I am fortunate to have become a physician in a time of great scientific progress. Back when I was in college and medical school, the thought that we would one day be able to sequence the human genome (and now sequence hundreds of cancer genomes), to measure the expression of every gene in the genome simultaneously on a single “gene chip,” and to assess the relative abundance of every RNA transcript, coding and noncoding (such as microRNAs) simultaneously through next generation sequencing (NGS) techniques was considered, if not science fiction, so far off in the future as to be unlikely to impact medicine in my career. Yet here I am, mid-career, and all of these are a reality. The cost of rapidly sequencing a genome has plummeted. Basically, the first human genome cost nearly $3 billion to sequence, while recent developments in sequencing technology have brought that cost down to the point where the “$1,000 genome” is within sight, if not already here, as illustrated in the graph above published by the National Human Genome Research Institute. Whether the “$1,000 genome” is truly here or not, the price is down to a few thousand dollars. Compare that to the cost of, for instance, the OncoType DX 21-gene assay for estrogen receptor-positive breast cancer, which costs nearly $4,000 and is paid for by insurance because its results can spare many women from even more expensive chemotherapy.
So, ready or not, genomic medicine is here, whether we know enough or not to interpret the results in individual patients and use it to benefit them, so much so that President Obama announced a $215 million plan for research in genomic mapping and precision medicine known as the Precision Medicine Initiative. Meanwhile, the deeply flawed yet popular 21st Century Cures bill, which passed the House of Representatives, bets heavily on genomic research and precision medicine. As I mentioned when I discussed the bill, it’s not so much the genomic medicine funding that is the major flaw in the bill but rather its underlying assumption that encouraging the FDA to decrease the burden of evidence to approve new drugs and devices will magically lead to an explosion in “21st century cures,” the same old antiregulatory wine in a slightly new bottle. Be that as it may, one way or the other, the federal government is poised to spend lots of money on precision medicine.
Because I’m a cancer doctor, and, if there’s one area in medicine in which precision medicine is being hyped the hardest, it’s hard for me not to think that the sea change that is going on in medicine really hit the national consciousness four years ago. That was when Walter Isaacson’s biography of Steve Jobs revealed that after his cancer had recurred as metastatic disease in 2010. Jobs had consulted with research teams at Stanford, Johns Hopkins, and the Broad Institute to have the genome of his cancer and normal tissue sequenced, one of the first twenty people in the world to have this information. At the time (2010-2011), each genome sequence cost $100,000, which Jobs could easily afford. Scientists and oncologists looked at this information and used it to choose various targeted therapies for Jobs throughout the remainder of his life, and Jobs met with all his doctors and researchers from the three institutions working on the DNA from his cancer at the Four Seasons Hotel in Palo Alto to discuss the genetic signatures found in Jobs’ cancer and how best to target them. Jobs’ case, as we now know, was a failure. However much Jobs’ team tried to stay one step ahead of his cancer, the cancer caught up and passed whatever they could do.
That’s not to say that there haven’t been successes. For instance, in 2012 I wrote about Dr. Lukas Wartman, at the time a recently-minted oncologist who had been diagnosed with acute lymphoblastic leukemia as a medical student, was successfully treated, but relapsed five years later. He underwent an apparently successful bone marrow transplant, but recurred again. At that point, there appeared to be little that could be done. However, Dr. Timothy Ley at the Genome Institute at George Washington University decided to do something radical. He sequenced the genes of Wartman’s cancer cells and normal cells:
The researchers on the project put other work aside for weeks, running one of the university’s 26 sequencing machines and supercomputer around the clock. And they found a culprit — a normal gene that was in overdrive, churning out huge amounts of a protein that appeared to be spurring the cancer’s growth.
That was 2011 as well. Today, the sequence could have been done much more rapidly. In any case, Ley identified a gene that was overactive and could be targeted by a new drug for kidney cancer. His cancer went into remission. Wartman is now the assistant director of cancer genomics at Washington University.
The technology now, both in terms of sequencing and bioinformatics, has advanced enormously even since 2011. With it has advanced the hype. But how much is hype and how much is really hope? Let’s take a look. Also, don’t get me wrong. I do believe there is considerable promise in precision medicine. However, having personally begun my research career in the 1990s, when angiogenesis inhibitors were being touted as the cure to all cancer (and we know what happened there), I am also skeptical that the benefits can ever live up to the hype.
The origin of “precision” medicine
“Precision medicine” is now the preferred term for what used to be called “personalized medicine.” From my perspective, it is a more accurate description of what “personalized medicine” meant, given that many doctors objected to the term because they felt that every good doctor practices personalized medicine. Even so, “precision medicine” is no less a marketing term than was “personalized medicine.” If you don’t believe this, look at the hype on the White House website:
Today, most medical treatments have been designed for the “average patient.” In too many cases, this “one-size-fits-all” approach isn’t effective, as treatments can be very successful for some patients but not for others. Precision medicine is an emerging approach to promoting health and treating disease that takes into account individual differences in people’s genes, environments, and lifestyles, making it possible to design highly effective, targeted treatments for cancer and other diseases. In short, precision medicine gives clinicians new tools, knowledge, and therapies to select which treatments will work best for which patients.
If you think this sounds like what alternative medicine quacks (but I repeat myself) routinely say about “conventional medicine,” you’d be right. It’s not that precision medicine advocates don’t have a germ of a point, but they fail to put it this criticism into historical context. Medicine has always been personalized or “precision.” It’s just that in the past the only tools we had to personalize our care were things like family history, comorbid conditions, patient preferences, and aspects of the patient’s history that might impact which treatment would be most appropriate. In other words, our tools to personalize care weren’t that “precise,” making our precision far less than we as physicians might have liked. Genomics and other new sciences offer the opportunity to change that, but at the cost that too much information will paralyze decision making. Still, at its best, precision medicine offers the opportunity to “personalize” medicine in a science-based manner, rather than the “make it up as you go along” and “pull it out of my nether regions” method of so many alternative medicine practitioners. It could also offer the clinical trials tools to do it, such as NCI-MATCH. At its worst, precision medicine is companies jumping the gun and selling genomic tests direct to the consumer without having an adequate scientific basis to know what they mean or what should be done with the results.
In any case, up until 2011, the term “personalized” medicine tended to be used to describe a form of medicine not yet in existence in which the each patients’ unique genomic makeup would serve as the basis to guide therapies. Then, the National Academy of Sciences Committee issued a report, “Toward Precision Medicine: Building a Knowledge Network for Biomedical Research and a New Taxonomy of Disease“, which advocated the term “precision medicine” and differentiated it from “personalized medicine” thusly:
“Personalized medicine” refers to the tailoring of medical treatment to the individual characteristics of each patient. It does not literally mean the creation of drugs or medical devices that are unique to a patient, but rather the ability to classify individuals into subpopulations that differ in their susceptibility to a particular disease or their response to a specific treatment. Preventive or therapeutic interventions can then be concentrated on those who will benefit, sparing expense and side effects for those who will not. (PCAST 2008) This term is now widely used, including in advertisements for commercial products, and it is sometimes misinterpreted as implying that unique treatments can be designed for each individual. For this reason, the Committee thinks that the term “Precision Medicine” is preferable to “Personalized Medicine” to convey the meaning intended in this report.
As I said, “precision medicine” is a marketing term, but it’s actually a better marketing term than “personalized medicine” because it is closer to what is really going on. That’s why I actually prefer it to “personalized medicine,” even though I wish there were a better term. Whatever it is called, however, the overarching belief that precision medicine is the future of medicine has led to what has been called an “arms race” or “gold rush” among academic medical centers to develop precision medicine initiatives, complete with banks of NGS machines, new departments of bioinformatics and genomics, and, of course, big, fancy computers to analyze the many petabytes of data produced, so much data that it’s hard to have enough media upon which to store it and we don’t know what to do with it. Genomic sequencing is producing so much data that IBM’s Watson is being used to analyze cancer genetics. It’s not for nothing that precision medicine is being likened to biology’s “moon shot“—and not always in a flattering way.
So what is the real potential of precision medicine?
Complexity intrudes
I discussed some of the criticism of precision medicine when I discussed the 21st Century Cures Act three weeks ago. I’ll try to build on that, but after a brief recap. Basically, I mentioned that I was of a mixed mind on the bill’s emphasis on precision medicine, bemoaning how now, at arguably the most exciting time in the history of biomedical research, the dearth of funding means that, although we’ve developed all these fantastically powerful tools to probe the deepest mysteries of the genome and use the information to design better treatments, scientists lack the money to do so. I even likened the situation to owning a brand new Maserati but there being no gasoline to be found to drive it, or maybe having the biggest, baddest car of all in the world of Mad Max but having to fight for precious gasoline to run it. I also noted that I thought precision medicine was overhyped (as I am noting again in this post), referencing skeptical takes on precision medicine in recent op-eds by Michael Joyner in The New York Times, Rita Rubin in JAMA declaring precision medicine to be more about politics, Cynthia Graber in The New Yorker, and Ronald Bayer and Sandro Galea in The New England Journal of Medicine. Basically, the number of conditions whose outcome can be greatly affected by targeting specific mutations is relatively small, far smaller than the impact likely would be from duller, less “sexy” interventions, such as figuring out how to get people to lose weight, exercise more, and drink and smoke less. The question is whether focusing in the genetic underpinnings of disease will provide the “most bang for the buck,” given how difficult and expensive targeted drugs are to develop.
Over the weekend, there was a great article in The Boston Globe by Sharon Begley entitled “Precision medicine, linked to DNA, still too often misses“, that gives an idea of just how difficult reaching this new world of precision medicine will be. It’s the story of a man named John Moore, who lives in Apple Valley, UT. Moore has advanced melanoma and participated in a trial of precision medicine for melanoma. His outcome shows the promise and limitations of such approaches:
Back in January, when President Obama proposed a precision medicine initiative with a goal of “matching a cancer cure to our genetic code,” John Moore could have been its poster child. His main tumors were shrinking, and his cancer seemed to have stopped spreading because of a drug matched to the cancer’s DNA, just as Obama described.
This summer, however, after a year’s reprieve, Moore, 54, feels sick every day. The cancer — advanced melanoma like former president Jimmy Carter’s — has spread to his lungs, and he talks about “dying in a couple of months.”
The return and spread of Moore’s cancer in a form that seems impervious to treatment shows that precision medicine is more complicated than portrayed by politicians and even some top health officials. Contrary to its name, precision medicine is often inexact, which means that for some patients, it will offer false hope rather than a cure.
On the other hand, in the Intermountain study, after two years, progression-free survival in the group with advanced cancer treated using precision medicine techniques was nearly twice what it was in those who underwent standard chemotherapy, 23 months versus 12 months. Moore himself reports that with a pill he had one year of improved health and quality of life before his cancer started progressing again. It’s not yet clear in this trial whether this will translate into an improvement in overall survival, the gold standard endpoint, but it’s a very promising start. It is, however, not a miraculous start.
Here’s the problem. I’ve alluded to it before. Cancer genomes are messed up. Really messed up. And, as they progress, thanks to evolution they become even more messed up, and messed up in different ways, so that the tumor cells in one part of a tumor are messed up in a different way than the tumor cells in another part of the tumor, which are messed up in a different way than the metastases. It’s called tumor heterogeneity.
Now enter the problem in determining which mutations are significant (commonly called “driver” mutations) and which are secondary or “just along for the ride” (commonly called “passenger” mutations):
But setbacks like Moore’s show that genetic profiling of tumors is, at this point, no more a cure for every cancer than angiogenesis inhibitors, which cut off a tumor’s blood supply, or other much-hyped treatments have been.
A big reason is that cancer cells are genetically unstable as they accumulate mutations. As a result, a biopsy might turn up dozens of mutations, but it is not always clear which ones are along for the ride and which are driving the cancer. Only targeting the latter can stop a tumor’s growth or spread.
Knowing which mutation is the driver and which are passenger mutations is so complicated that the Intermountain researchers established a “molecular tumor board” to help.
Composed of six outside experts in cancer genomics, the board meets by conference call to examine the list of a patient’s tumor mutations and reach a consensus about which to target with drugs. Tumor profiling typically finds up to three driver mutations for which there are known drugs, and the board reviews data on how well these drugs have worked in other patients with similar tumors.
And:
The next difficulty, Nadauld said, is that “the mutations may be different at different places in a tumor.” But oncologists are reluctant to perform multiple biopsies. The procedures can cause pain and complications such as infection, and there is no rigorous research indicating how many biopsies are necessary to snare every actionable mutation.
But a cancer-driving mutation that happens to lie in cells a mere millimeter away from those that were biopsied can be missed. Similarly, cancer cells’ propensity to amass mutations means that metastases, the far-flung descendants of the primary tumor, might be driven by different mutations and therefore need different drugs.
Or, as I like to say: Cancer is complicated. Really complicated. You just won’t believe how vastly, hugely, mind-bogglingly complicated it is. I mean, you may think it was tough to put a man on the moon, but that’s just peanuts to curing cancer, especially metastatic cancer. (Apologies to Douglas Adams.) Because of this, precision medicine as it exists now can lead to what Dr. Don S. Dizon calls a new kind of disappointment when genomic testing fails to identify any driver mutations for which targeted drugs exist because “discovery is an ongoing process and for many, we have not yet discovered the keys that drive all cancers, the therapies to address those mutations, and the tools to predict which treatment will afford the best response and outcome—an outcome our patients (and we) hope will mean a lifetime of living, despite cancer.”
Too true.
None of this is to say that precision medicine can’t be highly effective in cancer. I’ve already described one patient for whom it was. It’s also important to consider that even extra year of life taking a pill with few side effects is “not too shabby,” either, if the alternative is death a year sooner. Prolonging life with good quality is a favorable outcome, even if the patient can’t be saved in the end.
What is precision medicine, anyway?
As I thought about precision medicine during the writing of this post, one thing that stood out to me is that, although precision medicine is rather broadly defined, in the public eye (and, indeed, in the eyes of most physicians and scientists) its definition is much narrower. This narrower definition of precision medicine is the sequencing of patient genomes in order to find genetic changes that can be targeted for treatment, predict the response to therapy of various pharmaceuticals or dietary interventions, or predict disease susceptibility. In other words, it’s all genomics, genomics, genomics, much of it heavily concentrated in oncology. (I concentrated on oncology for this post because it is what I know best.) If you reread the definition from the National Academy of Sciences Committee report, you’ll see that precision medicine is defined much more broadly. Other similar definitions include metabolomics, environmental factors and susceptibilities, immunological factors, our microbiome, and many more, although even a recent editorial in Science Translational Medicine emphasized genomics more than other factors.
In fact, in the most recent JAMA Oncology, there are two articles, a study and a commentary, examining the effect of precision medicine in breast cancer. What is that “precision medicine”? It’s the OncoType DX assay, which is generically referred to as the 21 Gene Recurrence Score Assay.
Basically, this assay is used for estrogen receptor-positive (i.e., hormone-responsive) breast cancer that has not yet spread to the axillary lymph nodes. Twenty-one different genes related to proliferation, invasion, and other functions are measured, and an empirically derived formula is used to calculate a “recurrence score.” Scores below 18 indicate low risk of recurrence as metastatic disease and insensitivity to chemotherapy. Patients with low scores generally receive hormonal therapy but not chemotherapy. Scores over 30 indicate high risk and greater sensitivity to chemotherapy. For such patients, chemotherapy and hormonal therapy are recommended. Patients who score in the “gray” area from 18-30 remain a conundrum, but clinical trials are under way to better define the cutoff point for a chemo/no chemo recommendation. In any case, this study indicates that the use of OncoType DX is associated with decreased use of chemotherapy but because of limitations in the Surveillance, Epidemiology, and End Results (SEER) data set with linked Medicare claims, it wasn’t clear whether this decline was in appropriate patients. In any case, there’s no reason why genomic tests (like the Oncotype DX test) that are rapidly proliferating shouldn’t be considered “precision medicine,” and they are in practice already. Contrary to the image of oncologists wanting to push that poisonous chemotherapy, OncoType DX was designed with the intent of decreasing chemotherapy use in patients who will not benefit. Imagine that.
Conclusion: Medicine that works is just medicine
In the end, I don’t really like the term “precision medicine” that much. It seems to be a term that reminds me, more than anything, of Humpty Dumpty’s famously scornful boast, “When I use a word, it means just what I choose it to mean—neither more nor less.” It’s a sentiment that definitely seems to apply to the term “precision medicine.” To me, when new tests or factors that predict prognosis or response to therapy or suggest which therapies are likely to be most effective are developed and validated, it’s an artificial distinction to link them to genomics, proteomics, or whatever, as well as “big data” and refer to them as “precision medicine.” To me, medicine that works is just “medicine.”
803 replies on “Precision medicine: Hype over hope?”
“Precision medicine” is an unfortunate term for a variety of reasons, among which is that “precision” is not the same thing as “accuracy”. In a medical context, we can take “accuracy” to mean “treatment that addresses, if not cures, the underlying condition.” Some diseases have well-known cures that don’t need to be precise, and with others, like cancer, precision does not always help.
I like to illustrate the distinction between precision and accuracy by quoting Archbishop Ussher’s estimate for the creation of the Earth. He names a precise time (6 PM local time at the Garden of Eden; the often-quoted 9 AM, which contradicts “the evening and the morning were the first day”, is apocryphal) on a precise date about 6 ka ago, with the main uncertainty being due to not knowing exactly where the Garden of Eden was. That’s on the order of a part in 10^8, which is extraordinarily precise for Ussher’s day. But it’s not accurate; the actual age of the Earth is closer to 4.5 Ga.
I don’t know of any case in medicine where “precision” leads to a “precisely wrong” treatment in the way Ussher’s Bible studies led him to his precisely wrong answer about the age of the Earth, but the field is yet young, and there will likely be plenty of opportunities to make such a mistake.
Orac does stipulate that he is first discussing this in relation to his specialty, which is understandable. But for more general application– if this 1K figure is indeed realistic, we could sequence every child born in the US in one year for the cost of a few dozen F-35’s or similar tradeoffs.
Now that would be a study.
It might actually tell us something useful about autism and obesity and such, as well as more physically acute conditions, as we follow the cohort through life.
Gets my vote.
Ah, but medico-marketing can be so persuasive–if you practice precision medicine, then ain’t you a “precise doctor?” Yup, a sad state when marketing/propaganda trumps science.
It seems to me that would be an expensive way of generating vast amounts of data that no one would have any idea what to do with.
From Sam Kean’s ‘The Violinist’s Thumb’ (Venter and Collins were big players in the HGP):
I think we may have to wait until computer processing power has become even cheaper before that kind of venture would be worthwhile.
I thought this was also interesting (op cit):
It looks as if knowing a person’s genome isn’t quite as useful as one might think.
Krebiozen once again quotes out of context so he can reply with a non-sequitur.
Yawn.
One major problem with precision medicine is that it relies on the false idea that a complex disease requires a complex treatment. This is not true, since many tumors can be treated by surgery without extensive molecular knowledge.
The same principle can apply to chemotherapy, by using the fact that all cancers have a common feature, uncontrolled growth. So the future of cancer treatment, immunotherapy aside, will come from G2 checkpoint inhibitors and protection of normal cells by cell inflation, associated to chemotherapy targeting dividing cells.
http://www.ncbi.nlm.nih.gov/pubmed/24156014
zebra@5
He had a valid point regarding processing power. That much data would be difficult just to store let alone process. Why bother collecting all that data when we don’t even have the infrastructure to store it, let alone analyze it? From the conclusion of the study talked about in an article Orac linked to:
Let me calculate, by Fermi problem methods, how much information is involved here. For purposes of this post, cows are spherical, etc. (I am a physicist, after all).
A human has a few tens of thousands of genes. (Probably more than a zebrafish, which has about 20k, but probably less than 100k.) Let’s call it 30k, just to keep things in round numbers. Each gene codes for a protein that has between a few hundred and a few thousand amino acids–let’s take 1000 for an average figure. At three base pairs per amino acid, that’s around 100 million base pairs per genome, not counting junk DNA. There are four bases, so we are discussing something like 30 MB of data for one person. The US has a population of a bit over 300 million, which implies about 5 million births per year. So we are looking at 100-200 TB of data for a single year’s birth cohort, or around 100 PB of data for the entire US population. That’s large but not excessive for a Big Data project these days (many physics research projects will produce hundreds of terabytes per year, and some discard large amounts of data to keep the total that low).
But I agree that it won’t do any good to collect the data if you don’t know what you are going to do with it. At least with a Big Data physics project, you have some well-defined science question, and to undertake it you need to convince a leading funding agency that your project is worth funding. Zebra’s proposed data collection effort sounds (if I may put on my reviewer’s hat for a moment) like a solution in search of a problem. I can’t answer for NIH, but I know that NSF and NASA do not like to fund fishing expeditions like that.
Eric Lund,
It wasn’t storage I was thinking of so much as the processing power to find associations between groups of mutations and specific conditions. I thought it was interesting that Venter and Watson (as in Crick) both had mutations that are associated with serious physical conditions that they did not have – presumably this is some epigenetic phenomena that turns the relevant genes off (or on). When you add in the epigenetic data that would be required to figure out what is going on I don’t think current computers have the necessary power.
Krebiozen@9
From that PLoS Biology paper:
It goes on to say that this is an issue not necessarily solved by Moore’s law:
Krebiozen’s point was entirely valid, not a “non-sequitur”.
Eric Lund #8,
Eric, this would just be a database, like census information, that could be used by individual research projects. The sooner we have the data, the sooner that can begin to happen. Is the census a “fishing expedition”?
The numbers are big because this is a big country; maybe we could pay Canada to do it?
capnkrunch #10
Still having language problems? Look up “non-sequitur” and look up “valid”.
Eric Lund, I run a CLIA NGS lab, and you’re underestimating 🙂 We don’t just sequence each base once; we do it 30x, on average, for statistical power. Our latest exome data (which is what you’ve described) is ~15-20GB in it’s raw form, not to mention any files that are made for analysis purposes. Genomes are closer to 120 GB.
As everyone’s been describing though, the big reason we don’t just “sequence babies” – or the whole population, as some have suggested – now really is because sequencing is the easy part. We can generate genomes, and even store them (though that’s a pain), until we’re blue in the face, but determining the needle in the haystack causative mutation in sick people is hard enough, much less predicting what may go wrong in healthy folks. We just haven’t done enough of the (much harder) genetics work to figure out how to appropriately interpret the data.
Daniel, how’s that search for evidence demonstrating cell inflation represents a effective treatment for cancer coming? Got anything that approximates proof of concept, let alone that it has the potential (as you claimed when you first appeared on RI a couple of years ago that it represented a ‘universal’ treatment for cancer.
The numbers are big because this is a big country; maybe we could pay Canada to do it? Oh, yes, please! Our little hamlet will get right on that.
zebra@12
non-sequitur noun
: a statement that is not connected in a logical or clear way to anything said before it
valid adjective
: fair or reasonable
zebra@2
Krebiozen@4 (responding)
me@10
Swapping in definitions:
Krebiozen’s point was entirely reasonable, it is a statement that is connected in a logical or clear way to what was said before it.
I believe you misused “non-sequitur” to simply dismiss a valid point without addressing it.
Still having language problems? Look up “non-sequitur” and look up “valid”.
It would help if you looked up the former, as your attachment to that erroneous hyphen is quite grating.
^ Grumble grumble blockquote grumble.
JGC
What you do not seems to realize is that CIAC represents a lot of investment with no financial return. Fot the evidence, to make a comparison, it is like saying that gene therapy is the way to treat genetic disease: you don’t really need a proof of concept. The only thing is enough money to make things work. For me it’s better to work on G2 abrogation because, with drugs, you can attract investors, but I think that CIAC is safer. And I am quite optimistic that it will be done in one country or another.
capnkrunch #15
“Krebiozen’s point was entirely valid, not a “non-sequitur”.”
Is itself a non-sequitur.
“Krebiozen’s point is not a non-sequitur, [because it is] entirely valid.”
But “being valid” does not refute the claim of something being a “non-sequitur”.
Why don’t you just admit that you learned something again instead of wasting bandwidth? I already know how to suck eggs.
Are you really trying to correct someone over a word you can’t even spell correctly, or am I have a stroke?
While the computing power needed to analyze the data would be expensive, I’m not sure the algorithms needed for bulk comparison are there, and we likely don’t even know where to look, getting the data would be a first step when its cheap enough. We might not be able to use the full data set it in any good way for 10 or 20 years, but then the children won’t have developed all of the conditions one might correlate to the genetic data, either.
Other issues of such a study would be providing the ongoing follow-up and maintaining adequate confidentiality. Each genome would need to be linked to the individual’s medical records for the patient’s lifetime in order to get the best data. This has the potential for abuse or inadvertent disclosure.
@ Mephistoles
Another problem with big data is that the current academic reward system is based on experimental papers. If you just come up with a new interpretation of published data you will have hard time to publish.
sorry MephistoPHEles
Mephistopheles O’Brien #21
Basically correct on the first point. If we had the data tomorrow, it would be possible to begin preliminary sorting, which might well reduce computational cost later on as “sick” or otherwise characterized populations are identified over the decades.
Issues of confidentiality don’t seem that big a problem to me, unless is gets hacked and published on the internet… oh wait… . But realistically, no, assuming reasonable care and stiff penalties for misuse, I can’t see any real risk.
Mephistopheles O’Brien
One thing I would be concerned about is that I/O speed might be the bottleneck (see my post #10). It seems like a waste of resources to store data we can’t use and that will likely need to be copied to new hardware just to be usable. The logistics involved in a project like that would be a nightmare. Heck with that amount of data software changes would be a nightmare as well. With the amount of resources required it’s really best to have the proper container prepared before trying to fill it. I think it would be a far more efficient use of resources to sort out the hardware and software requirements prior to mass collection of data.
I totally agree with you about confidentiality. The government, insurers, hospitals, etc haven’t been inspiring much faith in their ability to protect confidential data.
No, because there are specified uses for that data set. In order to properly apportion representatives, we need to know how many people there are and where they live. In the US, the Constitution provides for an “actual Enumeration” every ten years. (Details are different in other countries, but any halfway functional democracy needs similar data at regular intervals for this purpose–the alternative is “rotten boroughs” and “pocket boroughs” such as existed in the UK at various times in history.) Other data collected by the Census Bureau is routinely used for a number of studies: demographics, wealth distribution, and many others of this kind. It’s also a much smaller data set than individual genomes: these days, you could store all of that data on one commercially available hard drive. There are also laws (at least in the US) requiring that the data remain confidential for a period of time (72 years IIRC), after which they are made public–those census records are handy for people who do genealogical research since they can often be used to track where certain people move.
A population-wide genome database would presumably also be confidential–HIPAA either would or should cover it. But it involves quite a bit more storage. As others note, data analysis gets a lot trickier; e.g., you would have to have some way of tying it to medical records for it to be useful in any way (as MO’B notes above). Comparisons are a hard problem as well; if you are not careful about how you design the algorithm, you will get something that scales as N^2 where N is the number of people in the database (because with N people you have N[N-1]/2 pairs of people), or worse if you are doing multi-way comparisons.
To me, the confidentiality issues MO’B brings up are sufficient reason not to collect the data any sooner than it would be of practical use, because IME any sufficiently large database of confidential information eventually will be abused in some fashion. Think hackers stealing credit card info, or the NSA’s dragnet collection of telephone metadata, but on a much larger scale.
Since this does begin to intrude on my area of expertise – I can say that Zebra has no idea exactly how much data he’s talking about – both storing and processing.
The data alone would take years to process – even the initial collection and export into a database. There are also few, if any, current database technologies that allow for the storing and analysis of datasets even approaching the size in question & none that would allow for the connection of so many disparate individual items of comparison.
By the time the technology “might” be available to do it, it is, in all likelihood, probably that better diagnostic tests would already be available to solve many of the issues that would have made this data interesting in the first place.
The Census is also a relatively small amount of data – meaning that the variables are both known and quantifiable (there are only a set number of questions on the forms & check boxes for the individual person).
Full gene sequencing for hundreds of thousands, if not millions, involves an unknown number of variables – and no idea, how any or all of the variables might be connected to each other.
Eric Lund@26
Therein lies the issue I was trying to get at in #25. I was once involved in a project to upgrade server hardware and software as well as migrating our code base from VB 6 to VB.NET. It was a mess. There’s no reason to set ourselves up for that when there’s no current use for the data. It is so mcuh easier to build the proper infrastructure (both hardware and software) the first time around than to have to upgrade later.
Lawrence #27,
What “disparate individual items of comparison” are you talking about?
I get the sense that people are projecting some complicated scenario onto a simple suggestion. You record the genome– admittedly a long bit of information– along with, say, social security number.
What’s the problem?
Lawrence@27
This is kind of zebra’s MO. I wouldn’t be surprised if he comes back and claims that he knows better than you.
Shorter Daniel @18
“No, I don’t have any evidence because MONEY.”
Where else have I heard this? Oh, yes–every alt-med proponent arguing that there are no funding for studies proving what they know to be true and that vitamin C/baking soda/aromatherapy etc. cures cancer because they aren’t patentable.
@zebra – and exactly how big is a single genome? How do all of the genes relate to one another & in what context?
You’ve put forth the idea that this data could be collected simply and just stuck somewhere – but by what method would you do so?
Having the data is merely one thing, but that data must be processed, stored and retrieved in some fashion for that information to be valuable – I am merely pointing out that the storage systems (i.e. databases) don’t exist to be able to handle this quantity of information in any meaningful way to allow for searching or using the results…..not in any sense that would take less than years – by which time, the information is no longer valuable.
Lawrence #33,
I just don’t understand what it is you are imagining.
Let’s begin like this: Can you tell me the maximum length a sequence would have to be in order for you (you imply you are an IT person) to be able to handle it?
JGC
The money argument is valid whoever uses it. And yours is obviously a fallacy:
https://en.wikipedia.org/wiki/Faulty_generalization
capnkrunch #32
“This is kind of zebra’s MO. I wouldn’t be surprised if he comes back and claims that he knows better than you.”
Given how easily I got him to fold, maybe I do.
Some of you may have missed malia’s comment at #13 which was held up in moderation. It’s worth reading, I think.
My point, which I thought was obvious, was that most people seem to think it’s simply a matter of getting lots of genomes and correlating it with physical illnesses, including autism and obesity, and figuring out which genes differing from the ‘standard’ version* are responsible. It is a great deal more complex than that, with some mutated genes being turned off or on by other genes and by other epigenetic factors we do not yet understand. I think there are better ways the NIH or whoever** could spend $5 billion (assuming $1,000 per genome and five million births per year).
* How do we establish what is the normal human genome? The current ‘standard’ HGP genome is an average of a number of different people’s genome, but since we all have dozens of serious mutations this is a somewhat moot point.
** Oddly it was the US Energy Department that started on the HGP, the rationale being that they were investigating the effects of radiation on DNA.
Sorry about the grammar fails in my last comment – rushed editing.
malia #13
It’s great to have a real expert pitching in.
“We just haven’t done enough of the (much harder) genetics work to figure out how to appropriately interpret the data.”
For those of us who are not experts (and don’t pretend to be), could you explain what the “genetics work” entails?
A quick question – we each have two copies of each chromosome (apart from the y chromosome in men, of course). Presumably both are sequenced – does anyone know how that works?
@ zebra – the reason the genetics work is hard is that there’s lots of ways to skin a cat, but I’ll try.
– A lot of it is basic genetics – we “break” a gene in a model organism and see what happens phenotypically. But this only works for genes that change a phenotype. Krebiozen’s post above, where he mentions epigenetics, talks about some of the reasons why it’s hard to correllate genotype and phenotype; but there are a myriad of others that we have to take into account – gene families where one gene can “rescue” another can hide a gene’s function, for instance, or genes that have such a subtle phenotype that we can’t pinpoint a change by looking.
– Some of it is looking at patterns in large cohorts of people – but again, a lot of that information can be masked by the same issues I mentioned above, and in many cases, when we start with “phenotype first”, there may be lots of different genes creating something that *looks* the same to us on the outside, which can confuse the issue.
These types of research aren’t sexy, nor do they use fancy machines, so they’re rather under-funded, to the frustration of every working geneticist, ever.
@Krebiozen – being diploid is one reason why we sequence at depth rather than just 1x. We physically chop all 46 chromosomes (23 pairs) in to manageable bits, and sequence them, presumably equally; then to put them back together, we compare the sequence data to the “human genome” (called hg19, which is really a mix of about 6 people) to find canonical differences from that reference, and we look for any differences in our patient’s sequence – where we have 50% of one nucleotide, and 50% of the other nucleotide, we know we have a difference between the maternal and paternal chromosome. But, what we can’t easily do is “phase” these differences – so, we don’t know whether a set of mutations that are physically close to one another live together on a single chromosome, or whether they’re dispersed between a chromosome pair. (FYI – this problem with phasing is also a contributing factor in determining if a mutation profile is “disease causing” or benign in some cases)
malia #43.
Your reply is greatly appreciated. But I remain puzzled as to why anyone would object to my suggestion, since I am offering what you appear to need. Let’s do this with Canada as a more manageable source of data:
Yearly births of 385,000 times 1,000 per genome is 385,000,000.
An F-35 (USAF, the cheaper model) is about 150,000,000.
So the US could buy 4 fewer of these (in a projected fleet of 450 plus) and easily cover data collection costs for our friendly neighbors to the north with their more rational health care system. Need more data, say from a larger country, lose a few more planes.
So this is what I don’t get. You say you are underfunded, but here I am giving you (and geneticists everywhere) free access to all the data you could possibly use. I understand that you need computing power to work with it, but since you aren’t paying for the sequencing, you have more funds to do the cat-skinning.
And the data will be useful even after every baby has grown old and died, assuming other records are maintained. The processing is only going to get easier and cheaper over time.
So really, what is the problem?
Thanks malia, that answers my question perfectly. It seems to me that phasing is going to be a serious issue in the future, unless/until someone finds an ingenious way of figuring it out.
And that the gene data is collected and labeled properly, and the other data is accurate, and that the other data can be perfectly correlated with the gene data, and that the other data is actually the data that is needed for the unforeseen analyses, and …
Think it through, don’t just go off half cocked, like you seem so fond of doing. Do like adults do: foresee problems and address them before they bite. This is your brain
fartstorm; be responsible rather than defensive.@ Krebiozen
Performing single sperm sequencing in the same male individuals?
That, historically, has been a very generous assumption. Storage media age–yes, even hard drives, but this was even more of an issue with magnetic tapes, which were standard for decades. Interface technologies change. Software that was designed for a particular computer architecture may not be maintained as computers using that architecture age out of service. Et cetera. Dealing with these issues takes time and resources. Only recently have people in my (relatively data-heavy) field begun to devote the necessary time and resources to addressing this problem.
Show of hands here: how many of you who are over 30 can read every single computer file you have created over the last 20 years? I certainly can’t. At least two pieces of software I used extensively in the late 1990s (ClarisWorks and Canvas) no longer exist, but I still have files I created with those programs. In 1995 my home machine was still a Mac Plus (new in 1988) with a 400k floppy drive and a 20 MB external hard drive with SCSI connection–I still have the machine in a box in my basement somewhere, but I have no way of exporting data on those media to something my current machine can read, without paying major bucks to somebody who has maintained such a machine. I also have zip disks.
I work with people who have decades worth of data collected, some of it on nine-track tapes. Nine-track tape readers were once ubiquitous in this field; today the number of still-operating readers in the world can be counted on the fingers of your hands. And many of those tapes are too brittle to read. Even when data are on media we can read, we have to hope that documentation was kept of the data format (the data is generally in a binary format, because data storage was at a premium in those days). In some cases software to read the data exists, but is in some ancient version of Fortran that won’t necessarily compile on a modern computer, even if it had a Fortran compiler (they are no longer automatically included with many operating systems). A significant fraction of the data were never examined more than superficially.
Now scale this problem up to the size that Malia mentions for the human genome. And ponder the question of who is going to maintain such a database, and who is going to cover the costs of maintaining it–which are likely to be the same order of magnitude, per year, as it would cost to collect all of that data in the first place.
There is no shame in underestimating how much of a problem this is–lots of people do that. I have had occasion to recommend rejection of a proposal that I thought was making that mistake. But it’s better to understand the magnitude of the problem before we collect a bunch of data we will never be able to use.
Eric Lund #48,
This is very strange reasoning. We would “be able to use” the data immediately– my suggestion that it might still be usable 100 years from now is only to illustrate that this is a long-term project.
I also think your experience with magnetic tapes and consumer-type software is truly irrelevant– this would be a serious scientific endeavor backed by world governments and scientific institutions. (In the 21st century– no “stone knives and bearskins”; no slide rules and punch cards.)
So I still await an objection from someone (who one hopes would be an actual expert) who can explain why he or she would not like to have this resource available for research.
Eric Lund,
After having just spent hours transferring files on floppy disks using a borrowed external floppy disk drive (because they no longer come installed in computers) I can very much relate to what you are saying. It also reminded me of how painfully slow the buggers are. Now all I have left to do is find a way to get files off of a zip disk I have. Yay.
zebra, I’m sure everyone would like this as a resource. However, yours is a hollow victory unless you can will it to happen or pony up the money and resources to make it happen.
Daniel Corcos,
Good thinking, but I’m not sure that would help. Even if a single sperm contained enough DNA to sequence (it doesn’t*) it will carry chromosomes randomly selected, so you wouldn’t know if a gene was from a maternal or paternal chromosome. Also you would only sequence half the man’s DNA, and sequencing multiple sperm to get the full genome would lead to the same problem i.e.not knowing which genes came from which chromosome. Until we can isolate a single chromosome and extract enough DNA to sequence that, I see no way of overcoming this, yet.
* Genome sequencing requires 250 ng DNA. A single sperm contains only about 3 pg i.e. 0.003 ng of DNA. That’s 4 orders of magnitude difference, which will doubtless take a few years to overcome.
Krebiozen
http://www.cell.com/abstract/S0092-8674(12)00789-1
Not a troll #50,
“zebra, I’m sure everyone would like this as a resource.”
Ummm…. no. Apparently several people think it would be a Bad Idea. Including Eric.
“Bad idea?” No, but it lands very much in the impractical category……
Daniel Corcos #52,
Wow! That’s impressive. I wondered about PCR but dismissed it. It still doesn’t really solve the problem though, since we still don’t know which genes came from which copy of each chromosome. Or am I missing something?
It’s the $5 billion cost that makes it a bad idea. I’m all for collecting data just in case it comes in useful, but not when it costs lots of money that could be spent on something with immediate practical uses.
Krebiozen
I would say that with enough sperms, you would be able to say that the genes come from the same chromosome and answer the question of whether several mutations are on the same chromosome or not.
zebra@49
No we wouldn’t. For a number of reasons that have been explained already.
Eric Lund’s comparison is apt. Recall the paper I linked to said I/O speed is likely to be a major bottleneck. Our current storage media is inadequate. To be able make practical use of the data it would need to be moved onto faster media when it is available. This too has already been explained.
Krebiozen is absolutely correct in #56
I would also add that doing the data collection now would also unecessarily incur additional future costs to upgrade the software and hardware infrastructure as better technology becomes available. As I said before, it would make much better use of resources to take those funds and put them towards creating the necessary big data technoogies before collecting the data.
capnkrunch #58,
No reasons have been “explained” at all.
Are you saying that malia is some kind of psycho troll who is claiming to use genomes when in fact she isn’t? Or any of the other “working geneticists” she mentions? You must be really out of touch with the 21st century, just like Eric appears to be.
Could you point me toward the part of Malia’s comment @#43 that you thought showed an apparent need for sequencing every child born in the US for a year?
Because I don’t see one. On the contrary. She seems to me to be saying that the data they already have is still way too much of a research imperative all on its own for there to be any need or use for more.
ann #60,
By “you”, I am (obviously to me at least) referring to malia and all those working geneticists she invokes, and all future geneticists who might be able to do research because this data is freely available. As I very clearly pointed out, the costs saved on sequencing should allow for expanding the more substantive research activity.
[Yes, obvious to me, but of course, we can always distract from the topic by now discussing whether I should have said “you geneticists”, or “y’all”, or something else, and then go on to whether y’all is properly used as singular or plural, and so on. Or is there a hyphen in there somewhere?]
@zebra: There is a definite way that you can settle this dispute in your favor. To wit: write a proposal to the NIH or NSF (or equivalent body if you are outside the US) in which you will describe how you will collect the data, and what science question you will use the data to answer. You will need to convince the funding agency that you can do it within the constraints of the program to which you propose, and that your science question is of sufficient interest that the agency should fund your proposal rather than one of the competing proposals of comparable merit that they would otherwise fund. Then go out and achieve the proposed goal. If you can do this, you will have proved yourself right. The various people who are skeptical of your proposal, myself included, have given reasons why we think you won’t be able to achieve the objective within the allotted resources.
Right now what you are proposing is an “underpants gnomes” scheme: 1. Collect large-scale genome data. 2. ??? 3. Science! I know from experience, as do several others in the commentariat, that funding agencies aren’t going to fund proposals like that when there are already many more proposals with an explicit step two than they can afford to fund.
Just because you have hand waved them away doesn’t mean we didn’t explain. First there’s the technology issues I’ve brought up numerous times. Read the PLoS Biology paper I linked to for more detail but here are some of the issues:
Protecting confidential data:
CPU speed:
I/O speed:
Database size and search speed:
On the other hand there’s the issue that malia brought up in #13:
Throwing more data at the problem isn’t going to solve it. Just because you didn’t understand malia’s explanation in #43 doesn’t make it wrong.
And as she very clearly pointed out, since there is no present need to spend any time, money, or energy sequencing more data, that actually wouldn’t be a saving costs. It would be a waste.
It’s basically like saying:
“I don’t have enough clothes. I need to buy some, which I can barely afford to do. But I know! I can save money by buying the clothes I’ll wear in thirty years now!”
Let me walk you through this.
(1) All those working geneticists she invokes have unfunded priorities right now.
(2) Having more data “freely available” would not help achieve them.
(3) It also wouldn’t be free. You’d have to spend money creating the database and making it available.
(4) That money is presently needed for other priorities.
(5) So spending it on something else now would detract from rather than aid presently ongoing research.
(6) Furthermore, there’s no way to even say whether the research being done now will result in findings that could be better translated to practical applications in the future if such a database were “freely” available.
(7) So the whole thing might easily be a great big waste of money, now and always. Because:
(8) Spending money supplying people with something for which there’s no demand just about always is.
Eric Lund #62,
Since I never proposed getting funding from any of those agencies, such a test would be irrelevant. I merely did a first approximation a la Enrico, see #44 for the less ambitious version.
If you would read carefully, you would see that I consistently have implied financing from the general fund, by invoking a metric– the much-maligned F-35– which is often used for this kind of analysis. If the right people got the contracts, I could imagine even this US Congress finding a way to fund the project. Probably by cutting food stamps and not airplanes, but you never know.
So the real issue is whether such a database would be useful.
“Probably by cutting food stamps and not airplanes, but you never know.”
“(4) That money is presently needed for other priorities.”
You heard it here first: Let them eat genome database entries.
“Sorting”? Sorting what into what?
You’re magically* going to get 4 million human genomes each with over 3 trillion base pairs, and then…. do 8 trillion whole-genome comparisons? Why? Babbling about “computational cost,” a subject that you may reliably be assumed to know nothing whatever about (what word size for the sequences?) doesn’t cut it.
What sort of data structure do you imagine resulting from this exercise?
That’s because you’re a simpleton. Remember:
No, the security would be on the level of that for access to the VSD. Eveything has to be deidentified, which is no small feat when one has a lifetime of medical records.
Speaking of which, how precisely do you figure that’s going to happen?
* You forgot about consent, now didn’t you?
And @#13, you have a person who’s in a position to know telling you that it wouldn’t, then explaining why @#43.
Where you underestimated the size of the U.S. birth cohort by an order of magnitude?
Capnkrunch,
Listing out-of-context [out of context] quotes doesn’t constitute an “explanation”, and anyway, whether I call it a non sequitur or a strawman or a Gish Gallop, this has nothing to do with my suggested project.
And, saying “it’s hard” is not an explanation. Nor is “it’s not perfect”.
And in particular, when we are talking about basic research, “but it might not yield useful results” is not just a poor argument, but actually stupid.
If this database existed, people would use it. It’s absurd to suggest otherwise. People would choose genetics as a career exactly because of the opportunity. And almost certainly, it would spur the kind of innovation and development of tools that you are talking about. Kind of like DARPA’s little experiment with connecting computers in different locations, you know…
I really do think a lot of people here are simply “stuck” with their attachment to 20th and even 19th century paradigms. You can’t imagine a different way of doing things, or it makes you uncomfortable, or you feel threatened. Too bad.
@Krebiozen/Daniel Corcos
Single cell sequencing is a thing; you can (and we have) sequenced a sperm, if one really wants to – and lots of animal science researchers want to. However, for humans, not super practical. First off, only useful in biosex males. Second off, those are germline cells, which are arguably different than the somatic cells (cells that make up the rest of your body) that you’d be interested in if you were doing diagnostic sequencing. We’re getting closer to being able to do phasing – there are some nifty biological tricks we can use with standard sequencing, and there is an adorable little sequencer, called the MinIon, that’s in beta testing right now – our lab got 30KB fragments off of it – but neither of these options are very cost or time effective….yet.
@zebra
Would such a database be useful in the real world?? Honestly, the answer is that we don’t know, because we don’t have enough of the biological groundwork to make that decision yet. Might it be useful in the future? Perhaps.
IF (and only if) money and time and storage space and processing power were not an limitation – AND doctors took a thorough, objectively defined, descriptive medical history that was always coded properly in an EMR that followed each person through their life so we had good phenotype data on every condition on every human ever – sure, future human genetic researchers would theoretically love a resource that could interrogate the genomes of all humans everywhere.
However, @ann has a pretty good run-down of the ideas for why it’s not being prioritized. Avenues of research that are arguably more fruitful are currently underfunded, and there are lots of technical hurdles that have been mentioned up-thread that would need to be innovated and properly managed in order to make such an endeavor feasible. Beyond that, there are some HUGE ethical considerations that are still being hammered out. Lots of people are categorically NOT OK with having their genome stored somewhere. Lots of insurance companies are looking to make unsubstantiated claims for denying coverage based upon preliminary genomic data as “pre-existing conditions”. There are questions about whether adults should be making decisions about whether a baby’s genome should be sequenced, rather than that baby when they reach majority. Etc, etc.
You can call something out of context but it doesn’t make it so. That paper quite clearly explains the technological challenges involved in big data genomics.
Similarly you can say people would use the data and they certainly would want to, but both the technology and our understanding of genetics is not at the level where this data would be useful. You have yet to provide any counterpoint to any beyond “I don’t think so.”
Our CPU’s, storage media, and database technology is not fast enough. Our security is not good enough. And even if it was we don’t understand enough to make use of the data. I provided references about the technology and malia is an expert in the field who told you how our fundamental genetics knowledge is lacking. You on the other hand have other nothing in defense of your idea.
Should be “…provide any counterpoint to any criticism beyond…”
@malia – a question almost, but not completely, off topic if you please.
Do you have any opinions on the commercial DNA testing companies that scan for genealogical ‘roots’? Any opinions on the validity of the results?
The word is that there is native American on both sides of my family tree, but as near as I can tell, it would be so far back, I’d probably be eligible for the Mayflower Society. I’d like to try to settle it one way or another.
It’s positively darling that Z. is now asshurt over this and doesn’t understand the error.
We’ve (tinw) been through this, but a careful prescriptivist would omit the apostrophe.
malia #72,
My comment about 20th century thinking wasn’t intended for you, but…”pre-existing conditions”* ?? I thought we were eliminating that little canard here in the USA.
But I get the same sense of Nirvana Fallacy/Grandiose Strawman from you that I do from others. Let’s say we collect the data as I described in 44, and sure there will be some opting out, and sure there will be errors– as happens now, but you keep working.
What I really don’t understand is why you think this only has utility for some great project involving all of humanity in the future. Assume the data is available; why will there not be young scientists (or old corporations) picking out sub-populations to study? I just don’t see the constraints described in any concrete form. What do I need more than a statistically significant sample, and just enough computing power to handle it?
*(Or “preexisting”, I’m sure Narad will be chastising you about that any time now.)
And thus comes the fantastic megalomania.
@Johnny
The current crop of geneological tests are pretty good at giving you an idea of ancestry, so I don’t see any reason why folks shouldn’t try it if they’re curious. They don’t, however, have good demographics for some smaller outgroup populations (and some Native populations are included in this statement), either because of lack of genotyped members that can be used in the database, or because the group has an aversion to genetic testing (as is the case in some SW-USian Native populations).
I’ve personally never done one (because I’m cheap); but others in my family have, and the emotional responses to the results have, in all cases, been the most interesting parts. My step grandma called me in tears after hers, thinking she must have misread it because it only told her she was of German-ish descent, and she *already knew that*! And my Uncle’s test started a small Facebook-family-feud because there was too much Celtic genetics, and not enough French/Gallic genetics. My family may need a new hobby.
That’s a stylistic choice, not rank ignorance.
capnkrunch #73,
See my response to malia. But maybe you can try explaining this.
What exactly does “our understanding of genetics is not at the level where this data would be useful” refer to???
How can genetic data be “not useful” in the study of genetics???
Not to repeat myself, but…
Not when it’s a huge cost- and labor-intensive fishing expedition for something the potential uses of which nobody even knows how to recognize, identify, define or describe yet.
Because in that case, you’d just be stating one of the reasons that putting the cart before the horse is a bad idea by saying it.
It would actually be — and is! — stupid to pretend otherwise.
When people can’t use it to study genetics.
Because, as she already clearly stated @#43, they don’t yet know what to look for and/or how to look for it in the data they already have.
Research is not being held up due to a lack of sequenced sub-populations As she also already clearly stated, sequencing is the easy part. The present imperative is interpreting the data they already have.
It’s actually the other way around. Supply does not create demand. It’s absurd to suggest otherwise.
What opportunity? People already — right now! — have more access to sequenced sub-populations than they know what to do with. Literally.
I don’t see how. Please elaborate.
Are you kidding? If there’s a single idea in existence that’s more 19th-century than definitively quantifying the genetic destiny of humankind in order to use it to build a better future through science, I don’t know what it is.
Storing and using huge amounts of data is a major technical challenge, one that both big tech companies (like Google) and government agencies (the NSA) are working very hard on right now.
I can only think of two uses for a database of just genomes (as opposed to genomes + medical data): for identifying bodies, and for identifying criminals.
Would sequencing everyone answer some scientific and medical questions? Probably yes. Are we capable of analyzing that data now? No.
To expand upon this further: Even if the data were available, there are resource costs (labor, if nothing else–people don’t work for free!) to searching the database. To pay for those costs, potential users would have to write a proposal demonstrating that (1) they have a well-posed research question, (2) the question is of sufficient importance to merit funding, and (3) the proposers have a methodology that they can show is likely to answer the question. At least that’s how the funding agencies I am familiar with work, and I have no reason to think NIH is different. Ann’s point is that researchers in the field don’t know what they are looking for, so they cannot write a proposal that satisfies the third point. It would be worse than looking for a needle in a haystack, because at least we know what a needle looks like.
I have been on review panels. I know what happens to proposals that don’t have a coherent methodology (or, as I described them above, “underpants gnomes” proposals). If you’re lucky, you’ll give the panel a good laugh for a couple of minutes or so before getting a rating that tells the program manager, “Don’t even think of funding this proposal, even if you have infinite resources.” For programs that practice proposal review triage, such as the NIH R01 program, you won’t even get that satisfaction. So nobody gets funding to look at the database, which just sits there consuming resources (as I pointed out above, there is a nontrivial cost to maintaining the data once you have collected it).
Maybe in a decade or two, once scientists in that field have figured out how to ask meaningful questions that can exploit such a database, we can talk about building that database. In the near- to mid-term, that money is better spent looking at data already in hand and trying to figure out what we can do with it. Only then will we be able to supply the second step in that business model.
Eric Lund@87
Not to mentiom that every action performed on a database has resource costs. In normal situations you don’t notice which is probably why zebra apparently is unaware. However, for such a large database every single query will cost a significant amount of CPU cycles, disk reads, etc. Until there’s a need to analyze such large amounts of data it is far more efficient to work with smaller datasets.
From what malia said it seems like research has not progressed to the point where such large amounts of data are necessary or even usable. So, I would say that even if there were such a database, researchers wouldn’t be scrambling to use it. It doesn’t make sense to use a huge database with its inherent latency when a much smaller dataset would suffice and be much easier to manipulate.
Heh, redundancy. Important for databases, not so much comments.
To add on to capnkrunch and Eric Lund: it is entirely likely (even probable) that doing the kind of Big Data deep-database search we’re talking about here will require not only new hardware and new software, but new mathematics.
Looking at data sets as large as the genome of every child born this year (for a small subset) will need new algorithms at the very least. My mathematician friends tell me this is an exciting area of research, but while math is faster than pretty much any other science, it will still take time to develop these new methods.
Eric Lund #87,
Let’s review what malia actually says at #43:
That doesn’t sound like someone saying “we don’t know what we’re doing we just run around like headless chickens”. It does sound like someone contending with agonizingly slow processing and horrendously “noisy” data and eye-straining poor resolution and stuff like that.
I find it difficult to reconcile this with what you are saying– that “these people don’t even know what they are looking for”.
What I am suggesting is that if we pick up the tab for the sequencing– at the cost of a few airplanes we don’t really need– and build a resource like the Census or NOAA/NASA and other such entities– there will be competent people applying for grants to make the data more usable, at least, and others with a cogent proposal for basic research, and others with medical and other applications. You are free to disagree, but you have to offer more than generalities that fit with your experience, which simply may not be applicable here.
just a tech, capnkrunch:
“the kind of Big Data deep-database search we’re talking about here”
Since you are obviously not talking about the same thing I am, I guess we’re both right.
As I said to malia, if I am looking for a correlation for example, I only need a statistically significant sample to work with. Do you guys not understand that it is trivial to extract that from the greater database?
The issue, which is probably above your heads, is what constitutes a significant sample, because of the noisiness of the genomic information. But, we are far more likely to figure that kind of thing out if we get multiple people working on multiple problems in the context I describe to Eric.
zebra@92
Two issues here. First, why waste all the resources building this database when we only ever need a small subset?
Second, querying a database is not zero cost, there costs for the retrieving information from the logical data structure as well as reading from the physical disk both of which scale with size. With a database that large even generating an arbitrary subset is not trivial. If you have specific parameters in mind it only gets worse. It’s not as simple as cutting a slice of pie. Count computer science as another topic zebra has no grasp of.
capnkrunch,
Did you really say “why waste all the resources building this database when we only ever need a small subset” ??
I hope the rolling doesn’t pop my eyes out of their sockets.
OK, tomorrow I will look for at least marginally rational responses from malia and Eric.
OK, let’s back this train up a bit, because I feel like I am missing something.
zebra@92: Please tell me if I am understanding your proposal correctly. You want to search our genome database a correlation. A correlation to what? Are you talking about search a subset of the database (say, children with a very specific genetic disease) to find common gene patterns?
Or are you searching the whole dataset for a specific coding sequence?
And how can we know how big a statistically significant sample will be before we know what we are looking for? If it is something common we might need a relatively small sample, while if it is something very rare, we might need a very large sample.
Usually you decide the level of statistical significance you want, then from that calculate the power you need to find that, and that in turn will let you calculate the necessary sample size. Is that what you mean?
By doing what? What would they be proposing to do to the data, using what methodology to accomplish what?
Which is what, exactly? As in “I propose to establish the genetic basis for…” And how do you imagine they would be cogently proposing to establish it? By looking for correlations?
Between what and what else? How would they look? What would they be looking for?
And you know this because you see it in your Magic 8 Ball?
Perfectly sensible question.
ORLY? How? I mean, it would be more straightforward to say what database?, given that all you have is yet more sophomoric posturing, but just for fun, show everybody what the query would be here.
Seriously, go fυck yourself. Your dismal performances here have only demonstrated that you seem to know nothing whatever about any topic that you choose to spout off on. I can scarcely imagine what, if anything, you have postsecondary training in.
OK, let’s see what’s over whose head. Define your terms.
^ Don’t forget “statistically significant sample,” either.
Oh, it’s vastly worse than that – remember the “preliminary sorting” bit? He has no understanding whatever of data structures or algorithms. (Fun fact: multiple sequence alignment with sum-of-pairs scoring is NP-complete.)
Oh dear, hoofbeats fading into the distance. I’d say “not enough carrots” if only Z.’s psychological dynamics weren’t so painfully obvious.
Behold, Z.’s comment 91:
This, of course, is yet another repetition of his ciphering in comment 44:
Note that the issue has been pointed out indirectly by others, and I did it explicitly in comment 70. Add “order of magnitude”* to the pile of things that Z. doesn’t understand.
* And, ironically, cost analysis, given the context for this idée fixe of a “yardstick”; he in fact posits $4 billion as the total initial cost from inception to end of initial sequencing. Absolutely classic Z.
In the absence of any notion of what to do with it, a hundredth or a thousandth of the data would meet the same criterion.
All this big-data talk always brings to mind the Maxwell’s Demon of the Second Kind from Cyberiad.
Spoiler alert: “The demon prints out this information on a long paper tape, but before the pirate realizes most of the information is completely useless (although strictly factual) he is buried under the endless rolls of tape, ceasing to bother anyone.”
herr doktor bimler@103
Don’t say that, zebra will roll his eyes right out of their sockets.
On that note, here’s an interesting case of zebra revealing his ignorance. In #93 I made two points. One was rather weak but required some knowledge of databases to rebut. zebra chose to ignore this one and instead opted to handwave away the much stronger, albiet simpler, argument (the same one herr doktor bimler made here).
zebra proving his lack of knowledge about a subject in one breath while insulting others in the next is nothing new. However, I think the way it came across in this case is somewhat novel.
The NP-hard problems are very likely going to remain NP-hard. New heurististics may be new mathematical applications, but I’m not so sure about the “new mathematics” part.
There’s a list of problems that were in need of attention a decade ago here (and many of the reference links are broken, rotted, or both), but I just don’t have the time at the moment.
Narad: Add “order of magnitude”* to the pile of things that Z. doesn’t understand.
I’m beginning to think he doesn’t understand anything at all. I mean, I don’t really understand computers, but I get the practical objections, not to mention the idea of obsolescence. I mean, does he seriously think computer tech is going to stand still for a hundred years? The computer I had ten years ago is vastly different from the one I have today, for example.
Eric and Justatech: I feel your pain. I’m trying to move files around, and even with two relatively close in age computers, it’s a gigantic pain. And, hey, I still have some floppies around. Don’t know what I’m going to do with them.
I have been a lurker here for years, yet never felt compelled to post before now. Sorry my first post is such a long rant. I realise that trying to dismount Zebra from his high horse is a futile task. But as a life-long geneticist/genomicist/molecular biologist or whatever it’s called these days, I just want to add my support to those who have already tried to explain how futile/wasteful Zebra’s idea is, at present. Better idea is to work on getting the ethics/consents and funding to collect high quality DNA (or at least blood) and immortalised cell lines from all births (or as many as consent), then when both the sequencing technologies plus data storage and analysis infrastructure are more mature, you can do all the sequencing AND make some sense from it. By then you might even have some decent phenotype data from this birth cohort which will help you select good subsets of the data to answer specific questions. I would also suggest that re-collecting samples from the cohort over time will yield even more useful data to track changes in epigenetic, RNA and protein expression over time. Ideally you would also want to track environmental and sociological data to work on gene-by-environment questions. Now we are talking about really REALLY big data, but potentially much more useful than just sequencing everyone born using current technology which is going to improve greatly over time. I am pretty worn out from having to re-impute genomic data from stuff done in the past. Imputation should only be done when you have no other choice.
I also see Zebra does not have any grasp of how big the computational and statistical challenges are. Think about 3 billion base pairs (that’s 6 billion bases) in an average human. Now think that each human has about 10 million of the base pairs as SNPs, plus CNVs, methylation differences and a whole host of other potential genomic differences between individuals. Let’s leave phasing out of it for the moment, though this is also a big problem. Now you need to screen all 3 billion base pairs to get the basic data that Zebra is talking about (keep in mind that is maybe up to 100 billion reads of DNA for decent filtering and mapping), then you need to do multivariate analysis of all the cross-wise comparisons between each base of “normal” DNA and affected individuals (whatever the effect is you are looking for), and do an enormous amount of correction for multiple comparisons to maybe get an idea of genetic difference that may be driving the effect. The more genes involved in a particular phenotype, the smaller the effect sizes and this is just the start of an answer to why it just doesn’t make any sense to do this right now. Do it when you have a specific question to answer, using the best technology you have available (and can afford) at the time to answer that question. And never, ever assume it is just about the plain text sequence of 3 billion base pairs that you can store in a database. That is a defunct idea spread by the hype of the HGP, which even people like me bought into at the time.
Or to maybe to put it in terms that Zebra can relate to, would you buy 5 million F-35s just because they were $1000 each, when you may not need them at all, or not for 30 years? Maybe you will need 100,000 of them before then, would you still buy all 5 million, just in case? Where will you store them, who will maintain them, and will they be of any use in 30 years’ time? Or will the war technology have changed so much by then that they are basically of little use except at air shows…Now keep in mind that genomic technology is evolving much faster than war technology at the moment, and you can see there are a few problems with just stock-piling for the sake of it, even if someone stumped up the money for it (which is unlikely right now). Using the F-35 analogy, wouldn’t it be better to put that money into buying what you need right now to fight your current wars, and investing some of it into research for future war technology improvements (if war was your business). That is all genomic researchers are saying. There are better uses for the money and technology right now, in both diagnostics (fighting the current wars) and research (improving technology for the future).
Narad@105
Personally, I like to dream that P=NP but realisticly you’re probably right. That said the work being done in compressive genomics is pretty interesting [1][2]. I don’t know enough to differentiate “new mathematics” from ” new application”. I would guess that new compression algorithms are more on the side of new application though.
Personally, I think the most interesting stuff is the work being done on homomorphic encryption [3]. That’s some seriously cool cryptography. Again though, not sure it constitutes “new mathematics”.
[1] h[]p://www.nature.com/nbt/journal/v30/n7/full/nbt.2241.html
[2] h[]p://m.genome.cshlp.org/content/21/5/734.full
[3] h[]p://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.309.1513
The SDSS pipeline, as of 2001, represented 25% of the shebang. The raw data aren’t really comparable (as the PLOS item notes;
datanoise has a dedicated garbage channel early in the chain), but, I mean come on, already.There’s something simple here, and it ain’t everybody else.
@Retro Pump:
I’m confident that unanimity will be found as to your doing it more often.
I think the fallacy of Zebra resides in the airplanes’ argument. Very few of us need these airplanes actually, and, personally, if I had the money of these airplanes, this would change my life; much more than if I had all these sequences, which I cannot say if they will be useful one day. Maybe we can use this blog to say that the money of the airplanes should be given directly to us. We certainly know better what to do with it (except maybe for Zebra), but I fear that some very powerful people really need these airplanes.
Retro Pump #107,
An excellent (and obviously knowledgeable) critique of the proposal. Before I respond, I’ll just ask– why didn’t you jump in right at the beginning and say: “Zebra, I see where you’re going, but here’s how it would have to work.”
The whole point of putting the idea out there is to promote this kind of discussion. Why lurk when you have real information to contribute?
Anyway, as to the substance. I don’t recall that I ever suggested that we would get all the samples and then have a crash program to sequence them all in one year. Even I am not that crazy, and to suggest that is what I call a grandiose strawman. The point, which you appear to understand and have no problem with, is to establish the cohort
So, what are the steps or components?
Getting the samples is trivial. Will some parents opt out? Stipulated. Will that skew the sample? Highly unlikely, except perhaps where you have a somewhat inbred religious or social group, and we would be aware of it
Developing a registry of phenotypes? Well that’s why I suggested a country with a rational health care system and cooperative citizens like Canada. Yep, I will also stipulate that in the USA there would be all kinds of irrational paranoia about such a project. Bad idea to do it here, numbers aside.
Why do it sooner rather than later? OK, that’s where I think we disagree.
As I’ve suggested, the first reason would be to stimulate research and the advancement of tools and techniques and lowering costs. It’s a big contract.
But the real benefit to me would be getting as much done before people in the cohort start manifesting whatever we are interested in. Are you saying that it wouldn’t help to have the genomes to hand (whatever subset of the data has been processed so far) in order to inform further action and study? This I don’t get.
If the data is there, and someone says “I think there may be a (genetic) correlation with x”, this can be examined initially without any patient interaction at all– that is, by people outside the clinical setting where confounding factors abound.
As to the analogy, no, it doesn’t work. How about “why subsidize rooftop solar when everyone knows how to make and distribute electricity from fossil fuels, and solar technology will be better in 20 years anyway.” (Or any number of examples like pc’s and internet and electric vehicles and so on.)
You don’t get the progress by sitting on your hands; solar panels et al are cheaper and better exactly because we started buying them even before they were “perfect”. Which is why I mentioned the Nirvana Fallacy along with grandiose strawmen.
[…] Orac is on vacation recharging his Tarial cells and interacting with ion channel scientists, as a good computer should. In the meantime, he is […]
Zebra @2
Zebra @112
D’oh!
The strategy in the UK and funded by the NHS (Government)is to target specific groups rather than just the population.
“The 100,000 genomes project.”
The project will sequence 100,000 genomes from around 70,000 people. Participants are NHS patients with a rare disease, plus their families, and patients with cancer.
I understood that to mean “a year’s worth of births.”
You say that as if it were a bad thing. The Dunning-Kruger is strong in this one.
As has been mentioned overnight, another area in which major advances would be needed before a large-scale genome database could be useful is algorithms for sorting and correlating the data. For instance, if the best available algorithm today has an O(N^2) run time, but an algorithm with an O(N log N) run time were possible at least in principle, it would be well worth spending money to develop the latter. For N of the order of the annual US birth cohort, the difference between N^2 and N log N is five orders of magnitude, or roughly the difference between having a query take one second (as our equine-pseudonym commenter seems to think) and one day (because 2^20 = 1048576). In a genome database, a more realistic N would be in the billions if not trillions–what would take the N log N algorithm one second would take the N^2 algorithm anywhere from a few years to a few thousand years.
We can’t count on Moore’s Law to hold forever. There are physical limits: signals cannot travel faster than the speed of light (about one foot per nanosecond), and a logic gate cannot be smaller than a few atoms in size. Maybe we can do better with quantum computers than with conventional computers, but that, too, is a long development road–the current state of the art in actual quantum computing hardware is a benchtop experiment that is barely able to tell us that 15 = 3 * 5. (I’m not being quite fair here: that computer was intended to demonstrate a factoring algorithm which is much faster for large numbers–O(log N) instead of O(N^1/2) where N is the number to be factored. Which is a big deal because encryption algorithms depend on the fact that factoring large numbers with non-quantum computers is computationally hard.) And of course, even if quantum computers are developed to a level where they might help, the data migration problem strikes again, in spades.
Those are all products that were developed after the technology and understanding that made them possible, not before.
The Nirvana Fallacy applies to things that are non-ideal, not things that are useless and unnecessary.
It just dawned on me that zebra’s thinking is essentially that if you put a bunch of stuff that uses the same code together and connect it up, it will be like the internet. (Hence the 21rst-century snark.)
Maybe everybody else already grasped that, though.
zebra@112
Hmmm. This doesn’t quite fit with what you were saying before.
zebra@31
And once again, I’ll bring up the confidentiality issue that you previously handwaved away:
zebra@23
Just because you think something doesn’t make it so. Are you beginning to see a theme here? Data breaches aren’t even the biggest issue, it’s ablut properly deidentifying the information. There’s a reason genomics is driving some real cutting edge crypto*. Since I apparently can’t quote without it being out of context here’s some required reading so you don’t embarass yourself again: Routes for breaching and protecting genetic privacy.
*It’s probably over your head but for extra credit go read the paper on homomorphic encryption I cited in #103.
capnkrunch,
That’s a dead link in your last comment, please repost.
There are already some interesting privacy issues emerging from sequencing people’s genomes. James Watson wanted his apoliprotein E status (associated with Alzheimer’s)withheld when his genome was published, but some geneticists pointed out that it was easy to figure out from the surrounding genes that had not been redacted. These and similar issues will doubtless become more prominent in the future.
capnkrunch #119,
No idea what you are getting at with your first two quotes. You need to elaborate.
But, since you appear to be part of the USA paranoid group I mentioned, let me ask something about “genetic privacy”.
I have a list that matches social security number with a genome. I have a list that correlates some medical condition with social security number. The social security number is encrypted, if you like.
Now, if it we go back on the momentum to eliminate the concept of pre-existing conditions as a way to deny insurance coverage or payment, I could imagine someone hacking the medical condition registry and selling the info to some nefarious insurance executive. I don’t think this will happen, but arguendo.
But could you please explain what possible deranged reasoning makes you think someone would hack the genome data, which you keep freakin telling me is impossibly difficult to turn into useful information in any useful time span??
My eye rolling is nothing compared to my headshaking at this point. [head-shaking]
Me, I think it would be neat to wear a t-shirt printed with my genome in tiny little letters– someday I expect one will be able to order such a thing from Amazon. What’s the problem?
Krebiozen@120
Oops. Here’s the link: http://www.nature.com/nrg/journal/v15/n6/full/nrg3723.html
Ann @115
If zebra were sensible then your inference would be reasonable. However, since zebra was responding to a point made by literally nobody, whilst ironically complaining that it was a “grandiose strawman”, I’m not convinced that your interpretation of his intentions is correct.
DrBollocks 123,
It was in response to Retro Pump pointing out (apparently obvious only to the two of us) that the genetic information is stored in the samples. He says basically “keep it stored that way until we reach some future capability” and I say no, lets get to work right away turning it into accessible data. For the reasons covered in 112.*
I never suggested, as some seem to keep implying, that we were going to have the entire databast digitized immediately, and that we would then do analysis on the entire thing. Hence “grandiose”.
*Note also that this is why all the nonsense about deteriorating media and changes in software is nonsense. The samples are there with the information to be extracted in the future, with future better tech, if the data gets corrupted.
So, I have to apologize, I was wrong about the mechanics of data storage.
According to my database systems engineer (I’ll call him DSE), you can store 1 petabyte (Pb) of data on one server rack of hard drives ( a server rack being the size of an overgrown filing cabinet). If you don’t care about your I/O, you can do that for about $100K. If you want a searchably useful I/O rate it will be more like a million dollars. (The DSE considered this chump change but then I reminded him this was science and not Silicone Valley.)
The much, much bigger problem in the opinion of my DSE is the issue of data entry. The USA does not currently have a unified EMR or EHR system (electronic medical record or electronic health record). While a universal EHR system has been on the WHO’s to-do list since at least 2012, not a lot of progress has been made on that front.
So it doesn’t matter than we can store the data and search the data, we can’t get the data *in* in the first place.
So zebra, I apologize, I was wrong to say that the storage problems would make your plan unfeasible. It’s the data entry that makes it unfeasible. Maybe a country like Canada could do it (if they had the money) but I still believe that there are issues beyond funding.
(A side note about starting with infants: for late-onset diseases like obesity, type II diabetes, CAD and dementia we would have to wait an awfully long time for diseases to manifest before we can determine anything about the genetic basis.)
zebra@121
That was my bad for botching the link. Do some reading. At the very least take a look at Figure 1. The issue isn’t exfiltrating the entire database, it’s that genomics can potentially be used to identify otherwise deidentified protected informtion. As to why anyone would want to do that, it doesn’t particularly matter because HIPPA says you need to protect that information. As I said, there’s a reason why there is serious cryptography research going on to allow queries without exposing the raw data.
As to the social security thing, I was under the impression you were suggesting that we only collect genome data because Lawrence said the database would get too complex if it included all the medical data. Apparently I misunderstood but your actual idea still doesn’t make sense. Using SSN’s to index the database unnecessarily exposes additional identifying information. Not to mention, it was the genome itself that Lawrence was referring to as being composed of huge amounts of variables (go reread Retro Pump’s #107; try reading for comprehension this time).
Justatech #126,
Remember, we, the wealthy USA, and I would hope the rest of the world, are paying the [Canadians] to do this. I would throw in even a couple more F-35’s if need be. And someone mentioned that the Brit NHS was doing something along these lines with phenotypically distinct populations. Rational healthcare systems do have advantages.
But your point about late-onset conditions is quite correct. Note that my initial comment referred to obesity and autism, the former unfortunately affecting more and more children. And that follows from Orac suggesting, IIRC, that genomics might be better applied to those kinds of less-acute-public-health-chronic issues.
So yes, maybe we will have figured out the genetic components of diseases of old and middle age before the cohort gets there. But I am also arguing that this project will help accomplish that indirectly by stimulating R&D.
capnkrunch 127,
I am really trying to comprehend what you are saying but it ain’t working.
There’s a government database of genomes indexed by ss#.
There’s a government registry of conditions or diagnoses indexed by ss#.
If I want to do research on condition x, the government sends me a list of the genomes indexed by a completely arbitrary set of numbers which the government indexes to ss#, so I can follow up if some need arises, but they could even leave that out and I could still do my research.
Where do I go to use the genomic information to find out what about what about any individual?
zebra@123
Again, there’s no reason to use SSN’s as the index. This system you’re proposing requores that every request requires the an additional column mapping the new arbitrary index to the SSN. There’s no need to use the SSN. You just set up a hash table for the index and you can then reuse the hashes as the index for a queried subset and there’s no need to map the subset’s index to the master databases.
Again, I’ll refer you to the paper I linked to in #123. There’s attacks that can be used to deindentify genomes or that can link a known person’s genome to their PHI. I’m not going to explain it all for you but here’s a very simplified explanation of one type of attack. Markers from a deidentified genome are referenced against information in publically available genealogical databases. These databases contain personally identifiable information. Because you requesting genomes from people with a certain condition you have correlated PHI with a specific person. HIPAA demands that not be possible.
This is not entirely theoretical either:
And researchers actually successfully used this method: Identifying Personal Genomes by Surname Inference (pdf).
Correction for #130
“The system you’re proposing requires that every request an additional column mapping the new arbitrary index to the SSN.”
I thought about it and there could also be just one additional column mapping the arbitrary index to the SSN. But then there’s no need for the SSN because this is the same I mentioned in #130 except it unnecessarily includes SSN’s as well.
Zebra:what possible deranged reasoning makes you think someone would hack the genome data, which you keep freakin telling me is impossibly difficult to turn into useful information in any useful time span??
First of all, they are assuming this can be turned into useable data, which in turn makes it vulnerable to hackers. As to why hackers would try to break it..uh, because it’s there? Because it could be used to embarrass and discredit people? I could imagine a lot of ways a break-in could get nasty fast.
Why would you even want your genetic data hanging out for all to see? What if you had schizophrenia or bipolar depression or a personality disorder running in the family?
I would certainly hope that there are no such government registries or databases, because as capnkrunch@127 notes, it would be illegal to maintain such databases in the US. There is a law (HIPAA) which requires medical information used for any form of research to be stripped of any and all identifying information. Social security numbers constitute identifying information, because they are unique numbers associated with specific people. For instance, anybody who knows your SSN can obtain credit in your name. (This is one of the ways that identity theft works.) If your medical history were also available to somebody who knows your SSN, he could use it to, e.g., legally obtain certain drugs that are not available over the counter, and sell them at a profit. Which leads to a nightmare scenario in which you can’t get the medication you need, because a program intended to sniff out prescription fraud has noticed that somebody using your identity is obtaining said medication in quantities well beyond what is needed for personal use.
Any database with financial information linked to individuals is a potential target for hackers. You need only pay attention to the news to see this: such databases are hacked on a regular basis. A database with everybody’s social security numbers and genomes/medical history in it might as well have a big sign on it saying “HACK ME” in letters big enough that, were it physically located in Washington, you could read it from Perth without reading glasses. No criminal penalty could deter all hackers, because the reward is so great.
There would have to be *some* unique identifier connecting the individual with his/her genome; otherwise there’d be no way to connect the individual’s medical records with his/her genome. Without that, all you have is a massive pile of bytes from which you could not learn anything about health.
But this whole project would require a database connecting every individual in the cohort with his/her medical records and that *would* be a target for hackers even if the genome info were not useful. Imagine the blackmail possibilities for a hacker who knew about treatment for venereal disease, drug addition, schizophrenia or bipolar depression or a personality disorder in the family as PGP suggested.
capnkrunch et al:
The hospital knows the ss# of the baby.
The hospital sends the ss# and the sample to the government.
The government attaches an arbitrary number (xss) to the sample and to the digital form of the data. But it must keep a table of ss# and xss#.
The doctor knows your ss#.
The doctor sends the information ss# and diagnosis.
The government converts the ss# to xss using the table.
It stores the diagnosis indexed by xss.
So, as the person doing the research, when the government sends me a list of genomes associated with the condition I am studying, I have no contact with ss#, and as I said, the government doesn’t even have to tell me the xss.
Somehow, you think this is less secure than the traditional method you are defending, where the subjects are directly involved with the researchers? Where “everybody knows your name”, and you can be secretly photographed or fingerprinted, and your credit card information and other easily readable health data is in the office, and your facebook page discusses your condition, and you order drugs online….
Yawn.
zebra@12
Nope. You still don’t understand what a hash table is. It stores the hashes without any need to keep the raw data (i.e. SSN). In any case, using the SSN is unnecessarily. It makes more sense to have a unique identifier known to healthcare providers (think MRN) that is standardized. That way it minimizes consequences in case there is leakage.
The traditional methods don’t work here either. As I told you before even just a genome is potentially personally identifiable. Hence the work on homomorphic encryption that would allow comparisons without exposing raw data. This is not advanced enough nor are computers powerful enough for this to be practical on a large scale. We can argue about your misunderstanding of how database indexing works until we’re blue in the face but this is the more difficult issue and it’s the one you haven’t even attempted to address.
Ooh! I just thought of a much better application of a genome database. I said earlier that there are issues with having to wait for diseases of adulthood to manifest in our hypothetical cohort.
Why not instead take an existing multi-generational study and sequence their genomes? Imagine the data you could learn from the Framingham Heart Study, with three generations of CV data! And since everyone there already has a study ID number (totally separate from any other identifying number), we eliminate all the SSN stuff.
I only see three issues with that: 1)a lot of the first generation are dead, so no genomic data, 2) getting people to volunteer their genomes, 3) it’s not all that diverse a place (which has always been a problem with the FHS) so there are a lot of population groups you would miss.
There is only one way to make a database like that secure: put it on a computer that is never connected to the internet. That’s how Los Alamos protects the computer that runs their bomb explosion simulations. But if you make it secure in that fashion, then it becomes a great deal less useful. If you try to make it useful to other researchers by putting it on the net, hackers will find a way to penetrate the security.
Admittedly, at the database sizes we are discussing, FedEx has more bandwidth than the internet. But you still have to pay the army of data technicians who input the queries and transfer the results to the hard drives which get shipped to researchers. And you have to pay FedEx (or UPS, or USPS, or whatever courier service is involved) to ship the disk to its destination. That gets expensive really fast–most likely, proposal budgets would have to include these things, which means less money to do the actual research. And when all is said and done, you have to make sure that the hard drives you are shipping to researchers all over the US (if not the world) don’t have any identifying data that somebody might accidentally put on a networked computer.
There are lots of problems like this that have to be solved. Feel free to argue that we (meaning NIH, NSF, and other funding agencies) should fund the research to address these issues–as noted in various posts, some of them have practical application in other areas, too. Don’t waste our time and money collecting the data before you have solved these problems.
This is a truly breathtaking level of cluelessness. No, you don’t get handed entire genomes for random conditions, because then – in your fantasy system – you can start doing reverse queries and not just deidentify them, but also piece together their complete medical histories in whatever noble land where adults have no control over their PHI.
There’s more, but I’m on deadline. Somebody with more time might want to look at how Denmark handles the information that it keeps; e.g., here one finds the following:
“Access to Danish registry data and data linkage requires authorization by the Danish Data Protection Agency (Datatilsynet) and in some cases, additional authorization from the Danish Health and Medicines Authority, typically when medical charts are to be accessed,[46] and/or authorization from the National Committee on Health Research Ethics (Den Nationale Videnskabsetiske Komité) if biological specimens are to be used or if living persons are to participate in clinical studies. The Danish privacy laws on the use of personal data are stipulated in The Act on the Processing of Personal Data (Act Number 429; May 31, 2000).[47,48]”
And once again, the slow loris demonstrates he has no clue how things work. Let’s go through these one by one.
1. in a research study, you absolutely cannot be photographed or fingerprinted without your consent. I have provided a few photos for research studies; in both cases, the doctors ASKED me, and assured me that my name would not be attached. Fingerprints were not taken, and very few medical studies would need them anyway.
2. Doctors do not accept credit cards, unless they’re named Sears, Byrzenski, or Gordon*. There’s this thing called insurance, or, you know, Medicaid. In any other country, there are national health systems. As for health information, it’s securely filed away. Yes, a sufficently motivated hacker could get into those files, but I don’t see why they’d want to, as it’s generally dullsville and only of interest to other doctors. There’s a huge glaring difference between office files and big fat database sitting there on the web.
3. Most of the time, you don’t order drugs yourself. You phone or click for a renewal and the pharmacist orders the drug. Unless you’re dealing with some fly-by-night compounding outfit, and like with Gordon or Sears, one could argue that anyone dealing with those outfits is already being robbed anyway, so they shouldn’t be surprised when additional chicanery occurs.
4. No one ever claimed facebook was confidential. Even Facebook doesn’t claim the pages are confidential, and there have been numerous warnings to that effect. If your facebook page has info on your medical condition, that’s because YOU put it there.
Anyone else like to weigh in?
capnkrunch 136,
I’m sure whatever involvement you have with data entry has interesting challenges, and requires some problem-solving skills, but you really are doing poorly at communicating. Which may be why I used the term non-sequitur earlier; I don’t see how any of this is related to whether my proposal is a good idea or not.
I can’t “address” some problem if you will not tell me what it is.
Anyone can access some random human dna in any number of settings, and, again, accepting your unlikely premise arguendo, learn something about some individual. In fact, the workers in the hospital where our cohort babies are born could scoop up all kinds of bodily fluids, and run a parallel zebra database. Wasn’t there a Thomas Pynchon novel along those lines, with a parallel post office? Is this the kind of thing that keeps you from sleeping at night?
PGP@140: Well, my doctor takes credit cards (for the co-pay). And yes, most medical files are super boring, but imagine if you wanted blackmail dirt on someone? “Does your wife know about your new case of herpes?” “Anti-retrovirals? Your mother will be so dissapointed.” Etc, etc.
There is also a law in the US that prohibits employers from sequencing you because that could be used to discriminate against you in hiring (or firing). “Oh, you have a very high likelyhood of cancer? We can’t have people here who won’t be able to give it their all…clean out your desk.”
And it is always possible that as our understanding of the human genome expands, what you can tell about a person from their genome will expand too. I’m not thinking GATTACA bad, but squicky.
This one is too good to pass up:
Hi, my name is Z., and I don’t know how Social Security numbers are issued.
The previous one seems to have vanished into the ether, so I’ll try again with minor variation.
Oh, Christ, not this sh*t again.
BTW:
Double fail by competent style authority. Clearly, Z. still fails to grasp the different nature of its original error.
Why? That’s the easy part, genius. What continues to perfectly elastically bounce off your skull is everything else.
The Crying of Lot 49
That’s what I was thinking of. There is a vast conspiracy of neonatal nurses tucking away bits of bodily fluid to create a Parallel Zebra Genomic Database.
Or at least, that’s what people should be more worried about than the actual Zebra Genomic Database, which is under strict (Canadian) government supervision [What could be more non-threatening than that, once they get rid of the current buffoons?]
It was called The Tristero Conspiracy, and it was either a parallel postal service or a paranoid fantasy.
Ah, I had previously missed the part where Z.’s fantasy involves the entire birth cohort being born in a single hospital. You can’t make this kind of desperately confused flailing up.
Narad: Ah, I had previously missed the part where Z.’s fantasy involves the entire birth cohort being born in a single hospital. You can’t make this kind of desperately confused flailing up.
Not to mention the outliers who get born on the road or at home. What sort of country just has one maternity hospital? I think even Luxembourg has multiple hospitals.
Justatech: And yes, most medical files are super boring, but imagine if you wanted blackmail dirt on someone? “Does your wife know about your new case of herpes?” “Anti-retrovirals? Your mother will be so dissapointed.” Etc, etc.
Yeah, but most offices are fairly well protected, and there are a lot of penalties for people who try that. Wasn’t there a case recently where the law came down really hard on someone who was trying to sneak records from Planned Parenthood?
Yes, there are differing state laws regarding Social Security numbers as unique identifiers. I’m not clear on the federal law for medical records since I think SSN’s are still being used as such in many podunk medical practices.
However, anything using SSNs would be a no go for me. A few years ago someone from the VA took a laptop containing veterans medical data home* to work on during off-hours. It was stolen and the way the government was able to locate me to let me know this was by using my tax records with SSN. It was almost 20 years since I had been in the military.
Moral of the story. TMI applies here. Too much information is at hand with SSNs already. No need to add more.
*Which I totally disagree with but totally understand if they are anything like business where they expect you to work in your sleep.
**Apologies if I posted this here before; my memory fails me, and often.
Thank you, malia, that’s the kind of answer I was looking for. I’ll be off to visit family later this month, so it looks like a few of us will be spitting into test tubes.
There is another way – you can connect it to an internet, just not the Internet. See https://en.wikipedia.org/wiki/SIPRNet
for an example. There are several others.
I made quite a good living helping to build a few private networks back in the day. But your other point is very valid. We had a saying ‘never underestimate the bandwidth of a truck full of mag tape’. There were times that a private armed courier with a pouch was faster and cheaper than 3 or 4 years of circuit charges. Ping times sucked.
Another point about Zebra’s silly plan – most people don’t have genetic anomalies, and beyond the number needed for a really, really good base line, I could see how, maybe 60 to 80% of the database would never need to be used (numbers pulled from my backside, maybe someone can offer up a better range if necessary). All the superfluous data would just sit there sucking up resources, both in the acquisition and the storage. The problem is that you don’t know which part you can leave out. Much better to sequence what you need as you need it.
I’m of two minds about the other half of his plan – his medical records database. Clearly, it violates the HIPAA laws, and mostly I think HIPAA is a good idea. But I also like to go out and spend an afternoon poking holes in a piece of paper (and sometimes tasty animals) with a few friends. But every once in a while, some nut case will decide to shoot up a church/ restaurant/town/policeman/school (and yes, you do have to be mentally broken on some level to use other humans for target practice). Everyone agrees that the mentally ill shouldn’t be allowed to buy guns. All we need is to have the government keep nice list of the ‘afflicted’, and Zebra has given us the rational (such as it is).
If by “mentally broken” you mean human, sure; I don’t see how it has anything to do with mental illness necessarily, though, especially given that people with psychiatric conditions are no more likely to be violent than “normal” people.
It’s an uncomfortable fact that pretty much any human is capable of atrocities, given the right set of circumstances, etc. The “just plain folks” soldiers in the Wehrmacht were just as awful, in fact, as the really committed SS guys. Then there are “crime of passion” impulsive murders, etc., which are also usually committed by “sane” individuals with a gun at hand during a critical moment.
I mean, if we’re going to profile people who buy guns based on how likely they are to commit a violent act, we shouldn’t be selling guns to men, actually.
Johnny @150. Here’s a better answer
http://real-psychiatry.blogspot.com/2015/08/anger-and-projection-are-not-political.html
Everyone agrees that the mentally ill shouldn’t be allowed to buy guns.
That’s all very well, but it gives the power to someone like me to decide if you’re mentally ill and to take away what was purportedly a constitutional right.
I’d estimate that, at a minimum, about fifty percent of the population will opt out when they hear the part about all their personal health information being sent to the government.
zebra@14 1
Here’s what I think is the most daunting confidentiality issue. The genome itself can be personally identifiable (i.e. by cross referencing against public genealogy databases). Giving researchers raw sequences is no go, and only giving them certain markers is risky because it’s not entirely certain what can be used to identify someone. This is an issue that already exists with our current data, as evidenced by how researchers were able to expose the identities of participants in the 1000 Genomes Project (see #130).
Right now there is no good solution to this problem. Homomorphic encryption is one potential solution. It allows comparisons to be done on encrypted data but with current technology the overhead is too high for it to be practical for large datasets. I’m sure there are other technologies being worked on but the problem of protecting genetic information is not solved.
I’ll say it again, if you want to talk about confidentiality issues it would behoove you to at least skim the article I linked to in #123. Here it is again for convenience: Routes for breaching and protecting genetic privacy.
Z.’s grandiosity is again noted. Of all the things I recall of Lot 49, though, this isn’t one of them.
Anyway, regarding my immediately preceding comment, maybe Z. didn’t mean “sequencing” at all, but rather “annotating” or something.
Or maybe he had no f*cking idea what he was talking about in the first place.
The Zebra Genome Project has already offshored its implementation. The fashion in which it’s “done so” is pretty embarrassingly funny, but I have get back to work.
Somebody with more time might want to look at how Denmark handles the information that it keeps
I guess that Icelanders hold the record for the fraction of the population with sequenced genomes, but IIRC they sold all the IP rights to a private company, so the company can do all their research away from the Intertubes and never have to worry about sharing data outside.
Wasn’t it the Mormons? IIRC they are busily collecting genealogical data so they can baptize everyone right back to Adam. Or is that a myth?
capnkrunch #155,
“This is an issue that already exists with our current data,”
Exactly.
If you were sincerely trying to answer my question (rather than offering a non sequitur because it’s a zebra suggestion and you want to be oppositional), you would explain why you think my project changes anything in a negative rather than positive way.
“Giving researchers raw sequences is no go”
Then, how are malia and Retro Pump doing their research?
How is what I suggest different from what people are doing now?
I would argue that my approach provides more, not less, security, for the reasons I explained.
So, unless you can actually demonstrate a net negative security effect from my approach, I will consider the security issue closed.
jp #151,
“I mean, if we’re going to profile people who buy guns based on how likely they are to commit a violent act, we shouldn’t be selling guns to men, actually.”
As a man, who has fired some guns in his time, I couldn’t agree more.
ann#154,
“I’d estimate that, at a minimum, about fifty percent of the population will opt out when they hear the part about all their personal health information being sent to the government.”
Especially the people on Medicare and Medicaid.
sigh
Right. Like I didn’t think of that.
Sigh.
Medicare and Medicaid are covered by HIPAA. What you’re proposing would require a waiver of that protection.
I do appreciate the concession of every single other point I’ve made however.
Speaking of which:
Do you mean people like malia and Retro Pump? Because they’ve both suggested otherwise. As in:
^^Retro Pump
And:
^^malia.
And (following up on malia’s “IF (and only if)”:
You haven’t addressed the substance of any of that, except by straw-manning. As in:
Blockquote disaster. Here’s that last part again, starting with malia’s quote:
How much clearer could that possibly be? I mean, what use do you expect people to make of data they don’t yet know how to interpret?
^^That second one’s a serious question. Please answer it.
@ Krebiozen:
It is the Mormons.
My cousin, who is researching our *interesting* family and her father’s (perhaps) even more intriguing clan, has used their resources for ( at last count) 3 countries- US, UK and Ireland- amongst other free on-line material she found. As we already knew, both families have been in the distilled hootch business ( gin and Irish whisky respectively). There are other businesses we knew about ( haberdashery) but some oddities ( a fruit merchant?) There may also be someone ( her family) who went to NSW .
So far though, no Norman Conquest.
And about Denmark:
a prof I knew used it for research about depression in families c. 1975-80.
ann163,
OK. We’ll use France or UK instead of Canada, and get about the same sample size.
Although I think you are incorrect that half of Canada’s citizens would be uncooperative. I’ve already said that USA is a bad choice because it is full of paranoid kooks, but nations with rational universal health care approaches I doubt would have such a rate of rejection.
To be clear, the Danish material didn’t involves the genome then.
AND I don’t think that the Mormon story is a myth.
My atheistic ancestors would not be thrilled.
ann
You haven’t made any points, so I can hardly answer them.
Cherrypicking quotes isn’t “making a point”.
As far as I know, the only commenter who has made a cogent response is Retro Pump.
And as far as I can tell, the only point about which we disagree is how quickly we would convert the data contained in the samples to digital format. I would love to have RP answer my query on that at #112. But you nor apparently anyone else has enough expertise to do that, as best I can tell.
Iceland, people, Iceland:
http://www.un.org/esa/population/publications/WFD%202008/Metadata/LB.html
Malia says that they don’t yet know how to appropriately interpret the data. That’s not cherry-picking. It’s her main point. She’s stated it concisely twice. And she’s also explained it at greater length twice.
You’ve ignored it. You’ve also misrepresented it by characterizing what she said as being about eye-strain, noisy data, and slow processing, none of which she mentioned. And when that’s been brought to your attention, you’ve mischaracterized the objection as being about chickens with their heads cut off.
I asked a question that you absolutely can answer. It is this:
What use do you expect people to make of data that they don’t yet know how to interpret?
This is also not cherry-picked. And it is a valid point:
You would not be saving costs on presently ongoing research by spending money on something that researchers presently don’t need and can’t use.
That’s a significant obstacle. To most people, it would be a dealbreaker, in fact.
How do you propose to overcome it?
Ann, I hesitate to respond quickly in case you are going to have one of your sequential commenting fits and stuff will be crossing on the wires, but anyway.
Look at the reference to the Icelandic study. Look at the number of “working geneticists” who apparently thought it was a good and useful idea. Go figure– is it some peculiar Icelandic genetic derangement that caused such agreement, or is it just scientists who want to move their discipline forward?
Now, I’ve dealt with the funding issue more than once, so you will have to go back and read more carefully. The data will be provided free or at a nominal fee to qualified researchers, and it will not take funding away from existing funding agencies. (And I still haven’t seen any evidence that operating budgets would be unmanageable at all.)
But as to malia and RP– the data isn’t for them specifically, it is for an expansion of research, so that people can figure out “what to do with the data” sooner. That’s how basic science works, by lots of little grad students working on lots of little projects and figuring out better ways to do things and contributing to the whole. Malia and RP can go on with their 20th-Century approach, and we will see which bears more fruit.
@#168 —
Canada:
Another 28% said that it would probably be the case.
Additionally, seven in ten Canadians think that protecting the personal information of Canadians will be one of the most important issues facing the country in the next ten years.
That was as of 2013.
>PDF link.
Per an even more recent survey, a majority of Canadians are also just distrustful of government generally.
What Iceland where their project to collect genetic data was ended thanks to precisely the kind of privacy issues you have dismissed out of hand?
Ann#175,
Since the information would not be available to the participants, so they couldn’t be asked for it, what possible relevance does this have?
Once again, like capnkrunch, you are providing non sequitur with respect to the specific plan I am proposing.
zebra@160
So the solution is to expand our data gathering efforts when there are already confidentiality issues with our current data? How exactly does that make anything better?
Yup, I was wrong here. It’s this data that can’t be publicly disclosed, not that it can’t be disclosed to researchers. Ideally, even researchers should not be accessing personally identifiable information. It’s a tenuous system already. Greatly expanding the amount of data will only worsen things.
For one, scale. On small scales some security measures work fine. For example there have been successful implementations of homomorphic encryption on datasets of 20 or so. Resource consumption scales with size. We’ve been telling you this the entire thread and somehow you still can’t grasp the concept.
More importantly, it doesn’t matter whether it is different. The current scheme has issues. You even agreed at the beginning of the post.
Look. I’ve given you plenty of references and encouraged you to read them multiple times. At this point it’s clear your ignorance is entirely by choice.
Krebiozen@176
Very interesting. o
Further @#168 —
The UK:
It’s already failed.
They actually proposed it. But they have just as much opposition to governmental invasion of privacy there as we do here, and it’s much better organized. Plus they have a very bad track record when it comes to keeping patient information private.
So the idea met with a lot of opposition due to widespread privacy concerns and expert opinion to this general effect:
So it never happened.
They do have a databank of half a million people, though.
zebra@177
Do you know what a non sequitur is? There are legitimate confidentiality concerns with current datasets. There are proof of concept attacks to deidentify genomic information. Starting a mass data collection campaign without solving these issues first is irresponsible in the extreme. And it makes even less sense to put the PHI of so many people at risk when you have not one but two experts in the field telling you they don’t even need the data.
My point was that almost half of the Canadian population has indicated that it would refuse to participate in the collection of genetic information due to privacy concerns, in which case they wouldn’t be participants.
This is relevant to your argument that “paranoia” in the US wouldn’t be an obstacle in countries where the government provides universal health coverage.
That’s untrue in both the UK and Canada. There are very high levels of distrust and protest regarding the databanking of personal health information generally and genetic information in particular in both.
France:
The direct transmission of genetic information by health-care providers to other persons or institutions is forbidden, apparently without qualification.
So strike three. It wouldn’t work there, either.
Any other ideas?
There’s a 186-page .pdf summarizing pertinent national regulations worldwide here, if it helps.
capnkrunch,
Yeah, I think you are dodging the question.
Is it a bad idea to expand genetic research?
Or
Is it a bad idea to expand genetic research using Zebra’s Database?
And you can’t say “both”.
The fact that you can’t directly respond to that question is why everything you’ve written is a non sequitur. It has no relevance to whether my way of doing it is better or worse for security.
If a researcher has N genomes, the security issue does not depend on whether she obtained them from the central database or by taking samples and sending them out for sequencing or doing the sequencing in her lab.
The fact that you refuse to acknowledge that demonstrates that you are not trying to make a sincere argument.
Also, wrt to this:
I’m not sure I even understand what you’re saying.
If they wouldn’t be asked to provide their personal health and/or genetic information, how could it be legally obtained by researchers?
If you’re suggesting that the government just hand it over, it’s precisely the fear of that kind of thing that makes almost half the Canadian population unwilling to get genetic tests.
So it’s still a relevant point.
And to avoid any purposeful misunderstanding, that’s “N genomes in digital format on her computer.”
I’ve already indicated that I think my method is more secure than either of the others in total.
zebra —
Please explain how you plan to overcome the widespread popular objection to genetic databanking in the UK and Canada.
Please also explain how you plan to overcome the legal obstacles to creating such a databank in France.
Or, alternatively, please suggest a nation where your project would be feasible.
PS —
Whether or not data is secure actually does depend on where it comes from, who collects it and where it goes.
zebra@183
Both you asshat. Until there are better privacy protections in place I think any mass collection of genomic data is irresponsible. Do I think we should stop using what data we have already? No. Do I think it would be reckless to collect additional sequences on a large scale? Hell yes.
Scale, scale, SCALE! you twat. There’s a difference between exposing a couple thousand people’s (about what the biggest datasets are now currently) PHI and exposing hundreds of thousands. Most of the current datasets were collected before the problem was well known. Those reseaechers had an excuse, no one knew the privacy imications of collecting genomics data. You have no such excuse.
There’s also a difference between privately held data (i.e. a researcher sequences genomes in her own lab) and shared data (i.e. a database that needs to be accessible by many different organizations). The attack surface is much greater in the latter scenario.
Using our current datasets, people can already be deidentified using their genome. Why the hell would we want to expose hundreds of thousands of more people to that? The fact that you choose not to answer that question means you are just being deliberately obtuse.
@185
Ah yes. I remember you saying that but you never explained why. I can’t imagine why you think that given that the attack surface is much greater. Please do enlighten me, great security guru zebra.
This thread is getting very tiresome. Barring a reply with some substance from zebra I’m bowing out.
No. It’s that you’re wrong to say that.
Flatly wrong.
The national Icelandic database was a government-backed commercial endeavor, and it was not supported by scientists or doctors:
Got that? The national database was not the one that was going to be used for diagnostic/therapeutic research.
And it was opposed by the people who do such research:
Link.
That’s why the project failed, just as it did in the UK.
As to this:
You have yet to produce an example of so much as one, single 21rst-century thinker who wants such a database besides you.
All the attempts to start one have been corporate-government partnerships the (ostensibly) scientific justifications for which were decried by scientists in terms such as “complete balls.”
I’ve read what you said. That the data would be provided free does not save costs unless people need and want but can’t afford it. And there’s not a whisper of a hint that that’s the case. On the contrary, all the evidence suggests — or even states — that such a database would be useless for research purposes. For example, as the article linked above says:
Got that? The kind of research you have in mind is presently impossible. So you would not be saving costs on it. It can’t be done.
That leaves you with the expense of compiling a database to make useless information freely available.
And if the money would not come from existing funding agencies, where would it come from? Setting up and staffing a new agency would just add to the costs.
Given that zebra can’t name a country where his idea is feasible or produce any evidence at all indicating that there’s any need, wish, or use for his project I think that unless he does, its uselessness has been too fully demonstrated to require further proof.
So I too am bowing out until then.
Take it away, z. The field is yours.
capnkrunch:
If you oppose expanding all genetic research because of security concerns, that’s fine, but you could have said that way back. I happen to disagree with your risk assessment, and that of the numbers of people ann cites as having concerns. It is often the case that people misperceive relative risks; I think that has been discussed here in the past.
I think I’ve expressed my take on this but lets see if I can briefly revisit it. There are “hundreds of thousands” (millions, actually) of medical records extant in many locations– not genomes, but actual medical records with easily understandable information about individuals and their health issues. So the “attack surface”, if I understand you meaning, of my database represents a trivial relative risk.
If there are any Willie Suttons out there looking to exploit and monetize medical information, they would be attacking Medicare and Medicaid, the VA, and the private insurance companies.
Why would they go after this not-very-liquid asset, which requires much more work before they can identify individuals, and which is tiny in “scale” compared to what they can get from any of the other large institutions, with many more avenues of access?
I’ve pointed this out in various forms more than once. I’ve also pointed out that the actual mechanics of my project keep things as arms-length as is possible, which ann is clearly befuddled by, and she needs to review how I’ve said it would work.
Relative risk– people just aren’t very good at thinking these things through.
Ann190,
I already mentioned the UK which has a large government-owned database which uses phenotypical grouping.
The Iceland study I talked about is here:
http://www.nature.com/ng/journal/v47/n5/full/ng.3247.html
Since your link doesn’t work, I am not sure what you are referring to.
@#192 —
That study only did whole-genome sequencing of 2,636 Icelanders, not the whole population. If it demonstrates anything, it therefore demonstrates that the kind of database you’re proposing isn’t necessary for genetically homogenous populations.
However, as it happens, your idea was attempted in Iceland. And it fell apart for the same reasons it did in the UK. Scientists and physicians opposed it, and there were privacy concerns.
The busted link is here:
http://www.the-scientist.com/?articles.view/articleNo/19517/title/Iceland-s-Public-Supports-Database–But-Scientists-Object/
^^As you might gather from that, the public was not initially opposed. This was in 1999. However (as explicated at krebiozen’s link) the Supreme Court put the kibosh on it in 2003. And concerns about privacy have greatly increased since then.
krebiozen’s link, in the event tht you need it, is here:
http://www2.law.ed.ac.uk/ahrc/script-ed/issue2/iceland.asp
SHORTER VERSION: Iceland didn’t need a national genome database to do that study. And when one was proposed, it failed due to the objections being raised here and everywhere else in the world that a corporate-government partnership tried to rustle one up.
In all cases I’ve seen so far, scientists and researchers didn’t want or favor the project. That includes Iceland. This:
is therefore flatly wrong. That study sequenced fewer than 3000 people. It did not require a national database of genomes. And the working geneticists who did it apparently were perfectly well able to move their discipline forward without one.
Ha.
I’m not the one who suggested that a study in which working geneticists were able to reach conclusions about the population of Iceland by whole-genome sequencing a mere 2636 people constituted proof that scientists wanted and needed a population-wide genome database in order to move their discipline forward.
ann,
First, the UK project here
http://www.genomicsengland.co.uk/
is alive and well, or at least its website is.
There was a commercial Iceland project that was sold off multiple times after not making money, but that is nothing like what I am suggesting, and I don’t know what connection there might have been with the Nature paper I referenced. That was the first thing I came across.
But as I said earlier, you don’t seem to grasp the concepts very well.
I am not suggesting that the entire population of Canada should be included in the database.
Nor have I ever suggested that any individual study would use the entire database.
I already went over this multiple times and refer to these ideas as grandiose strawmen, which accusing me of suggesting is ridiculous even by the standards of this blog’s comment threads.
You obviously haven’t comprehended what are essential elements, like the fact that the genetic information is completely isolated, including from the people contributing it.
You seem to think that if half the population refuses to participate, we can’t collect the data from the other half. It’s like gay marriage, ann, if you don’t believe in it, the law doesn’t require you to participate, but you can’t stop other people from doing it. And anyway, you and capnk keep complaining that there is too much data– ok, you should be happier with half as much, right? That’s something around 190K genomes.
So if you just want to keep repeating this stuff which is either wrong or irrelevant, I don’t know how to further help you.
Yes, I know. The one that failed was the one that was like what you’re proposing — government sponsored, all citizens, cross-referenced through the NHS, etc.
Read the link.
It’s the same project. The company is called DeCODE. It made a tremendous amount of money hyping itself, then crashed, leaving individual shareholders with trash.
For example:
http://www.theguardian.com/science/2002/oct/31/genetics.businessofresearch
Ha.
You may now troll yourself.
I’m bowing out.
IDK, zebra, maybe you need to ask those here to look at your genome db proposal while on…weed.
You’re beginning to sound like a communist. “Yeah, communism historically has caused untold misery but you just haven’t tried my communism yet.”
And you then you take it personally that they are against it because you mentioned it. You know, I originally thought the scientists here would take a database of this information if it auto-magically dropped in their laps. Not that this was ever in anyone’s power to do anyway, but they made a good case why they wouldn’t even want that. Data is not information. Throw in all the other unpractical reasons and this idea is dead in the water.
But don’t worry, it always was because there is no will, money or defining interest in it yet. The efforts are better spent elsewhere. Like, maybe, feeding people whose genes may or may not hold ticking time bombs. But as I have learned in resisting the never ending worry about my hypertension and cholesterol by MDGPs and naturopaths, it doesn’t matter to me what is going to kill me in ten years if I can’t survive in the present time.
zebra,
OK. There’s no “there” there. I’m following ann. Some parting comments:
-I’d challenge you to reexamine this belief that “I don’t agree” constitutes a valid argument.
-Comparing relative risk of storing personal medical data and of centralized collection of research data is meaningless. I’ll leave it as an exercise for you to figure out why (hint: you’re using the wrong risk assessment tool).
-The prevailing (and most prudent) paradigm in information security is to minimize all unnecessary exposure, not that additional exposure is ok so long as it is trivial compared to another.
Which, of course, is why Z. proposes a monolithic government project. Add in completely whimsical, magically free data access, and Problem Solved!
Oh dear, oh dear, Z. has demoted poor Malia from “real expert” to “20th century thinker.” How will her NGS lab go on?
(For those keeping score, I’d rank the juxtaposition of these two quotes as being a genuine non sequitur.)
It’s truly amazing the amount of hubris that one person who has no practical or theoretical understanding of any of the scientific disciplines involved* – indeed, who can’t even recognize a basic arithmetic error – much less the issues surrounding privacy and ethics in human subjects research can single-handedly generate.
* “capnkrunch 136, I’m sure whatever involvement you have with data entry has interesting challenges, and requires some problem-solving skills….” Sweet Jesus.
So the issues with the “birth cohort genome database” are:
1) We can’t get the medical records we would need to know if any given gene actually has a relationship with a disease.
2) We don’t have the processing bandwidth (technical or human) to actually analyze the data.
3) The cost of storing 1 cohort’s data is about $1million. Yes, I know Z said we could get it by not making F35s, but since when has DoD ever given up a single penny of their budget to someone else? See bake sales for bombs.
4) It would take generations to be able to learn anything about adult-onset diseases.
5) Acquiring the genetic material to sequence requires both an approved study and the informed consent of every single person in the cohort (or their parents, and given how protective people are of their children I think that a 20% enrollment rate would outstanding).
6) We already know that we cannot keep the data private, as is required *by law* for any human-subject study in the US (and most other countries).
So aside from all that, it’s a brilliant plan.
There was a commercial Iceland project that was sold off multiple times after not making money […] and I don’t know what connection there might have been with the Nature paper I referenced
Perhaps you should have read the paper.
That list has some omissions IMHO, but I’m certainly not going to fault anyone with losing interest in this Z. misadventure.
Not a Troll @198: I can’t speak for anyone else in the commentariat, but I suspect it would take LD50 levels of tetrahydrocannabinol to get me high enough to think that our equine friend’s database might be a good idea. Several commenters have raised a number of objections, any one of which should have been sufficient to sink the project, yet he remains as impervious to rebuttal as an old-fashioned vinyl record. (Or CD, in case you are too young to remember vinyl records.)
He reminds me not so much of Communists, as of political figures like Reagan and G. W. Bush. They would get certain ideas in their heads, and no amount of evidence to the contrary could get them to abandon those ideas. He seems to disdain those of us in the “reality-based community”, to use a phrase coined by an official in Bush’s administration.
Indeed, and not just for the punchline. Reference 18 looks totes kewl, as well, even if it is seven years old.
But this episode highlights, for me at least, Z.’s serious, ah, “oppositional” take on “20th century” notions regarding the order of carts and horses.
This one seems to mark the beginning of Z.’s realizing that Malia was getting uppity, or something:
Then again, the whole single-cohort routine does at least do away with the hoary 17th century dualist notion of comparing the size of the cart and the horse and thinking about maybe putting one on top of the other instead.
For those of you who think that z*bra is unable to learn may I point out a fact which TOTALLY destroys that hypothesis: z*bra changed from writing “non-sequitur” to “non sequitur” midway in this thread! Nothing else has penetrated its addled pate but s/he is demonstrably better informed than when this conversation began.
And yet, he’s dazzled unto blindness by the 21rst-century-ness of an idea that people have been using to fleece suckers, marks and governments since 1999 — eg, DeCODE — precisely because it elicits that response.
You’re leaping to the assumption that he’s figured out why.
[…] Orac is on vacation recharging his Tarial cells and interacting with ion channel scientists, as a good computer should. In the meantime, he is […]
A note on the quality of the responses, ann at 196
1) This is government sponsored and government owned and obviously they have access to the NHS data.
2) If anyone is smoking or imbibing something, it seems to be ann, who still hasn’t figured out– despite the fact that I just said it– I never suggested anything like “all citizens”. Grandiose strawman.
And various others presenting various strawmen and gish gallops too numerous to mention.
The good news is that RP, who is actually qualified, “got it”, and that makes it worth the trouble.
zebra,
You wrote something so idiotic it annoyed a long-term lurker enough to delurk and write:
Yet you somehow interpret this to mean RP agrees with you? Astonishing.
Question for non-zebra posters, what would the ethical implications of such a database be? I’d imagine that collecting medical information past the age of consent would require a new consent from the patient themselves but at that point could they request that information gathered with their parent’s consent be deleted? It seems a little questionable to me to allow a parent’s consent to be enough to collect the information and store it for an arbitrary amount of time. Maybe if it was collected with parent consent and couldn’t be used until the patient was at the age of consent and provided it.
Also, forgot to say it before, thanks malia and Retro Pump for chiming in. If nothing else, zebra at least stimulated some new people to delurk. I agree with Narad’s sentiment in #110.
Krebiozen #210,
“Yet you somehow interpret this to mean RP agrees with you.”
And yet another bizarre strawman, based on yet another cherrypicked quote.
Thanks for demonstrating my point.
I could have done without the high horse insults but I actually learned a great deal from this discussion. And for those who had a fair grasp of the subject before, I hope it strengthened your thinking on it.
Yes, I know.
But you’re proposing a government-funded DNA database of the entire national birth cohort for one year, with a view to creating a resource that’s large and nationally representative enough to provide researchers with the subpopulation sample of their choice.
The UK proposed something equivalent. And as I said @#179, it failed.
Read the link I provided. Here it is again.
The project you’re linking to now is also a government-sponsored large DNA database. But its exclusive research focus is cancer and rare disease. It recruits exclusively from a pool of patients who have already been diagnosed, plus their relatives.
Fergus mentioned it back @#115. And you ignored it. Because it’s not remotely like what you’re suggesting.
The entire point of your project is to assemble a database that represents something like all citizens — an entire birth cohort.
You directly admitted that it was akin to a population-wide*** project yourself. (“Iceland, people. Iceland.”)
***Or actually what you wrongly believed was one. But same difference.
zebra @#174:
And zebra @#209:
Ann
“Equivalent” is just your (yet again) ridiculous strawman. But putting that aside:
“The UK proposed something equivalent. And as I said @#179, it failed.”
In 1992 or so, the Clinton administration tried to institute a universal healthcare system. It failed.
So I guess that for you, that would be evidence that universal healthcare is a terrible idea. And that no progress could possibly be made towards that goal, under different conditions and incorporating lessons learned from the first attempt.
As I said, strawmen, non sequitur, gish gallop, yadda yadda.
After they somehow are able to a priori define meaningful subpopulations based on combinations of subsequence queries.* Unless, of course, the “results” are going to require genetic screening of everybody to have clinical utility.
* Again, nobody’s going to be handing out entire genomes willy-nilly based on fishing-expedition–level proposals.
There look to be a lot more questions than answers. Pages 323–24 here (PDF) are on point. (The Elger & Kaplan is here; “supra note 133″ in n.143 is a typo for 135.)
One key issue is that the sample donation, by definition, does not provide any benefit to the donor, although it does entail ongoing risk. For that matter, if things go swimmingly, the end result will likely be a private company reaping a handsome financial reward from all the donated samples.
^^ In fact, now that I think about it, Z. seems to have been awfully short on that “clinical utility” thingamabob in general.
Since it’s your bright idea and you’re invoking them, what would those “lessons” be?
capnkrunch,
In the UK the Nuffield Council on Bioethics has done a lot of work in this area. It is difficult for many reasons, for example because a person’s genome also gives information on their relatives’ health, thus impinging on their privacy too. There are also issues around informed consent, as we don’t really know yet what information might emerge from the genome in the future. Some embarrassing or even criminal characteristics might be connected to some constellation of genes – imagine if someone found an association with pedophilia, for example (as unlikely as that may be).
Narad #220,
Better politics. Duh.
Let’s see–
Death panels, keep the government’s hands off my medicare (ann might have been one of those), your giant corporate employer will drop your coverage, blah blah blah…
Here it’s some kind of ninja codebreakers….
1. Accessing the digitally encoded genome of a small random part of the population, either by getting into a secure database (or I think someone was worried about Fedex? trucks carrying hard drives being hijacked?)
2. Figuring out the medical information contained in the genome, which our experts say is excruciatingly difficult.
3. Determining who the individuals are from the genome.
4. Somehow turning all that into a profitable venture….
5. Instead of paying off some minimum-wage data entry person to get them access to medical records at the insurance company.
So yes, just like one set of irrational concerns was overcome, good politicians convincing enough people not to be stupid is what you need. Just like with the vaccination exception problem, as an even more recent example.
Re #222
I think we are up to ~221 posts trying to convince you not to be stupid. It’s no easy task when we are confronted with a D-K sufferer who is showing all signs of being in the top 1/10 of 1% of all those so affected.
As well you might, since it is equivalent, by your own admission.
Why, no. It would not. Because there’s abundant evidence that universal healthcare is a good idea, which can and does succeed time and time again.
But speaking of gish-galloping, cherry-picking, non sequiturs, and straw men:
As I’m sure you know, when I first raised the point it was in the context of pointing out that there were, are and have been such numerous and widespread objections to your tired old “21rst-century” idea everywhere in the world that anyone’s ever tried introducing it for the last sixteen years that that’s how long it’s been failing!
And as I said: Ha.
Narad@218 and Krebiozen@221
Thanks. That’s exactly what I was looking for. I made it through Narad’s links and have been skimming Krebiozen’s. It definitely seems like an interesting area in bioethics. Interestingly (to me at least) is that there doesn’t seem to be any issue with parents consenting to their children’s data being stored, as long as the child has the ability to opt out once they reach the age of consent.
I thought that would be more of a problem, especially in light of what Narad said:
I always thought the principle behind allowing parents to consent for children was that they could make decisions that are best for the child but the child wouldn’t make for themselves (i.e. no child would choose to get injections). In this situation where the benefit to the child is more unclear (there’s benefits for society but not necessarily the individual) I had figured the same principle might not hold. I’m not an ethicist though and it seems like the experts think otherwise.
You would have done yourself a favor to pretend that you had never seen the question.
I’ve already openly wondered here what on earth your college or university training was in; in point of fact, I often have a hard time convincing myself that you’re not a none-too-bright high-school student.
I confess that when I pointed to the Iceland red herring back in comment #158, it seemed too much to hope for that anyone would take the bait.
Opus,
That’s my comment at #222 – I do hope you aren’t referring to me.
HDB,
You did kindly point out that bear trap, but zebra just blundered on in anyway.
I do find it hilarious that zebra is now simply dismissing the enormous problem of privacy that hundreds of the best minds in genomics and bioethics are currently wrestling with.
Krebozien @ 229
My comment was to z*bra’s at 223.
Memo to self: check for typos before noting someone else’s stupidity.
Narad #227,
I was really surprised that an experienced drive-by troll like yourself would pitch me such a softball.
Although if it’s better politics he’s looking for, I’d suggest business-friendly Qatar. It’s an absolute monarchy without much in the way of civil liberties and a partnership with Weill-Cornell Medical College. The politics couldn’t be any better, really.
There’s even a regional precedent of sorts:
Kuwait, people. Kuwait.
Krebiozen #230
Why would any mature, rational (non-paranoid), non-Authoritarian adult do anything but dismiss this kind of silliness about “ethics” and “privacy”?
I also don’t pay much attention to the ruminations of very bright, very well educated Roman Catholic theologians, who are equally discussing meaningless concepts. Is that also “hilarious”?
To the extent that society is actually democratic, decisions can only be made on the basis of group self-interest. Crudely put, something like greatest good for the greatest number.
(I have no moral/ethical position like Utilitarianism, that’s just a familiar form of expressing a pragmatic approach.)
Sorry. That link should have been:
Kuwait.
If you’d like to ask some who don’t, the names of the ones who serve on the advisory panel of national leaders in medicine, science, ethics, religion, law, and engineering over at the Presidential Commission for Bioethical Issues are right here.
Ann @236,
Ah. The answer to a non-Authoritarian thinking something is unimportant is Appeal to Authority.
Well OK, I guess that’s settled.
Ann, you need to take a breath and think. Once in a while you demonstrate that you can write a complete paragraph that makes sense, but this kind of thing inclines one to not bother reading your comments.
Kuwait: I’m not going to waste my time researching the intricacies of the Kuwaiti political system, but I think it isn’t very democratic. Also, the actual citizens (not foreign labor) tend not to care that much because they are petro-wealthy. But maybe I will be corrected.
You should read about the very long battle to institute Universal Health Care in the US and the forces that opposed it. You should also, again, pay attention and think– 1992 was only 23 years ago, and everyone said UHC was never going to happen. And then there was don’t ask don’t tell, which was considered the best possible compromise at about the same time, and look how far we’ve come with respect to marriage equality. Not one person would have predicted where we are today.
So, I wouldn’t be so impressed that some attempts to do genetic research and collect data have been blocked; it’s early days.
It is also the case that GMO have been blocked in Europe. Does that mean GMO are a Bad Idea, and they will never be accepted?
For someone who complains about non-sequiturs….Zebra throws out quite of few of them, doesn’t he?
zebra,
I suspect explaining anything that a “mature, rational (non-paranoid), non-Authoritarian adult” might do would go right over your head. Let’s try this: how would you like it if it your genome was publicized and it was revealed that you had a constellation of genes associated with tiny-penis-syndrome or intractable-pig-headed-disease?
Concerns about privacy are not about being “Authoritarian”, they are about people being rightly worried that their privacy might be compromised by government and big business. That’s the opposite of “Authoritarian”.
What you seem to have a problem with is the idea that some experts know better than you do. Perhaps you have never studied any subject in enough depth to realize just how little you know and the need to have people specialize so they can advise those of us who have other areas to specialize in. I spent two years studying genetics, passed exams on the subject and have read dozens of books on the subject over the years, enough to know just how little I know. I would never have the hubris to accuse two geneticists of 20th century thinking, I am quite certain they know better about that area than I do. You appear to have no concept of the vastness of your ignorance.
You seriously think that privacy concerns about data that can be used to predict a person’s medical future and have real tangible consequences are “meaningless concepts” of a similar ontological status as souls and sins? If you do you are even dimmer than I thought. Once again you equate scientists with other groups, as if science is just like religion, or woo. Have you drunk from the PoMo cup?
What are you babbling about now? Sequencing the genome of millions of people isn’t going to give us useful data, for several reasons that have been explained. That isn’t group self-interest or the greatest good for anyone. Any normal person would have admitted they were wrong and joined a discussion about the best way to go forward instead of embarking on a moronic pantomime as is your usual MO. Not for the first time I find myself seriously wondering what is the matter with you?
You have been told, by two people who work in the field, why your suggestion is utterly impractical, yet your ego won’t let you admit you were wrong.
Not only that, but you are rude to people who have been perfectly polite to you, and accused those whose explanations have been easily understandable and make good sense of being bad at communicating, or of being on drugs. In short you are a twit of the highest order.
No. The answer to blind solipsistic bias is exposure to the thoroughly considered views of others, conveniently available online in .pdf form.
Also, I suggested that you ask them, not that you take their mere authoritative existence as proof of anything.
No, once again you’re using a straw man to avoid addressing the substance of the objections.
You wound me to my very core.
Was the fact that it has compulsory DNA testing your first clue?
Technically, it’s semi-democratic, which — if you ask me — means it’s an autocracy that can afford to allow a superficial and largely cosmetic veneer of freedoms in some areas.
The problem with talking about what the actual citizens care about is that it presumes that the concept of citizenship plays a part in the way Kuwaitis think about themselves, others, politics and/or where they live. It’s not that kind of place.
However, since I’m not sure what you’re saying they don’t care about, exactly, I guess it doesn’t matter anyway.
I’m a politically active person who has not only lived through but actually fought in some parts of that battle, which is — incidentally — not actually over, because guess what?
We don’t actually have universal health care in this country.
Yeah, well. I’m an optimist myself.
But I can see how 23 years of dealing with implacably ill-informed, self-regarding, and overly complacent bozos who evidently don’t even know what UHC is could make a person kind of dispirited.
Not by me.
I think you mean “not one person who knows so little about the fight for marriage equality that he thinks “don’t ask/don’t tell” had something to do with it would have predicted where we are today.”
Because although the outcome of Obergefell v. Hodges wasn’t certain, it was among the reasonably foreseeable options.
Speak for yourself, IOW.
Enjoyable as it’s been batting them around, those analogies are straw men. There’s no constituency fighting for the right to establish a DNA database of the entire birth cohort for one year. There’s no popular political demand for one. There’s no scientific demand for one. And not only that:
Widespread, well-grounded and rational political and scientific objections are actually what’s prevented private-sector corporate interests seeking profits from doing an end-run around democracy by partnering up with advocates for a surveillance state in order to set one up.
So get back to me when you can make a case for it being a cause worth fighting for that’s a little more persuasive than “I can see the future because I say so.”
Or make it now, if you have one.
No. But my point has never been that your proposal is a bad idea because it’s been blocked. It’s that it’s been blocked because it’s a bad idea.
So that’s just straw plus straw.
Your somehow managing to hit it directly into your foot was certainly impressive.
On the other hand, the fact that your grab-bag of language failures includes the word ‘troll’ is merely dirt-common.
^ Actually, it was closer to deciding on a sacrifice bunt with no runners on.
I tried to make this point back in comment 139, but Z. must have been too busy with some other facet of his brilliance to notice.
Krebiozen 239,
The issue is with “privacy” and “ethics” as concepts– they are just as vacuous as souls and sins. How is “being unethical” different from “sinning”? In either case, some authority has created a set of rules which don’t have legal consequences. If they do have legal consequences, we call them…you know…laws.
If you are asking whether I would vote for laws that restrict access to my medical information, that’s a different question. Of course I would, as a practical matter. But other than through the interpretations of SCOTUS in the USA, I have no “right to privacy” that I can characterize– I would have to go to court with standing in a specific case to find out what that would entail. Just like I suppose I would have to die to find out if I have an immortal soul.
Does that help with understanding my ontological perspective?
And of course, as should be clear from multiple comments on the topic, my vote concerning genomes would be influenced by what I consider the relative risks of any particular program. Since my clearly understandable medical information, not to mention my penis size, is on record with multiple entities, I consider the relative risk from those ninja hacker codebreaker criminal geneticists I described in 223 to be negligible. If you have concrete evidence (not speculation) to the contrary, let’s hear it.
By the way, if you don’t want to be characterized as befuddled (for whatever reason), or just being childishly dishonest yet again by taking quotes out of context and MSU:
See, I never said any of those thing. I equated ethics with morality. Nothing about scientists. Nothing about the practical matter of access to medical records being restricted. Grow up.
Ann
This is what I mean. What does one have to do with the other?
The howlers just keep coming.
If you’re not a member of congress, he probably wasn’t asking you whether you would vote for any laws.
How — how, ffs, how? — is dying like going to court to find out if you’re safe from illegal search and seizure in your own home?
I mean, that you’d have to [do something] in order to find [something] out is really not a unique enough distinction to be categorical.
No. I’m not sure I even see any ontology.
Unless you’re only weighing the risks to yourself, that would be an ethical consideration, by definition. BTW.
…
Well. That voting-for-laws thing makes more sense if you’re Anthony Weiner.
I suppose you might also be Iggy Pop. But it seems unlikely. He’s very articulate.
And there are, no doubt, other possibilities, too. Still. If you don’t mind my asking:
Exactly what entities keep records of your penis size? And in what form? (Meaning “in what form are the records?” not “in what form is the size of your penis recorded?”)
There’s no such thing as concrete evidence that a straw man you invented yourself @#223 does or does not pose a negligible risk. And can’t be.
Ontologically speaking.
@#245 —
A law requiring compulsory universal nationwide DNA testing with no exceptions, no informed consent, and no regulatory limits is so completely incompatible with the basic democratic principle of respect for human rights that any country that has one is, necessarily and self-evidently. not very democratic.
Human rights? Democracy? Vacuous concepts.
I couldn’t really tell whether his point was that all concepts are vacuous per se or whether it’s just the ones that can’t be instantiated he rejects or…I don’t know. I was baffled by that.
Because this part here…
…seems to suggest that because laws serve a practical purpose they are, though conceptual, not vacuous.
However, the same not only could be said of ethics, it would almost have to be if it was also said of law. They’re not entirely conceptually discrete.
I’m not going to get into whether that also applies to religious morality, because murkiness. But a case could be made.
The really confusing thing, though, is that starting here…
…it all of a sudden turns out that it’s the concepts that have legal consequences — or, you know, “laws,” as we call them — that are as vacuous as the wages of sin.
So I guess I would say that zebra just scorns the concept of concepts, generally. But I know that can’t be true. Because:
So apparently the thing that distinguishes a vacuous concept from the good kind is whether zebra is capable of conceiving of it unaided. Which is conceptually problematic, from an ontological perspective.
The whole thing left me befuddled, I don’t mind frankly confessing.
The issue is with “privacy” and “ethics” as concepts– they are just as vacuous as souls and sins. How is “being unethical” different from “sinning”?
Speeches like this really need to be delivered in a laboratory, in the bowels of a castle or an extinct volcano. With lightning crashing overhead.
YOUR PETTY HUMAN ‘LAWS’ and ‘MORALITY’! THEY CANNOT BLOCK THE ADVANCE OF SCIENCE!!
There’s something oddly appealing about zebra’s child-like naïveté around human nature (and human dignity). Yet since he is an adult, a case could be made that it is more like childish ignorance.
Ann,
I’ll leave you with this and check back tomorrow to see how you do.
Prior to the US Civil War, it was “illegal” to aid an escaped slave–punishable by imprisonment and a hefty fine.
Was it “unethical” or “immoral” to aid an escaped slave?
Prior to the US Civil War, it was “illegal” to aid an escaped slave–punishable by imprisonment and a hefty fine.
Was it “unethical” or “immoral” to aid an escaped slave?
What the everloving f*ck is this even supposed to mean in this context? Z. is trying to be all didactic about the difference between “legal” and “ethical” after just having declared the entire concept of ethical and unethical actions as being equivalent to “sin” in the religious sense, and therefore empty and meaningless? The mind boggles</b at such inanity.
What I'm wondering, actually, is just who Z. imagines his achingly tiresome sh!tfit of a performance is for. Is he trying to “educate” the lurkers, of whom a couple* have delurked specifically to explain just how wrong and ignorant Z. is? Is he trying to “educate” the regulars? Who does he imagine is laughing with him at home?
It all betrays a “See Noevo show” level of idiotic grandiosity.
*who happened to actually know what the f*ck they were talking about, to boot.
^Multiple tag fails are parse-able, I hope.
Another non-sequitur from Z, why am I not surprised?
Zebra,
I get your point that ethics, sin and law are malleable. Although I happen to be one who thinks that certain truths are self-evident, you can go on with your idea because you don’t get to say what my inalienable rights are.
Interestingly enough (or not) a couple of months ago I provided consent and some of my DNA for a study. However, I knew going in what it was for, that it is with one company, and under all the rules and regs regarding study participant’s information. But even I wouldn’t go in on your ‘master’ database. And not because it was your idea. It is because of all the other reasons commenters have raised here.
And, I’ll leave you with this riddle. If you convince the politicians to pass a law for my genetic material for your DB and I refuse to provide it, is that immoral or unethical or just illegal?
@#254 —
Unless you can tell me why we’re suddenly having the kind of deep conversation about ethics, morals and the law that most people leave behind when their YA-fiction-reading years are over, I’m not sure I see how it’s relevant.
I said “not entirely conceptually discrete” not “invariably one and the same, with no possibility of conflict either in theory or in fact ever, ever.”
In case that’s where this is coming from.
I do suddenly wonder whether someone has earned an advanced degree by elaborating the modern history of the use of scare quotes, given that they would have been of obvious value here to distract from the painful mimicry.
“They’re nihilists, Donny, nothing to be afraid of.”
Come on guys, don’t give him too hard of a time. We all know ethicists are just secular theologists and the Universal Declaration of Human Rights is their version of the Bible. When you think about it, isn’t the concept of human rights just as vacuous as transubstantiation?
That’s a good idea.
I sometimes idly wonder why reflexively throwing “teleological” in front of nouns like “perspective” and “argument” has never gotten vogue-ish. I mean, I personally prefer to use the word “f*cking” when I feel the need to preface my nouns with a couple-few empty adjectival syllables. But there’s certainly nothing wrong with “teleological.”
I’m a fool for idle thought, though.
^^That was @Narad, #261.
Better politics. Duh.
I’ve been know to use the T-word.
^ “known”
Not-very-democratic though it might be, you know what Kuwait’s got that we don’t?
Universal health care. That’s what.
Sometimes it’s T-word-ologically justified. That’s not what I meant.
I just read through this thread. Zebra, your ignorance and naivete are astonishing, and not in a good way. You know Jack Freaking Spit about IT. In #223 you say:
Here’s the thing. Substitute your Point 5 for Point 1. The idea of a team of super-hackers breaking systems and stealing data has been wrong for years. It is far faster to bribe or blackmail someone who has access to the database.
As capnkrunch mentioned in #187, the size of such a database combined with the number of researchers who would want access means a huge attack surface. Sooner or later, a determined criminal would locate someone with access who was open to bribery or at risk of blackmail. From there, it would be a simple matter to get the data. in addition, in order for data to be useful, it would have to be in an easily processed format. It would take a fair amount of digging, but eventually one could gain enough to identify (and blackmail) specific individuals.
Not A Troll #259,
Since I am not suggesting a law mandating that anyone, much less everyone, contribute DNA, it would definitely not be illegal.
I can’t very well be asked to apply labels like unethical or immoral since I have stated my position that they are vacuous.
But it would be like not vaccinating your child if you perceived that your child had a negligible risk of contracting the disease in question, and perceived a higher risk from the vaccination itself.
(You would be acting in your perceived self-interest, as all humans do.)
Since in the vaccine case, the perceived negative outcome (physical harm from the vaccine) is of greater negative consequence than the perceived negative outcome from submitting your DNA*, one might argue that you would be acting less rationally than the anti-vaxxer.
But as you say, this kind of decision is “malleable” or subjective. Who am I to judge?
*A perceived harm for which there is zero evidence, unlike the perceived harm from the vaccine.
capnkrunch #263
Well yes, we all know that if we look at reality, but some engage in self-delusion, just like the people who think that they have an immortal soul.
Neither your soul nor your “human rights” mean anything to a firing squad. Your “right to privacy”, which is such a big issue for you apparently, means nothing when you are stripped naked in a cell and a broomstick is shoved up your ass.
But carry on, someone has to man the barricades against the possibility that one’s genome will reveal embarrassing information. And then there’s the threat of Reiki to deal with…
Zebra @272:
“Who am I to judge?”
That’s an easy one. As a buffoonish, petulant, truculent blatherskite, you’re the best excuse I’ve had in a while to combine some of my favourite words.
So thank you for that.
(a) If that’s the criterion for conceptual vacuity, creating a DNA database for an entire year’s birth cohort is a vacuous idea.
(b) If you believe you have an immortal soul, it doesn’t matter what it means to a firing squad. That’s not the point.
(c) Execution by firing squad is not necessarily a human rights violation. I’m 100 percent opposed to capital punishment in all circumstances. It’s one of the issues I feel most strongly about. And even I don’t think so.
In my experience — which does not include the precise scenario described above, I admit — the reverse is true. Human rights never mean more than they do when they’re being violated. Or when they have been.
I mean, being subjected to sustained, systematic atrocities with no hope of escape or relief for a long period of time sometimes breaks people so that they no longer care. But assuming that there’s a semblance or possibility of human rights in the picture to begin with, what you’re saying is just false.
For example:
Abner Louima, whose experience does include something like what you describe, became an activist against police brutality because he survived it.
Not that it’s really material to the instant point, but fwiw, but he evidently also found meaningful aid in his belief in an immortal soul, according to wiki:
And finally:
A DNA database of an entire year’s birth cohort genuinely does mean nothing when you are stripped naked in a cell and a broomstick is shoved up your ass.
So what’s your point?
zebra@273
What the heck are you even talking about? My right to not be a slave is also a big issue to me and is similarly meaningless at gunpoint. For a guy who loves to complain about non sequiturs you sure make good use of them.
zebra # 272 says that not contributing your DNA for genome studies
“… would be like not vaccinating your child if you perceived that your child had a negligible risk of contracting the disease in question, and perceived a higher risk from the vaccination itself”
and you are right if you believe that
“…the perceived negative outcome (physical harm from the vaccine) is of greater negative consequence than the perceived negative outcome from submitting your DNA”.
This sort of reasoning probably would be justified if the person who decides is the same person who must bring the consequences of a wrong choice. May be this is understandable in a climate of “my son, my property”. But in today’s civilized countries this is no more considered acceptable.
Different ethics, perhaps?
Ann, now you are joining Krebiozen in out-of-context quotes with silly word games and irrelevancies.
I was responding to capnkrunch. The meaning is clear. There is no difference between UDHR and a bible. Neither matters. What matters are the choices of those who have control of what happens, which ultimately means the sovereign entity. “God is on the side of the big battalions” or some such quote. Napoleon?
And I never said people who delude themselves about souls and rights don’t benefit from the delusion; it is exactly my point that feeling better is obviously why they do it. That doesn’t make it less of a delusion.
#227 perodatrent,
“This sort of reasoning probably would be justified if the person who decides is the same person who must bring the consequences of a wrong choice.”
I think you meant “bear the consequences.”
But I don’t see how this relates to the reasoning itself. I am just comparing the two negative outcomes. In one case, there is a small chance of a bad reaction having a serious physical effect on the child.
In the other, there is some fantastic scenario (that not one person has been able to describe in even a tv-plot fashion) that leads to some future embarrassment or “loss of privacy”.
In both cases, the parent does make the decision for the child; but again, it is the perceived consequences that are being compared.
Like I said before calling something out of context doesn’t make it so. If that’s how you want to dismiss something you should provide the proper context and explain how the meaning of the quote has changed. It’s not difficult to do, and significantly strengthens your argument. Actually, dismissing something simply by yelling “out of context” or “cherry picking” just makes it seem like additional context actually has no bearing on the meaning and you simply don’t want to address inconvenient quotes.
Also, I have provided several references describing how confidentiality of genetic information can be breached including one actual proof of concept attack. The appropriate way to compare risks is cost/benefit comparisons. Benefits of vaccines far outweigh any risk. Several experts have told you that mass collection of genomes is useless at this time. Even if risk was purely theoretical (it isn’t; deidentification attacks have been proven as I already referenced) because there’s no benefit there’s no reason to take the risk. This is what I was alluding to before when I said you were using the wrong risk assessment tool. Comparing relative risk of storing personal medical records (or vaccinations) to a centralized research database is apples and oranges. When you compare cost/benefit it’s clear your idea carries unnecessary risk while in thethe other two benefit greatly exceeds risk.
capnkrunch,
I just did that. #278
Saying I didn’t doesn’t make it so.
See also Gish Gallop. The common practice here is to provide incomplete quotes– just phrases– and then riff on some interpretation of some word in the quote, or just start pontificating on something tangential to the meaning of the original comment. The result is that one would spend lots of time trying to refute all those irrelevancies, distracting from the core topic.
Another ploy is drive-by criticism, like what you just did, to create distraction.
“But it would be like not vaccinating your child if you perceived that your child had a negligible risk of contracting the disease in question, and perceived a higher risk from the vaccination itself.”
That’s a remarkably piss poor analogy. With vaccines there is a risk to the individual but also a known benefit to the him/her and society whereas your birth year gernome DB has no demonstrable benefit to a living individual. Sure, you can do something for the advancement of science (and that’s about all I’ll get out my study + 25 dollars), but that is no one else’s business but the individuals.
For one who speaks of what matters are the choices of those who have control of what happens, I don’t understand your mythical belief in no downsides. It isn’t like something such as eugenics never happened or that designer babies aren’t a thing or that the non-productive in society aren’t discriminated against or that even now there are those who speak of an age when people are expendable. I would love to see it (not) when they say those with certain genes are.
There’s better politics and there’s worse politics and neither of us are mind readers to know how that is going to play out. So for those who want to donate their DNA have at it and for those who don’t you can leave them alone. Unlike the unvaccinated who are a risk to others there are no issues with DNA non-donators. If the science gets better then I expect more people to be on board with it but to expect people to do so now is kind of a joke.
I’m sure you meant 277 but that reminds of how much I agree with Narad@227. Your nonsense sounds like the kind of half baked ideas I’d expect out of a student who just got an A on their first test in intro to philosophy.
No, you neither provided additional context nor explained how the meaning of the quote changed. ann already used the quote in the context of it being a reply to me otherwise the reference to vacuity doesn’t make any sense. If anything your additional comments make ann’s point even stronger. If all that matters is the choices of those in power than anything that doesn’t directly work towards gaining or maintaining power is a vacuous idea.
# zebra 279
“Bear the consequences”, of course.
My point wasn’t about which is the right choice in this question (in my personal view: to vaccinate and not to provide DNA).
But about who has the right to make the choices.
Giving my own DNA has consequences only for me, so the choice is very personal.
Not to vaccinate involves other people, too (our own children or non immune lay people). So it can be argued that the choice should be made not by parents, but by a public agency.
Speaking of creating distraction I don’t think I’ve yet seen you make an actual response to a single criticism of your idea. It’s always out of context this, non sequitur that, I don’t agree, 20th century thinking, where’s the evidence (ignoring multiple references provided of course). More recently it’s this pomo everything’s the same nonsense. Look, if you don’t think protecting privacy is an important that’s fine. HIPAA says otherwise and you seem to care about enforceable laws. How will your database protect confidential health information when genomes can be personally identifiable?
capnkrunch,
What you haven’t provided is any plausible scenario in which the project I described has any risk of harm to any individual. That would involve a specific narrative, which could even be quite hypothetical– as I said, like some tv crime or spy plotline. Nothing.
Your interpretation of what “several” experts have said is as irrelevant as your beliefs about what constitute human rights. I’ve answered Retro Pump way back at 112. The disagreement is over the rate at which the data is converted to digital format.
I’ve also pointed out that there are obviously experts who don’t agree that large, centralized databases of genetic information are useless at this time. If you want to argue the specifics of my idea v the Brit 100K genome project, that would be fine, but you’ve already said that you are against any further collection of genetic data. Which isn’t feasible anyway.
perodatrent,
OK. But the public agency could also decide that DNA must be given, as in the Kuwait example ann provided.
So, we are back to politics, and the power of the sovereign, whether that is a democratic entity or a king.
perodatrent,
I just realized that maybe you arrived late and were not clear on what the actual project was that I suggested. DNA would be collected from all the children born in a specific year, so again it would be a parental decision in both cases.
So?
I got that that was your point.
Mine was that if the criterion by which you decide whether a concept is vacuous or not is whether or not it saves you from a firing squad and/or being stripped naked in a cell and having a broomstick is shoved up your ass, the concept of establishing a DNA database for an entire year’s birth cohort is completely vacuous.
The concept of human rights, on the other hand, provides some protection to most people who live in a society that respects them, as well as some recourse to those whom they don’t protect.
IOW: You’re using what you call a grandiose strawman. Human rights also don’t save people from dying in car accidents. That doesn’t mean they’re completely useless.
I honestly don’t see how that was either out of context or silly or irrelevant. I addressed your entire argument, which was that ethics and human rights are vacuous because if you’re in front of a firing squad or being stripped naked in a cell and having a broomstick is shoved up your ass, they won’t help you.
In the event that my meaning wasn’t clear: While that may be narrowly true if you’re already in front of a firing squad or being stripped naked in a cell and having a broomstick is shoved up your ass, there’s not much about which the same couldn’t be said. And it’s entirely false if your aim is to avoid ending up in that kind of situation. The concept of human rights does more to keep people out of it than anything else, by greatest-good-for-greatest-number standards.
Ann,
That’s what I said in response to capnk, where his statement is in quotes within the blockquote.
I didn’t say that people’s beliefs didn’t give them comfort.
I didn’t say that the delusional beliefs of other people have no effect on the situation in which the individual finds himself.
So you are indeed the one strawmanning.
No, exactly no. What best keeps people from in front of the firing squad is self-interest. It is the experience of Martin Niemoller. It is when people stop following that lesson, and start using delusional, arbitrary, “beliefs” to guide their society, that problems arise.
You know, “an eye for an eye” pretty much justifies that death penalty you don’t like.
This is ridiculous. Not long ago I pulled up zebra for inaccurately paraphrasing people and putting those inaccurate paraphrases in quotation marks. He was apparently unaware that quotation marks generally denote a direct quote; he even claimed that putting paraphrases in quotes is common practice (it isn’t) and told me to “get with the modern era”.
Now he is complaining about accurate paraphrases of his comments that are not in quotes? Perhaps zebra would like to specify where I, or anyone else, have changed the meaning of his words by quoting him out of context (difficult when the context is right above on the same page), or where I, or anyone else, have made any argument that does not follow from its premises (i.e. a non sequitur). What zebra writes is quite ridiculous enough that no one has to change the meaning of his words to criticize them.
It seems to me that zebra is simply too dim to understand it is possible to paraphrase someone’s words without changing their meaning, and lacks the basic scientific knowledge required to see how some arguments do follow from their premises. Either that or he still hasn’t grasped what “out of context” and “non sequitur” mean.
Silly word games? I plead guilty, though not on this thread, other than a reference to PoMo and a hypothetical example of data that some might like to keep private as tiny-penis-syndrome, neither of which really count as word games.
As for irrelevancies, zebra has treated us to a plethora of those, from an irrelevant Pynchon novel to someone being physically assaulted in a cell, and other bizarre analogies that make no sense whatsoever.
Back to the issue under discussion: I don’t know how large the risks are because I don’t understand the details or scope of the problem well enough, which is why many countries have set up committees of experts to look into this, assess the risks and formulate necessary legislation. I don’t think we should ignore potential risks and just hope they come to nothing. We have already had some tastes of the possible problems we may face; here’s an example (adapted from a real case) of genomic information being used to discriminate against a person:
There are other examples of this kind of discrimination on the same page. Isn’t it best to figure out how to avoid more of this sort of thing in the future before we start sequencing the genomes of millions of people?
Speaking of the 100,000 Genomes Project and one such group of experts who Krebiozen referenced previously:
Krebiozen@293
You and your 20th century punctuation.
See also Gish Gallop. The common practice here is to provide incomplete quotes– just phrases– and then riff on some interpretation of some word in the quote, or just start pontificating on something tangential to the meaning of the original comment.
^ Well, that’s an odd blockquote failure mode.
“Well, that’s an odd blockquote failure mode.”
You just had an errant one that resulted in nested ones. Btw, did you figure out your issue with the winking face emoticon?
Okay, reading this long thread, I’m getting the impression zebra is unaware of exactly how much genetic information a human being has.
RE: JP #151
I’ve been away dealing with real life, but –
I wasn’t proposing that we should have a law to prevent the mentally ill from possessing firearms. We already have a suite of state and federal laws that say so, and it’s my understanding that the Supremes have said they are an acceptable restriction (HDB take note), so if you want to fight it, your argument is with your Representatives, not me (but I do think these laws are just fine).
You also may have the impression that I think all mental illness are the same, but both me and the law are well aware that there are many different types of mental illness, and not all (and maybe not even most) should lead to restrictions of any rights or freedoms.
You link doesn’t link. I agree that most mentally ill people are mostly harmless most of the time, and some are completely harmless all of the time, but I don’t agree that “the mentally ill” are no more violent than “normal” people. According to this http://www.bjs.gov/content/pub/pdf/mhppji.pdf ,
The same source says 61% of the state prison population who had current or past violent offenses had mental problems. This source ( http://www.nimh.nih.gov/health/statistics/prevalence/any-mental-illness-ami-among-adults.shtml ) says the prevalence of any mental illness among adults is 18%, so it would seem that the mentally ill are more likely to be violent than “normal” people. Or maybe the mentally ill are just more likely to get caught.
But none of the was the main point that I trying to make, which seems to have been lost. I was trying to offer a scenario where the existence of a complete medical database could (depending on your point of view) be used or abused. Let me try again.
We have laws that restrict some mentally ill from buying and possessing firearms. However, these laws are mostly toothless, because there is no mechanism for any gun seller to know if the purchaser is amongst those restricted by these laws. Zebra’s metadatabase would have the necessary information to enforce the law. Part of me thinks this would be a good thing to use this information to prevent some portion of violent crimes.
But a larger part of me thinks it would be bad. HIPAA laws make it clear that medical information should only be used to provide medical care. I like this law just fine, too. If we allow an “except for” to come in, we can expect others to follow. The government does have a record of using the data it holds to do bad things (census data and the Japanese internments come to mind). But Zebra seems to think that HIPAA should be darned to heck, and if y’all can’t convince him otherwise, I’m sure I can’t. Y’all have probably made this argument somewhere along the way (I hope to chew thru this in the next day or so) so I apologize for any redundancy.
Zebra may say that this is an argument against UHC. But again, it’s HIPPA that would be our protection, and it seems to me we should likewise protect it. Our medical information should only be used for benefit of the patient, unless the patient gives clear, informed consent otherwise.
“Or maybe the mentally ill are just more likely to get caught.”
In addition it may just be that treatments and social support for mental illness is vastly underfunded and they end up in prisons because they are nuisances and nobody else is taking them in.
Here is my link; with any luck, it’ll work.
“Mental disorder” is awfully broad and probably includes substance abuse disorders. People with mental illness who don’t have a substance disorder are, according to various studies, either no more likely or only slightly more likely to commit violent acts compared to the general population.
We’re talking about SMI here, though, also. There is *one* mental disorder which does correlate with increased violence, and that is antisocial personality disorder (or sociopathy), but that is not considered SMI.
In any case, sex (male), age (youth), and socioeconomic status (poor), correlate much more strongly with violent crime than mental illness does.
^ Substance disorders are considered “mental disorders” even on their own, not concurrent with an “Axis I” disorder. (I think psychiatrists have lately stopped using the Axis model, but you get the idea.)
I forget how this one got started, and I’m on deadline again, but I’ll briefly note that in my state, as I recall the FOID application, one has to have been involuntarily committed to be denied a license. This is an obvious, verifiable standard, but it represents a very small subpopulation, indeed.
No, that’s just you creating a straw man out of what I said by cherry-picking and paraphrasing. As I said:
^^See that right there? Please address it. It’s my main point.
But let it be duly noted that it’s no less true to say…
…that what you did say is. Because that’s my point. As a standard for establishing the vacuity of concepts, that’s a useless construction. All concepts fail it equally.
You’re therefore still one reasonable argument short of demonstrating that ethics and human rights are vacuous.
Please ante up.
FWIW, I don’t disagree that it’s in everybody’s self-interest to see that each and all are equally protected from abuse. But that’s the principle on which the laws and ethical standards you’re objecting to are based. Respect for persons, for example.
Pretty much. But since that particular concept goes back 4000 years and has never (afaik) been absent from any human society on record***, it’s probably not the best example you could choose of the kind of delusional arbitrary belief that leads to trouble when people start being guided by them. In order to know whether that was true, they’d have to stop first.
***Before you tell me that there are societies that don’t practice capital punishment: I know. I said “the concept.” It has numerous other iterations. Too numerous to count, really.
Anyway, back to the topic at hand for a moment, allow me to hearken back to carts and horses.
Has anyone figured out why Z. thinks a birth cohort is some sort of especially interesting sample per se? It can’t be pure size, given that other countries can randomly be plugged into the Master Plan (and given that Z. is demonstrably unclear about the size of the U.S. one).
You’re not going to capture any particularly granular environmental data specific to a generation unless, oh, say, the medical records are also going to geolocate the genome over time as it wanders to and fro, so, why?
The only thing I’m coming up with offhand is normalizing actuarial models.
Or maybe people who are incarcerated are likelier to have been evaluated and diagnosed than people who aren’t.
Or maybe being convicted of crimes that (in many more cases than one would like to think) you may not have committed and then locked up for years has a bad effect on your mental health.
Or maybe being in prison =/= being violent. There are a lot of people in prison for dealing drugs, for example.
Or maybe all of the above.
Except not maybe. JP is entirely correct. The mentally ill are no likelier to be violent than anybody else is.
More things zebra doesn’t get:
Huge government databases are hacked all the time. See the ever-expanding government employee personal information database hack.
If the medical records are linked to the genomes, that information alone is valuable enough to hack. And if any of it were attached to SSN? It could be used to blackmail or influence the parents of a child as well.
Ethics are not optional in human subject research. Not in the US, or the UK, or really anywhere in the world. There are standards and treaties and laws about these things. IRBs are not optional, and they are not optional for a reason.
Zebra: do you know why ethics and human rights must be considered *first* in all human subject research? If you don’t, and can’t find it in a 2-minute search, then you are a buffoon, a liar, or a monster.
And for public health surveillance (at least). I’ve gotta get my ass in gear, but I’ve already mentioned the Vaccine Safety Datalink. I don’t know whether the plan participants of the HMOs who are the data stream are represented on an opt-in, opt-out, or “neither” basis, but it strikes me as real-world example that Z.’s trip should at least be able to make specific contact with.
Not “big picture” enough, though, I suppose, or something.
ann,
But how is that my criterion? This is a truly bizarre interpretation, which is perhaps why I think you are strawmanning?
What makes “rights” vacuous is that they cannot be demonstrated, which is why I “equate” them with “souls”.
Sorry if that wasn’t clear enough to begin with.
You only have “rights” in the context of the legal system, (stipulating, of course, that the legal system operates the way it is supposed to.) Your “rights” are granted by the sovereign entity.
If you don’t get this I am happy to discuss it further.
“Well, that’s an odd blockquote failure mode.”
You just had an errant one that resulted in nested ones.
I meant the inversion. It’s neither here nor there; I just wanted to note the error.
^ I’m going to take that additional blockquote fail as a clear signal from the perceived world that this is the wrong time to “multitask.”
IIRC the mentally ill are far more likely to be victims of violence than perpetrators. That said, some years ago, as I have related here before, I had an unfortunate experience with a close friend who had some serious mental problems (delusions) but since he was not presenting a threat to himself or others, and despite my best efforts, I couldn’t get any doctors interested.
Eventually I contacted his mother in Scotland and paid his train fare to spend some time with here, thinking a bit of time out of London would do him some good. Sadly while he was there his condition worsened and he killed his mother, rather horribly and then calmly called the police.
I did visit him in the secure mental hospital he was placed in (the Scots sent him back to London), and kept in touch for a while after he was released. I never felt quite comfortable with him after that, even though he was on depot anti-psychotics and asymptomatic, and have since lost touch.
That has left me with an unease around people with SMI that I know isn’t entirely rational, but it’s still hard to shake off.
^ “some time with her”
@Krebiozen:
That’s terrible; I’m sorry to hear that. I know of a similar situation involving the older brother of a school friend, but I wasn’t nearly as close to what was going on as you were.
The point is that mental illness doesn’t cause violence over and above what you’ll find in the general population; it doesn’t mean the mentally ill aren’t ever violent, just like other people are sometimes violent. Young men have a particular risk of it in general.
As far as the SMI label goes, I mean, I’m pretty sure I’m probably in there. Severe recurrent depression and a nice case of PTSD counts as “serious” or “severe,” I’m pretty sure, even if I’m not having, say, command hallucinations. (Which also don’t incline people to be more violent, just by the by.)
I mean, most of my friends are crazy, too. I guess I sort of have a hard time grokking anybody who isn’t “broken” in some sort of profound way.
Justatech #309,
I offered to capnkrunch that he could make up even a far-fetched, tv crime or spy show scenario about how all this blackmailing and stuff would happen, but he couldn’t hack it. (pun intended)
I make you the same offer. I’ve watched my share of that kind of thing, and I can’t figure out what dark or deranged imagining is going on in your minds. How would it work? Why would someone go to my database instead of just bribing the person working for the local health insurance company, or the doctor’s office?
jp #316,
So why don’t you like me, phony?
“Hey, what’s up with that zebra, why doesn’t he want to just belong?” (#255)
Or is all your drama just middle-class spoiled brat social-media angst?
Zebra @317: Sure, I’ll invent you a crazy scenario involving a diplomat with an unknown genetic allergy to antibiotics and a terrorist group that wants him dead…
But ONLY after you answer my question about human subject research and ethics.
It can be answered in one word, if you’re lazy.
Do it.
Because you’re not terribly likable? I generally like people who are nice and smart and know what they don’t know.
Someone who refers to his wife as “perfectly serviceable” does not immediately strike me as friendship material either, just by the by.
Oh, Zony, stop it. My sides, they’re killing me.
zebra
All the pieces are there, I shouldn’t have to weave a f*cking narrative for you but here it is anyways. Insurance company (via some lab) requests information for, say diabetes. They do legitimate whatever with it but simulatenously use various methods to reidentify the genomes. This information is then used as a kind of blacklist, people they win’t sign. It’s illegal to deny coverage for pre-existing conditions but now they have access to information that they shouldn’t and mountains of plausible deniability. “We didn’t deny coverage because of the pre-existing condition. There’s no way we could have known,” (recall the data is ostensibly deidentified).
How about in the reverse. Some reserachers suspect they have discovered a mutation that greatly increases risk of leukemia. To help verify they request the histories of everyone with said mutation. Somehow an insurer gets a hold of the information and reidentifies it and hikes up everyone’s rates.
Heck, hackers comprimise healthcare servers (insurers, providers, etc) all the time; I don’t know what they do with the information but it’s certainly nothing good. Despite what you seem to think, I imagine bribing an employee probably puts the attacker at far greater risk than a spearphishing campaign; I don’t recall any recent attacks where bribery was the method of entry. Why give hackers another target? BCBS was too secure? Try the genomics database.
You may have watched you share of TV shows and movies but like Julian Frost noted before you appear to know jack sh!t about security. It’s common knowledge Hollywood rarely does any technology justice. You’re a fool to think that means anything.
In any case, a “TV show scenario” involving private health information isn’t hard to think up at all. We can even use SMI as an example.
What if, as has been brought up several times, scientists figure out how to read the genome for things like schizophrenia? I do in fact know a couple people who have, yes, schizophrenia, and are not “out” about it, either at work/school or with non-close friends. They have every right to keep that information private, given the kind of stigma it carries. I can well imagine that being “outed” would be an awful experience for them on a lot of levels.
Why would somebody use that information against somebody else? I mean, if they’re jerks, and enjoy the idea of making other people miserable and intimidating them out of their money, why wouldn’t they? It’s more information out there, your entire genetic code. Why wouldn’t people go after it, regardless of whether they also go after other health information? Again, we don’t know right now just how much information about a person is in their DNA.
^In any case, I gotta jet. I must bike to the Asian Market (I guess) and find a fruit I haven’t tasted in 9 months before I go to a Rosh Hashanah thing.
I looked for something recent on the subject of violence and mental illness and found what I think is one of the best overviews of the subject that I’ve ever seen here
Krebiozen, I’m sorry that all involved went through that. Truth be told I am also leery of those plagued by psychosis. But it is no more than I would feel with anyone else who I sense is unpredictable and/or acting erratically. That includes the police, business managers and angry people. It is just something instinctual and I doubt I will ever be able to change it.
I started wondering about Plomin, and his confident claims back at the end of the last century in 1993 and again in 1998 that he was about to discover the genes for intelligence, Real Soon Now. He seems to have found a fortunate niche where being wrong (and spending millions of dollars and decades of time) only increases his reputation, and his most recent, largest search for the genes for intelligence admitted total failure in 2010.
So he has sent the genomes to a Chinese colleague to be sequenced safely away from IRBs, and as of 2013 he was promising success within the year.
http://www.nature.com/news/chinese-project-probes-the-genetics-of-genius-1.12985
Of course it wasn’t clear. One of your examples was of a right being violated; and the other didn’t necessarily implicate any rights at all.
Neither illustrated the proposition that your rights can’t be demonstrated. And it’s not true that they can’t. For example:
Are you expressing your beliefs and opinions about the vacuity of rights on this very thread without fear of reprisal from the state?
Well, there you go. You’ve just demonstrated that one of your rights is alive and well.
Yes. You also only have citizenship in the context of the legal system. Ownership of property, too. It’s also what prevents landlords from shutting off the heat in the middle of the winter to save money and the reason why you don’t have to work a seventy-hour week to keep a job.
There are lots and lots of perks and benefits you only have in the context of the legal system. What of it?
In this country, your rights are granted by the (wait for it) Bill of Rights. And the US Constitution. Assuming that “sovereign entity” means “the state,” that’s not really the same thing.
But for the sake of argument, let’s say that it is. So what?
That’s okay. I’m good, actually. The “So what?” and “What of it?” were just rhetorical questions.
Anyway, if the thing that makes rights and ethics vacuous is that they (putatively) can’t be demonstrated, you need to make a case for it. Because you haven’t yet. So let’s just stick to that.
On further reflection, I realized that even if the vulnerability (as it were) used to compromise PHI was bribery, zebra’s data still greatly increases that attack surface. There’s a whole new set of people with acess to confidential data who might be susceptible to bribery. No one at UHC bites? Try the genomics guys. Of course, this bribing the peons discussion is vacuous for a number of reasons, not the least of which is that the idea is actually more Hollywood than elite ninja codebreakers or whatever zebra was going on about.
ann@326
I think what zebra is going for is that your rights only exist so long as those in power choose to allow them to. I get the feeling his AP History class just finished their section on Hobbes.
In the same sense that your running water does, sure. But you know. Your life only exists so long as someone with the power to kill you chooses to allow you to live. Other people are always around somewhere, having power to affect you some way. Can’t be helped. C’est la vie.
Details — such as how realistically likely it is that those in power will cancel the Bill of Rights, or be able to — really matter therefore.
[…] brief announcement, sure, that I was on vacation, but the rest of my posts were either reruns or a delayed crosspost from my not-so-super-secret other blog. As far as I can tell, that’s unprecedented. Even […]
capnkrunch,
Don’t quit your day job and try to become a scriptwriter. (But I appreciate that you made the attempt.)
The thing is, I asked you to do that for my project. That would be (let’s say, assuming lots of opting out) a round figure of 200K samples, derived from a particular year’s births.
I may be misinterpreting the specifics of what you suggest, but it sounds like an insurance company bribes a qualified academic researcher to submit a request for a set of genomes to be used in a “cover” project.
That data set would be limited to those individuals in the birth cohort with the specified (“cover”) medical condition, and probably a fraction of those if the number is large. Let’s say 5K to be generous.
So we are talking about all kinds of criminal risk in order to identify the fraction of 5K individuals with condition A who also happen to have the genetic risk factor for condition B? And who might be applying for insurance with that particular company? I just finished logic101, so I think I will call that reductio ad absurdum. (sarcasm)
There just is no way, no matter how many times you repeat “threat surface”, to claim that participating in my project adds anything to the existing risk of harm from unauthorized access to an individual’s health information. It just makes no sense, even if you could access the entire thing, to bother with such a restricted and really trivial amount of information for nefarious purposes.
And even though I don’t think the identification-through-the-genome route is a big problem, the existence of my database would reduce the risk to the general population. That should be obvious.
That’s because you don’t understand the basic issues, which in turn devolve to your wholesale failure to describe in even rudimentary fashion how the Bright Idea is supposed to work in practice, aside from “Computer, give me the entire genomes of all persons with condition X that satisfy this random list of natural-language terms.”
How many times do you have to be told that no real-world, arbitrarily whole-cohort, data bank linked to complete medical records is just going to barf up whole genomes? Why can’t you answer the simple question of what the interface is supposed to look like? With a genome in hand, can one “freely” pull the medical records? There might be something in there somewhere!
It’s not as though you’ve had a shortage of time or lack of genuine input with which to put together something resembling a contentful response, but instead you’re just jabbering incoherently about weird jail fantasies and so on.
I mean, yah, I think I’ve already noted that you’re Gumby, dammit, but WTF? If you’re going to whine about “the core topic” – and if the “core topic” is something other that Z. is so bright you have to wear shades – why are you so enthusiastically running the hell away from it?
ann,
“There are lots and lots of perks and benefits you only have in the context of the legal system. What of it?”
“Anyway, if the thing that makes rights and ethics vacuous is that they (putatively) can’t be demonstrated, you need to make a case for it. Because you haven’t yet. So let’s just stick to that.”
“Your life only exists so long as someone with the power to kill you chooses to allow you to live.”
OK, so you answered it yourself, gratis capnkrunch. You can’t demonstrate that you have a “right to life”.
Note to capnkrunch: If I have to end up sounding like philosophy101, perhaps it’s because everyone else sounds like they never took that class, and it is necessary to (re-)state the obvious?
JP,
I like to think she married me primarily because of my sense of humor, (as well as compassion and intelligence, of course). Not just that other thing.
Once again, zebra displays his ignorance of both IT and security risks.
Given the size of each DNA sample, we are talking petabytes, if not exabytes, of data. That will need storage space, electricity to run, and people to maintain both the physical hardware and administrate the software. Queries would take a very long time. It’s not yet practical.
That’s one of several possibilities. Another is a gang who blackmails or bribes either a researcher or an administrator into giving them certain data. Remember, in a database that big, the number of users and admins is huge, meaning a HUGE attack surface.
Or the data could be something like who meets the genetic risk criteria for a certain disorder like e.g. schizophrenia.
Except that your project is far less secure than you assume, and that the risk of the project getting hacked is far greater than the risk of someone’s medical files getting exposed and the data used nefariously.
It isn’t obvious. If anything, it is obvious that your proposed database significantly increases the risk to the general population.
If I recall correctly, there have been very few retractions from the GCN Circular.
Sweet G-d, do you still think that the U.S. birth cohort is “385,000“?
Oh, wait, insurance companies aren’t able to employ “qualified academic researchers”? The wholly unaddressed regulatory structure becomes more baroque by the moment.
zebra@331
Seriously? What don’t you get about additional targets equals more exposure? If hackers are interested in stealing PHI from hospitals they will be interested in stealing it from your database.
Regarding insurers, there have been cases of rates being increased due to genetic risk. Certainly the largest database of genomic information would be attractive but it is unlikely. That said, the reason I originally said these narratives don’t matter is that the onus is on you to ensure the information remains confidential, not on others to not abuse it. Regardless of risk, HIPAA says that legally you need to offer protections that our current tehnology cannot provide for a database that size.
If your counterpoint is the 100,000 Genomes Project there’s two problems. First is that privacy concerns are alive and well is that project (see the Nuffield Council link Krebiozen provided earlier). Second is that England has far more lax confidentiality laws.
@333
Or maybe it’s that most people graduate that kind of sophmoric babbling with high school. Don’t misunderstand. You don’t sound like philosphy or whatever 101. You sound like someone part way through the course with just enough knowledge to make yourself look like a fool and not enough to realize why.
Narad #337
Krebiozen doesn’t like me suggesting that people are CUI (whatever the kind of influence) but sometimes it is difficult not to conclude that.
You have sputtered and blustered about the number multiple times, so let’s read the reference you gave: (#44)
I take the rest of your blustering and sputtering to also be the result of whatever it is, and not worth wasting my time.
Julian Frost@335
You’re wasting your time. zebra thinks queries are zero cost actions and that selecting subsets with specific crtiteria is “trivial”. I gave up trying to explain the hardware and software limitations after he hand waved away my references as cherry picked and refused to even look at the sources I provided. Of course he’s done the same for the privacy concerns so it’s I guess I’m just as guilty of time wasting.
I’ll provide by references once more, mostly because I think Julian Frost might find them interesting in case he missed then earlier but also on the off chance that this time zebra will decide to at least make an attempt to educate himself.
Big Data: Astronomical or Genomical?
Routes for breaching and protecting genetic privacy
I work with a database for a department of a state government which only contains limited information on a small subset of the state’s population, and it takes quite a bit of time and effort to get information, as there are still millions of records. Imagine scaling that up to complete information on the population of an entire country.
That a right can be violated =/= it can’t be demonstrated. How does that even make sense? A right is a legitimate claim to consideration by others and the state wrt some aspect of individual self-interest, not a magic spell.
Also — and I don’t mean this in a nasty way — “gratis” does not mean “courtesy of” or “thanks to” (or anything else I can think of that would make sense as you used it). So unless you intended to say “OK, so you answered it yourself, capnkrunch at no additional charge,” I think you probably mean something else.
Oho! You’re correct; this level of derangement failed to sink in early on. Then again, I may have been conditioned by your comment 2:
There does remain the glaring issue of your failure to genuinely cost the Bright Idea out, of course. Barfing up the $1K genome doesn’t quite cut it.
But, so, just to quantify the terms, wouldn’t it make more sense to just trade F-35’s to Canada in exchange for all the biomedical data in perpetuity of a cohort from their, ah, more “manageable” population of “cooperative citizens”?
Am I really the only person who’s still curious to learn more about the multiple registries of penis size in which zebra’s records are kept?
Maybe everybody else just knows about them already. I guess I’ve led a sheltered life.
capnkrunch, thanks for those links. The second one is really fascinating. My comment was more about if a database like the one zebra proposes could be hacked and how easily (yes, and fairly). Nevertheless, it shows how wrong zebra is about how useless the data would be to a hack team.
I’m going with illuminated tracings on vellum and private collection.
ann,
“A right is a legitimate claim to consideration by others and the state wrt some aspect of individual self-interest, not a magic spell.”
“A legitimate claim to consideration” is yet another vacuous expression.
Sorry, but you’re not making sense with that. The right doesn’t exist until the sovereign entity (the state) grants it. The question is, do you have a “right to life”? If you have to “make a claim”, then you don’t have it.
And yes, “courtesy of” usually signifies gratis, but by itself gratis doesn’t signify “courtesy of”.
Which reminds me, just for future reference, although I’ve explained it before, “freely available” means “gratis” in my project design, so thanks for bringing this up– I will remember to use gratis in the future.
One could just as easily argue the perfect freedom is the natural state of human beings, and governments are formed when people decide to willingly give up certain rights.
capnkrunch 339,
It’s OK, lots of people give up when they are faced with making quantitative arguments.
If you think about USA plus Canada, that’s beginning to approach 400,000,000 actual health records that could be targeted. Being one of 200,000 individuals with genome information on file in fact represents a negligible incremental risk. Truly negligible.
zebra@348
Which is how you used it. Are you pathologically incapable of admitting that you got something wrong?
Gray Falcon@349
zebra’s class just started their social contract unit. You can’t expect him to understand everything yet.
capnkrunch:
Probably. In a previous thread, when pointed out that his comment was directly contracted by the article, he insisted he meant something else, and refused to tell us what, even going to so far as to suggest we were too stupid to understand what we said.
https://www.respectfulinsolence.com/2015/05/15/the-benefits-of-the-measles-vaccine-go-beyond-measles/
It didn’t work.
zebra@350
It’s ok, the difference between distributed and centralized isn’t that difficult but I’m not surprised you continue to fail to see the difference. There’s no centralized database of 400,000,000 records. If hackers are interested (they are) in compromising hospitals that might not contain even 300,000 archived records they will certainly be interested in your database. Plus, there’s no central collection of more than several thousand genomes which means your database represents a unique asset making it all the more valuable.
Sorry, 200,000.
Zebra, I see that you have still not answered my question from #319: Why are ethics and human rights at the forefront of human subject research?
I’ll give you a hint: it involves the major event of 20th century world history.
Tell me that and I’ll give you a lovely story about hacking your imagined database. It’ll be a right cracking tale!
On that note I remembered a continued failure to understand “order of magnitude”.
zebra@195
Justatech 355,
How would I know if ethics or human rights (which I’ve clearly stated are vacuous concepts in my thinking) are “at the forefront” of anything?
If I knew what “at the forefront” meant in this context, I might try, vacuity aside.
“Am I really the only person who’s still curious to learn more about the multiple registries of penis size in which zebra’s records are kept?”
There are certain medical conditions where it may be recorded. Could even be in a text book. But I’m not really interested in knowing.
“It’s ok, the difference between distributed and centralized isn’t that difficult…”
I didn’t think so either, and I thought my little vignette made that clear.
Not a Troll@358
I always chuckle when the review of systems says “Genitourinary: unremarkable”.
No it doesn’t. It suggests or implies it — ie, if something with a cost is provided gratis, it would be reasonable to infer that it’s courtesy of someone. But in order to signify that it has been, you would have to include some signifers to that effect — ie, “semantic hairsplitting provided gratis, courtesy of ann.”
We agree. It’s a red-letter moment in commenting history. Let’s rock out.
And people will comprehend you when you do. Because “gratis” doesn’t just mean “freely available” in your project design. That’s what it means.
I thought your argument was that it didn’t exist because it couldn’t be demonstrated. Have you abandoned that position? Because if not, you still haven’t made a case for it.
And if so, assuming that your position is now that rights don’t exist because they’re legitimate claims and if you have to claim something, you don’t have it:
Just because something is a claim, that doesn’t mean you have to make a claim in order to have it. That presumes the claim is not being honored.
So you’re basically just reverting to “rights can be violated, therefore they’re not real.” And how the effing eff does that make sense? Please elucidate.
I think we can add one more item to the growing list of topics that z*bra knows little about: basics of governmental contracting for high-cost items.
If the average cost of 100 F35 fighter planes is $150 million, one doesn’t save $150 million by reducing the order from 100 to 99. The actual cost would probably be $5.75 billion for the first plane and ~$75 million for each additional plane.
It’s no big deal: just reduces the funding for the Magical Mystery Genome Project by 50%.
ann,
Obviously, one cannot violate or take away something that doesn’t exist, and obviously that’s not my suggestion.
Do you have a “right to life”?
If yes, you would have to give me some way to test for the existence of this entity “a right”. Some way to demonstrate the difference between “having a right to life” and “not having a right to life”. I see no way for you to demonstrate that difference.
If I kill you, agreed, that’s not a valid test. But, nor is it a valid test if I don’t kill you.
You are making the claim for existence, so you must provide the test.
Zebra @357: I didn’t ask you *if* human rights must be considered first in human subject research. I asked you if you know *why* those laws are in place.
I have told you in several threads that any human subject research must respect the autonomy of all subjects, and that there are strict regulations and laws about this.
So, to re-phrase my question: Do you, zebra, know *why* there are rules and laws about the treatment of humans involved in human subject research? Do you understand how these rules came to be and their historical context?
The answer can be lazily summed up in one word.
(WRT claims, their inherent properties or lack of same, for the sake of example.)
I claim to be an American citizen. And in the event that a demonstration of that is required, here you go:
I’m an American citizen.
When returning to the United States from another country, however, I not only have to make that claim, I have to produce some evidence of it — ie, a passport, which I only have to begin with courtesy of the state’s recognition of my legitimate claim to one, on which its evidentiary value is entirely contingent.
So let’s say I go to Canada, inadvertently forgetting my passport. Because I’ve actually done that. And this is what happened:
Canada was so cool with it that, I didn’t actually have to make any citizenship claims in order to get in. I just said, “Oops, forgot my passport. But I’m going to be late! It’s a business thing! I have to be there! Let me in!” And they did.
On the way back, however, I had to both claim that I was an American citizen and back it up in order to be readmitted to the country.
Does that mean my American citizenship isn’t vacuous in Canada, although I don’t have it in the United States? Or is it fully pre-vacuous in its very nature because it’s a claim the legitimacy of which is contingent on recognition by the state? Or would I have it as long as I never actively claimed it? Or what?
Another thing that doesn’t exist by this logic: mathematics. How would one test for the existence of a purely conceptual framework?
Justatech #363,
There are laws about human subject research (or any other thing) because the sovereign entity establishes them. In a democracy (assuming it functions somewhat as we normally understand it should), that would be the result of citizens voting for their own perceived best interests.
You seem to be looking for some event that would influence that perception. There are plenty of instances where there were negative consequences to subjects– perhaps you are thinking of the Tuskegee Syphilis Study, which is pretty famous. I don’t know that that would be “the major event of 20th century world history”, though. I’m certainly not going to further waste my time trying to read your mind– “guess what number I’m thinking” is a pretty childish game.
And just a note– you hardly need something of that magnitude to get laws passed; just look at all the paranoia, including yours, surrounding my innocuous suggestion here.
ann,
#364 way too confusing in terminology and organization.
If you can answer #362, you’re done, so I will await that.
Ignoring #361to focus on vague philosophical ruminations? Why am I not surprised. . .
Not really. I’ve implicitly made that claim in passing in the context of rebutting yours, which is that rights don’t exist because they’re vacuous concepts because…Well. I’m not completely sure at this point. But I think it’s either “they can’t be demonstrated” ” or “claims are also inherently vacuous for reasons not yet stated.”
Correct me if I’m wrong, although I suppose I might as well go ahead and note that if it’s the latter, it’s fully self-negating by virtue of being itself a claim. Which you’re making.
In any event: Not really. I’m mostly rebutting your claimed grounds for the vacuity of rights and/or ethics and/or abstract concepts, as the case may be. (Again, I’m not completely sure. But it seems to be something in that general neighborhood. So I hope I’ve succeeded in covering it.)
No, I most certainly must not.
You contend that rights and ethics are vacuous concepts. Your arguments so far in support of that contention don’t make sense. And that would still be true no matter what I thought about it or why. So. On what do you base that assertion?
Fine. Let’s streamline it:
Is American citizenship a vacuous concept? If so, why? And if not, why and how does it differ from rights and ethics?
If you can tell me why I should disprove something you haven’t proved, your waiting will not be in vain. But otherwise it will.
So please support your contention that rights and ethics are vacuous concepts in a way that makes sense. Because you still haven’t done that.
Ann,
This is extremely simple and clearly stated:
If there’s no demonstrable difference between having a “right to life” and not having a “right to life”, the concept is meaningless.
Sorry if you are unwilling to acknowledge this, but I guess I’m the only one here willing to admit I got something wrong.
Zebra, you like to make things complicated don’t you?
There is a right to life and the demonstration of that is that someone or some thing is living. Then men and/or nature take that away for various reasons. Yet it still exists independently of either.
zebra- Do you know who else was famous for his efforts to advance medicine without concern for such things and ethics and rights of the patient? Joseph Mengele. Think about that.
It’s clearly stated. But I don’t see how any question about such a weighty subject could really be simple, except to the simple-minded.
But maybe you just mean that it’s easy to understand what you’re asking. And if so, I agree that it is.
Be that as it may.
And I don’t see why I am or should be obligated to disprove a claim I didn’t make in terms that I haven’t used, when the only reason I’m discussing it at all is that you made it but were unable to support it with an argument that made sense.
You say that rights are vacuous concepts. The reasoning behind that is..?
OK. Are we now back to “rights are vacuous because they can’t be demonstrated”?
Because it’s not true that they can’t. We’ve already gone over that. But we can do so again. Are you a commenter here at Respectful Insolence of your own volition, because you freely chose to be? Are you free to cease being one at any time you so choose? And in both cases, are you free to make your choice without fear of reprisal from the state?
Assuming that the answers are yes, yes, and yes, we have just demonstrated that you have the right of free association. Because you’re exercising it.
Indeed, your apparent unawareness of that fact comes pretty close to proving that you’re so securely convinced of your ability to do so that it’s never crossed your mind that it’s not among the natural powers you were born with. That’s a pretty damn impressive demonstration.
That’s very unfair. I admit that I’m wrong much more readily than the internet average. I just have to be wrong first.
In any event. I’m perfectly willing to acknowledge any point you’re capable of supporting with a sensible argument. But you haven’t yet made one for the claim that rights are vacuous concepts. So get to it.
Come on, now. How does a living thing demonstrate the right to life?
Life, in itself, does not demonstrate that the right to it does exist any more than death/killing demonstrates that it doesn’t. Be serious.
^ By virtue of it’s existence. A dead thing has no right to life. Only something living can have a right to life.
ann, please, you really are not being serious
I have acknowledged multiple times that rights exist in the context of the sovereign entity (SE) or state. Do I really have to go back and show you?
I said that they are meaningless as I described them, as qualities or attributes inherent to the individual. They only exist as granted by the state.
If there is no SE with a code of laws, and a legal system that works as intended, then “rights” is an empty concept. But it is a perfectly useful concept (kind of a shorthand, the way I see it) when there is the SE and legal system. Your problem is not being able to keep these two contexts separate.
Ding ding ding! Gray Falcon @373 has it in one: Why do we have major international declarations on what constitutes human rights? Nazis.
Zebra, in more than one thread I have tried to explain research ethics and the laws, standards and regulations surrounding human subject research. So far you have categorically refused to acknowledge that any of it exists.
Please go read the Declaration of Helsinki and think about how that applies to your proposed research database, as well as your ongoing argument with ann about the concept of rights.
And re: ” the paranoia, including yours, surrounding my innocuous suggestion here” – It’s not paranoia if there is ample evidence for past malfeasance. Or, is it still paranoia if they really are out to get you?
Of course human rights and ethics are not Platonic entities that exist “out there”; they are the result of agreement and consensus. Ethics are the basis of laws and professional standards that are enforced and have real consequences. How can anyone be so utterly confused about this?
The point of all the many committees and steering groups internationally that are wrestling with the thorny problem of genomic privacy is to establish an agreed ethical framework and to establish what legislation, if any, is required. Here’s a list of the different state statutes dealing with this issue that have been introduced over the past eight years.
You owe me a new irony meter. 20 posts or so ago you were unable to admit that you were wrong about your use of gratis even as you agreed with ann about the definition (a definition that doesn’t make sense in the context you used the word).
Zebra @371:
Please, I admitted I was wrong in #126.
All you want to do is look like you’re better than the rest of us.
Gosh. However did I get the idea that you weren’t originally making that distinction?
But OK. As long as your position is now that human rights are not actually a vacuous empty concept in countries that have them, so be it. I’ll make more of an effort to keep them separated.
@capnkrunch —
As I said earlier, I’m an optimist. So I could be wrong. But at least as I read it, the reason he said that is that he was admitting he was wrong. I mean, it really wasn’t all that big of a deal. Lots of remorseful detail wasn’t called for.
No argument here. My point was that its being dead doesn’t, ipso facto, prove that there is no such right. Including if the death was caused by an unjustified act of killing in a human-rights-having country. I mean, if unjustified acts of killing are recognized and punished as such, that’s actually proof that the right exists.
I guess I should really say “generally recognized and punished as such.” There’s always room for improvement.
Never let it be said that we don’t live in a country that protects the fundamental right of citizens in a free society to write curse words on a speeding ticket, at least in the Southern District of New York, which is probably more liberal wrt such things than some.
/all-but-completely off-topic.
@Not a Troll —
Hey, Not a Troll!
Please accept my apologies for that comment @#375. It came out more brusque and snippy than I meant it to or than it needed to be.
Ann, no worries. We’re good 🙂
Gray Falcon #300 “Okay, reading this long thread, I’m getting the impression zebra is unaware of exactly how much genetic information a human being has”
JustaTech #309 “Ethics are not optional in human subject research. Not in the US, or the UK, or really anywhere in the world. There are standards and treaties and laws about these things. IRBs are not optional, and they are not optional for a reason.”
JP # 322 “we don’t know right now just how much information about a person is in their DNA”
There are many good points arisen in this thread, including the above. My 20th century thinking, as Zebra calls it, is based on much recent NGS data trudging, including the use of the Oxford NanoPore Minion which is really the next NGS (about as far from 20th century thinking as you can get in genomics). I have been involved in the genomic study of a birth cohort, of 97% of people born in a single year in a single city. Note: the cohort is over 35 years old now (and has been tracked for health and sociological outcomes since birth), and we did not get genomic data from all of them. Consents and ethics are a big source of loss, as are death and inability to track individuals over their lifetime. However, even with this rich set of data from tracking a birth cohort over 35 years, there is really not much you can glean from the genetic data, aside from ethnicity and other stuff that makes a lot of people reluctant to participate in these kinds of genomic projects. The reasons for a general lack of clear actionable genomic outcomes are very complex. I could give you a long list, or you could just take my (and other contributors) word for it.
Our group is hardly alone in this dearth of actionable data. There are very large international consortia with very large data sets. COGS is one which is relevant to ORAC’s post (which was a very good synopsis IMO). Samples from 239,832 individuals from 167 research groups from all over the world (breast, ovarian and prostate cancer) have been used. In spite of this huge database, there are very few instances where a clinician can say, based on genetics alone, that an individual WILL get this cancer, or that a particular treatment WILL cure this person’s cancer. That’s due to the fact that cancer, like most diseases, is caused by multifactorial things, which may include genetics at birth, but is often over-shadowed by lifestyle factors and just bad luck. Genetics gets even more complicated when you are looking at diseases such as autism, schizophrenia, depression, obesity etc…And genomics is not just about a person’s DNA sequence which can be recorded in a 3 billion base pair text file derived from a much bigger NGS run. As Malia alluded early on, we just don’t know enough yet to make any sense of the data we already have. Generating even more just “because we can” makes no sense, is not ethically tenable (even if you don’t believe in ethics), and is not without risk to the individuals.
However, I will say that on some level I understand where you are coming from. I think most of us working in the field dream of a day when we can take blood from a person at birth, and use genomics to help guide that person in their lifestyle choices, prevention and screening programs, tailor drug treatments and generally help them to lead a healthy and long life. However mass genomic screening of people who are not yet sick, and may not be sick for many decades if ever, is not the way to go right now. We are working towards it (maybe). The hurdles are truly enormous. Generating the DNA sequence is NOT the bottleneck. Doing the genetic groundwork to make the data useful, consent and ethics, data storage, access, security and a whole host of other things are the current bottlenecks. So maybe I share your dream, but I don’t share your ideas on how to get there. I know the likes of Kaiser Permanente’s HUGE project are working towards this too. So it’s not a lack of people already working on it that is holding things up. It is the fact that humans are complicated, and there’s so much more than genetics that goes into it. It’s that there is never enough money to fund every blue-sky idea that pops up. And even given enough money, ethics and privacy will always raise its ugly head (unless more countries move to a totalitarian approach to the problem). It seemed a good idea at the end of the 20th century. Now we need to work smarter, not generate even more data that we don’t know what to do with and that many people don’t want us to have. If you think data security isn’t an issue, maybe you should brush up on Wikileaks or Edward Snowden to remind yourself how vulnerable sensitive data can be? Why would I say that genomics is complicated data, and then say that your genome is sensitive information? At the moment, it is mainly due to a plethora of really poor studies in the past that have inferred an association between single or a few genes, and certain health or social outcomes. A perfect example of this came up in our lab, where we used to have honours students extract their own DNA, then gave them some ‘mystery primers’ to amplify and sequence different genes. They then went away to identify their mystery gene. One of the students happened to get primers that amplified his DRD2 gene. He correctly identified his gene, then saw he had a variant that in past literature was associated with schizophrenia. Just so happened his mother had schizophrenia. He was beyond distraught, and we’ve since had to change our lab practice to make sure students only use de-identified DNA. Not because there is any real association with DRD2 and schizophrenia, but because spurious genetic efforts to interpret DNA sequence in the past had led to publications that such an association existed. We now refer to most diseases like schizophrenia as MAGOTS. Many Associated Genes Of Tiny Significance. And this is most diseases. And this opens a whole new can of worms. If we generate complex NGS data, who owns it? Can the person who donated the sample access this data and troll through it to find all sorts of worrying associations? And if we don’t let the individuals have their sequence data, is there an onus on those who control the data to let the individuals know if they have any actionable, pathogenic or incidental genetic information, assuming we even have the ability to recognise these? So to recap, there are basic genetic and environmental knowledge issues, data storage and processing issues, privacy, ethical and ownership issues, cost issues, and ummmm, issues galore to be sorted through.
Such projects require a perfect combination of artificial intelligence and human stupidity.
Retro Pump,
Thanks for acknowledging that I was making a positive suggestion.
I have to ask again– why didn’t you jump in sooner? If you had said you participated in exactly the kind of data collection I propose, it might have saved an awful lot of the silliness. At least they would have been reluctant to compare me to Mengele, since you would have been tarred with the same brush.
Just let me clarify the 20th century point, and an apparent misunderstanding. I didn’t say we need more data, although we might. I say we need more researchers, doing basic research, not necessarily directed towards finding medical cures.
Making the large amount of data available gratis would aid that.
The availability of that much data at a central source should, if I understand what you are saying correctly, reduce the obvious problems that you list. There would be uniform standards and uniform data, rather than a hodge-podge of sample collection and storage options and security options and privacy options and so on.
So it has nothing to do with what equipment you are using, and there is no criticism of your capabilities. But lots of things are changed by technology, and the structural and organizational aspects of the enterprise should reflect that.
This would be a use of government funding with a substantial multiplier effect.
Pointing out that a lack of ethical guidelines in medical research can lead to the horrors perpetrated by Mengele does not constitute comparing zebra to Mengele.
ann,
Sure, when I admit an error you have no trouble at all interpreting my words….
But I do appreciate your agreement.
I would note that the traffic ticket story is spot on with respect to what you quoted; for me this is where it gets interesting. The most convincing evidence that you have an actual right (granted or constructed by the SE) is when the issue is adjudicated, and even more so when there is a record of rulings that go both ways. In a sad way, the death penalty is ultimate confirmation of the claim that citizens have a “right to life”, if it is applied fairly.
I note also that there are obviously people who still don’t get it, who believe that “ethics” are the determinants of law. Just like the people who believe that the US constitution is derived from “Christianity”. Oh well.
zebra, if you don’t want to be compared to Mengele, then stop dismissing the concepts of rights and ethics.
zebra, # 289
I am not really able to follow your arguments about ethics.
I thought you could be happy to live in a country where
“…We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness.–That to secure these rights, Governments are instituted among Men, deriving their just powers from the consent of the governed…”
# 290
I was really lurking from the start, and I was aware of your proposal.
I wasn’t aware of the complexity of the matter too, and I am grateful to cognizant people who put it down right.
But I think something is missing from the discussion, and it is only surfacing from Retro Pump’s last post.
As i suggested in Orac’s last post about ductal carcinoma in situ, many medical procedures (in that case breast screening) are implemented without knowing all relevant consequences.
A proposal to gather DNA for genomic screening would bring the unwanted consequences Retro Pump found in his student: the discovery of pieces of information which rarely could benefit the donor, but more frequently would damage his psychological health.
And when humans have information at hand, they feel compelled to use it, even when the information is useless for their stated purposes.
This is the reason it is so hard to convince women not to have a biopsy after a positive mammography report.
It would be silly to say that the US constitution was merely Christianity transposed to another context. But there’s really not a whole lot of western thought that isn’t derived from Christianity. It’s kind of the you’re-soaking-in-it matrix of the contemporary west. For example: Prior to the rise of Christendom, the law — or, more specifically, Frankish law — did not distinguish between murder and manslaughter and when somebody got killed, the killer made restitution to their clan in whatever amount the loss of that person’s life represented. IOW, all lives were not regarded as equally valuable simply by virtue of being lives. That idea didn’t become current until c. the Holy Roman Empire, because it derives from the belief that since everyone has a soul like everyone else, everyone is an autonomously valuable individual of fundamentally equal worth.
So. The constitution wasn’t written until almost a thousand years after that. But inasmuch as it expands on the same concept, it is derived from Christianity. It’s also why most of the west rejected slavery on its own turf and eventually everywhere.
That’s not to say that all western thought is religious. Obviously it’s not. But Christianity is a very pervasive (if attenuated) influence. Omnipresent, pretty much.
The idea of government by an institutional hierarchy where the powers of a position and the respect due to it are vested in the office rather than the officeholder, who occupies it by appointment/election and not hereditary privilege — ie, the office of the presidency, etc. — is also derived from Christianity. Or actually, the Church.
Not purely. There’s some partial precedent in classical antiquity, too. But you know what I mean.
BTW:
^^That’s not willfully selective. I swear.
Perodatrent, welcome back.
What you quote would correctly be described as “propaganda”.
What makes me happy to live in this country is the Constitution itself and the development over the centuries of a structure of law that has, if imperfectly, granted and constructed that could be described in those terms.
It was not The Creator that gave the slaves life and liberty, or gave women the right to vote and own property, or gay people the right to be married– to pursue happiness.
It was the people who sacrificed and died to achieve those things. And they are only unalienable by virtue of eternal vigilance, as they say.
Saying that the rights are supernaturally extant, like souls, and we are “securing” those rights by forming a government, is a sop to those who need some kind of Authority figure around as a security blanket.
Your concern about the existence of the knowledge is understood. How does my proposal change anything? If you can get a genome done for $1,000 or even much less eventually, people will get them. Are you going to declare a War On Genomes, like the War On Drugs?
#395 “what could be described in those terms”
ann,
All valid. Once again I was using shorthand; Christianity in quotes as a stand-in for garbled misinterpretations of mostly the Old Testament that our resident Taliban types promote.
But you know, we could have another long (sophomoric according to capnkrunch I’m sure) discussion, about whether the Church was more influenced by Rome than Rome by the church. And Rome influenced by Greece, and then there’s the Eastern Church, and ….
Another time perhaps.
@zebra —
As long as I’m at it, since you mentioned it @#292:
^^The penalties for killing were calculated based on an-eye-for-an-eye principles, IOW. And that wasn’t because the Franks were reading the bible. Or even reading, for the most part. They were pre-Christian, and there weren’t really books yet.
Because “an eye for an eye” isn’t actually a religious sentiment and it doesn’t actually originate in the Hebrew bible. It’s there because it was a tenet of Babylonian secular law — eg, the Code of Hammurabi — that Jewish law picked up. But it’s also not inconceivable that it arose independently in other clan/tribe-based societies in other parts of the world subsequently.
Long story short: It sounds like a religious prescription to a contemporary western sensibility because most people in the contemporary west know it from the bible. But it’s not creator-mandated or anything like that. It’s just law that happens to be in the bible. And it’s been around a long time. I don’t know why that is. It just has a very enduring popular appeal, seemingly.
Maybe that’s dull, I don’t know. But if so, I apologize. I find that kind of thing interesting.
zebra, do you really want to work with a medical system that considers ethical behavior “twentieth-century thinking?”
Question for you, zebra: What, precisely, was wrong with the Tuskegee Syphilis Study? Answer that without bringing up ethics or the “right to life”.
I’ve heard the real understanding of “an eye for an eye” is that it was addressing the culture of extracting more from a perpetrator than what was lost “two eyes for one eye”.
I can’t say I vetted this yet but it wouldn’t surprise me if that is what was happening with vengeance and all but it is not something I’ll get into a debate about at this point.
ann,
I of course find these things interesting. I just don’t want to offend sensibilities much more than I already have, and spend too much time OT.
I don’t think there are many if any things that you could properly call “religious” in this context. As I suggest WRT the US constitution (#395), societies establish laws pragmatically, and attribution to some “higher power” or secular “moral/ethical” construct is simply an attempt to better achieve consensus and compliance.
As a non-Christian, I feel obligated to point out that the Old Testament is not the same thing as the Hebrew bible, even though it is.
Meaning: The popular belief that those books of the bible are all vengeful and wrathful and full of harsh, bloody and unforgiving eye-for-an-eye conflict is derived from Christianity, which has a much more literal and historicist approach to reading sacred texts than Judaism does. Plus, you know. Back in the origins-of-Christianity day, being an improvement on Judaism was an important brand attribute.
That’s not how Judaism reads or understands the same texts, however.
Well. That’s not necessarily a bad — or ftm, vacuous — thing, assuming that the consensus isn’t unduly restrictive and the compliance isn’t coerced.
I also don’t know about the “simply.” Ethics facilitate the functioning of civil society. And a functional civil society facilitates the preservation, maintenance and practice of fundamental freedoms.
It’s all pragmatic, in one way or another. Praxis is complicated. And also error-prone. If it wasn’t, everybody would just make a road-map to nirvana and settle in immediately.
ann,
Jesuitical or rabbinical; had to be one or the other….
But 404 doesn’t hold up to those standards. What exactly constitutes a “functioning civil society”? Societies that hold slaves and oppress women “function” just fine.
Grey Falcon 404,
I really don’t want to spend my time being philosphy101 professor, but you are insistent.
I can’t tell you what was “wrong” with the study because “right” and “wrong” are empty terms.
I can tell you why I would vote for laws prohibiting such practices– because the next time it could be me.
I don’t know enough detail to speculate on what laws it might have violated at the time, but that would be about whether it was illegal, rather than “wrong”.
They’re very similar. As it happens, I didn’t have that kind of religious education, though. Or any kind, in fact. It’s just the turn of mind I was born with.
Annoying, but not without its advantages.
One in which the non-governmental institutions and individuals that make up a society are able to function, within reasonable parameters. At a minimum, that requires a general ethical commitment to fairness and….I’m not sure what to call it. Something like “care/harm avoidance.”
Those obviously aren’t the only requirements. There has to be enough baseline security/stability wrt the resources necessary for survival first. For instance. But assuming that’s in place:
You really need those ethics to keep stuff up and running. It’s kind of like:
You can take the individuals out of the tribal/feudal society, but you can’t really take the tribal/feudal inclinations out of the individuals. Because at the individual level, that’s how self-interest tends to incline, due to the scope of consequences that are immediately within any individual’s sightlines being very narrow.
Ethical guidelines help. They’re a form of practical wisdom, basically.
Yeah, but they’re unfair.
zebra # 395
A long time ago I was teached that there were two sorts of Rights, Natural and Positive.
Consttutions were examples of positive rights. But I think they are based on some kind of natural right which is not completely vacuous, as you seem to believe. After all, people writing constitutions have to base their written words on shared beliefs.
As for your example, if Kuwaitians like it that way, who am I to argue?
As for the “right” to have one’s genome sequenced, I think it should be done only after specialist counseling; as already happens, for example, for HIV tests. Not a work for a family physician, but for a geneticist.
I have the “right” to have my genome sequenced. I do not have the *desire* to do so. And I would resent being forced to do so. I would resent any effort to make me have my children’s genome sequenced mandatorily. And certainly I wouldn’t give consent at their birth to have it taken and kept somewhere. At least not as things stand today.
In 50 or 100 years, my descendants might have a different view/desire. But I would never agree for it to be required.
Oh, G-d, it’s delusional. First the jaw-droppingly primitive performance about rights, and now ethics.
You’re arguing with a dining-room table, folks.
ann,
We’re just going to have to disagree.
Replacing a genuine, expansively empathic and compassionate psychology with the kind of Authoritarian rulebook you are talking about is both dangerous and degrading.
“Fairness is ‘good’ ” is trivially replaced with “greed is good”, as we have seen over the last few decades. I would prefer an effort to help people to escape adolescence, as much as possible.
I do enjoy this latter part of our conversation, but unless someone wants to discuss the on-topic Zenome project who can maintain an equivalent level of civility and knowledge as you have demonstrated on this, I’m done.
zebra, would you oppose anything like Tuskegee studies if you were assured you wouldn’t be subject to experimentation?
perodatrent,
If you never heard of “natural ‘right’ to life”, you would still put laws in your constitution prohibiting murder, and arbitrary execution by the government, so you would not be walking around in fear all the time.
Also, I have to say that thing about “get with the 21st century” again– you can buy HIV tests OTC for USD39.99 .
zebra@413: Or the ruling class could put in rules prohibiting murder and arbitrary execution of their own class, and to heck with everyone else.
Grey Falcon, you have to read my other comments and figure it out; I’m not going to keep repeating.
I would oppose them because I empathize with people suffering, and because, even if I am not directly involved, it causes disruption in the society. You can’t really be isolated from things– it’s like when the cop shoots the black guy for no good reason. Everyone picks up the tab, in multiple ways.
Done now.
Now there’s a failure of reading comprehension.
^ The “they” is particularly precious.
Perhaps zebra is unaware that the philosophical study of how we can minimize people’s suffering and reduce disruption in society is called ‘ethics’.
From ‘The Ethical, Legal, and Social Implications Program of the National Human Genome Research Institute: Reflections on an Ongoing Experiment’ published last year:
I note that “the need to pay close attention” to “the ethical, legal, and social implications of genomic science” is “almost universally appreciated”. Perhaps zebra didn’t get the memo.
Zebra @ 388
“I have to ask again– why didn’t you jump in sooner?”
Well, mostly I don’t have enough spare internet time to participate in these discussions, so I rarely even keep up with them. I usually hit them from my TOC alerts when they first come out, read the comments, then don’t check back again. When I first read this post there were not that many comments, and to address some of the questions raised adequately would have taken a book length post, and still not covered everything. Plus after 30 years working in the field I still don’t know close to everything. I know a whole lot less now than when I first learned as an undergraduate that DNA>RNA>Protein>human (which is now clearly not true). I have only touched on what I consider the tip of the ice-berg.
I don’t understand how I could be tarred with the same brush as Mengele, but then we perceive our own faults less than others perceive them. The student I mentioned was informed not only that he used his own DNA, but that there is also the possibility of incidental findings. He was also informed that the genes we were handing out had no real, established link with diseases. Part of the exercise was in fact for the students to trawl through the literature on their gene and realise how many false positive associations there are in the literature when you look at it in the light of more advanced research. And obviously, this person was doing a project in a genetics lab, so arguably had better knowledge to understand incidental findings in the context than most lay people.
To this day, twin studies are considered the gold standard in teasing out genetics and heritability from environmental factors. The difference today is ethics and consent. We have to make sure that any study participant (or patient sent for genetic testing) OR their parents, not only consents, but understands the possible positive and negative impacts of participating in the study. We have to take into consideration ethnic, cultural, religious and personal preferences. We never know all the potential pros and cons, but the concept of ‘first do no harm’ is as incumbent on researchers these days as it is on medical doctors. This is the 21st century thinking anyway.
Just for fun, let’s stick to schizophrenia. It is, judging by twin and family studies, the most highly heritable mental disorder we know of. But read this article http://psychcentral.com/lib/schizophrenia-and-genetics-research-update/
and have a good hard think about what malia said about doing the basic groundwork. We are so far from having any cogent answers to most complex diseases, that the question of what we do with this data, what are the benefits versus harm to the participants, who owns the data, how does a child who comes of age and decides they don’t want their data get it removed, who gathers not just the genetic data, but all the phenotypic data which will be needed to maybe make sense of the data someday. Hint: These targeted studies are a much better way forward to answer gene x environment questions, as much of the phenotype data needs people to actually go looking for it. You can’t just count on it being captured by your family doctor. So yes, we need more researchers on the job at ground level, but not necessarily for archiving scads of data that may be close to useless without closely monitored phenotypic data. But we also, in this day and age, need to have systems in place that give study participants the information and reassurances they need to feel comfortable participating in these kinds of studies. Please understand that in a civilised society THIS IS FIRST AND FOREMOST. We have to be very clear up front about who owns and can use the data, what types of analysis or studies can they be used for, how will the data be protected, what happens to the data and samples if the study winds down for whatever reason, and so on. For instance using my own personal experience, we had consent to collect DNA from our cohort for genetic analysis for a broad range of questions, but when we needed to send the DNA to another country to get the genetic analysis done cost-effectively, we had to go back to every person and get new consent. And some of them declined. Most interestingly this consent was to send the DNA to the USA (who then generated the data), and some people just didn’t feel at all good about that. With the size of the study you are proposing, it will almost certainly need international collaboration. How many Canadians in your proposal might say go ahead with your plan, as long as the samples and data stays in Canada? Quite a few would no doubt object to sending it to a US government body. You may think this is just nonsensical paranoia, but what if one the conditions you want to study is paranoia? Though more than ever I don’t think it is paranoid for people to worry about third hand parties getting hold of their data.
Last of all (for now) just think about the amount of data you are talking about. It can be trawled for so many things, and whether a researcher has legitimate or nefarious reasons for doing so, you can massage this vast amount of data to imply ethnic links with intelligence, violence, or socioeconomic outcomes, genetics of sexual preference, or pretty much anything else your heart desires. If you feed this kind of data back to participants, you set in place the perfect storm for eugenics or ethnic cleansing once again. We have to tread very carefully going forward.
Just this week in the BMJ was an article that is relevant to ORAC’s subject. It is about cancer genetics: http://www.bmj.com/content/351/bmj.h4805?etoc=
… cautioned oncologists on their use of multigene panel testing, which can turn up variants whose clinical significance has not been well established. “Because of the current uncertainties and knowledge gaps, providers with particular expertise in cancer risk assessment should be involved in the ordering and interpretation of multigene panels that include genes of uncertain clinical utility and genes not suggested by the patient’s personal and/or family history,” the statement said.
“Increasingly, we will be the recipients of data that we did not anticipate or, perhaps, even seek to know,” they wrote. “Accordingly, we will be in the uncomfortable position of reacting to that data on the basis of an immature and incomplete understanding of what [those] data mean.”
Retro Pump @419: “I don’t understand how I could be tarred with the same brush as Mengele, but then we perceive our own faults less than others perceive them.”
As one of the people who resorted to that simile to try to explain the need for IRBs to zebra I want to be very clear that I do *not* think the study you are involved with is unethical in any way. Obviously you have IRB approval, and based on your story about the student and the schizophrenia gene you really care about ethical conduct and the possibility of harm.
Thank you for posting here, it’s always great to hear from an expert! 🙂
Wait. What?
Fairness and care are universal moral fundamentals in all cultures at all times. Small children understand and appreciate that they’re good and useful qualities. It’s hardly a dictatorial imposition to suggest that bearing them in mind is generally conducive to successful societal functioning.
I mean, within very broad parameters, people should be free to go to hell their own way, if they like. (By which I don’t mean “hell’; it’s just a figure of speech.) Goes without saying.
But some basic acquaintance with the outlines of civics and ethics is useful. You never know when it might come in handy.
Yeah, well. If it all has to be reduced to a three-word motto, it’s never going to mean much to anybody. But it doesn’t. So moot point.
Adolescence has its pros and cons.
I hope I never completely stop being naive, personally. It’s hard to keep that alive sometimes, though. Times is tough.
Thank you. I enjoyed and appreciated it too.
FTFY. Leaving aside the fact that “the latter part of [the] conversation is completely on-point, you’ve had plenty of entirely practical questions about the Zanadugnome Project, which have been been completely ignored.
Describe the vaporware that “is” the interface.
^ “and has” and close quote after “[the] conversation.”
Retro Pump,
Again, your response is greatly appreciated.
WRT Mengele– perhaps you are not familiar with the dynamics of this group, so lets get that out of the way first. While I hesitate to compare myself with a young person for whom I have the greatest respect, what I experience on this blog can be compared to what our US president experiences– I think of it as ZDS, or zebra derangement syndrome.
So, when you participate in a birth cohort study, it is all well and good, but when I suggest a similar, completely voluntary program, with all the same or greater safeguards, it becomes a fantasy about Jack-Booted-Thugs forcibly taking samples from helpless infants. Perhaps they also think I’m in cahoots with Barack, and we’re going to store all the guns he confiscates in the same place as my DNA samples.
Can we move on to reality now?
What I would find extremely helpful is numbers. How many individuals in the cohort study you mention? What would be an ideal sample size to study schizophrenia? And so on.
When I read your description of the difficulties of the research, and your reference, I think: “how can I help”? My answer is that if we collect all these samples, and digitize some portion of them, and also create a registry of conditions, we *take away* many of the problems you describe.
If someone withdraws, for whatever reason, or dies, we can replace her. If someone objects to giving the data to a US researcher, we can replace him. The people doing the research do not have to deal with anything *but* the data; all the permissions and notifications are part of the centralized system…
Now, I could go on, but I’ll wait and see if you are able to engage further on this. I understand that your research project is extremely difficult, but as another pretty fair US president said– we aren’t going to the moon because it is easy.
Zebra, no matter what you are A. Always a victim B. Always claiming victory. Even in those rare moments when you are being kind. That’s quite a skill set to have in the business world, and it’s one of the many reasons I’m no longer in it.
This is spectacular.
Narad@410
Don’t insult dining room tables. At least they have a leg to stand on!
zebra
Do you not see the difference between Retro Pump’s birth cohort study (one city) and yours (one country)? Why do you think your idea solves problems that Retro Pump specifically said it doesn’t? How on earth does collecting more data (that even according the the experts we can’t use) solve storage, ethics, consents, security, etc problems?
Regarding Mengele, no one called you that. You couldn’t answer questions regarding privacy and ethics (no surprise, the experts can’t either) so you dismissed them as vacuous (then really made an ass of yourself by saying the same of human rights). The Nazis were just brought up as an extreme example of why ethics are so important. You can call this topic off topic (it is) but I’d note that you were all too happy to continually harp on it while on the other hand you were all too happy to drop any discussion of confidentiality issues beyond “I don’t agree” or “I don’t think…”.
The closest you’ve come to an actual defense is that 200,000 is only a small fraction of the total 400,000,000 population. This is nonsense there is no centralized medical record database of 400,000,000 people. Not 200,000 is several orders of magnitude greater than any current database so even if there were a central repository of medical records it would still represent a unique asset. Of course I already made and you already ignored both those points.
You keep saying that you don’t think your database poses a risk to the patients but have yet to provide any evidence to support that claim. There have been several people (myself included) with experience in infosec as well as one person with genomics experience telling you otherwise. I’ve provided several references explaining how confidentiality can be breached. If you’d like I can find references about hospitals being breached as a demostrarion that hackers would be interested in the PHI of 200,000 but I’m not particularly inclined to look given that you’ve summarily ignored every reference I’ve provided so far.
When several experts in a field tell you “we don’t need that right now. In fact, it’s a bad idea at this point in time,” the rational response would be to cut your losses not double down. You’re “the only one here willing to admit [you] got something wrong,’ my ass. To quote Narad, “[s]eriously, go f[*]ck yourself.”
Put another way, several issues with your
idea exist solely because of the size of the database (storage, processing) while others are made worse because of the size (consents, privacy, security). How exactly does gathering large amounts of data solve any aspect of any of those issues?
“So, when you participate in a birth cohort study, it is all well and good, but when I suggest a similar, completely voluntary program, with all the same or greater safeguards, it becomes a fantasy about Jack-Booted-Thugs forcibly taking samples from helpless infants.”
Umm, I never said and certainly don’t believe there is anything wrong with birth, or any other, cohort studies. I am just saying that you have to have proper ethical and other considerations in place, and these considerations need to be flexible into the future as ethics, technology and society change.
“how can I help”
You can volunteer to be in genetic studies that are already underway. If you don’t (yet) have any glaring health problems, you could always just be a healthy control.
“If someone withdraws, for whatever reason, or dies, we can replace her. If someone objects to giving the data to a US researcher, we can replace him.”
So this is no longer a birth cohort??
“My answer is that if we collect all these samples, and digitize some portion of them, and also create a registry of conditions, we *take away* many of the problems you describe.”
Well, the data is digitised to begin with, so not sure what you mean. That is what NGS data is. How will this registry of conditions be maintained. It takes a great amount of resources to follow a birth cohort and “update” their conditions as they develop. It needs to be done proactively.
More importantly, there is so much more to human wellbeing than just raw (digitised) DNA sequence. Properly designed studies will give you so much more bang for your buck than just collecting a whole bunch of random data. In the case of schizophrenia for example, you really need family based studies. That’s because there is not one gene, or even one set of many genes that leads to schizophrenia. It can be different in each family. One estimate is that you would need up to 50,000 sibling pairs to have 80% power to detect a locus accounting for 5% of variance in liability to schizophrenia at α = 0.001. And the best evidence is that a lot of the risk for schizophrenia is laid down in the prenatal period due to environmental factors (e.g. mum is infected with a certain virus at a critical in-utero period). So a best case scenario is that if you had these 50,000 sibling pairs, you *might* be able to detect a gene that *may* contribute up to 5% of the genetic risk of schizophrenia in the general population. Note the data from these sibling pairs is unlikely to come from a birth cohort. Unless the siblings are twins, they won’t be born in the same year, and even then you have to wait until both siblings are adults so you can assess whether or not they develop schizophrenia. So, better to spend the money finding these adult siblings with and without schizophrenia and work backwards from there. Now keep in mind that a 5% risk in one gene, is not saying that if you have this one gene you will get schizophrenia. It just means you are statistically slightly more likely to develop the disease. And even now, we can’t say for sure that THAT gene difference is the cause of your increased risk. That requires a lot more work in genetics at the level of epigenetics, RNA, protein and other more difficult and expensive tasks. The most we can hope for in complex diseases like schizophrenia is to try and understand the basic underlying biology and develop better treatments. Or maybe it’s better to spend the money on understanding and mitigating known environmental risk factors.
Good research quite simply requires good experimental design. You need to ask and answer the questions about what you intend to do with your data. What is the outcome you hope to achieve? How does knowing that out of 200,000 kids born in a single year, 50% of them will grow up to be obese, and about 30% of this risk of becoming obese is due to variation in maybe 300 genes. What if you have 150 out of 300 of these deleterious genes? What are the implications for you (or your children)? What do we decide is the cutoff for number of deleterious genes before we recommend ‘intervention’ to prevent you/your child from growing up obese?
Maybe a more concrete example from my own past will help you understand the genetic and ethical difficulties we have. After much genetic and phenotypic groundwork, a gene variant the MAOA gene is now pretty well established as a risk for abused or neglected kids (male children as it is on the X-chromosome) growing up with a variety of antisocial behaviours. Do we screen all male children at birth, and tell parents “don’t abuse or neglect THIS child as you may ruin them as adults? Or do we just skip the genetics altogether and tell all parents of all children not to abuse or neglect any child? Or do we do prenatal diagnostics and recommend terminating this child or adopting them out unless you intend to look after them properly? There have been court cases where this gene was used as a defence for antisocial behaviour. There was an ethnically divisive and dubious publication that implied a high rate of this variant in a Polynesian population explained their higher rates of convictions for violence and incarceration (dubbed “The Warrior Gene”). Do we really want to allow “my genes made me do it” as a defense, or “they” can’t help it, because ethnicity? There are so many legal and ethical consideration that need to go into how this kind of data is used. If we find your child has 150 out of 300 of the risk genes for obesity, do we say “make sure THIS child eats properly and gets plenty of fresh air and exercise”? Do we flag children with an increased risk of developing depression and let parents know that they should try and minimize life adversities for their child? Do we send children with an increased risk of developing alcoholism to be raised in a strict Muslim country?
Or do we spend the money on bettering the environments for our children. Do we try harder to mitigate the harms from increased food availability and screen time, drugs and alcohol, socioeconomic disparities, environmental contamination and degradation and all the other things that we know for sure can make a difference? Do we invest more in storing cord blood for future treatments that may become available? It may come as a surprise to hear this sort of thinking from a life-long geneticist, but so much of the disease burden we face now, though there is undeniably a genetic component, is better addressed through public health and social approaches. Some diseases could be prevented or treated better through a genetic approach, but these will be in the minority. We still don’t know what to recommend for women who have one of the known and major genes for breast cancer. Basically you still have to weigh up the costs of the Zebra project with the potential harms, and then address what benefits you envision will outweigh these costs and harms. You have to be convincing enough and show enough benefits, to get the US DoD to part with those fighter jets and sink the money into your project instead. You have to convince the parents of the children you want to recruit into your project, not with exaggerations or lies about the potential risks and benefits, but with some cogent and realistic reasons to participate (or not).
For Zebra and anyone else who wants a glimpse at just how hard the groundwork is for the kind of genomics in the Zebra project, I was just coincidentally reading this paper. I *think* it is publically available…basically it reiterates the idea that it is not raw DNA sequence that is holding us back, but really nailing the link between this DNA info and the ultimate results on phenotypes:
http://www.pnas.org/content/112/37/E5189.long
Comparison of predicted and actual consequences of missense mutations
Significance
Computational tools applied to any human genome sequence identify hundreds of genetic variants predicted to disrupt the function of individual proteins as the result of a single codon change. These tools have been trained on disease mutations and common polymorphisms but have yet to be tested against an unbiased spectrum of random mutations arising de novo. Here we perform such a test comparing the predicted and actual effects of de novo mutations in 23 genes with essential functions for normal immunity and all possible mutations in the TP53 tumor suppressor gene. These results highlight an important gap in our ability to relate genotype to phenotype in clinical genome sequencing: the inability to differentiate immediately clinically relevant mutations from nearly neutral mutations.
Abstract
Each person’s genome sequence has thousands of missense variants. Practical interpretation of their functional significance must rely on computational inferences in the absence of exhaustive experimental measurements. Here we analyzed the efficacy of these inferences in 33 de novo missense mutations revealed by sequencing in first-generation progeny of N-ethyl-N-nitrosourea–treated mice, involving 23 essential immune system genes. PolyPhen2, SIFT, MutationAssessor, Panther, CADD, and Condel were used to predict each mutation’s functional importance, whereas the actual effect was measured by breeding and testing homozygotes for the expected in vivo loss-of-function phenotype. Only 20% of mutations predicted to be deleterious by PolyPhen2 (and 15% by CADD) showed a discernible phenotype in individual homozygotes. Half of all possible missense mutations in the same 23 immune genes were predicted to be deleterious, and most of these appear to become subject to purifying selection because few persist between separate mouse substrains, rodents, or primates. Because defects in immune genes could be phenotypically masked in vivo by compensation and environment, we compared inferences by the same tools with the in vitro phenotype of all 2,314 possible missense variants in TP53; 42% of mutations predicted by PolyPhen2 to be deleterious (and 45% by CADD) had little measurable consequence for TP53-promoted transcription. We conclude that for de novo or low-frequency missense mutations found by genome sequencing, half those inferred as deleterious correspond to nearly neutral mutations that have little impact on the clinical phenotype of individual cases but will nevertheless become subject to purifying selection.
The rest of it goes into the nitty gritty, but the summary is “it’s complicated”
Retro Pump,
If you don’t mind sharing, what is your dream genetic research project?
“what is your dream genetic research project?”
I don’t think I can answer that question. When I first started in genetics in the late 80s, it was as a plant geneticist. I was working on pea genetics, and thought this was my dream job…in the footsteps of Mendel. The idea was one I loved, to use genetics to inform plant breeders at making and selecting better plants to help feed the world. Then the anti-GMO fever took hold (even though I wasn’t personally making GMOs, just helping breeders) and the whole field seemed to sour a bit for me. I still think using genetics to breed plants and animals for better, more nutritious yield in poorer soils using less water etc…is a noble one. I have moved into human genetics (decades ago) and I have gone from thinking that if we could get a handle on genetics, we could prevent or cure whatever ails us (the hype of the Human Genome Project Infected most of us in the field), to now feeling just plain inundated with data. We have too much of some data (such as the data Zebra wants more of), and no where near enough of other data (clinical, phenotypic, invitro, invivo, environmental, social).
So maybe my ideal genetic research project would be going back into the field of crop and food genetics. It is a field where then phenotypes, outcomes and endpoints are much easier to measure than in humans. It is really hard to control the environment and breeding of humans!!
Retro Pump@429
Speaking of raw sequences, if you were to request data from, say SHIP, would they give you the raw sequences? Is the ability to reidentify pseudonymous genomes (i.e. through surname inference) a concern? I’m curious if you can give some insight about how people in the field feel about attacks on genetic privacy. Like is it a concern but maybe tempered by controlling access to the data and IRB/ethics committee oversight or is it more regarded as like tinfoil hat paranoia?
What do you think of the 100,000 Genomes Project? The Nuffield Council paper that Krebiozen linked to before said that it was rushed because of political pressure and so the ethics weren’t given the time they should have been.
@430
The full text is publically available. It’s quite over my head though.
It is really hard to control the environment and breeding of humans!!
LOL. Indeed.
I don’t know how much of a role teaching plays in your profession now or how much of an interest it is to you, but you certainly demonstrate a talent for it. In any case, I wish you well in your endeavors whatever they may be.
Retro Pump,
Thanks for the added information. It must be weird to be in a field that promised so much that hasn’t panned out.
That was interesting, thanks, though I must admit skimmed the methods and results sections. The lack of a one to one relationship between genes or constellations of genes and specific conditions is precisely what I was getting at in my original comment at #4 that zebra apparently didn’t understand.
I guess we could conclude that one mouse’s (and man’s) mutation is another mouse’s polymorphism (sort of).
Retro pump,
You’ve provided lots of information, which again demonstrates the difficulty of genomic research in general, but you still seem to be “stuck” on what the actual proposal is.
This is not a “study”. It is simply a way of making the data available to researchers who will execute the study. It deals with many of the issues you discuss, so that researchers can concentrate on the experimental design. There is no “experimental design” beyond establishing what goes into the phenotype databases, which can be fairly broad.
I wonder, when you suggest that replacing one individual’s record with another would make it no longer a birth cohort, whether you have really thought it through. Can you explain just this point? Perhaps there is a disconnect because I am thinking of information/data more abstractly? Exactly what difference would it make?
And I really am curious as to the size of the city-cohort you were involved with.
436 To avoid misunderstanding:
This is not a “study”. It is simply a way of making the data available to researchers who will execute a study of their choosing.
And again, since misunderstanding is common:
This is not a “study”. It is simply a way of making the data available to researchers who will execute a study of their choosing with some subset of the data.
Good luck convincing an IRB or ethic committee that sequencing the genomes of hundreds of thousands of people isn’t a study.
Zebra doesn’t even know what constitutes a “study.”
Guess what, collecting data is a “study.”
How exactly? Other than dismissing those issues as vacuous concepts, I mean.
zebra # 413
I know some people are very jealous of their privacy, and use every means to not associate their name to a HIV test results.
Or other people “donate” blood to have HIV test made -and a few bucks in their pocket.
But in my view this should be strongly discouraged. For example by printing a well readable phrase on the packet/form: HIV (or Genome) testing can seriously damage your health. Just as for cigarettes.
perodatrent,
We agree that excessive screening is a bad idea. (I think your warning message is a bit extreme if you are being literal.) But again, this does not relate to my project, which is about basic research.
And really all I was trying to say, and I wish I knew the French for it, is “the cat is out of the bag” or “that train has left the station”.
I think even Not a Troll? reported taking USD 25 for a genetic sample. And RetroPump, who tells me that there is more data than they know what to do with, then also suggests that I can help by donating my genome.
I suppose zebra thinking that an Italian speaks French shouldn’t surprise me. It’s oddly apposite, actually.
Zebra, Retro Pump meant donating for specific studies not for casting a wide net. And, I’m unsure what the $25 has to do with people being inclined to donate. It wasn’t my reason because the time involved makes it a very poor investment.
As someone who is directly involved in the precision medicine initiative, I can tell you there are a lot of erroneous arguments presented here, both by zebra and against zebra. I’m not particularly interested in discussing those points, as I do enough of that during my day job, but just wanted to give everyone a heads up that there will be a major announcement from the White House regarding PMI in a few hours so stay tuned 😉
In Italian it would be: it’s useless to close the stable, after oxen escaped.
A stable is best kept closed, and a “right to know” is best made a little hard. In my opinion.
And it just dropped:
http://acd.od.nih.gov/reports/DRAFT-PMI-WG-Report-9-11-2015-508.pdf
I recommend that any further conversation on the viability of precision medicine refer to what the initiative actually aims to accomplish as described by this document.
Guys, zebra didn’t say it’s not a study, he said “study”. Not sure if those are scare quotes or a direct quote. Given his history of abusing quotation marks it would be rash to assume that ” study” has the same meaning as study.
AdamG447
Interesting. I hope it’s the draft privacy guidelines.
Ah. Cross posted there. Thanks for the link AdamG. Will put off posting in this thread until I’ve had a chance to peruse it.
Thanks, AdamG
OK, it’s official– I’m pathetic. 200,000? Hah! Piker!
And Canada? Who needs ’em.
Although I wish my concept had more support from experts in the field…
Zebra @436: “I wonder, when you suggest that replacing one individual’s record with another would make it no longer a birth cohort, ”
Generally when epidemiologists speak about a birth cohort it means “all of the people born between these dates”. Birth cohorts are inherently closed cohorts – you cannot be added to a birth cohort because it depends on when you were born.
Now, when you suggest adding people if some members of the study are lost, you are talking about an open cohort. That can be totally fine (it is a not-uncommon type of study group). I think what you mean (and please correct me) is that if someone from the study population dropped out, you would replace them with someone from their birth cohort.
Well, now that you have an actual proposal to hand, you’ve got a framework and all the time in the world to specifically demonstrate its inferiority to your own thoughtless babbling.
It was always just a dream for zebra. He couldn’t have pulled it off, but he will certainly do a happy dance around the blog. Which I’m fine with. That was going to happen regardless.
AdamG,
I very much like that the participants have a say in defining the rules of how their information will be used. But I’m not really a fan of this. I’ve already donated my DNA for one discreet study and may do so again, yet for this initiative count me out.
Care to say why? Not interested in debate, just genuinely curious.
Heh, I had missed this gem:
This is a classic. Apparently fed up with being aptly likened to a college sophomore, Z. is apparently now in his 70s or something, as 54 isn’t “young” by any stretch of the imagination. (Hint: try asking one.)
Even better, though, what the president, ah, “experiences” is named after Z.
Justatech,
Why would you think anything but that I would replace them from the birth cohort?
The database of 200,000 is a database, not a “study”. You would provide a replacement from the database of the Zenome Project to the study the researchers at university X are doing.
How many different ways would you like me to say that?
Perhaps for the same reason that RP did. Recall:
“Replace” for what? With what? Your comment was pure blobovianism. You seem to have meandered to this remark from schizophrenia, but if the relevant members of the cohort are completely interchangeable, why wouldn’t one be using all of them?
Your own brillian concept appears to be so ill-formed in your own head that you can’t even figure out what your own defenses are supposed to mean.
^ “brilliant”
So, that whole “sorting” thingamabob – i.e., data reduction and analysis – has been thrown overboard?
Perhaps you’d like to “define” your “terms.”
zebra@458
It might not be a “study” but collecting and sequencing genomes is certainly a study. You would need an IRB (one concern addressed in the PMI paper AdamG provided) and you would need to follow all the same legal and ethical rules that any other study.
On that note, I realize that you see this as nothing but a victory, but if you take the time to at least skim the PDF you’ll see that significant consideration was given to various issues that you outright dismissed. For example, privacy (including reidentifiction) and security. That’s the difference. You obstinately refused to acknowledge that there were any problems with your idea whereas the NIH produced a 105 page paper addressing these concerns. Even then there are some areas where their solution is along the lines of we will work with experts to figure out solutions.
@AdamG
I can’t speak for Not a Troll, but I wouldn’t participate mostly because the government has a very poor track record in infosec. I also think that access control and penalties for reidentification isn’t the be all end all. Especially when there is work being done to technologically provide better privacy guarentees.
capnkrunch 462,
The only thing I would consider a “victory” would be if people stopped making up bizarre strawmen and made an effort to have an adult debate that moved understanding of the issues forward.
So far, a couple of participants have demonstrated that capability.
I’m actually beginning to wonder if I can tell how much is ZDS and how much is just various forms of impairment.
My approach is probably more private and secure than BAU. It’s that simple. Apparently, others with actual expertise would not strongly disagree.
Zebra@458: I’m wanted to make sure that we were all one the same page and had clarified our terminology.
For people who work large study populations, like epidemiologists, it sounds wrong to say that you would add people to a birth cohort after the study has started.
You weren’t saying that. There was simply lack of clarity on the difference between the birth cohort of the proposed study population and the birth cohort from which that population is drawn. Now that we have cleared that up, we can address other questions.
Given that we are talking about an open-cohort design, that will complicate the calculations of things like incidence rate, that depend on person-time.
463 And, to avoid more wasted bandwidth, that’s: “how much of the bizarre commenting is ZDS ….”, not “how much of the adult discourse”
“infosec”
Yeah, “infosec”, that’s the ticket. I’m convinced.
j464 ustatech,
You would have to elaborate. Everyone is in the same birth cohort. Are you talking about the difference of <1 year?
zebra@463
Ha. Forgive me if I find this hard to believe. You’ve dismissed privacy as vacuous and security a minimal risk. I think the fact that the NIH specifically addressed these concerns shows that your dismissal was unwarranted.
You keep asserting that. Try defending it.
Where is this coming from? You’re approach was vague and you constantly refused to elaborate on how you would protect privacy or security. Instead you choose to say they were unimportant.
Table 5.3 is somewhat helpful here, although Z. has “opted out” from replying to questions about his vaporware interface.
1. You are now talking to yourself.
2. You don’t know what “bandwidth” means.
HTH. HAND.
^ The nonbroken part of the link resides in “463.”
@capnkrunch #43
“if you were to request data from, say SHIP, would they give you the raw sequences”
I have no idea what the acronym SHIP stands for, sorry.
“ Is the ability to reidentify pseudonymous genomes (i.e. through surname inference) a concern? I’m curious if you can give some insight about how people in the field feel about attacks on genetic privacy. Like is it a concern but maybe tempered by controlling access to the data and IRB/ethics committee oversight or is it more regarded as like tinfoil hat paranoia?”
All of these things are a concern. Most data is “leaky” at some level. If someone is determined enough, or someone is a bit slack at their job, there is scope for some pretty big screw ups. I see genomics data as being a bit like the internet. Don’t ever put something on the internet that you *might* someday regret or wish to retract. I think that as regulatory bodies and researchers become more aware of the issues, things will improve. But it will never be fail-safe.
“What do you think of the 100,000 Genomes Project? “
I like the idea of the project, I’m not informed about the ethical considerations. Its focus on rare diseases is a good way to find out lots of new things about, well, lots of things. We often get clues about the underlying biology of more common diseases from studying rare diseases, and rare diseases are more often phenotypically and genetically distinct enough that you can find that needle in the haystack, especially if you have familial genomes as well.
@ Not a Troll
I remembered last night that there is a dream genetics project in humans that I would love to do. I have always been fascinated by the possible genetics of the placebo response. A lot of pharmacology is muddied by this pesky but uniquely human trait, and I think knowing more about it could help inform the field of pharmacogenomics.
Teaching is a big part of my job, but not as a lecturer. I am more a mentor for grad students working in the lab. It is the aspect of my job that I love the most. Thanks for your kind words.
@Krebiozen
“I guess we could conclude that one mouse’s (and man’s) mutation is another mouse’s polymorphism (sort of).”
That’s a good way of thinking about it. Some gene variants are deleterious in certain environments, advantageous in others, or just plain neutral. Other gene variants are always deleterious. Sifting through this complexity in humans is daunting.
@ Zebra
“This is not a “study”.
Sigh. As other have pointed out, this IS a study. You can’t just collect/generate the data because you feel like it and have lots of money. Well, you probably could in some countries, but I’m working on some basic assumptions here. Maybe that was wrong of me.
“I wonder, when you suggest that replacing one individual’s record with another would make it no longer a birth cohort, whether you have really thought it through. Can you explain just this point? “
Well according to the original Zebra proposal as I understood it, you wanted to capture sequences from everyone born in a certain year. Presumably you would *somehow* be able to approach the parents of all these births, and consent as many into the study as you could. If some of these withdraw later on, do you plan on going back and harassing the parents who did not originally consent to join their kiddies up? I am not going to divulge the size of the study I worked on as I don’t want anyone here to identify the study through too much information, but suffice it to say that it was a medium sized city, and at the time the majority of births were in a single (socialised) health care system and most were not home births. To scale this up to a whole country would in itself be daunting. To follow them (I’m assuming you want this to be a longitudinal cohort) over their life span and record information about health, educational achievements, drug, alcohol and tobacco use, incarceration, abuse and neglect as a child, teen pregnancy, and many other things that would never show up in even the best of healthcare data, was even more daunting. But honestly, it is the richness of the data that has made this, and other birth cohorts like it, so powerful. Trying to do something like this in the US where healthcare disparities means you would even miss out on a lot of basic health data would be just generate rubbish. And trying to gather all this extra data is expensive and labour intensive. You may in theory get money to collect DNA samples and generate some sequence data at the start of the study, but it would take an enlightened government with a long term view to keep it going. It would cost a lot more than a few F-15s.
Now if you want to do an open study that is a different proposal.
“And RetroPump, who tells me that there is more data than they know what to do with, then also suggests that I can help by donating my genome.”
Umm, most well designed disease studies use a case-control design. You could find a genomics study that is looking for healthy/diseased people of a certain gender, age, ethnicity etc…that you fit into. You could volunteer for the PMI initiative, if and when that gets up and running. Or you could give some of your money to something like 23andme and help them build their data. 23andme is not NGS technology, but they are always happy to take people’s money and use their data. If you’re are interested in genetics and ancestry, you might find the $99 a good investment. Genetic data is always more fun when it’s your own
AdamG @456
It’s sharing too much of me for too little in return – for both me and society. For me, literally too much to share without a goal in sight.
For society, rightly or wrongly, I base my thoughts on the points raised here, and on the specific example of Dr. Thomas Insel at the NIMH and his search for biomarkers in mental illness. Psychiatric care has been severely negatively impacted by lack of funding yet this type of research appeared to be their main focus. It isn’t that it shouldn’t be done. Dr. Insel has gone on to Google and I say let him burn up their money on this; I wish them well in finding biomarkers if they exist. But as long as there is no investment in decent treatments and supportive assistance whether there is a biomarker or not it won’t make a much difference in the daily lives of the people affected.
If PMI turns out to be more a project of that project while other more immediate needs go unaddressed then I don’t wish to participate in it. Obviously I may change my opinion after seeing how it plays out over time but I’m not interested in being an early adopter. I’m sure you will have plenty though.
Retro Pump@471
My bad, I accidentally left a couple words out. It should have read “if you were to request data from one of the existing datasets, say SHIP, would they give you the raw sequences?” It probably would have made sense to say “the 1000 Genomes Project” but SHIP (Study of Health in Pomerania) came to mind instead because I had just been looking at a study that used data from it*.
Based on your response my guess is that the answer would differ based on where the data came from. It was a poorly worded, indirect question. I guess where I was trying to get at is what kind of protections are generally offered against reidentification. The PMI paper said that:
Is that pretty standard?
*For the sake of completeness the study was Genome-Wide Association Study with Targeted and Non-targeted NMR Metabolomics Identifies 15 Novel Loci of Urinary Human Metabolic Individuality. Not that it matters since I can’t quite remember how or why I got to that study.
Retro Pump,
The search for the genetics of the placebo response would be a very cool* study. As someone who doesn’t seem to have much of this type of response (rather more the null response), I’d volunteer for it.
*Americanism I still use.
zebra@465
Would “information security” be more acceptable? Either way, it doesn’t change the government’s poor track record. This is exactly what I mean about dismissing and handwaving. You could cut the condescension with a knife… if it wasn’t surrounded by an impenetrable layer of stupidity.
Regarding security:
Security is one of those things where the NIH said they’ll ask the experts. I’m curious what the subcommittee will look like and what their recommendations will be but it’s a much better response than “[b]eing one of 200,000 individuals with genome information on file in fact represents a negligible incremental risk. Truly negligible.”
This is what happens when you can’t admit that you don’t have every answer in areas you have litte to no expertise. You end up needing to dismiss things because you don’t know enough to solve the problem and you have too much hubris to admit that your half formed thought is anything but perfect.
One thing I do like about the PMI paper is this:
This is a good way to do it. Personally I think the risk is too high but there’s certainly people who feel otherwise. As long as people are educated enough to make an informed decision I think this is a perfectly fine way to go about it.
zebra@331
Another point where the NIH disagrees (and provides a solution instead of ignoring the problem).
Like I said, not strong enough protection for me to give my data but much stronger than your non-answers. I’d hope that as the crypto technology advances they implement technologic protection alongside the planned legislative ones.
NaT, thanks for your response. I hope you take some comfort in the fact that the PMI workgroup’s most heated debates have been about exactly the infosec issues you and others have raised here, and that this document is far from finished regarding these issues.
I urge you to take part in the Twitter chat happening next week: http://www.nih.gov/precisionmedicine/index.htm
We need more voices like yours (knowledgeable potential participants who have reservations regarding participation) to speak up about these issues. The committee takes these comments very seriously, as a primary goal of the initiative is to change the relationship between researchers and ‘subjects.’
As an aside, I know for a fact there are several folks involved with PMI at a high level that read this blog, but I’m the only one I know of who reads the comments. Please voice your opinions about PMI directly to NIH! Given the usual morass of red tape that defines the NIH, folks may be surprised with how important public feedback is for this project’s future.
Man, copy and paste from PDF’s is broken in such a weird way for me.
@capnkrunch
“Based on your response my guess is that the answer would differ based on where the data came from. It was a poorly worded, indirect question. I guess where I was trying to get at is what kind of protections are generally offered against reidentification.”
It definitely depends on who supplies the data. As does what kinds of protections are in place to prevent reID. Some data will only be made available in analysed and annotated form. Other providers will send you only the raw data and leave it up to the researcher to do analysis and annotation. From the POV of making research reproducible and fully open, it is best to have the raw data. From the POV of making life easier for the end user, the analysed/annotated data is best. Think of it as the difference between someone trying to find better ways to analyse the data, versus a clinician or other end user who really just wants a synopsis. The raw data can come in so many different form. The paper you cited was really just using a whole bunch of variants (about a million) based on array technology, as opposed to sequencing, so that data would look quite different to raw sequencing data.
I don’t know if the PMI approach to penalising reID is ‘standard”. The standards are constantly being refined and hopefully improved. At the very least, the people who collect personal information and allocate a study ID should have no access to the genomics data, and visa-versa. Even better if a third and independent party holds a ‘key’ that links personal info with data, and has no other knowledge about the participants or their data.
However it is still theoretically possible for full scale sequencing data to be used to identify individuals or families. It would take a lot of work, but some people seem to have too much spare time, and if there is enough of a money motive you can never say never. And there is always a risk that with social media, your aunt/brother/mother may post a link to some of their genetic/genomic results and in some way ‘implicate’ you and your genetics,and your children’s etc… This is a different kind of security concern, but no less real.
@Not a Troll
I think I would be a placebo non-responder too. I certainly don’t seem to respond well to homeopathy or acupuncture, or many other more SBM drugs. Please don’t give me paracetamol for any kind of pain or inflammation. I simply will not respond, though I’m sure it will still be hard on my liver. The flip side of the placebo response that I would like to include in my study is the nocebo effect. The power of suggestion is indeed powerful for both good and bad outcomes!
@Adam
I am glad to hear the PMI workgroup is thinking through these things carefully and taking public feedback. In this day and age, most people really want assurances that their information will be as secure as possible.
It does that for everybody.
Narad@479
It’s odd. There’s a character there and I can select and copy it but pasting it into Google doesn’t work but in text fields that allow line breaks it causes one. But my text editor doesn’t recognize it as a carriage return or a line feed. Curious.
My observations of its habits in the wild strongly suggest that Z. appears to consider concepts to be noumenalized and fully specified when he assigns them acronyms (vide “sovereign entity” supra), so you could try that, although I can’t remember the Hungarian version of the barn-door routine.*
* Which may have a distinctly different interpretation compared with the Romance language versions, despite the similar setups.
I have one concern: what if these sequences goes in the hands of INTELLIGENT people, able to interpret them? It is not possible to patent the sequences. Foreign (probably alien) scientists could make money by finding drugs against diseases common in the US, like obesity, creationism and quackery.
“go” not “goes”
zebra @452:
You’re amazing, and not in a good way. Don’t you understand what is blindingly obvious to the rest of us? If the “experts in the field” are not supporting your idea, it’s probably because said idea is a poor one.
Retro Pump #471,
I think you might have been reading some of the strawmen and quotemines as correctly reporting my actual comments. Correcting:
I think I only suggested US as the location once; I then started using the more manageable venue of Canada, and I also pointed out that it would be much more viable within Canada’s more rational health-care system.
As to whether it is a “study” or a database. That is a very easy distinction. The function of the project is not to answer any specific scientific question, so it is not a study to me. My goal is to be a facilitator for those who do have specific scientific questions.
Now, I don’t see the utility in saying “nyah-nyah that’s not what ‘study’ means to me”, as long as we both understand the intent– do we need to invent new words to communicate?
So, as to the specific question of replacement, as I already answered Justatech: Depending on the size of the database, and the prevalence of the phenotype or condition being studied, the researcher would likely only be using a subset, randomly selected, of the available relevant cases.
I think of a replacement drawn from the excess as still “being part of the birth cohort the researcher is studying”. If you don’t, that’s fine, but again, I’m interested in how you think that would affect results, not what we call it.
Related to that, I am having a hard time understanding the reasoning about acquiring all this other information. How does being abused or not as a child inform us about the genetic correlation, or not, with some physiological condition that develops later?
Those are the issues that I’m really interested in better understanding through your expertise, but I just want to point out that my position on privacy and security is being misrepresented in a ridiculous way, perhaps because ann and I had a more philosophical discussion about morals and laws that was too difficult for some to understand. I would vote, in so far as I have a vote, for very stringent restrictions to prevent misuse of the information, and for resources to be committed to aid in that. That was asked and answered more than once, so any report to the contrary is not to be believed.
zebra,
The problem is that as soon as you stick a needle into a patient with the intention of collecting blood for your database it becomes human research and you have a legal requirement to get IRB approval. It’s those pesky ethics again I’m afraid.
Well, now, isn’t that the sort of question a researcher might be interested in? Why do some abused children wind up in prison or an early grave, or struggle with substance abuse, while others shake off the worst of it and grow up as healthy productive adults? Just because you aren’t interested doesn’t mean no one is.
And there are other aspects of life too. One of my friends recently lost two aunts to a rare heriditary cancer; a third has just entered hospice for the same thing. His mother’s large family considers it significant that those three remained in their polluted home city whereas all the so-far-untouched siblings left while still young. If they are right, then to tease out the effect of that genetic inheritance from your vast cohort would require knowing where every member of the cohort lived throughout their lives.
For other genetic effects you might need their diet over their lifetime (more protein in childhood has what effect? More protein late in life has what effect?), their socio-economic status (stress due to economic uncertainty in formative years has what effect?), and so on.
Retro Pump,
I really would like to get your input on the questions I asked on the science part of this, but I just thought I would take the opportunity to illustrate why you need to read carefully, concentrating on where I directly reply to you, to avoid the wheat/chaff problem.
Almost instantly after I said this in 485…
…we are treated to the phenomenon I have described before, of someone taking an unrelated quote from the comment, and in some illogical construct, responding to it with something like “but what about laws protecting individuals from misuse of their genetic and health information?”
Perhaps we should study whether there is some genetic predisposition to ZDS; we can relate it to ODS and see if the President and I give off similar pheromones or something, to which sufferers respond.
zebra, just give it a rest. I know it’s a scary thought but this kind of research is already in the hands of people who are much smarter than you. None of the ideas you’ve presented here are novel or particularly good. If you’re actually interested in learning how this research is conducted, go read a textbook: http://amzn.com/0815341490
As Retro Pump said, abuse in conjunction with a variant of the MAOA gene is a predictor of antisocial behaviors.
But if it has to be physiological:
Abuse in conjunction with a variant of the MAOA gene alters NE, 5HT, and DA neurotransmitter systems, resulting in neural hyper-reactivity to threat, resulting in antisocial behaviors, such as violence.
LW 487,
Way back at the beginning, I addressed the possibility of some skewing of the data by, for example, a local somewhat inbred population that coincidentally refused to participate for religious reasons. I’m sure there are lots of interesting things to think about, and I’m sure there are lots of young scientists eager to explore them, particularly if there is genomic information available gratis.
But I don’t think you are answering my question. You can’t look for the needle until you find the haystack. Which Orac said in the first place, or so I interpret his post.
If your friend’s aunts have some genetic predisposition established by a legitimate study (of family history, twins, or whatever) how does that relate to my database? Just use that family as part of a conventional study, and acquire their genomes (voluntarily! voluntarily!) and work it out.
The MAOA story is a very interesting one. For a history of the genetic basis of this association, see http://omim.org/entry/309850#0002
Further to 490 —
FWIW, psychogenic dwarfism is also an example of emotional maltreatment in childhood being expressed physiologically. I don’t know if there’s a genetic predisposition to that. But I wouldn’t be surprised if there were.
It does kind of illuminate the complexity of the task to consider, though.
I mean, theoretically, emotional stressors in childhood might play a role in the expression of lots of things later on, but at a less dramatic level than extreme abuse, they’re very hard to quantify and track..
zebra,
You repeatedly claimed that collecting blood samples and sequencing their genomes is “not a study”. I pointed out that legally it is a study since it is classed as human research. If it is human research it is subject to all the rules that RT was referring to that you dismissed by writing:
Since this is clearly human research you would require IRB approval, and to get IRB approval you would have to demonstrate a robust experimental design, show that it would benefit the subjects, assess risks etc. etc..
How is that “unrelated” and what “illogical construct” are you referring to?
AdamG,
The only “idea” I have is that it would be helpful to have a large database, and I obviously don’t think that it is novel. Why you would describe it as a bad idea is beyond me if you are working on one.
Now, I’m counting on the fact that this research is in the hands of people far more capable than I am. But we are talking about political decisions, and we all know that the public isn’t going to read the textbook, so it always seems worthwhile to me to get information out in a form that might be more accessible.
You are obviously free not to participate, as is everyone else, thanks to the Constitution and legal system and so on. Do you have a problem with that?
ann #490,
Yeah but that doesn’t answer my question either. We’re not talking about what we know, but what we might find out. Haystack first.
Why do I need the information about the abuse to detect the genetic correlation?
zebra, your very first comment said
This is a terrible idea.
AdamG #497,
When someone pointed out that this would involve very large numbers, I immediately refined the concept. I guess you could also point out that I “nyah-nyah-nyah said ‘study’ ” in that first offhand comment.
If, in your expertise, you have something to contribute to the discussion where it is rather than where it began– help out by educating people. I suspect even the very educated people who first thought of your project started out with a napkin or envelope and a pencil stub. Or a tablet and a stylus, perhaps, these days.
Believe me, I do. It’s part of my job. I’m just not particularly interested in educating you given your failure to understand the importance of the obvious distinctions between a ‘database’ and a research study.
AdamG,
In fact, could you help out with the question I asked ann at 496?
AdamG, 499
I’m the one making that distinction.
If you really want to learn, you have to do the work. These are complex topics. The textbook I linked you to is what I use to introduce these concepts to undergrads, and is very accessible. You can obtain a used copy for $10.
502
Aww, bluff WRT claim of expertise is called.
I will see if ann can apply her rabbinical inclinations to the question.
“I urge you to take part in the Twitter chat happening next week
Thanks, Adam. I think I will attend this. There are the standard questions of course but there are additional questions I wish to ask about which have only been briefly alluded to here such as the accuracy of my EHRs. I know mine contain errors, and I also know that it’s very difficult to fix them.
“When someone pointed out that this would involve very large numbers, I immediately refined the concept.”
The trouble is that your refining of the concepts appears to be based on you being able to make yourself look as if you were correct all along and very seldom is it on your coming to an understanding.
Side note because you’ve mentioned this analogy more than once on the blog: Most of those here do bash anti-vaxxers and alt med proponets but they have information upon which to back up their claims how ever abrasive they may come across. But when someone just comes across as abrasive with only smoke-and-mirrors to defend their position it is a real turn off. That is why it would benefit you to read up on this subject. At this point you wouldn’t be able to convince me of joining PMI because it’s obvious you don’t know the subject you are discussing.
No, I just don’t have the desire or patience to explain the value of covariates in a genetic association model to you. Have you ever taken an upper level stats class on regression?
zebra@485
Isn’t that what you just did? You’re the one who is using a non-standard definition of study.
How exactly were your views misrepresented? You said multiple times that privacy concerns weren’t a big deal and security wasn’t a significant risk. Didn’t we already go over countering cherry-picked quotes? Please provide the additional context that changes the quotes I’ve used.
This is the first I recall you not dismissing privacy and security concerns or simply asserting that your idea is secure without any specifics. In fact, I doubt it’s coincidence that privacy and security have only become concerns for you after AdamG and I pointed out that the PMI working group takes them very seriously. Just in #465 you laughed at my use of the term “infosec” instead of making a substantive rebuttal of my point. Please provide evidence to the contrary.
Including yourself. You’re deluded if you think that did anything but provide ample evidence that philosphy is yet another subject of which you have a minimal knowledge and an even more minimal awareness of your lack of knowledge.
Here’s an interesting note. AdamG came into this pretty neutral but your obstinance seems to have changed that somewhat.
AdamG@502
This. 100 times this. I’ve been saying it all along and zebra still has yet to even skim any reference. But zebra is more concerned with proving his superiority than learning. Doing the work would only be an admission that there’s something he doesn’t know.
zebra@503
Seriously? Do you want him to teach you an intro to genetics class through RI comments? Can you see how your past behavior might be responsible for AdamG choosing not to answer your questions? Rhetorical question. Of course you don’t; you’re infallible in your own eyes.
AdamG,
You mean you don’t want to explain the value of covariates in a genetic association model as it pertains to the question of whether we have free will or not? That’s not very accommodating of you.
I bet I could get it out of you over a few beers…or a few pitchers. Maybe a keg?
#507…i was responding to zebra’s “Why do I need the information about the abuse to detect the genetic correlation?” at 496.
505,
Please, spare me the standard internet practices of deflection and distraction, huffing and bluffing, and just act like a grownup if you think you can explain it to us poor uneducated types.
In this context, as described more than once, explain why I would need to know about the abuse in order to detect the genetic correlation.
I’m willing to be found in error if it helps educate people– I don’t like it, but there’s always a cost to reducing one’s ignorance.
Because the relative risk for developing antisocial behaviors is modulated both by MAOA allele and previous abuse. Can you define relative risk in your own words?
I’m done here. Go read the original paper, zebra, and let us know what you’ve learned.
http://www.ncbi.nlm.nih.gov/pubmed/12161658
Adam G #508.
In my prior comment at #507, I was making a very poor joke regarding the discussion of science delving off into philosophy – of which there is a time and place for either and for both.
Both usually goes with late night drinking in my experience.
Zebra,
The effort given by those here in educating you always educates me. It’s just that I think there must be an easier way than the one-up-manship involved. Maybe not, and I’ll take what I can get. As long as they’re willing to put with it.
AdamG,
Can you describe the difference between
“why do I need the information about the abuse to determine the genetic correlation”
and
“why do I need the information about the abuse to determine the ‘relative risk’ once I have determined that there is a genetic correlation”
Haystack, needle. Asked and answered already.
But by being genuinely open to the possibility of a misunderstanding, I have realized that in the future I should use “detect the correlation” rather than “determine”. It would require a convoluted reasoning to make that mistake in this context, but anything is possible.
And this is the problem with the endless quotemining; I lose track of even my own language– I did say detect, but I think I used determine earlier. Anyway, I am not going to keep scrolling back to check these things.
If RP responds to my couple of questions, I will appreciate it. That’s it.
Oh, and capnkrunch– I found multiple comments where I responded to you about security. Disagreeing with you is not the same as not answering, quite the opposite. And in exchanges with ann, Grey Falcon? and perodatrent, it was clear that I favored laws discouraging abuse in studies. Laws, not moral pronouncements.
And he acts all butt-hurt when people treat him like a ill-mannered twit?
I think Krebiozen started that in post #4, to be honest.
I never said that, did I? Read carefully.
Prove me wrong.
This is a word game that only you are playing. The reason data on abuse is necessary is because that’s the population in which MAOA modulates risk of antisocial behavior. It’s right there in the title of the study that AdamG linked to, which you would have known if you made even a minimal effort to educate yourself. But instead you choose to play word games and whine about being misrepresented and insult people who actually work in the field.
Forgot to close the italics. Should have ended after “behavior”.
AdamG,
“That’s not very accommodating of you.”
Just to be clear this comment of mine was meant as sarcasm. I can understand perfectly well why you wouldn’t want to go into a basic education of genetics on this thread.
I got it NaT, no worries 🙂
Tone via text is harrrrrrd
Hm. Well. The answer to the question as phrased is:
Because absent the abuse, there’s nothing for it to correlate to. The gene variant alone doesn’t express itself that way if nothing turns it on.
It’s one of them there epigenetic factors about which one hears so much loose talk these days, in short.
But that’s not really a different answer than the one I already gave. So I have a feeling there may be some kind of miscommunication that I’m not picking up on. Let me know, if so.
I prefer to think of myself as Talmudic. Just to demonstrate I have them.
ann, you disappoint me. I was under the impression you had been raised to the archbishopric.
OK. Having read back through the comments looking for clues as to what the question was, I came up with this:
In which case the answer is:
In order to find most such things out, you need information about environmental factors that’s as close to comprehensive as you can get. Because epigenetics count. Genotypes and phenotypes alone don’t actually constitute a haystack that contains needles in many — possibly most — cases.
For example: Although there’s high concordance in monozygotic twins for schizophrenia and autism, it’s not 100 percent. So something apparently sometimes causes the genetic predisposition to zig rather than zag in one twin.
Plus of course, it might be more than one something. And/or more than one gene variant.
I mean, there are an awful lot of chronic, incurable little-to-partially understood conditions that are thought to have a genetic component that’s contingent on some other thing and/or things, but who knows exactly what?
I would imagine you’d have to cast a pretty wide net wrt environmental factors. Not that I’m an expert. But it makes sense to me.
ann,
You are the only one who could suck me back in, other than RP on this and the other question.
Instead of “missing”, how about “you are letting knowledge get in the way of knowing”? (trying to be Talmudic or Eastern Mystical here, since you didn’t get the haystack/needle point.)
In my database, there will be abused children who have this gene. So a researcher would detect a correlation between the negative subsequent behavior and the gene.
How could it be otherwise? And this is one of the things that recommended my approach to me in the first place.
Oh. My. G-d.
See above.
Read the paper, zebra. It’s free to access and addresses many of your questions.
You’re even more D-K than I thought given you don’t seem to know the difference between a gene and an allele. Everyone has MAOA, moron. Read a f-ing book before you try to design genomic databases-but-not-studies.
Maybe.
But let’s say for the sake of argument that he or she did:
Since searching the database for that polymorphism would show that there was no correlation between the negative subsequent behavior and the gene in all the non-abused children who had it, it wouldn’t look like — and, in point of fact, genuinely wouldn’t be — a meaningful correlation until the environmental factor was identified.
This is (at least as I understand it) exactly where research on a lot of conditions that are thought to have a genetic component that’s kinda-sorta-maybe already been identified has run aground. It’s not possible to point to the anomalies and say “This is the cause,” because lots of people without the condition also have that anomaly.
Well. Since the existence of unidentified environmental factors is a known obstacle research progress on the genetic causes of illness, you could make an effort to include as many of them in your database as you reasonably and possibly could.
Because otherwise you’d basically just end up stuck where you already were except on more fronts until you put together a complementary database, anyway. And why borrow trouble?
To use an example where knowledge won’t get in the way:
There are a number of autoimmune disorders — MS, rheumatoid arthritis, Addison’s — that are associated with changes to one or several genes. But not everybody with the disease has those changes. Not everybody who has those changes has the disease. And even among those who do, not everybody has the same one. Or the same course. And so on and so forth.
Just genotypes plus phenotypes don’t get you all that far. I mean, the goal is to find out something that facilitates prevention, ideally. Right?
@#AdamG —
I don’t know. I used “gene” the same way @#526 — ie, to mean the variant in question — and I do understand the distinction. It’s just that although my reading fluency is adequate, my understanding is too superficial for true speaking fluency.
You know how it is.
Zebra @466: “You would have to elaborate. Everyone is in the same birth cohort. Are you talking about the difference of <1 year?"
A birth cohort is all of the people born during a specific time period. That time period (and sometimes place, like a specific hospital) is defined at the beginning of a study, to determine who will be recruited into the study.
So if I say that a birth cohort is everyone born in a specific calendar year, then you and I are not in the same birth cohort.
You do not define who you mean by "everyone" when you say that "everyone is in the same birth cohort". Everyone in the world? No. Everyone in the study group? Yes, because that is how they were chosen.
Since you are such a stickler for precision of language, please define your terms, particularly when you are using them to mean things that they do not mean in the technical context of the conversation.
JustaTech@529
And yet (as you alluded to) he’s also the most egregious abuse of it (not just words but punctuation too!). He’s like the living embodiment of projection. Speaking of projection and word games, he accused everyone of being unable to admit mistakes yet he was unable to admit that his definition of study was wrong (instead choosing to claim that we were the ones at fault). Quite frankly that would have been an incredibly minor point to concede.
Oh, wait, now it magically has some sort of behavioral records, too? Do schools and parents and juvenile courts all now have to report to your fever dream as well? Are you under the further delusion that you’re going to get psychiatric records? And where are the records of childhood adversity or abuse going to come from?
You really haven’t picked up a single clue from all the time people have wasted replying to you, have you? Did it ever occur to you that there are all kinds of reasons for antisocial behavior? The fact that you could even ask this question pretty clearly reveals that your pig-ignorance has left you with no refuge but magical thinking.
It’s been pointed out before, but you’re doing it backwards. Since you’re obviously too damned lazy or incompetent to do it yourself, do you know where that signal came from in the first place? Here. Not by saying, “Computer, give me all genetic variants associated with data that you don’t have.”
What is? Be specific. It certainly isn’t MAOA, which you’ve just heard of. After all, given that you just blurted it out in the second comment of the thread, one might suspect that not only did nothing “recommend” it to you, but that you didn’t put a f*cking bit of thought into it in the first place and are now just stupidly digging in your heels, with a concomitant increase in your trademark obnoxiousness.
To be fair, in this particular case, there might be some indirect signs of both the maltreatment and the conduct/oppositional defiant disorder in the regular old medical records, since both are correlated with higher rates of accidental injury. (And ODD is correlated specifically with hospital admission for burns and poisoning, per one study, I just now learned from the internet, which is a very poignantly distressing little piece of quasi-knowledge, if true. Those poor kids.)
But there might not be. And obviously, it wouldn’t be specific enough to draw any clear inferences from even if there were. Kids with ADD also have higher rates of accidental injury. And so do any number of children for any number of social and/or environmental reasons, including — potentially — none.
You can’t really correlate without correlates. In a nutshell. At some point, somehow, you’d need to dredge them up from somewhere.
This is not my bailiwick at all, so if someone who knows what they’re talking about could enlighten me, I’d appreciate it. But am I wrong in thinking that for stuff like schizophrenia (and maybe autism?) there’s the additional complication of figuring out what’s genetic and what’s just innate — ie, the possible result of prenatal viral or bacterial exposure and so on?
Genetics, genomics and neurology are the three fields I most regularly come away from muttering, “Nobody’s ever going to understand this and trying will probably just end in tragic irony due to unanticipated consequences, like an episode of the Twilight Zone.”
That’s very 20th century of me, I readily admit. But I don’t really mean it. It’s just the kind of thing I say to myself before throwing my wooden shoe into a lace-making machine or whatever. Although that’s actually 19th century, I guess.
@ ann:
For a start, you can look at websites like schizophrenia.com and Wikip—- ( schizophrenia entry) for details about causation from genetics, other causes and ( possible) overlap with other neurodevelopmental condition.
I don’t think that this rises to being fair. Sure, there’s going to be some related data, but it’s going to be signal-poor and buried in noise as far as this example is concerned.
Z. apparently thinks that the way to arrive at study populations is to randomly shake huge barrels of data and hope that one pops out. One might note that – somewhat like the flirtation with “ontology” – Z. has elected to appropriate* the “needle in a haystack” observations directed his way and, bizarrely, do this:
It’s almost some sort of Flannery O’Connor
approachdemand.If I had Gaist’s talent for dialogue, I’d add it here.
* To truly grotesque proportions.
That video is unavailable to me. 🙁
Interestingly, “Haystack First” was the name of the O’Connor/Welty/McCullers salon/roundtable.
Ann, it is indeed nice to disagree with someone who knows what the f I’m talking about and can articulate a rational counterargument. (however right or wrong it may be).
“Meaningful correlation” is a little Scotsman-like for my taste.
The question is whether we would have a high degree of confidence in its validity. And the answer again is “of course we would”, not “maybe” as you say. You know that.
Let’s look at three things.
-my often repeated statement that I am talking about basic research
-Eric Lund’s commentary on accuracy and precision
-Orac– yes, Orac, who wrote the OP which I actually read carefully, apparently unlike everyone else- saying:
So, what you think of as a problem, I see as an advantage. On multiple fronts.
zebra@536
Ah… would that we could experience the same from this side of the fence. Anyone else note the parallels to See Noevo? Impervious to reason, not able to back up claims, ignores/insults people who disagree, and a weird fixation on ann.
No. The problem is that the correlation appears in the subpopulation of abused children. If you don’t have that data you don’t see the correlation. This would have been obvious to you if you had read the paper. It’s even in the title.
Seriously though, with a minimal skimming of some of the references provided you cluld have given a reasonable defense. Hint: check the PMI working group draft. In your immunity to education though you picked the clearly losing horse and made the unsupportable claim that the correlation between MAOA and antisocial behavior in abused children would be visible in the general population absent any environmental data (i.e. history of abuse).
Oft repeated, never supported. Recall that malia told you that mass quantities of data is not what we need for basic research. I know you asserted otherwise but never supported that assertion. I’m inclined to believe the geneticist over the layperson even absent your numerous failures of basic concepts.
Did you really? I fail to see how that quote offers you any support. In fact take a look at the last bit:
IDK. I don’t think you addressed Ann’s last point. I got the impression from this statement that you would disregard collecting information about child abuse in your database/study.
“Related to that, I am having a hard time understanding the reasoning about acquiring all this other information. How does being abused or not as a child inform us about the genetic correlation, or not, with some physiological condition that develops later?”
So, great, you have identified a correlation (not a causation) of an outlier gene change to antisocial behavior, but is there any other information available?
To use an analogy which I hate to do, but please bear with me. Several people have food poisoning. It is discovered that the majority of them but not all of them ate lettuce in the past two days. Yet others have eaten lettuce and haven’t gotten sick. So whats missing and what do you need to do next?
So I question the utility of your database/study beyond a certain point. If that’s how you envision it, that’s fine; it’s your invention. However, PMI is a very different beast and after reading more at AdamG’s link I’m fairly well intrigued by it now.
capnkrunch, we cross posted. Regarding your concern with the missing data of child abuse as you described:
“made the unsupportable claim that the correlation between MAOA and antisocial behavior in abused children would be visible in the general population absent any environmental data (i.e. history of abuse).”
I think he was blowing off knowing about the abuse because this particular gene (is it polymorphism?) is an already known correlation. It’s not as if we are starting from scratch in this case. Personally, I don’t agree with this because at the very least it would be confirmation of this correlation perhaps even leading to causation, but it’s his monster.
We can just make it “correlation.”
No, I really don’t. Correct me if I’m wrong. But as far as I can see:
A hypothetical researcher would initially either be looking at the subset of children with an MAOA variant, or the subset of male children with antisocial behavioral disorders. Right?
If the latter, they’d see that maybe 45% of them had a low activity allele.
In order to be confident in the validity of the association, they’d then have to look at a group of non-antisocial controls. And when they did, they’d see that maybe 34% of them also had a low-activity allele.***
Further complicating matters, 20-ish% of the antisocial sample has a high-activity allele. And while that would be much lower than the non-antisocial group’s 60-ish%, the high-activity allele kids in both groups would appear to have a significant predisposition to ADD and depression.
So. The researcher now has several suggestive and potentially significant indications that genetically determined variations in MAOA activity correlate to something neuropsychiatric. But it’s not completely clear what.
However, when 55% of the subset does not have the polymorphism, confidence in its validity would definitely be very rash. At the very least, you’d need to replicate the result several times before you could say the correlation was valid.
And even then, you would have to identify the swing factor that turned the correlation into causation.
If our hypothetical researcher instead started out looking into the genetic side of the equation — ie, all children with all MAOA variants, or boys with any MAOA variant, or whatever — it would be even more of a mess.
So. How do you figure differently? It seems pretty unambiguous to me. There’s not enough to hang your hat on and too many potential confounders for confidence.
***Wherever there’s no reference given for prevalence, I checked several studies and estimated the range. I could be somewhat off, though.
ann,
It’s worth noting, perhaps, that without childhood abuse those with low MAOA activity are less likely to exhibit antisocial behavior than those with high MAOA activity (Figure 1). That might well be enough to mask the correlation in the whole population.
So z*bra wants to give researchers access to child protective service records WITH IDENTIFYING INFORMATION? Jesus H Christ on a hyper speed pogo stick! I worked for 30 years in social services, with some of that time in MIS, and this idea is hypercube level craziness. These databases include unproven allegations of criminal activity, information about victims who are minors and information about siblings of those in our pseudo-cohort. What could ever go wrong with putting all that in one database?
Incidentally, if an additional reason for exercising caution wrt premature conclusions about validity is needed:
There evidently might be considerable racial and ethnic variation in the frequency of these alleles. And it would really be kind of dire to go around confidently proclaiming that there was a valid association between antisocial violence and an allele that appeared to be more common among African Americans than it is among Asians/Caucasians before you’d looked into it enough to know how, why and if it really expressed itself that way.
The maltreatment is really not an incidental or secondary factor. And neither are other cultural/environmental factors. At a glance, there also appears to be an association between low MAOA activity and male alcoholism in Scandinavian populations, for example.
@Krebiozen —
Thanks! I actually meant to mention that.
But that reading-vs-speaking fluency thing I mentioned @#528 is a real handicap. Stuff gets lost in translation. I probably miss a lot, too.
So corrections and additions are much appreciated.
Opus,
I don’t think zebra was/is saying that’s what he wanted social services data in his database/study. Rather the opposite. But he presumed to be able to make connections without this knowledge (not necessarily social services records but the knowledge someone was abused) and that’s where he ran aground IMHO.
Not a Troll@539
So he is talking about taking an already known correlation in a subpopulation and trying to see if it can be generalized to the general population? In that case, ann’s comment #540 is more on point (as well as Krebiozen@541).
This all started because someone (Narad maybe?) said that it would be difficult to collect environmental and psychiatric information. No matter how you a
slice it, saying we don’t need that data k
is a weak defense. Had he at least skimmed the PMI draft he would have seen that behavior health and environmental behavior will be among the data collected. Pointing that out would have been a far stronger counterpoint.
Of course, I’m sure DCFS records won’t be collected but abuse will probably be asked about in the self-reported data and may show up in medical records too. The psychiatric history is another animal given that release of psychiatric history usually requires an additional consent on top of the general one. From what I’ve read (admittedly not the whole report yet) this isn’t addressed specifically. Howeever, they do talk about granularity in the consents and I think it’s fair to assume that such granularity would include psychiatric/behavior health.
There you go zebra. Try doing the work yourself next time instead of blurting out the first thing that comes to mind and then digging your heels in. Your obstinance would be more understandable if there was more than a modicum of thought behind the things you say.
… There’s clearly some letters and line breaks in the second paragraph that shouldn’t be there.
As I understood it, the question was whether the correlation between genotype and phenotype would show up without knowledge of/information about the abuse, assuming that the antisocial behavior was known.
And as far as I can see, the answer to that is maybe, but it wouldn’t necessarily be obvious that it was the signal worth following up on. And even if it was, it wouldn’t be at all clear what it signified. Meaning:
Theoretically, assuming you were starting at square one and detected the correlation, you couldn’t confidently conclude that it was genetically dispositive at all, per se. Maybe it would turn out that children of alcoholic mothers were likelier to have that allele, as well as likelier to be poor and malnourished, hence the antisocial behavior. Etc.
Or at least I think so. But maybe I’ve gotten the whole thing wrong. Anything’s possible.
Also, though I don’t know whether this is true or not:
The percentages are not that high. And there’s a lot more than that one allele. Conceivably you’d be looking at other comparably suggestive correlations, just by the numbers.
Is that right, someone who knows?
I suspect explaining anything that a “mature, rational (non-paranoid), non-Authoritarian adult” might do would go right over your head. Let’s try this: how would you like it if it your genome was publicized and it was revealed that you had a constellation of genes associated with tiny-penis-syndrome or intractable-pig-headed-disease?
forget about that, let me plant his genome on a rape & murder crime scene. Then, if that doesn’t convince him of the need for ethics & privacy, it will leave me to ponder at the question: is he trying very hard to be a stubborn pigheaded id10t or does these qualitative come naturally to him.
Al
ann@548
Ah. Yup, I see that now. Your “maybe” is a much better answer than my “unsupportable”.
Makes sense. I think earlier in this thread (though I can’t find it) someone mentioned how without correcting for confounders it looks like coffee correlates with cancer but it is actually that smokers are disproportionately coffee drinkers. You need data about both things to reach an accurate conclusion.
Even if the specific instance being discussed turns out that environmental data is unnecessary there are likely others where it is. That’s why I think ‘environmental data is not impossible to collect; AdamG and friends are going to do it’ is a much more tenable position than ‘environmental data is unnecessary’.
“Anything’s possible.”
In genetics, and on this thread apparently.
Regarding the complexity of this particular gene and variants, I found two articles that may be of interest
http://www.nature.com/mp/journal/v14/n8/full/mp200944a.html
http://www.geneticliteracyproject.org/2014/11/04/does-the-human-warrior-gene-make-violent-criminals-and-what-should-society-do/
If Retro Pump didn’t convince anyone already, I think this one example alone highlights the massive questions/issues involved in genetic research. Even though the PMI will be knee deep in this as well I’m beginning to see it as much more than just a collect and sort through volunteers’ genomes study. It’s more like a pool of research subjects with as much information captured so they can be selected for further studies.
“As I understood it, the question was whether the correlation between genotype and phenotype would show up without knowledge of/information about the abuse, assuming that the antisocial behavior was known.”
ann, I took this into consideration of what he was saying for his database/study in general but when he kept emphasizing “what we already know” for this particular gene discussion, I took it one step further in that this was an already in-the-bag correlation that could be worked. I have no idea if I’m correct or if I was at t one time and now things have changed or if it is something entirely different.
You seem to speak zebra’s language so I will defer to your interpretation.
No, you wouldn’t. You were too lazy to read the Corsi et al., weren’t you? Your blob of genomes is filled with just about every confounder imaginable, plus it doesn’t contain the requisite data.
“Until this study’s findings are replicated, speculation about clinical implications is premature. Nonetheless, although individuals having the combination of low-activity MAOA genotype and maltreatment were only 12% of the male birth cohort, they accounted for 44% of the cohort’s violent convictions, yielding an attributable risk fraction (11%) comparable to that of the major risk factors associated with cardiovascular disease (37). Moreover, 85% of cohort males having a low-activity MAOA genotype who were severely maltreated developed some form of antisocial behavior. Both attributable risk and predictive sensitivity indicate that these findings could inform the development of future pharmacological treatments.”
Why? You’re perfectly happy to emit complete gibberish such as this:
It’s a two-repeat polymorphism in the MAOA promoter region. A really quick glance suggests that three or more repeats are OK on this front, but don’t hold me to that.
^ Oh, but naturally, the way to tease this out is by starting from a pile of whole genomes. Haystack first, people!
Z., quite simply, can’t take heat. Imagine this performance made incarnate, say, as the Q&A of a routine weekly departmental colloquium. “This week, we have a guest from the Department of Blobular Globularism, Professor Zebra….”
Actually, I’ve been there; a genuine comparison would require that the doors to the hall be locked for two hours. After frothing for a while at the questioners in the audience, Z. would be left with simply ignoring them, and then the poor bastard who introduced him would be left trying to deal with the awkward silence by signle-handedly trying to get him to fill the time or, perhaps, requiring that the increasingly impatient audience write their questions on 3-by-5 cards so that they could be translated into appropriately kowtowing terms.*
* This would be an example of what “interlocutor” actually means, Z.
Exactly right. Don’t bother listening to the folks doing the overhyping (“we’ll fix all the cancers!”), who are largely not involved and mainly just ego boosting. Everyone involved in PMI currently is on the same page about what we aim to create: 21st century Framingham.
“Let’s”? “Look”? This sort of construction is usually a prefatory remark meaning “I’m going to examine these things,” not left hanging in the air.
Oh, wait, you imagine yourself to be in a pedagogical role.* Gotcha.
OK, you bootstrap that accuracy-and-precision bit. I’m sure it will be eminently thought-provoking.
* Child psychologists don’t necessarily have fixed outcomes in mind.
Oh, Narad, you bring back frightening memories of Quarterly Meetings with the CEO of our small division. Most real questions were unwelcome so HR started the 3 x 5 card thing to review them beforehand.
But there was that time right after we were newly acquired by a different company when the one of their talking heads didn’t play that game. He took all questions. It was quite funny to watch the disarray of the HR people then. Although, it still wasn’t funny being locked in a room with them for hours.
Did you work in academia or something that just sounds like it, like the government?
My impression was that two-repeat is low activity and high-risk but rare; and that most of what they’re looking at is three-repeat (low) and four-repeat (high).
I also saw something about 3.5R and 5R. But I made an executive decision not to think about it.
Campi. But I know that you meant that.
ann@562
Caspi actually 😉
Also your link in #540 was broken and I forgot to mention it before. Could you repost it please?
@NaT:
The latter one has an interesting bit:
“I have read that MAOA-L is pretty common–one paper says 40 percent of the population possesses it. It gave no reference, and I haven’t been able to nail that number down for sure, but let’s assume it’s true.”
That paper, from EMBO Reports, is unpromisingly titled “The Psycho Gene.” I mention it only because I ran across Beaver et al. (PDF) earlier, which pegs the 2R allele at 0.1% of its Caucasian population.
Referring back to my caveat in comment 556, I suppose that leaves 3R to take up the slack.
@capnkrunch:
I’m not entirely certain about the antecedent of “he” here, but I at least was talking about Z.’s brilliant idea of shaking study populations out of randomly poking a giant whole-genome database with a stick. “Abusive environments” don’t simply reduce to things that are going to appear in medical records.
Z.’s “how could it be otherwise” was simply the impressive physical feat of putting the final nail in one’s own coffin.
Yes. But in reality, I imagine that most of the queries to such a database would be by researchers on a quest to find out the effect of low-activity MAO on dopamine in the nigrostriatal pathway as it relates to tardive dyskinesia.
Or what have you. It could be anything. My point is just that specialists specialize, so they’d have some idea of what they were looking for and at, presumably.
Thanks; I’m not sure where that one came from.
Oh, wait, no, that’s not the proper response:
Then again, I’m not sure what this automaton would actually emit in this situation.
Narad@565
My bad. Poor pronoun use on my part it was zebra I meant. And I went back through the thread and the route to where we are know was actually much more convoluted than I remembered (and the hole zebra’s in now was entirely dug by himself).
What I was commenting on was #531 where you said:
Had he not dug in his heels on that data being unnecessary I think we could have mounted a reasonable defense using Table 5.1. There’s a number of categories from which psychiatric history and family environment could come from. History of abuse would be much less reliably obtained because the main source would be self reporting.
Yeah, that’s why I figured it would more likely come from self reporting by the participants. Depending on the data gathered it could be gleaned from medical records; narratives*, repeated history of suspicious injuries or malnutrition, visits to abuse counselors, etc. Not a wide net nor a particularly reliable one, but it could supplement self reporting.
*Though it’s unlikely that they will get psychiatric notes it’s possible hints could be found in other providers’ notes. I document it in my PCR’s whenever I contact DCFS.
Though I’m generally skeptical of gene-environment-behavior associations in humans, this is one of the more believable ones.
As usual, the real meat of this paper is in the supplement (PDF). It’s important to remember that what they’re really associating here is antisocial behavior and MAOA (the protein’s) activity, but they’re using MAOA (the gene’s) alleles as a proxy for protein activity. This means that though there are several different alleles that can combine into a number of distinct genotypes, they can be generally grouped into 2 distinct phenotype categories, high and low activity.
This is especially true because the polymorphisms we’re talking about in particular involve a VNTR, which is a spot in the genome with a bunch of small repeats close together that is prone to mutations that alter its length, as illustrated here. Since only a small bit of sequence gets added or removed each time, some alleles end up having somewhat similar effects on the promoter region, and therefore transcription.
In this case, we have 5 distinct common alleles but only 2 phenotypes. There’s pretty solid evidence that these alleles directly alter expression and fall into these two groups, so it’s a pretty good proxy. Allele frequencies in the Caspi study are in Figure S1: 95.7% of their study population had one of the two common alleles, 3 (low) or 4 (high).
Perhaps zebra would like to explain how his database would be able to identify this association, given that the 3 groups in Figure 1 would be essentially collapsed into one.
Comment in moderation with some Saturday Afternoon Genetics…
@capnkrunch #563.
I don’t remember what I linked to. But I think it was this:
http://www.nature.com/npp/journal/v30/n9/full/1300785a.html
Or this:
http://archpsyc.jamanetwork.com/article.aspx?articleid=482035
Or maybe this:
http://www.nature.com/mp/journal/v11/n10/full/4001851a.html
The need for this sort of inference from an incomplete data set just goes to show how abysmal Z.’s Grand Idea is. Psych records? How about juvenile criminal records? Do the “more rational” Canadians treat these in a more freewheeling fashion than the “USA paranoid group“?
One of the first remarks that Caspi et al. make about DMHDS is that it is free from population stratification. Z., on the other hand, thinks it’s a better idea to smear biases all over the place and try to sort them out later, once the a priori inevitable result for which “we [sic] would have a high degree of confidence in its validity” pops out of the magic box.
I almost wrote that it would take more time to list the things that Z. for which has demonstrated a wholesale lack of understanding than the items of the complementary set, but then I realized that it’s not clear that the latter is nonnull.
Keep in mind that Z. has refused to so much as describe the imaginary interface to his magic box or the protocols, including comparisons with the VSD. The PMI report addresses forms of access, but reading is hard, or something.
I mean, I’m no great expert on computational complexity, but at least I’ve T.A.’d introductory algorithms for a bunch of master’s students.* Z. cannot be bothered with such minor issues – a haystack of things that reduce to the traveling-salesman problem must cause an NP= P needle to spring into being among them, or something.**
Christ, Eric Lund pointed out way back in
comment 62 that this is a whole lot of underpants gnomes.
Nothing has changed.***
* While I was in a nonacademic position. Long story. Cormen et al. as text.
** The comparison to S.N. is not inapropos; check out its recent performance at EvolutionBlog. This footnote has also been randomly moved up because I needed the final one at the last moment.
*** It doesn’t compare closely enough to “The Ballad of Frankie Lee and Judas Priest” to allow the phrasing that I reflexively desired.
^ “the things
that Z.for which Z. has”I think. I’m going to go clean the cat boxes and the ceiling fans to cleanse my palate.
Sometimes one is even expected to read papers.
OK, I mopped the bathroom ceiling and am moving on to the dishes, but this is another good one:
Oops.
With apologies to gaist.
At the annual International Genomics Conference in Fernando Po, a disheveled figure is on stage in one of the lecture theaters, rooting through some overhead projection transparencies. Projected onto the screen behind him, upside down, is an overhead stating ‘THE ZEBRA GEGNOMICS DATABASE PROJECT (NOT “A STUDY”)’, hand-written in marker pen, upside down. A small audience of professional geneticists watch with curiosity.
SCIENTIST 1: Who is this guy? Who uses an overhead projector these days. I’m surprised they even have one. Doesn’t everyone use PowerPoint these days?
SCIENTIST2: No idea, the program doesn’t say what his field is or where he works, just that he has an revolutionary and innovative idea that will, he claims, revolutionize genomics. Might be good for a giggle.
On stage zebra is ready to begin.
ZEBRA: Fellow scientists, good afternoon. Today I want to present to you my new idea for revolutionizing gegnomics. What I propose… [he pauses for effect] is to sequence the gegnomes of every child born in the US in a single year. This will give us a database of genes that we can simply match to obesity, autism and other conditions, [Zebra pauses beaming, looking for the adulation and
applause he anticipates. He is greeted with silence.]
SCIENTIST1: Your slide’s upside down, and you spelled genomics wrong.
ZEBRA: [Quickly removes transparency and replaces it with the next one.] Irrelevant non sequitur, and it’s out of context. That’s how I spell gegnomics, obviously, try to keep up. Any relevant comments?
SCIENTIST2: How are you going to fund this project?
ZEBRA: Easy, we just take it out of the defense budget.
SCIENTIST2: Does the Department of Defense know about this?
ZEBRA: Nitpicking, next.
SCIENTIST1: This will generate a vast amount of data, and we are having trouble storing and processing the data we already have. What do you propose to do with all this data?
ZEBRA: It will be a resource for researchers. It will stipulate research and answer all the gegnomic questions ever asked. You scientists are clearly too stupid to have thought of this before, so you need someone like me who can think out of the box.
SCIENTIST2: I think you mean ‘stimulate’…
SCIENTIST1: [sotto voce] Someone’s out of his box…
ZEBRA: More irrelevant nonsense – does anyone actually knowledgeable have any comments?
[A shocked gasp goes up from the audience]
SCIENTIST1: You do know this is Professor Craig Venter?
ZEBRA: Who?
SCIENTIST1: He’s one of the biggest names in genomics!
ZEBRA: Nonsense, appeal to Authority, and it’s gegnomics, I can make any word mean whatever I like. Anyway that’s an ad hominem, attacking me just because I don’t have a formal education in genetics. Typical Authoritarian fools. You wouldn’t treat President Obama like this, he gets it.
HECKLER: You know nothing about genetics, you’re an idiot!
ZEBRA: That’s typical of this meeting, you are all prejudiced against zebras from the start. I encounter intolerant idiots like you wherever, so I must be getting under their skin and making them realize how blinkered they are. Any sensible, knowledgeable comments?
SCIENTIST2: How are you going to get IRB approval for this project? You need to specify experimental design, do a risk assessment, show how the data will be secured…
ZEBRA (triumphantly): I don’t need IRB approval because it isn’t a study so the law doesn’t apply. No IRB, problem solved.
SCIENTIST2: Does it use human subjects?
ZEBRA: Well, yes, but just to create a gegnomics database.
SCIENTIST2: You take blood samples?
ZEBRA: Yes, but…
SCIENTIST2: Then it’s human research and you will need IRB approval, unless you do it in some country where there are no human rights..
ZEBRA: Why do I need IRB approval? Why are you picking on me?
SCIENTIST2: There are ethical issues you need to address, privacy for one.
ZEBRA: Ethics? Privacy? Vacuous concepts.
[Zebra frantically leafs through the overhead slides until he finds the one he is looking for – he places it on the projector and gestures at it triumphantly – it is titled ‘ETHICS – A VACUOUS CONCEPT’ clearly copied and pasted from a philosophy 101 text book.]
ZEBRA: We can safely ignore a vacuous concept like ethics, or do you clever scientists believe in God? [He smirks mockingly at the assembled throng]
You wouldn’t care about privacy or human rights if you were locked in a cell with a broom handle up your ass, would you? Thomas Pynchon wrote a novel about that, something about Broomhandle’s Rainbow – a bunch of geneticists steal blood samples from the world’s politicians, clone them all, and then send them to London in a V-2 rocket or something.
SCIENTIST1: It’s Gravity’s Rainbow, and that isn’t the plot, even if it was in any way relevant., which it isn’t What does privacy and human rights have to do with having a broom handle up your butt? Anyway, you can’t just ignore ethical issues! Just because they don’t exist doesn’t mean we don’t have a duty to create them? Look what the Nazis did!
ZEBRA: See! See! Now you are calling me a Nazi! This always happens, I make a sensible suggestion and people are so jealous they have to make up some stupid objection or compare me to Hitler. It’s 20th century thinking at its very worst.
[Realizing that the lecture is being held by a lunatic, people start filing out of the lecture theater.]
ZEBRA: Wait, come back, you haven’t heard the most brilliant bit yet, you fools! Ethics and privacy are very important, as I said, but my database overcomes all those ethical problems.
[Only a few scientists remain, retained by a horrified fascination at the bizarre spectacle.]
SCIENTIST1: You said ethics and privacy are vacuous concepts!
ZEBRA: No I didn’t.
HECKLER: It says so on the screen behind you you dickhead!
ZEBRA: [Immediately changes the slide] You’re taking that out of concept, and anyway that’s a non sequitur.
SCIENTIST2: [Realization dawning] You don’t know what a non sequitur is, do you? Or anything at all about genetics, or anything else from the look of it.
ZEBRA: You’re trying to change the subject. This database is not, I repeat not, any kind of study or any kind of human research that requires IRB approval, which it would get, obviously, though ethics is of course of immense importance as I keep saying if only you idiots would listen, this database solves all the problems that you fools have run into with genomics.
SCIENTIST1: How does it do that?
ZEBRA: By having such a large database. You see the risk of any individual patient’s data being exposed is reduced. Brilliant, you see.
SCIENTIST1: But by having such a large database you make it more likely that someone will have their privacy compromised.
ZEBRA: Yes, but it is much less likely to be me, I mean any specific person, because an individual’s likelihood of having their confidential health data exposed is reduced because there are so many other targets. It’s brilliant, why can’t you see that?
SCIENTIST1: [Laughing.] That’s a novel approach to data privacy I suppose…
SCIENTIST2: Why would you need an entire year’s birth cohort? That’s about 5 million children in the US. Wouldn’t it be better to focus on people with specific conditions?
ZEBRA: OK, I’m changing my project, now it’s going to be an entire year’s birth cohort from Canada, and it will have IRB approval, and we won’t sequence the genome, we’ll just keep blood samples, and if anyone opts out we will replace them with other people who opted out by er.. look a squirrel!
SCIENTIST3: What about Iceland?
ZEBRA: Iceland, of course, excellent point, er… One moment! [Zebra frantically taps at his phone for a minute.]
ZEBRA: Iceland, excellent idea. They sequenced every person, exactly as I suggested.
SCIENTIST3: No they didn’t, they sequenced a few hundred thousand and the project collapsed because of the privacy and ethical issues you said were vacuous concepts.
ZEBRA: I never said that, you took me out of context. I said that ethics and privacy are very important.
SCIENTIST3: What about phenotype data? How are you going to collect that?
ZEBRA: Pheno what? One moment! [Zebra consults his phone again] Phenotype data will go in the same database, obviously. Yawn.
SCIENTIST3: But where will it come from? Doctors records? Hospital records? An interview?
ZEBRA: Yes, yes, all of those, obviously. Duh. Yawn.
SCIENTIST1: Hold on a minute. You didn’t even know what a phenotype was until you Googled it just then, did you? You don’t have the faintest clue what you are talking about.
ZEBRA: Yes I did and yes I do. How hard can genetics be anyway? I’ve read the Wikipedia entry and it seems pretty easy to me.
[Exeunt remaining scientists shaking their head in disbelief ]
ZEBRA: Wait, come back you fools, you don’t understand. You are all stuck in a blinkered mind-set and only I have the vision, imagination and intelligence to help,,you see the error of your way? Hello?
[Crickets…]
Krebiozen, you’ve outdone yourself. Maybe stand-up is your second calling; this is hilarious. And I would say this even if you had written it about my comments had they been the same. It’s that good.
Now, now. Z. is “willing to be found in error,” so long as it “helps educate people” – viz., demonstrate that Z. is right. (In fact, he’s the href=”https://www.respectfulinsolence.com/2015/09/08/precision-medicine-hype-over-hope/#comment-416862″>only person here capable of the very task, qualification aside.)
^ Ahem.
Now, now. Z. is “willing to be found in error,” so long as it “helps educate people” – viz., demonstrates that Z. is right. (In fact, he’s the only person here capable of the very task, qualification aside.)
Time for me to make a shopping list before it’s too late.
Narad
Would you get us…some sour cream and onion chips with some dip, man, some beef jerky, some peanut butter. Get some Häagen-Dazs ice cream bars, a whole lot, make sure chocolate, gotta have chocolate, man. Some popcorn, red popcorn, graham crackers, graham crackers with marshmallows, the little marshmallows and little chocolate bars and we can make s’mores, man. Also, celery, grape jelly, Cap’n Crunch with the little Crunch berries, pizzas. We need two big pizzas, man, everything on ’em, with water, whole lotta water, and Funyons.
Thanks much!
He who acetates is lost!
“He who acetates is lost!”
LOL. If you breath that stuff in you certainly are. For hours.
Alright, I’m going to go now. I’ve overstayed my welcome for tonight. I think I’m just in an odd mood because Orac has been back for almost a week and still nothing about the bats. I’m hoping they’re ok.
My Russian students, especially the ones in STEM fields, always get a kick out the fact that there is a behemoth of an electric typewriter (circa 1980-something, I’d say) sitting amongst the four computers in the computer lab.
I’m not sure why it’s there, although I’ve heard several explanations, but it’s been there since I started and doesn’t seem to be going anywhere. (Still works just fine, too.)
^Russian language students, I should probably specify, not students from Russia.
JP — we keep an IBM Selectric D in the office, next to the superduper hi-speed, low-drag printers, because every so often somebody shows up with a form that can’t be filled in by computer.
It should surprise no one that two of the last five non-computerized forms were from the DOD.
@shay:
I’ve heard that theory; an alternate explanation that I’ve heard is that a certain (now late, sadly) Professor Emeritus used to use it for various things.
It can type in Cyrillic, evidently; there are mostly-worn-off Cyrillic stickers on the keys. The non-computerized form theory makes the most sense for me, especially if one considers that we deal with ex-Soviet countries on a regular basis, and not by any means only Russia.
It is kind of funny that it’s in the grad student lab, though. Doesn’t clutter up the main office that way, I guess.
Not a Troll,
That’s kind, but I’m sure could have done a lot better if I was willing to spend a bit more time on it. There is, after all, no lack of additional material 🙂
None required. In fact, I’ll happily direct to you, duly, the undeserved overflow of internets I got in the other thread.
I admit that trying to pick and choose which inanities to highlight seemed the biggest task with
See Noevothe dishonest misanthrope, the jokes on him pretty much wrote themselves.It’s weird how some people unwittingly keep roasting themselves with almost every comment they make.
Ann 540,
You are wandering a bit here. Remember, basic research. As I have said, lots of little grad students adding lots of bits of knowledge.
The “researcher” is just doing that one thing. Finding a correlation between one genetic characteristic and one phenotype. So, you can’t bring in all these other pieces of information that you know.
By doing that you confuse the validity of the correlation with its significance (not statistical).
You haven’t made a case that we wouldn’t have confidence in the detection of the correlation. On what possible basis would you challenge it? I would really like an answer to that, since I want to improve my database if necessary.
With respect to your points, separate from the above question: If I were doing research in this field, and I discovered this one correlation, I would then continue to look for others in the genome, until I was confident that I had well-characterized the relationships. I wouldn’t start chasing squirrels.
If I understood Retro Pump correctly, s/he said something like ” initially we all got excited thinking we were going to find magic cures and get rich and famous, but it sure didn’t work out that way”.
I wonder, if the gratis, expansive, clean, database I suggest had been available, how many resources would have been better spent.
Gratis?
Expansive??
Clean???
It looks like you have stopped your pseudo-cogitation and are now just throwing out material for Krebiozen.
My comment, still in moderation, does exactly this. Aside from the fact that the above statement is pretty close to stats word salad, the short answer is you have no statistical power to detect the association. This is because in your database, it would be impossible to separate cases into the 3 groups used by Caspi et al. for the analysis as shown in the x-axis of Figure 1.
Perhaps you’d like to tell us specifically what statistical method you would use on this “gratis, expansive, clean” (???) database to detect this association, given that low activity MAOA alleles are associated with less antisocial behaviors in individuals who fall in the most common subcategory (no maltreatment).
Later that day, the two Scientists are having dinner.
SCIENTIST1: I really enjoyed the presentation by Dr. Eric Green this afternoon.
SCIENTIST2: Indeed, an excellent presentation. Unlike, you know… [He points towards a table nearby, where Zebra is inserting himself, interrupting a lively discussion].
ZEBRA: No need to get up, we’re among friends here. Real scientists among peers.
DINER1: Quite. [clears throat, turning back to the others] So, as I was saying about the concerns that raises for the information security applic-
ZEBRA: Yes, yes, no doubt a fine subject, but rather peripheral to the real issue, I think.
DINER1: Excuse me?
ZEBRA: Infosec, silly acronym, and wholly unnecessary.
DINER2: But we were just discussing-
ZEBRA: Peripheral points of little interest, I’m afraid. Whereas the main point, quite clearly, is the utility and accessibility of my project. On gegnomes.
DINER1: On what?
ZEBRA: Gegnomes. Pay attention.
DINER2: What on earth are you talking about?
ZEBRA: I’m surrounded by idiots, again. My project, the Great Zebra Gegnomic Database.
DINER1: The what?
ZEBRA: You must be slow, I won’t bother explaining it to you.
DINER2: You’re being rude, sir, and I would like for you to le-
ZEBRA: It’s a wonderful project, much appreciated and applauded by the real experts in the field, like the esteemed Professor Greg Venter-
DINER2: Craig.
ZEBRA: Greg Venter, the esteemed Professor of Gegnomics personally complimented me on my project, and lamented how there are so called experts in the field who have not yet realized the full potential of my gratis, expansive, clean databa-
SCIENTIST2: Evening.
DINER1: Evening, Mr. Venter…
DINER2 Hello Craig.
SCIENTIST2: Hello.
ZEBRA: What? Who?
SCIENTIST2: I couldn’t help overhearing Mr. Zebra here, and I feel I must make it clear that I most certainly did not-
ZEBRA: So you disagree with some minor details, no biggie, there’s no shame in being wrong sometimes, even for an esteemed expert such as yourself.
SCIENTIST2: They are not minor details I disagree with, I assure you. Your project is ill-thought, gravely misrepresented even by you, and wholly untenable.
ZEBRA: It’s obvious there is some ungrounded hostility here, towards novel thinkers. I know when I’m not welcome. [stands up]. It’s a pity none of the real numerous experts who greatly appreciate my database showed up. Your “opinions” aren’t needed anyways. [Exits]
I don’t understand.
How can a valid correlation between a genetic characteristic and a phenotype be established if you don’t look at anything apart from the rate at which they co-occur? Even the most bare-bones inquiry would have to have a control group.
So at a minimum, assuming the inquiry had been in the form most favorable to you — ie, the researchers weren’t just looking for any genetic characteristic corresponding to antisocial behavior, but specifically for MAOA 3R and nothing else — what they’d get would be 45% in the sample, versus 34% in the controls.
There’s no way to say whether that’s valid without looking at a lot of other stuff. I mean, I’m assuming that “valid” means “validly shown to be among the causal or contributing factors for the behavior.” So that would actually be the case even if the numbers were more eye-popping. You’d need to have some testable idea of how it worked.
But never mind that.
I don’t really know enough about it to make a case one way or the other. I believe that if the sample was large enough, you could confidently conclude that the result represented something. Whether it was something that was valid for the purposes of your inquiry would be another question.
But my understanding of such things is basic at best.
AdamG 592,
We wouldn’t have confidence in the detection of a correlation we couldn’t detect?
Jeez, back to the drawing board. What was I thinking? Of course this idea is useless if it can’t detect the undetectable!
sigh
zebra:
Please stop. You are making an even bigger fool of yourself now. You are clearly showing you know nothing about IT.
Again, I don’t understand. There could be any number of correlations that had no relationship to each other, the behavior, or anything else. Plus if you did that, either you’d find the other stuff I mentioned or I have no idea what you’re talking about.
Ann 594,
So we are on the same page in using this particular correlation as an example of something a researcher might discover– AdamG doesn’t seem to get that.
Of course, no problem. I wasn’t questioning what you said about that.
But
Not at all. Valid means “I can publish this and someone isn’t going to point out that my sample size is insufficient, or there are confounding factors, or I engaged in selection bias…”
And since I am saving you the expense of buying one of those machines Orac talks about, you can put your funds into analyzing a sufficiently large sample. And if another underfunded researcher wants to challenge/verify the result for some reason, they have gratis access to a different set of data from the same cohort, if that suits their experimental design.
Is that making sense yet?
What do you even mean at this point? You asked:
What specifically do you mean by ‘the correlation’ here? If you mean the association between low MAOA activity and antisocial behaviors in a history with maltreatment, I already explained in 592 why it could not be confidently detected, as you ask. We would not be able to separate individuals into the 3 groups necessary to detect the association.
If what you’re trying to argue is ‘any results gleaned from my database would be significant, and robust’ that is incredibly naive, especially because you have yet to comment on precisely how any phenotype data would be collected. It’s not like you can just copy and paste this stuff, honey…
http://www.ncbi.nlm.nih.gov/pubmed?term=24987407
It is apparent, to this reader at least, that the incredibly perspicacious musings of Mssrs gaist and Krebiozen are deserving of much praise: indeed they are seemingly meritorious beyond measure.
I should be SO pleased – if they were ever appear in either a serialised web-based format or in print- to submit a preface and/ or introduction to this important work. AND I can assure you most confidently that my own efforts OBVIOUSLY will be intrinsically more thought-provoking and intriguingly apropos compared to anything written prologueally by Kennedy, McCarthy, Haley, Olmsted or Sears
( who habitually precede blather written by their comrades with blather all their own).
At the very least, it will be reality-based and spelt somewhat realistically: can you ask for more? I can’t.
Then there’s that. And there would be that. Because realistically speaking, the bare-bones search parameters I described only make even rudimentary sense if you already know there’s a correlation, contingent on some external factor.
Even then, they don’t make much sense. Though.
ann and Adam G:
what you say is precisely why so many amateurs get caught .
AdamG,
Since the genetics involved in antisocial behaviors is a hot mess* right now, would you speak to something simpler such as how zebra’s database could be used (or not) for finding the genes and alleles correlated to eye color? Assuming that we are starting from scratch and there is no knowledge of what genes impact eye color.
*my entirely unscientific phrase.
Denice,
You went high end. I’d be happy with a Krebiozen and gaist cartoon.
And that is something that is entirely possible (with the name changed to protect the anonymity of the pseudonymous of course).
I think he does, in the sense that he would grant that it’s possible to design a search of the database that might discover it.
But that’s not saying much. If a researcher who was just using the database to look for some (or any) correlation between some (or any) genetic factor and a particular phenotype would probably always find something.
And a researcher who was using it to look for some (or any) correlation between a low-activity MAOA allele and some (or any) behavioral or mental disorder would also probably find something most of the time.
But it still wouldn’t mean much. MAOA affects several neurotransmitters. One or more of them is implicated in virtually all major mental illnesses. That’s already known.
In order to find out anything validly of interest in relation to the object of your inquiry, you’d need to do more than query a database for a correlation.
Someone could point out that since you hadn’t looked for confounding factors, the validity of your finding was unknowable. And they’d be right.
Eye color is not the best example here, as it requires careful attention to subtle gradations in phenotype. For a super cool example of how this complexity can be unraveled, see http://www.ncbi.nlm.nih.gov/pubmed/23555287
A more straightforward example here would be a rarer, severe disease linked to a single event. For example, let’s say I knew absolutely nothing about Down Syndrome. Since DS would certainly be noted in the medical record, it would be easy to separate your data accurately into true cases and true controls. As it’s unlikely for someone to be misclassified clinically as having DS, even without a chromosomal assay, comparing genome-wide SNP genotypes would instantly reveal that nearly all your cases and none of your controls carry what appear to be 3 alleles for every variant on chromosome 21…boom, disease mapped.
Again this is a straightforward one…trisomy 21 was identified as the cause of DS in the 50’s as all it took was the development of the first technology that could routinely detect large chromosomal abnormalities: karyotyping.
@ Not a Troll:
I regularly emulate the queen’s English-
however I’m not saying *which* queen.
Unfortunately, Jameson at AoA is today spouting the erroneous belief that because something co-occurs it MUST be causative.
e.g. 20 years ago there were less vaccine as well as less autism, ADHD, obesity etc.
There are also more organic food stores, more natural health advocates, more social networks, University of G–gle degrees and more thinking moms.
Ann #607,
” If a researcher who was just using the database to look for some (or any) correlation between some (or any) genetic factor and a particular phenotype would probably always find something. ”
Maybe, maybe not. Remember, we are not assuming things we already know. But why is that a problem anyway?
“Someone could point out that since you hadn’t looked for confounding factors, the validity of your finding was unknowable. And they’d be right.”
What would be a confounding factor when using my database?
1. False positives.
2. What wouldn’t be? I dunno, because you haven’t said what phenotypes you’d measure and how.
If you really want to learn something, do the minimal amount of effort and watch this video on statistical power:
Unless you’d rather stick to your usual reading material.
I agree. I always wish that such studies looked more at factors like education, literacy and intellectual stimulation or exercise in childhood generally. As distinct from intelligence.
But that’s not a criticism of Caspi et al. I personally would just like to see it.
AdamG,
Let’s go as simple as I think is possible – or not. I have no idea.
The phenotypes in zebra’s database would be a person’s physical characteristics and the ICD-10 codes of any diseases they’ve had or currently have. Understanding that we’d have to pay 1,000s of Canadian and American grad students to capture and enter all of this data, and that some of the information will just be incorrect for various reasons.
Would this be a good resource for researchers? Worth the effort involved?
Potentially anything. Correlation by itself could always be due to either coincidence or factors unrelated to the inquiry.
Or maybe almost always. If you were looking at a nice straightforward single-gene disorder with a conveniently unmissable Mendelian pattern of inheritance, finding the single gene would do the trick.
But you wouldn’t need the database for that. You could just test the affected people and their immediate family. And it’s usually not the case.
Not A Troll,
You are making an excellent effort to clarify things– good question with eye color.
Just a point– there are no grad students involved in creating the original database. The samples get collected and processed. The data on phenotypes comes from the healthcare system.
Ann 615,
Ann, seriously. it might be coincidence? You’re rejecting all of statistics?
So, look, if “it could be anything”, just give me a couple of examples.
I’d be curious about the time complexity of this if actually carried out from scratch in the brute-force manner that Z., by default, envisions. Enumerating multiple-locus combinations scales intractably (PDF).
EMP-hardened irony meters all around!
By magic? It’s impressive that you’re still willing to say something this profoundly dense at this stage of the performance.
Not actually true. Most large health networks conducting research these days consent patients broadly to be part of biobanks for this exact sort of work. Since their EMR is already filled out by their physician, the data’s all there.
Then it’s just a matter of comparing the IC9/10 codes of people with a certain genetic variant to those without to see if the folks with the variant are more likely to have a certain code in their EMR.
not only is it a good idea, but it’s already been implemented rather successfully:
http://www.ncbi.nlm.nih.gov/pubmed/20335276
This approach is a cornerstone of PMI. One of the things that makes it work is an initial baseline exam with findings coded into a patient-accessible EMR. See the section starting on page 58 of the PMI document labeled “Recommendations for an initial PMI core data set”
as for zebra…
Finally, the true role of the gegnomes is revealed!
The paper you cite has to do with detecting associations that underlie primarily driven by three loci (here meaning three different polymorphisms)…If your goal is ‘discover which specific genes cause features of DS when found in triplicate’ then yes, you’ll have to do a much different study that models these relationships.
I was actually talking about using sequencing as a counting method in order to diagnose trisomy 21…this works by looking at the stoichiometry of fragments of cell-free fetal chr21 in the mother’s blood. It’s super neat!
More on this here: http://www.ncbi.nlm.nih.gov/pubmed/26332378
or an excellent lecture for those who prefer:
https://youtu.be/6P9AVGp6R5w?t=73
Ok, my mistake. In the US at least, I thought there would still need to be an effort involved for the switch from ICD-9 codes to ICD-10.
^Also, my point would be moot if starting from a brand new just born birth cohort. So, never mind.
This is indeed a challenge, but more in the scope of a single smaller workgroup tasked to build an algorithm to automate this than an undertaking of thousands. I’m simplifying here though…honestly neither ICD system is great, I’m glad there’s an increasing move towards using SNOmed codes which make everything a lot more comprehensible…ICD is a mess.
https://www.nlm.nih.gov/research/umls/Snomed/snomed_main.html
My previous comment regarding DS was directed to Narad if not obvious…
Right, but I was proceeding from the starting point of not knowing anything about the cause of Down Syndrome and getting it to fall out of Z.’s magic box, the interface to which he has proved unable to describe other than to intimate that people will be able to randomly query medical conditions and simply be handed whole genomes.
Actually, simply running mPileup on your mapped case genomes would instantly reveal not only that chr21 had way higher coverage on average than the cases, but your heterozygosity for the entire chromosome would be way off in cases.
The technology to do this is already extraordinary. Assuming the most basic type of database, a warehouse of raw genome sequencing data with annotated disease status, this could be done in about a day using freely available tools over the web:
https://usegalaxy.org/
Believe me, I’m not giving zebra any credit here, but the resources out there these days are kind of amazing.
“The samples get collected and processed.”
A simple lesson learned from a career in government: Assume that any proposal which cannot be expressed in simple sentences (subject/verb/object)is worthless.
I don’t think so. We’re not talking about overwhelming numbers or a huge sample. It’s kind of hard to calculate overall prevalence for “antisocial behaviors.” But responsibly defined, they’re not all that common.
I already gave one. It could be that boys born to women who drank or used drugs during pregnancy are likelier to have that allele (as a mutation, either as a direct result of the alcohol/drug use or something associated with it) as well as likelier to be exposed to one or more environmental factors that are (in turn) associated with higher rates of antisocial behavior, which would (in that case) not be genetically determined at all.
It could also be that boys with that allele are prone to some other behavior or have some other trait that predisposes them to sleep deprivation, which in turn predisposes them to yet another type of behavior, which in turn makes them prone to conflict, which in turn has an effect on endocrine function, which makes them even more prone to conflict, which (in conjunction with other factors) leaves them biopsychosocially prone to violence as adults at a disproportionate rate.
I believe, although I’m not certain, that you could also be looking at a genetic factor that was correlated to the behavior but didn’t appear to be because…Well. I think I read something about Alzheimers and epigenomics that suggested it was more about what you did with your genes than what they did with you. Maybe.
But I’m hazy on the details, due to having virtually no clue what I’m talking about. So never mind. I guess my point is just that I imagine that there are also probably scenarios I can’t even begin to conceive of. However, although I know what I don’t know, I still don’t know it. So I can’t elaborate.
The thing I don’t know is whether that kind of thing would be evident if you didn’t look for it, or whether looking for it is standard, and so on.
I mean, I can follow a line of reasoning if somebody else has already done all the work of layin. But as I’ve already said, my understanding is shallow.
Those last two paragraphs were an attempt to elaborate, on which I gave up.
Just ignore them.
By default? I had to sign off on several pages (presented by a chirpy grad student who also waltzed into the procedure room to see if she could score a brushing as well)* when I sent bits of my latest colonoscopy to be embalmed and sent forever to the Great Colon Bank
in the Skydown the street.Anyway, I was reminded again of the VSD, the participating HMOs in which have their own IRBs for independent researchers. Z. of course has specified that he would need a more
compliant“rational” population to ultimately have his Grand Vision come to fruition and spread its nutritive seeds far and wide to desperately hungry flocks of graduate students, but I was also reminded that he can’t even bring it to the Power—t level of description.* None of them said you got to watch, Peaches, and there’s no reason for you have been wearing a lab coat.
ann 629,
I appreciate that you are really trying to answer. I just don’t see how you think that would be a confounding factor. What would it be confounding?
We would still observe the correct correlation between the genetic information and the phenotype, even if the genetic information is the result of mutation.
It there really were some way that there would be confounding factors, someone would have suggested it by now.
I think AdamG pretty much sums it up with his disclaimer:
“Believe me, I’m not giving zebra any credit here, but the resources out there these days are kind of amazing.”
or
“Believe me, it pains me terribly to give zebra any credit here….”
AdamG,
I spent ten years running the laboratory end of a prenatal Down Syndrome screening program that used serum AFP and beta HCG to estimate risks of a Down Syndrome pregnancy (using multivariate analysis), so that’s of great interest to me. If I generated a positive screen result the woman would be advised to have amniocentesis and cytogenetics would karyotype the fetus, so she could make an informed decision as to whether to continue with the pregnancy. Even with fine tuning we only had a 75% true positive rate and a 5% false positive rate, so it wasn’t very good, though better than nothing. I always knew that some better and less invasive method would become available eventually, so it’s nice to see that happening.
I recently read (in ‘Mutations’ by Leroi) that the gene for superoxide dismutase 1 resides on chromosome 21, so people with Down Syndrome have three copies of the SOD1 gene. A simplistic view might assume that this would be a good thing, since SOD1 mops up oxygen free radicals, but we know that the free-radical theory of disease and ageing is flawed. It is thought that it is the extra copy of the SOD1 gene that has some of the most destructive effects of Down Syndrome the mental retardation associated with it may be because SOD1 may have a role in pruning neuronal architecture, which is also where autism may have its roots. Interesting, or at least I thought so. No doubt it will provoke a yawn form zebra.
I’m impressed, thank you. I imagine the fact that I’m thinking about computational complexity makes it obvious that I’m trying to work from first principles.
This has its pros and cons, and help bootstrapping things greatly ameliorates that latter.
I believe that I’ve already mentioned that you’ve built in nearly every confounder imaginable.
You have a “haystack” of genomes and a needle-sparse set of hypotheses to be examined against an information-sparse set of medical records. You may have noted that I’m not the only person here to have paired the words “cart” and “horse.”
I also find it interesting that it is a mutation in the SOD1 gene that leads to ALS (aka Lou Gehrig disease), “a particularly ferocious neurological disease in which the motor neurons of the spinal cord, brain stem and motor cortex are progressively destroyed, leading to paralysis and death”.
These kinds of single gene mutations appear to be in a tiny minority. Most genetic disorders are likely to be caused by MAGOTS, which are far harder to discover. The human genome consists of over 3 billion base pairs CG, GC, AT or TA, so finding correlations between human conditions (whether physiological or otherwise) and variations in these base pairs that may be modulated by environmental factors seems mind-bogglingly complex to me. I’m glad there are some amazing resources out there to deal with this!
Krebiozen, check out this paper.
“I think AdamG pretty much sums it up with his disclaimer:”
Or it could just be that they don’t give credit here for wild a** guesses. They may give credit for educated guesses but probably not after you’ve alienated them with difficult to decipher writings and arrogance.
If you pay attention, you can see that the credit goes to those who have some solid ground on the subjects they are speaking to either from experience, training or researching it and to those who have done the work such as creating the mPileup program.
^ Then again,
That is so
COBOL20th century. I still await the details of the post-“sorting” Z. object-oriented data structure.Narad,
Um. was that for me? I did learn COBOL long ago in what seems like another lifetime. All I remember is to make sure to put the period at the end of the sentence, dummy.
AdamG,
Thanks, that was interesting too, though I always take cell culture findings with a pinch of salt. You can to buy SOD in health food stores, and I seem to remember claims that copper salicylate mimics SOD. If so, and if any of it is actually absorbed, some people may be doing themselves more harm than good.
Zebra (616)
I don’t have time to comment here much, but thought I’d toss in a note tonight.
You state:
Thanks for offering a perfect example of why the course in writing for clarity I took 25 years ago included the rule
Use active voice, not passive voice.
It’s because in passive voice, it’s so easy to drop the subject entirely. (which you manage to do in a different context quite often IMHO)
You left the key part, by whom?
Who does all the work of collecting and verifying the data and who pays them to do it?
And that’s just the start-up cost of your little brainstorming exercise. Then of course you have yet to even describe a plan likely to achieve useful results from that start-up cost, etc.
’nuff said.
No, you wouldn’t. (Also, it’s immaterial that it was a mutation. That was just a narrative flourish.) You would observe what appeared to be a correlation between the genetic information and the phenotype, when in fact it was a correlation between the genetic information and one or more unknown, unidentified confounds, which were correlated to the phenotype.
Narad@635
I think I know why zebra thinks otherwise. He’s operating on the “if I can’t see it it’s not there” principle. His database doesn’t contain data on confounding factors (it’s just a medical record linked to a genone) so there’s no confounders there. He’s conflating data on confounders with the confounders themselves.
This is, of course, wrong. The confounders are there either way, the difference is that if you have data on them you can identify and control for them.
@Krebiozen and gaist
That alone made this whole thread worth it. I’m Not a Troll. A webcomic on the RI trolls would make for a fine read.
Ahem. I’m with Not a Troll. We are, in fact, two different people.
Dear gegnoramus Z.
If I look at your quote here:
“Believe me, it pains me terribly to give zebra any credit here….”
Iiiiii don’t think that’s the interpretation I understood from AdamG and I have my own idea about why you shouldn’t give yourself any credits here:
You don’t know what’s out there 3:)
even more so, you argue out of gegnorance 3:) (i.e. talking out of where the sun don’t shine).
why not getting a bit of education on the topic?
https://www.coursera.org/specializations/genomics
https://www.coursera.org/specializations/jhudatascience
Your friendly Gunnery Sergeant Hartman 😀
That alone made this whole thread worth it. I’m Not a Troll. A webcomic on the RI trolls would make for a fine read.
May I recommend this pharmadog (woof) for the drawing?
http://lepharmachien.com/produits-naturels/
Gunnery Sgt. Hartman
Zebra @617: Correlation and confounders:
As was mentioned by capnkrunch up at 550, there is a simple, classic example of a spurious correlation (a confounder).
In epidemiology studies of cancer coffee consumption will often appear to be strongly positively correlated with cancer and cardiovascular disease. The reason that coffee has this correlation is that most smokers drink a lot of coffee. Thus, while coffee is correlated to cancer, it is not the mechanism of action (that would be smoking), it is just a confounder.
So for ann’s example, the anti-social behavior in the boys could be caused by that gene mutation, or it could be caused by a violent upbringing. You would need to do more studies to determine if either is the sole cause of the behavior.
Confounding factors are always a huge issue in all research. That’s why studies are so carefully controlled.
Ann (et al):
If there is no mutation, there is no correlation.
Everyone keeps making– whether because of ZDS or simply unclear thinking– this fundamental error.
Said multiple times now: Basic research. Accumulating valid (robust) information. Not gold-rush looking for the miracle cure, as described by Orac in that quote I gave.
If I’m looking for a correlation, I’m looking for a correlation, not causality. So, there are no confounding factors, except as I have already suggested.
I mean, I mentioned an actual example of how the data might be distorted (in a minor way) at least a couple of times, and you people can’t even work from that to find some similar possibilities to beat me over the head with. That would be constructive.
AdamG,
Well, I did my part in the Twitter chat. The team did a good job and most of my questions were answered. I could have done without all of the cheerleading but that is to be expected.
Thanks for letting us know about this.
Dining. Room. Table.
zebra, I just want to make sure I am understanding your argument. Do you believe this statement to be true or false:
Confounding factors need only be considered in this context if one is trying to establish causality, and play no role in finding correlations.
Please, correct me if this is not what you are advocating.
NaT…thanks for chiming in. I’ll probably still be around here when it comes time for folks to start signing up…
There is no such thing as looking for a correlation while blind to confounds. That’s not research, basic or otherwise. It’s….I don’t know what it is, actually. It’s essentially a game of chance of some sort. Roulette. Slot machines. Something like that.
A correlation doesn’t necessarily have to be causal, exactly. But in order for an association between two variables to be correlative, A has to at least be demonstrably dependent on B in some way. If that can’t be demonstrated, it’s not one.
All of those things are non-optional. If you use the words “correlation” and “research,” that’s what you’re talking about.
I mean, they’re not my rules. But they’re not yours either. The words mean what they mean.
ann@653
Haystack first ann. It’s looking for hay in a haystack. You’re always successful but in the end you haven’t accomplished much.
“I’ll probably still be around here when it comes time for folks to start signing up…”
That’s good, AdamG. To clarify most of my questions asked in the chat were answered. I’m sure my questions will be a work in progress if I decide to sign up. But don’t worry, I don’t plan to abuse your presence here to answer them. There will be a contact for that through NIH, I’m sure.
For zebra’s conundrum, I think he is just looking for correlations between Col A (genomes/alles or however granular he plans) and Col B (coded medical conditions). I am not sure he grasps how far that will not get you or for the presence of red herrings.
Anyway, that’s my best guess.
The more I think about, the more this seems like the crowning moment of Z.’s “proposal.” An enitre birth cohort is going to be sequenced, magically have its members’ medical records thoroughly tracked* in a perfectly secure yet easily accessible fashion, and, at long last, the goal is to aimlessly churn out false positives. After burying them in noise for good measure, and ensuring that one has no way to easily identify screaming confounders such as, oh, say, population-level data. And this will cause people to flock to graduate study of this mess because, well, there’s no better way to get tenure than to spend years picking sh*t with the crows.
One could almost just say “The Aristrocrats” and stop there, but there is so much else wrong that it’s enough to drive a person to distraction.
Perhaps Z. would like to address this failure mode, and what it has to say – yet again – about the arrangement of carts and horses. L-rd knows he never got around to stating whether it has more than one dimension or not.
* BTW, returning to antisocial behavior, how complete is medical documentation of concussions?
^ “think about it”
(I was reminded of concussions by a truly impressive “data set” that Puliyel has on his Web site, but that’s for another time or, more likely, place.)
Relocated, although the monument to the gag reflex that is Z.’s comment 503. Allow me to review:
What’s the “correlation” with, again? Sweet G-d. Anyway….
—–
You know what? Since Z. didn’t have the damn sense to take advantage of an opportunity to stop publicly making a fool of himself, there’s another bit of utter fraudulence that I don’t believe I’ve commented on previously:
This is more than faintly insane, but I’ll write the bulk of it off to Z.’s situation at this juncture.* Resorting to weird persecution fantasies (which, as is par for the Zourse, are “concretized” and “defined” by virtue of being assigned acronyms) is beyond the scope of where I intended to go.
The garden-variety Bodhisattva concept is prima facie dualist, hydraulic, and pathognomic of Not Getting It, but here, Z. horks up some sort of freakish “operational definition” of empathy.
This reminds me of a story.
“‘You don’t understand,’ said the master. ‘My mind and the fawn’s mind are the same. It was very hungry. It wants milk, I want milk. Now it is dead. Its mind is my mind. That’s why I am weeping. I want milk.'”
Protip, Z.: Don’t try dropping the word “empathy” when your
entire, grotesque** sh*ttrip boils down to plain indignance over the failure of the perceived world to affirm your own glowing self-appraisal.
* Imagining how he would react to stopping up – or, better, causing to overflow late at night – the toilet at the home of somebody whom he was visiting for the for the first time, with first impressions on the line, is offered as a light-hearted exercise for the reader. Then again, he’s apparently now a septuagenarian or something.
** In the vernacular sense.
^ “although also having taken note of“
Hell, allow me to gratuitously call attention to a strange (to say the least) yet enthusiastic Z. tic:
- - -
- - -
- - -
- - -
There is something very simple going on, Z., but for some reason, you can’t figure it out:
1. “It” is not all about you.
2. “It” is all about you.
I am not a developmental psychologist, but my friends and neighbors have kids, and we hang out and work a little (or more if necessary) at enjoying our time together and so forth. I would guess, on this basis, that most 12-year-olds could authoritatively dispense with this “insolubilium” in passing between bites of carrot stick or whatever.
I mean, it would be vastly more interesting if you yourself would embark upon some “basic research,” by which I mean something along the lines of getting under a haystack and starting a bona fide blog about all the shiny things that you find and how you figure out whether they’re “needles” or random bits of leftover baling wire or something.
I cannot imagine any way that Dispatches from the Haystack could underform this wretchedness.
Idly advancing the notion that “hey, maybe we should sequence a U.S. birth cohort” is bullsh*tting. This is a good thing where I come from. Freaking right the f*ck out when people start kicking the idea around and finding it, ah, lacking in certain respects and then, in consequence, making up insane sh*t-brained “syndromes” might, briefly, have passed as a bit of horsesh*tting on the side, but this is ridiculous.
Not only have you been indulging a humorless, thoughtless, petulant tantrum, you apparently just couldn’t bear the notion that it might stop being reinforced to some sort of minimal gratification threshold.
Not all parasitism is truly obligate, Z.
^ Bit of close-ital failure, but it’ll do.
I am eager to see zebra’s response to AdamG’s question at #652. I won’t hold my breath though.
I have to say, I not only don’t see the problem with that, I think it’s an ingenious and viable work-around for the objectivist-libertarian tendency towards callous indifference — ie, it’s in your self-interest to oppose bad acts against.others because it could be you.
He cited Niemoller as a way of saying the same thing @#219. But you could also use “An injustice anywhere is a threat to justice everywhere.” And the Golden Rule would also do it. It comes off as more sanctimonious, but it’s the same principle.
I agree with it.
In Buddhist philosophy, this is considered the “conventional” or “relative” view: your actions or inactions affect others, which directly or indirectly comes back and affects you. We’re all in a complex web of relationships that can’t be untangled.
Narad is evidently speaking from the “absolute” viewpoint, in which It is me. Tat tvam asi, in so many words.
A reference to Sandokai is perhaps in order:
Adam 652:
In what context?
Ann:
It’s not easy being green. Thanks.
JP.
“In Buddhist philosophy.” Whoa, dude, that’s some deep shit.
In exactly the context you mean when you stated
Again, True or False:
Confounding factors need only be considered in the analysis of the database zebra has proposed if a researcher is trying to establish causality, and play no role in finding correlations.
If I’m misrepresenting your views on this, please feel free to to clarify your exact position.
AdamG,
If you don’t want to be accused of quotemining (taking a partial quote out of context), then don’t do it.
Did you miss the last paragraph?
BTW, Orac appears to be putting me at least in moderation. If he is growing impatient with this thread, it represents yet another thing he and I have some agreement on.
How would your database aimed at “accumulating valid (robust information” deal with false positives?
And BTW, silly zebra, it’s you typing “shit” without circumventing the word filter that put you in moderation, not Orac singling you out – for that you’re not significantly whiny a troll yet.
I can’t think of any context in which that paragraph makes any sense, so I await zebra’s explanation with interest.
zebra, your continued dodges are highly amusing. This time with no quotes whatsoever so nothing is ‘mined:’
True or False:
Confounding factors need only be considered in the analysis of the database zebra has proposed if a researcher is trying to establish causality, and play no role in finding correlations.
Great article Narad linked to @656 but over my head. Is there a relatively simple example of what the issues would be if an particular allele in Col A of zebra’s database was found to be a match with an illness in Col B for a significant percentage of the number of those with the illness?
Please don’t ask what percentage would be significant as I have no idea what that would be. Thanks.
AdamG,
I never said that. Here’s what I said.
Do you understand the meaning of the word “except”?
Do you understand “work from that to find some similar possibilities” ?
Why don’t you tell me– what is your interpretation of the actual comment? Do you think it says what you are paraphrasing it as: “no confounding factors except” means “no confounding factors”? “Work to find some similar possibilities” means “don’t bother looking for similar possibilities”?
You’re getting positively desperate-whacky trying to elicit some little turn of phrase or interpretation that will Put That As*hurt On Zebra! because well, back here he used this word and over there he used that word blah blah blah.
This from a supposed expert in the field.
At this juncture I’m reminded of something I read recently about the growth of PoMo in the social sciences and the attack on natural sciences (from ‘Higher Superstition: The Academic Left and Its Quarrels With Science’ by Paul R. Gross and Norman Levitt, please forgive the longish quote, but I think it’s apposite):
This is for Ann, if you are still there, and that is indeed it unless she replies or someone can rise to her level.
Ann, I think your problem again is in not “separating” things, as with so-called natural rights, and legal rights.
There are sources of error at different stages of the process. It isn’t that there aren’t confounding factors that might distort the data that is initially collected; one point of doing it my way is to eliminate what would normally be common sources of error.
Let’s consider schizophrenia, or, since I don’t want to get a lecture about how little I know about schizophrenia, some hypothetical similar diagnosis. So, in the usual way of doing things, what we do is go around finding people who have a condition, which may result in their being incompetent to make such a decision, and ask them if we can sequence their DNA.
The obvious problem with this is that we may then for example only get the DNA of patients for whom drugs work to make them competent to make such a decision, which of course is decided by the ethics committee of which everyone is so fond.
So, if I use that database, I am not completely confident that the statement (for example) “65% of those with the diagnosis have the genetic characteristic 1 (GC1), [while, say, only 35% of those without the diagnosis have GC1.”] And so on for GCn. It may well be that those who respond poorly to medication have different GC’s. That’s the kind of thing you are talking about, right?
But let’s say we do my project. We eliminate that source of potential bias, as well as the ethics question, because we have already asked: can we use your genome even if you become schizophrenic? So we can be much more confident in that statistical statement, made with respect to the cohort, absent some unlikely phenomenon like what I suggested earlier, or whatever someone can come up with, as requested.
BUT
This does not mean that [schizophrenia] might not also be correlated to environmental factors, for example, or that we don’t have to do much more work to sort things out.
It does mean that all the researchers trying to do that are working with the same “[people with schizophrenia] genome range” *, in which they can have more confidence than if they had to use a less comprehensive (and potentially contaminated) sample they collected themselves, to establish it themselves. And gratis, because it is published.
*Developed by the swarm of little “basic research grad students”, who got the database information gratis.
So, if you still disagree about the merits of my proposal, that’s OK, but that’s my best exposition of what we are disagreeing about.
And again, you have my gratistude for providing a coherent counterargument.
@Krebiozen:
I’m pretty deeply invested in the humanities, and I suppose I’m a “leftist,” and I see no evidence that this “growth” exists. As in, I have not come across a single person who quibbles with the scientific endeavor in this manner. Maybe there are a few people out there engaged in such a thing, but I have never met a single one.
Granted, when friends start talking about queer theory or “hegemonic something blah blah blah,” my eyes kind of glaze over, as it’s just not my thing, but I don’t really see how “feminist theory” is anti-scientific. It doesn’t properly apply to the study of, say, physics, sure, unless we are talking about the study of the culture of physics departments and why they are so heavily male, for instance.
And this:
doesn’t even make sense. Or the terms are so vaguely defined as to render the statement meaningless, whatever.
But anyway, if you are referring to zebra, he still hasn’t stated what his higher educational experience is in; I doubt he knows any more about postmodernism than he does about anything else.
I’ll say it again…if you want to learn, you have to do the work.
You do realize there are people whose entire career is based on unraveling confounding factors inherent in GWAS, right? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852732/
By the way that article has an actual, real life example of a spurious genotype/phenotype association that was published. This stuff CAN’T be explained via a few comments here. That’s why I linked you to a textbook that I legitimately think you would get a lot out of, if you are willing to do the work of reading it.
What you’re doing here is the equivalent of going to a particle physicist and saying “I have THE BEST idea! Let’s build something that smashes atoms together, wouldn’t that be helpful! And it would be gratis for basic research swarms!”
^ I mean, if you take a look at, say, the average university’s annual budget, and any budget cuts that have been made over the past ten years or so, the notion that science needs to defend itself from the humanities is pretty hilarious. We would just like to be allowed to exist, mostly. That would be nice.
In any case, a lot of the “scientific” arguments disparaging “humanists” or whatever just strike me as anti-intellectual and absurdly utilitarian*; I wonder if it has ever occurred to any of these guys (and they are mostly all guys) that if you are not interested in something or don’t get it, maybe it is not because you are too smart for it.
*I am reminded of a conversation I was having with an engineer friend of mine in which I mentioned that anthropology students often take at least a decade to get a PhD, since they have to do years of field work. His reaction: “That’s ridiculous! That means you’ll be in your thirties when you get a PhD. And sure, I mean, I guess it’s cool that you’ll have a PhD and all, but it won’t be useful or anything. I mean, come on.”
As though the only reason why one might study a culture and make a significant contribution to a field of knowledge is because it will have an immediately practical use…
*I am reminded of a conversation I was having with an engineer friend of mine There’s your problem right there.
Krebiozen, I think I can sum up the attitude referred to in your post above in just one sentence.
“We don’t understand this, but we’re smart, so we don’t need to understand it to critique it.”
JP,
I don’t agree with everything the authors say, and to be honest I got bored with the book after the first couple of chapters (its language reminded me of some impenetrable pomo texts, ironically). It’s an oldish book, and I’m aware that it somewhat indignantly tars too many with the same brush, but it has an element of truth in it and I found those passages amusing which is why I shared them.
It does seem snobbish to tell people that they don’t understand science well enough to criticize it, but it is also true that it takes years of study to properly understand things like statistics and genetics. It’s irritating to those of us that have spent years of hard work learning this stuff to encounter someone who thinks they can simply bluff their way through with the help of Google and Wikipedia.
Hopefully things in the unnatural sciences have improved a bit (post-Sokal) but I was surprised by some of the examples they gave in the book, though they are presumably extreme ones chosen for effect. I experienced some of this in the late 80s when I took a few years out of clinical biochemistry to study social anthropology, and had several heated arguments about whether science is just ‘another way of knowing’. I was surprised several times by the scientific ignorance of some of my fellow students and even my tutors.
There really are people who claim that Newtonian and Einsteinian physics were merely expressions of the social conditions at the time (see Stanley Aronowitz’s ‘Science and Power’), and bear no relation to ‘reality’. The number of social scientists who have horribly misunderstood quantum physics and especially the uncertainty principle is depressing.
There is also Bruno Latour whose anthropological studies of scientists are fun, but also contain gnomic statements such as, ““Since the settlement of a controversy is the Cause of Nature’s representation, not the consequence, we can never use the outcome—Nature—to explain how and why a controversy has been settled.” It seems that some people interpret science as nothing more than a cultural construction, but when you ask them how it is that science has led to so many technological innovations they usually fall silent.
BTW, regarding anthropology students taking a decade, I was offered a place to do Master’s and a PhD. but I couldn’t get a grant because the previous years’ students hadn’t completed theirs, and the funding body blacklisted my university until they did. I had a wife and child to support so I went back to lab work instead (after a brief sojourn working as a research anthropologist, but that’s another story).
This wasn’t my point; it takes years of study to understand a lot of things, for one thing, and this:
Still doesn’t make any sense. What do they imagine the “education and training that nurtures the average humanist (sic)” to be, and how on earth is it supposedly incompatible with understanding science? I have known “humanists” who went on to get advanced degrees in science or mathematics. They didn’t seem to be hobbled in any way by their prior education. (Which also belies the claim that one must “begin young” in scientific training if one is ever arrive at an understanding of a scientific subject.)
As regards snobbery, it does come off as rather self-congratulatory and clueless: we studied science, and it was a lot of hard work, and you just don’t realize that. It is as though they are assuming that people in the humanities don’t work hard, or don’t want to work hard, or don’t even understand how hard science is, or something. It’s childish and silly.
RE: Bruno Latour: It kind of depends on what era of his writing one gets into. I’m a fan of several of his books, but not so much his earlier work.
I dunno, maybe things have changed in 30 years, but like I said, I haven’t come across this argument. I mean, except perhaps in the rather obvious sense that there are other ways of knowing or ways of studying things; one does not study a sonnet (or whatever) in exactly the same way as one studies a chemical reaction, but it doesn’t mean there is no way to study literature, or that the endeavor isn’t valid. (It’s also the case that there are certain similarities between the study of a poem and the study of a chemical reaction, but that’s another subject.)
I dunno about the “nothing more” part, but I have a hard time seeing how science could possibly not be interpreted as a social construction. I mean, unless one believes that it was handed down from a pure Platonic realm of reason or something. Clearly science is the product of humans and their culture. I also can’t grok the notion that there’s any contradiction between the fact that it’s a cultural construction and the fact that it’s led to so many technological innovations; it’s a cultural construction that has led to a lot of technological innovations. That’s the only way to think of it that makes any sense, at least as far as I can see.
Oh:
And I am often surprised by, say, the ignorance of STEM students and even faculty when it comes to history, literature, art, all kinds of subjects. 🙂 There are a lot of things out there to study: nobody is an expert in everything. Which is to say that I don’t see STEM people as being any less prone to stunning Dunning-Kruger effect than humanities types when it comes to “alien” fields of study. Hubris is an equal-opportunity character flaw, I’m afraid.
JP,
I entirely agree that:
is a ridiculous statement. I’m well aware of the excellent work that the majority of social scientists do and of the hard work involved; I’m proud of my social anthropology degree. I’m also sure things have changed in 30 years (thanks for reminding me!) and I think the more extreme pomo attitudes were particularly prevalent in the late 80s at SOAS (where I studied).
It wasn’t science itself so much as the model of the universe that science has generated that some people claimed had no relation to ‘reality’. I honestly had arguments with people who claimed that the origins myths and other explanations of the world around them related by a hunter gatherer tribe were as valid as what scientists tell us about the universe, and that I was ethnocentric, Eurocentric and racist to argue otherwise.
I have no doubt that cultural factors sneak into science all the time, but claiming that Einstein’s equations were merely an epiphenomenon of bourgeois early 20th century society (as Aronowitz appears to do) seems ludicrous to me. I think the scientific method transcends culture (insofar as that is possible).
WRT to the people and science, viewpoints matter*.
Personally, I don’t think the Left handles this any better than the right’ it is a human failing. The anti-psychiatry crowd is largely left of center with some who identify as Marxist. They’re a very intelligent group as a whole and many are found in academia.
However, at many of their blogs, I’ve seen it too many times to count where scientific studies are critiqued as lies, manipulation, obfuscation or poor methodology as long as it is a point the community disagrees with. Yet they are more than happy to cite studies that agree with their viewpoints without ever looking into the same issues. I would feel more confident of their position if they would acknowledge the flaws in the research that agrees with them as much as they dissect the ones one the opposing side.
A more extreme example of an agenda flipping off science is the push to make carnivores into vegetarians and to stop animals from killing each other. Granted not mainstream environmentalism but who would think of such a thing to begin with. I doubt years ago people were entertaining this thought, and if it continues, it will be a laugh a minute for me until they get hold of a politician or two.
Forgot my footnote @684.
*This discussion fits really well ideas discussed on Orac’s most recent post)
@ Not a Troll:
re the “push to make carnivores into vegetarians”
Ha!
I just heard ( PRN) that Paleolithic folk REALLY weren’t meat eaters so much because they ate oats! ( Nearly vegan!)
and about 10 years ago, teach your cat to go vegan!**
Seriously. The cat will live to a grand old age!
Someone must have corrected that stupidity because he stopped and changed it to raw diets including fish.
HOWEVER the anti-psychiatry movement just explains itself if you catch my drift.
** don’t try this until you want one less cat.
Hmm. I guess I can see where a more tempered version of this attitude could be useful in a field like anthropology; certainly origin myths of hunter-gathering tribes, say, are as valid to them as the scientific explanation of the world, if not moreso. I mean, if you are actually studying a culture on its own terms, you can’t just dismiss myths as silliness; they’re hugely important cultural artifacts, and they have hugely important cultural functions.
Pitting one against the other (i.e., myths vs science) seems more like a category to me than anything else.
I haven’t read Aronowitz on Einstein (and likely never will), but if that is indeed his position, I agree that it is silly. I mean, Einstein’s equations indisputably are a product of early 20th century society (I dunno about the “bourgeois” part), but they also describe the physical world accurately.* Which is a grand thing.
Insofar as that is possible, I guess; but it’s still a product of culture. It wouldn’t have arisen in a culture that didn’t allow for free inquiry, for example. It’s not so much that culture sneaks into science, at least from my vantage point, as that the two things can’t really be separated. The political climate determines to a large extent what kind of science is funded, for example. And so on.
But yeah: the scientific method is really the only method we have to accurately describe and understand physical, “objective” reality. I’m glad that people came up with it.
*As far as they go, of course, like anything else in science.
**The quotation marks are just the epistemologist in me asserting itself. Sorry/not sorry.
I would be astonished if he made that claim, and utterly unsurprised if the word of someone who thought it worthwhile to write a book attacking the academic left was completely unreliable on that point. And probably on most others.
I mean, this…
…is what I would call ludicrous. Good scholarship is good scholarship.
Obviously, some — indeed many — academics are fools. But that’s not any commoner or less common in any department or discipline than it is in any other, in my experience and observation.
Furthermore, it doesn’t reflect very well on the training and education that nurtured the authors that they think this is an A-OK tactic:
Oh, really? You have secret knowledge of stuff that’s not in print? Please allow me to join your cult!
…
Seriously, do you have a quote that bears that out? I just glanced at a little bit of Science as Power online, and it does not look any likelier to contain statements that daft than I would have expected.
I give up. I’m surprised this thread has gone on so long. I don’t have the stamina to try and educate Zebra on the genomics of birth cohorts or the difficulties in linking complex diseases that have a gene-by-environment flavour.
So you collect genomic data on millions of kids. You don’t see the need to collect any other data aside from health records and let’s say on of your diligent grad students decides to study the association between schizophrenia and genes at age 25. How will you explain that less than half of your identical twins with schizophrenia have their twin also develop schizophrenia? Maybe it’s because one of the twins smoked too much pot when they were 17. Maybe it’s because the twins were adopted out at birth and were raised in different families, thus had different socioeconomic upbringings, different schools, different???. Maybe one of the twins suffered more traumatic events than the other (car crashes, divorce, death of a child, job loss…). Most of the time you will never know, as you haven’t actively monitored environmental and socioeconomic info. Maybe you should try to better familiarise yourself with the concept of ‘complex diseases’, which are in fact most diseases except some rare Mendelian ones. Though NGS data is a wonderful thing, we still need a lot more basic biology and environmental understanding to make the best use of it. We need better diagnostic criteria for sure. Is all heart disease the same? Is high blood sugar and insulin resistance a single disease? Is all schizophrenia, depression or bipolar disorder the same disease? Is all breast cancer the same? The clear answer is no.
This is aside from all the ethical issues involved, which are many.
Seriously, do you have a quote that bears that out?
There was this:
Sokal and Bricmont accused Luce Irigaray of describing E=mc2 as a “sexed equation” because “it privileges the speed of light over other speeds that are vitally necessary to us” — but it’s not clear whether she actually wrote that.
https://www.reddit.com/r/askphilosophy/comments/2hu5sb/did_luce_irigaray_ever_actually_say_emc2_is_a/
@#690 —
I meant “a quote from Aronowitz.”
I don’t doubt that it’s easy to find stupid quotes from identity-politics-oriented leftist academics. Or to cherry-pick them,, as the case may be. And while I’m not sure that’s a fair characterization, I’m not sure it’s not. Because I am sure that left-wing humanities professors are not actually any kind of threat to science.
However. Be that as it may. It’s been a long time since Sokal’s little exercise in trolling. The menace to progress that was Social Text has evidently been tamed. Everything’s fine. Why is it necessary to keep stomping the queer and feminist theorists?
What bothers me is really that from what I know of Aronowitz, which is limited, he’s a perfectly good thinker whose most prominent distinguishing characteristic is that he’s unreconstructed, old-school left, through and through. That he’s such a favorite target makes me suspicious. I find it very hard to believe that it’s not just a political act, masquerading as something else.
Also, as I’ve said before, Sokal made a bad impression on me from the get. I feel that if he really wanted to do something for science, he should have published something in his own damn field.
That the feminist theorists are always in there also raises a little bit of a red flag, tbh. There’s certainly no shortage of idiotic feminist theory. But feminist-bashing does not have a good pedigree.
I actually know the work of Aronowitz’s late wife, Ellen Willis, better than I know his. Speaking of feminists. She did very good work.
Well. Burn her, I say!
Come on. If they’re so fragile that they’re threatened by what some French feminist theorist that virtually nobody has ever heard of wrote in 1974, the problem is not on the academic left’s side. I mean, how did that statement injure science, precisely? Sokal and Bricmont probably did more to promote it than she did..
The Speculum of the Other Photon? Perhaps this really comes down to polarization.
Simply put, my take on Sokal is basically:
I don’t doubt that NYU gives Stanley Aronowitz all kinds of love and attention that it doesn’t give Sokal. But as far as I can see, that isn’t because leftist gangs got together and devalued science. It’s because Stanley Aronowitz is a much more accomplished and productive academic than Sokal is.
I mean, it’s not the Cultural Studies department’s fault that he hasn’t done star quality work. They didn’t even exist for most of the time he wasn’t doing it.
I read some Irigaray as an undergrad, almost a decade ago; my recollection is that I found her work interesting, if obnoxiously essentialist, which I think was my general feeling toward a lot of French feminism of the era. I confess to not having them revisited them recently; it could be an interesting exercise.
Speaking of anthropology, I actually read Irigaray in a class taught by an Evergreen professor who had gotten her PhD in anthropology in the 70s-early 80s, if memory serves. She got interested in feminism, epistemology, post-colonial theory, etc., because of her experience in anthropology; she related stories of having male colleagues pour out all kinds of personal difficulties they’d encountered in field work, sometimes literally crying in her lap.
The question of how possible it is to be “scientifically objective” during serious anthropological field work is certainly an interesting one. It definitely comes up in discussions over drinks with anthropology PhD student friends, especially wrt to sticky and sometimes traumatic experiences during field work.
Oh, and wrt to anthropology students taking a decade to finish (at least), that’s come up in discussions recently as well, with the university administration having recently decided to attempt to push a five-year finish time for PhD students across many fields. The issue is that it is generally understood that a PhD in anthropology will take substantially longer than this, and that current candidates entered the department under that general understanding.
Academics of the world unite: you have nothing to lose but your administrators!
@Not a Troll #684:
You’ve never seen the 1989 film “Shirley Valentine”, I assume. One of the jokes has Shirley Valentine (Pauline Collins) pet-sitting a bloodhound. Said bloodhound’s owners say that the dog is vegan. Now, I know life sometimes imitates art, but I would guess that that is at least partly based on reality.
@ Denice #686
Wait, aren’t cereals of any type definitively NOT paleolithic diet?
I think PRN got confused when someone told them that paleolithic people were huge believers in sowing their wild oats.
@ JP, ann and a few others
Nothing meaningful to add to your discussion, but to say I am learning lots about anthropology and other social sciences, beyond the clichés. Please continue 🙂
I’m going to restore the original boldface here:
My real ire was drawn by Z.’s nonsensical assertion that he “empathize[s] with people suffering.” This literally doesn’t mean anything, and Z. immediately abandoned it in favor of “discovering” some sort of monetized or convenience-oriented version of… the categorical imperative.*
This isn’t, in legal terms, “field preemption.” It’s stark idiocy. Nothing has gone before in Z.-land, or if so, it’s The Wrong Century, or Needlessly “Compicated,” or stop writing about this distraction from the Z. vision, stupid Orac.
Z.’s enthusiastic construction of what he imagines to be monuments to his pure brilliance at this point reminds me of neither more nor less than the beginning of The Monkey Wrench Gang, with the caveat that I’d be much more charitably inclined toward a billboard for an independent podiatrist.
* I inadvertently omitted this “because” in the original quote.
Yah, dogs. I would strongly advise against inadvertently bringing up Camille Marino.
sticky and sometimes traumatic experiences during field work.
I don’t want to behalf in this drunken and erratic way, but in the interests of the fieldwork I must try to blend into the milieu.
The ship was supposed to arrive and take me home but it is long overdue. Getting worried here.
I wish I hadn’t posted those quotes from Gross and Levitt, as I have no real interest in supporting their attack on what they term ‘the academic left’ They do spend some time (perhaps a little too much) explaining that they are not taking a political stance, and I should perhaps add that my personal politics are mostly leftist-liberalish. It was just that their exasperation with those attacking science without understanding it resonated with how I felt about zebra’s attempts to bluff his way through genomics and then statistics.
However, since I have stumbled down this road, I may as well be hung for a sheep…
Gross and Levitt don’t give many direct quotes (understandable given Aronowitz’s somewhat impenetrable style) but they paraphrase Aronowitz as follows:
Without reading the passages they refer to it is impossible to assess the accuracy of this claim. I did find this in Chapter 12 of ‘Science and Power’ (the only part I can find online), as perhaps one example of what Gross and Levitt claim:
I find it hard to conceive of gravitational theory, for example, as describing the relation of humans to gravity, not gravity itself.
Here’s another quote from ‘Science and Power’:
To be honest I’m not entirely clear what Aronowitz is suggesting here (despite having spent three years learning to understand that kind of language). It does appear to me that he is claiming facts have no objective reality, whereas I would argue E=MC^2, for example, is indeed “discovered” not “produced”. If that particular equation was “produced” out of whole cloth, how is it that nuclear fission works?
I also noticed a footnote in Chapter 12 that states:
That didn’t sound right to me, so I tracked down the quote here. What Heisenberg actually wrote was, in context (my emphasis) :
Firstly Aronowitz omits the word “our” from the quote, changing its meaning substantially from referring very specifically to subatomic phenomena, to experimental data in general. Heisenberg makes it clear that when Planck’s constant is introduced “the experimental data confirm the new theoretical concepts and principles”. It does look to me as if Aronowitz has misquoted and grossly misinterpreted Heisenberg in precisely the way Gross and Levitt claim.
Oops, only “subatomic phenomena” was supposed to be bold.
@ Helianthus:
Heh. Exactly.
PRN’s head honcho has however, an agenda which involves re-writing all scientific fields to fit his hobby horse’s needs so why not change this as well?
Supposedly scientists have got it all wrong:
– the paleo diet included oats ground with a pestle, little meat
– the Mediterranean diet is REALLY vegan
– cats can be vegan ( Oooops! Fix that one)
– if everyone became vegan, it would have a great impact upon AGW’s effects
– veganism prevents/ cures cancer and all other ills
.
I can’t believe I wrote “hung for a sheep”, I meant “hanged”, not “hung”. It isn’t important but it’s one of my bugbears – my neurological functioning isn’t at its best at present.
I’m not 100% sure whether it’s really essentialist or merely unfortunately capable of being understood that way. But that might be an excessively nuanced distinction, in that the latter case would just mean the essentialism was reflexive and unexamined.
I agree that it’s interesting. In fact, IIRC, some of it’s incredibly good. It’s been a while, though.
Based on the parts of the essay from which Sokal/Bricmont chose to pick a statement by her at which to laugh and point that are freely available on line, I would say that they’re doing exactly what they’re accusing her of — ie, throwing rocks at something they know little about and aren’t qualified to understand, out of purely personal hostility and arrogance.
It would not surprise me if the same was true for most of their targets.
But even without reading the whole thing, it’s completely clear that she’s not saying “Mass-energy equivalence is an artifact of the patriarchy! Take back the universe!” She’s talking primarily about how culture informs language, and hence perception.
It’s somewhat subjective. But as I read it, at least, that thing about the speed of light being privileged is not intended to be taken entirely serious. She’s being provocative.
There’s a defense of her work here:
http://www.newstatesman.com/voices/2014/05/jane-clare-jones-luce-irigaray-murder-mother
“entirely seriously“^^
That’s not what he means. I’m running out now, and I don’t want to express it imprecisely. But I’ll give it a (probably inadequate) go:
He’s just saying that the way people perceive/conceive of the world is culturally informed. There is thus an inherent distinction between the world as it is (nature) and knowledge of the world as it is (science).
^^Just as I thought. Inadequate. I’ll give it another try later.
No. He’s claiming that they acquire a subjective dimension when they’re discovered/described. But he’s not saying they’re objectively untrue or non-factual, therefore. He’s just saying that all human endeavor occurs in the context of culture, including human understanding.
Or maybe “human knowledge” — ie, science.
It’s not as hostile as you think it is. He’s on the side of knowledge.
The last quote appears to be a mistake, though. And probably a stupid one on his part. I’d say that overall, Sokal’s thinking is exponentially sloppier however.
Retro Pump @689.
Yes, this thread is still going. It’s not possible for me to learn genetics on this forum or most likely any other method, however, where I was leading in acting for a simpler example of where cofounders make/made all the difference is a question of logic and an educated guess.
It appears that zebra would be happy to learn almost half of the identical twins both have schizophrenia and then have some grad students launch into a research project on why this is so or why isn’t this percentage higher in identical twins. To him this wouldn’t even be known without the existence of his database and the brute force of numbers he is counting on to generate leads to research projects.
The logic question comes into play on where the tipping point is between a streamlined database with less data that can be matched but less time spent on teasing out correlations and more time spent on research projects vs one with enough data so that technology and statistics can be used to narrow down true correlations as much as possible before a research project is begun but where there are more security and ethical issues.
Who knows where that tipping point is but it appears that the PMI is aiming for the more robust database.
where I was leading in asking
Apologizes for my atrocious typos of late. Not exactly sure why that is.
ann,
I understand what you are saying but I’m not at all convinced. Aronowitz may be on the side of knowledge, but he doesn’t seem to think that science is capable of uncovering any. What else does he mean when he says scientific facts are “produced” not “discovered”? I’m pretty sure the planets were obeying Newton’s laws of motion long before he “produced” them. Then he comes out with statements like this:
It does look as if he is claiming that “physics, mathematics, and biology […] are rent” (i.e.torn into pieces), because of Heisenberg’s uncertainty principle. I wasn’t aware that quantum physics had led to the entire framework of understanding of science to be in contention.
He also writes:
So science “produces” the appearance of “natural facts” that are really “nothing more than the objectivization of the table of organization of the social world”. I struggle to find any other way to interpret this than that Aronowitz is claiming that science doesn’t discover real facts about objective reality.
BTW, I had forgotten just how frustrating this kind of writing is. It really seems to me that it deliberately makes its meaning obscure, and to make people feel dumb if they can’t make sense of it. Presumably I can’t be too dumb in this area since I got a decent grade and was encouraged to continue my studies, but who knows?
I think it’s worse than that. He seems to have utterly misunderstood quantum physics and is basing a large chunk of his writing on that misunderstanding.
Are you referring to his hoax, or his writing generally?
Personally I find Sokal’s more usual style of writing, for example this article about his notorious hoax, to be far clearer and more incisive than Aronowitz’s (for example the chapter of ‘Science and Power’ I linked to above), but of course YMMV.
I was following it in the sense of Representing Electrons (book review; PDF) up until the last sentence.
Speaking of fission (PDF),
“If we are to doubt the findings of the empirical sciences, we need to be given better reasons than that they have arisen from and been a necessary adjunct to capitalist social relations. Even if this latter is the case (and I doubt that it is, at least in the global, undifferentiated manner Aronowitz asserts), scientific discoveries could still give correct descriptions of (certain features in) nature. That the nuclear-power industry has attempted to impose on us a grossly undemocratic and capital-intensive form of energy production [If you say so] is no grounds for thinking that controlled fission reactions are just a capitalist plot.”
I’m referring to his thinking, as reflected in both. But that’s kind of awkward, because you agree with him. Although your iteration of it is honest, warm and intelligent, which does make a difference. And not a small one.
I really don’t want to bicker with you, or offend others here who admire and/or agree with Sokal. But fwiw, briefly:
I sincerely do not understand Aronowitz to be disputing or questioning that.
I think that that when he says facts are “produced” not “discovered,” he most probably just means that they’re a form of capital — ie, science is the means of production, facts are the product. If so, it has no implications for their factual-ness, one way or the other.
I would have to read the whole book to be sure, though. That’s just the meaning that seems likeliest to me.
It’s almost impossible to say what that means, absent context. And I’m not sure how much context would help, tbh.
However, I would again read that as simply meaning that objective facts acquire subjective dimensions and connotations when they’re described and formulated by human beings operating within the boundaries of the culture to which they belong.
It would really be such an enormous departure from form for him to be saying anything remotely like “facts don’t exist!” as to border on too bizarre to be credited. I mean, he’s a Marxist activist-intellectual. You can”t really count on his ideas being sensible. But you can at least count on their being oriented to three, wrt basic reality-testing.
Maybe I’ll read the book. But I’m almost sure that his target is power, not science. Because Marxism.
It’s difficult to get through. And I agree it’s frustrating. Hateful, even. But I don’t think it’s deliberate, in his case. I think he’s actually trying for clarity and precision, believe it or not.
It’s clearly stated. But it’s the opposite of incisive. He’s fine through to the “So what?” But after that, it’s unknowing bias all the way.
I realize that he probably doesn’t know what he doesn’t know. Even still, though. He’s making fun of stuff he doesn’t understand, which he’s selectively quoting for that very purpose. He’s going out of his way to do it. And that’s just not admirable, imo. It isn’t and can’t be productive of anything good.
I would personally say that some of his subjects are quite dreadul — even arguably fraudulent — on their own terms. I think Lacan is just awful, for example. But, you know, nobody has to read him if they don’t feel like it.
I frankly agree with Andrew Ross, as quoted by Sokal at that link. Maybe he himself (Sokal) doesn’t realize it, though. I don’t know.
@Narad —
It was nice to see Richard Rorty’s name. I knew him growing up. I don’t think he was a big deal yet at the time, but I might not have known. I was only, like, eight.
I tried to read an essay by him ten years or so ago. But I couldn’t understand one word of it.
Maybe I’m the only person on earth who thinks it. But nevertheless. I do think that he’s not asserting that they’re just a capitalist plot in the sense of “they are nothing but an abstract illusion, invented by capitalism for capitalist purposes.” He means functionally.
ann,
I’m more than happy to agree to disagree about Aronowitz and Sokal. I have no strong feelings either way, and in some ways I agree with Aronowitz more than I do with Sokal. Despite being very funny, I think Sokal’s hoax was a nasty trick for a physicist to play on social scientists who understandably assumed he was sincere. I also think that far more of our experience and our beliefs are culturally constructed than we generally realize, that metaphors (and the reality) of power, privilege and (white, older) male domination visibly and invisibly pervade our culture. I think you can find traces of that hegemony (cringe) in all sorts of cultural artifacts and detritus, including which scientific subjects exist and are studied, what gets published, which scientific findings are easily accepted, which are not etc. etc..
However, I struggle to see the influence of 17th century mercantilism in Newton’s equations, or of early 20th century Europe in Einstein’s. Would those equations be any different if an Arabic, Japanese, Russian or Indian scientist had “produced” them?
I remember during my anthropological studies, when we looked at Freud our professor (a woman who had studied as an Indian Saddhu and chain-smoked bidhis while she lectured) suggested we assess his work as if it were fiction, as literary critics, rather than fact, which I think helped. I wonder if the work of scholars like Aronowitz is better read as a sort of intellectual poetry.
I can follow the passages Narad linked to, though the first gives me nasty flashbacks to the semiotics class* I took, and what I read of the second before wearying baffled me a bit (WTF does “underlabour ” mean?). Do physicists still regard electrons as “theoretical entities”? I struggle to see why writing a biography of the electron is any different to writing a history of the scientific understanding of the electron. I can see some products of science, like the technological process to produce aluminum for example, as products in the Marxist sense, but the concept of an electron (cloud)?
* Perhaps I have a somewhat simplistic view of the signified, the signifier and the signal – is it really enough to base an entire field of study on? I had the very strong sense that the semiotics texts I read were simply trying to confuse me with long words of which I had learned to understand the meaning, but still couldn’t parse into anything meaningful in the sentences they were arranged in. Coming from a natural science background I was used to words and sentences having specific, unequivocal meanings, and found this confusing. I still have the uncomfortable, lingering feeling that there is some meaning in there that I have failed to grasp; I get a similar feeling reading zebra’s utterances at times. I can’t help wondering if some social scientists (and some commenters here) look at the sometimes impenetrable language of the natural sciences and construct a sort of cargo-cultesque simulation.
I think Lacan is just awful, for example.
I feel that I should be defending Lacan here, out of sheer contrarian perversity, because everyone hates him, but I can’t.
@Krebiozen —
You’re not only very smart and very gracious, but a better writer than Sokal, Aronowitz and myself at their best combined. There’s very little in your last post that I disagree with, although I diverge from most of it somewhat, just as a function of having my thoughts and not yours, if you know what I mean.
So although it’s very minor, the only thing I’d humbly ask you to reconsider is this:
Per Gross and Levitt, what Aronowitz actually said about Newton was that he “cannot be understood apart from an analysis of seventeenth-century mercantilism.”
There is nothing PoMo about Stanley Aronowitz’s work. He’s a Marxist theorist. Marxist analysis is socioeconomic. That he said that Newton could not be understood apart from an analysis of seventeenth-century mercantilism therefore almost couldn’t be more Marxist.
It has nothing to do with the influence of mercantilism on Newton’s equations, and suggests no such relationship. It’s just straight-up historical materialism.
And that’s as good an example as any of what I dislike about both Sokal and Sokal’s popularity in the skeptical community. He has a bias. It caused him to misconstrue the evidence he was examining. He created a myth based on his misconstruction. And as people are wont to do when myth-making, he invested it with emotional properties that he and others who see the world more or less as he does are bound to find both compelling and gratifying.
So naturally, they subscribe to it. And that’s really what I care about. Because it’s a myth based on personal bias, and that’s never helpful.
That leaves me in kind of an odd position, in that I end up defending a kind of work that I myself have no real affinity for and frequently dislike, in many regards.
But what can you do? If the worst consequence of it is that you now read Aronowitz in a state of Marxist-theory blindness that leaves you unable to imagine what he means by “produce” if it’s not what Sokal et al. think it is, I suppose that’s not so bad.
But fwiw, seriously. I’m 99% sure that he means “produce” in the Marxist sense of the word. Because he’s a Marxist.
The fancy, excessively complicated French theorists are up to something else entirely. And while (funnily enough), I personally think Freud can best be read from a quasi-Marxist perspective, I agree with you generally that that sort of thing works better in art. Ceci n’est pas une pipe. Pale Fire. Etc.
Everybody should therefore have artistic talent bordering on genius. Problem solved!
ann,
I’m gobsmacked at that – you are too kind! If you are correct in your interpretation of Aronowitz then I agree with you – of course Newton wouldn’t have been in a position to study science at all absent his social, economic and historical context – but I will still grumble that Aronowitz could have made himself a bit (or a lot) clearer.
Incidentally, Newton was not the ‘gentleman scholar’ of independent means I always assumed, He was a farmer’s son who worked as a subsizar (a sort of servant) at Trinity College to fund his studies before getting a scholarship.
Oh, what the hell. I really do object to it. So. Again. Simply put:
That Sokal doesn’t (and evidently can’t) distinguish Marxist theory from deconstructionism makes him guilty of exactly what he’s accusing his targets of doing — ie, swaggering into an unfamiliar field and saying “Oh, pish-tosh, what errant nonsense,” when, in fact, he has no idea what he’s talking about and doesn’t understand the material at even an elementary undergraduate level.
To make matters worse, as far as I can see, most of the time his targets actually aren’t doing what he accuses them of.
Therefore, the difference between Sokal on the academic left and Stanley Aronowitz on Heisenberg is that Heisenberg is not Aronowitz’s primary focus or — properly speaking — his subject. So his work doesn’t rise or fall on the error.
Kreb says:
“- is it really enough to base an entire field of study on?”
No.
Hilariously, I had to translate stuff like that as a degree requirement. And I was hoping for Piaget- silly me
At any rate, wouldn’t it just be easier to say that our thoughts/ words don’t correspond 1:1:1 to “reality” ( whatever that is) and we should just be aware of it and call it a day?
That to which we attend acquires increased significance to US but maybe not others. Cultures do that as well.
I am reminded of an old Confucian saying which states it much more eloquently which I suspect catches the drift but I never could get the words straight.
I’m not being entirely serious.
Most academics are not particularly gifted writers, sadly. I was really being way too snippy about Sokal in that regard before. He writes quite well. The problem is really that he’s not a gifted reader.
I’m inclined to believe that his intentions were more innocent than his actions. And I suppose it’s possible that he targeted the political left because it was there.
But I can’t really say much else about him that’s good. There were (and still are) plenty of people both within the academy and elsewhere who’d like to see cultural studies go away because they don’t like having their campuses sullied by what I once heard somebody characterize as “professors of hip hop.” Which meant “black people,” in context.
So, you know. He’s entitled to his opinion, that goes without saying. But where there are real consequences, there are also real responsibilities. Intellectuals aren’t exempt from that. At the very least, he could have been more diligent.
I actually very recently came to realize that there was more to semiotics than I’d been condescendingly thinking, lo these thirty-plus years. But I think the reason I underrated it was that completely idiotic and unnecessary semiotic analysis was so vogueish when I was in school.
So I think I agree with you.
Exactly.
Additionally, I am somewhat confused as to why many people seem to be offended by the notion that, say, Einstein’s equations are the product of early 20th century culture. It’s something that seems to me almost trivially true; Einstein was a product of early 20th century culture, for one thing. A real-life Mowgli would hardly be a practicing physicist, I think, what with the difficulty in acquiring language after the critical period.
It doesn’t make Einstein any less brilliant or his equations any less correct. I can’t really see how describing something accurately is an “attack” on it.
I mean, we are all communicating with each other by means of the Roman alphabet, which is a product of culture. We are products of culture. Almost everything we use, interact with, eat, etc., on a day-to-day basis is a product of human culture.
Like I said: the plain fact of it is almost trivially true. The specifics, I think, could be a worthy and interesting thing to study, if somebody were so inclined.
@ ann:
Believe it or not, I have an undergrad degree in a *liberal art*, although it also includes a great deal of life science/ social science, it was loaded with lit/ writing, visual arts and philosophy.
While I was later pursuing degrees in social science, one prof encouraged me to write about the psychology of visual arts which I did in order to fulfill independent study/ seminar requirement and up my street cred.
Thus I read semiotics and Gestalt works about art – graphic representations of emotions, some aesthetic styles and personality etc etc. At least HE liked it.
I do maintain a fond place in my heart for ‘culture and cognition’ but it is far more mundane than what is usually considered- purely that we pick and choose what we include in our own construction of the world- which exists quite independently despite our efforts.
I know that Eskimaux/ Northern Aboriginal People? have many words for snow but I don’t think that that necessarily changes what they actually SEE in a physical sense but they do attend to snow more and spend more time thinking about snow in all of its variability.
OBVIOUSLY there’s a lot more about Pomo ** which I have dis-remembered with great effort.
-btw- you can selectively forget but it ain’t easy.
** but not the tribal folk who make baskets
Eskimo or Inuit, mostly. It depends on which people you’re talking about.
But anyway: are you sure about that? What does it mean to see something? We are not camcorders, after all. Vision is something that happens in the brain, although the eyes are of course a necessary component.
Russian, for instance, has two words for what we would call in English “blue”: sinii and goluboi. The first one refers to a darker blue, and the second one to a lighter blue, but they are two different colors to a Russian speaker, the same as red and pink are to us. As it turns out, Russian speakers actually can distinguish shades of blue more quickly and accurately than English speakers can. Certainly the physical properties of whatever colored thing they are looking at are real physical properties “out there,”* but are Russian speakers and English speakers really seeing the same thing?
There are languages which use cardinal directions (PDF) rather than relational directions when describing where something is, and when thinking about where something is. I imagine speakers of those languages see things rather differently than I do.
*I had best not get started on this.
JP,
I don’t think that’s the notion people are offended by, it’s the notion that Einstein’s equations bear no relation to any objective reality. Whether that notion exists other than as a misunderstanding of some dense Marxist or pomo texts I am still unsure. I shan’t lose any sleep over it 🙂
Sapir-Whorff hypothesis?
Or even Sapir-Whorf hypothesis.
More or less, yeah. I mean, I would say that languages differ primarily in what they force people to attend to, like the gender of people doing verbs in Slavic languages, cardinal directions in certain aboriginal languages etc., rather than what they can express. But it does seem to me that language sort of inescapably shapes our cognition, perception, etc., at least to an extent. And of course our communication.
@ JP:
Sure. The language might lead a person to differentiate more; similarly an English-speaking artist might be more attuned to differences although there are not two words I English ( he/ she uses *qualifiers*- lighter/ darker- more, as well as other dimensions).
Still, the proximal stimulus is a particular tone of blue – some may attend to its particular-ness more or less. Similarly, skiers see different snow/ ice conditions. It’s what is attended to that determines the situation and labels, not just what is seen physically.
We use the word “see” to stand for different levels –
what’s on the retina, what we perceive it to be, then, as an opinion ( how we imagine/ surmise it)- ” I see that he’s on to his usual routine again”.**
Then again, there’s See Noevo.
** I shouldn’t get into this either.
JP:
Ha! We crossed paths in cyber space.
Way to go!
And I must GO as I am expected elsewhere and need to do something about my hair.
“That the nuclear-power industry has attempted to impose on us a grossly undemocratic and capital-intensive form of energy production…”
Hm? How’s that again? How many non capital-intensive forms of energy production can support modern society’s 24/7 electricity needs?
I thought the snow trope – which involves Whorf starting the game of Telephone from Boas – had been laid to rest some time ago (certainly when I was in grad school).
This is more HDB’s area, but most visual processing actually occurs in the retina.
^ Oh, it also turns out the W—dia mention of the Himba under “Color Vision” is, y’know, plain dumb.
I’m not the one who brought it up, and I thought about mentioning that it is more of a cliche than anything, but I was mainly responding to what seemed like a question of what is the “correct” thing to call speakers of Eskimo languages, which can be answered differently depending on where you are. “Eskimo” is an umbrella term including Inuit and Yupik peoples, some people find it offensive, it’s not used in Canada, but it is used in Alaska. There are also Aleuts, who speak a language which is part of the Eskimo language family, but are not considered to be culturally Eskimo.
Anyway. The “Russian blue” phenomenon which I did bring up is real.
“In fact, the word ‘deconstruction’ appears only once in my article, in the wry (wasn’t that clear?) confession that ‘I’m an unabashed Old Leftist who never quite understood how deconstruction was supposed to help the working class.'”
^ “My article” being the afterword, to which Aronowitz was responding.
^^ So, yah, I get the point now.
Indeed.
Huh. I am still under the impression, though, that vision is constructed, not physiologically direct; we don’t notice our blind spot, for instance.
but most visual processing actually occurs in the retina.
I don’t know if anyone has *quantified* the information-processing contributions of retina vs. lateral geniculate nucleus vs. visual cortex, there is *so much* of the brain given over to visual cortex, I suspect it’s doing most of the work.
I am still under the impression, though, that vision is constructed, not physiologically direct
That way lies the ‘homunculus’ fallacy, with a little JP inside your head, looking at the retinal image projected on a screen.
How so?
I thought most processing occurred in the brain. Or is that only the interpretation? Or did I totally miss the point?
http://www.theguardian.com/education/2012/nov/12/improbable-research-seeing-upside-down
Does that mean I don’t have to point out that he’s being disingenuous and evasive with that “In fact, the word “deconstruction” only appears once” routine?
That’s not a rhetorical question. I’m really not sure what you’re saying.
Bear in mind that the people I got mixed up with long ago would have assigned facial recognition to a Yale T predicate and hoped for the best.*
I did at least casually follow things from the LGN to V1, but in retrospect, I was relying on a subterranean, imaginary perceived visual realm in which nothing made sense. In retrospect, this still presumes object recognition.
* I wouldn’t say that the infiltration of Common Lisp was the beginning of the end, but nobody much seemed to use the Lisp Machine once it was procured.
I was at an intermediate point in reminding myself of the order of things and thought I had figured out “Sokal doesn’t (and evidently can’t) distinguish Marxist theory from deconstructionism” referred to Aronowitz’s statement that “Social Text was founded, and remains within, the Marxist project.”
My “thinking out loud” enshrined in that final comment was an ill-formed mile marker.
That way lies the ‘homunculus’ fallacy, with a little JP inside your head, looking at the retinal image projected on a screen.
How so?
For me at least, it is an insidious mental model, easy to fall into, best avoided by not thinking too much about the end results of visual processing. Perhaps it is a cultural construct.
http://www.theguardian.com/education/2012/nov/12/improbable-research-seeing-upside-down
In the middle of the 20th century, an Austrian professor turned a man’s eyesight exactly upside-down. After a short time, the man took this completely in his stride.
Marc Abrahams made a real dogs breakfast of that bit of Gosh-Wow fluff. Kohler’s study of mental plasticity and inverted vision was an attempt to *replicate* an original claim from Stratton, in 1897. And his collaborators did not describe a correction for the effect of the prism; they learned to adapt for them… but the world still looked upside down (or ambiguous).
There’s a been a series of inverted-vision attempts to replicate Stratton’s claim (because prism glasses are easy and fun), and this is the consistent result… the world stays looking upside-down.
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.294.9093&rep=rep1&type=pdf
Glad to see the genome question is settled and we are back to the fun philosophy stuff.
It should be noted that if you look at the development of physics over the centuries, there’s an awful lot of just the kinds of insulting back-and-forth disagreement that takes place on the internet, albeit written out in fine cursive on fine parchment, I suppose. This between the revered “giants” that preceded Newton, as well as those who followed.
But understanding that history, one has to recognize that talking about “objective reality” is a dangerous business. You know, we built that LHC partially with the hope that it would “break” physics, so there would be something for really clever physics grads to do besides creating financial disasters. Are we so sure that this might not have led to a different model of “reality” from the one we have now, had it happened? Are we quite sure that the dark matter/dark energy path might not lead us to a new construction of cosmology?
With respect to Ann’s interpretations, I would agree almost entirely, and I would just point out that social/economic structures are very much intertwined with the extant technology, and that technology informs physics. The “giants” who did the math were beholden, much as it irked them, to the “engineers” of their time, for the problems they had to solve.
So, was it the socio-economic structure that brought Einstein to his creation, or trains and clocks and telegraphs? Correlation, causality, complex symptoms/systems oh my. Perhaps that’s what some of these writers are missing.
# 739, 740
Indeed, I can confirm Italians use 3 different words for various hues of what in English is called “blue”.
Examples from football (soccer) jackets, which you could find on some video files:
Società Sportiva Lazio: “biancocelesti” (whiteblues)
Italian national team: “azzurri” (blues)
Bologna Football Club: “rossoblù” (redblues)
Aha.
That was a reasonable inference, but incorrect. I hadn’t seen that statement until you linked to it.***
I was speaking from personal observation, having…well, observed that Aronowitz was a Marxist in the course of encountering his work here and there (mostly in the popular press) over the years.
Same for Andrew Ross.
I think I’ve said this here in comments before. But one of the reasons I always thought Sokal was a troll was that I had some glancing familiarity with the work of both Ross and Aronowitz, which, though not extensive, was plenty enough to make it clear that he was definitely misrepresenting them.
I can no longer recall precisely why, but at the time, it seemed to me that Sokal’s principle target was actually Ross, not Aronowitz. NYU had just hired him to be the director of a big, new graduate program, and he was kind of a rock star — young, good-looking, sexy, sought after, and (in short) exceptionally glamorous for an academic.
Additionally, although some of his work was on conventionally weighty subjects — labor, class, etc. — he was unlike Aronowitz in that he also wrote about the kind of low pop-culture subjects that people love to hate. And not at all badly, I might add. Which is unusual.
In any event. At the time, it seemed to me that he was gunning for Ross because he was a player-hater, plain and simple.
Irrespective of which, what I said before still stands.
As far as I can tell, there’s no evidence whatsoever that the phenomenon he was purportedly exposing with his hoax even existed prior to it. Or ever has apart from it.
It therefore appears to me that he intentionally harmed a number of his colleagues for no good reason at all, simply in order to aggrandize himself beyond his real deserts.
And he not only got it completely wrong, he also refused to admit it, and — in fact — has been doubling down on the error out of sheer arrogance, plus either ignorance or something worse ever since.
*** It actually caused me to revise my opinion of Sokal, to his detriment.
That would be a serious hardship for me. Especially in museums.
If “it” is “the homunculus fallacy,” it definitely is. And I know that because one encountered it frequently in the movies and film strips they used to show middle-schoolers in health class, back in the day.
Or I did, at least. It might not have been specific to vision. But we definitely saw (IIRC) movies featuring a little man at a control board in the brain, turning stuff on and off.
Hormones, probably. Now that I come to think of it. But I would maintain that it still counts as evidence of cultural construction.
Hey! That reminds me of an excellent example of science repeatedly overlooking established facts out of cultural bias that’s been going on for centuries and persists even to the present day:
(Link).
In another paper, the same author gives a detailed account of the recurrent disappearance of the clitoris from medical texts each and every time anyone (re)discovered it over the centuries. But I can’t find a free online full-text version, atm.
I’m reasonably sure it’s still nowhere to be found in the diagrams and other materials used for most present-day health classes all across America. However.
That’s actually the same kind of thing that Luce Irigaray was trying to point out about language, more or less.
Summary from Psychology Today, two years ago:
That’s some pretty culturally determined science, you do have to admit.
Yeah, I was sort of confused by the idea that it must be a natural way of thinking of things that is easy to fall into. I looked it up on the Gazoogle, and saw one of those pictures of a little person inside a person’s head, looking out. Come to think of it, I may have seen a similar representation somewhere once or twice, but I certainly didn’t encounter it enough for it to stick; it’s honestly not something that occurred to me at, in terms of ways one might think about the mind or vision or what have you.
I definitely don’t think about (or experience) vision that way either.
My thoughts sometimes first occur as images or patterns in my mind’s eye rather than words, especially if I’m thinking about something complex. And that does feel more like I’m watching something happen than like I’m doing something, I guess.
I’m assuming that’s not super-duper unusual. So if it comes from within, maybe that’s where it comes from.
754 ann,
How do you know that they are thoughts?
I think in images sometimes if I am working on visual art, or thinking about working on visual art. I think in words if I’m sitting down to write something or if I’m having a conversation. Otherwise, I don’t really know how to describe my “thoughts” – and, actually, a lot of the time, if I’m not deliberately thinking about something, I am just perceiving things and not really thinking at all. I gather that this is in fact unusual, or that people who do not experience life this way can’t imagine it, because I have had people react in an incredulous way if I say it.
I actually find it very hard to imagine going through life with a constant monologue-type thing your head, which some people evidently experience.
This might have something to do with meditation practice, but it is also just sort of generally how things have always been for me, I think.
Incidentally, I think this is why I have never really found cognitive behavioral therapy to be particularly helpful. When I am really depressed or distressed or whatever, it is not because of negative thinking; it’s because I feel a certain way, often in an overwhelming way, and it seems to just be a background thing that’s there for no reason in particular. (Well, I’m sure there are reasons, but it isn’t typically triggered by thoughts.)
One of the times when my mind does get into a wheel of verbal-type thought is when I’m particularly anxious, though. But even in that case, it feels like the feeling of anxiety is there first, and then my mind goes crazy ruminating about all sorts of things and I guess looking for things to pin it on.
More things in heaven and earth…
http://www.bbc.com/news/health-34039054
@JP —
Word to all of that, especially this:
I too find it incredible that other people have some other kind of thought.
But that’s not what I meant. What I meant was:
@zebra:
It happens when I’m trying to solve a problem or figure something out from a starting point of little information, if that makes sense. I see images and/or patterns that represent the possibilities, then they either (a) dissolve, which = “I don’t know” (usual); or (b) cohere, which = “Wait! I know, I know!” (infrequent, but quite thrilling).
That’s when I’m most aware of it, anyway. It’s not something I do on purpose. It just happens sometimes. I think it maybe used to happen more when I was a child. But maybe I was just more frequently in situations about which I had little information.
@#757 —
Cool! Neither of those is me. But I do have ordinal linguistic personification synesthesia. And that’s kind of similar to the non-verbal thought, in that I see/perceive/recognize the personal qualities of (let’s say) 5 x 5 = 25*** rather than think them. Because I just do.
***Red, yellow, boisterous, noisy, a clattering sound, a happy little boy running downstairs, autumn, balloons.
Two is yellow, five is red, both are male. Etc.
@ann:
That’s interesting. I have a slightly similar thing, where I have a kind of feeling of a 3-D map in my mind (sounds weird, it’s hard to explain) and sometimes things “click” into place. I don’t “see” an image, though.
I think this is the first time I have actually sat down and tried to explain it before; usually it has just come up in the context of people asking me, “What are you thinking?” and me responding “nothing.” They usually interpret it as me being evasive or stoic or something, I think, but a few times they have interrogated further. Once was when I was seeing a therapist who asked me what I was thinking, like right at that moment, and I said “nothing really,” and he didn’t believe me – I think his words were “Come on, you’re not just having some kind of Zen moment,” and I tried to explain that no, I was aware of sitting in a chair and a room and looking at him and all, but I wasn’t thinking anything.
Man, other people are weird.
Ann 758,
I asked about the term “thoughts” because I have a similar phenomenon when encountering more complex math– an unconscious conversion to some kind of “mapping” that involves shapes arranged in a plane, with variations in hue and saturation.
But I can’t know whether the image contains actual information, or is just a “message” that my unconscious or mathematical intuition or whatever we call it has arrived at a conclusion about “where the answer lies”. (And it does only happen when I get that right.)
Perhaps it isn’t surprising that abstract inputs give abstract outputs; if the problem is verbal or more concrete, I often spontaneously see schematized versions on that screen behind the eyes. Still, there are no “steps” or consciousness about what I am seeing or how I am solving it.
More things in heaven and earth…
people asking me, “What are you thinking?”
Thoughts *happen* but I’m not sure that I can claim credit for thinking them.
@ JP and ann:
Believe it or not, people study stuff like that.
I interviewed people about their experiences with verbal thought vs imagery which was preliminary for something else.
Offhand, I’m trying to think about what would be interesting to look up. I always enjoy reading about how people use imagery or facility in language/ bilingualism to aid memory. Ability for mental rotation of images. Also the therapeutic implications for imagery/ language in meditation ( JP hints a little about this). Self regulation through inner speech. Day dreaming. The book, Memory Observed, may have something. Vygotsky?
@#761 —
That’s not dissimilar to what I’m talking about, actually. I see it like an equation, almost. And it is one, more or less. Logic is math, and it’s basically verbal logic without the words.
Maybe it’s just a mild form of the same phenomenon that enables people with savant syndrome to make complex calculations instantly. I believe that’s also said to be about “seeing” the answer. And it definitely does happen instantly — ie, before I’ve really formulated the question I’m trying to answer, on a conscious level.
It’s really never seemed like all that big of a deal to me. I mean, maybe it’s not universal. But I’m sure it can’t be exceptionally uncommon.
However, I didn’t realize I had synesthesia until well into adulthood because it simply never crossed my mind that everybody didn’t perceive that 16 was green and white/female. (I mean, that’s just who 16 is. Are they blind?)
So what do I know.
ann,
I was just reading about that (‘Dueling Neursosurgeons’, Kean); you might find it interesting too:
On the Sapir-Whorf perception thing, some years ago I read of an experiment that involved discharging an electroscope, but historically scientists reported seeing what they expected to see, i.e. what the prevailing theory said should happen, rather than what ‘really’ happens (either the foil arms of the electroscope fell instantly or slowly, I forget which). It would be an interesting example of belief affecting scientific practice, but sadly I have been unable to locate it since.
I may experience a minor, limited form of synaesthesia in that I “see” ( in my mind’s eye) certain musical passages as moving patterns of light that relate qualitatively to the music ( e.g. parts of Glass’ work “look” like spinning wheels of light/ sustained notes may “look” like a beam of light)
Go figure.
764 ann,
“And it definitely does happen instantly — ie, before I’ve really formulated the question I’m trying to answer, on a conscious level.”
Putting aside the matter of visual effects, “creative insight” or “the shower effect” or “intuition” is very likely the moment when you figure out, consciously or unconsciously, what the question is.
As to the prevalence of the actual visualization part, I don’t know, but actual problem solving as opposed to following algorithms or pattern recognition has been rare in my experience with students. It needs to be developed, rather than stifled, which is what happens with most of the population.
Yes. I discovered that there are some grapheme-color synesthetes in mine. I have that with numbers, though not letters.
But it’s really the personification that’s the most prominent — ie, if six was orange, that would be wrong and I wouldn’t like it, but it would still have six-ness. If it was male, however, it just wouldn’t be six. It would be some interloper using six’s form and name. And I would be hostile to it.
Happily, that circumstance doesn’t really arise.
@Denice —
There’s an instance of something like that in the lyrics to “Lola,” by the Kinks. (“I asked her her name and in a dark brown voice she said ‘Lola’.”)
That’s always just seemed very non-figurative to me. Unlike “silver bells,” for example.
I don’t think so. When it fails, it’s just a non-thing. When it works, it’s more like the answer to a question that wasn’t asked. So an insight, I suppose.
Wait. Scratch that, I misunderstood you.
Yes, I agree.
@ ann:
It makes me wonder if people with this ability express it somehow- I might imagine business/ finance as a series of pathways or “see” social interactions as a matrix- all in motion of course. I use visual metaphors often..
My thinking is a complex mixture of rapidly moving images, numbers, letters and dialog, but I can only see it dimly and fleetingly, though I can readily retrieve information from it, if that makes sense. I can put together a complex plan of action in detail, such as a complex computer program, or a work project, but may have trouble putting it in writing as it tends to be moving and in three dimensions. I have tried many different mind-mapping methods, but none seem to suit my style of thinking.
As for synesthesia, here’s the passage preceding the one I posted earlier, which may also be of interest:
Hmm. I can’t say as I’ve ever done much meditation which involved imagery or language. I guess I tried a few Tibetan-type meditation practices a long time ago, but they didn’t really catch me; it felt like more of a mental exercise than like, well, zazen. (The style of meditation I practice is called zazen or shikantaza in Japanese; I’m not sure what it is called in Korean, although by all rights I suppose I should know.) But it in any case, it is just sitting. That’s it. You’re aware of the breath, any passing thoughts, any emotions, etc., but you’re not fixating on them. Or at least that’s the idea. I’ve read somebody else who reported that after a couple decades of zazen (I’ve been at it since I was 15, with some hiatuses? hiati?), he started going through long periods in day-to-day life where no specific thoughts were really coming up. So the idea isn’t to try to stop thoughts on purpose – I can only suppose that would be some sort of psychological repression – but just to kind of let them subside on their own.
And of course I have random thoughts that come up and now and then, but even when I’m thinking, it’s almost never an “internal monologue.” I always thought that was just a voice-over device used in movies and TV, until I found out that a lot of people actually experience it, and even define it as consciousness or something. But anyway, say if I think about having a cup of coffee or something, I don’t think “Gee, I’m kind of tired, and a cup of coffee sounds nice.” I notice that I’m tired, and then maybe I imagine holding a cup of coffee and drinking it, and then I head to the kitchen.
As far as imagery goes, I can imagine things quite vividly, and I tend to recall what things look like with a high degree of accuracy, what color things are, etc. But when I imagine a thing, I don’t actually see it. When I close my eyes, all I see is black. So other people actually see things, like literally, when they imagine them?
^ Heh; tangentially how I tend to remember what things look like quite well, I also get tend to really absorbed in looking at things. The first or second time I saw the psychiatrist I’m seeing, he asked me what I like to do for fun, and I think one of the main things I said was “walk around and look at things.” Which probably sounds pretty weird, I suppose.
@ JP:
I meant the therapeutic use of meditation-like states which focus upon an image or words/ sounds in order to divert attention away from disturbing thoughts/ images that arise spontaneously or excessive worry. Paying attention to breathing or observing the external world is another method.
Right. People can use inner speech as well as imagery as rehearsal or planning as well as for repetition of past events. They also vary in how much they use imagery and how clear those images are..I haven’t really kept up with this research.
Personally I can sometimes evoke very clear images of what’ve I’ve already seen – it’s almost like ‘seeing’ but not exactly. “Mind’s eye’ is a good descriptive, I have excellent memory for maps and diagrammed material which means that I often function as navigator or instructor. People loved me in anatomy and physio classes. It’s easy for me to reproduce what I learn this way altho’ the maps may not really be in perfect proportion, the relationships between items are usually correct. Frequently I recall disturbing images better than I would choose .I can also plan things like creating an image with drawing materials or camera.
I discovered when studying that sometimes I would recall where a particular phrase or passage was located upon the page ( top/ bottom, left’right) even though I never intended to recall that.
Cham-seon, I guess, but it’s not really the same, as Korean meditation practice is koan-oriented – observing “the critical phrase,” not breathing. Sitting meditation also tends to be focused around seasonal retreats, rather than being a core practice (full-time meditation monks are a distinct minority).
Fourth declension; the nominative plural would also be “hiatus,” but with a long ‘u’.
Hmm. That explains all that stuff Haju was saying about thinking “Who am I,” etc. I remember the first time I went for an “interview” with her, she asked me to “practice out loud,” and I just sort of boggled and said I had no idea what that meant. It took a while to explain what I “do” in meditation.
In any case, though, although Ann Arbor ZBT is a Korean temple (sort of, I mean it’s a bit ecumenical and Americanized, you can look them up), they still definitely do at least morning and evening sitting meditation. And lots of bowing. Seriously, 108 full bows is kind of a b*tch on the knees. (One reason that I haven’t gone to early morning meditation there in a while…)
Japanese Zen also has retreats, actually – sesshin – but again, the meditate quite a bit every day as well. I’m really only familiar with the Soto school in practice, but I understand that the Rinzai school practices zazen as well, and after the student “finishes” koan study, they “move on” to shikantaza.
But anyway, yeah, it’s kind of funny that I think I have actually been associated with A2 ZBT probably for the longest chunk of time of any temple, but I still come at things in a very Soto way. I suppose that my introduction to Zen as a teenager was also in the Soto vein, through a book or two.
Ah.
Again, not to me.
Hmm. You know how you’re sometimes unaware of how much time has passed when you’re very absorbed in something?
Would you say that’s characteristic of you?
@Ann:
Yep, for sure.
My thinking is a complex mixture of rapidly moving images, numbers, letters and dialog, but I can only see it dimly and fleetingly
“My mind is a raging torrent, flooded with rivulets of thought cascading into a waterfall of creative alternatives.”
Yah, the Providence Zen Center, which is Kwan Um Central and thus nominally Chogye, seems to do the same sort of thing. A quick glance at this, which I have to hand, suggests nothing of the sort in the monastic environment, though.
Morning service (which the meditation monks skip) is three prostrations, a standard chant, brief prayer, recitation of the Heart Sutra, a bit of bowing, and off to the day. Then again, these Zen centers are largely nonvocational, so perhaps something has to substitute for more realistic temple rules.
One difference in Korean koan (hwadu) practice is that a student typically gets just one – it’s subitism, after all – so this can still be focused on outside of sitting-walking* meditation.
* These are paired; I don’t really know much of anything about Japanese-style practice.
^ “these Zen centers” meaning the U.S. ones.
There are different accounts of the precise inspiration for the lyrics, but I’m inclined to take this line as indicating that Lola’s black.
Wrt that pesky security issue. Received a letter in the mail today about this http://www.modernhealthcare.com/article/20150909/NEWS/150909880
It sucks.
Sitting and walking meditation are paired in Japanese-style practice, too. Typically you’ll have a 25-40 minute sitting period (depends on the temple), then 10 minuted of walking meditation (kinhin), then another zazen period, and so on. I think the typical Sunday morning routine at DRZC in Portland was 40 minutes sitting, 10 minutes walking, 40 minutes sitting, 15 minute chanting/bowing thing, coffee or whatever, then a Dharma talk. Similar thing at Olympia Zen Center, except it was much less well-attended, possible because it actually happened at 7:30 or so on Saturday morning. It was nice though; we would typically eat breakfast after sitting and then “study” after breakfast, which could get silly.
The Sunday service at AAZBT is like 20 minutes of sitting, I think, then Yebul and a little more sitting and a Dharma talk. Wimpy, I say, but I can always go for the more substantial Wednesday evenings and so on.
The Japanese monastic environment is kind of its own thing; mainly young monks go there for a period of time, then go back and run their dad’s temple or whatever. One hears from the Japanese teachers who came to America that they left in large part because there wasn’t much serious zazen practice going on in Japan, and they were sick of the bureaucracy and whatnot, the Soto-shu had just become a funeral guild, etc. Which I suppose explains the emphasis on sitting in American Japanese-style Zen.
There’s an interesting thing going on in American Zen wrt monks/priests, too, and how exactly people make it work in an American context. But I could go on for a long time in this vein.
^ Oh: in Soto Zen, at least (I dunno about Rinzai), one is also expected/encouraged to keep practicing outside of “formal” sitting and walking meditation practice.
Such as?
What does it look like when presented with the question what it could possibly mean to raise e to an imaginary power, as in Euler’s identity?
Anyway, more in the direction these comments have gone, I’ll mention – quite separately from internal dialogue, etc. – that I know there’s an opportunity to defeat an item of MDD anxiety when the somatic element rises from my solar plexus to my throat.
Whereas I’m just disappointed that nobody commented on my example of culturally determined science.
It is kind of a conversation stopper, I guess.
But seriously. Anatomy texts.
One would hope.
@ann:
I’m actually just sort of gobsmacked that there are anatomy textbooks that DON’T include the clitoris. And I totally agree that the oversight must be… culturally constructed.
Plural = ‘clitorides’. Before anyone asks.
@JP —
I know, it’s shocking. And yet, there are not. (Well. They include part of it.)
I gather that before Helen O’Connell MD began to agitate about it in 1998, it was even worse.
I mean, regular folk can figure out what they need to know without an illustration. But I would want a surgeon (for example) to be educated to know what the what was. For mercy’s sake.
@ ann re @791:
Oh I meant to say something along the lines that perhaps that explains why it is often overlooked in …er.. OTHER contexts.
BUT I am glad that you mentioned it.
-btw- way back in the mists of time, wasn’t there a feminist movement that .um.. focused its attention on it?
Not that I recall.
I mean, there was Our Bodies, etc. And Shere Hite, if she counts.
I’m a little too young for that stuff, though.
Only by jerks and totally clueless lovers at this point, I think? I mean, I remember being like 15 or 16, shortly before I moved away for school, riding around in a car with some friends (I slipped a lot of things past my mom, plus I think she gave up and stopped caring at some point) and talking about sex and my buddy Dylan remarking that “there’s always time to go for the clit.”
But anyway, I digress.
@ Narad
My interpretation was always that her voice was low and perhaps had a rough edge.
@ JP and ann:
OBVIOUSLY you missed my sarcasm signal.
@ Renate:
I read that as she was a guy trying to sound like a woman somewhat unsuccessfully.
It was in ” old Soho” so most likely white but could be black.
@ Denice, etc
Not sure about a real feminist movement, but in a strawman one in a movie or something… Although I’m not daring to search this on the internets.
It was at lest tangentially mentioned as one of the three things men were always missing (the other two being the toilet’s seat and birthdays).
Since I read it, I’m pleased to report I have become much better with one out of the three. Still have to work on the birthdays.
@Narad, Renate, re: “Lola”:
I’ve always taken it to mean that she had a husky or deep voice, prefiguring the “talk like a man” line two verses later.
re: malia @79
Well, I went out to see my sister, and we sat around and spit into a test tube. There were a few interesting things to come out, but mostly what we already suspected.
The big thing that I was looking for happened just as I expected – neither of us have any sign of Native American DNA, family stories to the contrary. 99.3% European for me, 99.6% for her. I know this doesn’t prove there is no Native American in my family tree, but if there is any, it’s way back, just as I expected.
One disappointing result is that I’m only 2.8% Neanderthal, and my sister clocked in at 3.1%. I was hoping to come in with a higher score than that, or at least higher than her. I understand that the 2.8% is about average for European stock.
The most unexpected result is that I’m descended from an Irish king (well, we share a Y, anyway). I am Haplogroup R1b1b2a1a2f2, very common in Ireland (and not uncommon on the west coast of Britain).
I guess that’s why I like a Guinness every now and then.