As predicted, Monday’s post about how the “lab leak” hypothesis for the origin of SARS-CoV-2, the coronavirus responsible for COVID-19, is becoming a conspiracy theory attracted trolls, although it did not go viral. This latter happening is probably fortunate for me. Given the volume of comments that this post got from just 50% or so more traffic than a typical post was more than enough for me to deal with. (Also, because I don’t have advertising, any increase in traffic that boosts my server costs comes straight out of my own pocket.) Be that as it may, given the protean nature of conspiracy theories and their unrelenting nature, it should surprise no one that, on the very same day I published my post on the “lab leak” hypothesis, elsewhere a new wrinkle to the conspiracy theory hit the press in the Wall Street Journal and the Daily Mail. (How appropriate.) The WSJ published an op-ed by Steven Quay and Richard Muller entitled The Science Suggests a Wuhan Lab Leak, while a headline blared from The Daily Mail, all touting how, supposedly, the presence of a “double CGG” sequence (CGGCGG) in the nucleotide sequence of SARS-CoV-2 was supposedly incontrovertible evidence that this coronavirus could not have arisen naturally and had to have been “engineered” in a laboratory (in Wuhan, wink, wink, nudge, nudge):
It wasn’t long before all the other usual suspects started amplifying this story, including stories with headlines like ‘Damning’ science shows COVID-19 likely engineered in lab: experts (from Fox News and the New York Post) and An unlikely genome sequence is evidence that COVID-19 leaked from a lab, two U.S. experts say (the National Post).
You get the idea.
So what is it about this “double CGG” sequence, basically a sequence of nucleotides, specifically CGGCGG, in the genome of SARS-CoV-2 that, if you believe Quay and Muller, is such compelling, slam-dunk evidence that this particular coronavirus could not possibly have arisen naturally through evolution and must therefore be the product of the nefarious Chinese fiddling with coronaviruses in Wuhan? (I am not exaggerating the rhetoric by very much at all here.) And who are Steven Quay and Richard Muller, anyway? Let’s find out!
A not-so-dynamic scientific duo of not virologists
I debated which of the two questions posed above to answer first, because if I point out how utterly unqualified Quay and Muller are to pontificate so confidently about the genomics and molecular biology of coronaviruses, conspiracy theorists will accuse me of ad hominem attacks. However, expertise matters, and neither of them has it in the relevant disciplines. So I consider it entirely appropriate to “consider the source” before I dive into the actual molecular biology, to explain what the CGGCGG sequence is and why what Quay and Muller write about it is nothing more than nonsense based on ignorance of molecular biology, evolution, virology, and genomics.
So who are the members of this not-so-dynamic scientific duo? Let’s start with Richard Muller, who, according to the WSJ byline, is an emeritus professor of physics at the University of California Berkeley and a former senior scientist at the Lawrence Berkeley National Laboratory. Reading that, I couldn’t help but roll my eyes, given my experience with physicists who think they have expertise in the biological sciences, such as cancer and evolution? Does anyone remember Paul Davies and Charles Lineweaver? They’re two astrophysicists who presume to lecture cancer scientists and evolutionary biologists about the “true” origin of cancer and how to treat it. I won’t go into a lot of detail, other than to say that their “discovery” was an idea about carcinogenesis that had been popular among cancer biologists over 100 years ago but found wanting based on accumulating evidence and abandoned. Yet Davies and Lineweaver treated it as some sort of brilliant and radical new insight that those hidebound cancer researchers just couldn’t accept, hence their negative reaction. I wrote about their “atavistic theory” of cancer on two occasions, explaining why it was nonsense not supported by what we know, as did evolutionary biologist P.Z. Myers. He was not impressed, either.
But what about Richard Muller? He has his own Wikipedia entry, which tells me that his areas of expertise are in physics, which is not surprising, including particle physics, mass spectroscopy, and areas of earth science. Interestingly, although apparently he now accepts the science showing that human activity is the main driver of global climate warming, back in the early 2000s he was a “climate skeptic” critical of the science supporting the conclusion of human-caused climate change and accused of “parroting” dubious attacks on the “hockey stick” curve developed by Michael Mann’s group. Later, he became a founder of the Berkeley Earth Surface Temperature Project, which had been intended to test the finding of climate scientists. At the time, Muller’s group was widely praised by climate science deniers, such as Anthony Watts, who said that he was “prepared to accept whatever result they produce, even if it proves my premise wrong.” Spoiler alert: Muller’s results agreed with the conclusions of the dreaded Intergovernmental Panel on Climate Change (IPCC), whose reports sound the alarm about climate change, and he even wrote an op-ed for the New York Times in 2012 portraying himself as a “converted climate skeptic,” even as he couldn’t help but add this qualification:
I still find that much, if not most, of what is attributed to climate change is speculative, exaggerated or just plain wrong. I’ve analyzed some of the most alarmist claims, and my skepticism about them hasn’t changed.
I suppose that it’s not surprising that Muller would become a COVID-19 crank and sign on to the claims about “CGGCGG” indicating a “lab leak” origin for SARS-CoV-2, given his history with climate science. Flirting with science denial is a bad thing, obviously, but somehow managing to come down on the right side of science after doing so is a good thing. However, the fact that Muller was once a “climate skeptic” (a.k.a. denier) suggests that he has a history of being susceptible to certain forms of science denial and conspiracy theory. At the very least, it suggests that he could be a “brave maverick scientist” who relishes being a contrarian. Whatever the case, Muller’s skills and knowledge as a physicist were far more closely aligned to the sort of scientific skillset needed to investigate climate change (and even then they weren’t that well aligned) than they are now to investigate the origin of a virus causing a pandemic. Sadly, his utter lack of expertise in the relevant scientific disciplines didn’t stop him from teaming up with Dr. Quay.
Speaking of Steven Quay, what about that other half of the “CGGCGG” duo? Just Google his name, and you’ll quickly find his website DrQuay.com. A perusal of that website should tell you all you need to know. Dr. Quay is the president and CEO of Atossa Therapeutics, a company that develops and sells contrast agents for MRI and ultrasound and nasal sprays to deliver vitamin B12 and calcitonin. These are all interesting products, but none requires complex knowledge of molecular biology of the sort that leads Dr. Quay to make such definite bold claims about CGGCGG.
Although he doesn’t mention it on his website, Google search results indicate that Dr. Quay is a board-certified pathologist, which might or might not give him some of the skillset needed to analyze a new virus. It would depend upon whether he is primarily a research pathologist and whether his interests involve the appropriate virology and molecular biology needed to analyze the genome of a coronavirus. (Spoiler alert again: He isn’t, and they don’t.) A PubMed search for his publications returns a number of publications, but none that would suggest that Dr. Quay has the necessary expertise to make the claims he makes in his WSJ op-ed.
Then there’s the grift. Yes, Dr. Quay is selling a book about how to survive the COVID-19 pandemic, because of course he is:
It’s advertised this way, with a part about supplements:
So, to boil it down, what we have here is a not-so-dynamic duo of not-virologists, not-molecular biologists, not-geneticists, who think they’ve found evidence of “engineering” in the CGGCGG sequence in SARS-CoV-2 that real virologists, molecular biologists, and geneticists have missed.
They haven’t, but I have to go into the weeds a bit to show why.
What the heck is this CGGCGG sequence, anyway?
Early in the pandemic, after SARS-CoV-2 was isolated and sequenced, scientists noted an interesting and very unusual feature. I went back to this article from May 2020 that identifies what’s so interesting about the CGGCGG sequence, which is in the center of what the article called CCU CGG CGG GCA: The Twelve Letters That Changed the World. This is the furin cleavage site. Does that term sound familiar? It should. I mentioned it in my last post, and it’s a trope that conspiracy theorists have been using for a long time and that was popularized by Nicholas Wade. It’s a site that allows an enzyme in nearly all human cells (furin) to cleave the S1 and S2 segments of the spike protein into their final form. To understand its significance, though, a bit of Biology 101 is required.
DNA and RNA are made up of building block molecules strung together called nucleotides, and the “letters” are abbreviations for the specific nucleotide (cytosine [C], guanine [G], adenine [A] or thymine [T]). RNA is similar to DNA, but differs in three main ways:
- RNA is usually a single-stranded molecule, unlike DNA, which most commonly takes the structure of a double helix. (There are exceptions, such as double-stranded RNA viruses. COVID-19 is a single-stranded RNA virus.)
- The sugar-phosphate “backbone” of DNA contains deoxyribose. RNA contains ribose instead. As a result, RNA is more chemically unstable, which is why messenger RNA half lives are generally short and the reason why the RNA in COVID-19 vaccines had to be chemically modified so as not to be degraded too rapidly.
- The complementary base (the base that pairs to it in a double strand) to adenine in DNA is thymine, whereas in RNA, it is uracil, which is an unmethylated form of thymine.
Proteins are encoded by DNA using the genetic code, in which three “letters” (nucleotides) provide the code for the protein translation machinery of the cell to incorporate one amino acid into a protein:
Thus CGGCGG codes for two arginine residues in a row. I’ll get into the significance of this in a moment. As a preview, I’ll note that the key to these claims is that CGGCGG is so rare in coronaviruses in nature as to be almost certainly due to lab manipulation. It’s not.
Let’s look at what Quay and Muller claim:
A genome is a blueprint for the factory of a cell to make proteins. The language is made up of three-letter “words,” 64 in total, that represent the 20 different amino acids. For example, there are six different words for the amino acid arginine, the one that is often used in supercharging viruses. Every cell has a different preference for which word it likes to use most.
So far, there’s nothing objectionable here. (Actually, I think they mean every organism, not every cell. Codon preference is baked into the genome of an organism.) unfortunately I knew where this not-so-dynamic duo were going:
In the case of the gain-of-function supercharge, other sequences could have been spliced into this same site. Instead of a CGG-CGG (known as “double CGG”) that tells the protein factory to make two arginine amino acids in a row, you’ll obtain equal lethality by splicing any one of 35 of the other two-word combinations for double arginine. If the insertion takes place naturally, say through recombination, then one of those 35 other sequences is far more likely to appear; CGG is rarely used in the class of coronaviruses that can recombine with CoV-2.
In fact, in the entire class of coronaviruses that includes CoV-2, the CGG-CGG combination has never been found naturally. That means the common method of viruses picking up new skills, called recombination, cannot operate here. A virus simply cannot pick up a sequence from another virus if that sequence isn’t present in any other virus.
No, this is not true at all, at least not exactly. First of all, CGGCGG is not all that uncommon. It has been found in other coronaviruses, for example, some isolates of MERS coronavirus. Furin cleavage sites are also found in a number of other coronaviruses, as discussed in this recent review article. Although uncommon, furin cleavage sites are not so uncommon in coronaviruses as to be any sort of strong evidence of laboratory manipulation.
Moreover, there are known mechanisms by which such a sequence could have arisen. This has been discussed extensively on Twitter, including the fact that this nonsense from Quay and Muller is not new and was debunked many months ago:
The CGGCGG sequence could have been caused by copy choice error or frame shift mutation, two very well-established mechanisms taught in basic molecular biology class:
The CGGCGG sequence is also not as uncommon as Quay and Muller claim:
Moreover, as has been pointed out by scientists, it’s not just the furin cleavage site that is unusual about SARS-CoV-2. There are a number of genetic features that, sadly for conspiracy theorists like Quay and Muller, look like nothing more than messy evolution doing its messy thing:
Or, as was described over a year ago (hence the reference to “my esteemed president” Trump):
The chance that someone would make all those changes in a laboratory is “far-fetched but not impossible,” says Nunberg, now director of the Montana Biotechnology Center. “Sadly, while I do not trust the Chinese to be transparent, I trust the conspiracy theorists (including my esteemed president) less. I don’t think anyone knows enough to purposely engineer a new virus that is so successful,” he says. Nunberg points out that viruses are mutating all the time. And a single infected living being can have up to a trillion infectious viral particles from any given virus in its body. “Never underestimate the ability of the virus to adapt,” he says. “It’s the 1,000 monkeys with typewriters who may eventually, at random, type out a Shakespeare play – stuff happens”.
And:
Actually, though, if you look at Quay and Muller’s core argument, it really does come down to an appeal to incredulity. Just because they can’t believe that this CGGCGG could have arisen naturally, they find specious reasons to argue that it didn’t:
Now the damning fact. It was this exact sequence that appears in CoV-2. Proponents of zoonotic origin must explain why the novel coronavirus, when it mutated or recombined, happened to pick its least favorite combination, the double CGG. Why did it replicate the choice the lab’s gain-of-function researchers would have made?
Yes, it could have happened randomly, through mutations. But do you believe that? At the minimum, this fact—that the coronavirus, with all its random possibilities, took the rare and unnatural combination used by human researchers—implies that the leading theory for the origin of the coronavirus must be laboratory escape.
Of course, I just cited examples of how the “novel coronavirus, when it mutated or recombined, happened to pick its least favorite combination, the double CGG. It’s not particularly mysterious, nor is it nearly as remarkable as Quay and Muller claim.
Note the last part though: “Yes, it could have happened randomly, through mutations. But do you believe that?” Quay and Muller admit that this combination could have happened randomly, and so it could. They just don’t believe that it could have, not because the CGGCGG sequence is in and of itself compelling evidence of lab manipulation, but because they want to believe that SARS-CoV-2 was engineered. This leads them to erroneously assert that this “rare and unnatural combination” must mean a laboratory origin. The problem, of course, is that this combination is not unnatural, not necessarily preferred by human researchers, and not as rare as Quay and Muller claim.
Another scientist weighed in on this very issue on Twitter:
Exactly. Random mutations happen all the time. That’s how evolution works.
Meanwhile, our esteemed breast health entrepreneur and our previously climate science-denying physicist (I couldn’t resist borrowing Dr. Maxmen’s phraseology but slightly altering it) continue their appeal to incredulity, this time incredulity that SARS-CoV-2 could have infected humans so efficiently right from the get-go:
Such early optimization is unprecedented, and it suggests a long period of adaptation that predated its public spread. Science knows of only one way that could be achieved: simulated natural evolution, growing the virus on human cells until the optimum is achieved. That is precisely what is done in gain-of-function research. Mice that are genetically modified to have the same coronavirus receptor as humans, called “humanized mice,” are repeatedly exposed to the virus to encourage adaptation.
This is, again, unscientific. I addressed it before when I noted earlier this week that one other claim that keeps popping up is that SARS-CoV-2 appeared “perfectly adapted” to humans as a host. (Wade alludes to this.) This study suggests a pathway by which natural selection in bats could have created a more “generalist” virus, rather than specifically adapted to humans. As I put it last week, SARS-CoV-2 is not “perfectly adapted to humans,” just well adapted enough to infect them efficiently. It did not have to be “optimized” to humans through serial passage in a laboratory.
It also turns out that the furin cleavage site is also not optimal:
Another key feature often cited as evidence of laboratory origin is the furin cleavage site, where the spike protein is cut in half to “activate” viral material for entry into cells. The viruses most closely related to SARS-CoV-2 don’t have this site, but many others do, including other human coronaviruses. The furin site of SARS-CoV-2 has odd features that no human would design. Its sequence is suboptimal, meaning its cleavage by the enzyme furin is relatively inefficient. Any skilled virologist hoping to give a virus new properties this way would insert a furin site known to be more efficient. The SARS-CoV-2 site has more of the hallmarks of sloppy natural evolution than a human hand. Indeed, a timely analysis last year showed convincingly that it is a product of genetic recombination, a natural feature of coronavirus replication and evolution.
No appeal to engineering is necessary.
CGGCGG: The resurrection of an early pandemic gambit
I’ll conclude by noting, as I did last time, that it is certainly possible that the origin of SARS-CoV-2 was a “lab leak” from the Wuhan Institute of Virology. That such an origin is possible, however, does not make it likely or even equally likely as a natural origin. Certainly, from what we know about the virus and its sequence, we can confidently conclude that it is incredibly unlikely that SARS-CoV-2 was “engineered.” It bears the hallmarks, as Angela Rasmussen and Stephen Goldman wrote in the article cited above, of the messiness of evolution, and “rare” combinations can be produced by evolution because evolution provides so much raw material to work on. It’s basically the law of large numbers, incredibly large numbers, that makes even “rare” outcomes not so rare. Scientists with the requisite expertise understand that.
Hacks like Quay and Muller do not, as Joshua Rosenau points out:
This last part is important to note:
Cranks like Dr. Quay:
I saw that 193-page preprint. I will admit that I didn’t read the whole thing. However, what I did read demonstrated to me that Dr. Quay, too, likes to abuse Bayesian analysis, just like the cranks I discussed last week. And, again, just because the most vocal proponents of the lab leak hypothesis are cranks, hacks, and grifters doesn’t mean that it’s impossible that SARS-CoV-2 escaped from a lab. It just means that the arguments in favor of the lab leak hypothesis are currently brain-meltingly stupid, both logically and scientifically.
Quay and Muller don’t help themselves with stuff like this, either:
I do love good sarcasm. I also like spot-on assessments like this;
Again, it is possible that SARS-CoV-2 escaped from a lab, although it is incredibly unlikely that it was engineered and the possibility that it was a natural coronavirus under study at the Wuhan Institute of Virology that escaped is only marginally less plausible and likely. Both of these “flavors” of lab leak hypothesis, though, the escaped engineered flavor and the natural escaped flavor, are far less likely and plausible explanations for COVID-19 than the long-known and long-studied mechanism of zoonotic transfer; i.e., a virus jumping from animal to human. A conspiracy theory can certainly be based on a claim that is possible. Barring compelling evidence making that “possible” explanation the most likely, it still remains a conspiracy theory, and currently the lab leak hypothesis is most definitely a conspiracy theory.
238 replies on “CGGCGG: The latest new-old wrinkle in the COVID-19 “lab leak” conspiracy theory”
This is a highly technical issue. The only people qualified to speak on it are people with a full understanding of viral molecular genetics and evolution.
However, as an investigation it does not require such extensive knowledge. It requires detective skills. We need our experts to tell us what are the modification and what is the likelihood of such a modification occurring in nature. It also requires a sensitivity to language.
What are the possibilities? The summation of possibilities must equal 1. These are the only 2 possibilities. The current virus is either of completely natural origin or engineered modification of a virus occurring naturally. (For this exercise we are excluding the possibility of a completely engineered virus).
What do we know (and I think all will agree): The basic virus is of natural origin, having high homology to bat coronavirus. The current virus has a modified spike protein that makes it particularly suitable for human hosts. Therefore we only need to look at the modifications to the spike protein.
What is the possibility that the spike protein was modified in a laboratory? Lab modification = 1 – natural modification.
The possibility of COVID-19 is 1 and is the summation of all probabilities.
Summation of all probabilities is 1.
So we can substitute: What is the probability of the spike protein being modified in a laboratory? Probability of lab modification = 1- probability of natural modification.
Probabilities are a statistical measurement of likelihood and for this we need to gather evidence.
What is the evidence for lab modification? For the virus to be of lab origin, it is necessary but not sufficient for a lab to be working on modification of the spike protein of a coronavirus.
There are two general categories. Circumstantial and technical.
Circumstantial: COVID-19 comes out of Wuhan. This is the general consensus that the disease is first identified in Wuhan. If it comes out of Wuhan, there are three possible sources: the wet market, importation from another site (such as the bat caves in southern China) and the viral laboratories.
What is the evidence it came out of the wet market? This requires an intermediate animal host. No such host has been identified despite extensive investigation. As the virus has an incubation period of several days, this requires the person to be infected prior going to the wet market. The probability of coming out of the wet market is near zero.
What is the evidence it came out of the viral laboratories? The viral laboratories in Wuhan are working on coronaviruses. Peer reviewed, scientific publications establish this fact. The viral laboratories are located in Wuhan. Viral escape from even high level BSL4 laboratories is a known phenomenon. One of the laboratories working on coronavirus was only a BSL2. Possible and of very high probability.
What is the evidence that COVID-19 came out of the bat caves in southern China? The backbone virus is identified as having originated from these caves, but not the highly human infectious form is not found. Possible but of very low probability.
Circumstantial evidence conclusion: The most likely origin of the virus is from a viral laboratory.
Molecular/evolutionary evidence: Here we must rely on our experts. There are variant opinions. But the experts arguing against engineered origin are all involved in this type of research and receive funding from the NIH/NAID to do this research. In a court of law, such expertise would be impeached due to distortion by the corrupting influence of money.
There are experts arguing for engineered origin. This includes the furan cleavage site of the S protein (never found in coronaviruses but common on human cells), the rarity of the CGGCGG coding, and several others, including six signatures of genetic manipulation.
Each modification can occur naturally But the likelihood or probability of all 6 occurring in the virus is about 1/64. Certain of these molecular signatures, although possible through natural origin, are not probable. This would need further modification for the likelihood of the molecular change to occur in the first place and there must be proper placement of key proteins. For this we need to defer to our experts. These further increases the likelihood of engineered origin and decreases the likelihood of natural origin
We can modify the above equation: The summation of all probabilities must equal 1. The likelihood of engineered origin = 1-probability of natural origin.
The probability of natural origin is <1/64 (or 0.015625). Due to the further restrictions, the likelihood of engineered origin is greater than 98.4%.
Legal evidence: The evidence in the laboratory was apparently purged. This is spoilage and in a court of law overwhelmingly indicates guilt.
The summation of all evidence strongly points to a laboratory origin.
Mandatory first response: “Experts.” You keep using that word. I do not think it means what you think it means.
Let’s just put it this way: Neither Nicholas Wade, Steven Quay, nor Richard Muller is an “expert” in any of the relevant scientific fields. Heck, Quay and Muller are risibly far from being experts, and I’m more of an expert in this than they are. Muller is a formerly bought-and-paid-for climate science-denying physicist, and Quay is a pathologist turned “breast health” entrepreneur with a side grift selling COVID-19 “survival tips.” Wade is a science journalist whom I used to rather like decades ago. (Betrayers of the Truth, which he co-authored with William Broad in 1982, was a great book about scientific fraud. I read it when I was in college studying chemistry as an undergraduate.)
As for the rest of your argument: In evolutionary terms, 1/64 is not a small likelihood. Far from it! When incredibly numbers of virus particles are multiplying, mutating, and recombining, a 1/64 chance is actually pretty likely. You simply do not understand how, when the numbers are large, small chances make it ultimately almost inevitable that we will see examples of the outcome.
I will thank you for making me laugh, even though this week has been a dark one. (My dog died on Tuesday, hence the paucity of blogging.) This quote is priceless:
I laughed out loud at the innumeracy and lack of understanding of genetics, virology, evolution, and, yes, Bayes’ theorem inherent in your statement. Indeed, the stupid there is so dense that it threatens to form a black hole, sucking all intelligence, reason, and science into it, past its event horizon.
There is only one response:
OK, maybe there is another:
My condolences with the death of your dog. Loosing a companion is always hard.
Thanks.
Please accept my condolences on your loss. May their memory be a blessing.
“My dog died on Tuesday.”
Orac,
I am very saddend to hear that. I don’t guess you are up for a ride with Bezos but something less costly might be soon behind and he may still be hanging out in the Heaviside Layer with some secret friends. Try to catch a sample of him on the way back down and put him in a cat. Just Sayin’.
https://old.reddit.com/r/aww/comments/ny1g0b/adopting_an_old_cat/
Of course, I don’t think I’d feel too much hate welling up if you also got a dog.
You have my deepest condolences for the loss of your family member. I hope you and your spouse are taking good care of yourselves.
I’m so very sorry to hear of your dog’s death. Sending sympathy & arohanui your way.
A fiinger in the air allows specifying probability to three significant digits?! I believe this is where the kids use “ROFLMAO.” It blows credibility to nanoparticles.
Yet another reason to laugh at Greg’s “1/64” probability argument.?
@Pathcoin
You can also add to that the fact that in 2018 US officials sounded alarm about Wuhan lab safety.
And virologists have been sounding alarms about potential zoonoses jumping to humans since at least the 1990’s.
Virologists like Raoult, of HCQ fame. To his credit.
With the first SARS and MERS as confirmation that these concerns were well-founded.
Followed by a long post full of speculation.
As someone who does have expertise in both molecular genetics and evolution, having published numerous scientific papers on the topic, I can confidently opine that the rest of your post is a load of nonsense. Especially this bit:
This is the sort of claim someone completely ignorant of both molecular genetics and evolution (oh and statistics for that matter) might make.
The wet market was a superspreader event. There was no infected animal at the wet market.
We know this because persons who caught it at the wet market were infected with both A and B strains.
Re: “There are experts arguing for engineered origin. This includes the furan cleavage site of the S protein (never found in coronaviruses but common on human cells), the rarity of the CGGCGG coding, and several others, including six signatures of genetic manipulation.
Each modification can occur naturally But the likelihood or probability of all 6 occurring in the virus is about 1/64.”
False, and I suspect you simply fabricated that calculation to suit your paranoid mindset. For example, template switching via copy-choice error (leading to an out-of-frame insertion) would bring those two codons to the site; i.e. each individual nucleotide would not need to independently mutate to form the codon. So doing a calculation that assume independent mutation is ridiculous.
Also, one could use your nonsensical reasoning to claim that all mutations are unlikely and thus did not occur naturally. As an analogy, any particular set of 5 cards in poker is equally unlikely. So you can’t infer cheating simply because your set of 5 cards is improbable. Similarly, you can’t infer design just because a set of nucleotide sequences is improbable. You’re this using the same fallacious arguments Intelligent Design proponents use for inferring design from ‘improbable’ aspects of life, the values for various physical constants, etc. Same trash Ebright attempted.
I could go on, but I’ve had plenty of paranoid conspiracy theorists who make stuff up about fields they don’t understand, so I know your type of beyond evidence and reasoned discussion. Like talking to a brick wall.
https://twitter.com/AtomsksSanakan/status/1394438888358391808
https://twitter.com/AtomsksSanakan/status/1397390147164033024
This was my response on the previous post. I admit to not having read the WSJ piece in full. I recognised the argument immediately and know from my own experience (and I work on plants, not virus) that lots and lots of mutations occur constrained only by the need for the protein produced to be functional. Claiming a single segment of 6 nucleotides as being a smoking gun for a lab construction is complete nonsense. I then checked who the authors were and rolled my eyes and didn’t bother with the rest of their article. Wanting something to be true, does not make it so.
Of course now I have COVID-19 deniers telling me the lab leak hypothesis is now a proper theory with more evidence than natural occurrence. I wish they would make up their mind. Is COVID-19 nothing to worry about, or is it a nefarious Chinese plot.
I do like the inconsistency. If COVID-19 is, as many deniers claim, no big deal, then who cares if it leaked from a lab in China? If we’re to believe the deniers, SARS-CoV-2 is essentially harmless, no worse than seasonal flu, and only kills those who have one foot in the grave anyway, who likely would have died of the flu or a cold. At the same time, these same deniers claim that SARS-CoV-2 is a horrific virus “engineered” using “gain of function” techniques that escaped from the lab, a crime for which those nefarious Chinese must pay!
I was cynically wondering about that. Could the Venn diagram of people saying “the virus is no big deal” and people saying “it’s a man-made virus engineered for lethality” be a perfect circle?
Are you sure you have a degree? Did you actually graduate high school?
If a plane crashed somewhere and everyone survived you would actually argue that there’s no need to investigate what happened?
I don’t know whether to laugh or feel depressed that Orac basically followed the lampoon template that I predicted. Here it is for those who may have missed it; you be the judge…
The point of my lampooning was to show that Orac will huff and puff, hurl insults and ad-homs, but never really addressing the issue at hand. This entire post was no exception and was also strawman. The issue is not whether a double CGG is possible. The issue is as Pathcoin above also points out is a matter of probability. Indeed, Quay and Muller are not arguing that a double CGG is not possible, they concede as much; they are arguing that it’s highly improbable. Throughout his entire mush, Orac postulates two mechanisms where it’s possible but without refuting the argument that it’s highly improbable. I might also ask, have scientists not argued all along the Covid-2 has a gene proofing mechanism that would mitigate the two errors that Orac described?
So, at the end of the day, where are we with the lab leak rebuttals? We have Orac and his ilk dismissing all the reasonable arguments showing how highly probably it is that Covid-2 could have originated in a lab with highly improbable arguments for a zoonotic explanation. They do so while dogmatically declaring that the zoonotic explanation is superior. Sigh!
PS: Reading the comments here, I did come across ‘Beth’ arguing how Nicholas Wade provided a masterful argument for a lab leak explanation for Covid. I only stumbled on it yesterday after opening a link that ‘Athaic’ sent me. Indeed, I have to say, ‘wow!’ Check out such objective, didactic writing, and compare it to the scams that Orac continues to barf up here.
“Reasonable arguments.” You keep using that term. I do not think it means what you think it means.
“‘Tis but a flesh wound,” said the Black Knight.
@Greg How many viral particles (not virus types) an infected human or animal has ? How many humans and animals are infected ? Multiply these with each other and result is much higher than 64. By your own argument, natural evolution of SARS CoV 2 is highly probable.
Conjecturing, Aarno! Easily defeated by the reality that a double CGG insert has never appeared in all the previous Coronas.
Except that, as I pointed out (with references) in my post and others have pointed out on Twitter (some quoted by me, many not) and here in the comments, the double CGG has been found in several coronaviruses, including MERS. It just haven’t been found in one subtype, betacoronaviruses, of which SARS-CoV-2, is a member. It is thus not particularly surprising or unusual that a betacoronavirus like SARS-CoV-2 could eventually acquire this sequence.?
Not only has double CGG been found in MERS (which is a betacoronavirus, but a different lineage than the SARS-related CoV), HKU-9 is in the closest related clade to the SARS-related CoV, has double CGG, has 10 of the 12 nucleotides in the PRRA* insert, AND is found circulating in the same region as RatG13. Wade lied to you, Greg.
*the insert is actually LLGG, but because it was inserted in the middle of a serine (S), the resulting residue became SPRRA
Again, clarification is in order. Is it that CGG code has never been found in Coronas’ genome, or two lined up in a row has never been found?
Dude, you’re the moron making the claim. Both of those positions are clearly false. CGG is found in just about every coronavirus. CGGCGG has been found in numerous coronaviruses, some quite closely related to SARS-CoV-2.
Quay and Muller:
@Greg:
There’s ya problem. As Orac points out:
Citing already discredited “experts” again damages your argument AND your credibility.
@Greg Read this article:
Gallaher, W.R. A palindromic RNA sequence as a common breakpoint contributor to copy-choice recombination in SARS-COV-2. Arch Virol 165, 2341–2348 (2020). https://doi.org/10.1007/s00705-020-04750-z
Go to figure 3b. You would see how CGGCGG would slip into SARS CoV 2.
Quay & Muller either lie or do not know anything (notice how old paper is)
Nicholas Wade’s lab-leak origin argument…
https://nicholaswade.medium.com/origin-of-covid-following-the-clues-6f03564c038
Yes, I’ve seen it. It’s bullshit, particularly the part about the furin cleavage site. (You do realize, don’t you, that his article is one reason why cranks are resurrecting the nonsense about the furin cleavage site being slam-dunk evidence that SARS-CoV-2 couldn’t have evolved naturally or that it was much more likely to have been “engineered”?)
Your scientific ignorance, as usual, is epic.
Orac, the chances that Greg or other trolls will benefit and learn from your explanations are lot less likely than the occurrence of that particular sequence.
I notice that the loons I survey often alight upon a detail that is unlikely to be understood by the general public so that they can confabulate elaborate structures unhindered that don’t exist in nature to their followers. Most of their objections follow this pattern and rely upon science-y sounding language..
I always imagine that self-taught, internet “scientist” contrarians become as unrealistic as they are because they alone select what parts of research they study unlike being in a survey course in which the curriculum is determined by experts in the field whom they don’t acknowledge. Thus, we have autism “experts” who know little about the development of the brain or variables that affect the rate of ASDs .
But your other readers learn and increase their level of understanding. Thanks!
-btw-
I’m so sorry to hear about your dog.
.
https://medika.life/debunking-nicholas-wades-origin-of-covid-conspiracy-theory/
https://medika.life/nobel-winning-virologist-david-baltimore-eats-wuhan-crow/
Great articles. The out-of-frame insertion which created the suboptimal furin cleavage site is key.
Many coronaviruses have furin cleavage site:
Yiran Wu, Suwen Zhao,
Furin cleavage sites naturally occur in coronaviruses,
Stem Cell Research, Volume 50,2021,102115,
ISSN 1873-5061,
https://doi.org/10.1016/j.scr.2020.102115.
(https://www.sciencedirect.com/science/article/pii/S1873506120304165)
Abstract: The spike protein is a focused target of COVID-19, a pandemic caused by SARS-CoV-2. A 12-nt insertion at S1/S2 in the spike coding sequence yields a furin cleavage site, which raised controversy views on origin of the virus. Here we analyzed the phylogenetic relationships of coronavirus spike proteins and mapped furin recognition motif on the tree. Furin cleavage sites occurred independently for multiple times in the evolution of the coronavirus family, supporting the natural occurring hypothesis of SARS-CoV-2.
So Wade is clearly wrong
A truck full of seeds explodes in a Walmart parking lot. Two seeds fall into a crack in the pavement and grow into flowers. One says to the other: “Look, we are perfectly adapted to living in this parking lot”!
Yep.
That’s one of the stupid argument from the lab-leak crowd reported by Orac in the previous thread.
“How comes the virus emerged with an optimized pathogenicity? That’s not natural!”
Aside from the fact that more “optimized” variants have since emerged, that’s basically saying that, before the epidemics exploded, there should have been epidemics of benign, weak, low-pathogenic infections.
IOW, a bunch of mild bronchitis, cold and other runny noses.
That could be true, but, so? That’s business as usual in Fall/Winter time. By definition, something benign is not worth much attention. It may pass completely unnoticed.
Maybe in retrospect, we will see there was an increase of respiratory ills, and maybe some of them were that. If we are lucky, there may be blood samples to analyze.
As arguments go, it’s a logical fallacy. Not sure which one. It’s “how come we didn’t notice it before it did something noticeable?”
I call dibs on cicada fallacy.
Just read about an analysis of returning bomber damage in WWII in order to determine where to increase resilience. The initial reaction was to reinforce the area with the holes but a smarter human correctly recommended reinforcing the “unholy” areas. They first idea forgot that there was no sampling possible from the planes that did NOT return.
The virus mutation that did not cause harm (or not much) never registered.
… and with this puddle nearby that’s just perfect for us…
Ok, Eric M’s nemisis.
I want to invent a lie detector that explodes when the testee is lying, and strap every disseminator of disinformation to it, and then question them about their assertions. The results will be either amusing or deadly
The problem is, I think most of them actually do believe the disinformation that they’re spreading.
Would Max Planck have survived the exploding lie detector?
He didn’t believe the theories that were implied, based on his own (accurate) measurements of the quantization of energy.
So we have those who:
– expound nonsense, knowing it’s nonsense.
– expound nonsense, thinking its true.
– expound truth, thinking it’s nonsense.
– expound truth, thinking it’s true.
IMO – If you’re going to expound nonsense – you should at least have the common decency to actually believe that it’s true.
@Cthulhu If you cite history of physics, get your facts right. Planck did not measure anything. He explained black body radiation, by assuming a quantum of light. This was then just a hypothesis, but things become more interesting when Einstein showed that quantum of light could explain photoelectric effect with quanta, too.
@Aarno Syvänen
“Planck did not measure anything”
OK
But he was unconvinced that energy could exhibit quantization – even though the phenomena he had observed could be explained by this.
vs
Now, is this another argument between ‘theory’ vs ‘hypothesis’ or, as I see it: Plank made an observation, it slapped him in the face because he didn’t like where it might lead because that is not how he thought, he published anyways with a sideways “gurumphh” kinda critique?
Whether he made “accurate measurements” or not, I seem to remember some equations and constants sitting around somewhere that has his name all over them. No idea if it is related.
— Have you ever thought, read, spoke, or written down “I’m in a pickle?”
If the sign says “you can’t put too much thought into it”, did you put too much thought into it?
{ok, that one’s from the weapons division. sorry.}
Steven Quay, the (ex?)-pathologist who co-authored the WSJ op-ed, also has the distinction of his firm being the recipient of an FDA warning letter in 2013. His company, Atossa Genetics, was calling a test it marketed for detecting malignant cells in nipple fluid “literally a Pap smear for breast cancer”. After the FDA got on its case, Atossa withdrew the product from the market.
https://www.fda.gov/consumers/consumer-updates/nipple-aspirate-test-no-substitute-mammogram
This sort of breast cytology testing seems to have fallen into general disfavor. I was (reluctantly) trained in interpreting nipple fluid aspirates years ago because one particular breast surgeon at our hospital was hot for the technique and wanted to send us samples to evaluate. When she left for another job, there was no one else interested and we thankfully stopped getting specimens, which were difficult to interpret and a poor substitute for fine needle aspiration or core biopsy of lesions.
Continue… moreso.
This is basically what underpins the “it’s a natural virus” theory.
Apparently 1,000 monkeys theory is more probable that it leaking from a lab that collected and worked on corona viruses.
“Apparently 1,000 monkeys theory is more probable”
Compare it to Trump appointees or Limbaugh filler.
You do understand the principles of evolution don’t you Dave? Or are you possibly in the intelligent design club?
Except that it’s not a hundred monkeys, but more like billions and billions of monkeys.
And if you add in a component of natural selection, retaining the letters that are “productive” and discarding those that aren’t, it’s possible to generate phrases from
Shakespeare in a relatively short time—like 40 generations. Of course, that’s working towards a predetermined end, while evolution has no predetermined goals, but it shows that this example isn’t as definitive as creationists would like to believe.
You do not understans eveolution, of course. It is random mutation and selective pressure. Random mutations that create furin cleavage site offer really great selective advantage.
One of the reasons that anti-vaxxers and other alties are able to cavalierly dismiss the material that Orac presents is because they do NOT accept expertise:
anti-vaxxers believe that an under educated parent knows more than doctors and researchers in the field and research shows that anti-vaxxers are more likely to reject hierarchies of expertise- to them, anyone can critique highly specialised scientific research and arcane mathematical concepts..
Thus, they ain’t great at self-evaluation and perceiving external reality..
I’m a physicist. I chuckled at the part where the 1000 monkeys with a 1000 typewriters will eventually type a work of shakespeare. no they won’t. ever.
it is extremely unlikely–so unlikely you could use it as an operational definition of “never.”
the chance that 10^10 monkeys typing 10 keys per second, ignoring caps and punctuation, typing for the age of the universe (about 10^18 seconds) to produce hamlet, which has about 10^15 characters is
10^−164316 (ten to the negative 164,316)
so you might expect them to take 10^164316 times the age of the universe to finish hamlet. that is 10^164334 seconds.
since the heat death of the universe is in some 10^107 seconds, you might expect the monkeys to type hamlet in about 10^164227 times the time is takes the universe to end.
even if you say you had 10^80 monkeys (which is the same number of particles in the universe) you could improve the time to type hamlet by that same factor, so it would only take 10^164147 times the time for the heat death of the universe. which is still not likely.
in conclusion, any number of monkeys will never type hamlet, given the constraints of the size and time to heat death of the universe.
of course, they may may be african, not european, monkeys and grasp the typewriters by the husk.
It is still a worthwhile task. While said monkeys are busy attempting to reproduce works from classic literature they are not free to join conspiracies and contribute their keyboard gymnastics to RI.
Actually said monkeys can write literature far quicker than you calculate. During their break periods they will spend their time frolicking and make more monkeys and some of them will be “better” monkeys. After only about 200,000 years of this you only need one of those improved monkeys to write Hamlet.
There is a theory that says this has already happened.
It’s still better than Trump appointees.
@Rob
I’m starting to think that articles on this site are written by 1,000 monkeys.
Maybe the monkey theory is right.
Certainly the 1,000 monkeys produce more coherent arguments than you do.
“After only about 200,000 years of this you only need one of those improved monkeys to write Hamlet.”
Ahh! But after 200,062 years, it will be the LifeTime Movie Network version.
You’ve got to have some sympathy for the monkeys that pretty much nailed Hamlet – but just screwed up in the final paragraph.
I know how they feel.
@Scientism Dave I think your responses are written by someone who has no substantial to say.
It takes a petabyte to represent Hamlet? I’m surprised then that my bookcase isn’t crushed by the weight of my printed copy of Shakespeare’s complete works!
I doubt that Hamlet would be 10^6 characters. It’s about 30000 words: https://www.statista.com/statistics/1061108/word-count-shakespeare-plays/)
10^15 bytes would easily accommodate a billion copies of Hamlet.
Still, the probability of the proverbial 1000 monkeys typing it before the heat death of the universe is still vanishingly small.
It’s ok to admit you might actually be wrong sometimes Orac. I admit I don’t know all the science that you know, but circumstantial evidence of a lab leak seems strong. Or maybe you rally do believe the timing and origins of the lab leak are just pure coincidence. WHO did such a great job “investigating” too. Is Jamie Metzl an evil anti-vaxxer?? Last I checked he’s a progressive Democrat.
There are antivax progressives and Democrats. Indeed, before the antivax movement co-opted the right wing 6 or 7 years ago with messages of “health freedom” and “parental rights,” the stereotype was that most antivaxxers were hippy dippy granola crunchers. (It wasn’t true then, but that was the stereotype because then the most prominent antivaxxers were lefties. Now, the loudest, most prominent antivaxxers are right wing conspiracy theorists.)
As for “admitting” I’m wrong. As I like to say, show me compelling evidence other than “circumstantial” evidence with bogus “Bayesian” calculations and insinuations of vast conspiracies, and I might just do that. Until then, I see no reason to, because there is no good evidence to make me think that I might be mistaken and force me to change my mind. Feel free to try to provide such evidence.
@Orac,
“Feel free to try to provide such evidence.”
Out of curiosity. What would you consider convincing evidence of a lab leak?
Out of curiosity, what would you consider convincing evidence of natural origin??
“Out of curiosity. What would you consider convincing evidence of a lab leak?”
Certainly not this hard documentary evidence of a lab leak in mid 2019, which includes an inspection report by the CDC that was redacted in order to hide the identity of the “select agent” (Baric’s chimeric SARS-CoV?) that breached BSL containment at USAMRIID: https://www.fredericknewspost.com/news/politics_and_government/military/cdc-inspection-findings-reveal-more-about-usamriid-research-suspension/article_6d1d316e-4989-5307-924c-8608c25ef6f7.html
I don’t study this stuff all the time. I have my hands full with 2 young kids who will both be fully vaccinated. However, I am slightly skeptical of these new vaccines for such a novel virus. I do believe these vaccines are mostly safe and effective but I also think we should trust the immune systems of young and healthy individuals before indiscriminately vaccinating large swaths of the population without screening them first. Studies have shown (don’t ask me to cite) that certain individuals have innate or adaptive immunity (i.e., O positive blood types and transferons that prevent spike protein from attaching to ACE2 receptors) to this virus.
Ivermectin has also been proven to be an effective treatment (see Bret Weinstein). Maybe you can write your next article complaining about him.
@Orac,
I knew you would not answer the question.
I get it, you don’t want to answer just in case that kind of evidence shows up.
I was making a point, and it has been made. Conspiracy theorists like you won’t accept any evidence against their conspiracy theory and will never tell you what evidence it would take to convince them.?
Just because hippy-dippy granola crunchers are not conservatives, does not make them “lefties”. There’s actually a tension between “hippy dippy” and “lefty’ that goes back to the 60s — dropping out v. sitting in, if you will. I’m thinking about the rank-and-file of the old pediatric antivax subculture, NoCal variety. What prominent AVs other than RFKJ would you categorize as lefties?
@Orac
“Conspiracy theorists like you won’t accept any evidence against their conspiracy theory and will never tell you what evidence it would take to convince them.?”
You do realize you never told us what evidence it would take to convince you….
You’re losing credibility with every post. Keep it up.
Can you just be indifferent to vaccines?
I had COVID19 last November. It didn’t affect me particularly badly. I still have mild olfactory hallucinations.
I’m not vaccinated because I didn’t fancy spending 2 days feeling rough – to gain absolutely nothing.
You would think those who survived COVID19 with little or no adverse effects would be a valuable commodity – and be pushed to be getting things back to normal with all urgency.
But nah. No-one has the slightest interest. Unless it comes to tarring you with the brush of being an antivaxxer / antimasker, when you point out your lack of hysteria is due to the fact you have already had the disease.
I had several phone calls from the British government COVID19 response team to make sure I was self-isolating throughout the period of my infection.
At the end of the period they told me this would be the final call they would be making.
I was expecting some advice on what I should be doing – now I was glowing with natural immunity. But … nothing was forthcoming.
Oh well.
@Scientism Dave I want too to know what evidence you need to accept natural origin theory. You did not have any credibility from the start.
@Cthulhu Everybody hope that your immunity would last very long time. But SARS CoV 2 is mutating fast. Only way to prevent is to have as many immune people as possible. Only way to quarantee this is vaccination.
@Aarno Syvänen
I’m not disputing that increasing the number of people immune to SARS-CoV-2 is a good idea.
I am pointing out that there exists a pervading attitude that the immunity provided by actually surviving the disease itself is dismissed as irrelevant, and the ONLY thing that can provide immunity is a dose of the vaccine.
I think this mindset is deliberately pushed by the authorities.
E.g. If you were to ask the public who they thought they would be most likely to catch SARS-CoV-2 from: An unvaccinated survivor of the disease, or a fully vaccinated individual who had never contracted the virus before vaccination, I feel sure most of them would say – the unvaccinated survivor.
I think I’m right in saying the opposite is actually true?
This is because the vaccine is being imbued with “whoo” by the authorities – and those that have survived are just an inconvenient “fly in the ointment” to their narrative.
If I was to ignore mask wearing rules – and when challenged point out I had already survived the virus – do you think the goons would say: Ah – accept our apologies for our intrusion! Please continue about your business, Sir! Have a nice day.
Of course not!
This attitude is not an accident, IMO.
“do you think the goons would say: Ah – accept our apologies for our intrusion! Please continue about your business, Sir! Have a nice day.”
“Around these parts”, nobody is even asking. And by “these parts” I mean a bunch of damn dirty fundamentalist trumspers who still think cannabis is the devil’s lettuce and yoga == masturbation + party with the devil and SIN(X) / N == SIX (the N’s cancel).
But, yes. For now, you should be conveyed the same ‘freedoms’. If only there were some kind of lidar-based hyperspectral scanner to identify the infected by their, otherwise undetectable by human noses, wicked stink…
No matter, I’m sure Amazon Ring will come out with something in the next couple quarters.
What “strong circumstantial evidence”?
Seriously, “strong circumstantial evidence” would be something like if everyone who worked at WIV and their families came down with a strange respiratory condition before anyone else in the world. (3 people doesn’t cut it, it would have to be at least 50% of the employees.)
Do you have any knowledge or experience with any level of BSL? Have you worked in any kind of biology lab?
Do you have any idea how many bats there are in the world? Bats are one fifth of all mammals. That’s a lot of bats. That’s plenty of room for evolution to come up with all kinds of viruses.
Not to mention the Gargoyles.
What if Gargoyles are escaped man-bats and they become the dominant species? Would you kill them then? Especially if they have cold sores?
No, I do not have any experience with BSL but does it not strike anyone as odd that the only BSL-4 lab in China is located in Wuhan and only a stone’s thrown from the wet markets?? I know this will probably raise some eyebrows but I work for the FDA, but not intimately involved in lab testing or approval processes but in drug imports compliance enforcement, so I do have some science background.
Can someone also explain why antibody dependent enhancement is not a valid concern with these vaccines (not trying to make this another anti-vax trope like gorski would say). I know nothing has stood out from current data, but there simply is no long term data available. Oh, and then there’s this: https://twitter.com/breaking911/status/1403421847388033024?s=21
If antibody-dependent enhancement after COVID-19 vaccination were an actual problem, we’d have seen it long before many hundreds of thousands of doses of vaccine were given. If it happens at all (which it appears not to), we can confidently say that it’s incredibly rare. It was a reasonable concern as the vaccines were being developed, but the large clinical trials to gain EUA for the vaccines failed to show a single case. The lack of cases of ADE since then after hundreds of millions of doses of vaccines have been administered confirms that ADE is not a problem.
@ Nike
(sigh)
Big cities tend to attract big sciency labs and plenty of traveling/trading people.
So the odds of a nasty virus starting its big tour in the same city where there is a virus lab, by pure coincidence, are not as low as you may think.
Two French cities which were hit hard by the virus are Lyon and Paris. Both cities host BSL-3 or BSL-4 labs. Should we go check them for a leak?
Listen, I’m not against the idea to go check the Wuhan lab. Just in case. But the pile of bullsh!t entering the discussion and presented as smoking gun by all these wannabe biologist is quite irking.
Especially since these are the same people who spent the whole last year telling us how the virus is harmless, the masks are suffocating us, and the vaccines are going to cyber us.
Also, there is a second BSL-something lab in China. Wuhan isn’t the only one.
@Nick Biosafety levels are explained here:
https://en.wikipedia.org/wiki/Biosafety_level
Go to level 4
It is not, like, I drop a testtube and started a pandemic.
Jamie Metzl’s expertise in this area is what exactly?
His take is simply another argument from incredulity.
The evidence for this being a laboratory-designed virus amounts to “I can’t believe this could happen naturally”. It is not a good argument and it lacks any evidence. Many years ago, I published this paper https://www.nature.com/articles/6800004 showing how easy it is for very rare events (in this case 1 in 20,000) to be common in large populations.
I trust him more than Peter Daszak. Watch the 60 minutes episode, reported by Leslie Stahl, covering this topic.
IKR? These ignoramuses think that a 1/64 chance is rare.?
When I heard it was rare I thought “Oh, it must be in the one in a million range or, at least, one in several hundred thousand”. Not one in sixty four. I’d put the lottery on five times a week with those odds.
And of course if something that is “rare” confers even a very small measure of increased fitness it can go from rare to very common very quickly as selection acts in its favor.
There is some suspicion, though nothing confirmed as far as I know, that the B.1.1.7 variant arose in an immunocompromised person. It didn’t take too long before it became the most prevalent variant in several places.
Now look, Marjorie Greene explained why Covid had to be engineered. God is true, not evolution. I guess she meant that things like mutations in a virus are impossible. You don’t think that that a US Congressman would be capable of spouting absolute nonsense, surely?
https://www.nbcnews.com/politics/congress/lunar-new-deal-gop-rep-gohmert-suggests-altering-moon-s-n1270219
Orac is a longtime master of ad hominem, but it still surprises me to see the “antivaxx” label applied to COVID skeptics. The science on mRNA vaccines is not settled; in fact in human subjects it’s brand new. We’re talking about a vaccine developed under the Trump administration, as part of a program named after a silly science fiction concept (“Warp Speed”). We’re talking about a vaccine given emergency use authorization, allowing it to bypass normal testing requirements. Surely I’m not the only one who remembers the “replication crisis” that most severely affects the field of medicine; so why should I believe Pfizer’s newfangled, half baked efficacy results are valid? Science is based on repeated observations. It is perfectly scientific to insist on repeated observations. It is totally unscientific to make an appeal to authority, to insist on the inerrancy of a preliminary result or hypothesis. Orac, you’re on the side of talking heads on TV. The same people who told us Saddam Hussein mailed the anthrax letters after 9/11. But of course the anthrax was later proven to have come from Fort Detrick.
Orac, are you familiar with the Salk institute study that claims the spike protein itself is pathogenic and causes vascular injury? You know, the same spike protein the mRNA vaccines force our cells to manufacture? Isn’t the CDC about to hold an emergency meeting regarding the incidence of myocarditis among young vaxx recipients?
Also, I’m happy for your dog, death must be quite a relief.
You really are an asshole.
All 9/11 troofers are ghouls, but this really takes the cake.
There were clinical trials for mRNA vaccines. Hundred million doses have been distributed .Safety problems should be clear now.
Anthrax is an actual bioweapon. It is used because its spores are very resistant. You can compare this to SARS CoV 2.
Orac actually had an article about spike protein, and about that Salk paper. Spike protein is present at the level of picograms, and even then only two weeks. Concentration is much lower than one used by Salk scientists.
@Sirius
Even worse. The emergency use authorization cannot be issued if there already are treatments available for a given disease. This explains why pharma went after HCQ and published a fabricated study in the lancet to discredit it.
Even if those vaccines are 100% safe (which they aren’t) they are completely unnecessary.
I’d like to see your proof that the study disproving HCQ was fabricated.
@Julian Frost
Really?! This is common knowledge….well unless you get you scientific news from CNN.
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)31324-6/fulltext
A study being retracted is not proof it was fabricated. I read through the retraction. The independent reviewers could not get the dat due to privacy concerns.
@Scientism Dave There is meta-analysis of HCQ and CQ trials:
Bignardi PR, Vengrus CS, Aquino BM, Cerci Neto A. Use of hydroxychloroquine and chloroquine in patients with COVID-19: a meta-analysis of randomized clinical trials. Pathog Glob Health. 2021 May;115(3):139-150. doi: 10.1080/20477724.2021.1884807. Epub 2021 Feb 11. PMID: 33573530; PMCID: PMC7885725.
Authors considered 120 papers. So it is not only one “fabricated” paper.
Intersting thing is, that HCQ did have EUA, but it was later revoked. HCQ is an antimalarial drug. Perhaps an antiviral would work better.
@Julian Frost
“A study being retracted is not proof it was fabricated.”
You are the target audience of this site. You do no research and believe everything you read.
https://www.sciencemag.org/news/2020/06/two-elite-medical-journals-retract-coronavirus-papers-over-data-integrity-questions
@Aarno Syvänen
Most recent study.
https://www.medrxiv.org/content/10.1101/2021.05.28.21258012v1
“Causal modeling establishes that weight-adjusted HCQ and AZM therapy improves survival by over 100%.”
“Casual modeling”? ???
Get back to me with double blind RCTs.
I think that latest pre-print is going to need some significant revision after peer review. They found that people who had received >3g cumulative dose of HCQ had a higher survival rate than those who didn’t. The problem is that “those who didn’t” appear to include those who didn’t live long enough to receive the threshold dosage. In other words, there was a survivor bias. Nor does the paper discuss the dosing regimen of the >3g HCQ group, so it’s difficult to assess where that point on the timeline is. We do know that most patients in the group were assigned to a regimen of 2.4g HCQ over 5 days, so we can guess that at least 6 days need to pass before patients can get to >3g HCQ. According to the figure, 20% of the cohort were dead before they even had a chance to reach the dose the authors recommend. If I were a peer-reviewer, I would definitely want to see that figure redone to account for the inherent bias (especially if there is no data on those assigned to the higher dose regimen but failed to attain that dose). The slopes of the curves appear to be similar once the patients that actually received the higher cumulative dose started dying, but it’s hard to tell how they line up without that part of the cohort who died early (or otherwise withdrew from the high dose protocol).
https://www.sciencemag.org/news/2021/01/many-scientists-citing-two-scandalous-covid-19-papers-ignore-their-retractions
Both of the retracted COVID-19 papers, one in The New England Journal of Medicine (NEJM) and the other in The Lancet, were based on what appeared to be a huge database of patient records compiled from hospitals worldwide by Surgisphere, a small company operated by vascular surgeon Sapan Desai, who was a co-author on each article. The 22 May 2020 Lancet paper ostensibly showed that hydroxychloroquine, an antimalarial drug promoted by President Donald Trump and others, could harm rather than help COVID-19 patients. Its publication led to a temporary halt in a major clinical trial and inflamed an already-divisive debate over the drug, which has proved to be no help against COVID-19. The 1 May NEJM article corroborated other evidence that people already taking certain blood pressure medicines did not face a greater risk of death if they developed COVID-19.
Questions soon arose about the validity, and even existence, of the Surgisphere database, however, and the retractions followed on 4 June. But of the 200 papers examined by Science—all published after the retractions—105 inappropriately cited one of the disgraced studies. In several cases it was a primary source for a meta-analysis combining multiple studies to draw overarching conclusions. In most, the studies were cited as scientific support or context. Science also found a handful of articles that uncritically cited an influential April preprint based on the same Surgisphere data set, which described the antiparasitic drug ivermectin as beneficial in critical COVID-19 cases. (There is no standard way to retract preprints, however.)
Ivan Oransky, co-founder of the website Retraction Watch, says such blunders occur because “people are either willfully or negligently not checking references.” Many authors copy and paste lists of apparently relevant citations from similar papers without actually reading them, he says. “It’s frightening. It’s terrible, but common.”
meanwhile,hcq is still useless-
https://pubmed.ncbi.nlm.nih.gov/33165621/
https://www.nature.com/articles/s41467-020-19056-6
https://pubmed.ncbi.nlm.nih.gov/32896292/
https://pubmed.ncbi.nlm.nih.gov/32706953/
https://pubmed.ncbi.nlm.nih.gov/32828135/
Dear God! Nonscientist here who tries to follow, but prefer not to read comments from such a malicious person! You can’t expect anyone to even want to hear what you have to say when you prove yourself so incredibly nasty.
Being extremely unpleasant to one another seems to be all part of the fun, here in the comments section: name calling, off-hand insults and so forth.
I too, was initially surprised by this.
@ Diana, Cthulhu
Ah, the title of the blog did mention “insolence”, isn’t it?
You can try Science-based Medicine, a series of blogs where a friend of Orac is posting similar articles. The comment section is usually more polite. Or more policed, one moderator is working fast at deleting comments which are nothing but insults.
Um, one of the latest article is quite controversial. Maybe avoid it.
That being said, as to here:
– a lot of people here have been posting regularly for 10+ years. So we have some… history. In a few cases, people are clearly entrenched in their opinions, and we are past the point of civil conversation
One guy is quite passive-aggressive and only interested in riling us up. And being banned.
– Whatever job you have IRL, picture some stranger barging in and telling you how to do your job. Repeatedly. And ignoring all your counter-arguments and sources and data.
At some point, you are left saying “you know nothing, Jon”. Sometimes in stronger words.
Or to put it another way, what do you call a misguided fool who thinks they are a genius but don’t even grasp the basic of a field?
I was very irked with the two scientists who claimed a sequence in the spike proteins was “impossible”. Looking at sequences in proteins is my job, and it’s clearly not their. Their “impossible”, I may see it every day.
So, what’s new here?
Orac, I am sorry to hear about the loss of your dog. Whether you lose your dog, or you are Narad and Renate who recently lost their dads, or you are a parent who lose your child to vaccine induced autism, you are all people with feelings who deserve sympathy.
Edit: ‘loss’ not ‘lost’
“For the autism parent, she will continue to live a life of hell until she also dies.”
So “vaccine induced autism” is equivalent to death, is it? Setting aside the fact that it does not exist, your characterization of persons with autism as dead to their parents is disgusting, as is your smarmy offer of sympathy.
I have experienced the loss of a number of people close to me. I know what grief is, and I have been grateful for the sincere expressions of sympathy that I have received. As far as I’m concerned, you can take your offer of “sympathy” and shove it where the sun don’t shine.
Greg was always like this.
As a parent of children with disabilities, his ableism is the main reason I despise him.
Yeah, maybe there is a difference. For Orac, Narad, and Athaic, the grief of losing their dog and dads will likely soften as time passes. They will also have fond memories of their dog and dads. For the autism parent, she will continue to live a life of hell until she also dies. A hell made even more excruciating by the likes of Orac, Narad, and Athaic. Especially, Orac!
Yeah, maybe I am and ‘asshole’, but I am proud one!
Agreed.
I sometimes think that Orac’s minions are being much too kind to anti-vax trolls who come here to spread mis-information/ doubt about vaccines and other medical topics that could hurt people who are misguided enough to follow their advice.
Why be civil to people who are not at all concerned about the welfare of others’ and cavalierly disseminate potentially harmful BS?
Edit to my previous post: Not Athaic’, ‘Renate’. But, I suppose ‘Athaic’ also does some bashing.
@ Denice
Speaking for myself, going all rilled-up and filling the thread with French expletives would be bad for my blood pressure and I would be afraid of outliving the welcome our host is extending to us on his blog.
Also, that would not be very constructive. Also, with newcomers, trying to be charitable. Maybe that one is somewhat honest instead of 100% trolling.
On Orac friend’s blog, one moderator is very consistent in replying politely to the most outrageous and aggravating visitors. Other commenters are also very steady in the face of adversity, constantly answering with cites and pubmed articles. I’m quite impressed by their patience and I’m trying to emulate their behavior.
Although recently, this moderator has been a little less polite. The constant, utterly repetitive barrage of stupid would damn an angel.
@ Athaic:
We don’t have to swear or get upset but we could merely point out how anti-vax causes real damage including death, unnecessary illness and keeps the pandemic alive. We aren’t debating a neutral topic in a university forum
sadmar shared a story about how Null’s protegee, Dolores Perri, and her husband died of Covid when a vaccine was readily available; they were both over 80 but apparently well enough to run small businesses until they got sick. They leave a son. ( The Daily Beast/ yahoo)
Anti-vax commenters at RI present themselves as experts and narrate horror stories of death and “vaccine injury” to scare other parents…
Following anti-vax mothers I learned of how they stop younger, naive women in shops or parking lots, leave literature in doctors’ waiting rooms, flood social media, support dodgy experts and testify at governmental hearings. They think of themselves as educators and whistleblowers when they are only mis-guided, unrealistic conspiracy theorists who lead other astray.
“Following anti-vax mothers I learned of how they stop younger, naive women in shops or parking lots”
We truckers call those types “lot lizzards” and they give some of the most fantastic flowjobs (siq. /s).
@Quasimodo
You say that
Present that evidence or go back to dusting off the gargoyles.
Comparing a child with autism to the death of a loved one is so odious, Greg. My younger son is not “lost” – he’s an intelligent, amazing little dude who happens to be autistic. You are an ugly person, as demonstrated by your consistent dehumanization of autistic people.
Scratch an anti-vaxxer and you’ll find a bigot. Greg is simply an extra-blatant version of this.
@moto_librarian, May you produce a tribe of intelligent, amazing little dudes who happen to be autistic – clearly there must be an evolutionary advantage to intelligent, amazing little dudes who happen to be autistic.
Of course, when you get old and feeble, surely your horde of intelligent, amazing little dudes who happen to be autistic will gladly and gratefully take very good care of you in your dotage, or at least utilise for a team of qualified caretakers and a comfortable dwelling some of the incredible wealth they’ve gained in their profitable pursuits of course aided and advantaged by their being intelligent, amazing little dudes who happen to be autistic.
Oh, the glories of fraternity, charity, statesmanship, science and technology intelligent, amazing little dudes who happen to be autistic bring to the world – which of course the world would never have seen if it wasn’t for the toxins injected in them when they were infants.
Quasimodo, vaccines do not cause autism. In fact, it has been hypothesised that many people throughout history were autistic, well before vaccination existed. Isaac Newton, Thomas Jefferson, William McGonagall, William Bligh. All engaged in behaviours that are today recognised as autistic.
@Julian Frost
Vaccines are toxins? Who knew… I spoke of toxins, explicitly, why do you knee-jerk assume something? Conditioned response a la Pavlov’s dogs?
“In fact, it has been hypothesised that many people throughout history were autistic” – key word, “hypothesised”.
But it’s interesting, have you considered, maybe that venerable list of (perhaps) autistic geniuses gained the attributes by exposure/ingestion of (neuro)toxins in some quantity that didn’t render them a drooling idiot (like mercury-mad-hatter) but disturbed them neurologically to the point of said alleged behaviours?
You must know that those figures you mentioned lived in periods where toxins such as arsenic, mercury, lead, etc. were considered medicinal for a host of maladies,
It’s likely, for example, that The Bounty Bastard, sailor that he was, would have picked up the clap somewhere and had the standard treatment for it.
Or maybe it was some syphilitic-type infection causing these symptoms in these men?
Fascinating, bears further investigation. Doubtless a good book’s worth.
Stay frosty, Julian.
First off, Quasimodo, many antivaxxers claim that vaccines are loaded with toxins that cause autism. You were following a well-worn path, which is why I responded the way I did.
Secondly, Bligh was not the monster popular fiction depicts him as. In fact, he was one of the most lenient Captains of his time, who seldom ordered floggings. Researchers have confirmed this.
What Bligh was was a technically highly skilled but very abrasive man who rubbed people the wrong way, including his subordinates. He had the habit of following orders to the letter. His journey after being set adrift by the Bounty mutineers was amazing. Everyone on that little boat survived until they made land.
The “Bounty Bastard” was a brilliant man.
@Julian Frost
Not very impressive how many assumptions you make, based only on your biased point of view (whatever it is). Can you show us on the doll where and how the bad “anti-vaxxer” touched you?
I’ll try to simplify for you, maybe you smoked a bowl and got too lyrical (see, not only you can speculate), but it wouldn’t be a surprise based on your previous responses if you then accuse me of ignoring the benefits of cannabis products and of traveling the well-worn path of the anti-tokers, or example.
Certain toxins cause certain effects.
It would be worthwhile to catalogue these causes and effects and investigate those less established causes and effects to confirm or dismiss.
The Bastard is what his contemporary disparagers called him, but even they don’t seem to have claimed that he wasn’t ‘brilliant’, but there seems to be a consensus that he was ‘abrasive’ (ie, an asshole).
In any case, my point is that my opinion regarding Autism, based on symptoms and prevalence is that there is evidence that seems to indicate a causative toxic environmental component (wheteher ingested . Pointing out historical figures displaying autism-symptomatic behaviours is worthy, perhaps to find a common exposure between them, whether it’s a substance or a pathogen of whatever kind, or even an heritable genetic component – as you know some of those seemingly autistic figures produced quite a few progeny.
Please note the lack of any reference in any of my comments to vaccines of any type except to dismiss your knee-jerk.
@Quasimodo:
Wow, that was ableist and bigoted.
Maybe you should take some time and think about why you say nasty things about people with autism, and why you say nasty things to strangers on the internet.
Quasimodo, the only assumption I made was that you were using “toxins” as a shorthand for vaccines. W.R.T. your snide comments about cannabis, I have never partaken of it in my life.
The question of what causes autism had been looked at. Overwhelmingly, the evidence points to a genetic cause. Many of the substances that were suspected of causing autism (like mercury) have very different symptoms from it.
@JustaTech
It’s demonstrated in several of your comments that you have an affinity for inveighing various forms of “bigot” towards those you seek to disparage.
Maybe you should think about, explain and define what “bigot” means to you and why usage of that concept as you understand it is so compelling for you, so as to simplify pitying you if apt rather than scoffing at you. Maybe sometimes you are actually even using the word correctly as defined, maybe not.
Reality is what it is – a defective organism is what it is – defective.
If such a defect is possibly induced – therefore, reasonably inferred to be able to be prevented if the cause is identified and avoided, effective persons of ability should pursue preventions and remedies rather than just accepting and even propagating at best through ignorance, such defects and resulting defectives.
Ableist – what does that even mean? You’d have to define that.
In any case, your stated feeling of being victimised by your perception of the nasty, bigoted ableism of strangers on the internet because you’re incapable of grasping the fundamental concepts posited doesn’t prove your subjective feelings realistic rather than delusional, though it could tend to demonstrate your hypersensitive feeble-mindedness to the objectively more able and less bigoted.
As one who “did it [his] way” quite successfully despite indications that he was “on the spectrum” famously sang, “That’s Life”…
Julian Frost, the only assumption I made was none. One can’t and should not need to be on constant alert for meaningless hypersensitive reflexive conditioned responses to trigger words, especially well understood and defined technical words like ‘toxin’ for example.
W.R.T. your fearful recoil from my illustrative cannabis example, you ought to know that nobody cares about your substance abuse habits or lack thereof, besides perhaps law enforcement authorities and your employer, of which I am neither.
“… Overwhelmingly, the evidence points to a genetic cause..” – Julian Frost
So, assuming you didn’t just pull that data out of your posterior annulus, and even if you had but after a quick yet thorough tidying the data is found to be legitimate, perhaps a genetic database of carriers of heritable autism genes and/or a laboratory test for the condition should be established in order to minimise the preventable propagation of these defectives through judicious selective breeding? Similar to the Tay-Sachs disorder and preventive measures taken.
@squirrelelite:
First, let’s fix your sloppy misquote of omission of some of my statements in an illustrative manner:
“[my opinion … is that] there is evidence that seems to indicate a causative toxic environmental component
…
Pointing out historical figures displaying autism-symptomatic behaviours is worthy, perhaps to find a common exposure between them, whether it’s a substance or a pathogen of whatever kind, or even an heritable genetic component”
Your obsession with one causative possibility out of several explicitly yet non-exclusively clearly and unambiguously specified as “my opinion”, has nothing to do with my solicitation of data on this topic.
All this time the conventional wisdom has squirrels, elite and proletarian alike, collecting nuts – yet here we have you, picking cherries – and failing at that, too.
A very interesting interview with Christian Drosten, for those who are able to read German. Perhaps Google translate can help. He also explains why it is higly unlikely, the virus was created in a labratory. He states the the furin cleavage site is not the only way the virus differs from other SARS viruses. If in a labratory, they would do an experiment with the furin cleavage site, they would take an available virus like SARS-1 and just change the furin cleavage site. He compares it with changing the car-stereo in an existing car. If you want to look if another car-stereo would work better, you are not building a new car, to try this, but take an existing car and just change the car-stereo.
https://www.republik.ch/2021/06/05/herr-drosten-woher-kam-dieses-virus
My comment is not meant to be an absolute scientific rebuttal in the sense of proving the virus is of laboratory origin. This requires a clear paper trail from the institute. Due to apparent spoilage this level of evidence is not available. It is a question of liability and legal culpability: Most of the dissenting comments seemed to have missed this. We are dependent on experts to tell us the possible mechanisms and pathways and to tell us the likelihood that such a pathway would or would not be followed. The fact that we have the virus means that such a pathway is possible. Clearly if a pathway is possible it may occur in our world; otherwise it would be supernatural. But I think everyone will agree that natural means purely random or by chance; whereas engineered means that is some degree of human intervention.
In the end there are two possibilities: the virus evolved naturally (without engineering) from a progenitor or the virus was engineered from a progenitor.
The purely natural origin: The virus arose by chance. This virus may have arisen in a zoonotic population and transmitted to a human or it may have arisen in a human harboring the virus and then gained infectivity. To this, one could add the initial ability to infect humans naturally occurred in the bat caves and this strain is the backbone virus to the virus we now know as SARS2. As far as I know, neither a zoonotic intermediate or origin in a bat cave that infected humans has been established.
The engineered pathway has two sub-pathways: direct manipulation with insertion of genetic material or indirect manipulation by culturing through human cells is done until a virulent strain emerged.
There should be no argument that one of these pathways needed to be followed. In a court of law, the fact that one of these possibilities (plus the hybrid pathway) needed to be followed in order that the COVID-19 virus could emerge.
In a court of law, agreed upon facts or facts that are established are stipulated facts. I think everyone should agree with this position.
These are the stipulated facts:
There is a Wuhan Institute of Virology.
Viral research was done at this laboratory.
Published, peer review articles by principles at the WVI indicate viral modification research on coronaviruses of bat origin.
COVID-19 is a coronavirus with high homology to identified bat coronavirus strains.
COVID-19 is a coronavirus exquisitely adapted to infect human AEC receptors.
COVID-19 is easily spread among humans.
Prior high virulent coronaviruses such as SARS1 and MER had readily identifiable zoonotic intermediates.
To date, no such intermediate has been found for SARS2.
Contested point: was the viral modification research gain of function or not? Here the experts disagree with the disagreement centering on the definition “gain of function”. The common understanding is giving a virus something it does not have. From a military point of view, modification of pathogen to a more lethal pathogen (gain of function) has dual function (it can be used in for either civilian or military use).
In order for the virus to have originated in a laboratory in Wuhan, two different necessary conditions are needed (but these are not sufficient);
For the virus to have emerged in Wuhan, the epicenter of the disease (and so called patient zero) should be in Wuhan. If this fact is not true, then Wuhan is not the origin center of the virus and the Wuhan Virology Institute is unlikely to be origin. (Discounting the possibility of making the virus and exporting it to another location prior to its emergence).
For the virus to have emerged in Wuhan it must have emerged in the wet market or in the laboratory. The wet market theory has been discounted for two reasons: no zoonotic intermediate has been found and the incubation period of the virus indicates that if it was first spotted in the wet market it actually emerged prior to the wet market.
In addition, the following conditions are necessary but not sufficient:
There must be a viral laboratory in Wuhan.
The viral laboratory should be engaging in coronavirus research.
These two conditions are established.
If any of the above are not true, then the virus is not of Wuhan laboratory origin. But all of the above are established. From the above it is clearly possible for the virus to be of WIV origin. The question then becomes which pathway is more likely. This is a question of probabilities not possibilities.
All the evidence strongly suggests (has a greater probability) that the Wuhan laboratory is the site of origin of the pathogen we know as COVID-19 than a purely natural origin.
In a court of law there are 3 levels of guilt:
Regulatory law: the fact speaks for itself. Example: speeding ticket. The level of proof required is 100%. The cop using laser technology clocks someone at 50 MPH in a 25 MPH. As long as there is no question of identity and the laws of physics hold, the defendant is guilty and the guilt is defined by and negated by the payment of a fine.
Civil litigation: more likely than not; usually quantified at 51% and assuming no shared liability. Here the defendant not committed an action in which liability to pay for damages is part of the liability.
Example: a moving vehicle crashes into a stationary vehicle. The law says the moving vehicle is always at fault. Here there may be shared culpability if the stationary vehicle stalled out at a site which it should have been moving.
A business fails to clear the ice off its sidewalk and fails to establish a warning. If it fails to clear the ice and the law says a business must clear the ice this is a regulatory violation subject to a fine. If a business sets up a warning it does not have further culpability. If it does not set up a warning it now has civil liability and is subject o much harsher penalties.
Homicide or the death of an individual: The death is classified as natural or unnatural. Natural death means the patient died from natural causes or more fundamentally, the action of another individual is not involved. Unnatural death requires the action of another and includes homicide, suicide. Finally a death may be unclassified.
Unnatural death bifurcates into lawful and unlawful homicide. Lawful homicide is the action of a soldier in war in accordance with the rules of engagement or a police officer protecting himself or another (in accordance with the standards of training).
Unlawful homicide includes murder, felony murder, manslaughter, reckless endangerment and suicide.
Murder 1: this requires intent and the level of proof is beyond a reasonable doubt. Note that it is not beyond doubt nor is it beyond a shadow of a doubt. It is beyond REASONABLE doubt.
Murder 2: something that is not murder 1 or murder 3. The exact legal definition is often one of statutory law. This requires the death of one by the hands of another and the action linking them is beyond reasonable doubt but there is a question of “mens rea” (intent) as opposed to a consequence of action.
Murder 3 or manslaughter: death by action but the action is the result of an accident (such as the head of an axe detaching from the handle and killing someone or hitting someone with a car).
Murder 4: Reckless endangerment: engaging in an action that is likely to result in death and in which only a depraved mind would do (such as poisoning a water reservoir with cyanide or driving drunk). In reality the standard of a deprived mind is difficult to establish and so this is rarely utilized in prosecution.
And finally we have the question of spoilage, wherein evidence is destroyed by the defendant (and its opposite, when exculpatory evidence is withheld by the prosecution). Spoilage is considered to a factor in determining guilt. The WHO investigation showed evidence of spoilage but lacked establishment of proof.
The question is not a question of absolute scientific establishment but of legal culpability.
Given these standards, it is clear that the laboratory origin of the virus is more likely than a natural origin and approaches the standard of beyond reasonable doubt.
Thank you, Pathcoin! It is people like you and Wade giving detailed assessments of why you believe the lab-leak hypothesis is true, and even if you’re coming from different angles. As for the zoonotic pushers, they will cease on any tidbit of such assessments to try and discredit it, and while dogmaticly declaring the zoonotic explanation superior, but giving little or no supporting evidence of their own.
Um, where’s the due diligence on the zoonotic origin? You’ve gone into great detail on your pet theory, but you’ve left out all the numbers that show the zoonotic as most likely? Are you usuing the judicial slant because you don’t understand the science and stats? I know they are complex fields, but science holds to a much higher standard than a court of law.
I want to know what is true, what is most likely, and whether there is anything that can be done to prevent. Basically,, seeing it as intentional bio weapon can be dismissed out of hand, as it’s highly inefficient. So two realistic option accidental leak and natural pathway. Two possibilities but NOT equal probability! Lots of animals, gazillions of virus vs one incidental lab leak that requires a uncontainable breach that is not even noticed or followed up on by the person responsible, that wasn’t noticed by any weird patterning of illness in the area all leading back to the lab.
So with no evidence of manipulation, the rare event that a natural sample from the lab, with the place where they got the sample to multiply billions of times outside the lab, and you think the lab leak is still responsible?
@Pathcoin Published paper do not indicate research of bat coronavirus. Backbomne of chimera virus came from mouse coronavirus. Quite natural, because mice are lab animals, bats are not.
Sequence similarity between this chimeric virus and SARS CoV 2 is low (80 %), much lower than between naturally occurred viruses and SARS CoV 2.
The image used at the beginning of this post is from the Wuhan Institute of Virology. The brick work is shoddy. Hmm, maybe that doesn’t matter.
@ Orac,
How old was your dog, in human years, when it passed? Likely had a damping effect on your respectful insolence over the years. A higher-frequency RI is noticeable.
This is completely off the main topic, but I feel the need for a little light relief from today’s array of small-minded cranks and the wilfully innumerate.
I don’t know how this company name reads to a North American audience, but for the British, Irish, Australians and New Zealanders it will raise a chuckle. Very apt.
“He runs Atossa?”
“He is Atossa!”
sb “tosser”
Stop Bowdlerizing stuff. It just makes it look like yu were born in the ’50s.
https://www.urbandictionary.com/define.php?term=tosser
This South African also laughed.
Oops, sorry, I forgot South Africa! You’d think I’d have learned by now…
This North American gets it!
In other news…
A few times a week, I listen to Mike Adams’ daily audios: usually I can only stand 10 minutes which I know is quite outstanding for a SB person. In yesterday’s episode, DROUGHT….” he began with an aside *that is now removed. He warned that soon, all hell will break loose and our very lives will be in danger, especially those who live in corrupt, evil crime syndicates ( cities) Drought, fire, no electricity, no food, roaming criminal gangs . Mike tells decent, clean living country folk how to prepare: Hhe paid for a prescription for ivermectin which is rather costly but he knows that there is a horse paste version that costs only a small fraction of that exorbitant price and is available at the feed store. He tastes some, declares it awful but says it’s better than paying pharma big money for human meds- he’ll
use it! He says he’s not telling anyone to do this but it seems he’s teaching them how. He notes that fish antibiotics are now banned by the FDA. I doubt this.
.
I wanted to replay that part today but noticed that the total time was less by 5-6 minutes, so checking I didn’t hear any of the ivermectin part- it was GONE! He rants on about liberal death traps and the total breakdown of society, the economy and fiat currency as he always does.
A few weeks ago, I discovered that the other idiot ( PRN) whilst showcasing his current rants ( a series of about 40 self-improvement tapes) predicts pretty much the same scenario with less guns BUT sandwiched within the layers of recent dreck were a couple of 1990s episodes in which he says the very same thing!
Disaster porn like this enables woo-meisters to frighten followers about their health or general life issues and then sell them relevant products and instructional videos/ books .Mike also now has a sponsor, a satellite phone system for when cell phone service disappears.
After momentary panic, I found that you can still buy fish antibiotics online, including such stapes as cephalexin, ciprofloxacin and clindamycin. I guess we should stock up in case the FDA bans the stuff, but am puzzled why we should trust Finned Pharma.
In Adams’ case, it might be appropriate to prescribe Super Ick Cure.
https://www.chewy.com/b/health-wellness-937?gclid=CjwKCAjwtpGGBhBJEiwAyRZX2kcJDbYMnEvZew74h4iNEk5_J6mzh4pux0ySHH5O5xAyr54G7QXz3BoC_gIQAvD_BwE
CGGG CGGG?
Super Ick?
Aaargh!
Bill the Cat for President!
https://i.pinimg.com/originals/26/dd/6c/26dd6c2048e32a7860b30179bda3c54c.png
“If you are trying to get at me as a public health official and a scientist, you’re really attacking not only Dr. Anthony Fauci, you are attacking science.”
— Anthony Fauci
I believe your religion is about to lose many of its followers as your cult leader just effectively said that he is “science” and people must never question him. (not very scientific).
You had a good run. You told men, women and children to cover their faces and many did. You didn’t quite get to stonings and public executions but maybe next time.
Ha ha ha ha ha ha. You’re right! Lets get rid of science. What America needs is witch craft trials and human sacrifice to make sure that spring returns after winter.
I presume you inveted the citation. Typical for Trump cult. (Masks and and stonings are quite diffrent.)
Still no argument I see
@Aarno Syvänen
As usual you are wrong. You didn’t even take 10 seconds to google it?
I guess presuming things is your scientific method.
That’s true but both are tools of radical religions like yours.
Let he who is without sin cast the first stone…. {god dammit, mom.}
No, the quote from Dr Fauci is genuine. Here it is with a bit more context:
From https://www.cnbc.com/2021/06/09/fauci-blasts-preposterous-covid-conspiracies-accuses-critics-of-attacks-on-science.html
https://www.cnbc.com/2021/06/09/fauci-blasts-preposterous-covid-conspiracies-accuses-critics-of-attacks-on-science.html
Quote taken out of contest. SOP for covidiots
Give him the money-shot here because he might be like Dory; A regal blue tang who suffers from short-term memory-loss and is a bit ditzy.
“A lot of what you’re seeing as attacks on me, quite frankly, are attacks on science, because all of the things that I have spoken about, consistently from the very beginning, have been fundamentally based on science,”
==/==
““If you are trying to get at me as a public health official and a scientist, you’re really attacking not only Dr. Anthony Fauci, you are attacking science.”
@TBruce
Thanks for providing another gem.
“A lot of what you’re seeing as attacks on me, quite frankly, are attacks on science…”
–Anthony “The Science” Fauci
You left something out, Dave:
Why?
See what I mean?
Because it’s a subjective statement that he makes about himself and which can easily be disproved.
His contradictory recommendations on masks had nothing to do with changing science.
Feb 8th 2020
“The typical mask you buy in the drug store is not really effective in keeping out virus, which is small enough to pass through the material. ”
Later on he started recommending that everyone should wear masks. Did the virus grow in diameter? Maybe the ‘1000 monkeys” theory that Gorski is promoting has caused the virus to balloon in size.
Also his push for prolonged lockdowns was anti-science. Even WHO is against lock-downs.
For the REAL story about the REAL Anthony Fauci, Mike Adams interviewed RFKjr who has a new book coming out, published by Skyhorse. ( yesterday, NN/ Brighteon). ‘Mass murderer’ and diverse appellations are tossed about by Kennedy as he weaves an intricate tale of crime, death, deceit, racketeering and vast wealth. Pre-order now! so it gets on the Best Sellers list.
The interview is 34 minutes long: I lasted about 10.
I thought Junior had hit rock bottom when he sucked up to Trump to head a “Vaccine Safety Commission”. Looks like he decided to get out the diamond drills and dynamite. What a creep.
@Scientism Dave You seems to think that changing your opinion is unscientific ? Quite contrary, if my opiniuons and facts contradict each other, I change my opinions.
CGGCGG hosted some pretty good rock and punk acts in its day.
The Ramones lyric this thread brings to mind:
Now I want to sniff some glue
Now I want to have somethin’ to do
All the kids want to sniff some glue
All the kids want somethin’ to do
One-two-three-four-five-six-seven-eight!
I am not falling into this. I am not going to round up all the CGG CGC GCC. I’m just not. https://youtu.be/AnWWj6xOleY?t=1
Yea? Stick it up your ass. And turn your dick around backwards to make a little click. God. Ihate my generation is a steotpe.l
https://xkcd.com/2475/
OT but not OT.
XKCD is never OT.
xkcd is on a roll: https://xkcd.com/2476/
How relevant/valid are reports that Covid-19 was circulating in other parts of the world (Italy) as early as September 2019? Some have found samples from other research that show antibody production or genome indicators. Would that provide the means for a mutation to occur that provides more aggressive spread and lethality over time? Apparently viruses are everywhere and make normal people sick.
https://www.reuters.com/article/health-coronavirus-italy-timing-idINKBN27V0KH
https://www.reuters.com/article/us-health-coronavirus-spain-science-idUSKBN23X2HQ
I’ve read a study of genomic variation in early samples from China that discussed two variants that were circulating in December. Unfortunately, I haven’t been able to relocate the link for it. Analysis of the genomic variations suggests they may have diverged in October 2019. So a September case is not wildly out of range.
It would certainly be interesting to review the chest X-rays of pneumonia patients from October-November and see if they look like Covid-19.
The Spain sewage sample pushes the bonds a lot and will require careful study and verification.
Yeah — not sure what that sewage excavation project is all about but interesting if that shyte has scientific value! Otherwise I accept that by nature there isn’t often a great meteor strike / smoking gub out there that we all agree is the culprit. I do think that enough similar virus was knocking around in our system way prior to Wuhan to discount a leak theory. I’m open to evidence to stomp my bias. Thanks for info!
The ‘worst’?! What?! Man – I suppose these scientists have never met Orac or been to this site.
Nice person’s thread up above has this
https://twitter.com/AtomsksSanakan/status/1403082217820246019
“Schmoke and a pankakke?” — Goldmember (probably)
Yet here you are.
In the absence of positive evidence, there is not much basis for a debate. If you do not assume a conspiracy, then you should presume that the Wuhan lab was being run in accordance with general international rules for handling biohazards, that the management and employees properly investigated any violations of those rules, and that they acted in good faith when they researched their collected samples in late December/early January 2020 to see if one of their samples might have been leaked.
That investigation identified the RaTG13 genome discussed in this paper.
https://academic.oup.com/nsr/article/7/6/1012/5775463
But that genome is only about 97% similar to the original Wuhan samples. And it lacks the furin cleavage site.
One paper I’ve seen cited as “evidence” involves several protocol violations at the U.S. AMRIID lab in Fort Detrick, Maryland.
https://wjla.com/news/local/cdc-shut-down-army-germ-lab-health-concerns
That lab also had problems with its steam sterilization system used to treat waste. But no human exposures resulted from those violations.
Those violations have been investigated and corrected and the various labs are fully operational again.
Without specific evidence, we are left to discuss the relative probabilities of a technically possible but infrequent and unlikely accident of the type these labs are specifically constructed to protect against versus disease transfer from animals to humans which happens practically every day around the world although highly infectious new diseases are relatively uncommon.
“You didn’t quite get to stonings and public executions but maybe next time.”
If the next pandemic involves an infectious disease which is much deadlier and more highly transmissible, tolerance for the obfuscating, lying and obstructive crap we’ve seen from denialists and antivaxers will be severely diminished.
This afternoon we were driving through a place in Kentucky that bills itself as the “Bourbon Capital of the World”. They had a set of public stocks downtown and someone was having his picture taken “locked’ in it.
Might be useful for dealing with a future edition of “America’s Frontline Doctors”.
Off topic:
@ Orac,
WTF, at the end of each comment I’ve noticed a “Like” feature that can be optionally clicked. This is surprisingly inappropriate for a blog titled, Respectful Insolence. Recommend that you remove the “Like” feature and replace it with “Dislike.” Let’s provide increased pleasure for the minions!
@ Denice Walter,
Can you do me a favor? Please ask Orac to answer at least two of my on-topic questions in the next 12 months. Thank you!
First of all, I have no impact on Orac’s decisions which are entirely HIS BUSINESS and even if I did, I wouldn’t be recommending your obsessive, mindless dreck when we have at least a score of regular, well-informed and usually quite hilarious commenters. Maybe more.
A federal judge has rejected the claims of over 100 staff members of a Houston hospital who challenged vaccine requirements for workers . .
So? They can get higher pay at MickyD’s now ( there are still no takers here). Imagine that. Essential workers.Pfft.
I wonder how many of the healthcare workers already have natural immunity to the virus. They need to be tested for antibodies and T-cell immunity. If positive, they do not need to be vaccinated. The vaccine is a sad attempt to duplicate superior natural immunity. Those who have had Covid 19 and recovered need to be counted. There are many of us. https://www.medpagetoday.com/infectiousdisease/covid19/92836
FYI
Kristian G Andersen whose tweets Orac uses in his article has deleted his account and I can only assume is currently searching for a criminal defense lawyer.
My understanding is that Dr. Andersen apparently left Twitter because of the harassment from “lab leak” proponents like you after Anthony Fauci’s emails were released. I don’t blame him at all if that’s the case.
Go home, young man:
https://youtu.be/8_qDYgEpEtY?t=368
Anderson to Fauci….
Never mind that two months later Anderson would go on to author a paper and –voila!– everything was now kosher, but, with the subsequent email fallout, something I am amazed he was never asked was what ‘small’ portion of the genome he initially thought looked engineered. If he were to truthfully answer, buckets to donuts I would expect him to say the furin insert.
Somebody should interview Eddie, Bob and Mike.
I’ll go even further, and predict that in addition to the furin cleavage site, they were looking at the three predicted O-linked glycan residues and at the six receptor binding domain residues as potentially engineered.
Of course, unlike Greg, I have actually read the paper in question, where they discussed why these sites looked like they might have been engineered, but ultimately concluded that they weren’t.
@Greg You forget this part
“But we have to look at this much more closely and there are still further analyses to be done, so those opinions could still change.”
Of course, Andersen is not only scientist opposing lab leak hypothesis, either.
And Dr Anderson responds…
https://www.nytimes.com/2021/06/14/science/covid-lab-leak-fauci-kristian-andersen.html
Kevin Vicklund also writes….
Indeed, in the paper those things were discussed, but language of them looking potentially engineered was never used. It’s in contrast with him being more ‘forthcoming’ with what he wrote Fauci, and now with this Times interview.
And, here is Pompeo telling Fox that the government has enormous evidence of a lab leak. Interestingly, though I agree that the circumstantial evidence pointing to a lab leak is quite strong, I have to agree with Orac that nothing new has cropped up to justify this about face with taking the theory seriously. Three scientists at the lab coming down with flu-like symptoms that they needed hospitalization? C’mon!
Could it be that Pompeo is right, and the government has more information than they’re letting on? Could it be with the investigation that Biden ordered, they are just trying to get ahead of the curve before really ‘damning’ stuff starts surfacing? Could it be that Pompeo is now serving a salvo.
https://www.foxnews.com/politics/pompeo-covid-leaked-wuhan-lab
Greg, what the fuck do you think “Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus” means? Dude, you’re grasping at straws in the middle of the ocean.
@Greg I have heard this argument any number of times, Wehave evidence. but we cannot publish it because it damages national security. In other words, zero evidence is given,
Kevin, you are missing my point. Reading the paper, it seemed all Anderson did was waive away the furin site and the other concerns; no language suggesting engineered was used despite him sharing that concern with Fauci. Anderson could’ve been a lot more forthcoming in his writing.
Greg, what the fuck do you think “This is strong evidence that SARS-CoV-2 is not the product of purposeful manipulation” means?
I’ll try again…
Anderson told Fauci that a certain portion of the genome looked engineered, and we are learning it was in reference to the furin insert, yet rather than letting on about this, in the paper he pretended it was all kosher and could be accounted for. How can one not conclude that he was deliberately over selling the zoonotic explanation by not being fully forthcoming?
Kevin, what’s your take?
Also, another writer asked, If it took Anderson only 3 days to resolve the ‘inconsistencies’ with the virus genome, why did he not put in the effort in the first place rather than bringing it to Fauci’s attention? Kevin, don’t you think that’s also a very good question?
@Greo Perpaps she did some genomic database searches ? Lysine repeats are common, CGGCGG is present in bat coronavirus, furin cleavage site has evolved multiple times among coronaviruses.
Like the election was going to be turned by supreme court? LOL,keep coping.
Maybe, Aarno. Or, maybe this is the true smoking gun that is now ‘prompting’ people, especially the US government, to take the lab leak theory seriously.
https://www.express.co.uk/news/world/1452011/China-spy-defection-US-latest-wuhan-lab-leak-Dong-Jingwei-joe-biden-world-war-3
Interesting, if true, as article itself states
Aarno, I think you are missing the point. Again, why yell ‘fire!’ at Fauci instead of doing those searches that apparently weren’t too arduous that they only took 3 days to complete?
We have news of another Covid-19 vaccine with reported 90+% effectiveness (Novovax).
In keeping with its policy of encouraging prolongation of the pandemic, the Fox News website has consigned this story to the bottom of its page, while hyping two other stories: one about a doctor and his wife who contracted Covid-19 a year and a half after being vaccinated (the vaccine isn’t perfect, so don’t get it, Fox fans), another with this headline:
“Coach says COVID vaccine had no role in star player’s sudden on-field collapse”
If you bother to check out that story (about a Danish soccer player who apparently suffered a cardiac event), the coach was quashing rumors, saying that the player “didn’t have Covid and wasn’t vaccinated either”. Fox would like casual readers to infer that a vaccine was involved.
Utter slime.
https://arstechnica.com/science/2021/06/we-have-another-highly-effective-covid-vaccine-based-on-different-tech/
Umm really?
Which COVID-19 vaccine was available in December 2019?
I can’t be bothered to wade through FOX news and find out what is being reported.
Yeah, I biffed the characters in Hamlet. It’s more like 10^5. Not 10^15. Oops.
The test of the math is still right.
Unless I mistyped another number….
Even if the rest of the maths is correct, using a number of characters that is too large by a factor of a billion will vastly inflate the result.
It turns out, though, that when actual monkeys are given access to a typewriter in experimental conditions, the output appears to be anything but random: https://en.wikipedia.org/wiki/Infinite_monkey_theorem#Actual_monkeys
The right wing weirdosphere is ganging up on Dr Fauci, predictably ignoring Trump’s failure of leadership that contributed substantially to the six hundred thousand lives lost from COVID-19 in the US.
https://www.vanityfair.com/news/2021/06/republicans-anthony-fauci-covid-19
RFK jr has joined the club. Junior’s new book is titled The Real Anthony Fauci and of course links Dr Fauci to Bill Gates and Big Pharma with the subtitle: Bill Gates, Big Pharma, and the Global War on Democracy and Public Health. Release expected around July 20.
Good beach book – to start a beach fire, maybe.
Farenheit 459 aside, if it is gossy, you probably should not allow a whiff. Prop 65 and all.
remember when cadence owens said she had bad experience from hpv vaccine at a age but the hpv vacccine wasn’t even market on that time-
RFK Jr.’s hit piece on Fauci will resonate with the same readership that glommed on to Charles Ortleb’s book comparing Fauci to Bernie Madoff (Ortleb’s impeccable scientific credentials include being an HIV/AIDS denier) and the book “Faucian Bargain”, written by a pair of right-wing talk show hosts, Steve Deace and Todd Erzen. Deace in particular is a real lulu, recently writing:
“Why are we so stricken with panic in our time, shutting down our entire way of life on unreliable and contradictory data, despite the technological advantages we have over them?”
“Because ours is a godless society, so we are afraid of our own mortality. Deep down we know we are not ready to meet our Maker after denying Him for so long. Therefore, we wait for our secular Messiah, government, to deliver us from that day. Or at least hold it off for as long as possible.”
Yeah, if you’re right with the Lord, you don’t need to worry about serious diseases and taking precautions to avoid even worse pandemic mortality and morbidity than we’ve already seen. Just calmly accept your fate, sheeple.
And if you don’t die, but develop long covid, it will make you humble, because you might get dependent from charity.
Why is it that those so fiercely pro-vaccine are willing to toss common sense out the window & hone in on “may be’s” & “could be’s” regarding cggcgg as evidence disputing lab origins? Why is it so important to you that it be zoonotic? It doesn’t make the vaccines less “needed” either way.
Seriously, if you think the geographical coincidence, findings of adenovirus vaccine sequences in early patients, the fact that Dr Shi’s first response was “Could this have come from our lab?”, the fact that she altered WIV computer databases on December 30, 2020, how China managed to contain covid so quickly AND the genetic signature are all dismissable, is confusing.
Whatever is it about the possibility of lab origin that makes the provaccine throw common sense out the window? No street smarts? My gosh this is sad.
I found this article to be a good overview of the lab leak speculation.
https://foreignpolicy.com/2021/06/15/lab-leak-theory-doesnt-hold-up-covid-china/
For me, I’m looking at/for evidence, clear and true, from those who promote the lab escape view. Still waiting for something about the lab theory that has certainty above the competing theories. Not produced yet, but obviously raged about by filthy fox media and other nuts.
Here’s a tissue to cry in for your sadness. Sorry you don’t understand how important the exchange and evaluation of evidence is for so many people. Sad you continue to be so happily misinformed. Most folks here are so credentialed, capable, and experienced to see what is real and what is not, based on evidence. Seriously, here is known common sense and data sense. You, not so sure. Bummer.
Funny, I am waiting too. Waiting for the zoonotic backers to give me a little more than that’s just how these pandemics occur. Desperately losing faith that those pesky bats will ever be found.
@1000 Links to a Furlong,
You “credentialed, capable, and experienced” posters here don’t seem to be able to see the forest for the trees.
This seems to be correlated with absolute faith in vaccines. It’s odd.
Something something Pasolini something.
There is the Narad that we all ‘love’. Where have you been, brother? It was starting to get boring understanding all the insults hurl my way.
@ Kincaid & Greg
Your shoes just don’t fit me.
Overwhelming evidence on zoontic transmission presented here. I dig it but you don’t. Are you qualified in any way to make an argument for or against anything that has to do with vaccines or COVID? Just let me know! That’s where I start.
So far you are you are just talking euphemisms and gardening tips at best.
Thanky!
Seriously ‘1000 links’, after Wade blew to smithereens your two main arguments from the Anderson ammunition chest, I am left wondering what else you guys have. You know, that if the virus was manipulated it would’ve left a trace and a backbone template would’ve also been obvious. I notice you guys have practically abandoned those talking points.
So, what else do you all have, ‘1000 links’? Just that animal spillovers are usually the culprit? Oh! — and two different strains were detected in Wuhan at the start of the pandemic? Don’t hold back now, ‘1000 links’, light me up with your ‘overwhelming evidence’, and even if I am too ‘stupid’ to understand it.
@Greg What two arguments of Andersen Wade destroyed ? I am curious
Anderson’s argument 1: Based on calculations, scientists wouldn’t have designed the virus that way..
Wade’s rebuttal….
Anderson’s argument two: If engineered, the backbone of the virus would’ve been obvious.
Wade’s rebuttal
@Greg
1 Wade says that SARS CoV 2 is a perfect virus, which shows it is enegineered. Then he says that a crucial piece of its infectivity need not be perfect, after all. An obvious contradiction.
2 A random backbone could indeed been used. A wellknown backbone would be better, however. Then you would know better what you get.
These are, of course, not her best arguments. Evolutionary tree of viruses is much better.
The chimeric virus produced by Wuhan lab has 80% sequence similarity, very low. This is because the backbone was mouse coronavirus.
“Signatures” : lysines in row are common, CGGCGG can be found ib bat coronaviruses (flying foxes, which are eaten as game).
China stopped coronavirus with total lockdown.
Who told you that dr. Shi destroyed research data ?
I’m just gonna copy paste it considering it’s 1.46 am where I’m. The links are here-https://medika.life/debunking-nicholas-wades-origin-of-covid-conspiracy-theory/#
Nobel-Winning Virologist David Baltimore Eats Wuhan Crow
The writing is here,only an excerpt of course-
More personal than molecular biology…
Wade spends much of his essay doling out personal takedowns of some key coronavirus researchers who have communicated scientific observations contrary to his opinions. The first of many victims is Dr. Peter Daszak, and the second is Dr. Kristian Anderson, followed by others.
Let’s focus on Wade’s attacks on Dr. Anderson since Wade presses several buttons here. First, Dr. Anderson and his team published a Nature letters article early during the pandemic explaining why an engineered origin of the virus was unlikely.
In the first step of Wade’s assault, he characterizes Anderson’s Nature letter as “…an opinion piece, not a scientific article…”. Wade’s Wikipedia page says that he was an editor at prestigious scientific journals Nature and Science, and therefore clearly knows better. Wade’s claim that a Nature letter like Anderson’s is only opinion and not a scientific article is not a small error, but an intentional assault on facts and truth.
A blog by Nature lays out the difference between these two formats quite clearly:
Articles are original reports whose conclusions represent a substantial advance in understanding of an important problem and have immediate, far-reaching implications.
Letters are short reports of original research focused on an outstanding finding whose importance means that it will be of interest to scientists in other fields.
Nature letters are NOT merely opinions. This has been a long-standing feature of Nature. As a prime example, the biggest biological discovery in the 20th century may be Watson and Crick’s discovery of the double-helical and complementary nature of DNA’s structure — published in a Nature letter. Clearly not just an opinion piece.
Any science writer knows that a couple of the most important science journals are called Physics Letters A and Physics Letters B.
These Nature letters represent important scientific reports. Clearly Wade found it necessary to jettison his editorial knowledge from working at that very journal in order to diminish and dismiss Anderson’s data, discussions, and conclusions.
Furthermore, when Wade tries to tackle Anderson’s data, he remains firmly in personal attack mode with comments like:
…Unfortunately this [Anderson’s article] was another case of poor science…
Wade liberally sprinkles much more of these snide and passive aggressive attacks throughout his essay. A journalist passing judgement on a scientist’s science, suggesting himself as more knowledgeable than the scientist, and co-opting a position as a science educator while peddling obvious errors and alternative facts as science.
A poor attempt at molecular biology…
When Wade finally argued Anderson’s data and discussions, we immediately saw how out of his depth and off target he was — and therefore why he spent so much time trying to damage those with opposing views. Wade clearly found that damaging reputations was much easier than arguing the points of a field in which he was unqualified.
The first argument Wade made with Anderson was about seamless methods of cloning or DNA manipulation. Wade referred to early methods of molecular cloning that left easily detected remnants or scars in the DNA sequence. The trouble with this is that Anderson never invoked genomic scars in his paper.
Perhaps Wade was familiar with seamless cloning technology — if your only tool is a hammer, everything is a nail. One such technology was called “No see’m” and was developed and used by coronavirus researchers. Aside from Wade’s error in calling it “No-see-um” which is a type of incredibly irritating biting gnat, his bigger error is that his argument was irrelevant.
Anderson’s article said nothing about seamless technology, and instead said the following:
…Furthermore, if genetic manipulation had been performed, one of the several reverse-genetic systems available for betacoronaviruses would probably have been used19. However, the genetic data irrefutably show that SARS-CoV-2 is not derived from any previously used virus backbone20.…
Anderson was referring to a characteristic set of restriction sites, natural or engineered, necessary to work with each of the reverse genetic systems — nothing to do with seamless cloning.
Reverse genetics covers a broad range of scientific methods, but common among all is the idea of changing the DNA sequence (what biologists call the genotype) and then looking for changes in the organism (its features, behaviors, chemistry, etc., all lumped under a typically obtuse scientific term, phenotype). When applied to viruses, often the goal is to see when a non-human virus becomes capable of infecting human cells.
Then Wade tried to falsely characterize one of Anderson’s arguments:
…they [Anderson et al] say that the spike protein of SARS2 binds very well to its target, the human ACE2 receptor, but does so in a different way from that which physical calculations suggest would be the best fit. Therefore the virus must have arisen by natural selection, not manipulation…
This is a major misrepresentation and oversimplification of Anderson’s argument. The S protein shows strong binding affinity for the human ACE2 protein, but ALSO to ACE2 proteins from other species. The viral S protein evolved in a way that bound well, but not optimally to human ACE2. Any synthetic S protein would have been engineered specific to human ACE2, and the binding would have been much more “tailored”.
What Anderson actually said was:
…SARS-CoV-2 …binds with high affinity to ACE2 from humans, ferrets, cats and other species with high receptor homology… SARS-CoV-2 may bind human ACE2 with high affinity, computational analyses predict that the interaction is not ideal7 and that the RBD sequence is different from those shown in SARS-CoV to be optimal for receptor binding7,11. Thus, the high-affinity binding of the SARS-CoV-2 spike protein to human ACE2 is most likely the result of natural selection on a human or human-like ACE2 that permits another optimal binding solution to arise. This is strong evidence that SARS-CoV-2 is not the product of purposeful manipulation…
What Anderson meant was that computational calculations show that the binding between the viral S (spike) protein and the human ACE2 protein are not “ideal” — ideal being what we expect from an engineered S protein. An engineered SARS virus might have used one of two routes:
Insert into the viral genome a known S protein with strong binding to human ACE2 protein.
Passage through cells and use only human ACE2 as the target.
Either route would have resulted in a much better, more customized fit of S protein to human ACE2.
Anderson argued that there were multiple ACE2 protein targets including those from human and other animals, which strongly suggests a natural origin.
The fact that Wade did not understand this basic biological concept shows how lacking his technical background is, and emphasizes his lack of qualification to pass judgement on the scientists or science being discussed.
The irony is that Wade tried hard to imply that it was Anderson, the Ph.D. virologist, who lacked technical understanding of virology. Wade says of Anderson:
…The authors’ basic assumption, not spelt out, is that anyone trying to make a bat virus bind to human cells could do so in only one way. First they would calculate the strongest possible fit between the human ACE2 receptor and the spike protein with which the virus latches onto it. They would then design the spike protein accordingly (by selecting the right string of amino acid units that compose it). But since the SARS2 spike protein is not of this calculated best design, the Andersen paper says, therefore it can’t have been manipulated…
Note how Wade tries to tell us what Anderson’s assumption is? He tells us that the “authors’ basic assumption, not spelt out, is that anyone trying to make a bat virus bind to human cells could do so in only one way.” That is emphatically NOT Anderson’s basic assumption.
Anderson et al are virologists and they know (far better than Wade) how scientists design viral proteins. Wade packed false assumptions into Anderson’s head and article, concepts which are clearly wrong.
Wade worked hard to tell us that a Nature-published virologist made incorrect assumptions about how virologists design and make viral proteins — and then wants to tell us how virologists really do this work?
Read what Wade goes on to say:
…But this ignores the way that virologists do in fact get spike proteins to bind to chosen targets, which is not by calculation but by splicing in spike protein genes from other viruses or by serial passage…
Anderson’s comment on computation had nothing to do with engineering the virus — Wade mischaracterized and twisted Anderson’s intent. Anderson only discussed the after-the-fact computation of protein binding.
By the way, Wade also erred by saying that virologists don’t use calculations to design protein binding. Here is only one example of many articles showing how virologists DO indeed use computation to design protein-protein binding interactions.
Wade was wrong TWICE in one argument — Wade was wrong because virologists do indeed use calculations and computation to design protein-binding interactions — and Wade was also wrong because Anderson’s article never discussed that kind of computation.
Wade then tried to argue further:
…the Andersen group writes, and since SARS2 is not derived from any of them, therefore it was not manipulated. But the argument is conspicuously inconclusive. DNA backbones are quite easy to make, so it’s obviously possible that SARS2 was manipulated using an unpublished DNA backbone…
Wade clearly doesn’t understand the field and assumes that any DNA backbone will work. That is not true and is why the few backbones developed took so long, and are still used. They work.
Development of mouse hepatitis virus and SARS-CoV infectious cDNA constructs – PubMed: The genomes of transmissible gastroenteritis virus (TGEV) and mouse hepatitis virus (MHV) have been generated with a…pubmed.ncbi.nlm.nih.gov
Here are some comments from a real virologist that directly refute what Wade says is “quite easy to make”:
… To reiterate, most of SARS-CoV-2 comes from a bat coronavirus closely related to RaTG13. This virus is not known to cause disease in humans. If we were virus engineers (and this actually happens to be my job in the Benhur Lee Lab) we would need to:
Make a virus backbone from a never-before-seen virus that looks like, but isn’t, RaTG13 without having any reason to believe it would be a better starting place than a previously characterized virus (like the original SARS-CoV)
Spend months to years building a system that is easy to engineer (reverse-genetics system) when there are other virus backbones readily available.
Choose the RBD region from an unknown pangolin coronavirus even though all computer models show it should be suboptimal at binding ACE2, and show that it binds well in spite of the models (paper 1, paper 2, paper 3, paper 4)
All of these steps sound like bad ideas from a scientist’s perspective: there were easier ways to engineer a coronavirus, and no one would have rationally chosen either the bat virus backbone or the pangolin portion of the spike protein. Therefore, SARS-CoV-2 is unlikely to be man-made from pieces of other viruses — we have zero evidence that any person or lab has attempted even one part of this process.…
Then Wade minimized Anderson’s paper as follows:
…And that’s it. These are the two arguments made by the Andersen group in support of their declaration that the SARS2 virus was clearly not manipulated. And this conclusion, grounded in nothing but two inconclusive speculations, convinced the world’s press that SARS2 could not have escaped from a lab. A technical critique of the Andersen letter takes it down in harsher words…
Wade clearly didn’t understand that Anderson discussed several other important points including something called a polybasic cleavage site. This is a short sequence of amino acids which is a target for protein scissors called proteases. Proteases clip proteins at specific cleavage sites defined by a short amino acid sequence. Anderson et al discuss how a cleavage site can be acquired by the influenza hemagglutinin protein by repeated passage in cell culture or animals. Anderson also talks about its absence in most viruses closest to SARS2, that the RaTG13 is 96% identical but differs significantly in the RBD, but the pangolin CoV are similar to SARS2 especially the 6 key resides in the RBD. Anderson also says:
…a hypothetical generation of SARS-CoV-2 by cell culture or animal passage would have required prior isolation of a progenitor virus with very high genetic similarity, which has not been described. Subsequent generation of a polybasic cleavage site would have then required repeated passage in cell culture or animals with ACE2 receptors similar to those of humans, but such work has also not previously been described. Finally, the generation of the predicted O-linked glycans is also unlikely to have occurred due to cell-culture passage, as such features suggest the involvement of an immune system18…
Now that we are aware of how shallow Wade’s understanding of biology is, it is no surprise that he completely missed the point about O-linked glycans, and that they only form when the virus is exposed to an immune system.O-linked glycans on viruses are thought to shield them from their host’s immune system. Therefore, the presence of these sugars (and the amino acids which host them), strongly point to the virus’s evolution in an adaptive immune system such as ours.
Halibut, I have read that confusing mess over and over again, and I must conclude that it was deliberately a mess because the writer had nothing of substance to rebut Wade. The most I got out of it was the denial that Anderson said that the virus was natural because based on calculations scientists would never had designed it that way. What exactly was Anderson’s argument about calculations then and how did it relate to the matter of whether the virus was of natural origin?
The writer next attempted to dispute Wade’s point about scientists not needing to make calculations to determine optimal genome by arguing that they do, yet, again, how did that refute Wade’s point about serial passage that may had been used to create the virus and leaving no trace of manipulation? Wasn’t that just a strawman point.
As to rebutting Wade that scientists could’ve created their own unpublished backbone for the Virus, the writer’s point was it wasn’t that easy. That’s it?! Like I said, just a strawman, red-herring, and ad-homs mixed in mess. Orac could’ve wrote it.
@Greg You will notice strange contradiction in Wade’s arguments. First the claim that SARS CoV 2 is a perfect virus, and thus it must designed. Second most crucial part of the virus need not to be perfect after all. Actually, you will notice a self refutation here.
Aarno, I think you’re nibbling at scraps. The point is, for over a year everyone ‘debunked’ the lab leak theory by bringing up Anderson. The two main points in that paper being the virus couldn’t have been manipulated because there was no trace, nor was there evidence of a published DNA backbone. Even Orac here cited those points. Along came Wade to eloquently demolish those points, and sans the mess that Halibut brought up, no one has countered with an effective rebuttal.
@Greg Actually, I consider Andersen’s main point was her evolutionary tree of coronaviruses. Wade did not mention this, strange ?
I’ve been having a hard go recently, but nothing to compare with the loss of a canine (or feline) companion. My sincere condolences.
[…] thing they don’t want to hear. Moreover, the WSJ editorial page itself has run full op-eds on hair-brained lab leak conspiracy theories. They have run numerous op-eds supporting the Great Barrington nonsense, including anti-vax […]