Germ theory denialism and the magical mystical microbiome

Whenever I point out that a very common thread of “thought”—if you can call it “thought”—in alternative medicine is nothing more than germ theory denialism, the usual reaction is incredulity. Newbies who haven’t encountered quacks before invariably do a double take when I inform them that germ theory denialism is a thing, particularly among antivaccine activists. (After all, vaccines don’t make sense if microorganisms don’t cause disease.) Yet, time and time again I find examples of quacks who deny that disease is a consequence of infection. In fact, some go so far as to try to argue in the other direction, that microorganisms are good for us. Of course, there is a grain of truth in this. We’ve known for a long time that one of the pernicious effects of antibiotics is that they kill the beneficial bacteria along with the pathogenic bacteria, leading to syndromes like antibiotic-associated diarrhea and C. difficile colitis, just to name an example. The problem is not so much that quacks claim that our microbiome can be beneficial, it’s that they basically deny that there are pathogenic bacteria, their usual spin on this claim being that these viruses and bacteria can’t cause disease if you’re truly healthy and your immune system is intact. Guess how you get that way? Of course. You have to do what they tell you to do to “strengthen your immune system” and make yourself resistant to them, of course!

Of course, many of these same quacks will blame chronic diseases on chronic candida infection. Oh, well, no one said they’re consistent.

Be that as it may, I came across a very silly bit of germ theory denialism that reminds me of a famous book by John Stauber and Sheldon Rampton entitled Toxic Sludge Is Good For You, except in this case it’s Measles and Mumps Are Good For You. Who, you might ask, could write something so off base, so full of cherry picked studies to back up utter nonsense? Who else? I’m talking Sayer Ji of GreenMedInfo, whom we’ve met many times before. This time around, he’s proclaiming The Healing Power of Germs. Not surprisingly, he starts out with a contemptuous attack on germ theory. After claiming that our fear of microorganisms is unfounded and stoked by the CDC through fears of antibiotic resistance, leading to the requirement for vaccines (which Ji clearly considers unnecessary), Ji launches into a familiar diatribe:

What makes this situation all the more surreal is the relatively recent discovery of the microbiome, namely, the 100 trillion viruses, bacteria, fungi, parasites, which outnumber our own cells 10-1, and which proves that we are more “germ” than “human,” and in many respects, would not be alive without them: e.g. about 8% of our genome is retroviral in origin, 90% of our immune system depends on bacteria in our gut. How, then, can these microorganisms be as deadly as we are told, while at the same time be responsible for making possible our life itself?

The cognitive dissonance generated by these diverging, if not diametrically opposed paradigms — “microbes as deadly” versus “microbes as essential to life” — is enough to drive the non-fluoridated mind a bit crazy. But so much is riding on belief in one narrative over another. If germs are not as deadly as we are told, how would we justify the 60+ vaccines in the childhood vaccination schedule, and the 250+ in the developmental pipeline? Clearly, there are biopolitical and economic motivations pushing the germ-centric ideology forward, even in the face of an accumulating body of contrary evidence.

Do you want to tell Ji, or should I? OK, it’s my blog; so I’ll tell him. Just because science is increasingly understanding the importance of the microbiome does not mean that bacteria and viruses are harmless. What it means is that many bacteria and viruses are harmless, able to live in various ecological niches on and in our bodies. Indeed, much about this microbiome is beneficial, assisting us with digesting food, modulating our immune systems, and carrying out functions important for health. However, one more time, that does not mean that pathogenic microbes are not harmful, that microbes are not a major cause of disease in the world. Indeed, one of the reasons why widespread antibiotic resistance is so terrifying is the possibility of a “post-antibiotic era,” where there are strains of bacteria that antibiotics can no longer treat. I worry about this myself, given my advancing age and impending increased susceptibility to infection.

Naturally, as is his wont, Ji cherry picks papers to support his viewpoint:

One such recent academic challenge to the germ theory can be found in a study published this year in Atherosclerosis titled, “Association of measles and mumps with cardiovascular disease: The Japan Collaborative Cohort (JACC) study,” which found that exposure to common infections during childhood could decrease risk of atherosclerotic cardiovascular disease (CVD).

Basically, this was a prospective observational study of 103,836 subjects (43,689 men and 60,147 women) aged 40–79 years in Japan, none of whom were vaccinated against the mumps or measles, because the MMR vaccine was not introduced to Japan until 1989. They were asked about their medical history, specifically whether they had ever had the measles or mumps and were were classified into the following four groups for comparison: those without a history of measles or mumps (reference group), those with a history of measles only, those with mumps only, and those with a history of both measles and mumps. The results are described in the charts below:


As you can see, it’s an interesting finding, a provocative finding even. The authors speculate that this effect might be due to the induction of regulatory T cells after an infection, leading to suppression of inflammation in the arterial wall, preventing the progression of atherosclerosis. One thing I noticed right away about this study is that the number of actual events was surprisingly small. For example, diving into the actual weeds of the numbers in Table 2, I find that there were only 1,212 deaths from myocardial infarction in the whole population over 20 years. Some of the categories have single digit numbers of subjects, such as only 8 men with mumps only who died of ischemic stroke, two of hemorrhagic stroke, five of myocardial infarction. In other words, as interesting as this study is, it’s by no means conclusive. It’s also hard not to point out (as the authors of this study do) that measles does indeed result in immunosuppression that persists at least two to three years after the infection and that this effect of measles leads children susceptible to a higher risk of death from other infectious diseases. It’s quite possible that, if this decrease in cardiovascular mortality that is associated with measles infection is real, it is part of the same phenomenon that leads measles to leave children immunosuppressed for as long as three years.

Of course, one can’t help but note that Ji only picks studies that appear to show a benefit from infection. I suppose that it’s not so odd then that he neglected to mention an article that appeared in the very same issue of the very same journal that the JACC study was published in, a review article about the association between periodontal disease and cardiovascular disease. Yes, it’s been suspected for a long time that periodontal disease is correlated with an increased risk of cardiovascular disease, and recent studies, although not conclusive, appear to bear out that relationship. Again, it’s not clear if this relationship is causative or not or due to some other confounding factor, but then the same thing can be said of the results of the JACC trial that Ji promotes.

Of course, Ji can’t resist making a certain analogy:

Germ theory has, in certain respects, taken on the characteristics of an infection itself. Not a physical one, but an ideological one, i.e. a meme. Ironically, these memes not only have a life of their own, and replicate like the very infectious entities they conceptualize, but they have physiological effects that can adversely affect immunity. A nebulous fear of “germs” (lethal, invisible, omnipresent), for instance, can contribute to a flight-or-fight/sympathetic dominant state and therefore can result in immune dysregulation, up-regulating cortisol and down-regulating the very cell-mediated immunity needed to prevent opportunistic infections.

Yes, that “fear of disease” can so amp you up that you suppress your own immune system. What rot.

Of course, it’s all about what’s natural:

As our scientific understanding of the microbe-dependent nature of our health continues to expand, and germ theory and its derivative agenda of vaccinology continues to confront evidence that contradicts its basic tenets, we finally can see a way past the increasingly dismal view projected by health authorities like the CDC and the WHO that germs will be the end of us all; that is, unless we employ “live saving” vaccines and drugs, or support global germ eradication campaigns that are not only not working, and by principle never will, but may actually be harming more than they are helping.

Ultimately, when we come to embrace the “germ” not so much as other but self, the endless war against microbes will give way to a type of peace and compassion between self, body, and the natural world that will be essential for true healing to take place.

That last link leads to an article by Ji that is amazing for its woo-fulness, How The Microbiome Destroyed the Ego, Vaccine Policy, and Patriarchy. It’s one of those quack masterpieces that tries to relate disparate bits of science into a unified whole where everything relates to everything else. In this case, Ji makes the amazing claim that “99% of what it means to be human is microbiome-based,” which is nonsense even knowing what we know now about the microbiome, and then goes on to “reason” that, because of mitochondrial DNA being maternally transmitted, plus maternal-fetal transmission of the biome, this must be true:

Moreover, the conditions surrounding gestation (important because of maternal-to-fetal microbiome trafficking in utero), her general health, and the way in which she gives birth (home, birth center, or hospital) now take on vastly greater importance than previously imagined. In other words, being born in a hospital via C-section and vaccination, will produce, genetically and epigenetically, a human that is so different – qualitatively – from one born at home, naturally, that they could almost be classified as different species, despite sharing nearly identical eukaryotic DNA (remember, only 1% of the holobiont’s total).

Yes, that’s how the title came about.

As fascinating as I find new research about the microbiome, it no more proves that the microbiome is more important to our biology than our own cells than epigenetics “proves” that we can “will” our own gene expression to change to whatever we want it to be. But quacks like Sayer Ji are all about the naturalistic fallacy. They also seem to forget that, microbiome or no microbiome, pathogenic organisms are pathogenic because they are able to over come everything standing in their way to causing infection—including the microbiome.

Ji’s posts are good teaching opportunities, though, particularly about alt-med germ theory denialism.