This week, we stumbled across a video that outlines a paradigm shift in the way that humans see viruses in the context of germ theory. The traditional explanation of disease is that it’s caused by microbial colonization of a healthy body. The immune system, then, is there to mount a defense against that pathogen. Since their discovery in the early 20th century, viruses have been included in this milieu as just another type of autonomous pathogen.

More recently, however, both the human microbiome and the human virome have been recognized as foundational elements of our biology. The “-ome” title is given in order to denote a network of interrelated viruses or microorganisms that are associated with the human body. In the case of the virome, this includes the viruses that target members of the gut microbiota (our intestinal bacteria). Viruses, however, unlike bacteria, archaea, and fungi are not organisms - rather, they are a process. During the viral process, target-specific, nucleotide-containing vesicles, virions, are secreted by one individual and can be taken up by another. 

The paradigm shift, that the viral program represents a wider communication network between organisms, has seen some press - but like all such shifts, is slow to be accepted. There are even tantalizing clues that viruses may have an evolutionary role that extends beyond mere pathology. 

In this video, Dr. Zach Bush points to this changing pathogenic narrative with enthusiastic certainty... and then adds some other less established assertions. The conversation that follows takes aim at some of these tendentious assertions. More importantly, we demystify Dr. Bush’s presentation, showing both the merits of his theory as well as his use of some rather common epistemological vices. Let us know your thoughts on social or in the comment section…

AB: We don’t really make it to the core of the presentation of the video until the very end - that the pathology of COVID-19 is due to the fact that humans live in a particularly toxic environment. This is maybe the strongest piece of his whole argument since there’s ample literature that suggests air pollution plays an important role in the lethality of COVID - as do pre-occurring conditions. [1][2][3]

MD: Yes, it seems like Dr. Bush is setting out to explain how COVID or pandemics in general are a natural response to a toxic environment. He sees viruses as a whole-species software update. If you get the update, your body will adapt. If you are unable to handle the update, your body self-destructs through widespread inflammatory disease. He presents this “update” notion as a matter of fact, but it’s quite hypothetical since we aren’t aware of any selective advantage of getting infected. It is an interesting theory but his conversion of hypothesis to fact sets off alarms.

AB: This sort of certainty is a common feature of scientific presentations - both fringe and mainstream, that leave me uneasy about the reliability of the presenter’s claims. For me, it shifts their presentation into one of belief. Ideally, when someone makes a presentation they’re doing so from the standpoint of possibility, rather than certainty, since the entire enterprise of science is one of “maybe.” 

MD: For me, the most valuable scholars are the ones that will not make a claim without scaling the uncertainty, either qualitatively or quantitatively. 

AB: And we see some of those issues here pretty early. He makes the claim that 50% of the human genome is viral, which is, at best, a 5X exaggeration. Then there are some non-specific claims about the fact that viral expression is induced by stress, which has only been shown in the case of herpes simplex, not across the board. Then there’s the nebulous presentation about these pools of pig feces where there’s a lot of “stress” that causes the viruses to jump into the human population. 

None of them would be deal-breakers if presented in an inductive lens. Say, “We know that stress causes flare-ups of the herpes virus, so..” or “a significant amount of the human genome is composed of viral DNA…” It makes it much harder for me to pay attention to the actual content of the presentation since I’m so busy searching PubMed for confirmation of the claims. 

MD: Right. And I feel like these are very common problems amongst both science popularizers and scientists themselves. They want so badly for their theory to be taken seriously that they’re willing to compromise their presentation’s accuracy. We see this all the time from institutional authorities as well. 

But underneath all the exaggerations and hypotheses converted to “facts,” we have a cool idea; one that’s rapidly gaining mainstream traction. Scientists are starting to realize that viruses aren’t jumping or doing anything active like an organism: they’re a targeted message system. Recall that a virus itself is a process; the physical objects secreted are called “virions” and they are not alive in the canonical sense.

AB: The question of viral “aliveness” has come up over and over again in our research on COVID and viruses, in general, these last few months. In order to be a living organism, you’d expect viruses to reproduce independently - but no, they can only do so by forcing a host cell to create them - lending credence to the idea that they’re little more than software.

That’s probably the biggest gem in this presentation - that viruses are a software program. But I’m not totally sure about the fact that they’re more damaging in the modern-day because we live in some kind of “toxic” world. After all, virions make up the majority of the nucleic acid content in the world. That there weren’t always some that could cause harm to humans just doesn’t scan for me. 

MD: I’m fairly sure that our industrial world is pumping out toxins on a level that our ancestors never imagined in their worst nightmares, but the link to viral expression or infection-mediated resilience, while interesting, is far from a settled matter. And this is why it’s so important to be transparent when presenting a new idea in science. If you want your idea to be taken seriously, you can’t oversell its merits. At best you can oversell its potential merits.

When you present a new mechanism in science, also called a theory, you have to be absolutely clear in the set up: here is what is known and apparent, and here is what could hypothetically, if shown to be true, provide for my explanation.

Honestly, if a presenter does not follow that simple method, it makes a lot of work for readers like us, trying to pluck the gold from the slag. And quite frankly, most scientists won’t have the patience for this at some point, which means that a lot of potentially brilliant leaps get relegated to the back pages.

AB:  It’s definitely not as sexy, to talk about possibility rather than certainty, or to avoid tendentious claims - those are basically the fritos of the intellectual world. But I think that there’s a lot to be said about the ideas that are produced by the “fringe” actually being useful for all of science. They’re analogous to the potentially pathological software updates that Dr. Bush suggests viruses act like!

I’d love to see a wider acceptance among audience members for what makes a good presentation - rather than allowing ourselves to be bowled over by big numbers and even bigger claims, I want to see a world where people clamor for a more reasonable, measured approach. 

I have a feeling it would go a long way towards reconciling the fringe with the mainstream.