What is in a Name? Is Virology an Ideology or Real Science?
Part 1: The Core of the Debate on Whether Viruses are Real or Not
COVID not only intensified the debate between the pro- and anti-vaccine camps, but it also extended the debate into the whole science of virology. Today, an increasing number of highly educated people including scientists, doctors and nurses, not only refuse vaccines (for themselves and for their children) but also question the whole field of virology and whether viruses really exist as standalone microbes (like bacteria or fungi). There are even those, like the author of Virology as Ideology, who use scientific and historic evidence to argue that virology is more of an “ideology” (based on certain dogma and profit/control motives) than science (based on objective empirical evidence unequivocally proving cause and effect). In this article, I explain why there is so much confusion about viruses and vaccines, and why many people on both sides (pro- or anti-) miss important facts about the realm of microbes.
20th Century
The controversy over the effectiveness of vaccines and the legitimacy of virology as real science is rooted in a relentless debate between advocates of the "Terrain Theory” and the “Germ Theory” (summarized in my earlier article). That debate started in late 19th century with a disagreement between two prominent scientists about the origin of disease-causing (pathogenic) microorganisms. Antoine Béchamp, the father of the microzymian theory, attributed pathogenic organisms to imbalances and dysfunctions between the host and his/her “environmental conditions” (The Terrain), whereas Louis Pasteur, the father of germ theory, blamed “exogenous” bacteria and microorganisms for disease.
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Although Pasteur, towards the end of his life, attached more significance to the ecosystem’s impact on the health of an organism, his Germ theory became mainstream in 1876 by Robert Koch, and later during the 20th century by academic and research institutions, which advocated reductionist science to isolate and study microbes, and pharmaceutical/chemical companies, marketing antibiotics, drugs and vaccines designed to neutralize isolated “exogenous” disease agents identified by universities and researchers.
By the second half of the 20th century, the Germ Theory became like a religion, so sacred that in most Western countries any criticism of the benefits or risks associated with broad-spectrum antibiotics or vaccines could make one labeled as anti-science or anti-vaccine, and even lose a medical license.
Yet, it was almost impossible for for the fans or critics of the Germ theory to rely on real epidemiological numbers to prove their case because by the time the Germ theory, antibiotics and vaccines became mainstream, the death rates from most infectious diseases had already plunged to a small fraction of what they were in the 19th century (see some interesting graphs here).
As the 20th century came to an end, new findings of the Human Genome Project, called “metagenomics,” using next-generation sequencing technologies to study both the organism and its ecosystem, have strengthened the position of Terrain Theory fans and critics of the Germ theory.
21st Century
Viruses are orders of magnitude smaller than microbes identified early on by Pasteur. Isolating and growing virions (viral particles) is also not as straightforward as isolating and growing (cultivating) bacteria. And even if we could identify and isolate certain viral particles in vivo (in the living system, as opposed to synthetically in the lab in vitro), their behavior could be quite unpredictable to observe or predict. These are some of the reasons that make viruses the focus of the microbiological debate in the 21st century.
An article by Ali Le Vere summarizes recent science-based arguments by Terrain Theory advocates which proves the infectivity of pathogenic viruses depends on the role of organisms of divergent kingdoms, such as bacteria and parasites, as well as host molecules such as interferons. She discusses how Helminths, for example, which are parasitic worms that infect mammals, can promote viral replication, because the virus senses and responds to the immunological milieu of the host, which is influenced by the helminth. On the other hand, certain viral infections such as latent murine herpesvirus 68 infection, induce high levels of the protective cytokine, IFNγ (interferon-gamma, a cytokine which the body produces upon viral exposure), which results in a reduction in mortality among certain mice during Listeria infection.
The article argues that:
“vaccinations may deprive the body of favorable immune-modulating effects of some viral infections. Contrary to the dualistic view of Western medicine, most viruses are neither innately good nor bad, as one virus could have multiple adverse and beneficial immunomodulatory effects on the host that are dependent on the anatomical location, host genotype, and the presence of other infectious agents and commensal microbes… This confirms what Louis Pasteur, the father of immunization and pasteurization himself, admitted on his death bed: that it is the biochemical context and physiological milieu that matters, rather than the infecting pathogen.”
Another article on the same platform titled “Why Everything You Learned About Viruses is WRONG!” refers to new scientific papers to show that viruses like the flu virus are “as much comprised of biological material from the host the virus 'infects,' as the viral genetic material of the virus per se.”
Even Germ Theory and vaccine advocates like Stephan Guttinger (a philosopher of science) see the problem with the old (20th century!) interpretations of the Germ Theory when it comes to viruses:
“During the past 15 or 20 years, results from new research disciplines such as metagenomics have initiated a paradigm shift in biology. Key to this shift has been new insights into the role and importance of microbes, which are now seen as an integral part of the human body rather than a mere component of its environment. This has led many scientists to adopt a different view of humans and their interactions with microorganisms, a change that has been noted and capitalized on by anti-vaccination advocates.
The term ‘microbiome’ was coined in 2001 by Joshua Lederberg and refers to the variety of microorganisms that are present in a particular environment—’human gut microbiome’, for instance, refers to the population of bacteria, archaea, fungi, viruses and protists that live in the human gut. Crucial to the development of microbiome research has been the emergence of a new postgenomic discipline called ‘metagenomics’. What is unique about metagenomics is that it does not focus on one particular organism as in traditional genomics, but that it uses next-generation sequencing technologies to analyze all the genomes present in an environmental sample, such as the human gut, skin and blood, but also ocean water or even air. Taking such a broad and inclusive approach has given researchers much insight into the abundance, diversity and dynamics of microbial populations in different environments and the vital roles microbes play in human health and development. This research is driving a transformation in our understanding of microbes and human health as it not only shows that microbes can be good for us but that they are an integral part of the human body.”
Although Guttinger asserts that research does not support the claim that “vaccinations may deprive the body of favorable immune-modulating effects of some viral infections,” he is aware of research in Ken Cadwell’s laboratory at New York University that shows at least in animals (mice studies) norovirus infections do not just have the well-known disruptive effects on the digestive system but can, like bacteria, restore normal gut morphology and T-cell repertoire in germ-free mice. In other words, any vaccine that would curb or stop this type of viral infection, would deprive the body of the favorable immune-modulating effect of this virus, exactly confirming the claim by Terrain Theory advocates, which Guttinger doubts.
The Source of Confusion About Viruses and Virology
Today, Terrain Theory advocates cannot deny the effectiveness of certain anti-bacterial antibiotics in mitigating the severity of infectious disease in certain immune-compromised individuals1, and Germ Theory advocates cannot deny the role of environmental factors and microbes (such as bacteria and parasites) and host’s condition (immune system and molecules such as interferons) on disease progress. Today, the realm of viruses is the main point of contention between the two camps and subsequently the effectiveness of vaccines and the whole field of virology which is called a pseudo-science by its critics.
The contention about viruses and the field of virology has to do with the ever-changing (dynamic) and complex ways that viruses (virion particles) supposedly impact their environment. I always think of virions as fragments/lines (codons) of a large coding/software system (not hardware like bacteria), the performance of which could only be assessed after running it in a specific application environment. The complexity is nicely summarized by Stephan Guttinger in “A Virus Is Not a Thing, Part 1: The case for a process view of viruses.” Although Guttinger seems too attached to the pharmaceutical industry’s positions on vaccines, his objective analysis of the complexity and ambiguity of the field of virology almost makes the case for anti-vaccine camps and Terrain Theory advocates:
“Viruses can be more or less virulent (i.e. able to cause disease), depending on the host organism they are infecting.. Over the 50 years of its application (roughly) there have been some successes, such as treatments for herpes simplex (Aciclovir) or the combination therapies used to suppress HIV expression. But in most cases, the antiviral drugs that are available on the market seem to have limited effectiveness .. viral strains can quickly develop drug-resistance. .. DNA and RNA sequencing technology have allowed researchers to assess the in vivo diversity of viral populations in more detail. These and other studies have shown that for many viruses, including influenza, HIV, or hepatitis, the viral population within an organism represents a highly diverse and, importantly, dynamic system. Rather than forming a collective of identical particles, these viruses form what researchers now call a ‘mutant cloud’ or ‘swarm’. ..
Understanding and measuring the reproductive success of a virus, therefore, depends on factoring in the relational and dynamic nature of the cloud, rather than just assessing the molecular ‘Bauplan’ of the individual viral particles… The developments discussed above are only part of the changes in virology that suggest the need to move from a thing-view to a more process-based understanding of viruses. Other developments, such as the discovery of viral epitranscriptomics, suggest that even at the level of the single viral genome a more relational and dynamic view is needed to understand basic features such as viral genome stability or gene expression.”
So by questioning the usefulness of focusing just on single viral genome, Guttinger is practically undermining the whole field of virology and vaccinology, which are mostly based on single/isolated viral genomics. And by pointing out the critical importance of “relational and dynamic” studies, Guttinger is practically repeating what Terrain Theory and anti-vaccine advocates point out!
Although naturalists can claim that natural antimicrobials like garlic can be as effective as synthetic antibiotics but with less harmful effects. See my June 2023 article about the miracles of garlic: https://simplescience.substack.com/p/learn-these-facts-before-using-garlic