3. Causality and the question of viruses

Some comprehension of what causality entails is needed to assess the quality of a scientific work. Logic and common sense, according to the Nyaya school,[1] tells us that mere invariance, antecedence or concomitance does not necessarily imply relevance: day always precedes night, but in no way explains the phenomenon of night; or for instance, the particular colour of a projectile is irrelevant to its motion. Ensuring unconditionality is thus essential to eliminate invariable but irrelevant antecedents or co-effects.[2]

This, as Nyaya philosophers realised and was reformulated some two millennia later by John Stuart Mill entails determining agreement in presence and agreement in absence; namely whether the presence, respectively absence, of one of the suspected cause and of its effect is necessarily accompanied with the presence, respectively absence, of the other.

Koch’s postulates

Hence, to attribute a disease to what are is termed a microbe, it must be found to be present abundantly in all who are suffering from the said disease, and to be absent in all who are not. These two criteria constitute Koch’s first postulate. Abundance is essential since all humans contain plenty of microbes.

But this is not sufficient. The verification of “agreement in presence” requires ensuring that no other phenomena is invariably present, and “agreement in absence” that all other factors remain present.

Koch’s other three postulates do not quite satisfy these requirements. Postulate 2 states that the pathogens must be isolated from every case of the disease and grown in pure culture by notably “transferring a small sample into new, sterile growth medium in such a manner as to disperse the individual cells across the medium surface” so that individual cells are separated and thus “when they multiply, each will form a discrete colony, which may then be used to inoculate more medium, with the assurance that only one type of organism will be present”.[3] This enables the different microorganisms present to be distinguished and those causing the desired clinical symptoms when inoculated into a healthy organism are the microbial cause (Postulate 3). To ensure this, they must be re-isolated from this new diseased host, and checked to be identical to the original ones (Postulate 4).

Whether or not the microorganisms play a role, these steps do not take into account that other factors may be necessary for the onset and evolution of the disease. Furthermore, Koch’s postulates, if satisfied, would only imply contagion through inoculation, which is not the usual natural mechanism for contagion, especially regarding respiratory diseases. To check human to human contagion, it is necessary to bring healthy organisms into close contact with diseased ones. Multiple experiments were carried out during the Spanish Flu epidemic in 1918, and in no case was contagiousness found.[4]

Are disease-causing viruses known to exist?

Now, Koch’s postulates were elaborated in the context of bacteria, whose existence was well documented since the advent of the microscope. In the case of viruses, showing presence and causality poses problems of an altogether different order.

But what is actually meant by a virus? In other words how do we know what to observe? With what standard “virus” can we compare our observation with to claim it is a virus? So has any virus ever been observed?

The hypothesis that tiny entities transmittable from organism to organism, not observable by light microscopes are the cause of diseases was hypothesized by Pasteur as no bacterial cause could be associated to Rabies. Consequently a number of diseases began to be attributed to these entities when inoculation with fluids from which bacteria and large molecules had been filtered out induced the desired symptoms.

In 1931, after the advent of the electron microscope, tiny entities were observed and thought to be bacteria killers. Although it was later experimentally found that these bacteriophages are transformations of the bacteria themselves, enabling these “to live and that bacteria themselves emerge from such structures”, belief in the assumption of pathogenic viruses, which had been reinforced by the former misconception, held strong. Yet, to this very day, no pathogenic virus, has seemingly never been observed, in other words, never “been isolated”, i.e. separated from the surrounding cellular material of the patient (see Addendum).[5]

As explained in the literature, the standard method for isolation is to filter the samples to be analysed through special devices to remove larger entities such as bacteria, the filtrate now only containing particles in the nanomillimetre range is then spun using a process known as density gradient centrifugation, which separates the particles according to density and weight, the more dense or heavy falling at the bottom.

The main point is that at no point should anything that can adulterate the process be added.

To further distinguish the viruses from other particles in specific density bands, it is however not possible to follow Koch’s requirement of a pure culture. Indeed, viruses are thought to be unliving and to reproduce only within cells. Hence, in 1937, Rivers modified Koch’s requirement of a pure culture into one consisting of host cells.

However, even this far weaker requirement is not followed. The initial samples, are invariably mixed with commercially prepared non-host mammal cells, notably Vero cell, i.e. monkey kidney cells, or primate cancer cells.[6] This appears to be the case when NGS is used.[7] [8] Note that these cells “have been maintained in vitro (in petri dish cultures) for many years.”[9] [10] In other words they have long been within an artificial mixture. In particular, in order to provide the cells with the nutrients they need, it contains serum, most commonly fetal bovine serum (FBS), or else newborn calf serum and horse serum[11]. So the cells are not getting their normal nutrients, those they would in their natural environment. Usually antibiotics are also added in the serum “to inhibit the growth of bacteria and fungi.”[12] Now all animal cells in damaged tissues secrete exosomes, i.e. extracellular vesicles, to help heal from diseases.[13] Antibiotics further generate exosomes. Nowadays, it is also common to gradually reduce nutrients to obtain a serum-free media for the cell culture.[14] [15] If the animal cells inoculated with the patient samples, purified or not, eventually show a cytopathic effect, i.e. mutation or degradation, then the particles are said to be viral once biological examinations have eliminated bacterial causes, even though no pathological virus has ever been observed, i.e. even though no evidence for their existence has been provided so far. In short the cytopathic effect is taken as proof of the presence of the virus.

Then enzymes are added to the lung fluid mixture in the cell culture (filtered or not) in order to dissolve cell membranes, so as to release genetic material, enabling the isolation of RNA. Then DNA oligonucleotides (PCR probes) are in turn added to amplify various segments, which may not even be complete, nor are they usually genes. These are then pasted together using a method of computer simulation “for constructing genomes from a large number of (short- or long-) DNA fragments, with no a priori knowledge of the correct sequence or order of those fragments.”[16] The end result is taken to depict the genome of the virus.

The amplified segments are compared with similarly obtained former genomes to eliminate these earlier artificial computer constructs of supposed viruses, or to find similarities with them. The latter are then claimed to further justify a virus has been identified and whether it belongs to this or that family of viruses.

The problem is that even if the mixture with non-host cells is purified, it would still not be possible to tell whether the particles observed under an electron microscope are from the original samples; nor is it possible to differentiate them from the exosomes, given we do not have any independent reference against which to judge what we are observing. According to a 2020 article published in the Journal ‘Viruses’: “to date, a reliable method that can actually guarantee a complete separation [a distinction between viruses and EVs] does not exist.”[17] This is confirmed by many other studies.[18] [19] In short, the assumed cause of the disease, the virus, is indistinguishable from the disease’s effect, the exosome.

Diseases until now have seemingly been claimed to be viral based on this kind of methodology. No evidence that the particles observed have an origin external and not internal to body or the cell culture has ever been provided. Viruses are thought not to be living outside cells, but tiny unliving matter are observable, e.g. inorganic nanoparticles, with the help of the electron microscope. Hence were these genomes of something that had entered the body from the external environment, the latter would contain unliving matter corresponding to each alleged pathological virus. Such matter has never been identified.

Furthermore, as mentioned, the virus is in effect defined to be its genome. This raises several questions. What is the genetic information obtained, living aside the fact that the enzymes added could affect the results? What is being observed and what is it being compared with, all the more so as PCR selectively multiplies and mass-produces specific DNA or RNA segments, i.e. it focuses on a single DNA or RNA locus among millions of similar but different loci? These tiny segments could be any cellular debris. PCR cannot tell us what these segments belong to.

Hence the genome is a computer simulation generated from a few sequences. To explain that this is a perfectly valid method, it is apparently compared to the identification of a unique book from the knowledge of sufficient sentences.[20] This comparison is totally erroneous given that the sentences can be observed in an existing book, and the rest of the sentences and the order they are in are not and could not be computer simulated. In the case of a virus, the rest of the sequences and the order they are in are computer simulated, i.e. based on our assumptions underlying the simulation, of what they would be and how they fit in together, but given the virus has never been observed, we cannot verify this against that which we say it is the genome of.

Furthermore, since the beginning of this century, it has been observed that a genome is not stable, but “in a state of constant transformation”. Genetic “processes are equipped with many degrees of freedom. They form an open system in which by no means everything is predetermined.” In other words, as had been formerly thought, a genome is not a static collection of sequences. “The assumption had been that the genetic material of any two people differed only by about one per mille of all DNA building blocks.” This has proved to be false. The differences are in fact tremendous, and are constantly changing. Each cell even “is a genetic universe in itself”. This certainly raises even more questions about our inference of an unobserved virus from its genome, and from comparisons with the genome of other unobserved viruses.[21]

Certainly none of this implies that pathological viral particles do not exist – non-existence has never been corroborated –, only that the methodology used commonly does not allow us to conclude they do.

In short: the methods usually used do not allow us to conclude that the particles observed are harmful and the cause of the infection. Furthermore, there appears to be no evidence that the particles observed have an external origin. Hence unless there are studies based on other appropriate methods and showing the external origin of the particles, Sars-Cov-2 and more generally other particles said to be pathogenic contagious viruses remain to this date figments of our imagination.

    1. One of the six systems of Indian philosophy, based on the writings of Gotama (3rd cent. B.C.)
    2. Ray, T. and U. Ray. 2020. On Science: Concepts, Cultures and Logic. London: Routledge.
    3. https://www.britannica.com/science/pure-culture
    4. Firstenberg, A. 2017. The Invisible Rainbow: A History of Electricity and Life. London: Chelsea Green, chapter 8.
    5. https://ourfreesociety.com/viruses/dismantling-the-virus-theory-dr-stefan-lanka.pdf
    6. https://www.biorxiv.org/content/10.1101/2020.01.22.914952v1
    7. https://www.mdpi.com/2076-393X/8/2/161/pdf
    8. https://www.nature.com/articles/s41598-019-53043-2
    9. https://in-this-together.com/covid-19-evidence-of-global-fraud/
    10. https://apps.who.int/iris/rest/bitstreams/1088173/retrieve
    11. https://www.sigmaaldrich.com/FR/fr/technical-documents/technical-article/cell-culture-and-cell-culture-analysis/mammalian-cell-culture/the-cell-environment
    12. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173454/
    13. https://www.sciencedirect.com/science/article/pii/S0753332219311990
    14. https://pubmed.ncbi.nlm.nih.gov/31756045/
    15. https://pubmed.ncbi.nlm.nih.gov/34068378/
    16. https://thesequencingcenter.com/knowledge-base/de-novo-assembly/
    17. https://www.mdpi.com/1999-4915/12/5/571
    18. https://www.pnas.org/content/113/33/9155
    19. https://rupress.org/jcb/article/162/6/960/33690/When-is-a-virus-an-exosome
    20. http://www.integralworld.net/visser197.html
    21. https://telegra.ph/Genetics-Genome-in-Dissolution-11-01