Virus, Bacteriophage and Single Virus Genomics by Dr. Mark Bailey. While the notional virus model has changed over time, the underlying premise of a contagious disease-causing entity has never been established. Nevertheless, its proponents have attempted to incorporate naturally observed particles such as bacteriophages into the virological realm without establishing they are viruses while portraying technological advances is the reason for their proportion discovery. Single Virus Genomics is yet another chapter in the technology-driven world of virology that remains embedded within a flawed model. Virus. The concept and meaning of virus have been through a number of iterations over several hundred years.

The appearance of the word in the English language in the 14th century derived from the Latin virus meaning poison, sap of plants, slimy liquid, a potent juice. It is said that the reference to an agent that causes infectious disease had emerged by the 1790s and the modern scientific use commenced in the 1880s. From the first purported discovery of a virus there has been no consistent definition of what a virus is because unlike other empirical biological sciences, there has never been a tangible viral particle that could be naturally observed, described, isolated, characterized and tested for pathogenicity.

Hence, without a tangible asset for virologists to engage with, the term virus has taken on a protein quality, shimmying its way from one definition to the next in order to keep up with the latest viral theory. A pervasive theme in virology’s development is that the notion of some invisible contagious entity was imagined and then subsequent indirect observations have been advanced to support the hypothesized entity. On this timeline, the tobacco mosaic virus was allegedly the first virus discovered in the 1890s. However, neither that first purported discovery nor any purported discovery since has demonstrated any virus that is consistent with the modern definition.

A particle that is disease-causing, replication competent and contagious through natural exposure routes. Note that the imagined transmissible particle itself is known as a virion. The Dutch microbiologist Martinus Bezierink used the term contagium vivum fluidum or contagious living fluid in the title of his 1898 paper concerning the cause of tobacco mosaic disease. He proposed it related to a form of sub microscopic infectious agent that was soluble but unable to be visualized by the technology of the time. In the body of his 1898 paper, Bezierink used the term contagium interchangeably with virus.

Although the archives of virology credits him with the first use of the word virus to mean a new class of pathogen, it is also acknowledged that Bezierink and his contemporaries would not have envisaged the virus model as it is known today. Bezierink’s claim of a fluidity of the contagium is a matter of semantics since he already used it interchangeably with solubility. His coining of the term virus for a new class of pathogens further marks the beginning of a new era in biology. Hence it is not very fertile to debate the issue who was first in discovering a virus.

None of the pioneers could have known what he was talking about. It is more than evident that the enigma of what has been talked about extends well beyond the so-called pioneers of virology and continues into the present day. Virology is a unique quote science within the field of biology because of the virologist’s propensity to redefine the supposed material nature of the entities they claim to be studying. Changing definitions and the use of linguistic ledger domain can make it difficult for the public to know what they are talking about if not for the virologists themselves as the following examples illustrate.

My ambition is to show that the word virus has a meaning and I shall defend a paradoxical viewpoint namely that viruses are viruses. Andrei Luoff 1957. A virus is what virologists say it is. It can be said that virologists invent and continually reinvent the concept of a virus as part of the normal progress of their science. William Summers 2014. Many host districts of the human body and its mucous membranes are heavily colonized by viruses that are not associated with any disease. Editorial Clinical Microbiology and Infection 2019. A coronavirus is just a piece of RNA molecule.

William Ruhlinson 2020. Whatever the virologists say or consider normal progress it is clear that they did not discover viruses in nature and then set about their study of them. The created paradigm is steeped in anti-scientific practices due to its typically unfalsifiable nature. The virologists do not perform experiments in an attempt to falsify their hypothesis because the material existence of viruses has always been assumed in advance. Apparently all that remains is for them to fill in the details. To the 19th century microbiologist virus was a useful but imprecise concept defined and operational rather than physical terms.

Viruses were thought of in terms of what they do, cause disease, produce lesions on tobacco leaves and the like. Not in terms of what they are. William Summers 2014. In order for viruses to do they must exist first and if they exist then they must have a specific biochemical composition and function. Since the 1800s their postulated nature has included the aforementioned fluid contagion, chemicals, infectious proteins and subcellular entities. It was not until the 1950s that the virologists started settling on the modern definition of virus meaning a resulting contagious particle consisting of a genome RNA or DNA surrounded by an encoded proteinaceous coat.

Salvador Luria having published his groundbreaking text General Virology in 1953 wrote to Andre LeBoffe in 1957 with his revised and admittedly clumsy construction of a virus. I would today define a virus as an element of genetic material capable of assuming a transmissible form by incorporation into a transmission apparatus synthesized under the viruses own control. The question still remains as to when the existence of viruses as physical entities was demonstrated. Good Pasture et al. reported on an alleged breakthrough with the cultivation of viruses in the Corioallantoic membrane of chick embryos in 1931.

However there was no evidence of any microbe being cultivated and their claim relied on the appearance of a vaccinal lesion that develops and spreads on the membrane. Here they simply made the assumption that the appearance of a lesion or damaged membrane tissue must have been caused by a virus that was present in their introduced sample. A footnote in the paper states that the sample was a strain of Levatitine neuro vaccine virus kindly supplied by Dr. T. M. Rivers. Dr. Thomas Rivers similarly asserted in advance that his supplied samples contained this quote virus and in his 1930 publication declared it to be a Levatitine neuro vaccine virus that had been propagated for six months in rabbit testicles.

It is clear that in all of these experiments the samples were mixed biological specimens and no specific independent variable had been identified. Neither Good Pasture nor Rivers could have possibly known the composition of the so-called Levatitine strain. The tissue in question was evidently diseased and if it caused other exposed tissue to exhibit signs of disease then the nature of the virus could not be said to be more than the original meaning of poison. It may be argued that this is an unfair charge against these early virologists as their experiments predated the availability of the electron microscope in the late 1930s.

However the new nanoscale imaging technology did not help their case as former virologist Dr. Stethon Lanke has explained. The pre-1951 theory of what a virus is supposed to be was refuted by the fact that no one could ever find or photograph anything different in people or animals supposedly infected with a virus from what can be found or photographed in healthy subjects using the electron microscope. This is still the case today. In the 1940s and 1950s the virologist started favoring the indirect cell culture technique in which specimens from diseased organisms were added to typically abnormal cell lines in the laboratory.

If the cells broke down under the microscope it was then declared that viruses were the cause. However the cells can also be shown to break down without the addition of any specimen. That is, the procedure itself can cause the same effects. Furthermore, as the present author argued in Virology’s Event Horizon, there are foundational logical flaws in the cell culture technique. The particles being declared as viral are seen for the first time as part of these cytopathic effect observations, i.e. they are dependent variables. It is preposterous to claim that they are also the independent variable in the same experiment.

The in-vitro laboratory observations cannot be known to replicate an in vivo within living process. The techniques involved in electron microscopy introduce further variables that are not controlled, in addition to technical artifact and the further limitation that they are static structures embedded in resin, not living tissue. Like all of the previous experimental methodologies in virology, the cell culture technique did not demonstrate the existence of viruses. It only served to perpetuate a reification fallacy, i.e. the imagined concept had been inappropriately declared to have a confirmed physical existence. Despite the absence of the requisite evidence, the intangible original formulations of virus from earlier eras was henceforth proclaimed to be a discrete particle possessing parasitic abilities.

The technique of electron microscopy has its own limitations with regard to whether the obtained images can inform us about living cellular biology. Even so, within these limitations, the technique should have spelt another dead end for the virus model. It was never able to deliver the anticipated decisive evidence being sought in direct specimens, such as sputum and blood, from people said to have viral illnesses. It was only the cell culture technique that allowed the proliferation of images in biology textbooks, purporting to depict viruses. However, by its very nature, the methodology cannot be controlled for an independent variable, and it is impermissible to invent one post hoc based on the cell breakdown appearances.

Thus, there is no evidence that any of the imaged vesicular structures are pathogenic and contagious entities of exogenous origin. The virologists employ the point and declare technique in these electron microscopy images, such as the example provided in figure 1. The particles are claimed to be SARS-CoV-2 variants, and yet there is no cooperation that they are infectious or disease-causing. A hypothetical genome is assembled, but as the imaged particles were not purified, the provenance of the genetic sequences remains unknown. They could have come from other constituents in the mixture. However, even if they were purified and their biochemical elements determined, that would not automatically qualify them as viruses.

The isolated particles would need to be shown to be capable of the required properties as an independent variable in controlled experiments. The claim that genomics proves the existence of viruses falls back into the same logical fallacy, involving the assertion that the viruses are already known to exist in advance. Within virology, this applies to both cell cultures and metagenomics, for example, sequencing of clinical samples. There cannot be any viral sequences unless viruses are first shown to exist. The central tenet of the virus model is mired in a fallacy of circular reasoning that its proponents appear unwilling to address.

In 2014, it was stated in the Annual Review of Virology that the basic idea that viruses are the material basis for disease transmission has changed little in the past 150 years. What has changed is our understanding of the essential properties and biological capacities of viruses. The concept of a virus has particularly been determined by technological advances rather than scientific understanding. However, this basic idea has never been established, and in accordance with the scientific method, the concept of virus remains as it was in the 1800s, a mental construct that attempts to explain why organisms become diseased.

Without a tangible independent variable, no other indirect observations or technological developments can rescue the model from this fatal gap in the evidence. Bacteriophage Bacteriophage literally means bacteria devourer or eater. The term was coined by Felix Terrell in 1917 when he declared, It was a nonsensical if not paradoxical statement as he did not demonstrate the physical isolation of anything. The invisible microbe once again invoked a reification fallacy where he attempted to materialize a mental construct through a linguistic sleight of hand. Nevertheless, the story was embraced by the virology establishment, and in the 2010 edition of the desk encyclopedia of general virology, we are told Terrell understood immediately that he had found a new category of viruses.

Terrell’s quote anti-siga microbe was created by adding four or five drops of feces to a broth, incubating the mixture at 37 degrees Celsius for 18 hours, and then passing the contents through a chamberlain candle filter to remove bacterial cells. He observed that the addition of the cell-free filtrate to a culture of Shigella bacteria inhabited their growth and resulted in their lysis. In line with other virologists, he had simply invented a hypothetical entity, the bacteriophage, to explain the cause of an observation in the bacterial culture. Rather than being skeptical of his own guesswork about a parasitic invisible microbe in his mixture, he continued to make all subsequent observations fit his unestablished premise.

The antagonistic microbe can never be cultivated in media in the absence of the dysentery bacillus. It does not detect heat-killed dysentery bacilli, but is cultivated perfectly in suspension of washed cells in physiological saline. Authors in the claims of Dharal as if they were unquestionable scientific facts. Some of them have made their own additions to the story, even going so far as to award teleological properties to the imagined bacterial viruses. Dharal quickly learned that bacteriophages are found wherever bacteria thrive, in sewers, in rivers that catch waste runoff from pipes, and in the stool of convalescent patients.

Like any predator, bacteriophages are best able to survive and multiply when they are in close proximity to their food supply, where they fulfill their evolutionary role of keeping bacteria in check. The first electron micrographs showing purported bacteriophages were published in 1940 in two papers from Germany, and according to the journal bacteriophage, proved the particulate nature of bacteriophages. One paper describes the imaging of a mixture made by adding a lysate to a broth culture of E. coli. Two images from the paper can be seen in figure two. The vesicular particles around the cells were declared to be viral in nature, presumably as this had already been decided in advance.

The possibility that the particles were originally endogenous and a result of the breakdown of the conclusions. The other 1940 publication reported on electron microscopy of a filtered bacteria-free phage lysate of a broth culture of coli bacteria. This imaging provided some evidence of homogenous particles around 60 nanometers in diameter. However, like the first paper, there was no demonstration that these were viral in nature. There are many known precipitants of cell membrane lysis, including pressure, heating, osmotic shock, alkali exposure, detergents, and enzymes, as well as sonic, optical, and electrical insults.

Figure three shows the breakdown of Escherichia coli cells following exposure to PVEC, a disrupting peptide that is 18 amino acids in length. Note that the particles surrounding the cells were not called bacteriophages in this instance. In 2015, Dr. Stefan Lanker outlined why the pre-conceived idea about predatory bacterial viruses led them to the wrong conclusions when interpreting the images. Due to the belief that these, at the time of their discoveries, still invisible structures, were killing the bacteria, they were called phages, bacteriophages, eaters of bacteria. Only later it was determined that merely highly inbred and therefore almost non-viable bacteria can be made to turn into phages or bacteria, which have been destroyed so fast that they do not have time to form spores.

Bacteriophages exist insofar as they can be found in nature, isolated, and characterized. They can and will be found everywhere that bacteria are found. In the ocean, they may be seen in quantities of up to 10 to the 8 per milliliter of water, and thousands have been described in phage databases. The fault lies in the name. They are not bacteria eating particles, and can only be said to be endogenous elements that are part of a reaction to environmental changes in microbiological systems. The virologists have never been able to show the existence of pathogenic viruses, and have compounded their errors by first claiming that bacteriophages are viral in nature, and then implying that there are equivalent viral particles that attack larger organisms such as humans.

Single virus genomics. Flow cytometry is a technique that allows for the analysis of single biological cells by passing a fluid sample through a narrow sheath. A laser beam is directed at the sheath, and detectors receive optical and impedance signals that provide information about the cells as they flow past. Some flow cytometry instruments can also be used to physically separate particular cell types. It is a tool that has been used for decades in medical diagnostics and scientific research. By the 1980s, flow cytometry was being used to quantify microscopic phytoplankton in natural water samples.

In the 1990s, it was claimed that flow cytometry was successfully used to enumerate viruses in sea water. However, the alleged viruses that were measured were of the phyocystis class, a vireoplankton or bacteriophage related to phytoplankton. Once again, and without substantive evidence, the virologists have declared that they are viral in nature, with bacteriophages being described as part of an infection cycle, rather than a microbial life cycle. Review papers such as this one published in 2000 continue to note that wherever microbes are active, so too are their bacteriophages. For aquatic viruses, abundance has, in nearly every case that has been examined, correlated most strongly with bacterioplankton concentration.

Furthermore, it appears that larger vireoplankton populations are found under conditions of high bacterial productivity. Many authors have speculated that bacteriophages comprise the majority of vireoplankton populations. Thus, it is not surprising that the abundance of aquatic viruses is closely correlated with the abundance and activity of bacterioplankton. As Dr. Stefa Lenka has explained, the existence of bacteriophages in giant viruses, as well-defined physical particles found in nature, is not being questioned. However, the names of these two related entities are misnomers, and their biological role has not been shown to be one of parasitism. The so-called giant viruses, i.e.

an enwrapped nucleic acid, that can be found everywhere in the sea and in basic organisms. Like all bacteriophages, not only they are harmless, but they have beneficial functions. They can be also isolated by using the density gradient centrifugation, which proves their existence. While these biological paradigms are ignored, further developments in flow cytometry led to the announcement of single-virus genomics in a 2011 public library of science publication. It was claimed that the benefits of single-virus genomics will be far-reaching, enabling novel virus discovery in a variety of clinical and environmental settings. The technique apparently isolated single particles into agarose droplets, which was confirmed by confocal laser scanning microscopy.

The isolated particles were then DNA-sequenced through genomic amplification. An incredible triumph of technology this may be, but the paper did not actually demonstrate these particles were viruses. The tested viral suspensions were E. coli T4 and lambda bacteriophages, the nature of which had been already discussed in the present paper. Single-virus genomics cannot enable virus discovery, unless it can be first shown that viruses as pathological microbial entities exist. The tautological declaration that a virus is what virologists say it is, is illustrative of a scientifically bankrupt paradigm. Humanity has been led to believe that virologists are studying microbes that are both contagious and disease-causing.

There has been a bombardment of information concerning genomics, proteomics, electron micrographs, alleged diagnostic tests and epidemiological data. The virologists may believe that such data continues to fit the model first conceived in the 19th century, but these imaginings have no bearing on biological reality. [tr:trw].

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