Philosophy of Science and Scientific Knowledge both Help to Solve Problems in Viral Taxonomy

Biological classifications are made up of abstract classes created by biologists such as species, genera, families, and orders. Members of the lower species class are also members of the classes above it and this class inclusion is responsible for the fact that genera and families, for example, have more members than species and therefore require fewer properties to meet the qualification for membership. Class membership is the logical relation that allows a link to be established between physical organisms and conceptual constructs such as classes and taxa. A philosophical approach to science is useful for analyzing the ontology and epistemology of viruses and of living organisms, and it has led to a processual interpretation of organisms and viruses in terms of continuous self-generating processes of development and evolution. The need to distinguish between the antigenicity and immunogenicity of viral proteins is emphasized because confusion between these two concepts makes it very difficult for vaccinologists to develop vaccines.

The biological sciences combine all the sciences that study living organisms such as animals, botany, microbes (microbiology) as well as viruses (virology). Viruses are too small to be seen with optical microscopes and they can infect animals, plants, and microbes, and can also kill the host they have infected. Viruses are genetic parasites that invade the genomes of their hosts but they do not reproduce themselves, since they are reproduced by the living cells of the hosts.

All biological classifications deal with abstract classes called taxa that are conceptual categories of the human mind. These hierarchical classes use the Linnaean format, from the lowest species class to the higher classes of genera, families, and orders universally used in biology. Philosophical precision is useful in biological classification because it clarifies that the vast majority of living organisms do not have common names that differ from the Latin names of the species to which the organism belongs [1]. As a result, it is commonly said that a person can be infected by the bacterial species Escherichia coli, as if a conceptual category could infect a physical organism. It is remarkable that virologists are the only biologists who can avoid such a logical confusion since every pathogenic virus has a common vernacular name that differs from the species name to which the virus belongs and that name should be used to refer to the infectious agent.

Viruses are chemical objects that parasitize the genomes of animals, plants, and microbial organisms they have infected. Viruses themselves are not alive since the living infected host cells do reproduce the viruses [2].

Viruses are classified using the hierarchical conceptual taxa of species, genera, families, and orders used in all biological classification [3]. Members of the lowest species class are also members of the classes above it and the relation between species and higher classes is called class inclusion. As a result of class inclusion, genera and families for instance, always have more members than species and they require, therefore, fewer properties to meet the qualification for membership. Since species always have fewer members than higher taxa, demarcating a new species always requires more properties than do higher taxa.

In 1975, the Virology Division of the International Union of Microbiological Societies established the International Committee on Taxonomy of Viruses (ICTV), which was responsible for the creation and naming of virus taxa. The ICTV developed a viral taxonomy using the hierarchical classes of species, genera, and families, the first ICTV reports used a Latinized virus nomenclature but virologists were opposed to the use of Latin for species names and only when the use of Latin in viral taxonomy was completely abolished [4] were English species names accepted in virology [5].

In biology, the vast majority of living organisms do not have common names that differ from the Latin name of the species to which the organism belongs [6]. Class membership is the logical relation that allows a link to be established between physical objects and conceptual constructs [7]. An infectious viral agent is a subcellular genetic parasite that can be incorporated into the genome of an infected living cell and the virus does not replicate itself since it is the living host that replicates the virus. Viruses should therefore not be considered to be subcellular organisms and they do not possess a so-called two-part heterogeneous ‘life’ cycle consisting of both non-living virions and living virus-infected host cells as was argued by Forterre P [8]. A virus present in a host cell is no more alive than a non-living virion and it makes little sense to claim that a non-living virion can be transformed by spontaneous generation into a type of living cell metaphorically labeled a virocell [9].

A virus species is defined as a polythetic class of viruses that has a variable distribution of properties, but which does not have a single common property present in all its members. Monothetic classes of viruses on the other hand are defined by one or a few properties that are both necessary and sufficient for membership in the class.

It should be stressed that the variable distribution of properties in one member of a polythetic species class as well as the absence of a single common property in all its members are characteristic of the class. Every membership condition determines a class although not being a member is not a defining property since there are no such things as negative properties. Membership of a polythetic class can thus be determined by one or many species membership conditions except one that is non-self-membership [10]. The absence of a single common property in all the members of a polythetic class does not make it possible to identify a polythetic class since this would lead to the well-known Russell paradox of the barber [11]. This paradox arises if one assumes, for instance, that a village barber shaves all and only those men in the village who do not shave themselves because this implies that the barber will need to shave himself only if he does not do so! This paradox is resolved only when it is realized that there is no such barber [7]. It is equally impossible to identify a polythetic virus species on the basis of a single unknown property that is absent in all its members. The term polythetic refers to a particular distribution of properties in the class and the members of that class do not themselves possess polythetic properties [6,12].

The term ontology is derived from the Greek word ontos (which means being) and logos (which means study) and refers to the branch of philosophy that analyses the nature of what exists in the world (i.e. substances, objects, organisms and abstract entities). The term epistemology is derived from the Greek words episteme which means knowledge and logos and refers to the branch of philosophy that analyses how humans acquire knowledge and determine its extent and validity for understanding the reality of the world we live in.

Epistemology views knowledge as a mental state in human minds that is acquired by personal experience and sound reasoning and it also analyses the methods used for acquiring knowledge and for analyzing its scope and limits. In recent years, a new ontology and epistemology of living organisms have been developed which argues that the living world consists of a hierarchy of processes rather than of things and substances as previously thought. Such a processual view of organisms is often compared to the ceaseless current and flow of a river, giving rise to the new concept of a stream of life. Although organisms may sometimes give the impression of being static, processes lead to perpetual changes that extend in time because organisms undergo continuous self-generating processes of development, metabolism, and evolution [13,14].

HIV proteins possess both antigenicity and immunogenicity which refer to their ability to bind to specific anti-HIV antibodies (antigenicity) and to induce in an injected host a variety of HIV antibodies when used as a vaccine (immunogenicity). It is often assumed that viral proteins are both antigenic as well as immunogenic and therefore able to elicit protective antibodies, although viral antigens are not necessarily also able to induce antibodies that protect against the relevant viral pathogen [15]. Vaccine developers often use a structure-based reverse vaccinology approach that uses a single viral antigen and disregards the fact that antibodies are always polyspecific and heterospecific and may not elicit protective antibodies that would require the use of hosts with relevant antibody gene repertoires as well as the presence of immune-active helper cells. Efficient vaccine immunogens, however, must be empirically tested beforehand to ascertain that the viral antigen is also an efficient vaccine immunogen which is actually only rarely the case [15,16].

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