Abstract
A common logical confusion is prevalent in the whole of biology, namely that biological species are viewed both as an abstract category in an hierarchical classifcation and as a concrete kind of organism. This is partly due to the fact that the vast majority of living organisms do not have common names that difer from the Latin name of the species to which the organism belongs. However, it is somewhat astonishing that the same confusion exists in virology since every virus has a common name, diferent from the species name to which the virus belongs, which could be used to refer to the infectious viral entity as a concrete material object. The original 1991 ICTV defnition of virus species stated that a virus species is a polythetic class of viruses and thus that a species is a class, namely a conceptual construction of the mind and not a physical, real object located in space and time. This is the reason why it is not possible to develop a vaccine against the HIV species. In 2013, the ICTV redefned a virus species no longer as a class but as a material object consisting of a monophyletic group of viruses that were all physically part of the species. This new defnition is reminiscent of an earlier school of thought known as bionominalism which considered species to be concrete individuals rather than classes. Both bionominalism and the new ICTV defnition are based on the logical fallacy of reifcation which treats abstractions such as classes as if they were concrete physical entities. The implications of this new ontology of virus species for virus taxonomy and for the possibility of incorporating nucleotide metagenomic sequences in the current ICTV classifcation is discussed.
Archives of Virology, 2018, volume 63, 2047–2054
Marc H V Van Regenmortel
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References
Adams MJ, Lefkowitz EJ, King AM, Carstens EB. Recently agreed changes to the international code of virus classification and nomenclature. Arch Virol. 2013;158:2633–9.
Amarasingham A, Geman S, Harrison MT. Ambiguity and nonidentifiability in the statistical analysis of neural codes. Proc Natl Acad Sci U S A. 2015;112:6455–60. https://doi.org/10.1073/pnas.1506400112.
Andrieu J-M, Lu W. A 30-year journey of trial and error towards a tolerogenic AIDS vaccine. Arch Virol. 2018;163:2025–31.
Azimzadeh A, Van Regenmortel MHV. Measurement of affinity of viral monoclonal antibodies by ELISA titration of free antibody in equilibrium mixtures. J Immunol Methods. 1991;141:199–208.
Baldwin JT, Lessmann O. What is Russell’s paradox? Scientific American; 1998. http://www.scientificamerican.com/article/whatis-russells-paradox/. Accessed 23 July 2018.
Ball LA. The universal taxonomy of viruses in theory and practice. In: Fauquet CM, et al., editors. Eighth ICTV report. Amsterdam: Elsevier; 2005. p. 11–6.
Brito AF, Braconi CT, Weidmann M, Dichler M, Alves JM, Gruber A, Zanotto PM. The Pangenome of the Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV). Genome Biol Evol. 2015;8:94.
Buck RC, Hull DL. The logical structure of the Linnaean hierarchy. Syst Zool. 1966;15:97–111.
Bunge M. Modes of existence. Rev Metaphys. 2016;70:225.
Daszak, et al. The global virome project. Intern J Infect Dis. 18.001. 2016; https://doi.org/10.1016/ijid.2016.11.096.
Du Sautoy M. What we cannot know. New York: Harper Collins Publishers; 2016. p. 36–73.
Finlay BJ, Esteban GF. Can biological complexity be rationalized? Bioscience. 2009;59:333–40.
Geoghenan JL, Holmes EC. Predicting virus emergence amid evolutionary noise. Open Biol. 2017:170189. https://doi.org/10.1098/rsob.170189.
Gibbs AJ, Gibbs MJ. A broader definition of the ‘virus species’. Arch Virol. 2006;151:1419–22.
Gibbs AJ, Armstrong JS, Gibbs MJ. A type of nucleotide motif that distinguishes tobamovirus species more efficiently than nucleotide signatures. Arch Virol. 2004;149:1941–54.
Gigerenzer G, Selten R. Bounded rationality. The adaptive toolbox. Cambridge, MA: MIT Press; 2002.
Green S. Can biological complexity be reverse engineered ? Stud Hist Phil Biol Biomed Sci. 2015;53:73–83.
King A. Comments to proposed modification to code rule 3.21 (defining virus species). ICTV Discussions; 2012. https://talk.ictvonline.org/ictv1/f/general_ictv_discussions-20/3930/comments-toproposed-modification-to-code-rule-3-21-defining-virus-species. Accessed 23 July 2018.
Korkut A, Hendrickson WA. Structural plasticity and conformational transitions of HIV envelope glycoprotein gp120. PLoS One. 2012;7:e52170.
Kurakin A. Self-organization versus Watchmaker: ambiguity of molecular recognition and design charts of cellular circuity. J Mol Recognit. 2007;20:205–114.
Kurakin A. Scale-free flow of life: on the biology, economics, and physics of the cell. Theor Biol Med Model. 2009;6:6–34.
Kurakin A. Order without design. Theor Biol Med Model. 2010;7:12–22.
Laubichler M. Tinkering: a conceptual and historical evaluation. Tinkering: the microevolution of development: Novartis Foundation Symposium, vol. 284. Chichester: Wiley; 2007. p. 20–9.
Ma B, Shatsky M, Wolfson HJ, Nussinov R. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci. 2002;11:184–97.
Mahner M, Bunge M. Foundations of biophilosophy. Springer: Berlin; 1997.
Nowak MA, McMichael AJ. How HIV defeats the immune system. Sci Am. 1995;273:42–9.
Olshansky SJ, Carnes BA, Butler RN. If humans were built to last. Sci Am. 2003;284:50–5.
Pulendran B. Systems vaccinology: probing humanity’s diverse immune systems with vaccines. Proc Natl Acad Sci U S A. 2014;111:12300–6. https://doi.org/10.1073/pnas.1400476111.
Richalet-Sécordel PM, Rauffer-Bruyère N, Christensen LL, Ofenloch-Haehnle B, Seidel C, Van Regenmortel MHV. Concentration measurement of unpurified proteins using biosensor technology under conditions of partial mass transport limitation. Anal Biochem. 1997;249:165–73.
Rios A. Fundamental challenges to the development of a preventive HIV vaccine. Curr Opin Virol. 2018;29:26–32.
Ruse M. All my love if for individuals. Evolution. 1998;52:283–8.
Simon H. The sciences of the artificial. 3rd ed. Cambridge, MA: MIT Press; 1996.
Simmonds P. A clash of ideas - the varying uses of the ‘species’ term in virology and their utility for classifying viruses in metagenomic datasets. J Gen Virol. 2018;99:277–87.
Simmonds P, Adams MJ, Benkő M, Breitbart M, Brister JR, et al. Consensus statement: virus taxonomy in the age of metagenomics. Nat Rev Microbiol. 2017;15:161–8.
Tsai CJ, Ma B, Nussinov R. Protein-protein interaction networks: how can a hub protein bind so many different partners? Trends Biochem Sci. 2009;34:594–600.
Umotoy J, Bagaya BS, Joyce C, Schiffner T, Menis S, et al. Rapid and focused maturation of a VRC01-class HIV broadly neutralizing antibody lineage involves both binding and accommodation of the N276-glycan. Immunity. 2019;51:141–54.
Van Regenmortel MHV. Antigenicity and immunogenicity of synthetic peptides. Biologicals. 2001a;29:209–13.
Van Regenmortel MHV. Pitfalls of reductionism in the design of peptide-based vaccines. Vaccine. 2001b;19:2369–74.
Van Regenmortel MHV. A paradigm shift is needed in proteomics: ‘structure determines function’ should be replaced by 'binding determines function. J Mol Recognit. 2002b;15:349–51.
Van Regenmortel MHV. Two meanings of reverse vaccinology and the empirical nature of vaccine science. Vaccine. 2011a;29:7875.
Van Regenmortel MHV. Limitations to the structure-based design of HIV-1 vaccine immunogens. J Mol Recognit. 2011b;24:741–53.
Van Regenmortel MHV. Basic research in HIV vaccinology is hampered by reductionist thinking. Front Immunol. 2012b;3:194. https://doi.org/10.3389/fimmu.2012.00194.
Van Regenmortel MHV. Specificity, polyspecificity, and heterospecificity of antibody-antigen recognition. J Mol Recognit. 2014a;27:627–39.
Van Regenmortel MHV. An outdated notion of antibody specificity is one of the major detrimental assumptions of the structure-based reverse vaccinology paradigm, which prevented it from developing an effective HIV-1 vaccine. Front Immunol. 2014b;5:593. https://doi.org/10.3389/fimmu.1014.00593.
Van Regenmortel MHV. The metaphor that viruses are living is alive and well, but it is no more than a metaphor. Stud Hist Philos Sci Part C Stud Hist Philos Biol Biomed Sci. 2016a;59:117–24. https://doi.org/10.1016/j.shpsc.2016.02.017.
Van Regenmortel MHV. Structure-based reverse vaccinology failed in the case of HIV because it disregarded accepted immunological theory. Int J Mol Sci. 2016b;17:1591–625. https://doi.org/10.3390/ijms17091591.
Van Regenmortel MHV. Immune systems rather than antigenic epitopes elicit and produce protective antibodies against HIV. Vaccine. 2017;35:1985–6. https://doi.org/10.1016/j.vaccine.2017.03.017.
Van Regenmortel MHV. Development of a preventive HIV vaccine requires solving inverse problems which is unattainable by rational vaccine design. Front Immunol. 2018a;8:2009.
Van Regenmortel MHV. Viral species, viral genomes and HIV vaccine design: is the rational design of biological complexity a utopia? Arch Virol. 2018b;137:2047–54.
Van Regenmortel MHV. The species problem in virology. Adv Virus Res. 2018c;100:1–18.
Zeder-Lutz G, Benito A, Van Regenmortel MHV. Active concentration measurements of recombinant biomolecules using biosensor technology. J Mol Recognit. 1999;12:300–9.
Zeder-Lutz G, Hoebeke J, Van Regenmortel MHV. Differential recognition of epitopes present on monomeric and oligomeric forms of gp160 glycoprotein of human immunodeficiency virus type 1 by human monoclonal antibodies. Eur J Biochem. 2001;268:2856–66.
Zolla-Pazner S, Cohen SS, Boyd D, Kong XP, Seaman M, Nussenzweig M, Klein F, Overbaugh J, Totrov M. Structure/function studies involving the V3 region of the HIV-1 envelope delineate multiple factors that affect neutralization sensitivity. J Virol. 2016;90:636–49.
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Van Regenmortel, M.H.V. (2019). Viral Species, Viral Genomes and HIV Vaccine Design: Is the Rational Design of Biological Complexity a Utopia?. In: HIV/AIDS: Immunochemistry, Reductionism and Vaccine Design. Springer, Cham. https://doi.org/10.1007/978-3-030-32459-9_24
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