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Arbitrariness is not enough: towards a functional approach to the genetic code

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Abstract

Arbitrariness in the genetic code is one of the main reasons for a linguistic approach to molecular biology: the genetic code is usually understood as an arbitrary relation between amino acids and nucleobases. However, from a semiotic point of view, arbitrariness should not be the only condition for definition of a code, consequently it is not completely correct to talk about “code” in this case. Yet we suppose that there exist a code in the process of protein synthesis, but on a higher level than the nucleic bases chains. Semiotically, a code should be always associated with a function and we propose to define the genetic code not only relationally (in basis of relation between nucleobases and amino acids) but also in terms of function (function of a protein as meaning of the code). Even if the functional definition of meaning in the genetic code has been discussed in the field of biosemiotics, its further implications have not been considered. In fact, if the function of a protein represents the meaning of the genetic code (the sign’s object), then it is crucial to reconsider the notion of its expression (the sign) as well. In our contribution, we will show that the actual model of the genetic code is not the only possible and we will propose a more appropriate model from a semiotic point of view.

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Notes

  1. In biology, the term “genetic code” is understood as a table of 64 codon triplets specifying amino acids or STOPs. The table is only a schematisation of a real connections between codon triplets and amino acids that exist in nature in form of strings (or folded strings). In this article, the term “genetic code” is used rather in reference to strings of codon triplets and strings of amino acids and relation between them, not in reference to its schematic representation.

References

  • Barbieri M (2002) The organic codes: an introduction to semantic biology. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Barbieri M (2005) Life is artifact-making. J Biosemiot 1:107–134

    Google Scholar 

  • Barbieri M (2008) Life is semiosis. The biosemiotic view of nature. Cosmos and history. J Nat Soc Philos 4(1–2):29–52

    Google Scholar 

  • Crick F (1968) The origin of the genetic code. J Mol Biol 38:367–379

    Article  CAS  PubMed  Google Scholar 

  • De Saussure F (1916) Course in general linguistics. McGraw-Hill Book Company, New York [Edited by C. Bally and A. Sechehaye, Transl. by W. Baskin]

    Google Scholar 

  • Eco U (1998) Segni, pesci e bottoni. Appunti su semiotica, filosofia e scienze umane. Sugli specchi e altri saggi. Il segno, la rappresentazione e l’immagine. Bompiani, Milan, pp 301–333

    Google Scholar 

  • Emmeche C (2004) A-life, organism and body: the semiotics of emergent levels. In: Bedeau M, Husbands PP, Hutton T, Kumar S, Suzuki H (eds) Workshop and tutorial proceedings. Ninth international conference on the simulation and synthesis of living systems (Alife IX), Boston Massachusetts, September 12th, 2004

  • Jakobson R (1971) Selected writings. Word and language, vol 2. Mouton, The Hague, pp 678–687

    Chapter  Google Scholar 

  • Ji S (1985) The bhopalator—a molecular model of the living cell based on the concepts of conformons and dissipative structures. J Theoret Biol 116:399–426

    Article  CAS  Google Scholar 

  • Ji S (1999) The linguistics of DNA: words, sentences, grammar, phonetics, and semantics. Molecular strategies in biological evolution. Ann N Y Acad Sci 870:411–417

    Article  CAS  PubMed  Google Scholar 

  • Ji S (2002) Microsemiotics of DNA. Semiotica 138(1/4):15–42

    Google Scholar 

  • Kull K (2005) Semiotics is a theory of life. In: Williamson R, Sbrocchi LG (eds) Proceedings of the National Academy of Sciences (PNAS), vol 111, no 25, pp 9265–9270

  • Kusebauch U, Ortega C, Ollodart A, Rogers RS, Sherman DR, Moritz RL (2014) Mycobacterium tuberculosis supports protein tyrosine phosphorylation. Proc Natl Acad Sci. doi:10.1073/pnas.1323894111

    PubMed  PubMed Central  Google Scholar 

  • Markoš A (2002) Readers of the book of life. Oxford University Press, New York

    Google Scholar 

  • Monod J (1970) Le hasard et la nécessité. Essai sur la philosophie naturelle de la biologie moderne. Éditions du Seuil, Paris

    Google Scholar 

  • Sarg B, Gréen A, Söderkvist P, Helliger W, Rundquist I, Lindner HH (2005) Characterization of sequence variations in human histone H1.2 and H1.4 subtypes. FEBS J 272:3673–3683. doi:10.1111/j.1742-4658.2005.04793.x

    Article  CAS  PubMed  Google Scholar 

  • Scherrer K, Jost J (2007) Gene and genon concept: coding versus regulation. A conceptual and information theoretic analysis of genetic storage and expression in the light of modern molecular biology. Theory Biosci 126:65–113. doi:10.1007/s12064-007-0012-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Searls DB (2002) The language of genes. Nature. doi:10.1038/nature01255

    PubMed  Google Scholar 

  • Sharov AA (2010) Functional information: towards synthesis of biosemiotics and cybernetics. Entropy 12:1050–1070. doi:10.3390/e12051050

    Article  PubMed  PubMed Central  Google Scholar 

  • Sharov AA (2016) Evolution of natural agents: preservation, advance, and emergence of functional information. Biosemiotics 9:103–120. doi:10.1007/s12304-015-9250-3

    Article  PubMed  PubMed Central  Google Scholar 

  • Sikorska B, Knight R, Ironside JW, Liberski PP (2012) Creutzfeldt–Jakob disease. Adv Exp Med Biol. doi:10.1007/978-1-4614-0653-2_6

    Google Scholar 

  • Stegmann UE (2015) ‘Genetic coding’ reconsidered: an analysis of actual usage. Br J Philos Sci. doi:10.1093/bjps/axv007

    PubMed  PubMed Central  Google Scholar 

  • Trifonov EN (1988) Codes of nucleotide sequences. Math Biosci 90(1–2):507–517

    Article  Google Scholar 

  • Trifonov EN, Kirzhner A, Kirzhner VM, Berezovsky IN (2001) Distinct stages of protein evolution as suggested by protein sequence analysis. J Mol Evol 53:394–401

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The production and publication of this paper was made possible thanks to the financial support of the Faculty of Arts of Palacký University Olomouc in 2014 from the Academic Research Support Fund. The name of the project is General Linguistics Prolegomena to the Making and Testing of Grammar.

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Correspondence to Ľudmila Lacková.

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Lacková, Ľ., Matlach, V. & Faltýnek, D. Arbitrariness is not enough: towards a functional approach to the genetic code. Theory Biosci. 136, 187–191 (2017). https://doi.org/10.1007/s12064-017-0246-1

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