Article

Name: Genome as a (hyper) text: from metaphor to theory

Authors: S. T. Zolyan, R. I. Zhdanov

Russian Institute for Advanced Study, Moscow Pedagogical State University and Institute of Fundamental Medicine and Biology, Kazan Federal University, 18, Kremlin St., Kazan 420008 Russian Federation

Abstract: The similarity between language and genetic information transmission processing was recognized from the very foundation of genetics. A lot of attempts have been made to use linguistics techniques for deciphering protein genes. A modest informative impact of various kinds of decoding of «protein language» was predictable: this kind of technique is limited by the processes of encoding and at best it helps to compile a dictionary of units, but is not able to describe a language and identify the semantic and textual structures which are decisive for communication. Thus, functions of the huge amount of non-coding DNA still remain unclear. A text but not a sign should be regarded as an object of creation – transmission – conservation – transformation of information. The general text theory should be capable to describe linguistic texts and the process of their structuring, functioning and transformation, and to represent a biochemical structure of genome as a hypertext consisting of ordered subset of other texts. The text can be considered as a quasi-organism having memory, creativecognitive characteristics and communicative force; the cell (ribosome) – as a quasi-intelligence capable to operate with abstract semiotic entities. Such an approach will require the construction of a new, multimodal and textocentric version of semiotics (the semiotics of the next generation), where text and context will be the basic concepts, and the signs and meanings will be considered as context-dependent variables, and at the same time as context-forming operators.

Keywords: genome, genetic code, biosemiotics, general theory of text, genome as а text

Bibliography:

Augustyn P. What Connects Biolinguistics and Biosemiotics? Biolinguistics, 2013, vol. 7, p. 96–111.

Barbieri M. A Short History of Biosemiotics. Biosemiotics. Berlin, Springer Science, 2009, no. 2, p. 221–245.

Barbieri M. Biosemiotics: A New Understanding of Life. Naturwissenschaften. Springer Verlag, 2008a, p. 577–599.

Barbieri M. Is the Cell a Semiotic System? Introduction to Biosemiotics. The New Biological Synthesis. M. Barbieri (ed.). Dordrecht, Springer, 2007.

Barbieri M. What is Biosemiotics? Biosemiotics (1). Springer, 2008b, p. 1–3.

Barthes R. From work to text. Barthes Rolan. Izbrannyye raboty. Semiotika. Poetika. Moscow, Progress, 1989, p. 413–423.

Barthes R. The death of the Author. Barthes Rolan. Izbrannyye raboty. Semiotika. Poetika. Moscow, Progress, 1989, p. 384–391.

Beaugrande R.-A. de, Dressler W. Introduction to Text Linguistics. London, Longman, 1994, 270 p.

Benveniste E. Obshchaya lingvistika [General linguistics]. Moscow, Progress, 1974.

Bertalanffy L. General Systems Theory. Foundations, Development, Applications. New York, G. Braziller, 1968, 289 p.

Bertalanffy L. Theoretische Biologie. Berlin, 1932.

Bickerton D. Some Problems for Biolinguistics. Biolinguistics, 2014, vol. 8, p. 73–96.

Chebanov S. Russian biosemiotics as a school: The problem of institualization. Nauchnye chteniya – 2003. Materialy konferentsii. St. Petersburg, Philological Department of St. Petersburg State Univ., 2004, p. 164–171.

Crick F. H. C. The Genetic Code – Yesterday, Today and Tomorrow. Cold Spring Symposium on Quantitative Cold Spring Harb. Symp. Quant. Biol., 1966, vol. 31, p. 3–9.

Crick F. Life Itself: Its Origin and Nature. Simon and Schuster, 1981, 193 p.

Dijk T. van. Some aspects of text grammars. A study in theoretical poetics and linguistics. The Hague, Mouton, 1972.

Elumalai A., Eswaraiah M. Review on application of bioinformatics. Journal of Science. Bioinformatics, 2013, vol. 3, iss. 1, p. 21–27.

Emmeche C., Hoffmeyer J. From language to nature – the semiotic metaphor in biology. Semiotica, 1991, vol. 84 (1/2), р. 1–42.

Favareau D. The evolutionary history of biosemiotics. Introduction to Biosemiotics. The New Biological Synthesis. M. Barbieri (ed.). Dordrecht, Springer, 2007, p. 1–69.

Galik D. Biosemiotics: A New Science of Biology? Filozofia, 2013, vol. 68, no. 10, p. 859–867.

Gamkrelidze T. «Paradigms» in Linguistics and the Problem of the Isomorphism between the Genetic Code & Semiotic Systems. Bulletin of the Georgian National Academy of Sciences, 2009, vol. 3, no. 2.

Gamkrelidze T. V. R. O. Jakobson and the problem of isomorphism between the genetic code and semiotic systems. Voprosy Jazykoznanija, 1988, no. 3, p. 5–9.

Garyaev P. P. Lingvistiko-volnovoi genom [Linguistic wave genome]. Kiev, The Institute of quantum genetics, 2009.

Gelfand M. S. Codes of genetic language and natural language. Voprosy jazykoznanija, 1990, no. 6, p. 60–70.

Gimona M. Protein Linguistics and the Modular Code of the Cytoskeleton. The Codes of Life: The Rules of Macroevolution. M. Barbieri (ed.). Berlin, Springer, 2008, p. 189–206.

Hjelmslev L. Prolegomena to the theory of language. Novoe v lingvistike. Moscow, Progress, 1960, no. 1, p. 264–389.

Ivanov V. V. «The frontiers of semiotics»: Questions for a preliminary discussion. Sovremennaya semiotika i gumanitarnye nauki. Moscow, Yazyki Slavyanskikh Kul’tur, 2010, p. 31–50.

Jakob F. The linguistic model in biology. Voprosy jazykoznanija, 1992, no. 2, p. 135–141.

Jakobson R. Linguistics in its relation to other sciences. Jakobson R. Izbrannye raboty. Moscow, Progress, 1985, p. 387–404.

Jaкobson R. Linguistics. Relationship between the science of language and other sciences. Main trends of research in the social and human sciences. Mouton, The Hague, 1970, p. 419–453.

Ji S. Isomorphism between Cell and Human Languages: Molecular Biological, Bioinformatic and Linguistic Implications. Biosystems, 1997, vol. 44, iss. 1, p. 17–39.

Ji S. The Linguistics of DNA: Words, Sentences, Grammar, Phonetics, and Semantics. Molecular Strategies in Biological Evolution. Annals of the New York Academy of Science, 1999, vol. 870, p. 411–417.

Kull K. A Sign Is not Alive – a Text Is. Sign Systems Studies, 2002, vol. 30.1.

Kull K. Organism as a Self-Reading Text: Anticipation and Semiosis. International Journal of Computing Anticipatory Systems, 1998, vol. 1, p. 93–104.

Kull K., Deacon K., Emmeche C., Hoffmeyer J., Stjernfelt F. Theses on Biosemiotics: Prolegomena to a Theoretical Biology. Biological Theory, 2009, vol. 4 (2), p. 167–173.

Lotman M. Yu. The dualistic nature of the text (discourse as a semiotic and communicative entity). Tekst i kul’tura: obshchie i chastnye problemy. Moscow, Institute of Linguistics, Academy of Sciences of the USSR, 1985, p. 3–20.

Lotman Yu. M. The semiotics of culture and the notion of text. Lotman Yu. M. Izbrannyye stat'i. Tallinn, 1992, vol. 1, p. 129–132.

Lotman Yu. M. Brain – text – culture – artificial intelligence. Semiotika i informatika. Moscow, All-Union Institute of Scientific and Technical Information, 1981, no. 17, p. 13–17.

Lotman Yu. M. On semiosphere. Uchenye zapiski Tartuskogo gosudarstvennogo uiversiteta, 1984, no. 641. (Trudy po znakovym sistemam. Vol. 17.), p. 5–23.

Luhmann N. Essays on Self-Reference. New York, Columbia University Press, 1990.

Luhmann N. Social Systems. Stanford, Stanford University Press, 1995.

Maturana H. R., Varela F. J. Autopoiesis and cognition: The realization of the living. Boston, D. Reidel, 1980.

Nikolaeva T. M. Text linguistics: Current status and prospects. Novoe v zarubezhnoi lingvistike. Moscow, Progress, 1978, no. 8, p. 5–42.

Nikolaeva T. M. Text linguistics and the problems of general linguistics. Izvestiya Akademii nauk SSSR. Seriya literatury i yazyka, 1977, vol. 36, no. 4, p. 304–313.

Pattee H. H. The Necessity of Biosemiotics: Matter-Symbol Complementarity the Physics and Metaphysics of Biosemiotics. Journal of Biosemiotics, 2005, vol. 1 (1), p. 223–238.

Propp Vladimir. Morphology of the Folktale. (Morfologiya skazki). Voprosy poetiki. Leningrad, Academia, 1928, iss. 12, p. 152.

Raible W. Linguistics and Genetics: Systematic parallels. Language Typology and Language Universals. An International Handbook. M. Haspelmath, E. König, W. Oesterreicher, W. Raible (eds.). Berlin, New York, Walter de Gruyter, 2001, p. 103–123.

Ratner V. A. Genetic code as a system. Sorosovskii obrazovatel’nyi zhurnal. Biologiya, 2000, vol. 6, no. 3, p. 17–22.

Ratner V. A. Genetic language: Grammar, sentences, evolution. Genetika, 1993, no. 29, p. 709–719.

Ratner V. A. Geneticheskie upravlyayushchie sistemy. Avtoref. kand. diss. [Genetic control sytems. Author’s abstract of the cand. diss.] Academy of Sciences of the USSR, Siberian Branch, Joint Council for Biological Sciences, Novosibirsk, 1965.

Ratner V. A. The Chronicle of the great discovery: the ideas and persons. Priroda, 2000, no. 6.

Ratner V. A. The comparative hierarchic structure of the genetic language. Genetika, 1993, no. 29, p. 720–739.

Rotshild F. S. Laws of symbolic mediation in the dynamics of self and personality. Annals of the New York Academy of Sciences, 1962, vol. 96 (3), p. 774–784.

Schrödinger E. Chto takoe zhizn’? Fizicheskii aspekt zhivoi kletki [What is life? Physical aspect of the living cell]. Moscow, Izhevsk, Scientific Research Center «Regular and chaotic dynamics», 2002.

Searls D. B. Formal Language Theory and Biological Macromolecules. Mathematical Support for Molecular Biology. American Mathematical Society Press, 1999, p. 117–140.

Searls D. B. Molecules, Languages and Automata. Grammatical Inference: Theoretical Results and Applications Lecture Notes in Computer Science, 2010, vol. 6339, p. 5–10.

Searls D. B. The Language of Genes. Nature, 2002. vol. 420 (6912), p. 211– 217.

Searls D. The Computational Linguistics of Biological Sequences. Artificial Intelligence and Molecular Biology, 1993, p. 47–120.

Sedov A. E. Hierarchic conceptions and cross-disciplinary connections of genetics embedded in its metaphors: Quantitative and structural analysis of terms and utterances. Naukovedenie, 2001, no. 1, p. 135–154.

Sedov A. E. Metaphors in genetics. Vestnik Rossiiskoi akademii nauk, 2000, vol. 70, no. 6, p. 526–534.

Shannon C. E. A mathematical theory of communication. Bell System Technical Journal, 1948, vol. 27 (379–423), р. 623–656.

Solov’ev V. V., Kel’ A. E., Rogozin I. B., Kolchanov N. A. Ispol’zovanie EVM v molekulyarnoi biologii. Vvedenie v teoriyu geneticheskikh tekstov [The use of computers in molecular biology. Introduction to the theory of genetic texts]. Novosibirsk, Novosibirsk Univ., 1988.

Stepanov Yu. S. Semiotika [Semiotics]. Moscow, Nauka, 1971.

Stjernfelt F. Tractatus Hoffmeyerensis: Biosemiotics as expressed in 22 basic hypotheses. Sign Systems Studies, 2002, vol. 30.1, p. 337–345.

Trifonov E. N. Codes of Biosequences. The Codes of Life. The Rules of Macroevolution. M. Barbieri (ed.). Springer, 2008, p. 3–14.

Trifonov E. N. Earliest pages of bioinformatics. Bioinformatics, 2000, vol. 16, no. 1, p. 5–9.

Trifonov E. N. Thirty Years of Multiple Sequence Codes. Genomics. Proteomics. Bioinformatics, 2011, vol. 9 (1–2), р. 1–6.

Vanyushin B. F. Metilirovaniye DNK i epigenetika (DNA methylation and epigenetics). Genetika, 2006, vol. 42, no. 9, p. 1–14.

Wiener N. Cybernetics: Or Control and Communication in the Animal and the Machine. Paris, Hermann & Cie, Camb. Mass., MIT Press, 1948.

Wittgenstein L. Tractatus Logico-Philosophicus. Moscow, Izd. inostrannoy literatury, 1958, 131 p.

Witzany G. Review: Marcello Barbieri (ed.) Introduction to Biosemiotics. The New Biological Synthesis. Dordrecht, Springer, 2007, triple C 5 (3), p. 104–109.

Zhdanov R. I., Ibragimova M. Y. New informational level at genomic DNA: lipids specifically bound to DNA. Genetics and Chemistry Sharing a Language of Discovery: Cell Symposium series, May 23–25, 2012. Boston, Marriott, Cambridge, 2014, p. 29.

Zhdanov Renad I. (ed.) Abstracts book of International Symposium «Language of Genome», Kazan Federal University. Kazan, 2014, 32 p.

Zolyan S. T. «The endless labyrinth of connections»: Text semantics as a multidimensional structure. Kritika i semiotika, 2013, no. 1 (18), p. 18–44.

Zolyan S. T. Rethinking the correlations between language and genetic code. Voprosy jazykoznanija, 2016, no. 1, p. 114–132.

Zolyan S. Text as a Multisemantic Entity – a Prolegomenon to Formalization. International Congress Cultural Poliglotism, tо the anniversary of Juri Lotman’s 90th birthday. Tartu, 2012, p. 57–62.