Abstract
The similarity between language and genetic information transmission processing has been recognized since molecular genetics was founded. Numerous attempts have been made to use linguistics techniques to decipher protein genes. The modest informational impact of various approaches to decoding the “protein language” was predictable: this type of technique is limited by the processes of encoding and at best helps compile a dictionary of units. However, this technique cannot describe a language and identify the semantic and textual structures that are decisive for communication. Thus, the functions of a large amount of non-coding DNA remain unclear. A text (but not a sign) should be regarded as an artefact of the creation, transmission, conservation and transformation of information. A general theory of text should be capable of describing linguistic texts and the process of their structuring, functioning and transformation. It should also be able to represent the biochemical structure of a genome as a hypertext that consists of an ordered subset of other texts. A text can be considered to be a quasi-organism that possesses memory, creative-cognitive characteristics and communicative force, and a cell can be considered as a quasi-intelligence capable of manipulating abstract semiotic entities. Such an approach requires the construction of a new, multimodal, and text-oriented version of semiotics (next-generation semiotics), in which text and context are the basic concepts and signs and meanings are considered to be context-dependent variables and, simultaneously, context-forming operators.
References
Augustyn, Prisca. 2013. What connects biolinguistics and biosemiotics? Biolinguistics 7. 96–111.10.5964/bioling.8957Search in Google Scholar
Barbieri, Marcello. 2007. Is the cell a semiotic system? In M. Barbieri (ed.), Introduction to biosemiotics: The new biological synthesis, 179–208. Dordrecht: Springer.10.1007/1-4020-4814-9_8Search in Google Scholar
Barbieri, Marcello. 2009. A short history of biosemiotics. Biosemiotics 2. 221–245.10.1007/s12304-009-9042-8Search in Google Scholar
Barthes, Roland. 1977. Image – Music – Text. London: Fontana.Search in Google Scholar
Beaugrande, Robert-Alain de & Wolfgang Dressler. 1981. Introduction to text linguistics. London: Longman.10.4324/9781315835839Search in Google Scholar
Benveniste, Emile. 1981 [1969]. The semiology of language. Semiotica 37(1). 5–24.10.1515/semi.1981.37.s1.5Search in Google Scholar
Bertalanffy, Ludwig von. 1932. Theoretische biologie. Berlin: Borntrager.Search in Google Scholar
Bertalanffy, Ludwig von. 1968. General system theory: Foundations, development, applications. New York: George Braziller.Search in Google Scholar
Bickerton, Derek. 2014. Some problems for biolinguistics. Biolinguistics 8. 73–96.10.5964/bioling.8993Search in Google Scholar
Crick, Francis. 1966. The genetic code: Yesterday, today, and tomorrow. Cold Spring Symposium on Quantitative Biology 31. 3–9.10.1101/SQB.1966.031.01.007Search in Google Scholar
Elumalai, A. & M. Chinna Eswaraiah. 2013. Review on application of bioinformatics. Journal of Science: Bioinformatics 3(1). 21–27.Search in Google Scholar
Emmeche, Claus & Jesper Hoffmeyer. 1991. From language to nature: The semiotic metaphor in biology. Semiotica 84(1/2). 1–42.10.1515/semi.1991.84.1-2.1Search in Google Scholar
Favareau, Donald. 2007. The evolutionary history of biosemiotics. In M. Barbieri (ed.), Introduction to biosemiotics: The new biological synthesis, 1–69. Dordrecht: Springer.10.1007/1-4020-4814-9_1Search in Google Scholar
Folcher, M., Sabine Oesterle, Katharina Zwicky, Thushara Thekkottil, Julie Heymoz, Muriel Hohmann, Matthias Christen, Marie Daoud El-Baba, Peter Buchmann & Martin Fussenegger. 2014. Mind-controlled transgene expression by a wireless powered optogenetic designer cell implant. Nature Communication 5. 5392.10.1038/ncomms6392Search in Google Scholar
Galik, Dusan. 2013. Biosemiotics: A new science of biology? Filozofia 68(10). 859–867.Search in Google Scholar
Gamkrelidze, Tomaz. 2009. “Paradigms” in linguistics and the problem of the isomorphism between the genetic code and semiotic systems. Bulletin of the Georgian National Academy of Sciences 3(2). 194–197.Search in Google Scholar
Garyayev, Petr. 2009. Lingvistiko-volnovoy genom. Kiev: In-t kvantovoy genetiki.Search in Google Scholar
Gel’fand, Mikhail. 1990. Kody geneticheskogo yazyka i yestestvennyy yazyk. Voprosy yazykoznaniya 6. 60–70.Search in Google Scholar
Gimona, Mario. 2008. Protein linguistics and the modular code of the cytoskeleton. In M. Barbieri & J. Hoffmeyer (eds.), Codes of life: The rules of macroevolution, 189–206. Berlin: Springer.10.1007/978-1-4020-6340-4_8Search in Google Scholar
Hjelmslev, Louis. 1961 [1943]. Prolegomena to a theory of language. Madison, WI: University of Wisconsin Press.Search in Google Scholar
Hogeweg, Paulien P. 2011. The roots of bioinformatics in theoretical biology. PLoS Computational Biology 7(3). e1002021.10.1371/journal.pcbi.1002021Search in Google Scholar
Jacob, François. 1977. The linguistic model in biology. In D. Armstrong & C. H. van Schooneveld (eds.), Roman Jakobson: Echoes of his scholarship, 186–192. Lisse: de Ridder.Search in Google Scholar
Jakobson, Roman. 1970. Linguistics. In Unesco (ed.), Main trends of research in the social and human sciences, Part one: Social sciences, 419–463. Paris, The Hague: Mouton.Search in Google Scholar
Ji, Sunghul. 1997. Isomorphism between cell and human languages: Molecular biological, bioinformatic and linguistic implications. Biosystems 44(1). 17–39.10.1016/S0303-2647(97)00039-7Search in Google Scholar
Ji, Sunghul. 1999. The linguistics of DNA: Words, sentences, grammar, phonetics, and semantics. Annals of the New York Academy of Science 870. 411–417.10.1111/j.1749-6632.1999.tb08916.xSearch in Google Scholar
Lotman, Juri. 1981. Mozg – Tekst – Kul’tura – Iskusstvennyy intellect. Semiotika i Informatika 17. 13–17.Search in Google Scholar
Keep, C., T. McLaughlin & R. Parmar (eds.). 1993. “Hypertext”. In The electronic labyrinth. http://www2.iath.virginia.edu/elab/hfl0037.html (accessed 19 August 2018).Search in Google Scholar
Kull, K. 1998. Organism as a self-reading text: Anticipation and semiosis. International Journal of Computing Anticipatory Systems 1. 93–104.Search in Google Scholar
Kull, K. 2002. A sign is not alive – A text is. Sign Systems Studies 30(1). 327–336.10.12697/SSS.2002.30.1.21Search in Google Scholar
Kull, K., K. Deacon, C. Emmeche, J. Hoffmeyer & F. Stjernfelt. 2009. Theses on biosemiotics: Prolegomena to a theoretical biology. Biological Theory 4(2). 167–173.10.1162/biot.2009.4.2.167Search in Google Scholar
Kurtz, Glenn. 1997. From work to hypertext: Authors and authority in a reader-directed medium. http://glennkurtz.com/cgi-bin/iowa/essays/work/index.html (accessed 11 April 2015).Search in Google Scholar
López-García, Ángel. 2005. The grammar of genes: How the genetic code resembles the linguistic code. Bern: Peter Lang.Search in Google Scholar
Lotman, Juri M. 1988 [1981]. The semiotics of culture and the concept of a text. Soviet Psychology 26. 52–58.10.2753/RPO1061-0405260352Search in Google Scholar
Lotman, Mihhail. 1985. Dvoystvennaya priroda teksta (svyaznyy tekst kak semioticheskoye i kommunikativnoye obrazovaniye). In Yu. Sorokin (ed.), Tekst i kul’tura: Obshchiye i chastnyye problem, 3–20. Moscow: Institute yazykoznaniya AN SSSR.Search in Google Scholar
Luhmann, Niklas. 1990. Essays on self-reference. New York: Columbia University Press.Search in Google Scholar
Luhmann, Niklas. 1995. Social systems. Stanford, CA: Stanford University Press.Search in Google Scholar
Maturana, Humberto & Francisco Varela. 1980. Autopoiesis and cognition: The realization of the living. Boston: D. Reidel.10.1007/978-94-009-8947-4Search in Google Scholar
Nikolayeva, Tat’yana. 1977. Lingvistika teksta i problemy obshchey lingvistiki. Izvestiya Akademii nauk SSSR: Seriya literatury i yazyka 36(4). 304–313.Search in Google Scholar
Pattee, Howard. 2005. The necessity of biosemiotics: Matter-symbol complementarity. Journal of Biosemiotics 1(1). 223–238.Search in Google Scholar
Peirce, Charles S. CP. 1931–1966. The collected papers of Charles S. Peirce, Vol. 8 C. Hartshorne, P. Weiss & A. W. Burks (eds.), Cambridge: Harvard University Press. [Reference to Peirce’s papers will be designated CP followed by volume and paragraph number.].Search in Google Scholar
Peirce, Charles S. MS. 1967. Manuscripts in the Houghton Library of Harvard University, as identified by Richard Robin, Annotated catalogue of the Papers of Charles S. Peirce. Amherst: University of Massachusetts Press. [Reference to Peirce’s manuscripts will be designated MS or L.].Search in Google Scholar
Propp, Vladimir. 1968 [1928]. Morphology of the folktale. Second Edition Revised and Edited with a Preface by Louis A. Wagner New Introduction by Alan Dundes. Austin: University of Texas Press. (American Folklore Society Bibliographical and Special Series Volume 9. Indiana University Research Center in Anthropology, Folklore, and Linguistics Publication 10).10.7560/783911Search in Google Scholar
Raible, Wolfgang. 2001. Linguistics and genetics: Systematic parallels. In M. Haspelmath, E. König, W. Oesterreicher & W. Raible (eds.), Language typology and language universals: An international handbook, 103–123. Berlin & New York: Walter de Gruyter.10.1515/9783110171549.2Search in Google Scholar
Ratner, Vadim. 1993a. Geneticheskiy yazyk: grammatika, predlozheniya, evolyutsiya. Genetika 29. 709–719.Search in Google Scholar
Ratner, Vadim. 1993b. Sravnitel’nyy iyerarkhicheskaya struktura geneticheskogo yazyka. Genetika 29. 720–739.Search in Google Scholar
Rothschild, Friedrich. 1962. Laws of symbolic mediation in the dynamics of self and personality. Annals of the New York Academy of Sciences 96(3). 774–784.10.1111/j.1749-6632.1962.tb50161.xSearch in Google Scholar
Saussure, Ferdinand de. 1959 [1916]. Course in General Linguistics Ferdinand. In de Saussure, Charles Bally & Albert Sechehaye (eds.), In collaboration with Albert Riedlinger Translated, with an introduction and notes by Wade Baskin. New York, Toronto, London: McGraw-Hill Book Company.Search in Google Scholar
Schrödinger, Erwin. 1944. What is life? The physical aspect of the living cell. http://whatislife.stanford.edu/LoCo_files/What-is-Life.pdf (accesed 10 June 2015).Search in Google Scholar
Searls, David. 1993. The computational linguistics of biological sequences. In Larry Hunter (ed.), Artificial intelligence and molecular biology, 47–120. Stanford, CA: AAAI Press.Search in Google Scholar
Searls, David. 1999. Formal language theory and biological macromolecules. Series in Discrete Mathematics and Theoretical Computer Science 47. 117–140.10.1090/dimacs/047/06Search in Google Scholar
Searls, David. 2002. The language of genes. Nature 420(6912). 211–217.10.1038/nature01255Search in Google Scholar
Searls, David. 2010. Molecules, languages, and automata. Lecture Notes in Computer Science 6339. 5–10.10.1007/978-3-642-15488-1_2Search in Google Scholar
Shannon, C. E. 1948. A mathematical theory of communication. Bell System Technical Journal 27. 379–423, 623–656.10.1002/j.1538-7305.1948.tb01338.xSearch in Google Scholar
Solov’ev, V. V., A. E. Kel’, I. B. Rogozin & N. A. Kolchanov. 1988. Ispol’zovanie EVM v molekulyarnoi biologii. Vvedenie v teoriyu geneticheskikh tekstov. Novosibirsk: Novosibirsk University.Search in Google Scholar
Stepanov, Juri. 1971. Semiotika. Moscow: Nauka.Search in Google Scholar
Stjernfelt, Frederik. 2002. Tractatus Hoffmeyerensis: Biosemiotics as expressed in 22 basic hypotheses. Sign Systems Studies 30(1). 337–345.10.12697/SSS.2002.30.1.22Search in Google Scholar
Trifonov, Edward. 2000. Earliest pages of bioinformatics. Bioinformatics 16(1). 5–9.10.1093/bioinformatics/16.1.5Search in Google Scholar
Trifonov, Edward. 2008. Codes of biosequences. In M. Barbieri & J. Hoffmeyer (eds.), Codes of life: The rules of macroevolution, 3–14. Berlin: Springer.10.1007/978-1-4020-6340-4_1Search in Google Scholar
Trifonov, Edward. 2011. Thirty years of multiple sequence codes. Genomics Proteomics & Bioinformatics 9(1–2). 1–6.10.1016/S1672-0229(11)60001-6Search in Google Scholar
Watson, D. 1965. Molecular biology of the gene. New York: Benjamin.Search in Google Scholar
Wiener, N. 1948. Cybernetics: Or control and communication in the animal and the machine. Cambridge, MA: MIT Press.Search in Google Scholar
Wittgenstein, Ludwig. 1922. Tractatus logico-philosophicus. C. K. Ogden (trans.). London: Kegan Paul, Trench, Trubner.Search in Google Scholar
Wittgenstein, Ludwig. 1958. Philosophical investigations. London: Basil Blackwell.Search in Google Scholar
Witzany, Günther. 2007. Review: Marcello Barbieri (ed.) (2007) Introduction to Biosemiotics. The New Biological Synthesis. Triple C 5(3). 104–109.Search in Google Scholar
Goethe, Johann Wolfgang. 2009 [1790]. The metamorphosis of plants. Cambridge, MA: MIT Press.Search in Google Scholar
Zolyan, Suren. 2012. Text as a multisemantic entity: A prolegomenon to formalization. In Proceedings of the international congress on cultural polyglotism, Tartu, February 28 – March 2, 57–62.Search in Google Scholar
Zolyan, Suren. 2013. “Beskonechnyy labirint stsepleniy”: Semantika teksta kak mnogomernaya struktura. Kritika i Semiotika 1(18). 18–44.Search in Google Scholar
Zolyan, Suren. 2014. Modalnaya semiotika: Osnovaniya I obosnovaniya. Il’in M. (ed.), Moskovskiy Yezhegodnik Trudov iz Obshchestvovedcheskikh Distsiplin (METOD), 97–120. Moscow: Rossiyskaya Akademiya nauk, INION.Search in Google Scholar
Zolyan, Suren. 2015. O Formal’nom apparate kontekstno-zavisimoy semantiki. Inostrannyye yazyki v vyshej shkole 2(33). 3–19.Search in Google Scholar
© 2018 Walter de Gruyter GmbH, Berlin/Boston