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Biocomputing: an insight from linguistics

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Abstract

This paper is placed in a formal framework in which the interdisciplinary study of natural language is conducted by integrating linguistics, computer science and biology. It provides an overview of the field of research, conveying the main biological ideas that have influenced research in linguistics. Our work highlights the main methods of molecular computing that have been applied to the processing and study of the structure of natural language: DNA computing, membrane computing and networks of evolutionary processors. Moreover, some new challenges and lines of research for the future are pointed out, that can provide important improvements in the understanding of natural language as a structure and a human capacity.

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References

  • Adleman LM (1994) Molecular computation of solutions to combinatorial problems. Sci Agric 226:1021–1024

    Article  Google Scholar 

  • Akman V, Surav M (1996) The use of situation theory in context modeling. Comput Intell 12(4):1–13

    Google Scholar 

  • Baxter G, Blythe R, Croft W, Nekane A (2008) Utterance selection model of language change. Phys Rev E 73:046118

    Article  Google Scholar 

  • Bel-Enguix G, Jiménez-López MD (2005a) Biosyntax. An overview. Fundam Informa 64:1–12

    Google Scholar 

  • Bel-Enguix G, Jiménez-López MD (2005b) Linguistic membrane systems and applications. In: Ciobanu Gh, Păun Gh, Pérez-Jiménez MJ (eds) Applications of membrane computing, Springer, Berlin, pp 347–388

    Chapter  Google Scholar 

  • Bel-Enguix G, Jiménez-López MD (2005c) Analysing sentences with networks of evolutionary processors. In: Mira J, Álvarez JR (eds) Artificial intelligence and knowledge engineering applications: a bioinspired approach. LNCS 3562, Springer, Berlin, pp 102–111

    Chapter  Google Scholar 

  • Bel-Enguix G, Jiménez-López MD (2006) Computing dialogues with membranes. Electron Notes Theor Comput Sci 157(4):57–73

    Article  Google Scholar 

  • Benerecetti M, Bouquet P, Ghidini C (2001) On the dimensions of context dependence: partiality, approximation, and perspective. In: Proceedings of CONTEXT 2001. Springer, Berlin

  • Beni G, Wang J (1989) Swarm Intelligence in cellular robotic systems. In: Proceedings of NATO advanced workshop on robots and biological systems. Tuscany, 26–30

  • Brendel V, Busse H (1984) Genome structure described by formal languages. Nucleic Acids Res 12(5):2561–2568

    Article  Google Scholar 

  • Brighton H, Smith K, Kirby S (2005) Language as an evolutionary system. Phys Life Rev 2:177–226

    Article  Google Scholar 

  • Cardelli L (2005) Brane calculi, interactions of biological membranes. In: Danos V, Schachter V (eds) Computational methods in systems biology. LNCS 3082, Springer, Berlin

    Google Scholar 

  • Castellanos J, Leupold P, Mitrana V (2005) Descriptional and computational complexity aspects of hybrid networks of evolutionary processors. Theor Comput Sci 330(2):205–220

    Article  MATH  MathSciNet  Google Scholar 

  • Castellanos J, Martín-Vide C, Mitrana V, Sempere JM (2003) Networks of evolutionary processors. Acta Inform 39:517–529

    MATH  MathSciNet  Google Scholar 

  • Cavalli-Sforza L (1981) Cultural transmission and evolution. Princenton University Press, Princeton

    Google Scholar 

  • Collado-Vides J (1989) A transformation-grammar approach to the study of regulation of gene expression. J Theor Biol 136:403–425

    Article  Google Scholar 

  • Collado-Vides J, Gutiérrez-Rios RM, Bel-Enguix G (1998) Networks on transcriptional regulation encoded in a grammatical model. BioSystems 47:103–118

    Article  Google Scholar 

  • Croft W (2000) Explaining language change. An evolutionary approach. Longman, Harlow

    Google Scholar 

  • Csuhaj-Varjú E, Dassow J, Kelemen J, Păun Gh (1994) Grammar systems. Gordon and Breach, London

    MATH  Google Scholar 

  • Csuhaj-Varjú E, Martín-Vide C, Mitrana V (2005) Hybrid networks of evolutionary processors are computational complete. Acta Inform 41(4-5):257–272

    Article  MATH  MathSciNet  Google Scholar 

  • Csuhaj-Varjú E, Mitrana V (2000) Evolutionary systems: a language generating device inspired by evolving communities of cells. Acta Inform 36:913–926

    Article  MATH  MathSciNet  Google Scholar 

  • Csuhaj-Varjú E, Salomaa A (1997) Networks of parallel language processors. In: Păun Gh, Salomaa A (eds) New trends in formal languages, LNCS 1218. Springer, Berlin, pp 299–318

    Chapter  Google Scholar 

  • Darwin Ch (2009) The origin of species: 150th anniversary edition. Signet classics. New American Library, New York (1st edition: 1859)

  • Dorigo M, Statzle T (2004) Ant colony optimization. MIT Press, Cambridge

    Book  MATH  Google Scholar 

  • Errico L, Jesshope C (1994) Towards a new architecture for symbolic processing. In: Plander I (ed) Artificial intelligence and information-control systems of robots 94, World Scientific Publisher, Smolenice, pp 31–40

    Google Scholar 

  • Hillis WD (1985) The connection machine. MIT Press, Cambridge

    Google Scholar 

  • Holland John H (1992) Adaptation in natural and artificial systems: an introductory analysis with applications to biology, control, and artificial intelligence. MIT Press, Cambridge

    Google Scholar 

  • Jacob F, Monod J (1963) Genetic repression, allosteric inhibition and cellular differentiation. In: Monod J (ed) Cytodifferentiation and macromolecular synthesis, Academic Press, New York, pp 30–64

  • Jakobson R (1973) Essais de Linguistique Générale. 2. Rapports Internes et Externes du Language. Les Éditions de Minuit, Paris

    Google Scholar 

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

    Article  Google Scholar 

  • Kirby S (2001) Spontaneous evolution of linguistic structure: an iterated learning model of the emergence of regularity and irregularity. IEEE Trans Evol Comput 5(2):102–110

    Article  MathSciNet  Google Scholar 

  • Knight C, Studdert-Kennedy M, Hurford J (eds) (2000) The evolutionary emergence of language: social function and the origins of linguistic form. Cambridge University Press, Cambridge

    Google Scholar 

  • Lieberman E, Michel JB, Jackson J, Tang T, Nowak MA (2007) Quantifying the evolutionary dynamics of language. Nature 449:713–716

    Article  Google Scholar 

  • López García A (2002) Fundamentos Genéticos del Lenguaje. Cátedra, Madrid

    Google Scholar 

  • Loreto V, Steels L (2007) Emergence of language. Nat Phys 3(11):758–760

    Article  Google Scholar 

  • Marcus S (1998) Language at the crossroad of computation and biology. In: Păun Gh (ed) Computing with bio-molecules, Springer, Singapore, pp 1–35

    Google Scholar 

  • Margenstern M, Mitrana V, Pérez-Jiménez M (2004) Accepting hybrid networks of evolutionary processors. In: Ferreti C, Mauri G, Zandron C (eds) DNA 10. Preliminary proceedings, University of Milano-Biccoca, Milan, pp 107–117

    Google Scholar 

  • Martín-Vide C, Mitrana V, Pérez-Jiménez M, Sancho-Caparrini F (2003) Hybrid networks of evolutionary Processors. In: Cantó-Paz E et al. (ed). Genetic and evolutionary computation, GECCO 2003, Genetic and evolutionary computation conference (Part I). LNCS 2723. Springer, Berlin, pp 401–412

  • Maynard Smith J, Szathmáry E (1997) The major transitions in evolution. Oxford University Press, New York

    Google Scholar 

  • Maynard Smith J, Szathmáry E (1999) The origins of life: from the birth of life to the origin of language. Oxford University Press, Oxford

    Google Scholar 

  • Monod J (1970) Le Hasard et la Nécessité. Éditions du Seuil, Paris

    Google Scholar 

  • Păun Gh (2000) Computing with membranes. J Comput Syst Sci 61:108–143

    Article  MATH  Google Scholar 

  • Păun Gh, Rozenberg G, Salomaa A (1998) DNA computing. New computing paradigms. Springer, Berlin

    MATH  Google Scholar 

  • Pawlak Z (1965) Gramatyka i Matematika. Panstwowe Zakady Wydawnietw Szkolnych, Warzsawa

    Google Scholar 

  • Regev A, Panina E, Silverman W, Cardelli L, Shapiro E (2004) BioAmbients: an abstraction for biological compartments. Theor Comput Sci 325(1):141–167

    Article  MATH  MathSciNet  Google Scholar 

  • Sakakibara Y, Brown M, Underwood R, Saira Mian I, Haussler D (1994) Stochastic context-free grammars for modeling RNA. In: Proceedings of the 27th Hawaii international conference on system sciences. IEEE Computer Society Press, Honolulu, pp 284–283

  • Schleicher A (1853) Die ersten Spaltungen des indogermanischen Urvolkes. Allgemeine Zeitung fuer Wissenschaft und Literatur

  • Searls D (1993) The linguistics of DNA. Am Sci 80:579–591

    Google Scholar 

  • Steels L (2000) Language as a complex adaptive system. LNCS 1917:17–26

    Google Scholar 

  • Uemura Y, Hasegawa A, Kobayashi S, Yokomori T (1999) Tree adjoining grammars for RNA structure prediction. Theor Comput Sci 210(2):277–303

    Article  MATH  MathSciNet  Google Scholar 

  • Victorri B (2007) Analogy between language and biology: a functional approach. Cogn Process 8:11–19

    Article  Google Scholar 

  • Watson J, Crick F (1953) The structure for deoxyribose nucleic acid. Nature 171:137

    Article  Google Scholar 

Download references

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Authors and Affiliations

  1. GRLMC-Research Group on Mathematical Linguistics, Universitat Rovira i Virgili, Av. Catalunya 35, 43002, Tarragona, Spain

    Gemma Bel-Enguix & M. Dolores Jiménez-López

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  1. Gemma Bel-Enguix
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  2. M. Dolores Jiménez-López
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Correspondence to Gemma Bel-Enguix.

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Bel-Enguix, G., Jiménez-López, M.D. Biocomputing: an insight from linguistics. Nat Comput 11, 131–139 (2012). https://doi.org/10.1007/s11047-012-9305-1

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