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Introducing Dynamics into the Field of Biosemiotics

A Formal Account with Examples from Language and Immunology

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Abstract

Coding plays a universal and pervasive role in biological organization, in forms such as genetic coding (DNA to protein translation), RNA processing, gene regulation, protein modification, cell signalling, immune responses, epigenetic development and natural language. Nevertheless, the ways and means by which organic codes are formed and used are still poorly understood. A formal model is presented in this paper to investigate the emergence of conventional codes among code users. The relationship between the formation and the usage of codes is discussed, and a biological mechanism involving coding is identified in the context of the immune system.

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Notes

  1. Noam Chomsky, one of the most influential linguists at that time, in fact explicitly wrote that the study of meaning and reference and of the use of language should be excluded from the field of linguistics (Chomsky 1977).

  2. For completeness we must mention that this Th1/Th2 model is a simplification, and it is recognized as such by biomedical researchers. For example, on the cellular level other Th cell subsets (Th3) also regulate the response by playing an inhibitory role (Benson et al. 2001). On the molecular level, the different cytokines may be down-regulated by other molecules, for example microRNAs (Lu et al. 2009). Additionally, the recruitment of Th1/Th2 cells to an inflammatory or malignant site in the body depends on yet another class of immunological mediators, namely chemokines (Kruizinga et al. 2009; Viola et al. 2008).

  3. One claim from Biosemiotics is that such mechanisms might be equally important as other well known primitives of evolution, like mutation and cross-over.

  4. The notation <.> denotes a sequence, i.e. an ordered list of elements.

  5. A kinetics specifies how reaction equations translate to concentration change equations.

  6. Note that, together, the first two reactions make that signs and adaptors live in an idiotypic relationship (i.e. one triggers the production of the other and vice versa), and that idiotypic relationships were also identified within the context of the adaptive immune system and the theory of clonal selection (Burnet 1959; Jerne 1955, 1985).

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Acknowledgements

The authors wish to thank the editor, Marcello Barbieri, as well as all of the anonymous reviewers for their invaluable comments and help to improve this document. The research reported in this paper was funded by the EU FP6 NEST/PATH project ComplexDis.

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Authors and Affiliations

  1. Artificial Intelligence Lab, Vrije Universiteit Brussel, Brussel, Belgium

    Joachim De Beule

  2. Iridia lab, Universite Libre de Bruxelles, Brussel, Belgium

    Joachim De Beule

  3. Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital Montebello, Oslo, Norway

    Eivind Hovig

  4. Department of Informatics, The University of Oslo, Oslo, Norway

    Eivind Hovig

  5. Unit for Clinical Systems Biology, Queen Silvia Children’s Hospital Gothenburg, Gothenburg, Sweden

    Mikael Benson

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Correspondence to Joachim De Beule.

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De Beule, J., Hovig, E. & Benson, M. Introducing Dynamics into the Field of Biosemiotics. Biosemiotics 4, 5–24 (2011). https://doi.org/10.1007/s12304-010-9101-1

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