Journal Title
Title of Journal: Biosemiotics
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Abbravation: Biosemiotics
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Publisher
Springer Netherlands
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Authors: Gérard Battail
Publish Date: 2014/08/29
Volume: 7, Issue: 2, Pages: 259-277
Abstract
Barbieri introduced and developed the concept of organic codes The most basic of them is the genetic code a set of correspondence rules between otherwise unrelated sequences strings of nucleotides on the one hand polypeptidic chains on the other hand Barbieri noticed that it implies ‘coding by convention’ as arbitrary as the semantic relations a language establishes between words and outer objects Moreover the major transitions in life evolution originated in new organic codes similarly involving conventional rules Independently dealing with heredity as communication over time and relying on information theory we asserted that the conservation of genomes over the ages demands that errorcorrecting codes make them resilient to casual errors Moreover the better conservation of very old parts of the genome demands that they result from combining successively established nested codes such that the older an information the more numerous component codes protect it Barbieri’s concept of organic code and that of genomic errorcorrecting code may seem unrelated We show however that organic codes actually entail errorcorrecting properties Errorcorrecting in general results from constraints being imposed on a set of sequences Mathematical equalities are conveniently used in communication engineering for expressing constraints but error correction only needs that constraints exist Biological sequences are similarly endowed with errorcorrecting ability by physicalchemical or linguistic constraints thus defining ‘soft codes’ These constraints are moreover presumably efficient for correcting errors Insofar as biological sequences are subjected to constraints organic codes necessarily involve soft codes and their successive onset results in the nested structure we hypothesized Organic codes are generated and maintained by means of molecular ‘semantic feedback loops’ Each of these loops involves genes which code for proteins the enzymatic action of which controls a function needed for the protein assembly Taken together thus they control the assembly of their own structure as instructed by the genome and once closed these loops ensure their own conservation However the semantic feedback loops do not prevent the genome lengthening It increases both the redundancy of the genome as an errorcorrecting code and the information quantity it bears thus improving the genome reliability and the specificity of the enzymes which enables further evolution
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