Origins of scaling in genetic code

Oliver Obst*, Daniel Polani, Mikhail Prokopenko

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference proceeding contributionpeer-review

3 Citations (Scopus)

Abstract

The principle of least effort in communications has been shown, by Ferrer i Cancho and Solé, to explain emergence of power laws (e.g., Zipf's law) in human languages. This paper applies the principle and the information-theoretic model of Ferrer i Cancho and Solé to genetic coding. The application of the principle is achieved via equating the ambiguity of signals used by "speakers" with codon usage, on the one hand, and the effort of "hearers" with needs of amino acid translation mechanics, on the other hand. The re-interpreted model captures the case of the typical (vertical) gene transfer, and confirms that Zipf's law can be found in the transition between referentially useless systems (i.e., ambiguous genetic coding) and indexical reference systems (i.e., zero-redundancy genetic coding). As with linguistic symbols, arranging genetic codes according to Zipf's law is observed to be the optimal solution for maximising the referential power under the effort constraints. Thus, the model identifies the origins of scaling in genetic coding - via a trade-off between codon usage and needs of amino acid translation. Furthermore, the paper extends the model to multiple inputs, reaching out toward the case of horizontal gene transfer (HGT) where multiple contributors may share the same genetic coding. Importantly, the extended model also leads to a sharp transition between ambiguous HGT and zero-redundancy HGT. Zipf's law is also observed to be the optimal solution in the HGT case.

Original languageEnglish
Title of host publicationAdvances in artificial life: Darwin meets von Neumann
Subtitle of host publication10th European conference, ECAL 2009, Budapest, Hungary, September 13-16, 2009: revised selected papers
EditorsGeorge Kampis, István Karsai, Eörs Szathmáry
Place of PublicationHeidelberg
PublisherSpringer, Springer Nature
Pages85-93
Number of pages9
VolumePart 2
ISBN (Electronic)9783642213144
ISBN (Print)9783642213137
DOIs
Publication statusPublished - 2011
Externally publishedYes
Event10th European Conference of Artificial Life, ECAL 2009 - Budapest, Hungary
Duration: 13 Sep 200916 Sep 2009

Publication series

NameLecture Notes in Computer Science
PublisherSpringer Berlin Heidelberg
Volume5778
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other10th European Conference of Artificial Life, ECAL 2009
CountryHungary
CityBudapest
Period13/09/0916/09/09

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