A model for the emergence of the genetic code as a transition in a noisy information channel

DOI10.1016/J.JTBI.2007.07.029MaRDI QIDQ2216309zbMATH OpenOpenAlexWikidataFDO

Authors Tsvi Tlusty

Publication date 15 December 2020

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1007.4122

zbMATH Keywords

biological information channelsgenetic coderate-distortion theory

Mathematics Subject Classification ID

Maps and general types of topological spaces defined by maps (54C99) Genetics and epigenetics (92D10) Problems related to evolution (92D15)

Abstract: The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. Some argue that the specific form of the code with its twenty amino-acids might be a 'frozen accident' because of the overwhelming effects of any further change. Others see it as a consequence of primordial biochemical pathways and their evolution. Here we examine a scenario in which evolution drives the emergence of a genetic code by selecting for an amino-acid map that minimizes the impact of errors. We treat the stochastic mapping of codons to amino-acids as a noisy information channel with a natural fitness measure. Organisms compete by the fitness of their codes and, as a result, a genetic code emerges at a supercritical transition in the noisy channel, when the mapping of codons to amino-acids becomes nonrandom. At the phase transition, a small expansion is valid and the emergent code is governed by smooth modes of the Laplacian of errors. These modes are in turn governed by the topology of the error-graph, in which codons are connected if they are likely to be confused. This topology sets an upper bound - which is related to the classical map-coloring problem - on the number of possible amino-acids. The suggested scenario is generic and may describe a mechanism for the formation of other error-prone biological codes, such as the recognition of DNA sites by proteins in the transcription regulatory network.

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Cited in

(9)

• Protein folding disorders: toward a basic biological paradigm
• Shannon information entropy in the canonical genetic code
• Translocation properties of primitive molecular machines and their relevance to the structure of the genetic code
• A genetic code Boolean structure. II: The genetic information system as a Boolean information system
• A solvable model of the genesis of amino-acid sequences via coupled dynamics of folding and slow-genetic variation
• `The frozen accident' as an evolutionary adaptation: a rate distortion theory perspective on the dynamics and symmetries of genetic coding mechanisms
• Extending Swerdlow's hypothesis: statistical models of mitochondrial deterioration and aging
• Equiangular lines via matrix projection
• Metabolic free energy and biological codes: a `data rate theorem' aging model

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