Arbitrariness is not enough: towards a functional approach to the genetic code

Abstract

Arbitrariness in the genetic code is one of the main reasons for a linguistic approach to molecular biology: the genetic code is usually understood as an arbitrary relation between amino acids and nucleobases. However, from a semiotic point of view, arbitrariness should not be the only condition for definition of a code, consequently it is not completely correct to talk about "code" in this case. Yet we suppose that there exist a code in the process of protein synthesis, but on a higher level than the nucleic bases chains. Semiotically, a code should be always associated with a function and we propose to define the genetic code not only relationally (in basis of relation between nucleobases and amino acids) but also in terms of function (function of a protein as meaning of the code). Even if the functional definition of meaning in the genetic code has been discussed in the field of biosemiotics, its further implications have not been considered. In fact, if the function of a protein represents the meaning of the genetic code (the sign's object), then it is crucial to reconsider the notion of its expression (the sign) as well. In our contribution, we will show that the actual model of the genetic code is not the only possible and we will propose a more appropriate model from a semiotic point of view.

On the Evolution of Symbols and Prediction Models

“…The convention defining the meaning of codons is implemented in the structure of tRNA molecules (Eigen, 2013) which during the translation process link the current codon to a certain amino acid included in the protein synthesis. In addition to this primary meaning, codons have a secondary, higher-level meaning in the functioning of the final protein (Lacková et al, 2017). In turn, the related hierarchy of meanings ultimately culminates in the organism's selective value and the associated phenotypic fitness landscape .…”

Natural languages and RNA virus evolution

“…Subsequently, the genetic code was regarded as a way of restricting to a single dictionary the different possibilities for the transfer of information from mRNA to proteins (Bateson, 1972;Barbieri, 2009). There is no deterministic, thermodynamically favoured link between tRNA codons and the specific amino acids that bind to each variant tRNA, a process catalysed by aminoacyl-tRNA (aa-tRNA) synthetases (Schimmel, 1987;Schimmel et al, 1993): the only connection between both sets of molecules seems to be historical (one of the frozen accidents referred to by Crick) or conventional (Barbieri, 2008;Lacková et al, 2017). Barbieri (2008) started a particular view of communication based on biological codes.…”

Participative opposition applied

“…Many other structuralist concepts can be taken to inspire or provide a new viewpoint to life phenomena. I can mention the concept of arbitrariness which was maybe the first one to link linguistics and biology: after the deciphering of the genetic code, many linguists became interested in seeking analogies between language and the genetic code, which has been viewed as a semiotic code in the strict sense (see Lacková et al 2017). Jakobson may have been one of the pioneers in finding analogies between language and the genetic code (Jakobson 1971a).…”