Linguistics of molecular interactions

Abstract

The most interesting biological molecules are long polymers. In analogy with human alphabetic languages, they can be called texts and analysed, as to the primary structure, as sequences of letters (monomers; nucleotides, aminoacids, etc.) or of words (codes of oligomers, of up to 5-6 letters). It is considered that the study of words, in a linguistic approach, may contribute positively to the understanding of molecular interactions (communication). The molecular and human languages and dialects are contrasted. The molecular one is peculiarly distinct from the human, for instance, by its use of a tridimensional morphology, temporal dynamics, absence of spacings and punctuation, and overlapping messages. A mathematical method is presented, for discovering words in texts. The word AAA (adenine triplets) was studied in the evolution of the 5S ribosomal RNA. It was shown that this word is more frequent in less complex organisms and less frequent in the more complex ones, in the fungi, plants, and vertebrates lineages. In the two latter ones, the degree of genie variability was also reduced. To the contrary, a moderate degree of usage of this word persisted in the whole invertebrates lineage, where a high degree of genie variability was maintained. In mitochondria, plastids and mycoplasmas, the frequency of the word AAA was increased, consistently with their need for interactions with a wider range of variation. These behaviors indicate that the monotonous AAA word allows for ambiguity in interactions. With the evolution of organic complexity and of greater molecular specificity, ambiguous words were progressively avoided.