Biological Evolution of Dialects of the Genetic Code

Biological Evolution of Dialects of the Genetic Code

Sergey Petoukhov (Russian Academy of Sciences, Russia) and Matthew He (Nova Southeastern University, USA)
DOI: 10.4018/978-1-60566-124-7.ch003
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Abstract

This chapter demonstrates results of a comparative investigation of characteristics of degeneracy of all known dialects of the genetic code. This investigation is conducted on the basis of the results of symmetrological analysis, which were described in Chapter 2, about the division of the set of the 20 amino acids into the two canonical subsets: the subset of the 8 high-degeneracy acids and the subset of the 12 low-degeneracy acids. The existence of numerical and structural invariants in the set of these dialects is shown. The derived results from the comparative investigation permit one to formulate some phenomenological rules of evolution of these dialects. These numeric invariants and parameters of code degeneracy draw attention to the formal connection of this evolution with famous facts of chrono-biology and chrono-medicine. The chronocyclic conception of the functioning of molecular-genetic systems is proposed on this basis. The biophysical basis of this conception provides connection to the genetic code structures with mechanisms of photosynthesis which produce living substance by means of utilization of solar energy. And the solar energy comes cyclically on the surface of the Earth. The revealed numeric invariants of evolution of the genetic code give new approaches to the fundamental question, why do 20 amino acids exist? We will demonstrate new patterns of the genetic code systems.
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Introduction And Background

Beginning with the level of the code correspondence between 64 triplets and 20 amino acids, some evolutional changes take place, which lead to many different dialects of the genetic code. Each amino acid is encoded in a concrete dialect by a certain quantity of triplets. This quantity of its triplets is called “number of degeneracy” of the genetic code. For example, the amino acid Thr is encoded by 4 triplets in one genetic dialect; the number of degeneracy of this amino acid in this dialect is equal to 4. But this amino acid is encoded by 8 triplets in another dialect of the genetic code, where its number of degeneracy is equal to 8, etc. Structures of the set of such dialects reflect features of biological evolution on very basic levels. It seems that the comparative analysis of these dialects can give important information about essence and mechanisms of biological organisms. The symmetry analysis of phenomenological data is useful for answering these questions as well.

One direction, where such information can be useful, is connected with knowledge about physiological rhythms in organisms. The statement that biological organisms exist in accordance with cyclic processes of environment and with their own cyclic physiological processes is one of the most classical statements of biology and medicine from ancient times. Many branches of ancient and modern medicine take into account the time of day especially, when diagnostic, pharmacological and therapeutic actions should be made for individuals. The set of this medical and biological knowledge is usually united under the names chrono-medicine and chrono-biology. But is it possible to spread this chrono-biological viewpoint from the usual level of macro-physiological systems into the molecular-genetic level? This chapter analyzes this problem.

The second direction, where results of the comparative analysis of the dialects of the genetic code can be useful, is connected with the question of internal structure of the set of 20 amino acids. This question is considered in the last paragraph of this chapter.

The third direction is related to algebraic foundations of the genetic code, which will be considered in Chapter 7.

So, the objectives of this chapter are, firstly, the comparative analysis of all known dialects of the genetic code, secondly, the utilization of its results to develop appropriate thoughts about chrono-biology at the molecular-genetic level and about the internal structure of the set of 20 amino acids.

The various dialects of the genetic code exist in different kinds of organisms or of their subsystems (first of all, in mitochondria, which play a role of factories of energy in biological cells). For this book all initial data about the dialects of the genetic code were taken by the authors from the website of the National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi. These dialects differ one from another through their specifics of the degeneracy (through concrete relations between 20 amino acids and 64 triplets). Based on these data, one can find that 17 dialects are known only which differ one from another by the numbers of the degeneracy of the amino acids (see these 17 dialects in Table 1). A small quantity of the dialects from the website differ one from another by their start-codons only but not by the numbers of the degeneracy of the amino acids; we consider these dialects as the same dialect in our investigation.

Concerning chrono-biology and chrono-medicine, literature sources have many brilliant words about the great importance of biological rhythms for organisms. For example, the famous Russian physiologist A. Bogomolets wrote about “universal rhythmic movement in biology”: “The world exists in rhythms, cosmic processes follow the law of rhythmic movement … The day replaces night, the time of activity replaces the dream ... The vital processes work in an organism rhythmically … A heart works rhythmically, and lungs breathe rhythmically, and processes of feeding of an organism are worked rhythmically, and nervous system follows the law of a rhythm, creating a rhythm of mental life” (Vogralik & Vogralik, 1978, p. 11).

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