Probable relationship between partitions of the set of codons and the origin of the genetic code.
Here we study the distribution of randomly generated partitions of the set of amino acid-coding codons. Some results are an application from a previous work, about the Stirling numbers of the second kind and triplet codes, both to the cases of triplet codes having four stop codons, as in mammalian mitochondrial genetic code, and hypothetical doublet codes. Extending previous results, in this work it is found that the most probable number of blocks of synonymous codons, in a genetic code, is similar to the number of amino acids when there are four stop codons, as well as it could be for a primigenious doublet code. Also it is studied the integer partitions associated to patterns of synonymous codons and it is shown, for the canonical code, that the standard deviation inside an integer partition is one of the most probable. We think that, in some early epoch, the genetic code might have had a maximum of the disorder or entropy, independent of the assignment between codons and amino acids, reaching a state similar to "code freeze" proposed by Francis Crick. In later stages, maybe deterministic rules have reassigned codons to amino acids, forming the natural codes, such as the canonical code, but keeping the numerical features describing the set partitions and the integer partitions, like a "fossil numbers"; both kinds of partitions about the set of amino acid-coding codons.
Centro de Investigación Biomédica, Facultad de Medicina, Universidad Diego Portales, Avda. Ejército 141, Santiago, Chile. Electronic address: dino.salinas@udp.cl.
Dino G
DG
Salinas
Centro de Investigación Biomédica, Facultad de Medicina, Universidad Diego Portales, Avda. Ejército 141, Santiago, Chile. Electronic address: mauricio.gallardor@mail.udp.cl.
Mauricio O
MO
Gallardo
Centro de Investigación Biomédica, Facultad de Medicina, Universidad Diego Portales, Avda. Ejército 141, Santiago, Chile. Electronic address: manuel.osorio@mail.udp.cl.
Manuel I
MI
Osorio
D000596:Amino Acids / Q000737:chemistry / Q000235:genetics*; D001483:Base Sequence; D003062:Codon / Q000235:genetics*; D003198:Computer Simulation; D019143:Evolution, Molecular; D005815:Genetic Code / Q000235:genetics*; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D000069497:Origin of Life; D017421:Sequence Analysis / Q000379:methods
D000596:Amino Acids; D003062:Codon
Entropy; Evolution; Genetic code; Integer partition; Origin; Stirling numbers of the second kind