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Published on: June 24, 2019
Genomic Codon Usage is Structurally Consistent with First-Classness Across the Tree of Life
1Independent Researcher, Brisbane, Australia. djhmoore@gmail.com.
Abstract:
Genome-scale codon usage data from 70,950 species spanning the tree of life allow a test of whether the standard genetic code's 21-family degeneracy partition is structurally consistent with the First-Classness (FC) framework, which derives that partition from conformal completion constraints on a four-element dispositional algebra without biological input. We report three findings. First, within-family codon usage uniformity, measured by coefficient of variation, follows a specific ordering across family sizes-2-fold < 4-fold < Ser 6-fold < 3-fold < Leu/Arg 6-fold-that is consistent with the architectural constraints of the FC-derived partition rather than being a simple monotonic function of family size. Second, the three split six-fold families (serine, leucine, arginine) exhibit four-codon sub-block dominance-pooled two-to-four ratios of 0.30--0.56-in archaea, bacteria and eukarya alike, though the strength of the dominance, most markedly for arginine, varies among the domains. Third, a family-balanced global FC ratio, tested against a null model preserving family-size architecture while randomising codon assignment, shows no separable statistical signal ([Formula: see text], [Formula: see text]); the possible interpretations, including limited sensitivity of the statistic at this level of aggregation and non-separability of the partition from the frequencies it governs, are discussed.
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