On the prevalence of certain codons ("RNY") in genes for proteins

J.C. Shepherd notes that codons of the type RNY (R = purine, N = any nucleotide base, Y = pyrimidine) predominate over RNR in the genes for proteins. He has hypothesized that RNY codons are the relics of "a primitive code" composed of repeating RNY triplets. He found that RNY codons predominated in fourfold RNN codon sets (family boxes). These family boxes code for valine, threonine, alanine, and glycine. We argue that the proposed "comma-less" code composed of RNY never existed, and that, in any case, survival of such a code would have long since been erased by mutations. The excess of RNY codons in family boxes is probably attributable to preference for the corresponding tRNAs.