Here is That New Paper on Synonymous Nucleotides

Evolutionists Are Bailing Out

One of the most common tests evolutionists use, when studying how genes are supposed to have evolved, is to compare the non-synonymous and synonymous genetic differences. That is, if a gene that codes for a particular protein is found in several species, then evolutionists interpret differences in the gene, across those species, as the result of mutations in the evolutionary process. And while most mutations cause a change in the resulting protein amino acid sequence, some mutations do not affect the amino acid that is coded for. These two kinds of mutations are referred to as non-synonymous and synonymous, respectively, and their relative proportions are important to evolutionists. They believe that the while the non-synonymous mutations are important, because they change the resulting protein, the synonymous mutations on the other hand are not important. Therefore, if the ratio of the non-synonymous to synonymous mutations is high, then evolutionists think most of the mutations are important and so the gene is undergoing strong selection which is driving significant evolutionary change. But if the ratio of the non-synonymous to synonymous mutations is low, then evolutionists think most of the mutations are not important and so the gene is undergoing purifying selection which rejects most changes because the lower fitness. In that case the synonymous mutations occur merely because they don’t change the protein. As you can see this entire approach is deeply wedded to evolutionary assumptions and its main result is an inference about how genes evolved. If evolution is true then that is useful information, but if not then the entire exercise is a waste. Well for several years evidence has been growing that this approach and its results do, in fact, have much less meaning than evolutionists believe and, as we discussed here, there is a much better way.

Very simply put, the problem with comparing non-synonymous to synonymous differences between genes is that synonymous differences are not unimportant as evolutionists have assumed. As we have discussed protein coding genes carry a multitude of signals and the resulting protein amino acid sequence is just one of many layers of information in the gene sequence. And for most of these signals, what are synonymous differences in the protein sequence are most definitely not synonymous in the message the signal sends.

All of this is highlighted in a new survey paper on messenger RNA, the copy of the DNA gene. As the paper explains:

There are several well-documented ways in which synonymous sites exert their impact on gene functions: effect on mRNA splicing, mRNA folding, stability and regulation of translation through utilization of preferred synonymous codons that translate more efficiently and accurately. Additional and sometimes opposing selective forces appear to affect codon frequency as well. Previous findings show roles for synonymous positions in RNA–RNA interactions, which influence the translation efficiency, and in RNA–RNA cross-talk, which is a key to biological regulation of expression and transcriptome complexity. Emerging evidence shows that “silent” substitutions carry a wealth of information, which is written over the encoded amino acid sequence, and that this information can be used to regulate translation speed, protein homeostasis, metabolic fate and even posttranslational modifications, which will be discussed in this review. Here we will focus on the RNA level of regulation and the role of synonymous sites and mRNA structure in generating biological complexity.

Once again evolutionary assumptions are being proven wrong by science. The facts of molecular biology make no sense on evolution, yet untold numbers of evolutionary studies, incorporating this test of the ratio of non-synonymous to synonymous mutations, are beholden to evolutionary assumptions.