Unfortunately, they examine the evidence incorrectly or incompletely. In the case of how genes allegedly evolved, scientists are finally learning that their presuppositions are getting in the way of true knowledge. They should have put aside their biases and examined the data more completely.
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.You can read the rest of "Here is That New Paper on Synonymous Nucleotides".