Theorists have not seen the light

It was long known that almost every amino acid can be encoded by multiple synonymous codons and that every organism, from humans to fungi, has a preference for certain codons.

My comment:
That fact underlies our representation of RNA-mediated cell type differentiation from our 1996 review From Fertilization to Adult Sexual BehaviorSee our section on molecular epigenetics. Our representation was subsequently linked to organization of genomes in insects and to life history transitions in honeybees and humans via single nutrient-dependent amino acid substitutions. Those links were fully established before microRNAs and adhesion proteins were linked via the octopus genome sequence from microbes to humans. All serious scientists now realize that the conserved molecular mechanisms of biophysically constrained RNA-mediated protein folding link the epigenetic landscape to the physical landscape of DNA in all living genera.

See also:

2011 We are not only eating ‘materials’, we are also eating ‘information’
Excerpt:

The finding is obviously very thought-provoking; for instance, it would indicate that in addition to eating “materials” (in the form of carbohydrates, proteins, etc), you are also eating “information” (as different miRNAs from distinct food sources could well bear different consequences on the regulation of host physiology once taken by the host due to potential regulation of different target genes as determined by the “information” contained within the miRNA sequence), thus providing a whole new dimension to “You are what you eat”.

Re: 1) Genes can adapt to different environmental changes by choosing the most optimal codon, which is counterintuitive to natural selection
My comment:  Ecological variation leads to ecological adaptation via nutrient-dependent RNA-mediated protein biosynthesis and degradation in the context of biophysically constrained thermodynamic cycles of protein biosynthesis and degradation that link the physiology of reproduction to biodiversity via organism-level thermoregulation.Genes cannot adapt outside that context, which helps to explain why Darwin insisted his “conditions of life” be placed before “natural selection.” If Darwin had known about genes he probably would have linked epigenetic effects of food to ecological adaptation even without knowing about nutrient-dependent RNA-mediated gene duplication and RNA-mediated amino acid substitutions that stabilize the organized genomes of all living genera.His book title might have been “Life is RNA-mediated.”
See also: Life is physics and chemistry and communication and Life as physics and chemistry: A system view of biology and Top-down causation: an integrating theme within and across the sciences? and Physiology is rocking the foundations of evolutionary biology
If life is not RNA-mediated in the context of what is known to serious scientists about physics, chemistry, communication, biology, top-down causation, and the physiology of nutrient dependent reproduction, life may have somehow evolved to link metabolic networks to genetic networks in all cells of all individuals of all living genera. However, no evidence of biologically-based cause and effect links anything encoded by multiple synonymous codons to RNA-mediated  gene duplications and the RNA-mediated amino acid substitutions that differentiate all cell types of all individuals of all species.
Re: 2) Genes can adapt to different environmental changes by choosing the most optimal codon, which is counterintuitive to natural selection
This statement can be placed into the context of what others have claimed about natural selection compared to ecological speciation July 2013 Carl Zimmer: “Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed “the blind watchmaker.” To some extent, it just happens.”June 2013 James Kohl “…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.”