For comparison to everything known about how chemotaxis and phototaxis must be linked to supercoiled DNA via the nutrient-dependent pheromone-controlled physiology of reproduction in the context of the microRNA/messenger RNA balance and RNA-mediated cell type differentiation, see:
Spectral Tuning of Killer Whale (Orcinus orca) Rhodopsin: Evidence for Positive Selection and Functional Adaptation in a Cetacean Visual Pigment
Excerpt: Using codon-based likelihood models, we also found significant evidence for positive selection in cetacean rhodopsin sequences, including on spectral tuning sites we experimentally mutated.
My comment: Pseudoscientists continue to link their mutagenesis experiments to natural selection and evolution without linking chemotaxis to phototaxis via nutrient-dependent microRNAs, adhesion proteins, and RNA-mediated cell type differentiation to the stability of all organized genomes via supercoiled DNA. The latest nonsense was reported as:
These functional aspects of protein evolution are often overlooked when selection signatures in genes or genomes are over-emphasized. “Bioinformatics and evolutionary statistics are hot areas of research now,” according to Dungan, “but to say anything about adaptation you need to also show how genetic changes may be of benefit to the organism, and that often requires an interdisciplinary approach.”
My comment: Claims about protein evolution do not take an interdisciplinary approach. They do not link atoms to ecosystems by what is known to all serious scientists about the biophysically constrained nutrient-dependent pheromone-controlled physiology of reproduction that links ecological variation to ecological adaptation.
Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].
The differences in amino acid composition among different tissues can lead to large differences in trophic discrimination .
My comment: Differences in hydrogen-atom transfer in DNA base pairs in solution link differences in the amino acid composition of proteins from RNA-mediated cell type differentiation to trophic discrimination in species from microbes to humans.
These results strongly indicate that profound changes in the chemosensory capabilities had occurred in the cetacean lineage during the period when ancestral whales migrated from land to water.
My comment: No experimental evidence of biologically-based cause and effect links the de novo creation of nucleic acids and de novo creation of chemosensory capabilities to anything else but hydrogen-atom transfer in DNA base pairs in solution and RNA-mediated events linked to supercoiled DNA in the organized genomes of all living genera via their nutrient-dependent physiology of reproduction and changes in the microRNA/messenger RNA balance. The changes exemplify how supercoiled DNA typically protects all cell types in all living genera from virus-driven pathology, except after the innate immune system is irreparably damaged by nutrient stress and or social stress, which are linked to the failure of nutrient-dependent RNA-mediated DNA repair.
The pleiotropic and often deleterious nature of most mutations may result in the long-term survival of substitutions at a limited number of sites, leaving a signature of molecular convergence within some coding genes. The parallel substitutions in 15 positively selected genes identified in this study likely represent a small proportion of the molecular changes underlying adaptive and convergent phenotypic evolution in marine mammals. Our data therefore indicate that, although convergent phenotypic evolution can result from convergent molecular evolution, these cases are rare, and evolution more frequently makes use of different molecular pathways to reach the same phenotypic outcome.
My comment: They tried to politely tell neo-Darwinian theorists that mutations are bad and nutrient-dependent RNA-mediated amino acid substitutions are good, but they did not make themselves clear. They could have speculatively linked hydrogen-atom transfer in DNA base pairs in solution from nutritional epigenetics to the physiology of reproduction. But instead, they placed their findings into the context of de Vries definition of mutation and the assumptions of population geneticists who decided to claim that accumulated mutations could lead to the evolution of one species from another. Simply put, they placed ecological variation and ecological adaptation into the context of evolution instead of linking morphological and behavioral phenotypes to the amino acid substitutions that stabilize the organized genomes of all living genera.
…our high-throughput approach for identifying generic features that define human pri-miRNAs can be modified to reveal specialized features required for regulated processing of certain mammalian pri-miRNAs, as well as the enigmatic features defining pri-miRNAs of other lineages, such as nematodes and plants.