Any model of biologically-based cause and effect must link atoms to ecosystems via the levels of organization in the diagram. That fact has been known to me since the early 1990s, when I was told that my model must start with sensory input linked to gene activation based on articles like this:
Excerpt: “The articles in this issue summarize the factors surrounding sex differences with respect to ontogeny, phenotype, and hormone-sensitive actions. They follow a sequence that begins with genetic sex differences and carries through to cell, tissue, organ and, finally, systemic effects of gender.”
My comment: Light-induced amino acid substitutions link cell type differences in plants and animals via the physiology of reproduction, which enables fixation of the amino acid substitutions in populations of organisms that exemplify how ecological variation is linked to nutrient-dependent pheromone-controlled physiology of behavior in species from microbes to man.
Excerpt (from 2008): “DNA achieves its high degree of photostability through its complex double-helix structure. The interactions between bases that are stacked one above another within a DNA strand, and the hydrogen bonds between the base pairs of the two complementary single strands in the double-helix play key roles.
Excerpt (from 2014): “The presence of charged radicals in DNA strands after light absorption may cause reactions—oxidative or reductive damage—currently not considered in DNA photochemistry.”
Excerpt (from 2015): “In our experiments, we showed that gene silencing is also maintained in the next generation, even when the original RNA molecule is no longer present. So what we’ve discovered is a wholly epigenetic mechanism: we can alter gene expression across generations – and thus influence cell development – without directly changing the DNA sequence.”
Excerpt (from 1996): “Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans. That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes” (see for references p. 337).
Excerpt (from 2015): “In most organisms, C nucleotides located next to G nucleotides have higher mutation rates than most sites in the genome, and this difference in mutability looks like it might be more extreme within chimp genomes than within human genomes. This is an example of a scenario where one mutation type – in this case, CG->TG – might have increased in rate along the chimp lineage relative to the rates of other mutation types.”
My comment: The ongoing misrepresentations of biologically-based cause and effect that link light-induced amino acid substitutions to cell type differentiation in all genera have become ever more ridiculous. The misrepresentations continue to be placed into the context of ridiculous evolutionary theory more than 40 years years after Dobzhansky wrote: “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla” (p. 127).
How much longer are serious scientists going to ignore or hide from the fact that the balance of microRNAs to nutrient-dependent microRNAs is altered by the sun’s biological energy and its epigenetic effects on nutrients and their metabolism, which links metabolic networks and genetic networks to the physiology of reproduction via RNA-directed DNA methylation and RNA-mediated amino acid substitutions in all genera?
Clearly, it is not the difference in mutation rates that links ecological variation to ecological adaptations. It is nutrient-dependent RNA-mediated amino acid substitutions and DNA repair linked to the physiology of reproduction. The physiology of reproduction is nutrient-dependent and pheromone-controlled in species from yeasts to primates. We reported the conserved molecular mechanisms of sex differences in cell types, which have since been linked to all cell type differentiation in all cells of all individuals of all species.
Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins
Excerpt: The switch between forms is ascribed to the insertion of a single amino acid in the open-form proteins. Thus, PBP quaternary structure controls excitonic coupling and the mechanism of light harvesting. Comparing organisms with these two distinct proteins will reveal the role of quantum coherence in photosynthesis.
My comment: Isn’t it time to link what is known about ecological variation and amino acid substitutions from atoms to ecosystems and to dispense with the pseudoscientific nonsense about mutations and evolution? Organisms ecologically adapt or die. Species don’t mutate and become other species.