We need pattern recognition, not a prologue

By: James V. Kohl | Published on: October 28, 2014

Prolegomenona preliminary discussion…; a prologue.”

“… we need a mapping from genotype to phenotype, from phenotype to what is selected, and from what is selected to the new genotype (Lewontin, 1961).
— cited in

Prolegomenon to patterns in evolution

Excerpt:  “…we cannot derive what selection, acting at the level of the whole organism in its world, will “select” among the possible but unprestatable…”
My comment: Organisms naturally select the nutrients that enable thermodynamic cycles of protein biosynthesis and degradation, which lead to the physiology of reproduction. Selection of nutrients by the whole organism leads from nutrient-dependent amino acid substitutions that differentiate the cell types of individuals and organisms via the metabolism of nutrients. This links the genetic networks and metabolic networks of cell type differentiation to the production of species-specific pheromones, which control the physiology of reproduction. Ecological variation in the availability of nutrients is thereby linked to pheromone-controlled biodiversity manifested in the morphological and behavioral phenotypes of species from microbes to man.
Nutrient uptake also epigenetically links genetic networks and metabolic networks to increasing organismal complexity via ecological, social, neurogenic, and socio-cognitive niche construction, which are controlled by nutrient stress and social stress. The balance is achieved when amino acid substitutions are fixed in the genome, which enables organism-level thermoregulation to build from its basis in nutrient uptake and to create new species that manifest their nutrient-dependent pheromone-controlled physiology of reproduction in the diversity of their morphological and behavioral phenotypes. Not only should the pattern of ecological speciation be clear, it has been modeled in the context of:

Nutrient-dependent/pheromone-controlled adaptive evolution: a model

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The model of adaptive evolution is actually a model of how ecological variation leads to ecological adaptations and ecological speciation via conserved molecular mechanisms in species from microbes to man. Minimally, several thousand people probably realize that the model refutes the pseudoscientific nonsense of neo-Darwinism via a pattern that links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. Therefore, serious scientists need more than just a Prolegomenon to patterns in evolution. What they need is something that suggests there is a pattern to evolution. If there is not, serious scientists and pseudoscientists should acknowledge what has already been detailed in articles like Combating Evolution to Fight Disease and RNA and dynamic nuclear organization. Simply put, there is no such thing as neo-Darwinian evolution. Darwin’s ‘conditions of life‘ should now be the focus of research on ecological variation and ecological adaptations that occur via amino acid substitutions in every cell of every tissue of every organ of every organ system of every organism that has ever existed on this planet.
Pattern Recognition: Conditions of life and ecological adaptations
ch 4 IF under changing conditions of life organic beings present individual differences in almost every part of their structure, and this cannot be disputed; if there be, owing to their geometrical rate of increase, a severe struggle for life at some age, season, or year, and this certainly cannot be disputed; then, considering the infinite complexity of the relations of all organic beings to each other and to their conditions of life, causing an infinite diversity in structure, constitution, and habits, to be advantageous to them, it would be a most extraordinary fact if no variations had ever occurred useful to each being’s own welfare, in the same manner as so many variations have occurred useful to man. But if variations useful to any organic being ever do occur, assuredly individuals thus characterised will have the best chance of being preserved in the struggle for life; and from the strong principle of inheritance, these will tend to produce offspring similarly characterised. This principle of preservation, or the survival of the fittest, I have called Natural Selection.
ch 5 “…the greater variability of species having wider ranges than of those with restricted ranges, lead to the conclusion that variability is generally related to the conditions of life to which each species has been exposed during several successive generations.”
“When a variation is of the slightest use to any being, we cannot tell how much to attribute to the accumulative action of natural selection, and how much to the definite action of the conditions of life.”
“Instances could be given of similar varieties being produced from the same species under external conditions of life as different as can well be conceived; and, on the other hand, of dissimilar varieties being produced under apparently the same external conditions. Again, innumerable instances are known to every naturalist, of species keeping true, or not varying at all, although living under the most opposite climates. Such considerations as these incline me to lay less weight on the direct action of the surrounding conditions, than on a tendency to vary, due to causes of which we are quite ignorant.”
ch 6 “By my theory these allied species are descended from a common parent; and during the process of modification, each has become adapted to the conditions of life of its own region, and has supplanted and exterminated its original parent-form and all the transitional varieties between its past and present states.”
Claims that species evolved over eons of time should be accompanied by biologically-based experimental evidence that links evolution to events that occurred across eons of time, or researchers should accept the obvious fact that a single nutrient-dependent base pair change can lead from an amino acid substitution to ecological speciation in a matter of a few generations in any organism from microbes to man.
Plants: Antheridiogen determines sex in ferns via a spatiotemporally split gibberellin synthesis pathway “Homosporous ferns have evolved a mechanism to favor cross-fertilization by controlling the sex ratio among individuals or prothalli within the population with the aid of antheridiogens. Antheridiogens are pheromones released in the aqueous environment by early-maturing fern prothalli in a colony, and they cause neighboring late-maturing prothalli in the colony to develop male organs (antheridia), thus promoting outcrossing in the colony (1–3).”
Algae: Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins “…cryptophytes have evolved a structural switch controlled by an amino acid insertion to modulate excitonic interactions and therefore the mechanisms used for light harvesting.”
Bacteria: Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB “Our findings demonstrate an unexpected role for aminoacyl-tRNA in the formation of dehydroamino acids in lantibiotics, and serve as a basis for the functional characterization of the many lantibiotic-like dehydratases involved in the biosynthesis of other classes of natural products.”
Lizards: Rapid evolution of a native species following invasion by a congener “These results illustrate that interspecific interactions between closely related species can drive evolutionary change on observable time scales.”

See also:

Birds: New insights into the hormonal and behavioural correlates of polymorphism in white-throated sparrows, Zonotrichia albicollis “…behaviour and endocrine function may be linked to a chromosomal rearrangement that determines plumage colour.”
Bees: Epigenomics and the concept of degeneracy in biological systems “The reiterations of living systems are developmentally constructed and come into being through internal interactions within organisms, interactions between organisms, and interactions between organisms and their surroundings. Novelty and variation arise from these interactions.”
Humans (development of behavioral phenotypes): Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults “Its function is known to be affected by a functional single nucleotide polymorphism (SNP) in COMT (G-to-A base-pair substitution) leading to a methionine (Met) valine (Val) substitution at codons 108/158 (COMT Val158Met). Carriers of the Met allele have been found to display a fourfold decrease in enzymatic activity compared to Val allele carriers going along with an increase of prefrontal DA activity (Lachman et al. 1996; Lotta et al. 1995).’

Humans (morphological phenotypes): Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

“Two additional recent reports link substitution of the amino acid alanine for the amino acid valine (Grossman et al., 2013) to nutrient-dependent pheromone-controlled adaptive evolution. The alanine substitution for valine does not appear to be under any selection pressure in mice. The cause-and-effect relationship was established in mice by comparing the effects of the alanine, which is under selection pressure in humans, via its substitution for valine in mice (Kamberov et al., 2013).

These two reports (Grossman et al., 2013; Kamberov et al., 2013) tell a new short story of adaptive evolution. The story begins with what was probably a nutrient-dependent variant allele that arose in central China approximately 30,000 years ago. The effect of the allele is adaptive and it is manifested in the context of an effect on sweat, skin, hair, and teeth. In other mammals, like the mouse, the effect on sweat, skin, hair, and teeth is due to an epigenetic effect of nutrients on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones control the nutrient-dependent hormone-dependent organization and activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates as previously indicated. That means the adaptive evolution of the human population, which is detailed in these two reports, is also likely to be nutrient-dependent and pheromone-controlled, since there is no other model for that.”
If adaptive evolution is placed into the context of ecological variation, there is no such thing as evolution. All that exists in the context of the amino acid substitutions that differentiate all cell types is ecolgical variation that leads to ecological adaptions. Nothing evolves, extant species adapt via nutrient acquisition and pheromone-controlled reproduction as they always have.
Other primates:
Nothing in Biology Makes Any Sense Except in the Light of Evolution “…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.”
Gibbon genome and the fast karyotype evolution of small apes: “We describe the propensity for a gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes and alter transcription by providing a premature termination site, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage.”
Dawkins eliminated the eons of time required for the evolution of lizards and others have confirmed that eons of time are not required for any species to ecologically adapt via the selection of nutrients and their pheromone-controlled physiology of reproduction. The challenge to evolutionary theorists and evolutionary theists has become one that must first involve a prologue to place their ridiculous claims into the perspective of what serious scientists recognize as ecological adaptations. Their inability to do so was predicted by Dobzhansky (1964) in Biology, molecular and organismic ” the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!”

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[…] report on lizards show that the morphology of two species diverged after only 20 generations. See We need pattern recognition, not a prologue for other examples of rapid nutrient-dependent pheromone-controlled ecological speciation that […]

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