From deep time into real time: What evolutionary processes?

Rapid evolution of a native species following invasion by a congener

Abstract excerpt: “…the lizard Anolis carolinensis moved to higher perches following invasion by Anolis sagrei and, in response, adaptively evolved larger toepads after only 20 generations.”

My comment: This indicates that the behavior evolved before the species, in response, evolved larger toepads.

Reported as: Florida lizards evolve rapidly, within 15 years and 20 generations

Karl Grammer’s comment: “Proofs for evolutionary processes…

What evolutionary processes?

RNA-directed DNA methylation links the epigenetic landscape to the ecological adaptations manifested in the morphology of the toepads. The changes require epigenetically-effected nutrient-dependent RNA-mediated amino acid substitutions that differentiate cell types. The morphological changes manifested in the cell types linked to larger toepads exemplify cell type differentiation that must be controlled by the physiology of reproduction and properly timed reproductive sexual behavior.

Everything currently known about biophysical constraints; the chemistry of protein folding; and the conserved molecular epigenetics of molecular biology attests to the fact that 1) moving to higher perches and 2) larger toepads requires a series of simultaneous nutrient-dependent pheromone-controlled ecological adaptations.

News Article excerpt: “To put this shift in perspective, if human height were evolving as fast as these lizards’ toes, the height of an average American man would increase from about 5 foot 9 inches today to about 6 foot 4 inches within 20 generations — an increase that would make the average U.S. male the height of an NBA shooting guard,” said Stuart.”

My comment: Sex differences in height and other morphological and behavioral traits assure us that the epigenetically-effected changes in the lizards cannot be put into any perspective outside the context of nutrient-dependent pheromone-controlled sex differences in cell type differentiation. All differences in cell types link ecological variation to ecological adaptations via the pheromone-controlled physiology of reproduction in species from microbes to man.

By reporting their findings outside the context of biologically-based cause and effect that links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man, the authors suggest that evolution somehow occurred. What they have actually shown is another example of nutrient-dependent pheromone-controlled ecological adaptations, which are manifested in the morphological and behavioral phenotypes of all species.

Journal article excerpt: “Brown and Wilson called evolutionary divergence between closely related, sympatric species “character displacement” (1), and our data constitute a clear example of this. Resource competition has been the interaction suggested most often as the source of divergent selection during character displacement [sometimes specifically called “ecological character displacement” (13)].”

Character displacement is a vague term used eight years before Dobzhansky (1964) claimed “…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!” Others have recently claimed “Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].”

Use of vague terms like character displacement, indirect genetic effects, cooperating genetic events, and genome dynamics events instead of ecological character displacement (i.e., ecological speciation) continue to contribute to the confusion manifested in yet another report of biologically-based cause and effect that is meaningfully interpreted as if the findings support a ridiculous theory of evolution. However, that theory must now be divorced from claims that evolution occurs over eons of time via mutations and natural selection, because no evolutionary events have been described that link one species to the evolution of another.

This statement makes that fact clear: “The rates of 4 types of elementary evolutionary events (hereinafter Genome Dynamics Events or GDE)…” That statement changes evolutionary events to the virtually unusable term genome dynamics events. It follows from the fact reported in A universal trend of amino acid gain and loss in protein evolution: “We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.” (So, why not use the term ecological speciation, since that is what obviously occurs via RNA-mediated genome dynamics events? Must researcher compete to invent new terms and claim that they are the first to detail the obvious?)

If it is not yet obvious to everyone that nutrient-dependent metabolism emerged as the link to ecological adaptations and ecological speciation “…before the last universal common ancestor of all extant organisms,” it might be clearer after reading Arrival of the Fittest: Solving Evolution’s Greatest Puzzle. Unfortunately, Wagner insists on using the terms commonly used by population geneticists. He focuses on “innovability” in that context. I’m not sure who invented that term for ecological speciation. However, for a quick claim that requires less thought about use of vague terms, see: “Genetic and metabolic networks drive all biological processes. You can think of them as bridges between the organism and the individual molecules – proteins and genes – that form all living cells.” — from the Genetic and Metabolic Networks page of Professor Andreas Wagner’s Wagner Lab Research site. You can also think of ecological speciation as the process that is driven by all biological processes that involve genetic and metabolic networks. (Hint: all biological processes clearly involve genetic and metabolic networks.)

The research reported here answers the question about “What evolutionary processes?” in the context of genetic and metabolic networks that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. See also, Dobzhansky (1973) “…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.” It was clear to Dobzhansky that the amino acid substitutions differentiated the cell types of these primates, although he could not have known what epigenetic effects led to the RNA-mediated amino acid substitutions and differentiation of the cell types.

What is the answer to questions about evolutionary processes in the context of these amino acid substitutions? See: From Fertilization to Adult Sexual Behavior (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…” To avoid further confusion about biologically-based cause and effect, which continues to be placed into the context of evolutionary theory, 41 years after Dobzhansky (1973) and 18 years after our Hormones and Behavior review, see Nutrient-dependent/pheromone-controlled adaptive evolution: a model. (2013).

Examples of amino acid substitutions, which differentiate the cell types of all individuals of all species from microbes to man, are included in the review. The examples answer the question “What evolutionary processes?” by placing biologically-based cause and effect into the context of Darwin’s ‘conditions of life’ and ecological speciation instead of the context of neo-Darwinism, which bastardized his theory by making it appear that mutations could lead from natural selection to the evolution of biodiversity over eons of time. That exemplifies pseudoscientific nonsense!

Ecological adaptations are nutrient-dependent and pheromone-controlled by the physiology of reproduction, which enables amino acid substitutions and chromosomal rearrangements to move what some people may still claim are evolutionary processes from deep time into real time via ecological speciation.

That forward movement into the scientific reality of real time has been mentioned in three recent reviews of biologically-based cause and effect that move Dobzhansky’s claims from 1964 and 1973 into the real time of today’s accurately reported research. See for example: Combating Evolution to Fight Disease and RNA and dynamic nuclear organization and Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans. See also Dobzhansky (1972) “Reproductive isolation evidently can arise with little or no morphological differentiation.”

Many serious scientists have realized that organisms like the lizards starve to death when competition for nutrients displaces them, unless they quickly adapt and establish a new ecological niche, which is obviously what all extant species have done via their nutrient-dependent RNA-mediated pheromone-controlled reproduction. The species that didn’t adapt are extinct, because too many individuals starved to death before their cell types could reproduce.

Rapid Evolution in Real Time

RNA-directed DNA methylation links the epigenetic landscape to the ecological adaptations manifested in the morphology of the toepads. The changes require epigenetically-effected nutrient-dependent RNA-mediated amino acid substitutions that differentiate cell types. The morphological changes manifested in the cell types linked to larger toepads exemplify cell type differentiation that must be controlled by the physiology of reproduction and properly timed nutrient-dependent reproductive sexual behavior, which probably occurs near the location of the higher perches.

Re: rapid evolution and character displacement (i.e., ecological speciation)

Everything currently known about biophysical constraints; the chemistry of protein folding; and the conserved molecular epigenetics of molecular biology attests to the fact that 1) moving to higher perches and 2) the ecological adaptation of larger toepads requires a series of simultaneous nutrient-dependent pheromone-controlled  RNA-mediated events that obviously have occurred.

The similarities to what also occurs in hummingbirds that ecologically adapt to higher elevations is clear. However, like all similarities manifested in morphological and behavioral phenotypes, which arise in the context of nutrient-dependent pheromone-controlled ecological adaptations, these lizards attest to the fact that the differences are due to RNA-mediated events, not to evolutionary events.

Creative use of the term “character displacement” can be compared to what Dobzhansky, a self-proclaimed creationist, wrote about amino acid substitutions in 1973. “…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.”

If he was not still dead, Theodosius Dobzhansky (January 24, 1900 – December 18, 1975), who was also a self-proclaimed evolutionist, would probably dismiss the observations of others who claim that ‘character displacement’ is proof of evolution, as he did in (1964) when he wrote:  “…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!” Observations that higher perches are linked to morphological phenotypes in these lizards are characterized by the observations of others who have virtually ignored the need for behavioral phenotypes to concurrently change to enable ecological speciation.

Moving forward

We can expect to see researchers report soon that a single nutrient-dependent RNA-mediated change leads from ecological variation to the morphological and behavioral phenotypes of these lizards, since that is how ecological adaptations occur in all species. However, we can also expect to see a few more attempts to place ecological adaptations into the context of evolutionary theories, since the theory has become more popular than biological facts.

Few people realize that Darwin’s theory placed ‘conditions of life’ before natural selection. Only after population geneticists bastardized his theory did it become popular enough to include in the context of:

1) “character displacement”

2) “indirect genetic effects”

and

3) “genome dynamics events.”

See also from the original news report: Florida Lizards Evolve Rapidly, Within 15 Years and 20 Generations

Excerpt: “This latest study is one of only a few well-documented examples of what evolutionary biologists call “character displacement,” in which similar species competing with each other evolve differences to take advantage of different ecological niches. A classic example comes from the finches studied by Charles Darwin. Two species of finch in the Galápagos Islands diverged in beak shape as they adapted to different food sources.”

My comment: Darwin did not study finches. Anyone who studies birds today has probably realized that nutrient-dependent pheromone-controlled RNA-mediated events link amino acid substitutions to chromosomal rearrangements that clearly differentiate the morphological and behavioral phenotypes of white-throated sparrows via the pattern of nutrient-dependent biologically-based cause and effect that Dobzhansky began to notice in 1964.

He wrote: “Ingram and others found that hemoglobin S differs from A in the substitution of just a single amino acid, valine in place of glutamic acid in the beta chain of the hemoglobin molecule.” What we continue to see reported as science is  ignorance associated with claims that “character displacement” is an evolutionary process, when it is evidence of nutrient-dependent pheromone-controlled ecological adaptations in species from microbes to man, which occur via conserved molecular mechanisms.

What then, is the link from amino acid substitutions to behavioral phenotypes?  Apparently, in human adolescents and adults it is a functional single nucleotide polymorphism (SNP) / a G-to-A base-pair substitution that leads from the amino acid methionine (Met) to a valine (Val) substitution. For example: 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).

The difference that the amino acid substitution makes is associated with metabolism (e.g., lower enzymatic activity) due to the difference a single base pair change makes in the context of thermodynamic cycles of protein biosynthesis and degradation. The substitution makes the nutrient-dependent pheromone-controlled organized genome less thermodynamically stable, which explains the difference in exploratory behavior.

If nutrient stress associated with “invasion of a congener” in lizards had not led to increased exploratory behavior and an amino acid substitution that stabilized the organized genome of the lizards with higher perches, there would be no biologically-based explanation of how one species climbed higher up the trees and established its pheromone-controlled ecological, social, and neurogenic niche without thought. Instead, the lizards that perched higher might appear to have automagically corrected a nutrient-dependent problem in their organism-level thermoregulation. The behavior that led them to climb higher up the tree led to a nutrient-dependent pheromone-controlled epigenetic correction in organism-level cell type differentiation via changes in metabolism that lead from RNA-directed DNA methylation to beneficial amino acid substitutions. Unfortunately, that is more difficult to explain via comparison to simply stating that “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.” And people already believe in constraint-breaking mutations.

Telling the truth

Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults was reported as Genes exhibit different behaviours in different stages of development, which links RNA-mediated events in our review From Fertilization to Adult Sexual Behavior to Organizational and activational effects of hormones on insect behavior and Honey bees as a model for understanding mechanisms of life history transitions.

The honeybee model organism links nutrient-dependent pheromone-controlled cell type differentiation via RNA-mediated events and what is currently known about 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. The functional redistribution of biological activity onto a group of interacting organisms and their environment effectively offloads a degree of genetic control onto epigenetic processes.’ The problem for evolutionary theorists who tout “character displacement” or anything else has become the fact that “The honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, and diseases of the X chromosome (Honeybee Genome Sequencing Consortium, 2006). Included among these different aspects of eusocial species survival are learning and memory, as well as conditioned responses to sensory stimuli (Maleszka, 2008; Menzel, 1983).” — Kohl (2012)

Links from nutrient-dependent pheromone-controlled morphological and behavioral phenotypes in the honeybee now extend across species via the conserved molecular mechanisms of RNA-mediated events that link amino acid substitutions to cell type differentiation and ecological speciation. Thus, it is clear that the popularity of evolutionary theory has prevented scientific progress that could have been made if all researchers were taught enough about biologically-based cause and effect to become serious scientists. Instead, many of them were taught to explain their findings as if organisms like lizards evolved into different species of lizards and dinosaurs evolved into different species of birds.

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Addendum: Val158Met polymorphism in COMT gene could be a candidate for low penetrance breast cancer susceptibility in Shanghai population, especially among premenopausal women and early-onset breast cancer patients.

The Val158Met amino acid substitution also shows up in the neurodegenerative disorder, Alzheimer’s disease.

A GOOGLE search for Val158Met might also surprise others who had no idea of how important a single amino acid substitution can be in the context of morphological and behavioral phenotypes because they were taught that species evolve via mutations and natural selection.

Fortunately, companies like Alpha Genomix are leading the way in attempts to link metabolism and pharmacogenetics to the RNA-mediated events that differentiate the cell types of all individuals of all species via amino acid substitutions, which are manifested as differences in genotypes and phenotypes as differences in morphological and behavioral phenotypes, not merely difference in the genes that evolutionary theorists still claim link mutations to the evolution of increasing organismal complexity.

Catechol-O-Methyltransferase (COMT) is an enzyme responsible for the metabolism of catecholamines and Catechol-estrogens in both the central nervous system and other organs. Dopamine is cleared mainly by COMT in the frontal cortex and a reduced activity of this enzyme results in higher synaptic levels of dopamine, which affects prefrontal cortex cognitive response to certain drugs. A single nucleotide polymorphism of the COMT gene produces an amino acid change from Valine to Methioinine (Val158Met) and reduces enzyme activity by 3 to 4 folds. The COMT assay tests for Mutations associated with decreased activity of COMT.

Several complex associations between COMT the Val158Met Variant as a risk factor for numerous diseases have been found but they all seem to have a limited predictive value. However, the response to some psychotropic medications seems to be dependent to some extent upon COMT status. In general, the wild-type genotype predicts a good response to methylphenidate and amphetamines in the treatment of attention deficit hyperactivity disorder.

About James V. Kohl 1307 Articles
James Vaughn Kohl was the first to accurately conceptualize human pheromones, and began presenting his findings to the scientific community in 1992. He continues to present to, and publish for, diverse scientific and lay audiences, while constantly monitoring the scientific presses for new information that is relevant to the development of his initial and ongoing conceptualization of human pheromones. Recently, Kohl integrated scientific evidence that pinpoints the evolved neurophysiological mechanism that links olfactory/pheromonal input to genes in hormone-secreting cells of tissue in a specific area of the brain that is primarily involved in the sensory integration of olfactory and visual input, and in the development of human sexual preferences. His award-winning 2007 article/book chapter on multisensory integration: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences followed an award winning 2001 publication: Human pheromones: integrating neuroendocrinology and ethology, which was coauthored by disinguished researchers from Vienna. Rarely do researchers win awards in multiple disciplines, but Kohl’s 2001 award was for neuroscience, and his 2007 “Reiss Theory” award was for social science. Kohl has worked as a medical laboratory scientist since 1974, and he has devoted more than twenty-five years to researching the relationship between the sense of smell and the development of human sexual preferences. Unlike many researchers who work with non-human subjects, medical laboratory scientists use the latest technology from many scientific disciplines to perform a variety of specialized diagnostic medical testing on people. James V. Kohl is certified with: * American Society for Clinical Pathology * American Medical Technologists James V. Kohl is a member of: * Society for Neuroscience * Society for Behavioral Neuroendocrinology * Association for Chemoreception Sciences * Society for the Scientific Study of Sexuality * International Society for Human Ethology * American Society for Clinical Laboratory Science * Mensa, the international high IQ society