Ecological speciation vs revised evolutionary syntheses

See: A universal trend of amino acid gain and loss in protein evolution (2005)


Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

My comment: The fact that something varies between taxa does not mean that it evolved.
Eugene Koonin is the senior author on an article, which appears to claim that something evolved that causes the amino acid compositions of proteins to vary. In the same article, however, this claim is made.

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.

My comment: How could the evolution of amino acid compositions or proteins evolve via a trend that emerged before the last universal common ancestor of all extant organisms. Koonin attempts to lead serious scientists to think that the emergence of biodiveristy manifested in morphological and behavioral phenotypes can be explained by evolution.

On 8/5/15 Andrew Jones (aka anonymous_9001) wrote:

Statement directly from Eugene Koonin to me:“I certainly have never even thought about “rejecting” neo-Darwinism. All I said, in this interview and many previous publications, is that neo-Darwinsim Is a rather narrowly constrained theoretical framework that, for various reasons, leaves out many key evolutionary processes. One of the primary reasons for that is simply that at the time neo-Darwinism took its shape (1950s), the salient theory and especially observations were unavailable.”

My comment: Koonin does not mention which previous publications claimed that neo-Darwinism left out many key evolutionary processes, which led others to call for an end to Koonin’s pseudoscientific nonsense.

See: Neo-Darwinism, the Modern Synthesis and selfish genes: are they of use in physiology?
See also: On 8/5/15, In “The extended evolutionary synthesis: its structure, assumptions and predictions, Laland et al (2015) wrote:

Excerpt 1)
The Modern Synthesis (MS) emerged in the first half of the twentieth century, with the integration of Darwinian natural selection, population-level thinking and Mendelian inheritance, and has provided the dominant conceptual framework for evolutionary biology [4,5].
Excerpt 2)
The EES will be of value in bringing together researchers from diverse fields who share its ecological-developmental perspective.

On 8/7/15 David W. Inouye wrote:

Early ecologists who thought about principles governing plant and animal communities never imagined that their ideas would provide the foundation for understanding the human microbiome, affecting our nutrition, immune system, and even psychological state.

My comment: Ecologists still cannot understand why evolutionary theorists refuse to accept the biological facts about biodiversity.
See, for example:
Olfactory receptor responding to gut microbiota-derived signals plays a role in renin secretion and blood pressure regulation
Abstract excerpts:

1) Olfr78, an olfactory receptor expressed in the kidney, responds to short chain fatty acids (SCFAs).
2) G protein-coupled receptor 41 (Gpr41), another SCFA receptor…

Journal article excerpt:

Antibiotic treatment reduces the biomass of the gut microbiota and elevates blood pressure in Olfr78 knockout mice. We conclude that SCFAs produced by the gut microbiota modulate blood pressure via Olfr78 and Gpr41.

My comment: Receptor-mediated behaviors must start with the de novo creation of a receptor. The article links molecules produced when gut bacteria digest components of plant-based foods to the creation of ligands for the Olfr78 olfactory receptor. If you alter the de novo creation of receptors in bacteria via antibiotic treatment, you alter all other metabolic networks that are linked to genetic networks in other species via changes in gut bacteria.
Olfactory receptors are G protein-coupled receptors and here the Olfr78 olfactory receptor is linked to another G protein-coupled receptor via the circulatory system.
This was reported in July 2013 as:

The startling sense of smell found all over your body


Pluznick’s research has revealed the existence of Olfr 78 receptors beyond the kidney, in blood vessels in the skin, heart and muscle. Scent receptors may be even more widely distributed, Firestein thinks, in blood vessels right across in the body. There’s no better place for a chemical sensor, he points out, as the blood is the highway by which substances move around the body. This could explain why the receptors show up in so many places, since tissues are shot through with blood vessels bringing in nutrients and ferrying away waste.

There’s no better place for a chemical sensor, he points out, as the blood is the highway by which substances move around the body. This could explain why the receptors show up in so many places, since tissues are shot through with blood vessels bringing in nutrients and ferrying away waste.What’s emerging is a picture of these receptors as a kind of general-purpose chemical sensor. Consider a doorbell: the button next to your front door is hooked up to a little machine that can be programmed to play almost any kind of tune, a clock chime, a fire alarm, or “Wild Thing” if so desired. The button doesn’t care what is being played – it just relays to the machine the message that a finger is pushing on it. These receptors are like that button, and the finger is anything with the right chemical structure to bind to it. The output might be the perception of a scent, the alerting of the immune system or the beating of cilia. “If you say olfactory receptors in the kidney, it sounds kind of nuts,” says Pluznick. “But if you say that chemical sensors are in the kidney, I think it makes a heck of a lot of sense.”

My comment: Ecologists have since linked the conserved molecular mechanisms of nutrient-dependent biophysically constrained RNA-mediated protein folding chemistry to fixation of RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all genera via the physiology of reproduction. That is why the de novo creation of olfactory receptor genes varies with exposure to food odors in the context of the physiology of reproduction.
See: Feedback loops link odor and pheromone signaling with reproduction and Estrogen Permits Vasopressin Signaling in Preoptic Kisspeptin Neurons in the Female Mouse
My comment: Sex differences in cell types and somatic differences are linked from food odors and pheromones via metabolic networks and genetic networks via hormone-organized and hormone-activated behaviors in all invertebrates and vertebrates.
An antagonist asked how the de novo creation of olfactory receptor genes occurs in the context of RNA-mediated gene duplication and RNA-mediated amino acid substitutions that are fixed in the organized genomes of all living genera.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
The ever more antagonistic Andrew Jones, whose Criticisms of the nutrient-dependent pheromone-controlled evolutionary model were simplistically addressed with this comment:

Editor’s note

The 2013 review article by James Vaughn Kohl published in Socioaffective Neuroscience & Psychology and criticized in the above Letter to the Editor was subjected to standard peer review and the revised version was accepted by me after it had been accepted by both reviewers.

See additional comments by Andrew Jones (aka anonymous_9001) in this discusssion. Mutant cells that can’t copy DNA somehow keep dividing when they shouldn’t—with disastrous consequences

His mutagenesis experiments and everything he learned at Carthage College, led him to believe that beneficial mutations may lead to the evolution of biodiversity at a time when all serious scientists have linked mutations to pathology and nutrient-dependent RNA-mediated DNA repair to healthy longevity. The facts about RNA-mediated gene duplication and RNA-mediated amino acid substitutions that link cell type differentiation in all cell types of all individuals of all genera have probably caused nightmares at the American Museum of Natural History, but they may be a dream come true at the Creation Museum.
Meanwhile, the moderator of the ISHE’s human ethology group appears to also be attempting to deal with his nightmares, by posting everything he can find to the group — if it attests to the facts about ecological variation and ecological adaptation.
See these examples from 8/8/15
But first see this from July 26, 2013:
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
The following examples attest to the foolish beliefs of theorists who must now attempt to make others think that they know something about ecology.
1) What defines an adaptive radiation? Macroevolutionary diversification dynamics of an exceptionally species-rich continental lizard radiation
2) What Drives Ontogenetic Niche Shifts of Fishes in Coral Reef Ecosystems?
3) Taylor’s law and abrupt biotic change in a smoothly changing environment
4) Gradual regime shifts in spatially extended ecosystems
5) Why dispersal should be maximized at intermediate scales of heterogeneity
6) Theory of early warning signals of disease emergenceand leading indicators of elimination

My comment: Meanwhile, the moderator of the Evolutionary Psychology Yahoo group continues to post links to articles like this one:

Natural selection, key to evolution, also can impede formation of new species

Nutrient-dependent RNA-mediated cell type differentiation is controlled by the physiology of reproduction in all living genera. Theories about natural selection have led to nightmares at the American Museum of Natural History, because none of the theories have been supported  by experimental evidence of biologically based cause and effect.
Instead, a report the the bacterial flagellum “re-evolved” in 4 days and a report that a species of bacteria has not changes in ~2 billion years will continue to challenge the credibility of pseudoscientists who must put both representations of biologically-based cause and effect into the context of their ridiculous theories, or abandon their ridiculous theories, which will require them to learn the difference between neo-Darwinian theories and facts.
Examples of the fossil record that are displayed at the American Museum of Natural History can be placed into the context of this report on RNA-mediated cell type differentiation.
Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees
and also this report:
Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates
These reports link nutrient-dependent RNA-mediated amino acid substitutions to the de novo creation of olfactory receptor gene families and to the mutation-driven loss of olfactory receptor genes when they are no longer required to stabilize the organized genomes.

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