Chromosomal rearrangements and ecological adaptations (part 2)

January 15, 2014 | James Kohl

I apologize for some of the repetition in the following post. Now that I have a reprint of the latest work from Donna Maney’s lab, I have more to say about it, and will again place it into context.

“Ecological variation is the raw material by which natural selection can drive evolutionary divergence.” – Tracking niche variation over millennial timescales in sympatric killer whale lineages.

Theories about mutations and selection cause many evolutionary theorists to simply ignore factors like ecological variation. For example, see:

Roles of Mutation and Selection in Speciation: From Hugo de Vries to the Modern Genomic Era

Article excerpt with my emphasis:

“...we will not consider geographical and ecological factors [e.g., ecological variation] because of space limitation. Our primary purpose is to clarify the roles of mutation and selection in the evolution of reproductive isolation and show that the molecular basis of speciation is more complicated than generally thought at present.”

My comment: It is academically irresponsible and unscientific to ignore ecological factors that epigenetically effect the conserved molecular mechanisms of reproductive isolation and speciation. Claiming that the primary reason for ignoring ecological variation is to clarify something is akin to men playing a card game with a magician who stacks the deck or hides a few cards. The magician then plays the winning hand as if he simply got lucky, until he gets caught cheating.  Whether or not he is cheating “Aces over eights” may still be a “dead man’s hand.”

PZ Myers is not a magician. He is a cheat who has been caught with his pants down while holding a ‘dead man’s hand’ — in the following context:

  • A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.
    • Wissenschaftliche Selbstbiographie. Mit einem Bildnis und der von Max von Laue gehaltenen Traueransprache. Johann Ambrosius Barth Verlag (Leipzig 1948), p. 22, as translated in Scientific Autobiography and Other Papers, trans. F. Gaynor (New York, 1949), pp. 33–34 (as cited in T. S. Kuhn, The Structure of Scientific Revolutions).

Myers is an atheistic biology teacher whose “dead man’s hand” is repeatedly played out on his blog “Pharyngula, which ”…is his outlet for venting his fury at faith, stupidity, and injustice…” His “venting” ignores ecological factors that contribute to chromosomal rearrangements, which John A. Davison proposed were a means by which species divergence occurred in the absence of mutations. In the context of PZ Myers’ furiously stupid faith in mutation-driven evolution, he insisted on portraying the late John A. Davison, and me, as “cranks.”

In more than 740 blog posts, PZ Myers and his minions subsequently refused to accept the fact that experimental evidence supports ecological variation as the driving force for species divergence.  In fact, experimental evidence provides overwhelming support for Davison’s idea, which links ecological variation to chromosomal rearrangements via the conserved molecular mechanisms in my model. For example, see:  Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes ”The ZAL2 and ZAL2m alleles code for 597 amino acids, with two fixed differences driving a Val73Ile and Ala552Thr polymorphism in ZAL2m.”

Fixed differences that drive the valine and alanine polymorphism (i.e., a Val73Ile and Ala552Thr polymorphism in ZAL2m) and the morphological and behavioral phenotype of sparrows, link other accumulated fixed polymorphisms to plumage color in other birds. For example, a single amino acid substitution has already been linked to alternative phenotypes manifested in different plumage color.

Unfortunately, statistical analyses placed the amino acid substitution into the ridiculous context of mutation-driven evolution in Difference in Plumage Color Used in Species Recognition between Incipient Species Is Linked to a Single Amino Acid Substitution in the Melanocortin-1 Receptor. PZ Myers would, no doubt approve of this blatant misrepresentation of biological facts:

Excerpt: ”…the clear and statistically significant association between the MC1R variants and plumage color strongly suggests that the Asp119Asn mutation contributes to the expression of the melanic plumage…”

My comment: Why isn’t the valine and alanine polymorphism (i.e., a Val73Ile and Ala552Thr polymorphism in ZAL2m) and the morphological and behavioral phenotype of sparrows attributed to a mutation or to accumulated mutations?  Could that be because there is no model of biologically-based cause and effect that suggests mutation-initiated natural selection is possible? If it occurs, mutation-driven evolution is like magic.

The “magic” of statistically significant associations and mutations theory in “bird-watching” is contextually comparable to the magician who stacks the deck or hides cards. The game that evolutionary theorists have continued to play is one that ignores the biological fact that Bird odour predicts reproductive success.  The theorists stack the deck against ecological variation and nutrient-dependent pheromone-controlled adaptations, which in my model are obviously the raw material by which natural selection for food drives evolutionary divergence. That’s how evolutionary theorists, atheists and the furious stupidity of biology teachers like PZ Myers contribute to another generation of students who are being taught to believe in a ridiculous theory of mutation-driven evolution. Simply put, they ignore the fact that all organisms must eat and that their reproduction must be controlled or they will run out of food.

For contrast to the nonsense touted by evolutionary theorists, serious scientists learned how to support their models with experimental evidence of how ecological variation contributes to species divergence via nutrient-dependent pheromone-controlled amino acid substitutions and chromosomal remodeling, which was again exemplified in the latest work from Donna L. Maney’s group: Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes.

What do people like PZ Myers do when they learn about more experimental evidence that refutes all the nonsense they’ve been trying to teach others to believe? In this case, he threatened to close the thread after I had already provided many other examples of experimental evidence that refute his idiotically simple-minded and unscientific beliefs. Myers wrote: I don’t know, this kook seems to have babbled repetitively enough. Time to close this thread? Is anybody still learning anything from engaging with the cabbage?

Summary: An atheistic biology teacher resorts to nonsense and name-calling, but ignores my model and experimental evidence of epigenetic cause and effect. My model and every bit of experimental evidence I have seen supports John A. Davison’s ideas about the importance of chromosomal rearrangements to ecological adaptations and species divergence.

Suggestions: I hope that others who understand the basic principles of biology and levels of biological organization that link sensory input to epigenetic effects on hormones that affect behavior will challenge evolutionary theorists who still believe in a ridiculous theory about mutation-driven evolution. It is long past time for others to enter discussion of the biological facts that must be taught to students so that the next generation can make bi0logically-based scientific progress that is not hindered by ridiculous theories of automagically-driven anything.

PZ Myers, and biology teachers like him, should be removed from their positions with extreme prejudice because they have continued to teach nonsense to unsuspecting students who are paying the high costs of tuition but currently remain largely unaware of established biological facts. After a few biology teachers like PZ Myers are used as examples, other entrenched academics will be more cautious about teaching nonsense, and they might even begin to learn about biological facts. John A. Davison addressed this with the provost of the university that still employs PZ Myers.  Davison died in 2012. Myers has continued to tout his nonsense and attacked me, apparently for the same reason he attacked Davison.  PZ Myers simply cannot comprehend biological facts or will not accept them. Whose version of biology is he teaching besides his own?  Why is he still employed?

See also, from Prof Weird:

“Not all changes to proteins are harmful – changing a valine to an alanine in a signal sequence has little effect….

From what fetid orifice did you pull the idea that all that is required for speciation is a single change of an amino acid in a single protein ?”


In my model, the valine to alanine change was used to help detail the common molecular mechanisms of nutrient-dependent pheromone-controlled differentiation of cell types in the mouse to human example. In a modern human population that appears to have adapted to ecological changes during the past ~30,000 years, a change in a single base pair resulted in substitution of the amino acid alanine for valine.

Excerpted from Kohl (2013) 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.


The idea that species divergence may result from a single change of an amino acid that is fixed in the organized genome of different species does not come from any “fetid orifice” as the weird doctor inferred.  Instead, the idea came with other examples I provided in the context of my recent review, such as this one:

“Species incompatibilities in nematodes are associated with cysteine-to-alanine substitutions (Wilson et al., 2011), which may alter nutrient-dependent pheromone production.”

And this one:  ”In Ostrinia moth species, substitution of a critical amino acid is sufficient to create a new pheromone blend (Lassance et al., 2013).”

If PZ Myers can manage to avoid termination by the university where he teaches, he may continue to exemplify an established academic standard of teaching nonsense to students who someday will demand a tuition refund because they were taught the ridiculous theory of mutation-driven evolution. However, there is still the opportunity to prevent the collapse of academia by replacing biology teachers who cannot comprehend anything more than the “evolution for dummies” that they believe in, and who also hope that they can convince their students to believe in the same nonsense. Unfortunately, the teachers of “evolution for dummies” have had many years of success. Change may come slowly, if at all.  Clearly, the dummies outnumber the serious scientists who have learned the biological facts that are required for them to make scientific progress.



James Vaughn Kohl

James Vaughn Kohl

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.