The irony and confusion of molecular epigenetics

March 20, 2014 | James Kohl

Science Table of Contents 21 March 2013 Volume 343, Issue 6177

Excerpted in sequence:

Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Escherichia coli Jessica Plucain et al.

The emergence of a stable polymorphism in bacteria involved a multistep process including three specific mutations.

Humans Can Discriminate More than 1 Trillion Olfactory Stimuli C. Bushdid et al.

The number of different odor mixtures people can distinguish is several orders of magnitude larger than anticipated.

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My comment: Ecological adaptations occur at the molecular level. They may become more or less obviously manifested in observable species diversity. However, if conserved molecular mechanisms did not link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man,  ecological variation could not result in the ecological adaptations that are manifested in observable species diversity.

The irony:  One report on ecological opportunity and nutrient-dependent pheromone-controlled ecological adaptations in Escherichia coli claims that synergistic interactions among beneficial mutations facilitates the epistasis of the adaptations. The report that follows it attests to the biological fact that the human sense of smell enables nutrient-dependent pheromone-controlled ecological adaptations.

The confusion: The molecular mechanisms of biophysically constrained life do not vary among species. If interactions among beneficial mutations somehow lead to epistasis and ecological adaptations linked to species diversity in microbes like E. coli, interactions among beneficial mutations must also lead to ecological adaptations and species diversity in other species.  If the human sense of smell enables ecological adaptations, the ecological adaptations of E. coli must also be enabled a primitive form of the human sense of smell. That’s why biologists place a high value on experimental evidence that links the molecular mechanisms of cause and effect.

The evidence: No experimental evidence supports ideas about mutations and evolution in species from microbes to man. The stable polymorphisms, which are reported in the context of population genetics, simply cannot arise from mutation perturbed protein folding, and that’s what mutations do — they perturb protein folding.  Thus, no matter how hard some researchers try to convince others that synergistic interactions among beneficial mutations might result in the organization of an organism’s genome, other researchers will continue to correctly represent how olfaction and odor receptors allow the combination of nutrient uptake and pheromone-controlled reproduction to organize the genomes of species from microbes to man. Organization occurs via nutrient-dependent changes in base pairs that lead to amino acid substitutions that stabilize protein folding, which stabilizes the organized genome.

In Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Escherichia coli, selective processes and glucose-dependent metabolism and secretion of by-products that generate negative frequency-dependent selection are placed into the context of mutations.  In Humans Can Discriminate More than 1 Trillion Olfactory Stimuli food odors and pheromones link nutrient uptake to metabolism and secretion of species specific pheromones that control reproduction in species from microbes to man. Removing the irony and confusion suggests that microbes select nutrients that metabolize to pheromones that control their reproduction, which is what all other organisms on this planet do. Nevertheless, it is interesting to see researchers continue to tout the role of mutations in evolution at the same time others are proving that ecological variation results in ecological adaptations via conserved molecular mechanisms in species from microbes to man.

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Humans can do what?

March 20, 2014 | James Kohl

Science 21 March 2014: Vol. 343 no. 6177 pp. 1370-1372

Humans Can Discriminate More than 1 Trillion Olfactory Stimuli

Reported as:

Humans can distinguish at least one trillion different odors, study shows

Excerpt: “You might move to some part of the world where you’ve never encountered the fruits and vegetables and flowers that grow there. But your nose is ready. With a sensory system that is that complex, we are fully ready for anything.” — Leslie Vosshall

My comment to Science Magazine  (submitted but not published to their site):

I would have erred had I not cited other works by Vosshall and Keller in the concluding sentence of my 2012 review: “Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors.”

“Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).”

Now that our detection abilities have been evaluated, I wonder why there is no mention of our ability to detect species-specific social odors, called pheromones. It’s become obvious that conserved molecular mechanisms link the epigenetic landscape to the physical landscape of DNA in species from microbes to man. Other recent reports attest to that fact:

1) “Detecting Fat Content of Food from a Distance: Olfactory-Based Fat Discrimination in Humans
2) “The Scent of Disease: Human Body Odor Contains an Early Chemosensory Cue of Sickness

Therefore, in the context of our detection abilities, I think others may have erred by not citing one of my other reviews: “Nutrient-dependent/pheromone-controlled adaptive evolution: a model

Clear attestations to the plasticity of our olfactory system, which links ecological variation to ecological adaptations, now suggest that “adaptive evolution” should be called ecological adaptation. In the presence of food odors and nutrients that metabolize to species-specific pheromones that control the physiology of reproduction, ecological adaptation is what’s expected to occur.

What this latest report now shows is the degree of fine-tuning that is possible after ecological, social, neurogenic, and socio-cognitive niche construction has already occurred — and resulted in the nutrient-dependent pheromone-controlled increased organismal complexity that is us.

Now that Mainland et al have published “The missense of smell: functional variability in the human odorant receptor repertoire” and Foote et al have published “Tracking niche variation over millennial timescales in sympatric killer whale lineages,” the similarities at the top of the aquatic and terrestrial food chains attest to the power of conserved molecular mechanisms to link cause and effect across all species via olfaction and odor receptors, which is what I detailed in the review I submitted last week.

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Addendum:

It’s been more than a week since I submitted the comment above. Since other comments I have submitted have always been published within 5 days of their submission, I published the comment above to The Scientist. See: The Nose Knows

The human nose can differentiate more than a trillion odors, a study finds.

By Rina Shaikh-Lesko | March 25, 2014

 

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Feierman’s pseudoscientific nonsense

March 20, 2014 | James Kohl

Re:  Nutritional intake, psychiatric traits and pseudoscientific nonsense

Follow up:

Feierman and his friend James Gray are attempting to extend Feierman’s pseudoscientific nonsense to reach equally uninformed participants in a yahoo group that is owned by Robert Stonjek.

See for example: “As the moderator of this list you are one of the gate keepers of what is defined as human ethology.”

Feierman is the moderator of the human ethology group, but this supposedly was inadvertently posted to the evolutionary psychology group. It seems more likely that this was a deliberate posting to another group so that Feierman could then continue to misrepresent human ethology and introduce others to the following nonsense about what he calls Type I Behavior.

Feierman writes: “I don’t think there is a definition of ethology in general and human ethology in particular that has universal agreement. From my perspective ethology in general started (by Lorenz and Tinbergen) as a method to understand the cause of instinctual behaviors, especially in vertebrates. To do this, they redefined the concept of an instinct from a motivational concept to a behavioral (movement) concept, which then generated the concept of the fixed/coordinated/modal action pattern, or what I now call Type I Behavior (definable by form and function in a natural environment and species-universal in form).”

Feierman has previously claimed that “…ISHE is “HBES Lite…” He denigrates the International Society for Human Ethology (ISHE),  which is the organization that owns the yahoo group he moderates, and touts the Human Behavior and Evolution Society (HBES), as if evolutionary theorists knew more about the biology of human behavior than human ethologists know. See:  ”My own personal impression at these three meetings was that there is very little difference between the types of papers presented at HBES and ISHE. In many ways, ISHE is “HBES Lite,” as in lite beer, less calories for those thermodynamically inclined. Said slightly differently and using a baseball analogy, the “heavy hitters” are members of HBES.

Is there a definition of human ethology? Human ethology focuses on the evolutionary and adaptive significance of human behavior. 

Who are the HBES “heavy hitters?” What have they contributed to understanding of the adaptive significance of human behavior? The question arises: What causes significant adaptations in human behavior? I think the answer is that ecological variation enables the adaptive significance of human behavior. For example, with co-authors, I published this award-winning review: Human pheromones: integrating neuroendocrinology and ethology 

We attempted to make it perfectly clear that the neuroendocrinology of human behavior must be included in any representations of biologically-based cause and effect. Feierman wants others to continue to look at human behavior as if it somehow evolved like all other ecologically adapted animal behaviors that supposedly somehow evolved.  Most others will not realize how twisted his thoughts have become.

For example, take the phrase (from his representation above): “definable by form and function in a natural environment and species-universal in form.” Compare that ridiculous misrepresentation of cause and effect to the fact that in any natural environment, ecological variation results in nutrient-dependent behaviors that are species-specific because the nutrients metabolize to species-specific pheromones that control the physiology of reproduction.

Why doesn’t Feierman simply admit to those facts?  I claim that Feierman wants others to continue to believe that “Random mutations are the substrates upon which directional natural selection acts.”  That means Feierman cannot admit to any biological facts because no experimental evidence supports the ridiculous idea that random mutations result in adaptations. And yet, Feierman now claims “…the Adapted Mind is really the Adapted Brain!

What kind of fool claims that natural selection acts on random mutations that result in the adapted brain? That was a rhetorical question.

The unanswered question is: Why does the ISHE allow Feierman to moderate their yahoo group, and denigrate the works that include the accurate representations of its members?

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Nutritional intake, psychiatric traits and pseudoscientific nonsense

March 20, 2014 | James Kohl

SLC6A4 polymorphism, population genetics, and psychiatric traits

Concluding sentence: “Interest in the gene determined the fate of the population genetics article, and resulted in a large number of citations to an unlikely candidate article.”

See also:

How does the social environment ‘get into the mind’? Epigenetics at the intersection of social and psychiatric epidemiology

Excerpt 1) “… increased DNA methylation at the SLC6A4 locus thus provides an additional example of how epigenetic processes may mediate social exposures in a manner salient to psychopathology.”

Excerpt 2) “These data confirm that nutritional intake — a process with clear social environmental contributions — can affect epigenetic processes, which have been associated with schizophrenia.”

My comment: The biological facts reported in the article excerpts attest to the need to understand the importance of nutritional epigenetics for comparison to the concluding sentence from the article about population genetics. For example, “Vitamin D-mediated production of serotonin may be critical for the production of serotonergic signals during neurodevelopment. This indirectly links vitamin D to the development of the brain and changes in the brain associated with skull architecture and brain development throughout adulthood because serotonin plays a critical role in regulating a variety of brain functions, which include social behavior.” — Kohl (under review)

Nutrient uptake clearly enables the metabolism of nutrients to species-specific social odors called pheromones that may epigenetically effect serotonin and brain development via the conserved molecular mechanisms associated with the epigenetic effects of:

1) food odors;

2) nutrient uptake and

3) the pheromone-controlled physiology of reproduction in species from microbes to man.

The epigenetic link from SLC6A4 polymorphism to schizophrenia may be as simple as that. Ecological variation in the availability of specific nutrients probably determines whether or not human populations ecologically adapt. Some individuals may not. However, it seems futile to try to find a mutation in cell types that may somehow cause a mental disorder in individuals that appear to be maladapted. It would be easier to trace a genetic predisposition and nutritional deficiency to cause and effect — not in human populations, or individual humans — but via the use of animal models.

However, when ecological variation leads to ecological adaptations, population geneticists tend to dismiss across species examples of ecological factors. When ecological variation appears to result in diseases and disorders, population geneticists attribute the diseases and disorders to mutation-driven evolution. The conserved molecular mechanisms of biophysically constrained cause and effect are removed as if psychiatry research had somehow become a branch of social science.

Nearly all social scientists are more likely to place the biologically based cause and effect manifested in diseases and disorders into the context of population genetics and constraint-breaking mutations. Most biologists and all psychiatrists should not do that. Parenthetically, it is okay for a few biologists to set a bad example, nonetheless. Someone must exemplify ignorance and arrogance so that others may recognize the difference in biologically plausible approaches.

No experimental evidence suggests that mutations, which perturb protein folding, are beneficial. However, the obviousness of biophysically constrained protein folding is only reassuring to those who are familiar with the basic principles of biology and levels of biological organization that link the sensory environment to behavior in species from microbes to man.

The obviousness of biophysical constraints can only disturb those who tout theories of mutation-induced SLC6A4 polymorphism that automagically include beneficial affects of polymorphisms on typical behavior. Those touting theories have begun to realize their theories are nothing more than pseudoscientific nonsense framed in the ridiculous context of mutation-driven evolution of human populations.

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ISHE: Two New Trustees

March 19, 2014 | James Kohl

The election for two International Society for Human Ethology (ISHE) Trustee positions ended with a welcome to newly elected trustees: Jan Havlicek and Nancy Segal

More on Nancy. See also this chapter on the Genetics of Olfactory Perception by​ Nancy L. Segal and Tari D. Topolski in Handbook of olfaction and gustation

More on Jan (try Google translate). See also the article that Jan co-authored: Olfactory Performance Is Predicted by Individual Sex-Atypicality, but Not Sexual Orientation

Excerpt: ”It has been suggested that many sex differences in psychology develop under the influence of context-dependent epigenetic factors.”

My commentThe Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences, details the involvement of species specific pheromones in sex differences in psychology in the context of nutritional epigenetics, which links food odors and the metabolism of nutrients to species-specific effects of pheromone on the physiology of reproduction and behavior. The current moderator of the ISHE’s yahoo group has consistently denigrated my contributions to human ethology, despite publication of the award-winning review:  Human pheromones: integrating neuroendocrinology and ethology, which was co-authored by others including Karl Grammer, who is one of the most highly regarded human ethologists in the world. Recently, Feierman had this to say about me:

Feierman: “I too am concerned that people who just read the group and don’t comment, and there are hundreds of them, will believe that what he is saying that is going unchallenged is correct. I’ve blocked 75% of what he has submitted to the group in the past few days because of my concerns.”

Now that two other people who are familiar with genetics and epigenetics are ISHE Trustees, I hope they will help alleviate the problems I have had with Feierman. Simply put, Feierman wants others to believe that his ridiculous opinions about biologically-based cause and effect should go unchallenged. However, I cannot recall Feierman ever stating why he was concerned that what I was saying might not be correct, or any discussion of why information in the award-winning review co-authored by respected ISHE member Karl Grammer, might be incorrect. For contrast, does anyone believe that this statement is correct, or that it reflects the beliefs of human ethologists?  Random mutations are the substrates upon which directional natural selection acts.

I suspect that Feierman is about to abandon the ISHE’s yahoo group. He already appears to be acting as co-moderator of the evolutionary psychology yahoo group moderated by Robert Stonjek. With new ISHE leadership, Feierman may be unable to continue to block my posts and prevent dissemination of accurate information on the role of “olfaction” and the de novo creation of olfactory receptor genes in species from microbes to man. Hopefully, he will not abandon the group so that all records of his deceit are untraceable.

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