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Nutrient-dependent chromatin organization?

Posted on June 24, 2014 by James Kohl.

Snf2h-mediated chromatin organization and histone H1 dynamics govern cerebellar morphogenesis and neural maturation open access

Conclusion: “…delineating the epigenetic regulation of neuronal development is crucial to our understanding of intellectual-disability disorders caused by mutations in epigenetic modifying enzymes. As a whole, our findings highlight the complexity and functional diversity of Snf2h-containing CRCs during brain development, and their roles in controlling chromatin organization as cells modulate their chromatin environment from a ‘largely open’ progenitor state to the ‘highly restricted’ state of a fully differentiated neuron during cerebellar morphogenesis and neural maturation (Fig. 9i)60.

Reported as:

Team finds gene critical for development of brain motor center

Excerpt: “ATP-dependent chromatin remodelling proteins that assemble, reposition and space nucleosomes, and are robustly expressed in the brain.”

My comment: ATP-dependent chromatin remodelling  seems likely to be nutrient-dependent.

If so, it might link ecological variation in nutrient availability to ecological, social, neurogenic, and socio-cognitive niche construction via the conserved molecular mechanisms of nutrient-dependent pheromone-controlled amino acid substitutions that differentiate the cell types of species from microbes to man.

Cell type differentiation appears to enable the ecological adaptations in morphological and behavioral phenotypes that are perturbed when nutrient stress or social stress alter protein folding, which leads to mutations.

It does not seem likely that mutations and natural selection somehow lead to the manifestation of biodiversity that theorists claim has evolved. If there is no model for that, this experimental evidence appears to refute neo-Darwinian theory (again).

As always, I would be grateful if anyone could tell me about any experimental evidence of biologically-based cause and effect that appears to support the invention of neo-Darwinian theory and definitions that were used to make it seem that mutations and natural selection are responsible for the evolution of biodiversity, which this report — and all others that I have read — suggest results from ecological variations that lead to ecological adaptations in species from microbes to man via nutrient-dependent chromatin organization, which appears to be pheromone-controlled.

See for instance our 1996 review for information on sex difference in cell type differentiation that are probably nutrient-dependent and pheromone-controlled in species from yeasts to mammals.

Excerpt: Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing …


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Drunks and monkeys (2): Seeing the light

Posted on June 24, 2014 by James Kohl.

Drunks and Monkeys

Understanding our primate ancestors’ relationship with alcohol can inform its use by modern humans.

By Robert Dudley | June 1, 2014

Excerpt:  “…the next time you enjoy a drink or two, think about primates enjoying the pleasure of ripe, squishy fruit in tropical rainforests. Realize that you are consuming the products of yeast metabolism.”

My comment: Drunks, monkeys, and evolutionary theorists are not capable of seeing the light of biologically-based cause and effect. Drunks and monkeys may not care. Evolutionary theorists seem to care enough to invent more theories. However,  nutrient-dependent pheromone-controlled protein biosynthesis and degradation in brewer’s yeast is linked to alcohol addiction and other addictions via conserved molecular mechanisms of cell type differentiation in species from microbes to man. The story that yeast tell us is one of how organisms respond to ecological variation with ecological adaptations.

Yeasts produce alcohol that kills bacteria. The molecular mechanisms of survival in yeasts also include cell type differentiation at the advent of sexual differentiation of cell types in a unicellular organism. Some evolutionary theorists seem to understand the importance of sexual behavior to species survival in species that sexually reproduce. However, I have never met an evolutionary theorist who could tell me how sex differences in morphological phenotypes, or in behavioral phenotypes “evolved.”  If yeasts could talk, they could probably carry on a more intelligent conversation about sexual reproduction compared to evolutionary theorists.

What’s known about yeasts already tells everyone that gene duplication is nutrient-dependent and pheromone-controlled, which means that sex differences in cell types arose from nutrient-dependent differences in alleles. For example,  “…yeast cells have developed multiple signaling pathways that respond to the availability of sugars, nitrogen, amino acids, and other nutrients.” Schmidt (2013) also noted that “The mechanism by which one signaling pathway regulates a second provides insight into how cells integrate multiple stimuli to produce a coordinated response.” That insight was included in his article “Signaling Crosstalk: Integrating Nutrient Availability and Sex.”

It should not be difficult, except for evolutionary theorists, to move forward from signaling crosstalk to an understanding of how Secreting and Sensing the Same Molecule Allows Cells to Achieve Versatile Social Behaviors.  Indeed, nearly all serious scientists realize that Feedback loops link odor and pheromone signaling with reproduction via changes in social behaviors and the nutrient-dependent pheromone-controlled physiology of reproduction. Social scientists, however, seem willing to continue telling us that mutations …


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Symbiosis and ecological adaptation

Posted on June 22, 2014 by James Kohl.

One Plus One Equals One

Symbiosis and the evolution of complex life John Archibald 224 pages | 216x135mm 978-0-19-966059-9 | Hardback | 26 June 2014

Excerpt from the book description: “All living organisms use the same molecular processes to replicate their genetic material and the same basic code to ‘read’ their genes. The similarities can be seen in their DNA. Here, John Archibald shows how evolution has been ‘plugging-and-playing’ with the subcellular components of life from the very beginning and continues to do so today. For evidence, we need look no further than the inner workings of our own cells. Molecular biology has allowed us to gaze back more than three billion years, revealing the microbial mergers and acquisitions that underpin the development of complex life. One Plus One Equals One tells the story of how we have come to this realization and its implications.

Readership: Popular science readership interested in biology and molecular biology, as well as students of these courses.”

My comment: Symbiosis exemplifies how ecological variation results in ecological adaptations, not how organismal complexity evolved. The problem with this book appears to be common to all books written for a “popular science readership.” The theory of evolution is popular, and most of the science readership does not realize that the theory was invented by population geneticists in an attempt to support Darwin’s claims.

To do that, they started with what he observed and began to suggest what caused the manifestations of morphological and behavioral phenotypes while focusing only on the morphological phenotypes. They ignored the physiology of reproduction that links nutrient-dependent morphological phenotypes to the pheromone-controlled behavior of reproduction via conserved molecular mechanisms in species from microbes to man.

If John Archibald does anything more that tell the same story of natural selection and the evolution of biodiversity, he may teach others what they need to learn about ecological adaptations under the guise of telling them about the evolution of complex life. However, until someone who is academically responsible puts some distance between evolutionary theory by teaching others about the biological facts, which link the epigenetic landscape to the physical landscape of DNA in organized genomes, we can expect nothing more than more pseudoscientific nonsense.…


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Basic biological needs and ecological adaptations

Posted on June 22, 2014 by James Kohl.

Stone age sex

When it comes to sex will humans ever be liberated from the basic biological needs that drove our evolutionary past?

by Neil McArthur

Excerpt: “Right now, there is no rival grand theory that promises to explain fully what we might call the ‘variability hypothesis’ – the view that humans are capable of adapting most or all aspects of their sexual behaviour to fit their historical and environmental context.”

My comment: There’s a model for that! Nutrient–dependent / pheromone–controlled adaptive evolution: a model

“Sex at Dawn” won the award that my book chapter in the Handbook of the Evolution of Human Sexuality won in 2007. In his book “Gay, Straight, and the Reason Why: The Science of Sexual Orientation,” Simon LeVay said this about my model:

“This model is attractive in that it solves the “binding problem” of sexual attraction. By that I mean the problem of why all the different features of men or women (visual appearance and feel of face, body, and genitals; voice quality, smell; personality and behavior, etc.) attract people as a more or less coherent package representing one sex, rather than as an arbitrary collage of male and female characteristics. If all these characteristics come to be attractive because they were experienced in association with a male- or female-specific pheromone, then they will naturally go together even in the absence of complex genetically coded instructions.”

However, LeVay quickly added a caveat that removed our 1996 model of cell type differentiation in yeasts and all other species from further consideration by sexologists. “Still, even in fruit flies, other sensory input besides pheromones — acoustic, tactile, and visual stimuli — play a role in sexual attraction, and sex specific responses to these stimuli appear to be innate rather than learned by association . We simply don’t know where the boundary between prespecified attraction and learned association lie in our own species, nor do we have compelling evidence for the primacy of one sense over another.”

The retraction of any explanation of biologically-based cause and effect (i.e., ecological variation that leads to ecological adaptations via conserved molecular mechanisms: a “…rival grand theory that promises to explain fully what we might call the ‘variability hypothesis’) may have led to Christopher Ryan’s and Cacilda Jethá’s claim that the permanently protruding/pendulous breasts of sexually mature human females resulted from mimicry of the fleshy buttocks — a ridiculous …


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Ecology is my theology

Posted on June 21, 2014 by James Kohl.

Rev. Michael Dowd (with my emphasis):

“Ecology is my theology.

Integrity is my salvation.

Ensuring a just and healthy future is my mission.”

James V. Kohl (Medical laboratory scientist) Ecological variation leads to ecological adaptations via conserved molecular mechanisms, not by random mutations and natural selection.

Professor Nava Ben-Zvi, said that learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.

Dr. 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.”

Only “Ecology is my theology” is supported by experimental evidence that attests to how ecological variation leads to biophysically-constrained ecological adaptations via natural selection for nutrients that are metabolized to the species-specific pheromones that control the physiology of reproduction in species from microbes to man.

The statement by Feierman about random mutations and natural selection may be supported by biology teachers and population geneticists who have not learnt anything about biology and genetics during the past decade or more. However,  “If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based.

If, for example, Feierman had learned anything about biology or genetics since 1964, he might have learned that without learning– according to Dobzhansky (1964) he could never be more than a bird watcher or butterfly collector. “The notion has gained some currency that 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!”

Instead, after a thorough review of my model in 1995 at a conference we both attended,  Feierman asked “What about birds?”  I have never taken him seriously since then, but as moderator of the International Society for Human Ethology’s yahoo group, he has seriously prevented my dissemination of accurate information about biologically based cause and effect for many years.

It is apparent that he represents the views of  ISHE and that members also prefer to not learn …


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