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Genes and Race: Human History?

Posted on May 26, 2014 by James Kohl.

Roundup of Book Reviews of Nicholas Wade’s A Troublesome Inheritance

My comment: Many reviewers of Wade’s book on genes and race appear to think he has accurately represented issues of differences in cell types that evolutionary theorists associate with mutations, natural selection, and the evolution of human biodiversity. This may be cause for concern among those who are interested in accurate representations of biologically-based cause and effect.

In this century, it has become clear that ecological variation results in biodiversity, which is manifested in morphological and behavioral phenotypes that exemplify ecological adaptations in species from microbes to man. Therefore, most people might want to escape the criticisms associated with evolutionary theories based on population genetics that have received no support from experimental evidence of biologically based cause and effect. Yet, Wade sticks with mutations and natural selection as the cause of differences that somehow evolved. Reviewers claim no knowledge of biological facts that refute Wade’s outdated assertions. That’s scary, but no one says, BOO!

Indeed, he even discusses the modern human population that arose in what is now central China as if mutations and natural selection enabled the changes that occurred in hair, teeth, sweat glands, and mammary tissue — supposedly during the past ~30K years. The changes followed the climate change associated with disappearance of Neanderthals. That climate change and the associated dietary change can clearly be linked to reproductive success via a change in a single base pair linked to the substitution of a single amino acid in the organized genome of what may be the most successful human population on this planet.

If humans were frugivorous bats that ecologically adapted due to the availability of dietary ascorbic acid via the de novo creation of olfactory receptor genes, the human population would represent another population of mammals, albeit without wings, that successfully radiated to different regions of the planet via the conserved molecular mechanisms that enable adaptive radiation. If humans were mice, the amino acid substitution would be manifested in the same changes in cell types. Humans are not mice, but the same changes in cell types occur due to the same amino acid substitution. Amino acid substitutions also differentiate the cell types of other human populations.

The question arises, do serious scientists still think that mutations and natural selection enable adaptive radiation? Is there a model for that? If so, the model could be compared to what …


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Another slap in the face for evolutionary theorists

Posted on May 24, 2014 by James Kohl.

From my invited and rejected submission on nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems. (The submission was rejected with another slap in the face to me because no one would review the submission.)

Excerpt: “The likelihood that eating lead- and manganese-contaminated leaves caused an ecological adaptation in moth larvae that led to a developmental change in morphology from fawn to peppered color in adults was dismissed when a replication attempt failed. Therefore, the displacement of the moths was attributed to predation more than 80 years ago. See for review . At that time, virtually nothing was known about nutrient-dependent pheromone-controlled biophysical constraints on the biochemistry of invertebrate morphology and behavior. Since then, others have leaned that morphology includes nutrient-dependent ecologically adapted pigmentation in insects ; in birds , and in humans .”

My comment: We now see that microRNAs are the most likely source of “Interspecies communication between plant and mouse gut host cells through edible plant derived exosome-like nanoparticles” Reported as: Amazing Food Science Discovery: Edible Plants ‘Talk’ To Animal Cells, Promote Healing

Excerpt: “With the recent discovery that non-coding microRNA’s in food are capable of directly altering gene expression within human physiology, this new study further concretizes the notion that the age old aphorism ‘you are what you eat’ is now consistent with cutting edge molecular biology.”

My comment: That biological fact links the epigenetic landscape of the moths — via contaminated plant leaves — to microRNA-induced changes in cell type differentiation and de novo creation of olfactory receptor genes. The olfactory receptor genes are linked to nutrient uptake and to the physiology of reproduction via the metabolism of nutrients to species-specific pheromones.

The extension from nutrient uptake to the pheromone-controlled physiology of reproduction in moths becomes clearer in mice. A nutrient-dependent amino acid substitution links the production of pheromones in mice to morphological and behavioral phenotypes associated with differences in teeth, sweat, hair, and mammary tissue. These changes are the result of the same nutrient-dependent amino acid substitution in humans and the changes have been exemplified in a human population that supposedly arose during the past ~30K years in what is now central China.

In his book “A Troublesome Inheritance,” Nicholas Wade repeatedly places the effect of the human nutrient-dependent amino acid substitution in the context of mutations and natural selection, which may make evolutionary theorists jump for joy. They …


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Epigenetic Transgenerational Actions

Posted on May 22, 2014 by James Kohl.

Michael Skinner (video)

2014 Forum: Epigenetic Transgenerational Actions of Endocrine Disruptors on Reproduction and Disease

The conserved molecular mechanisms of exposure-induced disease. A data-driven presentation that argues against the misrepresentations of evolutionary biology.

See also:

The natural history of transfer RNA and its interactions with the ribosome

Molecular mechanisms for the inheritance of acquired characteristics – exosomes, microRNA shuttling, fear and stress: Lamarck resurrected?

A symbiotic liaison between the genetic and epigenetic code

Epigenetic control of mobile DNA as an interface between experience and genome change

An invited but rejected review article about chemical ecology and nutritional epigenetics that encompasses all, or nearly all, of the accurate representations of epigenetic transgenerational actions above is available here:

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

Abstract: This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.…


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Neural systems are manifestations of ecological adaptations

Posted on May 21, 2014 by James Kohl.

The ctenophore genome and the evolutionary origins of neural systems

Excerpt: “More than 300 families of transposable elements constitute at least 8.5% of the genome (Supplementary Table 9 and Supplementary Data 2) with numerous examples of diversification of some ancient transposable element classes (for example, transposases and reverse transcriptases). Approximately 1.0% of the genome is methylated. Pleurobrachia also uses DNA demethylation during development, with both 5-hydroxymethyl cytosine (5-hmC) and its synthetic enzyme TET6 (Extended Data Fig. 2). The obtained genome and transcriptome data provide rich resources (http://neurobase.rc.ufl.edu/Pleurobrachia) for investigating both animal phylogeny and evolution of animal innovations including nervous systems2, 3, 7, 8, 9.”

My comment:  Since last year, attempts to comment on articles in published in Nature have resulted in the comment: “You are currently not allowed to comment owing to misuse”

Here is what I would have said about the article published earlier today.

“Researchers recently rediscovered a nutrient-dependent epigenetic variant that links vitamin C to what is probably a glucose and glucose dehydrogenase-dependent base pair change. The base pair change results in addition of a methyl group to a cytosine base, which takes on a hydroxyl group to form different 5-hydroxymethylcytosines (5hmCs). Different 5hmCs are associated with differences in cell types that have the same genetic backgrounds. Nutrient-dependent epigenetically-marked bases help to explain how hundreds of cell types in the human body and in the brain are differentiated and how they maintain their glucose-dependent and other nutrient-dependent receptor-mediated identities .” — Kohl (excerpt from an unpublished invited review) Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (submitted March 13, 2014)The focus of my model is on ecological adaptations not evolution because no experimental evidence supports the concept of biodiversity that arises from mutations and natural selection. Instead, all experimental evidence, which now includes the evidence in this article, suggests that ecological variation leads to ecological, social, and to neurogenic niche construction manifested in the ecological adaptations of neural systems in different species. Therefore, I wonder if the folks at Nature think ‘misuse’ equates with comments that argue against experimental evidence they publish by using experimental evidence that’s published elsewhere — even when it’s published by the Nature Publishing Group.  For example, in the past week, we’ve seen this experimental evidence of ecological adaptations manifested in neural systems in results published by the Nature Publishing Group as Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy


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Ecological adaptations link bats to humans

Posted on May 18, 2014 by James Kohl.

Is Evolution Predictable?

Excerpt:  “…evolution is not really predictable because too many chance events can knock it off course.”

My comment: Ecological variation predicts nutrient-dependent pheromone-controlled ecological, social, neurogenic, and socio-cognitive niche construction via conserved molecular mechanisms manifested in the morphological and behavioral phenotypes of species from microbes to man.

Examples (in the birds and the bees):

Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes

Epigenomics and the concept of degeneracy in biological systems

Other examples: “Nutrient–dependent / pheromone–controlled adaptive evolution: a model

Natural selection occurs for nutrients via experience induced de novo Creation of olfactory receptor genes in vertebrates and invertebrates.

What appears to be missing from evolutionary theory is any explanatory power whatsoever due to an overall lack of knowledge that must include what’s currently known about biophysically constrained nutrient-dependent amino acid substitutions and cell type differentiation in all species via an atoms to ecosystems model of biologically based cause and effect.

Theorists would rather believe in mutations and natural selection than biophysically constrained cause and effect. I think that’s because they didn’t understand biology, and will therefore never understand the physics and chemistry of molecular biology.

See also: Replace the Modern Synthesis (Neo-Darwinism): An Interview With Denis Noble. Neo-Darwinism can be replaced merely by consideration of what is currently known about biologically-based cause and effect. 

Maternal nutrition at conception modulates DNA methylation of human metastable epialleles and Genetic Interactions Involving Five or More Genes Contribute to a Complex Trait in Yeast link the nutrient-dependent differentiation of cell types in individuals of all species from ecological variation to pheromone-controlled ecological adaptations via conserved molecular mechanisms of signaling and sensing, which are manifested in Chemosensory Communication of Gender through Two Human Steroids in a Sexually Dimorphic Manner.

Frugivory in bats extends nutrient-dependent base pair changes and stabilization of the genome associated with vitamin C and the pheromone-controlled physiology of mammalian reproduction from the fossil record of bats to the fossil record of humans via the conserved molecular mechanisms of olfactory/pheromonal input.

Ecological adaptation determines functional mammalian olfactory subgenomes

The evolution of sensory divergence in the context of limited gene flow in the bumblebee bat

Molecular adaptation of telomere associated genes in mammals

A Cluster of Olfactory Receptor Genes Linked to Frugivory in Bats

Loss of Olfactory Receptor Function in Hominin Evolution appears to have occurred as sufficient dietary …


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