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Black Queen trumps the Red Queen

Posted on June 14, 2014 by James Kohl.

Earlier today, I wondered how best to note that the ridiculous misrepresentations in “Mutation-driven evolution” (2013) appeared in book publication on the same day my review article was published, which was one year ago.

This article, from “The Scientist Magazine” allowed me to vent some of my frustrations via my comments related to different hypotheses “Red Queen” and “Black Queen.”

Only the “Black Queen” hypothesis has been supported by experimental evidence of biologically-based cause and effect. The “Red Queen” hypothesis attests only to the theoretical nonsense that attests to the unwillingness of evolutionary theorists to learn about the basic principles of biology and levels of biological organization required to link sensory cause to behavioral affects via conserved molecular mechanisms in species from microbes to man.

My comment to The Scientist Magazine:

Re: “…none of us can actually tell how our experimental observations really relate to human disease, but we’re getting, all of us, closer to mechanistic insights…”

These mechanistic insights eliminate the “Red Queen” hypothesis and substitute biological facts about the molecular epigenetics of cause and effect, which can be accurately linked to the “Black Queen” hypothesis linked here. “The most likely explanation for the fitness advantage conferred by genomic and metabolic “streamlining” in both natural and experimental populations is that it reduces the amount of carbon and other limiting nutrients required to produce a new cell (12, 15, 16).

This “Black Queen” explanation of cell type differentiation and organization of the genome links the conserved molecular mechansims of sensing and signaling in species from microbes to man via the sensing of nutrients and their metabolism to pheromones that control the physiology of reproduction.

Nutrient-dependent base pair changes and amino acid substitutions link the microRNA/messenger RNA balance from alternative splicings of pre-mRNA to the de novo creation of olfactory receptor genes in invertebrates and vertebrates. The de novo creation of olfactory receptor genes enables the required receptor-mediated changes in behavior that link food acquisition and mate acquisition to biodiversity manifested in the morphological and behavioral phenotypes, which are life-support systems for their microbiomes.

Microbiome-dependent phenotypic expression shows how readily ecological variation enables the epigenetic landscape to become the physical landscape of DNA in the organized genome. (Nutrient-dependent pheromone-controlled phenotypic expression explains what is called the Cambrian “explosion” via the same model that explains the more recently reported differences in 500 species of fish in 15,000


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Mixing evolution and ecology

Posted on June 14, 2014 by James Kohl.

Population genetic structure of gray wolves (Canis lupus) in a marine archipelago suggests island-mainland differentiation consistent with dietary niche

Excerpt: “Evolutionary ecology and genetic differentiation between mainland and island wolves…”

My comment: This subheading mixes two different concepts.

1) Evolution of genetic differences in cell types between mainland and island wolves.

2) Ecological variation and epigenetic effects of diet, which are directly linked from food odors and pheromones to ecological adaptations in cell type differentiation. Cell type differentiation is manifested in morphological and behavioral phenotypes of species from microbes to man.

For example, in white-throated sparrows, research has shown that a difference in uniparental or biparental feeding results in fixed amino acid substitutions and different morphological and behavioral phenotypes. That suggests differences in wolves can also be linked to amino acid substitutions, but not to mutations and natural selection.

No experimental evidence of biologically-based cause and effect in any vertebrate links mutations and natural selection to the evolution of genetic differences in cell types, or to the evolution of different morphological and behavioral phenotypes like those of birds. All experimental evidence of biophysically-constrained cell type differentiation links nutrient-uptake, fixed amino acid substitutions, and the metabolism of nutrients to species-specific pheromones to cell type differentiation via conserved molecular mechanisms that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of the cell types of all species.

In the context of nutrient-dependent pheromone-controlled cell type differentiation and differences between wolves and dogs, I wrote (in Kohl, 2013):

“The epigenetic effects of nutrients on evolved differences in the diet and starch digestion of dogs and wolves (Axelsson et al., 2013) were detailed at the same time differences in the socialization of these subspecies were attributed to explorations involving only chemosensory input in 3 to 4-week-old wolf pups. For comparison, differences in starch digestion and exploration involving multisensory input in dogs begin a mere 2 weeks later (Lord, 2013). The differences in nutrient-dependent pheromone-controlled socialization, however, extend across a life-time of more aggressive behavior in wolves that have not been domesticated because less digested starch from their diet genetically predisposes infants to first respond to olfactory/pheromonal cues as they initially explore their postnatal environment.”

It should be obvious that prenatal cell type differentiation is quickly followed by postnatal cell type differentiation in vertebrates such as dogs and wolves, because larval cell type differentiation is followed by …


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A cradle of ecological adaptation?

Posted on June 13, 2014 by James Kohl.

High Tibet was cradle of evolution for cold-adapted mammals

News article excerpt:

“…the evolution of present-day animals of the Arctic region is intimately connected to ancestors that first became adapted for life in cold regions in the high altitude environments of the Tibetan Plateau.”

My comment: Does anyone else think that nutrient-dependent “ecological adaptation” is the term most appropriately used to replace the term “evolution” in the sentence above?

For example, there are 1180+ human hemoglobin variants that are directly linked to ecological variation, which includes elevation above sea level. If variants such as hemoglobin S are considered to be mutations,  present-day animals of the Arctic region could best be intimately connected to ancestors with mutations that were somehow naturally selected to enable adaptations in subsequent generations. However, there is no model for that.

Alternatively, the human hemoglobin variants could be compared to the variants in other species, like deer mice (see my comment to Science) and hummingbirds that appear to have ecologically adapted (e.g., in the absence of any experimental evidence that suggests they evolved via accumulated beneficial mutations that were somehow naturally selected). The alternative is consistent with Dobzhansky’s Creationist/Evolutionist approach in his 1964 (pdf) and 1973 (pdf) published works. It is also consistent with the labels he attached to those unfamiliar with conserved molecular mechanisms of Creation in 1964 when he wrote: “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!”

Current perspectives on evolution make me wonder if serious scientists are behind the recent change in the Israeli school system. Students in middle school will be taught about the theory of evolution so that it can be compared (e.g., earlier in life) to what they will learn is currently known about physics and chemistry in the context of the conserved molecular mechanisms of biophysically-constrained ecological adaptations.

This appears to be an attempt to ensure that future generations of Israeli researchers do not become bird-watchers and butterfly-collectors who might otherwise begin to tout the pseudoscientific nonsense of population geneticists and the theories they invented to replace Darwin’s accurate representations of his ‘conditions of life’ with the ridiculous theories of neo-Darwinian evolution.

At least one other cradle of ecological adaptation appears to have been recently discovered. However, …


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Nutrient-dependent cell type differentiation

Posted on June 12, 2014 by James Kohl.

Our Tastes For Certain Foods May Be Written in Our Genes

By Carl Engelking | June 5, 2014 3:41 pm

Excerpt: “Together, the series of studies bolsters a branch of research called nutrigenetics, which focuses on understanding the way our genes affect our choice of foods and our body’s ability to process these foods.”

My comment (Discover did not approve it):

jvkohl2 hours ago Hold on, this is waiting to be approved by D-brief.

Nutrigenetics is nutritional epigenetics because the nutrients epigenetically effect cell type differentiation, which is how they change behaviors.

Nutrient stress and social stress induce receptor-mediated changes in behaviors associated with ecological variations that must result in ecological adaptations via cell type differentiation for individuals of different species to survive. The result is biodiversity.

Taste receptors: Expression and nuclear translocation of glucocorticoid receptors in type 2 taste receptor cells

What could possibly go wrong?

Olfactory receptors: Mosaic Epigenetic Dysregulation of Ectodermal Cells in Autism Spectrum Disorder 

Are ASDs the disorders of nutrient-dependent cell type differentiation most closely linked to the epigenetic effects of pheromones on social behavior?

Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

———————————————————————————————————————————————————–

News sources often limit accurate representations of biologically based cause and effect and tout the pseudoscientific nonsense of population genetics.  The Discover blog D-brief reported that genes are responsible for the development of our food preferences. My comment cited works that link experience-dependent de novo creation of taste receptors and olfactory receptors to the hormone-organized and hormone-activated development of food preferences across species from insects to humans.

If my comment is not published, uninformed readers will continue to assume that food preferences are genetically determined despite experimental evidence that clarifies what is currently known about nutritional epigenetics, which they call “nutrigenetics” because they do not understand how the epigenetic landscape becomes the physical landscape of DNA  in the organized genomes of species from microbes to man.…


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Nutrient-dependent non-random personality differences

Posted on June 12, 2014 by James Kohl.

Personality: The Random Factor

Description: “Benjamin de Bivort, of Harvard, explores what fruit flies can tell us about personality, and also the random differences that develop between individuals and can’t be explained by genetics or environment.”

My comment: The differences are not random. The behavior of the flies exposed to a light stimulus does not address the conserved molecular mechanisms of insect behavioral development, which are nutrient-dependent and pheromone-controlled. For example, the complex wiring of the brain begins in insect larvae. See Nutrient-Sensing Neurons

Excerpt: “…Léopold’s group has found a path from food stimulus to behavior that is faster than predicted.”

My comment: The nutrient-dependent behavior is linked to ingestion of amino acids and a change in three dopamine-secreting neurons. In my model, nutrient-dependent amino acid substitutions stabilize cell type differentiation in the dopaminergic neurons and all other cell types.  That means the adult behavioral response to light reflects changes in the diet of the larvae, which are associated with feedback that epigenetically may effect the amino acid substitutions during life cycle transistions of organisms. Those changes result in transgenerational epigenetic inheritance of morphological and behavioral phenotypes during the development of offspring.

That fact links the ability of nutrient-sensing larvae to adult behavior via conserved molecular mechanisms of amino acid dependent alternative splicings of pre-mRNA, which link the epigenetic landscape to the physical landscape of DNA in the organized genomes of all species.

See also: Mechanism explains complex brain wiring

Conclusion: “These results indicate for the first time the significance of why different sets of the same protein variations can occur in one neuron and it could explain mechanistically how this contributes to the complex wiring in our brain.

Clinical impact

Although this research was done with fruit flies, it also provides new insights that help explain the wiring and complex interactions of the human brain and shine a new light on neurological development disorders such as autism. Thorough knowledge of nerve cell creation and their neural interactions is considered essential knowledge for the future possibility of using stem cell therapy as standard treatment for certain nervous system disorders.”

Journal article excerpt: “The Dscam1 gene uses combinatorial alternative splicing to generate tens of thousands of different receptor isoforms…”

My comment: 

The link from the experience-dependent de novo creation of olfactory receptor genes via alternative splicings of pre-mRNA to nutrient-sensing neurons in insect larvae  suggests the different receptor-mediated behavioral responses …


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What is the vomeronasal organ (VNO)?

The vomeronasal organ (VNO) is a cone-shaped organ in the nasal cavity, which is believed to be one of the body's receptors of pheromones. More, specifically, the VNO, which is part of the accessory olfactory system in the nose, does not respond to normal scents, but may detect odorless, barely perceptible pheromones.

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