Cognitive maps: insects to mammals

June 3, 2014 | James Kohl

Research shows bees might create cognitive maps

Excerpt: “…scientists studying the mammalian brain should bear in mind that bees might be able to create complex mental maps despite having brains many times smaller than the hippocampus of a rat.”

My comment: The honeybee model organism already extends the concept of nutrient-dependent pheromone-controlled ecological adaptations from species of microbes to man via conserved molecular mechanisms manifested in increasing organismal complexity (e.g., our socio-cognitive niche construction).

Evolutionary theorists simply refuse to discuss biological facts and want only for others to believe in the pseudoscientific nonsense of population genetics. The discussion section of this latest report may be the best indicator of how difficult it is for theorists to accept and integrate anything new into their approach to the study of how they think mutations and natural selection result in evolution.

The problem for them is that they have not learned anything about molecular biology during the past 50 years. Dobzhansky (1964) said it best in Biology, molecular and organismic.  “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!”  Denis Noble (2011) also wrote:  “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.”

The bird-watchers and butterfly-collectors who never learned anything about the amino acid substitutions that differentiate the cell types of individuals in all species will continue to come up with citations to works that deny what is known about the biological basis of nutrient-dependent pheromone-controlled ecological adaptations, but they will never tell you how mutations and natural selection lead to evolution and biodiversity because mutations don’t lead to biodiversity. Ecological variation leads to ecological adaptations that are manifested in biodiversity of the bees; the birds; and all other species on the planet via the conserved molecular mechanisms of ecological, social, neurogenic, and socio-cognitive niche construction detailed in Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems 

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From odors to autism spectrum disorder

May 31, 2014 | James Kohl

Mosaic Epigenetic Dysregulation of Ectodermal Cells in Autism Spectrum Disorder clearly links the de novo creation of olfactory receptor gene OR2L13, from decreased nutrient-dependent DNA methylation to sensory processing in ASD’s.

A series of published works I posted yesterday in Ecological variation leads to ecological adaptations links failed adaptations manifested in autism spectrum disorders (ASDs) via the sensing of chemicals that are typically called “odors.” Although the complexity of nutrient-dependent signaling and de novo creation of an olfactory receptor (OR) gene via conserved molecular mechanisms of cell type differentiation in species from microbes to man that lead to my atoms to ecosystems model is overwhelming, scientific progress is not made by ignoring the complexity.

That’s why I was surprised to read this sentence from Maximum information entropy: a foundation for ecological theory (in press).  “Given that there are so many mechanisms, processes, and trait-specific interactions at work in an ecosystem, they can effectively be ignored.”

Biophysical constraints on experience-dependent protein folding allow the natural genetic engineering of the cell to create the receptors that allows the nutrient(s) to enter the cell and to alter the microRNA/messenger RNA balance, which leads to the cell’s nutrient-dependent ability to create more ORs via gene duplication. However, gene duplication seems unlikely to occur in the context of entropy. I suspect that’s why a new definition of entropy is used in the context of maximum information entropy. What else can be done by theorists when what’s known about atoms and ecosystems refutes their theories with experimental evidence that appears to violate the Second Law of Thermodynamics, which implies that order does not arise from disorder. The molecular mechanisms of gene duplication show that order does result from disordered nutrient-dependent intercellular signaling in all cells of all individuals in all species. Since gene duplication defies entropy, it must now be defined in the terms of population genetics or neo-Darwinism will be exposed to be pseudoscientific nonsense.

Creation of ORs and other proteins via seemingly futile cycles of protein biosynthesis and degradation then stabilizes cell type differentiation that occurs with nutrient uptake and “pheromone”-controlled reproduction at the unicellular level (e.g., in bacteria and yeasts) and multicellular levels of organism-level sensing and signaling via the complexities of biophysically constrained thermodynamics and thermoregulation.

Transgenerational epigenetic inheritance of the molecular mechanisms required for organism-level thermoregulation enable ecological variation to be manifested in ecological adaptations. These ecological adaptations are found in the morphological and behavioral phenotypes of species from microbes to man.

ASDs represent failed ecological adaptations that are readily linked to nutrient stress and social stress, which link the epigenetic landscape to the physical landscape of DNA in organized genomes whether or not Darwin’s ‘conditions of life’ are all-together favorable.

His ‘conditions of life’ may require atomic level changes that link micronutrients and macronutrients from one-carbon metabolism, base pair changes, DNA methylation, and amino acid substitutions to the Creation of novel cell types via the differentiation of cell types during their nutrient-dependent maturation.

Use of the big “C” in the context of the Creation of novel cell types led to Dobzhansky’s claims. In 1973, he stated that he was a Creationist and an Evolutionist

Anyone who is not an evolutionary theorist now recognizes the likelihood that Dobzhansky and others like him have always been Creationists and Ecological Adaptationists who realize that mutations perturb protein folding, which means they are not naturally selected to become fixed in the organized genome of any species. Therefore, entropy must be redefined in another attempt to fit what population geneticists have ignored into their theories.

They have ignored the fact that only nutrient-dependent fixation of amino acid substitutions and the pheromone-controlled physiology of reproduction can result in increasing organismal complexity that is manifested in biodiversity via the conserved molecular mechanisms that link microbes to man. That fact led Queitsch & Rosenberg to conclude an article about Combating Evolution to Fight Disease with this statement, which echoes the sentiments I have repeatedly expressed: “The evolutionary biologist Theodosius Dobzhansky famously noted that “nothing in biology makes sense except in the light of evolution,” but perhaps, too, “nothing in evolution makes sense except in the light of biology.” Although the latter might be an exaggeration, an important gap is being filled by molecular understanding of the genesis of variation that confers the ability to evolve.”

Variation in the availability of nutrients confers the ability to ecological adapt. Nothing that makes sense in the light of biology  confers the ability to evolve. The theory of evolution was invented to explain what could not be explained by biology after the Scopes trial in 1925. Examples of ecological adaptations in species from microbes to man now explain how ecological variation leads to biodiversity via the nutrient-dependent pheromone-controlled physiology of reproduction. But:  “Given that there are so many mechanisms, processes, and trait-specific interactions at work in an ecosystem…,” they must be ignored by theorists, lest their theories be removed from any further consideration whatsoever in the context of biological facts about the origins of ASDs and other developmental disorders that theorists want others to attribute to mutations and natural selection.

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Ecological variation leads to ecological adaptations

May 30, 2014 | James Kohl

My published 2013 review  on ecological variation has been viewed more than 1000 times this month. It seems fitting that this is my 1000th blog post, since the time Dick Doty’s ridiculous assertions in “The Great Pheromone Myth” prompted me to begin adding experimental evidence to support my accurate representations of nutrient-dependent pheromone-controlled ecological adaptations.

Many of those who might otherwise be considered colleagues in academia are largely responsible for reporting biological facts in terms of evolutionary theory. They use the terms, although it has since become clear that those terms simply (and simple-mindedly) reflect the invention of theories associated with a neo-Darwinian perspective. Neo-Darwinism fails to incorporate anything Darwin wrote about the need to consider ‘conditions of life’ before going off half-cocked in attempts to explain cause and effect manifested in populations of living organisms.

Clearly, those populations cannot exist in the absence of Darwin’s ‘conditions of life’ which molecular biologists and intelligent non-scientists have probably always known are nutrient-dependent. Some molecular biologists also know that ‘conditions of life’ are controlled by the metabolism of nutrients to species-specific pheromones that control the physiology of reproduction in species from microbes to man.

That fact led me to submit an invited review on nutritional epigenetics at the request of a guest editor. The invitation was based on publication of facts in my 2013 review, and I added experimental evidence that had accumulated during another year — prior to submitting Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems in March 2014. I received notice of its rejection for publication in April 2014.

None of the reviewers who were asked to review the submission would read it, and I heard nothing about the submission from the guest editor who requested it. (We had discussed the fact that I would never submit anything for publication without a request, because of the nonsense I have been subjected to in the process of peer-review.) The ultimate nonsense of peer-review is when an invited submission is rejected without review. (Either I have no peers, or my peers want nothing to do with any new experimental evidence.)

Interdisciplinary research is the problem in that regard. It is difficult to find peers due to the scope of the review. However, it is easy to find critics who do not understand explanations of systems complexity because they have become too specialized to understand anything outside their field of expertise.

Arguably, however, I did not need to be so blatantly offensive by suggesting that evolutionary theory be replaced with Kohl’s “Laws of Biology” — so-named because the surname of the first author or sole author on each of 7 peer-reviewed publications in the paragraph that introduces the Laws is Kohl. However, I wanted to have some fun in the review. In an effort to bring home a point made clear by the experimental evidence I included, I wrote:

“The Kohls did not create the Laws of Biology; they merely independently incorporated what is known about them into what appears to be a cohesive series of published works.

Kohl’s Laws of Biology

Life is nutrient-dependent. That is a Biological Law. The ecological origin of all biological laws is apparent 1) in the context of systems biology [91]; 2) in the context of the metabolism of nutrients by microbes [157]; and 3) in the context of how the metabolism of nutrients results in species-specific pheromones that control the physiology of reproduction [158]. Taken together, the systems biology of nutrient metabolism to species-specific pheromones, which control the physiology of reproduction, can be expressed in a summary of Kohl’s Laws of Biology: 1) Life is nutrient-dependent. See for review [2, 31]. The physiology of reproduction is pheromone-controlled. See for review [30]. In the context of nutrient-dependent epigenetically-effected human reproduction, it is clearer that the epigenetic effects of human pheromones integrate neuroendocrinology and behavior [104], which includes the neuroendocrinology of mammalian behavior associated with the development of sexual preferences [159].

Kohl’s Laws help to explain what was missing from Darwin’s ‘conditions of life.’ Darwin knew nothing about genetics, which means he knew nothing about the epigenetic effects of food odors or pheromones. For contrast, the following representation of cause and effect acknowledges what is known today…”

——————————————————————-

In the months of March; April, and May (2014), experimental evidence that supports Kohl’s Laws of Biology in the context of Darwin’s ‘conditions of life’ overwhelmed me.  It has become increasingly difficult to consider all the support from different disciplines, although I have reported most of it on the PheromonesResearch Facebook page, and  some of it here at Pheromones.com

Here are links to the recently published articles that I may have missed reporting but that also support my explanation of how ecological variation results in ecological adaptations, which refutes ideas about mutations and natural selection in the context biophysically-constrained biodiversity that most people refer to as evolution.

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

Transgenerational Epigenetic Inheritance: Myths and Mechanisms

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

Mapping posttranscriptional regulation of the human glycome uncovers microRNA defining the glycocode

Nuclear compartmentalization of odorant receptor genes

Postnatal Odorant Exposure Induces Peripheral Olfactory Plasticity at the Cellular Level

The Molecular and Systems Biology of Memory

Long term functional plasticity of sensory inputs mediated by olfactory learning

Interspecies communication between plant and mouse gut host cells through edible plant derived exosome-like nanoparticles

Sex pheromone biosynthetic pathways are conserved between moths and the butterfly Bicyclus anynana

Hypothalamic response to the chemo-signal androstadienone in gender dysphoric children and adolescents

Chemosensory Communication of Gender through Two Human Steroids in a Sexually Dimorphic Manner

Odor Valence Linearly Modulates Attractiveness, but Not Age Assessment, of Invariant Facial Features in a Memory-Based Rating Task

Mosaic Epigenetic Dysregulation of Ectodermal Cells in Autism Spectrum Disorder

A symbiotic liaison between the genetic and epigenetic code Abstract excerpt: “the model is further extendable to virtually all traceable molecular traits.

The extension of Kohl’s Laws of Biology to virtually all traceable molecular traits via nutrient-dependent pheromone-controlled ecological adaptations is made possible because gene duplication is epigenetically effected by nutrient uptake and pheromones control the physiology of reproduction. However, researchers continue to approach the epigenetic regulation and dysregulation of morphological and behavioral phenotypes in species from microbes to man as if mutations and natural selection were somehow involved in perturbed protein folding that they think somehow leads to increasing organismal complexity and diseases.

For example, in Nicholas Wade’s book A Troublesome Inheritance: Genes, Race and Human History, he linked the nutrient-dependent pheromone-controlled advent of an ectodermal receptor to mutations and natural selection. In my model, I linked the receptor to morphololgical and behavioral phenotypes in a human population that appears to have arisen during the past 30,000 in what is now central China.

When I read the report that linked the olfactory receptor gene OR2L13, from decreased nutrient-dependent DNA methylation to sensory processing in ASD’s, I decided to update my blog posts with the experimental evidence that clearly shows how much pseudoscientific nonsense may continue to be touted as if it should make sense of what is clearly exemplified in all species.

This makes sense: Ecological variation leads to ecological adaptations unless the adaptations are prevented by mutations that perturb protein folding and cause physical and mental disorders and diseases.

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Genes and Race: Human History?

May 26, 2014 | 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 is known about the conserved molecular mechanisms of biolophysically constrained cause and effect. See for example: Interspecies communication between plant and mouse gut host cells through edible plant derived exosome-like nanoparticles. The article links genes to differences in morphology and behavior without resorting to claims made by neo-Darwinists.

Indeed, the focus is more on the fact that Darwin set forth when he repeatedly urged consideration of  the ‘conditions of life’ that must be met before natural selection could occur. His conditions of life require selection for food, which is manifested in changes in the microRNA/messenger RNA balance and cell type differentiation in bats and humans — if not all species, or some that might have mutated into existence. The report on the article mentions the fact that “With the recent discovery that non-coding microRNA’s in food are capable of directly altering gene expression within human physiology,[1] 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.”

Nicholas Wade’s book includes nothing known about the molecular biology of cause and effect. Reviewers seem to know about nothing but evolutionary theory.

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Another slap in the face for evolutionary theorists

May 24, 2014 | 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 [40]. 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 [41]; in birds [42-43], and in humans [44].”

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,[1] 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 typically like to read about things that appear to support their pseudoscientific nonsense. That’s why the peppered moth story is a favorite example of what they think is mutation-initiated natural selection. Theorists never think in terms of conserved molecular mechanisms that link the nutrient-dependent pheromone-controlled cell type differentiation of moths to mice and to other mammals via the epigenetic effects of ingested microRNAs on amino acid substitutions associated with food odors and with the metabolism of nutrients to species-specific pheromones in species from microbes to man.

Evolutionary theorists can only think in terms of mutations, natural selection, and biodiversity. They would not recognize a nutrient-dependent ecological adaptation if it slapped them in the face, which is metaphorically what just happened with publication of: “Interspecies communication between plant and mouse gut host cells through edible plant derived exosome-like nanoparticles.”

Nicholas Wade can now try to explain why he misrepresented the changes in the human population. They are not caused by mutations linked to racial differences and should be correctly represented as ecological adaptations that occur in all cell types of all individuals of all species via conserved molecular mechanisms. Trying to diffuse issues of racial differences while continuing to include any aspect of the pseudoscientific nonsense associated with neo-Darwinism, puts Wade in an awkward position. He’s stuck with theory at a time when biological facts clearly detail how ecological variation leads to ecological adaptations in microbes and all the races of man.

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