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Take two theories and call me in the morning

Posted on April 3, 2014 by James Kohl.

Science 4 April 2014: Vol. 344 no. 6179 pp. 19-20

Theoretical Physics

The Morning After, Inflation Result Causes Headaches

by Adrian Cho

Excerpt: “On one hand, the first thing you write down works. But then when you think about it, the first thing you write down doesn’t make any sense.”

My comment: When it was first proposed, mutation-initiated natural selection seemed to make sense. However, what’s been learned about physics, chemistry and molecular biology has since made ideas about mutation-driven evolution and ideas about natural selection seem to be examples of pseudoscientific nonsense. See, for example: Genes without prominence: a reappraisal of the foundations of biology.

Many physicists and most evolutionary theorists have already reached the point where they can no longer do anything but take two theories and add more theories that lead to diverging thoughts about reality. However, when it comes to the reality of physics, chemistry and molecular biology, experimental evidence is like a pill that resolves the headaches. Experimental evidence shows that life is nutrient-dependent and that reproduction is pheromone-controlled. All else is headache-causing theory.…


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Ecological adaptations incorrectly portrayed in terms of evolutionary advantages

Posted on April 3, 2014 by James Kohl.

Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans

Excerpt 1) “It is appealing to speculate that genetic variants affecting lipid catabolism in modern Europeans were acquired by modern human ancestors through genetic flow from Neanderthals, and then spread rapidly though the ancestral population by means of positive selection.”

Excerpt 2)  “If the lipid catabolism gene variants we find in Neanderthals and contemporary Europeans were already present in the ancestors of Neanderthals and out-of-Africa human populations, they may have independently increased in frequency in Neanderthals and humans situated in the European region. This scenario is probable if these genetic variants provided an adaptive advantage to both Neanderthal and human populations in the conditions of prehistoric Europe. While the presence of a recent positive selection signal in lipid catabolism gene variants containing NLS in modern Europeans supports such an adaptive scenario, the environmental pressures or functional mechanisms of this possible adaptive change remain elusive.”

My comment:

Excerpt 1) is biologically implausible speculation with no explanatory power. It is akin to what is typically discussed in terms of mutations and natural selection, which appears to occur only in the context of population genetics. For example, beneficial mutations must somehow supposedly result in natural selection for morphological and behavioral phenotypes that appear to result in increasing organismal complexity and species diversity.

Excerpt 2) includes what is currently known about biophysical constraints on protein folding that ensure the metabolism of  nutrients to species-specific pheromones controls the physiology of reproduction, which enables sexual selection for nutrient-dependent sex differences in pheromones. There is a model for that!

See, for example: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Experimental evidence now supports a revised view of adaptive evolution, because only ecological adaptations have been exemplified. See, if published: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (under review). While you wait, see Nutrient-dependent / Pheromone-controlled adaptive evolution: (a mammalian model of thermodynamics and organism-level thermoregulation).

See also: Genes without prominence: a reappraisal of the foundations of biology. It details aspects of biophysical constraints on protein folding and ecological adaptations that eliminate theories associated with mutations and evolution. Ecological adaptations result in species diversity, constraint-breaking mutations do not.

See also: A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution. Linking any nutrient to ‘evolution’ is a misrepresentation of the physics, chemistry, and conserved molecular mechanisms that enable ecological …


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Mutations in proteins that make all proteins

Posted on April 1, 2014 by James Kohl.

Cellular mechanisms for integral feedback in visually guided behavior Excerpt: “Visually driven behaviors of Drosophila have become a model system to study how neural circuits process sensory information.”

My comment: Perhaps they will link these “visually driven behaviors” to other behaviors that are driven by food odors and pheromones. This would reveal that conserved molecular mechanisms link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. Alternatively, they could simply claim that humans are primarily visual creatures, such as birds, but not dogs et al.

That claim might confuse people, but who cares? It’s only a theory. No experimental evidence support any model of visually driven behavior, and no biological facts about conserved molecular mechanisms need to be included in theories about visually-driven behaviors. There is no need to link visual input to DNA or anything else.

In a response to comments on

A Challenge to the Supremacy of DNA as the Genetic Material James V. Kohl says: March 29, 2014 at 6:42 pm

… Works by Lenski and Dunham are, of course, examples of how evidence from population genetics has confused evolutionary theorists who equate it with experimental evidence of biologically-based cause and effect reported by serious scientists.

Many of the academics have not updated their knowledge base by reading articles on yeasts, like “Signaling Crosstalk: Integrating Nutrient Availability and Sex” http://stke.sciencemag.org/cgi/content/abstract/sigtrans;6/291/pe28

Many theorists have not yet grasped the unicellular nutrient-dependent pheromone-controlled physiology of reproduction connection to “Feedback loops link odor and pheromone signaling with reproduction” http://www.ncbi.nlm.nih.gov/pubmed/16290036 …

March 31, 2014

Two days later I read about a model of cell type differentiation that makes no mention of nutrient-dependent pheromone-controlled cell types and posits that cancers evolve via one inherited or acquired mutation that is effected by a second mutation.

See:  Possible explanation for human diseases caused by defective ribosomes

The senior author states: “Our yeast work has established a new paradigm that we are now translating to humans.”

In the first sentence, this is what the report implies: “Ribosomes are essential for life, generating all of the proteins required for cells to grow. Mutations in some of the proteins that make ribosomes cause disorders…”

I’ll paraphrase that, since they are trying to translate it to humans:

1) Ribosomes… / generat… all of the proteins required for cells to grow.

2) Mutations in some of the proteins that …


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Theory presented in a book

Posted on March 31, 2014 by James Kohl.

Free Radicals: The Secret Anarchy of Science

Re: Lynn Margulis

Excerpt: “I was told by an NSF grants officer (after having been supported nicely for several years) that ‘important’ scientists did not like the theory presented in a book I had written and that they would never fund my work. I was actually told that I should never apply again to the cell biology group at NSF.” (p. 181)

I’ve never been told by anyone that they didn’t like the theory I presented with co-author Robert Francoeur in The Scent of Eros: Mysteries of Odor in Human Sexuality. However, I have often wondered why colleagues who appear to be friends do not cite my book or my subsequent published works. Then I see others report what I have detailed during the past two decades, as in Transgenerational Epigenetic Inheritance: Myths and Mechanisms.

Excerpt: “…there are many examples of quantitative epigenetic traits that appear to respond to environmental— and especially nutritional—cues experienced by former generations. For example, in the nematode C. elegans, exposure to an olfactory cue early in development affects behavior when encountering the chemical in adulthood, a process known as olfactory imprinting, and this behavior can then be transmitted over more than 40 generations (Remy, 2010).”

This is the nutrient-dependent pheromone-controlled ecological adaptation that I published as Nutrient-dependent/pheromone-controlled adaptive evolution: a model. It is somewhat expected that due to the increasing amount of published works, there will always be people who have not learned about my model or heard about my history of presentations during the past 22 years. But I’m beginning to think that details in a book should not precede a decade or more of presentations that familiarize others with what they eventually are going to be forced to accept. I didn’t realize that most people simply accept mutations and evolution as an explanation for species diversity, and don’t ask questions. They don’t want to know about anything else.

Re: Margulis, again“She describes the great evolutionary biologist John Maynard Smith as an engineer who ‘knows much of his biology second hand.’He and his fellow neo-Darwinists, Dawkins, Eldredge, Richard Lewontin and Stephen Jay Gould ‘codify an incredible ignorance.’ Their work is ‘reminiscent of phrenology’ and ‘will look ridiculous in retrospect, because it is ridiculous.’ “(p. 181)

Also, from the same book: “The scientific establishment, Lindgren decleared, ‘is permeated with opinions which pass for valid scientific inductions …


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Conserved molecular mechanisms: What is not clear?

Posted on March 31, 2014 by James Kohl.

Transgenerational Epigenetic Inheritance: Myths and Mechanisms

Heard and Martienssen (2014)

Excerpt 1): “…small RNA signals are highly mobile, being transmitted through the gut in C. elegans, through the vasculature and plasmodesmata in plants, and through exosomes and even serum in mammals. At least in C. elegans, these small RNAs or their derivatives can enter the germline and mediate heritable transcriptional silencing in subsequent generations using histone modification mechanisms analogous to fission yeast.”

Excerpt 2:) “Metabolites might also be transmitted from one generation to the next and participate in bioenergetic feedback loops. These could be propagated over generations and could also act as cofactors for chromatin modification or RNA processing, for example.”

My comment: In my model, nutrient-dependent pheromone-controlled changes in the microRNA/messenger RNA balance and seemingly futile cycles of thermodynamically controlled protein biosynthesis and degradation result in alternative splicings of pre-mRNA that contribute to organism-level thermoregulation. If the alternative splicings do not stabilize the genome via conserved molecular mechanisms in species from microbes to man, the alternative splicings do not link the epigenetic landscape to the physical landscape of DNA in the organized genome of any species.

Simply put, at best the alternative splicings are beneficial. At worst they result in perturbed protein folding and deleterious mutations.

Between the best and worst of nutrient-dependent pheromone-controlled alternative splicings lies the plasticity of intercellular signaling that may result in de novo creation of proteins that enable increasing organismal complexity in species from microbes to man.

Note however that Heard and Martienssen (2014) was reported as:

End the Hype over Epigenetics & Lamarckian Evolution

Excerpt: “Heard & Martienssen are not convinced. In their Cell review, they admit that epigenetic inheritance has been demonstrated in plants and worms. But, mammals are completely different beasts, so to speak.”

My comment: In our 1996 Hormones and Behavior review article, a section on molecular epigenetics attests to the fact that alternative splicing of pre-mRNA link the conserved molecular mechanisms of pheromone-controlled physiology of reproduction in species that sexually reproduce.

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 of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, …


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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.

Other schools of thought believe that it is not the VNO but rather cells in our main olfactory system and their affects on hormones secreted by the hypothalamus that are responsible for the affects of pheromones.

Learn more about the science behind pheromones here.

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