Nutrient-dependent origin of the genetic code

June 9, 2014 | James Kohl

RNA editing and modifications of RNAs might have favoured the evolution of the triplet genetic code from an ennuplet code

Original Research Article 
Journal of Theoretical Biology, Available online 6 June 2014, Pages 
Massimo Di Giulio, Marco Moracci, Beatrice Cobucci-Ponzano

Article excerpt: “The fact that today the anticodons are modified, and in particular modified by means of amino acids in a statistically significant way (Di Giulio, 1998), would make to presume in: (i) an intimate evolutionary relationship between amino acids and anticodons for the origin of the genetic code…”

My comment: That suggests the origin of the genetic code can be found in the context of ecological variation and nutrient-dependent amino acid substitutions that  differentiate cell types in individuals of all species in which the physiology of reproduction is controlled by the metabolism of nutrients to pheromones.

See also: Alternative RNA Splicing in Evolution to help transition from ideas about mutations, natural selection, and the evolution of biodiversity to facts about how ecological variation in the supply of nutrients leads to ecological adaptations via conserved molecular mechanisms in species from microbes to man.

Keep in mind the unenviable position of Jay R. Feierman, who is moderator of the International Society for Human Ethology’s yahoo discussion group. Like Jon Lieff, Feierman is a psychiatrist. Unlike Jon Lieff, Feierman knows nothing about the basic principles of biology and levels of biological organization required to link the epigenetic landscape to the physical landscape of DNA in the organized genome of species from microbes to man. However, Feierman makes claims like this in reference to my published works:

Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding Darwinian biological evolution. 

My comment: Feierman’s understanding of Darwinian biological evolution is what leads him to tout this ridiculous claim:

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.

Serious scientists continue to see experimental evidence that attests to the fact that Feierman and those who still share his ridiculous ideas about biologically based cause and effect are among the uneducated “know it alls” who think their academic credentials make up for their ignorance. They are also among the academically irresponsible educators who are teaching nonsensical theories to students who may never learn about how ecological variation leads to ecological adaptations and biodiversity because they’ve been taught to believe in “Evolution for Dummies.”

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Teaching of pseudoscientific nonsense earlier in Israeli schools

June 6, 2014 | James Kohl

Israeli Middle Schools School to Include Theory of Evolution

Excerpt: “… 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.”

My comment: This appears to be a blessing (e.g., in disguise) for Israeli children.  The earlier they learn the difference between the teaching of pseudoscientific nonsense that population geneticists used to invent neo-Darwinism, the more rapidly they will progress in quests for experimental evidence of biologically-based cause and effect that links what they’ve learned (or will learn) about physics and chemistry from ecological variation to ecological adaptations via Darwin’s ‘conditions of life.’

I noticed two years ago, after attending the Society for Neuroscience Annual Meeting in New Orleans, that researchers in Israel already were already consistently among those reporting experimental evidence that shows how ecological variation leads from the nutrient-dependent microRNA/messenger RNA balance to ecological adaptations. I did not know that students in Israel had not be burdened with implausible ideas about biologically-based cause and effect that population geneticists invented in their failed attempts to explain how Darwin’s ‘conditions of life’ led to biodiversity.

Now, it’s obvious that those who were not taught to believe in the pseudoscientific nonsense of neo-Darwinian evolution are among those most likely to be naturally selected to help science move forward. See for example: “Toward a combinatorial nature of microRNA regulation in human cells.”  Note the difference between the explanatory power of microRNAs compared to the inexplicable automagical effects of whatever causes changes in messenger RNA and mutation-driven evolution in this report: The Effects of Codon Context on In Vivo Translation Speed.

Here’s what happens when mutation-driven evolution is then used to explain the evolution of an organ in sheep.

The sheep genome illuminates biology of the rumen and lipid metabolism

Editor’s summary: Sheep-specific genetic changes underlie differences in lipid metabolism between sheep and other mammals, and may have contributed to the production of wool. Jiang et al. sequenced the genome of two Texel sheep, a breed that produces high-value meat, milk, and wool. The genome information will provide an important resource for livestock production and aid in the understanding of mammalian evolution.

My comment:  The connection between ecological variation and nutrient-dependent ecological adaptations manifested in the different morphological and behavioral phenotypes is short-circuited with mention of mutations that somehow cause changes in the hair of other mammals. The differences in hair are then loosely associated with mutation-driven evolution of an organ.

For contrast, in the mouse-to-human model of epigenetic effects via conserved molecular mechanisms, changes in hair, sweat glands, teeth, and mammary tissue are attributed to differences in diet. The differences in diet appear to cause a base pair change, an amino acid substitution, and receptor-mediated changes in morphology, which are clearly linked to receptor-mediated changes in behavior via the metabolism of nutrients to species-specific pheromones that control the physiology of reproduction. See for review: “Nutrient-dependent/pheromone-controlled adaptive evolution: a model”

The likelihood that species-specific pheromones control the physiology of reproduction in species from microbes to man via conserved molecular mechanisms suggests that attributing the evolution of any organ to a mutation is a miss-attribution. The miss-attribution appears to support a theory invented by population geneticists to explain nutrient-dependent pheromone-controlled biodiversity. But the theory explains nothing.

If the rumen is an ecological adaptation, any suggestion that it exemplifies mutation-driven evolution is one that can now be challenged by experimental evidence from the extant literature on how the nutrient-dependent microRNA/messenger RNA balance contributes to cell type differentiation in individuals of all species. Cell type differentiation links the finely-tuned balance from ecological variation to ecological adaptations and biodiversity via hormone-organized and hormone-activated behavior in sheep, all other vertebrates, and all invertebrates. See for example: “The ram as a model for behavioral neuroendocrinology

See also, our award-winning 2001 review article: Human pheromones: integrating neuroendocrinology and ethology and the author’s copy of my award-winning book chapter/journal article: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences.

When the pseudoscientific nonsense of mutation-driven evolution in microbes is taught and extended to mutation-driven evolution of an organ in a mammal, how could anyone subjected to the teaching of such a ridiculous theory not be left at least somewhat scientifically/intellectually disabled? If you look hard enough for evidence of what happens when “Evolution for Dummies” is taught to serious scientists, I think you will understand why that ridiculous theory will now be taught earlier to Israeli children. The sooner they recognize the difference between pseudoscience and scientific facts supported by experimental evidence of biologically based cause and effect, the sooner they can join their professors and continue to lead the field with new discoveries.
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What makes us human?

June 5, 2014 | James Kohl

Excerpt: “The belief that there is something inherently special about humans and the way we arose is more suited to creation mythologies and religious doctrine than to a scientific, testable view of the world.”

My comment: It is the belief in evolutionary theory that has not led to any scientific, testable view of the world. For example, Denis Noble stated that: “…gradual mutation followed by selection has not, as a matter of fact, been demonstrated to be necessarily a cause of speciation.” Challenges to the theory that mutations and natural selection lead to the evolution of biodiversity now incorporate quantum physics.  My comments on the misrepresentations in the news article linked above include a succinct apology to Luca Turin.

I criticized Turin in a 2003 book review. http://human-nature.com/nibbs/03/burr.html

“Turin never attempted to work within the system. Perhaps a future proponent of molecular vibration theory will manage better than Dyson, Wright and, most recently, Turin. Truly this theory may be years ahead of its time. It also may be a theory that cannot be sufficiently supported by scientific fact.”

Luca politely told me that his attempts to work within the system had failed — especially attempts that involved the Association of Chemoreception Sciences (AChemS). Two of my attempts to present have since been rejected and successful attempts have led to presentations that have been largely ignored. Dick Doty’s book “The Great Pheromone Myth” led more people to deny established facts from across disciplines that link Luca’s works to mine. http://www.amazon.com/Great-Pheromone-Myth-Richard-Doty/dp/080189347XI now criticize AChemS. Luca and I did all that’s expected of serious scientists.”

Here’s a link to information on the abstract of the poster presentation I submitted for the 2014 annual meeting: UNACCEPTABLE Presentation on nutrient-dependent pheromone-controlled ecological adaptations.

Our inability to accept scientific facts when the facts challenge our beliefs about pseudoscientific nonsense is what makes us human. The scientific facts link the epigenetic landscape to the physical landscape of the DNA in our organized genomes via the conserved molecular mechanisms and the biophysical constraints on mutation-initiated natural selection that are exemplified in the species-specific morphological and behavioral phenotypes of species from microbes to man.

Luca Turin tried to lead the way with information on the biophysical constraints of quantum physics. Hopefully, he will again attempt to do so, but if he does the outcome may still be the same.  For example, AChemS members are no more likely now than they were 15 years ago to understand the latest research from other disciplines.

Ask an AChemS member about this: Terahertz underdamped vibrational motion governs protein-ligand binding in solution or ask about this: A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution .

Don’t ask an AChemS member about this: Molecular Vibration-Sensing Component in Human Olfaction. All but a few AChemS members have learned to ignore new ideas. Most of them continue to promote ideas like those Dick Doty touts about differences between the epigenetic effects of food odors and the epigenetic effects of mammalian pheromones. Olfactory/pheromonal input alters levels of hormones that affect behavior via the conserved molecular mechanisms of biophysically-constrained cause and effect. Epigenetic effects link species of microbes to man via molecular vibrations that enable the experience-dependent de novo creation of olfactory receptor genes, which enable food odors and social odors called pheromones to alter the conserved molecular mechanisms of behavior.

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Models in biology vs pathetic thinking

June 4, 2014 | James Kohl

Models in biology: ‘accurate descriptions of our pathetic thinking’

Article excerpt: “…laying the foundations for rescuing Darwin’s theory from oblivion [67], a task later accomplished, in the hands of J. B. S. Haldane, R. A. Fisher and Sewall Wright, largely by mathematics.”

My comment: It is becoming clearer that:  “[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. The anglophone tradition was taught. I was taught, and so were my contemporaries, and so were the younger scientists. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another…. No, it wasn’t dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact.”

The idea that others needed to mathematically invent neo-Darwinism to rescue Darwin’s theory was accompanied by a requirement for the rescuers to ignore Darwin’s ‘conditions of life.’ That ignorance is now being considered in the light of molecular biology. What’s known about conserved molecular mechanisms and the de novo creation of olfactory receptor genes attests to this fact: No one can invent a theory that will be accepted indefinitely. Sooner or later, the theory must be supported with experimental evidence that fits a model of cause and effect. It is the lack of experimental evidence that represents the ‘pathetic thinking’ of those who should provide examples of critical thinking skills.

The tragedy of all this is exemplified in statements (below) made by Jay R. Feierman, the retired M.D. who is moderator of the ISHE’s human ethology group.

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. ” What Feierman is saying is that many others, perhaps even 100% of biology or genetics professors, also lack critical thinking skills.

For contrast: 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. 

Ecological variation confers the ability to ecologically adapt. Nothing supported by experimental evidence of biologically plausible cause and effect suggests that organisms evolve via the accumulation of genetic mutations.
Feierman:Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.Sadly, Feierman has led the ISHE’s human ethology yahoo group down a path towards its irrelevance as a source of accurate information or intelligent discussions. His bias prevents the purpose of the group from being achieved. Moreover, it is people like the biology and genetics professors who Feierman thinks share his beliefs who also are teaching today’s students to believe the same pseudoscientific nonsense that Feierman was taught to believe.  Pathetic thinking has been substituted for biologically plausible models in biology since the time of the Scopes trial.
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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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