Jon Lieff: ecologically adapted and masterfully prescient

March 24, 2014 | James Kohl

Q and A with William Miller about his new Book on the Microcosm and Evolution

by Jon Lieff
March 18, 2014 - See more at: http://jonlieffmd.com/blog/q-a-with-william-miller-about-his-new-book-on-microcosm-evolution#sthash.ktmxsMKI.dpuf

Excerpt: ”The major deficiency is what is considered the central paradox for Darwinian evolution based on natural selection. How does a mutation in a single individual ever become fixed in a population?”

Fifty years ago, Dobzhansky 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!”

Kudos to Jon Lieff for continuing to search the current extant literature and also ask the right questions so that he can provide others with detailed answers, which link Darwin’s ‘conditions of life’ in species from microbes to man.

Conditions of life are biophysically constrained. Simply put, they are nutrient-dependent and pheromone-controlled. The biophysical constraints of conserved molecular mechanisms have become clearer. So has the need for all cellular life to recognize self vs. other differences, which — as revealed in this blog post — is a function of the most primitive naturally engineered immune system.

Organisms that cannot recognize self vs. other differences would be more likely to literally eat themselves to death or to eat their conspecifics, which would not lead from ecological variation to ecological adaptations. Eating conspecifics would also not be likely to lead from ecological variation to mutation-initiated natural selection via any known conserved molecular mechanisms.

Therefore, in this Q & A, it quickly becomes clear that Lieff-via-Miller is addressing the first and most obvious need of all organisms, which involves natural selection of what to eat. If natural genetic engineering did not enable the ability to naturally select what to eat, it seems unlikely that it might somehow evolve.

However, bird watchers and butterfly collectors have continued to tout pseudoscientific nonsense in claims that the ability to naturally select what to eat did evolve. “It must have,” they claim. “We have observed that it did.” Therefore, since it is obvious to them that natural selection of what to eat is the RESULT of evolution, the ability to naturally select what to eat must also have somehow EVOLVED to cause evolution — via accumulated mutations, perhaps?

NO! Finally, Lieff-via-Miller attests to the obvious fact that organisms must naturally select what to eat or they cannot ecologically adapt and that means mutations do not enable species diversity. Mutations aren’t fixed in the organized genome of any species. Ecological variation and ecological adaptations via amino acid substitutions are responsible for species diversity. Mutations are responsible for pathology unless you’re a bird watcher or butterfly collector.

Anyone who has followed the blog posts by Jon Lieff has probably already concluded that he is a decade or more ahead of the understanding of his contemporaries. However, he is also helping them to catch up, which means that eventually he may be only a year or two ahead of them. At that point, others can ask him to help them get their grants funded so that scientific progress will no longer be stalled by the bird watchers and butterfly collectors.

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Cosmos and Feierman: Bamboozled Again

March 23, 2014 | James Kohl

Carl Sagan’s Two Warnings For Humanity In His Very Last Interview – You Might Want To Hear This

Excerpt: “One of the saddest lessons of history is this: If we’ve been bamboozled long enough, we tend to reject any evidence of the bamboozle. We’re no longer interested in finding out the truth. The bamboozle has captured us. It’s simply too painful to acknowledge, even to ourselves, that we’ve been taken. Once you give a charlatan power over you, you almost never get it back.” – Carl Sagan

My comment: Jay R. Feierman has been the charlatan / moderator of the International Society for Human Ethololgy’s yahoo group for more than 7 years. He continues to tout a ridiculous theory of evolution based on the biologically implausible role of mutations. For example:

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. 

All current extant literature attests only to the obvious role of ecological variation, which enables the ecological adaptations manifested in species diversity.

Foote et al (2013)Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].

Chung et al (2014) “…ecological divergence and mate choice may produce reproductive isolation and speciation….

Plucain  et al (2014) Ecological opportunities promote population divergence into coexisting lineages.

James V. Kohl: Evolution by natural selection cannot be the outcome if something is not first selected. Selection is always for nutrients. It is as simple as that.”

What explanation is there for Feierman’s refusal to accept what has become obvious about ecological variation to virtually everyone else? Why does he think mutations are somehow involved in species diversity, but that nutrient availability is not? Organisms that do not select food, do not vary from other organisms that have died from starvation. Why would anyone not realize that fact?

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 first encounter with Feierman led me to explain to him a mammalian model of hormone-organized and hormone-activated behavior. I was dumbfounded when after my conference presentation he asked “What about birds?” Although I had no reason to believe that the molecular mechanisms of hormone-organized and hormone-activated behavior varied across species, birds aren’t mammals. I can’t recall if I answered Feierman in 1995.

Experimental evidence has since linked ecological variation and selection for nutrients to ecological adaptations in birds. If experimental evidence did not link the conserved molecular mechanisms of biologically based cause and effect in all species, there would still be no evidence that human language is akin to birdsong in ecologically adapted birds. Instead, it has become clear that the nutrient-dependent  microRNA/messenger RNA balance links specific microRNAs (miRs) in birds (e.g. miR-9 and miR-140-5p) to the FoxP2 human ‘language gene[1].

For example, food rewards have been linked to hormone-organized and hormone-activated  neural circuitry and song neurons in Bengalese finches [2].  This link was expected, and nutrient-dependent pheromone production has also been linked to sexual selection in birds [3].

The link from nutrient uptake to pheromones that control the physiology of reproduction in birds and in humans links nutrient-dependent gene regulation in zebra finches from the social context of their singing behavior to the social context involved in the genetically predisposed development of human language via the same gene: FoxP2.

Conservation of the FoxP2 gene across mammals suggests that two amino acid substitutions differentiate the cell types associated with human language development from cell types with identical amino acid sequences in rhesus macaques, gorillas, and chimpanzees [4]. This is precisely what is expected in the context of conserved molecular mechanisms that epigenetically link species of microbes to man.

If Feierman understood anything at all about ecological adaptations, he probably would not continue to claim that I have an incorrect understanding of Darwin’s claims. Darwin wrote that ‘conditions of life’ must first be considered before natural selection is considered.

Whether the birds are singing or copulating and whether humans are talking about sex or ‘having it,” nutrient-dependent pheromone-controlled conserved molecular mechanisms of species diversity seem to underlie similarities and differences in species from microbes to man. Besides, nothing in the extant literature suggests that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.“ Instead, that statement suggests the question “What about birds?” is a foolish question. Obviously, Darwin’s ‘conditions of life’ apply to the birds and the bees and every other species.

Cited works

1.            Shi, Z.; Luo, G.; Fu, L.; Fang, Z.; Wang, X.; Li, X., miR-9 and miR-140-5p Target FoxP2 and Are Regulated as a Function of the Social Context of Singing Behavior in Zebra Finches. The Journal of Neuroscience 2013, 33 (42), 16510-16521. doi: 10.1523/jneurosci.0838-13.2013

2.            Seki, Y.; Hessler, N. A.; Xie, K.; Okanoya, K., Food rewards modulate the activity of song neurons in Bengalese finches. European Journal of Neuroscience 2014, 39 (6), 975-983. doi: 10.1111/ejn.12457

3.            Whittaker, D. J.; Gerlach, N. M.; Soini, H. A.; Novotny, M. V.; Ketterson, E. D., Bird odour predicts reproductive success. Anim Behav 2013, 86 (4), 697–703. doi: 10.1016/j.anbehav.2013.07.025

4.            Sherwood, C. C.; Subiaul, F.; Zawidzki, T. W., A natural history of the human mind: tracing evolutionary changes in brain and cognition. Journal of Anatomy 2008, 212 (4), 426-454. doi: 10.1111/j.1469-7580.2008.00868.x

 

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Cosmos: no facts; just theory

March 22, 2014 | James Kohl

Creationists demand equal airtime on Neil deGrasse Tyson’s ‘Cosmos’ to provide ‘balance’

By Travis Gettys
Friday, March 21, 2014 14:10 EDT

Excerpt: “Tyson recently said science reporting should not be balanced with nonscientific claims, so that seems unlikely he would offer that sort of fallacious argument on his own show.

“You don’t talk about the spherical Earth with NASA, and then say let’s give equal time to the flat Earthers,” Tyson told CNN. “Plus, science is not there for you to cherry pick.”

My comment: The entirety of neo-Darwism is based on cherry-picking of what population geneticists who bastardized Darwin’s theory have been telling us for the past 80 years. Darwin insisted that ‘conditions of life’ be given first consideration and population geneticists decided to forget ‘conditions of life’ and tell everyone that mutations somehow caused evolution. That’s not biologically plausible, but biological facts do not matter to theorists. They need only look at morphological differences to make their determination of cause and effect.

Yep, them there mutations did it; see here: the fawn-colored moths that ate the lead- and manganese leaves changed to peppered colored moths and predatory birds — not the pheromones of female moths — controlled the reproduction of the moths. And, if that’s not enough proof of mutation-driven evolution, just look at those folks with the mutated hemoglobin variant who have either sickle cell disease or the trait. If not for the mutation, they could not have evolved from other primates — unless dietary supplementation with fermented milk products containing higher levels of vitamin D stabilized their genome in areas where malaria is endemic. If that’s what happened, the sickle cell variant is like all other 1181 monoallelic hemoglobin variants, which are not mutations. But, like the theorist said, just look at the skin pigmentation in those folks. It’s like they were fawn colored moths that mutated into people with darker skin.

Enough sarcasm! Creationists do not need equal airtime. Neil deGrasse Tyson needs to learn about how ecological variation leads to ecological adaptations in species from microbes to man, and quit touting nonsensical theories that he thinks might be supported by experimental evidence. They never have been. The population geneticists just made up all their theories as if they were bird watchers and butterfly collectors.

“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!” Dobzhansky (1964)

Evidence of evolution from bird-watchers and butterfly-collectors probably should not be entered into evidence on Cosmos, or any other TV show.

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What causes evolution?

March 22, 2014 | James Kohl

See also: The irony and confusion of molecular epigenetics. This is a follow-up

Re: Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Escherichia coli

Abstract excerpt: “Ecological opportunities promote population divergence into coexisting lineages.”

My comment: I’ve attempted to discuss the change in this position, which is stated above — from previous claims about mutations and evolution to claims that ecological opportunities enable ecological adaptations associated with mutations. My attempts have failed for reasons that I think are exemplified in the following exchanges.

Sonny Williams: Kohl writes, “Richard Lenski’s group has all but abandoned the concept of mutations that somehow cause evolution.” This goes so far beyond Kohl’s frequent misrepresentation that it amounts to a blatant lie. Why do we permit someone who knowingly and repeatedly lies in posts to remain a member of this Yahoo discussion group?

Jay R. Feierman: Sonny, a lie is saying something that you know is false is true. If Kohl truly believes that Richard Lenski’s group “has all but abandoned the concept of mutations that somehow cause evolution” [sic] is a true statement, it is not lying. I actually don’t know what that phrase in quotes means because the grammar doesn’t make sense. I also don’t think that anyone believes that “mutations cause evolution.”

You can find many times when others have used the phrase: “has all but abandoned” in a google search. Feierman’s focus on my grammar is tactical. He knows that Lenski’s position has changed and knows the change conflicts with Feierman’s ridiculous stated belief that:  Random mutations are the substrates upon which directional natural selection acts. Thus, while Feierman did not say that “mutations cause evolution,” it is what he has clearly implied for several decades. The ridiculous claim that “mutations cause evolution”  is also implied in these statements from others…

Mutations are the ultimate source of heritable variation for evolution.

Mutations and genetic recombination provide the variation that fuels adaptation.

… and in the book title: Mutation-Driven Evolution

None of these claims are supported by experimental evidence. They are the claims typically made by population geneticists. The change in Lenski’s position, and what appears to be the change in position of Dominique Schneider, who is the senior author of “Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Escherichia coli” is clear —  in this excerpt: “…the ability of the S lineage to invade and coexist with the L lineage depended on both the ecological opportunity and synergistic interactions…

What causes evolution? There is across-species experimental evidence that ecological variation links the epigenetic landscape to the physical landscape of DNA in the organized genomes of all extant animal species. That’s obviously because epigenetic changes to DNA enable the maintenance of synergistic interactions among co-existing organisms in species from microbes to man. Therefore, the question arises: Does anyone know how mutations might lead to a stable polymorphism in any species?

The reason I asked that question was because Feierman had previously stated: Random mutations are the substrates upon which directional natural selection acts. Feierman’s reply was a  link to this article on mutations and evolution. Pictorial examples of moths and of sickle-cell disease misrepresent biologically-based cause and effect, but misrepresentations are all that people like Feierman have left.

I addressed the misrepresentations in an article I submitted that is currently under review. Feierman removed the next paragraph from my response to his link about mutations and evolution.

I wrote: The human sickle cell variant and the moth color morphs both exemplify how ecological variation and natural selection of nutrients results in sexual selection that involves the pheromone-controlled physiology of reproduction. Those facts have become clear with what has been learned about the importance of vitamin D to different human populations –especially where malaria is endemic — and also what’s been learned about the epigenetic effects of lead- and manganese-contaminated leaves in moth populations.

—————————————————————

My attempts to convey accurate information about biologically-based cause and effect have been thwarted by the moderator of the ISHE’s human ethology group. It seems unlikely that Feierman will ever allow the dissemination of any accurate information from me, and that he will continue to prevent discussion of any aspect of my model. However, two comments from him are all that’s necessary to reveal the nature of  his character and the change in his position.

1) Random mutations are the substrates upon which directional natural selection acts.

2) I also don’t think that anyone believes that “mutations cause evolution.

Those comments may be a fitting end to my participation on the ISHE’s yahoo group. Feierman’s behavior is so contemptible that I can only hope new ISHE leadership will end his tenure as the yahoo group’s moderator.

Nancy Segal and Jan Havlicek are now on the ISHE Board of Trustees. Both have expertise in genetics and olfaction. If they allow him to continue his reign of academic suppression, the ISHE’s position will continue to become clearer than it has already become since publication of the award-winning review: Human pheromones: integrating neuroendocrinology and ethology, which I co-authored with ethologists from Vienna. The article has been cited 78 times, but less than 5 times by anyone I know to be a member of ISHE.

We wrote: ” Human pheromones have more potential than any other social environmental sensory stimuli to influence physiology and, therefore, behavior.” Experimental evidence  in species from  microbes to man will continues to confirm that fact, whether or not people like Feierman allow others to learn anything new.

If the ISHE allows Feierman to continue as moderator, their position will become better known with each new review I publish.

Ignoring biological facts does not make them go away; it just makes the people who ignore them appear to be ignorant. Since I know that some of the people who are ignoring the biological facts are not ignorant, it seems that they want others to remain ignorant because people, like Feierman, who should know about the biological facts, don’t.

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Vitamin A causes mutations (or not)

March 21, 2014 | James Kohl

Vitamin A’s Influence on Immunity

Exposure to vitamin A in the womb influences immune system development and lifelong ability to fight infections, a mouse study shows.

By Ashley P. Taylor | March 19, 2014

Excerpt:  ”The present study is the first to suggest that this development can be altered by maternal behavior.”

My comment: There’s a model for that!  It links nutrient stress and social stress to mammalian immune system function and nutrient-dependent pheromone-controlled ecological adaptations via conserved molecular mechanisms in species from microbes to man.

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

Excerpt: “Embryos with retinoic acid receptor mutations had a smaller percentage of inducer cells than controls.”

My comment: That suggests the mutations do not contribute to adaptive evolution. Does anyone who is not a population geneticist think that mutation-driven evolution is biologically plausible?

Like all other experimental evidence, I think the results from this study show that ecological variation enables ecological adaptations. For contrast, only evidence from population genetics suggests that mutation-initiated natural selection is possible — and that evidence is not experimental evidence. Therefore, the idea that vitamin A causes mutations may seem like pseudoscientific nonsense to some molecular biologists, but not to those who believe in mutation-driven evolution.

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