Human ecological adaptations

By: James V. Kohl | Published on: February 1, 2014

ecological adaptations reported in the context of evolutionary theory

Science 31 January 2014: Vol. 343 no. 6170 pp. 471-472 
Human Evolution

Neandertals and Moderns Made Imperfect Mates

Ann Gibbons
Excerpt: “Finding traces of incipient speciation in human DNA is a stunning switch for biologists used to focusing on animals. “Seeing the signature of these rules of speciation in our own history is really amazing,” says speciation expert Daven Presgraves of the University of Rochester in New York.”

My comments to Science

1) (published 1/31/14): These results appear to conflict with previous reports of biologically plausible non-random experience-dependent receptor-mediated species divergence due to ecological variation and adaptations. At least two of those reports were co-authored by Dr. Akey.
The adaptations show up in nutrient-dependent pheromone-controlled differences in cell types, which appear to be due to alternative splicings of pre-mRNA and amino acid substitutions, and the adaptations also show up in chromosomal rearrangements like those recently reported in sparrows with different morphological and behavioral phenotypes (see Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes).
The differences in sparrows appear to be consistent with vertebrate-wide nutrient-dependent pheromone-controlled adaptations like those in the mouse-to-human example detailed in Kamberov et al (2013) and Grossman et al (2013) where a base pair change and single amino acid substitution showed up as differences in skin and hair, but also in teeth and mammary tissue in a population that arose during the past ~30,000 years in what is now central China.
Submitted on Thu, 01/30/2014 – 20:31
2) (published 2/1/14)
“…DNA from a small number of Neandertal ancestors might have been swamped later by the sheer abundance of modern human DNA.”
“Swamped” is an interesting word choice. Dr. Akey is senior author of the article with an abstract that states: ” We estimate that approximately 73% of all protein-coding SNVs and approximately 86% of SNVs predicted to be
deleterious arose in the past 5,000–10,000 years.”
Creationists might take that to mean the “swamping” occurred after a flood of Biblical proportions, which appears to be somewhat consistent with Dobzhansky’s “Creationist” belief. Clearly, however, that’s only if you place
his stated belief into the context of a shorter time frame, which enabled rapid ecological adaptations to occur via the nutrient-dependent pheromone-controlled physiology of reproduction, changes in base pairs, amino
acid substitutions, and chromosomal rearrangements.
“I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation.” — Dobzhansky (1973) in “Nothing in Biology Makes Any Sense Except in the Light of Evolution”
Somewhat like Dobzhansky, perhaps, I have been overwhelmed by the amount of experimental evidence that suggests food is the ecological variable which is naturally selected. If so, the selection of nutrient-rich foods might lead to “swamping” via ecological adaptations sans the theory of mutation-driven evolution.
Submitted on Sat, 02/01/2014 – 13:10
3) (published 2/2/14)
Adaptive changes during the past 10,000 to 5,000 years in genes associated with diet,immunity, skin pigmentation, and eye color were also recently reported in Olalde et al (2014):”Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European”.
Metabolic and immunological challenges appear to be reflected in epigenetically-effected ecological adaptations.  One adaptation appears to be the experience-dependent receptor-mediated ability to digest lactose.
That change and the other changes suggest an epigenetic effect of nutrient uptake was responsible for morphological and behavioral changes that could be sexually selected based on natural selection for food and its metabolism to species-specific pheromones that control the physiology of reproduction in species from microbes to man.
Submitted on Sat, 02/01/2014 – 22:35
I’ve also addressed a question posed in the context of the article.
4) published 2/3/14
In my model, the epigenetic effects of nutrient uptake and the metabolism of nutrients to species-specific pheromones link de novo creation of olfactory receptor genes in different cell types to infertility when spermatozoa are no longer able to “sniff out” an “egg” in invertebrates: Elekonich and Robinson (2000) and vertebrates: Diamond, Binstock and Kohl (1996).
If you look at the problem in the context of what we portrayed about the conserved molecular mechanisms at the advent of sexual reproduction in yeasts, you may see the continuum of ecological adaptations that began with
the nutrient-dependent pheromone-controlled chromosomal rearrangements that are required before sex chromosomes existed.
Submitted on Sun, 02/02/2014 – 14:34
In discussions elsewhere, I have asked that people address the perspective presented in the Science and Nature articles in the context of whatever opinion they have of how Mutation-driven evolution occurs.
Earlier, I provided this information in what has become an ongoing discussion of the topic:  Where is the proof in pseudoscience?

Mutation-Driven Evolution (p. 196): “Epigenetic control of development is very important…, alternative splicings of introns also plays an important role in generating polymorphic proteins…. These polymorphic proteins… are sometimes used for determining different developmental pathways, as in the case of sex determination in insects.”
Mutation-Driven Evolution (p. 196): “(1) Mutation is the source of all genetic variation on which any form of evolution is dependent… (2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation.”
I expect others to continue to ignore experimental evidence, despite Nei’s mention of it before he dismissed it and moved on to his statements of how mutation-driven evolution occurs. But, as you can see, he did not tell us anything about how mutation-initiated natural selection occurs. He says nothing about how  mutations are naturally selected. Mutations initiate and natural selection is an evolutionary process. What he’s telling us is that mutation-driven natural selection somehow occurs, which is a ridiculous theory to tout in a book-length version of more commonly touted nonsense.

See also: Diseases & disorders exemplify evolution
Note: As it becomes more difficult to deny that human ecological adaptations occurs via the conserved molecular mechanisms in species from microbes to man, Jay R. Feierman continues his attempts to prevent my model from being acknowledged by blocking many of my posts to the International Society for Human Ethology’s yahoo group. For example, yesterday he posted notice to the group of these publications: A game of thrones:Neural plasticity in mammalian social hierarchies (on social experience and neural plasticity) and Agency and Adaptation: New Directions in Evolutionary Anthropology (on phenotypic adaptation, cultural transmission, gene-culture coevolution, and niche construction.) 
He did not post 7 of my submissions, one of which was about: Single-molecule tracking of the transcription cycle by sub-second RNA detection

“FastFISH detection of nascent RNA, coupled to single-molecule detection of protein-DNA interactions will be particularly useful to study the dynamics of initiation, escape, elongation, and termination by multi-subunit RNAPs, and the coupling of the transcriptional steps to downstream RNA-processing events. The guidelines for designing fastFISH probe-target pairs can be used to efficiently detect endogenous RNAs in situ and in vivo, to silence gene expression, and to build novel nucleic acid nanostructures.”

Another submission was about The Makings of a Choosy Pathogen
The oomycete Phytophthora infestans is responsible for potato blight. A closely related pathogen afflicts the 4 o’clock flower. To assess why such similar pathogens are restricted to one host or the other, Dong et al. (p. 552; see the Perspective by Coaker) analyzed similar effectors from both pathogens. The results suggest that the host specialization that led to evolutionary divergence depends on reciprocal single–amino acid changes that tailor the pathogen effector to a specific host protease that is being disabled. Thus, small changes can open the door for a pathogen to jump to another species of host and, itself, diversify into another species of pathogen.

My comment: If evolutionary divergence resulted from single amino acid substitutions that were actually mutations, I would expect someone to explain how reciprocal mutations are involved in tailoring the required concurrent species-specific changes. Until then, the idea of concurrent reciprocal mutations in different species does not seem biologically plausible to me. Besides, I do not think that any experimental evidence supports the role of reciprocal mutations in ecological adaptations. Ecological variation leads to ecological adaptations via conserved molecular mechanisms in species from microbes to man, and that fact has been validated by experimental evidence. What biological facts have been included in theories of mutation-driven evolution? I’m only aware of the biological facts that have been excluded.

Researchers have moved quickly and are now examining biologically based cause and effect at levels from atoms to ecosystems. Feierman’s attempts to limit my dissemination of information that supports the model of cause and effect I have developed during the past few decades are as despicable as they have always been. The end result will be the same. Those who have continued to tout their nonsensical theories will be left behind, as they always have been when experimental evidence continues to support scientific progress and to expose the social pseuodoscience of theory.
Here is a recent 90 minute presentation about what is known at the atomic level of intracellular signaling.

Cellular Surgeons: The New Era of Nanomedicine

Addendum (2/2/14): In his despicable ongoing attempts to deny me credit for my refutation of mutation-driven evolution, Feierman has since posted links to these articles:
The evolutionary history of vertebrate cranial placodes I. Cell type evolution
The evolutionary history of vertebrate cranial placodes II. Evolution of ectodermal patterning
Single neuron dynamics and computation
Feierman’s behavior stems from our first encounter in 1995. After I explained the details of my model to him, he asked “What about birds?”  I have since portrayed that question in the context of how much nonsense evolutionary theorists have incorporated into their beliefs about mutation-driven evolution during the past decades of scientific progress, which has shown that conserved molecular mechanisms are responsible for ecological adaptations in birds and every other species on the planet.
Does anyone else still think it is likely to be mutations that are naturally selected to result in the evolution of neuronal cell types and the single neuron dynamics of computations that enabled nutrient-dependent pheromone-controlled what is now portrayed as the evolution of ectodermal patterning?   Is there a model for that?
See for example: Neural Crest Stem Cell-specific Deletion of the Pygopus2 Gene Modulates Hair Follicle Development

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