Diseases & disorders exemplify evolution

By: James V. Kohl | Published on: January 30, 2014

Neanderthal DNA hides in genes dictating our hair, skin

Researcher ‘quite proud’ of his above-average 2.9% Neanderthal genome
The Associated Press
Posted:Jan 29, 2014 3:50 PM ET
Excerpt: Harvard researcher Sriram Sankararaman, the lead author of the Nature study, said the place where Neanderthal DNA seemed to have the most influence in the modern human genome has to do with skin and hair. Akey said those instructions are as much as 70 per cent Neanderthal.
See: Resurrecting Surviving Neandertal Lineages from Modern Human Genomes
1) “To identify surviving Neandertal lineages, we developed a two-stage computational strategy…”
2)  ”This “fossil free” paradigm of sequencing archaic genomes holds considerable promise to reveal insights into hominin evolution, the population genetics characteristics of archaic hominins…”
My comment: The “fossil free paradigm” and insights revealed by populations genetics have become problematic because mutation-driven evolution appears to be proceeding too rapidly.  Joshua Akey has co-authored other articles that address the problem.
1) Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants
Excerpt: “Of the putatively deleterious protein-coding SNVs, 86.4% arose in the last 5,000 to 10,000 years, and they are enriched for mutations of large effect (Supplementary Fig. 14) as selection has not had sufficient time to purge them from the population.
My comment: This assumes only that deleterious mutations are purged, not that beneficial mutations exist or that they are somehow naturally selected to become fixed in the DNA of organized genomes.
2) Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution
Excerpt: “…simultaneous encoding of amino acid and regulatory information within exons is a major functional feature of complex genomes.”
My comment: Simultaneous encoding of regulatory information that leads to SNVs and the alternative splicings of pre-mRNA; fixed amino acid substitutions; and chromosomal rearrangements in my model, such as the achiral glycine substitution in the vertebrate gonadotropin releasing hormone (GnRH) decapeptide, enables rapid ecological adaptations without mutations. For example, the amino acid substitution in GnRH links olfactory/pheromonal input from the epigenetic landscape to the physical landscape of DNA in the organized genomes of all vertebrates via their nutrient-dependent pheromone-controlled physiology of reproduction.
No experimental evidence suggests that beneficial mutations are fixed in the DNA of any organized genome in any species. Mutations may or may not be removed but there are no fixed beneficial mutations that can be selected in any complex genomes. See Chelo et al (2013) for the only experimental test of that unsubstantiated hypothesis. (Note their experimental test was on the C. elegans model organism: The genome is small compared to humans (about 30 times smaller), yet it encodes over 22,000 proteins, only slightly fewer than humans. About 35% of C. elegans genes are closely related to human genes.)
See: The genomic landscape of Neanderthal ancestry in present-day humans
Excerpt: “The evidence for male hybrid sterility is particularly remarkable when compared with mixed populations of present-day humans in which no convincing signals of selection against alleles inherited from one of the mixing populations have been found…”
My comment: The focus on evidence for male hybrid sterility is particularly remarkable when compared to the lack of evidence to support the null hypothesis. The null hypothesis was typically accepted by evolutionary theorists in the context of the Bateson-Dobzhansky-Muller (BDM) proposal. Hybrid sterility and inviability are supposedly caused by incompatible alleles, which are also supposedly alternatively fixed in two previously geographically isolated populations. The BDM proposal excluded ecological factors but it was so straightforward that it became the null model of speciation. Blind acceptance of that proposal meant that my model of nutrient-dependent pheromone-controlled ecological adaptations and chromosomal rearrangements that lead to sex differences and other differences in cell types and to species diversity controlled by the nutrient-dependent physiology of pheromone-controlled reproduction has been largely ignored. In these two recent reports, it is also ignored in “Science” and in “Nature”.
The nature of scientific pursuits is that it does not ignore experimental evidence that does not fit with the theoretical approach of population genetics. What then can be said about a textbook author who previously stated with a co-author: “…we will not consider geographical and ecological factors because of space limitation. Our primary purpose is to clarify the roles of mutation and selection in the evolution of reproductive isolation and show that the molecular basis of speciation is more complicated than generally thought at present.” Did the failure to consider ecological factors lead to book publication of Mutation-Driven Evolution?
Excerpt:  ”(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. It does not have any creative power in contrast to the statements made by some authors.” p 196.
My comment: Did someone else mention skin and hair? I did in the context of the mouse-to-human model of ecological adaptations. I also mentioned teeth and mammary tissue. See, for example:  Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
Excerpt: ”These two reports (Grossman et al., 2013; Kamberov et al., 2013) tell a new short story of adaptive evolution. The story begins with what was probably a nutrient-dependent variant allele that arose in central China approximately 30,000 years ago. [Note: Neanderthals became extinct about 30,000 years ago.] The effect of the allele is adaptive and it is manifested in the context of an effect on sweat, skin, hair, and teeth. In other mammals, like the mouse, the effect on sweat, skin, hair, and teeth is due to an epigenetic effect of nutrients on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones control the nutrient-dependent hormone-dependent organization and activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates as previously indicated. That means the adaptive evolution of the human population, which is detailed in these two reports, is also likely to be nutrient-dependent and pheromone-controlled, since there is no other model for that.”
My comment: The latest works published in Science and in Nature ignore the fact that there is no experimental evidence to support a mathematical model of mutation-initiated natural selection or mutation-driven evolution.  The latest works published in Science and in Nature ignore the fact that my model is biologically plausible and ecologically validated across species via experimental evidence that links the sensory environment to amino acid substitutions. The amino acid substitutions appear to result in de novo gene creation and the chromosomal rearrangements that link nutrient-dependent pheromone-controlled adaptations in birds and in bees to their morphological and behavioral phenotypes sans mutations.
Perhaps researchers should ignore the latest works published in Science and in Nature and not ignore my model.  At some point, the level of ignorance becomes unbearable to anyone with enough common sense to realize that Darwin’s ‘conditions of life’ have always been nutrient-dependent and pheromone-controlled. The diversity of life is not likely to be the result of mutations that perturb the biophysics of protein folding and cause diseases and disorders associated with the thermodynamics of nutrient stress, social stress, and organism-level thermoregulation even if mathematical models indicate that mutation-driven evolution is possible. That long-standing but largely untested hypothesis is NOT biologically plausible nor has it been ecologically validated by experimental evidence.

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