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microRNAs and species relationships

Posted on July 30, 2014 by James Kohl.

Flaws emerge in RNA method to build tree of life

Study finds problems with alluringly simple way to tease out evolutionary relationships through microRNA. Amy Maxmen 28 July 2014

Excerpt 1:  “…some pieces of RNA are only expressed at particular moments in an animal’s lifetime, whereas genes in the genome are steady.” Excerpt 2): “…microRNAs cannot alone unveil species relationships.”

My comment: Until earlier today, I was not aware that anyone had been touting the evolution of microRNA (miRNA) or that that the role of miRNAs was being examined outside the context of the miRNA/messenger RNA (mRNA) balance. This report simply characterized the statistical behavior and phylogenetic utility of miRNA data. The researchers have not linked biologically-based cause and effect to biodiversity or exposed any flaws in works that do link the epigenetic landscape to the physical landscape of DNA in organized genomes via nutrient-dependent changes in miRNAs.

Journal article excerpt: “MicroRNAs originate from random hairpin sequences in intronic or intergenic regions (typically 60–80 bp in length) of the genome that become transcribed into RNA (14, 15).”

Some of the miRNAs found in human cell types, appear to come from plants. If the origin of miRNAs is placed into the context of random hairpin sequences, everything known about biophysical constraints on the carbon-hydrogen bonds essential to nutrient-dependent protein folding is removed from consideration. Thus, in this journal article, the evolution of biodiversity appears to begin sometime after the theromodynamics of protein folding  and organism-level thermoregulation have been dismissed — as if the Laws of Physics were nothing more than suggestions.

I’m not sure what any evolutionary theorists think about the required link from physics to chemistry and molecular biology, but I’ve seen no experimental evidence that suggests miRNAs originate from random hairpin sequences in intronic or intergenic regions of the genome.

“Consistently, plant miRNAs were detected in various tissues, including liver, intestine and lung. Different plant miRNAs accumulated at different levels, which also varied from one tissue to another, but their levels could reach up to one tenth of the most abundant human miRNA.”

Plant miRNAs do not seem to automagically appear in the cell types of different tissues, however. Thus, what is currently known about the gene-cell-tissue-organ-organ system pathway and the interactome points to functional miRNA/mRNA targets across genes in networks of genes that interact and link our nutrient-dependent metabolism via the circulatory system to miRNA functions in brain

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Yeast Genetics Meeting

Posted on July 29, 2014 by James Kohl.

The “Yeast Genetics Meeting” starts 7/29/14 and presenters will establish the unequivocal fact that the epigenetic landscape is linked to the physical landscape of DNA in the organized genomes of species from microbes to man via the conserved molecular mechanisms of nutrient-dependent pheromone-controlled reproduction. The pseudoscientific nonsense about mutation-initiated natural selection in the context of evolved biodiversity will be replaced with experimentally established biologically-based facts about how ecological variation and biophysically-constrained nutrient-dependent amino acid substitutions differentiate all cell types in all individuals of all species via the pheromone-controlled physiology of reproduction, which results in ecological adaptations.

See the Schedule of Events. Links to presentation abstracts are included. The presentations are being made to serious scientists who understand molecular biology and why Dobzhansky (1964) referred to those who do not understand molecular biology as “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!”

The poster presentation abstracts can be viewed at this link: Poster Session Listing

My comments on the posters that appeared to be particularly pertinent to what is known about Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems were removed from the Evolutionary Psychology News facebook page when an antagonist finally realized that neo-Darwinism was about to be eliminated from consideration via the presentation of facts that include: Kohl’s Laws of Biology

“Life is nutrient-dependent. That is a Biological Law. The ecological origin of all biological laws is apparent 1) in the context of systems biology ; 2) in the context of the metabolism of nutrients by microbes ; and 3) in the context of how the metabolism of nutrients results in species-specific pheromones that control the physiology of reproduction . Taken together, the systems biology of nutrient metabolism to species-specific pheromones, which control the physiology of reproduction, can be expressed in a summary of Kohl’s Laws of Biology: 1) Life is nutrient-dependent. See for review . The physiology of reproduction is pheromone-controlled. See for review . In the context of nutrient-dependent epigenetically-effected human reproduction, it is clearer that the epigenetic effects of human pheromones integrate neuroendocrinology and behavior , which includes the neuroendocrinology of mammalian behavior associated with the development of sexual preferences .”


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Comparing scientific claims

Posted on July 24, 2014 by James Kohl.

The Christian right’s 5 worst scientific claims

Excerpt: “This method of conducting science has led the Christian right to make some incredible — as in, not credible – scientific claims in the past, almost too many to document.”

My comments:  Evolutionary theorist’s worst misrepresentations of the Christian right’s scientific claims continue to be substituted for experimental evidence of biologically-based cause and effect that might otherwise support the pseudoscientific claims of social scientists. Attacks like this one commonly show up in discussion groups where theory is touted but scientific facts are never discussed. For example, see: Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins

Abstract excerpt:  “…cryptophytes have evolved a structural switch controlled by an amino acid insertion to modulate excitonic interactions and therefore the mechanisms used for light harvesting.”

My comment: The article also states “This strong connection between structural biology and physics means that ultrafast light-harvesting functions are under genetic and evolutionary control.”My claim: Amino acid insertions differentiate cell types of individuals of all species (see for examples in primates Dobzhansky, 1964 and in 1973: “Nothing in Biology Makes Any Sense Except in the Light of Evolution.” Attributing the control of ultrafast light-harvesting functions to genetics and evolution eliminates the epigenetic effect of light on amino acid substitutions in the context of “Let there be light” from Biblical Genesis.Eliminating the epigenetic effect of light on amino acid substitutions also eliminates the de novo creation of olfactory receptor genes that links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via conserved molecular mechanisms that are biophysically-constrained.

The misrepresentations of scientifically established cause and effect by evolutionary theorists led to this claim in a book published on June 14, 2013: “… genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.

For contrast, “Nutrient-dependent/pheromone-controlled adaptive evolution: a model” was published on the same day and it attests to the obvious link from ecological variation to ecological adaptations via amino acid substitutions with examples of biologically based cause and effect in different model organisms.

My conclusion: Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.Evolutionary theorists have had the opportunity for more than a year to compare …

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New trees of life

Posted on July 23, 2014 by James Kohl.

Untangling spider’s webs: Largest-ever study of spider genetics shows orb weaver spiders do not share common origins

Emphasis: “…contrary to long-held popular opinion, the two groups of spiders that weave orb-shaped webs do not share a single origin.”

My comment: Dobzhansky (1964) attested to the problem that evolutionary theorists have continued to incorporate into their skewed perspectives on biologically-based cause and effect. “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!”

Obviously, comparisons cannot be made based only on morphological phenotypes.

If the two groups of spiders do not share a single origin, what species do share a common origin?

In the journal article, compositional homogeneity in all of the amino acids and taxa included was addressed in the context of morphological similarities and behavioral diversities. The differences in the behavior of spiders is thereby readily linked to nutrient-dependent pheromone-controlled amino acid substitutions and cell type differentiation manifested in in the morphology and receptor-mediated behavior of white-throated sparrows.

This “…novel and radical hypothesis of spider evolution…” does more than simply “…set the roadmap toward an until-now elusive spider tree of life.” It reasserts a fact that evolutionary theorists refuse to accept. “Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).” — Kohl (2012)

See also: Organismal biologists needed to interpret new trees of life. “…biologists will best advance science if they ensure their proposals are consistent with evolutionary trees that are well supported by molecular data, if they look for incompatible evidence and obvious difficulties, and if they evaluate alternative scenarios, as well as their preferred ones.”

Nutrient-dependent pheromone-controlled ecological adaptations via amino acid substitutions that differentiate cell types in species from microbes to man is the only proposal that is consistent with what is known about how ecological variation results in the morphological and behavioral phenotypes of all species. Evolutionary trees need not be given further consideration because they have never consistently been linked by evidence of biologically-based cause and effect to biodiversity. biologists will best advance science if they ensure their proposals are consistent with evolutionary trees that are well supported by molecular data, if they look…
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Evolution of sex differences in cell types: more pseudoscientific nonsense

Posted on July 23, 2014 by James Kohl.

Demography can favour female-advantageous alleles

Excerpt: “Models with coevolution of local adaptation and dispersal very rarely include sexual reproduction , even though local variation in sex ratio have been identified as increasing extinction risks and can be a significant source of selection for or against dispersal .”

My comment: Evolutionary theorists seem to largely ignore the fact that sex differences in cell types are nutrient-dependent and pheromone-controlled, which means they must first be considered in the context of genetically predisposed natural selection for ecological variation in nutrients. In the context of natural selection for food, there is no such thing as the evolution of sex differences in cell types. Sex differences are based on the ability of odors to induce the de novo creation of olfactory receptor genes in other organisms, yeasts are a model organism for the differentiation of all cell types via conserved molecular mechanisms that link microbes to man.

For information about the nutrient-dependent advent of sex differences in the cell types of yeasts, which links conserved molecular mechanisms to sexual differentiation in cell types of all other species see: Gene duplication as a mechanism of genomic adaptation to a changing environment:  “One of the main duplicated gene families are the olfactory receptor proteins so perhaps their duplication may lead to an increase in sensitivity to a particular odour may be adaptive under certain conditions.”

Ignoring the conserved molecular mechanisms of sex differences in cell types has led evolutionary theorists to a dead end when it comes to attempts to explain homosexual orientation, which is probably the reason models of coevolution rarely include sexual reproduction. Besides, the claim that “Demography can favour female-advantageous alleles” has already been placed into the context of nutrient-dependent sex differences in cell types and the pheromone-controlled physiology of sexual reproduction in yeasts by serious scientists.

For example see: From Fertilization to Adult Sexual Behavior “Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.”

If you think that models of …

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