Chromosomal rearrangements and hibernation

July 31, 2014 | James Kohl

Prepped for the Long Sleep

Hibernation-related proteins are common even in non-hibernating animals, a study shows.

By Jyoti Madhusoodanan | July 30, 2014

Article excerpt: “These genes clustered on the same chromosome fairly near to one another, leading the researchers to at first believe they were conserved throughout mammalian evolution. But the researchers did not find these genes in the mouse, rat, dog, chicken, and human genomes.”

My comment: In the context of mutation-initiated natural selection and the evolution of biodiversity, do mutations lead to conserved chromosomal rearrangements in some mammals but not in others? I ask because of comments by PZ Myers from his attack on John A. Davison, which prefaced his attack on me.

Evolution was all due to chromosome rearrangements, which somehow are not mutations, and he also somehow ignored the existence of allelic differences between species:

In my model, the allelic differences between species of mammals and all vertebrates and invertebrates are nutrient-dependent and pheromone-controlled like they are in other species from microbes to man. Ecological variation leads to nutrient-dependent alternative splicings of pre-mRNA and pheromone-controlled amino acid substitutions that differentiate cell types, which are manifested in morphological and behavioral phenotypes.

What experimental evidence of biologically-based cause and effect led to PZ Myers attacks, and why didn’t he tell anyone about the biological basis for his ridiculously pseudoscientific opinion?

How can scientific progress be made if people like PZ Myers do not explain how experimental evidence led to their claims that serious scientists, like Dobzhansky are cranks?   “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.” (1973)

Read more

microRNAs differentiate neuronal cell types

July 31, 2014 | James Kohl

microRNAs: key triggers of neuronal cell fate

Excerpt: “In light of the fact that miRNAs have very precise expression patterns depending on the cell type, tissue and/or developmental stage; it is challenging to generalize a single mechanism to regulate their expression and to identify the target genes that each miRNA has during each stage of neurogenesis. Thus, the combination of bioinformatic tools and experimental techniques will help in the study of miRNAs role in early neurogenesis and how they, their target genes, and their regulators are integrated within the regulatory gene expression networks that determine each particular neuronal phenotype.”

My comment: In my model, the nutrient-dependent microRNAs (miRNAs) are the key triggers of all cell type differentiation in all cells of all individuals of all species. The epigenetically effected miRNA/messenger RNA (mRNA)  balance controls cell type differentiation by the metabolism of nutrients to species-specific pheromones. The physiology of reproduction is controlled by pheromones, which allows ecological variation to lead to ecological adaptations via the supply of nutrients. Simply put, microRNAs differentiate cell type via the pheromones that control the nutrient-dependent physiology of reproduction, which controls nutrient-dependent biodiversity.

Although it is becoming clear that Convergent microRNA actions coordinate neocortical development via cell type differentiation that is nutrient-dependent and pheromone-controlled, not all researchers agree that cell type differentiation should be removed from the context of mutation-initiated natural selection and the evolution of biodiversity. For example: in  A critical appraisal of the use of microRNA data in phylogenetics, the authors seemingly claim “…a Bayesian statistical approach that explicitly models the process of miRNA evolution may reveal the uncertainty of phylogenetic studies…” See also: Flaws emerge in RNA method to build tree of life.

By focusing on the evolution of microRNAs and statistics that link them to differentiation of cell types during different developmental stages in different species, the nutrient-dependent nature of the microRNAs that differentiate the cell types of all individuals in all species during their development is removed from consideration. There is no mention of nutrient-dependent pheromone-controlled epigenetic effects on microRNAs that link food odors to changes in the microRNA/messenger RNA balance and amino acid substitutions that differentiate cell types.

Thus, the most parsimonious and well detailed explanation of how ecological variation results in nutrient-dependent pheromone-controlled cell type differentiation via amino acid substitutions: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems, is replaced prior to its publication with statistical analyses that eliminate half of what occurs in the context of biologically-based cause and effect. Instead, we see another article that attributes biodiversity to mutation-initiated natural selection, which includes evolution of the human brain and behavior, or to some other theory with no explanatory power as first noted in the context of the prepublication of another work Estimating Phylogeny from microRNA Data: A Critical Appraisal.

It seems likely that “…a Bayesian statistical approach that explicitly models the process of miRNA evolution…” may convince evolutionary theorists that they can continue to tout the pseudoscientific nonsense of their theories based on what “… may reveal the uncertainty of phylogenetic studies…” unless the phylogenetic studies are placed into the context of what Dobzhansky (1973) noted in “Nothing in Biology Makes Any Sense Except in the Light of Evolution: “…the so called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.”

That parsimonious fact links nutrient-dependent pheromone-controlled ecological adaptations in yeasts to humans via the conserved molecular mechanisms of amino acid substitutions and cell type differentiation. See for examples: Signaling Crosstalk: Integrating Nutrient Availability and Sex and Feedback loops link odor and pheromone signaling with reproduction. Also, anyone who thinks that flaws have emerged in the method by which alternative splicings of pre-mRNA and amino acid substitutions that determine cell type differentiation in species from microbes to man is encouraged to look at the abstracts from presentations at the Yeast Genetics Meeting.

For example: Elucidating the Effects of Human Genetic Variation On Vitamin D Signaling links microbial fermentation of grains and yeasts from light-induced amino acid substitutions in plants and algae to the nutrient-dependent pheromone-controlled physiology of human reproduction via the conserved molecular mechanisms we detailed in our 1996 Hormones and Behavior review and adding the link across species to differentiation of cell types by vitamin-induced and sunlight-induced amino acid substitutions.

 

 

 

Read more

microRNAs and species relationships

July 30, 2014 | 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

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.  Changes in the nutrient-dependent miRNA/mRNA balance can therefore be linked via conserved molecular mechanisms of the nutrient-dependent pheromone-controlled physiology of reproduction to behavior in species with circulatory systems.

In my model, for example, nutrient-dependent pheromone-controlled ecological adaptations link ecological variation to pieces of RNA that are only expressed in some individuals of some species at particular moments in their lifetime.  The miRNA/mRNA balance changes with nutrient uptake in invertebrates and vertebrates which is how intercellular links the base pair changes and amino acid substitutions to cell type differentiation and ecological adaptations.

Abstract: This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

——————————————————————————————————–

Reports that characterize the statistical behavior and phylogenetic utility of miRNA data may make it appear that random hairpin sequences in intronic or intergenic regions of the genome that become transcribed into RNA are somehow linked to biodiversity. However, serious scientists know that nutrient-dependent changes in the miRNA/mRNA balance link ecological variation to ecological adaptations via conserved molecular mechanisms of alternative splicings, amino acid substitutions, and cell type differentiation in species from microbes to man.

Read more

Yeast Genetics Meeting

July 29, 2014 | 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 [91]; 2) in the context of the metabolism of nutrients by microbes [157]; and 3) in the context of how the metabolism of nutrients results in species-specific pheromones that control the physiology of reproduction [158]. 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 [2, 31]. The physiology of reproduction is pheromone-controlled. See for review [30]. In the context of nutrient-dependent epigenetically-effected human reproduction, it is clearer that the epigenetic effects of human pheromones integrate neuroendocrinology and behavior [104], which includes the neuroendocrinology of mammalian behavior associated with the development of sexual preferences [159].”

 

Read more

Comparing scientific claims

July 24, 2014 | 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 their claims about constraint-breaking mutations to what serious scientists know about biophysically-constrained ecological adaptations that are clearly linked from ecological variation via nutrient-dependent pheromone-controlled amino acid substitutions. Instead, we will probably continue to see the severity of their attacks increase as they are backed into a scientific corner from which they cannot emerge with their ridiculous theories about mutations and natural selection intact.

The refutations of evolutionary are in the news with a new refutation appearing almost daily. For example: This study is a great step towards the identification of genes related to olfaction stemming from the increasing number of sequenced mammalian genomes,” said Sergios-Orestis Kolokotronis, an assistant professor of biology at Fordham University in New York City, who was not involved in the study.”

Conserved molecular mechanisms can be compared to pseudoscientific nonsense about constraint-breaking mutations in any species or in all species (e.g., from insects to elephants). SIR – (Z)-7-dodecen-l-yl acetate is used by the females of more than 126 species of insects, especially Lepidoptera, as part of their pheromone blends to attract insect males1. Female Asian elephants, Elephas maximus, also use a pheromone to signal to males their readiness to mate2.”

For comparison, here is the only immediate challenge to my statement (with my emphasis)  thatEvolutionary 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.”

Response (with my emphasis): Your claims about “all” evolutionists are false and a lie.

Note the change from evolutionary theorist’s to evolutionists.

Perhaps someone with more personal integrity will answer this question: Which evolutionary theorist claims that ecological variation leads to ecological adaptations via the conserved molecular mechanisms of biophysically-constrained cause and effect in species from microbes to man?

Dobzhansky (1973) did that, but he claimed to be a Creationist and an Evolutionist, not an evolutionary theorist.

Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed “the blind watchmaker.” To some extent, it just happens.”

Attempts have failed each time I have asked any evolutionary theorist to explain how they think the observable complexity of biodiversity arose in the context of what might be considered by any molecular biologist (e.g, since Dobzhansky) to be biologically plausible. Thus, Dobzhansky’s (1964) denigration of evolutionary theorists appears to have stood the test of time (50 years). He 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!

I am merely seconding that notion about all evolutionary theorists because the claim has gone unchallenged for too long. If Dobzhansky’s claim was false or if he deliberately lied, someone should have by now defended evolutionary theorists by providing experimental evidence of biologically based cause and effect to support their theories about mutations, natural selection, and the evolution of biophysically-constrained biodiversity. Claims that I am a liar or that I am making false claims have never been supported by experimental evidence of biologically-based cause and effect. That’s why others are attempting to elicit answers from evolutionary theorists in the context of Dobzhansky’s works.

See for example: Combating Evolution to Fight Disease

Excerpt: “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.”

My 7/15/14 comment (#2) published to the Science Magazine site: Re: “Molecular biology and evolutionary biology have been separate disciplines and scientific cultures: The former is mechanistic and focused on molecules; the latter is theoretical and focused on populations.” Now see: A mechanistic link between gene regulation and genome architecture in mammalian development  for the refutation of neo-Darwinian pseudoscientific nonsense.

Experimental evidence of biologically-based cause and effect does not support ideas about mutations, natural selection, and the evolution of biodiversity.

Experimental evidence of biologically-based cause and effect supports the fact that ecological variation leads to nutrient-dependent pheromone-controlled ecological adaptations in species from microbes to man via conserved molecular mechanisms.

My 3/17/14 comment (#1) published to the Science Magazine site:

Darwin probably anticipated the insemination of population genetics that led to the bastardization of his detailed observations in the “Modern Synthesis.” He politely insisted that ‘conditions of life’ be considered before natural selection.

There are two ‘conditions of life.’ It is nutrient-dependent and pheromone-controlled. Rosenberg and Queitsch now note the work with Dobzhansky’s rarely acknowledged claim: “I am a creationist and an evolutionist.” They also declare the need for “Deep understanding of the mechanisms that generate variation at the molecular level…”

Deep understanding of the ‘conditions of life’ does not come from theory.

Problems with the “modern synthesis” now lead us back to the facts about biologically-based cause and effect that Darwin and Dobzhansky approached with humility, which are the same biological facts that evolutionists approached with ignorance about behavioral affects and the arrogance that accompanies that ignorance. Rosenberg and Queitsch echo the sentiments of those who have been subjected to academic suppression.

Clearly, however, “nothing in evolution makes sense except in the light of biology” is not an exaggeration. It is a common sense statement about the biologically plausible genesis of functional cell types. Population genetics and evolutionary theories abandoned the biophysical constraints of ecological variation and the physiology of reproduction, which enable epigenetically-effected nutrient-dependent pheromone-controlled receptor-mediated ecological adaptations and species diversity via the complexities of protein folding and niche construction.

It’s time for biophysicists to tell theorists and pathologists how to differentiate between theories about the genesis of different cell types and the biological facts about the nutrient-dependent pheromone-controlled ecological adaptations that enable the genesis of different cell types in individuals of different species. Simply put, it’s time to stop trying to explain ecological adaptations in the context of mutations and evolution.

My 7/24/13 conclusion to this blog post: A special issue on “The integration of evolutionary biology with physiological science” was published on June 1, 2014. See the table of contents:

Evolutionary theorists have had more than 50 years to respond to claims made about amino acid substitutions by Dobzhanzky that have been reiterated by me and by others who have no model that links atoms to ecosystems but who have somewhat blindly continued to present new experimental evidence from molecular epigenetics that refutes pseudoscientific nonsense when it is integrated into a model.  Claims that serious scientists are making false claims or that they are lying should be viewed in the context of scientific claims based on experimental evidence.

Clearly, the evolutionary theorists have never been more than bird-watchers or butterfly collectors. If they were anything more than pseudoscientists, they would be attempting to explain how biodiversity arose — as I did in the context of nutrient-dependent pheromone-controlled cell type differentiation that links ecological variation via amino acid substitutions, which are manifested in the morphological and behavioral phenotypes of all ecologically adapted species via the conserved molecular mechanisms of the nutrient-dependent pheromone-controlled physiology of reproduction.

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

Abstract: This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

Video representation (5.5 minutes) Published to figshare. com on 10 Oct 2013 Nutrient-dependent / pheromone-controlled thermodynamics and thermoregulation

Read more
Page 3 of 21012345...102030...Last »