Atoms to ecosystems: Evolutionary theory vs the coelacanth

Biodiversity: Life ­– a status report

“Species are disappearing quickly — but researchers are struggling to assess how bad the problem is.”

I want to eliminate some of the researcher’s struggles, but a moderator at Nature has blocked all my comments for several months, perhaps permanently. I think my past comments on articles, like this one, explain why other comments are blocked. In the past, I commented each time I saw a misrepresentation of biologically-based cause and effect. The misrepresentations are often found in their news features, which draw from publications in “Nature” and other well-respected sources of peer-reviewed information. Unfortunately, sometimes even peer-reviewed publications support ridiculous theories about the evolution of biodiversity. I suspect that “Nature” does not want critical comments on their representations of how biodiversity arose. For example, in the report published on December 10, 2014, Richard Monastersky wrote: “Of all the species that have populated Earth at some time over the past 3.5 billion years, more than 95% have vanished…”

He starts by setting up an argument for the evolution of biodiversity across 3.5 billion years. That argument has not been supported by experimental evidence of biologically-based cause and effect. Instead, evidence of at least one extant species attests to errors made by assuming that evolution occurred anytime during the past 65 million years. For example, Until 1938, the coelacanth was thought to have gone extinct with the dinosaurs 65 million years ago. This fact attests to the uncertainty about the past that is already incorporated into the Modern Synthesis, the evolutionary theory taught today.

Note, however, subtle changes to the Modern Synthesis are consistently being made to prevent the ridicule of theorists. They used to insist that mutations could somehow lead to increasing organismal complexity. But the nonsense about mutations is gradually disappearing and most of the nonsense about natural selection in the context of mutations has already disappeared. See for example: “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.” — Carl Zimmer (2013) However, the uncertainty from the past about how evolution might somehow have occurred have led to more uncertainty about the future.

Biodiversity: Life ­– a status report Excerpt 1) ““There is a huge uncertainty in projecting future extinction rates,” says Henrique Pereira, an ecologist…””

My comment: Errors made in representations of past extinction rates are exemplified by the coelacanth. They lead to uncertainty in projecting future extinction rates and the errors attest to problems associated with the pseudoscientific nonsense of population genetics. Without experimental evidence that links the epigenetic landscape to the physical landscape of DNA via what is known about physics and chemistry, pseudoscientists must guess about what already is understood by ecologists. They know that ecological variation leads to bio-physically constrained ecological adaptations.

For example, in my model of chemical ecology,  the conserved molecular mechanisms of bio-physically constrained nutrient-dependent amino acid substitutions are linked to cell type differentiation by the metabolism of nutrients to species-specific pheromones. The pheromones control fixation of the amino acid substitutions in the organized genomes of species from microbes to man. The nutrient-dependent pheromone-controlled physiology of reproduction links morphological and behavioral diversity across all species. An organism’s response to changes in the chemical ecology of its epigenetic landscape is enabled by the de novo creation of receptors. These creation of these receptors allows experience to dictate the organism’s response via the organisms innate ability to create the receptors that enable nutrient uptake. Unless you are an evolutionary theorist, you are more likely to attribute individual survival and species survival to nutrient uptake and the physiology of reproduction than to mutations.

If you are not an evolutionary theorist, you may already know that receptor-mediated behaviors are linked to biodiversity in species from insects to mammals. The behaviors appear to arise in the context of the nutrient-dependent chemistry of protein folding. Nutrient-dependent RNA-directed DNA methylation and RNA-mediated events link amino acid substitutions to the stability of protein folding in the DNA of organized genomes via alternative splicings of RNA linked to the de novo creation of olfactory receptor genes. But, I digress. What does “Nature” tell us about all this?

Richard Monastersky writes: “One approach is to develop comprehensive computer models that can forecast how human activities will alter ecosystems. These general ecosystem models, or GEMs, are in their infancy…”

My comment: Are general ecosystems in their infancy because pseudoscientists have assumed that extant species evolved across 3.5 billion years and that natural selection occurred in the context of extinctions? If so, it may be long past time to recognize the obvious role of ecological variation and nutrient-dependent ecological adaptation. For example, any species that cannot quickly adapt to ecological changes is already extinct. The coelacanth is not. WHY?

wrote in his comment about the article by Richard Monastersky:  “…apart from ecological modelling, what is critically needed is more effort in taxonomy.”
After my failed attempt to comment on the article, I also attempted to reply to that comment. I wrote: Taxonomy based on the nutrient-dependent de novo creation of receptors that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of all vertebrates via amino acid substitutions and GnRH seems to be a good place to start. http://www.sciencedirect.com/science/article/pii/S0016648014002986
My reply was blocked: “We are unable to post your comment because you have been blocked by Nature News. Find out more. Someday I might be inclined to find out more, but for now…
The link I provided is to GnRH receptors and peptides: Skating backward
Excerpt: “Skate and coelacanth are the only examples of animals with both type I and II GnRH receptors and all three peptide types, suggesting this was the ancestral condition in vertebrates.”
My comment: GnRH (gonadotropin releasing hormone) is the focus of my model. That fact suggests a model of chemical ecology could link taxonomy from the coelacanth to the skate via differences and similarities in the amino acid substitutions found in molecules of GnRH and GnRH receptors. Indeed, the differences in the amino acid substitutions might taxonomically link the epigenetic landscape to the physical landscape of DNA in organized genomes of species from microbes to man via an extant species, the coelacanth,  that researchers thought was extinct, unless they can explain why it is not.
I suspect the species ecologically adapted via the same conserved molecular mechanisms that link receptor-mediated behavior from nutrient uptake to the pheromone-controlled physiology of reproduction via feedback loops. There is a model for that!
There is no model for the evolution of biodiversity as it is portrayed in the context of neo-Darwinism. The Modern Synthesis assumed that mutations and natural selection of something led to the evolution of diversity or that evolution “just happened.” Theorists must now attempt to extract mutations from their theories, since serious scientists know that mutations perturb protein folding and amino acid substitutions stabilize it.
Still, extracting mutations from their theories leaves pseudoscientists likely to be the butt of jokes. Without mutations in their theory, how can they continue to claim that any species evolved. Clearly, in the context of feedback loops that link nutrient-dependent pheromone-controlled reproduction to RNA-medicated amino acid substitutions and biodiversity show that all species, including the coelacaths, must have adapted to ecological variation, which is why the adaptations are manifested in different morphological and behavioral phenotypes.
Indeed, a recent report attests to this fact. “Although the Type I receptors had previously been known only from mammals, we found full length sequences of this receptor type in the genomes of a coelacanth (Latimeria chalumnae) and a chimaera (the elephant shark Callorhinchus milii), as well as partial sequence orthologs in the genome of the little skate (Leucoraja erinacea)(see Additional file 1: Table S1 and below). Like the Type I receptor in mammals, those in coelacanths and chimaera lack the cytoplasmic tail, terminating at the same amino acid.”
That fact cannot simply be placed into the context of mutations and evolved biodiversity. Continuing to claim that evolution has occurred during millions to billions of years can be placed into the context of experimental evidence and biologically-based cause and effect that is irrefutable.
Attempts to refute the experimental evidence with arguments based on what was learned from population geneticists – in their day — would already have been dismissed if they had paid attention to one of their own. Dobzhansky (1973) wrote: “… 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.”
After the discovery of the coelacanth, a so-called “living fossil, theorists should have begun to pay more attention to claims about mutations. After 1973, theorists should have begun to ask questions about why nutrient-dependent pheromone-controlled RNA-mediated amino acid substitutions appear to be essential to the genomic stability of species from microbes to man.
Instead, this claim was made again, today: “The issue of human ‘pheromones’ is a controversial topic…. However, it is fair to say that, on balance, social odors play a much more subtle and much less critical role in human reproduction when compared to other mammals.” See: Introduction to the special issue on Chemosignals and Reproduction by Aras Petrulis. In Press, Accepted Manuscript, Available online 11 December 2014
Summary: Cell type differentiation occurs via conserved molecular mechanisms in species from microbes to man. It is nutrient-dependent and pheromone-controlled. The claim that social odors, which are commonly called pheromones in species from microbes to man, “…play a more subtle and much less critical role in human reproduction…” than they play in any other species is akin to claiming that food odors are less important to human reproduction.
Anyone who does not yet understand the difference between epigenetic effects of olfactory/pheromonal input on hormones and the affects of hormones on behavior should not make claims about biologically-based cause and effect. It has become too obvious that biologically-based cause and effect extends across all species. That includes those that are extinct and those that were thought to be extinct, like the coelacanth, and any that may become extinct due to the ignorance of theorists who continue to tout their pseudoscientific nonsense about the issue of human pheromones. It not a controversial topic among serious scientists. Only theorists claim that social odors play a less critical role in human reproduction than they play in the physiology of reproduction in other species. Only theorists are human pheromone-deniers.

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