‘Residual diversity estimates’ do not correct for sampling bias in palaeodiversity data

Abstract excerpt:

Evolutionary dynamics such as speciation are inherently a phylogenetic process, and only an explicitly phylogenetic approach will correctly model this process.

Reported as: Flawed analysis casts doubt on years of evolutionary research

The method assumes that variations in the number of different fossils at any given time are a reflection of how much rock was available. It has been used in more than 150 published research papers since it was first used in 2007.

For comparison: No assumptions about the fossil record are include in more that 54,000 published articles that link energy-dependent changes in the microRNA/messenger RNA balance to all biodiversity via the physiology of reproduction in all living genera.

See: microRNA

See also:

Published on 3 May 2016

Abstract:

Olfaction and the innate immune system link energy as information from the epigenetic landscape to the physical landscape of supercoiled DNA. The sun’s biological energy is the source of the information that links angstroms to ecosystems via physics, chemistry, and molecular epigenetics.

RNA-mediated protein folding chemistry and amino acid substitutions link the anti-entropic quantized energy of sunlight from the virucidal effects of ultraviolet (UV) light to healthy longevity via biophysically-constrained energy-dependent hydrogen-atom transfer in DNA base pairs in solution and cell type differentiation.

Biomarkers link energy-dependent differences in base pairs and amino acid substitutions to biosignatures across the healthy life span. RNA-mediated amino acid substitutions also reveal the increasing complexity of interactions among cell types as pathology progresses. For comparison, successful reproduction links energy from supercoiled DNA to protection of all organized genomes from virus-driven energy theft and pathology.

This model links the sun’s biological energy from top-down causation in microbes to the most recent model of bottom-up gene activation and cell type differentiation in vertebrates. Citations to extant literature provide examples of what is currently known about how ecological variation leads to biophysically constrained cell type differentiation in the context of nutritional epigenetics and Precision Medicine, which clearly link metabolic networks and genetic networks to pharmacogenomics.

See for comparison: Published on 26 Aug 2016

Description:

On July 11th 2002, then-Representative Mike Pence testified before the House of Representatives that public schools should teach the theory of evolution as if it were only one of multiple hypotheses regarding the origins of species. Now that Trump the Chump has chosen Pence the Dense as his vice presidential running mate, I felt obliged to address now-Governor Pence’s willful ignorance and deliberate misrepresentation of evolution.

He claims there is no other theory, but he also ignores publication of my model on June 14, 2013 for comparison to the textbook misrepresentations published in Mutation-driven evolution on the same day.

Similarly, in his Criticisms of the nutrient-dependent pheromone-controlled evolutionary model,  Andrew Jones cites Mutation-driven evolution, but does not provide an alternative model of biologically-based cause and effect.

Excerpt:

Based on his writings, both published and unpublished, James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research. It was a mistake to let such a sloppy review through to be published. Note: I concluded “…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

My comment: There is still no other model for comparison, and neo-Darwinian theory has been invalidated by all experimental evidence of biologically-based cause and effect. At every level of examination, serious scientists have linked energy-dependent changes from angstroms to ecosystems without the pseudoscientific nonsense about mutations and natural selection or evolution.

For comparison, this blog site focuses on mathematical models of observed phylogenetic differences. Reason Advocates.

If I were as biologically uninformed as this fool is, I would not have a blog site to advertise my ignorance via attacks on creationism.

He would only need to read one published work before he was forced to revise his ridiculous claims.

See: The phylogenetic utility and functional constraint of microRNA flanking sequences which was reported in advance as: All in the (bigger) family.

My comment:

The 2015 Society for Integrative and Comparative Biology (SICB) presenters may not recognize how much progress has been made since the 2013 ecological epigenetics symposium. For example, since then authors claimed “…ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.” http://dx.doi.org/10.1038/nature13400

Six months later, other authors traced signaling factors found in vertebrates to the origin of nerve cell centralization via the diffuse nerve net of animals like the sea anemone. http://dx.doi.org/10.1038/ncomms6536 That fact suggests ecological variation is linked to ecological adaptations in morphological and behavioral phenotypes via signaling protein concentrations that differentiate various cell types in body axes and the central nervous system.

Links across species from the epigenetic landscape to the physical landscape of DNA in organized genomes appear to have their origins in the conserved molecular mechanisms of  RNA-directed DNA methylation and RNA-mediated protein folding. Two weeks after the publication that refuted ideas about independently evolved neural systems or muscle specification — and perhaps refuted the independent evolution of anything else, SICB presenters linked crustaceans to insects.

Apparently, they’ve learned that the same set of microRNAs controls expression of the genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans.

Why were they left with  any questions about how crustaceans and insects could all be part of one big family? They linked RNA-mediated cell type differentiation to what we described in our section on molecular epigenetics in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior http://www.hawaii.edu/PCSS/biblio/articles/1961to1999/1996-from-fertilization.html

The report: Flawed analysis casts doubt on years of evolutionary research can be compared to what all serious scientists have claimed since 1964 or even earlier.

See for example: Biology, molecular and organismic

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 have heard a man whose official title happens to be Professor of Zoology declare to an assembly of his colleagues that “a good man cannot teach zoology. A good man can teach, of course, only molecular biology.

Such pronunciamentos can be dismissed as merely ridiculous. They are, however, caricatures of opinions entertained by some intelligent and reasonable people, whose views deserve an honest and careful consideration and analysis. Science must cope with new problems that arise and devise new approaches to old problems. Some lines of research become less profitable and less exciting and others more so.

My comment: Flawed analyses during years of “evolutionary research” attest to the fact that there is no such thing as “evolutionary research” and no such thing as evolutionary biology. Clearly, as Dobzhansky claimed in 1964, “…the only worthwhile biology is molecular biology.” Molecular biologists have since linked energy-dependent changes from angstroms to ecosystems in all genera.

Isn’t it past time for evolutionary theorists to admit that millions of lives have been lost due to pseudoscientific nonsense and billions of dollars have been spent on nothing but ridiculous claims about the emergence of life and the evolution of all biodiversity?

See also: New trends in evolutionary biology: biological, philosophical and social science perspectives

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