5th-6th Sept 2018 Dublin, Ireland

Ecological adaptations vs the randomness of evolution (3)

Summary: Fifty years later, only theorists and other pseudoscientists have failed to recognize the facts that link experimental evidence of differences in the energy of photons to the proton motive force, which links the potential of hydrogen (pH) to biophysically constrained viral latency and all biodiversity on Earth. In that context, Carl Zimmer serves as an important example of human idiocy each time he makes claims about evolution.
Serious scientists will meet during Schrödinger at 75 – The Future of Biology – September 2018 to discuss the overwhelming amount of human idiocy exemplified in the works of theorists who failed to learn that life is “All about that base.”
Without the quantized energy-dependent creation of the base pairs, viral latency could not be biophysically constrained and entropy would be used to explain the evolution of biodiversity manifested in sympatric speciation.
See for comparison: The costs of living at the edge: Seasonal stress in wild savanna-dwelling chimpanzees

Adaptations associated with shifting from a predominately forested habitat to a more open environment are considered a crucial step in hominin evolution.

The adaptations are food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans. For example, higher levels of dehydroepiandrosterone in humans are an adaptation.
See:  Dehydroepiandrosterone – is the fountain of youth drying out?

…humans are unique in having adrenals that secrete large amounts of the prohormone, dehydroepiandrosterone (DHEA) and its sulfate, DHEA-S, into the bloodstream of males and females. Even non-human primates produce only ~10% of the DHEA found in humans

Carl Zimmer places everything known about how ecological variation must be linked to energy-dependent ecological adaptations into the context of human evolution.
See: Hints of Human Evolution in Chimpanzees That Endure a Savanna’s Heat

Millions of years ago, our apelike ancestors gradually moved from woodlands to savannas and began walking upright at some point. The Fongoli chimpanzees demonstrate just how difficult that transition would have been — and how that challenge may have driven some major changes in our evolution, from evolving sweat glands to losing fur and walking upright.

Before she graduated from her medical technologist course (circa 2014), I mentioned to Misty ______ the importance of  β-lactamase testing to understanding how the energy-dependent creation of microRNAs would soon be linked to all biophysically constrained biodiversity on Earth via antibiotic susceptibility testing in the hospital medical laboratory.
Shared strategies for β-lactam catabolism in the soil microbiome

A hydrolase from the put operon was found to degrade in vitro benzylpenicilloic acid, the β-lactamase penicillin product.

This clearly exemplifies how the virus-driven degradation of messenger RNA in β-lactamase positive organisms is linked to antibiotic resistance via what all serious scientists know about the molecular mechanisms of energy-dependent cell type differentiation.
The findings were reported in the ridiculous context of claims about How Bacteria Eat Penicillin

…some of the bacteria could, in fact, eat the drugs… As it turned out, they were everywhere. He also found examples of the phenomenon in the scientific literature going back to the 1960s.

In 1964, McEwen et al, linked the creation of the sun’s anti-entropic virucidal energy from Schrödinger’s claims in What is Life? (1944) to the creation of ATP and the creation of RNA. Now, others like McEwen know that RNA interference biophysically constrains viral latency.
In 1968, Frohlich speculated that the highly ordered storage of quantized energy in species from microbes to humans linked hydrogen-atom transfer to the functional structure of cell membranes via the hydrogen bonds of molecules, or other dipolar constituents, which he linked to the shared energy supply that biophysically constrains life.
Fifty years later, only theorists and other pseudoscientists have failed to recognize the facts that link experimental evidence of differences in the energy of photons to the proton motive force, which links the potential of hydrogen (pH) to biophysically constrained viral latency and all biodiversity on Earth. In that context, Carl Zimmer serves as an important example of human idiocy each time he makes claims about evolution.
See also: UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs

By integrating proteomic and genomic analyses, we link these changes to UTX regulation of ATP-dependent chromatin remodeling, coordination of the COMPASS complex and enhanced pioneering activity of ETS factors during evolution to AML.

They linked the anti-entropic virucidal energy of sunlight from the creation of ATP to chromatin remodeling during the evolution of pathology, which all serious scientists know is biophysically constrained by the physiology of food energy-dependent pheromone-controlled reproduction.
See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] (1994)

A study of the influence of pheromone stressor(s) on proliferating germ and somatic cells was performed on laboratory lines of house mouse in the context of the physiological hypothesis of mutation process, proposed by M.E. Lobashev in 1947. Data from experiments are presented, and results obtained during last 10-15 years are discussed. The adaptive role of cytogenetic and other observed pheromonal effects is considered. The possible existence of interorganism systems of genetic regulation is discussed, the search for and study of which may help in more complete understanding of the regularities of functioning of genetic material.

The interorganism systems of genetic regulation have since been placed into the context of sympatric speciation by all serious scientists.
See: Direct estimation of mutations in great apes reveals significant recent human slowdown in the yearly mutation rate
See also: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

Sunlight as information

Proof: Sunlight is energy as information

Hypothesis: Kallmann’s syndrome is proof that virus-driven energy theft causes all pathology in species from archaea to humans via the degradation of messenger RNA and the loss of one allele.
 

Thought experiment:

Step 1) The loss of one allele and the transgenerational epigenetic inheritance of Zika virus-damaged DNA can be compared to the degradation of messenger RNA in bacteria that is manifested in archaea and L-forms.

Step 2) The degradation of messenger RNA in primates differentiates healthy longevity from pathology via a single amino acid substitution in gorillas compared to chimpanzees and modern humans.

Discussion:

Unless someone shows how mutation-driven evolution leads to increasing organismal complexity in species from microbes to humans, the speed of light on contact with water clearly establishes the link from the de novo creation of microRNA flanking sequences to hydrogen-atom transfer in DNA base pairs in solution and all energy-dependent morphological and behavioral phenotypes.

Conclusion:

Unless there is another model for comparison to Kohl (2013), energy as information will be established as the link from endogenous RNA interference to all biodiversity.  Until then, a natural law appears to link food odors and the pheromone-controlled physiology of reproduction from biophysically constrained RNA-mediated protein folding chemistry to feedback loops.

The feedback loops clearly link physics and chemistry to biodiversity from energy as information and food odors to pheromones that control the physiology of reproduction. Pheromones are the chemical signals that prevent virus-driven energy theft and genomic entropy in all living genera.

Filtering light through a prism to identify tissue type

Hydrogen-atom energy in DNA base pairs

See also: Consciousness is simply food rearranged
Role of Double Hydrogen Atom Transfer Reactions in Atmospheric Chemistry
Abstract excerpt: 

Hydrogen atom transfer (HAT) reactions are ubiquitous and play a crucial role in chemistries occurring in the atmosphere, biology, and industry.

My comment: The link from physics to chemistry and the conserved molecular mechanisms of biologically-based RNA-mediated cell type differentiation has been the focus my works for more than 20 years, even before I knew what I would need to explain about the energy-dependent links from angstroms to ecosystems via hydrogen-atom energy in all living genera.
See also: For first time, researchers see individual atoms keep away from each other or bunch up as pairs
Excerpt:

Different configurations of electrons give rise to specific elements, making carbon atoms, for instance, distinct from hydrogen atoms.

My comment: Without the different configurations of electrons,  energy-dependent changes in angstroms could not be linked from hydrogen-atom transfer (HAT) in DNA base pairs in solution to all biodiversity in all ecosystems. Simply put, the sun’s biological energy must be linked from atmospheric chemistry to biophysically constrained protein folding chemistry on Earth.
When these interactions are seen for the first time the experimental evidence must confirm theories. Otherwise physicists will try to come up with new untestable theories to stall scientific progress.  Serious scientists make progress when experimental evidence is accepted. Chemists typically know what to accept. So do molecular biologists.
What do evolutionary theorists or other social scientists know about physics, chemistry, or molecular epigenetics? How do pseudoscientists known what to accept when they already have accepted only theories?
For comparison, serious scientists know that angstroms measure distance, and every angstrom is dynamic in the context of energy-dependent RNA-mediated cell type differentiation. How can any serious scientist understand the claims of theorists made in the context of articles like this:
Humans and Neanderthals had sex. But was it for love? An investigation
Excerpt:

We know for sure humans and Neanderthals had sex because of a Swedish scientist named Svante Pääbo, who “more or less invented the field of paleogenetics,” Elizabeth Kolbert wrote in a terrific New Yorker article in 2011.

My comment:  Elizabeth Kolbert lied and used Svante Pääbo’s works to support her ridiculous claim:

We know for sure humans and Neanderthals had sex…

Serious scientists know that Svante Pääbo is the senior author of two articles. The two articles linked Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees and Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates.
Natural selection for the de novo creation of olfactory receptor genes and the loss of genes is not an indicator that humans and Neanderthals had sex. It is an indicator that natural selection for energy-dependent codon optimality occurred in the context of the physiology of reproduction in all primates. For contrast, all serious scientists know that members of two different species do not have sex. Chromatin remodeling and chromosomal rearrangements limit fertility among species via their nutrient-dependent pheromone-controlled physiology of reproduction and their behavior. The behavior is linked to energy-dependent codon optimality via the physiology of reproduction, not by sex between consenting humans and Neanderthals.
Is is silly to ask questions about sex for love without consideration of fertility, since the sexual interactions must be linked to survival of the species via biophysically constrained RNA-mediated protein folding chemistry in the context of the physiology of reproduction. The biophysical constraints are energy-dependent, but the theorists’ and journalists’ preference for fiction is clear.
Excerpt:

Robert Sawyer is a science fiction author who won the Hugo Award — one of sci-fi’s highest honors — for his 2002 book Hominids, a story that imagines a parallel world where Neanderthals survived and we didn’t. In the book (which spawned a trilogy), a Neanderthal physicist opens up a rift between the worlds and falls in love with a human.

For comparison, see this presentation text about Greg Bear’s novels in which he detailed for his non-technical audience how the nutrient energy-dependent pheromone-controlled physiology of reproduction is linked from RNA-amino acid substitutions to all cell type differentiation in all individuals of all species. The Darwin Code
See also: Structural and Functional MRI Differences in Master Sommeliers: A Pilot Study on Expertise in the Brain
Excerpt:

This study identified enhanced structural and functional patterns in the olfactory network of sommeliers. These findings are consistent with the learning they undergo in achieving the status of Master Sommelier. Furthermore, the volume of a region of the brain involved in olfactory memory was associated with experience, suggesting that the continued training results in morphological changes of the brain. These results speak to the plasticity of the adult brain in response to sensory expertise.

Reported as: Smelling Lots Of Wine Makes Your Brain Alzheimer’s Resistant

Overall, these differences suggest that specialized expertise and training might result in enhancements in the brain well into adulthood,” the study states. “This is particularly important given the regions involved, which are the first to be impacted by many neurodegenerative diseases.

See also:  What Sensory Receptors Do Outside of Sense Organs
My comment to the Scientist (I have posted: 361 comments so far)

20 years ago, we published: From Fertilization to Adult Sexual Behavior, which was a review of RNA-mediated cell type differentiation. We included a section on molecular epigenetic in the Hormones and Behavior review.

Unfortunately, few people realize that natural selection for energy-dependent codon optimality links the de novo creation of genes from the creation of G protein-coupled receptors to chemotaxis and to phototaxis before biophysically constrained energy-dependent biodiversity via RNA-mediated protein folding biochemistry can be linked to all biodiversity by amino acid substitutions.
When others report that mutations are linked to pathology, they seem to miss the fact that virus-driven energy theft causes the mutations. Nutrient-energy dependent viral latency has gone missing from explanations that would otherwise link what is known about biologically-based cause and effect from physics to chemistry and everything known about molecular epigenetics.
See also: Olfactory organ of Octopus vulgaris: morphology, plasticity, turnover and sensory characterization
My comment: Pseudoscientists could challenge representations like this if they had experimental evidence for comparison. They don’t. They have only their ridiculous theories, which they report in the story about sex between modern humans and Neanderthals. It is unadulterated pseudoscientific nonsense and nothing more than an unsubstantiated fictional account. It is not science fiction. The theorists claims are not scientifically based.
See for comparison: Role of olfaction in Octopus vulgaris reproduction and Two fatty acyl reductases involved in moth pheromone biosynthesis
Both articles cite Kohl (2013) Nutrient-dependent/pheromone-controlled adaptive evolution: a model
See also: The Ancient Origins of Consciousness: How the Brain Created Experience
Excerpt:

12. Plotnick, Dornbos, and Chen (2010). Others who advocate smell-first are Lucia Jacobs (Jacobs, 2012), who says the building of smell maps of environmental space came first and James Kohl (Kohl, 2013), whose model says chemical ecology is the main driver of adaptive evolution.  — p. 263

My comment: Chemical ecology is the main driver of energy-dependent ecological adaptations. It is not not the driver of mutation-driven evolution, and so far there is no other model for comparison to my model of chemical ecology. I deliberately used the term adaptive evolution to see if someone would take the bait and offer another model for comparison. No one did.
See also: How Psychiatrist Jon Lieff Turned an Interest in Cellular Intelligence into Award-Winning Blogging!
My comment: Lieff still presents cellular intelligence in the context of evolution. He ignores what is known about hydrogen-atom energy in DNA base pairs in solution. That shows how successful a blogger can be if they simply fail to address what is known about biophysically constrained RNA-mediated cell type differentiation. His focus is on evolution! That means he does not need to explain anything about how evolution occurs, or explain what he thinks cellular intelligence is or where it came from!
See for comparison: Direct interrogation of the role of H3K9 in metazoan heterochromatin function
Reported as: Tight DNA packaging protects against ‘jumping genes,’ potential cellular destruction
Tight DNA is supercoiled DNA and it protects the orgnaized genomes of all living genera from virus-driven energy theft and genomic entropy. Simply put, supercoiled DNA biophysically constrains virus-driven energy theft, which is the only way to establish a link from ecological variation to ecological adaptation without inventing another ridiculous theory.

… viral latency is responsible for life-long pathogenesis and mortality risk…

Nutrient energy-dependent microRNAs are the obvious link from olfaction to biophysically constrained RNA-mediated protein folding chemistry, plasticity, and prevention of all pathology.
See for example: Olfactory organ of Octopus vulgaris: morphology, plasticity, turnover and sensory characterization

Supercoiled DNA is the link to viral latency, which is the link to healthy longevity.

See also, from the Neuroscience FB group “As simple as random can be”
See also:  Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
My comment: There is no experimental evidence of biologically-based cause and effect that links anything except energy or energy theft to the species-specific COMT Val158Met amino acid substitution during life history transitions and the development of morphological and behavioral phenotypes.

COMT val158met polymorphism and molecular alterations in the human dorsolateral prefrontal cortex: Differences in controls and in schizophrenia
Excerpt:

…the COMT val158met polymorphism is not found in species other than humans (Palmatier et al., 1999).

My comment: That fact makes the COMT val158met polymorphism a “smoking gun” in the context of energy-dependent de novo gene creation and virus-driven energy theft that links gene losses to loss of function via differences in G protein-coupled receptors.
Dopamine Neuron-Specific Optogenetic Stimulation in Rhesus Macaques
G protein-coupled receptor kinases as regulators of dopamine receptor functions
Subsecond Regulation of Synaptically Released Dopamine by COMT in the Olfactory Bulb
Programmable RNA-binding protein composed of repeats of a single modular unit
Excerpt from the conclusion:

… Pumby may present a simplified context in which to insert Pumilio modules to study how specific amino acids contribute to the emergent properties of modular RNA binding, independent of position-specific effects.

See also: Another gate-keeping attempt by Feierman

human-evolution

Bringing RNA back to epigenetics (20 years later)

Has Contemporary Academia Outgrown the Carl Sagan Effect?  [Subscription required]
Excerpt (with my emphasis):

[Sean Carroll] offered 13 pieces of advice…: “Do good research; Make an impact in the field; Bring in grant money… Don’t be too well known outside the field; Don’t write a book; Choose your hobbies wisely.” Carroll argued that academics look askance at colleagues that have too high of a public profile. Not out of envy—but because they worry that public scientists care more about their media presence than about discovery.

Excerpt:

…institutions must find new incentives for dissemination, and the Royal Society has recommended the implementation of “a more effective support system” and “the introduction of significant departmental rewards” (Royal Society, 2006) for those who communicate. These are worthwhile goals, but more pressing perhaps is the need to overcome lingering ambivalence toward engagement in public discourse.

My comment: The book I wrote and published in 1995 with co-author Robert T. Francoeur is available here in an updated paperback from 2002. See: The Scent of Eros: Mysteries of Odor in Human Sexuality.  With other co-authors, I subsequently linked the nutrient-dependent physiology and behavior of species from microbes to humans via RNA-mediated events.
Metabolic networks and genetic networks are RNA-mediated. The networks link atoms to ecosystems in all living genera via the physiology of reproduction. Supercoiled DNA in organized genomes protects all genera against virus-driven pathology. Examples that link virus-driven pathology from bacteria to plants and animals have since repeatedly confirmed the links from atoms to ecosytems in the context of energy-dependent hydrogen-atom transfer in DNA base pairs in solution that link nutrient energy-dependent reproduction to RNA-mediated amino acid substitutions and all biomass and all biodiversity.
For comparison, see: 
RNA Epigenetics January 1, 2016

New RNA letter regulates gene expression: Discovery brings RNA to the fore of epigenetics February 16, 2016
My comment: RNA has been at the fore of epigenetics since our 1996 Hormones and Behavior review. In our section on molecular epigenetics, we wrote:

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). 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.

Among other published works, we cited:

Adler, B. K., and Hajduk, S.L. (1994). Mechanisms and origins of RNA editing. Curr. Opin. Genet. Dev. 4, 316-322.

Clemson, C. M., and Lawrence, J. B. (1996). Multifunctional compartments in the nucleus: Insights from DNA and RNA localization. J. Cell. Biochem. 62, 181-190.

Green, M. R. (1991). Biochemical mechanisms of constitutive and regulated pre-mRNA splicing. Annu. Rev. Cell Biol. 7, 559-599.

Guthrie, K. M., Anderson, A. J., Leon, M., and Gall, C. (1993). Odor-induced increases in c-fos mRNA expression reveal an anatomical “unit” for odor processing in the olfactory bulb. Proc. Natl. Acad. Sci. USA 90, 3329-3333.

Schneider-Gadicke, A., Beer-Romero, P., Brown, L. C., Mardon, C., Luoh, S. W., and Page, D. C. (1989). Putative transcription activator with alternative isoforms encoded by human ZFX gene. Nature 342, 708 -711.

Our focus was on sex differences in cell types. Others have since linked RNA-mediated events from the epigenetic landscape to the physical landscape of DNA in all living genera via the physiology of reproduction.
See for example:

  1. Sex-specific Patterns of the Epigenome as a Putative Mechanism in Fear-related Memory
  2. Exploring the role of histone demethylase, UTX, in mediating sex differences in fear-related learning and memory
  3. From Toxins to Culture: How Environment Shapes the Infant Brain
  4. En’Cas’ing The Stress: Engineering a Human Cell Line Knockout of Heat Shock Response Genes

See also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
My comment: Science news outlets appear to be following my series of more that 600 blog posts and my FB group posts at RNA-mediated. If I were following reports from other news services I would not already have linked: Watson–Crick Base Pairing Controls ExcitedState Decay in Natural DNA, which was reported as: Base-pairing protects DNA from UV damage, from microbes to mammals.
See for example: Applying humanized mouse models to immune therapy research
Excerpt:

Mouse models have been a mainstay in biomedical research for decades. As these models have become more sophisticated, their application has grown and now includes a wide variety of immunodeficient strains that can be used to examine the in vivo growth of human tumors and to test new cancer treatments.

My comment: I linked the mouse model organism to humans via one base pair change and one amino acid substitution in my 2013 review: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Excerpt:

The recently detailed mouse model (Li et al., 2013) builds on what is known about olfactory/pheromonal communication in species from microbes to man and incorporates works from mammals that elucidate the molecular mechanisms that are clearly involved. Sex-dependent production of a mouse ‘chemosignal’ with incentive salience appears to have arisen de novo via coincident adaptive evolution that involves an obvious two-step synergy between commensal bacteria and a sex-dependent liver enzyme that metabolizes the nutrient chemical choline.

See also: U of Chicago Researchers Discover Novel Polymorphisms Associated With VTE in African Americans

Excerpt:

They identified a link between VTE and three variants in a chromosome — rs2144940, rs2567617, and rs1998081 — associated with decreased expression of thrombomodulin, a protein that regulates clotting. Approximately 36 percent of American Americans have at least one of these variants, however, these variants were found in much lower frequency in other ethnicities from previous studies.
“This study not only brings us closer to understanding the cause of VTE in African Americans,” Perera said in a statement, “it demonstrates the importance of conducting populations-specific research in precision medicine.

My comment: Do neo-Darwinian theorists think that these variants are mutations?  Are they claiming that 36 percent of African Americans are mutants? If so, what are they claiming about the other 64 percent of African Americans who do not have these three variants in a chromosome?
See also: Transposons, and why you should love them

Although TEs can have deleterious effects, in higher animals they have become essential contributors to evolution, and have been described as the “motors of evolution”. By carrying out processes such as gene rearrangement, mutation of gene and regulatory sequences, genomic recombination, gene duplication, and other types of rearrangements, TEs have provided the adaptive benefit of increased genetic diversity and plasticity for their host species. TEs and their hosts have been forced to coevolve, and have achieved a fine balance between the potentially damaging and potentially beneficial effects of TEs.

My comment: They seem to be claiming that mutants co-evolved with organisms that ecologically adapted in the context of their nutrient-dependent physiology of reproduction, which is linked to the supercoiled DNA that protects all organisms from virus-driven entropy. Others have yet to link the virucidal effects of sunlight from hydrogen-atom transfer in DNA base pairs in solution to the physiology of nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation in soil microbes to the cancer treatment “taxol.” When someone else finally does that, their report will be a follow-up to this one: Discovery brings RNA to the fore of epigenetics.
Until then, see: Delving into dark matter
Excerpt:

Bhardwaj added, “The ncRNAs in cancers where odd RNAs were being activated and transcribed had unusual patterns that were similar to some pathogens, and this causes them to stimulate an innate immune response.”
“All in all, we believe these ncRNAs may play a significant role in mediating immune responses against cancer, but much work remains to describe their precise interactions,” said Greenbaum. “If we could characterize the ncRNA and link it with specific pathways, we could understand its role in the tumor environment and determine how it can be utilized for patient therapy.”

My comment: They fail to recognize the difference between nutrient-dependent microRNAs and viral microRNAs, which is why they cannot categorize the difference in pathways that lead to nutrient-dependent healthy longevity, which could be compared to virus-driven pathology. Instead, most researchers are still trying to determine how what they once called “Junk DNA” and now call “dark matter” links metabolic networks from genetic networks to supercoiled DNA that typically protects all organized genome from virus-driven entropy.
A new kind of periodic table
Conclusion:

According to Marsh, researchers are still very interested in trying to understand the evolutionary pathways of protein complexes, in particular heteromeric complexes. “We are currently doing some work on how the assembly pathways of heteromers are related to their evolution. Now that I’ve started my own research group in Edinburgh, one of my main focuses is on understanding how pathogenic mutations can disrupt the assembly of protein complexes, and how protein complex assembly and quaternary structure can influence the phenotypic impacts of mutations.”

See also: How to Build Life in a Pre-Darwinian World Perhaps chemistry played a more instrumental role in the origin of life than scientists thought.

Conclusion: Hud and his collaborators propose that RNA and proteins evolved in tandem, and those that figured out how to work together survived best. This idea lacks the simplicity of the RNA world, which posits a single molecule capable of both encoding information and catalyzing chemical reactions. But Hud suggests that facility might trump elegance in the emergence of life. “I think there’s been an overemphasis on what we call simplicity, that one polymer is simpler than two,” he said. “Maybe it’s easier to get certain reactions going if two polymers work together. Maybe it’s simpler for polymers to work together from the start.”

My comment: They fail to link sunlight and gravitational waves from hydrogen-atom transfer in DNA base pairs in solution and claim emergence and evolution. Since our 1996 review brought RNA to the fore of epigenetics, please return to this blog site to find information that others may still be missing during the next 20 years, or if I gave up trying to tell them anything more about about the obvious links from angstroms to ecosystems.

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

Excerpt:

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.

See for comparison: Evolution silences harmful mutations
Excerpt:

…researchers looked more closely at four synonymous but costly mutations in the gene for a ribosomal protein. They observed that the main problem with these mutations was that they caused a decrease in production of the mutated ribosomal protein. The cells entered into a vicious circle in which low protein levels resulted in defective ribosomes that in turn caused further problems with protein synthesis. By allowing these low fitness bacteria to grow for many generations it was possible to see that evolution solved the problem of synonymous mutations by creating compensatory mutations that restored the level of ribosomal protein to normal. In this way, the researchers have gained a greater understanding of why silent mutations might reduce fitness was and how bacteria could compensate for them.
My comment: Organisms that have enough food can reproduce. Successful reproduction links nutrient-dependent pheromone-controlled ecological adaptations to supercoiled DNA in species that control the replication of viruses and virus-driven genomic entropy.

See also: U of Chicago Researchers Discover Novel Polymorphisms Associated With VTE in African Americans

Excerpt:

They identified a link between VTE and three variants in a chromosome — rs2144940, rs2567617, and rs1998081 — associated with decreased expression of thrombomodulin, a protein that regulates clotting. Approximately 36 percent of American Americans have at least one of these variants, however, these variants were found in much lower frequency in other ethnicities from previous studies.
“This study not only brings us closer to understanding the cause of VTE in African Americans,” Perera said in a statement, “it demonstrates the importance of conducting populations-specific research in precision medicine.

See also: The mid-developmental transition and the evolution of animal body plans
Excerpt:

Embryos in a particular phylum of the animal kingdom tend to most resemble one another at a stage in the middle of embryogenesis known as the phylotypic period; a transcriptional analysis of embryogenesis from single embryos of ten different phyla reveals that the transcripts expressed at the phylotypic stage (or mid-developmental transition) differ greatly between phyla, and a ‘phylum’ may be defined as a set of species sharing the same signals and transcription factor networks during the mid-developmental transition.

My comment: All development transitions are nutrient-dependent and RNA-mediated. Other variants in chromosomes are reported in terms that link energy-dependent hydrogen-atom transfer in DNA base pairs to phenotypic changes in the mouse model that clearly are linked from amino acid substitutions to morphological and behavioral phenotypes via the physiology of nutrient-dependent phermone-controlled reproduction.
Again, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

Two additional recent reports link substitution of the amino acid alanine for the amino acid valine (Grossman et al., 2013) to nutrient-dependent pheromone-controlled adaptive evolution. The alanine substitution for valine does not appear to be under any selection pressure in mice. The cause-and-effect relationship was established in mice by comparing the effects of the alanine, which is under selection pressure in humans, via its substitution for valine in mice (Kamberov et al., 2013).

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. 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.

Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees
Functional characterisation of a SNP in the ABCC11 allele—Effects on axillary skin metabolism, odour generation and associated behaviours
Odor perception between heterosexual partners: its association with depression, anxiety, and genetic variation in odorant receptor OR7D4
Excerpt:

Genetic variants in OR7D4 receptor can modify the detection of the steroids androstenone and androstadienone, two pheromones that have the potential to evoke behavioral changes in many mammals, including humans, including mood changes (Kohl et al., 2001) and inter-sex communication (Kohl et al., 2001).

Excerpt:

…it was observed that the rating of partner odor was significantly associated with rs8109935 genotypes suggesting that genetic variability in the OR7D4 might have a role in the odor perception between partners. In fact, the data of this study replicate, for the first time, the results of Keller et al. (2007) about the influence of genotype variations in OR7D4 on odor perception.

See also:  Why Do Floral Perfumes Become Different? Region-Specific Selection on Floral Scent in a Terrestrial Orchid
Reported as: Orchid’s scent stronger in Swiss lowlands than mountains

The difference in pollinator communities between regions may indicate that different pollinators select for differences in floral scent chemicals, but further experiments would be required to test this theory. Nonetheless, the authors state their study is the first to find consistent regional differences in selection on floral scent, showing that this could be one mechanism behind geographical floral chemical scent divergence.
Karin Gross notes: “The observed regional differences in selection are an important evolutionary force contributing to divergence in floral fragrances. Other traits such as plant height were also affected by selection, but in a more uniform way.”

My comment: The changes in the orchid’s scent link ecological variation in the soil bacteria to the nutrient-dependent pheromone-controlled physiology of reproduction in mammals.
Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin
Repeated elevational transitions in hemoglobin function during the evolution of Andean hummingbirds
Evidence from cyclostomes for complex regionalization of the ancestral vertebrate brain
Reported as: Reported as: Jawless fish brains more similar to ours than previously thought
See also:  Distinct Circuits for the Formation and Retrieval of an Imprinted Olfactory Memory
Reported as: Neuroscience of Early-Life Learning in C. elegans
See alsoThe Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
The information that connects all of the above from ecological variation to ecological adaptation in all living genera via hydrogen-atom transfer in DNA base pairs in solution arrives so quickly that biologists must look at conference abstracts to stay current and they must also pay attention to advice like this:
Biologists urged to hug a preprint
Excerpt:

Both Vale and Vosshall think that preprints will become widely accepted only if the life-sciences community develops a consensus that preprint publication establishes a priority for any discovery.

See my invited review of nutritional epigenetics, which was published as a preprint when it was returned without review. Note, however, that Vosshall has referred to all my works as pseudoscience that she will not address. Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems. I would value her opinion if I thought she was a serious scientist. Instead, she is trying to genetically engineer mosquitoes to prevent the transmission of pathogens. Obviously, she doesn’t know enough about RNA-mediated cell type differentiation to predict that the pathogens will adapt faster than the organisms she genetically engineers.

rp_levels-of-organization.jpg

Supercoiled DNA constrains virus-driven genomic entropy

1) Genes linked with malaria’s virulence shared by apes, humans and
2) Supercoiled DNA is far more dynamic than the ‘Watson-Crick’ double helix were reported today.
One report (1) links viruses to the evolution of biodiversity in chimpanzees and humans compared to gorillas.
The other report (2) links nutrient energy-dependent base pair changes to RNA-mediated amino acid substitutions and DNA repair.

Both reports are linked to open access publications:

See 1)  Ape parasite origins of human malaria virulence genes
Excerpt:

This Laverania species diversity provides an unprecedented opportunity to study the origins of genomic features that previously seemed unique to P. falciparum, such as the var gene family encoding erythrocyte membrane proteins. Here we show that various aspects of the multi-scale modularity of these loci can be recognized in diverse Laverania species, with the implication that a var or var-like gene family already existed in their last common ancestor.

My comment: The implication that gene families already existed in a last common ancestor are linked to the theoretical ghosts of the evolution industry. Despite a century of scientific progress, the ghosts are still linked to the gene-centric views of population geneticists. They used de Vries (1904) definition of “mutation” as the basis for assumptions about how long it would take for all extant or extinct biomass to automagically arise from a primodial soup. Sometime during that time apes evolved from microbes and became modern humans.
See also 2): Structural diversity of supercoiled DNA
Conclusion:

Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

My comment: The data that links small molecules, such as microRNAs, from metabolic networks to genetic networks, makes the claims of neo-Darwinian theorists the theme of this parody. It is an accurate representation of how nutrient-dependent base pair changes link ecological variation to ecological adaptation and all biomass on earth via what is currently known to serious scientists about base pair changes and RNA-mediated DNA repair.

Last week, I recorded a less technical representation of biologically-based cause and effect that placed squirrel-centric evolution into the context of current philosophy (we don’t know how species evolved) and claims of evolutionary theorists (random mutations and natural selection led to the theoretical basis of the “walnut crush” phenomenon). Sarcasm alert: Creationist claims are vaguely presented with no experimental evidence to support the idea that the walnuts grew on and fell from trees.

Obviously, no one can be perfectly sure that what is known about RNA-mediated epigenetic regulation of gene expression and RNA-mediated gene silencing link base pair changes to all extant biodiversity, or if de Vries definition of “mutation” and theories are the best approach to understanding the pathology of malaria. However, the 2015 Nobel Prize winners in Physics, Chemistry, and Physiology and/or Medicine have linked neutrinos to mass and the speed of light on contact with water from the light’s virucidal properties to the effective treatment of malaria via a water-based chemical extraction procedure described 1600 years ago.
 

poster-from-jesse

Rejecting pseudoscientific nonsense

Rejecting Evolutionary Psychology is Rejecting Evolution

Discussion on the closed group Applied Evolutionary Psychology includes my comments on several other reports, beginning with:
My comments on:

Early Code

New research points to key properties of transfer RNA molecules and amino acids that may have supported the origin of life on Earth.

I wrote: Thanks for providing yet another reason to reject evolutionary psychology.  Acceptance of RNA-mediated links to cell type differentiation in all cells of all individuals of all genera is not optional. They link metabolic networks to genetic networks, which is required.
My comment to The Scientist:
Simultaneous emergence was suggested by Matti Pitkanen who pirated my model of biophysically constrained RNA-mediated cell type differentiation and claimed that “Hens and eggs emerged simultaneously.”
Serious scientists now appear to have discovered the link from the light-induced de novo creation of amino acids to the de novo creation of receptors that link RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of genera via the nutrient-dependent chemistry of RNA-mediated protein folding.
The nutrient-dependent physiology of metabolic networks and genetic networks link reproduction to fixation of the amino acid substitutions, which enables all extant biophysically constrained biodiversity, which is exemplified in differences in morphological and behavioral phenotypes.
Claims of simultaneous emergence should be supported by experimental evidence of biologically-based cause and effect, or abandoned along with claims of Mutation-Driven Evolution, like this one: “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.” (p. 199)
For comparison, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which was published on the same day as Nei’s textbook.
See also:

The Living Set

Mathematical and computational approaches are making strides in understanding how life might have emerged and organized itself from the basic chemistry of early Earth.

I wrote: Continuing to accept theory when facts about physics, chemistry, and the conserved molecular mechanisms of RNA-mediated protein folding attest to how ecological variation is epigenetically linked to ecologically adaptation is continuing to accept the pseudoscientific nonsense of the population geneticists who invented neo-Darwinism.

My comment to The Scientist:

Re:

Put some E. coli in a dish with appropriate nutrients, and after a few days the dish will be teeming with new bacterial offspring.

My comment: Put some genetically altered P. fluorescens in a dish and leave them without their flagella over-the-weekend. Forget to remove them from the incubator and find they have “re-evolved” their flagella.
See: Evolutionary Rewiring. Try to convince serious scientists that what “re-evolved” exemplies how autocatalycic processes link ecological variation to ecological adaptations via mutations that perturb the thermodynamic cycles of protein biosynthesis and degradation.
The thermodynamic cycles link the nutrient-dependent physiology of reproduction to RNA-mediated cell type differentiation in all cell types of all individuals of all genera.
SARCASM ALERT!
If you can successfully link mutations and evolution, you can teach neo-Darwinian theory to unsuspecting students who may think you are teaching them more about biodiversity than they might otherwise have learned if they knew: “[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another….  Assumptions, made but not verified, were taught as fact.
See also:

tRNA acceptor stem and anticodon bases form independent codes related to protein folding

Excerpt:

These and other results suggest that genetic coding of 3D protein structures evolved in distinct stages, based initially on the size of the amino acid and later on its compatibility with globular folding in water.

My comment: Sutherland’s group already linked the light-induced de novo creation of the smallest amino acid, glycine and what may appear to be the simultaneous de novo creation of three other amino acids.
Excerpt:

precursors of amino acids glycine, serine, alanine and threonine, are inevitable by-products of this RNA assembly chemistry

My comment: The de novo creation of the first amino acid does not appear to have been a random event.  Linking the light-induced de novo creation of glycine to globular folding in water, appears to link the speed of light, which slows on contact with water, to the de novo creation of the first amino acid and the creation of 19 others.  This is consistent with what has been portrayed in the context of a giant biogeochemical membrane.
See: Eukaryotic plankton diversity in the sunlit ocean
Excerpt:

The sunlit surface layer of the world’s oceans functions as a giant biogeochemical membrane between the atmosphere and the ocean interior (1).

My comment: It is difficult to not link the speed of light on contact with water to the de novo creation of amino acids and to RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to the creation of all cell type differences in all cell types of all individuals of all genera via their physiology of nutrient-dependent reproduction.
See also:

Human body epigenome maps reveal noncanonical DNA methylation variation

RNA-mediated gene activation

Excerpt:

The regulation of gene expression by non-coding RNAs (ncRNAs) has become a new paradigm in biology.

Scientists reveal epigenome maps of the human body’s major organs

My comment: The maps are linked from nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation in bacteria to humans. Evolutionary theorists recently tried to link “re-evolution” of the bacterial flagellum via mutations and evolution, which occurred in four days.

In the context of evolution in four days I admitted that I do not understand the abstractions and the assumptions made about the ability of de Vries definition of “mutation” to link biologically-based cause and effect.

I wrote: I’m a retired medical laboratory scientist who was never taught to believe in neo-Darwinism, which I still find unbelievable in the context of everything currently know about physics, chemistry, and molecular mechanisms. If the article clarified that evolutionary psychology was based on abstractions instead of what is known about ecological variation and ecological adaptations, I would not have commented.

But, as soon as someone misrepresents cause and effect, I think it benefits us both to clarify the difference between theory and biology. Anyone who wants to link theory to differences in behavior is welcome to continue doing so. However, serious scientists are Combating Evolution to Fight Disease because pseudoscientists have continued to claim that beneficial mutations can be linked to the evolution of increasing organismal complexity AND to pathology.

I added: Those who have children may also want to see: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

My comment: Without telling you that Va158Met is an amino acid substitution, they link it to cell type differentiation during life history transitions, which occur via the conserved molecular mechanisms of our 1996 model, which was linked to insects (2000) and to life history transitions in the honeybee model organism in 2005.

On a lighter note: If you think the behavior of some children can be linked via abstractions to the behavior of other species, you may want to consider how the immune systems links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. Signature Patterns of MHC Diversity in Three Gombe Communities of Wild Chimpanzees Reflect Fitness in Reproduction and Immune Defense against SIVcpz

Conclusion:

Well-illustrated by this study is how single events of recombination between MHC-B alleles can generate groups of MHC-B subtypes that offer different degrees of protection and susceptibility against an infecting pathogen. In both chimpanzees and humans, this is the major mechanism by which useful new variants are formed [20,66,71,72]. Reflecting the dynamic nature of the MHC-B gene, the majority of Patr-B alleles are specific to one subspecies of chimpanzee. It will therefore be of great interest to study Patr-B and other MHC genes in other subspecies of chimpanzee, as well in the second Pan species, the bonobo.

Re: “….inherited according to mendelian laws….” They were not part of Darwin’s theory.

My comment: See also: R2d2 beats Mendel: Scientists find selfish gene that breaks long-held law of inheritance

Mendel’s century-old “law of segregation,” which states that you have an equal probability of inheriting each of two copies of every gene from both parents is not a law of biology. Female mice pass on one copy of the R2d2 gene more frequently than the other copy. Cause and effect is nutrient-dependent and RNA-mediated, which means that you can’t get to an inherited “analytic gene” or anything else without explaining what you are trying to get to in the context of what serious scientists know about transgenerational epigenetic inheritance. But, let’s pretend that is not related to Glenn Geher’s post. Evolutionary psychology should be like magic.

I think if others follow the Psychology Today comments, they will be more likely to see that people aren’t buying into the pseudoscientific nonsense. Perhaps that is because of the links from nutritional epigenetics to pharmacogenomics that show how a single amino acid substitution can alter the response to medications used to treat behavioral disorders and disorders of cell type differentiation, like cancer.

Precision medicine is eliminating what’s now being taught as evolutionary medicine because serious scientists know the difference between mutations that perturb protein folding and amino acid substitutions that stabilize it. Test panels include testing for the Val158Met substitution, which is important to proper prescription medicine in ADHD and other developmental disorders linked to life history transitions via epigenetics, not by “analytic genes.”

UV-light mutations and gene loss (not gain)

The Neanderthals live on in us

March 13, 2015 Excerpt: “He opted instead for a medical degree and then a PhD at the University of Uppsala, where he was supposed to be probing the DNA secrets of a virus.”
My comment: If he had done what he was supposed to be doing, he might have learned how viral microRNAs and nutrient-dependent microRNAs contribute to cell type differentiation in all cells of all individuals of all species. If he had done that, he might never have started to confuse others with his nonsense about the evolution of human biodiversity. See also: Sunlight adaptation region of Neanderthal genome found in up to 65 percent of modern East Asian population.
Excerpt: “…the geographic distribution of the Neanderthal genomic region suggests that UV-light mutations were shown to be lost during the exodus of modern human from Africa, and reintroduced to Eurasians from Neanderthals. ”
My comment: The epigenetic effects of the sun link its anti-entropic energy to amino acid substitutions that stabilize the biophysically constrained RNA-mediated chemistry of protein folding. The amino acid substitutions differentiate all cell types in all individuals of all species.
Like all mutations, the UV-light mutations perturb protein folding. Mutations contribute to loss of function. Loss of function leads to the loss of the genes and also to the creation of pseudogenes. For example, humans have more olfactory receptor pseudogenes than other primates. Claims that “…UV-light mutations were shown to be lost during the exodus of modern human from Africa, and reintroduced…” are based on pseudoscientific nonsense. Mutations perturb protein folding. That’s why they are lost. No one has shown that they are lost and then reintroduced. However, population geneticists have convinced some theorists that their calculations show mutations are lost and gained in different populations.
Population geneticists must use calculations instead of experimental evidence of biologically-based cause and effect that links nutrient uptake to the pheromone-controlled physiology of reproduction.  Their calculations lead people to claim that have shown what they think might link mutations and lost genes to the evolution of new species. That is not possible. Ecological variation leads to ecological adaptations via the nutrient dependent link between the number of amino acids and the exponential increase in the number of proteins that is linked to increasing organismal complexity manifested in the morphological and behavioral diversity of all genera.
Clarification: “We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.” — A universal trend of amino acid gain and loss in protein evolution
Experience-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions link the de novo creation of olfactory receptor genes to differences in the number of olfactory receptor genes in primates and other animals. Odor exposure leads to the creation of receptors that enable nutrients to enter cells. Nutrients that contribute to the stability of DNA in organized genomes are metabolized to species-specific pheromones that control the physiology of reproduction in species from microbes to man. The physiology of reproduction enables nutrient-dependent fixation of the amino acid substitutions that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of all species.
The epigenetic landscape is linked to the physical landscape of DNA in the organized genomes of all species via RNA-mediated amino acid substitutions and the de novo creation of olfactory receptor genes, not by mutations and loss of genes.
Svante Paabo knows that, as well as anyone. He co-authored:  Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees and Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates.
If he does not know how the anti-entropic effects of light control the balance of viral microRNAs to nutrient-dependent microRNAs that leads to biodiversity, he should start  probing the DNA secrets of a viruses, which is what he was supposed to be doing decades ago.
August 18, 2014 Excerpt from the original article: Darwin had predicted that, like every other animal, human beings would have fossil ancestors. 
My comment: Darwin’s predictions were based on what he knew about links between ecological variation and their manifestations in ecological adaptations. This story and other ridiculous stories that link mutations to evolution have been told and retold so often that even some serious scientists believe the stories are true. Others are Combating Evolution to Fight Disease, because people like Svante Paabo didn’t do what they were supposed to be doing.
Obviously, it is more difficult to study viruses and molecular mechanisms than it is to invent stories based on de Vries definition of mutation and on assumptions about how long it takes for a new species to evolve. That explains why “[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another….  Assumptions, made but not verified, were taught as fact.
There is no explanation for why someone like Svante Paabo, who understands Natural Selection on.. Olfactory Receptor Gene(s) and the Loss of Olfactory Receptor Genes [that] Coincides with the Acquisition of Full Trichromatic Vision in Primates would continue to deceive others and misrepresent what is currently known about physics, chemistry, and conserved molecular mechanisms in all genera. Indeed, it has become perfectly clear that Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes is linked to the anti-entropic biological energy from the sun, not from mutations to the evolution of any species. The sun’s anti-entropic energy links viral microRNAs to entropic elasticity and to epigenesis and epistasis via nutrient-dependent microRNA’s and DNA repair mechanisms.
August 18, 2014 Conclusion (excerpt): ‘But there’s no doubt that Neanderthals live large in our imagination.”
My comment: This attests to the power of story-telling. It can lead others to imagine associations that are not possible. All associations between biologically-based cause and effect arise in the context of the biophysically constrained chemistry of nutrient-dependent RNA-mediated amino acid substitutions and protein folding.
For contrast, the story-telling appears to have led to the miss-identification of one species of snail as if it were “…different species and sub-species at least 113 times, more than any other animal or plant.”   It also appears to link microRNAs to the similarities of all crustaceans and insects. They now appear to be creatures of Biblical “like kind.” See: All in the (bigger) family
Excerpt: “In insects, falling levels of so-called juvenile hormone stimulate the transition to adulthood; the analogous hormone in crustaceans is methyl farnesoate, which spurs growth and molting. Juvenile hormone is thought to be specific to insects, whereas methyl farnesoate is inactive in that group. But researchers have learned that production of both hormones depends on the same rate-limiting enzymes. And Jerome Hui of the Chinese University of Hong Kong found that in both insects and crustaceans, the same set of micro RNAs control expression of the genes for those enzymes.”
The link from microRNAs to metabolic networks and genetic networks by enzymes is exactly what serious scientists would expect if chemical stimuli linked to food odors induced the de novo creation of receptors that allowed nutrients to enter the cell and fight the viruses the entered the cell via the same conserved molecular mechanisms of cell type differentiation that links species of microbes to man.
The lesson here seems to be “do what you are supposed to be doing” if you want to become a serious scientist. But, if you cannot do that, do not make up stories to explain what you did, instead. Your stories could lead others to become pseudoscientists who tell similar stories. In a short time, today’s students could evolve into nothing but pseudoscientists — if that has not already happened.

human-evolution

RNA-mediated repurposing in microbes and adaptations in primate brains

Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion

Excerpt: “…the C-terminal 47 amino-acids of ARHGAP11B (after lysine-220) constitute not only a unique sequence, resulting from a frameshifting deletion (fig. S10), but also are functionally distinct from their counterpart in ARHGAP11A.”
My comment: Co-author Svante Paabo is the senior author of this 2003 publication: Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees
The 2015 publication was reported as:

A gene for brain size only found in humans

Excerpt: “ARHGAP11B is the first human-specific gene where we could show that it contributes to the pool of basal brain stem cells and can trigger a folding of the neocortex. In that way, we managed to take the next step in tracing evolution”, summarizes Wieland Huttner.
My comment: The authors report the contribution of amino acid substitutions to primate brain development as if a human-specific gene had somehow automagically evolved outside the biophysical constraints of the chemistry of nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate the cell types of all individuals in all species.
Are they pretending not to know that 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.”
See also: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Excerpt: NtrC shares 30 percent amino acid identity with FleQ, suggesting the proteins may be able to minimally cross-react with each other’s target genes.
My comment: The fact that RNA-directed DNA methylation and RNA-mediated amino acid substitutions differentiate cell types in all individuals of all species from microbes to primates seems clear. Why would anyone continue to frame their results in the context of mutations and evolution?
See also: RNA-mediated “repurposing” is nutrient-dependent and pheromone-controlled

human-evolution

Genomic surveillance ends our world of RNA-mediated ecological adaptations

Why is this woman smiling?

1) Identifying Recent Adaptations in Large-Scale Genomic Data

Senior author: Sabeti with co-author Rinn
Excerpt: “As natural selection can only act on mutations that drive phenotypic variation…”.

2) Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak 

Senior author: Sabeti.
Excerpt: “Because many of the mutations alter protein sequences and other biologically meaningful targets, they should be monitored for impact on diagnostics, vaccines, and therapies critical to outbreak response.”

3) RNA and dynamic nuclear organization

First author Rinn.
Excerpt: “… it is becoming increasingly clear that lncRNAs are important at all levels of nuclear organization—exploiting, driving, and maintaining nuclear compartmentalization.”

4) ‘Oming in on RNA–protein interactions

First author Rinn.
Excerpt: “…the interactions between pre-mRNA and proteins fine-tune alternative splicing in a manner that can gradually create new protein functionalities without the need to create additional genes and without affecting existing proteins [4-6].”
My comment: Evolutionary theorists who think “…natural selection can only act on mutations that drive phenotypic variation…” may not realize that “…the interactions between pre-mRNA and proteins fine-tune alternative splicing in a manner that can gradually create new protein functionalities…” See our section on molecular epigenetics in 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…” (e.g., of cell types in species from yeasts to man).
Serious scientists may realize, too late, that nutrient-dependent RNA-directed DNA methylation — and pre-mRNA-mediated events that lead to mRNA-mediated amino acid substitutions — differentiate all cell types in all individuals of all living species. For example, without thinking, the non-living Ebola viruses may ecologically adapt with as little as a single amino acid substitution, like the one that differentiates all cell types of humans from chimpanzees and gorillas.
See: “…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.” Dobzhansky (1973).
What evolutionary theorists continue to think about natural selection acting on mutations that lead to the evolution of biodiversity will not matter if the Ebola viruses destroy humanity. People may ask as our species dies out: “What were the evolutionists thinking? Did they not know that Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution?
Did the theorists never ask: How does epistasis arise from an evolutionary process that is conceived as proceeding through the incremental accumulation of mutations?
Does any serious scientist still think that the accumulation of mutations leads to increasing organismal complexity? How could that happen?
Biophysically-constrained receptor-mediated nutrient-dependent pheromone-controlled ecological adaptations link the physiology of reproduction to behavioral phenotypes and morphological phenotypes in all living species based on the molecular mechanisms conserved in viruses.
Is there another model for that? Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems. See also: Origin of group identity: viruses, addiction and cooperation