5th-6th Sept 2018 Dublin, Ireland

The eternal significance of microRNAs (8)

Use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation and aging has been replaced by the use of model systems of biological processes.  Biological processes can be compared to so-called “evolutionary processes” to show that only biological processes need to be considered in the context of Darwin’s “conditions of life” or answers to the the question  What is Life? Schrödinger (1944).
K. L. Mettinger et al. (eds.), Exosomes, Stem Cells and MicroRNA, Advances in Experimental Medicine and Biology 1056, https://doi.org/10.1007/978-3-319-74470-4_6

This volume provides insight into the pivotal roles of stem cells, exosomes and other microvesicles in biofunction and molecular mechanisms and their therapeutic potential in translational nanomedicine. It further highlights evidence from recent studies as to how stem cell derived exosomes and microRNAs may restore and maintain tissue homeostasis, enable cells to recover critical cellular functions and begin repair regeneration.

Chapter 2 The Emerging Roles of microRNAs in Stem Cell Aging

involved in many biological processes such as developmental timing, differentiation, cell death, stem cell proliferation and differentiation, immune response, aging and cancer. Accumulating studies in recent years suggest that miRNAs play crucial roles in stem cell division and differentiation. In the present chapter, we present a brief overview of these studies and discuss their contributions toward our understanding of the importance of miRNAs in normal and aged stem cell function in various model systems.

Chapter 6  MicroRNAs, Regulatory Messengers Inside and Outside Cancer Cells

…like hormones, miRNAs can be secreted and regulate gene expression in recipient cells. Altered expression levels of miRNAs in cancer cells determine the acquisition of fundamental biological capabilities (hallmarks of cancer) responsible for the development and progression of the disease.

Model systems link the energy-dependent creation of microRNAs from microRNA biogenesis to the regulation of all cancer hallmarks. The virus-driven degradation of messenger RNA has been linked to all cancers and all other pathology in species from microbes to humans. Natural selection for energy-dependent codon optimality has been linked to healthy longevity.
See: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See for comparison:  The Neutral Theory in Light of Natural Selection May 2, 2018

…50 years after its introduction by Kimura. We argue that the neutral theory was supported by unreliable theoretical and empirical evidence from the beginning, and that in light of modern, genome-scale data, we can firmly reject its universality. The ubiquity of adaptive variation both within and between species means that a more comprehensive theory of molecular evolution must be sought.

The ubiquity of adaptive variation attests to the facts about how the creation of quantized energy is linked to biophysically constrained viral latency. Adaptive variation links energy-dependent changes from angstroms to ecosystems in all living genera  via the physiology of their food energy-dependent pheromone-controlled reproduction.

For comparison to mRNA stability during the maternal-to-zygotic transition, see: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

The energy-dependent molecular mechanisms of recombination clearly link microRNA biogenesis to the stability of organized genomes during the life histories of all genera. Serious scientists object to the use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation.

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

…it is tiresome to raise the same objections repeatedly, wondering why researchers have not fulfilled some of the basic requirements for establishing the occurrence of an autophagic process.

 

Alternative splicing of pre-mRNA

Do not refute cherished theories

Synopsis:
All serious scientist know that pre-mRNAs (now known as microRNAs in more than 70,000 published works) do not create themselves.
For comparison, Ricki Lewis fails to mention how fertility is biophysically constrained by by the creation of the sun’s anti-entropic virucidal energy, the creation of enzymes (e.g, ATP synthase), the creation of ATP, the creation of microRNAs, and the RNA-mediated creation of hormones and receptors that link achiral glycine in position 6 of the GnRH decapeptide to all experience-dependent receptor mediated structures and function in all vertebrates with jaws.

8 Simple mistakes that can delay peer review (and how to avoid them) (2018)

Add: Do not refute neo-Darwinian pseudoscientific nonsense or Big Bang cosmology. If we publish your work, we will retract it.
See for instance: Biomechanical Characteristics of Hand Coordination in Grasping Activities of Daily Living (2016) [retracted]

Following publication, readers raised concerns about language in the article that makes references to a ‘Creator’, and about the overall rationale and findings of the study.

For comparison, there was no need to mention a “Creator’ in  From Fertilization to Adult Sexual Behavior (1996)

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…

All serious scientist know that pre-mRNAs (now known as microRNAs in more than 70,000 published works) do not create themselves.
For comparison, Ricki Lewis fails to mention how fertility is biophysically constrained by by the creation of the sun’s anti-entropic virucidal energy, the creation of enzymes (e.g, ATP synthase), the creation of ATP, the creation of microRNAs, and the RNA-mediated creation of hormones and receptors that link achiral glycine in position 6 of the GnRH decapeptide to all experience-dependent receptor mediated structures and function in all vertebrates with jaws.
See: The Biology Behind the Fertility Clinic Meltdown

The spindle apparatus is among the most elegant structures in a cell, quickly self-assembling from microtubules and grabbing and aligning chromosomes so that equal sets separate into the two daughter cells that result from a division.

Self-assembling is a term often used by biologically uninformed theorists who do not understand what is known to serious scientists about cell type differentiation. See for an accurate representation of how fertility in all mammals is naturally biophysically constrained by FSH.
Regulation of FSH expression by differentially expressed miR-186-5p in rat anterior adenohypophyseal cells

Our results demonstrate that miR-186-5p regulates FSH secretion by directly targeting the FSHb 3′ UTR, providing additional functional evidence for the importance of miRNAs in the regulation of animal reproduction.

For more information about the virus-driven fertility meltdown that alters the structure and function of all mammalian genomes in every generation, see:
The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
and
Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
 

"Evolution of Man. - Undoubtedly there once lived upon the earth races of men who were much lower in their mental organization than the present inhabitants.

Natural selection for racism and all pathology

Why is natural selection hard to grasp? It is not what you think….

…human cognitive tendencies interfere more with deep understanding of how natural selection works.

Simply put, our intelligence and teleological reasoning interferes with the teaching of pseudoscientific nonsense. The nonsense does not place Darwin’s “conditions of life” before natural selection for reproductive fitness. Natural selection is food energy-dependent and pheromone-controlled in the context of biophysically constrained viral latency.
See for comparison: The vibrational theory of olfaction for the win

Darwin’s energy-dependent conditions of life link biophysically constrained viral latency to healthy longevity. Luca Turin’s works are among those that exposed the fraudulent claims of neo-Darwinian theorists.

See for example: Molecular recognition in olfaction

For physicists, maybe the single most important development that can be envisaged is the production of a high quality X-ray structure of a one or more olfactory receptors. This would open the door to large scale computer simulations that would help shed light on both the mechanical and electrical responses of olfactory receptors.

The X-ray structure of the virus that destroys olfactory receptors is more important. It can be viewed in the context of everything know to serious scientists who have linked quantum physics to quantum souls.
For example, see: Rosalind Franklin: The Hero Denied Her Due 

Franklin was also a brilliant chemist and a master of X-ray crystallography, an imaging technique that reveals the molecular structure of matter based on the pattern of scattered X-ray beams. Her early research into the microstructures of carbon and graphite are still cited, but her work with DNA was the most significant — and it may have won three men a Nobel.
Franklin left King’s in 1953 in a long-planned move to join J.D. Bernal’s lab at Birkbeck College, where she discovered the structure of the tobacco mosaic virus. But in 1956, in the prime of her career, she developed ovarian cancer — perhaps due to her extensive X-ray work. Franklin continued working in the lab until her death in 1958 at age 37.
“As a scientist, Miss Franklin was distinguished by extreme clarity and perfection in everything she undertook,” Bernal wrote in her obituary, published in Nature. Though it’s her achievements that close colleagues admired, most remember Franklin for how she was forgotten. — C.E.

For comparison, these authors take the ball that Nesse and other theorists put into play, and these theorists run with it. They even pretend to be “biologically informed,” in response to my oft repeated claim that people like them are biologically uninformed science idiots.
The Future of Secularism: a Biologically Informed Theory Supplemented with Cross-Cultural Evidence

…earlier trends toward secularization (due to science education surrounding advancements in science) are currently being counter-balanced by genetic and reproductive forces. The authors also propose that the inverse association between intelligence and religiosity, and the inverse correlation between intelligence and fertility lead to predictions of a decline in secularism in the foreseeable future.

The agenda of at least two co-authors: Nyborg and Ellis, is clear. See: Race and Sex Differences in Intelligence and Personality: A Tribute to Richard Lynn at Eighty 

Nyborg and Lee Ellis promote the works of J. Phillipe Rushton who was reported to be among the top racists of the 20th century.

See: Do pigmentation and the melanocortin system modulate aggression and sexuality in humans as they do in other animals?

Pigmentation of the hair, skin, cuticle, feather and eye is one of the most salient and variable attributes of vertebrates. In many species, melanin-based coloration is found to be pleiotropically linked to behavior. We review animal studies that have found darker pigmented individuals average higher amounts of aggression and sexual activity than lighter pigmented individuals. We hypothesize that similar relationships between pigmentation, aggression, and sexuality occur in humans. We first review the literature on non-human animals and then review some of the correlates of melanin in people, including aggression and sexual activity. Both within human populations (e.g., siblings), and between populations (e.g., races, nations, states), studies find that darker pigmented people average higher levels of aggression and sexual activity (and also lower IQ). We conceptualize skin color as a multigenerational adaptation to differences in climate over the last 70,000 years as a result of “cold winters theory” and the “Out-of-Africa” model of human origins. We propose life history theory to explain the covariation found between human (and non-human) pigmentation and variables such as birth rate, infant mortality, longevity, rate of HIV/AIDS, and violent crime.

Pigmentation is food energy-dependent and RNA-directed DNA methylation links food odors to pheromones and the physiology of reproduction in all living genera. It would be interesting to hear what Jay R. Feierman thinks about this since I met him at a 1995 conference that Lee Ellis organized and J. Phillipe Rushton also attended (by invitation only).

All (~90) attendees should be familiar with works that extended the social science theories to “hate-mongering.” I have tried to stop the hate-mongering, but history may repeat itself with Feierman’s help, of course.
See for comparison: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

Natural selection for energy-dependent codon optimality has been linked via olfaction from quantum physics to all biologically based RNA-mediated cell type differentiation via amino acid substitutions in organized genomes. But Nesse and others like him want to keep their teaching positions and that requires them to deny everything known to serious scientists about physics, chemistry, and molecular epigenetics.
See for comparison: A Civic Biology: Presented in Problems (New York, 1914): pp. 193-196, 253-254, 261-263.
Social scientists ignored Darwin’s “conditions of life.” Most of them don’t seem to understand why I claim that their ignorance has caused the deaths of millions.
See for comparison:  The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…
Will history repeat itself? Will most of us return to the racism of Hunter (1914)?

In the review The Future of Secularism: a Biologically Informed Theory Supplemented with Cross-Cultural Evidence, they obfuscate the claim that Muslims are less intelligent and more fertile than Jews or Buddhists. What will happen when their claim is linked to this claim from Hunter: “A Civic Biology: Presented in Problems” pp. 195-196 

Evolution of Man. – Undoubtedly there once lived upon the earth races of men who were much lower in their mental organization than the present inhabitants. If we follow the early history of man upon the earth, we find that at first he must have been little better than one of the lower animals.
Any and all links from intelligence to fertility are claims that attempt to support the pseudoscientific nonsense touted by neo-Darwinian theorists. Their ridiculous theories are the cause of all pathology.

The Root Cause Of Cancer and Why it Has Been Kept a Secret!

…the root cause of cancer is too much acidity in the body, meaning that the pH in the body is below the normal level of 7.365, which constitutes an “acidic” state. Warburg investigated the metabolism of tumors and the respiration of cells and discovered that cancer cells maintain and thrive in a lower pH, as low as 6.0, due to lactic acid production and elevated CO2. He firmly believed that there was a direct relationship between pH and oxygen.
Anyone who ever performed a blood gas analysis could have helped to establish the fact that the virus-driven degradation of messenger RNA is the cause of all pathology. See for instance: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”
 
The synthesis of RNA in isolated thymus nuclei is ATP dependent.

That fact made it obvious to all serious scientists that energy-dependent RNA mediated DNA repair was required for healthy longevity. The anti-entropic virucidal energy of the sun was linked to the creation of ATP by Schrodinger (1944) in “What is Life?” The food energy-dependent pheromone-controlled physiology of reproduction in species from microbes to humans now links the creation of RNA to all biodiversity, and that links pheromones to biophysically constrained transgenerational epigenetic inheritance of healthy longevity via viral latency.

Nothing has been hidden. There was no reason to hide the facts after theorists made it possible to teach their pseudoscientific nonsense to students in high school via the Scopes Trial in Dayton, TN (1925). Sinclair Lewis published “Arrowsmith” in 1925 and since then, ATP-dependent biophysically constrained viral latency has been detailed in the context of the cell biology game “Cytosis” with its “Virus Expansion.”
 

Cytosis: A Cell Biology Board Game

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

Alternative splicing of pre-mRNA

Methylation and the Innate Immune System

Free Webinar Training:

Methylation and the Innate Immune System

Please send your questions, comments and feedback to: support@qahomestudy.com

I sent these two questions in advance:

1) Does what organisms eat link food energy to RNA-directed DNA methylation and all healthy longevity via fixation of amino acid substitutions and transgenerational epigenetic inheritance in the context of the physiology of pheromone-controlled reproduction in species from microbes to humans?

2) Does the virus-driven theft of quantized energy link the loss of information from impaired methylation to all pathology?

——————————

See why I asked: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

The potential for sperm miRNA affecting zygote development has recently been reported in the literature [18] and has interesting implications for the use of sperm miRNA profiles as indicators of potential male fertility.

See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See also: Olfaction Warps Visual Time Perception



A rendering of how changes in an electron's motion (bottom view) alter the scattering of light (top view), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Credit: Extreme Light Laboratory|University of Nebraska-Lincoln

Energy-dependent physical and biophysical constraints (3)

See first: Energy-dependent physical and biophysical constraints (2)
Emily Balskus Pins Down the Chemistry and Metabolism of Human Microbiomes
Summary: The chemistry and metabolism of all microbiomes is food energy-dependent and pheromone-controlled via the physiology of reproduction.
See: Feedback loops link odor and pheromone signaling with reproduction

My comment to The Scientist:

…trans-4-hydroxy-L-proline (Hyp) dehydratase, a newly discovered member of an abundant family of proteins, produced by gut bacteria, known as the glycyl radical enzymes, helps in metabolizing trans-Hyp, an amino acid that is rare in bacteria but is common in eukaryotes.

The de novo creation of energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA protects the organized genomes of all living genera from the virus-driven degradation of messenger RNA, which has been linked from mutations to all pathology via the claims Schrodinger made in “What is Life?” (1944).

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.) (pp. 73 and 74)

See also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

Natural selection for food energy-dependent codon optimality links the sense of smell in bacteria to the biophysically constrained viral latency that links ecological variation to ecological adaptations in species from microbes to humans via the conserved molecular mechanisms of RNA-mediated cell type differentiation.

Sunlight has since been placed into the context of quantized energy as information, which links our visual perception of mass and energy from the space-time continuum to the concept of the energy-dependent creation of quantum souls.
See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (2016) and From Fertilization to Adult Sexual Behavior (1996)
 

terrarium-eco-system

Dobzhansky 1973 and precision medicine

MicroRNA-34 directly targets pair-rule genes and cytoskeleton component in the honey bee

Our findings point to miR-34-5p as novel regulatory component in the complex molecular cascade that governs insect segmentation and to a broader role of miRNAs in the early development due to the detection of mature transcripts from both 5p and 3p arms for several precursor miRNAs. Thus, this work encourages further investigation to pinpoint miRNAs as fine tuners of insect early development.

Anna Di Cosmo‘s group took the lead and already linked all invertebrates to all vertebrates via the conserved molecular mechanisms that link microRNA flanking sequences to all energy-dependent  biophysically constrained biodiversity.

See for example: Role of olfaction in Octopus vulgaris reproduction (January 1, 2015)

For a perspective, see: The phylogenetic utility and functional constraint of microRNA flanking sequences (February 18, 2015)

The majority of flanking sequences used in our analyses are composed of non-coding intergenic DNA, suggesting that conservation of these hairpin-loop flanking sequences is independent of either the presence of exonic sequence or protein-coding gene regions.

For the extension to humans, see:

Practical Approaches for Whole-Genome Sequence Analysis of Heart- and Blood-Related Traits

 …all amino acid substitutions or all promotor variants are not equal, and one can predict the impact based on knowledge of the location and type of substitution.

All cell type specific and tissue type specific amino acid substitutions in all individuals of all living genera are energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction. A long-time antagonist echoed that fact in the human ethology yahoo group, but he took facts about complex traits out of context. See: Practical application of whole-genome sequencing

The complex traits used here are heart and blood related ones, but the concepts are applicable to all complex genetically-sourced traits, including behavioral ones. — Clarence A. ‘Sonny’ Williams

Complex traits are not genetically sourced. The physiology of pheromone-controlled reproduction is clearly the link to the complexity of all nutrient energy-dependent morphological and behavioral traits.
See: No Genetics without Epigenetics? No Biology without Systems Biology?

…a unified understanding of life requires: (1) a view on its component parts, the cells, (2) a view on the life cycles of all cells—their formation, growth, development, and reproduction—as based in chemical reactions among similar sorts of molecules, (3) a view on the way in which amino acids are put together to form proteins, as specified by DNA and RNA according to a nearly universal and precise scheme.

That fact makes it perfectly clear that behavioral traits are not genetically sourced. All traits arise only in the context of systems biology, which links the epigenetic landscape to the physical landscape of supercoiled DNA in all living genera. For comparison, Clarence A ‘Sonny Williams wrote:

mutations in gene regulatory regions are the “driving force” behind human brain complexity. 

and

I do not reply to creationists or anyone who does not believe that humans evolved via Darwinian natural selection.

The facts about systems biology were stated clearly in Dobzhansky’s Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973)

Cytochrome C is an enzyme that plays an important role in the metabolism of aerobic cells. It is found in the most diverse organisms, from man to molds. E. Margoliash, W. M. Fitch, and others have compared the amino acid sequences in cytochrome C in different branches of the living world. Most significant similarities as well as differences have been brought to light. The cytochrome C of different orders of mammals and birds differ in 2 to 17 amino acids, classes of vertebrates in 7 to 38, and vertebrates and insects in 23 to 41; and animals differ from yeasts and molds in 56 to 72 amino acids. Fitch and Margoliash prefer to express their findings in what are called “minimal mutational distances.” It has been mentioned above that different amino acids are coded by different triplets of nucleotides in DNA of the genes; this code is now known.

See also:

For example, 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.

The de novo creation of amino acids has since been linked from chirality to autophagy and healthy longevity via chromosomal rearrangements.
See:
Light-Induced Opening and Closing of the Intramolecular Hydrogen Bond in Glyoxylic Acid
Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins
Dynamic control of chirality and self-assembly of double-stranded helicates with light
The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes

The cycle of interconversion of assemblies and helicities shown here holds promise to design other dynamic systems driven out of equilibrium by light energy.

See also: ATP hydrolysis by UPF1 is required for efficient translation termination at premature stop codons
The de novo creation of amino acids has since been linked from the energy-dependent creation of helicase to the structure of functional DNA. Theories about minimal mutational distances have been replaced by facts that link angstroms to ecosystems in all living genera via biophysically constrained RNA-mediated protein folding chemistry.

See: Structural diversity of supercoiled DNA

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.

They linked energy-dependent metabolic networks to genetic networks by recapitulating Dobzhansky’s claims and in this parody they add: “every angstrom is dynamic from the 5 prime to the three”

See also: Structure of eukaryotic CMG helicase at a replication fork and implications to replisome architecture and origin initiation

…definitive conclusions about the exact role of the N-tier in helicase mechanism will require higher resolution to identify candidate-specific amino acid residues, followed by direct mutagenesis and biochemical characterization.
 

Although the candidate-specific amino acid residues have not been identified, the energy-dependent creation of RNA-mediated amino acid “residues” links the anti-entropic virucidal energy of sunlight from angstroms to ecosystems in all living genera via chirality and autophagy, which protect all organized genomes from virus-driven entropy in the context of the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes.

See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

See also: Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes

The ZAL2 and ZAL2m alleles code for 597 amino acids, with two fixed differences driving a Val73Ile and Ala552Thr polymorphism in ZAL2m. valine to alanine substitution

How social learning adds up to a culture: from birdsong to human public opinion
Conclusion:

For human online cultures, we suggest that it may be useful to consider features of birdsong learning, which have been optimized over millions of generations to give rise to stable polymorphic cultures. Experimenting with implementation of similar features in online communication systems could potentially facilitate the design of more stable and balanced information systems, which can potentially promote distributed self-governance.

Public opinion (above) is based on bird-brained representations of pseudoscientific nonsense about “…balanced information systems, which can potentially promote distributed self-governance.” The information systems are not linked from energy-dependent changes in the microRNA/messenger RNA balance to all biodiversity via the physiology of pheromone-controlled reproduction. Instead the information systems automagically may promote “distributed self-governance” across all species in the context of millions of years of evolution.

In my model of biologically-based cause and effect, top-down causation is linked from natural selection for energy-dependent codon optimality to the physiology of reproduction and all biodiversity via supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.

For an example of medication-induced genomic entropy, see: Some Antibiotics Linked to Serious Nerve Damage

The FDA is strengthening its warning that a popular class of antibiotics, called fluoroquinolones, may cause sudden, serious, and potentially permanent nerve damage called peripheral neuropathy.

See also: There is nothing inevitable or natural about chronic disease

Causation at the molecular level, deep inside the body, appears to be beyond our current reach

See for comparison: Understanding and accounting for relational context is critical for social neuroscience

George Ellis:

This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: http://rsfs.royalsocietypublishing.org/content/2/1.toc

I wrote:

New data on how genetic predispositions are epigenetically linked to phenotypically distinct neuroanatomy and behaviors is provided in the honeybee model. Across-species comparisons from insects to vertebrates clearly show that the epigenetic influence of food odors and pheromones continues throughout the life of organisms that collectively survive whereas individuals do not. These comparisons also attest to the relative salience of sensory input from the rearing environment. For example, when viewed from the consistency of animal models and conditioned behaviors, food odors are obviously more important to food selection than is our visual perception of food. Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.

Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).” — Kohl, JV (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors
See also: Methylation Maestro

So are many others who do not understand how energy-dependent changes in chirality must be linked from autophagy to supercoiled DNA in the context of the physiology of reproduction and fixation of RNA-mediated amino acid substitutions.

They have failed to link the National Microbiome Initiative to the Precision Medicine Initiative via RNA-mediated protein folding chemistry and are trapped in theories with no explanatory power.

If you ask one of them about the virus-driven energy theft of quantized energy, which is linked to all pathology, they will run away. They cannot stand to think about how the potential of hydrogen (pH) must be linked from sunlight to all biodiversity via the claims of Schrodinger in What is Life? (1944)

Alternative splicing of pre-mRNA

Did evolution autophosphorylate your kinases? (2)

Hecatombic evolution

Deep-Sea Viruses Destroy Archaea

Excerpt:

Given the enormous scale of deep-sea ecosystems, the results indicate that archaea-virus relationships could be a major contributor to global biogeochemical cycles.

My comment:  I know that Anna Di Cosmo​ and John Hewitt​ are able to link virus-driven energy theft to all pathology in all living genera via the conserved molecular mechanisms they have already placed into their proper perspective on natural selection for energy-dependent codon optimality, which links the innate immune system to supercoiled DNA via the physiology of reproduction in the context of global biogeochemical cycles. Has anyone else already done that?
See for example:
1) Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
2) The Excitable Mitochondria by John Hewitt
3) Neuroendocrine–Immune Systems Response to Environmental Stressors in the Cephalopod Octopus vulgaris by Anna Di Cosmo and Gianluca Polese
4) Human pheromones: integrating neuroendocrinology and ethology
See for comparison:Did evolution autophosphorylate your kinases?
The idea the evolution could do what energy as information has done since the time that the energy was created, seems incredibly bizarre. It’s as if theorists still think they can explain away the role that virus-driven energy theft plays in all pathology by claiming that all species evolved from a common ancestor in the absence of biophysically constrained nutrient energy-dependent DNA repair. That’s why part two of Did evolution autophosphorylate your kinases?seems to be required.
Virus-mediated archaeal hecatomb in the deep seafloor
Excerpt:

Viruses are the most abundant biological entities in the world’s oceans, and they play a crucial role in global biogeochemical cycles. In deep-sea ecosystems, archaea and bacteria drive major nutrient cycles, and viruses are largely responsible for their mortality, thereby exerting important controls on microbial dynamics.

My comment: What, pray tell is a “hecatomb?” Does the word choice tell you anything about the difference between energy as information in the context of the polycomb repressive complex and energy theft linked to bloodshed, killing, havoc, slaughter, warfare, annihilation, et al.?
See: Gene Silencing Triggers Polycomb Repressive Complex 2 Recruitment to CpG Islands Genome Wide
See also: From Fertilization to Adult Sexual Behavior
Excerpt:

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.

My comment: The viruses in the deep blue see are still destroying archaea faster than they are destroying bacteria in the context of whatever the word hecatomb may mean for comparison to polycomb repression of virus-driven energy theft. Polycomb repression of virus-driven energy theft appears to be the link from bacteria and all other living genera to ecological adaptikon at a level above and beyond the failed adaptation to virus-driven energy theft in archaea that is almost literally and figuratively killing the archaea. Ecological adaptation in bacteria and all other living genera is nutrient energy-dependent and pheromone-controlled via the physiology of energy-dependent reproduction.
The death rate in archaea is an example of the fact that there is only one way to link energy as information to all biodiversity.  Autophagy links energy-dependent biophysically constrained viral latency from biodiversity in the ocean to all biodiversity on Earth via conserved molecular mechanisms.
For contrast, ask yourself again, Did evolution autophosphorylate your kinases?  A family member said she would need to learn what all these words meant before she might understand the basis for my claims or why I was joking about evolution. Many other family members have simply dismissed every claim I have ever made. This is for Melinda.

A protein kinase is a kinaseenzyme that modifies other proteins by chemically adding phosphate groups to them (phosphorylation). Phosphorylation usually results in a functional change of the target protein (substrate) by changing enzyme activity, cellular location, or association with other proteins. The human genome contains about 500 protein kinase genes and they constitute about 2% of all human genes.[1] Up to 30% of all human proteins may be modified by kinase activity, and kinases are known to regulate the majority of cellular pathways, especially those involved in signal transduction. Protein kinases are also found in bacteria and plants.

My comment: If bacteria automagically evolved into plants and humans, kinases must have been autophosphorylated outside the context of what is known about how quantised energy as information from the sun is linked from chemical ecology to all biodiversity on Earth by the polycomb repressive complex. In other words. if your kinases were not autophosphorylated by evolution, you did not evolve from a species of bacteria in the ocean.
‘That fact can be placed into the context of these two reports:
1) Sulfur-cycling fossil bacteria from the 1.8-Ga Duck Creek Formation provide promising evidence of evolution’s null hypothesis
2) Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

  1. On these bases and supporting lines of evidence, we interpret the striking similarities in organismal morphology, community structure, habitat, and evident physiology between the ancient and modern sulfur-cycling biotas as evidencing stasis resulting from adaptation to a physically quiescent subseafloor environment that has remained essentially unchanged over billions of years.
  2. Evolutionary Rewiring “… biological function—in this case, flagellar motility in Pseudomonas fluorescens—can re-evolve after the deletion of a seemingly critical gene. The bacteria regained motility not by reacquiring the lost gene . . . but instead by mutations in other genes that put their products to new uses.”

My comment: See my comments on “Evolutionary Rewiring.” They may still appear on the page from the article in The Scientist. The claim that mutations caused the weekend evolution of a irreducibly complex functional structure cannot be made by someone who is biologically informed. Statements such as that must come from biologically uninformed science idiots who know nothing about the phosphorylation of kinases, which links physics from chemical ecology to the molecular epigenetics of all cell type differentiation and all biodiversity on Earth.
The challenge to theorists is for them to explain the lack of changes in bacteria during ~2 billion years for comparison to the nutrient energy-dependent pheromone-controlled weekend resurrection of the bacterial flagellum in an organism that fluoresces on exposure to ultraviolet (UV) light, which is delivered at the speed of light on contact with water as information about quantized energy.
Experimental evidence that links femotosecond blasts of UV light might be considered in the context of all other refutations of pseudoscientific nonsense touted by neo-Darwinian theorists.
See: Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution and UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair
My comment: Alternatively, help pseudoscientists elect another Democrat to be President of the United States of America because the current regime has collectively probably already killed us all. Why not die laughing at them, if you can tolerate the suffering that has been caused by the failure of evolution to autophosphorylate your kinases?

Alternative splicing of pre-mRNA

Light energy-dependent active motifs

Active Motif claims that Active Motif is the industry leader in developing and delivering innovative tools to enable epigenetics and gene regulation research.

See how the role of light is portrayed in LightSwitch™ Luciferase Assay System (with my emphasis)

Excerpt 1) Combined with our large collection of miRNA Mimics and Inhibitors, you have everything needed to study miRNA-3´UTR interactions, validate miRNA targets, measure RNA stability, translation efficiency and the functional impact of miRNAs on a gene-by-gene basis.
Excerpt 2) The LightSwitch lncRNA Promoter Reporter Collection was designed to make it fast & easy to study the regulation of lncRNA promoters.
Excerpt 3) LightSwitch™ Validated Pathway Collections… have been experimentally validated to show significant activation or repression in response to pathway-specific induction conditions, so they are ideal when studying pathways such as inflammation, hypoxia, DNA damage, heat shock, etc.

My comment: They portray the light energy-dependent active motifs as switches. The switching is RNA-mediated. Fixation of RNA-mediated amino acid substitutions links the biophysically constrained chemistry of protein folding from the innate immune system to supercoiled DNA via the physiology of energy-dependent reproduction in all living genera.
The facts about “…everything needed to study miRNA-3´UTR interactions, validate miRNA targets, measure RNA stability, translation efficiency and the functional impact of miRNAs on a gene-by-gene basis” were included in this invited review of nutritional epigenetics. Active Motif repeatedly attests to the experimental evidence that attests to the facts in:

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.

My comment: Claims by Active Motif’are parroted by others. The facts can be linked from the LightSwitch™ Validated Pathway Collections to the study of pathways that link nutritional epigenetics to prevention of inflammation, hypoxia, DNA damage, heat shock, et al., via changes in pH. Femtosecond blasts of ultraviolet (UV) light link the changes in pH link from hydrogen-atom transfer in DNA base pairs in solution to RNA-mediated DNA repair in all living genera.
For example, all living genera reproduce. That’s a fact! That fact links the Laws of Biology in my model to all biodiversity. The Laws of Biology refute every aspect of neo-Darwinian theory with experimental evidence of biologically-based cause and effect. The facts were revisited in a series of presentations during Labroots virtual conferences. But remember this claim:

…everything needed to study miRNA-3´UTR interactions, validate miRNA targets, measure RNA stability, translation efficiency and the functional impact of miRNAs on a gene-by-gene basis…

The experimentally validated facts were linked from energy-dependent changes in angstroms to ecosystems in these 4 presentations.

The Origin of Information: How to Solve It

video

From hydrogen atom transfer in DNA base pairs to ecosystems

video

What is life when it is not protected from virus driven entropy

video

RNA-mediated physics, chemistry, and molecular epigenetics

video

For an easy to understand representation of facts that link angstroms to ecosystems in all living genera via nutrient energy-dependent supercoiled DNA, see:

For comparison, see: Active Motif Webinars
Excerpt:

Stay up-to-date with the latest tips & techniques from our Epigenetics experts.

My comment: If you find any information that suggests the representations at RNA-mediated.com are inaccurate or that the representations on the RNA-mediated FB group  are not supported by experimental evidence of biologically-based cause and effect, please comment on what you found for comparison Alternatively, watch for the results of the patent battle that will result if this patent application is successful.
See: RNA-Guided Human Genome Engineering reported in the context of this Secret meeting
Excerpt:

Why would a bunch of scientists need to exclude the media and the public from a meeting about something as ethically fraught as synthesizing a human genome?

The only reason to exclude anyone who could possible challenge the representations made at the secret meeting is to keep secrets about the facts. Those who keep secrets about energy-dependent RNA-mediated cell type differentiation have help from people who know nothing about the secrets that are being kept.
See also:  Evolution, Mutation, Super Bacteria, Oh My: When Mr. Jerry Coyne Shoots Himself in the Foot

September 14, 2016 Nathan van Ree wrote: Just to get it clear: do I understand correctly that Tomi got knowledge from your publication, misrepresented your publication by cherry picking parts of it and post those here, which made your presentation look so bad people outside of this group decided not to publish it?
What’s the difference between your conclusions and the way Tomi represents them and why would he do that?
Are your conclusions against the position of YEC, that of (neo) Darwinism, or neither?

My response: Thanks for helping to clarify what he has done, before asking. Tomi has only done the cherry-picking after the fact, and after publication of my 2013 review. Others cherry picked the information in the invited review that was returned without review.

The difference is the amount of secrecy used to mislead others who might decide to accept Tomi’s beliefs compared to the experimental evidence of biologically-based cause and effect. My conclusions are based on facts, which link my publication history across twenty years to the published works of other serious scientists.

See also the secretive approach by antagonist Tomi Aalto, who others seem to think is supporting my model with his plagiarism.

Mechanisms known to affect the phenotype

1. RNA methylation
2. DNA dinucleotide methylation
3. DNA CpG island methylation
4. Histone methylation
5. Chromatin remodeling
6. DNA coiling
7. MicroRNA regulation
8. Alternative splicing

All phenotypes are nutrient-energy dependent and virus-driven energy theft causes all pathology. In our 1996 Hormones and Behavior review, we wrote:

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.

The pre-mRNAs link energy-dependent changes in the microRNA/messenger RNA balance to all biodiversity, which is the next thing that Tomi Aalto will ineffectively try to do. Find out where Tomi got his information on energy-dependent RNA methylation and how he linked it to energy-dependent alternative splicings without mention of nutrient energy-dependent changes in hydrogen-atom transfer in DNA base pairs that link the physiology of reproduction to fixation of RNA-mediated amino acid substitutions in all organized genomes via supercoiled DNA, which protects all species from virus-driven energy theft and genomic entropy.

Genomic entropy is biophysically constrained by energy, not by evolution.

See for comparison: Brain evolution and development: adaptation, allometry and constraint

Excerpt:

2. What explains the presence of genetic correlations? Where present, the strength of genetic correlations between components could be combined with data on developmental (or evolutionary) origin and connectivity, to test whether genetic correlations evolve in response to functional integration (figure 1, scenario (v)), or reflect patterns of conserved developmental origin (figure 1, scenario (i)).

My comment: Energy-dependent RNA-mediated biophysically constrained protein folding explains genetic correlations, which arise only in the context of detailed links from the innate immune system to supercoiled DNA. Energy-dependent changes are linked to all cell type differentiation. Claims about evolution are the antithesis of claims that link ecological variation to energy-dependent ecological adaptations via what is known to all serious scientists about energy-dependent RNA-mediated protein folding chemistry.

See for comparison: Mutation-Driven Evolution

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements” (p. 199).

See also: Alternative RNA Splicing in Evolution

It now appears that alternative splicing is, perhaps, the most critical evolutionary factor determining the differences between human beings and other creatures.

My comment: Alternative RNA splicing is not an evolutionary factor. It links energy-dependent changes from angstroms to ecosystems in all living genera via fixation of RNA-mediated amino acid substitutions in the context of the physiology of reproduction, which is controlled by pheromones in species from microbes to humans.

From Fertilization to Adult Sexual Behavior

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

 See also: Circular RNAs: Novel Regulators of Neuronal Development

 

rp_levels-of-organization.jpg

Biophotonics, glycobiology, quantized biodiversity (2)

From Fertilization to Adult Sexual Behavior (1996)
In our section on Molecular epigenetics, we wrote:

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.

My comment: Serious scientists have since learned that all cell type differences arise from alternative splicings of otherwise identical genes. Pseudoscientists still make claims about the emergence of life and link natural selection to structural biology and the function of genome organization.

See for comparison: A Big Bang in spliceosome structural biology (2016)

Excerpt:

Splicing cycles through a series of steps in which the spliceosome assembles on the intron-containing pre-mRNA, defining the boundaries between exons—the sequences ultimately retained in the mature mRNA—and introns (see the figure, panel A).

My comment: Energy-dependent changes in angstroms to ecosystems link the defined boundaries between exons and introns from ecological variation to ecological adaptation and all biodiversity.  The “Big Bang” in structural biology is a contextualized polite way to tell theoretical physicists and other theorists that energy-dependent changes in functional structures must link ecological variation to ecological adaptation via what is known to serious scientists about all the links from angstroms to ecosystems in all living genera. Others have been trying to tell theorists how to link biologically-based cause and effect for several years.

See for example (2007): The MicroRNA miR-124 Promotes Neuronal Differentiation by Triggering Brain-Specific Alternative Pre-mRNA Splicing
Excerpt:

Both microRNAs and alternative pre-mRNA splicing have been implicated in the development of the nervous system (NS), but functional interactions between these two pathways are poorly understood.

My comment: All serious scientists know that the functional interactions among microRNAs and alternative pre-mRNA splicing are nutrient energy-dependent and controlled by the physiology of reproduction. Do you know how energy-dependent RNA methylation links biophysically constrained protein folding chemistry to cell type differentiation via RNA-mediated amino acid substitutions? If not, you probably do not know why  information about amino acid substitutions was left out of the claim that linked chromatin to the control of behavior in this misrepresentation:
Chromatin controls behavior
Conclusion:

…the discoveries of Yang et al. are an important addition to an emerging literature implying a dynamic epigenome in the central nervous system (14, 15), which is contrary to the prevailing dogma in the epigenetics field.

My comment: There is no prevailing dogma in the epigenetics field. The dogma was eliminated when serious scientists linked energy-dependent changes from angstroms to ecosystems via epigenetic effects of sensory input on the innate immune system; the de novo creation of G protein-coupled receptors; the physiology of reproduction, and fixation of RNA-mediated amino acid substitutions that link supercoiled DNA to protection from virus-driven energy theft and genomic entropy in all organized genomes of all living genera.
See also: Chromatin remodeling inactivates activity genes and regulates neural coding.
Summary: Epigenetic regulation in the brain

The activity of neurons in the brain controls the transcription of genes that influence the pruning of dendritic connections between neurons, and such modifications can influence animal behavior. Yang et al. propose a role for chromatin remodeling by the nucleosome remodeling and deacetylase complex (NuRD) in the inactivation of such activity-dependent transcription in the mouse cerebellum (see the Perspective by Sweatt). Deposition of the histone variant H2A.z at promoters of activity-dependent genes required the NuRD complex. Loss of the NuRD complex function resulted in hypersensitivity of mice to sensory stimuli and excessive neuronal connectivity in animals performing a task on a treadmill.

This article was reported as: Ability to turn off genes in brain crucial for learning, memory
Excerpt (with my emphasis):

One process that controls chromatin structure and transcription is chromatin remodeling by energy-dependent protein complexes (4). Such complexes that depend on adenosine 5′-triphosphate (ATP) can control gene expression by moving, ejecting, or restructuring nucleosomes, the scaffolds around which DNA wraps. Each nucleosome contains a core particle of eight histone protein subunits (5). Remodeling events include posttranslational modifications, swapping individual One process that controls chromatin structure and transcription is chromatin remodeling by energy-dependent protein complexes (4). Such complexes that depend on adenosine 5′-triphosphate (ATP) can control gene expression by moving, ejecting, or restructuring nucleosomes, the scaffolds around which DNA wraps. Each nucleosome contains a core particle of eight histone protein subunits (5). Remodeling events include posttranslational modifications, swapping individual histone subunit isoforms into and out of the core particle, and facilitating the unbinding of DNA from the core particle.
into and out of the core particle, and facilitating the unbinding of DNA from the core particle.

My comment: Chromatin remodeling is energy-dependent. But, they buried the facts about how energy-dependent chromatin remodeling links sensory input from learning and memory to fixation of RNA-mediated amino acid substitutions. The substitutions differentiate all cell types of all individuals of all living genera, which explains why they invented the term histone subunit isoforms.
Serious scientists understand why pseudoscientists bury facts by stringing words together without telling others what a histone subunit isoform is, or what differentiates one histone subunit isoform from any other histone subunit isoform. In this case, the wordplay prevents others from learning that the availability of nutrients and nutrient energy-dependent changes links link fixation of RNA-mediated amino acid substitutions from learning and memory to chromatin remodeling and the control of behavior. Pseudoscientists tend to remove facts from consideration and remove the facts from the context of via well established pathways that link the epigenetic landscape to the physical landscape of supercoiled DNA  in all living genera.
See for example: Roles of Mutation and Selection in Speciation: From Hugo de Vries to the Modern Genomic Era
Excerpt:

…we will not consider geographical and ecological factors because of space limitation. Our primary purpose is to clarify the roles of mutation and selection in the evolution of reproductive isolation and show that the molecular basis of speciation is more complicated than generally thought at present. (p. 813)

My comment: Inventing the term histone subunit isoform outside the context of geographical and ecological factors is another way to dismiss the complexity of speciation.
See for example: This article mentions a subunit isoform in the context of Loss of the V-ATPase B1 Subunit Isoform Expressed in Non-Neuronal Cells of the Mouse Olfactory Epithelium Impairs Olfactory Function
Excerpt:

The present study is the first to indicate the relevance of the VATPase, and presumably of V-ATPase-mediated proton secretion, in olfactory function. Undoubtedly, further functional and behavioral studies will allow a more comprehensive assessment of the physiological and clinical significance of V-ATPase expression in sustentacular and microvillar cells of the olfactory epithelium. At this point, we can only speculate on such possibilities. For example, modulating olfactory H+ secretion could offer the ability of up- or down-regulating the threshold of detection for certain odorants. Moreover, since the NML plays a role as a barrier against inhaled pathogens, and microbial and chemical toxins, regulating mucus pH may be relevant for protection against various specific diseases.

My comment: If you are unable to link the modulation of olfactory H+ secretion from hydrogen-atom transfer in DNA base pairs in solution to the de novo creation of G protein-coupled receptors and all energy-dependent biodiversity via RNA-mediated amino acid substitutions, please see:
Every amino acid matters: essential contributions of histone variants to mammalian development and disease.
Excerpt:

The introduction of these minor sequence variants into chromatin is physiologically relevant and fundamental to eukaryotic cellular plasticity. However, with the exception of substitutions towards modification permissive amino acids (for example, both H3.1A31 and H3.2A31 to H3.3S31, which can be phosphorylated), it remains unclear how histone variants acquire and/or differentially enrich for specific chemical modifications that are distinct from their canonical counterparts.

My comment: They just muddied the perfectly clear waters of how phosphorylation and fixation of RNA-mediated amino substitutions is links from biophysically constrained protein folding chemistry to all biodiversity via hydrogen-atom transfer in DNA base pairs in solution.   The claim that “every amino acid matters” is placed into the context of what is not known about biophysically constrained protein folding chemistry and biologically-based cause and effect. That is a way to help ensure these researcher get more funding. It’s a common tactic. If you focus on what is not known, people will think it’s not known to serious scientists who are funded to produce results that are supported by their experimental evidence of biologically-based cause and effect.

See also my comment on RNA and dynamic nuclear organization

Excerpt:

Moving forward, if RNA-mediated events organize the cell nucleus, mutations manifested in perturbed protein folding are not likely to lead to natural selection and the evolution of biodiversity. The requirement for DNA to be found in organized genomes is biophysically constrained via the conserved molecular mechanisms of protein biosynthesis and degradation in species from microbes to man.

For simplicity, see:

See also: Structural diversity of supercoiled DNA and m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs, which was reported as:

DNA’s dynamic nature makes it well-suited to serve as the blueprint of life.

My comment: The claim that DNA is the blueprint of life resurrects long-dead gene-centric theories. I expected others to make more rapid progress after the Zechiedrich lab linked energy-dependent changes from angstroms to ecosystems, but Al-Hashimi’s group is still reporting links in the context of pseudoscientific nonsense linked to neo-Darwinian theory. The theory does not address the need for biophysically constrained RNA-mediated protein folding chemistry in the context of the physiology of reproduction.
Perhaps Al-Hashimi’s group will be next to do that in RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly, which supposedly is “In Press.” RNA methylation is clearly the link to all biodiversity. But, until then, they may fall behind even further, especially if they keep trying to placate the neo-Darwinists.
See: ‘Quantum jitters’ could form basis of evolution, cancer
Excerpt:

“This is a remarkable study that illuminates a fundamental mechanism responsible for the random mutations that drive evolution and contribute to cancer,” said Bert Vogelstein, M.D., a cancer researcher at Johns Hopkins University School of Medicine who was not involved in this research.

My comment: How did Vogelstein arrive at his ridiculous conclusion? Did Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes inadvertently or deliberately lead him to it?
Excerpt:

These results, together with previous structural studies showing that WB and WC-like mispairs can exist within polymerase1–3 and ribosome5,6,13 active sites, strongly suggest that energetic competition between WB and WC-like mispairs is robust and is a key determinant of misincorporation probability during replication and translation (Supplementary Discussion 9).

My comment: How difficult would it have been to clarify the issues involved that suggest energetic competition causes the mutations, which means they do not randomly occur? I reiterate: Vogelstein thinks the “…study illuminates a fundamental mechanism responsible for the random mutations that drive evolution and contribute to cancer…”
Despite everything known to serious scientists about energetic competition for nutrients, I’m sure Vogelstein is not the only biologically uninformed cancer researcher who believes in neo-Darwinian theory. Others may also think that results framed in the context of energetic competition support ridiculous theories. Unfortunately, most people are not going to fight their way through an article like this one to discover that Vogelstein and all others like him are wrong.
Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios
Excerpt:

These observed protein dynamics are incompatible with random and cross-regulatory PU.1–GATA1 co-expression acting as the central mechanism that initiates MegE versus GM lineage choice3.

My comment: Most people may miss the fact that they claimed “…observed protein dynamics are incompatible with random… co-expression, which initiates lineage choice. Simply put, they eliminated Vogelstein’s ridiculous idea about random mutations from any further consideration.
See also: A miR-155–Peli1–c-Rel pathway controls the generation and function of T follicular helper cells, which was reported as A potential new way to sway the immune system found
Excerpt:

“People know miRNAs are involved in immune response, but they don’t know which miRNAs and how exactly,” explained TSRI Research Associate Zhe Huang, study co-first author with Liu and Seung Goo Kang of TSRI and Kangwon National University.

See also: Regulation of B-cell development and tolerance by different members of the miR-17~92 family microRNAs
Excerpt:

In this experimental setting, the changes in the ratio of virus-transduced CD45.2+ cells (GFP+) versus WT competitors (CD45.1+) during the pro- to pre-B transition provided a measurement for the developmental defect. In the control WT:WT mix group, as no major difference existed between these two populations, the GFP+/CD45.1+ ratios remained unchanged during the pro- to pre-B transition, resulting in a pre-B/pro-B ratio close to 1 (Fig. 5b upper panels and Fig. 5c). In contrast, cells derived from the Mb1tKO HSCs, when transduced with control virus, underwent a severe developmental block in competition with WT cells. Therefore, the GFP+/CD45.1+ ratio shifted drastically as WT cells became dominant in the pre-B population, resulting in a pre-B/pro-B ratio below 0.2 (Fig. 5b middle panels and Fig. 5c).

My comment: All serious scientists know that nutrient energy-dependent microRNA flanking sequences link the innate immune system to differences in morphological and behavioral phenotypes via the physiology of reproduction in species from microbes to man via supercoiled DNA, which protects organized genomes of all living genera from virus-driven entropy.
Recent reports, which link specific families of miRNAs to healthy longevity or to pathology will obviously lead mroe researchers to discover the specific miRNAs that link virus-driven energy theft to all pathology.
See: The phylogenetic utility and functional constraint of microRNA flanking sequences and Role of olfaction in Octopus vulgaris reproduction
Excerpt:

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

See for comparison: (2016) Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
Excerpt:

The bias between codons or amino acids, and mRNA expression levels has been previously recognized across species and is thought to result from selection for efficient, accurate translation, and folding of highly expressed genes (Ikemura, 1982; Akashi, 1994; Akashi & Gojobori, 2002; Drummond & Wilke, 2008; Kudla et al, 2009; Novoa & Ribas de Pouplana, 2012). The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

My comment: These authors echo the claim that random mutations are not the source of energy-dependent cell type differentiation. They add that the across-species bias of RNA-mediated amino acid substitutions offers an alternative to ridiculous claims about mutation-driven evolution. For another example of facts about RNA-mediated amino acid substitutions, see how Dobzhansky (1973) framed his claims.
Excerpt:

…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 (p. 127).”

If you don’t like Young Earth Creationists, see also: (2016) Major Evolutionary Blunders: The ‘Degenerate’ Genetic Code?
Excerpts:

A detailed literature review in 2014 found that even if different codons prescribed the same amino acid in a protein, the codon differences still mattered in how the protein was made. The final folding shape of proteins is vital to their function. David D’Onofrio and David Abel documented that the DNA and its corresponding RNA sequence carried information not only for the proper amino acid sequence but also to control the timing of its folding. They “demonstrate that this TP [translational pausing] code is programmed into the supposedly degenerate redundancy of the codon table.”8 What this means is that the code of differing codons, even if they specify the same amino acid, still supplies important information, information that “purposely slows or speeds up the translation-decoding process….Variable translation rates help prescribe functional folding of the nascent protein. Redundancy of the codon to amino acid mapping, therefore, is anything but superfluous or degenerate.”8
…if synonymous codons can have important functional meaning, then the whole methodology goes out the window, and hundreds of studies that used these methods to infer “selection” during the supposed “evolution of genes” could be wrong.11

If you like neo-Darwinian theorists, see: Tempo and mode of genome evolution in a 50,000-generation experiment
Excerpt:

One line of evidence derives from the expectation that synonymous substitutions—point mutations in protein-coding genes that do not affect the amino-acid sequence—are neutral and should therefore accumulate at a rate equal to the underlying mutation rate20,35. This expectation is not strictly true owing to selection on codon usage, RNA folding, and other effects, but…

My comment: Let’s tell the truth with no buts, rather the invent more reasons to lie. Creationists and other serious scientists seem to arrive at the same conclusion by citing different literature that adds another level of epigenetic complexity in the context of non-random selection of RNA-mediated amino acid substitutions, which must be fixed in the organized genomes of all living genera to link the innate immune system to supercoiled DNA, which protects all organized genomes from virus-driven entropy.
The literature includes details about how the across species bias between codons or amino acids and microRNA or pre-mRNAs and mRNA expression levels links selection to efficient, accurate translation, and folding of highly expressed genes.   For comparison, no serious scientist has ever suggested that virus-driven energy theft is linked from mutations and selection to the evolution of one species from another. Thus, it has become perfectly clear that the amount of pseudoscientific nonsense people must believe to continue to believe in mutation-driven evolution is based on definitions and assumptions. Serious scientists do not rely on definitions and assumptions to support their claims.
See for comparison: Mutation-Driven Evolution (2013)

Excerpt:

Mutation is the change of genomic structure and includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc. (2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation. —

Conclusion:

In other words, genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements.

See also: Replace the Modern Synthesis (Neo-Darwinism): An Interview With Denis Noble

[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. The anglophone tradition was taught. I was taught, and so were my contemporaries, and so were the younger scientists. 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…. No, it wasn’t dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact.

For more assumptions in the context of ridiculous theories, see: Phylogenetic plasticity in the evolution of molluscan neural circuits (2016)
Conclusion:

Molluscan neural circuitry represents a different evolutionary trajectory from vertebrates and even other lophotrochozoans. Using the same morphogenic genes as other phyla, molluscs have created novel nervous systems that control a wide variety of body forms. Yet the largest brained invertebrates, the cephalopods, have converged with insects and vertebrates on the organization of circuitry for learning and memory. Even with this cross-phyletic convergence, there are intra-phyletic differences between octopus and cuttlefish in the sites of plasticity. Phylogenetic plasticity is also found in gastropods where homologous neurons have been re-used for different functions and where neuromodulatory actions also display species-specificity. One outcome from this work is to show that there are many solutions to the same problem. The story of molluscs is about how looks can be deceiving; the same genes and neurons can be used and reused in different ways to create diverse nervous systems that sometimes converge on the same solution. I think it is more exciting to realize that octopus and mammals independently came up with a learning machine that has a fan-out/fan-in organization and LTP than to think that these similarities are just a family resemblance. Call me a splitter, but I believe that uncovering the many solutions that nature has found will tell us more about fundamental organizational properties than lumping them all together.

My comment: Anyone who makes a ridiculous statement like the one above should be ‘called out’ and questioned to learn how he or she has managed to maintain their overwhelming ignorance despite the availability of publications like this one:
The phylogenetic utility and functional constraint of microRNA flanking sequences and this one The octopus genome and the evolution of cephalopod neural and morphological novelties
Excerpt:

Among the octopus complement of ligand-gated ion channels, we identified a set of atypical nicotinic acetylcholine receptor-like genes, most of which are tandemly arrayed in clusters (Extended Data Fig. 7). These subunits lack several residues identified as necessary for the binding of acetylcholine26, so it is unlikely that they function as acetylcholine receptors. The high level of expression of these divergent subunits within the suckers raises the interesting possibility that they act as sensory receptors, as do some divergent glutamate receptors in other protostomes27. In addition, we identified 74 Aplysia-like and 11 vertebrate-like candidate chemoreceptors among the octopus GPCR superfamily of ~330 genes (Extended Data Fig. 6).

My comment: The GPCR superfamily links receptor-mediated signaling from chemotaxis to phototaxis and all energy-dependent biophysically constrained biodiversity via RNA methylation and RNA-directed DNA methylation, histone acetylation and every aspect of the energy-dependent physiology of reproduction. Taken together, everything known about the energy-dependent receptor-mediated physiology of reproduction links the innate immune system to supercoiled DNA.
Those who tout neo-Darwinian theories for comparison must continue to use definitions and assumptions as if that approach was acceptable to anyone else who was not also a pseudoscientist.
See also: (2016) 33. Octopus Signals
Excerpt:

We define a ‘signal’ as any act or structure which alters the behavior of other organisms, which evolved because of that effect, and which is effective because the receiver’s response has also evolved.

My comment: Via the bastardization of everything known to serious scientists about biologically-based cause and effect, the definition of signal is linked to its evolution via an effect, which is not linked from any epigenetic effect on hormones to any affect on behavior. That makes it impossible to link food odors to the energy-dependent de novo creation of olfactory receptor genes, which are GPCRs. The de novo gene creation of GPCRs links metabolic networks to genetic networks via the pheromone-controlled physiology of behavior in the context of epigenetic effects of pheromones on hormones. The hormones affect the species-specific behaviors of all invertebrates and vertebrates.
Definitions lead to confusion about the use of the terms “effect” and affect, which link epigenetic effects on hormones the the affects of hormones on behavior. Neo-Darwinian theorists skip everything known to serious scientists about the differences between effect and affect and link the definition of a ‘signal’ to species-specific behaviors and all biodiversity.
See for comparison: Feedback loops link odor and pheromone signaling with reproduction

Conclusion:

It appears that GnRH neurons integrate a variety of information about the internal state of the animal and its external environment. At least 10,000 neurons in 26 different brain areas appear to transmit signals directly to GnRH neurons. Among these are areas involved in
odor and pheromone processing, sexual behavior, arousal, reward, and other functions. This suggests that GnRH neurons are poised to modulate reproductive physiology and behavior in accordance with the overall state of the animal.
These studies also indicate that GnRH neurons are likely to influence numerous brain functions. They appear to transmit signals to as many as 30,000 or more neurons in 34 brain areas, consistent with previous studies showing GnRH+ fibers and GnRH receptors in multiple brain regions (Badr and Pelletier, 1987; Jennes et al., 1988; Jennes et al., 1997). BL+ neurons likely to receive synaptic input from GnRH neurons were seen in areas associated with numerous different functions, including odor and pheromone processing, sexual behavior, appetite, defensive behavior, motor programs, and the relay of information to higher cortical areas. These results may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.

My comment: Have neo-Darwinian theorists found a species in which feedback loops do not link what the organism eats to its physiology of reproduction? If not, what do they claim links energy-dependent changes in angstroms to ecosystems in all living genera?
Who cares?

See also: The scent of a hatchling: intra-species variation in the use of chemosensory cues by neonate freshwater turtles

The 5300-year-old Helicobacter pylori genome of the Iceman
Abstract excerpt:

The “Iceman” H. pylori is a nearly pure representative of the bacterial population of Asian origin that existed in Europe before hybridization, suggesting that the African population arrived in Europe within the past few thousand years.

See also: Evolution of gut bacteria in humans and hominids parallels ape evolution
See also: Rapid evolution of microbe-mediated protection against pathogens in a worm host

My comment: Taken  together, these two articles link the difference in the bacteria that nematodes eat to the morphological and behavioral diversity of C. elegans for comparison to the predatory nematode with teeth, P. pacificus. From there, the conserved molecular mechanisms link the gut bacteria of the “Iceman” to the morphological and behavioral diversity of all human populations.

See also:

Special Report on Cell Biology: Sweetening the pot

Glycosylation in cellular mechanisms of health and disease

Glycomics: A rapidly evolving field with a sweet future
Excerpt 1)

Glycans play many critical roles in both the normal function of cells and in disease. They assist in the folding of many proteins, aid in protein trafficking, mediate cell adhesion, differentiate blood groups, modulate the immune system, are implicated in many signaling pathways, and provide a protective extracellular matrix for many types of cells. Glycans are also implicated in the process of infectivity for many pathogenic bacteria (2) and most viruses (3), including those that cause the common cold, influenza, and HIV/AIDS.

Excerpt 2)

Glycomics is now being used in combination with genomics, epigenomics, proteomics, lipidomics and metabolomics to provide a more holistic view of how cellular pathways function and how they change in response to disease.

It has become nearly impossible for me to keep up with the information that refutes neo-Darwinian pseudoscientific nonsense at the same time more articles are published that tout the nonsense.
See for comparison: The role of microRNAs in metabolic interactions between viruses and their hosts
Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching
Conclusion:

epigenetic inheritance of active and repressed chromatin state during mitosis has been demonstrated (Cavalli and Paro, 1998; Grewal and Klar, 1996). Our measurements suggest that the timescale on which the relative accessibility of IGHC loci persists is ~10 somatic mutations. Calibration of the mutational clock should allow recovery of information about epigenetic state and phenotypic dynamics in units of time and cellular generations. Together with recent studies of mammalian (Spencer et al., 2009) and bacterial cells in culture (Hormoz et al., 2015), our work suggests that phenotypic correlations between sister cells due to shared inheritance are widespread. We predict that such correlations often will be detected when genealogical relationships between individual cells can be resolved. We propose that inheritance of epigenetic state provides a mechanism for orchestrating cellular behavior without the need for signaling.

My comment: Attempts to define the term “signal” will fail because everyone knows what a signal is and all serious scientists know that food odors and pheromones are signals that link feedback loops from the innate immune system to chromatin folding and supercoiled DNA, which protects organized genomes from virus-driven entropy. The proposal the “…inheritance of epigenetic state provides a mechanism for orchestrating cellular behavior without the need for signaling” exemplifies the ignorance of all neo-Darwinian theorists who have failed to link energy-dependent signals to biophysically contrained protein folding chemistry via RNA methylation and RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all living genera.
Finally,  see:Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters
It was reported on August 4, 2016 by Engaging Epigenetic Experts as:

…the authors say that they suspect such antisense transcription plays an important role in “in the regulation of gene expression and the maintenance of a promoter-associated chromatin environment.”

My comment: This site started removing my comments after several weeks of allowing me to accurately link articles like this one to what is known about RNA-mediated cell type differentiation. Others have already invented terms like oncohistones and histone subunit isoforms in attempt to continue obfuscating the links from energy-dependent RNA-mediated amino acid substitutions to healthy longevity because they know virus-driven energy theft has been linked to all pathology.

Engaging Epigenetics Experts appears to be caught in the crossfire. They’ve supported too much neo-Darwinian nonsense to suddenly admit that it never made sense, but that’s what antisense transcription confirms. There are many other sources of what should have been “Science” news but the news was placed into the context of pseudoscientific nonsense touted by neo-Darwinian theorists who have trapped themselves in their ignorance.
In the article mentioned by Engaging Epigenetics Experts, this claim is substantiated:

Despite differences in epigenetic features, tendency for association with transregulatory factors, and capacity to produce stable RNA transcripts, all three classes of TSS described in this work display similarities in sequence content, including enrichment for GC content and Pol II-associated sequence motifs (Fig 2). As such, antisense transcription appears to be encoded in genetic sequence. This connection between sequence content and epigenetic features provides the compelling suggestion that antisense transcription encoded by sequence may direct the positioning of nucleosomes and deposition of histone marks. Antisense transcription may also participate in signal-dependent modulation of epigenetic content where activation of sequence-encoded antisense TSS precedes nearby changes in chromatin structure. In this way, the collection of transcription initiation-associated sequence motifs near promoters may define regulatory potential for a given gene. This connection to sequence also provides a means to interrogate antisense transcription function. Future studies with selective mutation of associated sequence motifs may elucidate the function of antisense transcription and its coincidence with promoter-associated features. Directed mutagenesis could also establish the extent of the effect of antisense transcription on the chromatin environment at promoters.
We characterized downstream antisense transcription initiating near gene promoters in human T47D/A1-2 cells. daTSSs fall between regularly positioned nucleosomes downstream of gene TSSs. Histones within this region are enriched for marks closely associated with active promoter regions, such as H3K4me3 and H3K27ac modifications. Chromatin remodeling complexes show enriched binding upstream of observed daTSS positions, suggesting that antisense transcription contributes to the establishment and maintenance of a promoter-specific chromatin environment. Downstream antisense transcription is common to many human promoters, and daTSSs correlate with the downstream edge of promoter-associated chromatin features. Coincidence of daTSSs with these features suggests interplay between antisense transcription and regulatory pathways.

My comment: There are too many ways to obfuscate what is known about the epigenetically-effected links from energy-dependent changes in angstroms to ecosystems in all living genera. These two paragraphs are important to understand in that context. They link RNA methylation and RNA-mediated amino acid substitutions to cell type differentiation in all living genera via chromatin remodeling, but you will not be encourage to look at the facts because there is no mention of epigenetically-effected RNA-mediated amino acid substitutions in the context of chromatin remodeling.  That’s why I added emphasis to this claim: “…transcription initiation-associated sequence motifs near promoters may define regulatory potential for a given gene.” 
It links hydrogen-atom transfer in DNA base pairs in solution from energy-dependent changes in the microRNA/messenger RNA balance to gene regulation via everything known to serious scientists. It links RNA-mediated amino acid substitutions and morphological diversity by linking energy-dependent RNA methylation from learning and memory to behavior via chromatin remodeling. The chromatin remodeling occurs in the context of the physiology of reproduction and what is known about supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.
But their claim that “…transcription initiation-associated sequence motifs near promoters may define regulatory potential for a given gene” is placed into the context of a theory about the fact that energy-dependent RNA-mediated amino acids substitutions, which are referred to in the context of  transcription initiation-associated sequence motifs may define the energy-dependent regulatory potential of different genes in different individuals of different species. All pseudoscientists know how to obfuscate facts about the energy-dependent regulatory potential of different genes, because they have been placing them into the context of virus-driven energy theft and mutation-driven evolution since the time that de Vries (1902) defined “mutation.”
Addendum: People complain that I am not explaining how quantum physics, quantum chemistry, quantum biology, and quantum consciousness in terms they can understand. See:

Double slit experiment and the REAL secret

Real-world explanation: Brian Greene : What’s Beyond The Double Slit Experiment ?

See also:
 Our Reality Is Information Tom Campbell
Probability & Uncertainty: The quantum mechanical view of nature Richard Feynman
New Experiments Show Consciousness Affects Matter Dean Radin

Physics

Light 'drives' adaptation; nothing 'drives' evolution

Embedded Image

Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition

Abstract: Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal-to-zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by post-transcriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs, this pathway does not fully explain mRNA clearance. We investigated how codon identity and translation affect mRNA stability during development and homeostasis. We show that the codon triplet contains translation-dependent regulatory information that influences transcript decay. Codon composition shapes maternal mRNA clearance during the maternal-to-zygotic transition in zebrafish, Xenopus, mouse, and Drosophila, and gene expression during homeostasis across human tissues. Some synonymous codons show consistent stabilizing or destabilizing effects, suggesting that amino acid composition influences mRNA stability. Codon composition affects both polyadenylation status and translation efficiency. Thus, the ribosome interprets two codes within the mRNA: the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.

See also: Biological causal links on physiological and evolutionary time scales

Excerpt:

Occam’s Razor – the problem solving principle in philosophy that suggests that the theory with fewest assumptions should be preferred at first – could be helpful here in judging each potential causal direction. For example in the gene duplication and genetic dispensability problem presented above, the evolutionary causal effect requires the extra assumption that dispensable genes are more likely to undergo gene duplication during evolution; this is non-trivial.

My comment: Pseudoscientists have trivialized the link from the speed of light on contact with water to the de novo creation of nucleic acids and all biodiversity, which links the creation of the innate immune system to supercoiled DNA.  Science journalists report the trivialization in articles like this.

See: Do genomic conflicts drive evolution?

My comment: Nothing “drives” evolution across two billion years. Pennisi is in rare form.

She reports this:

Two billion years ago, an early cell swallowed an energy-producing microbe, giving birth to the mitochondria that are the hallmarks of all eukaryotes, from protists to people. Evolutionary biologists now think that was just the start of the influence that the cell’s “powerhouses” have on the tree of life.

In the same context, she reports:

…evidence that natural selection boosts mutation rates in the nucleus, apparently to keep up with mitochondrial evolution.

See for comparison: Virus-driven energy theft has been linked  to all pathology in Epigenetics and Genetics of Viral Latency.

Excerpt:

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

My comment: All serious scientists know that ecological variation must be linked to nutrient energy-dependent RNA-mediated ecological adaptation via biophysically constrained protein folding chemistry in all living genera. Only pseudoscientists and science journalists continue to report results in the context of two billion years of mutations, natural selection, and evolution.

See also: Inching toward the 3D genome; All in the (bigger) family — both articles were written by Pennisi, and the links are to my comments on the articles

See also: Combating Evolution to Fight Disease

My comment: Science journalists like Pennisi are supporting neo-Darwinian nonsense each time they report research in the context of two billion years of evolution.

See: Sulfur-cycling fossil bacteria from the 1.8-Ga Duck Creek Formation provide promising evidence of evolution’s null hypothesis

Excerpt:

…we interpret the striking similarities in organismal morphology, community structure, habitat, and evident physiology between the ancient and modern sulfur-cycling biotas as evidencing stasis resulting from adaptation to a physically quiescent subseafloor environment that has remained essentially unchanged over billions of years.

See for comparison: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

Excerpt:

A central process in evolution is the recruitment of genes to regulatory networks. We engineered immotile strains of the bacterium Pseudomonas fluorescens that lack flagella due to deletion of the regulatory gene fleQ. Under strong selection for motility, these bacteria consistently regained flagella within 96 hours via a two-step evolutionary pathway.

My comment: Compare the bacteria that recruited genes to re-evolve their flagellum via a two-step evolutionary process to the lack of any evolutionary process in the bacteria living in ocean sediments.  What was the two-step evolutionary process that was required for the weekend evolution of the bacterial flagellum? Why did nothing change in the other bacteria for ~ 2 billion years? If you ask answers to the right questions, you will find that theories about mutations, natural selection, and evolution have no explanatory power.

See: Mutation-Driven Evolution

Conclusion: 

genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements (p. 199).

My comment: In that view of evolution, there is no need to consider anything except the ridiculous conclusion, which can be placed into the context of what serious scientists can see. Occam’s razor suggests that all serious scientists should view ecological variation in the context of observed ecological adaptation. If they cannot see that their observations should be placed into the context of what is known  about biologically-based cause and effect, they may need to start looking under the light.

See for example: Gen9 “Our Founders

The founders of Gen9 include people who are likely to know that femotosecond blasts of UV light are linked to RNA-mediated DNA repair of all virus-driven pathology via energy-dependent changes in base pairs and RNA-mediated amino acid substitutions. Unfortunately, most people cannot see how that fact is connected to this fact:

Amino acid composition also influences mRNA stability in vertebrates.

My comment: Perhaps people should open their eyes; look up; and see the light. Quantized energy is difficult to ‘see’ if you live and die in the dark. Schrodinger (1944) and Dobzhansky (1973) reported what they saw. The links open the pdf of Schrodinger’s book “What is Life?” and Dobzhansky’s classic Nothing in Biology Makes Any Sense Except in the Light of Evolution.
In the forward to the reprint of “What is Life?” Roger Penrose asks:

“How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?”

Others still report that learning more about mutations and natural selection is the key to understanding how evolution occurs across millions of years — even after the report on weekend evolution of the bacterial flagellum in Pseudomonas flourescens which fluoresces when exposed to UV light. It seems that neo-Darwinian theorists and other theorists are not interested in linking Darwin’s “conditions of life” from Schrodinger’s claims about sunlight to Dobzhansky’s claims about the light of evolution. Do the theorists intend to keep ignoring everything known to serious scientists about the energy-dependent links from angstroms to ecosystems?
See: Structural diversity of supercoiled DNA
Excerpt:

Our cryo-ET, biochemical, and computational studies show the astounding versatility and dynamism of DNA depending on the degree of supercoiling. DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases. 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 differential structure features of DNA are RNA-mediated. Energy-dependent amino acid substitutions link angstroms to ecosystems in all living genera, and virus-driven energy theft links mutations to all pathology.
See for examples: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
My comment: For details on the conserved molecular mechanisms that link RNA-mediated amino acid substitutions to cell type differentiation in all cell types of all individuals of all species, see my invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Abstract 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: This protein designer aims to revolutionize medicines and materials

Excerpt:

Baker’s team has all but solved one of the biggest challenges in modern science: figuring out how long strings of amino acids fold up into the 3D proteins that form the working machinery of life.

Conclusion: Protein designers have shed nature’s constraints and are now only limited by their imagination. “We can now build a whole new world of functional proteins,” Baker says.”

My comment: RNA-mediated protein folding chemistry is biophysically constrained by nutrient energy-dependent microRNA flanking sequences, which link the details in our section on molecular epigenetics from our 1996 Hormones and Behavior review to all morphological and behavior diversity in all living genera via RNA-mediated amino acid substitutions.

Baker fails to mention that quantized energy is the link to energy-dependent changes and all links from angstroms to ecosystems via RNA-mediated protein folding chemistry in all living genera. That fact requires the ‘design’ of an innate immune system that protects all organized genomes from virus-driven energy theft and genomic entropy so that organisms can reproduce when enough food is available. If not enough food or energy is available to support the physiology of reproduction, metabolic networks cannot be linked to genetic networks via RNA-mediated amino acid substitutions and protein folding. But virus-driven energy theft can clearly be linked from the Zika virus to differences in craniofacial morphology and brain development by smaller skull size in victims of the transgenerational epigenetic inheritance of the virus.

The facts about the Zika virus-damaged DNA link virus-driven pathology to every aspect of development during life history transitions that are altered by the energy theft. Plasticity associated with olfactory input in this example, and many others, can be examined in the context of what is currently known to serious scientists, or it can be placed back into the context of the pseudoscientific nonsense touted by neo-Darwinian theorists.

See: Olfactory organ of Octopus vulgaris: morphology, plasticity, turnover and sensory characterization

See also:


See also: Light ‘drives’ adaptation; nothing ‘drives’ evolution (2)