Alternative splicing of pre-mRNA

Energy-dependent hydrogen bonds in supercoiled DNA

Chirality Check

Most biological macromolecules are homochiral, and enzymes help to maintain this state of affairs; for example, checkpoints ensure that only l-amino acids are incorporated into proteins during translation.

The fixation of the only achiral amino acid, glycine in position 6 of the gonadotropin releasing hormone decapeptide protein links the nutrient energy-dependent pheromone-controlled physiology of reproduction from yeasts to humans. That fact about RNA-mediated protein folding chemistry is missing from the chirality check, It also is missing from representations of the anti-entropic virucidal force that biophysically constrains all biodiversity by protecting all organized genomes from virus-driven energy theft and genomic entropy.
That’s why theories of evolution have no explanatory power. An unknown force of nature must be included the theories for comparison to Schrodinger’s claims in What is Life? (pp. 73 and 74)

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.)

See for comparison: Force of nature gave life its asymmetry

…even demonstrating how a common physical phenomenon would have favoured left-handed amino acids over right-handed ones would not tell us that this was how life evolved…

The fact that there is no explanation for how life evolved outside the context of an unknown force of nature can be placed into the context of the energy-dependent creation of all differentiated cell types in all living genera.
See: RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria (2016) by Junjie U. Guo and David P. Bartel,

Owing to the extensive hydrogen-bonding and base-stacking interactions, RG4 structures can be very stable, with in vitro melting temperatures well exceeding physiological temperatures. This stability typically depends on the presence of K+, which is the optimal size to bind at the center of two stacked G-quartets…

They fail to mention that energy-dependent hydrogen-atom transfer in DNA base pairs in solution must be linked to the stability of supercoiled DNA. Instead, the unfolding of the RNA G-quadruplexes was reported as: RNA Sequences Don’t Predict In Vivo Transcript Structure

Interactions between nucleotides can turn sections of transcripts into loops, bends, and knots, some of which have regulatory functions in the cell.

See for comparison: Electrolytes induce long-range orientational order and free energy changes in the H-bond network of bulk water.  K+ is an important electrolyte in the context of interactions in solutions. That fact was reported as:  A single ion impacts a million water molecules. The fact that the interactions between nucleotides are pH-dependent makes it important to consider what happens when slight changes in the cell types of species-specific tissues occur in the context of nutrient stress or social stress.
The stress causes changes in protein folding that predictably links energy-dependent interactions between nucleotides from natural selection for codon optimaility to fixation of RNA-mediated amino acid substitutions and healthy longevity? If pH does not facilitate energy-dependent codon optimality, a change in pH may predict a change in the structure of functional proteins, which can effect biophysically constrained cell type differentiation.
See for instance: 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.

Unfortunately, the nutrient energy-dependent interactions between nucleotides and amino acids, which are the building blocks of proteins, are typically not considered in the context of virus-driven energy theft, which has been linked from viral latency to all pathology via transgenerational epigenetic inheritance in species from archaea to humans.
See for instance: Epigenetics and Genetics of Viral Latency
… viral latency is responsible for life-long pathogenesis and mortality risk…
My comment to The Scientist on RNA Sequences Don’t Predict In Vivo Transcript Structure :

See also: MicroRNAs: Genomics, Biogenesis, Mechanism, and Function (2004) by David P. Bartel

…about a quarter of the human miRNA genes) are in the introns of pre-mRNAs. These are preferentially in the same orientation as the predicted mRNAs…

For comparison, see: From Fertilization to Adult Sexual Behavior

… epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans…  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.

Hydrogen-atom energy-dependent changes in base pairs have since been linked from RNA-mediated protein folding chemistry to all biophysically constrained cell type differentiation in all living genera via amino acid substitutions.

The RNA-mediated fixation of amino acids links autophagy from the innate immune system to supercoiled DNA. Virus-driven energy theft has been linked to all pathology via changes in the microRNA/messenger RNA balance. The changes link fertilization to adult sexual behavior.  See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems.
See also, the other publications by David P. Bartel
2016 Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression
Excerpt:

…we assumed that (1) molecular species are well mixed within the cytosol and their concentrations are not influenced by cell growth and division; (2) each mRNA and miRNA is produced at a constant rate, and unbound mRNAs and miRNAs undergo constant first-order decay; (3) upon association with a miRNA, the mRNA degradation rate increases, regardless of the site type; and (4) miRNA binding is reversible, and upon miRNA dissociation the mRNA degradation rate reverts to its original value. We also assumed that the Michaelis constant (KM) describing mRNA degradation with respect to the miRNA-mRNA complex is well approximated by the complex dissociation constant (KD), and that both bound and unbound mRNA are translated.

Simply put, they seem to have assumed that energy-dependent changes in the microRNA/messenger RNA balance need not be considered in the context of any model of biologically-based cause and effect.
See for comparison: 2014 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.

The clear difference between the assumptions made by Bartel (and others like him) and the facts about energy-dependent biophysically constrained RNA-mediated protein folding chemistry make it pointless for serious scientists to discuss experimental evidence of biologically-based cause and effect with anyone who does not agree that it is energy-dependent and biophysically constrained by the physiology of energy-dependent reproduction in all living genera.
See also: How the elite control the masses
Control involves giving the masses partial information, which is what Bartel and others appear to be doing in attempts to promote evolutionary theories.

See for comparison ( December 30, 2016 at 5:37pm):

Peter Berean wrote:

James, I have no problem with “energy-dependent RNA-mediated amino acid substitutions” … however, that does not show that energy = information.

And, neither does the article about “construction of phylogenetic trees”…

My recommendation is DO take the advice of your brothers in Christ… And correct your views and models accordingly.

IF you do so, you could actually have more people believe what you have to say about your models.

The comment about taking advice from my “brothers in Christ” is a classic. It comes from someone who may never understand anything about energy-dependent hydrogen bonds in supercoiled DNA, or how energy as information must be linked to all biodiversity.

Peter Berean is only one among many who are biologically uninformed. Their masses are not told that virus-driven energy theft can be linked to all pathology in the context of conserved molecular mechanisms, which have been detailed by all serious scientists. Peter Berean may think that his faith in God and/or his brothers in Christ will save him from his ignorance.

That may be true, but it may also not apply to those who have been told the truth and continue to ignore it. People like that encourage others to ignore the truth about energy-dependent hydrogen bonds in supercoiled DNA. The truth is that if you don’t know where that energy came from, you are no better off than any other theorist or atheist.

That makes this Chirality Check a reality check, and makes this a lie: “…checkpoints ensure that only l-amino acids are incorporated into proteins during translation.”

See: Evolution of constrained gonadotropin-releasing hormone ligand conformation and receptor selectivity as cited in Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor

When the chiral amino acid (Ala) in position six of Ciona I GnRH was substituted with the achiral glycine or with d-Ala, which enhances the type II’ β-turn conformation, there was a marked increase in the binding affinity of the peptides at the vertebrate GnRH receptor (Barran et al., 2005).

The substitution of achiral glycine and the increased binding affinity were placed into the following context in the Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor:

The discovery of the fact that one decapeptide molecule, among the GnRHs, was constructed perfectly at the beginning of 400 million years evolution and that it is not possible to improve its physiological potency using the any natural amino acid is, in my opinion, important, fascinating and beautiful.

The claim about 400 million years of evolution has not been substantiated by experimental evidence of biologically-based cause and effect and virus-driven energy theft was not considered in the context of the invention of neo-Darwinian theory.
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…
[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another…. Assumptions, made but not verified, were taught as fact.
See also: Spectrum of Antimatter Observed for First Time

The Standard Model predicts that there should have been equal amounts of matter and antimatter in the primordial Universe after the Big Bang, but today’s Universe is observed to consist almost entirely of ordinary matter. This motivates physicists to carefully study antimatter, to see if there is a small asymmetry in the laws of physics that govern the two types of matter.

Without the anti-entropic energy of the sun, the laws of physics could not be linked from chemistry to molecular epigenetics, which must link energy-dependent autophagy from the innate immune system to supercoiled DNA. If not, you are left with the magic of emergence and evolution instead of the fact that Life is physics and chemistry and communication in the context of energy as information.
In 2016, scientists collectively failed to link the anti-entropic virucidal energy of the sun to autophagy and all biophysically constrained biodiversity via the physiology of reproduction in all living genera. They also failed to link virus-driven energy theft from the negative supercoiling of DNA to all pathology.
Instead, most scientific successes are examples of politicized science. Congratulations to those who are willing to place politicized science into the context of their theories.  The theories make their World a better place for other theorists to live in. Serious scientists, for comparison, will remember the theorists who failed to make the Chirality Check a reality check.

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?

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)