rp_levels-of-organization.jpg

Energy dependent RNA-mediated immunity (3)

Viral ‘fossils’ in our DNA may help us fight infection

Excerpt:

The work suggests that these viral fossils probably played a key role in the evolution of our species…

My comment: The work shows that Greg Bear accurately portrayed virus-driven energy theft when he linked it to the creation of new species. In 1999 and 2003, he linked what is now known about the anti-entropic effects of sunlight and hydrogen-energy transfer in DNA base pairs in solution to the creation of a new human subspecies.
What’s currently known outside the context of science fiction also links Einstein’s math and physics to molecular mechanisms of adaptation via Schrodinger’s claims about sunlight when paired with Dobzhansky’s claims about amino acid substitutions in the context of transgenerational epigenetic inheritance.
For example, the Zika virus clearly links primate craniofacial morphology and brain development. DNA damage linked to variations can be compared in the context of the fossil record and what is known about how cell type differentiation occurs. Nutrient energy-dependent RNA-mediated DNA repair and amino acid substitutions are linked to species-wide ecological adaptations.
The energy-dependent adaptations link ecological variation to morphological and behavioral phenotypes in species from microbes to humans. Virus-driven energy theft links a single amino acid substitution to increased virulence when nutrient-stress and/or social stress cause changes in pH that favor viral replication instead of nutrient-dependent immune system-support of controlled cell type differentiation.
Simply put, Dobzhansky’s claims can be placed into the context of what is known about all virus-driven pathology. He wrote: “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla ( p. 127)” — See: Nothing in Biology Makes Any Sense Except in the Light of Evolution
The “light” is sunlight and it is linked to hydrogen-atom transfer in DNA base pairs in solution to fixation of amino acid substitutions and supercoiled DNA by everything currently known to physicists, chemists, and molecular biologists about biophysically constrained chemistry and the nutrient-dependent biological basis of the physiology of reproduction in all living genera.
Viruses increase their virulence via energy theft and base pair changes linked to a single amino acid substitution. All nutrient-dependent life must ecologically adapt by at least one nutrient-dependent base pair change and amino acid substitutions, which must be linked to supercoiled DNA via the physiology of reproduction in all living genera.
What some people call “viral fossils” are clear indicators of how the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding prevents virus-driven entropy of organized genomes in the context of the physiology of reproduction.
Suggested reading: RNA

Caption: A hairpin loop from a pre-mRNA. Highlighted are the nucleobases (green) and the ribose-phosphate backbone (blue). Note that this is a single strand of RNA that folds back upon itself.
 

Caption: Watson-Crick base pairs in a siRNA (hydrogen atoms are not shown)
My comment: Perhaps if they had showed the hydrogen atoms, neo-Darwinian theorists would not have ignored hydrogen-atom transfer in DNA base pairs in solution, which link the sun’s biological energy to all biomass and biophysically constrained nutrient-dependent biodiversity.
See also: Nucleotides and Bases
Excerpt:

 A nucleotide is the basic structural unit and building block for DNA. These building blocks are hooked together to form a chain of DNA. A nucleotide is composed of 3 parts:
* five-sided sugar
* phosphate group
* nitrogenous base (nitrogen containing)
The sugar and phosphate group make up the backbone of the DNA double helix, while the bases are located in the middle. A chemical bond between the phosphate group of one nucleotide and the sugar of a neighboring nucleotide holds the backbone together. Chemical bonds (hydrogen bonds) between the bases that are across from one another hold the two strands of the double helix together.

See also: From Fertilization to Adult Sexual Behavior
Excerpt:

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…. That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.


Organisms compete for food, heat, light and water. The innate immune system enables adaptations unless virus-driven energy theft overpowers the ability of organisms to reproduce in the context of their nutrient-dependent RNA-mediated protein folding chemistry, which links DNA repair to ecological adaptation in all living genera via what is known about supercoiled DNA in all living genera.
See also:

See also:

See also: McGovern Institute awards prize to neurogeneticist Cori Bargmann
Excerpt:

Building on her olfaction work, Bargmann has also studied the neural basis of social behavior, which in worms is strongly regulated by chemical cues. In one set of papers, for example, she identified a single neuron that integrates information from multiple chemical cues including food, oxygen and pheromones, to control the expression of social behavior.

See also:  Parallel Molecular Evolution in an Herbivore Community

Conclusion:

A decade-old debate centers around the relative importance of protein versus regulatory changes and the role of gene duplication in the evolution of novelties [e.g., (3, 8)]. Although our findings point to a certain level of predictability in evolution, they also reveal a plurality of evolutionary responses to a similar selective pressure, which demonstrates how adaptive evolution can leverage a combination of gene duplication, regulatory changes, and protein evolution. The genetic basis of repeated adaptations can be further elucidated by considering contexts where diverse groups of species are faced with a common selective pressure, such as insect-host specialization; cryptic melanism; or environmental gradients in oxygen, salinity, temperature, or acidity.

My comment: The expression of social behavior in nematodes links everything known about how ecological adaptation occurs in the context of chemical cues including food, oxygen and pheromones, which must be linked to salinity, temperature, and acidity via hydrogen-atom transfer in DNA base pairs in solution to avoid making claims about evolution that cannot be supported by experimental evidence of biologically based cause and effect that links atoms to ecosystems.

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

See for comparison:
Inside the secret defense systems of giant viruses

Excerpt: “Even if that search bears no fruit, Raoult thinks that MIMIVIRE is important for what it says about the evolution of giant viruses.
“It’s a witness of a very old life,” he said.”

My comment: Did someone change the definition of life to include viruses that must steal energy from living cells to replicate? If so, I think the pseudoscientific nonsense about use of de Vries (1904) definition of “mutation” and the assumptions about how long it takes accumulated mutations to lead to the evolution of a new species is about to come to an end. No one I know is ignorant enough to claim that viruses are alive in conversation with a serious scientist.

Zika virus infects human neural stem cells
Excerpt:

“We are trying to fill the knowledge gap between the infection and potential neurological defects,” says first author Hengli Tang, the team’s virologist whose lab studies RNA viruses like Zika, Dengue, and hepatitis C virus. “The questions we address here are among the very first questions people want to know the answers of.”

Zika virus kills developing brain cells

Excerpt:

The researchers noticed that the infected progenitor cells were not killed right away. Instead, the virus “hijacked the cells,” using the cellular machinery to replicate themselves, Song says. That helped the virus to spread quickly through the cell population, he says.  His team also reports that infected cells grew more slowly and had interrupted cell division cycles, which could also contribute to microcephaly.

My comment: I want someone to explain why they seem to know nothing about how nutrient-dependent microRNA flanking sequences prevent virus-driven entropy via energy-dependent hydrogen-atom transfer in DNA base pairs in solution that link physics, chemistry, and the conserved molecular mechanisms of cell type differentiation to the physiology of reproduction in species from microbes to humans.

See also: Widespread context dependency of microRNA-mediated regulation

Excerpt:

Expression of genes is not only regulated at the level of transcription but also post-transcriptionally in various ways, of which regulation mediated by microRNAs is one of the most prevalent (He and Hannon 2004). MicroRNAs are 20- to 24-nt long noncoding RNAs that have been found in animals and plants. They play a pivotal role in development, tumorigenesis, the immune system, and during viral infections (for a review, see Bartel 2004). Within the RNA-induced silencing complex (RISC), microRNAs are responsible for target recognition by binding to target sites, often located in the 3′-UTR of mRNAs. This is predominantly mediated by the so-called seed region (nucleotides 2–8 of the microRNA). In general, RISC causes down-regulation of the target mRNA either by inhibiting translation or promoting degradation (Bartel 2009). Neither the exact mode of binding nor the mechanisms of down-regulation are completely understood (Eulalio et al. 2008; Kozak 2008; Guo et al. 2010; Djuranovic et al. 2011; Mishima et al. 2012; Meijer et al. 2013).

My comment: Neo-Darwinists and all others who refuse to place their claims into the context dependency of microRNA-mediated regulation of ecological adaptation continue to defy the serious scientists who place their claims into the context of experimental evidence and common sense. All serious scientists are Combating Evolution to Fight Disease.

All pseudoscientists are combatants who are fighting to keep virus-driven pathology as the source of mutation-driven evolution.  They frame their explanations in the context of virus-driven evolution of mammalian development.

See for example: Viral Remnants Help Regulate Human Immunity (The Scientist)
Excerpt:

“These viral sequences have previously been linked to controlling early mammalian development and formation of the placenta, among other things.”

My comment: The other things link every aspect of RNA-mediated cell type differentiation from nutritional epigenetics to supercoiled DNA, which prevents virus-driven entropy of organized genomes.

Neuroscience of Early-Life Learning in C. elegans

My comment to “The Scientist”: See also:  Pan-neuronal imaging in roaming Caenorhabditis elegans
Reported as: Watching sensory information translate into behavior

“We have long been recording behavior in worms, but we and others have concluded that, if you want to get physiologically relevant neural activity patterns, you have to look at neurons inside a behaving animal,” Samuel explained. “Only in that context are all feedback loops intact, where behavioral output modulates neural activity which, in turn, shapes behavior.”

As all serious scientists continue to link ecological variation to ecological speciation via nutrient-dependent pheromone-controlled reproduction in species from microbes to humans, my antagonists have all but disappeared.
Clearly, it is time to finally begin discussion of how virus-driven energy theft links hydrogen-atom transfer in DNA base pairs in solution from mutations to pathology instead of from nutrient-dependent RNA-mediated DNA repair via amino acid substitutions to supercoiled DNA, which protects organized genomes from virus-driven entropy.
See the response to my comment by Roy Niles:

Clearly, since viruses weren’t discussed in this article, it is not time to begin discussion of how Kohl supposes that virus-driven energy theft “links” hydrogen-atom transfer in DNA base pairs in solution from mutations to pathology, although I suppose if anyone could figure out exactly what “links” are in Kohl’s imagination, we might find that he has mistaken the interconnectness of all universal systems as directed or directional links.
And I presume he knows that pathology is the science of the causes and effects of diseases, in which case he seems to be assuming that all virus-driven systems are diseased.  But hey, this kind of thing is what he does.

My comment: If you start from any other approach to healthy longevity for comparison to virus-driven pathology, your imagination, opinions and/or findings will not reflect what is known by serious scientists. All serious scientists know they must link angstroms to ecosystems across all living genera via hydrogen-atom transfer in DNA base pairs in solution.
Only pseudoscientists make claims about how virus-driven energy theft is linked to the nonsense about neo-Darwinian evolution. The pseudoscientists refuse to acknowledge that viruses like the Zika virus prevent ecological variation from becoming ecological adaptation. Serious scientists have continued to claim that pseudoscientists are typically found among the foolish theorists who knows nothing about physics, chemistry, or biophysically constrained RNA-mediated amino acid substitutions and cell type differentiation in all living genera, which is controlled by the physiology of nutrient-dependent reproduction. And, people like Roy Niles take their cues from the pseudoscientists.

rp_levels-of-organization.jpg

Effects on invertebrate GnRH and affects on primate behavior

Introduction: Energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution have again been linked to hormone-organized and hormone-activated behaviors by the conserved molecular mechanisms we detailed in the molecular epigenetics section of our 1996 Hormones and Behavior review. The practical application of those details has been reported in the context of this article, published in the New England Journal of Medicine.

Effects of Testosterone Treatment in Older Men

Daily Diagnosis is emailed each weekday to members of the American Society for Clinical Pathology (ASCP).
Information about the Effects of Testosterone Treatment in Older Men was reported in “ASCP Daily Diagnosis” as:
Testosterone Replacement Gel May Provide Some Benefits To Older Men With Low Testosterone, Study Suggests.

Excerpts:

The AP (2/17, Tanner):  … finding mostly modest improvement in the sex lives, walking strength and mood of a select group of older men.

NBC News (2/17, Fox, Derenowski, Costello)  …points out that that findings “are expected later from four other related studies, which tested the hormone’s effects on mental function, bone density, heart function and anemia.”

See also the reports from the New York Times (2/18, A17, Kolata, Subscription Publication), Forbes (2/17, Weintraub), Medscape (2/17, Tucker), HealthDay (2/17, Thompson), STAT (2/17, Swetlitz), the Pittsburgh Post-Gazette (2/17, Templeton), Reuters (2/17, Emery), the Wall Street Journal (2/17, Beck, Subscription Publication), The Oregonian (2/17, Terry), and the NPR (2/17, Streeter) “Shots” blog.

This is “Big Science” that is not placed into any other context whatsoever. See also, from the New England Journal of Medicine:

On Smell.

The sense of smell links energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution to testosterone levels during life history transitions in men.
Excerpt:

I should think we might fairly gauge the future of biological science, centuries ahead by estimating the time it will take to reach a complete comprehensive understanding of odor. It may not seem a profound enough problem to dominate all the life sciences, but it contains, piece by piece, all the mysteries” (p. 732).  — Lewis Thomas (as cited in The Scent of Eros: Mysteries of Odor in Human Sexuality).

My comment: Gonadotropin-releasing hormone (GnRH) is the link from the sense of smell to testosterone during life history transitions.
See also: From Fertilization to Adult Sexual Behavior (1996)
Excerpt:

For instance, Jakacki, Kelch, Sauder, Lloyd, Hopwood, and Marshall (1982) have shown that prepubertal children secrete luteinizing hormone (LH) and presumably gonadotropin-releasing hormone (GnRH) in a pulsatile manner, well before physical evidence of sexual maturation is apparent. Since the neuroendocrine mechanisms for the control both of gonadal and, in part, of adrenal steroidogenesis are active, if the Gd–H–B model is influenced by social-environmental sensory stimuli before puberty occurs, such stimuli also would be capable of influencing long-term behavior.

Cited in: Testosterone in utero and at birth dictates how stressful experience will affect learning in adulthood
Excerpt:

…the absence of testosterone shortly after birth organizes the ability to acquire trace memories in adulthood and dictates its modulation by stressful experience in females. These effects are generally consistent with those of sexual behaviors, which become masculinized by exposure to testosterone in utero and feminized by its absence shortly after birth (3, 9, 33, 34). Our data suggest that sexually dimorphic effects of emotional experience on cognitive behaviors in adulthood are similarly organized by a relatively brief exposure to testosterone during development.

See also: Feedback loops link odor and pheromone signaling with reproduction (2005)
Excerpt:

Indications that GnRH peptide plays an important role in the control of sexual behaviors suggest that pheromone effects on these behaviors might also involve GnRH neurons.  (p 683)

My comment: Additional findings that support claims about how nutrient energy-dependent hydrogen-atom transfer in DNA base pairs in solution are linked from RNA-mediated events to the pheromone-controlled physiology of nematodes and ecological adaptation during life history transitions in humans are included in the reports linked here:
Distinct Circuits for the Formation and Retrieval of an Imprinted Olfactory Memory
System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes
Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity
Mitochondrial functions modulate neuroendocrine, metabolic, inflammatory, and transcriptional responses to acute psychological stress
The Gonadotropin Releasing Hormone (GnRH)-Like Molecule in Prosobranch Patella caerulea: Potential Biomarker of Endocrine-Disrupting Compounds in Marine Environments
Cytogenetic approaches for determining ecological stress in aquatic and terrestrial biosystems
Summary: The benefits of testosterone therapy for those who are deficient have been placed into a model of biologically-based cause and effect of hormones linked to behavior. The hormones that affect behavior link physics and chemistry to every aspect of metabolic networks and genetic networks that has ever been linked to the physiology of reproduction in all living genera.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Conclusion:

…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

See for comparison: 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: The likelihood that anyone  who touts links from constraint-breaking mutations to biodiversity will “… fairly gauge the future of biological science, centuries ahead by estimating the time it will take to reach a complete comprehensive understanding…” can be compared to facts that link “…the future of biological science, centuries ahead…” to what is currently understood about the links from food odors and pheromones to the physiology of reproduction in all vertebrates and invertebrates. The food odors and pheromones link metabolic networks to genetic networks via RNA-mediated events linked to supercoiled DNA that protects all organized genomes from virus-driven entropy. The organized genomes are exemplified in the morphological phenotypes and the behavioral phenotypes of all living genera.
See for example: The Genetics of Society
Excerpt:

For the first time, scientists are investigating the molecules that underlie eusocial behavior at a depth that was previously unimaginable. New, affordable sequencing technologies enable scientists to examine how genes across the entire genome are regulated to generate different caste phenotypes, the roles of DNA methylation and microRNAs in this differential expression, and what proteins are synthesized as a result.

My comment: The molecules that underlie all behavior have already been linked from hydrogen-atom transfer in DNA base pairs in solution via the role that microRNAs play in RNA-directed DNA methylation, which links alternative splicings of pre-mRNA (the microRNAs) to cell type differentiation in all genera via RNA-mediated amino acid substitutions, DNA methylation, the creation of adhesion proteins and the nutrient-dependent pheromone-controlled creation and stability of supercoiled DNA.
See also:  Organizational and activational effects of hormones on insect behavior
Excerpt:

Effects of hormones on brain and behavior occur through three mechanisms: (1) behaviors both organized and activated by hormones, (2) behaviors only organized by hormones, and (3) behaviors only activated by hormones (reviewed in Arnold and Breedlove, 1985; Diamond et al., 1996).”

My comment: Although Gene Robinson cited our 1996 Hormones and Behavior review in the article he co-authored with Elekonich, neither of them has since acknowledged the basis for any of their subsequent claims. Gene Robinson has proceeded to tout the pseudoscientific nonsense of neo-Darwinism at a time when others are trying to eliminate it from any further consideration whatsoever.
See: Molecular evolutionary analyses of insect societies
Excerpt:

Our bee molecular evolution study revealed that genes involved in carbohydrate metabolism are evolving more rapidly in eusocial relative to noneusocial bee lineages and are evolving most rapidly in highly eusocial lineages (21).

My comment: Molecules do not evolve. Hydrogen-atom transfer in DNA base pairs in solution links energy-dependent changes in the microRNA/messenger RNA balance to the de novo creation of olfactory receptor genes in all vertebrates and invertebrates. Eusocial lineages do not evolve. Organisms and species adapt via the nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to humans via the conserved molecular mechanisms we detailed in the molecular epigenetics section of our 1996 review. That fact shows why the vision Sir Paul Nurse has for the Crick Institute will be skewed by the facts about RNA-mediated cell type differentiation.

See: Vision for the Crick Institute

…you can’t force people to work together, and just putting them in the same room doesn’t mean that is going to happen.

My comment: Gene Robinson, and many others, have pitted themselves against those who have been Combating Evolution to Fight Disease and those who have linked angstroms to ecosystems in all living genera via the Structural diversity of supercoiled DNA.
The vision for the Crick Institute requires cooperation among those who link RNA-mediated epigenetic regulation of gene expression; RNA-mediated gene silencing, RNA-mediated toxicity, RNA-mediated epigenetic heredity, via nutrient-dependent RNA-directed DNA methylation to life history transitions in levels of testosterone and behavior via RNA-mediated amino acid substitutions.
For example, see:
Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity
In the context of Combating Evolution to Fight Disease, especially age-related diseases that link epigenetic effects on hormones to the affects of hormones on behavior via COMT Val158Met or BDNF Val66Met, if you cannot accept the fact that energy-dependent base pair changes link RNA-mediated amino acid substitutions to all biodiversity, you should not consider trying to explain top-down causation to a serious scientist.
 
 

terrarium-eco-system

MicroRNA-mediated RNA epigenetics

RNA Epigenetics

DNA isn’t the only decorated nucleic acid in the cell. Modifications to RNA molecules are much more common and are critical for regulating diverse biological processes.

Excerpt:

…specific alternative splicing types, such as intron retention, exon skipping, and alternative first or last exon usage, were highly correlated with m6A decoration. And silencing the m6A methylating protein METTL3 affected global gene expression and alternative splicing patterns in both human and mouse cells.2

My comment: “Silencing” a protein effects global gene expression, which is how gene expression affects behavior.

See also: From Fertilization to Adult Sexual Behavior

Excerpt:

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: RNA methylation and DNA methylation are no longer just linked to sex difference in cell types. They are linked to all differences in biophysically constrained cell type differentiation in all individuals of all living genera.
It is perfectly clear that ecological variation links atoms to ecosystems via the ability of nutrient energy-dependent microRNAs and adhesion proteins to stabilize organized genomes in the context of the supercoiled DNA that protects all living genera from virus-driven genomic entropy.
Nothing currently known about biophysically constrained RNA-mediated protein folding chemistry during thermodynamic cycles of protein biosynthesis and degradation has changed in the past 50 years (see Dobzhansky, 1964).  When will everyone simply admit that Dobzhansky (1973) was correct when he reported that:

…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)

Are serious scientists trying to be polite when they destroy all the claims of neo-Darwinian theorists by doing it gradually?

October 2014

Perry Marshall: too much information for atheist PZ Myers

Atheist PZ Myers Debates Perry Marshall Darwinism vs. Evolution 2.0 on “Unbelievable?”
Excerpt:

Contrary to what PZ said, McClintock’s work is explicitly about cells engineering solutions! That is her point.

My comment: Perry Marshall shows how difficult it is to discuss biological facts with those who are biologically uninformed. PZ Myers ignores everything known about how the innate immune system is designed to ensure cell type stability and the nutrient-dependent stability of organized genomes.
That nutrient-dependent stability is maintained across species via the physiology of reproduction. Individuals of species that cannot find enough food to support their RNA-mediated physiology of reproduction do not mutate and become members of another species. They die!

When species do not become extinct, the nutrient-dependent physiology of reproduction links what organisms eat from RNA-mediated events to chromosomal rearrangements and biodiversity.
The systems complexity of the epigenetically-effected nutrient-dependent chromosomal rearrangements links everything known about physics, chemistry, and the design of the conserved molecular mechanisms of RNA-mediated cell type differentiation. Viruses can then be linked from mutations and perturbed protein folding to all pathology.
Viruses perturb protein folding, which is how they link the undifferentiated cell types of cancer to suffering and death. Viruses also perturb the nutrient energy-dependent mechanisms of DNA repair, which involve thermodynamic cycles of protein biosynthesis and degradation. Defects in degradation are linked to the pathology of neurodegenerative diseases, such as Alzheimer’s and Parkinson’s and all others.
When people like PZ Myers attempt to debate biological facts and to put mutations into the context of their neo-Darwinian nonsense about evolution, they always lose. The dialog between Marshall and Myers adds another decimating epic loss to the neo-Darwinian army of the biologically uninformed. Marshall’s accurate representations of biologically-based cause and effect encourage others who are interested in Combating Evolution to Fight Disease.
No biologically informed researchers are combating the representations in Evolution 2.0. All have either dismissed the representations of people like PZ Myers, or they will now do so more quickly. No serious scientists link atoms to ecosystems via mutation-driven evolution. Perry Marshall’s book will help you to dismiss the nonsense touted by PZ Myers and other pseudoscientists.
See also: One crank dies, another rises to take his place
Davidson (2006) Evolution was all due to chromosome rearrangements, which somehow are not mutations, and he also somehow ignored the existence of allelic differences between species
Excerpt:

It is no longer acceptable to regard evolution as a self-regulating phenomenon guided by random mutation and Natural Selection, especially since it has failed the acid test of experimental verification.

My comment:

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.
These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.
That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.

My comment: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system reported weekend evolution of the bacterial flagellum, which occurred via two nutrient-dependent pheromone-controlled RNA-mediated amino acid substitutions. The substitutions that enabled the ecological adaptation in the context of the bacterial flagellum were reported to be mutations.

PZ MYERS REVISITED

August 2015 I repeat: Octopuses are NOT aliens

Excerpt from my comment:

The problem for atheists becomes bigger almost every day.
Where is PZ Myers, when we need to learn more about cell type differentiation via mutations, now that all serious scientists have abandoned that pseudoscientific nonsense because they have learned about biologically-based cause and effect?

September 2015 Creationists are now actively propagating the claim that octopuses are aliens
Excerpt from my comment:

No experimental evidence of biologically-based cause and effect links evolution to the G protein-coupled receptors that link the de novo creation of nucleic acids to the de novo creation of olfactory receptor genes and the extant biodiversity exemplified in cephalopods, vertebrates, fruit flies, and all vertebrates.

Addendum: PZ Myers has continued to misrepresent what is known to serious scientists about biologically-based cause and effect since he attacked me for presenting accurate information about the role of nutrient-dependent pheromone-controlled chromosomal rearrangements that link ecological variation to ecological speciation in all living genera. He lives in a world of the biologically uninformed, which is why I was surprised to learn about the debate with Perry Marshall. Myers went into hiding over the issues brought forward in the context of the octopus genome sequencing, which linked nutrient-dependent microRNAs  and adhesion proteins to the supercoiled DNA that protects the organized genomes of all living genera from virus-driven entropy. But, he entered debate with Perry Marshall as if none of the claims by serious scientists had ever been made.

rp_levels-of-organization.jpg

Neo-Darwinism vs the neocortex

From Fertilization to Adult Sexual Behavior

Excerpt: (with my emphasis) Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to c in at least two species, Drosophila melanogaster and Caenorhabditis elegans…. That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

Alternative splicing as a switch to enhance neuroprotection under stress

Excerpt: Alternative splicing is an important post-transcriptional regulatory mechanism for cells to generate transcript variability and proteome diversity18, 19. It is estimated that 95% of multiexonic genes in humans and 65% in Drosophila are alternatively spliced20, 21. In the nervous system, this process is especially common for gene regulation.
Conclusion: Our identification of alternative splicing functioning as a switch to enhance the neuroprotective role of DmNmnat indicates that the neuronal maintenance capacity is regulated endogenously and enhanced under stress for neurons to confer self-protection and higher resistance to adverse conditions.

Reported as: “Under stress, RB is preferably spliced in neurons to produce the neuroprotective PB/PD isoforms. Our results indicate that alternative splicing functions as a switch that regulates the expression of functionally distinct DmNmnat variants.

My comment: Serious scientists have identified alternative splicing functioning as a switch to enhance the neuroprotective role of nutrient-dependent RNA-mediated protein folding chemistry. They have also linked the physiology of reproduction from microRNAs and cell adhesion proteins to supercoiled DNA, which protects organized genomes from virus-driven entropy during thermodynamic cycles of protein  biosynthesis and degradation.
Additional article excerpt:

To further investigate the mechanism of DmNMNAT localization, we analysed the C-terminal amino-acid sequence of PC and PD and identified a putative nuclear localization signal, a KKQK motif37, 38 encoded in exon 7 (Fig. 2a).

In all invertebrates and vertebrates, biophysically constrained nutrient-dependent RNA-mediated protein folding is controlled by the physiology of reproduction. The physiology of reproduction is controlled by pheromones in species from microbes to humans. That fact suggests that ecological variation can be linked from atoms to ecosystems via ecological adaptations. The ecological adaptations  require only a single nutrient energy-dependent base pair change and fixation of a single RNA-mediated amino acid substitution.
There is no need to ever again consider neo-Darwinian evolution in the context of what is known to all serious scientists about RNA-mediated cell type differentiation.
See also: Alternative RNA Splicing in Evolution and Mutation-Driven Evolution
Learn about the difference between mutations and amino acid substitutions and join others who are Combating Evolution to Fight Disease
My comment:
An alternative theory proposes environmentally induced change in an organism’s behavior as the starting point (1), and “phenotypic plasticity” that is inherited across generations through an unspecified process of “genetic assimilation” (2).
This is now more than merely an alternative theory of genetic assimilation. It links transgenerational epigenetic effects from nutrient uptake and RNA-mediated events to amino acid substitutions that differentiate the cell types of all cells in all individuals of all organisms. See, for example: Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans
The nutrient stress-induced RNA-mediated events, which link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man, also link morphological and behavioral diversity via conserved molecular mechanisms exemplified in the context of biologically plausible ecological speciation in nematodes.
See: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes
A difference in their feeding behavior and in the anatomy of their mouth parts is linked from nutrient-dependent pheromone-controlled feedback loops to ecological, social, and neurogenic niche construction. The change in focus from mutations, natural selection, and the evolution of biodiversity via unknown evolutionary events to nutrient-dependent pheromone-controlled RNA-mediated events that differentiate cell types may be required for others to realize the difference between evolutionary theories and biologically-based facts about RNA-mediated events.
RNA-mediated events are biophysically constrained, which means they are a biologically plausible way to link the physics and chemistry of protein folding to increasing organismal complexity via molecular biology. RNA-mediated events can also be compared to any unknown evolutionary events that might arise in the context of an alternative theory about constraint-breaking mutations, or other theories that include no mention of RNA-mediated events.
See also: Phosphorylation-Mediated Regulation of Alternative Splicing in Cancer
Abstract excerpt:

Alternative splicing (AS) is one of the key processes involved in the regulation of gene expression in eukaryotic cells. AS catalyzes the removal of intronic sequences and the joining of selected exons, thus ensuring the correct processing of the primary transcript into the mature mRNA. The combinatorial nature of AS allows a great expansion of the genome coding potential, as multiple splice-variants encoding for different proteins may arise from a single gene. Splicing is mediated by a large macromolecular complex, the spliceosome, whose activity needs a fine regulation exerted by cis-acting RNA sequence elements and trans-acting RNA binding proteins (RBP). The activity of both core spliceosomal components and accessory splicing factors is modulated by their reversible phosphorylation. The kinases and phosphatases involved in these posttranslational modifications significantly contribute to AS regulation and to its integration in the complex regulative network that controls gene expression in eukaryotic cells.

My comment:  Neo-Darwinian theorists continue to ignore everything currently known to serious scientists about RNA-mediated cell type differentiation. If you let them, they will teach another generation of students to become biologically uninformed science idiots.

amino acid homeostasis

Receptor methylation controls behavior

The protein arginine methyltransferase PRMT5 promotes D2-like dopamine receptor signaling

Excerpt 1)

The addition of a methyl group to an arginine residue can remove a hydrogen bond donor and decrease the electrostatic surface potential at the residue, resulting in a change in size and hydrophobicity that can affect its interaction with binding partners (21).

Excerpt 2)

Together, these results led us to propose that arginine methylation promotes D2-like dopamine receptor signaling and that this mechanism of receptor regulation is conserved between nematodes and humans. Moreover, our finding that several hundred mammalian GPCRs contain predicted methylation sites within their cytoplasmic domains (Fig. 1A and tables S1 and S2) suggests that methylation may broadly regulate GPCR signaling in a previously unappreciated manner.

My comment: This article links RNA-directed DNA methylation to G protein-coupled receptors via biophysically constrained nutrient-dependent pheromone-controlled protein folding chemistry in species from nematodes to humans. It was reported as:

Receptor methylation controls behavior

D2 dopamine receptors are targeted by antipsychotic agents to regulate behavior. Likhite et al. found putative arginine methylation motifs in some human G protein–coupled receptors (GPCRs), including the D2 dopamine receptor, and in homologs in the worm Caenorhabditis elegans. Methylation of the D2 dopamine receptor by the arginine methyltransferase PRMT5 enhanced D2 receptor signaling in cultured cells. C. elegans lacking prmt-5 had behavioral problems similar to those in worms deficient in the D2-like receptor DOP-3. Thus, methylation of GPCRs may be important for clinically relevant targets such as the D2 receptor.

My comment: The claim that Receptor methylation controls behavior can be placed into the context of MicroRNA-encoded behavior in Drosophila, and all other living genera. For example, Feedback loops link odor and pheromone signaling with reproduction.
Excerpt:

Indications that GnRH peptide plays an important role in the control of sexual behaviors suggest that pheromone effects on these behaviors might also involve GnRH neurons. (p 683)

My comment: The nutrient-dependent microRNA/messenger RNA balance links energy-dependent base pair changes to RNA-mediated gene duplication and fixation of RNA-mediated amino acid substitutions that differentiate all cell types of all individuals of all living genera in the context of the physiology of reproduction. Even when the physiology of reproduction does not involve neurons, it involves the conserved molecular mechanisms of nutrient-dependent pheromone-controlled reproduction in species from microbes to humans.
See for details: From Fertilization to Adult Sexual Behavior
Excerpt:

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 alternative splicing of otherwise identical genes links everything known about physics, chemistry, and biology via the conserved molecular mechanisms of biophysically constrained nutrient-dependent RNA-mediated protein folding to protection against virus-driven genomic entropy, which is ensured by supercoiled DNA.

terrarium-eco-system

eQTLs and ecological adaptation

Human Expression QTLs Are Enriched in Signals of Environmental Adaptation

eQTLs is the term used to link base pair changes via proxies to single-nucleotide polymorphisms (SNPs) associated with complex traits and diseases. The direct link from the epigenetic landscape to the physical landscape of DNA via nutrient-dependent protein folding biochemistry and RNA-mediated gene duplication and RNA-mediated amino acid substitutions goes missing in the context of term use confusion.

They link the epigenetic landscape to the physical landscape of DNA without the link from nutritional epigenetics to the pheromone-controlled physiology of reproduction and ecological speciation in species from microbes to man. But, they seem to be surprisingly close to realizing the difference between mutations and amino acid substitutions in the context of how ecological variation MUST lead to ecological adaptations via the conserved molecular mechanisms we detailed in our 1996 review of RNA-mediated cell type differentiation. From Fertilization to Adult Sexual Behavior
Excerpt:

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.

rp_levels-of-organization.jpg

Non-mainstream scientist shares Nobel prize in Medicine

Youyou Tu is the 12th women awarded the Nobel Prize in Physiology or Medicine (2015) for her discoveries concerning a novel therapy against Malaria.

Historical perspective: Lasker~DeBakey Clinical Medical Research Award

Excerpt:

Tu discovered a passage in the Handbook of Prescriptions for Emergencies (340 CE) by Ge Hong that referenced Qinghao’s malaria-healing capacity. It said “Take a handful of Qinghao, soak in two liters of water, strain the liquid, and drink.” She realized that the standard procedure of boiling and high-temperature extraction could destroy the active ingredient.

My comment: Recent learning about the thermodynamic stability of the active ingredient suggests that traditional Chinese medicine integrated what is now known about the biophysically constrained  chemistry of protein folding during thermodynamic cycles of protein biosynthesis and degradation in bacteria and plants.
The cycles link ecological variation to ecological adaptations via nutrient-dependent RNA-mediated amino acid substitutions in all living genera. The thermodynamic stability of the plant extract was maintained for medicinal use.
Excerpt 2)

Tu pioneered a new approach to malaria treatment that has benefited hundreds of millions of people and promises to benefit many times more. By applying modern techniques and rigor to a heritage provided by 5000 years of Chinese traditional practitioners, she has delivered its riches into the 21st century.

My comment: Other researchers from China recently linked everything else known about RNA-mediated protein folding biochemistry via amino acid substitutions to the thermodynamic stability of all organized genomes. The “Holy Grail” of nutrient-dependent RNA-mediated protein folding is thermodynamically regulated.
See:
Structural basis of pre-mRNA splicing 
Structure of a yeast spliceosome at 3.6-angstrom resolution
Reported as: Chinese Scientists Discover Structural Basis of Pre-mRNA Splicing

On August 21st, the research team led by Prof. Yigong Shi from School of Life Sciences, Tsinghua University in China published two side-by-side research articles in Science, reporting the long-sought-after structure of a yeast spliceosome at 3.6 angstrom resolution determined by single particle cryo-electron microscopy (cryo-EM), and the molecular mechanism of pre-messenger RNA splicing. Until now, decades of genetic and biochemical experiments have identified almost all proteins in spliceosome and uncovered some functions. Yet, the structure remained a mystery for a long time. The works, primarily performed by Dr. Chuangye Yan, and Ph.D students Jing Hang and Ruixue Wan under Prof. Yigong Shi’s supervision, settled this Holy Grail question and established the structural basis for the related area. This work was supported by funds from the Ministry of Science and Technology and the National Natural Science Foundation of China.

See also: Feedback loops link odor and pheromone signaling with reproduction and Sensory feedback shapes individuality to provide equal space for behavioral excellence
Other mainstream scientists continue attempts to genetically engineer mosquitoes to limit their nutrient-dependent physiology of RNA-mediated ecological adaptation. These mainstream scientists ignore the contribution of RNA-mediated amino acid substitutions reported in Amino Acid Residues Contributing to Function of the Heteromeric Insect Olfactory Receptor Complex.
They use viruses to genetically engineer mosquitoes with mutations that limit reproduction. See: orco mutant mosquitoes lose strong preference for humans and are not repelled by volatile DEET and Genome-engineering with CRISPR-Cas9 in the mosquito Aedes aegypti.
If this diagram looks impressively complex compared to claims that linked traditional medicine across 5000 years of what should have been advances in treatment of diseases made by mainstream scientists, realize is that mainstream scientists get paid to do work that is represented like this.

 
 
 
 
 

terrarium-eco-system

Exosomes and the RNA-mediated future of medicine

The Exosome Is Recruited to RNA Substrates through Specific Adaptor Proteins

Reported as:

The exosome regulates the processing, degradation, and surveillance of a plethora of RNA species.

Excerpt:

…the exosome employs a general mechanism of recruitment to defined substrates and that this process is regulated through adaptor proteins.

Journal article excerpt: (subscription required)

The nuclear exosome processes precursors of numerous stable RNA species (Allmang et al., 1999) (rRNA, snoRNA, and snRNA) and degrades by-products of RNA processing reactions. Additionally, it targets for surveillance numerous cryptic unstable transcripts (CUTs) (Wyers et al., 2005) and aberrant RNAs. In the cytoplasm the exosome degrades aberrant mRNAs identified by the NMD (nonsense-mediated decay) (Takahashi et al., 2003) and NGD (no-go decay) (Doma and Parker, 2006) pathways.

My comment: Attempts to place the general molecular mechanisms of biophysically constrained nutrient-dependent substrates’ RNA-mediated amino acid substitutions and protein folding chemistry that determines cell types in all individuals of all genera into the context of neo-Darwinian theories have continued to become increasingly more foolish.
See for example: Steven Tucker: The man who found the Homo Naledi fossils
When will students in your country be taught what is known about cell type differentiation instead of being taught to believe in ridiculous theories? See, for example:

Scientists home in on origin of human, chimpanzee facial differences

Excerpt:

The key lies in how genes involved in facial development and human facial diversity are regulated—how much, when and where the genes are expressed— rather than dissimilarities among the genes themselves.
My comment: The key to gene regulation has always been nutrient-dependent and RNA-mediated via gene duplication and RNA-mediated amino acid substitutions that are fixed in the organized genomes of species from microbes to humans via the biophysically constrained chemistry of protein folding and successful nutrient-dependent reproduction.
If you let pseudoscientists ignore that fact when they report results from fossil evidence, the evolutionary theorists will make monkeys of us all.

See instead:
International Society for Extracellular Vesicles (ISHE) exclusive video collection
includes the panel discussion: Exosomes Role in the Future of Medicine
See also: Context-specific microRNA function in developmental complexity
Excerpt:

When also considering the large number of primate-specific miRNAs expressed in the brain (Berezikov et al., 2006) and that a single pyramidal neuron in the cortex may form up to 10000 synapses with other cells, it is tantalizing to hypothesize a role for miRNA as key regulatory molecules in the development of the exquisitely complex programmes of gene expression and the decentralized modifications of individual synaptodendritic connections that are required for the cortical complexity observed in the human brain.

My comment: Do not be the last serious scientist in the world to learn how cell type differentiation occurs in all cells of all individuals of all living genera. Other serious scientists will think you have always been a biologically uninformed theorist.
See also: The Complexity of Human Ribosome Biogenesis Revealed by Systematic Nucleolar Screening of Pre-rRNA Processing Factors
Excerpt:

…among the human proteins identified, 59 have a yeast homolog that has not been examined for a role in ribosome synthesis. Significantly, these include putative methyltransferases, protein modification enzymes, and structural cellular components, as well as gene products
involved in translation, pre-mRNA splicing, or DNA replication. These are all cellular processes recently shown to share highly specific trans-acting factors with ribosome synthesis.

My comment: It should be obvious that mutations, which perturb thermodynamic cycles of RNA-mediated protein biosynthesis and degradation cannot be linked to the evolution of biodiversity, which is nutrient-dependent and controlled by the physiology of reproduction in all living genera.
See also: Viral and Cellular Genomes Activate Distinct DNA Damage Responses
and Loss of lamin A function increases chromatin dynamics in the nuclear interior, which was reported as: Preventing chromosomal chaos: Protein-based genome-stabilizing mechanism discovered
Excerpt:

According to Garini, this protein-mediated mechanism is fundamental to the stability of life as we know it.

The stability of life is nutrient-dependent, receptor-mediated and the stability of species is controlled by the physiology of reproduction in the context of chromosomal rearrangements, not mutations or natural selection or evolution.
See also:  Exosomes and the RNA-mediated future of medicine (2)
For a ridiculous misrepresentation of biologically-based cause and effect, see: One crank dies, another rises to take his place PZ Myers attacks anyone who does not support his ridiculous opinions.
Excerpt:
Behold James Vaughn Kohl. (my comment from Jan 3, 2014 may not appear unless you set the post rating to 1.0)

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.
These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.

See also: I repeat: Octopuses are NOT aliens

Excerpt:

The problem for atheists becomes bigger almost every day.
Where is PZ Myers, when we need to learn more about cell type differentiation via mutations, now that all serious scientists have abandoned that pseudoscientific nonsense because they have learned about biologically-based cause and effect?
See for example: DNA methylation pathways and their crosstalk with histone methylation http://dx.doi.org/10.1038/nrm4043
Why isn’t little PeeZee slamming down the creationists now that they reported the link from virus-driven entropic elasticity to genomic entropy?
Also:

August 25, 2015
The best way to refute pseudoscientific nonsense linked to evolutionary theories invented by neo-Darwinists is with facts about cell type differentiation in the context of climate change and the physiology of reproduction, which links ecological variation to ecological adaptations via the microRNA/messenger RNA balance. The balance is linked to biodiversity via chromosomal rearrangements, not by virus-driven mutations that cause gene loss.See: Mayo Clinic Researchers Find New Code That Makes Reprogramming of Cancer Cells Possible https://www.youtube.com/watch?v=yGYTLOGZ40U
Also:

August 23, 2015
See also: http://freethoughtblogs.com/pharyngula/2014/01/06/one-crank-dies-another-rises-to-take-his-place/“…he was actually a biologist, had a Ph.D. in zoology, and taught at the University of Vermont. He had a “scientific” theory, which was his, which he thought explained all that evolutionary change while refuting those silly scientists who believed that mutations occurred. No! Evolution was all due to chromosome rearrangements, which somehow are not mutations, and he also somehow ignored the existence of allelic differences between species…”Mutations perturb protein folding, which is why they cannot be linked to evolution.The differences in alleles are nutrient dependent and they link RNA-mediated events to the biophysically constrained chemistry of protein folding and the physiology of reproduction in all genera via amino acid substitutions and chromosomal rearrangements, which is what the octopus genome sequencing just showed.
Also:

August 21, 2015
Re: I just know this nonsense is going to be propagated by creationists everywhere, and I’m going to have to slam it down repeatedly.Thanks for acknowledging the fact you will be forced to address what is known to serious scientists about the link from microRNAs to biodiversity that refutes all claims of theorists about beneficial mutations.Jerome Hui and others linked all crustaceans to all insects via nutrient-dependent changes in the microRNA/messenger RNA balance. There is no reason to believe that anything else links marine invertebrates to primates.Besides, octopuses are referred to as the “primates of the sea.” The sequencing of the octopus genome links the conserved molecular mechanisms of biophysically constrained nutrient-dependent protein folding to RNA-mediated events and chromosomal rearrangements, which are clearly linked to all extant biodiversity without the nonsense about beneficial mutations and evolution.
Also:

August 27, 2015
The Octopus Genome: Not “Alien” but Still a Big Problem for Darwinism http://www.evolutionnews.org/2015/08/the_octopus_gen098681.html
Excerpt:
Whenever you see “de novo” origin of a gene invoked, you know that evolutionary biologists lack any explanation for how that gene arose.”
Slam ’em down, PZ. Alternatively, encourage your anonymous idiot minions to try.
Filtering light through a prism to identify tissue type

Riding the wrong direction

Riding the Evolution Paradigm Shift With Eugene Koonin

Excerpt:

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…

Excerpt:

[T]he entire ideology of personalized medicine should be taken with many grains of salt.

My comment: Personalized medicine links the conserved molecular mechanisms of biologically-based cause and effect from nutrient-dependent RNA-mediated gene duplication to RNA-mediated amino acid substitutions, which differentiate all cell types in all individuals of all genera. Fixation of the amino acid substitutions in the organized genomes of all genomes occurs in the context of their physiology of reproduction.
The idea that any aspect of this biophysically constrained chemistry of nutrient-dependent protein folding, which links atoms to ecosystems, should be taken with “…many grains of salt” is an idea commonly shared by those who do not understand how cell type differentiation occurs.
Koonin cannot yet be placed into the same category as other theorists. He clearly identified the problem with neo-Darwinian theories about a last universal common ancestor. See:

A universal trend of amino acid gain and loss in protein evolution

Excerpt: 

We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.

My comment: Claiming anything about “…a universal, intrinsic trend that emerged…” closely parallels the claims of creationists whose claims are supported by experimental evidence that links viruses to RNA-mediated cell type differentiation.
First, the de novo creation of amino acids must occur. Then viruses can perturb the creation of different cell types in different species by preventing proper RNA-mediated protein folding. The viruses can then be linked to all pathology at the same time that RNA-mediated amino acid substitutions are linked to healthy longevity.
See also: The Darwin Code by Greg Bear
Excerpt:

In fact, even in 1983, when I was preparing my novel Blood Music, I asked myself–what do viruses do ¬for us? Why do we allow them to infect us? I suspected they were part of a scheme involving computational DNA, but could not fit them in…not just then.

My comment: In his 1985 novel, Greg Bear linked RNA-mediated amino acid substitutions to learning and memory. He also linked learning and memort to cell type differentiation via RNA-mediated gene duplication.
See: RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon
At the same time, and since then, others began to learn that anything told to them by neo-Darwinian theorists had not been supported by experimental evidence. There is still no experimental evidence of biologically-based cause and effect that links mutations from natural selection to the evolution of different cell types in individuals of different species.
See also:

Mae-Wan Ho: No Boundary Really Between Genetic and Epigenetic

Excerpt:

Although Ho has not let up in her criticism of the Modern Synthesis, as our conversation reveals, she says evolutionary science has now “moved on to such an extent” that she and Peter Saunders don’t really care anymore about “trying to convince the neo-Darwinists.”

See also:

Luis P. Villarreal tells it like it is

Taken together, compare the experimental evidence for virus-driven ecological adaptation, which appears to occur via the anti-entropic epigenetic effects of nutrient-dependent microRNAs, and ask why any neo-Darwinian evolutionary theorist ever claimed anything without attempting to support the claim with experimental evidence that links biologically-based cause and effect. Instead, see this attempt to explain evolution in the ridiculous context of theory.