Amino acid modification FA_Epigenetics_Table1

Information and communication (2)

Leaving an Imprint

Among the first to discover epigenetic reprogramming during mammalian development, Wolf Reik has been studying the dynamics of the epigenome for 30 years.

By Anna Azvolinsky | August 1, 2015

Excerpt:

In the mammalian field, the imprinting field, together with the X-inactivation field, was the birthplace of epigenetics.

My comment: Researchers like Wolf Reik never mentioned the role viruses play in preventing cell type differentiation. The birthplace of epigenetics became associated with a “still-birth.” The still-birth continued to leave a horrid stain on every aspect of imprinting. Epigenetic effects on imprinting should have been placed into the context of what later came to be known about the RNA-mediated events that link nutrient-dependent RNA-mediated protein folding to the biophysically constrained chemistry of cell type differentiation that is perturbed by viruses.
For more than 30 years, the role of virus-perturbed protein folding has been placed into the context of mutations linked to biodiversity as if epigenetic imprinting attributed to viruses could link viruses from mutations to biodiversity in the context of transgenerational epigenetic inheritance. Epigenetic inheritance requires nutrient-dependent microRNAs that protect organized genomes from virus-driven damage to DNA. The damage to DNA links entropic elasticity to genomic entropy in all living genera.
Re: “X-inactivation field, was the birthplace of epigenetics.”
See also:  Sex differences in the brain: a whole body perspective
Excerpt with my emphasis: (Thanks to Teresa Binstock for calling my attention to this.)

Another example concerns one of the most pervasive sex differences: the inactivation of one X chromosome in every cell of the body in females. Random X inactivation is perhaps the prime example of a sex difference (in this case, a process that happens in all female cells and no male cells) that exists in order to make the sexes more similar (more or less equalizing the dosage of X chromosome genes). For the most part, nature does a great job in covering up the consequences of this. However, the inactivation of an entire chromosome in each female cell utilizes epigenetic machinery, and the inactivation state must be continually maintained[20], [21]. There is evidence that this affects the expression of autosomal genes [22], [23], presumably because there is a limiting supply of the DNA methyltransferases and histone-modifying enzymes required for the epigenetic changes that underlie the inactivation of an entire chromosome. It is not hard to see how this one event (usually thought of in terms of equalizing males and females) may have ripple effects that result in sex differences elsewhere.

My comment: Imprinting cannot automagically affect the expression of genes. Instead, nutrient-dependent RNA-directed DNA methylation links the epigenetic effect of sensory input to hormone-organized and hormone-activated behaviors via the effects of hormones on gene expression. Hormones are linked to affects on behavior.
The “ripple effects” of epigenetically-effected RNA-mediated gene duplication and RNA-mediated amino acid substitutions cause hormones to differentiate all hormone-differentiated cell types, which are linked to behavior during life history transitions. That fact was exemplified in: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults. 
The single amino acid substitution and human behavior were linked to the honeybee model organism in: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
Excerpt with my emphasis:

The honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, diseases of the X chromosome, learning and memory, as well as conditioned responses to sensory stimuli (Kohl, 2012).

My comment: All other model organisms with hormone-organized and hormone-activated behaviors present a problem to sex researchers. Most of them are among the best examples of human pheromone-deniers.
The pheromone-deniers try to link nutrient-dependent hormone-organized and hormone-activated behaviors without placing the behaviors into the context of feedback loops. All serious scientists know: Feedback Loops Link Odor and Pheromone Signaling with Reproduction.
Not much more can be said about sexologists whose fear of pheromones may lead them to continue touting pseudoscientific nonsense about X inactivation and everything else linked from RNA-mediated events to cell type differentiation in all cells of all individuals of all species.
Similarly, not much more can be said about molecular biologists who have failed to learn or failed to teach others about RNA-mediated events during the past 30 years.

See: Wolf Reik.

He appears to have left a stain on what should have become known to serious scientists about the role that viruses play in cell type differentiation. Viruses link entropic elasticity to genomic entropy. His focus appears to be only on the stability of organized genomes.

That must include the stability of organized genomes in heterosexuals and homosexuals during their epigenetically-effected life history transitions. If you don’t teach that fact to sexologists, they might think they can get away with touting their ridiculous theories about the sexual differentiation of cell types while linking their ridiculous theories to the expression of autosomal genes.

See: Global reorganization of the nuclear landscape in senescent cells.

Excerpt:

Comparison of embryonic stem cells (ESCs), somatic cells, and senescent cells shows a unidirectional loss in local chromatin connectivity, suggesting that senescence is an endpoint of the continuous nuclear remodelling process during differentiation.

See also: Selective impairment of methylation maintenance is the major cause of DNA methylation reprogramming in the early embryo.

Excerpt:

The dispersed patterns of CpG dyads in the early-cleavage embryo suggest a continuous partial (and to a low extent active) loss of methylation apparently compensated for by selective de novo methylation. We conclude that a combination of passive and active demethylation events counteracted by de novo methylation are involved in the distinct reprogramming dynamics of DNA methylomes in the zygote, the early embryo, and PGCs.

My comment: The concept of de novo methylation appears to lie outside the context of nutrient-dependent RNA-directed DNA methylation that links RNA-mediated amino acid substitutions to the stability of organized genomes in all genera via the protection of damage from viruses when proliferation of viral microRNAs overwhelms the thermodynamic stability of organisms, which is nutrient-dependent and controlled by the physiology of reproduction.

See also: Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation.

Excerpt:

Unexpectedly, we demonstrate that TET3 activity also protects certain CpG islands against methylation buildup.

My comment: Why was that unexpected? See:

Alteration of genic 5-hydroxymethylcytosine patterning in olfactory neurons correlates with changes in gene expression and cell identity

Excerpt: 

Tet3 overexpression disrupts olfactory receptor expression and the targeting of axons to the olfactory bulb, key molecular and anatomical features of the olfactory system. Our results suggest a physiologically significant role for gene-body 5hmC in transcriptional facilitation and the maintenance of cellular identity independent of its function as an intermediate to demethylation.

My comment: This report inadvertently linked viral microRNAs to Tet3 overexpression and nutrient-dependent microRNAs to protection of organized genomes via the respective roles of viruses and nutrients in cell type differentiation. Nutrient-dependent RNA-directed DNA methylation differentiates the cells of all individuals in all species from microbes to man via their receptor-mediated biophysically constrained chemistry of nutrient-dependent protein folding and amino acid substitutions that are fixed in organized genomes via the physiology of reproduction.

See for comparison: 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…

See also: Unmasking Secret Identities

Excerpt:

Epigeneticists don’t know yet how important it is to describe methylation at single-base resolution…

If they learn how important that is, they may also learn how important it is to include the links from viral microRNAs to energy-dependent changes at the atomic level of single-base resolution. They could then place the changes into a model that links atoms to ecosystems via the sun’s biological energy and the epigenetic traps that are perturbed by viruses.
See also: Signalling

The study of the proteins that control communication within and between cells

Excerpt:

For cells to grow there must be both available nutrients and positive signals from proteins responding to environmental stimuli.
Suppression of a single protein, mTOR, which acts as a quality control step activity can result in increased lifespan through an unknown mechanism and we will attempt to reveal this.

My comment: Are they pretending that they will reveal an unknown mechanism of signaling and suppression that already links the nutrient-dependent RNA-mediated cell type differentiation of nematodes from the pheromone-controlled physiology of their reproduction to the biodiversity of all species via this report: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes
See also: The neurobiological consequence of predating or grazing
Excerpt:

“The patterns of synaptic connections perfectly mirror the fundamental differences in the feeding behaviours of P. pacificus and C. elegans”, Ralf Sommer concludes.

My comment: If you know what naturally occurs to alter feeding behaviors you can link viruses and the proliferation of viral microRNAs to entropic elasticity that leads to genomic entropy — unless the entropy is biophysically constrained by ecological variation that leads organisms to find an alternative source of food and to reproduce in the context of Darwin’s “condition of life.”

Filtering light through a prism to identify tissue type

Viruses, amino acids, and somatic cell types (2)

Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain

Excerpt:

The RNA-seq data enabled us to detect a positive correlation between developmental changes in the magnitude of parental biases and overall gene expression for most imprinted genes.
Conclusion:

At the level of the organism, our data uncover how paternal and maternal alleles of Bcl-x make vastly different contributions to brain development, a result that has profound implications for the analysis of parentally-inherited polymorphisms in human health.

Reported as:

Expanding the brain: Research identifies more than 40 new imprinted genes

See also: The activity-dependent histone variant H2BE modulates the life span of olfactory neurons
The experience-dependent variant links what is known about the biophysically constrained chemistry of nutrient dependent RNA-mediated protein folding to imprinted cell types via amino acid substitutions that determine cell type differences in all cell types of all individuals of all organisms.
In this context, it has become clear that Every amino acid matters.
The physiology of reproduction links germ cells to somatic cells and to morphological and behavioral differences in the sexes during thermodynamic cycles of protein biosynthesis and degradation, which are perturbed by viruses. The viruses perturb the nutrient-dependent RNA-mediated events that link the fixation of amino acid substitutions to the stability of all organized genomes.
See also: Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells
The complexity of virus-driven entropic elasticity, which is modulated by the anti-entropic epigenetic effects of nutrient-dependent microRNAs, has been placed into the context of mutations and evolution by biologically uninformed theorists. Catherine Dulac is not one of them
For comparison, PZ Myers is a biologically uninformed theorist who attacked Nathaniel Jeanson, a Harvard-educated Ph.D
See: A first-hand report of Nathaniel Jeanson’s lecture in Boston
Excerpt:

As I told Catherine Dulac, his former dept. head at Harvard, it was an hour-long spectacle of misinformation, half-truths and what appeared to be deliberate obfuscation.

As is typical of PZ Myers and others who are equally biologically uninformed, he lets others attack. Then, Myers asserts his superior knowledge in the context of what he thinks is their superior knowledge.
He does not support his claims with experimental evidence of biologically-based cause and effect because he is not a scientist. He is an atheist blogger and is, or was, a biology teacher. If he were a serious scientist, PZ Myers would know that the link from Jeanson’s claims to the reports from Dulac on experience-dependent receptor-mediated differences in imprinted genes, cell type differences, and morphological and behavioral phenotypes can be placed into the context of virus-driven genomic entropy.
Genomic entropy is prevented by the nutrient-dependent de novo creation of olfactory receptor genes. RNA-mediated gene duplication and nutrient-dependent RNA-mediated fixation of amino acid substitutions links viruses and mutations to olfactory receptor gene loss. Nothing links mutations to the gain of structures or functions except the pseudoscientific nonsense of neo-Darwinian theory and the vague claims of the biologically uninformed.

For comparison, the light-induced de novo creation of amino acids links the creationist Biblical perspective from “Let there be light” to nutrient-dependent RNA-mediated amino acid substitutions that differentiate cell types via the experience-dependent de novo creation of olfactory receptor genes. Virus perturbed protein folding links mutations to the loss of olfactory receptor genes when they are no longer needed to support the organism-level genomic stability that is required for successful reproduction of all species.

The accumulation of viral microRNAs continues if it is not prevented by nutrient-dependent microRNAs that control the finely-tuned microRNA/messenger RNA balance. The nutrient-dependent microRNA/messenger RNA balance controls RNA-mediated cell type differentiation.
Neo-Darwinian theorists inadvertently placed the nutrient-dependent microRNA/messenger RNA balance into the context of mutations and evolution. Simply put, they ignored Darwin’s ‘conditions of life’ and removed nutrient-dependent RNA-mediated events from any further consideration whatsoever — before anything was known about RNA-mediated events. Fortunately, now that serious scientists are beginning to understand how cell type differentiation occurs, the neo-Darwinian theorists may soon be  stopped from presenting any more pseudoscientific nonsense.
See, for instance, Eugene Koonin’s recent claim:

Excerpt:

Can biologically uninformed science idiots like PZ Myers continue to retard scientific progress. Yes, history has a way of repeating itself when anyone challenges the dogma of pseudoscientists.
See for example:

Description: Elaine Morgan was a tenacious proponent of a theory that is not widely accepted. The aquatic ape hypothesis lays out the idea that humans evolved from primate ancestors who dwelt in watery habitats. Hear her spirited defense of the idea — and her theory on why science doesn’t take it seriously.
See also: “…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 place Dobzhansky’s claim into the context of the claim that Every amino acid matters, but try to link the claims of theorists to Mutation-Driven Evolution, do not expect serious scientists to take you seriously. Serious scientists are too busy Combating Evolution to Fight Disease.
Excerpt:

The evolutionary biologist Theodosius Dobzhansky famously noted that “nothing in biology makes sense except in the light of evolution,” but perhaps, too, “nothing in evolution makes sense except in the light of biology.” Although the latter might be an exaggeration, an important gap is being filled by molecular understanding of the genesis of variation that confers the ability to evolve.

The anti-entropic energy of nutrients confers the ability to ecological adapt. Ecological speciation arises via the fixation of RNA-mediated amino acid substitutions and chromosomal rearrangements during the life history transitions of species from microbes to man. That fact led the biologically uninformed science idiot, PZ Myers to attack me after he attacked John A. Davison for sharing similar views.
See: One crank dies, another rises to take his place
Excerpt:
Behold James Vaughn Kohl.
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.

See also:

Perhaps first, these researchers should consider how virus-driven RNA-mediated cell type differentiation occurs in species from microbes to man.

It is the viruses in the bacteria that drive the creation of new nutrient-dependent pheromone-controlled variants in bacteria. The new variants are ecologically adapted Biblical species of “like kind.” Anyone who claims that one species somehow evolved into another should start with an example and include experimental evidence of biologically based cause and effect. That should have been done ever since population geneticists invented neo-Darwinism.

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Becoming biologically informed (3)

See also: Becoming biologically informed and Becoming biologically informed (2)
Now available for free: New Perspectives on microRNA in Disease and Therapy (July 22, 2015)
My comments: Perhaps someone will correct me if I am wrong.
The microRNAs do not appear to participate in a direct response to viruses. But, over long periods of time they may fine-tune the microRNA/messenger RNA balance in the organized genomes of all living genera.  If so, the changes are manifested in morphology and in the transcriptome.
Dr. TenOever uses the influenza virus as an example. The addition of less than 45 nucleotides prevents viral replication. Adding to the host microRNA controls DNA viruses and RNA viruses in a tissue-specific species-specific manner. This is probably the best example of how nutrient-dependent energy alters base pairs that lead to the stability of organized genomes via RNA-mediated amino acid substitutions. The example cannot be compared to theories about mutations and evolution without clarification by the presenters who may be unwilling to discuss biologically-based cause and effect.
That may explain why the example of bird flu prevention is not linked to cancer prevention. Only 3 amino acid substitutions lead to gain of function that enabled human to human transmission, which probably scared the masses who were taught to believe in ridiculous theories about evolution. That scare appears to have led to banned research because evolutionary theorists have made ridiculous claims about beneficial (e.g., gain of function) mutations.
The clear threat is nutrient-dependent ecological adaptations by viruses that allow them to cross species by adapting to the supply of nutrients in specific cell types in different species. That threat is minimized by discusssion of the inability to create an escape mutant in the lab. Ecological variation leads to ecological adaptations in viruses that naturally adapt — but the adaptations are placed into the context of mutations.
Placing adaptations into the context of mutations will probably cause a problem with FDA approval. If it does not, it should. The different delivery strategies may “emerge” to kill us all.
SARCASM ALERT: Let’s try coupling a manufactured microRNA to cholesterol and see how it effects the liver. Keep in mind, however, that a single base pair change and one amino acid substitution may be all that links the nutrient-dependent natural body odor that we produce to the odor of mice. Nutrient-dependent/pheromone-controlled adaptive evolution: a model. 
Excerpt:

Sex-dependent production of a mouse ‘chemosignal’ with incentive salience appears to have arisen de novo via coincident adaptive evolution that involves an obvious two-step synergy between commensal bacteria and a sex-dependent liver enzyme that metabolizes the nutrient chemical choline.

The result of this synergy is (1) a liver enzyme that oxidizes trimethylamine to (2) an odor that causes (3) species-specific behaviors. Thus, the complex systems that biology required to get from nutrient acquisition and nutrient metabolism to species-specific odor-controlled behavior is exemplified by adaptive evolution of an attractive odor to mice that repels rats (see for review Li et al., 2013).

The mouse odor also repels humans.

However, if Eugene Koonin has correctly assessed the impact of viruses on personalized medicine, there will be no epigenetic effect of social odors on hormones that affect the development of species-specific behaviors. Thus, Koonin could support his claim that [T]he entire ideology of personalized medicine should be taken with many grains of salt.
Alternatively, the claims that currently link a single amino acid substitution to human life history transitions is closely linked to the nutrient-dependent pheromone-controlled changes in the context of the honeybee model organism.
See: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
Dr. Kasinski is looking at off-target effects, but Dr. TenOever is not concerned about epigenetic regulation of endogenous retroviruses in mammals or human endogenous retroviruses (HERVs). Like George Church, these researchers seem to be limited by their inability to link physics, chemistry, and the conserved molecular mechanisms of virus-driven RNA-mediated adaptations. For example, miR-34 down-regulates protein coating that may sensitize cells for more manageable chemotherapy.
If  knowledge of cell type differentiation were driving this research, their presentations could be linked from cell type differentiation in plants to nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation in animals.
For an example from Arabidopsis (Arabidopsis thaliana) that appears to link RNA-directed DNA methylation and phosphorylation to fixation of RNA-mediated amino acid substitutions and cell type differentiation, see: Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements
Examples from plant physiology can be linked via RNA-directed DNA methylation and phosphorylation to fixation of RNA-mediated amino acid substitutions in animals via the conserved molecular epigenetics of biophysically constrained protein folding chemistry. See also: Global Epigenomic Reconfiguration During Mammalian Brain Development.
Excerpt:

Here we provide integrated empirical data and analysis of DNA methylation at single base resolution, across entire genomes, with cell-type and developmental specificity.

The question arises: “Do the molecular mechansims of RNA-mediated gene duplication and RNA-amino acid substitutions that differentiate the cell type of plants vary in animals?”

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.

 
 

terrarium-eco-system

"New" epigenetic mechanism for lifelong learning?

Critical Role of Histone Turnover in Neuronal Transcription and Plasticity
Reported as:

Lifelong learning is made possible by recycling of histones, study says

Also reported as:

New epigenetic mechanism revealed in brain cells

Excerpt:
In humans, researchers used a technique called 14C/12C bomb pulse dating to measure turnover. The technique is based on the fact that high levels of radioactive carbon (14C) were released into the atmosphere during the 1950s and 1960s, when open-air nuclear bomb testing occurred following the Second World War. Researchers can take samples from cells – in this case, purified H3.3 samples from brain cells of postmortem human brains, and determine present 14C/12C ratios from the time of death against past atmospheric levels from the time of the subject’s birth. As with the rodent observations, the researchers found that H3.3 turnover occurs in the human brain throughout life.
Additionally, the researchers deliberately manipulated H3.3 dynamics in both embryonic and adult neurons, confirming the role of histone turnover in neuronal plasticity. The findings thus establish histone turnover as a critical, and new, regulator of cell-type specific transcription in the brain.
“Histone turnover, shown through our work with H3.3, is essential for the behavior of brain cells,” said Dr. Maze. “Furthering our understanding of how the brain works, learns, forms new memories and reacts to changes in the environment can help us to find new ways to treat neurodegenerative diseases and mental illness.”
Attempts to discuss this among neuroscientists can be found on this Neuroscience FB page.
Addendum:  My understanding of cancer links it from RNA-directed DNA methylation and RNA-mediated amino acids substitutions that are linked via “histone turnover” and cell type differentition in the brain.  My understanding is based on the young earth creationist perspective, which I learned about from a physician. He claimed that something more than sun exposure must be responsible for the different types and number of different non-malignant and malignant skin cell types that were removed during ~ 20 different surgeries. When I told him that I managed the medical laboratory at the Nevada Test Site, which is where open-air nuclear bomb testing occurred following the Second World War,  and that I had also worked in the down-wind area (Caliente, Nevada) and (Milford, Utah) for several years, he said: “That would do it!”
I hired other medical laboratory scientists to work at both locations, and they traveled from St. George, Utah. It is a “hotbed” of skin cancer and located between the two medical laboratory facilities that I subsequently managed.
Anecdotal and experimental evidence of biologically-based cause and effect have continued to support the views of the young earth creationists, who are less likely to believe in any pseudoscientific nonsense about mutations and evolution — compared to social scientists.
See also:
Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis
and
Histone Deacetylases Regulate Gonadotropin-Releasing Hormone I Gene Expression via Modulating Otx2-Driven Transcriptional Activity
The obvious epigenetic links from gut microbes to cell type differentiation in the human brain have been virtually ignored despite overwhelming experimental evidence of the systems complexity manifested in all genera. Evolutionary theorists are largely responsible for the overwhelming ignorance of how cell type differentiation occurs because they have placed it into the context of mutations and evolution.
See, for example: Mutation-Driven Evolution, which was published on the same day as: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Protein folding is biophysically constrained via RNA-mediated nutrient-dependent amino acid substitutions See also:

Published on 22 Oct 2013

For 50 years, the “protein folding problem” has been a major mystery. How does a miniature string-like chemical — the protein molecule – encode the functions of living organisms: how our muscles exert force, how our immune systems reject pathogens, how our eyes see our surroundings, how plants convert solar energy, and all the rest. Huge progress is being made. Moreover, these amazing nano-machines could play important roles in health and disease and commerce in the future.

 

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Unconscious affect (revisited)

Kohl et al., (2001)

…the importance of human non-verbal signals is based upon information processing, which occurs in the limbic system, and without any cognitive (cortical) assessment. Affect thus does not require conscious interpretation of signal content. Underlying this fact is that affect dominates social interaction and it is the major currency in social interactions [6]. Affective reactions can occur without extensive perceptual and cognitive encoding. They are made with greater confidence than cognitive judgments, and can be made sooner [5, 7].

A New Theory Suggests All Conscious Thoughts And Decisions Are Actually Made By Your Unconscious

Excerpt:

It may seem like your intelligence is being undermined at first, but that is not the case at all; in fact, this just goes to show what an amazing machine the brain is. We can create, process, and reason, all without ever knowing we’re doing it.

human-evolution

Uniquely epigenomic gene regulation

A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development

Excerpt:

Methylation at alternative promoters or splice sites can affect transcript variants expression, whereas enhancer methylation may modulate gene expression (Jones, 2012). These are potential mechanisms for translating DNA methylation information to phenotypes.

Reported as:

Reprogramming of DNA observed in human germ cells for first time

Excerpt:

…a notable fraction of the retroelements in our genome are ‘escapees’ and retain their methylation patterns – particularly those retroelements that have entered our genome in our more recent evolutionary history. This suggests that our body’s defence mechanism may be keeping some epigenetic information intact to protect us from potentially detrimental effects.

My comment: The conserved molecular mechanisms of cell type differentiation are RNA-directed and they link DNA methylation to RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all genera. The anti-entropic epigenetic effects of nutrient-dependent microRNAs prevents the entropic elasticity attributed to viral microRNAs from leading to genomic entropy.
The balance of nutrient-dependent microRNAs and viral microRNAs alters the thermodynamic cycles of protein biosynthesis and degradation. These cycles link fixation of amino acid substitutions to cell type differentiation. The thermodynamic cycles also link viruses and viral microRNAs to perturbed protein folding and pathology. Healthy cell type differentiation can be viewed in the context of how it occurs in species from yeasts to primates.
See: 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….

See: Feedback loops link odor and pheromone signaling with reproduction; Signaling Crosstalk: Integrating Nutrient Availability and Sex
See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
Cell type differentiation is typically biophysically constrained by the nutrient-dependent chemistry of RNA-mediated protein folding, which links RNA-mediated amino acid substitutions to morphological phenotypes and behavioral phenotypes via metabolic networks linked to genetic networks.
Past protection from the damage caused by viruses and viral microRNAs, which would otherwise be linked to genomic entropy, continues in the context of the physiology of nutrient-dependent reproduction.  Transgenerational epigenetic inheritance of organized genomes helps to ensure that what promoted survival in the past continues to promote it in future — until some day the viruses kill us all. Until then, claims like this one should be viewed with suspicion by serious scientists:
Excerpt from Mutation-Driven Evolution (p. 199):

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.

That suspicious claim can be compared to what was reported as “re-evolution” of the bacterial flagellum in 4 days. One mutation was not enough. Two were required and both were linked to amino acid substitutions. If the researchers had learned the difference between mutations that perturb protein folding and amino acid substitutions that stabilize it, they might have accurately reported that ecological variation led to ecological adaptation via the nutrient-dependent pheromone-controlled creation of the missing flagellum. Instead, see:

Evolutionary Rewiring

Strong selective pressure can lead to rapid and reproducible evolution in bacteria.

Excerpt:

Bacteria that lack a vital protein for growing flagella—tail-like structures that enable the microbes to swim—can attain flagella in as little as four days given enough pressure to evolve, according to a paper published in Science today (February 26).

 

diseases-disorders

Alternative splicings: epigenetics meets pharmacogenomics

Alternative splicing [is] …a regulated process during gene expression that results in a single gene coding for multiple proteins… [T]he proteins translated from alternatively spliced mRNAs will contain differences in their amino acid sequence and, often, in their biological functions….

See also: Alternative RNA Splicing in Evolution

Excerpt:

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

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: Sex differences in other species that are due to the alternative splicings of otherwise identical genes are linked to sex differences in cancers via RNA-mediated hormone-dependent cell type differentiation.  Higher levels of estrogen are linked to ovarian cancer. Higher levels of testosterone are linked to prostrate cancer. Estrogen and testosterone levels are nutrient-dependent and pheromone-controlled in mammals. Nutrient stress and social stress probably contribute to all cancers and all other pathologies linked from metabolic networks to genetic networks.

Ovarian cancer-specific markers set the stage for early diagnosis, personalized treatments

Excerpts:

While DNA carries all the instructions necessary for life, its actual sequence contains much more than just the genes that code for proteins. In contrast, mRNAs are complementary copies of just the genes. They carry the recipe for every protein that the cell will produce from the nucleus to the cytoplasm, where cellular machinery can read the recipe and build the corresponding proteins.
the researchers identified six mRNA isoform molecules that have the tumor specificity required for an early detection diagnostic of ovarian cancer.
These mRNA isoforms are predicted to encode proteins with unique amino acid sequences…

My comment: The link from viral microRNAs and entropic elasticity to the anti-entropic epigenetic effects of nutrient-dependent microRNAs is becoming clearer. The nutrient-dependent microRNAs control RNA-mediated cell type differentiation via amino acid substitutions.  That fact will come as a surprise to many people because scientists do not use terms consistently.
Some terms change when new information becomes available about links between protein structure and function.  You may never again see our phrase “alternative splicing techniques of pre-mRNA” in the context of an epigenetic “mechanism” linked to RNA-mediated amino acid substitutions and cell type differentiation. Some terms change because researchers need to report something new to help ensure future funding. If they can turn a phase, or invent a new term, it may confuse people. But, researchers must “follow the money.”
You may see mRNA isoforms linked to amino acid substitutions and reported as “amino acid sequences” in the context of difference in corresponding proteins. You may still see claims that proteins evolve.
What you are less likely to see is any additional claims that “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world” (p. 199).  You are more likely to see claims that “The expression of a gene is controlled by several other elements or factors such as microRNAs, transcribed small RNAs, and epigenetics.” Figure 6.1 (p. 114).
The claim on page 114 is made in the same book with the ridiculous conclusion about mutations on page 199. That is cause for concern.  The book is Mutation-Driven Evolution and it was published 40 years after Dobzhansky (1973) noted 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).
It is now clear to many serious scientists that cell type differentiation is RNA-mediated via nutrient-dependent amino acid substitutions that stabilize the organized genomes of all genera via the fixation of the amino acid substitutions in the context of the physiology of reproduction.
It is also clear that evolutionary theorists would rather have you continue to believe in their ridiculous theories than to accept the fact that their theories are horrid misrepresentations of biological facts. The facts must be considered in the context of disease prevention and treatment. The ridiculous theories must be discarded.
See also: Noncoding RNAs that associate with YB-1 alter proliferation in prostate cancer cells, which was reported as:

Team finds two new and very large classes of RNAs linked to cancer biomarker

Excerpt:

Many small RNAs known as microRNAs already have been shown to correlate with different grades of prostate cancer and could potentially serve as biomarkers for diagnosis and treatment,” Dr. John said. “We did this study after computer models led us to hypothesize that there was a connection between YB-1 and microRNAs. What started out as a curiosity-driven experiment ended up being an exhilarating treasure hunt over four years, culminating in the discovery of two big molecular finds from human cells.

My comment: The balance of viral microRNAs and nutrient-dependent microRNAs links the microRNA/messenger RNA balance to:
1) sex differences in alternatively spliced mRNAs;
2) sex differences in their amino acid sequences;
3) sex differences in their biological functions;
and
4) sex differences in cancers.
Ovarian cancer biomarkers and prostate cancer biomarkers link similarities and differences in viral microRNAs and nutrient-dependent microRNAs to RNA-mediated sex difference in cell type differentiation. RNA-mediated sex differences in cell types are linked to RNA-mediated differences in all cell types of all individuals of all species via the conserved molecular mechanisms of biophysically constrained nutrient-dependent protein folding chemistry. Progress in cancer research will not come from the evolution industry or from ridiculous theories.

rp_levels-of-organization.jpg

Epigenetic regulation of aging by glycine and GnRH

Summary:  “…the regulation of two genes involved with the production of glycine, the smallest and simplest amino acid, is partly responsible for some of the characteristics of aging. This indicates that the aging process in the mitochondrion is controlled by epigenetic regulation, not by mutations.”
My comment: The broad-based extension of the fact that aging is epigenetically controlled, extends everything known about RNA-mediated cell type differentiation across the life history transitions of all genera. The focus here is on vertebrates, but the conserved molecular mechanisms extend across all species.
———————————
Thanks to Teresa Binstock for alerting me to this. Epigenetic regulation of the nuclear-coded GCAT and SHMT2 genes confers human age-associated mitochondrial respiration defects
Excerpt:

Given that human aging can be seen as a consequence of a programmed phenomenon, it is possible that epigenetic regulation also controls human aging.

My comment:  See: Search Results for ‘glycine’ here at RNA-mediated.com and also Search Results for: glycine  in the “Science” section at Pheromones.com for additional information. It should become apparent why I started with the domain Pheromones.com in 1995 and linked nutrient-dependent RNA-mediated amino acid substitutions to cell type differentiation after addressing the control of nutrient-dependent reproduction. Others now realize that the physiology of reproduction biophysically constraints transgenerational epigenetic inheritance of morphological and behavioral phenotypes. The new information about the control of RNA-mediated cell type differentiation by pheromones and anti-aging medicine has been delayed for more than two decades by human pheromone-deniers and other pseudoscientists.
In 1994, for example: I presented “Olfactory-hormonal relationships in learning, memory, aging, and behavior” during the “2nd Annual Conference on Anti-aging Medicine & Biomedical Technology for the year 2010” and in 1995, I presented “Olfactory-genetic-neuronal-hormonal reciprocity in learning, memory, behavior and in immune function” at the “3rd Annual Conference on Anti-aging Medicine & Biomedical Technology for the year 2010.”
Teresa Binstock’s prescient contributions on RNA-mediated cell type differentiation in our 1996 Hormones and Behavior review article led me to examine the role of achiral glycine in vertebrates. See: From Fertilization to Adult Sexual Behavior
Excerpt:

Evolutionary conservation, both of pheromonal communication and its importance to behavior, is indicated by the involvement of a key mammalian reproductive hormone. For instance, a yeast pheromone, the alpha-mating factor, is very similar in structure to mammalian gonadotropic releasing hormone (GnRH). When injected into rats, this chemical binds to pituitary GnRH receptors and brings about the release of LH. Loumaye, Thorner, and Catt (1982) note: “GnRH and the yeast alpha-mating factor appear to represent a highly conserved effector system which includes the peptide ligand, the cell-surface receptor, and the physiological regulation of reproductive function” (p. 1325).

My comment: Substitution of the only achiral amino acid in the GnRH decapeptide of vertebrates links the light-induced de novo creation of glycine and other amino acids to the nutrient-dependent pheromone-controlled behaviors of species from microbes to humans. One need only consider that fact in the context of what is currently known about the biophysically constrained chemistry of RNA-mediated amino acid substitutions and protein folding in all genera.
1994 Abstract

The early prenatal migration of gonadotropin releasing hormone (GnRH) neurosecretory neurons appears to enable a neuroendocrine sequence of events that allows human pheromones to influence postnatal GnRH secretion, maturation of the hypothalamic-pituitary-gonadal axis; and, in part, the hypothalamic-pituitary-adrenal axis; hormone-dependent synaptogenesis and synaptolysis; neurotransmission; learning; memory; and behavior. That GnRH regulates the collective neural output manifest in reproductive behavior seems consistent with effects of drug therapies that influence the GnRH pulse, and which are used to treat disorders of neuroendocrine and reproductive maturation as well as dysfunctional behaviors. Is the hypothalamic GnRH pulse generator both the biologic and the psychologic core of mammalian reproduction? What is the contribution of extrahypothalamic GnRH? Is there a lack of “hard” scientific evidence for relationships between biologically relevant odors, olfaction, aging, and human behavior?

1995 Abstract

A five-step pathway allowing the social environment (“nurture”) to influence the genetic substrates (“nature”) of mammalian behavior is: gene->cell->tissue->organ->organ system. Though there are many environmental influences on the first step of this pathway, odors are the only known social-environmental stimuli that appear to activate gene expression in neurosecretory cells of tissue in the brain an organ that is essential to any organ system involved in learning, memory, and behavior. Olfaction appears to influence learning, memory, and behavior. Thus, the production and distribution of human odors may link two aspects of our social environment (e.g., olfaction and odors) to the genetic substrates of our behavior through a five-step pathway common to many other vertebrates. Olfactory input influences the gonadotropin-releasing hormone (GnRH)-directed regulation of gonadal and adrenal steroidogenesis. Thus, olfactory deficits associated with aging may be linked to a need for hormone replacement therapy, including dehydroepiandrosterone (DHEA). Similarly, olfactory deficits may be linked to immune system function. Many other hormones/neurotransmitters (e.g., melatonin and dopamine) feed back on the GnRH neuronal pathway. This pathway appears to be both the biological and the psychological core of mammalian, including human, behavior. Thus, the influence of odors and olfaction on levels of hormones, including neurotransmitters, may be linked to age-related changes in learning, memory, behavior, and immune system function.

2015

Scientists reverse aging in human cell lines and give theory of aging a new lease of life

Excerpts:

…the regulation of two genes involved with the production of glycine, the smallest and simplest amino acid, is partly responsible for some of the characteristics of aging.This indicates that the aging process in the mitochondrion is controlled by epigenetic regulation, not by mutations.

See for comparison: Mutation-Driven Evolution
Concluding sentences:

“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” (p. 199).

See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

Concluding paragraph:

Unconscious affects that are manifested during the development of diversified life and human behavior are, by their very nature, part of life that few people think about (Kohl et al., 2001). Therefore, the largest contributor to the development of our personal preferences may be the unconscious epigenetic effects of food odors and pheromones on hormones that organize and activate behavior. If so, the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

My comment: All accurate representations of biologically-based cause and effect have consistently shown that there are no other factual representations of epigenesis and epistasis that can be compared to my model.  The most recent report on glycine and cell type differentiation during the life history transitions of vertebrates also suggests that the honeybee model organism links nutrient-dependent base pair substitutions in yeasts to the RNA-mediated amino acid substitutions in vertebrates that differentiate nutrient-dependent pheromone-controlled cell types via the conserved molecular mechanism that Teresa Binstock detailed in the “molecular epigenetics” section of From Fertilization to Adult Sexual Behavior.

See also for comparison to published works by JW Locasale: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Excerpt:
Disease is associated with mutations exemplified in cancer where perturbations of the glucose-dependent thermodynamic/thermoregulatory equilibrium are equally clear (Locasale, 2012).

Excerpt:

Reprogramming of gene expression in elderly fibroblasts occurred in GCAT (Fig. 3b), which regulates glycine production in mitochondria17, 18. It was therefore likely that reduced glycine production in mitochondria by epigenetic downregulation of GCAT (Fig. 3a) resulted in the age-associated respiration defects (Fig. 1a).

My comment: Reference 17, is Locasale, J. W. Serine, glycine and one-carbon units: cancer metabolism in full circle. Nat. Rev. Cancer 13, 572583; doi:10.1038/nrc3557 (2013).
The barrage of pseudoscientific nonsense touted by evolutionary theorists and their idiot minions continues to test the patience of anyone who challenges ideas about cell type differentiation that link mutations to pathology and to aging, and RNA-mediated amino acid substitutions to health and longevity in all genera.
See for examples of nonsense touted by the biologically uninformed:
In evolution, ‘house of cards’ model wins
Tiny spheres of human cells mimic the brain, researchers say
Our bond with dogs may go back more than 27,000 years
John Glenn: Evolution should be taught in schools

terrarium-eco-system

Pattern recognition: biogeochemical structure and function

Microbes Effect on the Brain

Excerpt:

Recent research shows dramatic effects of microbe products from the gut on mental function—depression, stress, autism, and degenerative illness. In humans, many studies show microbes affect anxiety, mood, depression and social behavior. Direct effects are through secreted products, stimulation of the enteric nervous system and travel of microbes into the brain, while indirect factors are microbes’ influence on immune function affecting behavior. Microbes produce molecules that transform into hormones and neurotransmitters or they produce neurotransmitters themselves. Microbes effect on the brain includes fetal development and neurotransmitter function.

My comment: Thanks again for trying to lead others who are interested in learning about pattern recognition by providing them with facts. As you can see in the 5 articles linked below, you still are several years ahead of theorists who attribute increasing organismal complexity and biodiversity to mutations and evolution.
Like your articles, these articles individually and collectively attest to the importance of the anti-entropic energy of the sun to DNA repair and the physiology of reproduction, which links the creation of earth to the creation of amino acids and to the base pair substitutions and amino acid substitutions that differentiate all cell types.
Many others seem to have failed to notice that there is a pattern of creation. Nothing appears to be random. Viruses in the gut microbiome would link viral microRNAs from entropic elasticity to genomic entropy without the anti-entropic epigenetic effects of the sun and nutrient-dependent RNA-mediated amino acid substitutions that differentiate all cell types in all genera.
If anyone who has followed your accurate representations of biologically-based cause and effect placed them into the content of a book, it would be a best-selling way to connect your blog posts to everything known to serious scientists about biodiversity.
Patterns and ecological drivers of ocean viral communities
http://www.sciencemag.org/content/348/6237/1261498.abstract
Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links
http://www.sciencemag.org/content/348/6234/1253671.abstract
Structure and function of the global ocean microbiome
http://www.sciencemag.org/content/348/6237/1261359.abstract
Eukaryotic plankton diversity in the sunlit ocean
http://www.sciencemag.org/content/348/6237/1261605.abstract
Determinants of community structure in the global plankton interactome
http://www.sciencemag.org/content/348/6237/1262073.abstract

Excerpts, conclusions,  and comments:

Patterns and ecological drivers of ocean viral communities

Conclusion:

Such experimental and analytical progress, coupled to sampling opportunities from the Tara Oceans expedition, are advancing viral ecology toward the quantitative science needed to model the nanoscale (viruses) and microscale (microbes) entities driving Earth’s ecosystems.

My comment: This series of articles advances what is known about viral ecology and allows what is known to be placed into the context of science fiction that has become fact. See for example: The Darwin Code by Greg Bear.
Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links
Excerpt:

Here, we performed unbiased proteomic analyses of the dynamically changing protein landscape at damaged chromatin undergoing DNA replication. This yielded mechanistic insights into the pathways that ensure genomic stability during perturbed DNA replication.

My comment: Evolutionary theorists seem to have largely ignored the fact that genomic stability must be maintained throughout the life history transitions of organisms that mature and reproduce. For example, the bacterial flagellum reportedly re-evolved in 4 days. See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system.  That required orchestrated activity among many organisms with lineages that continued due to their nutrient-dependent pheromone-controlled physiology of reproduction.

Structure and function of the global ocean microbiome

Conclusion:

Finding that temperature drives microbial community variation and revealing the high functional redundancy in ocean microbial communities at global scale have wide-ranging implications for potential climate change–related effects. The Tara Oceans data set supports progress not only toward a holistic understanding of the ocean ecosystem but also of microbial communities in general, by facilitating comparative analyses between ecosystems.

My comment: I wonder who did not know until now that thermodynamic cycles of protein biosynthesis and degradation link temperature-dependent instability to organism-level thermoregulation and the stability of organized genomes via the biophysically constrained chemistry of protein folding. See also: Nutrient-dependent / Pheromone-controlled adaptive evolution: (a mammalian model of thermodynamics and organism-level thermoregulation)

Eukaryotic plankton diversity in the sunlit ocean

Excerpt:

…biotic interactions, rather than competition for resources and space (62), are the primary forces driving organismal diversification in marine plankton systems.

My comment: The primary forces linked to biodiversity were not described in the context of Darwin’s ‘conditions of life.’ However, Dobzhansky (1973) linked them to primate species diversity. In Nothing in Biology Makes Any Sense Except in the Light of Evolution, he claimed:
Excerpt: 

Molecular studies have made possible an approach to exact measurements of degrees of biochemical similarities and differences among organisms. Some kinds of enzymes and other proteins are quasiuniversal, or at any rate widespread, in the living world. They are functionally similar in different living beings, in that they catalyze similar chemical reactions. But when such proteins are isolated and their structures determined chemically, they are often found to contain more or less different sequences of amino acids in different organisms. For example, the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).

Determinants of community structure in the global plankton interactome

Conclusions: 

The global ocean interactome can be used to predict the dynamics and structure of ocean ecosystems. The interactome reported here spans all three organismal domains and viruses. The analyses presented emphasize the role of top-down biotic interactions in the epipelagic zone. This data will inform future research to understand how symbionts, pathogens, predators, and parasites interact with their target organisms and will ultimately help elucidate the structure of the global food webs that drive nutrient and energy flow in the ocean.

My comment: The structure of all functional ecosystems is nutrient-dependent. The function of successful ecosystems requires a direct link from nutrient-dependent structures to the physiology of reproduction. In all genera, the direct link is RNA-mediated amino acid substitutions that differentiate cell types via their fixation in organized genomes of species that mature and reproduce. Nothing except nutrient uptake ensures successful reproduction. It links RNA-directed DNA methylation and RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of all genera via what is currently known about the physics, chemistry, and conserved molecular mechanisms that link atoms to ecosystems. See for examples in species from microbes to humans: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
See also, the invited review of nutritional epigenetics that replaces evolutionary theories about mutations with facts that link ecological variation to metabolic networks and genetic networks that enable successful reproduction and ecological adaptations in all species.
Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

See also: Genome Digest

Unique miRNAs appear to link the nutrient-dependent pheromone-controlled life history transitions of bees to RNA-mediated metabolic networks and genetic networks in all genera via base pair substitutions and amino acid substitutions that differentiate cell types.
See for example: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
 See also:

TO UNDERSTAND IS TO PERCEIVE PATTERNS“TO UNDERSTAND IS TO PERCEIVE PATTERNS” – ISAIAH BERLIN
Posted by Jason Silva on Wednesday, May 20, 2015