Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

Exposing the 2nd Law to more ridicule (1)

Summary: Experiment demonstrates quantum mechanical effects from biological system

Schrödinger (1944) linked the anti-entropic virucidal energy of sunlight from the physiology of pheromone-controlled reproduction in soil bacteria to all biodiversity. He then began to suspect that his colleagues, who displayed human idiocy, would kill him – if ever again he reasserted the facts.

After 1944, Richard P. Feynman took a stand against the human idiocy, and lost. He was not killed, just ignored.

Ignorance prevails. It always has. The virus-driven degradation of messenger RNA ensures that organized genomes continue to become less organized and that biologically uninformed theorists continue to tout pseudoscientific nonsense.

New Genes and Functional Innovation in Mammals 21 July 2017

We identify several previously described cases of genes originated de novo from noncoding genomic regions, supporting the idea that this mechanism frequently underlies the evolution of new protein-coding genes in mammals. Finally, we show that most young mammalian genes are preferentially expressed in testis, suggesting that sexual selection plays an important role in the emergence of new functional genes.

Reported as: Genes identified that distinguish mammals from other animals  4 December 2017

They have also identified antimicrobial peptides, which participate in the body’s defence against pathogens.

The energy-dependent creation of “…antimicrobial peptides, which participate in the body’s defence against pathogens” already was linked from the sense of smell in bacteria to the physiology of pheromone-controlled reproduction and biophysically constrained viral latency, which protects all organized genomes from the degradation of messenger RNA. False assumptions about entropy for comparison to experimental evidence of the de novo creation of genes have been placed into the context of the “arrow of time.”

Scientists Experimentally Demonstrate the “Reversal of the Arrow of Time” 
4 December 2017

Through a remarkable experiment, an international team of scientists has found that it is possible to reverse the arrow of time without violating the second law of thermodynamics.

Pseudoscientists need no longer consider anything that cannot be linked to this experimental evidence of top-down energy-dependent causation and biophysically constrained viral latency/genomic entropy. Thank God, nothing but experimental evidence of the anti-entropic virucidal energy of sunlight has ever been considered by those who have linked feedback loops from odors and pheromones to all biodiversity on Earth.
See: QuEBS workshop

…has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has been developed in Lithuania for more than 20 years already. The beginnings could be associated with a series of “Light-harvesting Physics” international conferences, which were held in Lithuania (in Preila, 1992 and 1994, and in Birštonas, 1996). During these conferences, discussion of notable scientists and pioneers of Quantum Biology, such as Graham R. Fleming, Shaul Mukamel, Rienk van Grondelle, Richard Cogdell, Alfred Holzwarth and others, established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.

Quantum effects in biological light-harvesting systems have been linked from the de novo creation of sunlight to answers about all biophysically constrained biodiversity via Schrodinger’s What is Life? (1944).

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

See for comparison: 7/25/13 Jay R. Feierman:

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.

See also: What is life when it is not protected from virus driven entropy (video) 30 Mar 2016

The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

See for comparison: On causal roles and selected effects: our genome is mostly junk December 5, 2017

The idea that much of our genome is irrelevant to fitness—is not the product of positive natural selection at the organismal level—remains viable.

Conclusion:

That is to say, many of our uniquely human traits are probably the contingent products of drift and historical accidents—they make us us, but were not selected to have that, or necessarily any, effect. So we are back to Ohno’s conundrum. If lungfishes have junk, or at the least extraordinarily weakly or diffusely functional DNA in their genomes, why is it that we think we do not?

The concept of “junk DNA” is inconsistent with anything known to serious scientists about energy-dependent biophysically constrained viral latency.  Feedback loops link top-down causation to the pheromone-controlled physiology of reproduction via RNA-mediated fixation of amino acid substitutions in the organized genomes of all living genera.
See: Understanding and accounting for relational context is critical for social neuroscience
My comment: New data on how genetic predispositions are epigenetically linked to phenotypically distinct neuroanatomy and behaviors is provided in the honeybee model. Across-species comparisons from insects to vertebrates clearly show that the epigenetic influence of food odors and pheromones continues throughout the life of organisms that collectively survive whereas individuals do not. These comparisons also attest to the relative salience of sensory input from the rearing environment. For example, when viewed from the consistency of animal models and conditioned behaviors, food odors are obviously more important to food selection than is our visual perception of food. Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.
“Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).”

— Kohl, JV (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors Socioaffective Neuroscience & Psychology 2012 http://www.ncbi.nlm.nih.gov/pubmed/24693349

George F R Ellis This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: [Top-down causation: an integrating theme within and across the sciences?] http://rsfs.royalsocietypublishing.org/content/2/1.toc 25 Apr 2014 at 07:49am
See also: What Bacteria Can Tell Us About Human Evolution December 5, 2017

See for comparison: Learning from Bacteria about Natural Information Processing
The link from biological light-harvesting systems to the pheromone-controlled physiology of reproduction in species from microbes to humans exemplifies everything known to serious scientists about biophysically constrained viral latency, which links ecological variation to ecological adaptations in the context of physics, chemistry, and molecular epigenetics. The facts refute all neo-Darwinian nonsense and the nonsense touted by “Big Bang” cosmologists.
Sunlight is quantized energy as information and it is virucidal.
See also: Generation of photonic entanglement in green fluorescent proteins

…our prepared state is free from environmental decoherence because of the protective β-barrel structure that encapsulates the fluorophore in the protein. Our photonic entanglement generation and characterization indicate that the SFWM process in EGFP is a promising quantum process for developing quantum spectroscopic techniques and quantum-enhanced measurements in biological materials.

Reported as: Experiment demonstrates quantum mechanical effects from biological system

Nearly 75 years ago, Nobel Prize-winning physicist Erwin Schrödinger wondered if the mysterious world of quantum mechanics played a role in biology.

Schrödinger (1944) linked the anti-entropic virucidal energy of sunlight from the physiology of pheromone-controlled reproduction in soil bacteria to all biodiversity. He then began to suspect that his colleagues, who displayed human idiocy, would kill him.
After 1944, Richard P. Feynman took a stand against human idiocy, and lost. He was not killed, just ignored.

Ignorance prevails. It always has. The virus-driven degradation of messenger RNA ensures that organized genomes continue to become less organized and that biologically uninformed theorists continue to tout pseudoscientific nonsense.

See for comparison: Microbiome-Centric Human Health: A Call for Systems Biology
Stop calling for more microbiome-centric systems biology and link what is known about energy-dependent changes in electrons to ecosystems in all living genera via pheromone-controlled biophysically constrained viral latency.
See: [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)] 1994

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

diseases-disorders

Your indifference is killing you and others

Summary: Coherence-inducing mechanisms is double-speak for mechanisms that are nutrient-dependent and pheromone-controlled.
Feedback loops link odor and pheromone signaling with reproduction has been presented in double-speak as Looplessness in networks is linked to trophic coherence

We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

Feedback loops link the sun’s anti-entropic virucidal energy from the food that organisms eat to the physiology of pheromone-controlled reproduction in all living genera. The virucidal effect of ultraviolet light biophysically constrains viral latency. Energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA are fixed in organized genomes via the physiology of reproduction and supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA that links mutations to all pathology.
Coherence-inducing mechanisms is double-speak for nutrient-dependent and pheromone-controlled in the context of Nutrient-dependent/pheromone-controlled adaptive evolution: a model. 
Despite the validity of the model, it has not been accepted by neo-Darwinian theorists or “Big Bang” cosmologists. Ridiculous beliefs about emergence and evolution are pervasive and the pseudoscientific nonsense of their theories leads to claims about coherence-inducing mechanisms.
That is why I changed the FB page description at RNA-mediated after a series of posts (see below).

It took 20 years for others to realize that all life on Earth is food energy-dependent. Now, most people are indifferent to that fact. They refuse to learn anything about where the food energy comes from.

Differences in the energy of photons have been linked to quantized energy-dependent fixation of RNA-mediated amino acid substitutions. The substitutions biophysically constrain supercoiled DNA via the physiology of pheromone-controlled reproduction.

Virus-driven energy theft links the degradation of messenger RNA to mutations via amino acid substitutions in viruses. The substitutions in the viruses have been linked to all pathology via changes in the energy-dependent microRNA/messenger RNA balance.

For comparison, the pseudoscientific nonsense of neo-Darwinian theories links mutations from natural selection to the evolution of new species. In reality, light energy is quantized information. The information links physics, chemistry, and molecular epigenetics from the speed of light on contact with water and hydrogen-atom transfer in DNA base pairs in solution to learning, memory, and behavior via RNA-mediated events such as the energy-dependent creation of enzymes and the the de novo creation of G protein-coupled receptors such as olfactory receptor genes.

Top-down causation and de novo gene creation are exemplified by energy-dependent differences in the microRNA/messenger RNA balance that link natural selection for codon optimality to amino acid substitutions that link the physiology of reproduction to supercoiled DNA. Supercoiled DNA protects all organized genomes from virus-driven energy theft. That fact supports the beliefs of young earth creationists, which may be the only existing basis for discussion of quantum biology and refutations of neo-Darwinian theories that have linked olfaction to quantum souls. If there is another basis for the link from quantum physics to quantum souls, no one has detailed in in the context of top-down causation, which must include information about the creation of genes.

Most people seem unwilling to accept experimental evidence that attests to how genes are created or information that shows how virus-driven energy theft is linked to all pathology. Discussion of the energy-dependent paradigm shift would lead others away from pseudoscientific nonsense about emergence and/or beneficial mutations and evolution.

Only via discussion of facts about the paradigm shift will others learn what is currently known to serious scientists about the biophysically constrained nutrient energy-dependent chemistry of RNA-methylation and all biophysically constrained RNA-mediated protein folding chemistry. Simply put, the protein folding chemistry must be linked to all biodiversity by the physiology of energy-dependent pheromone-controlled reproduction in all living genera.

Your indifference to that fact is killing people.

See for comparison: Looplessness in networks is linked to trophic coherence (May 16, 2017)

Our theory correctly classifies a variety of networks-including those derived from genes, metabolites, species, neurons, words, computers, and trading nations-into two distinct regimes of high and low feedback and provides a null model to gauge the significance of related magnitudes. Because trophic coherence suppresses feedback, whereas an absence of feedback alone does not lead to coherence, our work suggests that the reasons for “looplessness” in nature should be sought in coherence-inducing mechanisms.

Reported August 14, 2017 as Trophic coherence explains why networks have few feedback loops and high stability

The researchers are also investigating whether negentropy – the opposite of entropy, and in which a physical, thermodynamic or biological process creates order – are affected by trophic coherence. “The modern concept of entropy,” Johnson points out, “comes from statistical physics and is a property of ensembles, as described above – that is, the entropy of an ensemble is simply a function of the number of elements it contains.” Moreover, he adds, graph ensemble entropy has proven to be a powerful tool for understanding various network properties. We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

See for comparison: Feedback loops link odor and pheromone signaling with reproduction

These studies also indicate that GnRH neurons are likely to influence numerous brain functions. They appear to transmit signals to as many as 30,000 or more neurons in 34 brain areas, consistent with previous studies showing GnRH+ fibers and GnRH receptors in multiple brain regions (Badr and Pelletier, 1987; Jennes et al., 1988; Jennes et al., 1997). BL+ neurons likely to receive synaptic input from GnRH neurons were seen in areas associated with numerous different functions, including odor and pheromone processing, sexual behavior, appetite, defensive behavior, motor programs, and the relay of information to higher cortical areas. These results may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.

See my posts on Discovering Vismodegib in the Fight Against Skin Cancer: The First Approved Inhibitor of the Hedgehog Pathway
No one I know is likely to understand this link from the anti-entropic virucidal energy of sunlight to prevention of all pathology because they must first understand the fact that proteins do not create themselves. There is no need for this inhibitor of the Hedgehog pathway or inhibition of any other pathway if cancer is prevented. But most people are not willing to learn about prevention because they think they can rely on medical practitioners to effectively treat their diseases. Do you think that your physician knows anything about light scattering characterization of glycoproteins and their interactions with other proteins and antibodies?
Absolute Characterization of Glycoproteins and their Interactions with Proteins and Antibodies by Light Scattering
Light scattering can now be linked to the characterization of glycoproteins and their immune system interactions in all species on Earth. That suggests the speed of light on contact with water links energy as information to the de novo creation of the glycoproteins,
If so, the physiology of reproduction links pheromones to biophysical constraints on the creation of more glycoproteins in the context of morphological and behavioral differences in species from microbes to humans. That suggests the refutation of neo-Darwinism is complete, since the virus-driven degradation of messenger RNA has been linked to all pathology in bacteria that become archaea before virus-driven energy theft causes them to become L-forms.
Simply put, Carl Woese was wrong. There is only one domain of life and virus-driven energy theft is what destroys all life on Earth.

 

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

Energy-dependent physical and biophysical constraints (5)

Summary: Emmy Noethe’s theorems were developed in the early 1900’s. Richard Feynman inadvertently or purposefully alluded to them as examples of human idiocy.
Discover Magazine resurrected the examples of human idiocy in a 2017 article. For comparison, Choi et al., (2017) support the claims that intercellular and interkingdom communication is energy-dependent and controlled by the metabolism of food energy to pheromones.
It is obvious that pheromones biophysically constrain the virus-driven degradation of messenger RNA. That fact links everything currently known about RNA-mediated cell type differentiation to human love in the context of established links from quantum physics to quantum souls. It may surprise some people to know that the virus-driven evolution of love is the antithetical to the food energy-dependent physiology of pheromone-controlled reproduction in all living genera. Indeed, some people may realize that the virus-driven evolution of anything is based upon ridiculous theories that were invented by Emmy Noethe.
See: Energy-dependent physical and biophysical constraints (4)
Natural selection links odors and the food energy from what organisms eat to the de novo creation of microRNAs. The creation of microRNAs is linked to biophysically constrained energy-dependent codon optimality.
Odor and food energy-dependent changes in microRNAs link hydrogen-atom transfer in DNA base pairs in solution from the creation of amino acids to the ability to sense energy and mass in the context of the space-time continuum. The sense of smell in bacteria has been linked to our food energy-dependent visual perception of the space-time continuum.
Publication of Olfaction Warps Visual Time Perception precedes the September 2017 release of the cell biology game Cytosis. The cell biology game links virus-driven energy theft to all pathology.

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

Taken together, the facts about olfaction link the sense of smell in bacteria from quorum sensing to our visual perception of mass and energy in the context of the space-time continuum. It is no trouble for a serious scientist to consistently link quantum physics from food energy to the creation of quantum souls via changes in the microRNA/messenger RNA balance and the pheromone-controlled physiology of reproduction.
Richard Feynman inadvertently did that when he claimed that the different measures for units of energy used by other theoretical physicists were examples of human idiocy.

See for comparison: The Universe According to Emmy Noethe (Discover Magazine, 2017)

…energy may not be conserved “locally” — that is, in an arbitrarily small patch of space — but everything works out when the space is sufficiently large. That was one of two theorems she proved that year in Göttingen, Germany. The other theorem, which would ultimately have a far greater impact, uncovered an intimate link between conservation laws (such as the conservation of energy) and the symmetries of nature, a connection that physicists have exploited ever since. Today, our current grasp of the physical world, from subatomic particles to black holes, draws heavily upon this theorem, now known simply as Noether’s theorem.

Emmy Noethe’s so-called theorems, which she developed in the early 1900’s, attempted to explain how the concept of entropy might not appear to defy everything known to serious scientists about the biophysically constrained energy-dependent physiology of pheromone-controlled reproduction, which links feedback loops from odors and pheromones to the creation of all energy-dependent biodiversity on Earth.
Simply put, more than 100 years ago Emmy Noethe’s theorems suggested that all representations of energy-dependent biologically-based cause and effect are wrong. For a current representation of what is known, see: Feedback loops link odor and pheromone signaling with reproduction.
The physiology of pheromone-controlled reproduction links what organisms eat to all energy-dependent biodiversity via the de novo creation of genes and gene activation that is biophysically constrained by the metabolism of food to pheromones which control the physiology of reproduction in all living genera.
See also: AMP-enabled FLT3-ITD detection

Independent and bidirectional probes are specifically optimized to detect internal tandem duplications (ITDs) of all sizes. The reads originating from these probes are bioinformatically assembled by Archer Analysis using a de novo assembler to form longer consensus sequences that span the ITD. These longer sequences are then aligned to the reference genome to identify the presence of even very large ITDs (> 250bp).a
a Only available on Illumina® instruments

Use of a so-called “de novo assembler” eliminates any consideration of energy as information that must be used in the context of bioinformatics and the identify of reference genomes that are used to identify pathological gene variants that arise in the context of energy-dependent de novo gene creation.  The link from Emmy Noethe’s theorems to the pseudoscientific nonsense about the  “de novo assembler” may not be clear without examination of facts about the physiology of reproduction.
For example, see: Physiology is rocking the foundations of evolutionary biology

Perhaps the elegant mathematics and the extraordinary reputation of the scientists involved blinded us to what now seems obvious: the organism should never have been relegated to the role of mere carrier of its genes.

For information on Emmy Noethe’s reputation and her elegant mathematics, see:

The Mighty Mathematician You’ve Never Heard Of (2012)

She invented a theorem that united with magisterial concision two conceptual pillars of physics: symmetry in nature and the universal laws of conservation.

Noether’s brilliance was obvious to all who worked with her, and her male mentors repeatedly took up her cause…

A Fight for the Soul of Science (2015)

Silk accused these theorists of “moving the goalposts” of science and blurring the line between physics and pseudoscience. “The imprimatur of science should be awarded only to a theory that is testable,” Ellis and Silk wrote, thereby disqualifying most of the leading theories of the past 40 years. “Only then can we defend science from attack.”

See for comparison:

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems April by James V Kohl

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.

From my publications alert: What’s new for ‘microRNA’ in PubMed on July 26, 2017
Tiny RNAs and their voyage via extracellular vesicles: Secretion of bacterial small RNA and eukaryotic microRNA

MicroRNAs are small non-coding RNAs that bind to the 3′-untranslated region of target mRNAs and have transcriptional or translational inhibitory function in eukaryotes. Before microRNAs were widely known, bacterial non-coding small RNAs around 50-200 nt in length were discovered whose mechanism of action resembled that of microRNAs. Recently, RNAs that are of similar size to or smaller than microRNAs have been discovered in bacteria and indeed, this class of small RNAs have been found throughout all domains of life. Moreover, recent findings suggest that these tiny RNAs can be released via extracellular vesicles (such as exosomes in eukaryotes and outer membrane vesicles in bacteria), which in turn heralds a new field of research, interkingdom communication. This review discusses two similar classes of small RNAs in evolutionarily distinct eukaryotes and bacteria. In addition to their biogenesis and regulation, we discuss small RNA vehicles and their secretion. Impact statement The possible endogenous functions of small RNAs such as regulatory small RNAs in bacteria and microRNAs in eukaryotes have been extensively studied since they were first discovered. However, their powerful functions should not be seen as limited to their cells of origin. Recently, several papers have demonstrated that small RNAs function as signaling molecules between cells. This is possible because small RNAs can be shuttled around after being incorporated into environmentally protective extracellular vesicles. It is now clearly plausible that secreted small RNAs can regulate other types of cells through biofluids. Given their “common molecule” status, the role of small RNAs in mediating bacteria-human crosstalk is an emerging and competitive area of genetic research. This review provides insight into the function of small RNAs in intercellular and even interkingdom communication.

See also:Impact statement

The possible endogenous functions of small RNAs such as regulatory small RNAs in bacteria and microRNAs in eukaryotes have been extensively studied since they were first discovered. However, their powerful functions should not be seen as limited to their cells of origin. Recently, several papers have demonstrated that small RNAs function as signaling molecules between cells. This is possible because small RNAs can be shuttled around after being incorporated into environmentally protective extracellular vesicles. It is now clearly plausible that secreted small RNAs can regulate other types of cells through biofluids. Given their “common molecule” status, the role of small RNAs in mediating bacteria-human crosstalk is an emerging and competitive area of genetic research. This review provides insight into the function of small RNAs in intercellular and even interkingdom communication.

As indicated in my 2014 invited review of nutritional epigenetics, which was returned without review, endogenous functions of regulatory RNAs such as small RNAs in bacteria and microRNAs in eukaryotes have been extensively detailed in the context of biophysically constrained biologically-based cause and effect. These authors attest to the fact that the structure and function of bacterial small RNAs and eukaryotic microRNAs are not limited to their food energy-dependent de novo creation in their cells of origin.
The fact that small RNA and micro-RNA-mediated cell type differentiation occurs in the context of hydrogen-atom transfer in DNA base pairs in solution links the information in this review to claims that small RNAs in seawater solutions and microRNAs in blood link “common molecule” status to “… the function of small RNAs in intercellular and even interkingdom communication.”  The fact that intercellular and interkingdom communication is energy-dependent and controlled by the metabolism of food energy to pheromones that biophysically constrain the virus-driven degradation of messenger RNA, links everything currently known about cell type differentiation from quantum physics to quantum souls via the food energy-dependent physiology of reproduction in all living genera.
See also: Choi JW[Author] microRNA
For example: MicroRNA profiling in the mouse hypothalamus reveals oxytocin-regulating microRNA
For comparison: @36:18 Larry Young explains the virus-driven evolution of love as if serious scientists had learned nothing about receptor-mediated behaviors.

Biology to a Physicist

Energy as information and constrained endogenous RNA interference (4)

Premise: Sunlight is the energy as information that is required to link endogenous RNA interference to healthy longevity
Counter claim:  The Quantum Thermodynamics Revolution: Information theory

Understanding entropy as a subjective measure allows the universe as a whole to evolve without ever losing information.

Precision Medicine virtual conference, Feburary 22-23, 2017

Title: Energy as information and constrained endogenous RNA interference

  •  James V. Kohl
  • RNA-mediated.com
  • jvkohl@bellsouth.net
  • Abstract describing the poster

 

Narrative: The term microRNA has been used in 58,000 indexed works. All the works support claims that link the anti-entropic virucidal energy of sunlight from endogenous RNA interference to biophysically constrained protein folding chemistry and cell type differentiation.
For comparison, news from last week reported: Physicists make the case that our brains’ learning is controlled by entropy.
On the same day, George Church spoke during the highest-profile lecture program at the NIH. His topic was “The future of genetic codes and BRAIN codes
But he failed to link energy-dependent endogenous RNA interference or exogenous RNA interference to the genetic codes or the brain codes.
For contrast, the systems complexity of energy-dependent top-down RNA-mediated causation is detailed here.
The details can be compared to claims that minimal mutational differences might link energy and/or entropy to the evolution of all morphological and behavioral diversity on Earth via DNA.
What I have done is to link Quantized Energy as Information from chirality and hydrophobicity to thermodynamic cycles of protein biosynthesis and degradation via the potential of hydrogen, which is referred to as pH.
pH links the sun’s anti-entropic virucidal energy from hydroxylation to the de novo creation of nucleic acids and hydrogen atom transfer in DNA base pairs in solution.
Photosynthesis links the creation of G protein-coupled receptor genes from the innate immune system to nutritional epigenetics and autophagy.
pH-taxis, chemotaxis, thermotaxis and phototaxis link microRNA biogenesis and microRNA flanking sequences from hydrogen energy-dependent changes in the microRNA/messenger RNA balance to autophagy.
Autophagy links everything currently known about nutritional epigenetics from alternative splicings of pre-messenger RNA to nutrient-dependent amino acid substitutions.
For example, feedback loops link odors and pheromones to the physiology of reproduction in all vertebrates via substitution of achiral glycine in position 6 of the gonadotropin releasing hormone decapeptide.
Simply put, endogenous RNA interference clearly links RNA-directed DNA methylation from DNA repair to supercoiled DNA and healthy longevity in all living genera via fixation of achiral glycine and/or fixation of other amino acid substitutions in all species.
For comparison, excess STRESS links reduced pH to virus-driven energy theft and genomic entropy via transgenerational epigenetic inheritance.
The cited works that support the details in this poster link epigenetically-effected changes in amino acid substitutions to cell type differentiation from archaea to Zika virus-damaged human DNA.
When that fact is considered in the context of the Precision Medicine Initiative it becomes clear that virus-driven energy theft links neural circuitry, odor hedonics, mood, memory, motivation, expressions of affect, cognitive behavioral state, and potentiating responses to other stimuli from nutritional and/or social stress to mutations and all pathology.
In the context of the Precision Medicine Initiative, prevention of pathology is achieved only in the context of nutritional epigenetics and the National Microbiome Initiative.
The National Microbiome Initiative links energy-dependent fixation of nutrient-dependent amino acid substitutions to supercoiled DNA, which protects all organized genomes from virus-driven entropy.
That fact helps to explain why exogenous RNA interference might sometimes be effective IF it restores nutrient-energy-dependent viral latency.
The failure to restore viral latency can now be placed into the context of three recent additions to the Merriam-Webster dictionary:
Phytoremediation,
Microbiome,
and CRISPR.
Taken together, the dictionary definition of these terms replaces ideas about evolved biodiversity that were based on de Vries 1902 definition of mutation. That definition led to the assumptions of population geneticists who never linked energy-dependent metabolic networks to genetic networks via endogenous RNA interference and the physiology of reproduction.
POSTER TEXT
Fact: The ribosome links the epigenetic landscape to the physical landscape of supercoiled DNA. The ribosome acts as a molecular decoder and as sensor that couples changes in the efficiency of messenger RNA (mRNA) translation to its biophysically constrained stability, which is regulated by energy-dependent stop codons.
1) ATP hydrolysis by UPF1 is required for efficient translation termination at premature stop codons
Alternative: Temperature-dependent biological processes could theoretically occur within a  range from –50°C, where cells vitrify or at +140°C when evolutionary theorists seem to think that nucleic acids spontaneously hydrolyze.
2)  Evolutionary drivers of thermoadaptation in enzyme catalysis
Elaboration: The speed of light on contact with water links adenosine triphosphate  (ATP) from energy-dependent changes in chirality and hydrolysis to phosphorylation. The anti-entropic virucidal effects of sunlight  link the energy-dependent creation of RNA to the innate immune system. For example, the de novo creation of G protein-coupled receptors (GPCRs) is energy dependent. Feedback loops link odor and pheromone signaling from ATP to the physiology of reproduction via GPCRs and nutrient energy-dependent phosphorylation.
The innate immune system links chirality to autophagy to biophysically constrained RNA-mediated protein folding chemistry in all living genera. Nutrient energy-dependent fixed RNA-mediated amino acid substitutions in supercoiled DNA protects all organized genomes from virus-driven energy theft.
For example, nutrient energy-dependent endogenous RNA interference (RNAi) has been linked to cell type differentiation and species diversity via nutritional epigenetics and the pheromone-controlled physiology of reproduction in nematodes.
3). Endogenous RNAi Pathways Are Required in Neurons for Dauer Formation in Caenorhabditis elegans
Example and summary: “….the epigenetic effects of food odors and pheromones are involved in neurogenic niche construction as exemplified in nematodes…”  See Bumbarger et al., (2013) as cited in Kohl (2013)
4) Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Nutrient energy-dependent pheromone-controlled quorum sensing links codon identity to the biophysically constrained stability of  mRNA. Natural selection for energy-dependent codon optimality appears to be the link from Darwin’s “conditions of life” to endogenous RNAi and all biodiversity via conserved molecular mechanisms in all living genera.
5) Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
The ATP-dependent creation of RNA links energy from endogenous RNAi to the stability of mRNA and  healthy longevity. That fact underlies every aspect of metabolic theory, which predicts how nutrient energy-dependent changes are linked from angstroms to ecosystems via genetic networks in all living genera.
6) Metabolic theory predicts whole-ecosystem properties
RNAi pathways appear to link ATP from hydrogen atom transfer in DNA base pairs in solution to microRNA flanking sequences and to all morphological phenotypes and behavioral phenotypes via the transgenerational epigenetic inheritance of healthy longevity.
7) The phylogenetic utility and functional constraint of microRNA flanking sequences
8) Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression
9) MicroRNA analysis in mouse neuro-2a cells after pseudorabies virus infection
10) microRNA-binding proteins: specificity and function
11) RNA in extracellular vesicles
12) Structural diversity of supercoiled DNA
Alternative facts and the ‘arbitrium’ system link communication among viruses and bacteria to all biodiversity on Earth inside and outside the context of quorum sensing. In the context of quorum sensing, viruses  decide how much energy to steal from cell types. Outside the context of quorum sensing in bacteria, the viruses must somehow tell each other exactly how much energy to use to link RNA-mediated amino acid substitutions to the stability of their organized genomes via minimal mutational distances and/or de novo mutations.
13)  Communication between viruses guides lysis–lysogeny decisions
14) The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters
15) Prevalence and architecture of de novo mutations in developmental disorders
In theory, until a specific cell type realizes that a change in chirality also indicates that energy is missing, the cell type does not decide to use autophagy to protect its supercoiled DNA from more energy theft. That theory links the alternative facts about the ‘arbitrium’ system from de novo mutations to evolution.
Theories of mutation-driven evolution fail to explain any aspect of what is known to those who have linked energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of reproduction. Two song parodies link the difference in theory and what is known about energy-dependent changes in base pairs to biophysically constrained protein folding chemistry. 16) All about the base and 17) Chemists know.
The diagram represents what is known about the systems complexity of energy-dependent changes in base pairs, amino acid substitutions and RNA-mediated cell type differentiation, which has been placed into the context of RNAi.
Two recently published articles by co-authors who are 2016 Nobel Laureates, link chirality to autophagy and endogenous RNAi. The current understanding of RNAi surpasses all understanding of systems complexity that was placed into the context of RNA-mediated DNA methylation.
18) Dynamic control of chirality and self-assembly of double-stranded helicates with light
19) The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes
Until now, most researchers have failed to link light induced changes in chirality to the biophysically constrained structurel of supercoiled DNA. That fact makes the difference between metabolic theory and the arbitrium’ system clear. All metabolic approaches explicitly and quantitatively link the natural selection of food to the control the carbon cycle at every level of examination that is required to link what organisms eat to supercoiled DNA via the physiology of reproduction. No alternative facts or theories are required. Supercoiled DNA links everything known about cell type differentiation in all  individuals of all species to energy-dependent ecosystems and the Earth’s biosphere.
Energy-dependent links from angstroms to ecosystem are clearly manifested in endogenous RNA interference, which links fixation of RNA amino acid substitutions in all differentiated cell types to the Precision Medicine Initiative. For comparison, links from virus-driven energy theft and gene-editing via the CRISPR-Cas9 technology are included in this proposal for the treatment of pathology. 20) RNA-Guided Human Genome Engineering
In the context of human genome engineering: “Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).”
Simply put, viruses are used to edit DNA in genomes that are damaged by virus-driven energy theft. Researchers using the technology think they can biophysically constrain virus-driven energy theft with directed virus-driven editing.
The current political climate in the USA indicates that a paradigm shift has already occurred. The National Microbiome Initiative and the Precision Medicine Initiative collectively appear to be blocking attempts to deliver an exogenous RNAi-based treatment. The treatment has been referred to as a “billion dollar baby.” The alternative to spending billions more dollars to perfect the treatment, which may cost more than what most people can afford, will require more scientists to learn what is known about how the microbiome and metabolic networks are linked to precision medicine by  genetic networks.
In the context of precision medicine, learning more about how ecological variation and endogenous RNAi link metabolism from ecological variation to energy-dependent  ecological adaptation  in species form microbes to humans may make more sense than learning more about the use of viruses to repair DNA damage caused by other viruses.
For example, Roger Penrose inadvertently linked energy-dependent endogenous RNA interference to exogenous RNA interference: How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?”(Roger Penrose 8 August 1991) in 20) What is Life?
See also: 21) Arginine 66 Controls Dark-State Formation in Green-to-Red Photoconvertible Fluorescent Proteins
22) Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor
The photoconvertible fluorescent proteins link energy-dependent endogenous RNAi to the substitution of achiral glycine in position 6 of the GnRH decapeptide, which links the pheromone-controlled physiology of reproduction in all vertebrates to the conserved molecular mechanisms of RNA-mediated protein folding chemistry in all living genera. Every aspect of every detailed link from angstroms to ecosystems involves the energy-dependent protein folding chemistry that links what organisms eat to the functional structure of supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.
23) A Big Bang in spliceosome structural biology

Alternative splicing of pre-mRNA

Sunlight: the essence of precision medicine and world peace

See for review: The essence of precision medicine
See for comparison:
We not only reject Trump’s values and policies, we also renew our commitment to a future where both the church and the academy will foster attitudes and actions so that human beings and the whole of creation can thrive. We join our hearts, our minds, our voices, and our actions with those of religious believers–Christians, Jews, Muslims, and
people of all faiths, as well as with secular people of good conscience, to resist the present destructive politics in our country and to seek reversal of their destructive consequences here and around the world.

This is unadulterated nonsense. Trump’s policies are clearly designed to protect us from the media-industrial complex that pervades the ivory towers of all pseudoscientists.

The “complex” has metaphorically choked the life out of millions of people who have needlessly suffered and prematurely died from virus-driven energy theft.

Anyone who signs this could potentially be convicted of sedition. Sorry if this warning is too late for those who may be the first to pay for their sins of ignorance.

See also: Viruses can Stimulate Photosynthesis in Bacteria  The ignorance overwhelms every discipline as it is included in everything that links the anti-entropic virucidal energy of sunlight to cell type differentiation and healthy longevity in all genera. Photosynthesis protects supercoiled DNA from virus-driven energy theft, and they report that fact as if viruses created the sun.

See also: L-form bacteria, cell walls and the origins of life

There is no mention of the energy-dependent origins of life and no mention of endogenous RNA interference, but they link

1) Invention of cell wall
2) Emergence of Archaea
3) Evolutionary development
 

That’s the magic of evolutionary development. First the cell wall is invented and then species emerge so that their emergence can be linked to their evolutionary develoment. For comparison, the works of all serious scientists link the virus-driven hecatombic evolution of all pathology to the destruction of the cell wall, which obviously was created to protect the supercoiled DNA from the threat of virus-driven energy theft.

The reverse logic is typical of theorists who do not understand why I claim that energy is information.

See for comparison: UV light activates 43 genes when DNA is damaged from The 2000 T. H. Morgan Medal Essay: H. J. Muller and the Nature of the Gene

The “nature” of the gene can now be compared to what is known about the energy-dependent de novo creation of genes  For example, a recent search for the termmicroRNA” returned a link to this published work. “Genetic 3’UTR variation is associated with human pigmentation characteristics and sensitivity to sunlight

One energy-dependent 3’UTR variation links sensitivity to the anti-entropic virucidal energy of sunlight to the physiology of reproduction in species from microbes to humans via microRNA flanking sequences and hydrogen-atom transfer in DNA base pairs in solution. Everything currently known to serious scientists appears to link endogenous RNA interference to healthy longevity. All experimental evidence of biologically-based facts also links virus-driven energy theft to all pathology.
My conclusion seems warranted. The energy-dependent de novo creation of genes links precision medicine to world peace by removing any religious views from the context of facts about creation.
For example, the newest member of my RNA-mediated FB group is from Turkey, which is where the Islamic creationist who wrote this book is gaining a large following. The Miracles of Smell and Taste
If the differences between Islam and Christianity can be linked from sunlight to the energy-dependent de novo creation of all biodiversity, could the similarities in the Abrahamic religions prevail? If so, I would use the similarities to link creation to the weekend resurrection of the bacterial flagellum in P. fluorescens, which gets its name from its innate ability to use light as a source of food energy?
See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

…this system enables us to understand the adaptive process in detail at the genetic and phenotypic level. We identified a tractable model for gene network evolution and observed…

This “tractable model” is important enough to be viewed in context of this claim about the genetic networks in E. coli.
See: Biodiversity is autocatalytic

…the metabolic network of Escherichia coli forms a large autocatalytic set of close to 1800 reactions (Sousa et al., 2015). As far as we know, this is the first formal proof that living organisms (or at least essential parts thereof) are indeed autocatalytic sets.

As far as I know, there is no such thing as an autocatalytic set. If all 1800 reactions are not energy-dependent, they must arise automagically in the context of virus-driven energy theft and genomic entropy. If not, pseudoscientists must expect serious scientists to believe in claims like this: Physicists make the case that our brains’ learning is controlled by entropy
The fact that RNA methylation links energy-dependent learning and memory to the survival of all living genera via the physiology of pheromone-controlled reproduction seems to be unimportant to journalists like Fiona Macdonald who also wrote this article.
We Just Got More Evidence That The 2 Human ‘Sex Pheromones’ Don’t Actually Exist

“My major concern with the experiments in this study is that they were not rigorously designed and conducted,” Zhou explained.

Martha McClintock, a behavioural neuroscientist at the University of Chicago in Illinois, who wasn’t involved in this research and has been the driving force behind promoting AND and EST as pheromones, also told Science that the effect of the two chemicals could be more subtle than we’re currently expecting.

“There’s no doubt that this compound, even in tiny amounts, affects how the brain functions,” she added.

How much of an effect on hormones could be linked to the affect of a pheromone behavior?
See for comparison: In Battle for Real Estate, a Disordered Protein Wins Out

“Discovering CITED2’s ability to win these battles is a paradigm shift,” said Wright, senior author of the new study.

The new study suggests that it may be more efficient to mimic nature’s own response and use a CITED2-like drug to knock HIF-1α away.

The paradigm shift can be viewed in the context of how “nature” used intrinsically disordered proteins to achieve the biophysically constrained nutrient energy-dependent stability of pheromone-controlled supercoiled DNA. The nature of the response must be linked to the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes in all living genera. That fact provides comic relief for serious scientists who understand how much pseudoscientific nonsense these authors included in a peer-reviewed publication in “Nature”
If you have a subscription, see: Hypersensitive termination of the hypoxic response by a disordered protein switch and watch for more reports on the “nature” and the magic of emergence and evolution of energy-dependent endogenous RNA interference and RNA-mediated cell type differentiation, which must link amino acid substitutions and chromosomal inheritance to all biophysically constrained biodiversity.
See also: Structural diversity of supercoiled DNA
See also: RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly
These authors claim that nature may have harnessed the ability to generate kinectically controlled alternative RNA structures such as riboswitches, which change the dominant pathway of chemistry folding to fit the response that links single nucleotide changes from RNA-mediated protein folding pathways to the structure and function of RNAs via ‘deconstruction and reconstitution.’ They suggest the magic of ‘deconstruction and reconstitution.’ is a viable strategy for understanding how the overwhelming systems complexity of molecular mechanisms links complex RNA structures to conformational transitions, which they do not seem to realize are energy-dependent and biophysically constrained.
See also: Why Evolution Is Ageist

Currently, Martin’s lab is searching for genes that maintain homeostasis. His hypothesis is that something occurs to these cells later in life that increases the molecular “drift” of old age that results in cell-to-cell variation. “This drift might take on a life of its own after the reproductive age,” Martin says, “And if you get drift outside of a certain window of homeostasis, it’s possible you can’t come back.”

Homeostasis is energy-dependent and it is maintained by supercoiled DNA. Nothing about healthy longevity compare to pathology occurs outside the context of energy-dependent changes in the microRNA/messenger RNA balance.
See for examples: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.

There are now more than 58,000 published works on microRNAs. This was published yesterday: Monitoring integrity and localization of modified single-stranded RNA oligonucleotides using ultrasensitive fluorescence methods.

The lifetime of the RNA in the cells could be explained by a balance between release of the oligonucleotides from endosomes, degradation by RNases and subsequent depletion from the cells.

The energy-dependent lifetime of messenger RNA links microRNAs to cell type stability via RNA-mediated amino acid substitutions in supercoiled DNA. Measuring fluorescence is an indicator of the differentiation of all cell types in all individuals of all living genera. Virus-driven energy theft links the degradation of messenger RNA to all pathology.

rp_levels-of-organization.jpg

The natural success of RNAi and failed treatment

see my other blog posts on m6A

Dynamics of Human and Viral RNA Methylation during Zika Virus Infection

Excerpt:

…ZIKV infection alters m6A location in mRNAs, methylation motifs, and target genes modified by methyltransferases. Our results identify a mechanism by which ZIKV interacts with and alters host cell functions.

Reported as: Zika virus infection alters human and viral RNA
Excerpt:

When Zika virus infects a human cell, Rana’s team found, the cell modifies viral RNA with m6A as a means to get rid of the infection. RNA tagged with m6A is a beacon for human enzymes that come along and destabilize it. In addition, they found that this host response to Zika viral infection also induced specific m6A modifications on human RNA. These human RNA changes were not present in the absence of Zika virus.

My comment: Energy-dependent cell type stability is RNA-mediated and linked from supercoiled DNA to protection from virus-driven energy theft in all living genera. The RNA-mediated cell type stability is consistently reported in the context of RNA interference.

RNA interference

Excerpt:

RNA interference (RNAi) is a biological process in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecules. Historically, it was known by other names, including co-suppression, post-transcriptional gene silencing (PTGS), and quelling. Only after these apparently unrelated processes were fully understood did it become clear that they all described the RNAi phenomenon.

My comment: All biological processes are nutrient-energy-dependent and controlled by the physiology of reproduction.

  1. Everything attributed to energy-dependent RNAi phenomenon has been linked from changes in base pairs and changes in the microRNA/messenger RNA balance to healthy longevity.
  2. Everything linked from virus-driven energy theft to changes in the microRNA/messenger RNA balance has been linked to all pathology.

Those 2 facts fact show that neo-Darwinian theorists and atheists know nothing about RNAi in the context of energy-dependent biologically-based cause and effect. Like all theorists, pseudoscientists have been forced to invent new theories about evolution that are even more ridiculous than the one Masatoshi Nei detailed in 2013 in his book “Mutation-driven evolution.”
On page 144 (see Figure 6.1), Nei wrote:

The expression of a gene is controlled by several other elements or factors such as microRNAs, transcribed small RNAs, and epigenetics.

On page 199, Nei concluded: 

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.

My comment: The conserved molecular mechanisms of gene expression are nutrient energy dependent and pheromone-controlled in species from microbes to humans. Constraint-breaking mutations are the link from controlled energy-dependent gene expression to all pathology.
See for example: Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria
Excerpt:

In the absence of the antibiotic, transcription is terminated prematurely by the ribo-regulator. However, upon exposure to lincomycin, drug-inhibited ribosomes stall over a conserved three-amino-acid upstream open reading frame found within the ribo-regulator, thus triggering a conformational change in the transcriptional terminator and inducing the expression of the full-length mRNA that encodes the resistance gene.

Reported in the context of neo-Darwinian nonsense by Ruth Williams | August 1, 2016 as Wanted: Transcriptional Regulators
Excerpt:

Nature has evolved a staggering array of mechanisms for regulating gene expression, but few are so simple and elegant as the riboswitch.

My comment: How could Nature evolve an energy-dependent three-position switch? The claim that the three position switch could be activated by exposure to lincomycin links everything known about autophagy from the innate immune system to supercoiled DNA, which prevents virus-driven energy theft from causing entropy in the organized genomes of all living genera. No matter how much effort is made to place new experimental evidence back into the context of neo-Darwinian pseudoscientific nonsense, the efforts will be ridiculed by serious scientists. But, the pseudoscientists may still cause the death of us all.
Another report on this same research claimed that

In order to describe the diversity of life, science differentiates, for example, between the plant and animal kingdoms.

See: Phys.org | October 20, 2016: Research delivers ground-breaking insights into evolution by studying transcription termination in archaea

Bacteria only have a very short end sequence, after the part responsible for coding the proteins. This study shows that Archaea, in contrast, have a long end sequence after the part responsible for coding the proteins in their mRNA similar to Eukarya. The supposedly uninvolved ends of the mRNA could also potentially contribute to gene regulation in Archaea. The scientists were also able to prove that over 30 percent of the genes in Archaea could be regulated by a series of consecutive alternative termination signals for transcription. Therefore, different lengths of end sequences are generated in response to environmental conditions.

My comment: No serious scientist ever suggested that the molecular mechanisms of cell type differentiation vary with domains-of-life or any species-specific level in any species of plant or animal. Instead, all serious scientists have linked energy-dependent changes from angstroms to ecosystems in species from soil bacteria to mammals via autophagy, supercoiled DNA, and chromosomal rearrangements that link feedback loops from odors and pheromones to the physiology of reproduction to the transgenerational epigenetic inheritance of healthy longevity or Zika virus-DNA damage manifested in craniofacial morphology and brain development in human infants.
If the conserved molecular mechanisms of Transcriptional Regulators could not be linked from transcription termination in archaea to transcription termination in human infants there would be no logical basis for claims about RNAi in the context of gene editing.
See for comparison: Gene Editing: From Roots to Riches
Excerpt:

The technique involved sandwiching an altered copy of a gene between two regions of code identical to those flanking the endogenous gene, which would be swapped out for its engineered counterpart.

My comment: The technique can be placed into the context of natural information processing and codon optimality, which links energy-dependent changes from hydrogen-atom transfer in DNA base pairs in solution to RNA-mediated DNA repair via microRNA flanking sequences, which prevent messenger RNA degradation in the context of virus-driven energy theft during autophagy.
See: The phylogenetic utility and functional constraint of microRNA flanking sequences
Excerpt:

Both miRNAs and their flanking sequences provide phylogenetic signals suitable for the inference of phylogeny with high levels of accuracy, when sufficient numbers of this type are concatenated. As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest.

My comment: Every aspect of energy-dependent RNAi links virus-driven energy theft to all pathology via conserved molecular mechanisms in species from microbes to humans. If that fact was not known to all serious scientists, pseudoscientists could continue to tout RNA-guided human genome engineering as if it would lead to the cure for most if not all virus-driven pathology.

All pathology is biophysically constrained by nutrient energy-dependent changes in cell types that allow all living organisms to adapt to the presence of viruses.

See for instance: Epigenetics and Genetics of Viral Latency
Excerpt:

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

My comment: The deliberate misrepresentation of biologically-based cause and effect is clear, since (I reiterate):

All pathology is biophysically constrained by nutrient energy-dependent changes in cell types that allow all living organisms to adapt to the presence of viruses. 

See also: Alnylam Pharmaceuticals: RNAi Failure Could Catch Monsanto Investors Off Guard?
Excerpt: It’s clear from the mistakes above that they really do not know and fully understand everything there is to know about how the genetic code works and our increase[d] understanding of epigenetic gene expression is proving that every single day.
My comment: Let’s place that into the context of Get Well in the RNAi Way-RNAi, A Billion Dollar Baby in Therapy  and this claim Last month, one of the top intelligence officials in the United States warned that genome-editing technology is now a potential weapon of mass destruction.
Co-suppression, post-transcriptional gene silencing, and every other aspect of biophysically constrained energy-dependent cell type differentiation can be placed into the context of:

How to Track Translation in Living Cells

Excerpt:

This domain, which the team dubbed “the spaghetti monster,” binds multiple FLAG-specific fluorescent antibodies that are injected into the cell, while the mRNA binds its own fluorescent antibodies. Thus, both the mRNA and its newly forming protein are observable at once (Science, 352:1425-29, 2016).

My comment: It’s as if serious scientists who are tracking translation in living cells are ridiculing theorists who chastise creationists for their belief in what theorists call the “flying spaghetti monster.” The theorists learned nothing about the complexity of RNA-mediated autophagy and joked about the creationist’s flying spaghetti monster.
See: The Flying Spaghetti Monster

…noticed that the Board only specified “Intelligent Designer” and not the specific name of any one known deity. This inspired Bobby to protest the proposal by creating the fictional deity named “Flying Spaghetti Monster.” In May of 2005, Henderson posted an open letter to the Kansas school board on his website[2], in which he addressed his opinion that intelligent design was no more valid than the belief that a Flying Spaghetti Monster created the universe.

My comment: How can any serious scientist enter into a debate with atheists who know nothing about biologically-based cause and effect; nothing about physics, and nothing about chemistry?
electra navarone wrote:
Ok, so from reading the contents of your site you are trying to communicate cellular processes that occur within all living beings called ‘autophagy’ that essentially involve recycling of nutrients within the being by breaking down old things and using them to build new things. Ok good. Now what do you want? Like · Reply · 29 mins
My reply: Nothing. It would be nice to have everyone else who is dying from virus-driven energy theft realize that we included every aspect of biophysically constrained RNA-mediated cell type differentiation in our 1996 Hormones and Behavior review — in a section on molecular epigenetics.  What we included has since been linked from autophagy to all healthy longevity or to all virus-driven pathology.
But I don’t care if pseudoscientists acknowledge that fact. Biologically informed serious scientists have already cited it our review, and my other works.

See also: Autophagy Pioneer Wins Nobel

October 3, 2016

…autophagy, the process by which a cell recycles unnecessary components. “His discoveries opened the path to understanding the fundamental importance of autophagy in many physiological processes, such as in the adaptation to starvation or response to infection…

My comment: How much more can be done without claiming that the energy-dependent changes link natural selection to codon optimality and codon optimality links fixed RNA-mediated amino acid substitutions to the stability of all cell types in all living genera via supercoiled DNA. The supercoiled DNA links ecological variation to ecological adaptation via the physiology of reproduction, which is the only way I know to prevent virus-driven energy theft from being transgenerationally inherited as it is with the Zika virus.

October 20, 2016

Research delivers ground-breaking insights into evolution by studying transcription termination in archaea
From the title above, would anyone recognize that this is a second report on the research reported in The Scientist on August 1, 2016 as Wanted: Transcriptional Regulators
The journal article was published on April 8, 2016. See Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria
Conserved molecular mechanisms of energy-dependent autophagy are obviously the link from virus-driven nutrient-dependent pheromone-controlled antibiotic resistance in bacteria to supercoiled DNA, which protects human infants from the transgenerational epigenetic inheritance of Zika virus damage.
But, in Research delivers ground-breaking insights into evolution by studying transcription termination in archaea we are told that…

In order to describe the diversity of life, science differentiates, for example, between the plant and animal kingdoms.

What differences does science introduce to remove the molecular mechanisms of autophagy from archaea before linking them to cell type differentiation in all other living genera?
See for comparison: Biologists first to observe direct inheritance of gene-silencing RNA
also reported as: RNA-mediated gene regulation across generations
 

Filtering light through a prism to identify tissue type

Countdown to Genetics and Genomics

RNA-mediated physics, chemistry, and molecular epigenetics (5) 5/10/16

Focus: Functional Implications of Human-Specific Changes in Great Ape microRNAs

RNA-mediated physics, chemistry, and molecular epigenetics (4) 5/9/16

Focus: Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein

RNA-mediated physics, chemistry, and molecular epigenetics (3) 5/9/16

Focus: Microtargeting cancer metabolism: opening new therapeutic windows based on lipid metabolism

RNA-mediated physics, chemistry, and molecular epigenetics (2) 5/6/16

Focus: Micron-scale plasma membrane curvature is recognized by the septin cytoskeleton

RNA-mediated physics, chemistry, and molecular epigenetics 5/4/16

for presentation on 5/11/16 and 5/12/16
Chemistry
Energy is INFORMATION
Hydrogen atom transfer in DNA base pairs in solution
Photosynthesis
Nutritional epigenetics
base pair substitutions
microRNA flanking sequence
miRNA/mRNA balance
RNA/DNA Methylation
RNA-mediated amino acid substitutions
Thermodynamic cycles of nutrient-dependent cell type differentiation
Quantum and Classical Physics
innate immune system
de novo creation of nucleic acids
microRNA (miRNA) biogenesis
alternative splicings / pre-mRNA
G protein-coupled receptor gene creation
Molecular Epigenetics
Olfactory receptor genes
Food odors & Pheromones
Feedback  loops
Physiology of Reproduction
RNA-mediated DNA repair
Supercoiled DNA
Healthy longevity
Excessive STRESS
changes in pH
Virus-driven energy theft
ENTROPY
Altered Brain development
Altered Learning and memory
Altered Life history transitions
Altered Feedback loops
Altered Reproduction & Aging
Transgenerational epigenetic inheritance

rp_levels-of-organization.jpg

MicroRNAs and/or QTLs: Who buried what?

Making precision medicine a reality: Genomics researchers unveil road map to disease origin

Excerpt:

This study highlights the significance of mechanistic similarities for uncovering additional interacting downstream effectors of intergenic SNPs…

My comment: Use of the term QTL may limit the understanding of how energy-dependent cell type differentiation occurs and how virus-driven energy theft is linked to all pathology.
It would be great if someone would explain the difference between what QTLs do and what microRNA flanking sequences  do in the context of the molecular mechanisms of energy-dependent cell type differentiation.
Excerpt 2)

The paper, “Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions,” has been identified as one of the best 30 of the year in computational biology and bioinformatics, and will be presented as a “highlight of the year” at the 2016 Intelligent Systems for Molecular Biology (ISMB) conference, the largest international conference of computational biology/bioinformatics, in July in Orlando, Fla.

My comment: Intelligent Systems? Intelligent Design? If virus-driven energy theft alters the quantitative trait loci and links angstroms to ecosystems via energy-dependent hydrogen-atom transfer in DNA base pairs in solution, will these research groups be accused of taking funds from young earth creationists who linked viruses to all pathology?

Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions

Excerpt:  Fourth, we performed the enrichment analysis again using an alternate reference human genome annotation, which includes coordinates for microRNA and lncRNA (GENCODE33 version 19; best OR=25.4, P=6.4×10−6 ) to establish that our results were not the result of miscategorising SNPs within this region as intergenic (Supplementary Figure S11).
Excerpt: SNP combinations showed evidence of synergistic effects using entropy-based measures of interaction information. This result showed that SNPs engage in cooperative or epistatic effects indicative of functionally similar mechanisms.
My comment: The disease-specific polymorphisms that are buried in intergenic regions must be resurrected to cause specific diseases linked from virus-driven energy theft to failed nutrient-dependent RNA-mediated DNA repair and all pathology.
See also: What is life when it is not protected from virus driven entropy Published on 30 Mar 2016

Poster Abstract: The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.
rp_levels-of-organization.jpg

From nothing to life and death everywhere

Astronomers in South Africa discover mysterious alignment of black holes

Excerpt 1)

This implies that there is a coherent spin in the structure of this volume of space that was formed from the primordial mass fluctuations that seeded the creation of the large-scale structure of the universe.

Excerpt 2)

“This is not obviously expected based on our current understanding of cosmology. It’s a bizarre finding.”

Excerpt 3)

A large-scale spin distribution has never been predicted by theories – and an unknown phenomenon like this presents a challenge that theories about the origins of the universe need to account for, and an opportunity to find out more about the way the cosmos works.

“We’re beginning to understand how the large-scale structure of the universe came about, starting from the Big Bang and growing as a result of disturbances in the early universe, to what we have today,” says Prof Taylor, “and that helps us explore what the universe of tomorrow will be like.”

My comment: The implications of unexpected creation of the large-scale structure of the universe cannot be placed into the context of “…our current understanding of cosmology.” With a little “spin-doctoring” (pun intended) Prof Taylor provides hope that what he and others are beginning to understand about creation “…helps us explore what the universe of tomorrow will be like.”

Note, however, unexpected findings from cosmology must first be linked to facts about cell type differentiation that include the role of virus-driven energy theft.

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… — Eugene Koonin

My comment: Each new “discovery” of what exists in the context of what cannot be explained about creation, attests to the likelihood that the explanatory power of theories will have no impact on what the universe of tomorrow will be like for people and every other form of life that becomes extinct due to virus-driven energy theft and the entropy of organized genomes.
Published on 2 Jan 2014
Celebrity Astrophysicist Neil deGrasse Tyson welcomes a distinguished panel of scientist to discuss and debate the Existence of Nothing.

Published on 12 Feb 2016

Richard Dawkins asks Neil deGrasse about what are his thoughts on the probability of life existing elsewhere in the universe. Neil is very positive about having life as the basic ingredients for having life are in abundance in the universe, as we are mostly made up of carbon.


See for comparison:

Published on 30 Mar 2016 (see above)

Abstract: The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

See also: Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats.

See also: Batman’s place in evolution

Excerpt:

Pettigrew doubts that molecular geneticists who have relied on DNA sequencing and other molecular evidence will take kindly to his explanation, first advanced in 1992, and since updated in the light of new findings about the nature of chromosomal DNA.

My comment: Pettigrew’s doubts are like the doubts of all serious scientists.  Serious scientists know that their works are not likely to be accepted if they challenge the dogma of pseudoscientists. Serious scientists have always been outnumbered by the pseudoscientists, and that’s why more money is spent on pseudoscience. Pseudoscientists may think that throwing more money at the current problem with transgenerational epigenetic inheritance of Zika virus pathology will help reduce the epigenetic effect on supercoiled DNA, which is manifested in craniofacial morphology and in brain development. But anyone who puts the threat into the context of the fossil record will recognize that the nutrient-dependent RNA-mediated innate immune systems of some human populations protected them, and some manifested the same diffferences in morphological phenotypes and brain development that are manifested today — for the same reason.  All populations of all organisms must ecologically adapt or become extinct. None has ever evolved into another species.” Batman’s place in evolution” is to show that ecological variation must lead from the nutrient-dependent pheromone-controlled physiology of reproduction in insects to ecological adaptation via the nutrient-dependent pheromone-controlled physiology of reproduction in mammals.

See also: U.S. Officials Warn Zika ‘Scarier’ Than Initially Thought

Excerpt:

Dr. Anthony Fauci, director of the U.S. National Institute of Allergy and Infectious Diseases, said if Congress does not provide emergency Zika funding, U.S. officials likely would be forced to redirect money currently dedicated for research into malaria, tuberculosis and a universal flu vaccine.

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

My comment: No matter how much more is spent, it is obvious that virus-driven energy theft will lead to the death of us all if serious scientists do not join the others who already are Combating Evolution to Fight Disease.

Millions of maternal and child lives could be saved every year for less than $5 a person

My comment: Dr. Anthony Fauci’s fundraising efforts should be placed into the context of what is already known about nutritional epigenetics and biophysically constrained protein folding chemistry, which links the innate immune system to supercoiled DNA. The supercoiled DNA protects all organized genomes from virus-driven entropy. That fact suggests government funding is being used for population control.
See also: Quantico
Jon Stewart interviews Greg Bear
See also: March 9, 2016 See Gene intelligence: The risks and rewards of genome editing resonate beyond the clinic.
Last month, one of the top intelligence officials in the United States warned that genome-editing technology is now a potential weapon of mass destruction.
See also: Genetic Resilience

“If you wanted to find clues to prevention,” study coauthor Stephen Friend, president of the nonprofit Sage Bionetworks and a geneticist Mount Sinai, said during a press briefing, “instead of looking at people with disease, you would want to look at individuals who should have gotten sick.”

My comment: All extant biodiversity exemplifies the fact that the nutrient energy-dependent RNA-mediated innate immune system is the key to healthy longevity and that virus-driven energy theft causes all pathology. If Fauci’s work with HIV did not already lead him to that conclusion, he should resign. If he already knows how to prevent all virus-driven pathology, he should simply change the policies that have been killing people in the context of neo-Darwinian pseudoscientific nonsense about beneficial mutations and evolution.

Broadcast: 8/10/1998 Rethinking Darwin

Description: Jennifer Byrne speaks to Professor Robert Blanden, co-author of ‘Lamarck’s Signature’; Dr Niles Eldredge from the American Museum of Natural History and Professor Evelleen Richards, science historian from the University of New South Wales about the latest challenge to Darwin’s theory of evolution.

Excerpt: 

…under normal circumstances, food is not thought to have an impact on his genetic makeup, nor is any other environmental influence on his non-reproductive cells.

What is Life?: With Mind and Matter and Autobiographical Sketches (Canto Classics) Reprint Edition

Excerpt: 

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

rp_levels-of-organization.jpg

Science vs semantics

Re-interpreting long-term evolution experiments — Is delayed adaptation an example of historical contingency or a consequence of intermittent selection?
Excerpt: “… the series of events used to explain adaptation in the short-transfer LTEE (and in speciation) might need to be revised. The amplification model supported by this article has already be proposed as a means of evolving new genes (1) and has been experimentally shown capable of generating a novel genetic function within as few as 3000 cell generations (11). Both of these processes are arguably more difficult to achieve than the ability to activate a single silent gene.”
My comment: In species from microbes to humans, physics and chemistry are linked to gene activation, the de novo creation of new genes, adaptation, and speciation by energy-dependent hydrogen-atom transfer in DNA base pairs in solution.
Nutrient-dependent microRNA flanking sequences help to ensure that adaptations and speciation occur only in the context of the physiology of reproduction, which links the nutrient-dependent pheromone-controlled biophysically constrained chemistry of RNA-mediated protein folding to cell type differentiation in all living genera via protection against virus-driven genomic entropy.
Species-specific cell type differentiation is linked from supercoiled DNA to biodiversity via chromosomal rearrrangements — not by mutations and evolution.
The primary message of the paper by Van Hofwegen et al.is that Lenski’s experiments clearly show that ecological variation leads to biophysically constrained ecological adaptation in the context of Darwin’s “conditions of life.” Any other interpretation of the results must involve the mathematical models, inferences, definitions, and assumptions of pseudoscientists who invented neo-Darwinism.
Reported as: Similar Data, Different Conclusions

By tweaking certain conditions of a long-running experiment on E. coli, scientists found that some bacteria could be prompted to express a mutant phenotype sooner, without the “generation of new genetic information.” The resulting debate—whether the data support evolutionary theory—is more about semantics than science.

Excerpt 1) “The resulting debate—whether the data support evolutionary theory—is more about semantics than science.”
My comment: Science has put an end to the semantics, and all serious scientists know that. No data from any experiment that links atoms to ecosystems has ever supported neo-Darwinian theory.
Here, they try to equate the pseudoscientific nonsense touted by Lenski’s idiot minions with what is known to serious scientists about energy-dependent biophysically constrained RNA-mediated protein folding chemistry. For example, thermodynamic cycles of protein biosynthesis and degradation link hydrogen-atom transfer in DNA base pairs in solution from ecological variation to ecological adaptation in all living genera via the physiology of reproduction.
Excerpt 2) “When natural selection—that is, differential survival and reproduction—favors bacteria whose genomes have mutations that enable them to grow on citrate, those mutations most certainly provide new and useful information to the bacteria,” Lenski and Blount countered in their blog post. “To say there’s no new genetic information when a new function has evolved (or even when an existing function has improved) is a red herring that is promulgated by the opponents of evolutionary science.”
My comment: Differential survival and reproduction is nutrient-dependent and pheromone-controlled in species from microbes to humans. Serious scientists do not put that fact into the context of evolutionary science. Nutrient-dependent de novo gene creation is required for experience-dependent RNA-mediated receptor-mediated morphology and behavior to link supercoiled DNA to protection from virus-driven entropy of organized genomes in all genera. Without the protection of supercoiled DNA, there is no sequence of events that links neo-Darwinian theory from ecological variation to ecological adaptations manifested in the stability of organized genomes. The sequence of events MUST link atoms to ecosystems via differential survival and reproduction, not via mutations linked to pathology and entropy.
See also: Evolutionary Rewiring
My comment: Next, the term “mutation” can be placed into the context of semantics vs science. That will makes it clear that RNA-mediated DNA repair via nutrient-dependent amino acid substitutions underlies all links from atoms to ecosystems in the context of what is known to serious scientists about the physiology of reproduction.
Excerpt:

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.

Mutation-Driven Evolution
Excerpt:

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


See also:
Combating Evolution to Fight Disease
My comment: (1 of 4)
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.