An evolutionary theory killer

A single base change refutes theistic evolution (2)

Announcing publication of a model that links the creation of quantized energy from changes in subatomic particles to biophysically constrained viral latency and sympatric speciation in all living genera.

Nutrient-dependent Pheromone-Controlled Ecological Adaptations: From Angstroms to Ecosystems

This angstroms to ecosystems model of ecological adaptation links nutrient energy-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA/messenger RNA balance and chromosomal rearrangements via the physiology of reproduction in species from microbes to humans.

The invited review of nutritional epigenetics was returned without review and the preprint was posted 4 years ago as:

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

The only significant change to the manuscript was a change in the title. Atoms to ecosystems became Angstroms to Ecosystems when quantized energy-dependent changes in angstroms were linked to ecological adaptation by what is known to all serious scientists in this 2014 parody.
All About that Base (Meghan Trainor Parody) 12/10/14
Repeat after them (and me): “… every angstrom is dynamic from the 5 prime to the three…”
See also the 2015 publication: Structural diversity of supercoiled DNA

DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases.

See also: RNA-Guided Human Genome Engineering

George Church and others may have been the first to place the naturally occurring biophysically constrained energy-dependent processes of ecological adaptations into the context of a patent. (It is extremely unusual for anyone to attempt to patent a naturally occurring process.) That explains why there is no patent litigation, which still plagues those who claimed to discover the CRISPR-Cas 9 innate immune system of bacteria, which biophysically constrains viral latency and prevents the degradation of messenger RNA that links the energy-dependent creation of bacteria to the virus-driven creation of archaea and L-forms. All biophysically constrained virus-driven pathology has since been placed back into the context of embryogenesis and the dynamics of energy-dependent gene expression at the level of single-cell resolution as if bacteria somehow evolved into humans.

See:

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis
Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo
The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution
Chronicling embryos, cell by cell, gene by gene
Reported as: How one cell gives rise to an entire body
See for comparison our section on molecular epigenetics in: From Fertilization to Adult Sexual Behavior (1996)
Watch pseudoscientists continue to make ridiculous claims that fail to link the creation of biophysically constrained thermonuclear energy to autophagy and all biodiversity in the context of the cell biology game Cytosis and most of the forthcoming presentations during Schrödinger at 75 – The Future of Biology – September 2018.
Remember to note that at the end of the parody All About that Base, the research group politely refers to Neil deGrasse Tyson as a big ass (er, a bass). Try not to use the acronym ROTFLMAO in attempts to discuss what is known to all serious scientists with theorists.

Cytosis

From base editing to RNA editing (2)

Summary: The link from the creation of the sun’s anti-entropic virucidal energy and the physiology of pheromone-controlled reproduction to fixation of RNA-mediated amino acid substitutions in the organized genomes of all living genera is all that is required to claim adaptation for comparison to Koonin’s moronic assertion that the amino acid composition of proteins varies because the composition evolved.
Digital reconstruction of the Ceprano calvarium (Italy), and implications for its interpretation

A “fresh” (i.e., not yet “fossil”) bone can be plastically deformed before it breaks because it is still rich in collagen and because the calcium crystals that constitute large part of the bony matrix are not yet substituted by other minerals, as happens during the process of mineralization34. Such a diagenetic process may occur in environments that are rich in water, like a riverbed or a perilacustrine paleosol; the latter was probably the case in the Ceprano area5.

The virus-driven degradation of messenger RNA links the diagenetic process in living tissue links to the fossil record via changes that appear to have occurred during the past 5-10,000 years.
See for instance: MicroRNA-32 promotes calcification in vascular smooth muscle cells: Implications as a novel marker for coronary artery calcification
The increased level of calcification in smooth muscle cells, which is associated with increased rates of coronary artery calcification is a clear indicator that the proliferation of viruses in organized genomes causes the negative supercoiling of DNA, which serious scientists have linked to all pathology.
See also: A Post Mortem Case Study: Diffuse Pulmonary Ossification and Sudden Death
Case studies have no explanatory power outside the context of models that link electrons to ecosystems in all living genera. In this case study, it is clear that the pulmonary ossification and sudden death can be placed into the context of my model of nutritional epigenetics.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

Attempts to support theories about random mutations and evolution have failed miserably and have largely been replaced with facts about energy-dependent RNA-mediated cell type differentiation.
See: RNA Editing Possible with CRISPR-Cas13

The tool itself could be further developed, adds computational biologist Eugene Koonin of the National Center for Biotechnology Information who also was not involved in the study. “This paper is not the end of the road,” he says. It’s possible that Cas13b could be fused to a variety of editing enzymes that would allow a range of different sequence changes. The possibilities are numerous, Koonin says, and “the best is still to come.”

This paper is the end of the road for pseudoscientists and biologically uninformed theorists, like Eugene Koonin, who made this ridiculous claim in 2005:
Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. –Jordan et al., (2005) A universal trend of amino acid gain and loss in protein evolution
See for comparison: The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis… (2015) — Eugene Koonin
See also Koonin’s attack on all models of ecological adaptation: Splendor and misery of adaptation, or the importance of neutral null for understanding evolution (2016)

…population genetic theory, combined with the data of comparative genomics, clearly indicates that such a “pan-adaptationist” approach is a fallacy. The proper question is: how has this sequence evolved? And the proper null hypothesis posits that it is a result of neutral evolution: that is, it survives by sheer chance provided that it is not deleterious enough to be efficiently purged by purifying selection. To claim adaptation, the neutral null has to be falsified.

The link from the creation of the sun’s anti-entropic virucidal energy and the physiology of pheromone-controlled reproduction to fixation of RNA-mediated amino acid substitutions in the organized genomes of all living genera is all that is required to claim adaptation for comparison to Koonin’s moronic assertion that the amino acid composition of proteins varies because the composition evolved.
Each time a new claim attests to the facts about energy-dependent RNA-mediated biophysically constrained cause and effect, remember how long those facts have been placed on hold by people like Eugene Koonin and Jay R. Fiereman, who is the moderator of the International Society for Human Ethology’s Yahoo Group.
See this attempt to discuss mysterious DNA changes with Jay R. Feierman who on 7/25/13 wrote:

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.

All DNA modifications are energy-dependent and RNA-mediated. Publications in Science and Nature attest to the foolishness of those who have tried to link base editing and RNA editing to human cell type differentiation without starting with the fact that RNA-mediated amino acid substitutions are food energy-dependent.
Clearly there are no mysterious stress-linked DNA modifications. Nutrient stress and/or social stress cause the proliferation of viruses. Typically the proliferation of viruses is biophysically constrained by food energy and the pheromone-controlled physiology of reproduction in species from microbes to humans.
See “Cytosis” for the game-ending details that placed the nonsense about neutral null falsification back into the historical perspective of the “Dark Ages.”
See also: Tempo and mode of genome evolution in a 50,000-generation experiment (with my emphasis)

Evidence for beneficial mutations

We sought to understand what proportion of the genomic changes in the non-mutator populations was adaptive, and how that proportion changed over time. One line of evidence derives from the expectation that synonymous substitutions—point mutations in protein-coding genes that do not affect the amino-acid sequence—are neutral and should therefore accumulate at a rate equal to the underlying mutation rate20,35. This expectation is not strictly true owing to selection on codon usage, RNA folding, and other effects, but it is generally thought that such selection is extremely weak, affects only a small fraction of sites at risk for synonymous mutations, or both 36,37.

RNA-mediated protein folding chemistry is biophysically constrained. It is nutrient energy-dependent and biodiversity is controlled by the energy-dependent physiology of reproduction. In 2015, Lenski’s group admitted to their lie about the beneficial mutations, with the claim “This expectation is not strictly true owing to selection on codon usage…”
No beneficial mutations have been found by serious scientists. But Lenski’s group clearly indicated they would continue to lie about all aspects of energy-dependent biodiversity. They hoped to make it appear that all energy-dependent biodiversity emerged and then automagically evolved. If they could do that, they knew that their idiot minions were not likely to examine selection for energy-dependent codon usage. But then,
See for comparison: The dynamics of molecular evolution over 60,000 generations
After 10,000 more generations, Lenski’s group reported that standard models of mutation-driven evolution has not been supported by their experimental evidence. Instead, they placed their results into the context of natural selection for energy-dependent codon usage and long-term adaptation, which obviously occurred outside the context of mutation–selection balance and neutral mutation accumulation.
They clearly indicated that the complexity of ecological variation and energy-dependent ecological adaptation must be considered before reporting anything in the context of natural genetic variation. Simply put, they refuted all the pseudoscientific nonsense their past claims caused to be touted by other biologically uninformed theorists. They reported that ecological adaptation occurs outside the context of the mutations and evolution.
But see: Molecular evolution: No escape from the tangled bank

Ecological interactions emerge spontaneously in an experimental study of bacterial populations cultured for 60,000 generations, and sustain rapid evolution by natural selection.

The claim that there is no escape from the tangled bank is true. Joshua B. Plotkin took Lenki’s group’s refutation of mutation-driven evolution and placed it back into the context of the spontaneous emergence of energy-dependent ecological interactions. And then, he again touted the nonsense about evolution by natural selection.
See also: Rapid and Inexpensive Evaluation of Nonstandard Amino Acid Incorporation in Escherichia coli (2017)

…we developed a toolkit for characterizing any Escherichia coli OTS that reassigns the amber stop codon (TAG). It assesses OTS performance by comparing how the fluorescence of strains carrying plasmids encoding a fused RFP-GFP reading frame, either with or without an intervening TAG codon, depends on the presence of the nsAA. We used this kit to (1) examine nsAA incorporation by seven different OTSs, (2) optimize nsAA concentration in growth media, (3) define the polyspecificity of an OTS, and (4) characterize evolved variants of amberless E. coli with improved growth rates.

Even with the tools available, which have refuted all ridiculous theories of mutation-driven evolution, the claims that variants “evolved” continues to plague all serious scientists. It seems that placing the claims that variants evolved into the context of natural selection for energy-dependent codon optimality and the physiology of pheromone-controlled reproduction in all living genera serves no purpose. However, even if biologically uninformed science idiots are not willing to admit that top-down causation requires first consideration for the energy source, there is hope for the future. Most people intuitively understand that the food energy from what organisms eat must be linked to the metabolism of food and the metabolism of food to species-specific pheromones is the only known link from the physiology of reproduction to all biophysically constrained biodiversity in the context of viral latency.
Epigenetic effects must be linked to affects on behavior and the difference between an effect on hormones and an affect of hormones on behavior must be considered in the context of how food odors and pheromones are linked to the physiology of human reproduction by serious scientists.
For example, see: Feedback loops link odor and pheromone signaling with reproduction
 
 

Alternative splicing of pre-mRNA

Evolutionary theories of epigenetic drift

Testing Two Evolutionary Theories of Human Aging with DNA Methylation Data
My summary: Outside the context of food energy-dependent biophysically constrained pheromone-controlled viral latency, mutation accumulation (MA) and disposable soma (DS) provide possible explanations for the existence of human aging. For example, age-differentially-methylated sites across the genome showed significant MA-consistent increases in heritability with age or significant DS-consistent decreases in heritability. Their results supposedly show that both MA and DS play a role in explaining aging and aging-related changes but their results do not link food energy-dependent RNA-directed DNA methylation to de novo gene creation or the virus-driven degradation of messenger RNA that serious scientists have linked from mutations to all pathology in all living genera.
See also: Caloric restriction delays age-related methylation drift

Epigenetic information encoded by DNA methylation is tightly regulated, but shows a striking drift associated with age that includes both gains and losses of DNA methylation at various sites.

Reported as: Researchers uncover mechanism behind calorie restriction and lengthened lifespan

Dr. Issa’s team made their discovery after first examining methylation patterns on DNA in blood collected from individuals of different ages for each of three species – mouse, monkey, and human.

Energy as information is epigenetically linked from the food that organisms eat to the physiology of pheromone-controlled reproduction in all living genera by RNA-directed DNA methylation and amino acid substitutions that differentiate all cell types in all individuals.
All serious scientists have linked RNA-mediated amino acid substitutions from the differentiation of cell types in yeasts to the differentiation of cell types in primates.
Nothing in Biology Makes Any Sense Except in the Light of Evolution 

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.

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

In the mouse model, the diet of the mice determines their nutrient-dependent pheromone production and social interactions with other mice. The mouse model also reveals something that was not revealed in the context of dogs and wolves (Axelsson et al., ; Lord, ). The aversive human body odor associated with fish odor syndrome can be epigenetically controlled by reducing dietary choline intake. It can also be controlled through antibiotic use (citations in Li et al., ). This may be important in the context of chemical ecology and epigenetic effects of genetically predisposed nutrient-dependent pheromone-controlled human interactions (Martin et al., ; Preti & Leyden, ).

See also the section on “An epigenetic continuum of nutrient-dependent / pheromone-controlled adaptive evolution”

Nematodes

Differences in the behavior of nematodes are determined by nutrient-dependent rewiring of their primitive nervous system…

Insects

The honeybee is currently an accepted model organism of nutrient-dependent pheromone-controlled adaptive evolution of the brain and behavior that is consistent with what is known about neurogenic niche construction in nematodes…

Mammals

Species-specific health and reproductive fitness is associated with nutrient-dependent amino acid substitutions and with pheromone-controlled reproduction. Disease is associated with mutations exemplified in cancer where perturbations of the glucose-dependent thermodynamic/thermoregulatory equilibrium are equally clear (Locasale, ).

Humans

Two additional recent reports link substitution of the amino acid alanine for the amino acid valine (Grossman et al., ) to nutrient-dependent pheromone-controlled adaptive evolution. The alanine substitution for valine does not appear to be under any selection pressure in mice. The cause-and-effect relationship was established in mice by comparing the effects of the alanine, which is under selection pressure in humans, via its substitution for valine in mice (Kamberov et al., ).

See for comparison: Feynman on social science
See also:

 

Alternative splicing of pre-mRNA

Inventing "Transcriptome Trajectory Turning Points"

Summary: They invented the term “Transcriptome Trajectory Turning Points” to prevent others from learning that virus-driven energy theft is the cause of all pathology.
Scientists discover genetic timetable of brain’s aging process

The biggest reorganisation of genes occurs during young adulthood, peaking around age 26, the team found. These changes affected the same genes that are associated with schizophrenia.

The team says this could explain why people with schizophrenia do not show symptoms until young adulthood, even though the genetic changes responsible for the condition are present from birth.

See for comparison: microrna schizophrenia 
 
There is no such thing as a genetic timetable of aging outside the context of epigenetic effects on hormones that affect behavior.
 

Food energy-dependent pheromone-controlled changes in the microRNA/messenger RNA balance link fixation of experience-dependent RNA-mediated amino acid substitutions to supercoiled DNA, which protects us from the virus-driven degradation of messenger RNA.

See also:  A genomic lifespan program that reorganises the young adult brain is targeted in schizophrenia

They invented the term “Transcriptome Trajectory Turning Points.” That is typical of what pseudoscientists must do to prevent others from learning that virus-driven energy theft is the cause of all pathology.

See for comparison: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults 

One amino acid substitution in supercoiled DNA can make the difference between healthy longevity and virus-driven pathology at any point in life. That is true for all individuals of all species and all serious scientists are using that fact as they continue Combating Evolution to Fight Disease.

See also: Microbial regulation of microRNA expression in the amygdala and prefrontal cortex

See also: Epigenetic Changes Caused by Occupational Stress in Humans Revealed through Noninvasive Assessment of DNA Methylation of the Tyrosine Hydroxylase Gene

See also: A new target for G protein signaling

The structure and mechanism of heterotrimeric G proteins has been studied at atomic resolution (Oldham and Hamm, 2008).

The energy-dependent de novo creation of G protein coupled receptors links the sense of smell in bacteria to our visual perception of mass and energy in the context of the physiology of pheromone-controlled reproduction and the time-space continuum. See: Olfaction Warps Visual Time Perception

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

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

Cytosis

Epigenetic effects of stress by Bruce McEwen (2)

Summary:

…rapid mRNA turnover starts with the energy-dependent de novo creation of microRNAs and ends with the virus-driven degradation of messenger RNA, which links mutations to all pathology.
 
This was reported in the following context: “RNA molecules live short lives” July 12, 2017

See also: Epigenetic effects of stress by Bruce McEwen (1)

Summary:

In the early 1990’s, Bruce McEwen inspired my life’s works, which link the epigenetic effects of nutrient-stress and/or social stress to the fact that RNA biosynthesis is ATP-dependent. That fact helped all serious scientists link the virus-driven energy theft of quantized energy to the degradation of messenger RNA, which links mutations to all pathology.

Pseudoscientists refuse to accept that fact.

New research uncovers the secrets of photosynthesis that could help develop computer technology

Energy and charge transfer is what drives photosynthesis and any solar-to-chemical or electrical-to-chemical energy conversion.

That fact links the anti-entropic virucidal energy of sunlight from the de novo creation of microRNAs to all biodiversity. Bruce McEwen published on the role that microRNAs play in: Characterization of the vulnerability to repeated stress in Fischer 344 rats: possible involvement of microRNA-mediated down-regulation of the glucocorticoid receptor (2008)

We also identified that microRNA (miR)-18a inhibited translation of GR mRNA in cultured neuronal cells and that increased expression of miR-18a in the PVN was observed in F344 rats compared with SD rats. These strain differences in GR protein levels were not found in the hippocampus and prefrontal cortex, and the expression of miR-18a was much lower in these brain regions than in the PVN. Our results suggest that F344 rats could be a useful animal model for studying vulnerability to repeated stress, and that miR-18a-mediated down-regulation of GR translation may be an important factor to be considered in susceptibility to stress-related disorders.

See also: Early Life Stress Enhances Behavioral Vulnerability to Stress through the Activation of REST4-Mediated Gene Transcription in the Medial Prefrontal Cortex of Rodents (2010)

Figure 3.

Expression analyses of mRNAs of RE-1-containing genes and brain-enriched pre-microRNAs in the mPFC of the maternally separated rats. A, B, The expression of mRNAs (A) and pre-microRNAs (B) of a variety of RE-1-containing genes in the mPFC of AFR, HMS15, and HMS180 rats at P14 were quantified by Q-PCR (n = 6 for all groups). C, D, The expression of mature microRNAs in the mPFC of AFR, HMS15, and HMS180 rats at P14 were quantified by Northern blotting analysis (n = 5–6 for each group). E, The mRNA and pre-microRNA expression of RE-1-containing genes in the mPFC of adult AFR, HMS15, and HMS180 rats were quantified by Q-PCR (n = 6 for all groups). *p < 0.05.

Bruce McEwen subsequently linked what is known about energy-dependent changes in single nucleotide polymorphisms to effects of hormones on behavior in mice and humans via a food energy-dependent biophysically constrained amino acid substitution.

See: Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity (2015)

Excitatory amino acids play a key role in both adaptive and deleterious effects of stressors on the brain, and dysregulated glutamate homeostasis has been associated with psychiatric and neurological disorders. Here, we elucidate mechanisms of epigenetic plasticity…  In WT mice after CRS and in unstressed mice with a BDNF loss-of-function allele (BDNF Val66Met), we show that the epigenetic activator of histone acetylation, P300, plays a pivotal role in the dynamic up- and down-regulation of mGlu2 in hippocampus via histone-3-lysine-27-acetylation (H3K27Ac) when acute stressors are applied. These hippocampal responses reveal a window of epigenetic plasticity that may be useful for treatment of disorders in which glutamatergic transmission is dysregulated.

See also: Multiplexed gene control reveals rapid mRNA turnover (open access)

The rapid mRNA turnover starts with the energy-dependent de novo creation of microRNAs and ends with the virus-driven degradation of messenger RNA, which links mutations to all pathology.
 
This was reported in the following context: “RNA molecules live short lives” July 12, 2017
“Sometimes it is hard to believe that scientists could have unknowingly worked with methods that produce inconsistent results for almost 30 years”, says Becskei.
 
Becskei adds insult to the injury, unnecessary suffering, and the premature death caused by misrepresentations of biologically-based cause and effect. An accurate representation was reported in 1964 as: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” 
 

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

The fact that some researchers still do not know that the synthesis of RNA is energy-dependent makes it impossible for them to link virus-driven energy theft from the degradation of messenger RNA to mutations and all pathology in all living genera.

It will soon become “child’s play” for anyone over 10 years old. See: Cytosis: A Cell Biology Board Game

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

achiral-glycine

Energy-dependent microRNA biogenesis

Published May 3, 2017 Genetic variation and RNA structure regulate microRNA biogenesis

…primary sequence determinants and RNA structure are key regulators of miRNA biogenesis.

Genetic variation aka primary sequence determinants are energy-dependent and RNA-mediated. Energy-dependent RNA methylation is an experience-dependent link from natural selection for energy-dependent codon optimality. Natural selection for energy-dependent codon optimality links ATP-dependent microRNA biogenesis to RNA biosynthesis.
Ridiculous attempts to portray energy-dependent top-down causation as if genetic variation came first may continue for another 52 years. But see this report from 1964 to help you recognize how much pseudoscientific nonsense has been touted since then.
See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

Isolated thymus nuclei transport amino acids into an intranuclear pool by a process which seems to depend on energy from nuclear ATP synthesis (20).

If any experimental evidence of biophysically constrained RNA-mediated cell type differentiation was not linked from an anti-entropic energy source to nuclear ATP synthesis that experimental evidence might support the claims of pseudoscientists who think that mutations link natural selection to evolution of different species.
See for comparison: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The bias between codons or amino acids, and mRNA expression levels has been previously recognized across species and is thought to result from selection for efficient, accurate translation, and folding of highly expressed genes…

My translation: Natural selection for energy-dependent and energy-efficient protein folding chemistry links what organisms eat to the energy that they require for reproduction via the accurate translation and folding of highly expressed genes.
Alternatively, virus-driven energy theft links the degradation of messenger RNA to all pathology via conserved molecular mechanisms in all living genera. Simply put, the molecular mechanisms of healthy longevity and biodiversity are nutrient energy-dependent and pheromone-controlled.

The fact that population geneticists have ignored what us known to all serious scientists about the controlled molecular mechanisms that link metabolic networks to genetic networks has led to the unnecessary suffering and premature death of millions to billions of people. If you are not willing to join those who are Combating Evolution to Fight Disease, you probably will be asked why you decide to ignore everything known about the energy-dependent de novo creation of genes. If you did not recognize your ignorance, try to find experimental evidence in the works of evolutionary theorists who did not start after the energy-dependent de novo creation of genes.

So far as I know, all pseudoscientists still consistently place the facts about de novo gene creation, which refute their nonsense about mutation-driven evolution, into the context of their published works. Those works will continue to cause the unnecessary suffering and premature death of millions to billions of people.

The fact that experience-dependent genetic variation does not create itself is a thorn in the side of all theorists who now recognize and must ignore the facts about RNA-mediated cell type differentiation. The facts link the energy-dependent RNA-mediated fixation of amino acid substitutions to all biodiversity.

The facts also link mutations to all pathology, which means the facts have always been evolutionary theory killers. The facts haven’t changed since Thomas Hunt Morgan presciently linked them to chromosomal inheritance and Schrodinger presciently linked the anti-entropic virucidal energy of sunlight to RNA-mediated DNA repair.

See also: Exiqon “Genome Web” This link opens the pdf for microRNA target identification by RNA pull down with biotinylated microRNA mimics

Approximately one in five microRNA interactions with mRNAs occur through non-canonical binding sites. Although of functional relevance these microRNA targets are not predicted by bioinformatics tools. Improved RNA pull-down techniques with biotinylated microRNA mimics open new possibilities to identify microRNA targets experimentally.

Download the tech note

My  comment: Although I have repeatedly mentioned works that link energy-dependent changes in the microRNA/messenger RNA balance to cell type differentiation and healthy longevity, I had not seen any mention of biotinylation, until today.

In biochemistry, biotinylation is the process of covalently attaching biotin to a protein, nucleic acid or other molecule. Biotinylation is rapid, specific and is unlikely to perturb the natural function of the molecule…

I do not know any theorists who are biochemists and suspect that all the ridiculous theories of pseudoscientists include nothing that is known about biotinylation. That may be why I did not hear the term mentioned, until today. What would happen if I heard it and failed to learn what it meant? God forbid, I might still be a biologically uninformed theorist
See for example: The landscape of sex-differential transcriptome and its consequent selection in human adults

This work provides a comprehensive overview of the sex-differential transcriptome and its importance to human evolution and human physiology in health and in disease.

Reported as: Researchers identify 6,500 genes that are expressed differently in men and women

The detailed map of these genes, reported in BMC Biology, provides evidence that males and females undergo a sort of separate, but interconnected evolution.

I thank God, for not allowing me to believe that males and females are different mutants of the same species.
See for comparison: We are all mutants

Darwin is a god in evolution, so you can’t criticize Darwin. If you do, you’re branded as arrogant.

But any time a scientific theory is treated like dogma, you have to question it. The dogma of natural selection has existed a long time. Most people have not questioned it. Most textbooks still state this is so. Most students are educated with these books.

You have to question dogma. Use common sense. You have to think for yourself, without preconceptions. That is what’s important in science.

Common sense? Masatoshi Nei’s textbook Mutation-Driven Evolution was published on the same day as my 2013 review: Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which is a refutation of mutation-driven evolution.

Excerpt:

…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.

Conclusion:

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

See for comparison: John Deely, from the Point of View of Biosemiotics

Conclusion:

….his unlimited but judiciously applied enthusiasm, his sterling example as  a scholar, and his inspirational support of semiotic colleagues, institutions, and the ongoing investigation into the reality of sign process at every level of life have been and will remain a force that both inspires and that sets the standard by which our colleagues continue with their important work.

My comment: The reality of sign process at every level of life is that it is energy-dependent, RNA-mediated, and biophysically constrained by the physiology of reproduction in species from archaea to humans.

Cytosis: Biology Content

 

Help Me Write Some Biology Content

Project Update #5: Cytosis: A Cell Biology Board Game by John Coveyou (Genius Games)

Many of you have mentioned that you’d like to have an explanation of the biology behind Cytosis available… and I think that is an AWESOME plan. Every time I’ve taught the game to non-science players in the past, they say gameplay made even more sense (and was so much more enjoyable) when I explained the science as well. This way they knew WHY they were doing what they were doing!

If you’ve got a strong background in biology, love explaining complexities in a way that someone unfamiliar with biology could understand, and would be interested in volunteering to help me write a page or two of science explanatory content for the rulebook, please shoot me an email… with the subject line “Cytosis Biology Explanations – [Your Name]” and we can start discussing!

I wrote: Kohl’s Laws of Biology may help. See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

1) Life is nutrient-dependent. See for review [2, 31]. The physiology of reproduction is pheromone-controlled. See for review [30].

In the context of the game “Cytosis,” Kohl’s Laws link the epigenetic effects of food odors and pheromones to changes in the mitochondria of all cell types. The energy-dependent changes in the mitochondria are linked to healthy longevity.
If the epigenetic effects of food odors and pheromones did not clearly link cytosis to healthy longevity, we would be left with only the link from virus-driven energy theft to all pathology. The explanation for all pathology involves more complexity than most people are willing to examine even when it is placed into the context of a book for a general, albeit educated, target audience.
See: The Scent of Eros: Mysteries of Odor in Human Sexuality

This is science at its best, with adventure, ideas, and lots of facts. — Helen Fisher

Details for other serious scientists:

The synthesis of RNA is nutrient energy-dependent. From 1964 Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

The anti-entropic virucidal energy of sunlight has since been linked to all biophysically constrained human cell type differentiation via representations in Feedback loops link odor and pheromone signaling with reproduction

The feedback loops link Dobzhansky’s claims about amino acid substitutions and RNA-mediated cell type differentiation from natural selection for energy-dependent codon optimality to the pheromone-controlled biodiversity of all living genera.

See: Combating Evolution to Fight Disease

…transient errors in mRNA synthesis can also cause heritable non-DNA-based phenotypic change. This is observed when low-abundance transcriptional regulators are affected by transcription errors. This disruption can cause a cell to alter its gene expression, resulting in a phenotype that may be heritable (2).

See also: Carl Woese, Evolution’s Golden Revolutionary

…there is probably no other scientist but Carl Woese who could write about having “no use for natural selection” and have Nature magazine respond with a Nobel endorsement. It is Carl Woese who first identified the Archaea and introduced us to horizontal gene transfer.

Virus-driven energy theft causes the degradation of messenger RNA, which links negative supercoiling of DNA in bacteria to the creation of archaea and links the conserved molecular mechanisms from archaea to the evolution of all pathology. For comparison, horizontal gene transfer links the nutrient energy-dependent de novo creation of genes from the pheromone-controlled fixation of RNA-mediated amino acid substitutions to supercoiled DNA, which prevents virus-driven energy theft from causing more degradation of messenger RNA.

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

This invited review of nutritional epigenetics includes a model that links nutrient energy-dependent changes from atoms to ecosystems. Most theorists have been caught with their pants down because they are still making claims about mutations and evolution. How can serious scientists compete with pseudoscientists who make claims that link mutations to millions of year of evolution?  Most serious scientists know how to link quantized energy from chemistry to biologically-based cause and effect. Most biologically uninformed people accept the claims of pseudoscientists, atheists, and other theorists.

Some Harvard researchers are still trying to hide facts that link research on the synthesis of mRNA to all biophysically constrained biodiversity on Earth via hydrogen-atom transfer in DNA base pairs in solution and RNA-mediated amino acid substitutions in supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. ATP-dependent cell type differentiation is placed into the context of conserved NAD+ and protein-protein interactions.

See:  A conserved NAD+ binding pocket that regulates protein-protein interactions during aging

See for contrast: Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention

It is now widely accepted that cancer is the result of the gradual accumulation of driver gene mutations that successively increase cell proliferation (1–3).

Johns Hopkins researchers framed everything known to serious scientists about cell type differentiation into the contest of cancer as ‘bad luck” as if cytosis was not energy-dependent and healthy longevity arose in the context of mutation-driven evolution — if species were lucky enough to evolve into other species.
No serious scientist has ever accepted that ridiculous claim.

See for comparison: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

…we characterize two distinct p120-associated complexes with antagonistic functions and we describe a microRNA (miRNA)-mediated mechanism through which the ZA suppresses transformed cell growth.

Backers and players of the game “Cytosis” will learn how the energy-dependent function of mitochondria must be linked to every aspect of healthy longevity or be linked from virus-driven energy theft to all pathology. They will be prepared to learn from the next game: “Photosynthesis,” which will link the sun’s anti-entropic virucidal energy to all biophysically constrained biodiversity via what is known to all serious scientists. They will not need to learn anything more than is required for them to reject the pseudoscientific nonsense of neo-Darwinian theories.

See what’s happened after 20 days of comments to this society. 

The information has been shared more than 450 times. The number of biologically informed students will force the biologically uninformed professors to stop playing the evolution game until they can begin supporting their ridiculous claims with facts. The facts must link ecological variation to ecological adaptations via what is known to serious scientists about hydrogen-atom transfer in DNA base pairs in solution.

Clearly, the facts tell us that all individuals of all species that live on Earth must eat and reproduce or they become extinct. None mutate and evolve into other species.

Thus, we regard as rather regrettable the conventional concatenation of Darwin’s name with evolution, because there are other modalities that must be entertained and which we regard as mandatory during the course of evolutionary time.

— Carl Woese and physicist Nigel Goldenfeld

I encourage others to support the development of games that teach what pseudoscientists do not want an interested target audience to learn. With enough support for an easy way to learn about energy-dependent cytosis compared to virus-driven pathology, the facts about RNA-mediated cell type differentiation will become clearer.

See also our section on molecular epigenetics in this review from 1996: From fertilization to adult sexual behavior

Every aspect of cytosis is food energy-dependent and RNA-mediated. Virus-driven energy theft cause all pathology. That fact makes sense in the context of all claims made by serious scientists. See for example:

 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)

— with forward by Roger Penrose who co-authored with George F.R. Ellis and Stephen Hawking

“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)

See also:

James Vaughn Kohl “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


    17 Apr 2014 at 03:07am

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: http://rsfs.royalsocietypublishing.org/content/2/1.toc 

See also:

…every angstrom is dynamic from the 5 prime to the three…

See also: Genetic 3’UTR variation is associated with human pigmentation characteristics and sensitivity to sunlight

Sunlight exposure induces signalling pathways leading to the activation of melanin synthesis and tanning response. MicroRNAs (miRNAs) can regulate the expression of genes involved in pigmentation pathways by binding to the complementary sequence in their 3′-untrastaled regions (3’UTRs).

Top-down causation starts from the creation of the sun’s anti-entropic virucidal energy. Hydrogen atom transfer in DNA base pairs in solution links energy-dependent changes in the microRNA/messenger RNA balance from microRNA flanking sequences to RNA-mediated amino acid substitutions that alter the stability of supercoiled DNA in the context of the physiology of reproduction.

One base pair change and a single amino acid substitution makes the difference between healthy longevity and pathology during life history transitions. See for example: Epigenetic Regulation of BDNF Gene during Development and Diseases
See also: Δ133p53 Functions to Maintain Redox Homeostasis in Response to Low ROS Stresses
https://www.omicsgroup.org/articles-images/single-cell-signaling-response-oxidative-stresses-5-154-g001.png
See also: Keep science a priority. Stand with ASCB at the March for Science rally April 22.
Amino acid modification FA_Epigenetics_Table1

Biologically uninformed biologists fight back and lose

Novel layers of RNA polymerase III control affecting tRNA gene transcription in eukaryotes 22 Feb 2017

A subset of tRNA genes shows low responsiveness to both environmental and cellular signals. Notably, this group contains at least one tRNA for each amino acid. Together these findings suggest the existence of a basal subset of housekeeping tRNA genes [36]. This concept is consistent with the mode of Maf1-mediated repression of actively transcribed tRNA genes in human cells subjected to serum starvation [104].

See also the citation to (with my emphasis): Kimura M, Ishihama A. 1995 Functional map of the alpha subunit of Escherichia coli RNA polymerase: amino acid substitution within the amino-terminal assembly domain. J. Mol. Biol. 254, 342–349.
The fact that an enzymatic reaction linked energy to the amino acid substitution seems to have been virtually ignored by theorists

See for example comparison: Richard Lenski – Evolution in a Flask

Published on 24 Feb 2017

Dr. Stan Maloy talks with Richard Lenski Ph.D., Hannah Professor of Microbial Ecology, Michigan State University, about his research into the evolution of bacteria and the new frontier of digital evolution.Episode 61 of MicrobeWorld Video, filmed at the American Association for the Advancement of Science Meeting in Vancouver, Canada on February 17th, 2012.

Lenski’s Long Term Evolution Experiment with E. coli has seen over 50,000 new generations since its inception in 1998. This has led to insights such as how viruses can evolve from types that don’t infect humans to ones that do.

Lenski’s work with E. coli has also led him into the digital world. Using computers, Lenski can achieve precise, rapid results by manipulating digital organisms. Software that evolves much like bacteria in the real world.

Lenski is optimistic about the future of evolution research. Applying the generalities that have resulted from his studies to any number of other microbial species. He also sees large potential in applying what he’s learned to the study of antibiotic resistance and bioengery.

The fact that Richard Lenski failed to acknowledge what was known about the nutrient energy-dependent RNA-mediated amino acid substitution that stabilized the organized genome of E. coli, his model organism, attests to how much pseudoscientific nonsense about mutations, natural selection, and evolution he has been touting for more than 2 decades.
For comparison, see: Measurements of translation initiation from all 64 codons in E. coli
Reported as: Start codons in DNA may be more numerous than previously thought
See also: Biodiversity is autocatalytic

…it was recently shown using the RAF algorithm that 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.

Reported as: Autocatalytic biodiversity hypothesis aims to supplant Darwin’s ‘war of the species (February 9, 2017)

A species emerges from this environment and is an expression of those interactions. In other words, species are expressed and maintained by a complex interacting ecological network.

Contrary to Darwin’s beliefs, biodiversity, according to Dr. Cazzolla Gatti, does not derive “from the war of nature, from famine and death,” but from the power of life to enable other life; not from war, but from coexistence; not from competition but from the avoidance of it, e.g. from cooperation and facilitation, i.e., by autocatalysis.

The power of life to enable other life is nutrient energy-dependent and controlled by the physiology of reproduction. That fact explains why virus-driven energy theft is being linked to all pathology in the science news that is reported each day. The obfuscation is clear in the fact that there is no such thing as a genomic pathway outside the context of epigenetic effects that link metabolic networks to genetic networks in all living genera. When you see a report that does not link energy-dependent epigenetic effects to supercoiled DNA or to virus-driven pathology, you should learn to recognize the tactics that are used to frame experimental evidence of biologically-based cause and effect in the context of evolutionary theories about evolutionary pathways and/or genomic pathways.
Faulty genomic pathway linked to schizophrenia developing in utero, study finds

“This research shows that there is a common dysregulated gene program that may be impacting more than 1,000 genes and that the great majority of those genes are targeted by the dysregulated nuclear FGFR1,” Stachowiak said.

When even one of the many schizophrenia-linked genes undergoes mutation, by affecting the INFS it throws off the development of the brain as a whole, similar to the way that an entire orchestra can be affected by a musician playing just one wrong note, he said.

See the obfuscatory attempt in:

See also: Epigenome: The symphony in your cells
The “symphony” is energy-dependent and RNA-mediated via endogenous RNA interference in the context of the physiology of reproduction.

 
 
 

rp_levels-of-organization.jpg

Science journalists or paid propagandists? (2)

Excerpt:

Riffell is interested in how chemical signals, like smells, affect behavior. Explore further: Researchers show that the mosquito smells, before it sees, a host.

This was reported last year in “Science” and on January 6, 2017 as Orchids mimic human body odor to attract mosquitoes
The year-long delay aroused my suspicion because everything known to serious scientists since 1996 has linked food odors and pheromones to reproduction in species from microbes to humans.
See for example: Insect pheromone in elephants (1996)

SIR – (Z)-7-dodecen-l-yl acetate is used by the females of more than 126 species of insects, especially Lepidoptera, as part of their pheromone blends to attract insect males1. Female Asian elephants, Elephas maximus, also use a pheromone to signal to males their readiness to mate2.

See also: Feedback loops link odor and pheromone signaling with reproduction (2005)
See also: Schedule 2016 and this search for pheromones: The Role of Pheromone Differences in Lineage Maintenance

…sex-specific pheromones used by plethodontid salamanders may play a role in sexual incompatibility and therefore the maintenance of isolated, genetically distinct populations.

…relative ratios of specific pheromone isoforms were compared across groups.

Species-specific pheromones must first epigenetically effect the nutrient energy-dependent hormone-organized function of the invertebrate and vertebrate brain. Then, pheromone isoform composition can affect energy-dependent male behavior or energy-dependent female behavior.
The evolutionary origins of social insect queen pheromones: honesty and dynamics of fertility signal production in a socially polyphenic Halictid bee.

…the evolution of these signaling channels given the potential for destabilizing dishonest signal production remains somewhat unclear. Fertility signal evolution may be at a nascent stage in primitively social insect societies…

They invented a nascent stage in an attempt to explain the nutrient energy-dependent pheromone-controlled behavioral development after claiming that facts about virus-driven destabilization of signal production were unclear.
Estrogen implantation alters putative pheromone composition in male brown tree snakes

Previous work in another snake species demonstrated that both estrogen implantation and testosterone removal (castration) could induce female pheromone expression in male red-sided garter snakes. It was thus the goal of this study to use estrogen implantation to manipulate putative pheromone expression in male brown tree snakes and determine the effect of implantation on male attractiveness. We implanted male brown tree snakes (n=7) with silastic implants (1 cm) containing estradiol and found that implanted males had significantly altered expression of long-chain methyl ketones, specifically the longer, monunsaturated ketones.

The hormone-dependent production of sex differences in pheromones has been linked from sex difference in yeasts at the advent of sexual reproduction to all sex differences in all cell types of all species that sexually reproduce.
Influence of female orientation and pigmentation on male positioning during courtship

We can modify the dummy’s appearance, pattern of motion, and pheromone coating. Males will robustly court the dummy, enabling us to delineate the relative contributions of visual and other sensory cues to male courtship behavior.

It is fascinating to see anyone pretend that the courtship behavior might depend on visual or other sensory cues without attesting to the facts about the classical conditioning of odor-driven changes in behavior that link chemotaxis to phototaxis in all living genera, not just organisms with eyes.
Cooperation and conflict in social insect societies: from genes to pheromones

Our studies provide novel insights into genomic, epigenomic, physiological and chemical mechanisms that regulate the variation in pheromone production and responses to these pheromones that shape social behavior in honey bees. We have extended these studies to other social insects (bumble bees, paper wasps, and fire ants) to begin to examine the evolution of the genomic pathways underpinning chemical communication and reproductive dominance…

Anna Di Cosmo’s group already linked everything known about ecological variation to ecological adaptation in species from marine invertebrates to terrestrial vertebrates in Role of olfaction in Octopus vulgaris reproduction
From the concluding paragraph:

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

Attempts to put facts like these back into the context of “…the evolution of the genomic pathways underpinning chemical communication and reproductive dominance…” are doomed to fail. There is no experimental evidence of biologically-based cause and effect that can be linked to the evolution of one species from another.
See also: Science journalists or paid propagandists? (3)
 

Biology to a Physicist

2016 obfuscated facts about energy as information

Zika infection may affect adult brain cells

Illumination of the fluorescent biomarker in green revealed that the adult mouse brain could be infected by Zika in a region called the subgranular zone of the hippocampus. Full of neural progenitor cells, this part of the brain is important in learning and memory. Credit: Laboratory of Pediatric Brain Disease at The Rockefeller University/Cell Stem Cell

As reported by Bob Yirka in: Best of Last Year – The top Medical Xpress articles of 2016

a team of MIT biologists reported that amino acids, not sugar, supplied most of the building blocks for tumor cells—cell mass was not mostly glucose, as they had expected.
In other news, at team at Duke University found a key protein for spinal cord repair

Most of the pseudoscientific nonsense reported in the top Medical Xpress articles from the past can be compared to the facts about how energy-dependent viral latency is required for ecological adaptation in the context of RNA-mediated amino acid substitutions.

The facts were reported as “New CRISPR–Cas systems from uncultivated microbes

See also: More refutations of neo-Darwinian nonsense and Dietary lutein and pheromone-controlled brain development

All serious scientists have learned there is no “new CRISPR–Cas” system. The de novo creation of the innate immune system links nutrient energy-dependent changes from angstroms to ecosystems via hydrogen-atom transfer in DNA base pairs in solution. The energy-dependent changes in base pairs are the obvious links to the development of morphological and behavioral phenotypes in all living genera. All phenotypic expression is energy-dependent, and it must link autophagy to the physiology of reproduction. For example, in species from microbes to humans Feedback loops link odor and pheromone signaling with reproduction

The pheromone-controlled physiology of reproduction links the energy-dependent creation of supercoiled DNA to protection from virus-driven energy theft and all pathology. Simply put, supercoiled DNA prevents the genomic entropy that is linked to all pathology.
 

For comparison, the link from the anti-entropic virucidal energy of sunlight to supercoiled DNA via the viral hecatomb in archaea is the link to the transgenerational epigenetic inheritance of Zika virus-damaged DNA in human infants. Facts about energy-dependent polycombic ecological adaptations will put an end to ridiculous theories about mutations and evolution. That will become perfectly clear if Gunter Witzany allows others to help present  what is known about energy-dependent changes in the microRNA/messenger RNA balance at the 2018 conference he reportedly is organizing.

See: Royal Society: The Public Evolution Summit (p. 12)

 … evolution of genome invading RNA networks that edit host g… Witzany is organizing a conference symposium for July 2018 “Evolution-genetic innovations without error replication”

Until everyone learns how energy-dependent autophagy and supercoiled DNA prevent error replication, pseudoscientists may continue to tout their ridiculous theories. Many more people will suffer and die prematurely due to biased reporting that supports the evolution industry and “big bang” cosmology industry.

But wait, 2016 is not over yet, is it?

See: Spatiotemporal antagonism in mesenchymal-epithelial signaling in sweat versus hair fate decision

This was reported by Bob Yirka as: Researchers identify signals during embryonic development that control the fate of skin cells to be sweaty or hairy

See also: Royal Society’s Sir Venki Ramakrishnan Agrees to Post Public Evo Audio

…public discussion from the recent “new trends” in evolution conference will be posted shortly online on the Royal Society event webpage.

The public discussion may help to reveal that the fate of all cell types is energy-dependent and RNA-mediated via natural selection for codon optimality linked to autophagy and to supercoiled DNA.
See for example: rs3827760, also known as 1540T/C, 370A or Val370Ala, is a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2.
This SNP and everything known about how chromosomal rearrangements are linked to energy-dependent  pheromone-controlled biodiversity, which links the mouse model of cell type differentiation to humans via what is known about energy-dependent RNA-mediated amino acid substitutions such as Val370Ala. The facts about the Val370Ala and other amino acid substitutions have been known since 1973 and four more decades of facts were detailed in the context of this 2013 review.
See for other examples: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

These two reports (Grossman et al., 2013; Kamberov et al., 2013) tell a new short story of adaptive evolution. The story begins with what was probably a nutrient-dependent variant allele that arose in central China approximately 30,000 years ago. The effect of the allele is adaptive and it is manifested in the context of an effect on sweat, skin, hair, and teeth. In other mammals, like the mouse, the effect on sweat, skin, hair, and teeth is due to an epigenetic effect of nutrients on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones control the nutrient-dependent hormone-dependent organization and activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates as previously indicated. That means the adaptive evolution of the human population, which is detailed in these two reports, is also likely to be nutrient-dependent and pheromone-controlled, since there is no other model for that.

Each week’s science news brings additional representations of facts that refute all neo-Darwinian pseudoscientific nonsense by linking Darwin’s “conditions of life” to all biodiversity. Most science news outlets still report and/or tout pseudoscientific nonsense because the reporters missed the fact that life is nutrient-dependent and the physiology of reproduction is controlled by pheromones in species from microbes to humans.
Can you imagine how embarrassed you would be if you had not learned to include the fact that all organisms must eat or they cannot reproduce in your reports. That fact means organisms cannot become part of a species if they can’t find food. What’s worst about having to explain that fact to reporters and/or pseudoscientists is that no experimental evidence of biologically-based cause and effect supports claims that one species ever evolved into another.
“The Battlefield”
I may have mentioned this before.  I’ve been banned from participation on this group, twice. Most recently, I complained that two other admins support Peter Berean’s attempts to denigrate my life’s works on energy as information-dependent changes in the microRNA/messenger RNA balance and denigrate me personally with his claims about “bio-functional information.”
By default, Larry Kisner Sr., and John L Leonard support the ignorant representations made by Peter Berean, and there is rarely any accurate representation of energy-dependent biologically-based cause and effect.

I’ve suggested several times that the group may be another “False Flag” group. Others can evaluate the claims made there for comparisons to the accurate claims of serious scientists who have linked hydrogen-atom transfer in DNA base pairs in solution to energy-dependent changes in microRNA flanking sequences and all biodiversity via natural selection for energy-as-information-dependent codon optimality.
You’ll be learning more about the facts as others try to obfuscate them in the weeks to come. Until then, see this conclusion from my 2013 review:

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