Alternative splicing of pre-mRNA

Food energy-dependent epigenetic adaptation (2)

Due to the overwhelming support for my model of top-down causation and all energy-dependent biophysically constrained biodiversity on Earth, I will replace
Food energy-dependent epigenetic adaptation (2)
with the more appropriately titled
God’s shrinking role in your salvation
See: Food energy-dependent epigenetic adaptation
and God’s shrinking role in your salvation (in prep)
before proceeding to the rest of this series on epigenetic adaptation.
 

Cytosis

Energy-dependent epigenetic translation to mRNA stability (6)

See: Energy-dependent epigenetic translation to mRNA stability (5)
Five energy-dependent amino acid substitutions are linked to differences in RNA content and biodiversity in 4 mammalian species.
Excerpt:

Species- and tissue-specific variation in mt-tRNA incorporation into the mt-LSU was analyzed….  Analysis of porcine dermal fibroblasts (C), human osteosarcoma 143B cells (D), bovine cardiac tissue (E), and rat hepatic tissue (F) depicts the relative abundance of each mt-tRNA across fractions (ImageQuant software); represented as a percentage of the total signal.

In my model, the metabolism of food to pheromones controls species specific and tissue specific variation in food energy-dependent mitochondrial transfer RNA (mt-tRNA) and the transgenerational epigenetic inheritance of morphological and behavioral phenotypes. In all models of biologically based cause and effect, the “RNA world” must be linked by metabolism to the pheromone-controlled fixation of RNA-mediated amino acid substitutions in supercoiled DNA. That is how the RNA world is linked from chromosomal rearrangements to energy-dependent RNA-mediated chromosomal inheritance and to protection from virus-driven energy theft, which links mutations to all pathology in species from microbes to humans.
See:  Nutrient-dependent/pheromone-controlled adaptive evolution: a model (published 2013 Jun 14)
My model of “ecological adaptation” was placed into the context of “adaptive evolution” because many theorists do not seem to understand why serious scientists do not believe in “Big Bang” cosmology or neo-Darwinian pseudoscientific nonsense about Mutation-Driven Evolution (also published 2013 Jun 14)
Anyone who tries to tell a theorist that no experimental evidence of biologically-based cause and effect supports their theories about mutation-driven evolution is not likely to see their work get past peer-review. And, when the threat to their ridiculous theories becomes known, theorists are more likely to accept criticisms of a model — even in the absence of a comparable model.
During the past 4 years, there has been no scientific support for neo-Darwinian theories and overwhelming support for the model of food energy-dependent amino acid substitutions and Darwin’s claims about “conditions of life.”
See for instance: Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization (published 2017 May 20)

…initiator-tRNA species proposed to participate in SOS reside in the cell nucleus, are found associated with supraspliceosomes (Table 2c), and appear not to be charged with an amino acid [87].

See also: Human mitochondrial ribosomes can switch their structural RNA composition

Our data demonstrate that only mt-tRNAVal or mt-tRNAPhe are found in the mitoribosomes of five different mammals, each mammal favors the same mt-tRNA in all tissue types, and strikingly, when steady-state levels of mt-tRNAVal are reduced, human mitoribosome biogenesis displays an adaptive response by switching to the incorporation of mt-tRNAPhe to generate translationally competent machinery.

The switches are food energy-dependent and they obviously link ecological variation to ecological adaptation via the Laws of Physics and basic principles of chemistry. In my model, for example, light-induced changes in hydrogen-atom transfer in DNA base pairs in solution cause initiator-transfer RNAs in the nucleus to become charged with an amino acid. Light energy-as-information subsequently appears to biophysically constrain all conditions of life in all living genera by protecting organized genomes from virus-driven energy theft and genomic entropy.
The link from quantum physics via electron resonance to quantum souls is clearer than it has ever been.
See: Electron resonance pervades the brain

Using molecular modeling, the US-Canadian team of Travis Craddock, Stuart Hameroff and Jack Tuszynski had previously shown anesthetic binding in ‘quantum channels’, non-polar arrays of amino acid pi resonance clouds, winding through microtubules.

See also: What is life when it is not protected from virus driven entropy
and
Energy as information and constrained endogenous RNA interference
An endogenous substrate was linked from the biosynthesis of RNA to endogenous RNA interference in this full text .pdf from 1963: PARTICIPATION. OF GLYCOLYSIS. AND THE CITRIC ACID CYCLE. IN NUCLEAR ADENOSINE TRIPHOSPHATE SYNTHESIS

…thymus nuclei appear to have an endogenous substrate, and some experiments are presented which suggest that this substrate is probably not glycogen or glucose.

I do not know any pseudoscientist who has linked the energy-dependent creation of nucleic acid precursors to the energy-dependent creation of new genes, or to the activation of genes via the endogenous substrate. Indeed, the fact that there is an endogeneous substrate has been ignored, unless it has been replaced by an alternative fact which was somehow linked to all biodiversity via the physiology of reproduction.
See for comparison: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”
Excerpt:

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

See for comparison: A scientist named George Church has a wild idea to upend evolution — here’s what you should know about him

Darwin explained how species evolve. Church wants to turbocharge that process by putting new genes into organisms rather than waiting around for them to evolve those genes on their own.

Darwin did not explain how species evolve. Darwin presciently linked natural selection for food energy-dependent codon optimality to RNA-mediated amino acid substitutions and the physiology of reproduction, which biophysically constrains the hecatombic evolution of all pathology. Nothing known to serious scientists suggests that new genes “evolve.”

In between tRNA and CRISPR, Church coauthored hundreds of scientific papers, from “Predicting regulons and their cis-regulatory motifs by comparative genomics” to “Characterization of Cas9-guide RNA orthologs.”

After he characterized naturally occurring energy-dependent changes in RNA orthologs, George Church refuted neo-Darwinian evolutionary theories when he and others filed this patent application. RNA-Guided Human Genome Engineering

FIG. 3A-1 and FIG. 3A-2 depict a human codon-optimized version of the Cas9 protein and full sequence of the cas9 gene insert.

Human codon-optimized changes in proteins are energy-dependent, RNA-mediated, and the changes are biophysically constrained by the food that organisms eat and the physiology of reproduction in all living genera. That fact was placed into the context of the Structural diversity of supercoiled DNA in the context of this review: Feedback loops link odor and pheromone signaling with reproduction
The review was co-authored by 2004 Nobel Laureate, Linda Buck who helped to link the sun’s anti-entropic virucidal energy to biophysically constrained cause and effect in all species that need to eat to reproduce. Richard Feynman may have been one of many others who also did that.

Richard Feynman was a Nobel prize winning Theoretical Physicist who popularized physics with his entertaining lecture style. This snippet is taken from one of his lectures in the series “The character of Physical Law” where he complains about all the different units that are used to measure the single concept of Energy.

See for comparison: George Church refutes theistic evolution

The future of genetic codes and BRAIN codes (video)

My comment on the video: Biophysically constrained genetic codes are brain codes. They link the epigenetic landscape to the physical landscape of supercoiled DNA via metabolic networks, which link energy as information to all cell type differentiation in all individuals of all living genera.

Virus-driven energy theft is linked from “gene vandalism” to epigenetically effected nutrient energy-as-information dependent RNA-mediated DNA repair.

Synthesis of nucleic acids became a “bigger deal” when Sutherland’s group showed that ultraviolet light was linked to the simultaneous de novo creation of nucleic acid precursors, which are the starting materials needed to make natural amino acids and lipids.

See also: Peter Godfrey Smith: “Other Minds: The Octopus, the Sea, and the Deep Origins…”

See for comparison:
Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge.” — Kalevi Kull
In this case, Anna Di Cosmo’s group already linked what is known about the physiology of pheromone-controlled reproduction from the gut bacteria of the octopus to the nutrient energy-dependent pheromone-controlled physiology of reproduction of the octopus. See: 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).

Her group also linked the conserved molecular mechanisms of chemical perception and gene expression in flies to consciousness in octopuses. See: Dose-Dependent Effects of the Clinical Anesthetic Isoflurane on Octopus vulgaris: A Contribution to Cephalopod Welfare via my model, albeit without citation to: Nutrient-dependent/pheromone-controlled adaptive evolution: a model or citation to Electron spin changes during general anesthesia in Drosophila.
Without an energy-dependent change in electron spin, the findings that link virus-driven energy theft to all pathology cannot be linked from cryo-EM to the biophysically constrained changes that link angstroms to ecosystems in all living genera. None of the claims that Richard Feynman made about energy, including his claims about food energy, can be linked from quantum physics to chemistry and biologically-based cause and effect via the physiology of reproduction.
Until recently, I thought that Eugene Koonin was prepared to challenge the nonsense about evolution. No other theorists seem to be willing to address the facts about energy-dependent increasing organismal complexity.
See: Riding the Evolution Paradigm Shift With Eugene Koonin

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…

Virus-driven energy theft links the degradation of messenger RNA to all pathology, which is biophysically constrained by conserved molecular mechanisms that link food energy from viral latency to all energy-dependent healthy longevity.
Watch for Koonin and other theorists to use experimental evidence of biologically-based cause and effect to eliminate the pseudoscientific nonsense about evolution touted by those who still know nothing about virus-driven pathology manifested in Alzheimer’s and other neurodegenerative diseases. Alternatively, watch for Koonin and other theorists to continue playing their evolution game until everyone who is more than one decade old learns to play this game:

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

Cytosis is a worker placement game that takes place inside a Human Cell! Players utilize the organelles within a cell to collect cellular resources such as mRNA from the Nucleus, Lipids from the Smooth E.R., ATP from the Mitochondria, etc. and score points when they use these resources to complete Hormones, Receptors or Enzymes! 2 to 5 Players, Ages 10 +, Plays in 50 to 75 mins – (Shipping Aug/Sept 2017 – US, EU, CA & AU will ship from WITHIN their country / region) 

See for comparison: How Statistics Weakened mRNA’s Predictive Power

More than 60,000 published works link food from energy-dependent changes in the microRNA/messenger RNA balance to differences in amino acid substitutions in mitochondrial transfer RNA (mt-tRNA).

The amino acid substitutions in different mammals appear to protect the mitochondria from virus-driven energy theft, which links the degradation of messenger RNA from mutations to all pathology.

The link from mt-tRNA to healthy longevity via species- and tissue-specific variation in the structure and function of supercoiled DNA may limit further consideration of neo-Darwinian theories because there is nothing to suggest that supercoiled DNA automagically evolved.

See for example: Figure 1

Species- and tissue-specific variation in mt-tRNA incorporation into the mt-LSU was analyzed….  Analysis of porcine dermal fibroblasts (C), human osteosarcoma 143B cells (D), bovine cardiac tissue (E), and rat hepatic tissue (F) depicts the relative abundance of each mt-tRNA across fractions (ImageQuant software); represented as a percentage of the total signal.

See also: Noncoding RNA Helps Cells Recover from DNA Damage

There is clear evidence that femtosecond blasts of UV light repair DNA in the context of energy-dependent changes in the microRNA/messenger RNA balance and autophagy, which protects all organized genomes from virus-driven energy theft and the degradation of messenger RNA.
The failure to integrate the Nobel Prize winning works of Ben Feringa (Chemisty 2016) and Yoshinori Ohsumi (Physiology or Medicine 2016) prevents theorists from linking what organisms eat to their pheromone-controlled physiology of reproduction in the context of Schrodinger’s claims in “What is Life?”(1944) and this claim by Roger Penrose in the reprint edition:

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: From Fertilization to Adult Sexual Behavior  In our section on molecular epigenetics, we wrote:

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans…

The food energy that is linked from alternative splicing techniques of pre-mRNA to the chemistry of protein folding and the pheromone-controlled physiology of reproduction in all living genera seems to be largely ignored by those who are not Nobel Laureates.

 

Alternative splicing of pre-mRNA

Energy-dependent epigenetic translation to mRNA stability (5)

Energy-dependent epigenetic translation to mRNA stability (4)
From Fertilization to Adult Sexual Behavior

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans….

See also: The Supraspliceosome – A Multi-Task Machine for Regulated Pre-mRNA Processing in the Cell Nucleus
Abstract conclusion:

…changes in these regulatory processing activities are associated with human disease and cancer. These findings emphasize the supraspliceosome as a multi-task master regulator of pre-mRNA processing in the cell nucleus.

Excerpt:

…the initiator-tRNA species proposed to participate in SOS reside in the cell nucleus, are found associated with supraspliceosomes (Table 2c), and appear not to be charged with an amino acid [87].

Energy-dependent regulation of the supraspliceosome and RNA-mediated amino acid substitutions is charge-regulated and the change in the charge must be linked to fixation of the amino acid substitution in the organized genomes of all living genera before energy can be linked to biologically-based cause and effect via what is known to all serious scientists about how the physiology of reproduction must be linked to biodiversity.
The changes in the supraspiceosome must then be linked from chromosomal rearrangements to morphological and behavioral diversity.
See also: New study helps solve a great mystery in the organization of our DNA, which is a report on this peer-reviewed published work: Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization

Beyond defining the functions of CTCF in chromosome folding, these results provide new fundamental insights into the rules governing mammalian genome organization.

My summary: The rules integrate what is known about energy-dependent adenosine to inosine RNA editing. See: Divergent prebiotic synthesis of pyrimidine and 8-oxo-purine ribonucleotides
Prebiotic synthesis starts with the sun’s anti-entropic virucidal energy.
See: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
RNA biosynthesis is energy-dependent and an endogenous substrate appears to be the link from sunlight to protometabolism. By starting from protometabolism, it is easy to link the energy from the innate immune system to polycombic ecological adaptations in all living genera via the physiology of reproduction.
See also: Polycomb Regulates Mesoderm Cell Fate-Specification in Embryonic Stem Cells through Activation and Repression Mechanisms

little is known about the mechanistic underpinnings of how differently composed Polycomb complexes instruct and maintain cell fate. Here we find that Mel18, also known as Pcgf2 and one of six Pcgf paralogs, uniquely regulates PRC1 to specify mesoderm cell fate in embryonic stem cells. Mechanistically, Mel18 functions as a classical Polycomb protein during early cardiac mesoderm differentiation by repressing pluripotency, lineage specification, late cardiac differentiation, and negative regulators of the BMP pathway. However, Mel18 also positively regulates expression of key mesoderm transcription factors, revealing an unexpected function of Mel18 in gene activation during cardiac differentiation. Taken together, our findings reveal that Mel18 is required to specify PRC1 function in both a context- and stage-specific manner.

The context- and stage-specific links from polycombic ecological adaptation are nutrient energy-dependent and the regulation of polycombic ecological adaptations is biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera.
See: Polycombic ecological adaptation as a science, not a theory
See also: Polycombic ecological adaptation as a science, not a theory (2)
See also: Search Results for “Polycombic ecological adaptation
For contrast, see: Is inference the best way to explain the origin of consciousness?

This conversation is connected to: Consciousness is not a thing, but a process of inference

My comments:

  1. Excerpt: “On this view, a loss of consciousness occurs whenever our models lose their ‘thickness’ and become as ‘thin’ as a virus’s.”

Consciousness is energy dependent and biophysically constrained by the ability of organisms to find food and reproduce. Consciousness is manifested as increasing organismal complexity in the context of links from quantum consciousness to quantum souls.

The fact that it took only one journalist to expose all the others who have not asked the right questions about consciousness so that the questions could be answered in the context of what is known to all serious scientists about virus-driven energy theft and all pathology is revealed here, and in the first interview from the week before.

Superbugs, Bacteriophages and Phage Therapy: An Interview with James Kohl

2. I just placed the essay on “Consciousness” into the context of “snake centric” evolution after scanning two published works by the author [Friston, Karl J.]

1) Top-Down Control of Visual Responses to Fear by the Amygdala http://www.jneurosci.org/content/33/44/17435.abstract

2) Bayesian inferences about the self (and others): A review http://www.sciencedirect.com/science/article/pii/S1053810014000105

See also: “Isbell calls these findings “the first neuroscientific support” for her snake-centric evolutionary theory.” excerpted from http://news.sciencemag.org/evolution/2013/10/did-snakes-help-build-primate-brain

For comparison see:

“Science is the belief in the ignorance of experts” — Richard Feynman

Feynman supported the efforts of those who laugh at ‘experts,’ especially when the experts are not among the serious scientists who were forced to link ecological variation to energy-dependent ecological adaptation in the context of what is now known about how to link food energy-dependent changes from angstroms to ecosystems in all living genera via feedback loops and the pheromone-controlled physiology of reproduction.

In “The Pleasure of Finding Things Out,” (see pages 124 and 125 for a summary) Richard Feynman presciently predicted that the ability to see interactions at the level of atomic energy would link quantized energy from sunlight to photosynthesis and pattern recognition by biologists, who would then link quantum physics from chemistry to the growth and movement of all organisms on Earth.
See also:

This comment was posted to my FB group on April 17, 2017
 

1) The findings reveal similarities and differences with a recently published report on the IP3R using a completely different method called cryo-electron microscopy.

2) The team identified an amino acid sequence in the leaflet that is conserved in parasites, suggesting structural insights that may assist in drug discovery for these devastating conditions.

By identifying the amino acid sequence, they inadvertently linked natural selection for energy-dependent codon optimality to all biodiversity via the biophysically constrained physiology of reproduction in the context of hydrogen-atom transfer in DNA base pairs in solution.

See also Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function as cited in:The Origin of Information: How to Solve It

Search Results for “hydrogen-atom transfer in DNA base pairs”

See also: Energy-dependent epigenetic translation to mRNA stability (5)
 

Filtering light through a prism to identify tissue type

Respiration-dependent endogenous RNA interference

If you are a theorist, please take a deep breath before beginning to read this.

The speed of light on contact with water has been linked from the level of oxygen on Earth to all biodiversity via the physiology of pheromone-controlled reproduction and the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes in all living genera.

15h15 hours ago  It’s “game over” for all theorists. There’s a new game in town. It’s an evolutionary theory killer.

12h12 hours ago Epigenetically-effected nucleosome repositioning sheds Dobzhansky’s light on evolution

Why are many mRNAs translated on or nearby mitochondria?

15h15 hours agoThanks for asking. Because otherwise one species could evolve into another species via natural selection for virus-driven energy theft.

35m35 minutes ago Replying to @jvkohl

how many times might a typical eukaryotic mRNA get translated? is it eventually degraded by RNAases? eroded from the ends?

Yes. Thanks for asking. Virus-driven energy theft degrades messenger RNA in the context of respiration and changes in pH in all cell types.

15m15 minutes ago The change to supercoiled DNA was energy-dependent. Where did the lost energy go? I need it back to support Schroedinger’s claims from 1944.

Re: Schodinger’s claims about sunlight: Practical application of the concept of energy as information sunlight.

Vitamin C is a natural antihistamine. It destroys the molecular structure of histamine, which decreases the amount of histamine in the blood. A diet that included the ingestion of leaves from the sago palm might have helped modern human populations in what is now Central China to ecologically adapt via energy-dependent changes in base pairs that link single nucleotide polymorphisms from natural selection for codon optimality to endogenous RNA interference and DNA repair via what is know about respiration in the context of the citric acid cycle.

See also: I forgot Wendy’s last name. She was a friend from Las Vegas, Nevada who died from lung cancer at an early age (38?).  We belonged to a public speaking group, which I was forced out of by my marriage in 1992, ~25 years ago.

The group was for single people only. Lung cancer has since caused the unnecessary suffering and premature death of many others because few people have learned that one energy-dependent base pair change can be linked from a single amino acid substitution to all RNA-mediated healthy longevity or from virus-driven energy theft to all pathology.

See for another example: Lkb1 inactivation drives lung cancer lineage switching governed by Polycomb Repressive Complex 2

The researchers linked sex differences in cell types to differences in the types of lung cancers. The differences were placed into the context of the nutrient energy-dependent metabolism of one amino acid, methionine. They suggest that methionine is essential to cell type differentiation in humans without placing that fact into the context of virus-driven energy theft, which links the degradation of messenger RNA from mutations to all pathology in all cell types of all living genera. It makes me very angry that they will not tell the truth about how energy-dependent endogenous RNA interference protects all organized genomes from virus-driven energy theft and genomic entropy. I’m beginning to wonder whether something more than ignorance is causing the misrepresentations of biologically-based cause and effect that are linked to the prevention and/or cure of cancer and all other pathology via nutritional epigenetics and the pheromone-controlled physiologoy of reproduction in all genera

.…one possibility is that metabolism of methionine is a link between LKB1 and EED. Studies with an inhibitor of S-adenosyl homocysteine hydrolase have demonstrated that decreased methionine metabolism can cause destabilization of the PRC2 components at the protein level61. Future studies will focus on identifying the link between the cellular genotype and the epigenetic identity of lung cancer cells from different subtypes of lung cancer…

Reported as: New study proves one lung cancer subtype can switch to another

“Now that we have a glimpse into the molecular mechanism of lineage switching, we can begin to learn how to manipulate this phenomenon for better therapeutic outcomes,” said Brainson.

My comment: In our 1996 Hormones and Behavior review we linked energy-dependent “lineage switching” to healthy longevity via alternative splicings of pre-mRNA and Polycomb.

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

See also: Thanks to everyone who helped fund the end of neo-Darwinian pseudoscientific nonsense and the end of the “Big Bang” theory. Viral latency is energy-dependent, RNA-mediated, and endogenous RNA interference is biophysically constrained by the physiology of pheromone-controlled reproduction.

The anti-entropic virucidal energy of the sun will be placed into its proper context by anyone who plays this game.

`6650 backers will receive the games and the number of biologically informed serious scientists will grow exponentially.
Anyone who plans to “March for Science” on Earth Day (April 22, 2017) is likely to be asked this embarrassing question. “Where did the energy in a hydrogen atom come from?”
Their answer will lead to a second question. “Where does the energy go when it no longer sustains the life of the organism?”
Alternative splicing of pre-mRNA

Theistic evolutionists fight back and lose (2)

For a historical perspective on the amount of ignorance theistic evolutionists and atheists have repeatedly displayed as they ignored everything known about the energy-dependent RNA-mediated de novo creation of genes, see:
The heat shock response is self-regulated at both the transcriptional and posttranscriptional levels (1982)
Thirty-five years later, there is another clear indication that theorists and atheists will never consider the fact that there must be an anti-entropic virucidal source of energy.
See for example: HSP90 Shapes the Consequences of Human Genetic Variation (2017)
Reported as: Researchers uncover a role for HSP90 in gene-environment interactions in humans

…uncovered a role for HSP90 in humans, not only as a modifier of the effects of mutations, but as a mediator of the impact of the environment on the function of mutant proteins. And these effects of HSP90 can alter the course of human diseases.

Serious scientists placed the effects of HSP90 and all other heat shock proteins into the context of thermodynamic cycles of microRNA-mediated protein biosynthesis and degradation. The fine-tuned cycles link virus-driven energy theft from the degradation of messenger RNA to all pathology via degrees of increasing genomic entropy in species from bacteria to Zika-virus infected humans.
Structural diversity of supercoiled DNA

Six decades after the elucidation of its double helical structure, DNA continues to surprise us by revealing new information. Our cryo-ET, biochemical, and computational studies show the astounding versatility and dynamism of DNA depending on the degree of supercoiling. DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases. Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

The metabolic processes are energy-dependent. See also: Functional Metabolic Analysis in Live Cells

The role of metabolism in cellular and physiological processes is well established, with many diseases now linked to metabolic dysfunction or reprogramming.

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

Our work identifies a mechanism through which adhesion complexes regulate cellular behaviour and reveals their surprising association with the microprocessor.

Reported as Researchers find new code that makes reprogramming of cancer cells possible

with my comments, such as this one:

Oct 14, 2015
“By administering the affected miRNAs in cancer cells to restore their normal levels, we should be able to re-establish the brakes and restore normal cell function,” Dr. Anastasiadis says.
This suggests nutrient-dependent microRNAs can stop the progression of virus-proliferation that links viral microRNAs to cancer pathology.
The suggestion comes from experimental evidence of how biophysically constrained nutrient-dependent RNA-mediated cell type differentiation occurs in the absence of viral proliferation, which young earth creationists have linked to all pathology.
For comparison, evolutionary theorists would probably tell you that the progression of cancer is inevitable via ongoing processes that link accumulated mutations to pathology except when beneficial mutations are linked to the evolution of a new species.
But, I can’t really attest to what theorists might say, and don’t really care what they claim. They are biologically uninformed.

See also:

See for comparison: Dominant evolutionary theme emerges to better predict clinical outcomes for cancer (October 13, 2015)
The only thing that has emerged from any evolutionary theme is the failure to predict outcomes of treatments, which is due to the ignorance of theorists who refuse to consider experimental evidence of energy-dependent biophysically constrained biologically-based cause and effect.
See: Viral and cellular messenger RNA targets of viral microRNAs and Virus-mediated archaeal hecatomb in the deep seafloor

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

Theorists continue to ignore the fact that energy-dependent biophysically constrained protein-folding chemistry, which is manifested in endogenous RNA interference, is the link from sunlight to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans.
Sunlight, for example, is the source of anti-entropic virucidal ultraviolet (UV) light that clearly links the nutrient-dependent pheromone-controlled physiology of reproduction to the weekend resurrection of the bacterial flagellum in P. fluorescens.
See also: Energy as information and constrained endogenous RNA interference (2/15/2017)

See also: A third of Americans don’t believe in evolution (January 1, 2014)
My comment:

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.

These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.
That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.
See the claims of PZ Myers and his idiot minions for comparison: One crank dies, another rises to take his place

IMG_2329-e1413855233208-958x718

Wikipedia refutes theistic evolution

RNA-Directed DNA Methylation

Besides RNA molecules, a plethora of proteins are involved in the establishment of RdDM, like Argonautes, DNA methyltransferases, chromatin remodelling complexes and the plant-specific Polymerase IV and Polymerase V. All these act in concert to add a methyl-group at the 5′ position of cytosines. In contrast to animals, cytosines at all sequence context (CG, CHG, CHH) may get de novo methylated in plants.

There is no such thing as de novo methylation. Methylation is energy-dependent. Virus-driven energy theft prevents methylation and links mutations to all pathology via everything known to young earth creationists, which some of them have been reporting since the late 1990’s. That fact explains why theorists were forced to change RNA-Directed DNA Methylation to RNA interference in a face-saving attempt. Many pseudoscientists have claimed the creationists cannot be scientists and their attacks on young earth creationists have been among the most vicious of all attacks. But now, the young earth creationists have this:

RNA interference (RNAi) RNA interference (RNAi) is a biological process in which RNA molecules inhibit gene expression or translation, by neutralizing targeted 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.

The so-called unrelated processes linked to RNAi phenomenon were place into the context of what was known about molecular epigenetics in our section on molecular epigenetics from this 1996 Hormones and Behavior review.
From Fertilization to Adult Sexual Behavior

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

The alternative splicings are energy-dependent.
See also: Contribution of epigenetic mechanisms to variation in cancer risk among tissues

Because de novo modification appears to take place almost exclusively on CpG islands that are already silenced by polycomb in the normal tissue (8), we suggest that this modification works by preventing these genes from becoming activated, thereby inhibiting normal tissue differentiation, causing clonal selection for cells that may predispose to cancer (31). Indeed, many of these methylation targets have been shown to be “driver” genes in a number of different cell types (Fig. S6).

Virus-driven energy theft prevents what they claim are the de novo modifications and the energy theft links contraint-breaking mutations from viral latency to all pathology. Only biologically uninformed pseudoscientists have continued to portray energy-dependent changes in methylation as if the changes occurred in the context of de novo modification.
See for comparison. These creationists start with energy and link it to experience-dependent cell type differentiation via what is known about sensing and signalling in all living genera.
Multipurpose plant sensors startle scientists

Evolutionary scientists did not predict such elaborate sensory integration in a single protein system.

Sensing and signalling in all living genera is links the physiology of reproduction in soil bacteria to the phyisology of pheromone-controlled reproduction in all livng genera. See for example:
The genome of Chenopodium quinoa

The TSARL1 transcript was alternatively spliced in the sweet progeny of Kurmi and 0654. A SNP in the last position of exon 3 (G2078C) co-segregates with the presence of saponins in the Kurmi × 0654 progeny. The G2078C SNP alters the canonical intron/exon splice boundary (Fig. 4e), probably leading to the alternative splicing at an upstream cryptic splice site in the sweet lines (Fig. 4e). This alternative splicing of TSARL1 results in a premature stop codon…

See also: Start codons in DNA may be more numerous than previously thought

Start codons are important to understand because they mark the beginning of a recipe for translating RNA into specific strings of amino acids (i.e., proteins).

See also: Codon optimality controls differential mRNA translation during amino acid starvation (2016)
They help to make the fact clear that all organisms must eat.
See also:Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (2016)
They make it clear that the bias between codons or amino acids, and mRNA expression is the link from natural selection for energy as information that links the selection of food to efficient, accurate translation, and folding of  expressed genes.  Simply put, the energy-dependent amino acid optimality code  differentiates between theories of evolution and facts about how ecological variation must be linked to ecological adaptation via the physiology of pheromone-controlled energy-dependent reproduction and supercoiled DNA in all living genera.
Obviously, pseudoscientists who cannot link energy-dependent changes in codon optimality have indirectly been responsible for all virus-driven pathology because they failed to link the viral hecatomb from archaea to the transgenerational epigenetic inheritance of Zika virus-damaged DNA or to all other pathology, including cancer and degenerative diseases.
Thank God, Bill Gates and President Trump are among the billionaires who have decided to help others who have been combating evolutionary theorists to fight disease for several decades.
See also: Combating Evolution to Fight Disease

Alternative splicing of pre-mRNA

Dobzhansky 1973 and Precision Medicine (2)

What Did Neanderthals Leave to Modern Humans? Some Surprises

A few years ago, the Swedish geneticist Svante Paabo received an unusual fossilized bone fragment from Siberia. He extracted the DNA, sequenced it and realized it was neither human nor Neanderthal.

Savante Paabo co-authored this refutation of neo-Darwinian nonsense in 2003.Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees

It links natural selection for energy-dependent codon optimality from the pheromone-controlled physiology of reproduction in species from archaea to humans via what is known to serious scientists about the de novo creation of olfactory receptor genes. He also co-authored this article: Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates It links the virus-driven energy theft to the mutation-driven loss of G protein-coupled receptors in all cell types of all individuals of all living genera.

John Anthony Capra, the expert on what Neanderthals left to modern humans is probably aware of this fact: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

One energy-dependent RNA-mediated amino acid substitution was linked from G protein-coupled receptors to differences in morphological and behavioral phenotypes and the “personality” difference in human adolescents compared to adults. Dobzhansky (1973) put that fact into the context of other facts that link fixation of amino acid substitutions to all cell type differences in all individuals of all living genera.

For example, the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).

The problem with this fact manifests itself in attempt by pseudoscientists to ignore it. At the same time, all serious scientists have place the facts into their perspectives on hemoglobin variants such as the hemoglobin S variant.

Genetic Variations: Heroes or Villains

Variations have not only been associated with diseases like cancer, turner syndrome, sickle cell anaemia, cystic fibrosis etc., but some of them have even been proved to be beneficial in certain cases like for increasing bone density, lowering down cholesterol level, and for developing malaria resistance.

Many pseudoscientists did not learn that there are now more that ~1200 hemoglobin variants, or that sickle cell anemia is an example of an ecological adaptation. Some have learned not to refer to variants as mutations in the context of mutation-driven evolution. But past claims about mutations and evolution have become a nightmare scenario for anyone who has ever made them.

What Did Neanderthals Leave to Modern Humans? Some Surprises (revisited)

But I received racist inquiries, too. I got calls from all over the world from people who thought that since Africans didn’t interbreed with Neanderthals, this somehow justified their ideas of white superiority.

What happens next will be more interesting. As people like John Anthony Capra and Svante Paabo try to extricate themselves from the muck of ridiculous theories, which they nearly let engulf them, they will be forced to start naming names. The people who taught them to believe in pseudoscientific nonsense about mutations and evolution will be reviled instead of revered for their expertise.  Ultimately, works by people like Masatoshi Nei will be viewed as if they were published by people who were biologically uninformed.

See for example: The neighbor-joining method: a new method for reconstructing phylogenetic trees(1987)

For comparison, see: Genomic locations of conserved noncoding sequences and their proximal protein-coding genes in mammalian expression dynamics (2016)

Naruya Saitou is the first author of the 1987 revised theory and the senior author of the accurate representations of biologically based cause and effect from 2016.

His co-author Masatoshi Nei published Mutation-driven evolution on the same day in 2013 that my review of everything known to serious scientists about biologically-based cause and effect was published. Nutrient-dependent/pheromone-controlled adaptive evolution: a model

See also: We are all mutants

Every part of our body is controlled by molecules, so you have to explain on a molecular level. That is the real mechanism of evolution, how molecules change. They change through mutation. Mutation means a change in DNA through, for example, substitution or insertion [of nucleotides]. First you have to have change, and then natural selection may operate or may not operate. I say mutation is the most important, driving force of evolution.

The changes are nutrient energy-dependent and RNA-mediated in the context of chromosomal rearrangements and the pheromone-controlled physiology of reproduction.

See for confirmation: Spliceosomal intronogenesis

The group II intron-derived features are likely to have degenerated over time, leading to a necessity for the development of the pre-mRNA splicing machinery composed of trans-acting snRNAs and trans-acting protein factors (11, 18). Within this context…
 
Every aspect of energy-dependent RNA-mediated life on Earth occurs “within this context.” Life is energy-dependent and biophysically constrained by the pre-mRNA splicing machinery in the context of the physiology of reproduction and chromosomal rearrangements.
See also: From Fertilization to Adult Sexual Behavior (1996)

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

The sex difference in cell types have since been linked via conserved molecular mechanisms to all differences in all cell types of all individuals in all living genera.

Virus-driven energy theft was rarely considered since the time of our 1996 review. It has now been linked from communication among viruses to nutrient-dependent pheromone-controlled ecological adaptation in species from archaea to humans. Archaea and Zika virus-damaged DNA of human infants exemplify how virus-driven energy theft links degenerated mRNA from failed DNA repair to differences in species of bacteria and difference between non-human primates and modern humans.

See also: Quantum leap: Physicists can better study the quantum behaviour of objects on the atomic scale.

…quantum behaviour: a microscopic mirror in a quantum superposition, created through interaction with a photon, would involve about 1014 atoms. And, letting their imaginations run wild, researchers have proposed a method to do the same with small biological structures such as viruses.

The quantum leap has never been imaginary. Schrodinger recognized that it was energy-dependent and many others have linked energy-dependent changes in angstroms to ecosystems. Theorists have been left with no excuses for their ignorance, which is still displayed in video representations such as this one.

See also:

See also: The tipping point? 50, 000 publications

Did Dobzhansky see the UV light of creation?

ALPHA GENOMIX

Conclusion from 2): “The ability to recognize endogenous RNAs within complex mixtures with high affinity and in a programmable manner paves the way for direct transcript detection, analysis and manipulation without the need for genetically encoded affinity tags.”

That ability to recognize endogenous RNAs within complex mixtures shows up in Alpha Genomix testing, which represents a quantum leap forward from what many experts inaccurately attribute to mutations, natural selection, and evolution. Instead, Alpha Genomix is leading the way by incorporating what is currently known about RNA-directed DNA methylation and RNA-mediated events that link enzymes to amino acid substitutions that differentiate cell types.

Evolving DNA before RNA

Any discovery that links a chain of evolutionary events to anything  known about gains and losses of abilities attributed to biologically-based cause and effect would be remarkable. So far, not even one evolutionary event has been described. Thus, linking the dawn of life to the food on our tables via evolutionary theory would represent a quantum leap from a ridiculous theory to what is known about biological facts by serious scientists.

For example, quantum physics is linked to quantum biology via a light-induced amino acid substitution that links cell type differentiation in plants from ecological variation in light-dark cycles to RNA-directed DNA methylation and RNA-mediated amino acid substitutions.

Order and disorder: Ecological adaptations not mutations

A microRNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides). Thus, the quantum leap from biophysically constrainted light-induced amino acid substitutions to the nutrient-dependent microRNA/messenger RNA balance that controls genome stability via epigenetically-effected amino acid substitutions is replaced with the concept of epigenetically-effected mutations, which are called epimutuations.

By mixing the theory of mutation-initiated natural selection and the evolution of biodiversity with biological facts about how ecological variation leads to epigenetically-effected ecological adaptations manifested in biodiversity, the senior author of the “epimutations” article sets the stage for his claim to be “the first” to find something new and important.

Alternative splicing of pre-mRNA

Autophagy: from pre-mRNAs to microRNAs, enhancers, QTLs et al.

Nothing known to serious scientists links anything except energy-dependent changes in chirality to autophagy and biodiversity via RNA-mediated amino acid substitutions that differentiate all cell types in all living genera. That fact forces pseudoscientists to invent new terms to confuse the biologically uninformed masses who were taught to believe in the neo-Darwinian pseudoscientific nonsense of mutation-driven evolution.
Autophagy in the liver: functions in health and disease 
See the section: Regulation of autophagy by amino acids

See for comparison: From Fertilization to Adult Sexual Behavior

Excerpt from our section on molecular epigenetics.

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

My family members and friends of Robin Williams might be appalled to learn that death from Parkinson’s and death from Lewy Body Disease both include instances of suicide that is caused by untreated virus-driven energy theft. The virus-driven energy theft also is the cause of all pathology in species from archaea to humans. It is manifested as energy-dependent changes in alternative splicings of otherwise identical genes.

The prevention of unnecessary suffering and death could be as simple as restoring the balance of amino acids and sugar to prevent all pathology via RNA-mediated cell type differentiation.

That’s not going to happen without some discussion of what is known to serious scientists about the links from angstroms to ecosystems. All of them are energy-dependent. So, “go ahead,  make my day!”

Ask your professors where the energy came from and how it is linked to the changes in pH that predict when difference in healthy longevity become differences in the types of pathology via links from autophagy to supercoiled DNA or to negative supercoiling.

See also: Processing and transcriptome expansion at the mRNA 3′ end in health and disease: finding the right end

This review suggests the term “pre-mRNA” changed to “microRNA” as serious scientists learned more about how energy-dependent cell type differentiation was biophysically constrained.

We illustrate the medical importance by presenting examples that are associated with perturbations of this process and indicate resulting implications for molecular diagnostics as well as potentially arising novel therapeutic strategies.

This was ~20 years after we linked alternative splicings of pre-mRNA to all cell type diversity via the pheromone-controlled physiology of reproduction in yeasts at the advent of energy-dependent sexual reproduction.

See also: Implications of polyadenylation in health and disease

This review addresses the key steps of polyadenylation and alternative polyadenylation in different cellular conditions and diseases focusing on the molecular effectors that ensure a faultless pre-mRNA 3′ end formation.

Watch as researchers continue to invent new names for the molecular effectors in attempts to obfuscated the facts about biophysically-contrained protein folding chemistry that have been known to all serious scientists since Schrodinger (1944) linked the anti-entropic energy of the sun to all biodiversity.

Epigenetic (re)programming of caste-specific behavior in the ant Camponotus floridanus

Abstract excerpt:

Eusocial insects organize themselves into behavioral castes whose regulation has been proposed to involve epigenetic processes…

Research article summary excerpt:

…behavioral plasticity can be manipulated in the ant C. floridanus by pharmacological and genetic tools that target chromatin regulatory enzymes to stimulate, inhibit, and reprogram behavior. These findings reveal the epigenome as a likely substrate  underlying caste-based division of labor in eusocial insects.

Conclusion:

…our ability to alter a canonical altruistic behavior in a truly social organism by experimental perturbation of a single gene suggests that the application of increasingly versatile reverse genetic approaches in eusocial insects will allow us to expose the general organizational principles underlying complex social systems (10).

See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
All general organizational principles underlying complex social systems are nutrient-dependent and pheromone-controlled in the context of the regulation of gene expression that enables the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes.

‘Mysterious’ non-protein-coding RNAs play important roles in gene expression

Berger and Daniel Bose, PhD, a postdoctoral fellow in her lab, study the regulation of gene expression from enhancers, non-coding regions of the genome more distant from protein-coding regions.

The only mystery should focus on why they thought they could continue to suppress the facts by referring to natural selection for energy-dependent codon optimality in terms like “enhancers.” Since 2013, everything known to serious scientists about nutrient-dependent microRNAs has been linked to all healthy longevity and virus-driven energy theft has been linked to to all pathology. Serious scientists are not using the term “enhancer.” See for example any of the 56,000 published works that use the term “MicroRNA

Ask why Phys.org / Medical Xpress must report old news from 2013 in the context of unpublished research by two people who cannot be found on the PubMed indexed list of research that links sunlight from chirality to autophagy and chromosomal rearrangements to all biodiversity via energy-dependent changes in the microRNA/messenger balance, which link supercoiled DNA to the protection of all organized genomes from virus-driven entropy.

See: Enhancer RNAs alter gene expression: New class of molecules may be key emerging ‘enhancer therapy’

Enhancers are sequences in the genome that act to boost or “enhance” the activity or expression of nearby genes. They “often behave in a cell-specific manner and play an important role in establishing a cell’s identity and functional potential,” said Christopher Glass, MD, PhD, a professor in the department of Medicine and Cellular and Molecular Medicine at UC San Diego and principal investigator of one of the papers.

Although enhancers have been recognized for more than 25 years, scientists have labored to fully flesh out the breadth and complexity of what enhancers do and how they do it. In 2010, it was discovered that enhancers directed expression of RNA on a broad scale in neurons and macrophages, a type of immune system cell. Dubbed eRNAs…

I do not know any serious scientists who accepts the term invented to replace pre-mRNAs after the term microRNAs was introduced at the turn of this century and more than 56,000 published papers now use the term microRNA in the context of links from metabolic networks to genetic networks in all living genera via non-coding RNAs..

SnapShot: Non-coding RNAs and Metabolism

In recent years, understanding the crucial role played by cellular homeostasis in disease initiation and progression became the focus of scientists and clinicians. This SnapShot sketches the involvement of both short microRNAs and long ncRNAs in the major metabolic pathways altered in diseases.

Functional Importance of eRNAs for Estrogen-dependent Transcriptional Activation Events

Who do they think does not know that the functional importance of microRNAs and the functional difference of eRNAs is the same. eRNAs are the term theorists use for microRNAs.

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

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

See also: SPECIAL ISSUE—THE ZIKA VIRUS GLOBAL PANDEMIC: THE LATEST EMERGING INFECTION
Placental Pathology of Zika Virus: Viral Infection of the Placenta Induces Villous Stromal Macrophage (Hofbauer Cell) Proliferation and Hyperplasia

It is still not well understood what role(s) the Hofbauer cell has in facilitating or inhibiting transplacental transmission of infectious agents such as the Zika virus. However, based on the demonstration in this communication of proliferation and prominent hyperplasia of Hofbauer cells in the placenta from a microcephalic fetus infected early in gestation, the identification of residual Zika virus in villous stromal cells, using an RNA probe, and the previously published results of in vitro infection and replication of Zika virus in human Hofbauer cells, it appears highly probable that the Hofbauer cell has an important, or even primary, role in those cases where transplacental transmission of the Zika virus does occur. The unexpected absence in placental tissues of any necrosis or leukocytic response by the mother or fetus to transplacental Zika virus infection is also interesting and of unknown significance.

The absence of a response in the organized genomes of the host clearly indicates ecological adaptation to the virus has already occurred and the supercoiled DNA of the host helps to protect a host from DNA damage. The infants are comparatively unprotected. If they survive to reproduce, and their bones turn up in what a future paleontologist thinks is a fossil record that spans hundreds of thousands of years, the paleontologist would almost undoubtedly claim to have found a new species of non-human primate.
For comparison, all serious scientists known that energy-dependent autophagy is the link to supercoiled DNA, which protects all organized genome from virus-driven energy theft and genomic entropy.
Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

human-evolution

Vietnam Veterans and others with glioblastoma

The Agent Orange Widows Club

After their husbands died of an aggressive brain cancer, the widows of Vietnam veterans have found one another as they fight the VA for benefits.

See also: Vietnam Veterans with Glioblastoma Multiforme Stage 4 Brain Cancer
This post was removed:

Targeting NF-κB in glioblastoma: A therapeutic approach

This is the level of complexity that the VA needs to understand and link to the treatment of this aggressive cancer, which is obviously caused by virus-driven energy theft. When the VA understands that, the treatment will open the floodgates of litigation for all the pathology in every veteran who ever served overseas and failed to adapt to the viruses encountered during the stressful conditions of war.

“…we used the NBD peptide, a peptide corresponding to the NEMO binding domain that specifically inhibits the induction of NF-κB activity (15). The NBD peptide has been used previously to inhibit inflammation in animal models such as acute inflammation in carrageenan-induced mouse paw edema and collagen-induced arthritis (31) or Duchenne muscular dystrophy (13). One of our main reasons for choosing the NBD peptide to treat GBM is the reported ability of NBD to enter into the CNS and exert an effect on NF-κB activation in a mouse model of Parkinson’s disease (14). Indeed, our results show that NBD treatment of mice with GBM significantly extended their survival, probably as a result of the specific inhibition of NF-κB not only in the tumor cells but also in the tumor microenvironment.”

My conclusion: Even if the VA understands what all serious scientists have learned about energy-dependent biophysically constrained biologically-based cause and effect, liberal academics will continue to try to prevent dissemination of accurate information. The facts about virus-driven energy theft compared to nutrient energy-dependent ecological adaptation refute every aspect of neo-Darwinian nonsense that is still being taught to your children and grandchildren if they are attending public schools.

Grady was the first person to get the treatment dripped through a tube into a space in the brain where spinal fluid is made, sending it down the path the cancer traveled to his spine.

This makes me wonder how Jimmy Carter’s brain cancer was cured. So far as I know, the cure must link genetically engineered cell type differentiation from viral latency in the cells dripped into the brain to the natural information processing.

Natural information processing can then link natural selection for energy-dependent codon optimality from base pair changes to RNA-mediated amino acid substitutions that stabilize the supercoiled DNA of all living genera, and prevent the accumulation of virus-caused mutations.

See for instance: DNAM-1-based chimeric antigen receptors enhance T cell effector function and exhibit in vivo efficacy against melanoma.

CAR is the acronymn for chimeric antigen receptor. See for an example of how CAR-T cell treatment must link energy-dependent changes in the microRNA/messenger RNA balance of the mouse model organism to vial latency via the anti-EGFRvIII chimeric antigen receptor.

Expression of miR-17-92 enhances anti-tumor activity of T-cells transduced with the anti-EGFRvIII chimeric antigen receptor in mice bearing human GBM xenografts

CONCLUSION:
These results warrant the development of novel CAR-T-cell strategies that incorporate miR-17-92 to improve therapeutic potency, especially in patients with GBM [glioblastoma].

Targeting NF-κB in glioblastoma: A therapeutic approach (revisited)

We have established a lentivirus-induced mouse model of malignant gliomas, which faithfully captures the pathophysiology and molecular signature of mesenchymal human GBM.

See also: MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination

Now that treatment is based on what was learned about virus-driven energy theft in the mouse model organism, how much longer will it be before viruses are linked to all pathology via changes in the microRNA/messenger RNA balance that clearly link virus-driven messenger RNA degradation to tissue-type specific pathology in all cells of all living genera?

See also: A Constitutive Intrinsic Inflammatory Signaling Circuit Composed of miR-196b, Meis2, PPP3CC, and p65 Drives Prostate Cancer Castration Resistance

Reported as: Scientists uncover new way to defeat therapy-resistant prostate cancer

In addition to IκBα/NF-κB, the signaling circuit includes the microRNA miR-196b-3p, Meis2 and PPP3CC. While miR-196b-3p promotes tumor development, Meis2, which is an essential developmental gene in mammals, can disrupt the circuit when overexpressed. The protein PPP3CC can inhibit NF-κB activity in prostate cancer cells.

The likelihood that all signaling circuits include either nutrient energy-dependent microRNAs, which are linked to healthy longevity or viral microRNAs that are linked from virus-driven energy theft to pathology peaked at the time that more than 50,000 published works had reported on differences in microRNAs that linked hydrogen-atom transfer in DNA base pairs in solution to healthy longevity or to all pathology. (May 2016)

See for comparison: microRNA. On December 29, 2016 there were more than 56,600 published works.

rp_levels-of-organization.jpg

Energy-dependent sensory maps (1996-2016)

Developmental broadening of inhibitory sensory maps

My summary: They help to detail how olfactory input causes the energy-dependent de novo creation of sensory maps, which are representations of the external world. The experience-dependent representations link chemotaxis and phototaxis to biophysically constrained behavior. The representations are systematically organized in brain structures throughout development. Simply put, the maps are links from the epigenetic landscape to the physical landscape of supercoiled DNA in organized genomes.
By investigating how ongoing neurogenesis in the mouse olfactory bulb is linked to existing circuitry, they found differences between excitatory and inhibitory neuronal networks. This led them to compare functional responses of both maturing and established granule cells. They confirmed previously observed refinement of excitatory maps but also found that inhibitory sensory maps became broader during experience-dependent maturation.
Abstract conclusion:

These data describe the development of an inhibitory sensory map as a network, highlighting the differences from previously described excitatory maps.

Summary: Energy-dependent RNA methylation links RNA-directed DNA methylation from learning and memory to the stability of the sensory maps.
See this report from 2005: Feedback loops link odor and pheromone signaling with reproduction

At least 10,000 neurons in 26 different brain areas appear to transmit signals directly to GnRH neurons. Among these are areas involved in odor and pheromone processing, sexual behavior, arousal, reward, and other functions. This suggests that GnRH neurons are poised to modulate reproductive physiology and behavior in accordance with the overall state of the animal.

See also:

…noradrenergic, dopaminergic, serotoninergic, and opiotergic pathways; inhibitory neurotransmitters (e.g., gamma aminobutyric acid) and excitatory amino acids (e.g., glutamic and aspartic acids); and other brain peptides including pineal secretions (melatonin) and corticotrophin releasing hormone, and the complex interactions among them are subtle but functional species-specific influences on the electrochemical transmission of neuronal signals that the hypothalamus translates to the chemical signal GnRH. Puberty: ontogeny, neuroendocrinology, physiology & disorders (1992, p. 1164)

–as cited in Kohl (2006) The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences (author’s copy) and in Handbook of the Evolution of Human Sexuality (2007, p. 350)
Pseudoscientists have ignored the fact that energy-dependent autophagy links the innate immune system to the de novo creation of G protein-coupled receptors (GPCRs). For example, achiral glycine in position 6 of the GnRH decapeptide links energy-dependent excitatory and inhibitory neuronal networks to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.
See for comparison: Novel candidate genes underlying extreme trophic specialization in Caribbean pupfishes

This greater phenotypic distance is primarily due to the large jaws of scale-eaters (Fig. S1B). Orr’s extension of Fisher’s geometric model predicts that de novo mutations with a large effect on phenotypic variation are more likely to be fixed during adaptation toward distant phenotypic optima than nearby optima (Orr 1998; Orr 2005). Based on this model, we predict more large-effect variants mediated the transition from generalist to scale-eater due to the greater phenotypic distance across the fitness valley separating these species.

Reported as: Jawing away: Bahama pupfish study identifies candidate genes driving food-niches

…each, through subtle jaw size differences, has carved out its own food niche —- all within the last 10,000 years. They specialize by their jaw size and food—algae, snails or quick-striking scale-eaters —- that like Darwin’s finches, reflect differences in seed choices by the size and shape of their beaks.

They claim their ridiculous theory of greater phenotypic difference extends to a model of how fixed de novo mutations predict what happened during 10,000 years of evolution in three variants of one vertebrate species. Their ridiculous theory can be compared to the works of serious scientists who have linked energy-dependent changes from angstroms to ecosystems in all living genera via food odors and pheromones.
For a comparison to energy-dependent changes in amino acid substitutions among three primate species, see: Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973)

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).”

Dobzhansky (1973) included more information on the importance of these nutrient energy-dependent RNA-mediated amino acid substitutions. He wrote:

Cytochrome C is an enzyme that plays an important role in the metabolism of aerobic cells. It is found in the most diverse organisms, from man to molds.

E. Margoliash, W. M. Fitch, and others have compared the amino acid sequences in cytochrome C in different branches of the living world. Most significant similarities as well as differences have been brought to light. The cytochrome C of different orders of mammals and birds differ in 2 to 17 amino acids, classes of vertebrates in 7 to 38, and vertebrates and insects in 23 to 41; and animals differ from yeasts and molds in 56 to 72 amino acids. Fitch and Margoliash prefer to express their findings in what are called “minimal mutational distances.” It has been mentioned above that different amino acids are coded by different triplets of nucleotides in DNA of the genes; this code is now known.

Dobzhansky (1973) may have knowingly linked light-induced energy-dependent changes in enzymes from Schrodinger’s claims about the anti-entropic energy of sunlight to selection for codon optimality via the “minimal mutational distances” reported in the context of Fitch and Margoliash (1967). But Dobzhansky reported the energy-dependent differences in the context of a model of links from energy-dependent changes in single nucleotide polymorphsims to amino acid substitutions. That fact should cause all pseudoscientists to wonder why Dobzhansky (1973) framed his review of cell type differentiation as an example of the need to start with an anti-entropic energy source.
Why did he choose this title: Nothing in Biology Makes Any Sense Except in the Light of Evolution Did he know that sunlight is the energy source for all biodiversity, or was he guessing?
See also my comments on: Combating Evolution to Fight Disease
For comparison to everything now known about energy-dependent RNA-mediated amino acid substitutions and cell type differentiation, Fitch and Margoliash (1967) determined the minimal mutation distance between two cytochromes in the context of a definition, which was linked from what they thought would be

“…the minimal number of nucleotides that would need to be altered in order for the gene for one cytochrome to code for the other. This distance is determined by a computer making a pair-wise comparison of homologous amino acids (8).”

Simply put, first they dismissed the need for an anti-entropic energy source. Then they took de Vries definition of “mutation” and linked energy-dependent changes in RNA-mediated amino acid substitutions to morphological phenotypes. They failed to link the energy-dependent changes in RNA-mediated amino acid substitutions to the physiology of reproduction, which is the only way to link the energy-dependent changes in morphology to changes in behavior.
If others had not linked the changes to reproductive sexual behavior, Linda Buck, who is the co-author of Feedback loops link odor and pheromone signaling with reproduction might never have linked every aspect of energy-dependent cell type differentiation to odors and pheromones. See for example: From Fertilization to Adult Sexual Behavior.

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans…

All serious scientists now know that the 2004 Nobel Laureate in Physiology or Medicine, Linda Buck clearly linked energy-dependent autophagy from substitution of achiral glycine in GnRH to all vertebrate biodiversity. With co-authors, she integrated what is known about the nutrient energy-dependent pheromone-controlled physiology of excitatory and inhibitory metabolic and genetic networks reproduction in yeast to non-human primates and humans.
If there is any experimental evidence that supports claims about 10,000 years of evolution and trophic specialization in Caribbean pupfishes or any other species, I have not seen it. All experimental evidence supports Dobzhansky’s claims and the claims of all others who have linked the anti-entropic virucidal energy of the sun to healthy longevity and also linked virus-driven energy theft to all pathology.
See also: Vietnam Veterans and others with glioblastoma