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

Is meat protein unhealthy? (2)

See also: Microbiome-Grade DNA Extraction Kits

…the thermal and chemical methods effectively lyse the gram-negative organisms and boost their population in the final profile, amplifying the bias.

This suggests that all links from food energy-dependent de novo creation of the pheromone-controlled biophysically constrained bull sperm microRNAome have been misinterpreted in the context of virus-driven fescue toxicosis.

The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

…the miRNA profile of mature ejaculated sperm may in fact have downstream consequences upon embryonic development. The potential for sperm miRNA affecting zygote development has recently been reported in the literature [18] and has interesting implications for the use of sperm miRNA profiles as indicators of potential male fertility.

Fescue toxicosis links the virus-driven creation of enzymes to the degradation of messenger RNA in bull sperm and to the transgenerational epigenetic inheritance of mutations, which all serious scientists have linked from damage to supercoiled DNA to all pathology in humans and other species.

Eating the meat from other animals that have not ecologically adapted to the virus-driven theft of quantized energy has been linked from the viruses in their genomes to human pathology via the degradation of messenger RNA in bacteria that become archaea and L-forms.

See also: Dobzhansky (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.

See also: The Breadth of Viruses in Human Semen

The presence of viruses in semen is probably more widespread than currently appreciated, and the absence of virus in genital secretions should not be assumed for traditionally non–sexually transmitted viruses. The investigation of virus detection and persistence in semen across a range of viruses is useful for clinical and public health reasons, in particular for viruses that lead to high mortality or morbidity rates or to epidemics.

No serious scientist has ever reported a link from the Virus-mediated archaeal hecatomb in the deep seafloor to the evolution of anything except pathology. All serious scientists have, for comparison, linked ecological variation to food energy-dependent  polycombic ecological adaptations via biophysically constrained viral latency in species from microbes to humans.

From Fertilization to Adult Sexual Behavior (1996)

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…

See also: Cytosis: A Cell Biology Board Game for ages 10+

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

5th-6th Sept 2018 Dublin, Ireland

Is meat protein unhealthy? (1)

Patterns of plant and animal protein intake are strongly associated with cardiovascular mortality
Reported as: Meat protein is unhealthy, but protein from nuts and seeds is heart smart

In the context of everything known about how the creation of anti-entropic virucidal light must be linked to all biodiversity on Earth, watch this ridiculous misrepresentation of the honeybee model organism. Food energy-dependent microRNA-mediated pheromone-controlled biophysically constrained viral latency is portrayed as if visual input was most important.

Bee swarms work like giant brains

See instead:

RNA-mediated nutritional psychiatry

RNA-mediated nutritional psychiatry (2)

Psychophysical Laws of Biology: RNA-mediated nutritional psychiatry (3)

Learn how to prevent more school shootings via what is known about how the “Psychophysical Laws” of Biology are linked to food energy-dependent biophysically constrained behaviors via microRNA-mediated cell type differentiation and the fixation of RNA-mediated amino acid substitutions like COMT Val158Met during the transition from adolescence to adulthood.

Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults (Epub Oct 16 2014)

Alternative splicing of pre-mRNA

Agilent technology and energy-dependent autophagy

The first step towards understanding the link from the creation of energy to metabolism-related cellular function is called energy phenotyping. It requires the  technology to measure energy-dependent changes in RNA-mediated metabolic switches via the RNA interference (RNAi) screening strategy. Endogenous RNAi must then be linked  to the prevention of the virus-driven degradation of messenger RNA that causes all pathology.
Scientists discover possible master switch for programming cancer immunotherapy

…they employed an RNA interference screening strategy which can test the actual function of thousands of factors simultaneously.

See also: Energy as information and constrained endogenous RNA interference (video 6:46 minutes)
Abstract:

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection. This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

See also: Measuring the Metabolic Switch in Cancer Cells – Agilent (pdf)

Yoshida used TRAP1-null cells and transient TRAP1 mutants on an Agilent Seahorse XF96 Analyzer to show that TRAP1 regulates a metabolic switch between oxidative phosphorylation and aerobic glycolysis in immortalized mouse fibroblasts and in human tumor cells. TRAP1 deficiency promotes increased mitochondrial respiration, fatty acid oxidation, accumulation of TCA intermediates, ATP, and ROS, while suppressing glucose metabolism.

The virus-driven degradation of messenger RNA is the only perfectly obvious reason for changes in oxidative phosphorylation and aerobic glycolysis that prevent the metabolism of glucose. Natural selection for energy-dependent codon optimality links the creation of energy to the metabolism of glucose via the creation of enzymes that metabolize food energy. Energy-dependent RNA-mediated error-free DNA repair and fixation of amino acid substitutions is required to link the creation of enzymes and the species-specific production of pheromones from the physiology of reproduction to biophysically constrained viral latency and all morphological and behavioral phenotypes in all living genera.
In that context, energy-dependent natural selection for codon optimality links biologically-based cause and effect from hydrogen-atom transfer in DNA base pairs in solution to the transgenerational epigenetic inheritance of healthy longevity. For contrast, the virus-driven theft of quantized energy links changes in non-coding RNAs to all pathology.
For example, see: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene
See also: A Concise Review of MicroRNA Exploring the Insights of MicroRNA Regulations in Bacterial, Viral and Metabolic Diseases
The link from the virus-driven theft of quantized energy to glioblastoma may be the best example of how viruses are readily linked to the cell death gene in all cell types of all individuals of all living genera. That fact is more obvious with further examination of details provided for free in book chapters from Codon Publishing.
See: Noncoding RNAs in Glioblastoma  Free book chapter from Codon Publishing

The vast majority of the human genome is transcribed into noncoding RNAs. Among these, microRNAs (miRNA) and long noncoding RNAs (lncRNA) are frequently deregulated in cancer, where they regulate a wide variety of functions.

See also: Epigenetic Mechanisms of Glioblastoma Free book chapter from Codon Publishing

Aberrant DNA methylation is a common event in the genesis and progression of tumors. The application of next-generation sequencing enables the identification and mapping of DNA methylation and its derivatives, 5fC and 5hmC, to base-pair resolution. This chapter describes nine novel hypermethylation genes and six hypomethylation genes, identified by constructing a DNA methylation profile, in glioblastoma. Abnormal promoter methylation and histone modifications were associated with differential expression of miRNAs in glioblastoma: miR-185 reversed global DNA methylation and the methylation level of the hypermethylation genes by targeting DNMT; and miR-101 regulated histone methylation of hypomethylation genes by targeting EED, EZH2, and DNMT3A. The long noncoding RNA CASC2c directly bound to miR-101 via microRNA response elements, and there was a reciprocal repression between CASC2c and miR-101. Despite being competitors they both led to the overexpression of their target hypomethylation genes CPEB1, PRDM16, and LMO3. Taken together, glioblastoma is a complicated pathological process with deregulated methylation and histone modifications. Focal differentially methylated region and differentially methylated site studies will be helpful for the identification of regulatory elements of transcription. Studies of intragenic and distant intergenic alterations in DNA methylation will help elucidate the nature of epigenetic deregulation in glioblastoma.

The Seahorse XF Cell Energy Phenotype Test kit is a simple assay kit that simultaneously measures the two major energy producing pathways in live cells – mitochondrial respiration and glycolysis, allowing rapid determination of energy phenotypes of cells and investigation of metabolic switching.
The simultaneous measurement of two major energy-producing pathways in live cells allows serious scientists to report their findings in the context of what is known about mitochondrial respiration and glycolysis. Glycolysis is epigenetically effected and RNA-mediated. No magic of evolution or nonsense about natural selection for anything except food and reproduction is required to explain how rapid metabolic switching determines whether or not viral latency is biophysically constrained across the time-space continuum.
See: From Fertilization to Adult Sexual Behavior (1996)

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: Epigenetic modifications poster (Abcam)
Also from Abcam: Mechanisms of Recombination conference
The bottom line is The secret to safe DNA repair  (2015)

…if you don’t have this enzyme, then this error-free repair is stopped. You can’t do it. If you can’t do the error-free repair, among other things that happen is that you expect these cells to be cancer prone.

Clearly, the creation of the enzyme is energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction. Pseudoscientists seem to know nothing about that, and most serious scientists are not telling you the facts that link the virus-driven degradation of messenger RNA to the “death gene” via the mechanisms that fail during recombination.
But see: microRNA autophagy  and also see: See:  Agilent Seahorse XF Publications Alert for December 2017
Selected publications
Autophagy maintains the metabolism and function of young and old stem cells
Ho, T. T., Warr, M. R., Adelman, E. R., Lansinger, O. M., Flach, J., Verovskaya, E. V., Figueroa, M. E. and Passegue, E.
Nature. 2017 Mar 9, 543 (7644):205-210.
Involvement of autophagy in the outcome of mitotic catastrophe
Sorokina, I. V., Denisenko, T. V., Imreh, G., Tyurin-Kuzmin, P. A., Kaminskyy, V. O., Gogvadze, V. and Zhivotovsky, B.
Sci Rep. 2017 Nov 6, 7 (1):14571.
Sugar or Fat?-Metabolic Requirements for Immunity to Viral Infections
Shehata, H. M., Murphy, A. J., Lee, M. K. S., Gardiner, C. M., Crowe, S. M., Sanjabi, S., Finlay, D. K. and Palmer, C. S.
Front Immunol. 2017 Oct 16, 8:1311.
System-wide Benefits of Intermeal Fasting by Autophagy
Martinez-Lopez, N., Tarabra, E., Toledo, M., Garcia-Macia, M., Sahu, S., Coletto, L., Batista-Gonzalez, A., Barzilai, N., Pessin, J. E., Schwartz, G. J., Kersten, S. and Singh, R.
Cell Metab. 2017 Dec 5, 26 (6):856-871 e5.
Late-onset Alzheimer’s disease is associated with inherent changes in bioenergetics profiles
Sonntag, K. C., Ryu, W. I., Amirault, K. M., Healy, R. A., Siegel, A. J., McPhie, D. L., Forester, B. and Cohen, B. M.
Sci Rep. 2017 Oct 25, 7 (1):14038.

BAG3 directly stabilizes Hexokinase 2 mRNA and promotes aerobic glycolysis in pancreatic cancer cells
An, M. X., Li, S., Yao, H. B., Li, C., Wang, J. M., Sun, J., Li, X. Y., Meng, X. N. and Wang, H. Q.
J Cell Biol. 2017 Dec 4, 216 (12):4091-4105.
Drug resistance induces the upregulation of H2S-producing enzymes in HCT116 colon cancer cells
Untereiner, A. A., Pavlidou, A., Druzhyna, N., Papapetropoulos, A., Hellmich, M. R. and Szabo, C.
Biochem Pharmacol. 2017 Oct 20, [epub ahead of print]
ISG15 governs mitochondrial function in macrophages following vaccinia virus infection
Baldanta, S., Fernandez-Escobar, M., Acin-Perez, R., Albert, M., Camafeita, E., Jorge, I., Vazquez, J., Enriquez, J. A. and Guerra, S.
PLoS Pathog. 2017 Oct 27, 13 (10):e1006651.
High throughput measurement of metabolism in planarians reveals activation of glycolysis during regeneration
Osuma, E. A., Riggs, D. W., Gibb, A. A. and Hill, B. G.
Regeneration. 2017 Nov 02, [epub ahead of print]
Current technical approaches to brain energy metabolism
Barros, L. F., Bolanos, J. P., Bonvento, G., Bouzier-Sore, A. K., Brown, A., Hirrlinger, J., Kasparov, S., Kirchhoff, F., Murphy, A. N., Pellerin, L., Robinson, M. B. and Weber, B.
Glia. 2017 Nov 7, [epub ahead of print]
Glucose-regulated protein 75 determines ER–mitochondrial coupling and sensitivity to oxidative stress in neuronal cells
Honrath, B., Metz, I., Bendridi, N., Rieusset, J., Culmsee, C. and Dolga, A. M.
Cell Death Discovery. 2017 Nov 06, [epub ahead of print]

Associations Between Microbiota, Mitochondrial Function, and Cognition in Chronic Marijuana Users
Panee, J., Gerschenson, M. and Chang, L.
J Neuroimmune Pharmacol. 2017 Nov 4, [epub ahead of print]
RNA cytosine methyltransferase Nsun3 regulates embryonic stem cell differentiation by promoting mitochondrial activity
Trixl, L., Amort, T., Wille, A., Zinni, M., Ebner, S., Hechenberger, C., Eichin, F., Gabriel, H., Schoberleitner, I., Huang, A., Piatti, P., Nat, R., Troppmair, J. and Lusser, A.
Cell Mol Life Sci. 2017 Nov 4, [epub ahead of print]
Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins
Samandi, S., Roy, A. V., Delcourt, V., Lucier, J. F., Gagnon, J., Beaudoin, M. C., Vanderperre, B., Breton, M. A., Motard, J., Jacques, J. F., Brunelle, M., Gagnon-Arsenault, I., Fournier, I., Ouangraoua, A., Hunting, D. J., Cohen, A. A., Landry, C. R., Scott, M. S. and Roucou, X.
Elife. 2017 Oct 30, 6.
The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12
Shen, H., Campanello, G. C., Flicker, D., Grabarek, Z., Hu, J., Luo, C., Banerjee, R. and Mootha, V. K.
Cell. 2017 Nov 2, 171 (4):771-782 e11.

See also: Research areas for this month include:

See for comparison: Autophagy

Autophagy is a process by which cellular material is degraded by lysosomes or vacuoles and recycled. Several autophagy pathways operate within a cell, including macroautophagy, microautophagy and chaperone-mediated autophagy.

Latest Research and Reviews

For example:

Dual role of autophagy in hallmarks of cancer

Quantitative assessment of cell fate decision between autophagy and apoptosis

The Nature Publications Group has fallen far behind the data and technical expertise of all the serious scientists in the world. It seems likely that they will attempt to portray autophagy as something besides the innate phage defense system and fail miserably.

Autophagy is the antiphage defense strategy December 8, 2016

What would you do if your publisher arrived at the “Autophagy Party” more than a year late and you had to introduce them as a supporter of neo-Darwinian nonsense and “Big Bang” cosmology?
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
 

Alternative splicing of pre-mRNA

Pseudoscientists hate what science explains! (3)

See also: Pseudoscientists hate what science explains (2)
Summary: In addition to germline silencing via information transfer to the physical landscape of supercoiled DNA, multicopy transgene arrays are linked from changes in the microRNA/messenger RNA balance to variation in their somatic expression level. That fact helps to establish the difference between healthy longevity and pathology across generations.
Problems with DNA replication can cause epigenetic changes that may be inherited for several generations
My summary: The polycomb repressive complex 2, additional chromatin- and small RNA–related pathways carry quantized energy as information from the epigenetic landscape. The information causes changes in microRNAs that modify histones, which links the energy to the transgenerational epigenetic inheritance of morphological and behavioral phentypes in the nematode model organism.
In addition to germline silencing via information transfer to the physical landscape of supercoiled DNA, multicopy transgene arrays are linked from changes in the microRNA/messenger RNA balance to variation in their somatic expression level. That fact helps to establish the difference between healthy longevity and pathology across generations.
The difference is food energy-dependent, RNA-mediated, and biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera.
See for comparison: From Fertilization to Adult Sexual Behavior (1996)

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

Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans

We propose that CNEs [conserved non-coding elements] represent the ‘hard-wired’ sequence traces of these core animal group-specific GRNs [gene regulatory networks]. The alternative core GRNs of different animal lineages are reflected in their having alternative CNEs. However, because of their co-evolution from a common metazoan ancestor, the core GRNs of different animal groups often utilize the same regulatory genes. As a result, distinct yet parallel sets of CNEs have become irreversibly associated with the same genes that coordinate core developmental networks in diverse animal groups. Indeed, this evolution of regulatory elements may underlie the astounding diversification of animal body plans that was seen during the Cambrian period approximately 550 million years ago.

No experimental evidence suggests that regulatory elements evolved.
Predicting phenotypic variation in yeast from individual genome sequences
No experimental evidence predicts a link from gain of function mutations to evolution
Differential DNA mismatch repair underlies mutation rate variation across the human genome
All experimental evidence links natural selection for energy-dependent codon optimality to mutation rate variation across species and to individual differences in the human genome via the pheromone-controlled physiology of reproduction.

3D structures of individual mammalian genomes studied by single-cell Hi-C

Reported as: Scientists have determined the 3D structures of intact mammalian genomes from individual cells, showing how the DNA from all the chromosomes intricately folds to fit together inside the cell nuclei. The research is published in Nature this week. http://go.nature.com/2n6psaw

My comments:

See also: 3D RNA and Functional Interactions from Evolutionary Couplings “…the ongoing explosion of available sequence data means that the outlook for elucidating functional interactions in mRNAs, lncRNAs, and viral genomes, as well as their protein-binding partners, is promising.” http://dx.doi.org/10.1016/j.cell.2016.03.030

Virus-driven energy theft causes the degradation of messenger RNA in all organized genomes. That fact threatens anyone who has ever reported results in the context of mutations, natural selection and evolution because natural selection occurs only for energy-dependent codon optimality.

It would be even more amazing if they told the truth about energy-dependent amino acid substitutions that stabilize supercoiled DNA, which links chromosomal rearrangement to all biodiversity via the physiology of reproduction in species from microbes to humans. See: http://science.sciencemag.org/content/355/6328/910

See other comments to this Nature Facebook page
Addendum: Say goodbye to mutation-driven evolution. Everything known to serious scientists about biophysically constrained endogenous RNA interference and the pheromone-controlled physiology of reproduction has been linked from the de novo creation of nucleic acids to energy-dependent amino acid substitutions that differentiate all cell types in all living genera via fixation in organized genomes.
See: Transgenerational transmission of environmental information in C. elegans
They link diet- and stress-induced changes in heterochromatin from repressed repetitive elements that escape epigenetic reprogramming to phenotypic variation in mammals. It is obvious that heterochromatin provides the link from the molecular mechanisms of biophysically constrained protein folding chemistry to the epigenetic transmission of information between generations. But they speculate that the transgenerational epigenetic inheritance of environmentally triggered changes in expression from repressed chromatin may be linked to ecological adaptations.
See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

 …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’.

Ben Lehner and his co-authors have consistently tried to sneak up from behind and link explanations of energy-dependent top-down causation from mutations to evolution.
Others are also ignoring the experimental evidence that links energy-dependent changes in microRNAs to healthy longevity or from virus-driven energy theft to all stress-linked pathology.
See: Stress-induced changes in miRNA biogenesis and functioning
See for comparison: I am not a story

Reported as: Life is not a neat narrative, it’s a patchwork of competing, even contradictory, forces. Sensations are too spurious and memory too fickle for the formation of reliable storylines. Reject the impulse to narrativise. Summer Reads from the Aeon archive: http://ow.ly/bLd430ekoJn

Re: Sensations are too spurious and memory too fickle for the formation of reliable storylines.

My comment: Too late for more of this nonsense. See: Olfaction Warps Visual Time Perception

 

The sense of smell in bacteria has been linked from the physiology of pheromone-controlled reproduction to our visual perception of mass and energy in the context of the space-time continuum via food energy.

See for comparison: Quantum common sense

We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking

My comment: No, it’s Santa Claus who sees you when your sleeping; He knows when you’re awake. And he knows if you’ve been bad or good, so be good for goodness sake.

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

Energy-dependent chirality

See also: Achiral glycine
Summary: Virus-driven energy theft alters the interactions between physics and chemistry that maintain biophysically constrained biodiversity. That’s how viruses are linked from mutations to all pathology. Nutrient energy-dependent changes in the context of the pheromone-controlled physiology of reproduction biophysically constrain biodiversity via the fixation of amino acid substitutions in supercoiled DNA, which protects organized genomes from virus-driven pathology.
Chirality (chemistry)

Two enantiomers of a generic amino acid that is chiral
The chirality of amino acids is energy-dependent and biophysically constrained by the physiology of reproduction in all living genera. For example, the substitution of achiral glycine in position 6 of the decapeptide gonadotropin releasing hormone (GnRH) stabilizes the organized genomes of all vertebrates by helping to protect them from virus-driven energy theft.

(S)-Alanine (left) and (R)-alanine (right) in zwitterionic form at neutral pH

See also:The acid-base behavior of amino acids

There is an internal transfer of a hydrogen ion from the -COOH group to the -NH2 group to leave an ion with both a negative charge and a positive charge.

Energy as information is placed into the context of the sun’s anti-entropic virucidal link from hydrogen-atom transfer in DNA base pairs in solutions. For example, as water in the ocean can be linked to all biodiversity via the physiology of reproduction and fixation of RNA-mediated amino acid substitutions in the supercoiled DNA of all living genera.

Any nutrient energy-dependent change in pH can be linked from hydrogen-atom transfer in DNA base pairs in solution to healthy longevity. All virus-driven energy theft can be linked from changes in pH and hydrogen-atom transfer in DNA base pairs in solution to pathology.
The difference between healthy longevity and pathology is viral latency. Unless the virus-driven energy theft is biophysically constrained by the anti-entropic virucidal force of the sun’s energy, life on Earth is not possible.
See also: A single ion impacts a million water molecules
That fact helps to explain what is intuitively obvious to all serious scientists. They understand how the energy-dependent difference between bacteria and archaea links the degeneration of messenger RNA from bacteria to the degenerate mophological and behavioral phenotypes of archaea.
See: Virus-mediated archaeal hecatomb in the deep seafloor
For comparison, see: From Fertilization to Adult Sexual Behavior

… 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.

All differentiation in all cell types of all living genera exemplifies nutrient energy-dependent pheromone-controlled RNA-mediated polycombic ecological adaptation. That fact can be compared to the fact that virus-driven energy theft exemplifies the hecatombic evolution of all pathology. Both facts can be placed into the context of everything known about energy-dependent alternative splicings and amino acid substitutions in supercoiled DNA.
For comparison, see this representation of how “minimal mutational distance” might still be used by biologically uninformed theorists who do not know the difference between a mutation and an amino acid substitution:
Construction of Phylogenetic Trees

Determining the Mutation Distance The mutation distance between two cytochromes is defined here as 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).

The choice is perfectly clear. You can accept the claims of theorists who use computers to make “…a pair-wise comparison of homologous amino acids,” or accept the claims of serious scientists who have linked energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which typically protects all living genera from virus-driven energy theft and all pathology.
See also: Multipurpose Plant Sensors Startle Scientists
See also: J. B. S. Haldane [“When I am dead,” in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209.
This discussion attempt failed to convince anyone that Haldane, who was one of the theorists who helped to invent neo-Darwinism, was like all the others who knew nothing about biophysically constrained energy-dependent cell type differentiation.

Peter Berean who invented the term “bio-functional information” concluded:

What is your chain of logic (in your own words) that leads to your belief that energy = information?

—————————–
DEFINITION

—————————–
in·for·ma·tion
1. facts provided or learned about something or someone.
“a vital piece of information”
synonyms: details, particulars, facts, figures, statistics, data; More
2.
what is conveyed or represented by a particular arrangement or sequence of things.
“genetically transmitted information”

—————————–
en·er·gy

1.
the strength and vitality required for sustained physical or mental activity.
“changes in the levels of vitamins can affect energy and well-being”
synonyms: vitality, vigor, life, liveliness, animation, vivacity, spirit, spiritedness, verve, enthusiasm, zest, vibrancy, spark, sparkle, effervescence, ebullience, exuberance, buoyancy, sprightliness; More
2.
power derived from the utilization of physical or chemical resources, especially to provide light and heat or to work machines.
—————————–

Conclusion: Energy and Information are two completely different things. They are NOT the same thing.

Claims that energy is not information, which are based on definitions, continue to frustrate the effort of intelligent scientists who are combating evolution to fight disease.
The casualties on the side of the serious scientists can be attributed to theorists and journalists who write articles with conclusions like this.
See: The queen does not rule

Division of labour is a human innovation, drawing on our ability to learn and improve by practice, and to trade goods and services. The growing recognition that natural processes work differently from our symphonies and armies will allow us to see the natural world more clearly. Ant colonies are not factories or fortresses; instead they use simple interactions to adjust to changing conditions. Ant societies, organised by distributed algorithms rather than division of labour, have thrived for more than 130 million years.

Division of labor is nutrient energy-dependent and pheromone-controlled via the physiology of reproduction in all living genera. For example XIST links differences in energy-dependent RNA-directed DNA methylation to chromosomal rearrangements and sex differences in species from yeasts to humans via the pheromone-controlled physiology of reproduction.
See: Chemical tags on RNA silence female X chromosome

“We found that methyl modification is a normal feature of most RNAs in the cell,” he said. “This includes messenger RNAs that encode proteins, as well as noncoding RNAs such as XIST.”

Others have shown that energy-dependent changes in the microRNA/messenger RNA balance link methylation to every aspect of healthy longevity and that they link virus-driven energy theft to all pathology via the conserved molecular mechanisms of cell type differentiation in all living genera.
See: microRNA
For one of 56,700 other examples see: MicroRNA-29 impairs the early phase of reprogramming process by targeting active DNA demethylation enzymes and Wnt signaling
See also: The real problem

…fundamental aspects of our experiences of conscious selfhood might depend on control-oriented predictive perception of our messy physiology, of our animal blood and guts. We are conscious selves because we too are beast machines – self-sustaining flesh-bags that care about their own persistence.

We are not self-sustaining. The real problem is the ignorance of theorists who have failed to tether their ridiculous theories to facts about Darwin’s “conditions of life” that have been detailed by serious scientists.
For example, see: Feedback loops link odor and pheromone signaling with reproduction
See also: Involvement of Host Non-Coding RNAs in the Pathogenesis of the Influenza Virus
See for comparison: My comment to the Science site and to the Atlantic site:

The idea of biophysical constraints seems antithetical to the idea of nature somehow selecting mutations that cause amino acid substitutions. However, I am not a biophysicist or evolutionary theorist.

The problem may be my focus on nutrient-dependent receptor-mediated amino acid substitutions in species from bacteria to humans (non-viral organisms). Since I am not a virologist or physicist, I’m not sure that the laws of physics apply to viruses and their replication.

If they do, natural selection for random mutations is not likely to result in amino acid substitutions because the thermodynamics of changes in organism-level thermoregulation preclude such randomness. Stability of protein biosynthesis and degradation that probably depends on protein folding must somehow be controlled. Besides, I don’t know how random mutations in viruses could be naturally selected for inclusion in the human virome (or in the virome of any organism capable of thermoregulating its thermodynamic intercellular signaling).

If the Second Law of Thermodynamics does not apply to viruses, which means the chemical bonds that enable the amino acid substitutions can form at random and somehow be naturally selected, the details of biophysical constraints in this article seems out of place, since I do not think in terms of constrained random mutations and natural selection in mutation-driven evolution.

Hopefully, someone with a background in biophysics will address my confusion in case others are confused. In addition, I wonder if the consequences of understanding the evolutionary mechanisms that govern viruses extend to consequences important to understanding the evolution of species from bacteria to humans via constrained random mutations and natural selection?

My comment was removed from the Science site and this appeared:

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

My comment is still available from the Atlantic site
See also: Virus-driven mutation or amino acid substitution
See also: Energy-dependent chirality (2)

Alternative splicing of pre-mRNA

Epigenetics and autophagy vs mutations and evolution (2)

Plants send light to roots to ‘see’ underground
My comment: Sending light requires an energy-dependent link from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects all organanized genomes from virus-driven energy theft and genomic entropy.
See Schrodinger (1944)
Excerpt:

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

Ongoing confirmations of facts have escaped the attention of most theorists.

My comment:  The physics of life is the same as the physics that underlies inorganic chemistry. There is no such thing as chemoautotrophic or chemoheterotrophic metabolism. Metabolism is energy-dependent. Chemosynthesis and symbiogenesis are energy-dependent and controlled by the physiology of reproduction, not by the magic of evolution.
How can anyone not understand the link from information transfer in the context of physics or not link quantized energy from chemistry to RNA-mediated cell type differentiation in species from microbes to humans via the physiology of reproduction.
If the anti-entropic virucidal effects of UV light did not cause RNA-mediated DNA repair in soil bacteria, plants could not grow. Instead, sunlight is the link from the nutrient-dependent pheromone-controlled physiology of reproduction in soil bacteria to all biodiversity via the conserved molecular mechanisms of epigenetics that we first detailed in our 1996 review.
See: From Fertilization to Adult Sexual Behavior
Excerpt:

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (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.

Alternative splicing of pre-mRNA

From Precis to Proof in 6000 years (3)

See first: Coulombic interactions facilitate polycombic adaptation
See also: From Precis to Proof in 6000 years (2)
See also: RNA catalyses nuclear pre-mRNA splicing 06 November 2013
Conclusion:

…our data indicate that the spliceosome, like the ribosome44,45, uses RNA to effect catalysis in the context of a complex ribonucleoprotein assembly. Moreover, the common catalytic mechanism used by the spliceosome and group II introns is consistent with a common evolutionary origin between the spliceosome and these ancient RNA retroelements46,47. Our findings thus support the idea that modern ribonucleoprotein enzymes evolved from a primordial ‘RNA world’ (ref. 48), in which catalysis was performed exclusively by RNA.

My comment: Claims that everything “evolved” are rarely seen in the context of data that links RNA-mediated physics, chemistry, and molecular epigenetics from the spliceosome and ribosome to catalysis and the complexity ribonucleoprotein assembly.  But here, they claimed: “Our findings thus support the idea that modern ribonucleoprotein enzymes evolved…”
See for comparison: Substantial contribution of extrinsic risk factors to cancer development 16 December 2015
Abstract conclusion

…rates of endogenous mutation accumulation by intrinsic processes are not sufficient to account for the observed cancer risks. Collectively, we conclude that cancer risk is heavily influenced by extrinsic factors. These results are important for strategizing cancer prevention, research and public health.

See for comparison: Cancer studies clash over mechanisms of malignancy 16 December 2015

Excerpt:

The authors also examined patterns in the mutations associated with certain cancers; ultraviolet light, for example, tends to create a tell-tale signature of mutations in DNA. And they used other mathematical models, expanding the data set used in the earlier work to include prostate and breast cancer — two of the most common cancers.

“There’s no question what’s at stake. This informs whether or not we expend energy on prevention.”

The models suggested that mutations during cell division rarely build up to the point of producing cancer, even in tissues with relatively high rates of cell division. In almost all cases, the team found that some exposure to carcinogens or other environmental factors would be needed to trigger disease.

My comment: Theories about mutation-driven evolution should have promptly been abandoned. Instead, this conference started on November 7, 2016: New trends in evolutionary biology: biological, philosophical and social science perspectives
 

rp_levels-of-organization.jpg

Light ‘drives’ adaptation; nothing ‘drives’ evolution (2)

See: Light ‘drives’ adaptation; nothing ‘drives’ evolution

See also: Who rules the waves? – Viruses might just be bit players in the drama of the seas. Then again, they could be major actors

Excerpt (from 1996): 

Most consider viruses to be a legion of cripples, sterilised by ultraviolet radiation and rendered impotent by hosts that are largely immune to their threat. But a few researchers take the opposite view. And if they turn out to be right, viruses could radically alter the balance of life in the oceans, ripping away huge parts of the food web that supports whales, sea birds and the fisheries on which many people rely.

See also: Riding the Evolution Paradigm Shift With Eugene Koonin

Excerpt: 

This is a good point to make. 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…

From 1996: 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.

Forthcoming, two decades later: New trends in evolutionary biology: biological, philosophical and social science perspectives
Excerpt:

Developments in evolutionary biology and adjacent fields have produced calls for revision of the standard theory of evolution…

My comment: Topics mentioned in the abstracts (my categories):

Science

The physics of organisms

multilevel and reciprocal causation

adaptability could influence the inherited characteristics of an organism’s descendants
phenotypic traits have complementary rather than antagonistic functions
‘second inheritance system’, built on the shoulders of the primary genetic inheritance system
adaptive design at the level of genes, individuals and societies
…niche construction co-directs adaptive evolution
integrated symbioses
‘developmental niche construction’ as a framework to integrate findings from fields ranging from molecular biology to developmental psychology
epigenetic inheritance
the involvement of epigenetic inheritance in adaptive evolutionary change
inherited yet non-genetic adaptation.
somatic inheritance, maternal effects and DNA methylation.
processes that sustain persisting lineages.
understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations

Pseudoscientific nonsense

a distinction between epigenetic and exogenetic inheritance

different narratives as to exactly what such an evolutionary approach entails.
how different mechanisms of inheritance contributes to evolution.
understanding of how important the process has been in shaping the evolution of animal form.
a closely allied distinction between ‘organic’ and ‘cultural’ evolution?
domestication to serve once again as a model system
‘human like’ modes of behaviour (and presumably more biocultural evolution)

See for comparison to everything currently known to serious scientists about biophysically constrained energy-dependent RNA-mediated protein folding chemistry.

A niche for the genome

Excerpt:

…the study of phenotypic plasticity, epigenetic and exogenetic inheritance, have not yet demonstrated the need for any revolutionary change in evolutionary thought. For us they highlight the extent to which proximate developmental mechanisms can inform ultimate biology.

My comment: Twenty years after our review of energy-dependent RNA-mediated molecular epigenetics and cell type differentiation, this exemplifies the overwhelming foolishness of theorists who seem to think that not all developmental mechanisms are energy-dependent and biophysically constrained by the physiology of reproduction.

See also the discussion attempt at: What does DNA have to do with the Origin of Life ?

Alternative splicing of pre-mRNA

Polycombic ecological adaptation as a science, not a theory (2)

Evolutionary Constraints in the β-Globin Cluster: The Signature of Purifying Selection at the δ-Globin (HBD) Locus and Its Role in Developmental Gene Regulation

Conclusion:

… the results here presented indicate that purifying selection is driving not only HBD evolution but also its neighbor pseudogene, HBBP1. In the light of recent advances in the characterization of the β-globin cluster, we propose that the complex patterns of diversity observed in this genomic region arose from distinct functional constraints related with the intricate process of chromatin and protein interactions coordinating the differential expression of genes at the β-globin cluster during development.

My comment: No experimental evidence of biologically-based cause and effect suggests that any locus of genes or any pseudogene has ever evolved. Purifying selection cannot drive evolution. Only energy-dependent variations can can be linked to polycombic ecological adaptation, and only virus-driven energy theft has been linked to the creation of pseudogenes in the context of biophysical constraints on viral latency.

See for comparison: microRNA Function Is Limited to Cytokine Control in the Acute Response to Virus Infection

Excerpt:

miRNA function is generally limited to cytokine levels in response to RNA viruses

Reported as: Mount Sinai Researchers Use Cellular miRNA-Elimination Tool to Study Viral Infection Dynamics

Excerpt:

…while the loss of miRNAs had a negligible impact on the cell’s immediate reaction to a virus or the short-term biology of the cell, sustained depletion had dramatic results on gene expression that was coupled to a burst of cytokines. The researchers concluded in the paper that miRNA function is limited to modulating the biology of the cell over long periods of time.

My comment: In my model, energy-dependent changes in the microRNA/messenger RNA balance link nutrient energy-dependent changes to all healthy longevity and virus-driven energy theft is linked to all pathology. Over long periods of time, autophagy is the link to polycombic ecological adaptation or virus-driven hecatombic evolution of pathology via energy-dependent biophysically constrained RNA-mediated protein folding chemistry. For example, fixation of amino acid substitutions differentiates all cell types in all individuals of all living genera in the context of the physiology of reproduction. For comparison, virus-driven hecatombic pathology is linked from mutations to all pathology.

Simply put, in my model of polycombic ecological adaptation, differential gene expression is nutrient-dependent and controlled by the physiology of reproduction.

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

Conclusion: 

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

My comment: Claims about RNA-mediated polycombic ecological adaptation were first placed into the context epigenetic imprinting in our 1996 review.

See: From Fertilization to Adult Sexual Behavior

Excerpt:

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (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.

My comment: Polycombic ecological adaptation appears to link energy-dependent epigenetic effects on hormones (i.e., proteins) to chromatin structure in telomeric regions, which links the effect on transcription and silencing of various genes to hormone-organized and hormone-activated affects on behavior. The hormone-organized and hormone-activated behaviors link the epigenetic landscape of yeasts to the physical landscape of supercoiled DNA in species from bacteria to invertebrates and all vertebrates via the de novo creation of G protein-coupled receptors, which link chemotaxis and phototaxis to all biodiversity.

For comparison, see: Mutation-Driven Evolution

Excerpt:

Mutation… includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc.

My comment: The definition above links mutations to any change in any genome.

See for comparison: Updates of the HbVar database of human hemoglobin variants and thalassemia mutations

Excerpt:

Single nucleotide substitutions or indels [insertions/deletions] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects [mutations] in either regulatory or coding regions of the human HBA2, HBA1, HBB or HBD genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.

My comment: The facts about nutrient energy-dependent amino acid substitutions link hemoglobin variants from ecological adaptation to healthy longevity and the facts also link molecular defects from mutations to the pathology of α-, β- or δ-thalassemia, respectively. It would be difficult to include facts about biophysically constrained energy dependent cell type differentiation in the context of any other model that links amino acid substitutions to healthy longevity and links mutations to all pathology in all living genera.

See for example:  Criticisms of the nutrient-dependent pheromone-controlled evolutionary model 

Excerpt:

…James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research.

My comment: The claims of a biologically uninformed undergraduate student reviewer were placed into the context of modern evolutionary theory, which involves Masatoshi Nei’s simple-minded revision of neo-Darwinian pseudoscientific nonsense. Nei does not compare his theory of mutations to the facts about nutrient energy-dependent fixation of amino acid substitutions in supercoiled DNA. The problem appears to be the use of the term “mutation” in the textbook published on the same day as my 2013 review was published.

I linked the energy-dependent fixation of amino acid substitutions to all healthy longevity. Nei’s textbook misrepresentations did not link anything to healthy longevity, but linked mutations to what I claimed are nutrient-dependent pheromone-controlled polycombic ecological adaptations.

I failed to include what is known about energy-dependent codon optimality in the context of polycombic ecological adaptations because there was no experimental evidence of biologically-based cause and effect to support those claims at the time of our 1996 review or my 2013 review. For comparison, there has never been any experimental evidence of biologically-based cause and effect to support claims about mutation-driven evolution. Simply put, nothing known to serious scientists about cell type differentiation suggest that mutation-driven evolution can occur.

For comparison, see: New analysis of big data sheds light on cell functions
Excerpt:

With today’s technology, scientists are able to generate data about a cell’s or organism’s complete set of genes, proteins, RNA profiles, metabolites and much more—known as omic data. Using omic data, scientists can model complex biological interactions and gain a more holistic view of different cellular processes.

See also: Research Topic Multi-omic Data Integration

Excerpt:

Stable, predictive biomarkers and interpretable disease signatures are seen as a significant step towards personalized medicine. In this perspective, integration of multi-omic data coming from genomics, transcriptomics, glycomics, proteomics, metabolomics is a powerful strategy to reconstruct and analyse complex multi-dimensional interactions, enabling deeper mechanistic and medical insight.

My comment: Glycomics, transcriptomics, proteomics, metabolomics and genomics have established fact about the biological basis of complex multi-dimensional interactions that link the nutrient-dependent pheromone-controlled physiology of reproduction in bacteria from quorum sensing to the molecular mechanisms that enable deeper mechanistic and medical insight in the context of the National Microbiome Initiative and Precision Medicine Initiative.

See for example: ‘Oming in on RNA–protein interactions

Excerpt:

…the interactions between pre-mRNA and proteins fine-tune alternative splicing in a manner that can gradually create new protein functionalities without the need to create additional genes and without affecting existing proteins [4-6].

See for comparison: From Fertilization to Adult Sexual Behavior

Excerpt:

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

My comment: Detailed examples of how the interactions between pre-mRNA and alternative splicings create new genes in the fine-tuned energy-dependent functional structure of supercoiled DNA explain how all cell types of all individuals of all living genera are protected from virus-driven energy theft. Energy-dependent RNA-mediated amino acid substitutions are fixed in organized genomes via the physiology of reproduction, which helps to prevent the transgenerational epigenetic inheritance of nearly all pathology by linking innate immune system to supercoiled DNA.

For comparison, viruses steal the energy that is required for cell type differentiation, which is how mutations are linked to all pathology. All differences between healthy longevity and virus-driven human pathology can be explained in the context of how nutrient energy-dependent microRNAs. The nutrient energy-dependent microRNAs are carried by erythrocytes in species with circulating blood.

See: Pitfalls of analysis of circulating miRNA: role of hematocrit

MicroRNAs are are delivered to the cell types on an as needed basis. When too few nutrient energy-dependent microRNAs are available, viruses use the existing energy they steal from cells to replicate. Eventually, the replication of the viruses causes the mutations, which are linked to all pathology. That’s why it is important to revisit the facts presented in the context of this article, which was published on 10/26/16

See: Multi-omic data integration enables discovery of hidden biological regularities
I reported this here as: Polycombic ecological adaptation as a science, not a theory for comparison to Biological evolution as a philosophy, not a science.
Despite several attempts to discuss the difference between science and philosophy, no progress was made.
See for example: Evolutionary assumptions (revisited)
See also the impasse that was reached in this attempt to discuss the anti-entropic virucidal energy of the sun.
It is worth joining The Battlefield FB group to see that others would rather hold on to their theories and opinions despite the overwhelming amount of experimental evidence that I have used to support my claims. For me, it is time to move forward and focus on the rediscovery of hidden biological regularities.
Finally, others have discovered that small intranuclear proteins generate alternative splicing techniques of pre-mRNA, which is how microRNAs link hydrogen-atom transfer in DNA base pairs in solution to the conserved molecular mechanisms of energy-dependent cell type differentiation, and to all cell type differences in all individuals of all living genera.
For comparison, this is an example of how virus-driven energy theft is linked viral replication and to virulence:
Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

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

For an example of how nutrient energy-dependent RNA-mediated amino acid substitutions are linked to healthy longevity via the physiology of reproduction, see:

…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).”

My comment: The facts stated above have forced theorists to invent evolutionary cell biology.
See Evolutionary cell biology: Two origins, one objective
Reported as: Why some junk DNA is selfish, but selfish genes are junk
Excerpt:

“A commonly held but incorrect stance is that essentially all of evolution is a simple consequence of natural selection.” They point out, for example, that many pathways to greater complexity of both genomes and cells don’t confer any selective fitness.

My comment: Greater complexity requires a link from ecological variation to polycombic ecological adaptation, which links supercoiled DNA to protection from the virus-driven hecatombic evolution of all pathology.
My comment: New theories are worthless if they do not include information on the role of energy in cell type differentiation or the role of virus-driven energy theft in all pathology.
See for comparison the facts about: Detection of hemoglobinopathies and thalassemias using automated separation systems
See also: In vivo correction of anaemia in β-thalassemic mice by γPNA-mediated gene editing with nanoparticle delivery
Excerpt: 

The combination of nanoparticle delivery, next generation γPNAs and SCF treatment may offer a minimally invasive treatment for genetic disorders of the blood that can be achieved safely and simply by intravenous administration.

My comment: That fact suggests all suffering and death caused by hemoglobin variants is caused by neo-Darwinian theorists who do not know how the variants link ecological variation to polycombic ecological adaptation.

Reported as: Scientists edit gene mutations in inherited form of anemia
Excerpt:

The researchers found that the technique corrected the mutation to such a degree that the mice no longer had symptoms of thalassemia. After 140 days, they tested hemoglobin levels in the animals and found them to be normal.
“The fundamental result here is that with nanoparticles containing PNAs, along with template DNA, and simple IV infusion of molecules, we achieved enough gene editing to effectively cure the anemia in mice that had thalassemia,” Glazer said.

My comment: The ability to correct the mutation requires a link from energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solutions such as blood. That’s how their IV therapy works. It changes the microRNA/messenger RNA balance and that forces the innate immune system to repair the damaged DNA.
See also:  Two novel loci, COBL and SLC10A2, for Alzheimer’s disease in African Americans
Excerpt:

Two SNPs at novel loci, rs112404845 (P = 3.8 × 10−8), upstream of COBL, and rs16961023 (P = 4.6 × 10−8), downstream of SLC10A2, obtained genome-wide significant evidence of association with the posterior liability.

Reported as: Study Identifies Two New Genes Responsible for Alzheimer’s in African Americans
Excerpt:

In 2013, a genome-wide association study of AD in more than 5,500 African Americans identified two genetic risk factors for AD. This study looked at genetic variants across subjects’ entire genome and compared their frequency in cases versus controls.
By doing so they were able to identify two new genes (COBL and SLC10A2) associated with risk of AD in African Americans.

My comment: The author’s study results link hydrogen-atom transfer in DNA base pairs in solution to energy-dependent changes in the microRNA/messenger RNA balance. The neuroscience news report claims they identified two new genes. The neuroscience news report then links the genes — instead of the energy-dependent changes — to the disease in a human population. Many African Americans are examples of how ecological variation has been linked to polycombic ecological adaptation via hemoglobin variants. The adaptations include amino acid substitutions linked to the stability of organized genomes in populations where malaria is endemic. Failed adaptations are included in examples of virus-driven energy theft linked to mutations and the pathology of Alzheimer’s disease.

My comment: The ability to edit out gene mutations clearly links RNA-mediated amino acid substitutions to supercoiled DNA and all biodiversity.
See also: Inventing neo-Darwinism
See also: Pioneering Geneticist Explains Ambitious Plan to “Write” the Human Genome

Excerpt:

…he notes that with an editing tool like CRISPR, one base out of many can be altered, but with a synthesis approach, a hundred edits could be made. This sort of change, he tells JAMA, could make a cell resistant to multiple viruses.

My comments: All the changes in base pairs may already have been linked from natural selection for codon optimality and energy-dependent changes in RNA-mediated cell type differentiation to supercoiled DNA, which links the physiology of reproduction from the innate immune system to fixation of the amino acid substitutions that differentiate the cell types of all living genera. If so, what might happen to an organized genome when a hundred edits are made?

Will anyone be able to stop the hecatombic evolution of pathology via the polycombic ecological adaptation, which links autophagy to healthy longevity via protection of organized genomes from virus-driven entropy?

See also: Yale scientists edit gene mutations in inherited form of anemia Genetics & Genomics

A new gene therapy is being tested for its ability to treat thalassemia, a form of anemia caused by genetic mutations. So far, scientists have successfully corrected gene mutations causing the disease in mice, and now researchers are interested in seeing if the same approach will work effectively in humans.
“The fundamental result here is that with nanoparticles containing PNAs, along with template DNA, and simple IV infusion of molecules, we achieved enough gene editing to effectively cure the anemia in mice that had thalassemia. We demonstrated we have extremely low off-target effects.”

See for comparison:

Product Development Pipeline

Excerpt:

Each microRNA mimic in our pipeline is designed to replicate the activity of a single tumor suppressor miRNA and regulate the expression of key oncogenes across multiple oncogenic pathways which can prevent proliferation and induce apoptosis in cancer cells.

See also: VACRC Projects

Excerpt: Future Projects

 The Influence of Carbon Dioxide Enhancement on Plant Growth
 Thermoregulation in Honey Bees
 Biochemistry and Taxonomy in Pine Trees
 The Formation of Multiple Tree Rings in Bristlecone Pine Trees

The VACRC suddenly seems willing to take everything I have claimed about RNA-mediated cell type differentiation during the past twenty years and begin to investigate the claims. This would have been a desirable outcome 20 years ago, but now it might prevent progress via use of my model. The model links energy-dependent changes from angstroms to ecosystems in all living genera, it and links virus-driven energy theft to all pathology.

The Pacific Yew Tree and production of taxol is an example of how the physi0logy of reproduction in soil bacteria can be linked from plant growth to the honeybee model organism of thermoregulation and behavior, which must be linked to the biochemistry and taxonomy of all species. That becomes meaningful via the explanatory power of a model that links RNA-mediated amino acid substitutions to all energy-dependent biodiversity via the conserved molecular mechanisms of polycombic ecological adaptation we detailed in our 1996 review.

However, when others wait too long to accept a model that may already have led to a paradigm shift, they may also realize it. That fact was addressed by Kaveli Kull in the context of next week’s meeting of the Royal Society.

See: Kalevi Kull: Censorship & Royal Society Evo Event

Excerpt:

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.

My comment: Some work by young earth creationists has been at the cutting edge since 1996, as indicated here: Where do viruses come from?

Excerpt:

‘Viruses tend to keep nutrients away from the big stuff and keep them going around in the little stuff,’ says Fuhrman. If so, viruses have shaped the entire structure of the ecosystem.”9

My comment: 9 is Holmes, B. (1996) Who Rules the Waves? New Scientist 152(2054):8-9, supp I have not read it in its entirety but the claim fits into the context of everything else I have learned about physics, chemistry, and conserved molecular mechanisms of RNA-mediated cell type differentiation, which appears to be biophysically constrained in all living genera via their nutrient-dependent pheromone-controlled physiology of energy-dependent reproduction.