Caption: Contemporary analyses of cell metabolism have called out three metabolites: ATP, NADH, and acetyl-CoA, as sentinel molecules whose accumulation represent much of the purpose of the catabolic arms of metabolism and then drive many anabolic pathways. Such analyses largely leave out how and why ATP, NADH, and acetyl-CoA (Figure 1) at the molecular level play such central roles. Yet, without those insights into why cells accumulate them and how the enabling properties of these key metabolites power much of cell metabolism, the underlying molecular logic remains mysterious. Four other metabolites, S-adenosylmethionine, carbamoyl phosphate, UDP-glucose, and Δ2-isopentenyl-PP play similar roles in using group transfer chemistry to drive otherwise unfavorable biosynthetic equilibria. This review provides the underlying chemical logic to remind how these seven key molecules function as mobile packets of cellular currencies for phosphoryl transfers (ATP), acyl transfers (acetyl-CoA, carbamoyl-P), methyl transfers (SAM), prenyl transfers (IPP), glucosyl transfers (UDP-glucose), and electron and ADP-ribosyl transfers (NAD(P)H/NAD(P)+) to drive metabolic transformations in and across most primary pathways. The eighth key metabolite is molecular oxygen (O2), thermodynamically activated for reduction by one electron path, leaving it kinetically stable to the vast majority of organic cellular metabolites

MicroRNA-mediated denuclearization (4)

April 24, 2018

by James Kohl with No Comment Adaptations biophotonics Cytosis Diseases & Disorders Ecology RNA Directed

Summary: Christ’s lab showed that in vivo formation of I-motif structures is pH dependent and helped to put the “fear of God” into atheistic communists.

I-motif DNA structures are formed in the nuclei of human cells (4/23/18)

Reported as: In human cells, scientists find DNA that looks like a twisted knot instead of a double helix (4/23/18)

Also reported as: New Twisted ‘Knot’ Human DNA Structure Discovered—and It Looks Nothing Like the Double Helix (4/23/18)

Christ’s lab showed that in vivo formation of I-motif structures is pH dependent. Clearly, the potential of hydrogen (pH) and pH-dependent cell cycles link the quantized energy of virucidal sunlight to protection from the degradation of messenger RNA that links mutations to all pathology.
In that context, denuclearization has been forced on North Korea and other communist countries by scientific creationists in South Korea. The creationists have indirectly revealed that they could decimate human populations in China via the creation of a virus with one base pair change linked to one amino acid substitution.
See also: 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.

Until recently, the pseudoscientific nonsense about vaccines that could protect human populations from the forthcoming viral apocalypse was tightly linked from communism to atheism. For comparison, Christ’s lab appears to have put the fear of God into its proper context; the 1918 Spanish flu.
Previously reported as: Structural diversity of supercoiled DNA (2015) and parodied in:

See also: The Pharmacology of Regenerative Medicine (2013)
See also: Energy as information and constrained endogenous RNA interference (2017)

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.

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.

Ecological adaptation: A new definition of heredity (3)

March 9, 2018

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy base editing biophotonics Diseases & Disorders Ecology Light Energy microRNA editing Model Organisms Neuronal Plasticity Nutrigenomics Physics RNA Directed RNA editing RNA interference Subatomic What's in the News

Excerpt:
Moving forward: Novel and Haplotype Specific MicroRNAs Encoded by the Major Histocompatibility Complex

…these data suggest that a subset of the identified novel miRNAs may contribute to the pathophysiology of numerous diseases, laying the groundwork for future studies to elucidate the functional connections of miRNAs to the numerous diseases associated with sequence variants within non-coding regions of the MHC.

OMCD: OncoMir Cancer Database

Dysregulation of miRNAs is commonly observed in cancers and it largely cancer dependent.

The virus-driven theft of quantized energy as information has been linked from changes in the microRNA/messenger RNA balance to all pathology. That fact replaces the circular logic that links cancer-dependent dysregulation of miRNAs to cancer. Simply put, the proliferation of viruses cause cancer. The proliferation of viruses is energy-dependent in the context of established links from atoms to ecosystems in all living genera.
See: Subatomic: An Atom Building Board Game

A deck-building game where particle physics & chemistry collide! Use quarks to build subatomic particles & particles to build Atoms!

Moving forward: Novel and Haplotype Specific MicroRNAs Encoded by the Major Histocompatibility Complex

My “Disqus” comment (and nearly 2000 others): Gene expression is energy-dependent, RNA-mediated, and biophysically constrained.
See: FUS Regulates Activity of MicroRNA-Mediated Gene Silencing.

MicroRNA-mediated gene silencing is a fundamental mechanism in the regulation of gene expression.

MicroRNAs do not create themselves.
See also: Energy as information and constrained endogenous RNA interference
8 of my 9 most recent comments to Disqus have been removed.
See for comparison: Incomplete host immunity favors the evolution of virulence in an emergent pathogen
Reported as: In nature, an imperfect immune system drives the evolution of deadly pathogens

…birds that eat at feeders are more likely to be infected with the disease, which causes red, swollen eyes and often blindness that results in death.

…lower virulence strains could be their own worst enemies, creating a population of hosts that are resistant to them but not the higher virulence strains that remain.

By removing my Disqus comments, the moderators limit discussion of the facts about virus-driven energy theft, which links mutations to all pathology. That allows the biased reporting on preprints that continue to try to support the ridiculous concept of neo-Darwinian evolution.
It also prevents the realization of goals by serious scientists who have linked the biogenic creation of uranium ores to the prevention of radiation sickness via microRNA therapy. See, for examples: miRNA-mediated therapies
A miRNA-145/TGF-beta1 Negative Feedback Loop Regulates the Cancer-Associated Fibroblast Phenotype

…miR-145 is a key regulator of the CAF phenotype, acting in a negative feedback loop to dampen acquisition of myofibroblastic traits, a key feature of CAF associated with poor disease outcome.

Gene-edited induced pluripotent stem cells (iPSCs) provide relevant isogenic human disease models in patient-specific or healthy genetic backgrounds. Towards this end, gene targeting using antibiotic selection along with engineered point mutations remains a reliable method to enrich edited cells. Nevertheless, integrated selection markers obstruct scarless transgene-free gene editing. Here, we present a method for scarless selection marker excision using engineered microhomology-mediated end joining (MMEJ). By overlapping the homology arms of standard donor vectors, short tandem microhomologies are generated flanking the selection marker. Unique CRISPR-Cas9 protospacer sequences nested between the selection marker and engineered microhomologies are cleaved after gene targeting, engaging MMEJ and scarless excision. Moreover, when point mutations are positioned unilaterally within engineered microhomologies, both mutant and normal isogenic clones are derived simultaneously. The utility and fidelity of our method is demonstrated in human iPSCs by editing the X-linked HPRT1 locus and biallelic modification of the autosomal APRT locus, eliciting disease-relevant metabolic phenotypes.

Reported as: Gene Editing Is Now Precise Enough to Modify a Single Letter of DNA

To make these very precise edits, an SNP modification is first inserted alongside a fluorescent reporter gene that helps researchers to identify modified cells. The researchers engineered a duplicate DNA sequence known as a microhomology (hence the technique’s name) on each side of the fluorescent gene, targeting sites for CRISPR to go in and cut DNA. The researchers were then able to use a DNA repair system known as microhomology-mediated end joining (MMEJ) to remove the fluorescent gene. That left only the single-base edit, in the form of an SNP, behind.

See also: Inhibition of the Host Translation Shutoff Response by Herpes Simplex Virus 1 Triggers Nuclear Envelope-Derived Autophagy
Nuclear envelope-derived autophagy (NEDA) appears to be a cellular stress response, which is triggered late during HSV-1 infection. An energy-dependent single nucleotide repeat (SNR) might compensate for the viral alteration of the macroautophagic response. At this level of hydrogen-atom energy transfer in DNA base pairs in solution, the link to supercoiled DNA and viral latency becomes increasingly important.
Theorists are angry because they have been left behind. They know very little about what is important. That was expected by all serious scientists, especially those who have accumulated decades of testing experience while working in medical laboratories.
See for example: Applications of ligation-mediated PCR

Using a molecular energy source (which differs depending on the enzyme source organism), DNA ligase reforms the missing covalent bond and the strand is whole again. Two aspects of this are critical:

The nick to be repaired occurs on a single strand but in the context of a double-stranded molecule.
The bases of the nicked strand, and particularly those directly flanking the nick site, must be properly base-paired to the opposite (un-nicked) strand.

It’s not hard to imagine why this is: the base pairing is required to hold the two parts (sugar 3′ -OH and the next phosphate) in place for the ligase enzyme active site to catalyze joining them. If either one of these isn’t base-paired down and is flopping about with thermal motion, the reaction geometry doesn’t occur, and no new bond can be made.

Biologically uninformed theorists cannot even speak the same language. They do not start with a molecular energy source for base pairing and microRNA-mediated amino acid substitutions that differentiate all cell types. Instead, mutations are linked to increasing organismal complexity via the magic of evolution.

Creating biophysically constrained viral latency (2)

February 28, 2018

by James Kohl with No Comment Adaptations Diseases & Disorders Ecology Model Organisms RNA Directed RNA-directed DNA methylation

Creating biophysically constrained viral latency (2)
Serious scientists have reached the point where they are finally ready to expose the pseudoscientific nonsense during Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses and also during Schrödinger at 75 – The Future of Biology – September 2018.
Until then, pseudoscientists may want to see these examples of accurate information about top-down causation.
MicroRNA Processing Gene Methylation and Cancer Risk

Methylation of three CpGs (DROSHA: cg23230564, TNRC6B: cg06751583, and TNRC6B: cg21034183) was prospectively associated with time to cancer development (positively for cg06751583, inversely for cg23230564 and cg21034183) whereas methylation of one CpG site (DROSHA: cg16131300) was positively associated with cancer prevalence.

Oncogene-induced regulation of microRNA expression: Implications for cancer initiation, progression and therapy

microRNAs are small non-coding RNAs that negatively regulate gene expression, assisting or antagonizing oncogenic signalling. The differential expression of microRNAs in cancer is well-documented and is considered a fundamental aspect of tumourigenesis.

Dengue virus causes changes of MicroRNA-genes regulatory network revealing potential targets for antiviral drugs

This study showed a preliminary support to suggest that the herbal medicine RDN combined with LRD can reduce both susceptibility and the severity of DENV.

Dampened STING-Dependent Interferon Activation in Bats
Reported as: How bats carry viruses without getting sick
There is a clear link from the gut bacteria of insects to food energy-dependent pheromone-controlled biophysically constrained viral latency in mammals.
See: Regulation of midgut cell proliferation impacts Aedes aegypti susceptibility to dengue virus

Our study demonstrates that the intestinal epithelium of the blood fed mosquito is able to respond and defend against different challenges, including virus infection. In addition, we provide unprecedented evidence that the activation of a cellular regenerative program in the midgut is important for the determination of the mosquito vectorial competence.

Amino Acid Residues Contributing to Function of the Heteromeric Insect Olfactory Receptor Complex
Our work suggests that the Or-Orco complex has two important characteristics. First, the biophysical properties of the channel vary according to subunit composition, even with highly similar proteins such as BmOr-1-Orco and BmOr-3-Orco. Second, because ligand-selective Or sequences within and between insect species are extremely divergent, the primary amino acid sequence of the ion-conducting pore is likely to differ according to the subunit composition of the Or-Orco complex.

Figure 1) Targeted mutagenesis of Ae. aegypti orco

a, Snake plot of Ae. aegypti Orco with amino acids colour-coded to indicate conservation with Drosophila melanogaster.

It should have been perfectly clear to Leslie Vosshall and others like her that the energy-dependent creation of microRNAs was the key to ecological adaptation via RNA-mediated biophysically constrained viral latency in all living genera. Instead, she attempted to make scientific progress by genetically engineering changes to the fertility of mosquitoes.
She appears to think that genetic engineering of the mosquitoes is the way forward.
Genetic engineering alters mosquitoes’ sense of smell 5/29/13

…the mosquitoes with orco mutations showed reduced preference for the smell of humans over guinea pigs, even in the presence of carbon dioxide, which is thought to help mosquitoes respond to human scent. “By disrupting a single gene, we can fundamentally confuse the mosquito from its task of seeking humans”…

Genetic engineering is gene-centric pseudoscientific nonsense. See: Nothing in cancer makes sense except…

An evolutionary logic pervades all major areas of cancer sciences including causation, cancer clone development and resistance to therapies [10] (Fig. 1).

What some people call evolutionary logic failed to link mutations to beneficial changes in behavior.

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.

George Church refutes theistic evolution (4)

February 15, 2018

by James Kohl with No Comment Adaptations Cytosis Diseases & Disorders Ecology Light Energy microRNA editing Model Organisms Nutrigenomics Physics RNA Directed RNA editing RNA interference

See: George Church refutes theistic evolution (February 9, 2017)
See also: Energy as information and constrained endogenous RNA interference (February 15, 2017)

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 for comparison: Church Speaks A Conversation With George Church (February 14, 2018)

[Arctic grass and] cyanobacteria, on the other hand, they fix [carbon]. Cyanobacteria turn carbon dioxide, a global warming gas, into carbohydrates and other carbon-containing polymers, which sequester the carbon so that they’re no longer global warming gases. They turn it into their own bodies. They do this on such a big scale that about 15 percent of the carbon dioxide in the atmosphere is fixed every year by these cyanobacteria, which is roughly the amount that we’re off from the pre-industrial era. If all of the material that they fix didn’t turn back into carbon dioxide, we’d have solved the global warming problem in a year or two. The reality, however, is that almost as soon as they divide and make baby bacteria, phages break them open, spilling their guts, and they start turning into carbon dioxide. Then all the other things around them start chomping on the bits left over from the phages.

The anti-entropic virucidal quantized energy of sunlight links the creation of ATP to the creation of microRNAs and changes in the energy-dependent microRNA/messenger RNA balance, which link what organisms eat to RNA-mediated fixation of amino acid substitutions that differentiate all cell types in all individuals of all living genera. Simply put, sunlight, food energy, and pheromones biophysically constrain the DNA damage that is done by phages.
Release of the cell biology game “Cytosis” and the forthcoming conference Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses (4 – 8 July 2018 Salzburg – Austria) have forced George Church and others like him to begin telling the scientific truth about how the virus-driven theft of quantized energy is either biophysically constrained, or linked from the virus-driven degradation of messenger RNA to mutations and all pathology.

Chantal Abergel >
Aix-Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Marseille, France
Gustavo Caetano Anolles >
Department of Crop Sciences, Evolutionary Bioinformatics Laboratory, University of Illinois at Urbana-Champaign Urbana, USA.
Marlene Belfort >
Department of Biological Sciences and RNA Institute, University at Albany, New York, USA
Felix Broecker >
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA

Irene Chen >

Department of Chemistry & Biochemistry, University of California, Santa Barbara, USA
Julian Chen >
Department of Chemistry and Biochemistry, Arizona State University, Tempe, USA
Jean-Michel Claverie >
Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille, France
Bryan Cullen >
Department of Molecular Genetics and Microbiology and Center for Virology, Duke University Medical Center, Durham, USA
Valerian Dolja >
Department of Botany and Plant Pathology, Oregon State University, Corvallis, USA
Cedric Feschotte >
Department of Human Genetics, University of Utah, School of Medicine, Salt Lake City, USA
Matthias Fischer >
Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Heidelberg, Germany

David Gilmer >
Institut de biologie moléculaire des plantes, Integrative virology, Strasbourg, France
Reynald Gillet >
Université de Rennes 1, Translation and Folding Team, Rennes cedex, France Institut Universitaire de France
Jordi Gomez >
Instituto de Parasitología y Biomedicina ‘López-Neyra’ (CSIC), Granada, Spain
Matti Jalasvuori >
Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Finland
I.King Jordan >
School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
Eugene Koonin >
National Center for Biotechnology Information, National Library of Medicine, Bethesda, USA.
Dusan Kordis >
Department of Molecular and Biomedical Sciences, Josef Stefan Institute, Ljubljana, Slovenia
Mart Krupovic >
Unit BMGE, Department of Microbiology, Institut Pasteur, Paris, France
Erez Levanon >
Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
German Martinez >
Dept. of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
John Mattick >
Garvan Institute of Medical Research, Darlinghurst, Australia
Jeff Miller >
California NanoSystems Institute, University of California, Los Angeles, USA

Karin Moelling >
Max Planck Institute for molecular Genetics, Berlin, Germany
Sabine Müller >
Universität Greifswald, Institut für Biochemie , Greifswald , Germany
Ulrich Müller >
Department of Chemistry & Biochemistry, University of California, San Diego, USA
Mariusz Nowacki >
Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
David Prangishvili >
Department of Microbiology, BMGE, Institut Pasteur, Paris, France
Lennart Randau >
Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
Forest Rohwer >
Department of Biology, San Diego State University, San Diego, CA, USA
Corrado Spadafora >
Institute of Translational Pharmacology, CNR, Rome, Italy
James Shapiro >
Department of Biochemistry and Molecular Biology , University of Chicago , IL , USA
Jason Shepherd >
Biochemistry and Ophthalmology & Visual SciencesUniversity of Utah, School of Medicine Salt Lake City, USA
Ravindra Singh >
Department of Biomedical Sciences, Iowa State University, Ames, USA
Keizo Tomonaga >
Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
Peter Unrau >
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
Luis P. Villarreal >
Center for Virus Research, University of California, Irvine, Irvine, CA, USA
Andreas Werner >
RNA biology group, Institute for Cell and Molecular Biosciences, Newcastle University, UK
Eric Westhof >
Architecture and Reactivity of RNA, Institute of Molecular and Cellular Biology of the CNRS, University of Strasbourg, France
Bojan Zagrovic >
Department of Structural and Computational Biology, Max F. Perutz Laboratories, Vienna, Austria

Steven Zimmerly >
Department of Biological Sciences, University of Calgary, Calgary, Canada

The MicroRNAome Strikes Back: A Sokalian hoax (10)

February 1, 2018

by James Kohl with No Comment Adaptations Autophagy biophotonics Cytosis Diseases & Disorders Ecology Model Organisms RNA Directed RNA-directed DNA methylation Variations

Linda Buck, Ben Feringa, Michael Gazzaniga, Christof Koch, Nick Lane and Svante Paabo are among the presenters who will almost undoubtedly discuss some or all of my claims.
Prepare to ask questions or intelligently discuss accurate representations of top-down causation by watching this:

The energy-dependent creation of the microRNAome protects the organized genomes of all living genera from the virus-driven degradation of messenger RNA that links mutations to all pathology.
See: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

MicroRNA present in mature sperm appears to not only be left over from spermatogenic processes, but may actually serve important regulatory roles in fertilization and early developmental processes. Further, our results indicate the possibility that environmental changes may impact the expression of specific miRNA.

We conclude that the enzymes involved took these alternatives by chance in independent populations that had already evolved distinct ion pumps. Our model offers a quantitatively robust explanation for why membrane bioenergetics are universal, yet ion pumps and phospholipid membranes arose later and independently in separate populations. Our findings elucidate the paradox that archaea and bacteria share DNA transcription, ribosomal translation, and ATP synthase, yet differ in equally fundamental traits that depend on the membrane, including DNA replication.

The microRNA-mediated creation of enzymes is quantized energy-dependent and biophysically constrained by phosphorylation in the context of food energy and the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes in species from bacteria to primates. Membrane divergence in archaea occurs via the virus-driven degradation of messenger RNA, which links the loss of quantized energy from mutations to all pathology. The degradation of the cell membrane links archaea to L-forms, the last remnant of the life of a cell. See: The Inner Life of the Cell (video)
See also: Virus-mediated archaeal hecatomb in the deep seafloor (2016)

So far as I know, none of the people who are presenting at “The Future of Biology” meeting have linked Schroedinger’s claims from the past to what is known about the conserved molecular mechanisms of energy-dependent biophysically constrained RNA-mediated cell type differentiation in species from microbes to humans. Even if they are not evolutionary theorists, most have not linked the energy-dependent fixation of RNA-mediated amino acid substitutions to increasing organismal complexity and some have even reversed what is known about top-down causation. For example, Nick Lane, like Gunter P. Wagner have used mathematical models of correlations.
See: Pervasive correlated evolution in gene expression shapes cell and tissue type transcriptomes
They start with this admission”

A major challenge for interpreting this data is that cell type transcriptomes may not evolve independently…

They seem to think they can use statistics and interpretations to address the challenge of facts about increasing organismal complexity.

Our study provides a statistical method to measure and account for correlated gene expression evolution when interpreting comparative transcriptome data.

See for comparison: From Fertilization to Adult Sexual Behavior and Nutrient-dependent/pheromone-controlled adaptive evolution: a model
The fact that what organisms eat has been linked from the food energy-dependent creation of enzymes, receptors, and hormones to the affect of hormones on behavior in all invertebrates and vertebrates was placed into the context of the cell biology game, Cytosis.

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

During the month of January (2018), 2831 people learned from my twitter profile about the domains RNA-mediated.com and Autophagy.pro and some of them learned from more than 100,000 impressions how energy must be linked to RNA-mediated biophysically constrained viral latency by autophagy.

Jan 2018 Summary

Tweets

1,199

Tweet impressions

102,000

Profile visits

2,831

Mentions

New followers

Why do I have only 29 new followers? Are theorists really that scared? If so, how will they help to prevent the next viral apocalypse, if it has not already started before September, 2018?

The tipping point (revisited): 68,000 publications

December 21, 2017

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy base editing biophotonics Cytosis Diseases & Disorders Ecology Human Pheromones Light Energy microRNA editing Model Organisms Neuronal Plasticity Nutrigenomics Pharmacogenomics Physics RNA Directed RNA editing RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Variations What's in the News

MicroRNA Items: 1 to 20 of 68011 (earlier today, on 12/21/17)

See for example: In Vitro Validation of miRNA-Mediated Gene Expression Linked to Drug Metabolism 12/20/17

The approaches described can be employed broadly for the validation of miRNA-mediated negative regulation of any gene. Determining miRNA-mediated regulation of enzymes and transporters affecting drug metabolism is a critical step in designing personalized therapy and for understanding the mechanisms responsible for variations in the responses to therapeutic agents.

The “…miRNA-mediated regulation of enzymes and transporters affecting drug metabolism…” links the National Microbiome Initiative to the Precision Medicine Initiative and to all healthy longevity or to all virus-driven pathology in all living genera via differences in energy as information.
For review, see: Energy as information and constrained endogenous RNA interference

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.

For a historical perspective on what is known about energy-dependent RNA-mediated (aka microRNA-mediated) cell type differentiation, see:
The quantum / classical RNA-mediated ‘tipping point’ 3/26/15
The tipping point? 50, 000 publications 5/16/16
The tipping point? 50, 000 publications (2) 5/16/16
The tipping point? 50,000 publications (3) 5/17/16
The tipping point? 50,000 publications (4) 5/26/16
The tipping point? 50,000 publications (5) 7/27/16
The tipping point (revisited): 60,000 4/20/17
By May 16, 2016, the innate antiphage defense strategy was linked from quantum physics to classical physics by 50,000 publications that mentioned microRNAs. Nineteen months later, every aspect of the microRNA-mediated gene expression that had already been linked to drug metabolism attests to the fact that not all scientists have followed the extant literature.
Many scientists are still among the pseudoscientists who who failed to notice the most obvious links from the antiphage defense strategy to healthy longevity. Perhaps they were also too busy to notice the most obvious links from the virus-driven degradation of messenger RNA to the need for drug therapies.
If so, that may explain why the drug therapies have been largely ineffective. The drug therapies may be like vaccinations. They appear to link the virus-driven degradation of messenger RNA to more mutations, which clearly link the virus-driven theft of quantized energy to all pathology.
With more than 18,000 published works in the past 19 months, (8,000 in the past 8 months) it is time to again address the tipping point between quantum physics and classical physics in the context of food energy-dependent pheromone-controlled microRNA-mediated cell type differentiation via what is known about autophagy.
In the context of drug metabolism, the energy-dependent microRNA-mediated creation of enzymes was linked from the metabolism of food to all biodiversity on Earth via pheromone-controlled physiology of reproduction.
See for example page 19 of the sample report from Alpha Genomix that you can download as a pdf here. The food energy-dependent creation of the CYP enzymes protects our organized genome by biophysically constraining viral latency.

See for comparison: Our Top 17 in ’17: The Year in Science at PLOSBLOGS

…the far-reaching war on science being conducted by the Trump administration, an assault on facts which, as several of our bloggers have noted, constitutes a removal of scientific evidence from the formation and discussion of public policy and an evisceration of funding and communication of vital research in medical research and regulation, public health, climate, energy, agriculture and education.

The only war on science that I know about, is the one in which serious scientists are Combating Evolution to Fight Disease. To place that claim into the context of what has happened during 2017, see the retraction of this article.
Biomechanical Characteristics of Hand Coordination in Grasping Activities of Daily Living [retracted]
It was retracted because the authors mentioned the creator of the hand. The creation of the hand occurs only in the context of biophysically constrained viral latency.

See for comparison: Retraction Watch

In retrospect, we were totally blinded by our belief [in our findings]…we were not as careful or rigorous as we should have been (and as Tivoli was) in interpreting these experiments.

Where else besides PLOS have you seen a retraction for the mention of a creator? Where did PLOS report on the retraction for misrepresentations in “Nature Chemistry?” Who still believes that microRNA and messenger RNAs created each other so that they could automagically constrain viral latency?
Who else besides PLOS is waging a far-reaching war on science?
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems 4/10/14

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.

Obama Advisers Urge Action Against CRISPR Bioterror Threat 11/17/16

Scientific advisers to President Obama warn that the U.S. urgently needs a new biodefense strategy and should regularly brief President-elect Donald Trump on the dangers posed by new technologies like CRISPR, gene therapy, and synthetic DNA, which they say could be coöpted by terrorists.

See for comparison: 2017 Global Infectious Diseases Threats to the United States 12/22/16

Flu. Influenza remains one of the greatest threats to the US population killing on average 3,000-49,000 Americans annually. People at the greatest risk of severe flu and death are pregnant women, residents of long-term care facilities, the very old (adults over the age of 65), the very young (children less than 2), Native American populations, and those with underlying chronic conditions such as asthma, COPD, heart disease, obesity, and other conditions. Timely vaccination remains the most proven and effective way to avoid serious injury from influenza.

The new Trump Administration will face a formidable array of global and indigenous infectious disease threats in 2017. A Global Health Security Agenda will help provide a framework for tackling some of these tough issues, but enhanced efforts will be needed to prevent new epidemics, especially from vector-borne and zoonotic neglected tropical diseases, measles, and the ever-constant threats from AMR and flu.

The biggest threat that the Trump administration has faced in the first year is the fake news. The most recent example accused him of censorship at the CDC for his director’s efforts to biophysically constrain energy-dependent viral latency. The CDC director’s efforts to help others with budget concerns were linked to censorship, and the President of the United States was compared to Hitler. Wake up and “Remember the Alamo.”
SARCASM ALERT: No, that was a different war. Wake up and remember the Manhattan Project, which also linked censorship about energy to the winning of a war.

The overwhelming ignorance of sex researchers (2)

December 13, 2017

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy Diseases & Disorders Ecology Model Organisms RNA Directed Variations

Conclusion: There is a clear link from Estrogen receptor α polymorphism in individuals and in species with differences in behavioral phenotypes. The differences are food energy-dependent and RNA-mediated. The differences link the sense of smell and the pheromone-controlled physiology of reproduction in soil bacteria from The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression to the report on the Obligatory role of hypothalamic neuroestradiol during the estrogen-induced LH surge in female ovariectomized rhesus monkeys

Reported on December 12, 2017 as: Estrogen discovery could shed new light on fertility problems

Estradiol builds in the bloodstream until it reaches a concentration that causes a surge of the hypothalamic and pituitary hormones, including one called luteinizing hormone, which in turn trigger an ovary to release an egg.

“It’s a feedback loop…

From our section on “Neurosteroids” in this December 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior

Perhaps significantly, neuron-specific transcription regulation of neurosteroidogenic enzymes and subsequent neurosteroids production suggest clues to mechanisms that allow some persons to develop in accord with typical gonadal male-pattern or female-pattern hormones and have appropriate male-typical or female-typical physiques nonetheless have parameters of their sexual behavior profile quite opposite to their physical phenotype. For instance, it might be possible for local neurosteroid action in CNS loci specific for sexual orientation to operate independently of other hormonal production and separately from gross body morphology in general. This could, for instance, account for different manifestations of transsexualism and homosexuality.

The “gay agenda” served its proponents well as they attempted to bury the facts that link feedback loops from odors and pheromones to biophysically constrained viral latency.

See: Feedback loops link odor and pheromone signaling with reproduction

Most sex researchers still live in fear that the biologically uninformed masses will learn that homosexual orientation is nothing more than another variation of what happens in the context of transgenerational epigenetic inheritance.

See: The overwhelming ignorance of sex researchers (December 8, 2016)

All serious scientists link food energy to the pheromone-controlled physiology of reproduction and autophagy, which protects all organized genomes from the virus-driven degradation of messenger RNA. The virus-driven degradation of messenger RNA links mutations to all pathology in species from microbes to humans.

If you try to make any aspect of pathology specific to any group of individuals in any human population, you challenge the totality of experimental evidence that links top-down causation to healthy longevity. You be forced to admit that you are not perfectly healthy, which means you are not qualified to judge the mental health or judge the physical health of others. The take home message is stop judging anyone based on your ignorance.

See also the author’s copy of this award-winning review: The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences

Abstract:

The across-species genetic conservation of intercellular and extracellular chemical communication enables unicellular and multicellular organisms to functionally distinguish between self and non-self. Non-self olfactory/pheromonal input from the social environment elicits a vertebrate neuroendocrine response. The organization and activation of this neuroendocrine response modulates the concurrent maturation of the mammalian neuroendocrine system, the reproductive system, and the central nervous system during the development of sexual preferences that may be expressed in sexual behavior. Psychophysiological mechanisms for the development of these sexual preferences include focus on unconscious affects that are detailed in reciprocal cause and effect relationships. Olfactory/pheromonal conditioning elicits neuroendocrine effects accompanied by unconscious affects on the development of sexual preferences. Integrating these unconscious affects extends to humans a developmental model of behavior that includes the development of male sexual preferences for other males.

Conclusion:

ISSUES FOR FURTHER CONSIDERATION

Rarely do sex researchers address the ongoing philosophical debate between canonical neo-Darwinism and Biblical creation. Perhaps this is because any debate between scientific theory and religion arises from distinctly different domains of cognitive thought. Does the acceptance of Darwin’s theory represent the glorification of Science pitted against religion, or is it a means by which Science and religion might be integrated? Integration of Science and religion might be achieved by recognizing that the key components of this olfactory/pheromonal model appear to be as irreducibly complex as the basic tenets of evolution and the basic tenets of religion.

From an evolutionary perspective, highly conserved GnRH peptide ligand/receptor signaling mechanisms are the molecular biochemical mechanisms for sexual reproduction in all organisms. These signaling mechanisms also appear to play an integral role in the development of sexual preferences. From a religious perspective, these signaling mechanisms dictate that the creation of life, which begets life, also allows for the creation of diversified life through the same mechanisms. These mechanisms allow life to recognize the difference between self and non-self and to respond to this difference.

Perhaps the creation of diversified human life gave us the ability to recognize differences between our sexual behavior and the sexual behavior of others. Since all life does not beget diversified life, those who judge sexual preferences that do not seem to result in diversified life may be judging creation itself.

It is easy to understand how someone could judge a particular sexual preference, without thought. Unconscious affects that are manifest in the development of human sexual preferences are, by their nature, a part of diversified life that few people think about. What we think about human sexual preferences becomes less meaningful when we realize that most of sexual behavior is not what we cognitively think it should be. Indeed, the largest contributor to sexual preferences that are manifest in the sexual behavior of any species appears to be unconscious affect. This also appears to be the basis for diversified life.

See this claim about diversified life for comparison: New Zealand discovery of fossilised ‘monster bird’ bones reveals a colossal, ancient penguin

Insights into penguin evolution

The other startling thing about the new colossal fossil is its ancient age. At 55 to 60 million years old, it is nearly as old as the earliest penguin ancestors ever found. It would have lived during a geological period known as the Paleocene, just after the mass extinction 66 million years ago that wiped out non-bird dinosaurs.

The most startling thing about this ridiculous claim is that it cannot be linked from anything known to serious scientists about biophysically constrained viral latency to all biodiversity on Earth via the pheromone-controlled physiology of reproduction and chromosomal rearrangements in birds.

See for comparison: Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes

Two fixed differences among 597 amino acids drive a Val73Ile and Ala552Thr (valine to alanine) polymorphism in ZAL2m that distinguish its morphological and behavioral phenotype from ZAL2.

Pheromones biophysically constrain base editing and RNA editing

November 2, 2017

by James Kohl with No Comment Adaptations Alternative Splicings base editing biophotonics Cytosis Diseases & Disorders Ecology Human Pheromones Model Organisms Nutrigenomics Physics RNA Directed RNA editing What's in the News

Summary: …they [Koonin’s group] substitute what they consider to be a plausible hypothesis. It places their observations into the context of a universal trend that is conserved in all life after the trend emerged, which was sometime before the last universal common ancestor of all extant organisms emerged and began to evolve.

Social behaviour shapes hypothalamic neural ensemble representations of conspecific sex Published online 18 October 2017

The vibrational theory of olfaction for the win Published 31 October 2017

Neuronal Representation of Social Information in the Medial Amygdala of Awake Behaving Mice Publication stage: In Press Corrected Proof

Two of the three articles above were reported to the Human Ethology Yahoo Group on November 1, 2017.

89773 Mini-microscopes reveal brain circuitry behind social behavior

See: Mini-microscopes reveal brain circuitry behind social behavior Posted: 31 Oct 2017 12:12 PM PDT

A microscope lens implanted deep inside a mouse’s brain shows different patterns of neural activity when the mouse interacts with males, females, or other stimuli. Now, researchers have discovered that sexual experience can trigger long-term changes in these brain patterns.

Here is the comment I submitted to the Human Ethology Yahoo group, which is moderated by Jay R. Feierman, who (since 1995) I have used as an example of a biologically uninformed science idiot. Feierman, for example, consistently ignores any science news that does not support the pseudoscientific nonsense of his ridiculous theories. For comparison, I wrote:

The creation of quantized energy (i.e., sunlight); the creation of ATP; the creation of RNA; and the physiology of pheromone-controlled biophysically constrained viral latency have been placed into the context of the epigenetically effected changes in brain patterns.

See: The vibrational theory of olfaction for the win

The vibrational theory of olfaction was placed into the context of how Olfaction Warps Visual Time Perception via publication of Feedback loops link odor and pheromone signaling with reproduction

The feedback loops link natural selection for energy-dependent codon optimality from the sense of smell in bacteria to the physiology of pheromone-controlled reproduction in all living genera via naturally occurring base editing, RNA editing, and RNA-directed DNA methylation, which links amino acid substitutions in organized genomes to protection from the virus-driven degradation of messenger RNA. The virus-driven degradation of messenger RNA causes the mutations that cause all pathology in species from bacteria to humans.

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

For comparison see: Single rat muscle Na+ channel mutation confers batrachotoxin autoresistance found in poison-dart frog Phyllobates terribilis

Scientists changed the 1,584th amino acid found in most animals (asparagine) to the amino acid that the poison frogs have at that spot (threonine). The link from all vertebrates to mammals was exemplified when rats with the frog’s version of this protein survived exposure to the toxin. Survival of all species has always been placed into the context of Darwin’s ‘conditions of life.” His conditions are food energy-dependent and pheromone-controlled in the context of the physiology of reproduction. Only biologically uninformed theorists have claimed that mutation-driven evolution somehow occurs in the context of their mathematical models, which have no explanatory power whatsoever. All extant life is ecologically adapted to ecological variation. Extinctions exemplify the exceptions.

Previously, Feierman’s claims became increasingly more foolish. See for example:
7/25/13
Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.
7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
I’m not sure if there is any experimental evidence of biophysically constrained biologically-based cause and effect that supports Feierman’s ridiculous claims, but they may be based on this claim:

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

That claim comes from A universal trend of amino acid gain and loss in protein evolution, which is an example of overwhelming ignorance.
Simply put, they substitute what they consider to be a plausible hypothesis. It places their observations into the context of a universal trend that is conserved in all life after the trend emerged, which was sometime before the last universal common ancestor of all extant organisms emerged and began to evolve.

From base editing to RNA editing (4)

November 1, 2017

by James Kohl with No Comment Adaptations Alternative Splicings base editing Cytosis Diseases & Disorders Ecology Human Pheromones Light Energy Model Organisms Neuronal Plasticity Nutrigenomics Pharmacogenomics Physics RNA Directed RNA editing RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA-mediated toxicity RNA–Mediated Epigenetic Heredity Variations

Summary: To claim evolution, Koonin must link food energy from the pheromone-controlled physiology of reproduction to fixation of a beneficial mutation in the organized genome of one species that evolved into another species.
Search Results for “base editing” = 82 blog posts starting with Cell-type differentiation on February 7, 2014
Search Results for “RNA editing” = 95 blog posts starting with In theory, or supported by experimental evidence? October 22, 2014
See for comparison PubMed: “base editing” (33 citations) and “RNA editing” (4222 citations)
The failure to link energy-dependent base editing to RNA editing and RNA-mediated cell type differentiation in all publications about healthy longevity compared to pathology can be attributed to the pseudoscientific nonsense touted by theorists. In their ridiculous mathematical models, they claimed the emergence of energy could be linked to the evolution of all biodiversity. Their lack of experimental evidence, which is required to link biologically-based cause and effect to biodiversity, was placed into the context of “human idiocy” by Richard P. Feynman.

See Richard P. Feynman’s lecture on: Food energy. See for comparison see: Energy as information and constrained endogenous RNA interference.

The failure to link energy-dependent base editing and energy-dependent RNA editing to healthy longevity predicted the failure to link the virus-driven degradation of messenger RNA to all pathology. See for instance: The Science of Personalized Nutrition

A single nucleotide polymorphism (SNP) or change occurs in nearly 1 in 1,000 base pairs and accounts for much of an individual’s uniqueness. Research on SNPs and other genetic variations like deletions, inversions, duplications and copy number variations (CNV), which represent up to 9.5 percent of the human genome, have changed the face of human nutrition and validated the concept that nutrition could and should be personalized. (Mullally, 2007)

A single nucleotide polymorphism (SNP) is a single base-pair difference in the DNA sequence of individual members of a species. SNPs in genes may lead to variations in the amino acid sequence, but SNPs can also occur in noncoding regions of DNA. Base editing of A•T to G•C in genomic DNA was linked from RNA editing to the physiology of pheromone-controlled reproduction and fixation of amino acid substitutions in organized genomes. The amino acid substitutions differentiate all cell types in all individuals of all living genera.
See: Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage
Reported as: Base Editing Now Able to Convert Adenine-Thymine to Guanine-Cytosine

Bioengineer Feng Zhang of MIT’S Broad Institute notes in an email that the team employed “a comprehensive and creative approach” to achieve such precision. “As a field, we have been looking for ways to precisely rewrite parts of the genetic code,” writes Feng, whose own, CRISPR-based method to edit single bases in RNA was published today in Science. “Base editors move us closer to this goal.”

The CRISPR-based editing of single base pairs in RNA links the energy-dependent function of the innate immune system to all biophysically constrained biodiversity via the pheromone-controlled physiology of reproduction, which biophysically constrains viral latency. Natural selection for energy-dependent codon optimality, links the editing of single base pairs in RNA to every aspect of healthy longevity via RNA editing.
See: RNA editing with CRISPR-Cas13
Reported as: RNA Editing Possible with CRISPR-Cas13

“This work is an impressive study from a highly productive research group that suggests the possibility of editing RNA transcripts to alter their coding potential in a programmable manner,” David Liu…[who] has a report out today in Nature describing specific nucleotide editing of DNA by a similar method.

Feng Zhang (base editing) gives a pat on the back to David Liu (RNA editing), and Liu reciprocated, or vice versa. Taken together, they are making face-saving attempts that ignore everything known to serious scientists about biophysically constrained viral latency.

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

Koonin is a biologically uninformed science idiot who has followed in the footsteps of others like him. Their computations link mutations to evolution across millions of years. The computational biologists are evolutionary biologists who have failed to link food energy from the creation of enzymes and the the RNA-mediated editing of the enzymes, which is required to link differences in sequence changes from fixation of RNA-mediated amino acid substitutions in organized genomes to the prevention of virus-driven messenger RNA degradation. All serious scientists have linked the virus-driven degradation of messenger RNA from mutations to all pathology. Koonin’s claim that “the best is still to come” is moronic.
Every link to energy-dependent RNA-mediated cell type differentiation via the pheromone-controlled fixation of amino acid substitutions has been detailed in the context of experimental evidence. But, Koonin (2016) made this ridiculous claim:

The proper question is: how has this sequence evolved? And the proper null hypothesis posits that it is a result of neutral evolution: that is, it survives by sheer chance provided that it is not deleterious enough to be efficiently purged by purifying selection. To claim adaptation, the neutral null has to be falsified.

To claim evolution, Koonin must link food energy from the pheromone-controlled physiology of reproduction to fixation of a beneficial mutation in the organized genome of one species that evolved into another species.
If Koonin and others like him cannot provide an example of how biologically-based evolution occurs, there is only the pseudoscientific nonsense of their mathematical models for comparison to facts about: How flu shot manufacturing forces influenza to mutate

“Now we can explain — at an atomic level — why egg-based vaccine production is causing problems,” said TSRI Research Associate Nicholas Wu, Ph.D., first author of the study, published recently in the journal PLOS Pathogens.

Clearly, an explanation — at the atomic level — of how viruses adapt to the cell types of one species during the production of an egg-based vaccine must be linked from atoms to ecosystems in all living genera via adaptations in the host.
See for example: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

The genesis of variation is manifested in ecological variation, which confers the ability to adapt via nutrient-dependent epigenetically-effected pheromone-controlled ecological, social, neurogenic, and socio-cognitive niche construction. Niche construction is manifested in organismal complexity. Everything about ecological adaptation appears to make sense in the light of what is currently known about molecular biology. What is currently known about the conserved molecular mechanisms that link the epigenetic landscape to the physical landscape of DNA can now be compared to any forthcoming explanations that attempt to make sense of how mutation-driven evolution might occur.

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

From base editing to RNA editing

October 27, 2017

by James Kohl with No Comment Adaptations Alternative Splicings base editing biophotonics Diseases & Disorders Ecology Light Energy Physics RNA editing RNA-directed DNA methylation RNA–Mediated Epigenetic Heredity Variations

Base Editing Now Able to Convert Adenine-Thymine to Guanine-Cytosine

“Nature conveniently provides us with cytosine deaminase enzymes that operate on DNA,” Liu tells The Scientist.

The creation of quantized energy in sunlight links energy as information from electrons to ecosystems via the physiology of reproduction in all living genera. The claim that “Nature” provides us with cytosine deaminase enzymes makes it seem that the enzymes emerged and automagically evolved to become purposeful and meaningful in the context of ridiculous theories about mutation-driven evolution.
See for comparison: All about that base (video parody)
See also: RNA Editing Possible with CRISPR-Cas13

Introducing specific sequence changes into RNA molecules could allow researchers to answer questions about alternative splicing mechanisms, translation, and even editing, he says. “There’s a lot of scope.”

The entirety of that scope was addressed in the context of energy-dependent RNA-mediated cell type differentiation in our section on molecular epigenetics from this 1996 Hormones and Behavior review. 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 (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 biophysically constrained RNA-mediated energy-dependent cell type differentiation has since been linked from the pheromone-controlled physiology of reproduction to supercoiled DNA via the fixation of amino acid substitutions and chromosomal rearrangements.
The facts about the amino acid substitutions in the context of transgenerational epigenetic inheritance link electrons to ecosystems via the cryo-EM technology that won the 2017 Nobel Prize in Chemistry.
See: Chemists know (video parody)
See also:

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

Scent of Eros

Posts tagged: mutations