viral microRNAs Archives

The MicroRNAome Strikes Back: A Sokalian hoax (3)

January 24, 2018

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy biophotonics Cytosis Diseases & Disorders Ecology Human Brain Human Pheromones Light Energy microRNA editing Model Organisms Neuronal Plasticity Physics RNA Directed RNA interference RNA–Mediated Epigenetic Heredity

One way to recognize a Sokalian hoax is to determine whether the claims can be linked from gravity or from the speed of light on contact with water to feedback loops that biophysically constrain viral latency and all biodiversity in all living genera.

See: Feedback loops link odor and pheromone signaling with reproduction

See for comparison: Chiromagnetic nanoparticles and gels

Reported as: Nanoparticle gel controls twisted light with magnetism

The trick, the researchers found, was to twist the nanoparticles themselves by coating them with amino acids.

What kind of carefully-designed “trick” is that? Could it be linked by serious scientists to the prevention of all pathology?

See:

Energy-dependent light-modulated reversible chemical changes in the chirality of the nanoparticles produces is linked to a heightened sensitivity to magnetism that strengthens the interactions with circularly polarized light. That suggests the next thing that theorists will learn about is achiral glycine in position 6 of the gonadotropin releasing hormone decapeptide. Achiral glycine is the food energy-dependent pheromone-controlled RNA-mediated amino acid substitution that stabilizes all organized genomes in vertebrates that supposedly evolved during the past 600 million years.

See: Evolution of Constrained Gonadotropin-releasing Hormone Ligand Conformation and Receptor Selectivity

These findings indicate that the substitution of glycine for a chiral amino acid in GnRH during evolution allows a more constrained conformation for receptor binding and that this subtle single amino acid substitution in a site remote from the ligand functional domains has marked effects on its structure and activity.

In the context of food and pheromones the “nanoparticles” are microRNAs that link what organisms eat from the pheromone-controlled physiology of reproduction to all biophysically constrained biodiversity via the anti-entropic virucidal effects of sunlight.

There is a model for that:

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.

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.

If serious scientists are right about the protection of organized genomes that has repeatedly been place into the context of feedback loops and autophagy, which protects all orgnanized genomes from virus-driven degradation of their messenger RNA, the recent series of Abcam buyouts can readily be explained.

See: Abcam acquires rights to over 700 Roche products in new licensing deal

The deal marks the latest in a series of moves by Abcam to expand its portfolio, which now includes more than 120,000 products. Since 2011, the biotech has made a number of acquisitions to this end, including AxioMx, Ascent Scientific, Epitomics, Firefly Bioworks and MitoSciences.

This is a fitting end to my efforts to inform others about the amount of pseudoscientific nonsense they have been subjected to during the past few decades. The discovery of the death gene was made by serious scientists working for Abcam in the early 1990s. It was linked from the discovery of pre-mRNAs (now called microRNAs and many other things) and prevention of cancer cell type proliferation in glioblastoma.

See: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene (2011)

It is time for anyone still touting the pseudoscientific nonsense about mutation-driven evolution to prepare for this conference. Mechanisms of Recombination conference

The first preparatory step should be to admit that your commercial interests or your interest in pursuing an academic career in the academic swamp prevented you from examining truth or telling it to help stop the unnecessary suffering and premature death of millions. The next step should be to find a place to hide until all other pseudoscientists proclaim that evolution is ecological adaptation and that they have always known that.

See for comparison: Study finds convergent evolution of gene regulation in humans and mice January 18, 2018

Organisms that aren’t closely related may evolve similar traits as they adapt to similar challenges. It’s called convergent evolution…

No, ecological adaptation is not called convergent evolution.

Legionella pneumophila RpoS (LpRpoS), an alternative sigma factor of RNA polymerase (RNAP), is essential for virulence and stress resistance. To investigate the mechanism of RpoS in the intracellular pathogen L. pneumophila, we determined the high-resolution crystal structure of the LpRpoS 95–195 containing a partial region 1.2 and region 2. The structure of LpRpoS 95–195 reveals that the conserved residues are critical for promoter melting, DNA and core RNAP binding. The differences in regulatory factor binding site between Escherichia coli RpoS and LpRpoS suggest that LpRpoS may employ a distinct mechanism to recruit alternative regulatory factors controlling transcription initiation.

Compare the claims about the “alternative sigma factor of RNA polymerase” and virulence or stress resistance in the context of what is known about food energy-dependent microRNA-mediated biophysically constrained viral latency and healthy longevity.

microRNA Items: 1 to 20 of 69027

See also: The Postmodernism Generator web page (generates a random postmodernist article each time loaded)

Via the use of terms for microRNA that have bastardized the concept of energy-dependent biophysically constrained viral latency, you might be able to create a Postmodernism Generator for pseudoscientists who do not want anyone to know that Abcam applications of current technology will help to prevent or effectively treat activation of your death gene.

At a time when all food energy-dependent pheromone-controlled biodiversity has clearly been linked from the speed of light on contact with water to biophysically constrained viral latency in all genera, what excuse is left for the ignorance of theorists who have never examined the facts in published works like these:

Virus-mediated archaeal hecatomb in the deep seafloor

Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

The "walking fish" walks straight from quantum physics to quantum souls (5)

January 4, 2018

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

Evolutionary determinants of genome-wide nucleotide composition January 1, 2018
1) They place their thoughts about mutation rates into the context of compatibility with mutational spectra.
2)They claim the mutation rate can be linked to mutational spectra that may be free to wander across evolutionary time.
3) They ignore facts that link the energy-dependent maintenance of a suppressed constant genome-wide deleterious rate that obviously occurs in the context of the Virus-mediated archaeal hecatomb in the deep seafloor
4) They eliminate the need for food energy and the pheromone-controlled physiology of reproduction, which protect all organized genomes from the virus-driven degradation of messenger RNA.
5) They link the mutations caused by the degradation of messenger RNA to increasing organismal complexity via mutational spectra.
Summary, these researchers appear to be biologically uninformed science idiots.
See also Luo lab at CUHK publications Microbial Evolution and Ecology
The fact that microbes do not evolve and the fact that ecological variation is biophysically constrained by the food energy-dependent pheromone-controlled physiology of reproduction does not appear to have occurred to any coauthors of any articles from this group with one notable exception.
Single–cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton

Viruses are the most abundant biological entities on Earth, surpassing the number of their potential host cells by at least one order of magnitude (Suttle, 2005). In the ocean, viral infections kill ~10–20% of planktonic biomass each day (Suttle, 2007; Evans and Brussaard, 2012). These infections are believed to have a major impact on microbial community composition, evolution and global geochemical cycles (Jover et al., 2014).

See also: Marine phage genomics: the tip of the iceberg
At some point, all serious scientists expect others to acknowledge the fact that the role bacteriophages play in pathology extends from marine phage genomics to the energy-dependent antiphage defense mechanism referred to as autophagy. Autophagy links food energy from the biophysically constrained pheromone-controlled physiology of reproduction to healthy longevity in all living genera. The facts about autophagy refute all the pseudoscientific nonsense touted by theorists.
See for instance: Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods

By resolving carbon and nitrogen enrichment in viral particles, we demonstrate the power of nanoSIMS tracer experiments in obtaining quantitative estimates for the total number of viruses produced directly from a particular production pathway (by isotopically labeling host substrates). Additionally, we show through laboratory experiments and a pilot field study that BONCAT can be used to directly quantify viral production (via epifluorescence microscopy) with minor sample manipulation and no dependency on conversion factors. This technique can also be used to detect newly synthesized viral proteins. Together these tools will help fill critical gaps in our understanding of the biogeochemical impact of viruses in the ocean.

The resolve of the carbon and nitrogen enrichment in P. fluorescens was linked to autophagy via the nutrient-dependent pheromone-controlled weekend resurrection of the bacterial flagellum. See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
The claim about the “evolutionary resurrection” exemplifies the amount of pseudoscientific nonsense that theorists have placed into the context of energy-dependent pheromone-controlled fixation of RNA-mediated amino acid substitutions that differentiate the cell types of all individuals of all living genera.
A single nucleotide polymorphism (SNP) in ntrB in strain AR2S caused an amino acid substitution [Thr97→Pro97 (T97P)] within the PAS domain of the enzyme sensor NtrB. Another SNP in the fast-spreading strain AR2F in the σ54-dependent EBP gene ntrC alters an amino acid (R442C) within the DNA binding domain. The alteration in the two amino acids were reported as if they were mutations in the context of evolution, which occurred over-the-weekend.
See for comparison Diet and cancer prevention: Dietary compounds, dietary MicroRNAs, and dietary exosomes October 4, 2017

,,,a variety of dietary compounds such as curcumin, green tea, folat, selenium, and soy isoflavones show a wide range anti-cancer properties. It has been showed that these compounds via targeting a sequence of cellular and molecular pathways could be used as suitable options for cancer chemoprevention and cancer therapy. Recently, dietary microRNAs and exosomes have been emerged as attractive players in cancer prevention and cancer therapy. These molecules could change behavior of cancer cells via targeting various cellular and molecular pathways involved in cancer pathogenesis. Hence, the utilization of dietary compounds which are associated with powerful molecules such as microRNAs and exosomes and put them in dietary patterns could contribute to prevention or treatment of various cancers.

Natural agents mediated autophagic signal networks in cancer

When growth factors are withdrawn, the autophagosome forms to induce autophagy [14].

A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution
Classical physics cannot explain how Darwin’s “conditions of life” are linked to the biophysically constrained energy that is released during cell type signalling, which appears to be absolutely and precisely quantized in the context of tunnelling. However, nothing known to serious scientists about tunneling has been linked from experimental evidence of top-down causation to the energy-dependent tunneling. The spurious use of the term “evolution” should be placed into that context.
Docosahexaenoic acid–mediated, targeted and sustained brain delivery of curcumin microemulsion

Conclusion: The superiority of CUR DHA ME in enabling targeted brain delivery of CUR by both intravenous and intranasal administration presents this new formulation as a promising and versatile formulation for application in brain cancer.
MicroRNA: A Novel Target of Curcumin in Cancer Therapy

…curcumin has a variety of pharmacological effects such as antioxidant, anti-cancer, anti-inflammatory, and anti-microbial activities. Anti-cancer effects of curcumin are due to targeting of a wide range of cellular and molecular pathways involved in cancer pathogenesis including NF-kB, MAPK, PTEN, P53, and microRNAs (miRNA) network. Multiple lines of evidence have indicated that curcumin exerts its therapeutic effects via regulating miRNA expression (e.g. miR-1, miR-7, miR-9, miR-34a, miR-181, miR-21 and miR-19) which could lead to the regulation of underlying cellular and molecular pathways involved in cancer pathogenesis.

At some point, the facts must be recognized by even the most biologically uninformed researchers in the world. See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

Electron cloud superimposed on the yin yang symbol

The "walking fish" walks straight from quantum physics to quantum souls (3)

January 3, 2018

by James Kohl with No Comment Adaptations Alternative Splicings Autophagy base editing biophotonics Cytosis Diseases & Disorders Ecology Light Energy microRNA editing Model Organisms Nutrigenomics 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 Subatomic Variations

The molecular dynamics of the hydrophobic amino acid, valine, link the anti-entropic virucidal energy of sunlight from the Second Law of Thermodynamics to the energy-dependent and temperature-dependent orientational dynamics of the structure of water via methylation and acetylation in the C and N terminus, respectively.
The quantized energy of sunlight must be linked from energy as information to energy-dependent methylation and acetylation to all biodiversity via the effect of the energy on contact with water and the physiology of pheromone-controlled reproduction in the context of changes in base pairs and fixation of RNA-mediated amino acid substitutions that differentiate all cell types in all living genera.
Philip Ball inadvertently claims to have missed all the scientific progress during the past 5 decades in: Chiral water in DNA’s hydration shell

I missed previously this nice paper from H. F. M. C. Martiniano and Nuno Galamba in Lisbon on the structure and dynamics of water around a hydrophobic amino acid…

Philip Ball’s admission can be linked to the ignorance of food energy-dependent pheromone-controlled biophysically constrained viral latency in all living genera. Food energy links sunlight on contact with water to hydrophobicity in supercoiled DNA.
From last year: Worms dine on nanoparticles to help test biological force sensor technology

Adding to Goodman’s previous research on how neurons process the sensation of touch, this technique could also enhance our understanding of the forces involved in sensing the world around us. “More detail about how we experience touch could inform the translation of touch into non-biological systems, like prosthetics,” Goodman said.

The spurious link from touch to biological systems and/or non-biological systems makes it seem that — like Philip Ball — they are oblivious to the fact that serious scientists linked

1) the de novo creation of anti-entropic virucidal light to

2) chirality, which links

3) the speed of light

4) on contact with water from the

5) de novo creation of G protein coupled receptors and

6) all energy-dependent biodiversity via

7) the innate immune system,

8) autophagy,

9) the physiology of reproduction, and

10) supercoiled DNA, which

11) protects all organized genomes from

12) virus-driven energy theft and

13) genomic entropy.

The thirteen steps that link sunlight to healthy longevity and the virus-driven theft of quantized energy to all pathology were placed into a context of a section in the news report on worms:

From worm food to human health

The fact that worms and humans must eat to be healthy was not included in the publication on touch in July 2017 as Upconverting Nanoparticles as Optical Sensors of Nano- to Micro-Newton Forces.
The link from nanoparticles to optical sensors via micro-Newton forces preceded retractions of two works that reported on the automagical creation of RNA.
The creation of RNA is food energy-dependent and it was linked from the creation of ATP to all biodiversity in 1964.
See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

See for comparison: ”Definitely embarrassing:” Nobel Laureate retracts non-reproducible paper in Nature journal

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.

Philip Ball has now linked what he calls Chiral water from the structure and dynamics of water around a hydrophobic amino acid to supercoiled DNA, which links sunlight and food energy to protection of all organized genomes from the virus-driven degradation of messenger RNA. The virus-driven degradation of messenger RNA links the theft of quantized energy from mutations to all pathology. Nothing from the claims about optical sensors is pertinent outside the context of the fact that all organisms must find food and reproduce for any species to survive.

That is why I am adding my comments from last year on: Worms dine on nanoparticles to help test biological force sensor technology. Philip Ball must have missed these facts, also.

Two epigenetic traps are required to link hydrogen-atom transfer in DNA base pairs in solution to the energy-dependent physiology of pheromone-controlled reproduction. It is unlikely that the traps automagically emerged and more unlikely that any species has ever evolved from any other species via mutations and natural selection. Instead, the epigenetic traps make it perfectly clear that evolutionary theorists and “big bang” cosmologists know nothing about energy-dependent biophysically constrained RNA-mediated cell type differentiation.

That fact may explain why Vice-President Pence wants the students in public schools to be taught how ecological variation must be linked to ecological adaptation via everything known to physicists, chemists, and biologists. All serious scientists have linked what is known about molecular epigenetics from energy-dependent changes in electrons to to ecosystems in all living genera.

If we raise another generation of students who are biologically uninformed, some human populations in the USA might as well agree to be the naturally selected victims of the forthcoming viral apocalypse. When large populations begin to suffer unnecessarily and die prematurely, the 1918 Spanish flu will be remembered as the harbinger of ignorance that led to the suffering and death of millions, mostly in the cities of the USA. That’s where the panic and riots start.

You’ve read about this in books (Arrowsmith, 1925) and seen the movies. Prepare yourself for the reality of energy-dependent chirality. It’s the First Law of Thermodynamics that everyone must eventually accept. Food energy is biophysically constrained in all cell types until the virus-driven theft of quantized energy links the degradation of messenger RNA from mutations to all pathology.

It would be great if that fact was taught in public schools instead of teaching students to believe in pseudoscientific nonsense. In any case, the sun’s anti-entropic virucidal energy cannot simply be removed from consideration by theorists and/or so called science journalists who have failed to link quantum physics to quantum souls.

See: Grandfather Paradox, Time Travel, Energy, Life, Death and the Mobius Strip (video)

See for comparison: Quantum secret sharing for a multipartite system under energy dissipation

… noise is associated with energy dissipation and hence, loss of probability to distinguish and decode the information at the receiving end. Finally, we make this task possible through an optimization algorithm.

In their optimization algorithm, a mathematical model is applied to all forms of life on Earth but the dissipation of energy is not linked to death. Everyone who believes that energy cannot be created or destroyed knows that there is no “quantum secret.” Dissipated energy does not vanish in the context of any model that links the functional structure of supercoiled DNA to the protection of all organized genomes from the virus-driven degradation of messenger RNA.
When theorists tout secrets in the context of quantum physics, the secrets of their mathematical models can be compared to facts. See: Structural diversity of supercoiled DNA
The functional structure and the diversity of supercoiled DNA is energy dependent and biophysically constrained by temperature dependent changes in amino acid substitutions.
See also: Temperature dependence of amino acid hydrophobicities
Reported as: Early Code

“Our work shows that the close linkage between the physical properties of amino acids, the genetic code, and protein folding was likely essential from the beginning, long before large, sophisticated molecules arrived on the scene,” Carter said in a statement. “This close interaction was likely the key factor in the evolution from building blocks to organisms.”

The pseudoscientific nonsense of the historical perspective on evolution was included in this 2005 claim: Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.
My comment to The Scientist on the Early Code:

Simultaneous emergence was suggested by Matti Pitkanen who pirated my model of biophysically constrained RNA-mediated cell type differentiation and claimed that “Hens and eggs emerged simultaneously.”

Serious scientists now appear to have discovered the link from the light-induced de novo creation of amino acids to the de novo creation of receptors that link RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of genera via the nutrient-dependent chemistry of RNA-mediated protein folding.

The nutrient-dependent physiology of metabolic networks and genetic networks link reproduction to fixation of the amino acid substitutions, which enables all extant biophysically constrained biodiversity, which is exemplified in differences in morphological and behavioral phenotypes.

Claims of simultaneous emergence should be supported by experimental evidence of biologically-based cause and effect, or abandoned along with claims of Mutation-Driven Evolution, like this one: “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.” (p. 199)

For comparison, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which was published on the same day as Nei’s textbook: June 14, 2013.

Historical perspective from Jon Lieff who is a very confused award-winning blogger: Synchronizing with Brain Clocks

The three previous posts have described new research that each living cell has its own individual clocks based on genetic feedback loops combined with epigenetic loops. The three posts described the discovery of individual clocks, the relation to metabolic cycles in tissues and other cells, and the way immune cell cycles alter responses based on clocks.

The three posts he mentioned fail to include any citations, such as a citation to my published 2013 review, which was a refutation of the neo-Darwinian pseudoscientific nonsense. Jon Lieff has continued to tout his pseudoscietific nonsense after I told him about food energy-dependent Alternative Splicings of RNA on October 27, 2013.
See my comment on his misrepresentations of: Alternative RNA Splicing in Evolution

In our 1996 Hormones and Behavior review, we wrote:”Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans.”

From Fertilization to Adult Sexual Behavior

The alternative splicings are nutrient-dependent and appear to be enabled by the experience-dependent de novo creation of olfactory receptor genes, which enable additional receptor-mediated nutrient uptake and the metabolism of nutrients to species-specific blends of pheromones that control reproduction in species from microbes to man.

Your focus on the importance of pre-mRNA and alternative splicing is exemplary, especially in the context of neuronal plasticity.

C. elegans is the model organism of neurogenic niche construction that links nutrient-dependent ecological and pheromone-controlled social niche construction to socio-cognitive niche construction in vertebrates and invertebrates. See for review:

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

What you are helping to detail is self-assembly with evidence of olfactory/pheromonal self-organization that is currently missing from evolutionary theory, which attributes speciation to mutation-initiated natural selection even though there is no experimental evidence for that (as I mentioned elsewhere).

See for comparison: Promises and Challenges in Continuous Tracking Utilizing Amino Acids in Skin Secretions for Active Multi-Factor Biometric Authentication for Cybersecurity
In Figure 1., they link the biophysically constrained biocatalytic cascade via two optical detection pathways to the energy-dependent creation of three amino acids. This extends what is known about natural selection for food energy-dependent codon optimality to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans.
The key to understanding how ecological variation must be linked to ecological adaptations is the role played by fixation of RNA-mediated amino acid substitutions. The measurement of NADH (energy) at 340 nm (ultraviolet), and the conversion of NADH (energy) to a observable yellow color at 580 nm links quantized energy as information from ultraviolet (UV) light to the visible spectrum. That fact is also manifested in results from chemistry testing and other laboratory testing that helps physicians diagnose and effectively treat their sick patients.
Chemists and molecular biologists must know how to link physics to results of diagnostic testing.
See: The Gene Polymorphism of VMAT2 Decrease the Risk of Developing SCZ in Male Han Chinese (link opens pdf)

A GWAS research found an female-specific association with rs7341475 in reelin (RELN ) gene [30]. Most interestingly, in a study show in a same gene, different SNPs conduct different sex-spefic effect: eg, SNPs rs3891636, rs7728773, rs2189663,rs3864283, and rs2526303 of HINT1 gene significant among the female subjects alone, whereas SNP rs7735116 was significant among males alone [31]. These studies indicate there may exit sexspecific genetic risk and protective factors to SCZ.

I placed the failure of all theorists to link energy-dependent changes in base pairs from SNPs to the RNA-mediated amino acid substitutions that differentiate all cell types in all living genera into the context of this invited review of nutritional epigenetics,

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

For comparison to the VMAT2 polymorphism linked to thje decreased risk of schizophrenia, I took a broad-based approach. The ingestion of sago palm-like leaves linked increased endogenous vitamin C from the stablility of the organized genome in mice to the stability of the organized genome in a modern human population via this report: Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant.
They linked one a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2 to differences in the morphological and behavioral phenotypes of species from mice to humans. Note: rs3827760 is also known as 1540T/C, 370A or Val370Ala. Nothing known to serious scientists about biophysically constrained biologically-based cause and effect suggest that base pairs and amino acid substitutions evolved to create proteins.
For comparison to Szostak’s retracted claims about RNA, see: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism and compare what is known to serious scientists to the claims of creationists.
Oops! Scientific retraction a major blow to evolution theory

The finding is the latest in a “replication crisis” sweeping the scientific community in which apparent breakthroughs cannot be repeated by other researchers.

Szostak’s study reopens what is perhaps the largest hole in evolutionary theory, as scientists remain unable to explain how the building blocks of life were “spontaneously” created.

Szostak’s comment that his team was “blinded by our belief” is significant. Previously, he condemned “belief systems based on faith” as “inherently dangerous, as they leave the believer susceptible to manipulation when skepticism and inquiry are discouraged.”

My invited review of nutritional epigenetics was returned without review, and no one has commented on the representations in Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems that link energy-dependent changes from electrons to ecosystems in all living genera via more than 68,000 published works on microRNAs.
See for instance: Two-Color-Based Nanoflares for Multiplexed MicroRNAs Imaging in Live Cells

…two-color-based nanoflares can simultaneously detect miR-21 and miR-141 expression levels in various live cancer cells successfully. Compared to the traditional single-color-based nanoflares, the two-color-based nanoflares could offer more reliable and practical information for cancer detection, improving the accuracy of early disease diagnosis.

Diagnostics: The changes in the the two-color-based nanoflares will eventually be used to determine the differences in the number of viral microRNAs compared to the number of food energy-dependent microRNAs. The differences will link the weekend resurrection of the bacterial flagellum in P. fluorescens to cell type differentiation in the “walking fish” via dietary differences and biophysically constrained pheromone-controlled reproduction, which requires a source of ingested iodine for the maturation of sex differences in cell types.
Treatment: Exosomes from human umbilical cord blood accelerate cutaneous wound healing through miR-21-3p-mediated promotion of angiogenesis and fibroblast function

Faith in evolution: Paleontology as a molecular science

October 16, 2017

by James Kohl with No Comment Adaptations Cytosis Diseases & Disorders Ecology Human Pheromones Model Organisms RNA Directed RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Subatomic

Keeping the faith

For the last 20 years, Mary Schweitzer, a paleontologist at North Carolina State University in Raleigh, has amassed a wealth of evidence that she’s isolated protein fragments from dinosaurs as much as 80 million years old. That bucks the conventional wisdom among paleontologists who argue that proteins, which are made of chains of amino acids, can’t survive more than 1 million years or so. So far, no group other than Schweitzer and her collaborators has managed to replicate the findings. She contends that’s because others don’t follow her methods. If Schweitzer is right and outside researchers eventually do confirm her findings, it could transform dinosaur paleontology into a molecular science. That, in turn, could help researchers answer long-standing questions, such as whether dinosaurs were warm- or cold-blooded, and work out the dinosaur family tree.

The evidence does not show that the protein fragments are from dinosaurs as much as 80 million years old. No experimental evidence of biophysically constrained biologically-based cause and effect suggests that is possible. But she is keeping her faith in evolution despite the fact the nothing but mathematical models support that pseudoscientific nonsense.
See for comparison: Paths of the Trinity: Being-in-Relationship as Theology, an Answer to Zen Buddhism
In the comments, Jay Kimooyoung wrote:

As people get more informed of the range of interpretive tools that have been avalialbe across different times and different cultures, with their commonality and distinctions, both apparent and real, hopefully they will interact with the world more freely, and then collectively enter into a more ‘enlightend’ stage in the next chapter of our history.

The 2017 Nobel Laureates in Chemistry shared their prize for linking energy-dependent changes from electrons to ecosystems in all living genera via the cryo-EM technology that enables observation at the level of changes in atoms and hydrogen-atom transfer in DNA base pairs in solution. Virus-driven theft of quantized energy occurs at that level of examination, which is how the degradation of messenger RNA is linked to all pathology. If you are not willing to “inform yourself” or to believe serious scientists, do not wait for anyone to “…enter into a more ‘enlightend’ stage in the next chapter of our history.”
Energy is information. The virus driven energy theft that links the degradation of messenger RNA to all pathology is proof that the number of biologically uninformed science idiots who claim to be scientists is greater than the number of serious scientists. The number of self-serving theologians is of secondary concern.
Jay Kimooyoung

New discoveries are made through numerous attempted experiements. Such attempts require huge investment of energy and accumulated information. In the development of science, they are as much the integral part as pigeonhalling confirmed data. Attempted memes are the background soil for the progress in science.

And more so is with the situation of theology. What ultimately validates is not correspondence according to objectified criteria. It is the extent of sincere dedication that serves to carry the weight of life. In that sense, every theology contains element of self-service. Concern could be a matter of degree rather.

To my horror, “Answers in Genesis” just published Celebrate Your Inner Virus — a reversal of their long-standing theological perspective that links the “Curse” from the virus-driven degradation of messenger RNA to all pathology.

It is important that we understand the design present in viruses because God made them

See for comparison: Did God Make Pathogenic Viruses?

Pathogenesis is evidence of something gone wrong, a mutation or the accidental movement of genes, and not evidence of a system deliberately designed to cause human disease and suffering.

My life’s works have served to refute all the pseudoscientific nonsense touted by neo-Darwinists and “Big Bang” cosmologists. “Answers in Genesis” now appears to be supporting them.
See for comparison: https://www.youtube.com/watch?v=HaKf2VuOyl0&feature=youtu.be Video interview about the death of Robin Williams Quantum Souls Published on 10 May 2017
https://www.youtube.com/watch?v=OIkbH9dcAkw&feature=youtu.be Superbugs, Bacteriophages and Phage Therapy: An Interview with James Kohl Published on 17 May 2017
https://www.youtube.com/watch?v=iTvT0p9Q5TY Food Energy-Dependent Cell Type Differentiation Refutes Theory of Evolution
https://www.youtube.com/watch?v=wfPy5QDJp7w&feature=youtu.be How to Treat Cancer as a Disorder of Energy Transfer
https://www.youtube.com/watch?v=s7_fQ2fS5UY&feature=youtu.be Charles Darwin Taught Conditions of Life, Not Mutations
https://www.youtube.com/watch?v=HCQI7fMi8ts Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 1
https://www.youtube.com/watch?v=ObHVOdi99Rw Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 2
See also: Base-pair opening dynamics of the microRNA precursor pri-miR156a affect temperature-responsive flowering in Arabidopsis

Based on these results, we propose that fine-tuning of the base-pair stability at the cleavage site is essential for efficient processing of pri-miR156a at a low temperature and for reduced flowering sensitivity to ambient temperature changes.

All the co-authors are from South Korea and so is Jay Kimooyoung.
I ride for God and country with the American Legion Riders. See for comparison: Energy as information and constrained endogenous RNA interference

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

Re: The viral hecatomb
In his 2010 publication “The Great Pheromone Myth“, Richard L. Doty challenged all accurate representations of the top-down energy-dependent creation of RNA and biophysically constrained pheromone-controlled biodiversity.
On 5/16/17, he published: Olfactory dysfunction in neurodegenerative diseases: is there a common pathological substrate?

…antibodies or other evidence of viral infection have been found to be higher in the autopsied brains of people with neurodegenerative diseases with the most smell loss (figure 2), relative to the brains of healthy controls. Whether a close relationship exists between smell dysfunction and antibodies or other indicators of viral involvement is unknown.

The close relationship that exists between smell dysfunction indicators of viral involvement has been exquisitely detailed in my life’s history of published works and presentations. All of them link what is now known about the virus-driven degradation of messenger RNA from mutations to all pathology in species from microbes to humans.
See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

Currently, only a limited number of miRNA and miRNA-like RNAs have been found in bacteria and viruses, a number that is sure to increase rapidly in the future. The interactions of these small noncoding RNAs in such primitive species have wide-reaching effects, from increasing viral and bacterial proliferation, better responses to stress, increased virulence, to manipulation of host immune responses to provide a more ideal environment for these pathogens to thrive. Here, we explore those roles to obtain a better grasp of just how complicated disease truly is.

…inducible provirus-host interactions occurring in these systems can profoundly influence the functioning of the microbial food web and the efficiency in the energy transfer to the higher trophic levels.

Summary: The virus-driven theft of quantized energy prevents the efficient transfer of energy that is required to link the physiology of pheromone-controlled reproduction to all biodiversity on Earth. Instead, the virus-driven degradation of messenger RNA has been linked to all pathology.
Remember, anytime a pseudoscientist like Richard L. Doty claims that mammalian pheromones and/or human pheromones do not exist, that pseudoscientist is trying to cover up a history of ignorance. The history of ignorance has caused the unnecessary suffering and premature death of millions of people during the past two decades. Pseudoscientists have placed their faith in evolution and in the nonsense touted by people like Doty, who never learned to link the metabolism of food energy to pheromones or linked species-specific pheromones from the physiology of reproduction to biophysically constrained viral latency and all biodiversity.
See for comparison: “Cytosis”

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

Energy-dependent physical and biophysical constraints (6)

July 27, 2017

by James Kohl with One Comment Adaptations biophotonics Diseases & Disorders Ecology Light Energy Model Organisms Nutrigenomics RNA Directed RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression Variations

Conclusion: Like Richard Dawkins, Magnus S. Magnusson is a pseudoscientist.

A light-induced change in an endogenous substrate found in all cell types of all living genera links femtosecond blasts of UV light from the de novo creation of the innate immune system to RNA-mediated DNA repair in species from microbes to humans. The theft of quantized energy by viruses has been linked to all pathology.

The speed at which quantum decoherence occurs makes it difficult for virus-driven energy theft to be carried from one generation to the next via chromosomal inheritance, which is the only way that nutrient-dependent pheromone-controlled transgenerational epigenetic inheritance occurs — if it does not occur automagically in the small minds of theorists.

See first: Energy-dependent physical and biophysical constraints (5)
See next: Design of a synthetic yeast genome
They use what occurs in the context of natural selection for quantized energy-dependent changes in base pairs and link RNA-mediated amino acid substitutions from changes in enzymes and feedback loops. The feedback loops link the pheromone-controlled de novo creation of more receptors via the physiology of reproduction, which biophysically constrains viral latency in all organized genomes.
Their work was reported today, July 26, 2017 in the context of Scientists build DNA from scratch to alter life’s blueprint with my emphasis

Boeke, a researcher at New York University, directs an international team of 11 labs on four continents working to “rewrite” the yeast genome, following a detailed plan they published in March.

The research may reveal basic, hidden rules that govern the structure and functioning of genomes.

All serious scientists known that the structure and function of all organized genomes is energy-dependent and RNA-mediated. For example, in all animals the functional structure of supercoiled DNA is controlled by food odors and pheromones in the context of the physiology of energy-dependent reproduction that links food energy-dependent changes in the microRNA/messenger RNA balance to healthy longevity. Alternatively, virus-driven energy theft links the degradation of messenger RNA from mutations to all pathology.

See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

The question arises: Does Boeke or anyone like him know that the organized genome of yeast is rewritten only in the context of the food energy-dependent pheromone-controlled biophysical constraints on viral latency? I ask because he may be hiding something. Anyone who does not know how chirality and autophagy biophysically constrain viral latency is not likely to have written a book chapter like this, which was co-authored by J.D. Boeke in 1988.

See: Yeast Ty Elements as Retroviruses in Viruses of Fungi and Simple Eukaryotes

The title of J.D. Boeke’s latest effort: Design of a synthetic yeast genome, would make any young earth creationist proud of his Boeke’s accomplishment. It attests to facts about “design” that atheistic hate mongers like Richard Dawkins and other pseudoscientists have linked from mutations and natural selection to evolution.

See: Mutation-Driven Evolution

See also for example: Magnus S. Magnusson’s comments on Richard Dawkins event cancelled over his ‘abusive speech against Islam’ Magunsson started removing my responses a few hours ago.

I attempted to discuss the fact that Boeke and others use base substitutions within ORFs to introduce or remove enzyme recognition sites. That is how they facilitate the energy-dependent assembly of synthetic chromosomes.

But there’s more! Boeke’s history of publications links nearly 30 years of pseudoscientific nonsense to an impressive refutation of neo-Darwinian theory. The design of the synthetic yeast genome via the energy-dependent assembly of synthetic chromosomes attests to the fact that natural selection for energy-dependent codon optimality is the link to the design of all biophysically constrained biodiversity.

See for instance: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

Some people might think that pseudoscientists can recover from refutation linked to the stability of messenger RNA (mRNA), but the recovery time ended two decades ago with publication of From Fertilization to Adult Sexual Behavior

See our section on molecular epigenetics.

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…

The proteins do not automagically create themselves. Energy-dependent changes in chirality must be linked from autophagy to biophysically constrained viral latency. In that context, this report is another clear refutation of mutation-driven evolution.

See: Lipophilic siRNA targets albumin in situ and promotes bioavailability, tumor penetration, and carrier-free gene silencing

These data reveal the immense promise of in situ albumin targeting for development of translational, carrier-free RNAi-based cancer therapies.

The increased amount of information on naturally occurring energy-dependent RNA interference (RNAi) linked to cancer treatment was reported as: Molecular hitchhiker on human protein signals tumors to self-destruct

“What fascinates and excites me most about this approach, in addition to improved tumor penetration, is lack of toxicity at a relatively high dose,” she said. “We could potentially use our siRNA delivery system to target several genes simultaneously or sequentially. Most cancers are driven by multiple abnormal genes, so targeting one often leads to activation of others as the tumor adapts.”

Tumors do not adapt. Viruses quickly adapt via energy theft and the substitutions of amino acids in their genomes. The amino acid substitutions in the tumors cause the tumors to adapt to the lack of energy-dependent microRNAs carried by albumin. That is how virus-driven energy theft is linked to the proliferation of undifferentiated cell types in all tissues of all organisms.

See: The phylogenetic utility and functional constraint of microRNA flanking sequences

As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.

The energy-dependent microRNA flanking sequences do not evolve and genes do not assemble themselves. Quantized energy as information biophysically constrains virus-driven energy theft, which would otherwise link mutations to all pathology.

Young earth creationists recently placed the virus-driven theft of quantized energy into the context of Cancer Research Confirms the Curse.

…the cancer-suppressing molecule NAD+ diminishes with age appeared in the same Science issue.³Harvard Medical School News summarized the findings. As NAD+ lessens, “DNA breaks go unrepaired and, as these breaks accumulate over time, precipitate cell damage, cell mutations, cell death and loss of organ function.”⁴ It seems the only way to cure cancer would be to somehow reach into and constantly correct every cell’s mutations.

Carrier-free gene silencing links femtosecond blasts of UV light from the anti-entropic virucidal effects of sunlight on contact with water to everything serious scientists know about food energy-dependent top-down causation and changes in the microRNA/messenger RNA balance, which have been linked to all biophysically constrained biodiversity via what organisms eat and the physiology of their pheromone-controlled reproduction.

See: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

The sequences have been selected according special charge distributions and lifetimes of excimer states previously characterized by femtosecond infrared spectroscopy.(3a, 3c, 3d) With these selected sequences we demonstrate that repair occurs when the intrastrand charge transfer leads to a suitably charged nucleotide adjacent to the lesion.

A femtosecond is the SI unit of time equal to 10⁻¹⁵ or ¹/_{1,000,000,000,000,000} of a second; that is, one quadrillionth, or one millionth of one billionth, of a second.^[1] For context, a femtosecond is to a second as a second is to about 31.71 million years; a ray of light travels approximately 0.3 µm (micrometers) in 1 femtosecond, a distance comparable to the diameter of a virus.^[2]

For comparison: One picosecond is equal to 1000 femtoseconds (fs). Theoretical physicists who thought they knew something about the nature of quantum coherence based their theories on measurements of timescales up to 1.5 picoseconds (ps), but they have since learned that decoherence occurs within 60 fs. The transfer of energy in the context of photosynthesis clearly links the anti-entropic virucidal energy of UV light to RNA-mediated DNA repair in much less time than theorists realized.

See: Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer

Given the relatively well-defined structure of the FMO protein, and comparative couplings between chlorophylls to other photosynthetic systems, the observed extremely fast decoherence should be viewed as general, bringing to question any significant quantum coherent transport contributions to photosynthesis.

…unlike the theoretical predictions, analysis of the OLYMPUS measurements suggests that, most of the time, only one of the photons has high energy, while the other must carry very little energy indeed…

The differences in the energy of photons and the amount of time it takes for energy-dependent RNA-mediated DNA repair link displays of ignorance by Magnus S. Magnusson and other atheistic hate-mongers that can be compared to any display by anyone who has ever been involved in linking pattern recognition to biophysically constrained life on Earth.

For comparison, that is what young earth creationists have done with the information about energy as information from Biblical Genesis.

The light’s coming off at different angles, with different colors, depending on how bright it is.

That phenomenon stemmed partly from a change in the electron, which abandoned its usual up-and-down motion in favor of a figure-8 flight pattern. As it would under normal conditions, the electron also ejected its own photon, which was jarred loose by the energy of the incoming photons. But the researchers found that the ejected photon absorbed the collective energy of all the scattered photons, granting it the energy and wavelength of an X-ray.

See: The Reality of Color Is Perception

Color is one of the longstanding puzzles in philosophy, raising doubts about the truthfulness of our sensory grasp on things, and provoking concerns as to the metaphysical compatibility of scientific, perceptual, and common sense representations of the world. Most philosophers have argued that colors are either real or not real, physical or psychological. The greater challenge is to theorize the subtle way that color stands between our understanding of the physical and the psychological.

See for comparison: Olfaction Warps Visual Time Perception

The fact that olfaction warps visual time perception links the speed of light on contact with water from the visual appeal of a rainbow to the integration of all sensory input and our appreciation of how energy and mass are linked across the time-space continuum via what is known about the sense of smell in bacteria and the food energy-dependent pheromone-controlled physiology of reproduction in all living genera.

For comparison, Magnus S. Magnusson co-authored “Complex spike patterns in olfactory bulb neuronal networks” He and his colleagues failed to link fast decoherence from the anti-entropic virucidal energy of sunlight to all biodiversity via the physiology of reproduction and RNA-mediated DNA repair.

In the world of those who have consistently linked olfaction to our visual perception of energy and mass in the context of the space-time continuum, Magnusson can be referred to as a biologically uninformed science idiot — if only because he has no expertise in any scientific discipline.

Conclusion: Like Richard Dawkins, Magnus S. Magnusson is a pseudoscientist.

Although that fact has been repeatedly revealed in the extant scientific literature, which includes texts like the Holy Bible, atheistic hate-mongers refuse to read anything that challenges their beliefs at the same time they either claim to believe in nothing or attack the beliefs of intelligent scientists.

See for examples of what pseudoscientists are likely to believe.

This New Equation Could Unite The Two Biggest Theories in Physics

Quantum entanglement… describes the way that two particles can interact in such a way that they become inexorably linked, and essentially ‘share’ an existence.

The Universe According to Emmy Noethe

…energy may not be conserved “locally” — that is, in an arbitrarily small patch of space — but everything works out when the space is sufficiently large.

That claim forced others to make their ridiculous theories fit into the context of “…the idea that the Universe expanded just like a balloon shortly after the Big Bang.”

Stephen Hawking And 32 Top Physicists Just Signed a Heated Letter on The Universe’s Origin

…three physicists heavily criticised inflation theory – the idea that the Universe expanded just like a balloon shortly after the Big Bang. The article went as far as claiming that the model “cannot be evaluated using the scientific method” – the academic equivalent of saying it isn’t even real science.

God's shrinking role in salvation (2)

June 14, 2017

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

Conclusion: There is no such thing as a blind dance of atoms. Quantized energy-dependent changes link angstroms to ecosystems in all living genera via the physiology of reproduction. Serious scientists do not link “high-level cause and purposes” to anything that does not link what organisms eat from food energy to the physiology of reproduction. Only pseudoscientists claim that ideas about “emergence” are “…a remarkable synthesis across fields and levels.”
See: God’s shrinking role in salvation

These 6 Common Vegetables Are Actually All The Same Plant Species
The morphological traits are quantized energy-dependent, They link the de novo creation of plant microRNAs from the anti-entropic virucidal energy of sunlight to the physiology of reproduction in all living genera via the energy-dependent creation of microRNAs in animals.
See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

The interactions of these small noncoding RNAs in such primitive species have wide-reaching effects, from increasing viral and bacterial proliferation, better responses to stress, increased virulence, to manipulation of host immune responses to provide a more ideal environment for these pathogens to thrive. Here, we explore those roles to obtain a better grasp of just how complicated disease truly is.

Disease is much more complicated when it cannot be linked from top-down causation via physics, chemistry, and molecular biology. See for comparison; ‘Liquid Light’ Can Bend Around Objects in a Frictionless Flow
Thanks to Fiona Myrglwitz for calling attention to this claim that they can:

…conceive and design future photonic superfluid-based devices where losses are completely suppressed.

That suggests they may link the metabolism of bacteria from the creation of uranium isotopes to the errors made in mathematical models of evolved traits. The errors in mathematical models fail to link quantized energy-dependent changes in the microRNA/messenger RNA balance to the biophysically constrained by the physiology of reproduction.The errors are magnified by the fact that they fail to link incompletely suppressed energy losses to all pathology via the virus-driven degradation of messenger RNA.

For comparison, the physiology of reproduction links the solar analemma to the biophysically constrained energy in uranium, which is the reason that radiation therapy is used to treat cancer. Everything known about the link from sunlight to radiation therapy can be placed into context via use of the Mobius strip.
It is an example of how nutrient energy-dependent pheromone-controlled choices made by all living genera must link feedback loops to the biophysically constrained virucidal energy of sunlight. Any loss of energy can potentially be linked to the proliferation of viruses via a slight drop in the potential of hydrogen (pH).

That fact makes it more be obvious that God’s shrinking role in salvation can be viewed in the context of medical practices that appear to make physicians and/or other medical professionals your savior(s). They will warn you to avoid too much sun exposure and treat your cancer with radiation because you did not get enough sun exposure to protect you via the increased production of Vitamin D.
They will tell you to use a chemical “sun-screen” and treat your cancer with chemotherapy that was caused by the chemical imbalance your body could no longer cope with.
See also: Electrolytes induce long-range orientational order and free energy changes in the H-bond network of bulk water
This was reported as: A single ion impacts a million water molecules
So far as I know there has been no discussion of the link from free energy changes in the H-bond network to the hydrophobicity of supercoiled DNA, which links quantum physics to the protection of all organized genomes from the virus-driven degradation of messenger RNA and genomic entropy.
Could the lack of discussion be attributed to the claim that no one understands quantum mechanics in an age where the speed of light on contact with water has been linked to all biodiversity via energy-dependent changes in angstroms to ecosystems in all living genera?
From last year: How Can Physics Underlie the Mind? Top-Down Causation in the Human Context

My review on Amazon (6/12/16)

Others linked the sun’s anti-entropic virucidal energy from energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.

Ellis comments on at least one of Schrodinger’s claims from “What is Life?” but he largely ignores the energy-dependent links from ecological variation to ecological adaptation that also were reported in two recent publications. See: “Structural diversity of supercoiled DNA” and “Epigenetics and Genetics of Viral Latency.”

Ellis cannot be held accountable for not knowing the most recent work (May 11, 2016) reported that “…viral latency is responsible for life-long pathogenesis and mortality risk…”

However, it seems inappropriate for anyone whose opinions are held in high regard to ignore everything else that is known about energy-dependent RNA methylation and the biophysically constrained morphological and behavioral diversity of all living genera. Experimental evidence has established facts that are being used to link the Precision Medicine Initiative to the National Microbiome Initiative via attempts to crack the olfactory code.

When researchers report the direct link from energy-dependent RNA methylation to differences in behavior, this book will be compared to Masatoshi Nei’s “Mutation-driven evolution.” The biggest difference between the two seems to be that Ellis tries to link emergence to evolution via Darwin’s “conditions of life.”

But he now bears the burden of the report in “Science” of nutrient energy-dependent pheromone-controlled weekend evolution of the bacterial flagellum: “Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system.”

The “resurrection” is obviously energy-dependent and it also links the innate immune system to biophysically constrained biologically-based cause and effect in species from microbes to humans via RNA-mediated amino acid substitutions. Resurrecting Darwin’s “conditions of life” after they were ignored by neo-Darwinists for many decades should not be attempted by physicists, cosmologists, or biologically uninformed theorists from any other discipline without first learning more about what is known about the RNA-mediated links from physics and chemistry to molecular epigenetics.

See for comparison, this review by Giulio Tononi

An admirable, systematic approach to the issue of emergence from physics to sociology, of great originality, broad scope, and deep understanding. George Ellis argues with admirable clarity of thought that much of the world we live in is governed not by the blind dance of atoms, but by high-level causes and purposes. This is a much needed book and a remarkable synthesis across fields and levels. I know of no other book where the evidence for emergence is presented so thoroughly and with as much insight.

There is no such thing as a blind dance of atoms. Quantized energy-dependent changes link angstroms to ecosystems in all living genera via the physiology of reproduction. Serious scientists do not link “high-level cause and purposes” to anything that does not link what organisms eat from food energy to the physiology of reproduction. Only pseudoscientists claim that ideas about “emergence” are “…a remarkable synthesis across fields and levels.”

See: God’s shrinking role in salvation (3)

Amino acid modification FA_Epigenetics_Table1

Food energy-dependent cell type differentiation (2)

June 6, 2017

by James Kohl with One Comment Adaptations Alternative Splicings base editing Diseases & Disorders Ecology Human Brain Human Pheromones Light Energy Model Organisms Nutrigenomics Physics RNA Directed RNA editing RNA-directed DNA methylation RNA–Mediated Epigenetic Heredity Variations

Summary: The concept of “faster-evolving DNA” regions in the context of nucleotide variation in both the 16S and 12S sequences is not consistent with any accurate representation of how the functional structure of supercoiled DNA must be linked from energy-dependent changes in angstroms to ecosystems in all living genera. Conserved molecular mechanisms link the sense of smell in bacteria from the de novo creation of olfactory receptor genes to the physiology of reproduction via the microRNA/messenger RNA balance and Feynman’s claim about the human idiocy of theoretical physicists who use different terms for their measurements of food energy.
See first: Food energy-dependent cell type differentiation
See also: Bacterial Communication And Relevance Of Quantum Theory
Thanks to antagonist Jay R. Feierman for calling this to my attention, See: Fwd: Bacterial Communication And Relevance Of Quantum Theory

The recent findings confirm that bacteria communicate each other through chemical and electrical signals. Bacteria use chemical signaling molecules which are called as quorum sensing molecules (QSMs) or autoinducers. Moreover, the ion channels in bacteria conduct a long-range electrical signaling within biofilm communities through propagated waves of potassium ions and biofilms attracts other bacterial species too. Both communication process are used by bacteria to make their own survival strategies. In this article, we model this bacterial communication mechanism by complex Ginzburg-Landau equation and discuss the formation of patterns depending on kinematic viscosity associated with internal noise. Again, the potassium wave propagation is described by the non-linear Schrodinger equation in a dissipative environment. By adding perturbation to non-linear Schrodinger equation one arrives at Complex Ginzburg-Landau equation. In this paper we emphasize that at the cellular level (bacteria) we use Complex Ginzburg-Landau equation as a perturbed Non-linear Schrodinger equation to understand the bacterial communication as well as pattern formation in biofilms for certain range of kinematic viscosity which can be tested in laboratory experiment. Here, the perturbation is due to the existence of nonthermal fluctuations associated to the finite size of the bacteria. It sheds new light on the relevance of quantum formalism in understanding the cell to cell communication.

For everyone who does not follow my posts on groups and in forums where they are not commonly edited or fail to appear because the moderators and administrators are biologically uninformed theorists, I reiterate:
Natural selection for energy-dependent codon optimality and nutrient energy-dependent quorum sensing have been linked from the pheromone-controlled physiology of reproduction in bacteria that naturally produce a uranium isotope to all morphological and behavioral biodiversity via an atoms to ecosystems model that refutes every aspect of neo-Darwinian theory and all theories linked to the claims of “Big Bang” cosmologists.
Clearly, Feedback loops link odor and pheromone signaling with reproduction (2005) in all living genera can be compared in the context of two claims, which were made by the moderator of the ISHE’s human ethology group, soon after I published Nutrient-dependent/pheromone-controlled adaptive evolution: a model (6/14/13)
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.
See for comparison: Quantum Souls

The sun’s energy flows to Earth as information that is absorbed by energy-dependent organisms. Along with nutrient-dependency and pheromones, it effects all living genera and ensures reproduction. God’s “conditions of life,” described in part by Darwin, come before natural selection.

For additional evidence that links the anti-entropic virucidal energy of sunlight to all biodiversity and the concept of quantum souls, I reiterate:
Figure 4: Conceptual model of uranium roll-front deposit formation. — from Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits (open access)

Precursors and conditions favouring the formation of uraninite, biogenic uraninite and non-crystalline U^(IV) are illustrated.

The nutrient energy-dependent pheromone-controlled physiology of reproduction of bacteria that live underground was linked from thermodynamic cycles of RNA-mediated protein folding chemistry to the production of uranium isotopes. The obvious link from the quantized energy of sunlight to the de novo creation of all biodiversity also was reported in the context of 16S rRNA microbial community analysis in fish. Most authors report this in the context of a “DNA-based” analysis. That way, there is no need to differentiate between abiogeneis and biophysically constrained biogenesis. Start with genes and you do not need to explain how DNA was created.

See for comparison: Evaluation of the 16S and 12S rRNA genes as universal markers for the identification of commercial fish species in South Africa

The nucleotide variation in both the 16S and 12S sequences was suitable for identifying the large majority of the examined fish specimens to at least the level of genus, but was found to be less useful for the explicit differentiation of certain congeneric fish species. It is recommended that one or more faster-evolving DNA regions be analysed to confirm the identities of closely-related fish species in South Africa.

The concept of “faster-evolving DNA” regions in the context of nucleotide variation in both the 16S and 12S sequences is not consistent with any accurate representation of how the functional structure of supercoiled DNA must be linked from energy-dependent changes in angstroms to ecosystems in all living genera. Conserved molecular mechanisms link the sense of smell in bacteria from the de novo creation of olfactory receptor genes to the physiology of reproduction via the microRNA/messenger RNA balance and Feynman’s claim about the human idiocy of theoretical physicists who use different terms for their measurements of food energy.
The amount of food energy, measured in calories, is linked to whether or not the organism starves to death before it reproduces. That’s how ecological variation in the supply of nutrients may lead to extinction of any species that fails to evolve into another species. So far, no experimental evidence of biologically-based cause and effect suggests that any species has ever evolved into another species.
Claims about the need for energy-dependent changes in supercoiled DNA to protect all organized genomes from the virus-driven degradation of messenger RNA, which is linked to mutations and all pathology may have have peaked with this publication:
Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs (5/25/17)

Over the last decade, it has become increasingly apparent that miRNAs have many important roles in the development of disease and cancer. Recently, however, their role in viral and bacterial gene regulation as well as host gene regulation during disease progression has become a field of interest.

More than 61,000 works published peer-reviewed works show why differences in the types of microRNAs are the most important consideration to energy-dependent healthy longevity or to virus-driven pathology.
MicroRNA Items: 1 to 20 of 61426
See for comparison: It’s Time to Start Calling Evangelicals What They Are: The American Taliban

Atheistic hate-mongers like Magnus S. Magnusson continue to disseminate this nonsense and encourage attacks on any views that link Creationism to Americanism. The hate-mongers don’t know who created energy or how energy-dependent ecological adaptation is linked from changes in base pairs to all biodiversity, but they will claim that American evangelicals are like the Taliban.

See for comparison: The in vivo structure of biological membranes and evidence for lipid domains

The structure and organization of the cell membrane are central to many biological functions, and although they have been extensively studied, there is still much that we don’t understand. A wealth of detailed information has been obtained from studies of model lipid membranes. However, these systems are often highly simplified in composition and always lack the active processes found in cells. The major obstacle to studying membranes in vivo in living cells has been that high-resolution physical methods used to investigate membrane structure are not compatible with living organisms. To overcome this obstacle, we employed a new in vivo approach that allows membrane structure to be observed directly in the gram-positive bacterium B. subtilis. This approach relies on tuning the isotopic content of hydrogen within the membrane, and other parts of the bacterium, to generate neutron scattering spectra exclusively from the membrane. Using this approach, we confirmed that the structure of the B. subtilis membrane is lamellar and has an average hydrophobic thickness of 23.9 ± 0.9 Ångstroms (Å). We were also able to observe nanoscopic lateral membrane structures, consistent with the notion of lipid rafts. This experimental approach will allow for a wide range of future structural studies of the cell membrane (and possibly other classes of biomolecules) without the need for extrinsic probes or labels. In this way, it fundamentally changes the scope of nanoscale structural questions that can be addressed in vivo.

Reported as: This Is The First Ever Nanoscale Image of a Living Cell Membrane

They link the energy-dependent de novo creation of the cell wall in Bacillus subtilus, a Gram-positive, catalase-positive bacterium, found in soil and the gastrointestinal tract of ruminants and humans, to all biodiversity on Earth via differences in hydrogen ions, hydrogen atom transfer in DNA base pairs in solution, and the pheromone-controlled physiology of reproduction.

Hydrogen ions are made by the removal of one electron from atomic hydrogen. That fact supports the the claims of those who have linked energy-dependent changes from atoms to ecosystems in all living genera via what occurs at the level of changes in angstroms. The changes in angstroms are linked to the innate ability of all cell types to signal other cell types via changes in the membrane that biophysically constrains the contents of the cell.
Although it is important that these researchers showed how the role of quantized energy from the sun is linked to biophysically constrained hydrophobicity in supercoiled DNA, anyone who has ever performed a “catalase” test to distinguish between pathogenic and non-pathogenic strains of Staphlococcus and Streptococcus before testing for beta-lactamase and resistance to oxacillin/methicillin has observed the release of hydrogen caused by the breakdown of the cell membrane.

“Catalase is a common enzyme found in nearly all living organisms exposed to oxygen (such as bacteria, plants, and animals). It catalyzes the decomposition of hydrogen peroxide to water and oxygen.[3]”

“Beta-lactamase provides antibiotic resistance by breaking the antibiotics’ structure. These antibiotics all have a common element in their molecular structure: a four-atom ring known as a β-lactam. Through hydrolysis, the lactamase enzyme breaks the β-lactam ring open, deactivating the molecule’s antibacterial properties.”

Congratulate the researchers who have just refuted every aspect of neo-Darwinian theory as was predicted by any intelligent microbiologist who has ever needed to identify and perform susceptibility testing on a pathogen to help a physician keep the pathogen from killing the patient.

And, remember the Hippocratic Oath. First, do no harm. If you are a physician who thinks that people evolved from bacteria, learn something about cell type differentiation via a visit to the microbiology lab at a local hospital. Most medical laboratory scientists will be happy to help you stop killing people with your ignorance.

Serious scientists have forced theorists to change their claims about the gene editing technology called CRISPR Cas9 to reflect the fact that the reason the technology failed miserably. The technology was based on naturally occurring endogenous RNA interference. It is now being reported as CRISPRi in the context of identifying new genes but outside the context of their energy-dependent de novo creation.

See: High-throughput CRISPRi phenotyping identifies new essential genes in Streptococcus pneumoniae

Genome‐wide screens have discovered a large set of essential genes in the opportunistic human pathogen Streptococcus pneumoniae. However, the functions of many essential genes are still unknown, hampering vaccine development and drug discovery. Based on results from transposon sequencing (Tn‐seq), we refined the list of essential genes in S. pneumoniae serotype 2 strain D39. Next, we created a knockdown library targeting 348 potentially essential genes by CRISPR interference (CRISPRi) and show a growth phenotype for 254 of them (73%). Using high‐content microscopy screening, we searched for essential genes of unknown function with clear phenotypes in cell morphology upon CRISPRi‐based depletion. We show that SPD_1416 and SPD_1417 (renamed to MurT and GatD, respectively) are essential for peptidoglycan synthesis, and that SPD_1198 and SPD_1197 (renamed to TarP and TarQ, respectively) are responsible for the polymerization of teichoic acid (TA) precursors. This knowledge enabled us to reconstruct the unique pneumococcal TA biosynthetic pathway. CRISPRi was also employed to unravel the role of the essential Clp‐proteolytic system in regulation of competence development, and we show that ClpX is the essential ATPase responsible for ClpP‐dependent repression of competence. The CRISPRi library provides a valuable tool for characterization of pneumococcal genes and pathways and revealed several promising antibiotic targets.

The de novo creation of essential genes has been placed into the context of a problem with antibiotic sensitivity testing.

The problem was introduced into susceptibility testing by biologically uninformed theorists who still may not know the difference between energy-dependent ecological adaptation and mutation-driven evolution.

Cell-type-specific genome editing with a microRNA-responsive CRISPR-Cas9 switch

The transient and conditional expression of our system using synthetic RNA could provide genome editing as a potentially ‘one-shot therapy’ to treat numerous genetic diseases. In conclusion, our miR-Cas9 switch combined with a RNA-delivery approach can selectively engineer genomes of target cells by detecting an endogenous miRNA signature, with potential benefits for synthetic biology, genome editing field and future therapeutic applications.

The conditional expression of genes is linked from food energy-dependent pheromone-controlled biophysically constrained viral latency to healthy longevity or from virus-driven energy theft to constraint breaking mutations and all pathology.

People like Jay R. Feierman and Magnus S. Magnusson tout the pseudoscienitific nonsense of theories in books such as this one. The Biology of Religious Behavior: The Evolutionary Origins of Faith and Religion
Their atheistic agenda is the antithesis of any factual representation of anything known to serious scientists about biophysically constrained energy-dependent biologically-based cause and effect.
See for comparison: Mechanism of transmembrane signaling by sensor histidine kinases reported as:Scientists investigate how the sense of smell works in bacteria

…the signaling and inactive states differ only very slightly at the nitrate-binding site – by 0.5-1 angstroms, which is approximately one fifth of the size of the ion itself (1 angstrom is 10-10 meters). However, when this ion binds to the sensor, it causes huge changes in the protein: The helices of different monomers begin to move in different directions, like pistons. These “pistons” transmit the small change of 0.5-1 angstroms through the membrane, and their outer ends shift by approximately 2.5 angstroms in different directions. Inside the cell, in the HAMP domain, these shifts are converted into the rotation of two parts of NarQ relative to each other. Ultimately, the positions of the output helices change by as much as 7 angstroms, thus completing the signal transmission.

See also: Eros is a novel transmembrane protein that controls the phagocyte respiratory burst and is essential for innate immunity
For a non-technical representation of everything currently known to serious scientists about the energy-dependent biophysically constrained physiology of pheromone-controlled biodiversity in all living genera see: The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002)
Could any serious scientist fail to link the novel transmembrane protein “Eros” from what organism eat to innate immunity via the non-technical representations in The Scent of Eros? If you know someone who you think is a serious scientist ask them about the representations made in The Biology of Religious Behavior: The Evolutionary Origins of Faith and Religion. If you learn that they think Faith and Religion “evolved,” I will add them to my growing list of pseudoscientists who continue to tout ridiculous theories.

Theistic evolutionists fight back and lose (2)

February 27, 2017

by James Kohl with 2 Comments Adaptations Alternative Splicings biophotonics Diseases & Disorders Ecology Light Energy Model Organisms Physics RNA Directed RNA interference RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing RNA–Mediated Epigenetic Heredity Variations

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

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

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

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

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

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

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

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

with my comments, such as this one:

Oct 14, 2015

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

See also:

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

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

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

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

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

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

Vietnam Veterans and others with glioblastoma

December 30, 2016

by James Kohl with One Comment Adaptations Alternative Splicings Autophagy Diseases & Disorders Ecology Model Organisms Neuronal Plasticity Nutrigenomics RNA Directed RNA methylation RNA-directed DNA methylation RNA-mediated epigenetic regulation of gene expression RNA-mediated gene silencing Variations What's in the News

The Agent Orange Widows Club

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

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

Targeting NF-κB in glioblastoma: A therapeutic approach

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

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

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

This post also was removed: Cells dripped into the brain help man fight a deadly cancer

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Theories vs facts about polycombic adaptation

December 6, 2016

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

See: Demoncrats fight polycombic ecological adaptation

Exosomes as miRNA Carriers: Formation–Function–Future

Important aspects will be highlighted as a take-home message (THM) at the end of each paragraph.

THM: Extracellular vesicles transport miRNA in a paracrine and endocrine manner. Questions regarding the cellular options of producing either microvesicles or exosomes and their difference in miRNA composition and number are still unknown.

In my 2014 invited review, the four F’s, Formation–Function–Future and Copulation were included in details about how the nutrient energy-dependent de novo creation of microRNAs must be linked to nutritional epigenetics. My invited review was returned without review by the guest editors of a special issue of “Nutrients.”
I realized the guest editors had “baited me” into providing them with all the available current information and published my submission to Figshare. That’s how I show the level of deception that biologically uninformed theorists still use to obfuscate what is known to serious scientists about biologically-based cause and effect.

See for example: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (April 10, 2014)

Abstract: “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.”

Lynnette Ferguson, was one of two guest editors that invited my review.

She is the co-author of The Interaction between Epigenetics, Nutrition and the Development of Cancer This article belongs to the Special Issue NutritionalEpigenetics

Conclusion:

…it is imperative to understand the implications of diet on epigenetic modifications, and the effect of those modifications on the development of cancer today and in future generations. Such an understanding and an appropriate resultant response would help decrease the level of risk in future generations.

There would be no future generations if diet could not be epigenetically linked from metabolism to the pheromones that control the physiology of reproduction in species from microbes to human via energy-dependent changes in the microRNA/messenger RNA balance. The microRNA/messenger RNA balance biophysically contrains RNA-mediated protein folding chemistry.

Protein folding chemistry links energy-dependent changes from angstroms to ecosystems in all living genera via the innate immune system and fixation of RNA-mediated amino acid substitutions in supercoiled DNA. Supercoiled DNA exemplifies natural section for energy-dependent codon optimality, but theorists will not accept that fact. They would rather believe that the mutations in DNA are naturally selected and that mutation-driven evolution automagically occurs outside the context of energy or the virus-driven energy theft that causes all mutations and all pathology.

This scenario challenges the assumed value of extant blastoporal behaviours for explaining the evolutionary origin and diversification of Bilateria that has been presumed for over 100 years^{4,5,6,7,9,10,11}. Freeing the constraint that the mouth and anus have a necessary association with the embryonic blastopore will help in understanding the developmental events underlying the evolution of an alimentary canal^5,20,21,50, and ultimately the appearance and diversification of bilaterian body plans.

All scenarios that failed to link energy-dependent behavior to the physiology of reproduction and also failed to link virus-driven energy theft to all pathology have always been based on questionable assumptions. The assumptions fall outside the context of Darwin’s “conditions of life,” which require links from what organisms eat to signaling and sensing and the behavior of other organisms.

For example, Schrodinger (1944) linked excretion from mammals to sunlight as the source of anti-entropic virucidal energy used to support all ecosystems. All serious scientists have done that since Thomas Hunt Morgan won the 1933 Nobel Prize in Physiology or Medicine for linking chromosomes to transgenerational epigenetic inheritance long before most people understood what the term autophagy means.