Watering Young Plant - Vintage Effect

A single base change refutes theistic evolution

Everyone who failed to learn how light-activated endogenous substrates biophysically constrain viral latency is playing “catch up” to serious scientists. The serious scientists know how quantized energy-dependent RNA-mediated cell type differentiation occurs in the context of the physiology of reproduction in all living genera. Rather than accept the fact that the innate immune system of bacteria (CRISPR) linked the pheromone-controlled physiology of reproduction from autophagy to biophysically constrained viral latency, theorists decided to waste money on virus-assisted gene-editing attempts to repair virus-damaged DNA.

Mammoth Biosciences launches a CRISPR-powered search engine for disease detection

Jennifer Doudna, George Church and many others still refuse to admit that they have refuted theistic evolution. They are just beginning to accurately portray the how detection of changes in the microRNA/messenger RNA balance links virus-driven energy theft to the degradation of messenger RNA. Clearly, however, they know how the degradation of messenger RNA is linked to all pathology.

Had they followed the works of Christ et al. (2013), The Pharmacology of Regenerative Medicine and Christ et al., (2018) Western Diet Triggers NLRP3-Dependent Innate Immune Reprogramming, they could intelligently interact with those who are scheduled to present during Schrödinger at 75 – The Future of Biology – September 2018.

(Nick Lane excepted.) He appears to be a biologically uninformed theorist who does not realize that Fast food makes the immune system more aggressive in the long term

Unhealthy eating causes some of these normally hidden pieces of DNA to unwind, similar to a loop hanging out of a ball of wool. This area of the genetic material can then be read much easier as long as this temporary unwrapping remains active. Scientists call these phenomena epigenetic changes. “The inflammasome triggers such epigenetic changes,” explains Dr. Latz. “The immune system consequently reacts even to small stimuli with stronger inflammatory responses.”

The immune system reacts to the proliferation of viruses. The viruses cause the inflammation, which has been linked to all pathology in more than 72,500 published works. See microRNA.

See also: Field-deployable viral diagnostics using CRISPR-Cas13

…the Cas13-based SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) platform can detect Zika virus (ZIKV) and dengue virus (DENV) in patient samples at concentrations as low as 1 copy per microliter. We developed HUDSON (heating unextracted diagnostic samples to obliterate nucleases), a protocol that pairs with SHERLOCK for viral detection directly from bodily fluids, enabling instrument-free DENV detection directly from patient samples in <2 hours. We further demonstrate that SHERLOCK can distinguish the four DENV serotypes, as well as region-specific strains of ZIKV from the 2015–2016 pandemic. Finally, we report the rapid (<1 week) design and testing of instrument-free assays to detect clinically relevant viral single-nucleotide polymorphisms.

Pardis C. Sabeti’s group already linked the anti-entropic virucidal energy of sunlight from the creation of enzymes to natural selection for energy-dependent codon optimality via the pheromone-controlled stability of organized genomes in a human population in what is now Central China.
See this report from 2013 on fixation of the EDAR V370A substitution.
Following the footprints of positive selection February 15th, 2013.
For comparison to positive selection for food and fixation of the EDAR V370A amino acid substitution, the pseudoscientific nonsense about evolution touted by Pardis C. Sabeti’s group appears in this YouTube video report: 2 Cell Studies Reveal Genetic Variation Driving Human Evolution
In the mouse model of food energy-dependent pheromone-controlled ecological adaptations, they replaced the valine normally found in mouse EDAR with the alanine that’s under selection in humans. They got mice with thicker hair, changes in mammary tissue, and and increased  number of eccrine sweat glands. Those changes parallel phenotypic changes in humans. The phenotypic changes in humans link the quantized energy-dependent creation of microRNAs to biophysically constrained viral latency in all living genera.
In humans, the changes are linked to visual perception of mass and energy and the perception of physical features that are sexually selected.
See: Olfaction Warps Visual Time Perception
A single base change results in the valine to alanine substitution, which changes the ancient mammalian gene EDAR and the EDAR encoded protein.
That fact was reported in the context of links from subatomic particles and all levels of biophysically constrained viral latency and biological organization in my 2014 invited review of nutritional epigenetics.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (unpublished)
Conclusion:

The ecological adaptations, which appear to be manifested in the human population are detailed in these two reports [162-163]. The ecological adaptations are likely to be nutrient-dependent and pheromone-controlled. If so, ecological variation probably leads to ecological, social, neurogenic, and socio-cognitive niche construction, which is manifested in increasing organismal complexity and species diversity. If not, there may be something as yet unknown about mutations and evolution that makes sense in the light of what is known about nutritional epigenetics and the molecular biology of species from microbes to man

162. Kamberov, Yana G.; Wang, S.; Tan, J.; Gerbault, P.; Wark, A.; Tan, L.; Yang, Y.; Li, S.; Tang, K.; Chen, H., et al., Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant. Cell 2013, 152 (4), 691-702. doi: 10.1016/j.cell.2013.01.016
163. Grossman, Sharon R.; Andersen, Kristian G.; Shlyakhter, I.; Tabrizi, S.; Winnicki, S.; Yen, A.; Park, Daniel J.; Griesemer, D.; Karlsson, Elinor K.; Wong, Sunny H., et al., Identifying Recent Adaptations in Large-Scale Genomic Data. Cell 2013, 152 (4), 703-713. doi: 10.1016/j.cell.2013.01.035
See also:
161. Rosenberg, S. M.; Queitsch, C., Combating Evolution to Fight Disease. Science 2014, 343 (6175), 1088-1089. doi: 10.1126/science.1247472
Kalevi Kull: Censorship & Royal Society Evo Event

Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull

Serious scientists from South Korea are the winners. Two recent publications forced the denuclearization of North Korea.
Emergence of Human G2P[4] Rotaviruses in the Post-vaccination Era in South Korea: Footprints of Multiple Interspecies Re-assortment Events

Compared to the G2 RotaTeq vaccine strain, 17-24 amino acid changes, specifically A87T, D96N, S213D, and S242N substitutions in G2 epitopes, were observed. These results suggest that multiple interspecies re-assortment events might have contributed to the emergence of G2P[4] rotaviruses in the post-vaccination era in South Korea.

A Single Amino Acid at the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses

When analyzed using reverse-genetically rescued viruses, it was shown that PA K338R alone could increase the pathogenicity of both IBVs in mice and viral replication property in the respiratory tracts of ferrets. In a subsequent mini-replicon assay, the effect of PA K338R was highlighted by the enhancement of viral polymerase complex activity of both Vc_BR60 and Ym_WI01 viruses. These results suggest that the PA K338R mutation may be a molecular determinant of IBV pathogenicity via modulating the viral polymerase function of IBVs.

Mutations are known to be the molecular determinants of all pathology in species from microbes to humans. See:  Virus-mediated archaeal hecatomb in the deep seafloor
Watch as Hashem Al-Ghaili puts everything known to serious scientists about the virus-mediated archaeal hecatomb back into the context of neo-Darwinian evolution.

See also: Study offers new approach to starve p53 deficient tumors

One major hallmark of cancer cells is their ability to adapt to stressful conditions such as nutrient deprivation. Rapidly growing tumor cells must compete for the ever-diminishing supply of nutrients in the surrounding environment to survive and proliferate. Targeting these adaptive mechanisms represents a promising approach for cancer therapeutics.

It’s a little late to claim that the virus-driven theft of quantized energy is linked from autophagy to adaptations in viruses. All serious scientists know that food energy-dependent pheromone-controlled biophysically constrained autophagy has been linked to viral latency and to ecological adaptations in all living genera. Intelligent people know that viruses have been linked to all pathology.
See also: From Istanbul, Turkey. Respect for all human life has been placed into the context of the energy-dependent de novo creation of microRNAs and the works of an Islamic creationist in Turkey.

Autophagy-Regulating microRNAs and Cancer
Cancer researchers in other countries clearly are approaching the cure for all pathology from a scientific creationist perspective despite being forced to place their claims into the context of evolution to get their works past peer review.
The Trump administration has been working towards world peace with other leaders for more than a year. See for example:
May 3, 2017
LIVE: President Donald J. Trump and Palestinian President Mahmoud Abbas make a joint statement at the White House.
Who does not want World Peace? Why The End of the Korean War Is Bad News for the United States
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Environmental selection is natural selection

Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk was published on April 23, 2018

The ectodysplasin A receptor (EDAR) gene has a range of pleiotropic effects, including sweat gland density, incisor shoveling, and mammary gland ductal branching. The frequency of the human-specific EDAR V370A allele appears to be uniquely elevated in North and East Asian and New World populations due to a bout of positive selection likely to have occurred circa 20,000 y ago. The dental pleiotropic effects of this allele suggest an even higher occurrence among indigenous people in the Western Hemisphere before European colonization. We hypothesize that selection on EDAR V370A occurred in the Beringian refugium because it increases mammary ductal branching, and thereby may amplify the transfer of critical nutrients in vitamin D-deficient conditions to infants via mothers’ milk. This hypothesized selective context for EDAR V370A was likely intertwined with selection on the fatty acid desaturase (FADS) gene cluster because it is known to modulate lipid profiles transmitted to milk from a vitamin D-rich diet high in omega-3 fatty acids.

The authors placed my claims about the mouse-to-human model of the EDAR V370A variant back into the context of an evolutionary adaptation. They seem unwilling to accept the fact that the  EDAR V370A variant is a nutrient-dependent pheromone-controlled ecological adaptation in mice and in humans. It links energy-dependent changes from angstroms to ecosystems in all living genera via natural selection for energy-dependent codon optimality.
The EDAR V370A allele is also known as rs3827760, 1540T/C, 370A, or Val370Ala. It is a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2.
See the author’s copy of my invited review of nutritional epigenetics, which was returned without review :
Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

In the context of climate change and changes in diet, the story began with what probably was a nutrient-dependent base pair change and a variant epiallele that arose in a human population in what is now central China. Apparently, the effect of the epiallele was adaptive and it was manifested in the context of an effect on sweat, skin, hair, and teeth. In another mammal, such as the mouse, the effect on sweat, skin, hair, and teeth is probably due to a nutrient-dependent epigenetic effect on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones appear to control the nutrient-dependent epigenetically-effected hormone-dependent organization and hormone-activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates and in microbes as previously indicated.

The ecological adaptations, which appear to be manifested in the human population are detailed in these two reports [162-163]. The ecological adaptations are likely to be nutrient-dependent and pheromone-controlled. If so, ecological variation probably leads to ecological, social, neurogenic, and socio-cognitive niche construction, which is manifested in increasing organismal complexity and species diversity. If not, there may be something as yet unknown about mutations and evolution that makes sense in the light of what is known about nutritional epigenetics and the molecular biology of species from microbes to man.

More than four years later, biologically uninformed theorists have again tried to make natural selection something different than environmental selection. Nina G. Jablonski is one of the co-authors. I’m tempted to think that all the others also are biologically uninformed science idiots who cannot link physical and chemistry from subatomic particles to ecosystems via what organisms eat and the physiology of pheromone-controlled reproduction, which biophysically constrains viral latency in all living genera.
See also: microRNA and ADAR1 microRNA
For example:
Combinatory RNA-Sequencing Analyses Reveal a Dual Mode of Gene Regulation by ADAR1 in Gastric Cancer (April 25, 2018)
Virus-encoded miRNAs in Ebola virus disease (April 24, 2018)

High-throughput sequencing and analysis of microbial community cDNA (#metatranscriptomics) are providing valuable insight into in situ microbial activity and metabolism in the oceans.

The eternal significance of microRNAs (4)

Conclusion: Conserved energy biophysically constrains viral latency.
Metatranscriptomics

High-throughput sequencing and analysis of microbial community cDNA are providing valuable insight into in situ microbial activity and metabolism in the oceans.

When faced with the eternal significance of quantized energy-dependent natural selection for codon optimality, theorists must attack the basics of what is known to serious scientists about biophysically constrained life on Earth.
See for example: Virus-mediated archaeal hecatomb in the deep seafloor
By starting with “raw assemblies” instead of the energy from sunlight that must be linked to the “Assemblies Trinity,” pseudoscientists link “data” to codon optimality. They fail to link the creation of virucidal light from differential gene expression before they link the data to results that are meaningless outside the context of an energy source.
All results can be predicted only in the context of the energy-dependent biophysical constraints that prevent the virus-driven degradation of messenger RNA from destroying the supercoiled DNA that is required to maintain viral latency and healthy longevity.
Nutrition, microRNAs, and Human Health (2017)

MicroRNAs (miRs) hybridize with complementary sequences in mRNA and silence genes by destabilizing mRNA or preventing translation of mRNA.

The authors recapitulate the claims from my 2014 invited review of nutritional epigenetics but fail to address the most important aspect of biophysically constrained viral latency, which requires the energy-dependent creation of microRNAs that prevent the translation of mRNA. The destabilizing effects of viruses are eliminated when enough food energy is available to support RNA-directed DNA methylation and fixation of amino acid substitutions in organized genomes.
See:  Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.

See for comparison: Prediction of 5-Fluorouracil Toxicity Associated With Dihydropyrimidine Dehydrogenase Gene (DPYD) Polymorphism Using the Secondary Structure Prediction Programs
The predicted toxicity must be linked from the energy-dependent creation of dehydrogenase gene polymorphisms. The failure to do that has led to class action litigation.
See also:  DPYD dihydropyrimidine dehydrogenase [ Homo sapiens (human) ]

The protein encoded by this gene is a pyrimidine catabolic enzyme and the initial and rate-limiting factor in the pathway of uracil and thymidine catabolism. Mutations in this gene result in dihydropyrimidine dehydrogenase deficiency, an error in pyrimidine metabolism associated with thymine-uraciluria and an increased risk of toxicity in cancer patients receiving 5-fluorouracil chemotherapy. Two transcript variants encoding different isoforms have been found for this gene.

Finding isoforms is of little use if researchers do not know how the isoforms are created.
medical Definition of isoform.:

any of two or more functionally similar proteins that have a similar but not identical amino acid sequence and are either encoded by different genes or by RNA transcripts from the same gene which have had different exons removed.

Most researchers know nothing about energy-dependent biophysical constraints on the creation of amino acid substitutions in the isoforms.
See for example: NSF’s Big Ideas: Understanding the Rules of Life and The Quantum Leap
The rules of life that include fixation of amino acid substitutions in organized genomes could have been linked from the quantum leap to biophysically constrained viral latency and healthy longevity in all living genera. Instead the presenters failed to answer any of my questions.

1) Has anyone place the rules of Life and the Quantum Leap into the context of food energy-dependent biophysically constrained viral latency and sympatric speciation?
2) Do you think that this parody accurately represents what was known in 2014 about the importance of energy-dependent base pair changes to biophysically constrained protein folding chemistry? All About that Base (Meghan Trainor Parody) 12/10/14
3) Do you agree that questions about genome adaptations compared to the evolution of organized genome are ambiguous in the context of what is known about natural selection for quantized energy-dependent codon optimality?
4) Has the difference in the energy of two photons been linked from altered proton gradients to the protential of hydrogen (pH) and RNA-mediated DNA repair via the creation of microRNAs and enzymes?
NSF funding is largely used to support theories about the emergence of energy and evolution of all biodiversity.
This work would be funded by NSF: The evolutionary history of vertebrate RNA viruses
They claim that the evolutionary history of vertebrates matches the history of the RNA viruses, which they claim is because the viruses evolved. Viruses must steal the quantized energy of sunlight from cell types or they cannot replicate. Does that sound like vertebrate viruses are capable of evolution?
That nonsense was reported as: New study transforms understanding of virus origins and evolution
See also: Estimating evolutionary rates in giant viruses using ancient genomes

…this suggests that these viruses could have diverged at least hundreds of thousands of years ago, and hence have evolved over longer time-scales than previously suggested. We propose that the evolutionary rate and time-scale of pithovirus evolution should be reconsidered in the light of these observations and that future estimates of the rate of giant virus evolution should be carefully examined in the context of their biological plausibility.

All their suggestions have become more ridiculous as more facts about the creation of microRNAs have been placed into the context of biophysically constrained viral latency.
See: MicroRNAs in neural development: from master regulators to fine-tuners

The proper formation and function of neuronal networks is required for cognition and behavior. Indeed, pathophysiological states that disrupt neuronal networks can lead to neurodevelopmental disorders such as autism, schizophrenia or intellectual disability. It is well-established that transcriptional programs play major roles in neural circuit development. However, in recent years, post-transcriptional control of gene expression has emerged as an additional, and probably equally important, regulatory layer. In particular, it has been shown that microRNAs (miRNAs), an abundant class of small regulatory RNAs, can regulate neuronal circuit development, maturation and function by controlling, for example, local mRNA translation. It is also becoming clear that miRNAs are frequently dysregulated in neurodevelopmental disorders, suggesting a role for miRNAs in the etiology and/or maintenance of neurological disease states. Here, we provide an overview of the most prominent regulatory miRNAs that control neural development, highlighting how they act as ‘master regulators’ or ‘fine-tuners’ of gene expression, depending on context, to influence processes such as cell fate determination, cell migration, neuronal polarization and synapse formation.

See also: Learning-dependent chromatin remodeling highlights noncoding regulatory regions linked to autism
They identified a single nucleotide polymorphism known as rs6010065. It is associated with differences in microRNAs linked to autism spectrum disorder.
See also: A Common Allele in FGF21 Associated with Sugar Intake Is Associated with Body Shape, Lower Total Body-Fat Percentage, and Higher Blood Pressure
A single nucleotide polymorphism known as rs838133 was linked from food energy-dependent changes in microRNAs to biophysically constrained viral latency and healthy longevity in the mouse-primate-human model of pheromone-controlled reproduction.
I reiterate: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

In the context of quantized energy as information-driven changes in the microRNA/messenger RNA balance, a single nucleotide polymorphism known as rs3827760, 1540T/C, 370A, V370A, and/or Val370Ala was linked to conserved morphological and behavioral phenotypes in mice and humans.

See: Epigenetics and Autism Spectrum Disorder: Is There a Correlation?

At a time when all serious scientists have linked energy-dependent changes in electrons to ecosystems, questions about correlations are irrelevant.

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

Functional connectivity is energy dependent and biophysically constrained by by the energy-dependent physiology of reproduction.

It is time for all biologically uniformed science idiots to admit that the source of all energy-dependent changes in every organism on Earth is sunlight.

See: Resolving sub-cellular miRNA trafficking and turnover at single-molecule resolution

Regulation of microRNA (miRNA) localization and stability is critical for their extensive cytoplasmic RNA silencing activity and emerging nuclear functions. Here, we have developed single-molecule fluorescence-based tools to assess the subcellular trafficking, integrity, and activity of miRNAs.

The regulation of microRNA (miRNA) localization and stability is quantized energy-dependent and pheromone controlled in the context of everything known to serious scientists about biophysically constrained protein folding chemistry and supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.
Why symmetry gets really interesting when it is broken

Energy is conserved…because the laws of physics are the same now as they were a millennium ago…

Long-range coherence and energy storage in biological systems (1968)

The supplied energy is thus not completely thermalized but stored in a highly ordered fashion.

Conserved energy biophysically constrains viral latency.

APS 2018

From photons to the proton motive force (2)

If you know someone who has linked differences in the energy of photons from the proton motive force to the physiology of reproduction and all biophysically constrained biodiversity, ask if they will attend Schrödinger at 75-The Future of Biology
For contrast, touting genetic evolution is not the future of biology.
See: Abstract: K06.00013 : A Path Integral Method for Analytically Tractable Inference of Evolutionary Dynamics

Understanding the forces that shape genetic evolution is a subject of fundamental importance in biology and one with numerous practical applications. Modern experimental techniques give insight into these questions, but inferring evolutionary parameters from sequence data, such as how an organism’s genotype affects its fitness, remains challenging. Here we present a method to infer selection from genetic time-series data using a path integral approach based in statistical physics. Through extensive numerical tests we find that our method exceeds the current state of the art in the successful classification of mutations as beneficial or deleterious in a variety of scenarios, while also yielding orders of magnitude improvements in run time. Our approach can also be extended to jointly infer other evolutionary parameters such as the effective population size and mutation rates.

Serious scientists do not infer evolutionary parameters using sequence data. They link natural selection for energy-dependent codon optimality to biophysically constrained viral latency. Virus-driven energy theft is linked from mutations to all pathology. There is no such thing as a beneficial mutation.
See also: Abstract: K06.00001 : Coarse-grained models coupling cell cycle and gene expression*

During a cell cycle, cells grow and divide. Recent single-cell experiments show that gene expression levels depend on the cell cycle. Particularly important is the proportion of the number of mRNA and protein to the cell volume. It is not clear how cells maintain a constant mRNA and protein concentration as the cells grow. Here we propose a coarse-grained gene expression model incorporating ribosomes and RNA polymerases, which captures the exponential growth of mRNA and protein number. We show that the homeostasis of mRNA and protein concentrations during the cell cycle can be achieved in a robust manner independent of cell shape. Furthermore, we show that the fluctuations in ribosome and polymerase numbers do not propagate to protein concentrations while the fluctuation in cell density does. Furthermore, our model reconciles the discrepancy between the experimentally observed negligible correlations between mRNA and protein levels, and the predicted positive correlations from previous models

Energy-dependent changes in the microRNA/messenger RNA balance have been linked from RNA-mediated cell cycles to gene expression in more than 70,000 published works. See: microRNA
See also: Applications of ligation-mediated PCR

A nick in a strand is any place where there’s a missing covalent bond between a sugar and the next adjacent phosphate. Nicks can arise from DNA damage, during normal DNA replication, or from the action of nuclease enzymes. Since a nick breaks the continuity of the backbone of one strand, it must be repaired by re-forming the missing covalent bond in order to make the DNA molecule intact again. This job of sealing nicks (specifically, nicks that occur between a sugar 3′ -OH group and the adjacent phosphate attached to the preceding sugar’s 5′ -OH group) is the function of DNA ligase. Using a molecular energy source (which differs depending on the enzyme source organism), DNA ligase reforms the missing covalent bond and the strand is whole again. Two aspects of this are critical:

The nick to be repaired occurs on a single strand but in the context of a double-stranded molecule.

The bases of the nicked strand, and particularly those directly flanking the nick site, must be properly base-paired to the opposite (un-nicked) strand.

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

Simply put: It’s all about that base and energy-dependent RNA-mediated DNA repair.
If you are still trying to put what is known about DNA repair and cell type differentiation back into the context of neo-Darwinian evolution, you are not a winner.
See: Kalevi Kull: Censorship & Royal Society Evo Event

Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull

See also: The spread of true and false news online
Reported as: Researchers call for large-scale scientific investigation into fake news

Additionally, the article’s authors point out that false information affects not only the political sphere but also areas not previously regarded as political, such as public health topics like nutrition and vaccinations, as well as the stock market.

Do you know someone who has consistently touted the use of vaccinations compared to nutrition? Are they paid to do that or are they biologically uninformed?

Alternative splicing of pre-mRNA

Diet-driven RNA interference and cancer prevention (3)

Excerpt: They claim to have found novel autoregulatory feedback loops that link changes in microRNAs to the alternative splicing factors SRSF1 and SRSF2.  Ectopic expression of SRSF1 can automagically repress the level of multiple microRNAs and SRSF2 can automagically upregulate miRNA expression.

The fact that a peer-reviewed work published in 2018 links autoregulatory feedback loops to automagically altered gene expression and apoptosis via alternative splicings of pre-mRNAs suggests it is time for all serious scientists to retire. The magic of pseudoscientists has prevailed for more than 2 decades.

See for comparison: In clinical trial, cream reduces squamous cell carcinoma risk

Results of a new randomized, double-blinded, controlled clinical trial in veterans showed a 75 percent reduction in the risk of needing surgery to treat a squamous cell carcinoma for a year after applying a skin cream for up to four weeks.

How Fluorouracil Works: (with my emphasis)

The ability of chemotherapy to kill cancer cells depends on its ability to halt cell division. Usually, the drugs work by damaging the RNA or DNA that tells the cell how to copy itself in division. If the cells are unable to divide, they die. The faster the cells are dividing, the more likely it is that chemotherapy will kill the cells, causing the tumor to shrink. They also induce cell suicide (self-death or apoptosis).

Chemotherapy drugs that affect cells only when they are dividing are called cell-cycle specific. Chemotherapy drugs that affect cells when they are at rest are called cell-cycle non-specific. The scheduling of chemotherapy is set based on the type of cells, rate at which they divide, and the time at which a given drug is likely to be effective. This is why chemotherapy is typically given in cycles.

Chemotherapy is most effective at killing cells that are rapidly dividing. Unfortunately, chemotherapy does not know the difference between the cancerous cells and the normal cells. The “normal” cells will grow back and be healthy but in the meantime, side effects occur. The “normal” cells most commonly affected by chemotherapy are the blood cells, the cells in the mouth, stomach and bowel, and the hair follicles; resulting in low blood counts, mouth sores, nausea, diarrhea, and/or hair loss. Different drugs may affect different parts of the body.

Fluoruracil belongs to the category of chemotherapy called antimetabolites. Antimetabolites are very similar to normal substances within the cell. When the cells incorporate these substances into the cellular metabolism, they are unable to divide. Antimetabolites are cell-cycle specific. They attack cells at very specific phases in the cycle. Antimetabolites are classified according to the substances with which they interfere. Fluoruracil is classified as a pyrimidine analog because it interferes with DNA and RNA synthesis by mimicking the building blocks necessary for synthesis.

The term antimetabolites is confusing. Metabolism is enzyme-dependent. Cell type differentiation is energy-dependent and the creation of microRNA links ATP to the creation of enzymes that metabolize food to the species-specific pheromones.
Pheromones biophysically constrain viral latency. That is how they prevent all pathology in the context of metabolism. Enzyme-dependent cycles of metabolism are the key to healthy longevity. Simply put, pheromones prevent the transgenerational epigenetic inheritance of nearly all viruses that have not been biophysically constrained by food energy-dependent metabolism.

Hardin, Hall and Rosbash (1990) put that fact into the perspective of Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels. The feedback loops are food energy-dependent and biophysically constrained by naturally occurring RNA interference (i.e., natural selection for energy-dependent codon optimality). The feedback links the metabolism of food to pheromone-controlled biophysically constrained viral latency.
 

Rosbash shared the 2017 Nobel Prize in Chemistry, which attests to the fact that all serious scientists probably know how to prevent or to effectively treat cancer as a disorder of cyclic changes in the chemistry of energy-dependent RNA mediated cell type differentiation. Prevention should include limiting exposure to nutrient stress and/or social stress because stress alters microRNA-mediated alternative splicings that link food energy to the biophyiscally constrained chemistry of protein folding.

See: Microrna-mediated regulation of splicing factors SRSF1, SRSF2 and hnRNP A1 in context of their alternatively spliced 3’UTRs

The microRNAs targeting SRSF1 and SRSF2 are involved in a regulatory feedback loop. microRNAs miR-183-5p and miR-200c-3p that target SRSF2, affect the expression of genes involved in apoptotic regulation.

They claim to have found novel autoregulatory feedback loops that link changes in microRNAs to the alternative splicing factors SRSF1 and SRSF2.  Ectopic expression of SRSF1 can automagically repress the level of multiple microRNAs and SRSF2 can automagically upregulate miRNA expression.

The fact that a peer-reviewed work published in 2018 links autoregulatory feedback loops to automagically altered gene expression and apoptosis via alternative splicings of pre-mRNAs suggests it is time for all serious scientists to retire. The magic of pseudoscientists has prevailed for more than 2 decades.

See for comparison:

From Fertilization to Adult Sexual Behavior (1996)

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two [model organisms.]

See also:
Feedback loops link odor and pheromone signaling with reproduction (2005)
The feedback loops are food energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans.

Sarcasm alert: The treatment of automagically dysregulated apoptosis should probably begin with a change in diet.

Changes in diet have been linked from the energy-dependent creation of enzymes that specifically link an energy-dependent base pair change to microRNA-mediated DNA repair via fixation of an RNA-mediated amino acid substitution. The substitutions are linked to energy-dependent cell type differentiation and healthy longevity without the magic.

Just add food energy or the virus-driven theft of quantized energy to eliminate the term autoregulatory and you could prevent or effectively treat all virus-driven pathology. 

Energy-dependent RNA interference links the enzyme-dependent metabolism of food and drugs to cell type differentiation via feedback loops that link pheromones to biophysically constrained viral latency.

Do not claim to have a logical philosophy if you cannot link the creation of the sun’s anti-entropic virucidal energy to every aspect of the biophysically constrained pheromone-controlled physiology of reproduction in species from microbes to human by starting with the obvious need to control viral replication in the ocean and linking the control to healthy longevity in modern human populations via fixation of RNA-mediated amino acid substitutions in all differentiated cell types.

See also: Metabolic Labeling and Profiling of Transfer RNAs Using Macroarrays

Transfer RNAs (tRNA) are abundant short non-coding RNA species that are typically 76 to 90 nucleotides in length. tRNAs are directly responsible for protein synthesis by translating codons in mRNA into amino acid sequences.

See also: Molecular mechanism of promoter opening by RNA polymerase III

RNA polymerase III (Pol III) and transcription factor IIIB (TFIIIB) assemble together on different promoter types to initiate the transcription of small, structured RNAs.

Nothing happens without the energy-dependent creation of the enzymes and the biophysically constrained viral latency that links the creation of G protein-coupled receptors to the functional structure of supercoiled DNA. The claims about molecular mechanisms of promoter opening appear to be deliberate attempts to obfuscate cause and effect.
Activation of G protein-coupled estrogen receptor signaling inhibits melanoma and improves response to immune checkpoint blockade

Female sex and history of prior pregnancies are associated with favorable melanoma outcomes. Here, we show that much of the melanoma protective effect likely results from estrogen signaling through the G protein-coupled estrogen receptor (GPER) on melanocytes. Selective GPER activation in primary melanocytes and melanoma cells induced long-term changes that maintained a more differentiated cell state as defined by increased expression of well-established melanocyte differentiation antigens, increased pigment production, decreased proliferative capacity, and decreased expression of the oncodriver and stem cell marker c-Myc. GPER signaling also rendered melanoma cells more vulnerable to immunotherapy. Systemically delivered GPER agonist was well tolerated, and cooperated with immune checkpoint blockade in melanoma-bearing mice to dramatically extend survival, with up to half of mice clearing their tumor. Complete responses were associated with immune memory that protected against tumor rechallenge. GPER may be a useful, pharmacologically accessible target for melanoma.

Sex-specific cell type differentiation links yeasts to primates via the nutrient-dependent pheromone-controlled physiology of reproduction that links the food energy-dependent structure and function of enzymes and G protein-coupled receptors to the biophysically constrained Structure and dynamics of GPCR signaling complexes, which are required to biophysically constrain viral latency in the context of effect of androgens and estrogens on difference in the cell type of males and females.
Any focus on G protein-coupled estrogen receptors compared to G protein-coupled androgen receptors  should be viewed with suspicion in the context of what has been known to all serious scientists about hormones and behavior since our Hormones and Behavior review of RNA-mediated cell type differentiation. From Fertilization to Adult Sexual Behavior (1996)
Simply put, the alternative splicings of pre-mRNAs, which are now called microRNAs, biophysically constrain energy-dependent viral latency and prevents the transgenerational epigenetic inheritance of nearly all virus-driven pathology until excess nutrient stress or social stress takes its toll on the innate immune system.
Eventually, our food energy-dependent RNA-mediated DNA repair fails, and the accumulation of viral microRNAs predicts the failure of cell type differentiation in the tissues that are required to sustain our physical health and mental health.

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

Elsevier fails to support the concept of autophagy

Summary: Who lets biologically uninformed theorists make presumptions about evolution after all serious scientists have linked light-harvesting from energy-dependent changes in electrons to ecosystems in all living genera via natural selection for food energy-dependent codon optimality. Who lets them pretend not to know that the pheromone-controlled physiology of reproduction links autophagy to the transgenerational epigenetic inheritance of healthy longevity? Who is causing the unnecessary suffering and premature death of your loved ones?
Elsevier publishing supports the pseudoscientific nonsense touted by theorists by who publish articles like this:
Neurotransmitter Funneling Optimizes Glutamate Receptor Kinetics (open access) Published Online: December 14, 2017 (with my emphasis)

These studies suggest that neurotransmitter binding is a directed process for which kinetics have been optimized (presumably by evolution)…

Our experiments reveal a strikingly elaborate management of ligand transport by AMPA receptors, whereby flexible positive charges ensure that glutamate binding reactions are fast. The existence of these pathways is surprising, and the fact that they alter the kinetics of receptor activity indicates that the molecular mechanisms that determine the action of neurotransmitters at receptors are more complex than previously thought. R660 is conserved between AMPA and NMDA receptors; in kainate receptors, R660 and R661 are replaced by lysine residues (Figure S8). It is possible that these helix F interactions also coordinate ligand binding in kainate and NMDA receptors. Given that electrostatic interactions are also important for coordination in other neurotransmitter binding sites (McCammon, 2009), these principles of ligand funneling may be general.

They linked the lysine residues (i.e., amino acid substitutions)  from electrostatic interactions to RNA-mediated cell type differentiation in all living genera. Their studies do not link any experimental evidence from electrostatic interactions or optimized kinetics to evolution. Evolution cannot optimize any aspect of energy-dependent kinetics. Evolution cannot optimize any aspect of energy-dependent RNA-mediated cell type differentiation, which is biophysically constrained by the physiology of pheromone-controlled reproduction.
The nonsense about evolution was reported as: Scientists chart how brain signals connect to neurons (with my emphasis)

Scientists at Johns Hopkins have used supercomputers to create an atomic scale map that tracks how the signaling chemical glutamate binds to a neuron in the brain. The findings, say the scientists, shed light on the dynamic physics of the chemical’s pathway, as well as the speed of nerve cell communications.

See: Life is physics and chemistry and communication
All experimental evidence of top-down causation links quantized energy from the speed of light on contact with water to energy as information-dependent changes in electrons and all ecosystems via the physiology of pheromone-controlled reproduction, which biophysically constrains viral latency. The use of supercomputers led the researchers to report findings that eliminate everything known to serious scientists about energy-dependent RNA-mediated cell type differentiation. It is common for theorists to eliminate energy as information-dependent changes and replace facts with mathematical models.
See for comparison: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (open access)

The bias between codons or amino acids, and mRNA expression levels has been previously recognized across species and is thought to result from selection for efficient, accurate translation, and folding of highly expressed genes (Ikemura, 1982; Akashi, 1994; Akashi & Gojobori, 2002; Drummond & Wilke, 2008; Kudla et al, 2009; Novoa & Ribas de Pouplana, 2012). The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

This is not just an alternative perspective. It is a refutation of neo-Darwinian pseudoscientific nonsense that was reported as: Codon optimality at genome transition

Nucleotide triplets, or codons, designate specific amino acids for protein synthesis. However, that is not their only job. In yeast and bacteria, codons contribute to RNA stability, with “optimal” codons stabilizing RNAs and “suboptimal” codons destabilizing RNAs. This is possible because multiple codons can encode the same amino acid.

See also: Human GW182 Paralogs Are the Central Organizers for RNA-Mediated Control of Transcription Elsevier — Cell Reports (August 15, 2017)

Nuclear RNAi, regardless of whether it is controlling splicing, transcription, or some other nuclear process, would have distinct advantages as a mechanism for evolution, because it would expand sequence-specific control of gene expression by miRNAs.

No experimental evidence of biologically-based cause and effect suggests that microRNAs evolved to control sequence-specific gene expression. The authors linked TNRC6, MED14, NAT10, and WDR5 to RNA-mediated gene activation. They inadvertently linked the energy-dependent de novo creation of microRNAs to Trinucleotide Repeat Containing (TNRC) 6A expression.  See: miR-26a-5p Regulates TNRC6A Expression and Facilitates Theca Cell Proliferation in Chicken Ovarian Follicles
The anti-entropic virucidal energy of sunlight links the creation of microRNAs and multiple codons to the creation of differences and similarities in the same amino acid. That fact has been ignored.
See also: MicroRNAs recruit eIF4E2 to repress translation of target mRNAs

There is increasing evidence indicating that translation initiation is a major target of miRNA repression…

…we provide evidence indicating that TNRC6A, the core component of RISC, can directly recruit eIF4E2 to target mRNA to repress translation.

They provided evidence that the energy-dependent de novo creation of microRNAs represses the expression of the mutations that cause all pathology.
See for example: Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention
Reported as: New Study Finds That Most Cancer Mutations are Due to Random DNA Copying ‘Mistakes’

John Hopkins Kimmel Cancer Center scientists report data from a new study providing evidence that random DNA copying “mistakes” account for nearly two-thirds of the mutations that cause cancer. Their research is grounded on a novel mathematical model based on DNA sequencing and epidemiologic data from around the world.

This was reported in the context of the “bad luck” theory of cancer (video).
For comparison see:  Why Is This Bacterium Hiding in Human Tumors?

 “The whole idea of bacteria in tumors is fascinating and unexpected,” said Dr. Bert Vogelstein, a colon cancer researcher at Johns Hopkins.

See for comparison: QuEBS: Workshop on Quantum Effects in Biological Systems  has established itself as an outstanding stage to present the research in the intersection of physics, chemistry and biology. This field has… established excitons in biology as the “must-talk-language” when describing the quantum effects in biological light-harvesting systems.
All serious scientists have linked the anti-entropic virucidal energy of sunlight from physics and chemistry to biophysically constrained viral latency via the de novo creation of microRNAs and the physiology of pheromone-controlled reproduction, which links autophagy to fixation of amino acid substitutions that stabilize the organized genome of all living genera in the context of autophagy.
Only biologically uniformed researchers, like Bert Vogelstein are surprised to find bacteria in tumors, because all serious scientists have link the viruses in bacteria from the degradation of messenger RNA in bacteria to the degradation of messenger RNA that causes all pathology in all living genera.
 
 
 

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

Two retractions of human idiocy

Excerpt: …she was interested in the PNAS research because it identified a potential inhibitor of the hepatitis C virus…

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

1)

This retraction marks the second in six months for Nature Chemistry after having none for eight years.

2)

In 2009, Szostak also retracted a 2008 paper in Proceedings of the National Academy of Sciences after an outside researcher could not replicate the results. The retraction notice credited Katherine Berry, then a doctoral student at the University of California, Berkeley, for bringing the issues to their attention. (Full disclosure: RW’s Victoria Stern and Berry were roommates freshman year of college).

Berry, who’s now an assistant professor of biochemistry at Mount Holyoke in South Hadley, Mass., told us that she was interested in the PNAS research because it identified a potential inhibitor of the hepatitis C virus…

Comment awaiting moderation

James V. Kohl December 7, 2017 at 4:35 am

The Science Behind the Game “Cytosis,” pits the collaborative efforts of 20 serious scientists against the pseudoscientific nonsense touted by theorists. The serious scientists know how energy-dependent RNA-mediated cell type differentiation occurs.

Resources (e.g., mRNA, ATP) are used to build enzymes, hormones, and/or receptors. Health points accumulate to show why food energy must be linked from the physiology of pheromone-controlled reproduction to biophysically constrained viral latency.

For comparison, Szostak and other theorists have been stuck with their ridiculous misrepresentations of emergence and neo-Darwinian evolution, which failed to consider Darwin’s “conditions of life.”

“Conditions of life” are energy-dependent. The energy is Schrodinger’s anti-entropic virucidal energy. It comes from sunlight and is epigenetically “trapped” in food via the physiology of reproduction.

Board Game:
Cytosis: A Cell Biology Game
Title:
Cytosis – The Science Behind the Game https://boardgamegeek.com/filepage/155090/cytosis-science-behind-game

Addendum: Naturally occurring base editing, microRNA editing, and RNA editing link the energy-dependent creation of microRNAs from natural selection for energy-dependent codon optimality to the physiology of pheromone-controlled reproduction, which biophysically constrains viral latency. Constraint breaking mutations have been linked to all pathology. The misrepresentations of Szostak and others like him have contributed to a history of unnecessary suffering and premature death. Richard Feynman helped to place their claims into this perspective:

 

 

diseases-disorders

Your indifference is killing you and others

Summary: Coherence-inducing mechanisms is double-speak for mechanisms that are nutrient-dependent and pheromone-controlled.
Feedback loops link odor and pheromone signaling with reproduction has been presented in double-speak as Looplessness in networks is linked to trophic coherence

We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

Feedback loops link the sun’s anti-entropic virucidal energy from the food that organisms eat to the physiology of pheromone-controlled reproduction in all living genera. The virucidal effect of ultraviolet light biophysically constrains viral latency. Energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA are fixed in organized genomes via the physiology of reproduction and supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA that links mutations to all pathology.
Coherence-inducing mechanisms is double-speak for nutrient-dependent and pheromone-controlled in the context of Nutrient-dependent/pheromone-controlled adaptive evolution: a model. 
Despite the validity of the model, it has not been accepted by neo-Darwinian theorists or “Big Bang” cosmologists. Ridiculous beliefs about emergence and evolution are pervasive and the pseudoscientific nonsense of their theories leads to claims about coherence-inducing mechanisms.
That is why I changed the FB page description at RNA-mediated after a series of posts (see below).

It took 20 years for others to realize that all life on Earth is food energy-dependent. Now, most people are indifferent to that fact. They refuse to learn anything about where the food energy comes from.

Differences in the energy of photons have been linked to quantized energy-dependent fixation of RNA-mediated amino acid substitutions. The substitutions biophysically constrain supercoiled DNA via the physiology of pheromone-controlled reproduction.

Virus-driven energy theft links the degradation of messenger RNA to mutations via amino acid substitutions in viruses. The substitutions in the viruses have been linked to all pathology via changes in the energy-dependent microRNA/messenger RNA balance.

For comparison, the pseudoscientific nonsense of neo-Darwinian theories links mutations from natural selection to the evolution of new species. In reality, light energy is quantized information. The information links physics, chemistry, and molecular epigenetics from the speed of light on contact with water and hydrogen-atom transfer in DNA base pairs in solution to learning, memory, and behavior via RNA-mediated events such as the energy-dependent creation of enzymes and the the de novo creation of G protein-coupled receptors such as olfactory receptor genes.

Top-down causation and de novo gene creation are exemplified by energy-dependent differences in the microRNA/messenger RNA balance that link natural selection for codon optimality to amino acid substitutions that link the physiology of reproduction to supercoiled DNA. Supercoiled DNA protects all organized genomes from virus-driven energy theft. That fact supports the beliefs of young earth creationists, which may be the only existing basis for discussion of quantum biology and refutations of neo-Darwinian theories that have linked olfaction to quantum souls. If there is another basis for the link from quantum physics to quantum souls, no one has detailed in in the context of top-down causation, which must include information about the creation of genes.

Most people seem unwilling to accept experimental evidence that attests to how genes are created or information that shows how virus-driven energy theft is linked to all pathology. Discussion of the energy-dependent paradigm shift would lead others away from pseudoscientific nonsense about emergence and/or beneficial mutations and evolution.

Only via discussion of facts about the paradigm shift will others learn what is currently known to serious scientists about the biophysically constrained nutrient energy-dependent chemistry of RNA-methylation and all biophysically constrained RNA-mediated protein folding chemistry. Simply put, the protein folding chemistry must be linked to all biodiversity by the physiology of energy-dependent pheromone-controlled reproduction in all living genera.

Your indifference to that fact is killing people.

See for comparison: Looplessness in networks is linked to trophic coherence (May 16, 2017)

Our theory correctly classifies a variety of networks-including those derived from genes, metabolites, species, neurons, words, computers, and trading nations-into two distinct regimes of high and low feedback and provides a null model to gauge the significance of related magnitudes. Because trophic coherence suppresses feedback, whereas an absence of feedback alone does not lead to coherence, our work suggests that the reasons for “looplessness” in nature should be sought in coherence-inducing mechanisms.

Reported August 14, 2017 as Trophic coherence explains why networks have few feedback loops and high stability

The researchers are also investigating whether negentropy – the opposite of entropy, and in which a physical, thermodynamic or biological process creates order – are affected by trophic coherence. “The modern concept of entropy,” Johnson points out, “comes from statistical physics and is a property of ensembles, as described above – that is, the entropy of an ensemble is simply a function of the number of elements it contains.” Moreover, he adds, graph ensemble entropy has proven to be a powerful tool for understanding various network properties. We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

See for comparison: Feedback loops link odor and pheromone signaling with reproduction

These studies also indicate that GnRH neurons are likely to influence numerous brain functions. They appear to transmit signals to as many as 30,000 or more neurons in 34 brain areas, consistent with previous studies showing GnRH+ fibers and GnRH receptors in multiple brain regions (Badr and Pelletier, 1987; Jennes et al., 1988; Jennes et al., 1997). BL+ neurons likely to receive synaptic input from GnRH neurons were seen in areas associated with numerous different functions, including odor and pheromone processing, sexual behavior, appetite, defensive behavior, motor programs, and the relay of information to higher cortical areas. These results may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.

See my posts on Discovering Vismodegib in the Fight Against Skin Cancer: The First Approved Inhibitor of the Hedgehog Pathway
No one I know is likely to understand this link from the anti-entropic virucidal energy of sunlight to prevention of all pathology because they must first understand the fact that proteins do not create themselves. There is no need for this inhibitor of the Hedgehog pathway or inhibition of any other pathway if cancer is prevented. But most people are not willing to learn about prevention because they think they can rely on medical practitioners to effectively treat their diseases. Do you think that your physician knows anything about light scattering characterization of glycoproteins and their interactions with other proteins and antibodies?
Absolute Characterization of Glycoproteins and their Interactions with Proteins and Antibodies by Light Scattering
Light scattering can now be linked to the characterization of glycoproteins and their immune system interactions in all species on Earth. That suggests the speed of light on contact with water links energy as information to the de novo creation of the glycoproteins,
If so, the physiology of reproduction links pheromones to biophysical constraints on the creation of more glycoproteins in the context of morphological and behavioral differences in species from microbes to humans. That suggests the refutation of neo-Darwinism is complete, since the virus-driven degradation of messenger RNA has been linked to all pathology in bacteria that become archaea before virus-driven energy theft causes them to become L-forms.
Simply put, Carl Woese was wrong. There is only one domain of life and virus-driven energy theft is what destroys all life on Earth.

 

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

Energy-dependent physical and biophysical constraints (6)

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.

See also: OLYMPUS experiment sheds light on structure of protons

…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.

See also: One billion suns: World’s brightest laser sparks new behavior in light

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.

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 via the difference between “Nature” and God’s perfect “Creation.”

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.

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.

rp_levels-of-organization.jpg

What energy source do proteins prefer?

Quantized energy as information is the anti-entropic virucidal source of healthy longevity. All pathology is caused by virus-driven energy theft.
Impact of cytosine methylation on DNA binding specificities of human transcription factors

…many developmentally important proteins display preference for mCpG-containing sequences.
 

How do proteins display a preference for anything except food and codon optimality?

Natural selection for quantized food energy-dependent codon optimality links the structure and function of supercoiled DNA to protection from virus-driven energy theft.

That fact was obfuscated in this report: Scientists reveal how epigenetic changes in DNA are interpreted

…some ‘master’ regulatory proteins can activate regions of the genome that are normally inactive due to epigenetic changes. Their findings contribute to a better understanding of gene regulation, embryonic development and the processes leading to diseases such as cancer.

Don’t miss the claim that links epigenetic changes from normally inactive genes to cancer. See also the section on molecular epigenetics from this 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior

Early in embryonic development attached methyl groups become removed from most genes. Several days later, methyl groups are reattached in appropriate sites. Fascinatingly, some such genes reestablish methylation patterns based upon whether the chromosomal segment carrying the gene came from maternal or paternal chromosomes. These sexually dimorphic patterns are labeled genomic or parental imprinting, and these imprintings are inheritable but non-genetic modifications of specific genes…

If you were an inherited protein in an organized genome, would you prefer to protect yourself from virus-driven energy theft? If the transgenerational epigenetic inheritance of virus-damaged DNA left you, an organism will a debilitating or deadly form of protein-based pathology, would you consider an attempt to eliminate the virus? How could you do that?

Most people are taught to believe that they have no choice but to accept the virus-caused pathology. They do not know that the way to eliminate the pathology is energy-dependent. That’s what they will learn by playing the game Cytosis.

 

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

When not enough food energy as quantized information is available to the cell, the virus-driven degradation of messenger RNA prevents the DNA code from correctly building more proteins that are found as enzymes, hormones, and receptors. For example, without the energy-dependent de novo creation of more G protein-coupled receptors, the ability of all cell types that contribute to the physiology of pheromone-controlled reproduction is compromised.
See: Feedback loops link odor and pheromone signaling with reproduction

These results may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.

Even in bacteria, the feedback loops link quantized energy as information from what organisms eat to the pheromone-controlled physiology of reproduction. The fact that achiral glycine in position 6 of the GnRH decapeptide is linked to the stability of all organized genomes in all vertebrates from what is known about invertebrates suggest that mutation-driven evolution is the most ridiculous manifestation of human ignorance that could be imagined by serious scientists who have linked energy-dependent changes from angstroms to ecosystems via supercoiled DNA.
For comparison, the virus-driven degradation of messenger RNA links mutations to loss of function and all pathology in all genera via the transgenerational epigenetic inheritance of biophysically constrained viral latency. In cases where viral latency is not biophysically constrained or when stress links the lack of nutrients and/or ongoing social stress to the virus-driven degradation of messenger RNA, organisms die. The death rate is determined by the nutrient energy-dependent ability of organisms to ecological adapt and reproduce.

The technicalities of accurate representations of biologically-based interactions among the birds and the bees and all other living genera have been established. The sun’s anti-entropic virucidal energy links hydrogen-atom transfer in DNA base pairs in solution to nutrient energy-dependent RNA-mediated DNA repair via protein folding chemistry in the context of amino acid substitutions in supercoiled DNA. Simply put, energy as information is linked to all biodiversity via the physiology of reproduction.

But, as Roger Penrose once asked: How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?

All ecological models that link what organisms eat to biophysically constrained biologically-based RNA-mediated protein folding chemistry and the amino acid substitutions have been validated by all serious scientists who have learned that cell type differentiation is nutrient energy-dependent in all cell types in all individuals of all living genera.

For comparison, all theories that fail to link what organism eat to the ecological adaptations manifested in differences in morphological and behavioral diversity havce been removed from any further consideration whatsoever, except for consideration by pseudoscientists.

See for example:

James V. Kohl:

Evolution by natural selection cannot be the outcome if something is not first selected. Selection is always for nutrients. It is as simple as that.

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.

See also: Virus linked to food sensitivity

“This study clearly shows that a virus that is not clinically symptomatic can still do bad things to the immune system and set the stage for an autoimmune disorder, and for celiac disease in particular,” Jabri says. “However, the specific virus and its genes, the interaction between the microbe and the host, and the health status of the host are all going to matter as well.”

Pre-order here: Cytosis: A Cell Biology Game

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

The facts about how nutrient energy-dependent biophysically constrained biologically-based cause and effect controls viral latency via the physiology of pheromone-controlled reproduction have been detailed in the extant peer-reviewed literature during the past century. Most people wonder why they have not been taught to believe in the facts. Simply put, there are too many pseudoscientists who want people to believe in the pseudoscientific nonsense touted by neo-Darwinian theorists, and too few who have joined the serious scientists who are: Combating Evolution to Fight Disease
For a recent example of those who are fighting to keep disease, see these comments, which were removed from an attempt to discuss ecological models of top-down causation and biophysically constrained RNA-mediated healthy longevity for comparison to virus-driven pathology.
See also: Your comment on ‘No, epigenetics and environmental responsiveness don’t undermine Darwinian evolution’ has been removed.

What is life when it is not protected from virus driven entropy https://www.youtube.com/watch?v=K35THJtlhoE

Published on 30 Mar 2016

Poster: The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

See also: Your comment on ‘No, epigenetics and environmental responsiveness don’t undermine Darwinian evolution’ has been removed.

What experimental evidence of biologically-based cause and effect suggests that it might take a thousand generations? See for comparison: Transgenerational transmission of environmental information in C. elegans http://science.sciencemag.org/content/356/6335/320

Clearly, others have placed the facts about transgenerational epigenetic inheritance into the context of chromosomal inheritance via energy-dependent endogenous RNA interference across life-history transitions. See: Endogenous RNAi Pathways Are Required in Neurons for Dauer Formation in Caenorhabditis elegans http://www.genetics.org/content/early/2017/01/25/genetics.116.195438?papetoc

Is there a model organism that you would like to compared to Caenorhabditis elegans, or do you ignore it and others that do not support theories about mutation-driven evolution?

See also: Your comment on ‘No, epigenetics and environmental responsiveness don’t undermine Darwinian evolution’ has been removed.

As a medical laboratory scientist who linked the anti-entropic virucidal energy of sunlight to all biodiversity via the potential of hydrogen (pH), I viewed people like you with suspicion.

If you cannot link the creation of energy to all healthy longevity via the physiology of reproduction in all living genera, you cannot link virus-driven energy theft from the degradation of messenger RNA to mutations and all pathology.

But, you earned the title of pathologist, anyway. Congratulations! You show others where demanding their respect for your credentials will lead them. To the grave via evolutionary processes!

See also: Your comment on ‘No, epigenetics and environmental responsiveness don’t undermine Darwinian evolution’ has been removed.

You claim to be a “Retired physician-scientist-academic; active tree-grower.”

Do you realize that the production of taxol from the Pacific Yew Tree links the physiology of reproduction in soil bacteria to the treatment of cancer in humans via the conserved molecular mechanisms of energy-dependent cell type differentiation I have detailed?

Simply put, taxol is a link from the anti-entropic virucidal effects of ultraviolet light in plants to changes in the microRNA/messenger RNA balance in all living genera. That fact allowed me to link microRNAs from chirality to autophagy and inhibition of apoptosis via signal transduction and activation of transcription in vascular smooth muscle cells and all other cell types.