The problem with -omics has repeatedly been detailed in articles from social scientists and other theorists who fail to link what is known to serious scientists about the microRNAome to their theories. Pseudoscientists continue to create bricks that clutter the metaphorical physical landscape and prevent the epigenetic landscape from being linked from the physiology of nutrient energy-dependent pheromone-controlled reproduction to all cell type differentiation via energy-dependent changes in atoms to ecosystems in all living genera.
On 1/22/18, I discussed this with a plumber and his assistant, who is –like me– a veteran of the US Military. The plumber, prefaced the discussion with a comment about adaptations for comparison to evolution. The veteran provided supportive comments from his expertise in history, which he hopes will not repeat itself in the context of the 1918 Spanish flu, smallpox, or the bubonic plague.
I learned the value of social science because he believes that vultures put an end to the bubonic plague in the context of their unique ability to thermoregulate their organized genome by spreading their wings to create what most people would refer to as a virus-killing fever. I may not be so critical of other social scientists after meeting one that was not biologically uninformed.
There may be others, but I doubt it.
See: Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay
We identified and confirmed orthologous gene pairs with 3′-UTR SINEs that independently function in SMD control of myoblast metabolism. Expanding to other species, we demonstrated that SINE-directed SMD likely emerged in both primate and rodent lineages >20-25 million years ago. Our work reveals a mechanism for the convergent evolution of posttranscriptional gene regulatory networks in mammals by species-specific SINE transposition and SMD.
…one SNP in the promoter, three SNPs in the coding region, and one in 3′-UTR were novel and reported for the first time in this study.
[…]The expression of Hsp90AA1 in cow bearing mutant allele C was higher (4.18 +/- 0.928) than cows bearing wild-type allele G (1.008 +/- 0.0.129) in stress season. In summary, there was an association between genetic variations in the Hsp90AA1 and thermoresistance. This association could be used as a marker in genetic selection for heat tolerance in Chinese Holstein cattle breeds.
There is no such thing as genetic selection for heat tolerance. The limits of food energy-dependent thermotolerance are biophysically constrained in the context of food energy that biophysically constrains viral latency,which typically limits or prevents activation of the death gene.
Preventing activation of the death gene was reported as: 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, and familiar examples include the wings of birds, bats, and insects, and echolocation in bats and dolphins. Now, molecular biologists have found evidence of convergent evolution in an important mechanism of gene regulation in humans and mice.
Serious scientists do not call ecological adaptation convergent evolution, and serious scientists do not claim to discover important mechanisms of gene regulation. All the mechanisms are biophysically constrained by ecological variation in the availability of food and the physiology of pheromone-controlled reproduction in species from mice to humans (and from microbes to humans).
But see for comparison: A simple explanation of Born’s rule
…the agreement between quantum theory and experiments follows from a one-to-one correspondence between the logical possibilities and the physical possibilities and, in particular, implies that the outcomes of quantum measurements are not constrained by any physical reason.
Thanks to so-called science journalist Philip C. Ball for calling this to my attention. In my first blog post about Nonomura’s Sokalian hoax, I mentioned Frohlich (1968). Long-range coherence and energy storage in biological systems. I do not expect pseudoscientists or so-called science journalists to accept the facts about constrained energy storage. The facts are neo-Darwinian theory killers. Once again, the theorists have a problem understanding how the creation of energy must be linked from energy storage to biophysically constrained viral latency and all biodiversity. Nonomura’s hoax links the energy-dependent epigenetic silencing of transposable elements to the central events of germline transmission via the creation of sunlight, the creation of ATP, and the creation of microRNAs. The light energy-dependent creation of microRNAS must be linked to RNA-mediated DNA repair and to the relatively error-free genome of the next generation via the pheromone-controlled physiology of reproduction that biophysically constrains viral latency.
Unanswered questions about viral latency and transcriptional quiescence (aka gene silencing), which is a hallmark of the biophysically constrained germ cell lineage in many organisms, are the clear link to my claim that Nonomura has published a Sokalian hoax as Small RNA pathways responsible for non-cell-autonomous regulation of plant reproduction — as a peer-reviewed monograph.
The unanswered questions allow biologically uninformed peers to accept the claims of non-cell-autonomous regulation as if they could be part of an evolutionary approach to energy-dependent reproduction. For comparison, the first question a serious scientist would ask is about how non-cell-autonomous pathways compensate for ecological variation, which must be linked to energy-dependent ecological adaptation via the availability of some nutrients, materials and signals. Most serious scientists will realize that non-cell-autonomous pathways link sunlight to the activation of endogenous substrates (e.g., enzymes) that are created in the context of what happens when the speed of light hits water.
See: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
Reported as: … the conditions that produce nucleic acid precursors also create the starting materials needed to make natural amino acids and lipids. That suggests a single set of [light activated] reactions could have given rise to most of life’s building blocks simultaneously.
I noticed that this pinned post now appears first @rnomics:
This was a report on Non‐enzymatic glycolysis and pentose phosphate pathway‐like reactions in a plausible Archean ocean
Fabrice Leclerc @rnomics seems to be ignoring the retractions of Jack Szostak’s works. See: Retraction Watch
Researchers who study the origins of life on Earth have hypothesized that RNA evolved before DNA or proteins. Szostak’s works seemed to suggest that RNA replicated itself without enzymes. Supposedly, a certain type of peptide — which may have existed in our early history — made it possible for RNA to copy itself. But where did the peptide come from?
Who cares? In subsequent experiments, no one reproduced the 2016 findings. Indeed, the peptide did not appear to provide an environment that fostered RNA replication. With two retraction of his groups works, claims about the microRNAome should have been placed into the context the energy-dependent creation microRNAs and enzymes.
The problem that serious scientists expect to be addressed is the one that links the nutrient-energy dependent source of the materials for developing germ cells to the development of differentiated cell typed in the context of metabolism and signaling. Again, we see how Nonomura helps to eliminate the magic of evolution without admitting to the hoax. Light energy is required, and he did not mention that fact.
For comparison, science journalist Philip Ball took the the magic several steps further. He placed the availability of the quantized energy as information, which is required for the creation of nutrients, into this context:
Nonomura claims that little is known about the mechanism that promotes the energy-dependent intercellular movement of small RNAs in plant reproductive organs. But, he also claims that the mechanism in humans is part of an energy-dependent exosome-mediated system, which was recently reported in the context of small RNA transfer in organ cross-talk. Philip C. Ball’s claims are based on the automagical creation of an environment full of stuff.
The link from the availability of nutrient-energy in pollen (i.e., Ball’s environment full of stuff) to energy-dependent foraging behavior and the pheromone-controlled physiology of reproduction in the honeybee model organism is missing. Nonomura’s conclusion is another example of Sokal-like wit. The cell membrane must automagically create itself before direct evidence for energy-dependent microRNA-mediated cell type differentiation can be linked to healthy longevity in all living genera via the physiology of reproduction in grasses like fescue.
The energy source for the transfer of materials or information between SCs [somatic cells] and the vegetative cell (VC) nucleus in not mentioned in Nonomura’s attack on the intelligence of theorists and science journalists who have failed to link the virus-driven theft of quantized energy from mutations to the transgenerational epigenetic inheritance of all pathology.
For comparison: My top tweet from this month was posted on January 5, 2018. So far it has accumulated 1484 impressions. In case you missed it:
A cartoon representation of “Long-range coherence and energy storage in biological systems” (1968) might help others establish facts about how the construction of the cell membrane protects against virus-driven genomic entropy. A comic about the problems with the -omics, illustrated by Matteo Farinella
The problem with -omics, and especially with the ridiculous representation from 2014 as a pinned post @rnomics, has repeatedly been detailed in articles from social scientists and other theorists who fail to link what is known to serious scientists about the microRNAome to their theories. Pseudoscientists and biologically uninformed science journalists continue to create bricks that clutter the metaphorical physical landscape (an environment full of stuff) and human idiocy prevents the epigenetic landscape from being linked to all cell type differentiation via the nutrient energy-dependent pheromone-controlled links from atoms to ecosystems in all living genera.
The MicroRNAome Strikes Back: A Sokalian hoax (3)
See also: The Postmodernism Generator web page (generates a random postmodernist article each time loaded)
See also: Social science is pseudoscience
Summary: Identical nucleotide sequences link energy-dependent changes in binding sites to different amino acids in different proteins.The binding sites are conserved in the orthologous mammalian genes.
As presciently predicted in the works of Richard Feynman and Bruce McEwen, bacteria feed on something that allows them to produce uranium isotopes in the context of their food energy-dependent biophysically constrained pheromone-controlled physiology of reproduction. The link from a light-activated endogenous substrate in all cell types must be viewed in the context of energy-dependent feedback loops that link sunlight to the anti-entropic constraint of atomic energy in uranium isotopes. Chromosomal inheritance prevents the evolution of one species into another.
What it could mean is this: that the human mind (consciousness) isn’t made up of the same matter governed by physics. Furthermore, it could suggest that the mind is capable of overcoming physics with free will. This could potentially be the first time scientists gain a firm grasp on the problem of consciousness. “It wouldn’t settle the question, but it would certainly have a strong bearing on the issue of free will,” said Hardy.
The idea that the mind isn’t made up of matter, which is governed by the Laws of Physics is ridiculous. You cannot take such a ridiculous idea and make it meaningful via experiments. The experiment would be meaningless. All experiments must start with a rational hypothesis or something that is known. Then you must attempt to add scientific support for extending what is known to something that becomes known via your experiment. Otherwise, you start with a theory and add nothing more than another theory. You don’t get answers to any questions.
See for example: Did humans evolve in Europe rather than Africa? We don’t have the answer just yet
Charles Darwin believed that humans evolved in Africa, because that’s where our closest ape relatives the chimpanzees and gorillas live. And during the twentieth century he was vindicated through a combination of fossil and genetic discoveries.
Darwin placed his energy-dependent “conditions of life” first. .
While our place in the tree of life is now well established – chimpanzees being our closest relatives – the beginning of the human line millions of years ago continues to be shrouded in mystery.
Charles Darwin had a theory about how his “conditions of life” might be linked to biodiversity via natural selection. Others thought that his theory could be linked from natural selection to the evolution of humans from ape relatives. They claimed that Darwin thought humans evolved during millions of years of natural selection for small changes. De Vries (1902) defined the small changes as mutations. Biologically uninformed neo-Darwinian theorists still claim that mutation-driven evolution is supported by the fossil record and genetic discoveries.
See for comparison: Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees Svante Paabo is one of the paleoanthropologists who has a grasp of cell biology, which links energy to RNA-mediated biodiversity via the sense of smell. When someone with his level of expertise refutes all neo-Darwinian nonsense with experimental evidence of biologically-based cause and effect, how can others justify their lack of acceptance for the facts? Paabo’s facts link natural selection for energy-dependent codon optimality to all biodiversity via the claims in Feedback loops link odor and pheromone signaling with reproduction.
Genetically engineered “disco bacteria” sense and respond to different colors of light, creating both stunning art in the culture dish and new possibilities for synthetic biology.
See for comparison:Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates
Who engineered the energy-dependent acquisition of RGB color vision in E. coli and full trichromatic RGB color vision in primates? What prevents the biophysically constrained loss of the engineered receptors for RGB color vision in E. coli that are linked from the de novo creation of olfactory receptor genes to the loss of the genes that coincides with the advent of RGB (Trichromatic) color vision in primates?
Pseudoscientists might claim that evolution engineers the acquisition of all morphological and behavioral traits, but they won’t make verifiable claims about biophysical constraints or loss of the genes after the genes are created. Instead, see: Mutation-Driven Evolution.
Theorists start with genes that were somehow created and then claim:
…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations…
After the energy-dependent de novo creation of genes, genomic conservation continues to be nutrient energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction in all living genera. Chromosomal inheritance prevents the evolution of one species into another — unless it occurs via magic traits. In the context of mutation-driven evolution species must have magic traits.
See for example: Evolution on the fast lane—One flounder species became two
“The answer may lay in so called magic traits, meaning traits that are under selection which at the same time cause reproductive isolation as a byproduct. In theory, selection on such traits could play a central role in rapid speciation events. The mating strategies and reproductive traits of the two flounder species could act as magic traits,” clarifies Momigliano.
Despite its appearance, amphioxus is not a fish. It has a primitive spinal cord which runs down its back, but no clearly defined face, no bones or jaws and a small brain with a single light-sensing “frontal eye”. It has changed so little for hundreds of millions of years that it has been described as a “living fossil”.
See for comparison to the report of a hundreds of million years-old “living fossil:”Bacteria evolve over a weekend (video) Serious scientists know that the bacteria that reportedly “evolved” adapted to ecological variation in their food supply. Adaptation is nutrient energy-dependent and pheromone controlled via the physiology of reproduction in all living genera. It occurs over-the-weekend in P. fluorescens, but it is still reported to be mutation-driven evolution by biologically uninformed theorists.
Biologically uniformed theorists also make claims like those found here: The Physics of Everything
For comparison: This is the Physics of Everything, outside the context of the magic of evolution in the context of magic traits.
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).
Average hydrophobic thickness cannot be linked from energy-dependent changes in the cell membrane to biophysically constrained cause and effect via the pheromone-controlled physiology of reproduction in any organism.
See for comparison: 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.
Serious scientists do not link average hydrophobic thickness from the sense of smell in bacteria to all biophysically constrained energy-dependent biodiversity via the physiology of reproduction in species from microbes to humans. Serious scientists link the energy-dependent changes from angstroms to ecosystems in the context of RNA-mediated amino acid substitutions in supercoiled DNA.
See: Structural diversity of supercoiled DNA
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 and biophysically constrained.
In recent years, scientists had uncovered new evidence that bacteria – living microorganisms – could generate a different kind of reduced uranium that is non-crystalline and has very different physical and chemical properties.
…using new techniques including synchrotron radiation-based spectroscopy and isotope fingerprinting. They found that up to 89 percent of the uranium from their 650-foot-deep samples wasn’t crystalline uraninite at all, but rather, a non-crystalline uranium that was bound to organic matter or inorganic carbonate. Most of the uranium they found in that unmined site is estimated to be 3 million years old, and formed via reduction by microorganisms – microbes that respire not on oxygen, but on uranium.
They linked the nutrient energy-dependent pheromone-controlled physiology of reproduction in bacteria and all other living genera to the creation of differences in the 238U to 235U isotope ratio. The differences in the 238U to 235U isotope ratio discriminate between the abiotic and biotic transformation of uranium. But, they placed their findings on abiogenesis into the context of ridiculous theories of evolution and ignored everything known to serious scientists about the energy-dependent biotic transformation of uranium and all energy-dependent biogenesis.
For any example of how placing their results into the context of abiogenesis supports ridiculous theories about emergence and evolution, see: Uranium–lead dating
The method relies on two separate decay chains, the uranium series from 238U to 206Pb, with a half-life of 4.47 billion years and the actinium series from 235U to 207Pb, with a half-life of 710 million years.
NtrC shares 30 percent amino acid identity with FleQ… the re-evolved flagella enabled the bacteria to access food supplies…
Natural selection for food energy-dependent codon optimality links ultraviolet light (UV) to the nutrient energy-dependent pheromone-controlled physiology of reproduction in P. fluorescens, which links UV light to the weekend resurrection of the flagellum because P. fluorescens fluoresces with exposure to UV light.
Differences in the nutrient energy-dependent RNA-mediated amino acid substitutions link differences in supercoiled DNA to the protection of all organized genomes from viruses. Virus-driven energy theft causes the degradation of messenger RNA, which links mutations to all pathology.
See Feynman’s comments about food energy:
Could any other physicist but Feynman have guessed that bacteria feed on something that allows them to produce uranium isotopes in the context of their food energy-dependent biophysically constrained pheromone-controlled physiology of reproduction?
Could any other molecular biologist but Bruce McEwen have linked an endogenous substrate from the energy-dependent biophysically constrained pheromone controlled physiology of reproduction to all biodiversity in all living genera?
Binding sites of miR-619-5p in the 3’UTRs of all human target genes are also present in the 3’UTRs of orthologous genes of mammals. The completely complementary binding sites for miR-619-5p are conservative in the orthologous mammalian genes.
CONCLUSIONS:(with my emphasis)
The majority of miR-619-5p binding sites are located in the 3’UTRs but some genes have miRNA binding sites in the 5’UTRs of mRNAs. Several genes have binding sites for miRNAs in the CDSs that are read in different open reading frames. Identical nucleotide sequences of binding sites encode different amino acids in different proteins.The binding sites of miR-619-5p in 3’UTRs, 5’UTRs and CDSs are conservative in the orthologous mammalian genes.
To help differentiate between evolution and adaptation in the context of natural selection for food energy-dependent codon optimality in the context of the physiology of pheromone-controlled reproduciton, see: Metrics of assay accuracy
Neo-Darwinian evolution occurs only in the context of this “Magic Box” example. Each time you look at the “+” sign on the box, you are taught to believe in evolution.
This evidence supports the idea that progressive epigenetic dysregulation may be the key driver of organismal aging and challenges the conventional view of aging as an irreversible process. The model of aging as an epigenetic process provides an elegant explanation of a number of age-related processes difficult to explain by conventional theories of aging.
Conventional theories of aging have failed to link the nutrient energy-dependent pheromone-controlled physiology of RNA-mediated protein folding chemistry to all biodiversity via biophysically constrained chromosomal inheritance. That’s how conventional theories left all of humanity waiting for cures that will never become available. Biologically uninformed theorists still do not know how protein folding chemistry is linked from changes in the microRNA/messenger RNA balance to healthy longevity via cell type differentiation or from the virus-driven degradation of messenger RNA to mutations and all pathology.
See: Genome editing: That’s the way the CRISPR crumbles
Review of A Crack in Creation: Gene Editing and the Unthinkable Power to Control EvolutionThis title will be released on June 13, 2017.
Not since the atomic bomb has a technology so alarmed its inventors that they warned the world about its use.
…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.
(1) Mutation is the source of all genetic variation on which any form of evolution is dependent. Mutation is the change of genomic structure and includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc. (2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation. It does not have any creative power in contrast to the statements made by some authors.
…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.
The researchers from Russia link energy-dependent changes in angstroms to ecosystems in all living genera. See this parody for fun.
Listen for her to repeat the claim that “,,,every angstrom is dynamic from the 5 prime to the three…”
See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013) and see this invited review of nutritional epigenetics from 2014: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems All adaptive evolution is epigenetically-effected ecological adaptation. In my model, adaptive evolution equates with epigenetic adaptation for claims that can be compared to claims about mutations and evolution. In 2013, I placed my claims into the context of adaptive evolution because many people did not realize that organized genomes must be protected from virus-driven energy theft at the level of energy-dependent changes in the microRNA/messenger RNA balance. Other researchers have since begun to realize that virus-driven energy theft causes the degradation of messenger RNA. Every level of examination links the loss of quantized energy from angstroms to ecosystems via mutations, which are linked to all pathology. If my invited review had not been returned without review, other researchers probably would have linked the peer-reviewed publication from 2013 and virus-driven energy theft from the hecatombic evolution of pathology in archaea to all pathology via the degradation of messenger RNA and negative supercoiling of DNA.
Gyrase is a molecular motor that harnesses the free energy of ATP hydrolysis to perform mechanical work on DNA. The enzyme specifically introduces negative supercoiling in a process that must coordinate fuel consumption with DNA cleavage and religation and with numerous conformational changes in both the protein and DNA components of a large nucleoprotein complex. Here we present a current understanding of mechanochemical coupling in this essential molecular machine, with a focus on recent diverse biophysical approaches that have revealed details of molecular architectures, new conformational intermediates, structural transitions modulated by ATP binding, and the influence of mechanics on motor function. Recent single-molecule assays have also illuminated the reciprocal relationships between supercoiling and transcription, an illustration of mechanical interactions between gyrase and other molecular machines at the heart of chromosomal biology.
It has also become clear that no experimental evidence links the degradation of messenger RNA from mutations to evolution via natural selection or any other claims that have been made by biologically uninformed theorists. No experimental evidence that supports evolution via natural selection has been published in a peer-reviewed journal. Natural selection for energy-dependent codon optimality is the experimental evidence-based link to healthy longevity and all biodiversity. Theorists might complain that their absence of experimental evidence is not evidence of absence. But that is how theorists try to keep serious scientists waiting for pseudoscientists to make a contribution to what is known about energy-dependent biologically-based cause and effect. Theorists are pseudoscientists who cannot do that. For instance, and for an example, in the conclusion of Mutation-Driven Evolution, which was published on the same day as my 2013 review, Masatoshi Nei suggested that other theorists and everyone else should simply ignore the need to consider teleological elements. Teleology is the philosophical attempt to describe things in terms of their apparent purpose, directive principle, or goal. For instance, in 2012, Thomas Nagel proposed a neo-Darwinian account of evolution that incorporates impersonal, natural teleological laws to explain the existence of life, consciousness, rationality, and objective value.
So far as I know, Nei is still biologically uninformed and Nagel is still looking for his Darwin. See: Awaiting a New Darwin
For comparison, here is an example of what happens when other researchers from Russia included a link from the teleological elements to the purpose of life. Keep in mind that every aspect of neo-Darwinian theory must eventually incorporate “Laws of Biology” that link energy from quantum physics to ecological adaptation via quantum physics and the chemistry of biophysically constrained pheromone-controlled reproduction. For example, in my model of how to link angstroms to ecosystems, Kohl’s “Laws of Biology” are Darwin’s “conditions of life.” The term “epigenetic adaptation” suggests that others have accepted all the facts about RNA-mediated cell type differentiation. The facts link nutrient energy-dependent changes from angstroms to ecosystems via food energy and the physiology of reproduction, which is controlled by pheromones in species from microbes to humans.
The three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution – adaptation to a freshwater environment. While genetic adaptations to freshwater environments are well-studied, epigenetic adaptations have attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of the marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into a freshwater environment and freshwater sticklebacks placed into seawater. We showed that the DNA methylation profile after placing a marine stickleback into fresh water partially converged to that of a freshwater stickleback. For six genes including ATP4A ion pump and NELL1, believed to be involved in skeletal ossification, we demonstrated similar changes in DNA methylation in both evolutionary and short-term adaptation. This suggested that an immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. For the first time, we demonstrated that genes encoding ion channels KCND3, CACNA1FB, ATP4A were deferentially methylated between the marine and the freshwater populations. Other genes encoding ion channels were previously reported to be under selection in freshwater populations. Nevertheless, the genes that harbor genetic and epigenetic changes were not the same, suggesting that epigenetic adaptation is a complementary mechanism to selection of genetic variants favorable for freshwater environment.
Although they try to separate microevolution and macroevolution, the authors refute every aspect of neo-Darwinian pseudoscientific nonsense. They inadvertently link the quantized energy of sunlight to the creation of ATP, which links food energy-dependent biophysically constrained RNA-directed DNA methylation biosynthesis from RNA to cell type differentiation in all living genera via my series of blog posts here. See: Search Results for “rna directed DNA methylation”
Anna Di Cosmo’s group linked all invertebrates to all vertebrates via my model in Role of olfaction in Octopus vulgaris reproduction
From the concluding paragraph:
Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).
RNA-directed DNA methylation links the nutrient-dependent pheromone-controlled weekend resurrection of the bacterial flagellum in P. fluorescens to all biodiversity on Earth via conserved molecular mechanisms of controlled cell type differentiation in all living genera. From a teleological perspective, supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA, which links virus-driven energy theft to all pathology in all living genera. See: Structural diversity of supercoiled DNA
See also: Engineering RGB color vision into Escherichia coli, which was reported as Bacterial Photography Goes Technicolor http://mobile.the-scientist.com/article/49481/bacterial-photography-goes-technicolor
The requirement for a light-activated endogenous substrate in all cell types has been known to serious scientists who have linked chromosomal inheritance to all biodiversity during the past century. The de novo creation of the endogenous substrate links the de novo creation of G protein-coupled receptors to all energy-dependent cell type differentiation via chemotaxis and phototaxis, which link the ability of microbes to find food to the creation of supercoiled DNA. The supercoiled DNA protects all living genera from the virus-driven degradation of messenger RNA, which is linked from mutations to all pathology.
Indeed, the success of optogenetics is based on the fact that femtosecond blasts of UV light were been linked to RNA-mediated DNA repair. The light activated DNA repair has been linked to the weekend resurrection of the bacterial flagellum in P. fluorescens. That fact refutes all claims about mutation-driven evolution.
Facts that refute mutation-driven evolution are a nightmare for theorists who failed to link sunlight to the life-sustaining energy that Richard Feynman and others placed into the context of food energy. Feynman used that fact as an example of how to “get” physicists who present themselves as know-it-alls. See the video clip, below.
See also: Advances in Non-Viral DNA Vectors for Gene Therapy
…synthetic messenger RNAs (mRNAs), which are delivered to the cell and translated in vivo, offer potential for expressing proteins. The nucleotides in these mRNA molecules must be modified to avoid immune detection through pattern recognition receptors…
…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).”
Similarly, if all of life’s processes were not nutrient energy-dependent and pheromone-controlled, this research could not link pheromones to the control of antibiotic resistance, which is caused by virus-driven energy theft.
See:
It is likely that viral miRNAs help viruses enter the latent phase of their life cycle and become undetected by the host’s immune system, while increasing the host’s risk for cancer development.
Many human viruses of clinical importance including polyomaviruses, hepatitis B virus, hepatitis C virus, human papillomavirus, human immunodeficiency virus produce viral miRNAs (Louten et al., 2015). These specific viral miRNAs have likewise been explored as potential diagnostic platforms (Lagatie et al., 2014, Zhu et al., 2017, Takahashi et al., 2013, Kumar Gupta and Kumar, 2015, Dahiya and Atreya, 2014).
Scientific advisers to President Obama warn that the U.S. urgently needs a new biodefense strategy and should regularly brief President-elect Donald Trump on the dangers posed by new technologies like CRISPR, gene therapy, and synthetic DNA, which they say could be coöpted by terrorists.
The CRISPR Bioterror Threat links all current technology to refutations of every aspect of neo-Darwinian pseudoscientific nonsense and the pseudoscientific nonsense touted by “Big Bang” cosmologists. That fact has forced those who once led the scientific advances in technology to place them into a teleological perspective.
For example, I suspect that is what George Church and others are trying to do.
See: Human Genome Project 2: Synth meeting takes place in Boston16 May 16
Yes, the meeting was behind closed doors, but it’s not quite what you’d call a ‘secret meeting’. Word has it, that the organisers have a high impact publication in the works that they can’t talk about openly yet.
Harvard biologist George Church burst into the headlines (yet again) last week when he helped organize a closed-door meeting of scores of top scientists to discuss accelerating efforts to create synthetic DNA — including a complete human genome.
Begley reports that a meeting held last year was held last week. I think I can explain why placing her report into the context of George Church’s business practices is good business for people like her. For example, George Church already refuted every aspect of neo-Darwinian pseudoscientific nonsense when he and others filed the patent for ‘RNA-guided human genome engineering,’ which is an energy-dependent naturally occurring RNA-mediated process. It links natural selection for energy-dependent codon optimality to supercoiled DNA and every aspect of biodiversity.
That fact forces many of the world’s top experts to acknowledge that Darwin’s ‘conditions of life’ are nutrient energy-dependent and pheromone-controlled. That fact links quantum physics to quantum consciousness via claims made by Richard Feynman. For example, he claimed that theoretical physicists exemplify idiocy by using too many different terms for the measurement of “energy.”
The “…proof that physicists are human…” he claims, “… is the idiocy of all the different units which they use in measuring energy.”
The apparent corruption among evolutionists may simply be another example of what Richard Feynman placed into the context of idiocy. In any case, we will continue to see attempts to make it appear that neo-Darwinian theorists have not displayed that same level of idiocy.
They have failed to link ecological variation to energy-dependent ecological adaptation via the physiology of pheromone-controlled reproduction in all living genera. The report by Begley could be “spin-doctoring” at its finest, or it could simply be her mistake.
In either case, those who have been caught touting alternative facts about evolution must now try to make it appear that they have not done that during the past year. During the past year many academics and liberals have been fighting against the claims of corruption made by the Trump administration when the corruption obviously extends to academia.
The fact that reports from researchers in Russia and researchers in China consistently have linked what is known about energy-dependent changes in the microRNA/messenger RNA balance from ecological variation to ecological adaptation or to pathology is not well known to all researchers in the United States. That problem led to accusations that the Russians had hacked the election of our President.
Those accusations can now be placed into the context of Combating Evolution to Fight Disease and support for the State of Israel.
See: Israeli Middle Schools School to Include Theory of Evolution
…learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.
The 2015 Society for Integrative and Comparative Biology (SICB) presenters may not recognize how much progress has been made since the 2013 ecological epigenetics symposium. For example, since then authors claimed “…ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.” http://dx.doi.org/10.1038/nature13400
Six months later, other authors traced signaling factors found in vertebrates to the origin of nerve cell centralization via the diffuse nerve net of animals like the sea anemone. http://dx.doi.org/10.1038/ncomms6536 That fact suggests ecological variation is linked to ecological adaptations in morphological and behavioral phenotypes via signaling protein concentrations that differentiate various cell types in body axes and the central nervous system.
Links across species from the epigenetic landscape to the physical landscape of DNA in organized genomes appear to have their origins in the conserved molecular mechanisms of RNA-directed DNA methylation and RNA-mediated protein folding. Two weeks after the publication that refuted ideas about independently evolved neural systems or muscle specification — and perhaps refuted the independent evolution of anything else, SICB presenters linked crustaceans to insects.
Apparently, they’ve learned that the same set of microRNAs controls expression of the genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans.
Why were they left with any questions about how crustaceans and insects could all be part of one big family? They linked RNA-mediated cell type differentiation to what we described in our section on molecular epigenetics in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior
I will add that the number of terms that could be reduced to link claims about energy to claims about cell type differentiation increasing. Attempts to avoid making claims that link energy-dependent changes in microRNAs from RNA-directed DNA methylation to amino acid substitutions and healthy longevity are prevented by researchers use these different terms for the same thing. MicroRNAs are contextualized as enhancers, promotors, quantitative trait loci, RNA-based switches. mobile elements, extra-coding RNAs, CRISPR effectors, Oncocers, oncomiRNA, regeneration enhancer elements, isomiRs, regulatory polymorphisms, c-fos enhancers, potential signatures of environmental exposure or effect, key triggers of neuronal cell fate, and many other terms for the same thing.
…primary sequence determinants and RNA structure are key regulators of miRNA biogenesis.
Genetic variation aka primary sequence determinants are energy-dependent and RNA-mediated. Energy-dependent RNA methylation is an experience-dependent link from natural selection for energy-dependent codon optimality. Natural selection for energy-dependent codon optimality links ATP-dependent microRNA biogenesis to RNA biosynthesis.
Ridiculous attempts to portray energy-dependent top-down causation as if genetic variation came first may continue for another 52 years. But see this report from 1964 to help you recognize how much pseudoscientific nonsense has been touted since then.
See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”
Isolated thymus nuclei transport amino acids into an intranuclear pool by a process which seems to depend on energy from nuclear ATP synthesis (20).
If any experimental evidence of biophysically constrained RNA-mediated cell type differentiation was not linked from an anti-entropic energy source to nuclear ATP synthesis that experimental evidence might support the claims of pseudoscientists who think that mutations link natural selection to evolution of different species.
See for comparison: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
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…
My translation: Natural selection for energy-dependent and energy-efficient protein folding chemistry links what organisms eat to the energy that they require for reproduction via the accurate translation and folding of highly expressed genes.
Alternatively, virus-driven energy theft links the degradation of messenger RNA to all pathology via conserved molecular mechanisms in all living genera. Simply put, the molecular mechanisms of healthy longevity and biodiversity are nutrient energy-dependent and pheromone-controlled.
The fact that population geneticists have ignored what us known to all serious scientists about the controlled molecular mechanisms that link metabolic networks to genetic networks has led to the unnecessary suffering and premature death of millions to billions of people. If you are not willing to join those who are Combating Evolution to Fight Disease, you probably will be asked why you decide to ignore everything known about the energy-dependent de novo creation of genes. If you did not recognize your ignorance, try to find experimental evidence in the works of evolutionary theorists who did not start after the energy-dependent de novo creation of genes.
So far as I know, all pseudoscientists still consistently place the facts about de novo gene creation, which refute their nonsense about mutation-driven evolution, into the context of their published works. Those works will continue to cause the unnecessary suffering and premature death of millions to billions of people.
The fact that experience-dependent genetic variation does not create itself is a thorn in the side of all theorists who now recognize and must ignore the facts about RNA-mediated cell type differentiation. The facts link the energy-dependent RNA-mediated fixation of amino acid substitutions to all biodiversity.
The facts also link mutations to all pathology, which means the facts have always been evolutionary theory killers. The facts haven’t changed since Thomas Hunt Morgan presciently linked them to chromosomal inheritance and Schrodinger presciently linked the anti-entropic virucidal energy of sunlight to RNA-mediated DNA repair.
Approximately one in five microRNA interactions with mRNAs occur through non-canonical binding sites. Although of functional relevance these microRNA targets are not predicted by bioinformatics tools. Improved RNA pull-down techniques with biotinylated microRNA mimics open new possibilities to identify microRNA targets experimentally.
My comment: Although I have repeatedly mentioned works that link energy-dependent changes in the microRNA/messenger RNA balance to cell type differentiation and healthy longevity, I had not seen any mention of biotinylation, until today.
I do not know any theorists who are biochemists and suspect that all the ridiculous theories of pseudoscientists include nothing that is known about biotinylation. That may be why I did not hear the term mentioned, until today. What would happen if I heard it and failed to learn what it meant? God forbid, I might still be a biologically uninformed theorist
See for example: The landscape of sex-differential transcriptome and its consequent selection in human adults
This work provides a comprehensive overview of the sex-differential transcriptome and its importance to human evolution and human physiology in health and in disease.
The detailed map of these genes, reported in BMC Biology, provides evidence that males and females undergo a sort of separate, but interconnected evolution.
I thank God, for not allowing me to believe that males and females are different mutants of the same species.
See for comparison: We are all mutants
Darwin is a god in evolution, so you can’t criticize Darwin. If you do, you’re branded as arrogant.
But any time a scientific theory is treated like dogma, you have to question it. The dogma of natural selection has existed a long time. Most people have not questioned it. Most textbooks still state this is so. Most students are educated with these books.
You have to question dogma. Use common sense. You have to think for yourself, without preconceptions. That is what’s important in science.
…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution.
Conclusion:
…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.
….his unlimited but judiciously applied enthusiasm, his sterling example as a scholar, and his inspirational support of semiotic colleagues, institutions, and the ongoing investigation into the reality of sign process at every level of life have been and will remain a force that both inspires and that sets the standard by which our colleagues continue with their important work.
My comment: The reality of sign process at every level of life is that it is energy-dependent, RNA-mediated, and biophysically constrained by the physiology of reproduction in species from archaea to humans.
No experimental evidence of biophysically constrained biologically-based cause and effect supports claims that the mammalian placenta “evolved.”
All experimental evidence of biophysically constrained biologically-based cause and effect supports claims that the mammalian placenta is an energy-dependent pheromone-controlled ecological adaptation.
See also: Discovery of chemoautotrophic symbiosis in the giant shipworm Kuphus polythalamia (Bivalvia: Teredinidae) extends wooden-steps theory
Chemoautotrophic symbiosis is nutrient energy-dependent and pheromone-controlled. Nothing about life involves autotrophy. Everything known to serious scientists links chirality to autophagy, which protects the supercoiled DNA of all organized genomes from virus-driven energy theft and genomic entropy that links extinction to the fossil record. Claims about the last known common ancestor of shipworms are the clearest indicator that pseudoscientists do not realize no last known common ancestor has ever been found for any form of energy-dependent RNA-mediated life.
See “March for Science: Dispatches from Washington, DC”
“We made history!” marchers chanted at the terminus of a mile-and-a-half walk from the Washington Monument to Capitol Hill in Washington, DC.
“We just watched a documentary on Charles Darwin the other night, and my older daughter, when I told her that in some countries—Turkey, Russia, and parts of the United States—evolutionary theory is taken out of the school curricula, she said, ‘We have to make a sign!’ And we [created] these ones.” —Percy Rohde
The science march in Chicago was was a blend of scientists and nonscientists alike. Peggy Mikros, a caterer, came up from the south side of the city because she said she cares about the environment and “science is everything.” The event has inspired her to continue to advocate for science.KERRY GRENS
“I’ve never done this and I am so excited to be here.” —Peggy Mikros, caterer from Chicago
The ARID1A gene, encoding a subunit of the ATP-dependent chromatin remodeling complex SNF/SWI, has recently been identified as a tumor suppressor in multiple cancers. Despite studies that elucidate the mechanism of ARID1A’s tumor suppressor function, little is known of the genes/events that regulate ARID1A expression. Using the HEK293 cells as a model, we discovered novel aspects of ARID1A transcription regulation in response to cell cycle progression, DNA damage, and microRNAs, exemplifying the potential of our strategy in providing new insight to the mechanism of gene transcription regulation.
The synthesis of RNA in isolated thymus nuclei is ATP dependent.
Connecting energy as information to ATP-dependent synthesis of RNA and healthy longevity is not difficult unless you do not know where the energy comes from. If you do not know or fail to acknowledge the creation of energy as the source that links the anti-entropic virucidal effects of sunlight to all biodiversity via what is known to serious scientists, you will not understand what serious scientists know about how to prevent all virus-driven energy theft from linking mutations to all pathology in all living genera
See also: Individual Bromodomains of Polybromo-1 Contribute to Chromatin Association and Tumor Suppression in Clear Cell Renal Carcinoma
The architecture of chromatin is governed, in part, by adenosine triphosphate (ATP)-dependent chromatin remodelers. These multi-protein complexes contain targeting domains that recognize posttranslational marks on histones. One such targeting domain is the bromodomain (BD), which recognizes acetyl-lysines and recruits proteins to sites of acetylation across the genome. Polybromo1 (PBRM1), a subunit of the polybromo-associated BRG1- or hBRM-associated factors (P-BAF) chromatin remodeler, contains six tandem BDs and is frequently mutated in Renal Clear Cell Carcinoma (ccRCC). Mutations in the PBRM1 gene often lead to loss of protein expression; however, missense mutations in PBRM1 have been identified and tend to cluster in the BDs, particularly BD2 and BD4, suggesting that individual BDs are critical for PBRM1 function. To study the role of these six BDs, we inactivated each of the six BDs of PBRM1 and re-expressed these mutants in Caki2 cells (ccRCC cells with loss of function mutation of PBRM1). Four of the six BDs abrogated PBRM1 tumor suppressor, gene regulation, and chromatin affinity with degree of importance correlating strongly to rate of missense mutations in patients. Furthermore, we identified BD2 as the most critical for PBRM1 and confirmed BD2 mediated association to histone H3 peptides acetylated at lysine 14 (H3K14Ac), validating the importance of this specific acetylation mark for PBRM1 binding. From these data we conclude that four of the BDs act together to target PBRM1 to sites on chromatin; when a single BD is mutated, PBRM1 no longer controls gene expression properly, leading to increased cell proliferation.
The American population developed, during thousands of years, free of epidemics that had been attacking Europe, Asia and Africa. The European and African migrations, after Columbus’s first trip, produced an epidemic invasion of influenza, smallpox, measles, yellow fever, malaria, diphtheria, typhus, and other diseases that attacked the immunologically virgin populations and produced a very high mortality, with a diminution of the indigenous population of more than 90% in many places. According to historical evidence, the first epidemic was influenza, produced by swine strain of virus, immediately followed by smallpox. The Spaniards mated freely with the Indians producing a mixed race called the Mestizo, who were immunologically more capable of defending themselves against various viruses, bacteria, and parasites brought over from the Old World. Marriage between the races also was sanctioned by Queen Isabella (1503) and Fernando I (1515). With these new genetic immunologic defenses against infections, the Mestizo eventually made up the majority of the population of Indians in the New World.
Viruses are the most abundant biological entities in the world’s oceans, and they play a crucial role in global biogeochemical cycles. In deep-sea ecosystems, archaea and bacteria drive major nutrient cycles, and viruses are largely responsible for their mortality, thereby exerting important controls on microbial dynamics. However, the relative impact of viruses on archaea compared to bacteria is unknown, limiting our understanding of the factors controlling the functioning of marine systems at a global scale. We evaluate the selectivity of viral infections by using several independent approaches, including an innovative molecular method based on the quantification of archaeal versus bacterial genes released by viral lysis. We provide evidence that, in all oceanic surface sediments (from 1000- to 10,000-m water depth), the impact of viral infection is higher on archaea than on bacteria. We also found that, within deep-sea benthic archaea, the impact of viruses was mainly directed at members of specific clades of Marine Group I Thaumarchaeota. Although archaea represent, on average, ~12% of the total cell abundance in the top 50 cm of sediment, virus-induced lysis of archaea accounts for up to one-third of the total microbial biomass killed, resulting in the release of ~0.3 to 0.5 gigatons of carbon per year globally. Our results indicate that viral infection represents a key mechanism controlling the turnover of archaea in surface deep-sea sediments. We conclude that interactions between archaea and their viruses might play a profound, previously underestimated role in the functioning of deep-sea ecosystems and in global biogeochemical cycles.
Autophagy is activated by virus-driven energy theft. Click on the term “Autophagy” That fact is clear in the diagram of systems complexity and in my model.
A key question in virology, that is potentially answerable using paleovirological analyses, is what caused the elimination of extinct viral lineages?
Conclusion:
The selection pressures acting on hsaHTenv, its orthologs and progenitors might have been complex. Loss of fusogenicity but retention of receptor binding activity are, in a sense, opposing influences in terms of maintenance of the ORF and its function. Moreover, although some purifying selective pressure (low dN/dS) can be detected in hsaHTenv and its orangutan ortholog, a relaxation of those forces might be expected to have occurred after HERV-T extinction, perhaps leading to reduced antiviral activity observed in modern hsaHTenv. Finally, as MCT-1 is a moncaboxylate transporter that is upregulated in human cancers (Halestrap, 2013), the ability of hsaHTenv to deplete MCT1 from cell surfaces may suggest an additional or alternative metabolism-related cellular or even anti-tumor functions and selective pressures. Such an activity might have continued to shape hsaHTenv sequence independent of anti-HERV-T activity. In either case, this study highlights the potential importance of ERV proteins as raw material for the innovation of new functions in human ancestors.
All energy-dependent cell type differentiation is receptor-mediated. The nutrient energy-dependent de novo creation of receptors in cell types links metabolic networks to genetic networks via RNA-mediated protein folding chemistry, which biophysically constrains virus-driven energy theft. The energy theft links viral replication to the degradation of messenger RNA and mutations, which are linked to all pathology.
My comment:jvkohl•an hour ago Hold on, this is waiting to be approved by eLife.
Rarely do we see this degree of prescient raw insight displayed by a non-scientist who predicted the claims about viruses in the manuscript reviewed.
Please see: Evolution rising from the grave http://dx.doi.org/10.1038/3… Excerpt: “Reactivation of a dormant message signals the dawn of a new humanity.”
See also: Living with the Neanderthals http://www.nature.com/natur…
My competing interests include ownership of domains that disseminate accurate information about energy-dependent biologically-based cause and effect, which is biophysically constrained. My publication history extends across twenty years during which I have refuted every aspect of neo-Darwinian nonsense.
The nonsense places claims about evolution into the context of what is known to serious scientists about the links from angstroms to ecosystems in all living genera. Serious scientists start with hydrogen-atom transfer in DNA base pairs in solution.
The potential of hydrogen is referred to as pH. Virus driven energy theft links changes in pH to the degradation of messenger RNA and the mutations that are linked to pathology in all living genera.
My comments are rarely published here.
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See, for comparison, my comment to Greg Bear’s FB page: Darwin’s Radio and Darwin’s Children (revisited)
“Viral Fossils Reveal Immune Capabilities of Our Ancestors” http://buff.ly/2nT1osY
Hi Greg. Nutrient energy-dependent pheromone-controlled RNA-mediated viral latency became the focus of my published works and presentations after you linked pheromones to ecological adaptations in a new human subspecies.
My 2017 Labroots Precision Medicine presentation is an extension of facts you helped to detail for your target audience. https://www.youtube.com/watch?v=cdtsfweO5SQ
“Energy as information and constrained endogenous RNA interference” is being ignored because it refutes every aspect of pseudoscientific nonsense that has ever been touted by neo-Darwinian theorists. I continue to be amazed by those who claim to be scientists who cannot begin to understand what you understood at the time you wrote “Blood Music.” Like others, I am also somewhat scared of what you predicted in “Quantico.”
Despite the substantial systematic uncertainty that affects our measurement, our work has demonstrated the potential that future MUSE observations have in constraining the intensity of the UVB in the local Universe.
This is a report on the Multi Unit Spectroscopic Explorer (MUSE) instrument. The preposterous claim is not supported with experimental evidence that observations made in the context of the instrument somehow constrain the intensity of UV light.
That unsupported claim is worth placing into the context of other preposterous claims about the mutation-driven evolution of all biodiversity on Earth. See: Mutation-Driven Evolution
The picture below represents facts about UV light that link energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of reproduction.
Galaxy UGC 7321 is surrounded by hydrogen gas, and as this gas is irradiated with UV radiation, it emits a diffuse red glow through a process known as fluorescence. This image shows the light emitted by stars inside the galaxy, surrounded by a red ring that represents the fluorescent emission induced by the UV radiation. Credit: M. Fumagalli/T. Theuns/S. Berry
Simulations show that there should be more small galaxies in the Universe, but UV radiation essentially stopped them from developing by depriving them of the gas they need to form stars.
I saw no mention of the missing galaxies until 3/21/17. I only knew that the anti-entropic virucidal energy of ultraviolet light biophysically constrains all life on Earth via nutrient energy-dependent endogenous RNA interference and the physiology of pheromone-controlled reproduction.
Now that information on the missing galaxies has been presented in the context of observations, those observations can be correlated with evidence from observations of individual bones, which exist only in the context of the observable fossil record evidence.
Observers tell us those bones come from species that became extinct millions to billions of years ago. Dobzhansky (1964) told us about those observers.
“The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists! I have heard a man whose official title happens to be Professor of Zoology declare to an assembly of his colleagues that “a good man cannot teach zoology. A good man can teach, of course, only molecular biology.
Such pronunciamentos can be dismissed as merely ridiculous. They are, however, caricatures of opinions entertained by some intelligent and reasonable people, whose views deserve an honest and careful consideration and analysis. Science must cope with new problems that arise and devise new approaches to old problems. Some lines of research become less profitable and less exciting and others more so.”
Indeed, it would be hard to miss the fact that current lines of research are expected to be much more profitable that the observations of theorists. For example, RNA-mediated amino acid substitutions in supercoiled DNA link energy-dependent changes in angstroms to ecosystems. Clearly, if organisms within an ecosystem cannot find food, they will not have the energy to reproduce.
The pheromone-controlled physiology of reproduction will no longer prevent the transgenerational epigenetic inheritance of virus-driven energy theft, and all individuals of the species may eventually become extinct. Observable evidence that some individuals died led observers to claim that many species became extinct during millions of years of evolution. No experimental evidence of biologically-based cause and effect supports those claims. Instead, facts about how quickly virus-driven energy theft continues to degrade their messenger RNA suggests that the fossil record of bones exemplifies how quickly ossification occurs in the absence of sunlight.
For comparison, anti-entropic virucidal UV light still appears to be the source of all biodiversity because all biodiversity appears to be energy-dependent and biophysically constrained.
See: Nerve Dependence: From Regeneration to Cancer
Reported as: How the nervous system controls tumor growth
At the dawn of cell differentiation, mitochondria from a particular donor cell may have been the only source of some particular proteins for a new host cell that could no longer make them.
John Hewitt made this fact perfectly clear. Cell type differentiation has always been energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction.
Observers claims that fossilized bacteria could be used as evidence to support millions to billions of years of evolution were replaced when chemists provided experimental evidence that the observers were wrong. Fossil or inorganic structure? Scientists dig into early life forms
Oliver Steinbock and Professor Juan Manuel Garcia-Ruiz of the Consejo Superior de Investigaciones Cientificas (Spanish National Research Council) in Granada, Spain published an article in Wednesday’s edition of Science Advances that shows fossil-like objects grew in natural spring water abundant in the early stages of the planet. But they were inorganic materials that resulted from simple chemical reactions.
For example, the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).
Obviously, he was joking about 10 billion years of evolution when he made this claim:
I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation.
Anyone who ever linked sunlight to energy-dependent biodiversity on Earth via endogenous RNA interference and the physiology of reproduction knows the difference between jokes about evolution and facts about cell type differentiation. For example, biophysically constrained cell type differentiation is energy-dependent and viruses steal the energy for replication. That’s why all serious scientists have linked supercoiled DNA to viral latency without making claims about mutations, natural selection, and/or evolution. Serious scientists do not simply link observations from intruments, such as the Multi Unit Spectroscopic Explorer (MUSE) instrument, to missing galaxies. Serious scientists link facts about virus-driven energy theft from mutations to all pathology.
See for example: The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
Yuste and Eberwine would like to see 3D reconstructions of individual neurons compared to analyses of the genes expressed in those neurons. This may offer clues as to the type and function of each cell.
The nutrient energy-dependent structure and function of all cell types in all living genera links biodiversity from the physiology of pheromone-controlled reproduction in C. elegans to the predatory behavior of P. pacificus, a predatory nematode with teeth.
All ecological adaptations, such as teeth, exemplify what is required to link energy-dependent endogenous RNA interference to supercoiled DNA, which protects all organized genome from virus-driven energy theft and genomic entropy.
Predictably, Paul Allen will be the next to start funding works that might help to prevent the viral apocalypse, now that Bill Gates is mentally prepared to do so.
The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
The antigenic changes are clearly nutrient energy-dependent, as are all changes in all cell types of all living genera. Their results link virus-driven energy theft to all pathology, which is why Sinclair et al (2017) must put his mathematical model back into the context of evolution across billions to millions of years.
They conclude that no discussion of nutrient energy-dependent species-specific pheromone-controlled viral latency should allow others with critical thinking skills to challenge their ridiculous claims about the energy-dependent RNA-mediated signals that link virus-driven energy theft to dysfunctional relationships among structure, amino acid sequence, and coding sequences.
They prefer that others, like Masatoshi Nei in “Mutation-driven evolution” (2013) place their claims into the context of how discussions about signaling between viruses and the supercoiled DNA of all organized genomes can be placed into the context of possible evolutionary relationships.
The evolutionary relationships do not link energy-dependent changes in chirality from autophagy via the innate immune system to endogenous RNA interference and all biodiversity on Earth.
Without the energy-dependent changes, the virucidal effects of femtosecond blasts of UV light on energy-dependent codon optimality and DNA repair cannot link the de novo creation of the energy in hydrogen atoms to the biophysically constrained coding sequence in all living genera via the physiology of reproduction.
The energy-dependent coding sequence links the physiology of reproduction to RNA-mediated amino acid substitutions and cell type differentiation in all living genera.
…the epigenetic effects of food odors and pheromones are involved in neurogenic niche construction as exemplified in nematodes (Bumbarger, Riebesell, Rödelsperger, & Sommer, 2013), and in flies (Swarup et al., 2013).
Three recent studies find that the single-pass transmembrane protein HAP2 mediates gamete fusion and is remarkably similar to class II fusion proteins found in viruses such as dengue and Zika.
In-vitro-fertilized human embryos often acquire large structural and numerical chromosomal abnormalities. Liu et al. now show that multiple smaller copy number variations may also arise in in-vivo-conceived embryos. Analysis of these variations provides insight into the DNA mutational processes occurring in early embryos and the mechanisms underlying them.
I repeat: “…evolutionary relationships do not link energy-dependent changes in chirality from autophagy via the innate immune system to endogenous RNA interference and all biodiversity on Earth.” Similarly, “DNA mutational processes occurring in early embryos…” cannot shape the genome because mutations prevent biophysically constrained protein folding chemistry.
Exposure to ultraviolet light leads to a cell-wide DNA damage response that includes a global reduction in transcription. Williamson et al., identify a protein involved in this process as well as a noncoding RNA produced by alternative processing of RNA transcribed from the same gene that promotes recovery from the repressed state.
Femtosecond blasts of UV light have already been linked to DNA repair via alternative processing of RNA transcribed from the same gene.
The fact that UV-light induced charge transfer states in DNA control pH responsive RNA-mediated DNA repair seems to have escaped the notice of those who tout selective repair via effective gene transfer without mentioning the source of energy for the transfer.
It’s the anti-entropic virucidal energy of sunlight!
…in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.)
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How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy? (Roger Penrose 8 August 1991)
…variability is generally related to the conditions of life…
…we cannot tell how much to attribute to the accumulative action of natural selection, and how much to the definite action of the conditions of life.
…during the process of modification, each has become adapted to the conditions of life…
Charles Darwin placed his energy-dependent “conditions of life” first. He knew that natural selection could not occur outside the context of the conditions of life, which are nutrient energy-dependent and pheromone-controlled via the physiology of reproduction in species from microbes to humans.
For information on how ecological variation is linked to ecological adaptation in the context of what is known about Darwin’s and God’s “conditions of life” see:
Specifically, this talk will focus on proteins that interact with the human Na,K-ATPase (NKA). An active plasma membrane ion pump, the NKA is required for life. Without it, the cell cannot maintain a proper ion potential and the cells dies by a natural death process known as necrosis.
…the world now has an emergency medical response team – which, astonishingly, it never had before.
Pardis Sabeti may still be part of the response team, and most of them still may not know how to link energy-dependent changes in SNPs from angstroms to ecosystems in all living genera via RNA-mediated hydrogen-atom energy transfer in DNA base pairs in solution.
… EBOV is able to generate and fix nucleotide and amino acid variation within co-circulating viral lineages on the time-scale of individual outbreaks, including the presence of country-specific lineages, and which may ultimately produce variants with important fitness differences.
What about those fitness differences? What don’t fitness experts know about nutrient energy-dependent amino acid substitutions? Who is Amir Siddiqui, really? Is everyone who calls me a religious nut actually a terrorist, or are they simply too ignorant to learn how to link what people eat to their reproductive fitness via amino acid substitutions in supercoiled DNA?
Reported as: Start codons in DNA may be more numerous than previously thought
The measurements of energy-dependent translation initiation in E.coli must be linked from changes in the start codons to supercoiled DNA. That requires fixation of RNA-mediated amino acid substitutions in the context of the physiology of pheromone-controlled reproduction, which is linked to nutrient energy-dependent ecological adaptations in all living genera.
The fact that there are more energy-dependent start codons to be considered in the context of biophysically constrained protein folding chemistry became important to Bill Gates in the context of virus-driven energy theft and the forthcoming viral apocalypse.
See: Bill Gates refutes theistic evolution
