…these data suggest that a subset of the identified novel miRNAs may contribute to the pathophysiology of numerous diseases, laying the groundwork for future studies to elucidate the functional connections of miRNAs to the numerous diseases associated with sequence variants within non-coding regions of the MHC.
Dysregulation of miRNAs is commonly observed in cancers and it largely cancer dependent.
The virus-driven theft of quantized energy as information has been linked from changes in the microRNA/messenger RNA balance to all pathology. That fact replaces the circular logic that links cancer-dependent dysregulation of miRNAs to cancer. Simply put, the proliferation of viruses cause cancer. The proliferation of viruses is energy-dependent in the context of established links from atoms to ecosystems in all living genera.
See: Subatomic: An Atom Building Board Game
A deck-building game where particle physics & chemistry collide! Use quarks to build subatomic particles & particles to build Atoms!
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.
…these data suggest that a subset of the identified novel miRNAs may contribute to the pathophysiology of numerous diseases, laying the groundwork for future studies to elucidate the functional connections of miRNAs to the numerous diseases associated with sequence variants within non-coding regions of the MHC.
…birds that eat at feeders are more likely to be infected with the disease, which causes red, swollen eyes and often blindness that results in death.
…lower virulence strains could be their own worst enemies, creating a population of hosts that are resistant to them but not the higher virulence strains that remain.
By removing my Disqus comments, the moderators limit discussion of the facts about virus-driven energy theft, which links mutations to all pathology. That allows the biased reporting on preprints that continue to try to support the ridiculous concept of neo-Darwinian evolution.
It also prevents the realization of goals by serious scientists who have linked the biogenic creation of uranium ores to the prevention of radiation sickness via microRNA therapy. See, for examples: miRNA-mediated therapies A miRNA-145/TGF-beta1 Negative Feedback Loop Regulates the Cancer-Associated Fibroblast Phenotype
…miR-145 is a key regulator of the CAF phenotype, acting in a negative feedback loop to dampen acquisition of myofibroblastic traits, a key feature of CAF associated with poor disease outcome.
Gene-edited induced pluripotent stem cells (iPSCs) provide relevant isogenic human disease models in patient-specific or healthy genetic backgrounds. Towards this end, gene targeting using antibiotic selection along with engineered point mutations remains a reliable method to enrich edited cells. Nevertheless, integrated selection markers obstruct scarless transgene-free gene editing. Here, we present a method for scarless selection marker excision using engineered microhomology-mediated end joining (MMEJ). By overlapping the homology arms of standard donor vectors, short tandem microhomologies are generated flanking the selection marker. Unique CRISPR-Cas9 protospacer sequences nested between the selection marker and engineered microhomologies are cleaved after gene targeting, engaging MMEJ and scarless excision. Moreover, when point mutations are positioned unilaterally within engineered microhomologies, both mutant and normal isogenic clones are derived simultaneously. The utility and fidelity of our method is demonstrated in human iPSCs by editing the X-linked HPRT1 locus and biallelic modification of the autosomal APRT locus, eliciting disease-relevant metabolic phenotypes.
To make these very precise edits, an SNP modification is first inserted alongside a fluorescent reporter gene that helps researchers to identify modified cells. The researchers engineered a duplicate DNA sequence known as a microhomology (hence the technique’s name) on each side of the fluorescent gene, targeting sites for CRISPR to go in and cut DNA. The researchers were then able to use a DNA repair system known as microhomology-mediated end joining (MMEJ) to remove the fluorescent gene. That left only the single-base edit, in the form of an SNP, behind.
See also: Inhibition of the Host Translation Shutoff Response by Herpes Simplex Virus 1 Triggers Nuclear Envelope-Derived Autophagy
Nuclear envelope-derived autophagy (NEDA) appears to be a cellular stress response, which is triggered late during HSV-1 infection. An energy-dependent single nucleotide repeat (SNR) might compensate for the viral alteration of the macroautophagic response. At this level of hydrogen-atom energy transfer in DNA base pairs in solution, the link to supercoiled DNA and viral latency becomes increasingly important.
Theorists are angry because they have been left behind. They know very little about what is important. That was expected by all serious scientists, especially those who have accumulated decades of testing experience while working in medical laboratories.
See for example: Applications of ligation-mediated PCR
Using a molecular energy source (which differs depending on the enzyme source organism), DNA ligase reforms the missing covalent bond and the strand is whole again. Two aspects of this are critical:
The nick to be repaired occurs on a single strand but in the context of a double-stranded molecule.
The bases of the nicked strand, and particularly those directly flanking the nick site, must be properly base-paired to the opposite (un-nicked) strand.
It’s not hard to imagine why this is: the base pairing is required to hold the two parts (sugar 3′ -OH and the next phosphate) in place for the ligase enzyme active site to catalyze joining them. If either one of these isn’t base-paired down and is flopping about with thermal motion, the reaction geometry doesn’t occur, and no new bond can be made.
Biologically uninformed theorists cannot even speak the same language. They do not start with a molecular energy source for base pairing and microRNA-mediated amino acid substitutions that differentiate all cell types. Instead, mutations are linked to increasing organismal complexity via the magic of evolution.
Summary: It has been 75 years since Erwin Schrödinger exposed the pseudoscientific nonsense of mutation-driven evolution in the lecture series that was published as What is Life? (1944)
The mental health of so-called science journalists must be addressed. Many of them seem to be pathological liars or, at best biologically uninformed science idiots who cannot link physics and chemistry from molecular epigenetics to all energy-dependent biodiversity on Earth. The Biggest Myth In Quantum Physics by Ethan Siegel
Conclusion:
Take ourselves out of it, and all we have are the equations, the results, and the answers that the physical Universe gives. Physics cannot answer questions about “why” the Universe works the way it does; it can only explain how it works at all. If you’re interested in the fundamental nature of reality, ask the Universe questions about itself, and when it tells you its secrets, listen. Anything else that you layer atop it was put there by you, not by the Universe. Avoid that temptation, and you’ll never fall for the greatest myth about quantum physics: that it needs an interpretation at all.
The claim that quantum physics does not require a meaningful approach to explaining how energy is linked to all biodiversity in the context of interpretation of facts is ridiculous. Astrophysicist and author Ethan Siegel is the founder and primary writer of the blog “Starts With A Bang!” His books include Treknology and Beyond The Galaxy, Simply put, he is a biologically uniformed science idiot, like others who have failed to link their ridiculous theories to all biodiversity on Earth.
See for comparison: Refined control of cell stemness allowed animal evolution in the oxic realm
Reported as: Why animals diversified on Earth: Cancer research provides clues
Just the presence of free oxygen is the result of some microbes finding a way of using sunlight to get energy. This was also a biological event.
The difference between how animals diversified and why they diversified is perfectly clear to all serious scientists. Energy is required! McEwen et al (1964) linked the biological event from the creation of ATP to the creation of RNA and the creation of all biophysically constrained biodiversity. All other serious scientists have since followed his lead. Dobzhansky (1964) suggested that would happen.
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.
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).”
The anti-entropic virucidal effect of sunlight was linked from ecological variation to ecological adaption in all living genera via the pheromone-controlled physiology of reproduction in soil bacteria in: What is Life? (1944)
Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.)
Today, a team of geneticists reveals a remarkable mechanism that enables plants to count their chromosomes, solving a century-old mystery.
Molecular mechanisms are energy-dependent. That’s no mystery. See: How an RNA gene silences a whole chromosome (2015)
Most science journalists have refused to inform themselves. They have not linked sunlight on contact with water to all energy-dependent biodiversity via the physiology of reproduction. For example, John Hewitt wrote:
If anything we know the Sky Fathers totally forgot about selenium during most of the design phase and then had to write him in at the end as a walk-on.
I was surprised by his sarcastic attack on religion and wrote:
Those who do not believe in evolution understand that energy-dependent RNA-mediated amino acid substitutions must be linked from the physiology of reproduction to chromosomal rearrangements that biophysically constrain viral latency. If you can place your claim about selenium into the context of protection of all life on Earth from the virus-driven degradation of messenger RNA, we could discuss your claim. What is it?
John Hewitt wrote:
Sky Daddy likes cranberries so much he gave them sequence-level machinery for producing selenocysteine in their mitochondrial genome
I could not get him to make sense. I wrote:
This is the type of cryptic sarcastic claim that kills people. Thousands of them. Quit playing your silly games. Who are you calling “Sky Daddy?” Sequence-level molecular machinery does not exist outside the context of the creation of the sun’s anti-entropic virucidal energy.
For comparison, Roger M. Pearlman wrote:
name one person you know that can explain Neo-Darwinian Theory (NDT) so it adds up, and how you know it adds up otherwise don’t knock the NDT adherents here as they are equally inept at making NDT add up as are the leading NDT scientists
… 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.
Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.
If the differences in the amino acid sequences are energy-dependent and RNA-mediated, NDT is the most ridiculous example of pseudoscientific nonsense that has every been touted by people who claim to be more intelligent than their primate ancestors.
..we demonstrate an immediate survival benefit conferred by the enhanced redox reactivity of the modern amino acids tyrosine and tryptophan in oxidatively stressed cells. Our data indicate that in demanding building blocks with more versatile redox chemistry, biospheric molecular oxygen triggered the selective fixation of the last amino acids in the genetic code. Thus, functional rather than structural amino acid properties were decisive during the finalization of the universal genetic code.
Selective fixation of amino acid substitutions in organized genomes is energy-dependent and controlled by the physiology of reproduction.
If you were representing the amino acids as circles, they could be drawn as multiple concentric circles representing differing energy levels, rather than one single circle of the same chemical hardness and energy level – kind of like in the photo below.
Few people would make the connection from the amino acids as circles representing different energy levels to the claim that de Vries (1902) made when he invented the term mutation.
But about forty years ago the Dutchman de Vries discovered that in the offspring even of thoroughly pure-bred stocks, a very small number of individuals, say two or three in tens of thousands, turn up with small but ‘jump-like’ changes, the expression ‘jump-like’ not meaning that the change is so very considerable, but that there is a discontinuity inasmuch as there are no intermediate forms between the unchanged and the few changed. De Vries called that a mutation. The significant fact is the discontinuity. It reminds a physicist of quantum theory -no intermediate energies occurring between two neighbouring energy levels. He would be inclined to call de Vries’s mutation theory, figuratively, the quantum theory of biology. We shall see later that this is much more than figurative. The mutations are actually due to quantum jumps in the gene molecule. But quantum theory was but two years old when de Vries first published his discovery, in 1902. Small wonder that it took another generation to discover the intimate connection!
It has been 75 years since Erwin Schrödinger exposed the pseudoscientific nonsense of mutation-driven evolution in the lecture series that was published as What is Life? (1944)
In the 1991 reprint edition, a forward by Roger Penrose who has co-authored with George F.R. Ellis, Stephen Hawking, Stuart Hameroff and others wrote:
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?
It is worth repeating the claim the food energy is required to link quantum physics from quantum chemistry to quantum biology and quantum souls until all pseudoscientists lean the difference between a mutation and an amino acid substitution. Until then, the mental health problem at the highest level will be maintained at the highest level by the highest level of human idiocy every known to have eliminated common sense from consideration in the context of biologically based cause and effect.
For example, Darwin’s claims were based on “conditions of life” that required all organisms to find food and reproduce. Nothing was known about mutations, and even then Darwin could not possibly have been foolish enough to put them first in the context of natural selection for mutation-driven pathology.
Visual system development is light-experience dependent, which strongly implicates epigenetic mechanisms in light-regulated maturation. Among many epigenetic processes, genomic imprinting is an epigenetic mechanism….
…through which monoallelic gene expression occurs in a parent-of-origin-specific manner.
See: An Epigenetic Signature for Monoallelic Olfactory Receptor Expression
This explains why John Hewitt claims I’m providing BS. He is a biologically uninformed science journalist who does not understand the facts about light energy-dependent changes in organized genomes.
Any journalist who publishes anything like The vibrational theory of olfaction for the win should prepare to defend his claims in the context of serious scientists who know how energy must be linked to the vibrations and how the vibrations link quantum physics from quantum chemistry to quantum souls via the physiology of pheromone-controlled reproduction and fixation of RNA-mediated amino acid substitutions.
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.
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.
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.
“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.
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.
…it was recently shown using the RAF algorithm that the metabolic network of Escherichia coli forms a large autocatalytic set of close to 1800 reactions (Sousa et al., 2015). As far as we know, this is the first formal proof that living organisms (or at least essential parts thereof) are indeed autocatalytic sets.
A species emerges from this environment and is an expression of those interactions. In other words, species are expressed and maintained by a complex interacting ecological network.
Few people recognize how difficult it is to link experimental evidence across disciplines. It is discouraging to to find that neo-Darwinian theorists have consistently done it with their claims about minimal mutational distances and the magic of evolution. Theorists link the natural selection of surviving organisms to biophysically constrained viral latency via nutrient energy-dependent RNA-mediated DNA repair and amino acid substitutions in supercoiled DNA.
The theistic evolutionists have made it almost impossible to refute their claims because their claims are not evidence-based. No experimental evidence of biologically-based cause and effect has been linked from energy-dependent biophysically constrained protein folding chemistry to all biodiversity. For example, energy-dependent changes in the microRNA/messenger RNA balance, which links natural selection for energy-dependent codon optimality has not been considered by theorists. The start without energy A sudden drop in outdoor temperature increases the risk of respiratory infections Sarcasm alert: If this is true, global warming may be the solution to all virus-driven pathology. If it is based on the alternative facts touted by neo-Darwinian theorists, your aging relatives are more likely to die than your children — until the advent of something like the 1918 Spanish flu, which was more deadly to younger populations.
See also: Targeting Parkinson’s-linked protein could neutralize two of the disease’s causes
You cannot target a protein without consideration for energy-dependent endogenous RNA interference (i.e., biophysically constrained RNA-mediated cell type differentiation).
It is not the proteins that cause the diseases. It is the failure of energy-dependent RNA-mediated DNA repair. Surprise: Femtosecond blasts of UV light have been linked to natural selection for codon optimality and all biodiversity by serious scientists who have linked energy-dependent changes in angstroms to ecosystems in all living genera. Keep in mind that the serious scientists are not going to stop laughing about the claims of pseudoscientists. See for example, this attack on the claims made by Neil deGrasse Tyson. It’s subtle, but that’s how serious scientists have fun. They know that most pseudoscientists won’t get their jokes.
Try to get used to the fact that theistic evolutionists don’t get the jokes, But first, you may need toi get over the fact that you probably were taught to believe in the pseudoscientific nonsense of neo-Darwinian theories. Admit it, you probably believed the nonsense even before it was linked to theories about Intelligent Design by alternative facts about evolution across millions of years. Some biologically uninformed theorists still seem to think led to the evolution of birds from dinosaurs.
1. See also: DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification
Can you link their findings to autocatalytic biodiversity?
Can you avoid linking their findings to drug therapy-induced DNA damage that was not repaired in the context of endogenous RNA interference?
If you can avoid linking the findings from these three articles to biophysically constrained energy-dependent RNA-mediated amino acid substitutions and biodiversity in all living genera, you might be able to co-author an article on autocatalytic biodiversity and make people think it was possible for everything that emerged to automagically evolve into every species that has ever existed on Earth. But, why would you want to do that?
Studying bacterial effects on cancer are very complex, because there is no one clear mechanism
Jon LIeff has again obfuscated the clarity of facts about energy-dependent conserved molecular mechanisms. These are the facts:
1) Closed feedback loops link nutrient energy-dependent pheromone-controlled quorum sensing in bacteria to supercoiled DNA in all living genera.
2) Virus-driven energy theft causes the degradation of messenger RNA in bacteria that is manifested in the morphology and behavior of so-called archaea.
3) Archaea are bacteria with less supercoiling in their DNA. (For comparison to bacteria the so-called archaea are less well-adapted. They must struggle harder to avoid extinction.)
4) Negative supercoiling in the organaized genomes of bacteria has been linked to communication among viruses.
5) Viral signaling pits energy theft against the nutrient energy- dependent signaling that links quorum sensing from ecological variation to ecological adaption in all cell types of all individuals of all species on Earth.
Healthy longevity is linked from the nutrient-dependent pheromone-controlled physiology of reproduction in bacteria to supercoiled DNA, which prevents the transgenerational epigenetic inheritance of Zika virus-damaged DNA.
To his credit, this is the first time I have seen Jon Lieff attempt to distance himself from ridiculous theories about evolution.
He concludes:
All of these interactions are based on the natural communications between bacteria and human cells.
…Sorek reports in the journal Nature that his team has found the protein that viruses used to communicate. His team has called the protein arbitrium, which is Latin for “decision.”
They conclude with this ridiculous claim about viruses as a primitive life form instead of realistically linking virus-driven energy theft from mutations to all pathology.
Even though viruses are the most primitive form of life, they infect and harm millions of people every year. The possibility of tapping into viral communication has many scientists excited, because it offers new ways to build drugs that could defeat viruses.
Quorum sensing in bacteria is the nutrient energy-dependent pheromone-controlled link from the innate immune system of all living genera to the physiology of reproduction. Ecological variation must be linked to ecological adaptation via conserved molecular mechanisms of RNA-mediated protein folding chemistry in the context of the physiology of reproduction. If the physiology of reproduction is not biophysically constrained by the availability of nutrients, you are left with a ridiculous theory about mutation-driven evolution.
See also: Alternative RNA Splicing in Evolution (2012)
On 10/27/13 Jon Lieff wrote:
I very much appreciate your comments on pheromone communication and its rapid and critical link to the olfactory brain. I look forward to any current references and future work to help understand the immune brain connection as well as communication in general.
That comment was edited, and now appears as:
Thanks for the current article and information. I very much appreciate your important information and will try to learn more about it.
Another pertinent current article was published in May 2016
See: Spliceosomal intronogenesis
Unfortunately, Jon Lieff and many others have tried to link alternative RNA splicings to the evolution of morphological and behavioral phenotypes outside the context of the energy-dependent physiology of reproduction. Attempts to make viruses the cause of evolution are even more ridiculous, since virus-driven energy theft is the cause of all pathology.
See for comparison: Stromal cues regulate the pancreatic cancer epigenome and metabolome
…these studies raise the possibility that microenvironmental context broadly influences the epigenetic state of tissue-resident cell types under physiological and pathological conditions.
If you had a molecule that could drive viruses into complete latency, it would be a good drug.
Viral latency is nutrient energy-dependent and it is controlled by the physiology of reproduction. There is no need for a good drug until virus-driven energy theft causes the accumulated mutations that all serious scientists have linked to all pathology. For comparison, all pseudoscientists have linked the mutations to evolution.
Pseudoscientists abandoned every aspect of nutrient energy-dependent healthy longevity and focused on drug development. For a track record of pseudoscientific nonsense, see:
Masatoshi Nei and Naruya Saitou (1986) Genetic relationship of human populations and ethnic differences in reaction to drugs and food
…variant alleles at the pseudocholinesterase locus seem to be maintained by the balance between mutation and weak selection.
CNS-flanking genes were often found in evolutionarily conserved genomic neighborhoods. ChIP-Seq signal and gene expression patterns also suggested that CNSs regulate nearby genes. Interestingly, genes with more CNSs have more evolutionarily conserved expression than those with fewer CNSs. These computationally obtained results suggest that the genomic locations of CNSs are important for their regulatory functions. In fact, various kinds of evolutionary constraints may be acting to maintain the genomic locations of CNSs and protein-coding genes in mammals to ensure proper regulation.
Conserved non-coding sequences, which are typically reported as microRNA flanking sequences, are reported as CNS-flanking genes. Two decades after we reported how alternative splicings of pre-mRNA were linked from RNA-mediated cell type differentiation to biodiversity via sexual differentiation of cell type in species from yeasts to mammals, the experimental evidence forced Masatoshi Nei’s 1985 co-author to admit that the statistical evidence matches the facts. At first glance, it mght appear that Saitou and Nei never heard about virus-driven energy theft in the context of neo-Darwinian evolution. But wait, instead, they chose to ignore what they knew.
See: Naruya Saitou and Masatoshi Nei (1986) Polymorphism and evolution of influenza A virus genes
See also: Naruya Saitou and Masatoshi Nei (1986) The number of nucleotides required to determine the branching order of three species, with special reference to the human-chimpanzee-gorilla divergence
When these five different tree-making methods, as well as Fitch and Margoliash’s method, are applied to the mitochondrial DNA data (1834 bp) obtained by Brown et al. and by Hixson and Brown, they all give the same phylogenetic tree, in which human and chimpanzee are most closely related. However, the trees considered here are “gene trees,” and to obtain the correct “species tree,” sequence data for several independent loci must be used.
In optogenetics, neurons are genetically modified to express light-sensitive ion channels (proteins that conduct electricity), such that light exposure may be used to activate or inhibit electrical activity.
The fact that femotosecond blasts of virucidal UV light have been linked from quorum-sensing in bacteria to repair of virus-driven DNA damage in species from archaea to humans, suggests the understanding of optogenetics has moved far beyond what was specific to neuronal activation.
By varying the time between two pulses of light, serious scientists saw how the structure of the protein morphed over time. They did not extend the time to millions of years and suggest that protein evolution had occurred during that time because they are serious scientists, not pseudoscientists.
See: Dobzhansky 1973 and precision medicine (4) in prep
Religious texts, such as The Holy Bible appear to be like a Precis of works from God. He seems to be explaining energy-dependent creation in the context of what is currently known to serious scientists about biophysically constrained RNA-mediated protein folding chemistry, healthy longevity and RNA-mediated biodiversity.
God made it perfectly clear, in advance, that all miraculous biodiversity is energy-dependent. Energy as information is the theme that extends to the weekend resurrection of the bacterial flagellum in P. fluorscens. Biologically uninformed theorists are beginning to realize the importance of a simplistic version of biologically-based systems complexity.
Energy as information can be understood by non-scientists whether or not they are interested in further examination of top-down causation at every level of subsequent interactions among subatomic particles and macroscopic biodiversity. See for instance:Protein Folding Using Quantum Topology which is linked to this video as a part of a series from “Serious Science” Description:
Matematician Jørgen Andersen on local geometry of hydrogen bonds, quantum states of proteins and future methods of predicting the macromolecules structure.
Excerpt:
There are about 2000 local patterns that we’ve seen popping out now and we are trying to understand what is the correlation between the primary sequence of these patterns. Some of them have a clear significance. We’re trying to devise energy contributions for each of such patterns and then trying to see if we can create algorithms that generate all structures with a certain sequence of patterns. And this is a combinatorial problem that we’ve actually solved very recently.
My comment: Does he realize he is giving the bird to all pseudoscientists with both fingers?
The book was written for the general readership (as indicated by the Table of Contents). This precis is designed to elicit responses from the scientific readership.
This Precis provides an overview of the book “The Scent of Eros: Mysteries of Odor in Human Sexuality,” which details for a general audience a five-step biological pathway that allows the social environment to influence the genetic nature of mammalian behavior. This pathway is: gene-cell-tissue-organ-organ system. Moreover, though there are many environmental influences on genes, mammalian pheromones are the only known social-environmental stimuli that appear to activate gene expression in neurosecretory cells of tissue in the brain, an organ that is essential to any organ system involved in behavior. Human pheromones appear both to elicit a homologous “neuroendocrine” response and to influence behavior. Thus, human pheromones may fulfill the biological criteria required to link at least one aspect of a sensory-based, nurturing, social environment: olfaction, to the genetic nature of human behavior through a five-step pathway common to all terrestrial mammals and to many other vertebrates.
Full text:
1. This book incorporates both non-human animal and human models of reciprocity among odors, olfaction, neuroendocrinology, and behavior. It details the likely influences both of human chemical communication and of olfaction on genes in neurosecretory neurons. These neurons are found in brain tissue responsible for integrating, coordinating, and directing reproductive endocrine function in organs that comprise the organ systems known to influence mammalian reproductive sexual behavior and human sexuality. Though this book is not written to meet any requirements of a “hard scientific” approach to interdisciplinary topics, it is fully referenced for the knowledgeable scientist and for those interested either in further study or in support for any conclusions. Also included are chapter notes, a glossary, and an index.
2. After a Foreward by William E. Hartman and Marilyn A. Fithian and an Introduction by the co-author, Chapter 1 begins with commentary on previously published works by various scientific authorities who have offered their insights into the importance of human chemical communication. Among these authorities are Havelock Ellis, Irving Bieber, and Lewis Thomas, who offered the following statement: “I should think we might fairly gauge the future of biological science, centuries ahead, by estimating the time it will take to reach a complete, comprehensive understanding of odor. It may not seem a profound enough problem to dominate all the life sciences, but it contains, piece by piece all the mysteries.” (Thomas, 1980)
3. In Chapter 1, there are fourteen examples of the many questions that may be answered when one considers the likelihood of odorous human communication. Most of these questions concern different aspects of human sexuality. Briefly deliberated are concerns about an ineffective “language of olfaction” and errors in the logic that has been used in the past to deny the importance of odor in human sexuality. The introductory focus then turns to biological consistency among species; the common basis for scientific advancements; and the development of the working hypothesis that odors are a primary influence on human sexuality.
4. Chemical communication and its importance in other species from insects to mammals is more fully detailed in Chapter 2. The term pheromone is defined, with added emphasis of one basic causal relationship, namely, that mammalian pheromones appear to influence the secretion of gonadotropin releasing hormone (GnRH), a hormone with both short-term and long-term effects on neurotransmission. Distinguishing characteristics of pheromones like species-specificity, and the differences between signalling and releasing pheromones are added to the definition. After a brief discussion of mammalian pheromones, the natural production of human odors is discussed and anecdotal evidence of some of their effects are offered as support for the concept of human pheromones.
5. Chapter 3 alludes to Greek mythology; the story of Ariadne’s thread, which metaphorically addresses the issue of biological consistency among species. The development of the mammalian sense of smell is detailed from its beginnings in single-celled organisms. Olfactory transduction is briefly discussed. Four crucial turning points in the development of mammalian chemical communication systems, which contribute to species survival, are: (1) the release of pheromones to attract another organism, which occurs in single-celled non-motile organisms, (2) the ability to detect and respond to chemical messengers with movement, which occurs in motile single-celled organisms (3) the development of neural networks devoted to processing chemical signals, which occurs in brainless invertebrates, and (4) phylogenetic advances in the development of these neural networks to include development of the vertebrate brain. Species-specific comparisons and contrasts in structure and function are provided.
6. Chapter 4 offers an ontogenetic perspective on development, both of the mammalian olfactory systems and of the GnRH neuronal system. The ontogenetic connection between the structure and function of olfactory sensory systems and brain development ascends in its significance because it allows the odorous social environment to directly and indirectly influence brain function by acting on GnRH, which in turn has short-term effects on neurotransmission and long-term effects on the hypothalamic-pituitary-gonadal (HPG) axis.
7. Kallmann’s syndrome represents a failure of GnRH neuronal migration. Correlates with anosmia and the inability to fall in love are noted, as are correlates with the GnRH neuronal system and brain development in other species. Additional aspects of olfactory transduction and signal processing are discussed. There are differences between the main olfactory system and the accessory olfactory system. The importance of the vomeronasal organ (VNO) for pheromone detection in other species and renewed interest in the recently confirmed presence of the human VNO add to the argument for the influence of odors on human sexuality.
8. Chapter 5 begins with anthropological folklore associated with odor and human behavior and progresses to a discussion of empirical evidence for this link. The metabolism of hormones into pheromones is noted. Specifically addressed are experiments with putative human pheromones and the likelihood of causal physiological and behavioral relationships. Comparisons and contrasts among species again are offered in this regard. The use of mammalian pheromones in fragrances designed to enhance the sexual appeal of humans is examined. The naturally occurring fragrance of musk, present in the secretions of many species, is held in high regard for its universal sex-attractant properties.
9. Chapter 6 reports on experiments with consciously processed human odors, beginning with the classically-conditioned response of infants to their mothers’ naturally-scented or artificially-scented breasts. Olfactory imprinting and the importance of the mother-infant bond are linked through non-human animal models to the development of neural templates and the human “love map”. Aspects of odor hedonics are detailed.
10. Children can determine the genetic sex of adults, and adults can distinguish between different people using their sense of smell. The importance of mammalian odors in aggression and in other contexts besides the mother-infant bond suggests human correlates. Similarly, clinical and anecdotal evidence that humans are culturally aware of odor-associated customs enhances a more scientific approach to the link between sex and the human sense of smell. Odors and fetishism are linked. The natural superiority of women’s olfactory acuity and specificity is linked to estrogen levels and to an important role in female choice: What human beings lack in acuity they make up for in powers of discrimination, which rival those of any other mammal.
11. Chapter 7 is a simplistic overview of prenatal GnRH neuronal system development. Included are genetic predisposition and the importance of GnRH pulsatility in the regulation of the HPG axis. This chapter begins, however, with the importance of chemical communication between ovum and spermatozoa and progresses through basic genetics, neuroanatomy, endocrinology, and endocrine aspects of neurotransmission. Postnatally, odor input is linked to human HPG axis function. Pheromone input appears to be indirectly measurable in assays of luteinizing hormone.
12. Beginning with the “nature” versus “nurture” controversy, Chapter 8 proceeds to the important issue of finding a link between the social environment and genes. The likelihood that genes are involved both in physiological and in behavioral cause and effect relationships is detailed. The influence of pheromones on genes and on concurrent neuroendocrine, reproductive system, and central nervous system development is proposed.
13. Twin studies are discussed, as is recent evidence of master genes that may allow chemical communication at the cellular level to play a primary role in behavioral development and in sexual orientation. Genetic conservation among species, specifically with regard to chemical communication, is addressed. Enzymes and chemical responses are linked with human behavior, as are genes and G protein-coupled receptors through an example of familial precocious puberty. Correlates between adrenal androgen metabolism, pheromone production, sexual dimorphism in the human hypothalamus, and human sexual orientation are offered.
14. Chapter 9 details aspects of human consciousness and of limbic learning and memory. Olfaction plays a key role by providing input to the medial preoptic area of the hypothalamus. Comparisons and contrasts among species and among theories of consciousness are offered.
15. The importance of linking specialized research in diverse disciplines is made known, namely, how a “gay gene” might influence both human neuroanatomy and human sexuality. Dean Hamer has proposed the following: “The most simple hypothesis would be that the Xq28 makes a protein that is directly involved in the growth or death of neurons in the INAH-3. Alternatively, the gene could encode a protein that influences the regulation of this region by hormones.” (Hamer & Copeland 1994).
16. Effects of pheromones on other species are favorably compared to the effects of putative human pheromones. A consciously-processed odor stimulus has been used as an adjunct to classically condition the human immune response, thereby adding clinical significance to the effects of odors.
17. Chapter 10 reveals evidence of odor-driven hormonal effects on human behavior and on sexuality, again using cross-species comparisons that link information provided in earlier chapters. Examples supporting a link between pheromones and human sexuality are discussed. The “Law of Propinquity” appears to be invalidated by experience with pheromones that create more of a friendship or kinship bond, perhaps also creating an antibond effect on love. There is evidence that humans mate for genetic diversity on the basis of unconscious odor associations, and that odors may be involved in the Coolidge effect.
18. The sources of human pheromones are detailed in Chapter 11, with a discussion of the role of glandular secretions, fatty acids, bacteria, skin cells, and the relationship between levels or ratios of sex hormones and pheromone production. Important aspects of pheromone distribution are then linked to intimate behavioral associations. Androgenization appears to stimulate secretion of a more masculine pheromone signature. Odors can be used in clinical diagnostics. The inherent difficulties of human pheromone research are briefly discussed.
19. Chapter 12 links human pheromones to various courtship behaviors (e.g., dancing, kissing, et al.,) that appear to become progressively more intimate with increasing exposure to pheromones. Stereotypic attractive qualities (e.g., large breasts or hair color and distribution) with anecdotal evidence of causal relationships between pheromones, attraction, and intimacy are represented both positively and negatively. Culturally, negative representations often appear to correlate well with sexual repression. Racial differences in odor production that may contribute to racial prejudice are briefly addressed.
20. Included in Chapter 13 is a discussion of results from the National Geographic Smell Survey. Data was collected from approximately one and a half million people worldwide. Causes of anosmia and its link both to genetics and to the GnRH neuronal systems are detailed, as are links between damage to the VNO, age-related disorders, olfactory deficits, and behavior.
21. Chapter 14 provides both a historical and a modern-day overview of aromatherapy. Cultural differences in odor hedonics are explained by odor-associated classical conditioning. The roles of chemicals now known to function as human pheromones and of putative human pheromones in fragrances for commercial use is discussed. A brief summation of current research supporting the hypothesis that human pheromones are a primary influence on human sexuality is provided.
22. I believe that “the pheromones of other mammals are the only social-environmental stimuli to influence genes [in GnRH neurons].” Accordingly, human pheromones are the most likely link between the “nature” and the “nurture” of human sexuality. However, a typographical error: insertion of “not” on page 189, in paragraph 2, line 4 (intended to read as above) detracts from the concluding paragraphs.
REFERENCES
Thomas, L. (1980) Notes of a biology-watcher: on smell. New England Journal of Medicine 302: 731-733.
Hamer, D. & Copeland, P. (1994) The Science of Desire, Simon & Schuster: 163.
My comment: Claims that my Precis is linked to proof of biophysically constrained energy-dependent causd and effect can be viewed in the context of the video representation by Jorgen Anderson for comparison to this detailed representation of my model and/or this video:
See the discussion attempt here before it is removed via suggestion by an unfriendly administrator who claims he is my friend. I’ve already given him the bird (in the cartoon representation from this blog post).
In 1960, the eminent Oxford marine biologist Sir Alister Hardy proposed a revolutionary idea: that our human ancestors had not started their existence on the wide savannahs of Africa, but had become accustomed to living alongside water – swimming and diving in the shallows, collecting the abundant food, and learning to use language and fashion tools. Hardy asserted that this adaptation to living at the waterside –whether by rivers and pools or by the ocean – would also account for a whole range of peculiarities about the human form, including the layers of fat beneath the skin, the relative lack of body hair, the development of language and speech, and what he called our “runaway brains”.
Perhaps surprisingly, it was a screenwriter rather than a scientist, Elaine Morgan, who took up Hardy’s theory and, for over 40 years, progressively refined the evidence for the idea. Most mainstream paleo-anthropologists ridiculed and rejected the Hardy-Morgan thesis for decades, but some influential scientists asked for the proposal to be approached with an open mind.
Sir David Attenborough first considered the controversial theory on Radio 4 in 2004, and in this new two-part series, he brings listeners up-to-date with the story and the evidence put forward since then – for both the hypothesis and also for its continuing detractors. Back in 2004, Sir David asked Elaine Morgan how long it would take for the aquatic adaptation theory to become a mainstream account of human origins. She answered: “I’ll give it ten years.” As the programme reviews the new evidence, has she been proved right?
Presenter/Sir David Attenborough, Producer/Richard Collins for Pier Productions
Re: As we review the new evidence, has she been proved right?
My comment: No experimental evidence of biologically-based cause and effect ever suggested that Elaine Morgan was wrong. She accurately predicted that 2014 would be the year in which she was proved right. As far as I know, she was predictably right.
See this 2014 invited review of nutritional epigenetics (and energy-dependent RNA-mediated cell type differentiation):
…the largest contributor to the development of our personal preferences may be the unconscious epigenetic effects of food odors and pheromones on hormones that organize and activate behavior. If so, the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.
My 2014 invited review was returned without review. No factual representations of epigenesis and epistasis have been offered for comparison to the ridiculous claims of theorists. For example:
In Mutation-Driven Evolution, which was published on the same day as my 2013 review, Masatoshi Nei concluded:
…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements.
In my model, and in the context of Elaine Morgan’s claims, viral latency is biophysically constrained by the nutrient energy-dependent physiology of reproduction in all living genera.
See also: Epigenetics and Genetics of Viral Latency
… viral latency is responsible for life-long pathogenesis and mortality risk…
For brief reviews of Elaine Morgan’s claims, see:
I do not believe any experimental evidence of energy-dependent biologically-based cause and effect suggests that we evolved from any other species. I suspect that Sir David Attenborough will not be the first to consider my model in the context of his review of Darwinian and/or neo-Darwinian theories. There is too much known to serious scientists about energy-dependent RNA-mediated cell type differentiation to reach any other conclusion than the one reached by Paul M. Lieberman in Epigenetics and Genetics of Viral Latency.
I reiterate:
… viral latency is responsible for life-long pathogenesis and mortality risk…
See for comparison:
See also:
The idea that Elaine Morgan can be proved right without proving that Darwian and neo-Darwinian theories are overwhelmingly wrong is an idea that should have been considered during the past 40 years. Instead, consideration of the claims made by theorists have left theorists with nothing more than their ridiculous theories. See for comparison:Structural diversity of supercoiled DNA, Glucose Tightly Controls Morphological and Functional Properties of Astrocytes, Tight DNA packaging protects against ‘jumping genes,’ potential cellular destruction Thanks to Teresa Binstock for bringing this article about supercoiled DNA to my attention.
“Tight DNA packaging” and “tightly coiled DNA” are terms used to obfuscate the facts about supercoiled DNA that have already linked viral latency to all pathology.
Supercoiled DNA protects the organized genomes of all living genera from virus-driven entropy. That fact has been the focus of my efforts here and at RNA-mediated.com
Why is Teresa Binstock — co-author of our 1996 Hormones and Behavior review — the only one who seems to be following the literature on RNA-mediated cell type differentiation?
When Schreiber’s team looked for compounds that met both criteria – displaying a novel mechanism of action and activity during all three disease stages – a series of compounds stood out. All of them acted on the same target, phenylalanyl-tRNA synthetase, a complex enzyme that contributes to protein synthesis. When they tested the compounds in mice, it eradicated the malaria parasites during all three stages of the disease.
Cause and effective treatment are RNA-mediated via links from metabolic networks to genetic networks across species.
This interaction raises the possibility that particle velocity information and electrical information, and interactions between them, can be encoded by a single hair.” It also raises the possibility that “electroreception is widespread in arthropods, fulfilling functions beyond the detection of floral electric fields.
My comment: Energy-dependent microRNA flanking sequences linked all invertebrates to all vertebrates in the context of what was published as: The phylogenetic utility and functional constraint of microRNA flanking sequences and reported in advance (with my comment) as All in the (bigger) family and later as ‘Junk DNA’ Used To Sort Species The Creation Evolution editor removed my comment about the “Epigenetics and Genetics of Viral Latency.” I tried to focus attention on this. On May 11, 2016, Paul M. Lieberman claimed that “…viral latency is responsible for life-long pathogenesis and mortality risk…” But the Creation Evolution editor didn’t ask me what I thought the widespread conservation of electroreception in arthropods had to do with physics in nature. The editor’s claim was that:
jvkohl, your comment had nothing to do with the article….
That ended my attempt to discuss what Jeffrey Tomkins reported about the epigenetics and genetics of viral latency in: “Viral Genome Junk Is Bunk.” Tomkins included an important quote: “As molecular biologist and biochemist Peter Borger notes, “The most parsimonious answer is: the RNA viruses got their genes from their hosts.” 6 Other molecular biologists understand the importance of providing quotes and citations. Journalists and editors may not. See for example: “Quantum mechanical DNA. The weird world of quantum mechanics operates in DNA, the molecule of life.” That statement was not linked to this report Sound-like bubbles whizzing around in DNA are essential to life.
I added this comment on the Creation Evolution site:
Thanks. The article failed to provide a link to this information.
Sound-like bubbles whizzing around in DNA are essential to life http://phys.org/news/2016-06-sound-like-whizzing-dna-essential-life.html
Excerpt: “It is believed that DNA has regions where a specific sequence of bases modifies the stiffness of the double helix favouring the formation of bubbles. This causes a break of the weak bonds between the strands showing the transcription and replication enzymes where to start their task.”
That’s what I tried to address in my comment. Why introduce the topic of Quantum mechanical DNA if you would rather it not be discussed in the context of “Masters of Physics in Nature?”
My comment about a new book by George Ellis was simply removed, and I suspect my second comment will also be removed. The problem for anyone touting Intelligent Design for comparison to Creation is that the book How Can Physics Underlie the Mind?: Top-Down Causation in the Human Context fails to link virus-driven energy theft to all pathology. Instead, it places all biophysically constrained protein folding chemistry and constraint-breaking mutations into the context of evolution. See also:
…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements (p. 199).” Mutation-Driven Evolution (published June 14, 2013)
…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’.
The conclusions from 3 years ago vary significantly. One eliminates consideration of teleological elements (e.g., biologically-based cause and effect), and the model demands consideration of everything known to serious scientists about energy-dependent RNA-mediated amino acid substitutions and cell type differentiation in the context of the physiology of reproduction, which links olfaction from the innate immune system to supercoiled DNA. Supercoiled DNA links everything known to serious scientists about energy-dependent cell type differentiation and virus-driven energy theft, which links mutations to all pathology. In that model of how ecological variation must be linked to ecological adaptation by the physiology of energy-dependent reproduction, the facts speak for themselves. They link the incredibly complexity of metabolic networks to genetic networks via the innate immune system, and link all pathology to the effect of virus-driven energy theft.
Creationists who don’t think it is important to learn what other creationists are claiming in the context of facts that link nutritional epigenetics to healthy longevity — as in Biblical Genesis are more likely to be among those who will discuss Intelligent Design, but deny the existence of a Creator. They are also more likely to miss the misrepresentations that other creationists, like George Ellis, use to support their claims of theistic evolution.
Advance praise for the book I co-authored in 1995 included this: “This is science at its best, with adventure, ideas, and lots of facts”. — Helen Fisher (biological anthropologist)
I was happy when George Ellis responded to my comment about food odors and pheromones with this claim from 2012:
This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: http://rsfs.royalsocietypublishing.org/content/2/1.toc
and then this:
Great links, thanks. I’m intrigued by your work on pheromones. It is just possible it might relate to the issue of primordial emotional systems, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3540967/ – See more at: http://community.frontiersin.org/people/GeorgeEllis_1/51729#sthash.RcztWMUN.dpuf
I thought that by now, 2 decades after book publication and nearly 2 decades after publication of our 1996 review of molecular epigenetics, that George Ellis and I might share the same perspective.
I was wrong, as anyone can see if only they read the Advance Praise for his book Excerpt: 1)
A stark lacuna lies at the heart of science: half the causal narrative has been omitted! — Paul Davies, Beyond Center, Arizona State University
My comment: The half that’s missing is virus-driven energy theft, which is linked to all pathology. Excerpt 2)
The sweep of the book is enormous as it details the evidence and the impact in each area of science. It forms a major landmark, and it does so at an exciting time, when the purely gene-centric views of biology are being seriously challenged. — Denis Noble, CBE FRS, University of Oxford
My comment: Gene-centric views of biology have not been considered by serious scientists who began to learn about molecular epigenetics in the mid-1990’s. Excerpt 3)
…this defense of “strong emergence” sets a high, perhaps unreachable bar for scientific reductionists. –Philip Clayton, author of Mind and Emergence
My comment: Claims about “strong emergence” are meaningless when placed into the context of evolution. Angstroms and ecosystems have been linked via the de novo creation of genes — the “holy grail” of biology. The genes are olfactory receptor genes that link food odors and pheromones to energy-dependent RNA-mediated cell type differentiation in species from microbes to humans. Excerpt 4)
…other modes of explanation, including those based on emergence and top-down causation, are vital for a fully orbed account of the natural world. — Ard Louis, Rudolph Peierls Centre for Theoretical Physics University of Oxford
My comment: Claims about “emergence and top-down causation” do not account for energy theft. Supercoiled DNA prevents it. Viruses cause it. Nothing evolves! Every species must adapt to the threat viruses pose to nutrient energy-dependent survival via the physiology of reproduction. Excerpt 5)
George Ellis argues with admirable charity of thought that much of the world we live in is governed not by the blind dance of atoms, but by high-level causes and purposes. — Giulio Tononi, University of Wisconsin-Madison
My comment: Is he claiming that George Ellis is arguing for non-random creation and a purpose-driven life? Excerpt 6)
A carefully crafted argument, steeped in the scholarly literature, yet accessible to the ordinary reader. — Alister E. McGrath, University of Oxford
My comment: What carefully crafted argument is he claiming that George Ellis developed in the context of the scholarly literature? What scholarly literature still touts emergence and evolution in attempts to craft arguments that all serious scientists dismiss because they fail to include experimental evidence of facts that link energy-dependent changes from angstroms to ecosystems? Summary. If those who offered their advance praise had been more specific about what they were praising, their comments would not appear to me to be coming from a “good old boy’s club” of those who agree with each other because that is what they agreed to do — sometime before the turn of this century. I suspect that they agreed to ignore what is known about energy-dependent biophysically constrained cell type differentiation and virus-driven energy theft, which links mutations to all pathology.
What’s left is emergence and natural selection with or without mutations, which means the evolutionary theorists and big bang cosmologists can have it both ways. Both ways are theoretical. I don’t think that serious scientists will accept any more claims from either group of theorists.
Energy-dependent RNA methylation has emerged from the ranks of serious scientists as the obvious link from ecological variation to nutrient-dependent biophysically constrained ecological adaptations. Virus-driven energy theft has emerged as the obvious link from mutations to all pathology. If the facts about energy-dependent cell type differentiation cannot be placed into a model that links physics and chemistry to what is already known about molecular epigenetics, theorists must agree to stay at least 20 years behind the experimental evidence of biologically-based cause and effect. Will you join their club, or join the serious scientists who are Combating Evolution to Fight Disease? My comment:
“An alternative theory proposes environmentally induced change in an organism’s behavior as the starting point (1), and “phenotypic plasticity” that is inherited across generations through an unspecified process of “genetic assimilation” (2).” http://www.sciencemag.org/content/332/6034/1161.short
This is now more than merely an alternative theory of genetic assimilation. It links transgenerational epigenetic effects from nutrient uptake and RNA-mediated events to amino acid substitutions that differentiate the cell types of all cells in all individuals of all organisms. See, for example: Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans http://www.cell.com/cell/abstract/S0092-8674(14)00806-X
The nutrient stress-induced RNA-mediated events, which link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man, also link morphological and behavioral diversity via conserved molecular mechanisms exemplified in the context of biologically plausible ecological speciation in nematodes.
See: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes http://linkinghub.elsevier.com/retrieve/pii/S0092867412015000
A difference in their feeding behavior and in the anatomy of their mouth parts is linked from nutrient-dependent pheromone-controlled feedback loops to ecological, social, and neurogenic niche construction. The change in focus from mutations, natural selection, and the evolution of biodiversity via unknown evolutionary events to nutrient-dependent pheromone-controlled RNA-mediated events that differentiate cell types may be required for others to realize the difference between evolutionary theories and biologically-based facts about RNA-mediated events.
RNA-mediated events are biophysically constrained, which means they are a biologically plausible way to link the physics and chemistry of protein folding to increasing organismal complexity via molecular biology. RNA-mediated events can also be compared to any unknown evolutionary events that might arise in the context of an alternative theory about constraint-breaking mutations, or other theories that do not mention RNA-mediated events. Summary: Theories are like stories that tell people about only half of what must be epigenetically linked from energy-dependent changes in angstroms to ecosystems. For example, George Ellis now includes information on energy-dependent emergence and evolution.
But he seems unwilling to tell people anything about the virus-driven energy theft that others have linked to all pathology in all living genera. The pathology exemplifies the fact that some species have not adapted via their nutrient-energy dependent innate immune system. There are missing links between metabolic networks and genetic networks, which fail to support the physiology of reproduction and the functional structure of supercoiled DNA.
It is time for Ellis and his cronies to admit that they know nothing about how energy-dependent RNA methylation is linked to behavior and successful reproduction by RNA-mediated amino acid substitutions. The substitutions link hydrogen-atom transfer in DNA base pairs in solution to energy-dependent ecological adaptation via DNA repair in the context of quantized energy from the sun on contact with water. From the time others learned about the de novo creation of nucleic acid precursors, which was detailed in Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism to the time that the information on the origins of RNA was linked to healthy longevity can now be compared to how quickly others have learned that virus-driven energy theft links viral nucleic acids to all pathology.
When the link from olfaction and the innate immune system to RNA methylation and behavior establishes an even clearer path from the epigenetic landscape to the physical landscape of supercoiled DNA, those who have told only half the story will be exposed by those who tell others the truth and the consequences of ignorance.
Trying to resolve the stubborn paradoxes of their field, physicists craft ever more mind-boggling visions of reality
Excerpt 1) with my emphasis
Physicists are deeply aware of the schizophrenic nature of their science and long to find a synthesis, or unification. Such is the goal of a so-called ‘theory of everything’. However, to non-physicists, these competing lines of thought, and the paradoxes they entrain, can seem not just bewildering but absurd.
Excerpt 2)
Based in mathematics, the classifications of physicists are supposed to have a rigour that other sciences lack, and a good deal of the near-mystical discourse that surrounds the subject hinges on ideas about where the mathematics ‘comes from’.
We demonstrate the self-organization of these connectome-specific harmonics patterns from the interplay of neural excitation and inhibition in coupled dynamical systems as described by neural field models. Interestingly, due to the emergence of these harmonic patterns in various natural phenomena, ranging from acoustic vibrations, electromagnetic interactions and electron wave functions to morphogenesis, it is tempting to suppose that human brain activity might also be governed by the same underlying principles as other natural phenomena.
My comment: Self-organization and emergence are included in mathematical models that fail to link atoms to ecosystems via energy-dependent hydrogen-atom transfer in DNA base pairs. Does the emergence of self-organized connectomes in the context of a mathematical model make sense to schizophrenic physicists with their “theories of everything” else?
…allele frequencies at polymorphic CpG sites can distinguish between maintenance of CpG islands by selection and stabilization of CpG islands through mere hypodeamination. As demonstrated by evolutionary simulations (Figures 7A and 7B , Figure S6A and S6B ), both low level of deamination and selection for minimal CpG content will result in high steady state CpG content. However, in the selective regime, polymorphic CpGs are expected to have significantly lower allele frequencies (average heterozygosity), and thus a higher frequency of low heterozygosity alleles than that observed in G/C dinucleotides.
My comment: The allele frequencies are nutrient energy-dependent and the different alleles link hydrogen-atom transfer in DNA base pairs to RNA-mediated cell type differentiation via the physiology of reproduction and fixation of amino acid substitutions that stabilize the organized genomes of all living genera.
The 100 year stand-off between theoretical physicists, evolutionary theorists, and serious scientists ended. But, few serious scientists are trying to win any confrontations over ridiculous theories compared to facts. The theorists simply add another theory and tell the serious scientists to prove that their theory is not important to understanding how to link physics and chemistry to biologically-based cause and effect. Their ridiculous theories never link hydrogen-atom transfer in DNA base pairs to all biomass via the sun’s biological energy. Thus, no matter what a serious scientist like Ricki Lewis does to promote the serious science produced by others, the pseudoscientists run away and try to start a fight somewhere else.
The news last week seemed to validate Drs. Annila and Baverstock’s concern about genome sequencing entering the clinic when we don’t fully understand how genes interact at the level of their products, the proteins.
See the comments. PZ Myers attacks the expertise of Drs. Annila and Baverstock, whose works have since been linked from nutrient-dependent microRNAs and hydrogen-atom transfer in DNA base pairs to RNA-mediated cell type differentiation via adhesion proteins and supercoiled DNA, which protects organized genomes from virus-driven entropy.
Baverstock tells people how epigenetically-effected RNA-mediated events are linked from amino acid substitutions to cell type differentiation in all cell types of all individuals of all species, and Myers claims: “Your version of the central dogma is idiosyncratic and wrong.” Myers has also since done that to Perry Marshall, author of “Evolution 2.0.”
But first, look at these comments from Ricki Lewis’ site:
I’m not sure if I understand your point, as I’m still an undergrad student. I think the chaperones are a measure to widen a possible proteome (as alternative splicing), and since chaperones and alternative splicing factors are passed on through cytoplasmatic continuity, these should be also considered as an unit of heredity. I agree with this view, but I think it is already a predominant view with, lets say, developmental biologists – who seek out for function of certain genes during morphogenesis, for example. The same gene in different also locations can give rise to different structures – and this is certainly due to different proteomes in these locations.
:
In our view genes do not have a function. Function arises from a process entailing the interaction of active and information bearing proteins (mainly) and it is this process that we propose is the “unit of inheritance”. It can be regarded as a unit because it can be encapsulated by a quasi-stable state of the cell and as we said at the outset of the piece: it is the state of the cell that is inherited at cell division. as well as the DNA. I think you are pretty close to the idea. Good luck with your studies.
Say what? Perhaps you need to go back and read what biologists were saying in the 1950s and 1960s. Your version of the central dogma is idiosyncratic and wrong.
Chaperones do not violate the central dogma.
Alternative splicing does not violate the central dogma.
There are bits of what you wrote that I think you’d find most biologists would agree with, because they’ve been saying them for years. But that nonsense about finding a violation of the central dogma, and then listing phenomena do not refer at all to the fact that information does not flow from protein sequence back into nucleotide sequence, tells me that you really do not have enough respect for the discipline of biology to bother examining what we actually say.
We will agree to disagree then.
PZ Myers decided to tell his minions I am a ‘crank’ based on my detailed model of nutrient-dependent pheromone-controlled epigenetic effects on genome organization in species from microbes to man. Thus, it is appropriate for you to agree to disagree with him, unless you want to be subjected to unceasing attacks from those he has recruited to his blog.
Thank you for bringing biophysical constraints back into what recently became mutation-driven evolution via “constraint-breaking” mutations. Perhaps theorists will now address how mutations lead to species diversity in cases where they do not lead to physical diseases and mental disorders.
The duality of their proposed function(s) still goes far beyond my ability to grasp in the context of biologically-based receptor-mediated cause and effect. But I’m certain that PZ is not going to try to explain anything that, in his world, “just happens.”
Thanks James for the warning!
See others and also:
A single–amino acid change enabled a unicellular pathogen to effect a specific host by disabling an enzyme in the host. The tragic result was the Irish Potato Famine. Although no epigenetic effect of a specific nutrient on a specific base pair that conclusively led to a specific amino acid substitution was demonstrated, nutrient-dependent amino acid differences link algae to cell type differentiation in plants (okay, viruses, too). Thus, the atoms to ecosystems approach continues to be based on some speculation, but it is also based on experimental evidence, which comes from others who also have speculated about the thermodynamics of intercellular signaling, which leads to organism level thermoregulation, in species from microbes to man via amino acid substitutions.
Had I known about this excellent work by Annila and Baverstock, which fills in all, or nearly all the required details of biophysical constraints on ecological adaptations, I would probably violated copyright laws by including too much of what they have accurately represented in an already submitted invited review in an attempt to move evolutionary theorists forward into the 21st century.
“Attributing cause and effect to microbes that have somehow mutated and become resistant to antibiotics is pseudoscientific nonsense.”
Well, I think trying to explain all resistence and adaptation with no recourse to mutation is pseudoscientific nonsense too. Anyway, as long your work provides new insight, regardless of what survives later on, I’m all for it.
