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

Energy-dependent physical and biophysical constraints (8)

Summary: The role of vitamin C in the treatment of pain: new insights links what is known about the “superfood” Spirulina (blue-green algae), which is grown in marine and freshwater environments, to the stability of all organized genomes via its biological activities, such as antioxidant, anti-diabetic, cholesterol-controlling and insulin resistance effects. The biological activities are energy-dependent and they link the anti-entropic virucidal energy of sunlight to all biodiversity via the pheromone-controlled physiology of reproduction and microRNAs in plants and animals.
For example, see: Hypothalamic stem cells control ageing speed partly through exosomal miRNAs

Energy-dependent physical and biophysical constraints (7)

7/26/17 Brain’s stem cells slow ageing in mice

…these cells may have a role in regulating the neurons that release a hormone called GnRH, which is secreted by the hypothalamus and is associated with ageing. Imai would also like to know whether the microRNAs from the cells can pass into the bloodstream, which would carry them throughout the body.

I would like to know why Shin-ichiro Imai, who studies ageing at Washington University in St Louis, Missouri, claims to know nothing about food energy-dependent pheromone-controlled RNA-mediated biophysically constrained viral latency, which prevents the degradation of messenger RNA. I expect that anyone who studies aging to learn that the virus-driven degradation of messenger RNA links mutations to all pathology via effects on all cell types in all individuals of all living genera. Perhaps Shin-ichiro Imai, and others who have not learned anything about energy-dependent cell type differentiation can play the game “Cytosis” when it is released in September, 2017. Or, perhaps they all are neo-Darwinian theorists who prefer not to examine any of the experimental evidence that links energy-dependent microRNAs to healthy longevity and virus-driven energy theft to all pathology.

See for 63,127  examples: MicroRNA
See for comparison: The NAD World 2.0: the importance of the inter-tissue communication mediated by NAMPT/NAD+/SIRT1 in mammalian aging and longevity control by Shin-ichiro Imai

See also: 7/27/11 via my Pheromones Research FB page and Pheromones.com
This is very technical, but begins to address the role of pheromones in anti-aging medicine, particularly with regard to neurodegenerative diseases. Pheromones are used to increase neurogenesis in the area of the brain that is responsible for learning and memory.

Jo Rockafellor Is this the stuff you created James?

James Kohl I have nothing to do with the patent, but am responsible for the concept and first linking pheromones, luteinizing hormone, and neurodegenerative disease associated with aging.

Coleen Powell Keep searching for a cure!

7/27/17 James Kohl The cure is treatment with food energy-dependent microRNAs. See:Hypothalamic stem cells control ageing speed partly through exosomal miRNAs. Liberals hate that fact because it refutes their ridiculous theories about the emergence of energy and the evolution of all biodiversity via mutations and natural selection. They would rather watch people like Dick suffer and die prematurely from cancer than admit that they are biologically uninformed science idiots. (idiot: someone with no professional expertise)
Without labeling them, Feynman claimed that liberals were examples of human idiocy. He failed to differentiate between the beliefs of conservatives and liberals, but those differences have become perfectly clear.
Even those who have learned nothing about “The character of Physical Law” understand that all organisms must eat. That is why Feynman complained about the different units that are used to measure the single concept of energy. The energy that sustains life and all biodiversity via the physiology of reproduction comes from food.
Reported by James Kohl on 7/27/14 Study shows epigenetic changes can drive cancer
“Potential applications of this novel mouse model include the testing of targeted epigenetic therapies for prevention and treatment of human cancer.” http://www.jci.org/articles/view/76507
“Our straightforward approach to epigenetic engineering should be useful in testing the causal role of other epigenetic alterations implicated in carcinogenesis, and broadly applicable toward elucidating epigenetic etiology in a wide range of diseases.”
Their straightforward approach confirms that cell type differentiation is nutrient-dependent and pheromone-controlled in species from microbes to man, which refutes any aspect of mutation-initiated natural selection in the context of the evolution of biodiversity.

Ecological variation in the nutrient supply leads to ecological adaptations via the pheromone-controlled physiology of reproduction. Evolutionary theory should have been replaced by biological facts more than 18 years ago. We could have avoided the past 18 years of pseudoscientific nonsense about mutations and cancer and learned more about its origins, prevention, and effective treatments.
7/27/15 Reported by James Kohl
New Technology Lets Scientists Easily Rewrite Living Organisms’ Genetic Code
[For scientists to rewrite the genetic code, they must know how it was created.] 7/22/15 Sexuality is fluid – it’s time to get past ‘born this way’ reported 7/27/15 by James Kohl
[For people to get past the ‘born this way’ pseudoscientific nonsense, they must learn how energy-dependent RNA-mediated cell type differentiation occurs in the context of the nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to humans.] Bacterial Hunger Games reported 7/27/15 by James Kohl
[Survivors find enough food to reproduce in the context of quorum sensing and the weekend resurrection of the bacterial flagellum, which was reported in P. fluorescens.] Go ahead, be sarcastic: Research uncovers creative benefits in using sarcasm when people trust each other reported 7/27/15 by James Kohl
[I’ve tried presenting facts; using examples of top-down causation, and discussing the facts and examples with biologically uninformed science idiots after sarcasm did not work.
Study identifies ‘major player’ in skin cancer genes reported 7/27/15 by James Kohl
[The virus-driven degradation of messenger RNA causes all pathology] Honeybees Show Evidence of Insecticides reported 7/27/15 by James Kohl
[I used the honeybee model organism as an example of nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation in Nutrient-dependent/pheromone-controlled adaptive evolution: a model
CONCLUSION:
An environmental drive evolved from that of nutrient ingestion in unicellular organisms to that of pheromone-controlled socialization in insects. In mammals, food odors and pheromones cause changes in hormones such as LH, which has developmental affects on pheromone-controlled sexual behavior in nutrient-dependent reproductively fit individuals across species of vertebrates.]

Addendum: Environmental drives are food energy-dependent and pheromone-controlled in the context of feedback loops linked from supercoiled DNA to chromosomal rearrangements and all biodiversity. I used the term evolved to get past the ignorance of any potential reviewers who would most likely be theorists. In “The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002) we used the term mutation for the same reason. The editor at Continuum rightfully insisted.

The CRISPR craze: genome editing technologies poised to revolutionize medicine and industry reported 7/27/15 by James Kohl
[The CRISPR craze of using viruses to edit organized genomes is the example of more ignorance in medicine and industry than most people can comprehend.] See also: CRISPR–Cas systems exploit viral DNA injection to establish and maintain adaptive immunity

The acquisition of new spacer sequences from foreign DNA elements, also known as adaptation, is a hallmark of the CRISPR–Cas immune response1.

Any intelligent scientist would ask where the spacer sequences came from and learn that the spacers are food energy-dependent microRNAs that prevent the virus-driven degradation of messenger RNA and all pathology in all genera.
See Energy-dependent physical and biophysical constraints (9) (in prep) for examples of those who might otherwise seem to be intelligent scientists.
 

Cytosis

God's shrinking role in salvation

God’s shrinking role in salvation can temporarily be placed into the context of what serious scientists are reporting for comparison to the claims of pseudoscientists.
See: Quantum Simulation (free download)

It presents several examples of experiments using both density and momentum imaging and quantum gas microscopy to study the motion of atoms in optical lattices.

The energy-dependent motion of atoms must be linked to ecosystems by the physiology of pheromone-controlled reproduction in all living genera. That fact requires extended consideration of helicity, chirality, autophagy, and hydrophobicity in supercoiled DNA
Helicity – the projection of the spin onto the direction of momentum. ie. spin direction depends on direction of motion;
Chirality – not identical to its mirror image, ie. left-handed vs right-handed;
Cool animation of a particle where the Helicity matches the Chirality.

I’m not sure how to start an attempt to finalize ongoing comments on what has been learned during the past century about  energy-dependent RNA-mediated cell type differentiation, which is manifested in the complexity of the animation. I would like to move forward without the redundancy of explaining everything each time a new finding links quantized energy from physics to chemistry and the facts link molecular epigenetics to the biologically-based energy-dependent creation of microRNAs and RNA-mediated cause and effect.
The energy-dependent creation of microRNAs is missing in this representation of energy-dependent internal motion in DNA.
DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid

The internal motions of DNA appear to be governed by strong internal forces arising from being crowded into the small space of the nucleoid.

God’s shrinking role in salvation can be placed into the context of works published by those who fail to link the creation of energy as information to the packed nucleoid via DNA internal motion in the context of the creation of microRNAs.
See for example: microRNA
Everything known to serious scientists about the creation of microRNAs links the sun’s anti-entropic virucidal energy from the solar analemma to representations of the time-space continuum in a Mobius strip and to this solution to the grandfather paradox, which is based on quantum entanglement, which includes quantum entanglement in DNA.
The solution to the grandfather paradox links quantized energy from quantum entanglement to energy-dependent changes in the structure and function of supercoiled DNA, which helps to ensure the survival of individuals and species, but only if the anti-entropic virucidal energy of sunlight was created before anything else.
The creation of quantized energy also must be biophysically constrained by the physiology of reproduction in all living genera.
See: Light Modulates the Biosynthesis and Organization of Cyanobacterial Carbon Fixation Machinery through Photosynthetic Electron Flow, which was reported as: Illuminating the inner ‘machines’ that give bacteria an energy boost
See also: Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes, which was reported as: Nanotechnology reveals hidden depths of bacterial ‘machines’ and subsequently placed into the context of the nonsense touted by theorists on June 8, 2017 as  Revealing the Structure of Bacterial Machines
The structure and function of the bacterial machines depends on the innate ability of the species to find enough food. If an organism fails to find food, it cannot adapt to ecological variation and reproduce in the context of the pheromone-controlled physiology of reproduction. For example, this species finds food that it metabolizes to create a uranium isotope.
See: A new twist on uranium’s origin story, by CSU scientists

…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.

The energy-dependent creation of the isotope exemplifies how the energy of sunlight is biophysically constrained in the context of quantum physics and the physiology of energy-dependent reproduction, which Richard Feynman linked to the creation of the atomic bomb — even though he did not know where the energy in a hydrogen atom came from. I have asked others where the energy came from, but the question has not been answered.
The estimate that the uranium was formed by bacteria 3 million years ago is based on pseudoscientific nonsense touted by neo-Darwinian theorists and “Big Bang” cosmologists. Taken together those who are biologically uninformed are now attempting to separate everything known to serious scientists about the energy-dependent creation of all life on Earth from the quantized energy required for creation and the physiology of reproduction.
If quantized energy is not information, the loss of energy from the sun via thermal entropy could create life and all biodiversity, at least in theory. But who believes in theories that are this ridiculous?
See: Information entropy and thermal entropy: apples and oranges

…the change of information entropy and the related change of thermal entropy can be separated in space and time leading to the break of Brillouin’s negentropy principle. iv) The information entropy can increase without triggering any change of the thermal entropy indicating that information erasure does not necessarily require energy dissipation.
v) There is no case where Landauer’s principle of erasure dissipation is even seemingly valid because erasing of the memory does not yield change in the information entropy. vi) The information entropy can violate the Third Law of Thermodynamics.

When theorists are allowed by others who are biologically uninformed to tout the amount of pseudoscientific nonsense contained in this excerpt (above), everyone who believes that the Laws of Thermodynamics can be violated is an example of what Feynman claimed is a form of human idiocy.

See also, from 2-3 years ago in the science news:

The first ever photograph of light as both a particle and wave 3/2/15

Scientists see ripples of a particle-separating wave in primordial plasma 6/10/15

Scientists find genetic basis of brain networks seen in imaging studies 6/11/15
Cell density remains constant as brain shrinks with age 6/12/15
This Nifty Infographic Is a Great Introduction to Neuroplasticity and Cognitive Therapy
New immunoregulation and biomarker 6/12/15

Cell type stability is receptor-mediated and biophysically constrained.

DNA data explosion lights up the Bronze Age 6/10/15

Quantized energy-dependent amino acid substitutions are still being reported as if they are mutations.

See for comparison: The Molecular Nutrition of Amino Acids and Proteins, 1st Edition

See also: The Ancient Origins of Consciousness: How the Brain Created Experience 3/25/16
See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model 6/14/13 My review is cited in the context of:

12. Plotnick, Dornbos, and Chen (2010). Others who advocate smell-first are Lucia Jacobs (Jacobs, 2012), who says the building of smell maps of environmental space came first and James Kohl (Kohl, 2013), whose model says chemical ecology is the main driver of adaptive evolution.  — p. 263

The concept of smell-first was linked from energy-dependent changes in angstroms to ecosystems in all living genera.
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.

The signal transmission was linked from the physiology of reproduction in soil bacteria to fertility in mammals via changes in the bull sperm microRNAome. See: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
Outside the context of the creation of quantized energy and the de novo creation of genes linked to increasing organismal complexity, there is no need to discuss God’s shrinking role in salvation. You can, instead, link the Stepwise Evolution of a Buried Inhibitor Peptide over 45 My from the de novo evolution of genes and the novel proteins they encode to the innovations that automagically contribute to the diversity of life via The evolution of social behavior in microorganisms.
See also: Metabolism and the evolution of social behavior

…using experimental evolution, we followed the joint evolution of the genome, the metabolome and the social behavior as swarming re-evolved. New variants emerged spontaneously with mutations that reorganized the metabolome and compensated in distinct ways for the disrupted metabolic prudence. These experiments with a unicellular organism provide a detailed view of how metabolism—currency of all physiological processes—can determine the costs and benefits of a social behavior and ultimately influence how an organism behaves towards other organisms of the same species.

Simply put, the quantized energy of the smell-first model of energy-dependent ecological adaptation in species from microbes to humans can be compared to the metabolism-first theory of de novo gene evolution. Both can be compared in the context of the joint evolution of the genome, the metabolome and the evolution of social behavior, which is portrayed as swarming in the bacterium Pseudomonas aeruginosa. The swarming behavior re-evolved in an evolution experiment.
The re-evolved ability to swarm can be compared to the report on the weekend resurrection of the bacterial flagellum in Pseudomonas fluorescens.
See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
The weekend resurrection of the bacterial flagellum suggests that virtually any change in an organized genome can be linked to the pheromone-controlled the physiology of reproduction. If not, the claims about evolution can be linked from the wrong choice of food to the virus-driven degradation of messenger RNA, which links mutations to all pathology. But claims about the virus-driven degradation of messenger RNA are rarely made by theorists.
When the missing information about the virus-driven degradation of messenger RNA is placed into the context of the the solar analemma, a Mobius strip, and the solution to the grandfather paradox, quantum entanglement appears to link all changes in the amount of quantized energy that comes from sunlight to biophysically constrained energy theft and viral latency, which prevents pathology.
For comparison, see: A New RNA Synthesis of Cells: A Possible End of Birth Defects

…an estimation of these two above elements [nitrogen and phosphorus] as a chemical compound leads a human’s birth defect to have the correct amino acid sequence as previously mentioned and then become a normal trait. With the correct calculation of the compound of nitrogen and phosphorous for an unstable RNA messenger, which is traced to a birth defect, a researcher can discover the ideal growth rate for its stability as an RNA messenger and then its end as a birth defect.

The quantized energy-dependent biosynthesis of RNA is food energy-dependent and pheromone-controlled in species from microbes to humans and virus-driven energy theft appears to cause the degradation of messenger RNA, which has been linked to all pathology. The report of the evolutionary resurrection of flagellar motility clearly exemplifies how energy-dependent changes in RNA-mediated amino acid substitutions are linked to survival of the species outside the context of the “magic traits.” The “magic traits” do not link nutrient-dependent pheromone-controlled cell type differentiation to all biodiversity in reports like this one: Magic traits in speciation: ‘magic’ but not rare?
The “magic traits” have been linked to rapid speciation in bacteria and vertebrates
See: Extraordinarily rapid speciation in a marine fish

We evaluated different possible evolutionary scenarios under the approximate Bayesian computation framework and estimate that the speciation process started in allopatry ∼2,400 generations ago, following the colonization of the Baltic by the demersal lineage. This is faster than most known cases of ecological speciation and represents the most rapid event of speciation ever reported for any marine vertebrate.

Reported as:“Evolution on the fast lane—One flounder species became two” May 30, 2017

“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.

Quantum Physics News (see for discussion on this group)
The Quantum Physics News was created by Robert Karl Stonjek, whose atheistic pseudoscientific nonsense is pervasively distributed among several other Facebook groups and yahoo groups. His influence has caused the unnecessary suffering and premature death of millions of people who think God’s shrinking role in salvation can best be viewed in the context of the “magic traits” of neo-Darwinian theorists.
 

Hard Science vs the neo-Darwinian "magic box"

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.

  1. The in vivo structure of biological membranes and evidence for lipid domains
  2. Scientists investigate how the sense of smell works in bacteria
  3. Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits

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.


at futurism.com

See:  Scientists Have an Experiment to See If the Human Mind Is Bound to the Physical World

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.

See also: Engineering RGB color vision into Escherichia coli reported as: Bacterial Photography Goes Technicolor

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.

See for comparison: Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain

Reported as: Living fossil challenges thinking on brain evolution

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.

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

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.

For another example of biogenic metabolic processes, see: Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits

This was reported as: A new twist on uranium’s origin story, by CSU scientists

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.

For comparison, see: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

This was reported as: Evolutionary Rewiring: Strong selective pressure can lead to rapid and reproducible evolution in bacteria

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?

See also: The Binding Sites of miR-619-5p in the mRNAs of Human and Orthologous Genes

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.

For comparison, see: The Emerging View of Aging as a Reversible Epigenetic Process

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 Evolution This 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.

June 14, 2013 Nutrient-dependent/pheromone-controlled adaptive evolution: a model

…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’.

 June 14, 2013 Mutation-Driven Evolution

(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.

 

Cytosis

From E. coli to monkeys and mankind: Theories vs models (2)

Dedicated to Dr. Tom Jordan and Priscilla Jordan on the day of their retirement from the Baptist ministry, May 28, 2017. They always encouraged me to learn more about the “Laws of Biology” and link the Laws from energy as information to all biodiversity on Earth via the physiology of reproduction.

See also: From E. coli to monkeys and mankind: Theories vs models

High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding (5/23/127)

…changes in observed association and dissociation, suggesting the possibility of kinetic and thermodynamic tuning of Cas9 behavior.

Simply put, the technology didn’t work. That’s a problem for CRISPR/Cas9 advocates (see the incessant barrage of CRISPR/Cas9 promotion on the closed FB group CRISPR Cas9).

Advocates will be forced to accept the fact that natural selection for energy-dependent codon optimality has always been the link from ecological variation to ecological adaptation via food odors and pheromones.

Suggesting the possibility of kinetic and thermodynamic tuning is akin to telling all serious scientists that, until now, the innate immune system of bacteria and the CRISPR Cas technology has not been examined inside the context of the Laws of Physics and the Basic Principles of chemistry. The Laws and the Basic Principles must link RNA-mediated protein folding chemistry from the physiology of reproduction to all food energy-dependent pheromone-controlled behavior in species from microbes to humans via amino acid substitutions in supercoiled DNA.
 

That fact separates the serious scientists from the pseudoscientists who have refused to examine other facts about biologically-based biophysically constrained protein folding chemistry. The facts start with the sun’s anti-entropic virucidal energy as information and the energy as information has been linked to all cell type differentiation by these researchers.

See: Mechanism of transmembrane signaling by sensor histidine kinases (5/18/17)

Reported as: Scientists investigate how the sense of smell works in bacteria

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.

My summary of the signalling mechanism, which links subatomic particles to cell type differentiation in all living genera via the sense of smell in bacteria:

The active and inactive signaling states link energy-dependent changes from angstroms to ecosystems via slight variations at the nitrate-binding site. When the ion binds to the sensor, a change in 0.5-1 angstroms (approximately one fifth of the size of the ion itself) causes a change in the protein that links input from the sensor to a change in the output that varies by as much as 7 angstroms.

In the context of what is known about food energy-dependent pheromone-controlled quorum sensing in bacteria, the change in 0.5-1 angstroms can be linked from the changes in 7 angstroms to base pair changes and amino acid substitutions that stabilize the organized genomes of species from E. coli to primates in the context of all energy-dependent interactive ecosystems, which appear to have existed from the dawn of Creation.

For example, the link from energy-dependent changes in angstroms to ecosystems in all vertebrates is mentioned in the title of this published work: The zinc spark is an inorganic signature of human egg activation. 

The spark that links inorganic material to organic life was placed into the context of our 1996 Hormones and Behavior review of RNA-mediated cell type differentiation. See our section on molecular distance in: From Fertilization to Adult Sexual Behavior.

Molecular distance. As measured in centimorgans, human and other species’ male and female chromosomes, including the autosomes, tend to have different lengths in various segments. To some extent, this suggests a correlation with physical distance but instead the differing lengths are based upon rates of recombination; although sections of most female chromosomes are longer than their homologous counterparts in male chromosomes, in some segments of various chromosomes opposite length-difference occurs, with males having larger centimorgan values than females in those regions (Lawrence, Collins, Keats, Hulten, and Morton, 1993; Murray, Buetow, Weber, Ludwigsen, Scherpbier-Heddema, Manion, Quillen, Sheffield, Sunden, and Duyk, 1994; Straub, Speer, Luo, Rojas, Overhauser, Ott, and Gilliam, 1993). While ramifications of these centimorgan sexual dimorphisms are not yet clearly established, in recent years cis- and trans-acting factors contributing to these recombination length differences have been reported for a specific part of the murine major histocompatibility complex (MHC) (Shiroishi, Sagai, Hanzawa, Gotoh, and Moriwaki, 1991).

Simply put, the cited works linked energy-dependent changes from angstroms to ecosystems via the innate immune system of bacteria, which was linked to sex differences in chromosomes. Note the difference between our accurate representation of biophysically constrained energy-dependent chromosomal inheritance and the claims in: Sex chromosome evolution: historical insights and future perspectives

Conclusion:

…a direct experimental test of the steps in sex chromosome evolution constitutes more robust evidence than a comparative study, especially considering the new manipulative possibilities opened up by the CRISPR/Cas9 system [105]. In any case, the field of sex chromosome evolution seems likely to remain active and dynamic for many years to come.

Reported as: Knowledge gap on the origin of sex

The review shows that the significance of ecology has not been sufficiently noted. Therefore, the biologists in Lund call for more research on how the living environment of a population affects the development and evolution of sex chromosomes. This could include factors such as access to food, age variations within a population or the consequences for sex chromosomes when populations that have lived separately meet and mix.

The fact that others still claim that the origin of sex has not already been linked from factors such as access to food, age variations within a population or the consequences for sex chromosomes attests to the ignorance of theorists. The fact that theorists want to attempt to evoke aspects of the CRISPR Cas9 technology in attempts to explain sexual differentiation attests to the ignorance of those who think more research is required to link energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of pheromone-controlled reproduction and chromosomal inheritance.

Energy-dependent changes were linked from angstroms to ecosystems in all living genera in this published work: Structural diversity of supercoiled DNA (10/12/15) and in this parody from 12/10/14.

See also: Origins of Life: A Problem for Physics

The hope is that a theory akin to our other theories in fundamental physics might one day emerge to explain the phenomenon of life, and in turn finally permit solving its origins.

See for comparison: The Chirality Of Life: From Phase Transitions To Astrobiology

A key missing piece is the origin of biomolecular homochirality: permeating almost every life-form on Earth is the presence of exclusively levorotary amino acids and dextrorotary sugars.

Watch as Jeremy England eliminates any discussion of light activated endogenous substrates in the context of microRNAs linked to the energy-dependent creation of exclusively levorotary amino acids and dextrorotary sugars.

A New Physics Theory of Life

You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant.

If another ridiculous theory emerged, will it explain anything outside the context of experimental evidence that links energy as information to biophysically constrained cell type differentiation via the physiology of reproduction in all living genera? For example, what theory might emerge to explain how an infection in the throat is linked to mental disorders in adults.

See: Streptococcal throat infection linked to mental disorders

The researchers found that the risk of any mental disorder was increased for individuals with a positive streptococcal test compared to those without a streptococcal test…

Watch a biologist fail to link physics and chemistry from the strep infection to brain development via the innate immune system and molecular epigenetics as he explains CRISPR at 5 different levels of his ignorance. 5/24/17

 

The speaker is a co-author of: Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis 3/5/15

In all of these experiments, the effect of mutations on primary tumor growth positively correlates with the development of metastases. Our study demonstrates Cas9-based screening as a robust method to systematically assay gene phenotypes in cancer evolution in vivo.

Reported as: In vivo CRISPR-Cas9 screen sheds light on cancer metastasis and tumor evolution

The results highlighted some well-known tumor suppressor genes in human cancer, including Pten, Cdkn2a, and Nf2, but included some genes not previously linked to cancer. Unexpectedly, the screen also implicated several microRNAs — small RNA segments that are functional in the cell.

Neville E Sanjana, has now linked his ignorance from 2015 to assays that link energy-dependent microRNAs to healthy longevity or from virus-driven energy theft to all pathology. Kaveli Kull attests to the fact about what loser must do, when facts replace their ridiculous theories about genome editing.

Kalevi Kull: Censorship & Royal Society Evo Event

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

Anyone who has tried to explain what humans are made of without linking energy from the light activated endogenous substrate that links ATP to the creation of RNA via microRNAs in the context of what is now being referred to as endogenous RNA interference may not recognize how desperate evolutionary theorists have become in their attempt to make others think that all neo-Darwinian theorists are not losers.

See (link opens .pdf) Participation of glycolysis, and the citric acid cycle, in nuclear adenosine triphosphate synthesis (1963)

…thymus nuclei appear to have an endogenous substrate, and some experiments are presented which suggest that this substrate is probably not glycogen or glucose.

See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

Isolated thymus nuclei transport amino acids into an intranuclear pool by a process which seems to depend on energy from nuclear ATP synthesis (20).

fruit-dove

Food energy-dependent epigenetic adaptation (3)

Food energy-dependent epigenetic adaptation (2)

On 5/24/17 I attempted to post this to the ISHE’s human ethology group in response to the post on How concepts of God have developed: God’s shrinking role. God’s survival. Conclusions.

For comparison, see the expanding role of anti-entropic virucidal energy that theorists claim automagically emerged to sustain all evolved biodiversity.

I included a link to:


I also included a link to:

The moderator of the group responded quickly: Jay R. Feierman wrote:

What you are posting has nothing to do with the thread article.

See also: 7/25/13
Jay R. Feierman:

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution. 

My summary of past interactions with Jay R. Feierman:

He refuses to accept the fact that conditions of life are energy-dependent. He refuses to accept the fact that other biologically uninformed science idiots and many anonymous fools have consistently removed Darwin’s ‘conditions of life’ and replaced them with ridiculous theories about mutations and evolution.

At a conference we both attended in 1995, Jay R. Feierman was the first to challenge the entirety of the model I presented with the question “What about birds?”

He has continued to prevent dissemination of accurate representations of energy-dependent biologically-based cause and effect since then. He exemplifies the impact that one biologically uninformed science idiot can have across an entire generation of unsuspecting anonymous fools who are likely to believe that the creation of energy has nothing to do with the claims in: How concepts of God have developed: God’s shrinking role. God’s survival. Conclusions.

See also: The general form of Hamilton’s rule makes no predictions and cannot be tested empirically

Hamilton’s rule asserts that a trait is favored by natural selection if the benefit to others, B, multiplied by relatedness, R, exceeds the cost to self, C. Specifically, Hamilton’s rule states that the change in average trait value in a population is proportional to BR−C. This rule is commonly believed to be a natural law making important predictions in biology, and its influence has spread from evolutionary biology to other fields including the social sciences. Whereas many feel that Hamilton’s rule provides valuable intuition, there is disagreement even among experts as to how the quantities B, R, and C should be defined for a given system. Here, we investigate a widely endorsed formulation of Hamilton’s rule, which is said to be as general as natural selection itself. We show that, in this formulation, Hamilton’s rule does not make predictions and cannot be tested empirically. It turns out that the parameters B and C depend on the change in average trait value and therefore cannot predict that change. In this formulation, which has been called “exact and general” by its proponents, Hamilton’s rule can “predict” only the data that have already been given.

Simply put, the authors attest to the fact that every aspect that has ever been included in mathematical models of natural selection cannot link natural selection to anything that could not be predicted by what is known about how food energy must be linked from ecological variation to ecological adaptation by the sense of smell in all living genera. The sense of smell predictably links what is known about natural selection for energy-dependent codon optimality to biophysically constrained viral latency via publication in 2005 of Feedback loops link odor and pheromone signaling with reproduction.

There has never been any experimental evidence of biologically based cause and effect that link anything but olfaction, food odor, and pheromones directly to the survival of all species. Yet Feierman’s claim continues to be echoed in the claims of all others who are biologically uninformed:

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. — Jay R. Feierman

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.

 

Alternative splicing of pre-mRNA

Food energy-dependent epigenetic adaptation (2)

Due to the overwhelming support for my model of top-down causation and all energy-dependent biophysically constrained biodiversity on Earth, I will replace
Food energy-dependent epigenetic adaptation (2)
with the more appropriately titled
God’s shrinking role in your salvation
See: Food energy-dependent epigenetic adaptation
and God’s shrinking role in your salvation (in prep)
before proceeding to the rest of this series on epigenetic adaptation.
 

fruit-dove

Food energy-dependent epigenetic adaptation

Mechanism of transmembrane signaling by sensor histidine kinases, was reported as Scientists investigate how the sense of smell works in bacteria

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

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.

See for example: Structural Dynamics and Mechanochemical Coupling in DNA Gyrase

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.

Here’s an example of how the “Laws of Biology’ are linked to energy-dependent ecological adaptation: Genome-wide DNA methylation profiling reveals epigenetic adaptation of stickleback to marine and freshwater conditions

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 fact that synthetic amino acids have been used to create vaccines that may prevent all pathology, links current technology and teleology to pattern recognition across all species that must find food to reproduce.
See: Generation of influenza A viruses as live but replication-incompetent virus vaccines, which was reported as: Engineered virus has artificial amino acid allowing it to serve as a vaccine
See also: A semisynthetic organism engineered for the stable expansion of the genetic alphabet, which was reported as: Scientists create first stable semisynthetic organism

“We can now get the light of life to stay on,” said Romesberg. “That suggests that all of life’s processes can be subject to manipulation.”

If all of life’s processes were not energy-dependent, the processes could not be manipulated by light in the context of Dobzhansky’s claims in Nothing in Biology Makes Any Sense Except in the Light of Evolution.

…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:

Drugs which affect bacteria’s “sense of smell” could potentially be used as substitutes for modern antibiotics. They do not kill bacteria; they simply give them signals that render them harmless to the human body. In theory, in this case it would be impossible for resistance to be developed.

See also:
Bacterial Quorum-Sensing Network Architectures
Social Evolution Selects for Redundancy in Bacterial Quorum Sensing
Killing by Type VI secretion drives genetic phase separation and correlates with increased cooperation
Unfortunately for you and all your dying or deceased loved ones, mathematical model of evolution failed to link nutrient energy-dependent pheromone-controlled ecological adaptations in all genera to healthy longevity. Fortunately, the creation of vaccines via substitutions with artificial amino acids attests to the fact that all of life’s processes are energy-dependent. That may be sufficient proof that RNA-mediated amino acid substitutions protect supercoiled DNA from virus-driven energy theft and the degradation of messenger RNA, which links mutations to all pathology. If not, there will be more proof each day.
See: microRNA
Earlier today, this appeared on my alert. The evolutionary origin of plant and animal microRNAs
The idea that microRNAs automagically evolved appears to be linked to the foolishness of theories that tried to link mutations from natural selection to evolution.  For comparison, see: Genome-wide discovery of viral microRNAs based on phylogenetic analysis and structural evolution of various human papillomavirus subtypes

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.

See also: viral microRNA
For example: Presence of Viral microRNA in Extracellular Environments

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).

See also: Modified mRNA Vaccines Protect against Zika Virus Infection, which was reported as: More evidence that Zika mRNA vaccines can stop viral replication in mice
The potential for side effects of the vaccines can be evaluated in the same context as the potential for detrimental uncontrolled ecological adaptation of viruses that could be caused by the CRISPR Cas9 gene-editing technology.
See: Obama Advisers Urge Action Against CRISPR Bioterror Threat 

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.

See: “This is not a secret meeting” – George Church 29 Jun 2016
See: George Church refutes theistic evolution 9 Feb 2017
See also: A scientist named George Church has a wild idea to upend evolution — here’s what you should know about him

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.

For review see: Virus-driven energy theft Archives and RNA directed DNA methylation Archives
Finally see: The phylogenetic utility and functional constraint of microRNA flanking sequences (2015) reported as: All in the (bigger) family
My comment: 

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.
Cytosis

Energy-dependent epigenetic translation to mRNA stability (6)

See: Energy-dependent epigenetic translation to mRNA stability (5)
Five energy-dependent amino acid substitutions are linked to differences in RNA content and biodiversity in 4 mammalian species.
Excerpt:

Species- and tissue-specific variation in mt-tRNA incorporation into the mt-LSU was analyzed….  Analysis of porcine dermal fibroblasts (C), human osteosarcoma 143B cells (D), bovine cardiac tissue (E), and rat hepatic tissue (F) depicts the relative abundance of each mt-tRNA across fractions (ImageQuant software); represented as a percentage of the total signal.

In my model, the metabolism of food to pheromones controls species specific and tissue specific variation in food energy-dependent mitochondrial transfer RNA (mt-tRNA) and the transgenerational epigenetic inheritance of morphological and behavioral phenotypes. In all models of biologically based cause and effect, the “RNA world” must be linked by metabolism to the pheromone-controlled fixation of RNA-mediated amino acid substitutions in supercoiled DNA. That is how the RNA world is linked from chromosomal rearrangements to energy-dependent RNA-mediated chromosomal inheritance and to protection from virus-driven energy theft, which links mutations to all pathology in species from microbes to humans.
See:  Nutrient-dependent/pheromone-controlled adaptive evolution: a model (published 2013 Jun 14)
My model of “ecological adaptation” was placed into the context of “adaptive evolution” because many theorists do not seem to understand why serious scientists do not believe in “Big Bang” cosmology or neo-Darwinian pseudoscientific nonsense about Mutation-Driven Evolution (also published 2013 Jun 14)
Anyone who tries to tell a theorist that no experimental evidence of biologically-based cause and effect supports their theories about mutation-driven evolution is not likely to see their work get past peer-review. And, when the threat to their ridiculous theories becomes known, theorists are more likely to accept criticisms of a model — even in the absence of a comparable model.
During the past 4 years, there has been no scientific support for neo-Darwinian theories and overwhelming support for the model of food energy-dependent amino acid substitutions and Darwin’s claims about “conditions of life.”
See for instance: Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization (published 2017 May 20)

…initiator-tRNA species proposed to participate in SOS reside in the cell nucleus, are found associated with supraspliceosomes (Table 2c), and appear not to be charged with an amino acid [87].

See also: Human mitochondrial ribosomes can switch their structural RNA composition

Our data demonstrate that only mt-tRNAVal or mt-tRNAPhe are found in the mitoribosomes of five different mammals, each mammal favors the same mt-tRNA in all tissue types, and strikingly, when steady-state levels of mt-tRNAVal are reduced, human mitoribosome biogenesis displays an adaptive response by switching to the incorporation of mt-tRNAPhe to generate translationally competent machinery.

The switches are food energy-dependent and they obviously link ecological variation to ecological adaptation via the Laws of Physics and basic principles of chemistry. In my model, for example, light-induced changes in hydrogen-atom transfer in DNA base pairs in solution cause initiator-transfer RNAs in the nucleus to become charged with an amino acid. Light energy-as-information subsequently appears to biophysically constrain all conditions of life in all living genera by protecting organized genomes from virus-driven energy theft and genomic entropy.
The link from quantum physics via electron resonance to quantum souls is clearer than it has ever been.
See: Electron resonance pervades the brain

Using molecular modeling, the US-Canadian team of Travis Craddock, Stuart Hameroff and Jack Tuszynski had previously shown anesthetic binding in ‘quantum channels’, non-polar arrays of amino acid pi resonance clouds, winding through microtubules.

See also: What is life when it is not protected from virus driven entropy
and
Energy as information and constrained endogenous RNA interference
An endogenous substrate was linked from the biosynthesis of RNA to endogenous RNA interference in this full text .pdf from 1963: PARTICIPATION. OF GLYCOLYSIS. AND THE CITRIC ACID CYCLE. IN NUCLEAR ADENOSINE TRIPHOSPHATE SYNTHESIS

…thymus nuclei appear to have an endogenous substrate, and some experiments are presented which suggest that this substrate is probably not glycogen or glucose.

I do not know any pseudoscientist who has linked the energy-dependent creation of nucleic acid precursors to the energy-dependent creation of new genes, or to the activation of genes via the endogenous substrate. Indeed, the fact that there is an endogeneous substrate has been ignored, unless it has been replaced by an alternative fact which was somehow linked to all biodiversity via the physiology of reproduction.
See for comparison: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”
Excerpt:

 …Isolated thymus nuclei transport amino acids into an intranuclear pool by a process which seems to depend on energy from nuclear ATP synthesis (20).

See for comparison: A scientist named George Church has a wild idea to upend evolution — here’s what you should know about him

Darwin explained how species evolve. Church wants to turbocharge that process by putting new genes into organisms rather than waiting around for them to evolve those genes on their own.

Darwin did not explain how species evolve. Darwin presciently linked natural selection for food energy-dependent codon optimality to RNA-mediated amino acid substitutions and the physiology of reproduction, which biophysically constrains the hecatombic evolution of all pathology. Nothing known to serious scientists suggests that new genes “evolve.”

In between tRNA and CRISPR, Church coauthored hundreds of scientific papers, from “Predicting regulons and their cis-regulatory motifs by comparative genomics” to “Characterization of Cas9-guide RNA orthologs.”

After he characterized naturally occurring energy-dependent changes in RNA orthologs, George Church refuted neo-Darwinian evolutionary theories when he and others filed this patent application. RNA-Guided Human Genome Engineering

FIG. 3A-1 and FIG. 3A-2 depict a human codon-optimized version of the Cas9 protein and full sequence of the cas9 gene insert.

Human codon-optimized changes in proteins are energy-dependent, RNA-mediated, and the changes are biophysically constrained by the food that organisms eat and the physiology of reproduction in all living genera. That fact was placed into the context of the Structural diversity of supercoiled DNA in the context of this review: Feedback loops link odor and pheromone signaling with reproduction
The review was co-authored by 2004 Nobel Laureate, Linda Buck who helped to link the sun’s anti-entropic virucidal energy to biophysically constrained cause and effect in all species that need to eat to reproduce. Richard Feynman may have been one of many others who also did that.

Richard Feynman was a Nobel prize winning Theoretical Physicist who popularized physics with his entertaining lecture style. This snippet is taken from one of his lectures in the series “The character of Physical Law” where he complains about all the different units that are used to measure the single concept of Energy.

See for comparison: George Church refutes theistic evolution

The future of genetic codes and BRAIN codes (video)

My comment on the video: Biophysically constrained genetic codes are brain codes. They link the epigenetic landscape to the physical landscape of supercoiled DNA via metabolic networks, which link energy as information to all cell type differentiation in all individuals of all living genera.

Virus-driven energy theft is linked from “gene vandalism” to epigenetically effected nutrient energy-as-information dependent RNA-mediated DNA repair.

Synthesis of nucleic acids became a “bigger deal” when Sutherland’s group showed that ultraviolet light was linked to the simultaneous de novo creation of nucleic acid precursors, which are the starting materials needed to make natural amino acids and lipids.

See also: Peter Godfrey Smith: “Other Minds: The Octopus, the Sea, and the Deep Origins…”

See for comparison:
Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge.” — Kalevi Kull
In this case, Anna Di Cosmo’s group already linked what is known about the physiology of pheromone-controlled reproduction from the gut bacteria of the octopus to the nutrient energy-dependent pheromone-controlled physiology of reproduction of the octopus. See: 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).

Her group also linked the conserved molecular mechanisms of chemical perception and gene expression in flies to consciousness in octopuses. See: Dose-Dependent Effects of the Clinical Anesthetic Isoflurane on Octopus vulgaris: A Contribution to Cephalopod Welfare via my model, albeit without citation to: Nutrient-dependent/pheromone-controlled adaptive evolution: a model or citation to Electron spin changes during general anesthesia in Drosophila.
Without an energy-dependent change in electron spin, the findings that link virus-driven energy theft to all pathology cannot be linked from cryo-EM to the biophysically constrained changes that link angstroms to ecosystems in all living genera. None of the claims that Richard Feynman made about energy, including his claims about food energy, can be linked from quantum physics to chemistry and biologically-based cause and effect via the physiology of reproduction.
Until recently, I thought that Eugene Koonin was prepared to challenge the nonsense about evolution. No other theorists seem to be willing to address the facts about energy-dependent increasing organismal complexity.
See: Riding the Evolution Paradigm Shift With Eugene Koonin

The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…

Virus-driven energy theft links the degradation of messenger RNA to all pathology, which is biophysically constrained by conserved molecular mechanisms that link food energy from viral latency to all energy-dependent healthy longevity.
Watch for Koonin and other theorists to use experimental evidence of biologically-based cause and effect to eliminate the pseudoscientific nonsense about evolution touted by those who still know nothing about virus-driven pathology manifested in Alzheimer’s and other neurodegenerative diseases. Alternatively, watch for Koonin and other theorists to continue playing their evolution game until everyone who is more than one decade old learns to play this game:

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

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

See for comparison: How Statistics Weakened mRNA’s Predictive Power

More than 60,000 published works link food from energy-dependent changes in the microRNA/messenger RNA balance to differences in amino acid substitutions in mitochondrial transfer RNA (mt-tRNA).

The amino acid substitutions in different mammals appear to protect the mitochondria from virus-driven energy theft, which links the degradation of messenger RNA from mutations to all pathology.

The link from mt-tRNA to healthy longevity via species- and tissue-specific variation in the structure and function of supercoiled DNA may limit further consideration of neo-Darwinian theories because there is nothing to suggest that supercoiled DNA automagically evolved.

See for example: Figure 1

Species- and tissue-specific variation in mt-tRNA incorporation into the mt-LSU was analyzed….  Analysis of porcine dermal fibroblasts (C), human osteosarcoma 143B cells (D), bovine cardiac tissue (E), and rat hepatic tissue (F) depicts the relative abundance of each mt-tRNA across fractions (ImageQuant software); represented as a percentage of the total signal.

See also: Noncoding RNA Helps Cells Recover from DNA Damage

There is clear evidence that femtosecond blasts of UV light repair DNA in the context of energy-dependent changes in the microRNA/messenger RNA balance and autophagy, which protects all organized genomes from virus-driven energy theft and the degradation of messenger RNA.
The failure to integrate the Nobel Prize winning works of Ben Feringa (Chemisty 2016) and Yoshinori Ohsumi (Physiology or Medicine 2016) prevents theorists from linking what organisms eat to their pheromone-controlled physiology of reproduction in the context of Schrodinger’s claims in “What is Life?”(1944) and this claim by Roger Penrose in the reprint edition:

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)

See also: From Fertilization to Adult Sexual Behavior  In our section on molecular epigenetics, we wrote:

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans…

The food energy that is linked from alternative splicing techniques of pre-mRNA to the chemistry of protein folding and the pheromone-controlled physiology of reproduction in all living genera seems to be largely ignored by those who are not Nobel Laureates.

 

Amino acid modification FA_Epigenetics_Table1

Energy-dependent epigenetic translation to mRNA stability (4)

See first: Energy-dependent epigenetic translation to mRNA stability (3)
First-ever direct observation of chiral currents in quantum Hall atomic simulation

The report on the simulation fails to address the facts about what happens at the level of hydrogen-atom transfer in DNA base pairs in solution when you have an MRI. Perhaps the link from chirality to autophagy and all cell type differentiation in all living genera is not obvious.
 

See: Magnetic resonance imaging

MRI is based upon the science of nuclear magnetic resonance (NMR). Certain atomic nuclei can absorb and emit radio frequency energy when placed in an external magnetic field. In clinical and research MRI, hydrogen atoms are most-often used to generate a detectable radio-frequency signal that is received by antennas in close proximity to the anatomy being examined. Hydrogen atoms exist naturally in people and other biological organisms in abundance, particularly in water and fat. For this reason, most MRI scans essentially map the location of water and fat in the body. Pulses of radio waves excite the nuclear spin energy transition, and magnetic field gradients localize the signal in space. By varying the parameters of the pulse sequence, different contrasts can be generated between tissues based on the relaxation properties of the hydrogen atoms therein.

For comparison, see: Affective Neuroscience with Jaak Panksepp (BSP 65)

1 page 7

My feeling is that the social brain has many levels. If you don’t understand the foundational level, then you can do brain imaging until you’re blue in the face, but you still will not understand the process at a deep causal level.

If you understand the fact that quantized energy must be linked from the anti-entropic virucidal energy of sunlight to diagnostic testing by what is known to serious scientists about the effects of energy on hydrogen-atom transfer in DNA base pairs in solution, you may understand how frustrating it is to see people report pseudoscientific nonsense like this:

The Life of A Thought in the Brain and this: ‘Humanlike’ ways of thinking evolved 1.8 million years ago, suggests new study

See also: MicroRNA GnRH

I urge others who are interested in learning more about energy-dependent endogenous RNA interference and biophysically constrained viral latency to search for the term microRNA and the form of pathology that links the failure of RNA-mediated protein folding chemistry to the disease. You can be as specific or as general as you wish and you will still find that the energy-dependent creation of G protein-coupled receptors, enzymes, hormones et al., must be linked from ecological variation to ecological adaptation by the physiology of reproduction. That fact refutes the pseudoscientific basis for the CRISPR threat to humanity.

See for comparison the never ending nonsense touted by theorists who know nothing about mRNA stability:

Evolution by Gene Duplication

Emergence and evolution of an interaction between intrinsically disordered proteins

ModelFinder: fast model selection for accurate phylogenetic estimates

Other Minds: The Octopus, the Sea, and the Deep Origins...

Novel approach to study the perception of animacy in dogs

We suggest that dogs spontaneously recognized the chasing-like pattern and thus they may have considered the interacting partners as animate agents. This methodological approach may be useful to test perceptual animacy in other non-human species.

rp_tumblr_ngykp0yfND1r5gzz6o1_500.jpg

Energy-dependent epigenetic translation to mRNA stability (3)

Energy-dependent epigenetic translation to mRNA stability (2)

Energy-dependent epigenetic translation to mRNA stability (2)


See for comparison this treatise on climate change packaged as information on the evolution of a flying snake.
Fossil ‘winged serpent’ is a new species of ancient snake

At the time that Zilantophis dwelled there, the site was a sinkhole surrounded by forest, attracting a variety of animals. The local fauna included ancient representatives of familiar North American creatures such as bears, beavers and salamanders. Others were more exotic, including unique species of rhinoceros, alligator and the site’s famous red panda.

“This is a time when the world was moving in the direction of a modern climate and modern fauna,” Jasinski said.

For information on the evolution of the flying snake’s behavior see Robert Sapolsky: The biology of our best and worst selves

How can humans be so compassionate and altruistic — and also so brutal and violent? To understand why we do what we do, neuroscientist Robert Sapolsky looks at extreme context, examining actions on timescales from seconds to millions of years before they occurred. In this fascinating talk, he shares his cutting edge research into the biology that drives our worst and best behaviors.

I did not learn anything about cutting edge research from this TED talk. I learned that Robert Sapolsky believes in the evolution of human behavior. That surprised me because Robert Sapolsky is one of the most famous students of Bruce McEwen, who linked a single amino acid substitution (BDNF Val66Met) from nutrient energy-dependent biophysically constrained biologically-based top-down causation to behavior in the dramatically different pheromone-controlled ecosystems of mice and humans.
See: Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity

in unstressed mice with a BDNF loss-of-function allele (BDNF Val66Met), we show that the epigenetic activator of histone acetylation, P300, plays a pivotal role in the dynamic up- and down-regulation of mGlu2 in hippocampus via histone-3-lysine-27-acetylation (H3K27Ac) when acute stressors are applied. These hippocampal responses reveal a window of epigenetic plasticity that may be useful for treatment of disorders in which glutamatergic transmission is dysregulated.

See also: Correction for McEwen, Brain on stress: How the social environment gets under the skin

The authors note that on page 17184, right column, first paragraph, line 4, “effect” should instead appear as “affect.”

Until Robert Sapolsky helps others to make sense of how the energy-dependent pheromone-controlled de novo creation of olfactory receptor genes is linked to differences in epigenetic effects that link sensory stimuli from hormones to the affects of hormones on animal behavior, his lectures will be of little use to those who study the biology of behavior.
In all vertebrates, the study of behavior begins with the epigenetic effects of food odors and pheromones on gene activation that link changes in microRNAs from gonadotropin releasing hormone to the physiology of reproduction. In the early 90’s, Bruce McEwen told me that my model of biologically-based cause and effect could not be validated unless I found experimental evidence that could be linked to gene activation in gonadotropin releasing hormone (GnRH) neurosecretory neurons.
The late Robert L. Moss provided preprints from his group that now link everything known about energy-dependent RNA-mediated cell type differentiation in all vertebrates to the pheromone-controlled physiology of reproduction in mice and in humans via amino acid substitutions.
The early gene expression of cFos has since linked the Fos protein to proof of the concept that links food odors and pheromones to all receptor-mediated behavior in all living genera via what is known about vertebrate GnRH.
See: Induction of FOS immunoreactivity in central accessory olfactory structures of the female rat following exposure to conspecific males
See: A hypothalamic circuit that controls body temperature

…we used cFos staining to identify neurons that are activated by a thermal challenge and found induced expression in subsets of neurons…

See: Researchers discover neuronal targets that restore movement in Parkinson’s disease model

The research group used optogenetics, a technique that turns genetically tagged cells on and off with light.

See also: Hypothalamic microRNAs flip the switch for fertility
See also our section on molecular epigenetics in: From Fertilization to Adult Sexual Behavior
More than 60,000 published works on microRNAs link cutting edge research to energy-dependent healthy longevity or from virus-driven energy theft and the degradation of messenger RNA to all pathology. Who is discussing that fact?
See for comparison: Behave: Why do we do the things we do?

Over a decade in the making, this game-changing book is Robert Sapolsky’s genre-shattering attempt to answer that question as fully as perhaps only he could, looking at it from every angle. Sapolsky’s storytelling concept is delightful but it also has a powerful intrinsic logic: he starts by looking at the factors that bear on a person’s reaction in the precise moment a behavior occurs, and then hops back in time from there, in stages, ultimately ending up at the deep history of our species and its genetic inheritance.

And so the first category of explanation is the neurobiological one. What goes on in a person’s brain a second before the behavior happens? Then he pulls out to a slightly larger field of vision, a little earlier in time: What sight, sound, or smell triggers the nervous system to produce that behavior? And then, what hormones act hours to days earlier to change how responsive that individual is to the stimuli which trigger the nervous system? By now, he has increased our field of vision so that we are thinking about neurobiology and the sensory world of our environment and endocrinology in trying to explain what happened.

Sapolsky keeps going–next to what features of the environment affected that person’s brain, and then back to the childhood of the individual, and then to their genetic makeup. Finally, he expands the view to encompass factors larger than that one individual. How culture has shaped that individual’s group, what ecological factors helped shape that culture, and on and on, back to evolutionary factors thousands and even millions of years old.

The result is one of the most dazzling tours de horizon of the science of human behavior ever attempted, a majestic synthesis that harvests cutting-edge research across a range of disciplines to provide a subtle and nuanced perspective on why we ultimately do the things we do…for good and for ill. Sapolsky builds on this understanding to wrestle with some of our deepest and thorniest questions relating to tribalism and xenophobia, hierarchy and competition, morality and free will, and war and peace. Wise, humane, often very funny, Behave is a towering achievement, powerfully humanizing, and downright heroic in its own right.

See also: CRISPR kills HIV and eats Zika ‘like Pac-man’. Its next target? Cancer

Researchers paired proteins with a process that amplifies RNA which could be used to detect cancer cells

One of the most fascinating things that I have repeatedly encountered is the failure to link CRISPR from the nutrient-dependent pheromone-controlled physiology of reproduction to the biophysically constrained viral latency that links ecological variation to ecological adaptation via natural selection for energy-dependent codon optimality in all living genera.
It’s as if the gene-editing technology could not be understood in the context of femtosecond blasts of virucidal UV light and RNA-mediated DNA repair, which has been linked to the prevention of all pathology until stress overwhelms the immune system.