An evolutionary theory killer

How to create biologically uninformed theorists

Summary: On March 2, 2018, Philip C. Ball and Nick Lane started making claims about proton gradients. Their claims are based on my model of quantized energy as information. This post includes added support for what is known to all serious scientists about the light-activated endogenous substrates that link molecular epigenetics to RNA-mediated autophagy.
See first: Energy as information and constrained endogenous RNA interference (audio/visual aid 2017)

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy.

The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.

This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes.

For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

Added support for the light-activated molecular epigenetics of autophagy:
Light-powering Escherichia coli with proteorhodopsin (2007)

…we quantify the coupling between light-driven and respiratory proton currents… and show that light-driven pumping by PR can fully replace respiration as a cellular energy source in some environmental conditions.

Structure of the Deactive State of Mammalian Respiratory Complex I (2018)

…the deactive state arises when critical structural elements that form the ubiquinone-binding site become disordered, and we propose reactivation is induced when substrate binding to the NADH-reduced enzyme templates their reordering. Our structure both rationalizes biochemical data on the deactive state and offers new insights into its physiological and cellular roles.

Global collective motions in the mammalian and bacterial respiratory complex I (2018)

…we identify here transitions between experimentally resolved structures of the mammalian complex I as low-frequency collective motions of the enzyme, highlighting similarities and differences between the bacterial and mammalian enzymes. Despite the reduced complexity of the smaller bacterial enzyme, our results suggest that the global dynamics of complex I is overall conserved.

The conservation of light-powered functional structures and energy-dependent proton gradients link the deactive state in critical structures to the active state via the creation of enzymes in species from bacteria to mammals. The energy-dependent creation of the enzymes links metabolism of the energy (e.g., food energy) from pheromones to biophysically constrained viral latency in the context of the physiology of reproduction.
The pheromone-controlled physiology of reproduction in species from microbes to humans links our visual perception of energy and mass in the context of how ecological variation must be linked to energy-dependent ecological adaptations in all living genera.
See: Olfaction Warps Visual Time Perception

Our perception of the world builds upon dynamic inputs from multiple senses with different temporal resolutions, and is threaded with the passing of subjective time. How time is extracted from multisensory inputs is scantly known. Utilizing psychophysical testing and electroencephalography, we show in healthy human adults that odors modulate object visibility around critical flicker-fusion frequency (CFF)-the limit at which chromatic flickers become perceived as a stable color-and effectively alter CFF in a congruency-based manner, despite that they afford no clear environmental temporal information. The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity. These findings point to a neuronal network in the right temporal cortex that executes flexible temporal filtering of upstream visual inputs based on olfactory information. Moreover, they collectively indicate that the very process of sensory integration at the stage of object processing twists time perception, hence casting new insights into the neural timing of multisensory events.

See also: Odors Alter Subjective Time Experience Author: Dr. ZHOU Wen’s Research Group Update time: 2017/05/15

The brain is not a timepiece. Whereas it is equipped with senses like vision, audition, touch, smell, and taste, it has no direct access to or measure of the physical time (unless you read from a clock). Rather, it constructs the subjective “time” of an event from the dynamic multisensory inputs associated with that event. Yet different senses come with different temporal precisions. For instance, when standing near an apple tree, you can detect the falling of an apple much better with your eyes or ears than the nose. How does the brain coordinate multisensory signals entering different brain regions with different temporal resolutions, and come up with the subjective time?

A team at the Institute of Psychology at Chinese Academy of Sciences tackled this issue using odors and images. Specifically, Dr. Bin Zhou, the study’s lead author, and his colleagues examined whether odors could modulate one’s temporal sampling and subjective duration of visual objects. In their study, participants viewed two series of flickering isoluminant images in red and green (Figure 1A). One of the series contained opposite images of an apple or bananas; the other contained only images of red and green fields. When the images alternated at a frequency beyond 20 Hz, the participants started to have difficulty reporting which series contained an object. Indeed, for most people, chromatic flicker fusion frequency (CFF), the limit at which alternating colors become perceived as a stable fused color, falls somewhere between 20 and 25 Hz. Interestingly, the participants’ object detection accuracies around CFF were improved under the exposure of a congruent, as opposed to an incongruent, odor. In other words, the participants detected a rapidly flickering apple better when they smelled an apple odor rather than a banana odor, and vice versa (Figure 1B, left panel). In effect, the presence of a congruent odor facilitated the brain’s temporal sampling of a visual object and elevated its CFF (Figure 1B, right panel). Based on electrical activities recorded from the participants’ scalp, the researchers found that the integration between smell and vision strengthened the signals of the corresponding object in a brain region heavily implicated in object representations called the right temporal cortex, about 150-300 ms after object onset. They further showed that such integration lengthened one’s subjective duration of the corresponding object in a duration comparison task. The researchers concluded that subjective time is warped by the neural energy involved in representing multisensory inputs at subsecond scales.

Until Philip C. Ball mentioned that Nick Lane believed proton gradients came before the energy-dependent creation of RNA, I did not realize how little they knew about this link from differences in the energy of photons to consciousness.
See: What Affective Neuroscience Means for Science Of Consciousness (2013)

The coupling of the two circuits promotes an endogenous feedback that supports conscious processes. Within this framework, we present the defence that detailed study of both affective and cognitive processes, their interactions, as well of their respective brain networks, is necessary for a science of consciousness.

The coupling of the two circuits links differences in the energy of photons from the proton motive force to the light-activated endogenous feedback loops and Feedback loops link odor and pheromone signaling with reproduction.
It is extremely difficult for intelligent people to not link this experimental evidence to biophysically constrained viral latency in the context of reports that claim “Creatures’ Adaptability Begins with Their Sensors.”
But, see for comparison: David Attenborough on creationsim May, 2015

My comment on his nonsense: First steps to neutralizing Zika: How highly potent antibody neutralizes Zika infection discovered

This is framed within the context of energy-dependent changes in pH, which facilitate receptor-mediated entry of nutrients or viruses into specific cell types of species-specific tissues via stress-linked changes in hydrogen-atom transfer in DNA base pairs.

Virus-driven energy theft has been linked to all pathology in all living genera via the conserved molecular mechanisms of RNA-mediated polycombic protein folding chemistry compared to the hecatombic evolution of pathology manifested first in the differences between archaea and bacteria. Admitting that Carl Woese was wrong about the different domains of life is the first step towards understanding the difference between healthy longevity and the evolution of all virus-driven pathology.

Carl Woese was wrong

God did not create the viruses. He created the anti-entropic virucidal energy of sunlight, which protects all organized genomes from virus-driven entropy. Only the choices of our ancestors could have led to the increasing amout of virus-driven pathology during the past ~6000 years that pseudoscientists place into the context of millions of years of evolution. Then, they blame God, like these two pseudoscientists do. Darwin knew they would do that, which is why he insisted that others put conditions of life before natural selection. But they bastardized his theory anyway and taught their revision to anyone who was foolish enough to believe in it. It’s called the “Modern Synthesis” and was based on de Vries 1902 definition of “mutation.”

Celebrate Your Inner Virus

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

It is no wonder that Sir David Attenborough and many others like Philip C. Ball and Nick Lane are confused about the energy-dependent creation of healthy longevity and consciousness. Even some young earth creationists have failed to link the creation of the sun’s anti-entropic virucidal energy from changes in electrons to ecosystems via the proton motive force. That leaves every aspect of creation to be placed back into the context of ridiculous theories. The theories start with the virus-driven theft of quantized energy as information. The energy theft links mutations to all virus-driven pathology. The theft of quantized energy as information cannot be linked by serious scientists from beneficial mutations to the evolution of one species from another.
For comparison, pseudoscientists have no problem touting this confusing nonsense:
Sign of selection on mutation rate modifiers depends on population size (
1)  Genetic variation—the raw material for evolution—is ultimately generated by mutation.
2). …beneficial alleles never become deleterious and deleterious alleles never become beneficial.
Conclusion:

Whether these phenomena can be united in a single theoretical framework remains an open question that we are actively exploring. In any case, our results add to a growing appreciation of nonclassical population size dependence in evolution by natural selection (41, 42).

Funding for research that attempts to link natural selection to evolution via mutation-driven genetic variation should be used to link food odors and pheromones from the physiology of reproduction to biophysically constrained viral latency and ecological adaptations. It is time to stop creating more biologically uninformed theorists.

5th-6th Sept 2018 Dublin, Ireland

Light-activated carbon fixation did not evolve (4)

Summary: Dobzhansky was joking about the time it would take for the creation of light to cause the energy-dependent fixation of RNA-mediated amino acid substitutions, which link food energy to the creation of enyzmes that metabolized food. His joke extends from the creation of sunlight — as the “light of evolution” — to the species-specific pheromone-controlled physiology of reproduction and cell type differentiation in chimpanzees and humans compared to gorillas via one amino acid substitution. The joke was played on theorists who, in 1973, still believed that mutations could be linked to evolution despite the claims in Schroedinger: What is Life? (1944).
See: Light-activated carbon fixation did not evolve (3),(2),(1) and RNA mediated molecular epigenetics and virus driven entropy and The origin of information (2)
For comparison, see: Genome editor CRISPR’s latest trick? Offering a sharper snapshot of activity inside the cell

…this tool can record exposure to light, antibiotics, and viral infection or document internal molecular events.

The “tool” links the anti-entropic virucidal energy of sunlight to the creation of enzymes, which link the metabolism of food energy to the physiology of reproduction in the context of autophagy and viral latency.

The facts about autophagy and biophysically constrained viral latency have been placed into the context of phage-activated continuous evolution (PACE) by people who do not want others to learn the facts about how autophagy protects all organized genome from the virus-driven degradation of messenger RNA.
See: Evolution in Action – Literally

The idea is that you use bacteriophage as your vehicle for evolving proteins, because of their extremely short generation time. These infect E. coli bacteria, and the two of them are modified in this system so that you can use selection pressure to get to a protein with specific binding properties. It’s been used to look at protease inhibitor resistance and DNA-binding specificity, and now it’s put to work for a protein-protein interaction.

All protein-protein interactions are energy-dependent, RNA-mediated and biophysically constrained in the context of the physiology of reproduction and transgenerational epigenetic inheritance.
See for contrast: Church Speaks George Church [2.14.18]

  1. Maybe it would help if the very top scientists believed in neo-Darwinism or something.
  2. We found the enzymes that occur in nature, which was not obvious, and both companies have patents on making those alkanes.

Top scientists who believe in neo-Darwinism are more likely to believe Church’s claim that the anti-entropic energy of sunlight was not the obvious link to the creation of enzymes and all biophysically constrained life on Earth. The creation of enzymes was required to biophysically constrain viral latency.

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

See: Regulation of the unfolded protein response by noncoding RNA
See: Endoplasmic reticulum stress signaling: the microRNA connection
See also: ER homeostasis and autophagy

The endoplasmic reticulum (ER) is a key site for lipid biosynthesis and folding of nascent transmembrane and secretory proteins. These processes are maintained by careful homeostatic control of the environment within the ER lumen. Signalling sensors within the ER detect perturbations within the lumen (ER stress) and employ downstream signalling cascades that engage effector mechanisms to restore homeostasis. The most studied signalling mechanism that the ER employs is the unfolded protein response (UPR), which is known to increase a number of effector mechanisms, including autophagy.

Place the unfolded protein response (UPR) into the context of how virus-driven energy theft links the degradation of messenger RNA from mutations to all pathology. Link femotosecond blasts of ultraviolet light to the creation of enzymes and energy-dependent RNA-mediated DNA repair to complete the picture of creation vs neo-Darwinism.
See: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair
If you are a top scientist who believes in neo-Darwinism, retire as soon as possible to avoid the ridicule that will be linked to the lack of funding for your so-called research.
See also: miRs-103/107 regulate autophagy in the epidermis

We found that antagomir-107 treatment in epidermis: (i) depleted endogenous miR-107; (ii) increased GFP-LC3 puncta in epidermal basal layers of GFP-LC3 transgenic mice, indicative of an accumulation of autophagosomes; (iii) inhibited LC3 turnover and increased p62, suggesting an inhibition of autophagy flux; and (iv) increased phosphorylated dynamin (p-dynamin, an inactive form), a key enzyme in end-stage autophagy. Conversely, miR-107 mimic treatment in mouse epidermis: decreased GFP-LC3 puncta in basal layer as well as p62 protein levels; and diminished p-dynamin, indicative of activation of this enzyme.

See also: CCPG1: A new breed of autophagy cargo receptor: 3:00pm GMT / 10:00am EST / 7:00am PST on Thursday 1st March
The anti-entropic energy-dependent creation of receptors is enzyme-dependent and RNA-mediated in the context of the physiology of reproduction and autophagy, which biophysically constrains viral latency.
The overwhelming complexity prevents most attempts to link quantum physics from quantum chemistry to the molecular mechanisms of epigenetically-effected cancer prevention and treatment. Despite that fact, prevention and effective treatments will continue to link the speed of light on contact with water from hydrogen-atom transfer in DNA base pairs in solution via the creation of microRNAs linked to biophysically constrained viral latency.
Do you remember what Barry J. Marshall did to link H. pylori to prevention of gastric cancer?
See: Neutrons identify critical details in bacterial enzyme implicated in gastric cancer

Ronning’s team focused on H. pylori’s use of a unique biosynthetic pathway to synthesize vitamin K2, which aids in the electron transfer processes, or chemical reactions, of all organisms.

Ronning’s team linked Barry J. Marshall’s energy-dependent changes (e,g., hydrogen-atom transfer in DNA base pairs in solution) from electrons to ecosystems and healthy longevity in all living genera via the physiology of pheromone-controlled reproduction in species from microbes to humans.
I asked the evolutionary theorist, John Hewitt (a so-called science journalist): “Are you still planning to do that by starting with the magical creation of selenocysteine?”
I’ve heard nothing from him, since then.
See also: Is Maternal Food Security a Predictor of Food and Drink Intake Among Toddlers in Oregon? (2012)

CDC Disclaimer: The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention.

The 35-year-old author works as a team lead for the CDC’s Division of Population Health.

Authorities say he called in sick on February 12, 2018 and has not been heard from since.

In 2014 he was the first author of: Sex-specific relationships between adverse childhood experiences and chronic obstructive pulmonary disease in five states

This work adds to a growing body of research suggesting that ACEs may contribute to health problems later in life and suggesting a need for program and policy solutions.

The link from the anti-entropic virucidal energy of sunlight to healthy longevity and the link from stress-induced biophysical constraint-breaking mutations reaffirms that suggestion.
Cunningham’s brother, Anterio Cunningham, does not want to assume the worst, yet he is worried something horrible has happened for him to leave his family and prized job with no notice.
The CDC did not immediately respond to ABC News’ request for comment.

Anyone with information is urged to call 911 or the Atlanta Police Homicide/Adult Missing Persons Unit at 404-546-4235.

The need for program and policy solutions at the CDC could bring the current practice of medicine to an end. The end requires all practitioners to acknowledge the facts about disease control. The facts link the creation of sunlight from fixation of light in cyanobacteria to the physiology of reproduction in humans and to all biodiversity via biophysically constrained viral latency.
See also: Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973)

 I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation.

Dozhansky supposedly assumed that:

Creation is not an event that happened in 4004 B.C.; it is a process that began some 10 billion years ago and is still under way.

But he may also have been joking. He wrote:

…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.

Dobzhansky was joking about the time it would take for the creation of light to cause the energy-dependent fixation of RNA-mediated amino acid substitutions, which link food energy to the creation of enyzmes that metabolized food. His joke extends from the creation of sunlight — as the “light of evolution” — to the species-specific pheromone-controlled physiology of reproduction and cell type differentiation in chimpanzees and humans compared to gorillas via one amino acid substitution. The joke was played on theorists who, in 1973, still believed that mutations could be linked to evolution despite the claims in Schroedinger: What is Life? (1944).
Anyone who places Dobzhansky’s claims from 1964 and the claims of McEwen et al. (1964) into the context of Frohlich’s assertions in 1968 would close the door on evolutionists in three steps.
Dobzhansky compared theorists to bird watchers and butterfly collectors.
McEwen et al., (1964) linked the creation of ATP to the creation of RNA.
Frohlich (1968) linked the creation of RNA to all biophysically constrained biodiversity.
The cell biology game “Cytosis” can be used to teach people like George Church about cell biology. Alternatively, Church could ask a serious scientist what was known about the energy-dependent creation of naturally occurring enzymes.
For comparison, retracted works by Jack Szostak’s group are the only works that might make that fact not obvious (e.g., to other theorists). Serious scientists know that all enzymes naturally occur in the context of their energy-dependent microRNA-mediated creation. If George Church shared Dobzhanky’s creationist beliefs, he might have avoided the shame that comes from his claim that it was not obvious where all naturally occurring enzymes come from.
See: Retraction Watch Also reported as: Oops! Scientific retraction a major blow to evolution theory

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

Jack W. Szostak—a professor of chemistry and chemical biology at Harvard University,  shared the 2009 Nobel Prize in Physiology or Medicine. It seems likely that he influenced the works by George Church — also at Harvard, and the claims Church made about the “not obvious” creation of naturally created enzymes.
See for comparison: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
Reported as: Researchers may have solved origin-of-life conundrum

…the conditions that produce nucleic acid precursors also create the starting materials needed to make natural amino acids and lipids. That suggests a single set of [light activated] reactions could have given rise to most of life’s building blocks simultaneously.

The difference between George Church’s neo-Darwinian approach, and the approach that serious scientists have taken, may be as simple as the difference between a creationist and an evolutionary theorist.
 
For comparison, see: What is life when it is not protected from virus driven entropy Published on 30 Mar 2016

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

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

Elsevier fails to support the concept of autophagy

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Nature vs Science and Autophagy.pro

Conclusion: The anti-entropic virucidal energy of sunlight links food energy directly from the innate immune system to all morphological and behavioral diversity. It all about energy. It’s all about the creation of enzymes. It’s all about the base pairs.


Until the day that I launched Autophagy.pro, I had only one or two Facebook posts that were marked as spam. Since December 11, 2017, I have had ~5 posts marked as spam.

See for example: This comment was marked as spam at Ciência Biomédica, when I responded to  Synthetic protein packages its own genetic material and evolves

Packaging is energy-dependent and biophysically constrained. Nothing evolves. The concept is foolish. See: A universal trend of amino acid gain and loss in protein evolution 
Excerpt: Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.
 
Laboratory co-oximeters determine the %HbO2 (%SaO2 ) by measuring the amount a specific frequency of light is absorbed as it passes through a known volume of blood. In contrast, pulse oximetry (SpO2) measures the change in light absorbed at systole and diastole. This allows the pulse oximeter to distinguish between the constant amount of light absorbed by the tissue, bone, venous blood, etc. from the arterial blood (the blood in the volume change due to the pulse).
 
The amount of light absorbed by the tissue, bone, venous blood etc., varies in the context of hydrogen-atom transfer in DNA base pairs in solution. Blood gas analysis in the medical laboratory links differences in hydrogen (H2) — as in H2O from quantized energy-dependent changes in the potential of hydrogen (pH) to all biophysically constrained biodiversity.
 

Measuring pH links what is known about nutritional epigenetics from the innate immune system to healthy longevity via everything known about autophagy. The measurements can be compared in the context of  what is known about virus-driven energy theft, which links stress from the replication of viruses to all pathology via critical care testing of other blood gas analytes such as pCO2, pO2, Sodium, Potassium, Chloride, Calcium, Glucose, Lactic Acid, and Hematocrit.

For example in a mammal, see: Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin (June 14, 2013)

See Fig. 2 Difference in the network of hydrogen bonds between high- and low-altitude Hb variants, HH-H and LL-L, respectively.

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My comment to the Science site (submitted 6/14/13 published 6/20/13):

In my model species-specific epistasis is nutrient-dependent and pheromone-controlled. An additional example of this showed up earlier this week in the context of the epigenetically-effected microRNA/messenger RNA balance: “miR-124 controls male reproductive success in Drosophila”

miR-14 acts in neurosecretory cells in the adult brain to control metabolism and miR-124 acts in the context of brain-directed neuroendocrine control of sexual differentiation and male pheromone production, which is controlled in mammals by gonadotropin-releasing hormone (GnRH) neurosecretory cells of the hypothalamus.

We can anticipate extension to mammals of the Drosophila model from the abstract of a forthcoming Science article: “MiR-200b and miR-429 Function in Mouse Ovulation and Are Essential for Female Fertility.” Given our earlier work in the context of molecular epigenetics and the concept of alternative splicings and sexual differentiation in Drosophila and C. elegans, I suspect we will see evidence for nutrient-dependent adaptive evolution of GnRH pulse frequency-controlled LH secretion and pheromone-controlled female fertility in mice.

If I’m correct, this evidence will link glucose and pheromones to feedback loops that control reproduction in invertebrates and vertebrates. (See Nutrient–dependent / pheromone–controlled adaptive evolution: a model). Model organisms exemplify these feedback loops in microbes, nematodes, insects, and other mammals. The mouse to human example that Kamberov et al., and Grossman et al., detailed is the most telling.

A single amino acid substitution appears to result in what seem to be nutrient-dependent changes in the thermodynamics of intracellular signaling, intranuclear interactions, stochastic gene expression, and selection for phenotype via organism-level thermoregulation in a human population that arose in what is now central China during the past ~30K years.

Using a model that integrates what is known about the common molecular mechanisms may help establish whether adaptive mutations lead to thermodynamic effects on organism-level thermoregulation and epistasis, or whether epigenetic effects of nutrients and their metabolism to species-specific pheromones that control reproduction via changes in the microRNA/messenger RNA balance are the driving force behind adaptive evolution in species from microbes to man.

See: Obligatory role of hypothalamic neuroestradiol during the estrogen-induced LH surge in female ovariectomized rhesus monkeys
Reported as:  Estrogen discovery could shed new light on fertility problems December 12, 2017

Estradiol builds in the bloodstream until it reaches a concentration that causes a surge of the hypothalamic and pituitary hormones, including one called luteinizing hormone, which in turn trigger an ovary to release an egg.

“It’s a feedback loop…

The feedback loop is food energy-dependent and pheromone-controlled.
See: Feedback loops link odor and pheromone signaling with reproduction
Energy-dependent autophagy is the link from feedback loops to ecological adaptation. Science Magazine now has the opportunity to challenge the pseudoscientific nonsense of published works from the Nature Publishing Group. There is no need to consider mutations and evolution outside the context of virus-driven energy theft, which links the degradation of messenger RNA from mutations to all pathology.
See also: Combating Evolution to Fight Disease

Darwin probably anticipated the insemination of population genetics that led to the bastardization of his detailed observations in the “Modern Synthesis.” He politely insisted that ‘conditions of life’ be considered before natural selection.

There are two ‘conditions of life.’ It is nutrient-dependent and pheromone-controlled. Rosenberg and Queitsch now note the work with Dobzhansky’s rarely acknowledged claim: “I am a creationist and an evolutionist.” They also declare the need for “Deep understanding of the mechanisms that generate variation at the molecular level…”

Deep understanding of the ‘conditions of life’ does not come from theory.

Problems with the “modern synthesis” now lead us back to the facts about biologically-based cause and effect that Darwin and Dobzhansky approached with humility, which are the same biological facts that evolutionists approached with ignorance about behavioral affects and the arrogance that accompanies that ignorance. Rosenberg and Queitsch echo the sentiments of those who have been subjected to academic suppression.

Clearly, however, “nothing in evolution makes sense except in the light of biology” is not an exaggeration. It is a common sense statement about the biologically plausible genesis of functional cell types. Population genetics and evolutionary theories abandoned the biophysical constraints of ecological variation and the physiology of reproduction, which enable epigenetically-effected nutrient-dependent pheromone-controlled receptor-mediated ecological adaptations and species diversity via the complexities of protein folding and niche construction.

It’s time for biophysicists to tell theorists and pathologists how to differentiate between theories about the genesis of different cell types and the biological facts about the nutrient-dependent pheromone-controlled ecological adaptations that enable the genesis of different cell types in individuals of different species. Simply put, it’s time to stop trying to explain ecological adaptations in the context of mutations and evolution.

The retraction of Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication attests to the amount of pseudoscientific nonsense published by the “Nature Publications Group” during the past few decades.
See: Retraction Watch

In retrospect, we were totally blinded by our belief [in our findings]…we were not as careful or rigorous as we should have been (and as Tivoli was) in interpreting these experiments.

How many others who published via the Nature Publishing Group were blinded by their belief in pseudoscientific nonsense that failed to link the food energy-dependent creation of enzymes and the creation of RNA from blood gas analyses to patient outcomes?
See for comparison: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

Who did not know that? How did non-enzymatic RNA replication become a non-energy-dependent consideration for anyone associated with the Nature Publishing Group?
See for comparison: Mechanisms of mTORC1 activation by RHEB and inhibition by PRAS40

Here we present the 3.0 ångström cryo-electron microscopy structure of mTORC1 and the 3.4 ångström structure of activated RHEB–mTORC1. RHEB binds to mTOR distally from the kinase active site, yet causes a global conformational change that allosterically realigns active-site residues, accelerating catalysis.

The global conformational change that allosterically realigns active-site residues (i.e., amino acids), accelerating catalysis, is an energy-dependent change.
Reported as:  Scientists unlock structure of mTOR, a key cancer cell signaling protein

1) Like many proteins, mTOR is an enzyme, which binds to target molecules called substrates in a precise way to hasten chemical reactions. Specifically, it is a type of kinase, which removes phosphates (P) from ATP, the cell’s energy currency, and places them on other molecules.

The creation of the enzymatic activity of mTOR is quantized energy-dependent and it links the pheromone-controlled physiology of reproduction to biophysically constrained viral latency via autophagy. The retractions of Jack Szostak’s nonsense about the magical creation of enzymes after the energy of life emerged and organisms subsequently evolved in the context of differences in H2 to all biodiversity on Earth, can be placed into the context works by serious scientists.

2)  …mTOR is an enzyme, which binds to target molecules called substrates in a precise way to hasten chemical reactions. Specifically, it is a type of kinase, which removes phosphates (P) from ATP, the cell’s energy currency, and places them on other molecules. From that 2013 study, which took more than five years to complete, the team learned some key things about the protein, such as what the ATP-binding site looks like…

The study that took more than 5 years to complete was published as: mTOR kinase structure, mechanism and regulation

The structures also reveal active-site residues and conformational changes that underlie inhibitor potency and specificity.

They had experimental evidence of energy-dependent changes in active-site residues (i.e., amino acids). They subsequently failed to link anything known to serious scientists about the energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of pheromone-controlled reproduction. They seemingly ignored all claims about RNA-mediated amino acid substitutions in the context of autophagy, which links base pair changes from changes in the microRNA/messenger RNA balance to RNA editing.
How could the Nature Publishing Group not know what all serious scientists know?
See for example: All Nobel Laureates in Physiology or Medicine

The Nobel Prize in Physiology or Medicine 2017

Jeffrey C. Hall, Michael Rosbash and Michael W. Young

“for their discoveries of molecular mechanisms controlling the circadian rhythm”

The molecular mechanisms are energy-dependent.
Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels  (1990) Hardin, Hall and Michael Rosbash
Who, besides Jack Szostak, does not know that the creation of energy must be linked to RNA-mediated cell type differentiation via messenger RNA levels?

The Nobel Prize in Physiology or Medicine 2009

Elizabeth H. Blackburn, Carol W. Greider and Jack W. Szostak

“for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase”

Where did the enzyme telomerase come from?
Face the facts, Jack (Szostak) and others. Cell type differentiation is food energy-dependent and biophysically constrained at every level of examination. Biophysical constraints on viral latency are required for ecological adaptation. The anti-entropic virucidal energy of sunlight links food energy directly from the innate immune system to all morphological and behavioral diversity. It’s all about energy. It’s all about the creation of enzymes. It’s all about the base pairs.
See:  Structural diversity of supercoiled DNA

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.
 

Functionally interdependent editing and methylation

Editing and methylation at a single site by functionally interdependent activities

…cytosine 32 in the anticodon loop of Trypanosoma brucei tRNAThr is methylated to 3-methylcytosine (m3C) as a pre-requisite for C-to-U deamination. Formation of m3C in vitro requires the presence of both the T. brucei m3C methyltransferase TRM140 and the deaminase ADAT2/3. Once formed, m3C is deaminated to 3-methyluridine (m3U) by the same set of enzymes. ADAT2/3 is a highly mutagenic enzyme4, but we also show that when co-expressed with the methyltransferase its mutagenicity is kept in check.

They showed how natural selection for energy-dependent codon optimality is linked from autophagy to RNA-directed DNA methylation and supercoiled DNA, which protects all organized genomes from virus-driven energy theft.
Reported as: Electric DNA, Circular RNA, and Other Epigenetic Wonders

…some non-coding RNAs are now known to be ‘guardian RNAs’ according to the modifications on their bases or sugars with methyl groups that act as tags.

The energy-dependent de novo creation of nucleic acids links microRNAs in flanking sequences to hydrogen-atom transfer in DNA base pairs in solution. Virus-driven energy theft causes the failure of hydrogen-atom transfer in DNA base pairs in solution, which links mutations to all pathology.
For additional claims about all pathology see: The Most Transformational Biologist of Our Era?
Dr Zhang: I worked with John to figure out how the HIV virus put different components together. We used the retrovirus as a model, and that formed the basis for the project.
Dr Zhang: …I realized that psychiatric disease is very much a physical illness, just like cancer or diabetes.
Dr Zhang: Optogenetics allows us to use light to stimulate specific groups of cells to be able to systematically map out how the brain is wired and how things work.
Dr Zhang: I did not know what CRISPR was. I went to look it up. Around that time, a paper from Sylvain Moineau in Canada was published describing how it was RNA-guided endonuclease.
Dr Zhang: Editas Medicine is a gene-editing company that I cofounded with George Church, Jennifer Doudna, Keith Joung, and David Liu. The mission of Editas is to develop the CRISPR genome-editing system for clinical applications. More than 5000 genetic diseases are caused by specific mutations in our cells. We thought it would be great if we could build a platform that systematically developed this to treat the many diseases for which we know the cause but have no way of treating.
Dr Topol:

We applaud you for what you have done to transform this field, along with so many others around the world. You really have been a pioneer. We look forward to seeing your work translated into something that will be therapeutic for people; especially the people who are often neglected—those with rare, Mendelian diseases. Congratulations on what you have already achieved. Just think what is in store.

For an example of what is for sale in Harvard’s store, see:
RNA-Guided Human Genome Engineering

…use of gRNAs [guide RNAs] provide the ability to multiplex than mRNAs in part due to the smaller size—100 vs. 2000 nucleotide lengths respectively. This is particularly valuable when nucleic acid delivery is size limited, as in viral packaging. This enables multiple instances of cleavage, nicking, activation, or repression—or combinations thereof. The ability to easily target multiple regulatory targets allows the coarse-or-fine-tuning or regulatory networks without being constrained to the natural regulatory circuits downstream of specific regulatory factors (e.g. the 4 mRNAs used in reprogramming fibroblasts into IPSCs).

5. Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).

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.

Natural selection for energy-dependent codon-optimality links feedback loops from food odors and pheromones to the physiology of reproduction in all living genera.
Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

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

Get Well in the RNAi Way-RNAi, A Billion Dollar Baby in Therapy

Disease therapy based on genetic materials is now a reality. The technique of gene silencing also called as RNA interference (RNAi) keeps our hopes alive. RNAi based drugs have now advanced steps closer towards clinical trials. The powerful in-vivo RNAi machinery and its delicate factors apprehend that RNAi-dependent therapies might create a billion dollar business against the pathogenic organisms and disease for which treatment options are currently restricted conventionally. Recent years have highlighted both the promises and challenges in delivery of different RNAi therapeutics. Apart from the delivery, the design, stability and degradation of RNAi based effective molecules appears to be the major lime light to challenge the conventional drug safety concerns and ensures to be the most powerful gene recovery in future which execute billion dollar business hope.

The billion dollar business hype exemplifies the failure of all pseudoscientists to recognize the fact that energy-dependent changes in microRNAs link hydrogen-atom transfer in DNA base pairs in solution to all biodiversity via the physiology of reproduction in species from microbes to humans.
See for comparison: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis
Feedback loops link odor and pheromone signaling with reproduction (2005)
Dynamic control of chirality and self-assembly of double-stranded helicates with light
Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

A protein conjugation system essential for autophagy (1998)

This conjugation can be reconstituted in vitro and depends on ATP. To our knowledge, this is the first report of a protein unrelated to ubiquitin that uses a ubiquitination-like conjugation system. Furthermore, Apg5 and Apg12 have mammalian homologues, suggesting that this new modification system is conserved from yeast to mammalian cells.

The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes 

One hallmark of autophagy is sequestration of a portion of cytoplasm by de novo formation of a double-membrane structure, the autophagosome, which fuses with lytic compartments (vacuoles in yeast and plants; lysosomes in mammals), leading to degradation of its contents.

The senior author is the 2016 Nobel Laureate, Yoshinori Ohsumi. He placed these findings into the context of the de novo formation of a double-membrane structure and supramolecular assembly of intrinsically disordered proteins. The authors make no mention of the facts about how the energy-dependent biosynthesis of RNA must be linked to supercoiled DNA, which protects all organized genomes from virus-driven energy theft in the context of autophagy and the physiology of reproduction.

Sunlight as information

Proof: Sunlight is energy as information

Hypothesis: Kallmann’s syndrome is proof that virus-driven energy theft causes all pathology in species from archaea to humans via the degradation of messenger RNA and the loss of one allele.
 

Thought experiment:

Step 1) The loss of one allele and the transgenerational epigenetic inheritance of Zika virus-damaged DNA can be compared to the degradation of messenger RNA in bacteria that is manifested in archaea and L-forms.

Step 2) The degradation of messenger RNA in primates differentiates healthy longevity from pathology via a single amino acid substitution in gorillas compared to chimpanzees and modern humans.

Discussion:

Unless someone shows how mutation-driven evolution leads to increasing organismal complexity in species from microbes to humans, the speed of light on contact with water clearly establishes the link from the de novo creation of microRNA flanking sequences to hydrogen-atom transfer in DNA base pairs in solution and all energy-dependent morphological and behavioral phenotypes.

Conclusion:

Unless there is another model for comparison to Kohl (2013), energy as information will be established as the link from endogenous RNA interference to all biodiversity.  Until then, a natural law appears to link food odors and the pheromone-controlled physiology of reproduction from biophysically constrained RNA-mediated protein folding chemistry to feedback loops.

The feedback loops clearly link physics and chemistry to biodiversity from energy as information and food odors to pheromones that control the physiology of reproduction. Pheromones are the chemical signals that prevent virus-driven energy theft and genomic entropy in all living genera.

terrarium-eco-system

Dobzhansky 1973 and precision medicine

MicroRNA-34 directly targets pair-rule genes and cytoskeleton component in the honey bee

Our findings point to miR-34-5p as novel regulatory component in the complex molecular cascade that governs insect segmentation and to a broader role of miRNAs in the early development due to the detection of mature transcripts from both 5p and 3p arms for several precursor miRNAs. Thus, this work encourages further investigation to pinpoint miRNAs as fine tuners of insect early development.

Anna Di Cosmo‘s group took the lead and already linked all invertebrates to all vertebrates via the conserved molecular mechanisms that link microRNA flanking sequences to all energy-dependent  biophysically constrained biodiversity.

See for example: Role of olfaction in Octopus vulgaris reproduction (January 1, 2015)

For a perspective, see: The phylogenetic utility and functional constraint of microRNA flanking sequences (February 18, 2015)

The majority of flanking sequences used in our analyses are composed of non-coding intergenic DNA, suggesting that conservation of these hairpin-loop flanking sequences is independent of either the presence of exonic sequence or protein-coding gene regions.

For the extension to humans, see:

Practical Approaches for Whole-Genome Sequence Analysis of Heart- and Blood-Related Traits

 …all amino acid substitutions or all promotor variants are not equal, and one can predict the impact based on knowledge of the location and type of substitution.

All cell type specific and tissue type specific amino acid substitutions in all individuals of all living genera are energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction. A long-time antagonist echoed that fact in the human ethology yahoo group, but he took facts about complex traits out of context. See: Practical application of whole-genome sequencing

The complex traits used here are heart and blood related ones, but the concepts are applicable to all complex genetically-sourced traits, including behavioral ones. — Clarence A. ‘Sonny’ Williams

Complex traits are not genetically sourced. The physiology of pheromone-controlled reproduction is clearly the link to the complexity of all nutrient energy-dependent morphological and behavioral traits.
See: No Genetics without Epigenetics? No Biology without Systems Biology?

…a unified understanding of life requires: (1) a view on its component parts, the cells, (2) a view on the life cycles of all cells—their formation, growth, development, and reproduction—as based in chemical reactions among similar sorts of molecules, (3) a view on the way in which amino acids are put together to form proteins, as specified by DNA and RNA according to a nearly universal and precise scheme.

That fact makes it perfectly clear that behavioral traits are not genetically sourced. All traits arise only in the context of systems biology, which links the epigenetic landscape to the physical landscape of supercoiled DNA in all living genera. For comparison, Clarence A ‘Sonny Williams wrote:

mutations in gene regulatory regions are the “driving force” behind human brain complexity. 

and

I do not reply to creationists or anyone who does not believe that humans evolved via Darwinian natural selection.

The facts about systems biology were stated clearly in Dobzhansky’s Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973)

Cytochrome C is an enzyme that plays an important role in the metabolism of aerobic cells. It is found in the most diverse organisms, from man to molds. E. Margoliash, W. M. Fitch, and others have compared the amino acid sequences in cytochrome C in different branches of the living world. Most significant similarities as well as differences have been brought to light. The cytochrome C of different orders of mammals and birds differ in 2 to 17 amino acids, classes of vertebrates in 7 to 38, and vertebrates and insects in 23 to 41; and animals differ from yeasts and molds in 56 to 72 amino acids. Fitch and Margoliash prefer to express their findings in what are called “minimal mutational distances.” It has been mentioned above that different amino acids are coded by different triplets of nucleotides in DNA of the genes; this code is now known.

See also:

For example, the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.

The de novo creation of amino acids has since been linked from chirality to autophagy and healthy longevity via chromosomal rearrangements.
See:
Light-Induced Opening and Closing of the Intramolecular Hydrogen Bond in Glyoxylic Acid
Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins
Dynamic control of chirality and self-assembly of double-stranded helicates with light
The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes

The cycle of interconversion of assemblies and helicities shown here holds promise to design other dynamic systems driven out of equilibrium by light energy.

See also: ATP hydrolysis by UPF1 is required for efficient translation termination at premature stop codons
The de novo creation of amino acids has since been linked from the energy-dependent creation of helicase to the structure of functional DNA. Theories about minimal mutational distances have been replaced by facts that link angstroms to ecosystems in all living genera via biophysically constrained RNA-mediated protein folding chemistry.

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.

They linked energy-dependent metabolic networks to genetic networks by recapitulating Dobzhansky’s claims and in this parody they add: “every angstrom is dynamic from the 5 prime to the three”

See also: Structure of eukaryotic CMG helicase at a replication fork and implications to replisome architecture and origin initiation

…definitive conclusions about the exact role of the N-tier in helicase mechanism will require higher resolution to identify candidate-specific amino acid residues, followed by direct mutagenesis and biochemical characterization.
 

Although the candidate-specific amino acid residues have not been identified, the energy-dependent creation of RNA-mediated amino acid “residues” links the anti-entropic virucidal energy of sunlight from angstroms to ecosystems in all living genera via chirality and autophagy, which protect all organized genomes from virus-driven entropy in the context of the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes.

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

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

See also: Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes

The ZAL2 and ZAL2m alleles code for 597 amino acids, with two fixed differences driving a Val73Ile and Ala552Thr polymorphism in ZAL2m. valine to alanine substitution

How social learning adds up to a culture: from birdsong to human public opinion
Conclusion:

For human online cultures, we suggest that it may be useful to consider features of birdsong learning, which have been optimized over millions of generations to give rise to stable polymorphic cultures. Experimenting with implementation of similar features in online communication systems could potentially facilitate the design of more stable and balanced information systems, which can potentially promote distributed self-governance.

Public opinion (above) is based on bird-brained representations of pseudoscientific nonsense about “…balanced information systems, which can potentially promote distributed self-governance.” The information systems are not linked from energy-dependent changes in the microRNA/messenger RNA balance to all biodiversity via the physiology of pheromone-controlled reproduction. Instead the information systems automagically may promote “distributed self-governance” across all species in the context of millions of years of evolution.

In my model of biologically-based cause and effect, top-down causation is linked from natural selection for energy-dependent codon optimality to the physiology of reproduction and all biodiversity via supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.

For an example of medication-induced genomic entropy, see: Some Antibiotics Linked to Serious Nerve Damage

The FDA is strengthening its warning that a popular class of antibiotics, called fluoroquinolones, may cause sudden, serious, and potentially permanent nerve damage called peripheral neuropathy.

See also: There is nothing inevitable or natural about chronic disease

Causation at the molecular level, deep inside the body, appears to be beyond our current reach

See for comparison: Understanding and accounting for relational context is critical for social neuroscience

George Ellis:

This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: http://rsfs.royalsocietypublishing.org/content/2/1.toc

I wrote:

New data on how genetic predispositions are epigenetically linked to phenotypically distinct neuroanatomy and behaviors is provided in the honeybee model. Across-species comparisons from insects to vertebrates clearly show that the epigenetic influence of food odors and pheromones continues throughout the life of organisms that collectively survive whereas individuals do not. These comparisons also attest to the relative salience of sensory input from the rearing environment. For example, when viewed from the consistency of animal models and conditioned behaviors, food odors are obviously more important to food selection than is our visual perception of food. Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.

Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).” — Kohl, JV (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors
See also: Methylation Maestro

So are many others who do not understand how energy-dependent changes in chirality must be linked from autophagy to supercoiled DNA in the context of the physiology of reproduction and fixation of RNA-mediated amino acid substitutions.

They have failed to link the National Microbiome Initiative to the Precision Medicine Initiative via RNA-mediated protein folding chemistry and are trapped in theories with no explanatory power.

If you ask one of them about the virus-driven energy theft of quantized energy, which is linked to all pathology, they will run away. They cannot stand to think about how the potential of hydrogen (pH) must be linked from sunlight to all biodiversity via the claims of Schrodinger in What is Life? (1944)

Alternative splicing of pre-mRNA

Mutations: the "driving force" behind human brain complexity?

Evolutionary Psychology Crap in New Scientist

There is a reason why domestic violence is so widespread, says David Buss, an evolutionary biologist at the University of Texas in Austin: it carries a selective advantage, tied with reproductive success.

Larry Moran wrote:

There’s something seriously wrong with evolutionary psychology. And there’s something seriously wrong with respectable science magazines who promote this crap.

Are the science magazines that promote this crap respectable? I lost respect for anyone who still uses de Vries 1902 definition of mutation in attempts to explain how the emergence of life links natural selection from mutations to all extant biodiversity.

Evolutionary psychology Group Description

Evolutionary Psychology is an approach to psychology, in which knowledge and principles from evolutionary biology are put to use in research on the structure and function of the human mind.

Information and vision

Excerpts:

RKS: The retina turn light into visual information which is then processed by specific brain areas dedicated to this task, known as V1 through to V9. 

RKS:
This is established by neuroscience, yet another entire branch of science you dismiss in its entirety in an effort to prove your own feeble points…

RKS:

This involves previous experience, current mood and emotional status, previous behaviour (what you were doing when the visual stimuli occurred) and so on.  In other words there is an entire world of cognitive processing that needs to be consulted before behaviour occurs or is modulated as a result of visual stimuli.

RKS:

Information is also modified in the brain.  Visual information is filtered, in other words the visual information is processed, the colour of scenes is modified to compensate for the changing colour of light through the day (redder in the morning and night, bluer in the middle of the day)…

RKS:
We were discussing information processing with regard to the handling of information gleaned by the senses.  You are discussing in the above the decision making processes which occur in response to sensory stimulation and after that stimulation has been processed.
No supporting argument?  Perhaps you should try reading what I write…
I think it is safe to say that we can group behaviour into three steps:
1) Sensory stimulation;
2) Decision making, Behavioural response;
3) behavioural output.
The information processing being discussed previously concerns the (1) and (3), what happens to sensory stimulation on its way to the decision making process and on its way from the decision making process.  We have not discussed, except for your last statement above, the decision making process per se.

Other discussion groups owned and/or moderated by Robert Karl Stonjek include: Yahoo! Groups
Climate Change Forum
Cognitive NeuroScience
Evolutionary Psychology News Only
Mind and Brain
Physical Sciences
Psychiatry Research

See for comparison: Networks of Cultured iPSC-Derived Neurons Reveal the Human Synaptic Activity-Regulated Adaptive Gene Program

Clarence A. ‘Sonny’ Williams: wrote this to the Neuroscience FB group moderated by Robert Karl Stonjek

Interesting research adding to other evidence revealing that mutations in gene regulatory regions are the “driving force” behind human brain complexity. Please note that this research does not identify uniquely human genes, but rather the comparison is between mice and humans. For all we know, the identified genes are present in all primates.

Here, the regulatory region changes found in humans but not mice are involved in activity-dependent synaptic changes (roughly, plasticity).

I responded:

No experimental evidence of biologically-based cause and effect links mutations to anything except pathology. Activity-regulated gene expression is nutrient energy-dependent and controlled by the physiology of reproduction in all living genera.

I added: The Odyssey of Autophagy

Excerpt: “ask a simple question about an interesting phenomenon, pick the right model organism in which that question can be approached genetically and biochemically, and let the grand unity of biology do the rest.”

The question is: Where did the quantized energy in a hydrogen atom come from and where does it go when it is stolen by viruses?

I added: Theorists sell hidden energy

Conclusion: Neo-Darwinian theorists invented ridiculous theories because they did not know where energy came from or where it goes when it no longer sustains life. They sold their theories to the biologically uninformed masses and will continue to sell theories about hidden energy until serious scientists put a stop to the nonsense touted by the evolution industry and the “big bang” cosmology industry.

See also: Structural diversity of supercoiled DNA

Clarence A. ‘Sonny’ Williams (with my emphasis)

Thanks for your contributions, Mr. Kohl, but I do not reply to creationists or anyone who does not believe that humans evolved via Darwinian natural selection. Others may want to respond to any comments you make on posts from others, even if they often do not relate to the subject at hand, but this is the last time I will respond to any posts or comments you make.

James Kohl

Thanks for your ongoing antagonism and atheistic nonsense. If not for you and others like you, serious scientists would have nothing to offer to those who want to become biologically informed. See also: http://onlinelibrary.wiley.com/doi/10.1002/bdrc.21146/full Excerpt: “Studies conducted in various animal models have revealed the importance of ncRNAs during gonadal determination and differentiation process. However, the functions of these RNAs in the human sex determination are still not known.”

How much longer will anyone pretend not to know that hydrogen-atom energy in DNA base pairs in solution links nutrient energy-dependent changes in microRNA flanking sequences to all biodiversity via what is known to all serious scientists about autophagy and how the pheromone-controlled physiology of reproduction is linked to supercoiled DNA? When virus-driven energy theft causes malfunctions in receptors, the receptor-mediated events are linked from mutations to pathology, not to the evolution of a new species. I’ve published award-winning review of these facts and other reviews for more than 20 years. And Mr. Williams has come here to plague others with more of his pseudoscientific nonsense.

See for comparison our section on molecular epigenetics from this 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior

The phylogenetic utility and functional constraint of microRNA flanking sequences

Excerpt: “…miRNAs and their flanking sequences provide phylogenetic signals suitable for the inference of phylogeny with high levels of accuracy, when sufficient numbers of this type are concatenated. As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.”

The de novo assembly of genomes is energy-dependent and biophysically constrained by the physiology of reproduction whether or not you believe in creation. But if you believe that humans evolved via Darwinian natural selection, you should probably learn that Darwin put his energy-dependent “conditions of life” first. He did not seem to believe that anything created itself or any species outside the context of what is now known about autophagy and supercoiled DNA.

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

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

I wrote: Robert Karl Stonjek  Attacks on the beliefs of others should not be tolerated, and supposedly, that is why you removed me from your Evolutionary Psychology News FB group.

Please address this attack by Clarence A. ‘Sonny’ Williams, who wrote: “I do not reply to creationists or anyone who does not believe that humans evolved via Darwinian natural selection.”
 

Robert Karl Stonjek Are you trying to get yourself removed from this group as well??
James Kohl  Thanks for asking. No.
I think this group is a great way to inform others who want to learn what is known to those who have linked energy-dependent changes in angstroms to ecosystems via autophagy and supercoiled DNA, as represented in this parody. https://www.youtube.com/watch?v=gwy2lD1reos&feature=youtu.be
James Kohl See also: https://www.youtube.com/watch?v=iM_I6rtIgn0
The alternative may be to remove anyone from this group who has already linked 2016 Nobel Laureate, Ben Feringa’s works to 2016 Nobel Laureate Yoshinori Ohsumi’s works. See for example: Dynamic control of chirality and self-assembly of double-stranded helicates with light

The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes

See also the section on Regulation of autophagy by amino acids in: Autophagy in the liver: functions in health and disease

James Kohl They make it perfectly clear that autophagy is the only obvious link from the fixation of RNA-mediated amino acid substitutions in the cell types of all living genera to their morphological and to their behavioral diversity. In the same article, they help to show that virus-driven energy theft is the link to all pathology. See also: https://www.ncbi.nlm.nih.gov/pubmed/?term=microrna+autophagy (534 published works link energy-dependent changes in microRNAs to autophagy.

See also: https://www.ncbi.nlm.nih.gov/pubmed/?term=microrna 56723 published works link nutrient energy-dependent microRNAs to all cell type differentiation in all living genera and they also link virus-driven energy theft to all pathology.

Kalevi Kull: Censorship & Royal Society Evo Event

Excerpt: “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

Clarence A. ‘Sonny’ Williams is still touting “…evidence revealing that mutations in gene regulatory regions are the “driving force” behind human brain complexity.”

He has ignored all the experimental evidence of biologically-based cause and effect during the past twenty years. I don’t know what else to do besides cite Kull’s comment and point out that Clarence A. ‘Sonny’ Williams is not even trying to move forward with “cutting edge” knowledge about RNA-mediated cell type differentiation. He is stuck trying to sell hidden energy — as if he were even less informed than most theorists.

See for comparison: Cultural differences may leave their mark on DNA

This is a big advancement of our understanding of race and ethnicity,” Burchard said. “There’s this whole debate about whether race is fundamentally genetic or is just a social construct. To our knowledge this is the first time anyone has attempted to quantify the molecular signature of the non-genetic components of race and ethnicity. It demonstrates in a whole new way that race combines both genetics and environment.
Alternative splicing of pre-mRNA

Mutations: the "driving force" behind human brain complexity?

Evolutionary Psychology Crap in New Scientist

There is a reason why domestic violence is so widespread, says David Buss, an evolutionary biologist at the University of Texas in Austin: it carries a selective advantage, tied with reproductive success.

Larry Moran wrote:

There’s something seriously wrong with evolutionary psychology. And there’s something seriously wrong with respectable science magazines who promote this crap.

Are the science magazines that promote this crap respectable? I lost respect for anyone who still uses de Vries 1902 definition of mutation in attempts to explain how the emergence of life links natural selection from mutations to all extant biodiversity.

Evolutionary psychology Group Description

Evolutionary Psychology is an approach to psychology, in which knowledge and principles from evolutionary biology are put to use in research on the structure and function of the human mind.

Information and vision

Excerpts:

RKS: The retina turn light into visual information which is then processed by specific brain areas dedicated to this task, known as V1 through to V9. 

RKS:
This is established by neuroscience, yet another entire branch of science you dismiss in its entirety in an effort to prove your own feeble points…

RKS:

This involves previous experience, current mood and emotional status, previous behaviour (what you were doing when the visual stimuli occurred) and so on.  In other words there is an entire world of cognitive processing that needs to be consulted before behaviour occurs or is modulated as a result of visual stimuli.

RKS:

Information is also modified in the brain.  Visual information is filtered, in other words the visual information is processed, the colour of scenes is modified to compensate for the changing colour of light through the day (redder in the morning and night, bluer in the middle of the day)…

RKS:
We were discussing information processing with regard to the handling of information gleaned by the senses.  You are discussing in the above the decision making processes which occur in response to sensory stimulation and after that stimulation has been processed.
No supporting argument?  Perhaps you should try reading what I write…
I think it is safe to say that we can group behaviour into three steps:
1) Sensory stimulation;
2) Decision making, Behavioural response;
3) behavioural output.
The information processing being discussed previously concerns the (1) and (3), what happens to sensory stimulation on its way to the decision making process and on its way from the decision making process.  We have not discussed, except for your last statement above, the decision making process per se.

Other discussion groups owned and/or moderated by Robert Karl Stonjek include: Yahoo! Groups
Climate Change Forum
Cognitive NeuroScience
Evolutionary Psychology News Only
Mind and Brain
Physical Sciences
Psychiatry Research

See for comparison: Networks of Cultured iPSC-Derived Neurons Reveal the Human Synaptic Activity-Regulated Adaptive Gene Program

Clarence A. ‘Sonny’ Williams: wrote this to the Neuroscience FB group moderated by Robert Karl Stonjek

Interesting research adding to other evidence revealing that mutations in gene regulatory regions are the “driving force” behind human brain complexity. Please note that this research does not identify uniquely human genes, but rather the comparison is between mice and humans. For all we know, the identified genes are present in all primates.

Here, the regulatory region changes found in humans but not mice are involved in activity-dependent synaptic changes (roughly, plasticity).

I responded:

No experimental evidence of biologically-based cause and effect links mutations to anything except pathology. Activity-regulated gene expression is nutrient energy-dependent and controlled by the physiology of reproduction in all living genera.

I added: The Odyssey of Autophagy

Excerpt: “ask a simple question about an interesting phenomenon, pick the right model organism in which that question can be approached genetically and biochemically, and let the grand unity of biology do the rest.”

The question is: Where did the quantized energy in a hydrogen atom come from and where does it go when it is stolen by viruses?

I added: Theorists sell hidden energy

Conclusion: Neo-Darwinian theorists invented ridiculous theories because they did not know where energy came from or where it goes when it no longer sustains life. They sold their theories to the biologically uninformed masses and will continue to sell theories about hidden energy until serious scientists put a stop to the nonsense touted by the evolution industry and the “big bang” cosmology industry.

See also: Structural diversity of supercoiled DNA

Clarence A. ‘Sonny’ Williams (with my emphasis)

Thanks for your contributions, Mr. Kohl, but I do not reply to creationists or anyone who does not believe that humans evolved via Darwinian natural selection. Others may want to respond to any comments you make on posts from others, even if they often do not relate to the subject at hand, but this is the last time I will respond to any posts or comments you make.

James Kohl

Thanks for your ongoing antagonism and atheistic nonsense. If not for you and others like you, serious scientists would have nothing to offer to those who want to become biologically informed. See also: http://onlinelibrary.wiley.com/doi/10.1002/bdrc.21146/full Excerpt: “Studies conducted in various animal models have revealed the importance of ncRNAs during gonadal determination and differentiation process. However, the functions of these RNAs in the human sex determination are still not known.”

How much longer will anyone pretend not to know that hydrogen-atom energy in DNA base pairs in solution links nutrient energy-dependent changes in microRNA flanking sequences to all biodiversity via what is known to all serious scientists about autophagy and how the pheromone-controlled physiology of reproduction is linked to supercoiled DNA? When virus-driven energy theft causes malfunctions in receptors, the receptor-mediated events are linked from mutations to pathology, not to the evolution of a new species. I’ve published award-winning review of these facts and other reviews for more than 20 years. And Mr. Williams has come here to plague others with more of his pseudoscientific nonsense.

See for comparison our section on molecular epigenetics from this 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior

The phylogenetic utility and functional constraint of microRNA flanking sequences

Excerpt: “…miRNAs and their flanking sequences provide phylogenetic signals suitable for the inference of phylogeny with high levels of accuracy, when sufficient numbers of this type are concatenated. As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.”

The de novo assembly of genomes is energy-dependent and biophysically constrained by the physiology of reproduction whether or not you believe in creation. But if you believe that humans evolved via Darwinian natural selection, you should probably learn that Darwin put his energy-dependent “conditions of life” first. He did not seem to believe that anything created itself or any species outside the context of what is now known about autophagy and supercoiled DNA.

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

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

I wrote: Robert Karl Stonjek  Attacks on the beliefs of others should not be tolerated, and supposedly, that is why you removed me from your Evolutionary Psychology News FB group.

Please address this attack by Clarence A. ‘Sonny’ Williams, who wrote: “I do not reply to creationists or anyone who does not believe that humans evolved via Darwinian natural selection.”
 

Robert Karl Stonjek Are you trying to get yourself removed from this group as well??
James Kohl  Thanks for asking. No.
I think this group is a great way to inform others who want to learn what is known to those who have linked energy-dependent changes in angstroms to ecosystems via autophagy and supercoiled DNA, as represented in this parody. https://www.youtube.com/watch?v=gwy2lD1reos&feature=youtu.be
James Kohl See also: https://www.youtube.com/watch?v=iM_I6rtIgn0
The alternative may be to remove anyone from this group who has already linked 2016 Nobel Laureate, Ben Feringa’s works to 2016 Nobel Laureate Yoshinori Ohsumi’s works. See for example: Dynamic control of chirality and self-assembly of double-stranded helicates with light

The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes

See also the section on Regulation of autophagy by amino acids in: Autophagy in the liver: functions in health and disease

James Kohl They make it perfectly clear that autophagy is the only obvious link from the fixation of RNA-mediated amino acid substitutions in the cell types of all living genera to their morphological and to their behavioral diversity. In the same article, they help to show that virus-driven energy theft is the link to all pathology. See also: https://www.ncbi.nlm.nih.gov/pubmed/?term=microrna+autophagy (534 published works link energy-dependent changes in microRNAs to autophagy.

See also: https://www.ncbi.nlm.nih.gov/pubmed/?term=microrna 56723 published works link nutrient energy-dependent microRNAs to all cell type differentiation in all living genera and they also link virus-driven energy theft to all pathology.

Kalevi Kull: Censorship & Royal Society Evo Event

Excerpt: “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

Clarence A. ‘Sonny’ Williams is still touting “…evidence revealing that mutations in gene regulatory regions are the “driving force” behind human brain complexity.”

He has ignored all the experimental evidence of biologically-based cause and effect during the past twenty years. I don’t know what else to do besides cite Kull’s comment and point out that Clarence A. ‘Sonny’ Williams is not even trying to move forward with “cutting edge” knowledge about RNA-mediated cell type differentiation. He is stuck trying to sell hidden energy — as if he were even less informed than most theorists.

See for comparison: Cultural differences may leave their mark on DNA

This is a big advancement of our understanding of race and ethnicity,” Burchard said. “There’s this whole debate about whether race is fundamentally genetic or is just a social construct. To our knowledge this is the first time anyone has attempted to quantify the molecular signature of the non-genetic components of race and ethnicity. It demonstrates in a whole new way that race combines both genetics and environment.