Alternative splicing of pre-mRNA

Psychophysical Laws of Biology: RNA-mediated nutritional psychiatry (3)

Psychophysical Laws and the Superorganism  (open access)

…superorganisms may also exhibit such behaviour, suggesting that these laws arise from fundamental mechanisms of information processing and decision-making.

Reported on Jun 14, 2013 as Nutrient-dependent/pheromone-controlled adaptive evolution: a model

and again on: Mar 27, 2018 as Honeybees may unlock the secrets of how the human brain works

The study… found that superorganisms may obey the same laws as the human brain.

Kohl’s “Laws of Biology” and Darwin’s “conditions of life” can now be compared in the context of how quantized energy as information was linked to biodiversity in this invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)
See also for review:

Functional and evolutionary aspects of chemoreceptors (2012)
Sensory receptors—design principles revisited (2013)
Moving forward: See: Tuning Insect Odorant Receptors (in press)

Among the insect olfactory receptors the odorant receptors (ORs) evolved in parallel to the onset of insect flight. A special property of this receptor type is the capability to adjust sensitivity of odor detection according to previous odor contacts. This article presents a current view on regulatory processes affecting the performance of ORs and proposes a model of mechanisms contributing to OR sensitization.

Future attempts to place psychophysical laws of biology back into the context of neo-Darwinian pseudoscientific nonsense will continue to pit ridiculous theories about experience-dependent tuning of odor receptors against everything known to serious scientists about RNA-mediated biophysically constrained viral latency and supercoiled DNA.
See for comparison:
Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment (2003)
Seeking the foundations of cognition in bacteria: From Schrödinger’s negative entropy to latent information (2006)
Learning from Bacteria about Natural Information Processing (2009)
Stability of the hybrid epithelial/mesenchymal phenotype (2016)

Epithelial-to-Mesenchymal Transition (EMT) and its reverse – Mesenchymal to Epithelial Transition (MET) – are hallmarks of cellular plasticity during embryonic development and cancer metastasis.

Cellular plasticity was linked from the energy-dependent pheromone-controlled physiology of reproduction in bacteria to our visual perception of energy and mass in the context of the space-time continuum.
See: Olfaction Warps Visual Time Perception (2017)

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.

See also: Schrödinger at 75 – The Future of Biology – September 2018
The scheduled speakers will undoubtedly link the Science Behind the Game “Cytosis” to the Science Behind the Game “Subatomic” via everything known to all serious scientists based on Schrodinger’s prescient claims in What is Life? (1944).
See also: What is life when it is not protected from virus driven entropy

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

See also: Energy as information and constrained endogenous RNA interference

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.

See also “Outer Membrane Vesicles” microRNA (4 of 4 from a 3/27/18 search)

How Our Other Genome Controls Our Epi-Genome (2016)

Secretable Small RNAs via Outer Membrane Vesicles in Periodontal Pathogens (2017)

Tiny RNAs and their voyage via extracellular vesicles: Secretion of bacterial small RNA and eukaryotic microRNA (2017)

Molecular Paths Linking Metabolic Diseases, Gut Microbiota Dysbiosis and Enterobacteria Infections (2018)

See also: March 28, 2018 sponsored by System Biosciences
Webinar: Deciphering how bacteria utilize outer membrane vesicles (OMVs) to communicate and infect
 
Outer Membrane Vesicles (OMVs) are membrane vesicles secreted by bacteria that contain DNA, RNA, proteins and endotoxins. Bacteria respond to many environmental factors by secreting specifically-enriched OMVs, which makes these bacteria more fit for their environment. For example, OMVs may be enriched with invasion proteins at the host-pathogen interface. OMVs have recently gained attention as a novel mechanism for transmission of molecular information within bacteria as well as between bacteria and mammalian cells. Owing to their similarities to well-studied extracellular vesicles (EVs), OMVs are being utilized by researchers to study host-bacterial interactions in pathogenesis, cancer therapy, host immune response modulation, as well as bacterial OMV engineering for use as vaccines. This webinar will give an overview of recent studies on the role of OMVs in host-pathogen interactions and discuss their bioengineering potential as vehicles for cargo delivery. We will also introduce our new & revolutionary ExoBacteria™ OMV Isolation Kit, which will enable you to achieve faster, simpler & better OMV isolation.
Learn how OMVs are being utilized by researchers to study host-bacterial interactions in pathogenesis, cancer therapy, host immune response modulation, as well as bacterial OMV engineering for use as vaccines.
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.

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

Darwinian adaptation: a clear evolutionary trail?

Summary: The light harvesting occurs in the ocean and on land. It links the creation of sunlight from food energy to the physiology of pheromone-controlled viral latency in all living genera, and all serious scientists know that.
 

Origins of photosynthesis in plants dated to 1.25 billion years ago

The world’s oldest algae fossils are a billion years old, according to a new analysis by earth scientists. Based on this finding, the researchers also estimate that the basis for photosynthesis in today’s plants was set in place 1.25 billion years ago.

A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

See for comparison:  Energy as information and constrained endogenous RNA interference (video)
For contrast, Philip Ball separates the origin of photosynthesis in plants from the origin of bioluminescence in bacteria in the ocean.
See: Water is an active matrix of life for cell and molecular biology

1) Water is a complex fluid in its own right (4, 5), and Darwinian adaptation to a complex milieu might be expected to generate much the same kind of enmeshing and interplay of the biological and environmental at the molecular scale that we find at higher levels of life’s organizational hierarchy.

Higher levels of organization are no different than other levels of organization. Organization is organization. But Philip Ball is a deceptive journalist. Neo-Darwinian evolution becomes Darwinian adaptation, which links the sun’s anti-entropic virucidal energy from feedback loops and the physiology of pheromone-controlled reproduction to microRNA-mediated autophagy and biophysically constrained viral latency in species from microbes to human. That causes the biologically uniformed journalist to claim:

2) All of this touches on the astrobiological question mentioned at the outset: should we, like Henderson (88) in 1913, regard water as uniquely “biophilic” and “fit” to act as life’s matrix?

There is no astrobiological question.  See the comments section on Understanding and accounting for relational context is critical for social neuroscience
George F R 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 25 Apr 2014 at 07:49am
I wrote:  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).
Philip Ball has since changed the clear evolutionary trail that links the sense of smell to ecological adaptation. Ecological variation links the creation of enzymes that metabolize food and drugs to his claim about  Darwinian adaptation.
See also for a recent representation of his word-play: Quantum common sense

We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking

There are stark difference in his claims about a Universe that is always looking that can be compared via claims about the creation of a universe in which viral latency is biophysically constrained by feedback loops. The feedback loops link food odors and pheromones from the physiology of reproduction in all living genera to all biodiversity via autophagy and the microRNA-mediated creation of supercoiled DNA.
In the spirit of the Christmas season and an attempt to stop the pseudoscientific nonsense touted by biologically uniformed theorists and journalists like Philip Ball, see: Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 2 (video excerpt <2 minutes long)
Remember, Santa Claus (or someone like him) is coming soon. Philip Ball may not be prepared for that. He has been a very bad boy. At the same time that President Trump, who tries his best to be good, has been accused of censorship and compared to Hitler.  I do not think that President Trump would try to change neo-Darwinian evolution to Darwinian adaptation without mentioning how the speed of light on contact with water changes everything.
Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
Reported as: … the conditions that produce nucleic acid precursors also create the starting materials needed to make natural amino acids and lipids. That suggests a single set of [light activated] reactions could have given rise to most of life’s building blocks simultaneously.
All the theories can be linked via facts to creationist science that has been supported with experimental evidence of biophysically constrained viral latency as presciently foretold by
1) Schrodinger,
2) Feynman,
3) Dobzhansky
4) McEwen,
and by
5) Eshel Ben-Jacob, who wrote: Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment 
Note his use of the term adaptability. It may have led Philip Ball to change Darwinian evolution to Darwinian adaptation.
See also: Learning from Bacteria about Natural Information Processing

Focusing on the energy, matter, and thermodynamic imbalances provided by the environment, Schrodinger proposed that life required the consumption of negative entropy, that is, the use of thermodynamic imbalances in the environment. From the perspective of thermodynamics, each bacterium can be viewed as a complex system that is composed of an “engine” that uses imbalances in the environment to do work, and a “machine” that uses this energy (to act against the natural course of entropy increase) for the synthesis of organic substances.13 A third information-processing system is also needed for the coordination and synchronization of the functioning of the engine and the machine. Namely, a living cell is analogous to a complex man-made cybernetic system, or a “chimera,” composed of information processing systems and of at least two thermodynamic elements. In addition, using the outer membrane, cells sense the environment.

We proposed that, besides “negative entropy,” organisms sense the environment to extract latent embedded information.13 By latent information we refer to data embedded in the environment that, once processed cognitively, initiates change in the organism’s function or behavior. Information induces changes; hence it can be used to generate an internal condensed description (model or usable information) of the environment, which guides the organism’s functioning.

See also: QuEBS 2018: 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.
The light harvesting occurs in the ocean and on land. It links the creation of sunlight from food energy to the physiology of pheromone-controlled viral latency in all living genera, and all serious scientists know that. If Philip Ball just realized that, he knows he has a long-standing problem with misrepresentations of  top-down causation. In any case, it is important to know that he has forced all theorists and journalists to acknowledge the likelihood that Santa Claus is not just a figment of a child-like imagination, and that the creation of sunlight must be linked from its contact with water to the physiology of pheromone-controlled reproduction and biophysically constrained viral latency in all living genera.
 

Alternative splicing of pre-mRNA

Energy-dependent alternative splicings 1996 – 2016 (2)

See also: Energy-dependent alternative splicings 1996 – 2016

Re: Rs3827760 is Val370Ala and EDARV370A

No matter what it is called, Val370Ala may be the best example of how nutrient energy-dependent biophysically constrained pheromone-controlled viral latency protects all organisms from virus-driven energy theft and all pathology.
For example, see: Genome recoding by tRNA modifications

The succession of mRNA codons controls the synthesis of polypeptides through the complementarity between each of the 64 possible codon triplets and the tRNA anticodons that decode the 20 amino acids of the cellular proteome. Central to the mRNA decoding process is the backward compatibility of the codon : anticodon recognition that is mediated by tRNA.

See also: In the loop: how chromatin topology links genome structure to function in mechanisms underlying learning and memory

Highlights:

•    Epigenetic regulation represents a key mechanism of learning, memory and cognition.
•    Chromatin topology is emerging as a major regulator of neuronal gene expression.
•    Dynamic chromatin topology changes correlate with activity-dependent transcription.
•    DNA double-strand breaks facilitate induction of immediate early gene transcription.

All their highlights can be placed into the context of this article from 2005.
Feedback loops link odor and pheromone signaling with reproduction
The feedback loops determine whether of not a species survives via links from energy-dependent autophagy to learning, memory, RNA-mediated amino acid substitutions and supercoiled DNA.
BDNF Val66Met and COMT Val158Met are also examples that link energy-dependent changes in base pairs from single nucleotide polymorphisms to life history transitions in morphological and behavioral phenotypes.

See also: Spatiotemporal antagonism in mesenchymal-epithelial signaling in sweat versus hair fate decision

Our findings revealed a differential impact of BMP signaling on appendage fate specification that has ancient roots and occurs repeatedly throughout vertebrate evolution.

This was reported by Bob Yirka as: Researchers identify signals during embryonic development that control the fate of skin cells to be sweaty or hairy

The fate of all cell types is energy-dependent and RNA-mediated via natural selection for codon optimality. See for example:
rs3827760, also known as 1540T/C, 370A or Val370Ala, is a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2. This SNP links the mouse model of cell type differentiation to humans. That fact has been known for at least 3 years.
See:

  1. Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant
  2. A genetic basis of variation in eccrine sweat gland and hair follicle density
  3. A genome-wide association scan implicates DCHS2, RUNX2, GLI3, PAX1 and EDAR in human facial variation

Other energy-dependent base pair changes link natural selection for codon optimaility from SNPs to RNA-mediated amino acid substitutions and differences in intelligence and/or unexplained death risk.
A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence
An insertion/deletion polymorphism within 3’UTR of RYR2 modulates sudden unexplained death risk in Chinese populations
Few people can place the findings on energy-dependent codon optimaility into the proper context of natural information processing. How many do you know who might claim that natural selection links mutations to evolution?

Compare the people who think in terms of mutation-driven evolution to those who know the energy-dependent differences between archaea and bacteria. The greater energy-dependent stability of organized genomes in bacteria can be liked to the stability of eukaryotes. The instability of archaea genomes can be linked from virus-driven energy theft to the degradation of messenger RNA and negative supercoiling of DNA.
All cell type stability link the sun’s anti-entropic virucidal energy from the creation of all biodiversity to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy, which links mutations to all pathology.
See for instance, (2013) MicroRNA-based regulation of epithelial-hybrid-mesenchymal fate determination

The authors

…address long-standing fundamental questions linked to compelling clinical needs—how to distinguish between the aberrant dynamics of epithelial–hybrid–mesenchymal transitions during tumorigenesis vs. the normal programs of embryonic development and tissue regeneration.

The “normal programs” are energy-dependent and biophysically constrained by the physiology of reproduction.The senior author should have received the 2016 Nobel Prize for linking energy-dependent autophagy to supercoiled DNA, but the Prize is not awarded posthumously, as I recall.

Politicized “science” often prevents the Prize in Physiology or Medicine from being awarded to anyone whose works challenge the ridiculous theories about mutation-driven evolution. Those who present experimental evidence of how cell type differentiation is biophysically constrained by energy-dependent changes in the microRNA/messenger RNA balance tend to be virtually ignored.

Even some of the creationists I have encountered want others to keep thinking in terms of evolution rather that energy as information. Peter Berean, for example, decided to invent the term “bio-functional information” when he realized that the sun’s anti-entropic virucidal energy was the only obvious link from microRNA flanking sequences to all healthy longevity and that virus-driven energy theft was the link to all pathology.If you want to learn how serious scientists are combating evolution to fight disease on two fronts, see any claim made by an old earth creationist, or any claim made by any atheist. The similarities led Peter Berean to substitute “bio-functional information” for de Vries 1902 definition of “mutation.”

See for comparison:

2003 Bacterial self–organization: co–enhancement of complexification and adaptability in a dynamic environment

2006 Seeking the foundations of cognition in bacteria: From Schrödinger’s negative entropy to latent information

2009 Learning from Bacteria about Natural Information Processing

See also: CRISPR study reveals unexpected roles of non-coding RNAs

Royal Society’s Sir Venki Ramakrishnan Agrees to Post Public Evo Audio

…the public discussion from the recent “new trends” in evolution conference will be posted shortly online on the Royal Society event webpage.

Suzan Mazur helped force them to do what they claim they would do:

Recorded audio of the presentations are available below.

It’s been six weeks and the recorded audios from the audience are not available.

If the recorded comments become available, the public discussion may help to reveal that the fate of all cell types is energy-dependent and RNA mediated via natural selection for codon optimality and autophagy.

See for other examples: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

These two reports (Grossman et al., 2013; Kamberov et al., 2013) tell a new short story of adaptive evolution. The story begins with what was probably a nutrient-dependent variant allele that arose in central China approximately 30,000 years ago. The effect of the allele is adaptive and it is manifested in the context of an effect on sweat, skin, hair, and teeth. In other mammals, like the mouse, the effect on sweat, skin, hair, and teeth is due to an epigenetic effect of nutrients on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones control the nutrient-dependent hormone-dependent organization and activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates as previously indicated. That means the adaptive evolution of the human population, which is detailed in these two reports, is also likely to be nutrient-dependent and pheromone-controlled, since there is no other model for that.

Each week’s science news brings additional representations of facts that refute all neo-Darwinian pseudoscientific nonsense by linking Darwin’s “conditions of life” to all biodiversity. Most science news outlets still report and/or tout pseudoscientific nonsense because the reporters missed the fact that life is nutrient-dependent and the physiology of reproduction is controlled by pheromones is species from microbes to humans.
Can you imagine how embarrassed you would be if you had not learned that all organisms must eat or they cannot reproduce, which means they could never have become an organism of a species? What’s worst is that no experimental evidence of biologically-based cause and effect support claims that one species evolved into another. For comparison, this recent report shows changes in organized genomes that link the nutrient-dependent pheromone-controlled physiology of reproduction in moths to bacteria and from bactreria to humans via conserved molecular mechanisms of RNA-mediated protein folding chemisrty.

Engineers create programmable silk-based materials with embedded, pre-designed functions

… the researchers created a surgical pin that changes color as it nears its mechanical limits and is about to fail, functional screws that can be heated on demand in response to infrared light, and a biocompatible component that enables the sustained release of bioactive agents, such as enzymes.

The news article cites: Directed self-assembly of silk fibroin into bulk materials: with the subtitle: Programming function into mechanical forms from the nano- to macroscale,
I look forward to learning why they are claiming that energy-dependent assembly is “directed self-assembly.”

rp_levels-of-organization.jpg

Light ‘drives’ adaptation; nothing ‘drives’ evolution (2)

See: Light ‘drives’ adaptation; nothing ‘drives’ evolution

See also: Who rules the waves? – Viruses might just be bit players in the drama of the seas. Then again, they could be major actors

Excerpt (from 1996): 

Most consider viruses to be a legion of cripples, sterilised by ultraviolet radiation and rendered impotent by hosts that are largely immune to their threat. But a few researchers take the opposite view. And if they turn out to be right, viruses could radically alter the balance of life in the oceans, ripping away huge parts of the food web that supports whales, sea birds and the fisheries on which many people rely.

See also: Riding the Evolution Paradigm Shift With Eugene Koonin

Excerpt: 

This is a good point to make. The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…

From 1996: From Fertilization to Adult Sexual Behavior

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

Forthcoming, two decades later: New trends in evolutionary biology: biological, philosophical and social science perspectives
Excerpt:

Developments in evolutionary biology and adjacent fields have produced calls for revision of the standard theory of evolution…

My comment: Topics mentioned in the abstracts (my categories):

Science

The physics of organisms

multilevel and reciprocal causation

adaptability could influence the inherited characteristics of an organism’s descendants
phenotypic traits have complementary rather than antagonistic functions
‘second inheritance system’, built on the shoulders of the primary genetic inheritance system
adaptive design at the level of genes, individuals and societies
…niche construction co-directs adaptive evolution
integrated symbioses
‘developmental niche construction’ as a framework to integrate findings from fields ranging from molecular biology to developmental psychology
epigenetic inheritance
the involvement of epigenetic inheritance in adaptive evolutionary change
inherited yet non-genetic adaptation.
somatic inheritance, maternal effects and DNA methylation.
processes that sustain persisting lineages.
understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations

Pseudoscientific nonsense

a distinction between epigenetic and exogenetic inheritance

different narratives as to exactly what such an evolutionary approach entails.
how different mechanisms of inheritance contributes to evolution.
understanding of how important the process has been in shaping the evolution of animal form.
a closely allied distinction between ‘organic’ and ‘cultural’ evolution?
domestication to serve once again as a model system
‘human like’ modes of behaviour (and presumably more biocultural evolution)

See for comparison to everything currently known to serious scientists about biophysically constrained energy-dependent RNA-mediated protein folding chemistry.

A niche for the genome

Excerpt:

…the study of phenotypic plasticity, epigenetic and exogenetic inheritance, have not yet demonstrated the need for any revolutionary change in evolutionary thought. For us they highlight the extent to which proximate developmental mechanisms can inform ultimate biology.

My comment: Twenty years after our review of energy-dependent RNA-mediated molecular epigenetics and cell type differentiation, this exemplifies the overwhelming foolishness of theorists who seem to think that not all developmental mechanisms are energy-dependent and biophysically constrained by the physiology of reproduction.

See also the discussion attempt at: What does DNA have to do with the Origin of Life ?