Electron cloud superimposed on the yin yang symbol

The "walking fish" walks straight from quantum physics to quantum souls (3)

The molecular dynamics of the hydrophobic amino acid, valine, link the anti-entropic virucidal energy of sunlight from the Second Law of Thermodynamics to the energy-dependent and temperature-dependent orientational dynamics of the structure of water via methylation and acetylation in the C and N terminus, respectively.
The quantized energy of sunlight must be linked from energy as information to energy-dependent methylation and acetylation to all biodiversity via the effect of the energy on contact with water and the physiology of pheromone-controlled reproduction in the context of changes in base pairs and fixation of RNA-mediated amino acid substitutions that differentiate all cell types in all living genera.
Philip Ball inadvertently claims to have missed all the scientific progress during the past 5 decades in: Chiral water in DNA’s hydration shell

I missed previously this nice paper from H. F. M. C. Martiniano and Nuno Galamba in Lisbon on the structure and dynamics of water around a hydrophobic amino acid…

Philip Ball’s admission can be linked to the ignorance of food energy-dependent pheromone-controlled biophysically constrained viral latency in all living genera. Food energy links sunlight on contact with water to hydrophobicity in supercoiled DNA.
From last year: Worms dine on nanoparticles to help test biological force sensor technology

Adding to Goodman’s previous research on how neurons process the sensation of touch, this technique could also enhance our understanding of the forces involved in sensing the world around us. “More detail about how we experience touch could inform the translation of touch into non-biological systems, like prosthetics,” Goodman said.

The spurious link from touch to biological systems and/or non-biological systems makes it seem that — like Philip Ball — they are oblivious to the fact that serious scientists linked 

1) the de novo creation of anti-entropic virucidal light to

2) chirality, which links

3) the speed of light

4) on contact with water from the

5) de novo creation of G protein coupled receptors and

6) all energy-dependent biodiversity via

7) the innate immune system,

8) autophagy,

9) the physiology of reproduction, and

10) supercoiled DNA, which

11) protects all organized genomes from

12) virus-driven energy theft and

13) genomic entropy.

The thirteen steps that link sunlight to healthy longevity and the virus-driven theft of quantized energy to all pathology were placed into a context of a section in the news report on worms:

From worm food to human health

The fact that worms and humans must eat to be healthy was not included in the publication on touch in July 2017 as Upconverting Nanoparticles as Optical Sensors of Nano- to Micro-Newton Forces.
The link from nanoparticles to optical sensors via micro-Newton forces preceded retractions of two works that reported on the automagical creation of RNA.
The creation of RNA is food energy-dependent and it was linked from the creation of ATP to all biodiversity in 1964.
See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

See for comparison: ”Definitely embarrassing:” Nobel Laureate retracts non-reproducible paper in Nature journal

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.

Philip Ball has now linked what he calls Chiral water from the structure and dynamics of water around a hydrophobic amino acid to supercoiled DNA, which links sunlight and food energy to protection of all organized genomes from the virus-driven degradation of messenger RNA. The virus-driven degradation of messenger RNA links the theft of quantized energy from mutations to all pathology. Nothing from the claims about optical sensors is pertinent outside the context of the fact that all organisms must find food and reproduce for any species to survive.

That is why I am adding my comments from last year on: Worms dine on nanoparticles to help test biological force sensor technology. Philip Ball must have missed these facts, also.

Two epigenetic traps are required to link hydrogen-atom transfer in DNA base pairs in solution to the energy-dependent physiology of pheromone-controlled reproduction. It is unlikely that the traps automagically emerged and more unlikely that any species has ever evolved from any other species via mutations and natural selection. Instead, the epigenetic traps make it perfectly clear that evolutionary theorists and “big bang” cosmologists know nothing about energy-dependent biophysically constrained RNA-mediated cell type differentiation.

That fact may explain why Vice-President Pence wants the students in public schools to be taught how ecological variation must be linked to ecological adaptation via everything known to physicists, chemists, and biologists. All serious scientists have linked what is known about molecular epigenetics from energy-dependent changes in electrons to to ecosystems in all living genera.

If we raise another generation of students who are biologically uninformed, some human populations in the USA might as well agree to be the naturally selected victims of the forthcoming viral apocalypse. When large populations begin to suffer unnecessarily and die prematurely, the 1918 Spanish flu will be remembered as the harbinger of ignorance that led to the suffering and death of millions, mostly in the cities of the USA. That’s where the panic and riots start.

You’ve read about this in books (Arrowsmith, 1925) and seen the movies. Prepare yourself for the reality of energy-dependent chirality. It’s the First Law of Thermodynamics that everyone must eventually accept. Food energy is biophysically constrained in all cell types until the virus-driven theft of quantized energy links the degradation of messenger RNA from mutations to all pathology.

It would be great if that fact was taught in public schools instead of teaching students to believe in pseudoscientific nonsense. In any case, the sun’s anti-entropic virucidal energy cannot simply be removed from consideration by theorists and/or so called science journalists who have failed to link quantum physics to quantum souls.

See for comparison: Quantum secret sharing for a multipartite system under energy dissipation

… noise is associated with energy dissipation and hence, loss of probability to distinguish and decode the information at the receiving end. Finally, we make this task possible through an optimization algorithm.

In their optimization algorithm, a mathematical model is applied to all forms of life on Earth but the dissipation of energy is not linked to death. Everyone who believes that energy cannot be created or destroyed knows that there is no “quantum secret.” Dissipated energy does not vanish in the context of any model that links the functional structure of supercoiled DNA to the protection of all organized genomes from the virus-driven degradation of messenger RNA.
When theorists tout secrets in the context of quantum physics, the secrets of their mathematical models can be compared to facts. See: Structural diversity of supercoiled DNA
The functional structure and the diversity of supercoiled DNA is energy dependent and biophysically constrained by temperature dependent changes in amino acid substitutions.
See also: Temperature dependence of amino acid hydrophobicities
Reported as: Early Code

“Our work shows that the close linkage between the physical properties of amino acids, the genetic code, and protein folding was likely essential from the beginning, long before large, sophisticated molecules arrived on the scene,” Carter said in a statement. “This close interaction was likely the key factor in the evolution from building blocks to organisms.”

The pseudoscientific nonsense of the historical perspective on evolution was included in this 2005 claim: Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.
My comment to The Scientist on the Early Code:

Simultaneous emergence was suggested by Matti Pitkanen who pirated my model of biophysically constrained RNA-mediated cell type differentiation and claimed that “Hens and eggs emerged simultaneously.”

Serious scientists now appear to have discovered the link from the light-induced de novo creation of amino acids to the de novo creation of receptors that link RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of genera via the nutrient-dependent chemistry of RNA-mediated protein folding.

The nutrient-dependent physiology of metabolic networks and genetic networks link reproduction to fixation of the amino acid substitutions, which enables all extant biophysically constrained biodiversity, which is exemplified in differences in morphological and behavioral phenotypes.

Claims of simultaneous emergence should be supported by experimental evidence of biologically-based cause and effect, or abandoned along with claims of Mutation-Driven Evolution, like this one: “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.” (p. 199)

For comparison, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which was published on the same day as Nei’s textbook: June 14, 2013.

Historical perspective from Jon Lieff who is a very confused award-winning blogger: Synchronizing with Brain Clocks

The three previous posts have described new research that each living cell has its own individual clocks based on genetic feedback loops combined with epigenetic loops. The three posts described the discovery of individual clocks, the relation to metabolic cycles in tissues and other cells, and the way immune cell cycles alter responses based on clocks.

The three posts he mentioned fail to include any citations, such as a citation to my published 2013 review, which was a refutation of the neo-Darwinian pseudoscientific nonsense. Jon Lieff has continued to tout his pseudoscietific nonsense after I told him about food energy-dependent Alternative Splicings of RNA on October 27, 2013.
See my comment on his misrepresentations of: Alternative RNA Splicing in Evolution

In our 1996 Hormones and Behavior review, we wrote:”Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans.”

From Fertilization to Adult Sexual Behavior

The alternative splicings are nutrient-dependent and appear to be enabled by the experience-dependent de novo creation of olfactory receptor genes, which enable additional receptor-mediated nutrient uptake and the metabolism of nutrients to species-specific blends of pheromones that control reproduction in species from microbes to man.

Your focus on the importance of pre-mRNA and alternative splicing is exemplary, especially in the context of neuronal plasticity.

C. elegans is the model organism of neurogenic niche construction that links nutrient-dependent ecological and pheromone-controlled social niche construction to socio-cognitive niche construction in vertebrates and invertebrates. See for review:

Nutrient-dependent/pheromone-controlled adaptive evolution: a model

What you are helping to detail is self-assembly with evidence of olfactory/pheromonal self-organization that is currently missing from evolutionary theory, which attributes speciation to mutation-initiated natural selection even though there is no experimental evidence for that (as I mentioned elsewhere).

See for comparison: Promises and Challenges in Continuous Tracking Utilizing Amino Acids in Skin Secretions for Active Multi-Factor Biometric Authentication for Cybersecurity
In Figure 1., they link the biophysically constrained biocatalytic cascade via two optical detection pathways to the energy-dependent creation of three amino acids. This extends what is known about natural selection for food energy-dependent codon optimality to all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans.
The key to understanding how ecological variation must be linked to ecological adaptations is the role played by fixation of RNA-mediated amino acid substitutions. The measurement of NADH (energy) at 340 nm (ultraviolet), and the conversion of NADH (energy) to a observable yellow color at 580 nm links quantized energy as information from ultraviolet (UV) light to the visible spectrum. That fact is also manifested in results from chemistry testing and other laboratory testing that helps physicians diagnose and effectively treat their sick patients.
Chemists and molecular biologists must know how to link physics to results of diagnostic testing.
See: The Gene Polymorphism of VMAT2 Decrease the Risk of Developing SCZ in Male Han Chinese (link opens pdf)

A GWAS research found an female-specific association with rs7341475 in reelin (RELN ) gene [30]. Most interestingly, in a study show in a same gene, different SNPs conduct different sex-spefic effect: eg, SNPs rs3891636, rs7728773, rs2189663,rs3864283, and rs2526303 of HINT1 gene significant among the female subjects alone, whereas SNP rs7735116 was significant among males alone [31]. These studies indicate there may exit sexspecific genetic risk and protective factors to SCZ.

I placed the failure of all theorists to link energy-dependent changes in base pairs from SNPs to the RNA-mediated amino acid substitutions that differentiate all cell types in all living genera into the context of this invited review of nutritional epigenetics,

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

For comparison to the VMAT2 polymorphism linked to thje decreased risk of schizophrenia, I took a broad-based approach. The ingestion of sago palm-like leaves linked increased endogenous vitamin C from the stablility of the organized genome in mice to the stability of the organized genome in a modern human population via this report: Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant.
They linked one a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2 to differences in the morphological and behavioral phenotypes of species from mice to humans. Note: rs3827760 is also known as 1540T/C, 370A or Val370Ala. Nothing known to serious scientists about biophysically constrained biologically-based cause and effect suggest that base pairs and amino acid substitutions evolved to create proteins.
For comparison to Szostak’s retracted claims about RNA, see: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism and compare what is known to serious scientists to the claims of creationists.
Oops! Scientific retraction a major blow to evolution theory

The finding is the latest in a “replication crisis” sweeping the scientific community in which apparent breakthroughs cannot be repeated by other researchers.

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.

Szostak’s comment that his team was “blinded by our belief” is significant. Previously, he condemned “belief systems based on faith” as “inherently dangerous, as they leave the believer susceptible to manipulation when skepticism and inquiry are discouraged.”

My invited review of nutritional epigenetics was returned without review, and no one has commented on the representations in Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems that link energy-dependent changes from electrons to ecosystems in all living genera via more than 68,000 published works on microRNAs.
See for instance: Two-Color-Based Nanoflares for Multiplexed MicroRNAs Imaging in Live Cells

…two-color-based nanoflares can simultaneously detect miR-21 and miR-141 expression levels in various live cancer cells successfully. Compared to the traditional single-color-based nanoflares, the two-color-based nanoflares could offer more reliable and practical information for cancer detection, improving the accuracy of early disease diagnosis.

Diagnostics: The changes in the the two-color-based nanoflares will eventually be used to determine the differences in the number of viral microRNAs compared to the number of food energy-dependent microRNAs. The differences will link the weekend resurrection of the bacterial flagellum in P. fluorescens to cell type differentiation in the “walking fish” via dietary differences and biophysically constrained pheromone-controlled reproduction, which requires a source of ingested iodine for the maturation of sex differences in cell types.
Treatment: Exosomes from human umbilical cord blood accelerate cutaneous wound healing through miR-21-3p-mediated promotion of angiogenesis and fibroblast function

 
Cytosis

MicroRNAs light up life

Summary: Every aspect of cell type differentiation or mutation-driven pathology occurs downstream from the de novo creation of energy-dependent microRNAs. That fact should be considered in all aspects of top-down causation, which must link the sun’s energy to behavior via the physiology of reproduction and chromosomal inheritance.

On a relational theory of biological systems: a natural model for complex biological behavior (5/29/17)

In this paper, we develop a natural (empirical) relational theory for describing and modeling complex biological phenomena. We have as stepping stone the assertion: function implies structure. The theory is built upon a graph’s theory structure in which a diffusion model of information takes place, and where dynamics can be investigated in order to generate steady quantifiers. In this context, we improve a seminal work by adding a free context biological importance measure given by the Shannon’s Entropy. We also introduce the concept of biological loci. Such concept stands for closely related biological agents which plays a role as an agent by itself. Our results allow us to synthesize a natural model for complex biological behavior that takes into account: system’s update, irreducibility, and exploit of the dynamical behavior mounted over a diffusion model. The model deals in final terms to its natural capacity to model plasticity and environmental changes, which has an intrinsic relationship with Shannon’s Entropy and the sort of dynamics that biological systems can display.

It’s too late for any more of this pseudoscientific nonsense about entropy and increasing organismal complexity, which is energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction.

See also: Evolution Not Only About Natural Selection but Also Improvisation, Says Israeli Scientist

Evolution, he argues, is not limited to families of plants and animals, but also occurs inside individual living things – whether they are, say, cells, plants, horses or people.

It is too late for people like him to redefine “evolution” in the context of a theory of adaptive improvisation at the level of links from energy-dependent changes in angstroms to ecosystems. All biologically informed researchers have followed the lead of the late Eshel Ben-Jacob, who realized that natural selection for energy-dependent codon optimality links what organisms eat to the physiology of their pheromone-controlled reproduction. All serious scientists have known that for more than two decades.

To start from cell type differentiation in bacteria, see: Seeking the foundations of cognition in bacteria: From Schrödinger’s negative entropy to latent information (2006)

…it is widely accepted that there is no need for some unknown laws of physics to explain cellular ontogenetic development. We take a different view and in Schrödinger’s foot steps suggest that yet unknown physics principles of self-organization in open systems are missing for understanding how to assemble the cell’s component into an information-based functioning “machine”.

If your ridiculous theory does not explain how the virus-driven degradation of messenger RNA is biophysically constrained by the physiology of nutrient-dependent pheromone-controlled reproduction in species from microbes to humans, you must start learning what serious scientists have learned during the past century.

Simply put, the last universal common ancestor had the ability to find food. That fact attests to the glory of all Creation, which starts with the Creation of sunlight. The claims of some creationists can be placed into the context of a light-activated endogenous substrate in all cell types that links energy as information to endogenous RNA-interference and all biophysically constrained biodiversity via the pheromone-controlled physiology of reproduction.

Theorists can continue to claim whatever they wish. But none of their claims make sense if they cannot link energy to healthy longevity via the physiology of reproduction and also link the virus-driven degradation of messenger RNA from mutations to all pathology.

Serious scientists have done that. See: 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.

Disease Awareness Months Work, Even If You Don’t Wear The Ribbon

For the people living with an illness that may lack effective treatments, much less a cure, even small increases in awareness are valuable. And that’s true whether or not anybody remembers what disease they’re supposed to be thinking about this month.

Think about this. Serious scientists have published more than 61,000 papers that link nutrient energy-dependent microRNAs to healthy longevity and virus-driven energy theft from the degradation of messenger RNA to mutations and all pathology. A PubMed search for “microRNA” and the name of the pathology you would like to cure will show you that the cure is always energy-dependent biophysically constrained viral latency.
autism
Myasthenia gravis
Congenital Cytomegalovirus

See for comparison:


 

fruit-dove

Happy Darwin Day (2017)

My series of blog posts about the refutation of theistic evolution by George Church led him to contact me via email.

  1. He asked why he would get credit for or against the refutations
  2. He claimed he was trained in quantum physics.
  3. He claimed that he has authored peer reviewed papers on protein folding, biodiversity, supercoiling, etc.
  4. He wanted to know more but did not know enough about my target audience to realize why I included information about the viral hecatomb.
  5. He also claimed to have written more on what is known about endogenous RNA interference than on exogenous RNA interference.

I invited him to discuss this further on my FB group, or on this domain. He declined. That was a great end to my 2017 Darwin Day.
See Evolution-guided optimization of biosynthetic pathways, which was co-authored by George Church and published December 1, 2014.
There is no such thing as evolution-guided optimization. Natural selection for energy dependent codon optimality is the only link from ecological variation to ecological adaptation in all living genera. That means we can move forward without George Church and still place his comments into the context of “Trust me, I’m a biologist.
I think that most serious scientists agree that you can’t trust evolutionary theorists For comparison, you can trust Darwin’s “conditions of life.”
Darwin’s “conditions of life” link the anti-entropic virucidal energy of sunlight to the physiology of reproduction in all living genera. Can you trust anyone who claims evolution did that?
See: RNA-Guided Human Genome Engineering 

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).

Nutrient energy-dependent microRNAs link natural selection for energy-dependent codon optimality to viral latency and protection of organized genomes from endogenous viral elements. Targeting endogenous viral elements with RNA-mediated amino acid substitutions is the key to biophysically constrained cell type differentiation. Fixation of amino acid substitutions prevents problematic nearly identical copies. There is no need for uncontrolled copies if there is no need to find another energy source. Uncontrolled copies link virus-driven energy theft from mutations to all pathology in all genera.
For example, energy theft from bacteria links messenger RNA degradation to morphological and behavioral phenotypes of archaea. Similarly, messenger RNA degradation in humans links the transgenerational epigenetic inheritance of Zika virus-damaged DNA to craniofacial morphology and brain development in infants.
Taken together with what is known about differences in energy-dependent endogenous RNA interference in nematodes, all ridiculous misrepresentations of Darwin’s works must be reversed to show the truth about what virus-driven energy theft does. It links RNA-mediated cell type differentiation from the energy-dependent creation of bacteria to the energy-dependent creation of humans and it links virus-driven energy theft to all pathology.
Riding the Evolution Paradigm Shift With Eugene Koonin

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

Is Eugene Koonin joking about what was left out? If not, big bang cosmologists and neo-Darwinian theorists have never tried to support their ridiculous theories with any experimental evidence of biologically based cause and effect. They never examined the role of energy-dependent microRNAs or virus-driven energy theft. Instead, they invented gene-centric theories of mutation-driven evolution.

See for comparison: Membrane Patterns Carry Ontogenetic Information that is Specified Independently of DNA
Reported as: Peer-Reviewed Paper: Development Needs Ontogenetic Information that Cannot Arise from Neo-Darwinian Mechanisms

With over 400 citations to the technical literature, this well-researched and well-documented article shows that embryogenesis depends on crucial sources of information that exist outside of the DNA.

A 16 page monograph with 12 pages of citations is an unparalleled achievement for anyone who is not a polymath or someone who has not already linked physics and chemistry from molecular epigenetics to all biophysically constrained cell type differentiation in all living genera via fixation of nutrient energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA.
None of the cited works appear to link what is known about virus-driven energy theft to all pathology. Again, it is time to move forward.
See: Charles Darwin’s Ocean Upwelling

It’s hard to overstate how vital Darwin’s coral reef theory was in developing his career and thinking. It paved the way, conceptually and methodologically, for everything to come — particularly his transmutation theory [natural selection]. The likenesses startle. Like the transmutation theory, the coral reef theory described how small, virtually unnoticeable changes could create differences of essential type in seemingly immutable forms — and in doing so, account for broad patterns of development and difference.

Changes in coral reefs are nutrient energy-dependent and controlled by the physiology of reproduction. De vries defined “mutation” in 1902, which means that Darwin could not have had a transmutation theory. Also, Darwin repeatedly asserted the claim that his “conditions of life” must come before any claims about natural selection.
Darwin Day 2017 may become known as the day George Church refused to publicly discuss evolution or to admit there is no such thing as evolution outside the context of virus-driven energy theft and the evolution of  pathology. On the same day, The Smithsonian National Museum of Natural History blog site published a post that misrepresented everything known to serious scientists about biophysically constrained energy-dependent RNA-mediated cell type differentiation and healthy longevity.  Who could ask for a better Darwin Day than one during which Darwin’s “conditions of life” clearly triumphed over the ridiculous claims made by neo-Darwinian theorists and others who refuse to admit to the facts that link energy-dependent changes in chirality from autophagy to endogenous RNA interference and to supercoiled DNA, which prevents virus-driven energy theft from causing the mutations that all serious scientists have linked to all pathology?
 

Alternative splicing of pre-mRNA

Energy-dependent de novo creation and neurogenesis (2)

See also: Energy-dependent de novo creation and neurogenesis
12/7/16 Atlas of the RNA universe takes shape
Excerpt:

MicroRNA are very mysterious. They are really relics of the RNA world—pieces of RNA that are highly reactive, very small and which pair and bind other RNA and facilitate catalytic reactions,” Mangone says. “We don’t know much about them—where they come from or how they regulate gene expression, but they are very misregulated in many diseases.

See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model Published 14 Jun 2013
Excerpt:

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.

My comment: Only if you lived among wolves or among theorists for the past 10 years would you not know that more than 55,000 indexed publications link energy-dependent changes in the microRNA/messenger RNA balance to healthy longevity. For comparison, all serious scientists also know that virus-driven energy theft links viral microRNAs from mutations to all pathology.
You need only search for “RNA mediated” to find information on how cellular and viral microRNAs are linked from energy-dependent changes to RNA-mediated amino acid substitutions and biophysically constrained protein folding chemistry. For example, this is all it takes to recognize the amount of pseudoscience that is packaged in claims that we don’t know much about microRNAs.
See also: Published to Figshare 10 April 2014

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.

See also: MicroRNAs: the future of genomic science?
Excerpt:

The ubiquity of miRNA occurrence is reflected in the current literature, which reports a wide range of potential biomarker applications for this highly conserved molecule.

My comment: MicroRNAs are biomarkers that clearly link energy-dependent biophysically constrained changes in base pairs from RNA-mediated amino acid substitutions to cell type differentiation in all living genera. The energy-dependent links from the innate immune system to the physiology of reproduction also link all metabolic networks to all genetic networks in species from microbes to humans.
See for comparison: A single splice site mutation in human-specific ARHGAP11B causes basal progenitor amplification

…we hypothesize that the novel, human-specific C-terminal sequence of modern ARHGAP11B has a key role in the mechanism by which this protein promotes BP amplification. In this regard, the present data show that this sequence is due to a single C→G base substitution, which creates a novel splice donor site that results in the replacement of the ancestral C-terminal sequence of the ARHGAP11B GAP domain. The present data also demonstrate that this single C→G base substitution underlies the ARHGAP11B-mediated BP amplification implicated in neocortex expansion.

Reported as: Small Mutation Contributed to Evolution of Bigger Human Brains
Excerpt:

A single base change in a human gene likely played an important role in evolutionary expansion of the human brain, researchers say.

My comment: They claim that a single cytosine to guanine substitution created a novel splice site. They failed to mention that base pair (BP) amplification is nutrient energy-dependent. They also failed to mention that the de novo creation of a novel splice donor site must be linked from the energy-dependent fixation of an RNA-mediated amino acid substitution to the physical landscape of supercoiled DNA via the physiology of reproduction.

Svante Paabo is one of the co-authors who reported this:

Hence, it is not the ARHGAP11 partial gene duplication event ~5 million years ago, as such, that impacted human neocortex evolution. Presumably, ARHGAP11A and ancestral ARHGAP11B coexisted as functionally similar proteins for some time after the gene duplication event. The ability of ARHGAP11B to amplify BPs likely arose more recently from a change that is tiny on a genomic scale but substantial in its functional and evolutionary consequences.

My comment: No experimental evidence of biologically-based cause and effect suggests that any partial gene duplication event ~5 million years ago could have linked a mutation and the altered de novo creation of genes that Svante Paabo (and co-authors) placed into the context  of biophysically constrained biodiversity in:

Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees

My comment: Natural selection for energy-dependent codon optimality is the only way to link the de novo creation of genes from autophagy to RNA-mediated amino acid substitutions and nutrient-dependent polycombic ecological adaptation.
See: 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.

See also: PTBP1 and PTBP2 Serve Both Specific and Redundant Functions in Neuronal Pre-mRNA Splicing
Excerpt:

…the two paralogs displayed similar RNA binding across the transcriptome, indicating that their differential targeting does not derive from their RNA interactions, but from possible different cofactor interactions.

My comment: The cofactors are nutrient energy-dependent microRNAs, which are linked to healthy longevity and all biodiversity and viral microRNAs, which are linked from mutations to all pathology.
See also: Viral and cellular messenger RNA targets of viral microRNAs

…viral miRNAs may be particularly important for regulating the transition from latent to lytic replication and for attenuating potentially inhibitory host antiviral immune responses.

See also: Nothing in Biology Makes Any Sense Except in the Light of Evolution
Excerpt:

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).”

See also: Light- and Carbon-Signaling Pathways. Modeling Circuits of Interactions

…carbon either attenuated or potentiated light repression of ASN1 in light-grown plants. These studies indicate the interaction of carbon with blue, red, and far-red-light signaling and set the stage for further investigation into modeling this complex web of interacting pathways using systems biology approaches.

My comment: When did theorists decide to take the light as information and energy out of systems biology and ecological adaptations? Who decided to replace the anti-entropic virucidal energy of light with mutations and evolution?