Light-induced-conformer-intercoversion-of-hydrogen-bond

Open Science: Closed to facts about microRNAs

See my 5-part series on: The tipping point? 50, 000 publications

Imagine how we could accelerate innovation, stimulate economic growth and all the solutions we need to live on a healthy and sustainable planet, if we were to open up our science fully and allow a free flow of scientific knowledge.” says Kamila Markram, a neuroscientist and the CEO of Frontiers, one of the largest Open Access science publishers in the world and a leader in the Open Science movement.

Talk is cheap. See: Understanding and accounting for relational context is critical for social neuroscience
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 Socioaffective Neuroscience & Psychology 2012

Open access publication in Frontiers has not led to any discussion of facts represented since 2005 in articles like this and this one which was co-authored by 2004 Nobel Laureate, Linda Buck. Feedback loops link odor and pheromone signaling with reproduction.
See for comparison, the validation of my model and its importance in the context of integrating disparate disciplines.
George F R Ellis wrote:

“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 [Top-down causation Organized by George F. R. Ellis, Denis Noble and Timothy O’Connor]: http://rsfs.royalsocietypublishing.org/content/2/1.toc ” 25 Apr 2014 at 07:49am

See also, my comment posted to YouTube:

Talk is cheap. I am a medical laboratory scientist whose efforts to use open access publication have not led to any discussion of facts about energy-dependent biophysically constrained RNA-mediated cell type differentiation or facts about how virus-driven energy theft can be linked from the degradation of messenger RNA to mutations and all pathology in all living genera. See: Energy as information and constrained endogenous RNA interference https://www.youtube.com/watch?v=cdtsfweO5SQ

Q: What happened to the facts about energy as information?

See: A different tack for Alzheimer’s research

“Despite observations that link mitochondrial dysfunction and sporadic neurodegenerative disease, there hasn’t been a robust hypothesis that could explain the origin of mitochondrial stress associated with human aging and able to account for neurological disease observed across the entire human population,” Larsen continues. “The ‘Alu neurodegeneration hypothesis’ provides this link. Alus belong to a class of retrotransposons or mobile elements. They get the name ‘jumping gene’ because they can move about the genome and insert themselves into new locations. Alus are found only in primates, and they are abundant in the human genome (approximately 11 percent of human DNA). For a long time, they were considered junk DNA because their function was largely unknown. Only recently has the scientific community begun to appreciate how much Alu elements have influenced human evolution.”

A: The assumption that humans evolved has influenced the interpretation of any facts based on experimental evidence of energy-dependent de novo creation and/or maintenance of organized genomes. The facts have repeatedly showed that supercoiled DNA protects organized genomes from virus driven degradation of messenger RNA and that the degradation of messenger RNA links mutations to all pathology. The facts also links natural selection for energy-dependent codon optimality to the transgenerational epigenetic inheritance of all biophysically constrained biodiversity.

See also:  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.

See also: The Excitable Mitochondria by science journalist, John Hewitt.

…the brain’s logical architecture may, in the end, be familiar to us. We do not, after all, have that many models for computation.

Also, there is only one model that links what organisms eat from food energy to the biophysically constrained brain development of humans. Nutrient-dependent/pheromone-controlled adaptive evolution: a model

…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.

See also: MicroRNA Items: 1 to 20 of 59836

What can be said about researchers who fail to use any model of biophysically constrained biologically-based cause and effect to link energy to supercoiled DNA and virus-driven energy theft to all pathology?

See for example: Mutation-Driven Evolution

Mutation is the change of genomic structure and includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc. (2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation.

See also and combination of these search terms for articles that have been published about clear links to energy-dependent increasing organismal complexity and how virus-driven energy theft contributes to all pathology.

microRNA; miRNA; virus; viruses; psychiatric disorders; autism spectrum disorder; biomarkers; genetic variation; expression profiling; animal studies

Location, Location, Location

Since first proposing that a cell’s function and biology depend on its surroundings, Mina Bissell continues to probe the role of the extracellular matrix.

Virus-driven energy theft prevents the typical interactions that link the function of the extracellular matrix to healthy longevity. As predictably occurs at the time of completion for any paradigm shift, Mina Bissell and others like her will claim that they have known about the role of viruses in cell type differentiation for several decades.

Revealing literature gaps. At UCB, Bissell became interested in cell culture techniques and how viral transformation changes metabolism, working with virus-transformed chicken cells to study how glucose metabolism differs from that of normal cells in culture. She began to read the literature on the Warburg effect—the observation that cancer cells produce energy by aerobic glycolysis and lactic acid fermentation rather than through the typical ATP-producing oxidative phosphorylation cycle.

Bissell’s lab again confirmed that transformed cells rely more heavily on aerobic glycolysis for energy, but that the switch to this energy pathway did not result from the impairment of the hydrogen-transfer pathway. The results, says Bissell, went against the other half of Warburg’s hypothesis: that the reason for the increased glycolysis is impaired hydrogen transfer.

Her lab could not have confirmed anything associated with Warburg’s hypothesis (in 1976). The differences in the energy of photons had not yet been linked from hydrogen-atom transfer in DNA base pairs in solution to the biophysically constrained physiology of reproduction and all biodiversity via changes in base pairs and fixation of amino acid substitutions in supercoiled DNA that protect all organized genomes from virus-driven energy theft and genomic entropy. Since then, the Nobel Prize-winning works of Thomas Hunt Morgan (1933 Physiology or Medicine) and Schrodinger/Dirac (1933 Physics) have linked changes in atomic energy from chirality (Ben Feringa, Chemistry 2016) to autophagy (Yoshinori Ohsumi, 2016 Physiology or Medicine and chromosomal inheritance via the pheromone-controlled physiology of nutrient energy-dependent reproduction in species from microbes to humans.

According to Bissell’s ‘dynamic reciprocity’ model, signals from the ECM traveled through transmembrane receptors to a cell’s interior and nucleus, altering its gene expression.

According to my model of biophysically constrained biologically-based cause and effect Bissell’s ‘dynamic reciprocity’ model fits into the context of neo-Darwinian pseudoscientific nonsense instead of into the context of established facts.

See: Feedback loops link odor and pheromone signaling with reproduction

See for comparison:

Cytosis: Biology Content

 

Help Me Write Some Biology Content

Project Update #5: Cytosis: A Cell Biology Board Game by John Coveyou (Genius Games)

Many of you have mentioned that you’d like to have an explanation of the biology behind Cytosis available… and I think that is an AWESOME plan. Every time I’ve taught the game to non-science players in the past, they say gameplay made even more sense (and was so much more enjoyable) when I explained the science as well. This way they knew WHY they were doing what they were doing!

If you’ve got a strong background in biology, love explaining complexities in a way that someone unfamiliar with biology could understand, and would be interested in volunteering to help me write a page or two of science explanatory content for the rulebook, please shoot me an email… with the subject line “Cytosis Biology Explanations – [Your Name]” and we can start discussing!

I wrote: Kohl’s Laws of Biology may help. See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

1) Life is nutrient-dependent. See for review [2, 31]. The physiology of reproduction is pheromone-controlled. See for review [30].

In the context of the game “Cytosis,” Kohl’s Laws link the epigenetic effects of food odors and pheromones to changes in the mitochondria of all cell types. The energy-dependent changes in the mitochondria are linked to healthy longevity.
If the epigenetic effects of food odors and pheromones did not clearly link cytosis to healthy longevity, we would be left with only the link from virus-driven energy theft to all pathology. The explanation for all pathology involves more complexity than most people are willing to examine even when it is placed into the context of a book for a general, albeit educated, target audience.
See: The Scent of Eros: Mysteries of Odor in Human Sexuality

This is science at its best, with adventure, ideas, and lots of facts. — Helen Fisher

Details for other serious scientists:

The synthesis of RNA is nutrient energy-dependent. From 1964 Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

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

The anti-entropic virucidal energy of sunlight has since been linked to all biophysically constrained human cell type differentiation via representations in Feedback loops link odor and pheromone signaling with reproduction

The feedback loops link Dobzhansky’s claims about amino acid substitutions and RNA-mediated cell type differentiation from natural selection for energy-dependent codon optimality to the pheromone-controlled biodiversity of all living genera.

See: Combating Evolution to Fight Disease

…transient errors in mRNA synthesis can also cause heritable non-DNA-based phenotypic change. This is observed when low-abundance transcriptional regulators are affected by transcription errors. This disruption can cause a cell to alter its gene expression, resulting in a phenotype that may be heritable (2).

See also: Carl Woese, Evolution’s Golden Revolutionary

…there is probably no other scientist but Carl Woese who could write about having “no use for natural selection” and have Nature magazine respond with a Nobel endorsement. It is Carl Woese who first identified the Archaea and introduced us to horizontal gene transfer.

Virus-driven energy theft causes the degradation of messenger RNA, which links negative supercoiling of DNA in bacteria to the creation of archaea and links the conserved molecular mechanisms from archaea to the evolution of all pathology. For comparison, horizontal gene transfer links the nutrient energy-dependent de novo creation of genes from the pheromone-controlled fixation of RNA-mediated amino acid substitutions to supercoiled DNA, which prevents virus-driven energy theft from causing more degradation of messenger RNA.

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

This invited review of nutritional epigenetics includes a model that links nutrient energy-dependent changes from atoms to ecosystems. Most theorists have been caught with their pants down because they are still making claims about mutations and evolution. How can serious scientists compete with pseudoscientists who make claims that link mutations to millions of year of evolution?  Most serious scientists know how to link quantized energy from chemistry to biologically-based cause and effect. Most biologically uninformed people accept the claims of pseudoscientists, atheists, and other theorists.

Some Harvard researchers are still trying to hide facts that link research on the synthesis of mRNA to all biophysically constrained biodiversity on Earth via hydrogen-atom transfer in DNA base pairs in solution and RNA-mediated amino acid substitutions in supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. ATP-dependent cell type differentiation is placed into the context of conserved NAD+ and protein-protein interactions.

See:  A conserved NAD+ binding pocket that regulates protein-protein interactions during aging

See for contrast: Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention

It is now widely accepted that cancer is the result of the gradual accumulation of driver gene mutations that successively increase cell proliferation (1–3).

Johns Hopkins researchers framed everything known to serious scientists about cell type differentiation into the contest of cancer as ‘bad luck” as if cytosis was not energy-dependent and healthy longevity arose in the context of mutation-driven evolution — if species were lucky enough to evolve into other species.
No serious scientist has ever accepted that ridiculous claim.

See for comparison: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

…we characterize two distinct p120-associated complexes with antagonistic functions and we describe a microRNA (miRNA)-mediated mechanism through which the ZA suppresses transformed cell growth.

Backers and players of the game “Cytosis” will learn how the energy-dependent function of mitochondria must be linked to every aspect of healthy longevity or be linked from virus-driven energy theft to all pathology. They will be prepared to learn from the next game: “Photosynthesis,” which will link the sun’s anti-entropic virucidal energy to all biophysically constrained biodiversity via what is known to all serious scientists. They will not need to learn anything more than is required for them to reject the pseudoscientific nonsense of neo-Darwinian theories.

See what’s happened after 20 days of comments to this society. 

The information has been shared more than 450 times. The number of biologically informed students will force the biologically uninformed professors to stop playing the evolution game until they can begin supporting their ridiculous claims with facts. The facts must link ecological variation to ecological adaptations via what is known to serious scientists about hydrogen-atom transfer in DNA base pairs in solution.

Clearly, the facts tell us that all individuals of all species that live on Earth must eat and reproduce or they become extinct. None mutate and evolve into other species.

Thus, we regard as rather regrettable the conventional concatenation of Darwin’s name with evolution, because there are other modalities that must be entertained and which we regard as mandatory during the course of evolutionary time.

— Carl Woese and physicist Nigel Goldenfeld

I encourage others to support the development of games that teach what pseudoscientists do not want an interested target audience to learn. With enough support for an easy way to learn about energy-dependent cytosis compared to virus-driven pathology, the facts about RNA-mediated cell type differentiation will become clearer.

See also our section on molecular epigenetics in this review from 1996: From fertilization to adult sexual behavior

Every aspect of cytosis is food energy-dependent and RNA-mediated. Virus-driven energy theft cause all pathology. That fact makes sense in the context of all claims made by serious scientists. See for example:

 in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.) (pp. 73 and 74)

— with forward by Roger Penrose who co-authored with George F.R. Ellis and Stephen Hawking

“How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?”(Roger Penrose 8 August 1991)

See also:

James Vaughn Kohl “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 Socioaffective Neuroscience & Psychology 2012


    17 Apr 2014 at 03:07am

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 

See also:

…every angstrom is dynamic from the 5 prime to the three…

See also: Genetic 3’UTR variation is associated with human pigmentation characteristics and sensitivity to sunlight

Sunlight exposure induces signalling pathways leading to the activation of melanin synthesis and tanning response. MicroRNAs (miRNAs) can regulate the expression of genes involved in pigmentation pathways by binding to the complementary sequence in their 3′-untrastaled regions (3’UTRs).

Top-down causation starts from the creation of the sun’s anti-entropic virucidal energy. Hydrogen atom transfer in DNA base pairs in solution links energy-dependent changes in the microRNA/messenger RNA balance from microRNA flanking sequences to RNA-mediated amino acid substitutions that alter the stability of supercoiled DNA in the context of the physiology of reproduction.

One base pair change and a single amino acid substitution makes the difference between healthy longevity and pathology during life history transitions. See for example: Epigenetic Regulation of BDNF Gene during Development and Diseases
See also: Δ133p53 Functions to Maintain Redox Homeostasis in Response to Low ROS Stresses
https://www.omicsgroup.org/articles-images/single-cell-signaling-response-oxidative-stresses-5-154-g001.png
See also: Keep science a priority. Stand with ASCB at the March for Science rally April 22.
Light-induced-conformer-intercoversion-of-hydrogen-bond

Light-activated feedback loops vs self-organization of ecosystems

John Lieff has been trying to update his ridiculous misrepresentations of biologically-based cause and effect to match the accurate representations we made in a section on molecular epigenetics in our 1996 Hormones and Behavior review.

From Fertilization to Adult Sexual Behavior

Nothing can stop him, but this will provide the next source for material that he must borrow as if he learned about it somewhere else.

Apoptosis analysis guide | Free ebook download

Virus-driven energy theft causes apoptosis, which releases cell contents for recycling in the context of autophagy, which helps to ensure food energy-dependent pheromone-controlled RNA-mediated DNA repair in species from microbes to humans.

Gene bivalency at Polycomb domains regulates cranial neural crest positional identity

Journal article abstract excerpt (figure: Epigenetic regulation of cranial NC cell identity.)

A Polycomb-dependent poised chromatin organization underlies the positional plasticity of cranial premigratory NC cell progenitors. This chromatin prepattern is maintained through migration. In response to local cues encountered by the NC cells during or after their migration, the regulatory elements (E) and promoters (P) of differentially expressed genes switch from a poised to an active chromatin state, establishing transcriptional identities specific to subpopulations of NC cells.

The use of the term “chromatin prepattern” must be linked from endogenous RNA interference to all all biodiversity via transgenerational epigenetic inheritance. Watch closely as all pseudoscientists, atheists and other biologically uninformed theorists finally realize there is no such thing as mutation-driven evolution except in the context of virus-driven energy theft, apoptosis, and the evolution of pathology. Virus-driven energy theft causes degradation of messenger RNA in the absence of nutrient energy-dependent pheromone-controlled RNA-mediated amino acid substitutions and DNA repair.

MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos

Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We discovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability.

Reported as: The role of tiny RNA in genetic diversity March 28, 2017

All species, from zebrafish to humans, possess a genetically diverse collection of traits that allow them to adapt to changing environments. Yet scientists do not fully understand how organisms reach a state of optimal diversity—just enough variability to respond to environmental risks but not too much to function properly.

Natural selection for energy-dependent codon optimality is the link to optimal diversity. Conserved molecular mechanisms of nutrient-dependent pheromone-controlled biodiversity have been linked from quorum sensing in bacteria to all cell type differentiation in all individuals of all species.
See: Feedback loops link odor and pheromone signaling with reproduction

These studies reveal a complex interplay between reproduction and other functions in which GnRH neurons appear to integrate information from multiple sources and modulate a variety of brain functions.

Escherichia coli and the peppered moth typically are typically used by biologically uninformed theorists as examples of mutation-driven evolution.
See: The Man Who Bottled Evolution
See the refutation: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

…this system enables us to understand the adaptive process in detail at the genetic and phenotypic level [over the weekend]. We identified a tractable model for gene network evolution and observed, in real time, the rewiring of gene networks to enable the incorporation of a modified component (NtrC′) creating a novel regulatory function by a highly repeatable two-step evolutionary pathway with the same point mutations often recurring in independent lineages.

They failed to differentiate between the term mutation and what occurs in the context of energy-dependent pheromone-controlled changes in the microRNA/messenger RNA balance via fixation of RNA-mediated amino acid substitutions in supercoiled DNA.
See: Structural diversity of supercoiled DNA

Six decades after the elucidation of its double helical structure, DNA continues to surprise us by revealing new information. Our cryo-ET, biochemical, and computational studies show the astounding versatility and dynamism of DNA depending on the degree of supercoiling. DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases. 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.

See for comparison: Helicoverpa armigera images

Identification and Evaluation of Suitable Reference Genes for Normalization of MicroRNA Expression in Helicoverpa armigera (Lepidoptera: Noctuidae) Using Quantitative Real-Time PCR

…10 candidate genes of H. armigera were selected and analyzed for their expression stability under different biotic and abiotic conditions….  miR-9 and U6 snRNA for developmental stages, miR-100 and U6 snRNA for larval tissues, miR-100 and miR-305 for adult tissues, miR-9 and miR-279 for parasitic treatment, miR-998 and U6 snRNA for nuclear polyhedrosis virus infection, miR-9 and U6 snRNA for insecticide treatment, miR-92a, miR-100, and miR-279 for temperature treatment, miR-92a, miR-305, and miR-998 for starvation treatment, miR-9 and miR-279 for light treatment, miR-305 and miR-998 for hormone treatment, and there was not one reference gene suitable for all samples.

Nutrient-dependent pheromone-controlled reproduction in this moth species links the works of Karlson and Luscher (1959) Pheromones: a new term for a class of biologically active substances to the Bruce McEwen’s works on stress via Effects of Carnitine on Fatty-Acid Oxidation by Muscle (1959) and 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.

Taken together, these works are linked to energy-dependent Normalization of MicroRNA Expression. The anti-entropic virucidal energy of sunlight is the obvious link from the de novo creation of microRNAs to the ATP-dependent biosynthesis of messenger RNA and healthy longevity.  Virus-driven energy theft clearly links the degradation of messenger RNA, which would otherwise link the creation of microRNAs from sunlight to the nutrient energy-dependent pheromone-controlled biosynthesis of ATP and all cell type differentiation in all living genera.

For example see: Genetic 3’UTR variation is associated with human pigmentation characteristics and sensitivity to sunlight

To our knowledge, this is the first time that these two 3’UTR SNPs have been associated with sun-sensitivity traits. We state the potential implication of these SNPs in human pigmentation and sensitivity to sunlight, possibly as a result of changes in the level of gene expression through the disruption of putative miRNA-binding sites.

See also:: Race-dependent association of sulfidogenic bacteria with colorectal cancer

reported as: Study links sulfide-producing bacteria and colon cancer in African-Americans

“These bacteria are using nutrients associated with an animal-based diet,” Gaskins said.

For information on the biophysically constrained energy-dependent origins of race-dependent associations see:

Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism

…precursors of amino acids glycine, serine, alanine and threonine, are inevitable by-products of this RNA assembly chemistry…

Like all chemistry, this can be placed into the context of how quantum physics must be linked from quantum chemistry to quantum biology via food as energy.

The link from food enery to the nutrient-dependent pheromone-controlled physiology of reproduction and racial differences in colon cancer was predicted based on difference in diet and links from the National Microbiome Initiative to the Precision Medicine Initiative.

See for comparison: Sonny Williams

Re: … much ado about nothing — Jay R. Feierman.

SONNY [NEW]: As we’ve discussed many times, I reject your criteria for judging the merits of a scientific observation.  Arguing that something is “much ado about nothing,” if “the results can’t be predicted by common sense or by simple observation and deductive reasoning,” is exceptionally poor reasoning.  Frankly, I’m bewildered that someone like you would cling to it.  I’ll repeat:  any judgment that includes an evaluation based on “common sense” is DOA.  It’s useless.  Whose “common sense” do you intend to use?

More importantly, the authors DID establish a pre-observation “prediction.”

They predicted that young children will show the same variation in temperament as adults, and which is associated with the various BDNFval/66met polymorphisms.  They wrote, “To the best of our knowledge, there are no studies investigating the role of BDNFval66met with regard to individual differences in temperament during infancy, a period in which genetically-based behavioral traits are hypothesized to be more easily observed (Posner & Rothbart, 2009; Rothbart et al., 2000). Hence, the purpose of the current study was to explore the association between the BDNFval66met polymorphism and individual differences in temperament in a sample of healthy 4-month-old full-term infants.”

Moreover, the authors did a far better job than you did in discussing limitations.

They wrote as follows: “The current study had some limitations. First of all, due to sample size findings cannot be generalized and future studies with larger samples are needed in order to differentiate the impact of met-homozygous and heterozygous profiles of BDNFval66met genotype. Second, infants’ temperament was measured through a parent-reported measure. A more direct account of the effects of BDNF met allele on observed temperament and regulatory behavior is warranted to be investigated in future research. Finally, single polymorphism studies are at risk of underrepresenting the role of environmental conditions, including maternal caregiving behavior. As the quality of early caregiving has been found to regulate BDNF transcriptional functioning (Unternaehrer et al., 2015), we suggest that upcoming studies should target gene x environment interactions using genetic and epigenetic approaches.

To the best of our knowledge, this study is unique in providing evidence of an association between the BDNFval66met polymorphism and infants’ temperament at 4 months of life. The present study adds to previous genetic association research on temperament in infants looking at other polymorphisms (Auerbach et al., 2001; Ivorra et al., 2011), preliminarily suggesting a further genetic factor involved in temperament. Future research is warranted to investigate the BDNF-temperament association in greater populations of infants at low- and high-risk (e.g., preterm infants) and assuming a gene-x-gene and gene-x-environment approach (Papageorgiou & Ronald, 2013).”

Sonny Williams and Jay R. Feierman are antagonists who ignore the facts that link our predictions to all energy-dependent biophysically constrained biodiversity from our 1996 Hormones and Behavior. Our predictions were based on Bruce McEwen’s advice to start with the activation of genes. That is why we included a section on molecular epigenetics.

From Fertilization to Adult Sexual Behavior

All predictions have since been linked from the anti-entropic virucidal energy of sunlight to biophysically constrained RNA-mediated biodiversity by changes in base pairs linked from amino acid substitutions to differences in morphological and behavioral phenotypes during the development of moths and humans. The epigenetic effects of sunlight were predicted in the context of the nutrient energy-dependent de novo creation of microRNAs.
Anything ever linked to the gene-centric theories of neo-Darwinists has been replaced by what is known about energy-dependent endogenous RNA interference and all biophysically constrained biologically-based biodiversity on Earth. For example, pheromones biophysically constrain the physiology of reproduction in all living genera. They protect against virus-driven entropy by linking what organisms eat to the species-specific pheromone-controlled transgenerational epigenetic inheritance of species from microbes to humans.
See also: Epigenetic regulation of face formation
See also: Explaining the accelerating expansion of the universe without dark energy

See also: A distinct role for Lgr5+ stem cells in primary and metastatic colon cancer
Reported by Genentech as: Cancer stem cells have long been thought to influence tumor growth, but a clear link has been difficult to show. Now, in a new study in Nature, our scientists show for the first time that removing cancer stem cells in a model of colorectal cancer can indeed reduce tumor growth. See how these findings could help guide new therapies aimed at targeting cancer stem cells.
What took them so long to link virus-driven energy theft from messenger RNA degradation to the negative supercoiling of DNA via G protein-coupled receptors?
Feedback loops link odor and pheromone signaling with reproduction

At least 10,000 neurons in 26 different brain areas appear to transmit signals directly to GnRH neurons.  GnRH neurons appear to transmit signals to as many as 30,000 or more neurons in 34 brain areas, consistent with previous studies showing GnRH+ fibers and GnRH receptors in multiple brain regions. These results may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.

 

Alternative splicing of pre-mRNA

The essence of precision medicine

…Trump’s labeling of the media as the enemy of the state was unfortunate and dangerous.

It was an accurate label that has been supported by Bill Gates and the Allen Institute in the context of the forthcoming viral apocalypse.
See for comparison this enemy of the state-issued media representation:
 

“We are all proud of professor Filipp’s accomplishments,” Vice Chancellor for Research Samuel Traina said. “He exemplifies the attributes of a great UC professor.”

 This biased representation was framed in the context of: The histone demethylase KDM3A regulates the transcriptional program of the androgen receptor in prostate cancer cells

Filipp misrepresented everything known to serious scientists about energy-dependent RNA-mediated cell type differentiation and supercoiled DNA when he made this claim:
 
 

The Precision Medicine Initiative and National Microbiome Initiative link food energy to biophysically constrained RNA-mediated protein folding chemistry and viral latency. Virus-driven energy theft has been linked to all pathology in all living genera via the molecular mechanisms of chromosomal inheritance.

Evidence of chromosomal inheritance led to the 1933 Nobel Prize in Physiology or Medicine, which was awarded to Thomas Hunt Morgan.

The essence of precision medicine involves an understanding of how atomic energy-dependent RNA-mediated fixation of amino acid substitutions differentiates all cell types in all individuals of all living genera in the context of the physiology of reproduction, which has been linked to chromosomal inheritance by all serious scientists since Schrodinger (1944) in What is Life?.
 
For example, Horton et al (2014) put the facts about chromosomal inheritance into the context of epigenetic effects of food and pheromones on estrogen receptors and biodiversity of behavior in a single species.
 
 

…our results illustrate a detailed chain of events linking a chromosomal rearrangement to changes in overt social behavior.

Filipp and others like him probably do not want the details of chromosomal rearrangements to be linked from energy-dependent changes in estrogen receptor polymorphism to virus-driven energy theft and androgen receptor polymorphism in prostate cancer. 
For an example of threat to pseudoscientists posed by facts about sex differences in androgen and/or estrogen receptor polymorphism and healthy longevity compared to virus-drive pathology, see: A third of Americans don’t believe in evolution
My comment to Phys.org:

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.

These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.

That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.

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

There is no other model or model organism that so clearly integrates what is known to all serious scientists about energy-dependent endogenous RNA interference at a time when Church et al (2015) are waiting to cash in on this patent application. RNA-Guided Human Genome Engineering

Anyone who claims to be proud of professor Filipp’s accomplishments should be asked how he thinks the essence of precision medicine will link drug targets from each person’s unique genetic and epigenetic makeup to what others have claimed is a “billion dollar baby.”

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

RNAi has targeted exogenous genes in models of viral infection…

See also: Obituary: Robert L. Moss

 Most recently, his efforts were directed towards establishing the role of pheromonal signals in activating GnRH neurons.

The nutrient energy-dependent pheromone-controlled activation of GnRH neurons links the androgen and/or estrogen receptor context of different tissues to healthy longevity or to virus-driven pathology in all vertebrates via substitution of achiral glycine in position 6 of the GnRH decapeptide.

Other energy-dependent RNA–mediated amino acid substitutions also link morphological and behavioral phenotypes to all biodiversity via conserved molecular mechanisms in the context of the physiology of reproduction.

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

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.

Amino acid modification FA_Epigenetics_Table1

Theistic evolutionists fight back and lose (3)

See also: Theistic evolutionists fight back and lose
See also: Theistic evolutionists fight back and lose (2)
For succinct representations of the claims made by people who are obviously biologically uninformed, see:

7/25/13
Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.
See for comparison:

How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy? — Roger Penrose (8 August 1991)

7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
See for comparison:

…in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.) — Erwin Schrodinger (1944)

See also: Nutrient-dependent / Pheromone-controlled thermodynamics and thermoregulation (August 3, 2013)
Abstract excerpt:

Resurrected proteins reveal that ancestral uricases have steadily decreased in activity since the last common ancestor of mammals gave rise to descendent primate lineages. We were also able to determine the 3D distribution of amino acid replacements as they accumulated during evolutionary history…

The amino acid substitutions are not accumulated during evolutionary history. The substitutions link nutrient energy-dependent RNA-mediated top down causationk from ecological variation to ecological adaptation via the creation of heat shock proteins. The heat shock proteins “buffer” organized genomes to protect them from virus-driven energy theft and genomic entropy via the physiology of reproduction, which is controlled by pheromones in species from microbes to humans.
See also this discussion attempt: An epigenetics gold rush: new controls for gene expression
Sonny:

The other day, I read a new paper from a sociologist who wrote that epigenetics reveals that the environment is “more important than genes” in constructing the phenotype.  That is an egregiously misleading statement.

James Kohl

m6A is the link from energy-dependent changes in angstroms to ecosystems via learning and memory, which links ecological variation to ecological adaptation in the context of the physiology of pheromone-controlled reproduction.

Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice

Excerpt: “The differential effects of m6A may depend on distinct cis-acting elements that are present on the RNA molecule which may interact with m6A, including micro-RNAs (Alarcón et al., 2015; Chen et al., 2015).” p. 6776

James Kohl: Ultimately, the biggest embarrassment to scientists who have linked energy-dependent changes from angstroms to ecosystems via chirality, autophagy, and supercoiled DNA is that other scientists start with the de novo creation of copy variants.

Sinclair et al., (January 25, 2017) Nucleic and amino acid sequences support structure-based viral classification

They conclude that no discussion of nutrient energy-dependent species-specific pheromone-controlled viral latency should allow others to challenge their claims about the energy-dependent RNA-mediated signals that link virus-driven energy theft to dysfunctional relationships among structure, amino acid sequence, and coding sequences.
 
They prefer that others, like Masatoshi Nei in “Mutation-driven evolution” (2013) place their claims into the context of how discussions about signaling between viruses and the supercoiled DNA of all organized genomes can be placed into the context of possible evolutionary relationships.
 
The evolutionary relationships do not link energy-dependent changes in chirality from autophagy via the innate immune system to endogenous RNA interference and all biodiversity on Earth.
 

Without the energy-dependent changes, the virucidal effects of femtosecond blasts of UV light on energy-dependent codon optimality and DNA repair cannot link the de novo creation of the energy in hydrogen atoms to the biophysically constrained coding sequence in all living genera via the physiology of reproduction.

See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model and this presentation. Energy as information and constrained endogenous RNA interference

Keeping up-to-date with the primary literature just got a little easier

Today, Springer Nature is pleased to announce the launch of an innovative service which we believe will significantly improve the workflows of researchers by saving time and enabling access to the most relevant content, allowing users to access a new way to keep up to date without visiting any new websites.

Recommended is a service which we believe will help all primary researchers in the natural sciences keep up to date with the literature that really matters to them.  It is a personalised service that suggests relevant papers for users, regardless of publisher, based on what they have previously read across all Springer Nature services.

The “Nature Publications Group” banned me from commenting on their publications several months ago.
Comments on this news are disabled for everyone, which means the Nature Publications Group knows how to hide from any accountability for the lies they have told in the context of gene-centric theories.
See: The RNA code comes into focus Published online
See also:

The presence of an N1 methyl group on adenine bases in DNA and RNA was thought to be a form of damage. Results now show that it also occurs at specific sites in messenger RNAs, where it affects protein expression.

This nutrient energy-dependent methyl mark link RNA methylation from learning and memory to biophysically constrained RNA-directed DNA methylation, which is now represented in the context of endogenous RNA interference (RNAi). The link from the epigenetic landscape to RNAi and to the physical landscape of supercoiled DNA has repeatedly been placed into the context of via RNA-mediated protein folding chemistry and amino acid substitutions that differentiate all cell types in all living genera via the physiology of reproduction.
Typically, the physiology of reproduction prevents the transgenerational epigenetic inheritance of virus-driven pathology in all living genera — until the landscape changes to one in which energy-dependent RNA-mediated DNA repair can no longer keep up with the virus-driven energy theft.

Amino acid modification FA_Epigenetics_Table1

Francis S. Collins refutes theistic evolution

Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

Based on his writings, both published and unpublished, James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research. — Andrew Jones, BA

Editor’s note

The 2013 review article by James Vaughn Kohl published in Socioaffective Neuroscience & Psychology and criticized in the above Letter to the Editor was subjected to standard peer review and the revised version was accepted by me after it had been accepted by both reviewers.

See for comparison: The Language of God: A Scientist Presents Evidence for Belief, by Francis S. Collins. The current director of the NIH also is a co-author of Genetic regulatory signatures underlying islet gene expression and type 2 diabetes

…T2D risk alleles that overlap with RFX footprints uniformly disrupt the RFX motifs at high-information content positions. Together, these results suggest that common regulatory variations have shaped islet TF footprints and the transcriptome and that a confluent RFX regulatory grammar plays a significant role in the genetic component of T2D predisposition.

No experimental evidence of biologically-based cause and effect suggest that any common regulatory variations has ever evolved. Let me make that fact perfectly clear in the words of the co-authors:

“Individuals who are heterozygous for a frameshift mutation in RFX6 have increased 2-h glucose levels (33). Importantly, rare autosomal recessive mutations that alter DNA-contacting amino acids in the DNA binding domain of RFX6 result in Mitchell–Riley syndrome, which is characterized by neonatal diabetes (29).

The frameshift mutation and rare autosomal recessive mutations occur outside the context of energy-dependent endogenous RNA interference (RNAi). For comparison RNA-directed DNA methylation (aka endogenous RNAi) typically links DNA-contacting amino acids to healthy longevity via the transgenerational epigenetic inheritance of morphological and behavioral phentoypes in species from microbes to humans. It is difficult to describe all the links, but it is clear that RNAi links RNA-directed DNA methylation from energy-dependent changes in chirallity to base pairs, single nucleotide polymorphisms (SNPs) and autophagy via the innate immune system.
Without any mention of how virus-driven energy theft links mutations from SNPs to pathology, Francis S. Collins and his co-authors link the rare autosomal recessive mutations to altered DNA-contacting amino acids. Apparently, they do not want to mention anything about the fact that natural selection for energy-dependent codon optimality is the link from RNA-mediated protein folding chemistry to all biophysically constrained healthy longevity. Instead, they seem willing to ignore the facts about energy-dependent fixation of RNA-mediated amino acid substitutions in cell types.
Indeed, they seem to put everything known to serious scientists into the context of the theistic evolution of pathology. Serious scientists know that nutrient energy-dependent pheromone-controlled cell type differentiation is the link from atoms to ecosystems in models of ecological adaptation.
Clearly, anyone who does not want to expose the pseudoscientific nonsense touted by neo-Darwinian theorists and theistic evolutionists should not mention “amino acid” and “mutation” in the same context. Using only the definitions of both terms in the same sentence (above) alerts all serious scientists to the fact that nutrient energy-dependent amino acid substitutions are not the same as mutations, which are caused by virus-driven energy theft.
Reported as: Diabetes in your DNA? Scientists zero in on the genetic signature of risk

…for now, it’s the first demonstration that many Type 2 diabetes-linked DNA changes have to do with the same DNA-reading molecule. Called Regulatory Factor X, or RFX, it’s a master regulator for a number of genes.

The regulation of genes is energy dependent.

“RFX is probably unable to read the misspelled words, and this disruption of regulatory grammar plays a significant role in the genetic risk of Type 2 diabetes.”

The concept of “misspelled words” is appropriate for use only in the context of pseudoscientific nonsense that fails to address facts about natural selection for energy-dependent codon optimality. Codon optimality links the speed of light on contact with water to biophysically constrained RNA-medidated cell type differentiation in all living genera.

They characterized differences not just in DNA sequences, but also in the way DNA was packaged and modified by epigenetic factors, and the levels of gene expression products that indicated how often the genes had been read and transcribed.

Epigenetically-effected reading and transcription is energy dependent and biophysically constrained via the speed of light and hydrogen-atom transfer in DNA base pairs in solution such as seawater and blood. Serious scientists noticed that pattern and linked virus-driven energy theft from pathology in bacteria to archaea and from the transgenerational epigenetic inheritance of Zika-virus damaged DNA in human infants. The craniofacial morphology and brain development of infected human infants clearly links energy-dependent fixation of amino acids to the morphological and behavioral phenotypes of all living genera.
See: Nothing in Biology Makes Any Sense Except in the Light of Evolution

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.

Facts about nutrient energy-dependent codon optimality also are known to be refutations of neo-Darwinian pseudoscientific nonsense because codon optimality links Darwin’s “conditions of life” to the physiology of reproduction in all living genera.
See: Codon optimality controls differential mRNA translation during amino acid starvation and Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See for comparison: Epigenetic Editing of Ascl1 Gene in Neural Stem Cells by Optogenetics

Each DNA change might alter this binding in a different way, leading to a slightly different effect on Type 2 diabetes risk or blood sugar regulation. But the common factor for many of these changes was its effect on the area where RFX is predicted to bind, in the cells of pancreatic islets.

So, says Parker, this shows how the genome – the actual sequence of DNA—can influence the epigenome, or the factors that influence gene expression.

The sequence of DNA cannot influence the epigenome before the energy-dependent sequence has been created via natural selection for codon optimality. That is why epigenetically-effected nutrient-dependent pheromone-controlled energy-dependent changes in supercoiled DNA were linked from the weekend resurrection of the bacterial flagellum in Pseudomonas fluorescens to all biodiversity in all living genera via the conserved molecular mechanisms that link light energy-induced changes in microRNAs to all biodiversity.
See also: Optokinetically encoded nanoprobe-based multiplexing strategy for microRNA profiling
Programmable artificial phototactic microswimmer

For active drug delivery, the nanomotor should be able to orient towards specific chemical signals, such as those demonstrated in chemotaxis21–25 and pH taxis26.

See also: pH-Taxis of Biohybrid Microsystems

…assuming that it is possible to tune the preferred pH of bioactuators by genetic engineering, these biohybrid microsystems could potentially be applied to sense the pH gradient induced by cancerous cells in stagnant fluids inside human body and realize targeted drug delivery.

If naturally occurring chemotaxis could not readily be linked from pH-taxis and phototaxis to natural selection for codon optimaility and supercoiled DNA, light energy as information could not be linked to communication between the microscopic and the macroscopic world.
Light Could Propel Nanorobots on a “Fantastic Voyage” Through the Human Body

“Light is a more effective option to communicate between the microscopic world and the macroscopic world,” said Tang.

The fact that the energy-dependent virucidal effects of sunlight have been linked to the weekend resurrection of the bacterial flagellum in an organism that fluoresces on exposure to UV light was placed into the context of claims about two amino acid substitutions that were reported as if they were mutations.
Summary: Francis S. Collins, current NIH director, is a theistic evolutionist. He should not use his position to tout the pseudoscientific nonsense of evolution. He is supposed to link experimental evidence of biologically-based facts to healthy longevity or to pathology.
See also: United states health care reform: Progress to date and next steps

All of the individuals who assisted with the preparation of the manuscript are employed by the Executive Office of the President.

Former President Barrack Obama should not have used his position or his employees to mislead the voters in the United States of America. He correctly stated that “…partisanship and special interest opposition remain…,” which ensured that “…experience with the Affordable Care Act…” would demonstrate “…that positive change is achievable on some of the nation’s most complex challenges.” That claim was placed into the context of misrepresentations made by ~50% of people who are biologically uninformed theorists and/or those who are atheists. Clearly there is overlap among those groups of people. Hopefully, others will see why. They’ve been taught to believe in theistic evolution or nothing.
Experimental evidence of biologically-based cause and effect refutes theistic evolution by linking virus-driven energy theft to all pathology in all living genera. In the context of  Genetic regulatory signatures underlying islet gene expression and type 2 diabetes, Francis S. Collins revealed either his ignorance or his treachery.
The article links the nutrient energy-dependent pheromone-controlled physiology of reproduction to the weekend resurrection of the bacterial flagellum in P. fluorescens via RNA synthesis, not mutations.
Virus-driven energy theft influences energy-dependent RNA-mediated gene expression, and the energy theft is clearly linked to mutations. See for example: DEPENDENCE OF RNA SYNTHESIS IN ISOLATED THYMUS NUCLEI ON GLYCOLYSIS, OXIDATIVE CARBOHYDRATE CATABOLISM AND A TYPE OF “OXIDATIVE PHOSPHORYLATION”

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

See also: microRNA “Regulatory Factor X” 
 

Amino acid modification FA_Epigenetics_Table1

Physicists: Desperate Acts (revisited)

Physicists: Desperate Acts
Light-induced endogenous RNA interference in bioluminescent microbes links Schrodinger’s claims in “What is LIfe?” (1944) from a light-to-chemical pathway of information exchange in all living genera via amino acid substitutions in supercoiled DNA.
All subsequent works on the evolutionary synthesis failed to link  the anti-entropic virucidal energy of sunlight to Darwin’s “conditions of life” from the claims of Schrodinger (1944) or the claims of any other serious scientist.

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.) (pp. 73 and 74)

See also: A theoretical physicist approaches the complexity — and mystery — of quantum gravity head-on

We thought that matter was continuous, and it took quite some time to realize that matter is not continuous,” he explains. “It’s atomic, it’s made by atoms and molecules, by particles. This was only understood about the beginning of the 20th century, not before that. It’s one of those ideas that is very old. It was suggested in ancient times. But it was realized recently.”

“So matter is discrete, and light is discrete, it’s made by photons. A wave of light is actually a cloud of photons. And it’s not surprising, after all, that space itself is sort of a cloud of little teeny small things.
Serious scientists used what is known about subatomic particles to show that all the assumptions of pseudoscientists have always been wrong. The pseudoscientists now must deal with serious scientists who have linked the creation of energy as information to all biodiversity and others who linked virus-driven energy theft to all pathology.
Some of the best among the serious scientists scientists who did that are young earth creationists who have always been right. They somehow knew that gravity did not create itself and most of them began to realize that hydrogen-atom transfer in DNA base pairs in solution must be linked from energy-dependent changes in chirality to autophagy.
When pseudoscientist failed to link chirality from autophagy to endogenous RNA interference and supercoiled DNA, which prevents virus-driven energy theft and genomic entropy in all organized genomes of all living genera, the serious scientists started to ridicule the theorists in parodies.
For a historical perspective on the ridicule, see Was ribosome the first self-replicator?

Two years ago, I asked Matti Pitkanen if differences between biophotons were recognized by the photons at the quantum level of their interactions. His response was a classic example of evading the question with claims that theoretical physicists tout in their pseudoscientific nonsense.

To how high level can one continue this parallelism. For instance, does it make sense to talk about dark variants of cell and cell membrane? Can one tell whether it was pro-cell or bio-molecules that emerged first? It seems that all these structures could have emerged simultaneously. What emerged was dark matter and its emergence involved the emergence of all the others. Hens and eggs emerged simultaneously.

See for comparison: “How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?” — Roger Penrose (8 August 1991)

See also: Why metabolism and what happens in bio-catalysis? Matti Pitkanen (2 February 2017)

  1. The simplest and at the same time most difficult question that innocent student can make about biology class is simple: “Why we must eat?”
  2. …the energies of the hydrogen atom depend on hbareff=n× h in as hbareffm, m=-2<0. Hydrogen atoms in dimension D have Coulomb potential behaving as 1/rD-2 from Gauss law and the Schrödinger equation predicts for D≠ 4 that the energies satisfy En∝ (heff/h)m, m=2+4/(D-4). For D=4 the formula breaks since in this case the dependence on hbar is not given by power law. m is negative only for D=3 and one has m=-2. There D=3 would be unique dimension in allowing the hydrino-like states making possible bio-catalysis and life in the proposed scenario.
  3. The condition that the dark binding energy is above the thermal energy gives a condition on the value of heff/h=n as n≤ 32. The size scale of the dark largest allowed dark atom would be about 100 nm, 10 times the thickness of the cell membrane.

Pitkanen is unable to grasp the fact that the speed of light on contact with water is the source of all binding energy, which links hydrogen-atom transfer in DNA base pairs in solution from endogenous RNA interference to healthy longevity in all living genera via chromosomal inheritance. His attempts to place dark binding energy above the anti-entropic virucidal energy of sunlight is still one of the most foolish attempts I have seen anyone make to deny that the energy in a hydrogen atom has been there from the time God created the heavens and the earth — as detailed in Biblical Genesis.
Matti Pitkänen What new physics do you want to introduce to support your claims about dark energy and dark matter for comparison to the claims of Schrodinger about the anti-entropic energy of sunlight?

I call it adelic physics or number theoretic physics.

Does everyone who knows you except Ulla Mattfolk laugh at your pseudoscientific nonsense?

Matti Pitkänen …one must assume that space-time is what topologist calle n-fold covering space. n sheets of covering effectively multiply Planck constant by n to give h_eff. The quantum of action is n-fold since there are n sheets.

I told him that all the assumptions made by others have been wrong.

Matti Pitkänen  It took more than 10 years to deduce this from adelic physics which is fusion of real physics for matter and various p-adic physics for cognition, p = prime.

Matti Pitkänen I think very few laugh to my theory now. If they do so I can safely conclude that they are idiots.

Matti Pitkänen …your understanding of physics could be better. One must distinguish between continuity at space-time level and continuity of matter.

Matti Pitkänen  The cognitive representations defined by the intersections of real and p-adic space-time surfaces as intersection of reality and imagination/cognition are discrete: points have coordinates in extension of rationals. In this sense discreteness makes sense but is has nothing to do with the quantum mechanical discretization of quantum numbers.

Matti Pitkänen …the odor of nutrients is determined by pheromones. Is this true. This would be nice since pheromones could provide information about distribution of h_eff=n*h and thus about the number theoretic evolutionary level of food or potential mating partner. Good odors would correspond to large average n. Bad odors to low value of n and low negentropy.

Matti Pitkänen  TGD predicts both dark matter and energy naturally and this explanation leads to vision about quantum biology and cognition unlike other proposals.

The pre-publication reviews of this book came from people who I think George FR Ellis and others probably believe are serious scientists. I do not believe those people are anything more than theorists. When they include claims about viruses, serious scientists may discuss the reality of pattern recognition with them. But not until then. Energy vs virus-driven energy theft must be considered in the context of adaptive changes in the brain, June 12, 2016

See for comparison: Thomas Hunt Morgan

Morgan contributed to the neo-Darwinian synthesis, despite his criticism of Darwin at the beginning of his career. Much work on the Evolutionary Synthesis remained to be done.

See also: Gamma oscillations organize top-down signalling to hypothalamus and enable food seeking
Reported as: Gamma oscillations coordinate food seeking

 “Preferential and selective control of feeding-related cells by rhythmic inputs to hypothalamus demonstrates a beautiful interaction of structure and function in the brain” says Alexey Ponomarenko. “Here we see how fast synchronization, combined with a precise information transfer between brain regions and cells types, drives behaviors crucial for survival.”

Coevolutionary dynamics of phenotypic diversity and contingent cooperation
Reported as: Study finds mutual reinforcement of phenotypic diversity and cooperation

A new model exploring how evolutionary dynamics work in natural selection has found that phenotypic diversity, or an organism’s observable traits, co-evolves with contingent cooperation when organisms with like traits work together to protect themselves from outsiders, according to a Dartmouth-led study published in PLOS Computational Biology. The study also finds that diversity helps prevent the collapse of cooperation.

Achieving Reversible H2/H+ Interconversion at Room Temperature with Enzyme-Inspired Molecular Complexes: A Mechanistic Study
Reported as: Catalyst mediates energy-efficient proton transport for reversibility

Scientists at Pacific Northwest National Laboratory built a catalyst that mimics nature’s hydrogen-splitting enzymes—working reversibly at room temperature and pressure without added energy. This was achieved by stabilizing the catalyst’s structure by attaching an amino acid…

Increasing Type 1 Poliovirus Capsid Stability by Thermal Selection

Our data show that some capsid mutations stabilize the ECs and could be applied as candidates to synthesize stable VLPs as future genome-free poliovirus vaccines.

‘Virus-Like Particle’ Method to Make new Polio Vaccines Proven Effective

The investigators have demonstrated that stabilized VLPs can be utilized effectively under controlled conditions. Additional research with model organisms like mice and rats will be necessary and is planned as an important part of crucial procedure of ensuring the safety and efficacy of these new VLPs for use in people.

All experimental evidence of biologically-based cause and effect has shown that controlled conditions are not exemplified in the context of how ecological variation must be linked from natural selection for energy-dependent codon optimality to the physiology of reproduction. Energy-dependent changes must be linked from chirality to autophagy by natural information processing. The control of information processing links energy-dependent endogenous RNA interference from amino acid substitutions in supercoiled DNA to all healthy longevity in all living genera. Negative supercoiling links virus-driven energy theft from mutations to all pathology.

If you would like to learn more about how virus-driven energy theft is linked to messenger RNA degradation and all pathology in species from microbes to humans, see: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
The resurrection clearly links energy-dependent RNA-mediated amino acid substitutions to the functional structure that enables the search for nutrients, which are metabolized to pheromones that control the physiology of reproduction in species from microbes to humans.

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.