Light-activated feedback loops vs self-organization of ecosystems

By: James V. Kohl | Published on: March 30, 2017

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.


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