Open Science: Closed to facts about microRNAs

By: James V. Kohl | Published on: April 20, 2017

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]: ” 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

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:

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