Hypothesis free pseudoscience vs facts (5)

By: James V. Kohl | Published on: October 4, 2016

See first: Hypothesis free pseudoscience vs facts (4)
Re: There is literally nothing left of neo-Darwinian pseudoscientific nonsense, and yet pseudoscientists still make the same ridiculous claims.

See for comparison:  Current Drug Design Studies for Hsp70 in Oncological Applications

SBD [substrate binding domain] contains hydrophobic amino acid residues, and this hydrophobic cavity helps unfolded substrate proteins to fold their native structure. Thus, exposed part of the folded proteins may not interact with each other and cause aggregation [in the context of the nucleotide binding domain (NBD)].

My comment: Anyone who thinks that this will not end up explaining every aspect of energy-dependent biophysically constrained RNA-mediated protein folding chemistry and the effects of virus-driven energy theft on all pathology should begin to explain the conflict between their ridiculous opinions and the facts presented in the context of Nobel Prize winning research in Physiology or Medicine and in Chemistry and in Physics during the past 12 years.
But first, see: the video representation of results from this study: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

They found the existing code that links energy-dependent changes in the microRNA/messenger RNA balance from codon optimality and RNA-mediated amino acid substitutions to the physiology of reproduction and reported the obvious link from virus-driven energy theft to all pathology as if no one had ever heard of it.
See for comparison: The phylogenetic utility and functional constraint of microRNA flanking sequences

Structural Basis for Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates
Yeast mating pheromone activates mammalian gonadotrophs: evolutionary conservation of a reproductive hormone?
–as cited in our 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior
See also: MicroRNA-21 protects against cardiac hypoxia/reoxygenation injury by inhibiting excessive autophagy in H9c2 cells via the Akt/mTOR pathway
Abstract conclusion:

“We showed that miR-21 could inhibit H/R-induced autophagy and apoptosis, which may be at least partially mediated by the Akt/mTOR signalling pathway.”

My comment: They linked energy-dependent changes in the microRNA/messenger RNA balance from the innate immune system to supercoiled DNA via RNA-mediated amino acid substitutions that stabilize the biophysically constrained chemistry of organized genomes in all living genera. The supercoiled DNA protects organized genomes from virus-driven energy theft and genomic entropy.
See also: Autophagy microRNA (482 publications)
My comment: It has become much easier for serious scientists to link molecular epigenetics to biologically-based cause and effect in all living genera.
See for example: Role of olfaction in Octopus vulgaris reproduction

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

My comment: The physiology of reproduction in yeast is nutrient energy-dependent and pheromone-controlled. That fact links the conserved molecular mechanisms of RNA-mediated cell type differentiation from microbes to humans via a work co-authored by 2004 Nobel Laureate, Linda Buck.
See: Feedback loops link odor and pheromone signaling with reproduction
See also: Decoy DNA Binding Sites Subtly Impact Gene Expression

Re: The 2005 Nobel Prize in Physiology or Medicine. This is what it took to share it with someone who was equally interested in advancing science at great risk to both their careers.

“… in 1984, Marshall… drank a Petri dish containing cultured H. pylori…. He was surprised when, only three days later, he developed vague nausea and halitosis (due to the achlorhydria, there was no acid to kill bacteria in the stomach, and their waste products manifested as bad breath)…. On days 5–8, he developed achlorydric (no acid) vomiting. On day eight, he had a repeat endoscopy, which showed massive inflammation (gastritis), and a biopsy from which H. pylori was cultured, showing it had colonised his stomach. On the fourteenth day after ingestion, a third endoscopy was done, and Marshall began to take antibiotics.[12] Interestingly, Marshall did not develop antibodies to H. pylori, suggesting that innate immunity can sometimes eradicate acute H. pylori infection. Marshall’s illness and recovery, based on a culture of organisms extracted from a patient, fulfilled Koch’s postulates for H. pylori and gastritis, but not for peptic ulcer. This experiment was published in 1985 in the Medical Journal of Australia[13] and is among the most cited articles from the journal.[14]

My comment: If others had learned that virus-driven energy theft is the cause of the RNA-mediated changes in gut microbes, the publication of results in 1985 might have prevented the death of Robin Williams from Lewy Body Disease. His first symptom was gut discomfort.

Had the viruses in the bacteria been killed by killing the bacteria with an effective antibiotic, Robin Williams and many others would still be alive — like Barry Marshall. Instead, many researchers are still stuck with the irrelevant theories touted by neo-Darwinists.

See for comparison: Morphometricity as a measure of the neuroanatomical signature of a trait

…the proposed framework will be significant in dissecting the functional, morphological, and molecular underpinnings of different traits.

See also: A cross-modal genetic framework for the development and plasticity of sensory pathways

…first-order nuclei in mice are genetically homologous across somatosensory, visual, and auditory pathways, as are higher order nuclei. We further reveal peripheral input-dependent control over the transcriptional identity and connectivity of first-order nuclei by showing that input ablation leads to induction of higher-order-type transcriptional programs and rewiring of higher-order-directed descending cortical input to deprived first-order nuclei. These findings uncover an input-dependent genetic logic for the design and plasticity of sensory pathways, in which conserved developmental programs lead to conserved circuit motifs across sensory modalities.

‘By observing neuronal gene expression in these distinct pathways during development, we detected common patterns, as if an underlying genetic language was bringing them together.’

My comment: Common patterns of biophysically constrained cell type differentiation are not observed in the context of gene expression unless the observers know what causes the gene expression.
See also: Nobel honors discoveries on how cells eat themselves

Yeast species typically do not eat themselves to extinction like some human populations seem to be doing. Instead, they seem to exemplify energy-dependent biophysically constrained pheromone-controlled reproduction. That is an ecologically appropriate way to continue adapting to the epigenetic landscape by linking the innate immune system to supercoiled DNA, which protects all organized genomes from virus-driven entropy.
Neo-Darwinian theorists have never linked their theories of morphological change from the behavior of yeasts to human behavior. Scientists have linked nutrient energy-dependent RNA methylation from the innate immune system to learning, memory, and species-specific behaviors in the context of their pheromone-controlled physiology of reproduction and supercoiled DNA.
See for comparison. This link downloads the pdf: “The Inapplicability of the Biogenetic Rule to Behavioral Development
If Darwin’s “conditions of life” link ecological variation to ecological adaptation manifested in morphological and behavioral phenotypes, the 2015 and 2016 Nobel Prize-winning works from the hard sciences, already refute every aspect of neo-Darwinian theories.
See also for comparison: Autophagy Pioneer Wins Nobel

…autophagy, the process by which a cell recycles unnecessary components. “His discoveries opened the path to understanding the fundamental importance of autophagy in many physiological processes, such as in the adaptation to starvation or response to infection…

How much more can be done without claiming that the energy-dependent changes link natural selection to codon optimality and codon optimality links fixed RNA-mediated amino acid substitutions to the stability of all cell types in all living genera via supercoiled DNA. The supercoiled DNA links ecological variation to ecological adaptation via the physiology of reproduction, which is the only way I know to prevent virus-driven energy theft from being transgenerationally inherited — as it is with the Zika virus.
See also this discussion of Barcode trick traces paths of thousands of neurons in brain
The anonymous Pat Sweeney (aka Pat’s Weeny) claims he can teach me about cytology.
See for comparison: Chemosignals from isolated females have antimutagenic effect in dividing the cells of bone marrow from male mice of the CBA strain
Excerpt: Humans also have various pheromone-induced physiological effects, especially those associated with reproduction [46, 47]. This suggests that the human olfactory system is still an effective pathway for influencing environmental factors on the human nervous system. Various psychoemotional states of the human nervous system can, in turn, disrupt the integrity of the chromosomal apparatus of target cells, for instance lymphocytes [41, 42]. Therefore, studies on the oppositely directional modulation of the mutagenic consequences of stress in rodents with the use of specific, volatile, and zoosocial important chemosignals are a promising approach both to modeling posttraumatic stress disorders in humans [36] and to searching for mehods of their treatment.
[46] is Kohl, J.V., Atzmueller, M., Fink, B., and Grammer, K., Human pheromones: integrating neuroendocrinology and ethology, Neuroendocrinol. Lett., 2001, vol. 22, pp. 309–321.
Sweeney knows nothing about this, and my works have been cited by experts across disciplines. The antimutagenic effect of pheromones is just one other way to control pathology that  others like you have dismissed.
See also: Pheromones And The Luteinizing Hormone For Inducing Proliferation Of Neural Stem Cells And Neurogenesis

The present invention provides a method of increasing neural stem cell numbers or neurogenesis by using a pheromone, a luteinizing hormone (LH) and/or a human chorionic gonadotrophin (hCG). The method can be practiced in vivo to obtain more neural stem cells in situ, which can in turn produce more n…

Conclusion: Until the announcement earlier today about the 2016 Nobel Prize in Physiology or Medicine, few people realized that the nutrient-dependent pheromone-controlled physiology of reproduction in yeasts was the key to all energy-dependent healthy longevity compared to all virus-driven energy theft and pathology.  Many still will not find answers to their questions in the context of technically dense texts, but the refutations of neo-Darwinian nonsense are still rather clear.

Organisms that do not eat do not have the energy to reproduce. Virus-driven energy theft and autophagy cull them from the populations of organisms that cannot find enough food. They eat themselves compared to organisms that find an alternative food source.

Humans have the most alternatives and are typically the dominant species in any ecosystem. All that changes when virus-driven energy theft takes its toll on biodiversity, and eventually takes its toll on us.

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