5th-6th Sept 2018 Dublin, Ireland

The eternal significance of microRNAs (8)

Use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation and aging has been replaced by the use of model systems of biological processes.  Biological processes can be compared to so-called “evolutionary processes” to show that only biological processes need to be considered in the context of Darwin’s “conditions of life” or answers to the the question  What is Life? Schrödinger (1944).
K. L. Mettinger et al. (eds.), Exosomes, Stem Cells and MicroRNA, Advances in Experimental Medicine and Biology 1056, https://doi.org/10.1007/978-3-319-74470-4_6

This volume provides insight into the pivotal roles of stem cells, exosomes and other microvesicles in biofunction and molecular mechanisms and their therapeutic potential in translational nanomedicine. It further highlights evidence from recent studies as to how stem cell derived exosomes and microRNAs may restore and maintain tissue homeostasis, enable cells to recover critical cellular functions and begin repair regeneration.

Chapter 2 The Emerging Roles of microRNAs in Stem Cell Aging

involved in many biological processes such as developmental timing, differentiation, cell death, stem cell proliferation and differentiation, immune response, aging and cancer. Accumulating studies in recent years suggest that miRNAs play crucial roles in stem cell division and differentiation. In the present chapter, we present a brief overview of these studies and discuss their contributions toward our understanding of the importance of miRNAs in normal and aged stem cell function in various model systems.

Chapter 6  MicroRNAs, Regulatory Messengers Inside and Outside Cancer Cells

…like hormones, miRNAs can be secreted and regulate gene expression in recipient cells. Altered expression levels of miRNAs in cancer cells determine the acquisition of fundamental biological capabilities (hallmarks of cancer) responsible for the development and progression of the disease.

Model systems link the energy-dependent creation of microRNAs from microRNA biogenesis to the regulation of all cancer hallmarks. The virus-driven degradation of messenger RNA has been linked to all cancers and all other pathology in species from microbes to humans. Natural selection for energy-dependent codon optimality has been linked to healthy longevity.
See: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See for comparison:  The Neutral Theory in Light of Natural Selection May 2, 2018

…50 years after its introduction by Kimura. We argue that the neutral theory was supported by unreliable theoretical and empirical evidence from the beginning, and that in light of modern, genome-scale data, we can firmly reject its universality. The ubiquity of adaptive variation both within and between species means that a more comprehensive theory of molecular evolution must be sought.

The ubiquity of adaptive variation attests to the facts about how the creation of quantized energy is linked to biophysically constrained viral latency. Adaptive variation links energy-dependent changes from angstroms to ecosystems in all living genera  via the physiology of their food energy-dependent pheromone-controlled reproduction.

For comparison to mRNA stability during the maternal-to-zygotic transition, see: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

The energy-dependent molecular mechanisms of recombination clearly link microRNA biogenesis to the stability of organized genomes during the life histories of all genera. Serious scientists object to the use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation.

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

…it is tiresome to raise the same objections repeatedly, wondering why researchers have not fulfilled some of the basic requirements for establishing the occurrence of an autophagic process.

 

Alternative splicing of pre-mRNA

Explorers who do not know what is known (2)

See: Explorers who do not know what is known
See also: Energy-dependent polycombic ecological adaptation

Now see: The B/Z reaction, and the problem with peer review December 9. 2016 by John Leonard

  1. … oscillating chemical reactions predictable by mathematical formula are partially responsible for organizing cells to form organs, bone, and tissue.
  2. Alan Turing didn’t live to see the publication of evidence that would have validated his theory almost immediately.
  3. …when Belousov attempted to have his research published in 1951, the leading scientific journals flatly rejected his work, based on the assumption that the experiment results were “impossible.”
  4. Only a single paragraph from Belousov’s analysis was finally published four years later, in 1955. Alan Turing was already dead. And so was the career of Boris Belousov,  so disgusted the editors of the leading journals had flatly rejected his work without even trying to replicate the results that he stopped performing scientific research.
  5. A horribly flawed peer review process utterly failed Boris Belousov. The editors of science journals successfully asserted themselves as the arbiters of what may be considered acceptable science, and their power remains largely unchecked even today.
  6. Rather than simply assuming that some process or claim  is “impossible,” perhaps we should seriously consider at minimum a cursory investigation of the alleged evidence.
  7. Peer review is a horribly flawed system, but unfortunately, it remains the best system we have.
Peer-review fuels plagiarism. Plagiarism fuels ignorance when what is known about physics, chemistry, and conserved molecular mechanisms is placed back into the context of ridiculous theories. People and plagiarists like John L. Leonard fuel ignorance when they refer to me as an ill-mannered idiot.
October 24, 2016 at 1:15 pm he wrote:

And I don’t like ill-mannered idiots.

Less than two months later, John L. Leonard plagiarizes my detailed model and referenced claims about energy-dependent cell type differentiation. He put them into the context of failed peer review, Turing’s suicide, and the reason why Boris Belousov stopped his research.  I think that if Facebook groups had been available so that people like John L.Leonard could criticize his works, Boris Belousov might also have committed suicide.
Clearly, the amount of overwhelming ignorance displayed in the context of peer review now extends across many more forms of communication in which the opinions of the biologically uninformed prevail. See for example my invited review of nutritional epigenetics, which was returned without review. Then see the subsequent publications from two guest editors of the journal “Nutrients” who requested my review: Lynnette Ferguson and Justin O’Sullivan.
Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Genomic instability in human cancer: Molecular insights and opportunities for therapeutic attack and prevention through diet and nutrition
Insights from Space: Potential Role of Diet in the Spatial Organization of Chromosomes

See for comparison: A protein conjugation system essential for autophagy (1998)

This process is crucial for survival during starvation and cell differentiation.

See also: A Harvard scientist just won $3 million for discovering the hidden ‘intelligence’ that defends our cells (2016)
He discovered nutrient energy-dependent autophagy, again.
See for instance: How autophagy both activates and inhibits cellular senescence (2016)

Although autophagy was originally recognized as a nonspecific lysosomal degradation pathway (general autophagy), increasing evidence supports a selective form of autophagy that mediates the degradation of specific targets (selective autophagy).

Yoshinori Ohsumi won the 2016 Nobel Prize in Physiology or Medicine for experimental evidence that links selective autophagy to supercoiled DNA, which protects all organized genomes from virus-driven energy theft.
See: Structural Basis for Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates (2016)

Selective autophagy mediates the degradation of various cargoes, including protein aggregates and organelles, thereby contributing to cellular homeostasis.

Others have helped to establish the fact that energy-dependent receptor-mediated selective autophagy is RNA-mediated.
Schrodinger (1944)  What is life?

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)

Diamond et al. (1996) From Fertilization to Adult Sexual Behavior

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

Ben-Jacob et al. (2006) Seeking the foundations of cognition in bacteria: From Schrödinger’s negative entropy to latent information

We proposed that, besides “negative entropy,” organisms sense the environment to extract latent embedded information.13 By latent information we refer to data embedded in the environment that, once processed cognitively, initiates change in the organism’s function or behavior. Information induces changes; hence it can be used to generate an internal condensed description (model or usable information) of the environment, which guides the organism’s functioning.

Ben Jacob (2009) Learning from Bacteria about Natural Information Processing

It seems that bacteria have some sort of collective memory by which they keep track of how they handled their previous encounters with antibiotics. They know how to collectively glean information from the environment, “talk” with each other, distribute tasks, generate collective memory, and turn their colony into a “cybernetic system”—a massive “brain” that can perform natural distributed information processing, learn from past experience, and possibly alter the genome organization or even create new genes to better cope with novel challenges.8–13,17,18

Fortunately, serious scientists are now limiting attempt by pseudoscientists and opinionated laypeople to present more pseudoscientific nonsense about mutations, natural selection, and evolution. Those attempts may stop here.
See: The complex evolutionary history of aminoacyl-tRNA synthetases November 29, 2016
This article includes ongoing misrepresentations of how biophysically constrained protein folding chemistry is linked from RNA-mediated amino acid substitutions to the nutrient-dependent pheromone-controlled weekend resurrection of the bacterial flagellum.
Everything known to serious scientists is again placed back into the context of theories and “complex evolutionary histories.”
But the resurrection of the flagellum occurred within 96 hours in an organism (P. fluorescens) that fluoresces with exposure to ultraviolet light.
The failure to link the anti-entropic virucidal energy of sunlight to healthy longevity is the reason some researchers still frame their results in the context of ridiculous theories. In this article, they could refute the theories by the mere mention of the energy source that powers all cell type differentiation in all cell types of all individuals of all living genera.
Instead of the explanatory power of energy as information, an “evolutionary history” approach is used, which ignores the weekend evolution of the irreducibly complex bacterial flagellum.
The journal article was reported as: Ancient enzyme morphed shape to carry out new functions in humans

 Schimmel compared it to reshaping an airplane’s wing to serve as the airplane’s tail instead. “Nature has provided ways for reshaping objects, like C-Ala, and when that happens, new functions occur,” he said.

Selective autophagy is akin to the complete destruction of the airplane, which is rebuilt in its entirety via energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution in all living genera. All the reassembled parts must be linked from energy transfer to functional structures at every level of examination. In the context of biologically-based cause and effect, angstroms must be linked to ecosystems in all living genera via conserved molecular mechanisms.
Attributing all that to “Nature” is an example of the pervasive ignorance that is common among theorists. That ignorance should probably never be displayed by creationists, especially if they attempt to argue with theorists.
Instead, all creationists can stay silent or they can learn about the experimental evidence that has linked selective autophagy to chromosomal rearrangements since the time of the 1933 Nobel Prizes for Physiology or Medicine (Thomas Morgan Hunt) and for Physics (Schrodinger/Dirac).
See also: “aminoacyl-tRNA synthetase” microRNA
miR-15a and miR-16-1 down-regulation in pituitary adenomas (2005)
Feedback loops link odor and pheromone signaling with reproduction (2005)

From Fertilization to Adult Sexual Behavior December 1996

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

The alternative splicings are energy-dependent. Virus-driven energy theft causes all pathology by using the energy to stabilize the genomes of viruses. If not for the atheists, plagiarists, and other creationists who would rather steal the information or fight against its dissemination, the neo-Darwinists would never have stood a chance.Watch for more reports that link energy-dependent RNA-mediated amino acid substitutions to supercoiled DNA, which protects all organized genomes from virus-driven entropy.

Someone else will also soon expose the fact that what theorists are calling ancient aminoacyl tRNA synthetases are the enzymes in bacteria that decode genetic information to help produce amino acids in all living genera. The nutrient energy-dependent fixation of the RNA-mediated amino acid substitutions links selective autophagy from nutritional epigenetics to healthy longevity via the physiology of reproduction in all genera.