RNA-mediated theory killers

By: James V. Kohl | Published on: December 11, 2015

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Brain-manipulation studies may produce spurious links to behaviour

Study shows that controlling neurons with light or drugs may affect the brain in more ways than expected.

Excerpt:

Given that many experiments build on existing knowledge about circuits involved in a behaviour, he cautions, experimental scientists should be particularly careful when using transient techniques to map entirely new circuits in the brain.
“This study nicely reminds us that there is no perfect technique,” says Evan Feinberg, a neuroscientist at the University of California, San Francisco.

My Summary of this blog post:

The arguments of serious scientists must include experimental evidence of facts that link physics, chemistry, and the conserved molecular mechanisms of biologically-based cause and effect from atoms to ecosystems.

Epigenetic effects on biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry during thermodynamic cycles of protein biosynthesis and degradation link the epigenetic landscape to the physical landscape of supercoiled DNA in the organized genomes of all living genera.

Biologically-based cause and effect cannot be established in the context of metaphors.

An Ecology of Beauty and Strong Drink

Excerpt (with my emphasis):

The following presents several ecological metaphors for ritual adaptation: sexual selection, the isolated island, and the clearcut forest. Once these metaphors are established, I will explain how they apply to ritual, and suggest some policy recommendations based on this speculation.

Metaphors

Excerpt:

…this echoes a tension at the heart of philosophy between two modes of philosophizing: a speculative-revisionary mode that is metaphorical and an analytic-explanatory mode that is conditional. The tasks are generally complementary so that the difference can be ignored with impunity. However, if we do not respect that difference, we may find ourselves analyzing metaphors and seeing logical analyses as metaphorical, and thus missing the point on both fronts.

My comment: Logical analyses of biologically-based cause and effect are not metaphorical. Any theorist or philosopher whose arguments are based on ecological metaphors that attempt to link ecological variation to ecological adaptations via selection in the context of speculation can be compared to any serious scientist. The difference between theorists, philosophers and serious scientists is clear.
The arguments of serious scientists must include experimental evidence of facts that link physics, chemistry, and the conserved molecular mechanisms of biologically-based cause and effect from atoms to ecosystems.
Serious scientists do not use metaphors linked to speculation in the context of their models of top-down causation or bottom-up effects on cell type differentiation. Top-down causation is the sun’s biological / virucidal energy and bottom-up effects always must include epigenetic effects.
Epigenetic effects on biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry during thermodynamic cycles of protein biosynthesis and degradation link the epigenetic landscape to the physical landscape of supercoiled DNA in the organized genomes of all living genera.
For an example of why all serious scientists are Combating Evolution to Fight Disease by accurately representing biologically-based cause and effect, see: Structural diversity of supercoiled DNA
Excerpt:

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.

My comment: Their ABILITY to present data that links atoms to ecosystems via RNA-mediated events in an entertaining way is exemplified in less than 4 minutes. See: All About that Base (Meghan Trainor Parody) 10 Dec 2014
The INABILITY of theorists and philosophers to address any aspect of that data is represented in less than 2 minutes. See: Bacteria evolve over a weekend.
The ability of bacteria to recognize all proteins, nucleic acids, and small molecules that modulate DNA metabolic processes is miraculous. The miraculous ability can be viewed outside the context of the magic of evolution. For example, if all organisms did not have the innate ability to recognize all proteins, nucleic acids, and small molecules that modulate DNA metabolic processes, there would be no examples of what is obviously required to link the epigenetic landscape to nutrient-dependent RNA-mediated protein folding chemistry, which is biophysically constrained by the physiology of reproduction. Without fixation of RNA-mediated amino acid substitutions in different species, there is no link from the epigenetic landscape to the physical landscape of differences in the supercoiled DNA of organized genomes. Without fixation of amino acid substitutions, only ridiculous theories are left to consider. Serious scientists don’t consider ridiculous theories.
Instead, for example, serious scientists have linked the sequencing of the octopus genome to the nutrient-dependent pheromone-controlled physiology of all invertebrates and vertebrates via nutrient-dependent microRNAs and cell adhesion proteins that link supercoiled DNA to the protection from virus-driven entropy in the organized genomes of all living genera.
See: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity
Excerpt 1

In the present study, we sought to reconcile the apparently contradictory observations and clarify the roles of p120 and E-cadherin in epithelial cell behaviour. Recently, the p120 binding partner PLEKHA7 was shown to specifically localize at the apical zonula adherens (ZA) but not along lateral surfaces of epithelial cells, as for p120 or E-cadherin21,22. By using PLEKHA7 as a marker of the apical ZA in mature epithelial cells,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.

Conclusion:

Taken together, our data untangle the complicated roles of E-cadherin and p120 in the context of distinct junctional complexes, spatially separating their functions and providing an explanation for their conflicting behaviour in cell growth. In addition, they identify PLEKHA7 as a specific marker of ZA that mediates suppression of growth-related signalling. Finally, they reveal an interaction of the ZA with the microprocessor complex, and uncover a mechanism whereby the ZA regulates a set of miRNAs to suppress cellular transformation and maintain the epithelial phenotype.

Serious scientists have describes a microRNA (miRNA)-mediated mechanism of transformed cell growth that links viral microRNAs to pathology and nutrient-dependent microRNAs to healthy longevity. However, I may need to keep reminding others of this fact:
More than 45,000 published journal articles indexed on PubMed already contained the term microRNA before evolutionary theorists declared the microRNAs were linked from their emergence to all biodiversity via mutations and evolution in: MicroRNA mechanisms of action: what have we learned from mice?
I do not mind repeatedly reminding others of the fact that these theorists are biologically uninformed science idiots because they may be responsible for teaching yet another generation of unsuspecting students to become biologically uninformed science idiots.
Please remind any biologically uniformed student that you encounter that RNA-mediated theory killers will kill their chance of a successful career in any scientific discipline unless someone shows that the speed of light on contact with water cannot be linked from quantum physics to biologically-based cause and effect via RNA-mediated events in all living genera. The number of published works that help to establish that fact in the context of what is known about RNA-mediated amino acids substitutions has reached the tipping point where theorists must fight to their death against the paradigm shift that comes from their death in the context of Max Planck’s oft-echoed claim.
Guide to Thomas Kuhn’s The Structure of Scientific Revolutions
Excerpt:

19. How Communication is Restored by Conversion to the New Paradigm: What I want to highlight here is the further thesis that (p.150) “before they can hope to communicate fully, one group or the other must experience the conversion that we have been calling a paradigm shift.” For example, (p.151) “Max Planck … sadly remarked that ‘a new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.’” Or, (p.152) “Conversions will occur a few at a time until, after the last hold-outs have died, the whole profession will again be practicing under a single, but now different, paradigm.” Partly by way of explication, and partly by way of argument, Kuhn tells us how conversion is induced and how resisted.

My comment: Pseudoscientists resist converison, serious scientists usher in the paradigm shift despite that resistance. A phone call from a contractor whose efforts I agreed to help promote without the conflict of interest that financial considerations would create reminded me to first restate the fact that all experimental evidence of biologically-based cause and links the Precision Medicine Initiative to preventative medicine in the context of this brief video representation.
https://www.youtube.com/watch?v=fGjG_9EEeeA
If the contractor begins to pay me, pseudoscientists and all theorists may continue to claim that my commercial interests invalidate my representations, which is what they have done since 1995. I would like to wrap up my attempts to refute them and enjoy my retirement, even more than I already have. My wrap-up will include examples of RNA-mediated theory killers in a series of blog posts and on my FB group until someone makes me an offer to purchase the domain and continue to use it for dissemination of accurate information about biologically-based cause and effect.