Biophysical constraints on RNA synthesis (1)

By: James V. Kohl | Published on: March 5, 2019

(click to enlarge)

Includes:

Constraints on amino acid substitutions in peptides

Constraints on nanocomplexes

Constraints on systems complexity

Summary: The role that energy-dependent changes in the microRNA/messenger RNA balance plays in ecological adaptation established the facts about biophysically constrained viral latency and healthy longevity in the context of the cure for cancer and links to neurodegenerative diseases.
See: Virus-driven downsizing of the human brain parts 1-6 at RNA-mediated.com
Theme: MicroRNAs are the pre-mRNAs from the past. That fact has since been buried in the patent on RNA-interference (aka RNA-guided human genome engineering).
Historical perspective: There were ~25,000 publications that mentioned the term microRNA by the time I published Nutrient–dependent / pheromone–controlled adaptive evolution: a model on 6/14/13. Mutation-driven evolution, a textbook of pseudoscientific nonsense was published on the same day.
Since 6/14/13 the number of publications that mention microRNA has increased to nearly 84,000.
In an attempt to move forward, is it wrong for me to claim that all biologically uninformed theorists have failed to link the light-activated Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism to the light-activated assembly of the microRNA-RNA-peptide nanocomplex? If so, have they also failed to link biophysically constrained viral latency to all biodiversity on Earth via the physiology of reproduction?

…precursors of amino acids glycine, serine, alanine and threonine, are inevitable by-products of this RNA assembly chemistry…

Have biologically uninformed theorists found another logic-based pathway that links RNA assembly chemistry to cell type differentiation in all cell types? After three questions with no immediately apparent answers, see also: Dual-microRNA-controlled double-amplified cascaded logic DNA circuits for accurate discrimination of cell subtypes

(1) the dual-microRNA-controlled strategy provides an impressive improvement over the single-input-controlled system by increasing specificity and inhibiting off-target effects; (2) the double-amplified assay offers efficient signal amplification and enables ultrasensitive fluorescence activation of target microRNAs with a picomolar detection limit…

This is the level of detection that led to claims from: Accelerated Evolution Biotechnologies

The ability of different peptides to inhibit autophosphorylation of EGFR is presented by the decrease of the fluorescent signal (Y axis).

That means the fixation of RNA-mediated amino acid substitutions in the peptides can be linked from a measurement of fluorescence to everything that happens in the context of the space-time continuum of energy-dependent top-down causation.
See also: Olfaction Warps Visual Time Perception (3/17/17) link opens pdf and see other publications by Wen Zhou et al. (2008-2019)
Summary: Her group’s findings suggest that the concept of the space-time continuum from physics, in which space-time is warped by the distribution of mass and energy in it, extends from the creation of the sense of smell to our visual perception of mass and energy in the context of time.

Simply put, “…subjective time is “warped” by the neural energy involved in representing multisensory inputs at subsecond scales.’

That claim about olfaction is consistent with all other claims about the creation of sunlight and neural energy. The claims link the light-activated assembly of the microRNA-RNA-peptide nanocomplex to the neural energy that allows the fixation of RNA-mediated amino acids to differentiate all cell types in all individuals of all living genera via the neural energy of peptides (two or more amino acids). The neural energy of peptides must be viewed as an extension of the creation of sunlight in the context of autophosphorylation and the prevention of all pathology.
See: Autophosphorylation

en.wikipedia.org

Autophosphorylation is a biochemical process in which a phosphate is added to a protein kinase by itself. In eukaryotes, autophosphorylation takes place by the addition of a phosphate group to serine, threonine, or tyrosine residues in protein kinases.
Serine and threonine are polar amino acids. Many people will not understand how the precursors of amino acids glycine, serine, alanine and threonine led to the creation of the so-called serine, threonine residues.
Definition of residue

a constituent structural unit (such as a group or monomer) of a usually complex molecule amino acid residues from hydrolysis of protein

Definition of isoform:

any of two or more functionally similar proteins that have a similar but not an identical amino acid sequence

These definitions do not include anything that is known to serious scientists about the food energy-dependent structure of amino acids in proteins. That is why biologically uninformed theorists make claims like this from: A universal trend of amino acid gain and loss in protein evolution 2/10/2005

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

How much more would you need to learn about biophysically constrained protein folding before you realized that every aspect of biophysically constrained protein folding chemistry must be linked from the creation of sunlight to autophagy and to cell type differentiation via energy-dependent changes that link autophosphorylation to the fixation of RNA-mediated amino acid substitutions? The energy-dependent changes differentiate all cell types in all individuals of all living genera.

At what point might you be able to link nutrient stress or social stress from energy-dependent changes in autophagy to the appropriate abiotic and biotic stress responses and ecological, social, neurogenic, and sociocognitive niche construction? The use of definitions is confusing. Could it be that some people make money by deliberately confusing others. Do they use terms such as residues or isoforms and hope no one would notice they are making claims about energy-dependent effects on protein folding chemistry? Do they not want you to learn about what it takes to link stress to appropriate responses. Do they not want you to learn that inappropriate responses link the virus-driven theft of energy from mutations to all pathology?

You need only look for the use of terms such as quantitative trait loci and nonhomologous end joining to see examples of confusion. WARNING: You must enter the world of biologically uninformed theorists to learn how they think in the context of meaningless terms and vague definitions. Some people become too confused and they start to think like theorists. When that happens, they may never be able to return to the reality of serious scientists.

Did that happen to you? For a test, try to think about: Linking Autophagy to Abiotic and Biotic Stress Responses

…an interplay between reactive oxygen species (ROS) and autophagy is observed, ROS being able to induce autophagy and autophagy able to reduce ROS production. We also highlight the importance of osmotic adjustment for the successful performance of autophagy…

Autophagy is energy-dependent. It does not perform itself in the context of autophophorylation. An energy-source is required. The energy source is light. Osmotic adjustments to the availability of water do not automagically occur.

Light activates the assembly of the microRNA-RNA-peptide nanocomplex that links biophysical constraints on the creaton of RNA and amino acids from peptides to cell type differentiation via the energy-dependent fixation of amino acids in peptides. Indeed, the potential of hydrogen (pH) appears to link hydrogen-atom transfer in DNA base pairs in solution from osmotic adjustments to the hydrophobicity of supercoiled DNA.

To clarify: A peptide is a compound consisting of two or more amino acids linked in a chain. If you refer to the amino acids as anything except amino acids, you escape from the facts about biophysically constrained cell type differentiation. That escape route may be linked to how people become neo-Darwinian evolutionary theorists.

Theorists need an escape route. Most cannot accept the reality of their ignorance.

They tell fanciful stories about things that happen to genes. See for examples: Mutation-Driven Evolution 6/14/13

They include stories about nucleotide substitutions, insertions/deletions, gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer and virtually anything else you can think of. Whatever else you can think of will still allow theorists to claim that mutations are the source of all genetic variation and theorists will link the mutations to evolution via natural selection. Simply put, theorists think that natural selection automagically saves advantageous mutations and eliminates harmful mutations.

If you ask a theorist how natural selection occurs outside the context of the light-activated assembly of the microRNA-RNA-peptide nanocomplex, the theorist can evoke claims of “magic traits.”

For instance, see: Genetic dissection of assortative mating behavior 2/7/19

Ecologically relevant mating cues (sometimes known as “magic traits” [2,6]) are now predicted to be widespread in nature [6,7]

Cited works with my emphasis:

2. Gavrilets S. Fitness Landscapes and the Origin of Species. Princeton University Press; 2004.

6. Servedio MR, Van Doorn GS, Kopp M, Frame AM, Nosil P. Magic traits in speciation: “magic” but not rare? Trends Ecol Evol (Amst). 2011;26: 389–397.

7. Thibert-Plante X, Gavrilets S. Evolution of mate choice and the so-called magic traits in ecological speciation. Ecol Lett. 2013;16: 1004–1013.

See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model 6/14/13

…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.

If you believe in the “magic traits” of ecological speciation, you do not need to learn about energy-dependent biophysical constraints on ecological adaptations and sympatric speciation. You will function well among other academics who believe in magic. With their “magic” theorists need not consider the role of the energy-dependent microRNA/messenger RNA balance.

For example: A postdoctoral researcher threatened me with litigation if I did not remove his name and the name of his institution after he wrote:

We house our animal mouse models in pathogen free environments (aside from transponson). They still age and die with pathological features. Sorry

He made an ignorant attempt to refute the entirety of my model.

See for comparison: RNA Polymerase II (video)

For details, see: Phosphorylation and functions of the RNA polymerase II CTD

Changes in phosphorylation patterns, as polymerase transcribes a gene, are thought to orchestrate the association of different sets of factors with the transcriptase and strongly influence functional organization of the nucleus.

Every interactive aspect of the energy-dependent functional organization of the nucleus and every aspect of protein folding chemistry is biophysically constrained in the context of the light-activated assembly of the microRNA-RNA-peptide nanocomplex. For comparison, theorists claim that the interactions are controlled by mutations and the evolution of the amino acids in different peptides.
See: A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

Biophysically constrained endogenous retroviruses have been linked to healthy longevity in all living genera. The virus-driven degradation of messenger RNA has been linked from constraint breaking mutations to all pathology.

The fact that mice used in experiments are housed “in pathogen free environments” is not irrelevant. It attests to the fact that stress links endogenous retroviruses in mice and humans to the pathological features of aging and death, which are caused by constraint-breaking mutations.

For an example of someone who studies aging, but does not know what causes it, see:

1) Ku80 facilitates chromatin binding of the telomere binding protein, TRF2 (2010)

The Ku70/80 heterodimer is central to non-homologous end joining repair of DNA double-strand breaks and the Ku80 gene appears to be essential for human but not rodent cell survival.

That suggests the creation of a new gene is essential to differences in the survival of humans compared to rodents. It’s wrong, but see what’s partially right:

Intriguingly, aging and age-related diseases can be delayed by modulating nutrient signaling pathways converging on the target of rapamycin (TOR) kinase, either by genetic or dietary intervention.

Rather than accept all the facts that link Nutrient-dependent Pheromone-Controlled Ecological Adaptations: From Angstroms to Ecosystems, one of the co-authors of both these published works threatened litigation. His so-called attorney claimed I misrepresented his claims without specifying which claims I had misrepresented in a Facebook discussion.

What can be done about such malicious threats? I’ve found it does no good to expose examples of human idiocy.

For comparison, via publication on 4/18/18, I linked the nutrient-dependent pheromone-controlled EDAR V370A variant from the mouse-to-human model of biophysically constrained viral latency in human populations from North and East Asia to the New World. Support for my claims was published on 4/23/18 as: Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk

The frequency of the human-specific EDAR V370A allele appears to be uniquely elevated in North and East Asian and New World populations due to a bout of positive selection likely to have occurred circa 20,000 y ago.

This was reported as: Human Genome Structural Variation Patterns Vary by Population, Optical Mapping Study Shows

A phylogenetic analysis of these maps indicated that some SVs and CNVs show variable population patterns. The researchers were also able to characterize SVs in typically intractable regions of the genome, including spots not covered by the human reference genome.

The problem they encountered was simple:

A major limitation of optical mapping is its lack of sequencing data, such that it does not have single basepair resolution.

The link from an energy-dependent change in as single base pair to the EDAR V370A and differences in the phenotype of mice and humans was established in my review.

Nutrient-dependent Pheromone-Controlled Ecological Adaptations: From Angstroms to Ecosystems

Others, for comparison, have attempted to dismiss my refutation of neo-Darwinian pseudoscientific nonsense and Big Bang cosmology. People like their ridiculous theories. It doesn’t matter how much experimental evidence invalidates their theories and their world-view.

That fact helps to explain why President Donald Trump recently claimed

“I will be signing an executive order requiring colleges and universities to support free speech if they want federal research dollars”

I replied:

This is the beginning of the end to neo-Darwinian theory and Big Bang cosmology. If discussion of the light-activated asssembly of the microRNA-RNA-peptide nanocomplex continues to be linked to the cure for cancer, everyone will learn that viruses cause all pathology.

See: A16Z Bio Fund’s Pande Sees A.I. as Way to Ride Bio Innovation

…many aspects of biology (biochemical pathways, for example) have become so big, complicated, and messy that understanding the system is beyond what a human being can comprehend.

All are light-activated and microRNA-mediated. I wrote: The energy-dependent light-activated assembly of the microRNA-RNA-peptide nanocomplex links achiral glycine from the EDAR V370A allele to human populations in the New World from populations in North and East Asia. With that understanding, biochemical systems are comprehensible.

See for example: Human chemosignals modulate emotional perception of biological motion in a sex-specific manner link opens pdf

See: Biophysical constraints on RNA synthesis (2)
Includes:
Constraints on sexual orientation
Constraints on subatomic particles
David Sloan Wilson’s comment on gamification

Biophysical constraints on RNA synthesis (1)

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