Navigable networks as Nash equilibria of navigation games

Nature Communications | Article  Open

Excerpt:

Here we show that the ideal maximally navigable networks do share some basic structural properties with the Internet, E.coli metabolic network, English word network, US airport network, the Hungarian road network and a structural network of the human brain.

Reported as:

Researchers find the organization of the human brain to be nearly ideal

Excerpt:

“An optimal network in the brain would have the smallest number of connections possible, to minimize cost, and at the same time it would have maximum navigability—that is, the most direct pathways for routing signals from any possible source to any possible destination,” says Krioukov. It’s a balance, he explains…

My comment: It is the failure to link the nutrient dependent changes in the microRNA/messenger RNA balance to virus-driven entropic elasticity that leads to portrayals  of links from E. col to human brain development in the context of the pseudoscientific nonsense about evolution of the brain.

For contrast, see: 

Genome-wide microRNA screening reveals that the evolutionary conserved miR-9a regulates body growth by targeting sNPFR1/NPYR

Abstract conclusion:

We show via an in vitro binding assay that miR-9a binds to sNPFR1 mRNA in insect cells and to the mammalian orthologue NPY2R in rat insulinoma cells. These findings indicate that the conserved miR-9a regulates body growth by controlling sNPFR1/NPYR-mediated modulation of insulin signalling.

Reported as:

Control of body growth by miRNA

MicroRNAs (miRNAs) regulate many physiological processes including body growth. Insulin/IGF signalling is the primary regulator of animal body growth, but the extent to which miRNAs act in insulin-producing cells (IPCs) is unclear.

Scientists identify miR-9a as an evolutionarily conserved regulator of insulin signalling and body growth.

IPC-specific miR-9a overexpression reduces insulin signalling and body size. Of the predicted targets of miR-9a, authors find that loss of miR-9a enhances the level of sNPFR1.

They show that miR-9a binds to sNPFR1 mRNA in insect cells and to the mammalian orthologue NPY2R in rat insulinoma cells.

These findings indicate that the conserved miR-9a regulates body growth by controlling sNPFR1/NPYR-mediated modulation of insulin signalling.

My comment: The microRNA-controlled growth of insects and mammals links the anti-entropic epigenetic effects of nutrient-dependent microRNAs to the control of viruses and viral microRNAs that contribute to entropic elasticity and genomic entropy. Without the anti-entropic epigenetic effects of nutrient-dependent microRNAs, the microRNA/messenger RNA balance could not lead to cell type differentiation in the context of RNA-directed DNA methylation and the fixation of RNA-mediated amino acid substitutions that differentiate all the cell types of all individuals of all living genera.

Without the anti-entropic epigenetic effects of nutrients, no one would be Celebrating independence from ridiculous theories, and there would be no link from physics to chemistry and to the beauty of biological diversity.

Instead see:

A post-transcriptional mechanism pacing expression of neural genes with precursor cell differentiation status

Excerpt:

We conclude that the newly identified miR-9/TTP circuitry limits unscheduled accumulation of neuronal mRNAs in non-neuronal cells and ensures coordinated upregulation of these transcripts in neurons.

Reported as:

Micro RNA Controls Neural Development

Excerpt:

…miR-9/TTP circuitry ensures coordinated up-regulation of neuronal mRNAs in neurons and limits unscheduled accumulation of these transcripts in non-neuronal cells.

My comment: It has become obvious to many serious scientists that microRNAs control the development of the body and the brain in insect species and in mammals. Control appears to involve the finely tuned balance of viral microRNAs and nutrient-dependent microRNAs. That balance links the microRNA/messenger RNA balance to RNA-mediated cell type differentiation via amino acid substitutions in the context of the biophysically constrained chemistry of protein folding. Proper protein folding (sans mutations) links the physiology of reproduction to the fixation of amino acid substitutions in the organized genomes of all living genera. Viruses and accumulated viral microRNAs perturb protein folding, which links them to pathology instead of to healthy longevity via what is known about nutritional epigenetics and pharmacogenomics.

Physics: The impulse of beauty

by Joseph Silk

Excerpt 1):

“…colour, the epicentre of beauty, unites art with biology, chemistry and physics.

Note from “Nature”: You are currently not allowed to comment owing to misuse.

My comment: I think “misuse” means providing comments that link physics, chemistry, and molecular epigenetics via RNA-mediated cell type differentiation in all genera. Reports in “Nature” publications are taking a slow approach to what has already been done in publications in “Science.”

Publications in “Science” have followed the current experimental evidence and have encouraged others to join the serious scientists who are Combating Evolution to Fight Disease.

The difference between “Nature” and “Science,” is that “Science” allows me to comment on the latest experimental evidence that links the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding without the pseudoscientific nonsense about mutations and evolution that continues to be touted by those who support the evolution industry and big bang cosmology industry.

See the additional comment from the article by Joseph Silk.

Excerpt 2) Persistent voices insist that a theory of physics must lead to experimental verification. Wilczek is emphatic about this, as was Isaac Newton, who would like us to see empiricism as the search for truth. If truth and beauty are inseparable, that circle is closed.

My comment: The scientific truth about the beauty of the circle that links nutrient-dependent feedback loops to the physisology of reproduction is exemplified by the facts that link microRNAs to RNA-mediated cell type differentiation via the conserved molecular mechanisms of protein folding in all genera. I included what I know about the facts in my response to an article published in Science.

My comment to Science:

Submitted on Sat, 09/13/2014  Published  9/24/14

“An alternative theory proposes environmentally induced change in an organism’s behavior as the starting point (1), and “phenotypic plasticity” that is inherited across generations through an unspecified process of “genetic assimilation” (2).” http://www.sciencemag.org/content/332/6034/1161.short

This is now more than merely an alternative theory of genetic assimilation. It links transgenerational epigenetic effects from nutrient uptake and RNA-mediated events to amino acid substitutions that differentiate the cell types of all cells in all individuals of all organisms. See, for example: Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans http://www.cell.com/cell/abstract/S0092-8674(14)00806-X

The nutrient stress-induced RNA-mediated events, which link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man, also link morphological and behavioral diversity via conserved molecular mechanisms exemplified in the context of biologically plausible ecological speciation in nematodes.

See: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes http://linkinghub.elsevier.com/retrieve/pii/S0092867412015000

A difference in their feeding behavior and in the anatomy of their mouth parts is linked from nutrient-dependent pheromone-controlled feedback loops to ecological, social, and neurogenic niche construction. The change in focus from mutations, natural selection, and the evolution of biodiversity via unknown evolutionary events to nutrient-dependent pheromone-controlled RNA-mediated events that differentiate cell types may be required for others to realize the difference between evolutionary theories and biologically-based facts about RNA-mediated events.

RNA-mediated events are biophysically constrained, which means they are a biologically plausible way to link the physics and chemistry of protein folding to increasing organismal complexity via molecular biology. RNA-mediated events can also be compared to any unknown evolutionary events that might arise in the context of an alternative theory about constraint-breaking mutations, or other theories that include no mention of RNA-mediated events.

Summary. What we now have in the articles from “Nature” attests to the facts about Control of body growth by miRNA, and that Micro RNA Controls Neural Development. Taken together with the articles published in “Science,” it may be possible for a collaborative effect that encourages all serious scientists to join those who are Combating Evolution to Fight Disease, regardless of where they are publishing, or attempting to publish their works.

See for example, my invited review of nutritional epigenetics.  Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

Abstract: 

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

See also:

Popcorn: critical temperature, jump and sound

Abstract excerpt:

…popcorn is midway between two categories of moving systems: explosive plants using fracture mechanisms and jumping animals using muscles.

This is the description of the journal that published the article on popcorn.

Cross-disciplinary research at the interface between the physical and life sciences

My comment: At the turn of this century, I judged posters at a middle-school “Science Fair.” The one I rated highest was on the claims made about different yields from different brands of popping corn.

As it turns out, the young lady appears to have anticipated what is now known to serious scientists about the biophysically constrained cell type differentiation that links RNA-mediated events from the metabolic networks and genetic networks of plants to animals via conserved molecular mechanisms.

She may, by now, be one of the serious scientists who is helping to lead others away from ridiculous theories and lead them towards the examination of facts about biologically-based cause and effect in the context of RNA-mediated organism-level thermoregulation.

In that context, heat stress, nutrient stress, social stress, and evolutionary theory are killers. For example, in theory diverticulitis may lead to diverticulosis or colon cancer via mutations caused by popcorn hulls, small seeds, et al. Typically, nothing is mentioned about links from the gut microbiome to RNA-mediated morphological changes in cell types linked to changes in behavior. No mention of facts means that the link from vitamin D to the stability of organized human genomes may be missing when you are advised to change your diet — albeit, typically, only after-the-fact.

See, instead:

MicroRNA-627 Mediates the Epigenetic Mechanisms of Vitamin D to Suppress Proliferation of Human Colorectal Cancer Cells and Growth of Xenograft Tumors in Mice

Chromatin acetylation at transcription start sites and vitamin D receptor binding regions relates to effects of 1α,25-dihydroxyvitamin D3 and histone deacetylase inhibitors on gene expression

Using components of the vitamin D pathway to prevent and treat colon cancer.

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