Filtering light through a prism to identify tissue type

From fertilization to RNA-mediated events and back

My comment: The RNA-mediated events that link all biodiversity from it’s nutrient-dependent origins to the physiology of reproduction in all living genera (from octopuses to insects in this video), were detailed in:
From Fertilization to Adult Sexual Behavior
See also:
Organizational and activational effects of hormones on insect behavior
Honey bees as a model for understanding mechanisms of life history transitions
Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors.
Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
Role of olfaction in Octopus vulgaris reproduction
The octopus genome and the evolution of cephalopod neural and morphological novelties
My comment: For an attempt to make everything known about how ecological variation is linked via RNA-mediated events to ecological adaptation fit into a mathematical model of “emergence,” see:
Stability analysis of a model gene network links aging, stress resistance, and negligible senescence
Excerpt 1)

The most important results of this study are Eq. (4), phenomenologically describing aging of a gene network, and the concept of fundamental genomic instability described by Eq. (6).

Excerpt 2)

Although unstable gene networks exponentially accumulate gene expression errors and eventually disintegrate, the growth exponent is nevertheless small and the characteristic mean lifespans can be made sufficiently large and weakly dependent on genotoxic stress factors in the Gompertz limit. This may be an explanation of the apparent prevalence of Gompertzian aging in Nature.

My comment: Gene expression errors is used instead of mutations in the context of metabolic networks linked to genetic networks that disintegrate, which replaces the term genomic entropy. Their team makes it clear why mathematical models that phenomenolgically describe aging of gene networks have no explanatory power in the context of biologically-based cause and effect.
Biologically based cause and effect must link RNA-mediated DNA repair to healthy longevity via metabolic networks and genetic networks that do not disintegrate due to gene expression errors. The metabolic networks and genetic networks link the conserved molecular mechanisms of RNA-mediated cell type differentiation to the nutrient-dependent origin of life in all living genera.
See also: A Surprise Source of Life’s Code

In 2006, Begun found some of the first evidence that genes could indeed pop into existence from noncoding DNA.

My comment: That’s phenomenologically ridiculous. Never in history have the simple-minded so greatly influenced young scientists who have learned how to become biologically uninformed science idiots.
The article concludes:

“How does novel gene become functional? How does it get incorporated into actual cellular processes?” McLysaght said. “To me, that’s the most important question at the moment.”

My comment: The nutrient-dependent de novo creation of olfactory receptor genes links The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression to the pheromone-controlled physiology of reproduction via RNA-mediated molecular mechanisms of cell type differentiation that link species from microbes to man.
Duplicate genes that are not required for survival of organisms and species accumulate virus-driven mutations that lead to the formation of pseudogenes or gene loss in the context of biophysically constrained thermodynamic cycles of protein biosynthesis and degradation.
See also: DNA methylation pathways and their crosstalk with histone methylation

Histone and DNA methylation have important and connected roles in the epigenetic control of gene expression in all three kingdoms of eukaryotic organisms. In some cases the relationships between these two epigenetic marks are linear.

My comment: In cases where the relationships between these two epigenetic marks do not appear to be linear, preventing food acquisition or reproduction would quickly establish a link between biologically-based cause and effect in the context of everything known to serious scientists about top-down causation and biophysically constrained ecological speciation.

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