From Precis to Proof in 6000 years (2)

By: James V. Kohl | Published on: November 7, 2016

See: From Precis to Proof in 6000 years
Why now? See from 2014 Israeli Middle Schools School to Include Theory of Evolution

“…learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.”

See also: President Obama on Atheism
We have since seen the rise of claims about natural information processing link energy-dependent changes to healthy longevity in species from microbes to humans via the physiology of reproduction. We have also seen facts presented that link virus-driven energy theft to all pathology. After everyone else in the world has learned about the failure of neo-Darwinian pseudoscientific nonsense, who thinks a Democrat can save us from the viral apocalyse that has been predicted for at least two decades?

See for comparison: Regulation of RNA-binding proteins affinity to export receptors enables the nuclear basket proteins to distinguish and retain aberrant mRNAs

Following transcription, messenger ribonucleic acids (mRNAs) are transported to the cytoplasm to transfer genetic information and direct synthesis of functional proteins1. Multiple co-transcriptionally occurring processes applied on precursor mRNA (pre-mRNA) are followed by the engagement of several key proteins and complexes, including RNA-binding proteins (RBPs), along the length of pre-mRNA2,3, eventually forming an export-competent ribonucleoprotein (mRNP) prepared for efficient export through the nuclear pore complex (NPC). Splicing, 5′ capping, 3′ cleavage and polyadenylation are the four well-known processing steps prior to nuclear export, while failure in any of these steps yields aberrant mRNAs1,3. These processes are quality controlled by various evolutionary conserved and highly efficient mechanisms in eukaryotic cells3,4.

My comment: The processes are quality controlled by the availability of energy. They do not control themselves without it and nothing is conserved outside the context of the energy-dependent pheromone-controlled physiology of reproduction in species from microbes to humans.
Reported as: New Details on how Cells Keep RNA Errors in Check

…many interactions between proteins allow the cell to ensure the quality of mRNA. RNA-binding proteins bind to every strand of mRNA and aid in the recruit of export receptors. Nuclear basket proteins use the interaction between export receptors and RNA-binding proteins to locate and retain aberrant mRNA.

My comment: Conserved molecular mechanisms link nutrient energy-dependent autophagy from the innate immune system of bacteria to the pheromone-controlled physiology of cell type differentiation in all living genera. The innate immune system is the link from energy-dependent changes in pre-mRNAs to supercoiled DNA prevents virus-driven energy theft from causing all pathology in species from archaea to humans.
See: 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.

See: Virus-mediated archaeal hecatomb in the deep seafloor

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

See also: Dynamics of Human and Viral RNA Methylation during Zika Virus Infection

…we investigated the role of m6A during ZIKV infection of human cells. We found that the depletion or overexpression of the central RNA methylation enzymes impacts viral replication, demonstrating that the host RNA methyltransferase machinery acts as a negative post-transcriptional
regulator of ZIKV virus.

See for comparison: Uncovered: the mysterious killer triffids that dominate life in our oceans

Based on our findings, we have proposed a new model for life in our oceans, arguing that the traditional split between the “plant-like” phytoplankton (microalgae) and the “animal-like” microzooplankton used to describe the oceanic food-web is no longer tenable. This model could overturn a century’s worth of our understanding of marine biology.

My comment: The fact that only one domain of life exists has forced theorists to invent a new player in their game of who can invent the next best theory.

See for comparison: Nobel prize-winning autophagy research laid groundwork for potential Parkinson’s treatment


During starvation, cells break down proteins and nonessential components and reuse them for energy. Cells also use autophagy to destroy invading viruses and bacteria, sending them off for recycling. And cells use autophagy to get rid of damaged structures. The process is thought to go awry in cancer, infectious diseases, immunological diseases and neurodegenerative disorders. Disruptions in autophagy are also thought to play a role in aging.

See this discussion attempt: “WHY don’t we have a plethora of random life forms alive today… nor in the fossil record”?

My comment: The more people learn about the birds and the bees, the more biological regularities attest to the fact that birds did not automagically evolve from dinosaurs during the past 6000 years, or ever.

Chemical composition of preen wax reflects major histocompatibility complex similarity in songbirds


The salience of MHC genotype to fitness in songbirds [45] suggests that selection should favour the ability to signal and assess MHC profiles. The relationship between MHC and chemical distances for mixed-sex dyads suggests that provided song sparrows can detect chemical cues, this information should be useful in the context of mate choice, regardless of whether a self-referent or a known-kin criterion is used. By contrast, chemical cues do not appear to reflect MHC diversity. Our findings implicate preen secretions as potential semiochemicals in songbirds, a group in which chemical communication has only recently been explored. Further testing is warranted to determine if songbirds can perceive MHC-related variation in chemical profiles. Still, our findings suggest that chemosignalling may be more taxonomically widespread than previously thought, and could help to maintain adaptive genetic diversity in natural populations.

My comment: In my model, nutrient energy-dependent chemosignalling links the pheromone-controlled physiology of reproduction from species of microbes to humans via the conserved molecular mechanisms known to all serious scientists.

See also: Thomas Hunt Morgan (September 25, 1866 – December 4, 1945)[1] was an American evolutionary biologist, geneticist, embryologist, and science author who won the Nobel Prize in Physiology or Medicine in 1933 for discoveries elucidating the role that the chromosome plays in heredity.[2]

See also:  Genes located in a chromosomal inversion are correlated with territorial song in white-throated sparrows

The white-throated sparrow is a useful model system in which to study the consequences of an inversion on gene expression. By suppressing recombination between alleles, chromosomal rearrangements can foster the evolution of co-adapted alleles, or ‘supergenes’ (Dobzhansky, 1970). Inversions that encompass multiple genes involving a suite of phenotypic traits might therefore maintain both behavioral and color polymorphism within a species (reviewed in McKinnon & Pierotti, 2010). Alternatively, a single gene with pleiotropic effects might be responsible for both behavioral and color polymorphism. Likely candidates are transcription factors and hormones. Transcription factors have the capacity to coordinate the expression of multiple genes that share a cis-regulatory region. Hormones can activate transcription factors and act through nongenomic signaling pathways. We cannot determine from our current study whether co-adapted alleles or a small number of pleiotropic genes can explain the behavioral polymorphism. It will be interesting to determine in future studies the extent to which manipulating expression of a single gene can influence behavior in this species.

My comment: A single base pair change and single RNA-mediated amino acid substitution link energy-dependent changes in morphological and behavioral phenotypes  across all species.
See for example: Genome divergence and diversification within a geographic mosaic of coevolution

Our results further characterize a striking example of coevolution driving speciation within perhaps as little as 6000 years.

Reported as:   Biologists Use Genomics to Identify Evolving New Bird Species in Southern Idaho

The finch feeds voraciously and exclusively on the pine seeds, which caused the tree to evolve seed defenses that make it harder for the birds to harvest the seeds. The birds counter-evolved against those defenses as evolution favored deeper-beaked crossbills, resulting in a coevolutionary arms race that has driven evolutionary divergence of this unique bird population.

My comment: The idea that bird species and trees co-evolved during the past 6000 years is one that can be placed into the context of nutrient-dependent pheromone-controlled weekend resurrection of the bacterial flagellum because all individuals in all species must eat to reproduce and pheromones control the physiology of nutrient-energy reproduction.
Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Reported as: Evolutionary Rewiring
See my comments. For example:

The ‘backup system’ appears to protect against the damage caused by viruses and viral microRNAs that perturb the biophysically constrained chemistry of nutrient-dependent protein folding and reproduction in species from microbes to humans.

See: Viruses and cell type differentiation

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