Alternative splicing of pre-mRNA

The MicroRNAome Strikes Back: A Sokalian hoax (6)

The nature of nurture: Effects of parental genotypes Science  January 26, 2018

…nontransmitted alleles can affect a child through their impacts on the parents and other relatives, a phenomenon we call “genetic nurture.”

It doesn’t matter what they call it, since there is no defined boundary between genetics and epigenetics.
Reported as: You Are Shaped by the Genes You Inherit. And Maybe by Those You Don’t by Carl Zimmer January 25, 2018

A calf may inherit those milk-boosting variants from its mother. But just because the calf carries them doesn’t mean they directly make the calves bigger.

Compared to other mammals, Dr. Bijma observed, human children are especially dependent on their parents — not just for food and other essentials, but for social development. So it stands to reason that they’d experience similar effects.

“Humans provide substantial care to their offspring, and so the nurture they create is very likely to have a genetic component,” said Dr. Bijma.

Dr. Harden said that taking account of genetic nurture could improve research on the effects of poverty on how children do in school, as well as studies of methods to improve educational attainment.

“It’s so obvious in retrospect, and so elegant,” she said. “A lot of people are going to say, ‘I can see my data in a new light with this.’”

See for comparison: No Boundary Really Between Genetic and Epigenetic

…evolutionary science has now “moved on to such an extent” that she and Peter Saunders don’t really care anymore about trying to convince the neo-Darwinists.

The reporting on genetic nurture by Carl Zimmer appears to be a ploy to soften the impact of his past misrepresentations and the misrepresentations of all theorists and most so-called science journalists. He now reports on biophysically constrained energy-dependent events that link ecological variation to ecological adaptation in all living genera. See for example the The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression.
Included in the New York Times online article is a picture of a cow and a calf that tells less than half of what we detailed in From Fertilization to Adult Sexual Behavior (1996). The remaining details include how molecular mechanisms of RNA-mediated cell type differentiation are conserved in the bull.
Without food energy-dependent changes in the bull’s microRNAome, no one, including Carl Zimmer can get from the energy-dependent zinc spark at fertilization to the microRNAs in cow’s milk. And now, Carl Zimmer knows it!
See: The zinc spark is an inorganic signature of human egg activation (2016)
See also: MicroRNAs: Milk’s epigenetic regulators (2017)
See also: Maternal BRG1 regulates zygotic genome activation in the mouse (2006)

Genes involved in transcription, RNA processing, and cell cycle regulation were particularly affected. The early embryonic arrest is not a consequence of a defective oocyte because depleting maternal BRG1 after oocyte development is complete by RNA interference (RNAi) also resulted in two-cell arrest. To our knowledge, Brg1 is the first gene required for ZGA in mammals.

But wait, there’s more than just RNA interference involved. The energy-dependent zinc spark is linked from the energy-dependent creation of microRNAs to the creation of  monoallelic olfactory receptor genes via the biparental contribution to chromosomal rearrangements. If not, Carl Zimmer and other science journalists cannot get from the epigenetic effects of food odors and pheromones to the feedback loops that link chromosomal rearrangements to the protection of all organized genomes from the virus-driven degradation of messenger RNA and all pathology.
If Carl Zimmer appears to have had a sudden epiphany that led him to see the light of evolution is actually sunlight in the context of ecological adaptation, his ability to see the how the facts extend to humans cannot be attributed only to a recent publication.
See also: Fine-scale recombination rate differences between sexes, populations and individuals (2010)

Comparisons of our maps with two LD-based maps inferred from data of HapMap populations of Utah residents with ancestry from northern and western Europe (CEU) and Yoruba in Ibadan, Nigeria (YRI) reveal population differences previously masked by noise and map differences at regions previously described as targets of natural selection.

Human population differences were linked to natural selection and the energy-dependent spark at fertilization. What, besides natural selection for energy-dependent codon optimality, could have been linked to the spark at fertilization?  Why would there be any questions about whether the findings in other animals extend to the findings on the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes in species from yeasts to mammals that we reported in 1996? See our section on molecular epigenetics in  From Fertilization to Adult Sexual Behavior.
I wonder if Carl Zimmer was one of the people who may have seen my tweets during the past 28 days (80,000 impressions). There is no way to be certain that the timing of his epiphany is anything more than coincidental. But that doesn’t matter.
He is now well on his way to reporting the facts about biophysically constrained viral latency and biodiversity after decades of reporting on the pseudoscientific nonsense touted by neo-Darwinian theorists.
it seems just as likely that he has been following my blog posts here and is scared to death not to report the facts before the forthcoming conference: Mechanisms of Recombination After that, everyone in the world of intelligent science journalism will know that energy-dependent epigenetic effects link food odors and pheromones from feedback loops to biophysically constrained cell type differentiation and viral latency in all living genera.
See also: Epigenetic modifications poster
Anyone who continues to report findings in the context of neo-Darwinian pseudoscientific nonsense about mutations and/or evolution is unlikely to be employed as a science journalist.


The radical pair mechanism of ecological speciation

The radical pair mechanism and the avian chemical compass: Quantum coherence and entanglement


Radical pairs are usually produced as short-lived intermediates through decomposition, electron transfer, or hydrogen transfer reactions from singlet or triplet excited states.

My comment: The radical pair mechanism appears to be another link from nutrient energy-dependent hydrogen-atom transfer in DNA base pairs to ecological speciation. However, the hydrogen-atom transfer in DNA base pairs mechanism seems to have gone unrecognized despite this report.

Induction of micronuclei and superoxide production in neuroblastoma and glioma cell lines exposed to weak 50 Hz magnetic fields


The radical pair mechanism (RPM) is considered as a plausible mechanism for explaining the biological effects of weak MFs [7]. Based on quantum mechanics, the RPM predicts MF effects on the lifetime of radical pairs. This mechanism is theoretically well known [7,33–34] and has been experimentally demonstrated in chemical systems [35]. In biology, the RPM seems to be involved in animal navigation, through detection of the geomagnetic field in specific magneto-sensitive molecules [35].

My comment: Disorienting epigenetic effects of weak magnetic fields (MFs) that are known in theory could be linked from atoms to ecosystems via what is known about the biophysically constrained nutrient energy-dependent physiology of reproduction and ecological speciation in white-throated sparrows and other model organisms. However, the advantage of the white-throated sparrow model is the link from atoms to ecosystems that appears to be manifested in different morphological phenotypes and different behavioral phenotypes in the same species.
Odour-based discrimination of subspecies, species and sexes in an avian species complex, the crimson rosella
Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes
New insights into the hormonal and behavioural correlates of polymorphism in white-throated sparrows, Zonotrichia albicollis
Evaluation of reference genes for quantitative real-time PCR in the brain, pituitary, and gonads of songbirds
Estrogen Receptor Alpha as a Mediator of Life-History Trade-offs
The perfume of reproduction in birds: chemosignaling in avian social life
My comment: Taken together, it is less likely that serious scientists will miss the link from atoms to ecosystems via chromosomal rearrangements and biodiversity in birds that links their biodiversity to the biodiversity of microbes via RNA-mediated amino acid substitutions linked to chromosomal rearrangements. The conserved molecular mechanisms of quantum physics link nutrient energy-dependent hydrogen-atom transfer in DNA base pairs across all living genera via their physiology of reproduction.
See also: Pathogenetics. An introductory review

10.7.2. RNA repair/editing system
RNA editing refers to molecular modifications of nucleotides of RNA through chemical changes in the base makeup of the molecule. Such changes appear to be present in all three domains of life, and involve both coding, mRNA, and non-coding, tRNA and mRNA, types of small or microRNA. RNA editing occurs in the cell nucleus and the cytosol, as well as in mitochondria and is mediated by a complex repair system comprising many species of small RNA (guide RNA) and large protein complexes known as the editosomes. The pathways of RNA editing include many diverse processes: nucleoside base modifications such as cytidine (C) to uridine (U) and adenosine (A) to inosine (I) deaminations, as well as non-templated insertions of nucleotide. RNA editing in mRNAs effectively alters the amino acid sequence of the encoded protein so that it differs from that predicted by the genomic DNA sequence. Though mRNA editing is used in many instances to allow for synthesis by the cell of more than one protein from the same mRNA transcript, e.g. synthesis of both apolipoprotein B-100 and apolipoprotein B-48 from the same mRNA in liver cells, it can also be used to repair missense or termination mutations of the molecule which can have deleterious effects on the synthesized protein. Specific endonucleases and ligases for double stranded species of RNA have been defined in many prokaryotes and it might be just a matter of time before defining their functional counterparts in eukaryotes and human cells.

My comment: RNA-mediated DNA repair is nutrient energy-dependent and it is linked from ecological variation to ecological adaptation via the physiology of reproduction in all living genera. The physiology of reproduction links atoms to ecosystems via nutrient energy-dependent hydrogen-atom transfer in DNA base pairs.
If you do not understand that fact, you cannot understand how cell type differentiation occurs in the context of healthy longevity compared to pathology. Neo-Darwinists, for example, link mutations to healthy longevity via evolution.