Light-activated PTEN-dependent viral latency (2)

(click to enlarge)

See first: Light-activated PTEN-dependent viral latency (1) 12/25/19
On 12/26/19, Cold Spring Harbor Laboratory responded to my accurate representations of light-activated energy-dependent biophysically constrained viral latency with a report on Biophysical models of cis-regulation as interpretable neural networks 11/8/19
See: Finally, machine learning interprets gene regulation clearly 12/26/19

“…understanding how something like gene regulation works—is very often the difference between being able to develop molecular therapies against diseases, and not being able to,” Kinney said.

Cold Spring Harbor Laboratory is a safe haven for researchers who do not seem to know that gene regulation is energy-dependent and/or that the Creation of energy biophysically constrains viral latency. That knowledge led intelligent serious scientists to link the Creation of sunlight and water from oxidative phosphorylation to differences in the morphology and behavior of all oxygen-dependent life on Earth.
Gregg L. Semenza shared the 2019 Nobel Prize in Physiology or Medicine for starting to do that in 1991.
See: Semenza, G.L, Nejfelt, M.K., Chi, S.M. & Antonarakis, S.E. (1991). Hypoxia-inducible nuclear factors bind to an enhancer element located 3’ to the human erythropoietin gene. Proc Natl Acad Sci USA, 88, 5680-5684
See also: A genetic mechanism for Tibetan high-altitude adaptation (2014)
All adaptations are epigenetically effected by the energy that links the physiology of reproduction to all biodiversity via biophysically constrained viral latency.
I reiterate: PTENα, a PTEN Isoform Translated through Alternative Initiation, Regulates Mitochondrial Function and Energy Metabolism 4/24/14
You can follow the extant literature on ecological variation and ecological adaptations, or take what Greg Bear learned from CSHL researchers, when he linked the extant literature on light-activated biophysically constrained energy-dependent microRNA-mediated pheromone-controlled quorum sensing in P. fluourescens to viral latency and the rise of a new food energy-dependent ecologically adapted group of humans via gene duplication in two books reviewed in Nature.
See: Evolution rising from the grave (2000) and Living with the Neanderthals (2003)
But wait. A 2019 news article in Nature bastardized everything known to Greg Bear, and everything known to all serious scientists, by claiming that evolution builds genes from scratch.
See: How evolution builds genes from scratch 10/16/19 Clarification 11/13/19

After publication of our story, we learnt that another scientist had suggested the de novo origin of antifreeze protein genes before Helle Baalsrud’s team.

Biologically uninformed science idiots link the de novo origin of proteins to all extant biodiversity via the de novo creation of genes.
de novo means that the genes create themselves. Eliminating that nonsense is the key to explaining why CSHL researchers and reporters are still misrepresenting cause and effect via claims based on “big data.”
For comparison to “big data-based” reports, no experimental evidence suggests that any microRNA, any RNA, any amino acid, any protein, or any gene has ever created itself.
Instead, see this Historical perspective (works published from 2003 to 2018). Start with:

• Fischer SE. Small RNA-mediated gene silencing pathways in C. elegans. Int J Biochem Cell Biol. 2010 Aug; 42(8):1306-15.

• Newman MA, Ji F, Fischer SEJ, Anselmo A, Sadreyev RI, Ruvkun G. The surveillance of pre-mRNA splicing is an early step in C. elegans RNAi of endogenous genes. Genes Dev. 2018 05 01; 32(9-10):670-681.
• Fischer SEJ. RNA Interference and MicroRNA-Mediated Silencing. Curr Protoc Mol Biol. 2015 Oct 01; 112:26.1.1-26.1.5.
• Billi AC, Fischer SE, Kim JK. Endogenous RNAi pathways in C. elegans. WormBook. 2014 May 07; 1-49.
• Fischer SE, Pan Q, Breen PC, Qi Y, Shi Z, Zhang C, Ruvkun G. Multiple small RNA pathways regulate the silencing of repeated and foreign genes in C. elegans. Genes Dev. 2013 Dec 15; 27(24):2678-95.
• Zhang C, Montgomery TA, Fischer SE, Garcia SM, Riedel CG, Fahlgren N, Sullivan CM, Carrington JC, Ruvkun G. The Caenorhabditis elegans RDE-10/RDE-11 complex regulates RNAi by promoting secondary siRNA amplification. Curr Biol. 2012 May 22; 22(10):881-90.
• Montgomery TA, Rim YS, Zhang C, Dowen RH, Phillips CM, Fischer SE, Ruvkun G. PIWI associated siRNAs and piRNAs specifically require the Caenorhabditis elegans HEN1 ortholog henn-1. PLoS Genet. 2012; 8(4):e1002616.
• Fischer SE, Montgomery TA, Zhang C, Fahlgren N, Breen PC, Hwang A, Sullivan CM, Carrington JC, Ruvkun G. The ERI-6/7 helicase acts at the first stage of an siRNA amplification pathway that targets recent gene duplications. PLoS Genet. 2011 Nov; 7(11):e1002369.
• Zhang C, Montgomery TA, Gabel HW, Fischer SE, Phillips CM, Fahlgren N, Sullivan CM, Carrington JC, Ruvkun G. mut-16 and other mutator class genes modulate 22G and 26G siRNA pathways in Caenorhabditis elegans. Proc Natl Acad Sci U S A. 2011 Jan 25; 108(4):1201-8.
• Sebastiani P, Montano M, Puca A, Solovieff N, Kojima T, Wang MC, Melista E, Meltzer M, Fischer SE, Andersen S, Hartley SH, Sedgewick A, Arai Y, Bergman A, Barzilai N, Terry DF, Riva A, Anselmi CV, Malovini A, Kitamoto A, Sawabe M, Arai T, Gondo Y, Steinberg MH, Hirose N, Atzmon G, Ruvkun G, Baldwin CT, Perls TT. RNA editing genes associated with extreme old age in humans and with lifespan in C. elegans. PLoS One. 2009 Dec 14; 4(12):e8210.
• Fischer SE, Butler MD, Pan Q, Ruvkun G. Trans-splicing in C. elegans generates the negative RNAi regulator ERI-6/7. Nature. 2008 Sep 25; 455(7212):491-6.
• Vastenhouw NL, Fischer SE, Robert VJ, Thijssen KL, Fraser AG, Kamath RS, Ahringer J, Plasterk RH. A genome-wide screen identifies 27 genes involved in transposon silencing in C. elegans. Curr Biol. 2003 Aug 05; 13(15):1311-6.
• Fischer SE, Wienholds E, Plasterk RH. Continuous exchange of sequence information between dispersed Tc1 transposons in the Caenorhabditis elegans genome. Genetics. 2003 May; 164(1):127-34. 

See for comparison: System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes 1/17/13
Reported as: The neurobiological consequence of predating or grazing 1/17/13

“The patterns of synaptic connections perfectly mirror the fundamental differences in the feeding behaviours of P. pacificus and C. elegans”, Ralf Sommer concludes. A clear-cut result like that was not what he had necessarily expected.

See also: Evolution of neuronal anatomy and circuitry in two highly divergent nematode species 9/17/19

These findings demonstrate the existence of several constraints in patterning the nervous system and suggest that major substrates for evolutionary novelty lie in the alterations of dendritic structures and synaptic connectivity.

No experimental evidence of biophysically constrained energy-dependent ecological adaptations suggests that differences in neuronal anataomy and circuitry evolved. Biophysical constraints on viral latency and ecological adaptations are nutrient-dependent and pheromone-controlled in species from microbes to primates.
Clearly, however, those who were taught to believe in ridiculous theories of evolved biodiversity are stuck with the language used by theorists at a time when all serious scientists have replaced the term evolution with ecological adaptation.

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