Two photon-linked biodiversity (1)

Excerpt: Photochromic photoreceptors, called phytochromes, perceive changes in the ratio of red and far-red light. The perceived changes help to control light-activated microRNA biogenesis in the context of the shade avoidance reaction of plants. If plants avoid the shade, they grow in the amount of light that is readily available.

Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments

…two amino acid changes responsible for the red-shift have independently occurred…

Nothing known to serious scientists suggests that the changes are not linked directly from the creation of sunlight and ATP to microRNA biogenesis and the creation of RNA.

Indeed, Ewan Birney was made a Commander of the British Empire despite his 2012 refutation of neo-Darwinian nonsense about mutation-driven evolution.

He placed ecological variation into the context of ecological adaptation.

See: The genomic basis of adaptive evolution in threespine sticklebacks

It was published a few weeks after I published Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors.

…the gene, cell, tissue, organ, organ-system pathway that links food odors and pheromones to the brain and to behavior does not change from insects to mammals.

To place that fact from 2012 into the context of different light environments, see: Hard two-photon contribution to elastic lepton-proton scattering determined by the OLYMPUS experiment

Reported as: OLYMPUS experiment sheds light on structure of protons

…two photons are indeed exchanged during electron-proton interactions.

However… most of the time, only one of the photons has high energy, while the other must carry very little energy indeed…

The difference between the theoretical and experimental results means further experiments may need to be carried out in the future, at even higher energies where the two-photon exchange effect is expected to be larger, Hasell says.

In the immediate future, the researchers plan to see how the theoretical physics community responds to the data, before deciding on their next step, Hasell says.

I do not think that the theoretical physics community can help to link theories to biophysically constrained cause and effect. Theoretical physicists typically do not start with the creation of energy or with food energy. They use mathematical models.

See for instance: Leptonic radiative corrections to elastic deuteron-electron scattering

Formulas for the relevant kinematical variables, the cross section, and the radiative corrections are derived and numerical results are presented.

At some point, everyone should expect to see the mathematical models be declared worthless when compared to how the creation of sunlight is linked from the creation of ATP to light-activated microRNA biogenesis and the creation of RNA, which has been linked from RNA interference to biophysically constrained viral latency and all extant biodiversity via energy-dependent protein-folding chemistry.

See for instance: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

John Hewitt could have helped to link the creation of RNA to all biodiversity on earth when he wrote about Using the ‘deuterium switch’ to understand how receptors work. Clearly the creation of receptors must be linked to what he wrote about The vibrational theory of olfaction for the win.  But, John Hewitt is a biologically uninformed theorist, a so-called science journalist, who failed to link light-activated structural changes in biomolecules and chromophore heterogeneity.

Everything known to serious scientists about the energy-dependent creation of the sense of smell was put on hold until a truthful science journalist helped me try to stop others from touting the pseudoscientific nonsense of neo-Darwinian theories.

See:  Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 1 Jun 23, 2017 and Part 2 Jun 24, 2017

Moving forward, see: Light-Driven Domain Mechanics of a Minimal Phytochrome Photosensory Module Studied by EPR

They used a special form of mass spectrometry, called electron paramagnetic resonance (EPR) spectroscopy and also electron spin resonance spectrometry to measure changes in the dynamics of  interspin distances, which have been linked to biophysically constrained protein folding chemistry.

DEER (double electron-electron resonance), which is also known as pulsed electron-electron double resonance (PELDOR), showed that phytochromes exhibit more chromophore heterogeneity compared to other photoreceptors.  The creation of sunlight and links energy to the creation of chromophore heterogeneity and to all receptor-mediated biophysically constrained biodiversity via the efficiency of RNA interference, which modulates light-driven structural changes in biomolecules.

That fact was reported as: Uncovering Reasons for Light-Driven Structural Changes in Biomolecules for Use in Optogenetics

Photoreceptors capture and transduce the information of light. The creation of the photoreceptors mediates ecological adaptations to the environment in the host organisms by enhancing the efficiency of photosynthesis and/or by enhancing protection against harmful UV radiation.

Photochromic photoreceptors, called phytochromes, reportedly perceive changes in the ratio of red and far-red light. The ‘perceived’ changes help to control light-activated microRNA biogenesis in the context of the shade avoidance reaction of plants. If plants avoid the shade, they grow in the amount of light that is readily available.

Phytochromes are also found in photosynthetic and non-photosynthetic bacteria, including cyanobacterial species (see below), and even several fungi. They are largely responsible for the light-activated fixation of carbon that Church et. al., linked to naturally occurring energy-dependent RNA interference, which biophysically constrains the virus-driven degradation of messenger RNA.

Church Speaks: A Conversation With George Church [2.14.18]

The cyanobacteria fix [carbon via] light as well or better than land plants. Under ideal circumstances, they can be maybe seven to ten times more productive per photon.

See also: RNA-Guided Human Genome Engineering

5. Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).

The plans to deliver this therapy to an unsuspecting world of theorists were reported as: Get Well in the RNAi Way-RNAi, A Billion Dollar Baby in Therapy

RNAi has targeted exogenous genes in models of viral infection (hepatitis B virus (HBV), influenza virus, Ebola virus) and in tumor xenografts. Initial, RNAi-dependent trials aimed at the delivering siRNA locally or on objects, such as vascular endothelial growth factor (VEGF), for the treatment of the wet age-related macular degeneration and the respiratory syncytial virus (RSV) for the treatment of RSV infections but lately the efficient delivery of VEGF-specific siRNA is done by a direct injection into the vitreal cavity to the eye [55]. RNAi therapeutics through the direct delivery of siRNA into the lungs can treat RSV infection [56]. However, the fruitful and feasible RNAi dependent therapeutics for many other diseases, particularly like cancer, require a more precise delivery to the tissues, remains yet to be realised.

See also: Aging-Related Changes in Cognition and Cortical Integrity are Associated With Serum Expression of Candidate MicroRNAs for Alzheimer Disease

…serum expression of AD-related miRNAs are biologically meaningful in aging and may play a role as biomarkers of cerebral vulnerability [to viruses] in late life.

For comparison, claims about mutation-driven evolution are meaningless.

If you’re not prescribed a therapy that limits viral replication, you will probably suffer unnecessarily and die prematurely.

See also: Multiscale Analysis of Independent Alzheimer’s Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus

Reported as: New study suggests viral connection to Alzheimer’s disease

Without a cure or effective treatment, AD is expected to strike a new victim in the United States every 33 seconds by mid-century and costs are projected to exceed $1 trillion annually.

Author: James Kohl

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