Biology to a Physicist

The C. elegans Taste Receptor Homolog LITE-1 Is a Photoreceptor

“In Brief: A taste receptor homolog absorbs UV light and mediates avoidance behavior in C. elegans in response to light exposure.”

Excerpt: Light sensation is critical for all phyla of life, ranging from bacteria to humans (Wang and Montell, 2007; Yau and Hardie, 2009). Organisms have evolved various types of photoreceptor proteins…

Photoreceptors are G protein-coupled receptors (GPCRs). No experimental evidence of biologically-based cause and effect links the evolution of any type of photoreceptor to any other type of G protein-coupled receptor (GPCR). Nothing except energy-dependent hydrogen-atom transfer in DNA base pairs in solutions like sea water and blood links the de novo creation of olfactory receptor genes, which are GPCRs, to all biodiversity via the physiology of reproduction and supercoiled DNA in all living genera.

The facts about supercoiled DNA link energy-dependent RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of all living genera via the claim that “…a taste receptor homolog absorbs UV light and mediates avoidance behavior in C. elegans in response to light exposure.”

That claim can be readily linked to the energy-dependent experience-dependent nutrient-dependent RNA-mediated de novo creation of all GPCRs and experience-dependent behavior that links chemotaxis from the de novo creation of olfactory receptor genes to phototaxis via the nutrient energy-dependent de novo creation of photoreceptors and/or all other receptors.

Reported as: Tasting light: New type of photoreceptor is 50 times more efficient than the human eye

1) …within the protein, having the amino acid tryptophan in two places was critical to its function.

2) Breaking it apart, or “denaturing” it, completely stops its ability to absorb light, rather than just diminishing it — showing that it really is a different model, Xu said.

The two nutrient energy-dependent RNA-mediated amino acid substitutions link UV light from DNA repair to all biophysically constrained pheromone-controlled biodiversity via the innate immune system and supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. The claim that the are using a different model to do that should be placed into the context of the only model that links angstroms to ecosystems in all living genera to all nutrient energy-dependent RNA-mediated amino acid substitutions and pheromone-controlled biodiversity.

Also reported as: Powerful New Photoreceptor Found in Roundworms

Because the “genetic code” of these photoreceptor proteins are so much different than that of other photoreceptors found in the animal kingdom, there is a ton of untapped potential in this discovery.

There is only one genetic code. It links the epigenetic landscape to the physical landscape of supercoiled DNA via energy-dependent changes in base pairs, which link natural selection for codon optimality to the physiology of reproduction by protecting the organized genomes of all living genera from virus-driven energy theft.

See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

Conclusion:

…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

See also: Meaning = Information + Evolution

Notions like meaning, signal, intentionality, are difficult to relate to a physical word. I study a purely physical definition of “meaningful information”, from which these notions can be derived. It is inspired by a model recently illustrated by Kolchinsky and Wolpert, and improves on Dretske classic work on the relation between knowledge and information. I discuss what makes a physical process into a “signal”.

Energy as information becomes a signal via its effect on hydrogen-atom transfer in DNA base pairs in solution. The information links the anti-entropic virucidal energy of sunlight to all biophysically constrained cell type differentiation in all living genera via the innate immune system, which links the physiology of reproduction to supercoiled DNA.

For more experimental evidence of this established link to biologically-based cause and effect, which was not presented in the context of my model from 2013, see:

Dynamic control of chirality and self-assembly of double-stranded helicates with light

Physicochemical mechanism of light-driven DNA repair by (6-4) photolyases

Clearly, if one photon provides just enough energy to perform repair, two photons are even better. However,
these are speculations…

UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

Control of pH responsive peptide self-association during endocytosis is required for effective gene transfer

Analysis of Viral and Cellular MicroRNAs in EBV-Infected Cells

A Framework for integrating multiple biological networks to predict microRNA-disease associations

Without a framework that links energy-dependent changes from angstroms to ecosystems in all living genera via their physiology of reproduction and fixation of RNA-mediated amino acid substitutions in supercoiled DNA, which protects organisms from virus-driven energy theft and genomic entropy, all that’s left is the pseudoscientific nonsense of neo-Darwinian theories.

For comparison, with a framework that links the sun’s anti-entropic virucidal energy to cell type differentiation in all genera, it is likely that the cure for all pathology is within sight. For example all pathology appears to be is epigenetically controlled at the level of quantized energy.

See also: Melanocytic Nevi and the Genetic and Epigenetic Control of Oncogene-Induced Senescence

Melanocytic nevi represent benign clonal proliferations of the melanocytes in the skin that usually remain stable in size and behavior or disappear during life. Infrequently, melanocytic nevi undergo malignant transformation to melanoma. Understanding molecular and cellular mechanisms underlying oncogene-induced senescence should help identify pathways underlying melanoma development, leading to the development of new strategies for melanoma prevention and early detection.

See also: microRNA

More than 55,000 published works link energy-dependent changes in the microRNA/messenger RNA balance to the framework that links amino acid substitutions to cell type differentiation and healthy longevity compared to virus-driven energy theft, which has been linked to all pathology by amino acid substitutions that stabilize viruses.

Here is some background on the concept of sunlight as energy that links information to all biodiversity via natural selection for energy-dependent RNA-mediated codon optimaility.

Light Absorption, Reflection, and Transmission

If a light wave of a given frequency strikes a material with electrons having the same vibrational frequencies, then those electrons will absorb the energy of the light wave and transform it into vibrational motion. During its vibration, the electrons interact with neighboring atoms in such a manner as to convert its vibrational energy into thermal energy. Subsequently, the light wave with that given frequency is absorbed by the object, never again to be released in the form of light. So the selective absorption of light by a particular material occurs because the selected frequency of the light wave matches the frequency at which electrons in the atoms of that material vibrate. Since different atoms and molecules have different natural frequencies of vibration, they will selectively absorb different frequencies of visible light.

The absorption of ultraviolet light links the anti-entropic virucidal energy of the sun to all biophysically constrained biodiversity.

What is life when it is not protected from virus driven entropy

The anti-entropic force of virucidal ultraviolet light (UV) links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

See also: Royal Society: The Public Evolution Summit  Page 12

Witzany is organizing a conference symposium for July 2018 “Evolution-genetic innovations without error replication”

The title may change to “You are what you eat.” He has already linked energy and information-dependent changes from physics to chemistry and all the biodiversity of life.

See also: Life is physics and chemistry and communication

Manfred Eigen extended Erwin Schroedinger’s concept of “life is physics and chemistry” through the introduction of information theory and cybernetic systems theory into “life is physics and chemistry and information.” Based on this assumption, Eigen developed the concepts of quasispecies and hypercycles, which have been dominant in molecular biology and virology ever since. He insisted that the genetic code is not just used metaphorically: it represents a real natural language. However, the basics of scientific knowledge changed dramatically within the second half of the 20th century. Unfortunately, Eigen ignored the results of the philosophy of science discourse on essential features of natural languages and codes: a natural language or code emerges from populations of living agents that communicate. This contribution will look at some of the highlights of this historical development and the results relevant for biological theories about life.

Biological facts about life link energy-dependent changes from angstroms to ecosystems in all living genera via the physiology of reproduction and supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. Why hasn’t everyone already accepted the facts that Schrodinger helped to detail in What is Life?

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight.) (pp. 73 and 74)

See also from the forward to the reprint edition:

“How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?” (Roger Penrose 8 August 1991)

Eliminating energy-dependent creation and Darwin’s “conditions of life” was probably not de Vries intention when he defined the term mutation in 1902. But, neo-Darwinian theorists took his claims about sudden energy jumps and assumed the jumps could explain what would happen if accumulated random mutations had somehow caused one species to evolve into another.

In that view of evolution, millions of years are required to link the sudden energy jumps to all morphological and behavioral diversity. Serious scientists have since learned that all energy-dependent changes in organized genomes link what organisms eat to their physiology of reproduction. That is how biodiversity is biophysically constrained by the availability of food and how food odors and pheromones are linked to the physiology of reproduction by feedback loops.

See: Feedback loops link odor and pheromone signaling with reproduction

Neo-Darwinian theorists eliminated energy and the nutrient energy-dependent feedback loops that link odors and pheromones to biophysically constrained biologically based cause and effect.

See for comparison: Scientists Seek to Update Evolution and Genetic and mechanistic diversity of piRNA 3′-end formation.

The news article by Carl Zimmer and the journal article ignore all accumulated experimental evidence of biologically-based energy-dependent top-down causation. The authors of the journal article invent the term “egoistic genes” as if no one had refuted the pseudoscientific nonsense of Richard Dawkins’ “The Selfish Gene.”

Pseudoscientists seem to think that serious scientists must prove their pseudoscientific nonsense is nonsense. Serious scientists do not try to do that because they are not taught to believe in theories. Serious scientists are taught to find experimental evidence of biologically-based cause and effect that supports their claims.

See for an example of the energy-dependent de novo creation of G protein-coupled receptors: Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo

See for comparison: Mutation-Driven Evolution

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements” (p. 199).

See also: 30 Reasons to Never Put Another M&M in Your Mouth Ever Again

See also: The Sea Slug That Eats The Sun

See also: Sci-hub  Our mission is to remove any barrier which impeding the widest possible distribution of knowledge in human society!

See also: Purkinje effect: Physiology:

The effect occurs because the color-sensitive cones in the retina are most sensitive to green light, whereas the rods, which are more light-sensitive (and thus more important in low light) but which do not distinguish colors, respond best to green-blue light.[4] This is why humans become virtually color-blind under low levels of illumination, for instance moonlight.

The effect links the sun’s anti-enrtopic virucidal biological energy to all biophysically constrained cell type differentiation via the physiology of reproduction in all living genera.

Light and Color – Detailed Help

Jack is wearing a red shirt. The shirt is illuminated with white light. Jill views Jack’s shirt while looking through a magenta filter. To Jill, Jack’s shirt will appear ____.

If you look at a red shirt through a red filter, you will most likely claim that the shirt is white. If you eliminate the sun’s biological energy from your claims about evolution, you will eliminate everything known to serious scientists about the energy-dependent creation of all biodiversity.

The fact that light and color are clearly linked to the morphological and behavioral phenotypes of the fruit dove, pictured above, is hard to dismiss, no matter how biologically uninformed others are.

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