Amino acid modification FA_Epigenetics_Table1

Ab initio cell wall invention, emergence, and evolution (2)

Peter Berean Answer my question above please, or we will have to part company. You are wasting my time and those of our readers when you make assertions that are false, and that you do not defend. These are all just a distraction and a waste of our time.

1) Are you saying that Viruses create energy?
2) Or that Viruses destroy energy?
In response to your questions
1. Yes, God created the process of Entropy for our physical universe.
2. Yes, God may have directly created viruses, and/or some viruses may be a side-effect of other processes that God created for/in this universe.

See for comparison, the claims made by the Fourth Estate via the media-industrial complex.

Viruses can Stimulate Photosynthesis in Bacteria 02/26/17

This work has demonstrated how a viral protein can stimulate the construction complexes that work to harvest light. “This gives the virus an evolutionary advantage,” Frankenberg-Dinkel said. “They ensure a high rate of photosynthesis in the bacteria during infection, meaning sufficient energy is available for the production of new viruses.”

The amount of ignorance about energy-dependent viral replication overwhelms every discipline. The ignorance is included in everything that would otherwise link the anti-entropic virucidal energy of sunlight to cell type differentiation and healthy longevity in all genera.
What is known about biophotonics links photosynthesis from supercoiled DNA to protection from virus-driven energy theft. They report that fact as if viruses created the sun.

“They [viruses] ensure a high rate of photosynthesis…”

See also: Ab initio cell wall invention, emergence, and evolution (1)
A Chat with Leeuwenhoek Medalist Jeffery Errington (February 22, 2017)

Suzan Mazur: Do viruses play a role in regulating L-form bacteria?

Jeffery Errington: That’s a good question. Of course, much of the research on bacteriophages has shown that they tend to bind to components of the cell wall, so certainly you’d anticipate that L-forms would be resistant to many forms of virus. But I don’t know if much work has been done on this.

See: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
The work that has been done on this links the speed of light on contact with water from its anti-entropic virucidal effects to the  de novo creation of nucleic acids, which are the “…starting materials needed to make natural amino acids and lipids. That suggests a single set of [light energy-activated] reactions could have given rise to most of life’s building blocks simultaneously.”
See also: Light-Induced Opening and Closing of the Intramolecular Hydrogen Bond in Glyoxylic Acid

“…the isomerization processes slow down in the case of the Tc conformer, whereas for the Tt-based complex the influence of water is negligible on the isomerization process.

My summary: An intramolecular hydrogen bond characterizes the most stable glyoxylic acid (GA) conformer. The stability of the hydrogen bond changes when hydrogen and oxygen form water. Hydrophobicity may be the key to the energy-dependent stability of supercoiled DNA.
See also: Near-Infrared Laser-Induced Structural Changes of Glycine·Water Complexes in an Ar Matrix
The stability of the glycine-water complex in the gonadotropin releasing hormone (GnRH) decapeptide found in all vertebrates is nutrient energy-dependent and pheromone-controlled. Fixation of the achiral amino acid glycine in position 6 of the decapeptide occurs via the physiology of reproduction. In all vertebrates, GnRH is the central regulator of genetically predisposed nutrient-dependent individual survival and pheromone-controlled species survival.
See Obituary: Robert L. Moss  1940 – 1999. He died of complications while awaiting a heart transplant.

Most recently, his efforts were directed towards establishing the role of pheromonal signals in activating GnRH neurons.

See for comparison: The ASBMB remembers Susan Lindquist 1949 – 2016 She died from cancer.

Many of Sue’s most insightful discoveries were enabled by her devotion to her favorite organism, Saccharomyces cerevisiae, and her fearlessness to jump to mice, iPS-derived human cells or whatever organism was most appropriate to demonstrate the relevance of her findings in yeast.

The obvious cause of death in both cases is virus-driven energy theft. Posthumous publication of this article by senior author Susan Lindquist, makes that fact perfectly clear. HSP90 Shapes the Consequences of Human Genetic Variation

We conclude that a single amino-acid change in FANCA can increase the dependence of the entire FA pathway on HSP90.

Fixation of energy-dependent RNA-mediated amino acid substitutions in the supercoiled DNA of heat shock proteins occurs in the context of the pherormone-controlled physiology of reproduction in species from microbes, such as yeasts, to humans.
See also: Yeast mating pheromone activates mammalian gonadotrophs: evolutionary conservation of a reproductive hormone? (1982)

The ability of the yeast pheromone to reproduce the biological actions of GnRH in the mammalian pituitary gland indicates that the structural and functional properties of GnRH-related peptides may have been highly conserved during evolution.

For the current perspective on evolution, see: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
From the Editor’s Summary with my emphasis:

Losing and then regaining flagella

The ability to adapt to changes in the function of gene regulators, as opposed to structural genes, is a crucial aspect of evolutionary change. Taylor et al. mutated a central regulator for the formation of flagella in the bacterium Pseudomonas fluorescens. They then put the mutated flagella-free bacteria under strong selection pressure to regain mobility. The mutated bacteria regained the lost flagella, and motility, within 4 days.

The mutagenesis experiment linked the speed of light on contact with water to the light-Induced opening and closing of the intramolecular hydrogen bond that links the nutrient energy-dependent pheromone-controlled fixation of RNA-mediated amino acid substitutions in supercoiled DNA to all cell type differentiation in all cells of all individuals of all living genera via the conserved molecular mechanisms reported in the context of this news release: A single ion impacts a million water molecules
See also: Origin of hydrophobicity and enhanced water hydrogen bond strength near purely hydrophobic solutes
Reported as: New research explains hydrophobicity

Ab initio molecular dynamics simulations were used to investigate the possible structural and electrostatic changes of D2O near methane at various temperatures. These studies showed that the electrostatic potentials of water nearest to the methane molecules were lower than bulk water. Specifically, they noted that four of the nearest water molecules surrounding the tagged water in the first hydration shell interacted more strongly with the tagged water molecule. This particular result seemed to indicate a tendency of hydration water to form locally more stable tetrahedral structures relative to bulk.

See for comparison: L-form bacteria, cell walls and the origins of life

The peptidoglycan wall is a defining feature of bacterial cells and was probably already present in their last common ancestor. L-forms are bacterial variants that lack a cell wall and divide by a variety of processes involving membrane blebbing, tubulation, vesiculation and fission. Their unusual mode of proliferation provides a model for primitive cells and is reminiscent of recently developed in vitro vesicle reproduction processes. Invention of the cell wall may have underpinned the explosion of bacterial life on the Earth. Later innovations in cell envelope structure, particularly the emergence of the outer membrane of Gram-negative bacteria, possibly in an early endospore former, seem to have spurned further major evolutionary radiations. Comparative studies of bacterial cell envelope structure may help to resolve the early key steps in evolutionary development of the bacterial domain of life.

See also: Errington’s section heads

8. Invention of the peptidoglycan wall and the bacterial radiation

9. Emergence of archaea by invention of a different cell envelope structure(s)?

10. Evolutionary development of the bacterial cell envelope

Serious scientists have a disadvantage. They are required to link experimental evidence of top-down causation from the sun’s anti-entropic virucidal energy to the creation of all cell types before they find evidence that virus-driven energy theft causes all pathology.

That fact shows why Errington and others like him do not understand anything about how ecological variation must be linked to energy-depenent and ecological adaptation. They start with theories about the invention of the cell wall, the emergence of archaea, and the evolution of all biodiversity.

See also: A Chat with Leeuwenhoek Medalist Jeffery Errington (February 22, 2017)

Suzan Mazur: So you tend to think L-forms were extensive in earlier evolutionary time.

Jeffery Errington: Yes. For example, what we’re finding is that very similar triggers to those that will turn a Gram-positive bacterium [i.e., bacteria with a single thick peptidoglycan wall] like Bacillus subtilis into an L-form will also convert E. coli into the L-form state. And these two species of bacteria are separated by about a billion years of evolution.

See also: A Revised Tree of Life, L-form bacteria, chronic diseases and the origins of life, and Biodiversity is autocatalytic

Biodiversity is not autocatalytic. It is energy-dependent and virus-driven energy theft has been linked to all pathology. When are the sources of science “information” going to admit that the networks are energy-dependent and RNA-mediated in the context of links from the physiology of reproduction to pheromone-controlled chromosomal inheritance?

The researchers found that many of the genes proved to be working together in large networks. It was particularly striking that some of them served as ‘master regulator switches’ for many other genes. When they were ‘switched off”, the other gene variants in the network had no effect on the traits studied.

“It was remarkable that the effects of these genes were entirely dependent on the other genes in the networks. Along with certain variants, they seemed to have a tremendous effect, while they hardly had any effect at all in combination with others,” says Simon Forsberg.

The study shows that, in many cases, it is difficult to predict the outcome for an individual by summarising the effects of individual genes.

“We hope that what we’ve arrived at here will help others to analyse and interpret results from genetic studies in humans, plants and animals too, in a better way. It’s important for us to become aware of what risks there may be if we don’t consider the way genes work together. This applies, for example, when the aim is to use DNA information to predict how high a risk there is of an individual falling ill or suffering severe side-effects from a drug treatment,” Carlborg concludes.

See also: Invisible Nature: The Glowing Squid 02/21/17
See also: Electrons Use DNA Like a Wire for Signaling DNA Replication  02/23/2017

You have to get the DNA primase off the DNA quickly—that really starts the whole replication process,” says Barton. “It’s a hand off of electrons from one cluster to the other through the DNA double helix.

The hand off is energy-dependent and linked from the bioluminescence of bacteria in the light organ of Hawaiian bobtail squid to all energy-dependent biodiversity via feedback loops that link quorum sensing in bacteria to the physiology of reproduction in all living genera.

February 23, 2017 See what’s missing from Eric Lander’s works, which were based on the gene-centric theories of morphological and behavioral diversity.

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

How could award-winning researchers, like Eric Lander, ignore the fact that the interactions among energy, endogenous RNA interference and the functional structure of supercoiled DNA clearly link virus-driven energy theft to all pathology?

Reported February 25, 2017 Dr. Wendy Suzuki is studying the extraordinary effects of exercise on the brain. Watch the full interview here: Exercise Changed This Neuroscientist’s Life And Now She Wants To Change Yours
Video  She links exercise to the de novo creation of G protein-coupled receptors in the brain.

The effect must be linked from GnRH to behavior via epigenetic effects on supercoiled DNA.

Minireview: Metabolic control of the reproductive physiology: Insights from genetic mouse models

See also: This article belongs to a special issue  Energy Homeostasis in Context 

This special issue of Hormones and Behavior therefore contains 9 review articles and 7 data articles that consider energy homeostasis within the context of other motivations and physiological processes, such as early development, sexual differentiation, sexual motivation, reproduction, seasonality, hibernation, and migration. Each article is focused on a different species or on a set of species, and most vertebrate classes are represented.

See also: The [4Fe4S] cluster of human DNA primase functions as a redox switch using DNA charge transport

The eukaryotic DNA primase is involved in DNA replication and contains a [4Fe4S] cluster that is required for its RNA primer synthesis activity. O’Brien et al. show that the [4Fe4S] cluster in DNA primase can regulate the protein’s DNA binding activity through DNA-mediated charge transfer.

RNA primer synthesis is energy-dependent and linked to biophysically constrained protein folding chemistry in all living genera via the physiology of reproduction. That fact consistently is missing from reports that fail to link the anti-entropic energy of sunlight  to all biodiversity on Earth.

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