A rendering of how changes in an electron's motion (bottom view) alter the scattering of light (top view), as measured in a new experiment that scattered more than 500 photons of light from a single electron. Previous experiments had managed to scatter no more than a few photons at a time. Credit: Extreme Light Laboratory|University of Nebraska-Lincoln

Energy-dependent physical and biophysical constraints (4)

Energy-dependent physical and biophysical constraints (3)

Summary:

Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull

Microbiota Manipulations

…modified an endogenous Bacteroides promoter sequence to be inducible—it could be turned on or off in mice by adding or omitting an effector molecule in the animals’ drinking water (see illustration). Sonnenburg’s system, on the other hand, used a viral promoter that upregulated gene expression to 70-fold higher than the type of promoter used by Goodman’s team. The viral promoter had the power to drive levels of fluorescent protein expression high enough to visualize bacteria in the mouse gut—a previously impossible feat.

See: bacteriodes and microRNA
The “effector molecule” links the food energy-dependent physiology of reproduction to all biodiversity via changes in the microRNA/messenger RNA balance, which biophysically constrain the virus-driven degradation of messenger RNA that causes all pathology. The viral load of cell types can be measured via fluorescence but the measurements of energy refute every aspect of all claims placed into the context of neo-Darwinian evolution.
Anyone still touting any aspect of neo-Darwinian evolution can now be categorized as a “loser.” But, be careful. There are more of them than those who have been Combating Evolution to Fight Disease
My comment to Science:

Darwin probably anticipated the insemination of population genetics that led to the bastardization of his detailed observations in the “Modern Synthesis.” He politely insisted that ‘conditions of life’ be considered before natural selection.

There are two ‘conditions of life.’ It is nutrient-dependent and pheromone-controlled. Rosenberg and Queitsch now note the work with Dobzhansky’s rarely acknowledged claim: “I am a creationist and an evolutionist.” They also declare the need for “Deep understanding of the mechanisms that generate variation at the molecular level…”

Deep understanding of the ‘conditions of life’ does not come from theory.

Problems with the “modern synthesis” now lead us back to the facts about biologically-based cause and effect that Darwin and Dobzhansky approached with humility, which are the same biological facts that evolutionists approached with ignorance about behavioral affects and the arrogance that accompanies that ignorance. Rosenberg and Queitsch echo the sentiments of those who have been subjected to academic suppression.

Clearly, however, “nothing in evolution makes sense except in the light of biology” is not an exaggeration. It is a common sense statement about the biologically plausible genesis of functional cell types. Population genetics and evolutionary theories abandoned the biophysical constraints of ecological variation and the physiology of reproduction, which enable epigenetically-effected nutrient-dependent pheromone-controlled receptor-mediated ecological adaptations and species diversity via the complexities of protein folding and niche construction.

It’s time for biophysicists to tell theorists and pathologists how to differentiate between theories about the genesis of different cell types and the biological facts about the nutrient-dependent pheromone-controlled ecological adaptations that enable the genesis of different cell types in individuals of different species. Simply put, it’s time to stop trying to explain ecological adaptations in the context of mutations and evolution.

 

diseases-disorders

The Aquatic Ape / Waterside Ape divergence

See also: The Aquatic Ape: New evidence? (9/8/16)
Walt Patrick 

Now that I’m semi-retired…. My major focus is the development of village-scale energy sovereignty.
I believe that sustainable community stands on an interlocking foundation of effective and sustainable energy systems, and I’m working to develop ways that a community can meet its energy needs without having to rely on multi-national energy corporations.

My comment: Thanks to Walt for introducing me to Elaine Morgan’s work. He loaned me his copy of “The Aquatic Ape” in 1982. Thanks to Janissa Wilson for introducing me to Walt Patrick. Thirty-four years have passed, and I remember their friendship and their influence as if it was only yesterday.
See (from yesterday and earlier today):
The Waterside Ape — Sir David Attenborough considers whether new evidence will help a once widely ridiculed theory of human origins move towards to mainstream acceptance.
My comment: He takes a giant step forward in an obvious attempt to keep biologically uninformed theorists from being subjected to ridicule because they missed the paradigm shift.
He then takes small steps backwards to put the “The Aquatic Ape” back into the context of ridiculous theories, which he uses to link his divergence from claims in the “The Aquatic Ape.” He needs an evolutionary theory to evolve one theory into a new theory that becomes “The Waterside Ape.” Otherwise, he gets credit for nothing more than finally acknowledging what serious scientists have known for several decades.
The reports on the efforts of the serious scientists are exemplary. So is the attempt to put them all into the context of evolutionary theory at a time when energy-dependent changes have been linked from angstroms to ecosystems in all living genera in the context of energy as information.
See also:  A Chat with Information Scientist Pedro Marijuán
I’ve commented twice on this article, which is  on Suzan Mazur’s blog site, and both comments were promptly removed.
See for comparison: Kalevi Kull: Censorship & Royal Society Evo Event
My Jul 31, 2016 11:51am comment has not yet been removed:

James Kohl Founder at RNA-mediated.com

This response may not, at first, appear to be directed against the claims you have supported with your series of interviews. But watch closely as they squirm under the weight of experimental evidence that collectively refutes their ridiculous theories and philosophy.

The Origin of The Extended Evolutionary Synthesis: An Interview with Massimo Pigliucci

Moving forward:

Claims linked to the Extended Evolutionary Synthesis have since run out of “wiggle room”. Listen to: The Waterside Ape, which closes the case on how the nutrient-energy-dependent pheromone-controlled physiology of reproduction links ecological variation to ecological adaptation via RNA methylation and RNA-mediated amino acid substitutions in supercoiled DNA, which differentiates all cell types in all living genera.

part 1
part 2
Ongoing attempts have failed to place everything known about biophysically constrained RNA-mediated protein folding chemistry and epigenetic effects on supercoiled DNA into the context of evolution. The attempts will continue to fail until researchers and theorists stop trying to make what is known fit into their theories about millions of years of evolution. No experimental evidence of biologically-based cause and effect links what is known about energy-dependent changes from angstroms to ecosystems in all living genera.
See also: Elaine Morgan is a tenacious proponent of the aquatic ape hypothesis: the idea that humans evolved from primate ancestors who dwelt in watery habitats. Hear her spirited defense of the idea — and her theory on why mainstream science doesn’t take it seriously.

See for comparison: Study Links RNA Alterations to Stomach Cancer  September 14, 2016

Written By: Xuan Pham Science Writer, PhD LabRoots

Description: I am a human geneticist, passionate about telling stories to make science more engaging and approachable.

For comparison: I am a medical laboratory scientist who has followed the literature on biologically-based cause and effect since 1982.

The historical perspective on the current literature clearly states this:

For several years it has been apparent that an ecological approach is imperative for all studies in population genetics, including those pertaining to man. It also offers a potentially useful point of view to the physical anthropologist, the ethnologist, and the archeologist, and it should provide an important integrative bridge between the various fields of anthropology. — Blood, Bulbs, and Bunodonts: On Evolutionary Ecology and the Diets of Ardipithecus, Australopithecus, and Early Homo

See also: Unravelling the genetic mystery behind mitochondrial disease

Excerpt:
Mitochondrial disease is an illness that robs its sufferers of energy, and damages muscles and major organs like the brain and heart. About one in 5000 babies – or one Australian baby born each week – are born with a severe form of the disease, which can often lead to an early death.

My comment: Virus-driven energy theft of quantised energy is the cause of all pathology. That fact is not a genetic mystery. It is fact known to all serious scientists who understand why Church et al., (2015) applied for this patent RNA-Guided Human Genome Engineering.

Viruses steal the energy that all cell types require for cell-type differentiation, which links ecological variation to ecological adaptation and healthy longevity in the absence of excess nutrient-stress and/or excess social stress. Stress-linked pathology is manifested when changes in hydrogen-atom transfer in DNA base pairs in solution facilitate codon usage in codon usage that enables their proliferation and prevent cell type differentiation.

The energy stolen by viruses is quantised energy:

See: A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution

My comment: This is not a quantum theory of neural cell signalling throughout evolution. It exemplifies what is know to serious scientists about the obvious links from ecological variation to ecological adaptation, which is nutrient-energy-dependent and pheromone-controlled in species from microbes to humans.

See also: Two fatty acyl reductases involved in moth pheromone biosynthesis 7/18/16

Studies over the last two decades have pinpointed that the epigenetic effect of pheromone-driven adaptive evolution is one of the major factors driving the successful diversification of Lepidopteran insects10. In moths, a few substitutions in critical amino acids in the key pheromone biosynthetic enzymes are sufficient to create a novel pheromone component11,12.

See also: Role of olfaction in Octopus vulgaris reproduction 1/1/15

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

Kohl (2013) Nutrient-dependent/pheromone-controlled adaptive evolution: a model is also cited in Two fatty acyl reductases involved in moth pheromone biosynthesis.

In my 2013 review, I concluded:

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’.

The criticisms of my 2013 review may be of interest in the criticisms of Elaine Morgan’s works, since there is still no other model that links ecological variation to ecological adaptation.

In his Criticisms of the nutrient-dependent pheromone-controlled evolutionary model, Andrew Jones wrote:

James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research. It was a mistake to let such a sloppy review through to be published.

Andrew Jones did not offer any other model for comparison. He seemed to think that he could support his criticisms via his claim in his thesis:

Despite their challenges, ribozymes have made an interesting niche for themselves in the field of abiogenesis. The evolution of a successful RNA polymerase ribozyme is a lofty goal. While its discovery would not be the be-all and end-all of abiogenesis research, it would represent an important stepping stone between prebiotic chemistry and life. The encapsulation of such a ribozyme is also an important step, as it would enable a system of heredity and evolution through natural selection. Based on progress in current research, it is only a matter of time before that ribozyme is discovered.

The current state of college education in the United States of American and perhaps elsewhere is reflected in the thesis by Andrew Jones as a continuation of the pseudoscientific nonsense that is used to support hypothesis-free science with claims that a system of heredity and evolution through natural selection may exist outside the context of any model that links energy-dependent changes from angstroms to ecosystems in all living genera.

See this invited review of nutritional epigenetics, for example: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems 4/10/14

Abstract:

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

In 2004, Elaine Morgan suggested it might be another 10 years before her concept of ecological adaptation gained more acceptance. If not for students like Andrew Jones, acceptance of historical works that link angstroms to ecosystems in all living genera via experimental evidence of biologically-based cause and effect would already be accepted. Until the experimental evidence is accepted and the theories are declared by all serious scientists to be ridiculous, you and your loved ones will suffer and die from virus-driven pathology. Why aren’t you already as sick of that as I am after 40 years experience as a medical laboratory scientist?

 

rp_levels-of-organization.jpg

Ecological speciation. Get it, theorists?

A Prkci gene keeps stem cells in check

Excerpt:

In the presence of Prkci, the Notch pathway remains silent, and stem cells differentiate into specific cell types.

My comment: Several days of attempted discussion led to this question
Do you get it now, jvk?
My response: Everyone who is not a biologically uninformed science idiot gets it. The Zechiedrich lab‘s focus links energy-dependent base pair changes from atoms to ecosystems. The Rosenberg lab‘s focus on stress shows why others must eliminate any focus on population genetics to fight disease.
“Combating Evolution to Fight Disease” cites Dobzhansky (1973) who wrote: “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.”
The nutrient-dependent link from microRNAs to base pairs and RNA-mediated amino acid substitutions links metabolic networks from atoms to ecosystems via cell adhesion proteins and genetic networks that protect organized genomes from stress-linked virus-driven genomic entropy.
Energy-dependent supercoiled DNA and cell type differentiation via the physiology of reproduction and fixation of RNA-mediated substitutions lead to ecological speciation. Theft of energy by viruses links the proliferation of viral microRNAs to failed DNA repair and pathology. Across a lifetime of nutrient-stress and/or social stress, the innate immune system of all cells in all tissues of all organs in all our organ systems is suppressed and we often needlessly suffer and die because neo-Darwinian theorists claim that random mutations are sometimes beneficial when the stress-driven accumulation of mutations always leads to pathology.

terrarium-eco-system

Protein folding and Google page rank

Pheromones.com has been on the first page of a Google search for “pheromones” for several months. See: https://www.google.com/?gws_rd=ssl#q=pheromones
Today, RNA-mediated.com appeared on the first page of a Google search for “RNA mediated” See: https://www.google.com/?gws_rd=ssl#q=RNA+mediated
My domains may remain in a key position for information dissemination, or they may be placed into the background by Google’s algorithms. In either case, it has become clear that RNA-mediated events link the nutrient-dependent pheromone-controlled physiology of reproduction to biodiversity in species from microbes to man via amino acid substitutions.
Claims by theorists can now be viewed in the context of a model that links biologically-based cause and effect to biophysically constrained cell type differentiation in all genera.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Abstract: This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.
For comparison, see:  Mutation-Driven Evolution
Conclusion:

In other words, 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 (posted yesterday, June 29, 2015):

Introduction: Proteins are complex structures folded from a linear strand of amino acids. These structures are involved in almost every process in the cell. In this iBiology talk, Susan Lindquist discusses the incredible diversity of protein structures, the importance of proper protein folding, and the problems that arise when proteins are misfolded.
My comment: Do you think the mutations that link perturbed protein folding to pathology can also be linked to “…the enormous amount of biodiversity in this world” via “biological innovations?” If so, you may also think there is a model of protein folding that links mutations to something besides pathology.
There is no model of biologically-based cause and effect that links mutations to the organized genomes of all genera.
What is the basis for your ridiculous belief in the pseudoscientific nonsense of population genetics?
It is disingenuous for anyone to place protein folding into the context of “music” after the excellent representations of Denis Noble did so in a series of presentations that established the changes required to link physiology to cell type differentiation.
See also: In conversation with Denis Noble, about “The Music of Life

achiral-glycine

Physics, Chemistry, and Molecular biology (PCMb)

Physics, Chemistry, and Molecular biology (PCMb) link ecological variation to ecological adaptations via a model of gene-cell-tissue-organ-organ system complexity that I first presented in 1992. After adding gene activation by pheromones, I co-authored a book that linked the pheromone-controlled physiology of reproduction across species from microbes to man: The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002)
Since then, others have written books that claimed that pheromones evolved: Pheromones and Animal Behaviour (2003/2014) and one claimed that mammals don’t produce or respond to pheromones: The Great Pheromone Myth (2010).
Ignorance of biophysically-contrained biologically-based cause and effect continue to prevent scientific progress. Others have started to speak out against the pseudoscientific nonsense of evolutionary theorists and psychologists who have limited progress that could have been made by serious scientists from many disciplines. The theorists have continued to tout their pseudoscientific nonsense about mutations, natural selection and evolution, for more than 17 years after we detailed the facts about how epigenetically-effected RNA-mediated events link nutrient-uptake to the pheromone-controlled physiology of reproduction in species from microbes to man.

Many others must speak up each time they read or hear about the statistical nonsense of evolutionary theory as if it were supported by experimental evidence of biologically-based cause and effect. Tell the theorists to start making sense. Cite Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes and quote from it: “The rates of 4 types of elementary evolutionary events (hereinafter Genome Dynamics Events or GDE)…”
Help make others approach the psychology and the practice of medicine from the only perspective that makes sense: Physics, Chemistry, and Molecular biology (PCMb) — not the pseudoscientific nonsense of theorists. RNA-directed DNA methylation links RNA-mediated events to amino acid substitutions that differentiate the cell types of all individuals in all species.

See also: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.