Caption: Contemporary analyses of cell metabolism have called out three metabolites: ATP, NADH, and acetyl-CoA, as sentinel molecules whose accumulation represent much of the purpose of the catabolic arms of metabolism and then drive many anabolic pathways. Such analyses largely leave out how and why ATP, NADH, and acetyl-CoA (Figure 1) at the molecular level play such central roles. Yet, without those insights into why cells accumulate them and how the enabling properties of these key metabolites power much of cell metabolism, the underlying molecular logic remains mysterious. Four other metabolites, S-adenosylmethionine, carbamoyl phosphate, UDP-glucose, and Δ2-isopentenyl-PP play similar roles in using group transfer chemistry to drive otherwise unfavorable biosynthetic equilibria. This review provides the underlying chemical logic to remind how these seven key molecules function as mobile packets of cellular currencies for phosphoryl transfers (ATP), acyl transfers (acetyl-CoA, carbamoyl-P), methyl transfers (SAM), prenyl transfers (IPP), glucosyl transfers (UDP-glucose), and electron and ADP-ribosyl transfers (NAD(P)H/NAD(P)+) to drive metabolic transformations in and across most primary pathways. The eighth key metabolite is molecular oxygen (O2), thermodynamically activated for reduction by one electron path, leaving it kinetically stable to the vast majority of organic cellular metabolites

Kohl's Laws of Biology (codon-optimality revisited)

Summary: Kohl’s Laws help to explain what was missing from Darwin’s ‘conditions of life.’ Darwin knew nothing about genetics, which means he knew nothing about the epigenetic effects of food odors or pheromones.
Ancient hepatitis B viruses from the Bronze Age to the Medieval period 5/7/18

We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.

The complexity of biophysically constrained viral latency in all living genera refutes all pseudoscientific nonsense touted by neo-Darwinian theorists and Big Bang cosmologists.
See for example: Who were the Neanderthals? 5/5/18

Current evidence from both fossils and DNA suggests that Neanderthal and modern human lineages separated at least 500,000 years ago. Some genetic calibrations place their divergence at about 650,000 years ago.

No serious scientists believe in the nonsense that links genetic calibrations to “divergence” at about 650,000 years ago.
See for comparison: Efficient coding explains the universal law of generalization in human perception 5/11/18
Everything known to serious scientists about natural selection for energy-dependent codon optimality and RNA-mediated DNA repair is placed back into the context of evolution, which is subject to constraints (finding food and reproduction).
See also: Olfaction Warps Visual Time Perception (2017)
The creation of visual perception starts with the energy-dependent creation of enzymes.

High-resolution cryo-EM analysis of the yeast ATP synthase in a lipid membrane 5/11/18

…the enzyme transduces the energy of a proton gradient, generated by the electron transport chain, into the major energy currency of the cell, ATP.

The quantized energy-dependent creation of the enzyme was linked to the creation of ATP and RNA
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.

Natural selection interacts with recombination to shape the evolution of hybrid genomes 5/11/18

Hybridization is an important force in evolution.

That is a ridiculous assumption. Quantized energy is an important force in ecological adaptation. That is a fact.

Metabolic regulation of transcription through compartmentalized NAD+ biosynthesis 5/11/18

Competition between the NAD+ precursors—nuclear NMNAT-1 and cytosolic NMNAT-2…, regulates the balance between nuclear NAD+ synthesis for adipogenic gene regulation and cytosolic NAD+ synthesis used in metabolism.

Every aspect of what is currently know about life on Earth begins with the creation of quantized energy.
Energy efficiency drives the global seasonal distribution of birds 5/7/18
Reported as: A Thermodynamic Answer to Why Birds Migrate 5/7/18

…research makes a forceful argument that energy supply and demand is a driving ecological principle shaping the global structure of biodiversity.”

See also: The histone demethylase KDM6B regulates temperature-dependent sex determination in a turtle species 5/11/18

In this 1996 review, we linked the sex differences in yeasts to sex differences in humans via alternative splicings of pre-mRNAs, which are now called microRNAs. From Fertilization to Adult Sexual Behavior

I linked quantized energy from subatomic particles to all biodiversity via the creation of  microRNAs in:
2014 Preprint: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
2018 Publication: Nutrient-dependent Pheromone-Controlled Ecological Adaptations: From Angstroms to Ecosystems

Biological Laws

Biophysical constraints and biological laws appear to link ecological variation to ecological adaptations via conserved molecular mechanisms in all species. For example, nutrient-dependent ecological niche construction leads to pheromone-controlled social niche construction via the nutrient-dependent pheromone-controlled physiology of reproduction. The nutrient-dependent origin of amino acid substitutions in viruses [149-152], which also are manifested in plant and animal interactions, exemplifies a continuum of biological plausibility and ecological validity in the context of Laws of Biology. These Laws of Biology include Kohl’s Laws of Biology, which are so named because the surname of the first author or sole author on each of 7 peer-reviewed publications in the paragraph below is Kohl. The Kohls did not create the Laws of Biology; they merely independently incorporated what is known about them into what appears to be a cohesive series of published works.

Kohl’s Laws of Biology
Life is nutrient-dependent. That is a Biological Law. The ecological origin of all biological laws is apparent 1) in the context of systems biology [87]; 2) in the context of the metabolism of nutrients by microbes [153]; and 3) in the context of how the metabolism of nutrients results in species-specific pheromones that control the physiology of reproduction [154]. Taken together, the systems biology of nutrient metabolism to species-specific pheromones, which control the physiology of reproduction, can be expressed in a summary of Kohl’s Laws of Biology: 1) Life is nutrient-dependent.

See for review [27,155]. The physiology of reproduction is pheromone-controlled. See for review [26]. In the context of nutrient-dependent epigenetically-effected human reproduction, it is clearer that the epigenetic effects of human pheromones integrate neuroendocrinology and behavior [100], which includes the neuroendocrinology of mammalian behavior associated with the development of sexual preferences [156].

Kohl’s Laws help to explain what was missing from Darwin’s ‘conditions of life.’ Darwin knew nothing about genetics, which means he knew nothing about the epigenetic effects of food odors or pheromones.

 

Watering Young Plant - Vintage Effect

Laws of Biology / Rules of Life

Summary: Slide number 6 clearly states the “Levels of Biological Organization” that the “NSF’s 10 Big Ideas” finally places into the context of what has been known to all serious scientists for more than a century. Simply put, Hugo de Vries definition of mutation (sudden energy jumps) should never have been accepted as anything besides the claim of a biologically uninformed science idiot. Instead, the definition bastardized every aspect of what is now known about biophysically constrained viral latency and all epigenetically-effected biodiversity on Earth.
The epigenetic effects start with the creation of quantized energy as information carried in sunlight.
Understanding the Rules of Life: Predicting Phenotype

Rules of Life projects… may have these characteristics:

Addresses a fundamental question in the life sciences

Crosses different scales (spatial, temporal, levels of biological organization and complexity)

Generates results that will be broadly generalizable beyond the system under investigation, so that a rule can be formulated

Enables the forecasting or prediction of change in a biological system

The characteristics of the so-called “Rules of Life” were predicted in the context of Darwin’s “conditions of life,” and in What is Life? (1944)
Biologically uninformed science idiots took this claim from 1944 and placed it into the ridiculous context of mutation-driven evolution:

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.)

See for comparison: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

Kohl’s Laws of Biology

…summary of Kohl’s Laws of Biology: 1) Life is nutrient-dependent. See for review (J. V. Kohl, 2012; M. Lynch, 2007). The physiology of reproduction is pheromone-controlled. See for review (J. V. Kohl, 2013). In the context of nutrient-dependent epigenetically-effected human reproduction, it is clearer that the epigenetic effects of human pheromones integrate neuroendocrinology and behavior (J. V. Kohl, et al., 2001), which includes the neuroendocrinology of mammalian behavior associated with the development of sexual preferences (J.V. Kohl, 2007).

Kohl’s Laws help to explain what was missing from Darwin’s ‘conditions of life.’ Darwin knew nothing about genetics, which means he knew nothing about the epigenetic effects of food odors or pheromones.

M. Lynch (2007) is The frailty of adaptive hypotheses for the origins of organismal complexity

…emergent biological features such as complexity, modularity, and evolvability, all of which are current targets of considerable speculation, may be nothing more than indirect by-products of processes operating at lower levels of organization.

See for comparison:  Evolutionary determinants of genome-wide nucleotide composition (2018) with senior author Michael Lynch
Reported as: Scientists explore mysteries behind diversity of DNA composition among species

…mutation drives the overall pattern, but selection for G’s and C’s over A’s and T’s boosts the genome content above the neutral mutational expectation.

Natural selection for energy-dependent codon optimality is the driving force that links the sun’s anti-entropic virucidal energy to  biophysically constrained viral latency and all biodiversity via the physiology of pheromone-controlled reproduction in species from microbes to humans.
I reiterate:

“…selection for G’s and C’s over A’s and T’s boosts the genome content above the neutral mutational expectation.”

Selection is quantized energy-dependent and RNA-mediated. The energy comes from sunlight!
See also: Cytosis and Subatomic
See also: Human Pheromones: Linking Neuroendocrinology and Ethology (revisited) (2010)
Slide number 6 clearly states the “Levels of Biological Organization” that the “NSF’s 10 Big Ideas” finally places into the context of what has been known to all serious scientists for more than a century. Simply put, Hugo de Vries definition of mutation (sudden energy jumps) should never have been accepted as anything besides the claim of a biologically uninformed science idiot. Instead, the definition bastardized every aspect of what is now known about biophysically constrained viral latency and all epigenetically-effected biodiversity on Earth.
The epigenetic effects start with the creation of quantized energy as information carried in sunlight.

5th-6th Sept 2018 Dublin, Ireland

Less evolvable RNA-mediated ecological adaptations

No experimental evidence of biophysically constrained RNA-mediated cell type differentiation supports the claim about “…the evolutionary plasticity of the regulatory regions involved in transcriptional regulation…” The overwhelming systems complexity of energy-dependent RNA-mediated cause and effect can no longer be placed into the context of the pseudoscientific nonsense touted by theorists. Watch Andrea Wagner’s group try to escape from the claims made by losers.
But first see: Kalevi Kull: Censorship & Royal Society Evo Event

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

RNA-mediated gene regulation is less evolvable than transcriptional regulation

…nucleic acid binding sites of RNA-mediated gene regulation are less evolvable than those of transcriptional regulation. This observation is consistent with the high levels of mRNA target conservation for RBPs (10, 82, 83) and the evolutionary plasticity of the regulatory regions involved in transcriptional regulation (84⇓–86) as well as their role in the evolution of myriad adaptations and innovations (11, 87, 88).

It is obvious to anyone who has followed the works of Andreas Wagner that his group has reached an impasse.
See: Evolution of Viral Proteins Originated De Novo by Overprinting (2012)

We found that young de novo genes have a different codon usage from the rest of the genome.

There is no such thing as a de novo gene.
See: From de novo to “de nono”: most novel protein coding genes identified with phylostratigraphy represent old genes or recent duplicates

I collectively refer to the putative de novo genes that failed to pass the validation criteria as the ‘de nono’ genes.

See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

Natural selection for energy-dependent codon optimality links what organisms eat to their pheromone-controlled physiology of reproduction in species from microbes to humans. Ecological variation is linked to ecological adaptations only in the context of biophysically constrained viral latency. That fact is now perfectly clear in the context of more than 71,000 indexed published works that link the energy-dependent creation of ATP synthase to the creation of ATP and the creation of RNA in the context of McEwen et al., (1964) and Frohlich (1968).
People like Andreas Wagner are stuck with their ridiculous claims about evolution, when all serious scientists know that only the hecatombic evolution of virus-driven pathology is possible. Healthy longevity requires food energy-dependent biophysically constrained polycombic ecological adaptations. The metabolism of food to species-specific pheromones links RNA-mediated autophagy to all biodiversity. The virus-driven degradation of messenger RNA is linked to all pathology.
Andreas Wagner reversed every aspect of what is known in: Arrival of the Fittest: Solving Evolution’s Greatest Puzzle (2014)

…he has found that adaptations are not just driven by chance, but by a set of laws that allow nature to discover new molecules and mechanisms in a fraction of the time that random variation would take.

See for comparison: Kohl’s Laws of Biology in Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

Life is nutrient-dependent. That is a Biological Law. The ecological origin of all biological laws is apparent 1) in the context of systems biology (P. Kohl, et al., 2010); 2) in the context of the metabolism of nutrients by microbes (K. D. Kohl, 2012); and 3) in the context of how the metabolism of nutrients results in species-specific pheromones that control the physiology of reproduction (J. Kohl, Ostrovsky, Frechter, & Jefferis, 2013). Taken together, the systems biology of nutrient metabolism to species-specific pheromones, which control the physiology of reproduction, can be expressed in a summary of Kohl’s Laws of Biology: 1) Life is nutrient-dependent. See for review (J. V. Kohl, 2012; M. Lynch, 2007). The physiology of reproduction is pheromone-controlled. See for review (J. V. Kohl, 2013). In the context of nutrient-dependent epigenetically-effected human reproduction, it is clearer that the epigenetic effects of human pheromones integrate neuroendocrinology and behavior (J. V. Kohl, et al., 2001), which includes the neuroendocrinology of mammalian behavior associated with the development of sexual preferences (J.V. Kohl, 2007).

Andreas Wagner, and others like him, will probably continue to misrepresent what is known about how the creation of sunlight must be linked to food energy-dependent pheromone-controlled reproduction by natural selection for codon optimality. But the facts about how energy must be linked to increasing organismal complexity are not going to change.
See: Schrödinger at 75 – The Future of Biology – September 2018
and/or Cytosis: A Cell Biology Board Game

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

 
 
 

Cytosis: Biology Content

 

Help Me Write Some Biology Content

Project Update #5: Cytosis: A Cell Biology Board Game by John Coveyou (Genius Games)

Many of you have mentioned that you’d like to have an explanation of the biology behind Cytosis available… and I think that is an AWESOME plan. Every time I’ve taught the game to non-science players in the past, they say gameplay made even more sense (and was so much more enjoyable) when I explained the science as well. This way they knew WHY they were doing what they were doing!

If you’ve got a strong background in biology, love explaining complexities in a way that someone unfamiliar with biology could understand, and would be interested in volunteering to help me write a page or two of science explanatory content for the rulebook, please shoot me an email… with the subject line “Cytosis Biology Explanations – [Your Name]” and we can start discussing!

I wrote: Kohl’s Laws of Biology may help. See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

1) Life is nutrient-dependent. See for review [2, 31]. The physiology of reproduction is pheromone-controlled. See for review [30].

In the context of the game “Cytosis,” Kohl’s Laws link the epigenetic effects of food odors and pheromones to changes in the mitochondria of all cell types. The energy-dependent changes in the mitochondria are linked to healthy longevity.
If the epigenetic effects of food odors and pheromones did not clearly link cytosis to healthy longevity, we would be left with only the link from virus-driven energy theft to all pathology. The explanation for all pathology involves more complexity than most people are willing to examine even when it is placed into the context of a book for a general, albeit educated, target audience.
See: The Scent of Eros: Mysteries of Odor in Human Sexuality

This is science at its best, with adventure, ideas, and lots of facts. — Helen Fisher

Details for other serious scientists:

The synthesis of RNA is nutrient energy-dependent. From 1964 Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

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

The anti-entropic virucidal energy of sunlight has since been linked to all biophysically constrained human cell type differentiation via representations in Feedback loops link odor and pheromone signaling with reproduction

The feedback loops link Dobzhansky’s claims about amino acid substitutions and RNA-mediated cell type differentiation from natural selection for energy-dependent codon optimality to the pheromone-controlled biodiversity of all living genera.

See: Combating Evolution to Fight Disease

…transient errors in mRNA synthesis can also cause heritable non-DNA-based phenotypic change. This is observed when low-abundance transcriptional regulators are affected by transcription errors. This disruption can cause a cell to alter its gene expression, resulting in a phenotype that may be heritable (2).

See also: Carl Woese, Evolution’s Golden Revolutionary

…there is probably no other scientist but Carl Woese who could write about having “no use for natural selection” and have Nature magazine respond with a Nobel endorsement. It is Carl Woese who first identified the Archaea and introduced us to horizontal gene transfer.

Virus-driven energy theft causes the degradation of messenger RNA, which links negative supercoiling of DNA in bacteria to the creation of archaea and links the conserved molecular mechanisms from archaea to the evolution of all pathology. For comparison, horizontal gene transfer links the nutrient energy-dependent de novo creation of genes from the pheromone-controlled fixation of RNA-mediated amino acid substitutions to supercoiled DNA, which prevents virus-driven energy theft from causing more degradation of messenger RNA.

See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

This invited review of nutritional epigenetics includes a model that links nutrient energy-dependent changes from atoms to ecosystems. Most theorists have been caught with their pants down because they are still making claims about mutations and evolution. How can serious scientists compete with pseudoscientists who make claims that link mutations to millions of year of evolution?  Most serious scientists know how to link quantized energy from chemistry to biologically-based cause and effect. Most biologically uninformed people accept the claims of pseudoscientists, atheists, and other theorists.

Some Harvard researchers are still trying to hide facts that link research on the synthesis of mRNA to all biophysically constrained biodiversity on Earth via hydrogen-atom transfer in DNA base pairs in solution and RNA-mediated amino acid substitutions in supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. ATP-dependent cell type differentiation is placed into the context of conserved NAD+ and protein-protein interactions.

See:  A conserved NAD+ binding pocket that regulates protein-protein interactions during aging

See for contrast: Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention

It is now widely accepted that cancer is the result of the gradual accumulation of driver gene mutations that successively increase cell proliferation (1–3).

Johns Hopkins researchers framed everything known to serious scientists about cell type differentiation into the contest of cancer as ‘bad luck” as if cytosis was not energy-dependent and healthy longevity arose in the context of mutation-driven evolution — if species were lucky enough to evolve into other species.
No serious scientist has ever accepted that ridiculous claim.

See for comparison: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

…we characterize two distinct p120-associated complexes with antagonistic functions and we describe a microRNA (miRNA)-mediated mechanism through which the ZA suppresses transformed cell growth.

Backers and players of the game “Cytosis” will learn how the energy-dependent function of mitochondria must be linked to every aspect of healthy longevity or be linked from virus-driven energy theft to all pathology. They will be prepared to learn from the next game: “Photosynthesis,” which will link the sun’s anti-entropic virucidal energy to all biophysically constrained biodiversity via what is known to all serious scientists. They will not need to learn anything more than is required for them to reject the pseudoscientific nonsense of neo-Darwinian theories.

See what’s happened after 20 days of comments to this society. 

The information has been shared more than 450 times. The number of biologically informed students will force the biologically uninformed professors to stop playing the evolution game until they can begin supporting their ridiculous claims with facts. The facts must link ecological variation to ecological adaptations via what is known to serious scientists about hydrogen-atom transfer in DNA base pairs in solution.

Clearly, the facts tell us that all individuals of all species that live on Earth must eat and reproduce or they become extinct. None mutate and evolve into other species.

Thus, we regard as rather regrettable the conventional concatenation of Darwin’s name with evolution, because there are other modalities that must be entertained and which we regard as mandatory during the course of evolutionary time.

— Carl Woese and physicist Nigel Goldenfeld

I encourage others to support the development of games that teach what pseudoscientists do not want an interested target audience to learn. With enough support for an easy way to learn about energy-dependent cytosis compared to virus-driven pathology, the facts about RNA-mediated cell type differentiation will become clearer.

See also our section on molecular epigenetics in this review from 1996: From fertilization to adult sexual behavior

Every aspect of cytosis is food energy-dependent and RNA-mediated. Virus-driven energy theft cause all pathology. That fact makes sense in the context of all claims made by serious scientists. See for example:

 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)

— with forward by Roger Penrose who co-authored with George F.R. Ellis and Stephen Hawking

“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)

See also:

James Vaughn Kohl “New data on how genetic predispositions are epigenetically linked to phenotypically distinct neuroanatomy and behaviors is provided in the honeybee model. Across-species comparisons from insects to vertebrates clearly show that the epigenetic influence of food odors and pheromones continues throughout the life of organisms that collectively survive whereas individuals do not. These comparisons also attest to the relative salience of sensory input from the rearing environment. For example, when viewed from the consistency of animal models and conditioned behaviors, food odors are obviously more important to food selection than is our visual perception of food. Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.

Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).”

— Kohl, JV (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors Socioaffective Neuroscience & Psychology 2012


    17 Apr 2014 at 03:07am

George F R Ellis This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics.
This is explored here: http://rsfs.royalsocietypublishing.org/content/2/1.toc 

See also:

…every angstrom is dynamic from the 5 prime to the three…

See also: Genetic 3’UTR variation is associated with human pigmentation characteristics and sensitivity to sunlight

Sunlight exposure induces signalling pathways leading to the activation of melanin synthesis and tanning response. MicroRNAs (miRNAs) can regulate the expression of genes involved in pigmentation pathways by binding to the complementary sequence in their 3′-untrastaled regions (3’UTRs).

Top-down causation starts from the creation of the sun’s anti-entropic virucidal energy. Hydrogen atom transfer in DNA base pairs in solution links energy-dependent changes in the microRNA/messenger RNA balance from microRNA flanking sequences to RNA-mediated amino acid substitutions that alter the stability of supercoiled DNA in the context of the physiology of reproduction.

One base pair change and a single amino acid substitution makes the difference between healthy longevity and pathology during life history transitions. See for example: Epigenetic Regulation of BDNF Gene during Development and Diseases
See also: Δ133p53 Functions to Maintain Redox Homeostasis in Response to Low ROS Stresses
https://www.omicsgroup.org/articles-images/single-cell-signaling-response-oxidative-stresses-5-154-g001.png
See also: Keep science a priority. Stand with ASCB at the March for Science rally April 22.
Light-induced-conformer-intercoversion-of-hydrogen-bond

Energy-dependent pheromone-controlled entropy (2)

See also: Energy-dependent pheromone-controlled entropy (1)
Let’s make peer review scientific

…peer review is often biased and inefficient. It is occasionally corrupt, sometimes a charade, an open temptation to plagiarists. Even with the best of intentions, how and whether peer review identifies high-quality science is unknown. It is, in short, unscientific.


The androgynous baby-faced boy or girl pictured among those wearing pink “crotch” hats appears to representing others at the March for Women. The sign may also be representing the intent of one of the organizers whose support for terrorists became better known after this March.
Next comes the March for Science, where anyone whose photo appears can be asked what area of scientific expertise most interested them. Attempts will be made to learn more about what they did to link energy-dependent changes in angstroms from sunlight to ecosystems in all living genera via hydrogen-atom transfer in DNA base pairs in solution.

See for example: Quantifying Intracellular Rates of Glycolytic and Oxidative ATP Production and Consumption Using Extracellular Flux Measurements

Abstract excerpt:

Measurement of ATP use revealed no significant preference for glycolytic or oxidative ATP by specific ATP consumers. Overall, we demonstrate how extracellular fluxes quantitatively reflect intracellular ATP turnover and cellular bioenergetics.

The energy-dependent extracellular fluxes link pheromone-controlled entropy from cellular bioenergetics to the physiology of reproduction. Virus-driven energy theft compromises the conserved molecular mechanisms of cellular bioenergetics.
See for example: Endothelial cell tropism is a determinant of H5N1 pathogenesis in mammalian species

…our study demonstrates that endothelial cell tropism is a determinant of the high virulence associated with HPAI H5N1 infection in mammalian hosts. By utilizing endogenous miRNA mediated restriction of viral tropism, we demonstrate that H5N1 infection of endothelial cells results in increased cytokine production in the lungs and loss of endothelial barrier function, which culminates in vascular leakage in the lungs. In addition, extrapulmonary spread of H5N1 virus likely occurs via the hematogenous route by infection of endothelial cells.

They link virus-driven energy theft from microRNAs in bacteria to messenger RNA degradation in archaea and L-forms (cells without walls). They fail to link energy theft to the substitution of nutrient energy-dependent amino acid substitutions in viruses, which links viruses to pathology in all living genera.
See for example: Identification of amino acid substitutions supporting antigenic change of influenza A(H1N1)pdm09 viruses

In conclusion, substitutions in or near the RBS can influence the antigenic properties of A(H1N1)pdm09 viruses. Based on the current and previous studies of antigenic change of influenza A viruses (11, 12), it is probable that emerging antigenic variants of A(H1N1)pdm09 viruses will escape from population immunity because of substitutions in or near the RBS. However, our results also suggest that the presence of antibodies directed to epitopes on seasonal A(H1N1) and A(H1N1)pdm09 viruses in much of the population limits the number of antigenic variants that can emerge to cause new epidemics.

Antigenic variants that are biophysically constrained cannot “emerge.” Nutrient stress or social stress must first break the biophysical constraints or there would be no new epidemics. That fact means that nutrient-dependent pheromone-controlled neurogenesis links the physiology of reproduction to ecological adaptations in all cell types of all individuals of all living genera, including organisms with no brain. If you start from neurogenesis in the human brain without realizing that it is pheromone-controlled, you may never learn how food odors and pheromones link the physiology of reproduction to the transgenerational epigenetic inheritance of all morphological and behavioral diversity via conserved molecular mechanisms of endogenous RNA interference.
See also from 6 years ago: Reproduction: A New Venue for Studying Function of Adult Neurogenesis?

Recent studies disclose that SVZ neurogenesis is under regulation of reproductive cues like pheromones.

Some recent debate about this fact was published to the Discover Magazine blog site in the context of accurate claims that Ben Carson made about learning and memory. A anonymous character with the screen name “Neuroskeptic” caused me to voice some concerns about the intelligence of people who accused Ben Carson, a pediatric neurosurgeon, of being wrong about anything.
See: Ben Carson and the Power of the Hippocampus 3/10/17

See also: Social phobia: Indication of a genetic cause — reported on “medicalxpress”
Excerpt: The cause of genetic illnesses often lies in the SNPs.
My comment: The energy-dependent differences in the SNPs is RNA-mediated. In this case, the differences link RNA methylation from endogenous RNA interference to learning and memory via experience-dependent cell type differentiation during life history transitions.
For example, one amino acid substitution (COMT Val158Met) was already linked to differences in the behavior of adolescents and adults. When will Neuroskeptic and others admit that they need to learn more about biologically-based cause and effect before they attack people like Ben Carson.

My comment from 3/11/17
See also:Reproduction: A New Venue for Studying Function of Adult Neurogenesis?” (2011) Cell Transplant

Excerpt: …the number of dividing neurons in the hippocampus of female sheep increased robustly (43), which is accompanied with a sharp increase in circulating luteinizing hormone. Additionally, luteinizing hormone level and hippocampal neurogenesis were also upregulated by the soiled bedding. With the use of prolactin and leutinizing hormone receptor knock-out mice, it was confirmed that the hippocampal neurogenesis is due to the increase of the luteinizing hormone but not prolactin; in contrast, prolactin is the regulatory factor of SVZ neurogenesis (69).

Neuroskeptic displayed the ignorance of all theorists and left them with no excuse to say anything more about Ben Carson, or anyone else who intends to help the President of the United States “Make America Great Again.” Only biologically uniformed liberals will continue their attempts to stop President Trump. The anti-entropic effect of pheromones on GnRH and luteinizing hormone links food odors and pheromones from feedback loops to the physiology of reproduction in all vertebrates via the substitution of the achiral amino acid glycine in position 6 of the GnRH decapeptide.

With co-authors, Donald Pfaff did this in the context of autism. For example, substitution of the achiral amino acid glycine in position 6 of the GnRH decapeptide also links food odors and pheromones from stress-linked changes and feedback loops to sex-specific gene–environment interactions via the hypothalamic-pituitary-gonadal axis.
See: Sex-specific gene–environment interactions underlying ASD-like behaviors

…we found a significant three-way interaction on corticotropin-releasing hormone receptor-1 (Crhr1) gene expression, in the left hippocampus specifically, which co-occurred with epigenetic alterations in histone H3 N-terminal lysine 4 trimethylation (H3K4me3) over the Crhr1 promoter. Although it is highly likely that multiple (synergistic) interactions may be at work, change in the expression of genes in the hypothalamic–pituitary–adrenal/stress system (e.g., Crhr1) is one of them. The data provide proof-of-principle that genetic and environmental factors interact to cause sex-specific effects that may help explain the male bias in ASD incidence.

This was reported as: Study tests the ‘three-hit’ theory of autism

…the researchers looked for molecular changes within these rodents’ brains that might help to explain the differences in behavior. They found an increase in the expression of a gene that helps to kick off stress responses, in a brain region called the left hippocampus. With help from C. David Allis’s lab, they looked for chemical alterations in the packaging of DNA that might explain this uptick in gene activity. This effort revealed one particular chemical change in the nerve cell nucleus that encourages the expression of this stress-relevant gene.

The chemical alterations are energy-dependent and RNA-mediated via methylation, which alters gene activation to help ensure that all organisms of all living genera have the best opportunity to ecologically adapt. If they fail to adapt, they die. They do not mutate and become another species.
See: Every amino acid matters: essential contributions of histone variants to mammalian development and disease  (2014) by senior author C. David Allis.
Conclusion:

…numerous histone variants seem to be restricted to specific cell lineages or tissue types, yet it remains unclear how such expression patterns are maintained and what the consequences are of increasing or reducing combinatorial variant deposition across cell types. Aberrations in these processes result in detrimental phenotypic outcomes across numerous mammalian systems, including humans. Although we are clearly still in the infancy of this ever-expanding and diverse field, we imagine that future endeavours related to histone variant biology will hold great promise for human health and disease.

The tag-team of Pfaff and Allis will continue to prevent others from what is known to all serious scientists about epigenetically-effected gene-environment interactions among all living genera. The interactions are nutrient-energy-dependent and pheromone controlled by the physiology of reproduction.
I posted this question to the CRISPR Cas 9 FB group and to the miRNA & siRNA FB group

Does any experimental evidence of biologically-based cause and effect suggest that microRNA-mediated host-induced gene silencing is not linked from biophysically constrained viral latency to energy-dependent RNA-mediated cell type differentiation via amino acid substitutions in the cell types of all living genera?

For example, could host-induced gene silencing occur outside the context of natural selection for energy-dependent codon optimality and endogenous RNA interference and the physiology of reproduction?

See also: What’s Next for Diagnostic Patents After Ariosa v. Sequenom

…we should use language that highlights the inventive piece of the invention rather than the natural law underlying it.
 
The natural law underlying all links from ecological variation to ecological adaptation could be applied to the patent for RNA-Guided Human Genome Engineering. If so, the examiners will find that host-induced gene silencing is the obvious link from nutrient energy-dependent RNA methylation to the pheromone-controlled physiology of reproduction in all living genera via Kohl’s Laws of Biology.
 
Simply put, Kohl’s Laws includes two facts:
 
1) all organisms must eat or they die.
2) all species must reproduce or they become extinct.
 

Can you imagine what the value of future patents on drugs will be if researchers continue to deny what is known about those two natural laws?

Biology to a Physicist

Coulombic interactions facilitate polycombic adaptation

RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly
Summary: Everything known to serious scientists about energy-dependent biophysically constrained RNA-mediated protein folding chemistry is attributed to “Nature” and evolution with no consideration for where the energy came from or where it goes when viruses use it for their replication.

See also: War Games: False Flag Terrorism (2)

I baited Sean Ovis, and caused him to join a discussion on “The Battlefield.Sean Ovis regurgitated parts of my model when he wrote:
Excerpts:

  1. This scenario is explored fully within my model which links virus-driven energy theft and genomic entropy in all ecosystems on Earth to energy-dependent RNA-mediated amino acid substitutions via olfaction and the innate immune system in the context of the physiology of reproduction, and is fully known to all serious scientists.
  2. In this model all organized genomes in all tissues of all living genera are linked to nutrient-dependent RNA-mediated amino acid substitutions via symbiosis and the pheromone-controlled physiology of nutrient-dependent reproduction in biochemically-based ecosystems which protects energy-dependent ecological adaptations from virus-driven energy theft and genomic entropy. The model was about to be published when due to an unfortunate accident, I tripped and the only copy of the manuscript fell out of my pocket and was eaten by a small dog.

My reply: Please note: After my last encounter with Sean Ovis, he wrote:

“If you are a creation scientist, you can take comfort in the fact that as you get older, the control of these viral fragments is considerably weakened, and eventually one or more of these jumping genes will be let loose in your body to wreak havoc on your DNA. When that happens, you can thank God, because they will have brought you closer to him.”

Addendum: That will remain as one of the most vicious of all atheistic attacks on my model.

I’ve since added information on coulombic interactions to help others link angstroms to ecosystems in all living genera via the physiology of reproduction and fixation of RNA-mediated amino acid substitutions in supercoiled DNA, which protects all organized genomes from virus-driven entropy.

Sean Ovis bastardized the discussion of Quantum Consciousness, so I ended comments on the threat after attempting to get him and others to start their own OP.

See: James Kohl

Was Hitchens a self- described marxist-trotskyist who regarded the materialist conception of history as legitimate for explaining the human condition?

Sean Ovis “Language is elitist,” says Marx; however, according to la Tournier , it is not so much language that is elitist, but rather
the rubicon, and some would say the defining characteristic, of language. Bataille’s analysis of neocultural textual theory states that consciousness may be used to marginalize minorities. Thus, Lacan suggests the use of postsemantic feminism to challenge hierarchy.
If one examines dialectic nationalism, one is faced with a choice: either accept postsemantic feminism or conclude that the task of the poet is social comment, given that culture is interchangeable with sexuality. The within/without distinction which is a central theme of Tarantino’s Pulp Fiction emerges again in Reservoir Dogs, although in a more mythopoetical sense. Therefore, if Lacanist obscurity holds, we have to choose between subpatriarchialist narrative and the capitalist paradigm of discourse.

In an attempt to move forward, I started a new OP based on the claims in: Peptides design based on transmembrane Escherichia coli’s OmpA protein through molecular dynamics simulations in water-dodecane interfaces

It seems futile to continue to address questions about the transfer of energy as information, when people cannot seem to grasp the fact that transfer must be biophysically constrained in the context of RNA-mediated protein folding chemistry that links coulombic interactions to polycombic adaptation, which prevents the hecatombic evolution of all virus-driven pathology.

Matthew Hunt, who is the co-author of “Electrostatic effects on linear and nonlinear waves in hanging film flows” (link opens pdf paper) continued to ask questions like this: You talk about the transfer of energy, but what is physically being transferred?

One of the administrators, Larry Kinser Jr., began to provide vague answers. His vague answers and proselytizing are all that I’ve seen come from the administrators of the group.

James Kohl Thanks for asking. Energy as information is being physically transferred as in the context of the Laws of Physics, which must be linked from the fundamentals of what is known about organic chemistry to Kohl’s Laws of Biology or Darwin’s ‘conditions of life,” which God established in the context of His Creation. Chemists know that — see for example:


See also: Gianmarc Grazioli YouTube Channel for Chemistry AND Guitar Tutorials!
See also: m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs
Excerpt:

These observations provide a mechanism for disrupting RNA structure through post-transcriptional modifications. The different propensities to form Hoogsteen base pairs in B-DNA and A-RNA may help cells meet the opposing requirements of maintaining genome stability, on the one hand, and of dynamically modulating the structure of the epitranscriptome, on the other.

My comment: For several years, others have also attempted to portray what they think are novel mechanisms of RNA-mediated cell type differentiation in the context of the epitranscriptome and epitranscriptomics. Their attempts seem to be nothing more than attempts to obfuscate the facts that have been known about the molecular epigenetics of RNA-mediated cell type differentiation for at least two decades.
See for example:  From Fertilization to Adult Sexual Behavior
Excerpt:

Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

My comment: See also this report on “m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs”
DNA’s dynamic nature makes it well-suited to serve as the blueprint of life
Excerpt:

“For something as fundamental as the double helix, it is amazing that we are discovering these basic properties so late in the game,” said Al-Hashimi. “We need to continue to zoom in to obtain a deeper understanding regarding these basic molecules of life.”

Excerpt:

“The team believes that RNA doesn’t form Hoogsteen base pairs because its double helical structure (known as A-form) is more compressed than DNA’s (B-form) structure. As a result, RNA can’t flip one base without hitting another, or without moving around atoms, which would tear apart the helix.” That means fixation of RNA-mediated amino acid substitutions is the basis of life and all biodiversity.

My comment: That fact means DNA cannot serve as the “blueprint of life” outside the context of biophysically constrained energy-dependent fixation of RNA-mediated amino acid substitutions that differentiate all cell types in all living genera. Science journalists continue to twist the facts to support the pseudoscientific nonsense of neo-Darwinian theories.
For musical fun with those who cannot link energy-dependent changes from angstroms to ecosystems in all living genera, see what intelligent people are doing with their experimental evidence of biologically-based cause and effect, which must start with changes in base pairs and link hydrogen-atom transfer from natural selection for energy-dependent codon usage to RNA-mediated amino acid substitutions in supercoiled DNA, which protects all organized genomes from virus-driven entropy.
 

To be continued.
 

2008 01 Mat & Helse

Energy dependent RNA-mediated immunity (6)

Alzheimer’s disease could be caused by herpes virus, warn experts
Excerpt:

Professor Douglas Kell of the University of Manchester’s School of Chemistry, said “We are saying there is incontrovertible evidence that Alzheimer’s Disease has a dormant microbial component. We can’t keep ignoring all of the evidence.”

My comment: What evidence? Microbes and Alzheimer’s Disease is still listed as an in-press publication. Perhaps they are telling others to stop ignoring all my evidence.
See for example: Energy dependent RNA-mediated immunity (2)
Excerpt:

If you only look at the works cited in this poster session, you could link everything known about nutrient-dependent cell type differentiation to healthy longevity. You could also link everything known about viruses to all pathology. For example, the nematode model of learning and memory links amino acid sensing to RNA-mediated amino acid substitutions that protect our organized genomes from virus-driven changes in nerve cells that alter olfactory acuity and specificity in Alzheimer’s disease.

For comparison, Greg Bear made the connection from viruses to all pathology in a series of science fiction novels that began with “Blood Music” in 1985. It took evidence of the transgenerational epigenetic inheritance of Zika virus pathology to prompt serious scientists to expose the pseudoscientific nonsense that has been touted by neo-Darwinian theorists during the past 30 years of scientific progress. All scientific progress has continued to support obvious links from atoms to ecosystems, which are perturbed by virus-driven energy theft.

Ecological adaptations are nutrient-dependent and cannot be placed into the context of theories about beneficial mutations and evolution, which is pseudoscientific fiction.

Gene intelligence

Last month, one of the top intelligence officials in the United States warned that genome-editing technology is now a potential weapon of mass destruction. Techniques such as the emerging CRISPR–Cas9 system, US director of national intelligence James Clapper warned in an annual threat-assessment report to the US Senate, should be listed as dangers alongside nuclear tests in North Korea or clandestine chemical weapons in Syria (see go.nature.com/jxuyev).
Jon Stewart interviews Greg Bear. They discuss Quantico.  So does the US director of national intelligence James Clapper. See “Statement for the Record Worldwide Threat Assessment of the US Intelligence Community Senate Armed Services Committee”
Excerpt:

Genome Editing
Research in genome editing conducted by countries with different regulatory or ethical standards than those of Western countries probably increases the risk of the creation of potentially harmful biological agents or products. Given the broad distribution, low cost, and accelerated pace of development of this dual-use technology, its deliberate or unintentional misuse might lead to far-reaching economic and national security implications. Advances in genome editing in 2015 have compelled groups of high-profile US and European biologists to question unregulated editing of the human germline (cells that are relevant for reproduction), which might create inheritable genetic changes. Nevertheless, researchers will probably continue to encounter challenges to achieve the desired outcome of their genome modifications, in part because of the technical limitations that are inherent in available genome editing systems.

See also: Ecology: Biology distilled

Excerpt:

Carroll has made a strikingly clear case that ecology is a science on a par with molecular biology and genetics. In many ways, this book is a homage to Charles Elton, who helped to define ecology as the study of species interactions in a ‘trophic’ network shaped by the environment (see E. Marris Nature 459, 327–328; 2009). Building on his vision, Carroll provides a passionate motto for the twenty-first century: “better living through ecology”.

My comment: I placed his passionate motto and six rules of regulation (his “Serengeti Rules”) into the context of this invited review of nutritional epigenetics.

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

The rules of regulation are Kohl’s “Laws of Biology.”
Excerpt:

Kohl’s Laws of Biology… are so-named because the surname of the first author or sole author on each of 7 peer-reviewed publications in the paragraph below is Kohl. The Kohls did not create the Laws of Biology; they merely independently incorporated what is known about them into what appears to be a cohesive series of published works.
Kohl’s Laws of Biology
Life is nutrient-dependent. That is a Biological Law. The ecological origin of all biological laws is apparent 1) in the context of systems biology (P. Kohl, et al., 2010); 2) in the context of the metabolism of nutrients by microbes (K. D. Kohl, 2012); and 3) in the context of how the metabolism of nutrients results in species-specific pheromones that control the physiology of reproduction (J. Kohl, Ostrovsky, Frechter, & Jefferis, 2013). Taken together, the systems biology of nutrient metabolism to species-specific pheromones, which control the physiology of reproduction, can be expressed in a summary of Kohl’s Laws of Biology: 1) Life is nutrient-dependent. See for review (J. V. Kohl, 2012; M. Lynch, 2007). The physiology of reproduction is pheromone-controlled. See for review (J. V. Kohl, 2013). In the context of nutrient-dependent epigenetically-effected human reproduction, it is clearer that the epigenetic effects of human pheromones integrate neuroendocrinology and behavior (J. V. Kohl, et al., 2001), which includes the neuroendocrinology of mammalian behavior associated with the development of sexual preferences (J.V. Kohl, 2007).
Kohl’s Laws help to explain what was missing from Darwin’s ‘conditions of life.’

See also: Gone is the solitary genius – science today is a group effort
Excerpt:

Seeking general patterns and processes responsible for these patterns has long been the holy grail of ecology. Collaboration makes this quest achievable.

My comments: Group efforts have focused on making claims that are consistent with neo-Darwinian pseudoscience. The groups hope their efforts will continue to be funded by unsuspecting government agencies.
Recently, private parties with billions to spend have contributed prize money to academics in groups. Many people seem to think the groups will accomplish something faster that has always been accomplished by individuals.
One passionate individual who is not stopped by “group think” or ridiculous theories can disseminate more accurate information than any group. Monographs can help individuals jump at least two decades ahead of those who should be peers, but can’t be. Co-authors can always be helpful, but ultimately someone like me must work alone, albeit with the support of others like Teresa Binstock, who also works alone.
Academics in groups are constrained by other academics, which makes progress painfully slow and ridiculously expensive. The best example of this slow progress is found in the obvious links from ecological variation to ecological adaptation that many ecologists are still trying to put into the context of neo-Darwinian nonsense.
See: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons
Excerpt:

Because of gar’s phylogenetic position, slow rate of sequence evolution, dense genetic map and ease of laboratory culture, this resource provides a unique bridge between tetrapods and teleost biomedical models. Our analyses show that gar bridges teleosts to tetrapods in genome arrangement, allowing the identification of orthologous genes by possessing ancient VGD ohnologs lost reciprocally in teleosts and tetrapods and elucidating the evolution of vertebrate-specific features, including adaptive immunity and mineralized tissues, and the evolution of gene expression.

My comment: This group of 61 authors seems to not know anything about the nutrient-dependent RNA-mediated innate immune system links the ecological landscape to the physical landscape of supercoiled DNA in the organized genomes of all living genera.  They make a claim about the evolution of gene expression, when all serious scientists know how to link the de novo creation of nucleic acids to the nutrient-dependent de novo creation of genes. All serious scientists also know that virus-perturbed protein folding chemistry leads to gene loss or to the creation of pseudogenes. Anyone who still claims that vertebrate-specific features “evolved” has missed all the experimental evidence from physics and chemistry that links the conserved molecular mechanisms of biologically-based cause and effect from hydrogen-atom transfer in DNA base pairs to all biomass and all biodiversity.
The missing evidence shows up in this report of the group’s work. Finding our genomic inner fish with the spotted gar
Excerpt:

We were interested in regulatory elements known as enhancers, which are genetic switches that turn certain genes on or off. In particular, we were looking for enhancers that regulate genes involved in limb development. Without them, limb formation can’t occur.

My comment: Similarly, formation of the bacterial flagellum cannot occur outside the context of the nutrient-dependent pheromone-controlled physiology of reproduction that links hydrogen-atom transfer in DNA base pairs to RNA-mediated cell type differentiation in the context of supercoiled DNA that protects all organized genome from virus-driven entropy. The flagellum formed over-the-weekend.
See:

For other example of what is known about biolgoically-based cause and effect, see the works of Anna Di Cosmo’s group; Eugene Daev’s group, and Bruce McEwen’s group.
 
 

terrarium-eco-system

In theory, or supported by experimental evidence?

Carl Zimmer typically makes statements like the one below without prefacing them with “in theory.” That’s how he establishes the bias towards evolutionary theory in nearly everything he reports.
For example: “During the development of eggs and sperm, each pair of chromosomes swaps pieces of their DNA. Over the generations, long stretches of DNA get broken into smaller ones, like a deck of cards repeatedly shuffled.
Inaccurate statements like that one make it appear that the evolution of biodiversity occurs across millions of years during which accumulated mutations somehow lead to fixed changes in the amino acid substitutions that differentiate the cell types of all cells in all individuals of all different species. Accurate representations of biologically-based cause and effect include RNA-mediated events, which link ecological variation to nutrient-dependent amino acid substitutions and chromosomal rearrangements.
The amino acid substitutions and chromosomal rearrangements occur in the absence of mutations that perturb protein folding. Instead, they help to ensure biodiversity via the metabolism of nutrients to species-specific pheromones. Pheromones control the physiology of reproduction in species from microbes to man, which is how they lead from nutrient-uptake to the control of biodiversity via conserved molecular mechanisms of cell type differentiation in all species.
The alternative that Zimmer and others like him continue to tout involves a ridiculous theory that accumulated mutations somehow lead to natural selection and the evolution of biodiversity. No experimental evidence of biologically-based cause and effect suggests that is possible. Furthermore, the amino acid-dependent protein folding that links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man is biophysically-constrained. Simply put, that means the Laws of Physics prevent mutation-driven evolution by placing chemical ecology in a position that ensures what Darwin called his ‘conditions of life’ have been met. Minimally, his ‘conditions of life’ have always been nutrient-dependent, which is probably why evidence of RNA-mediated events clearly links nutrient uptake to ecological adaptations.
Until 1973, most evolutionary theorists could have excused themselves from intelligent conversations about the conserved molecular biology of amino acid substitutions and cell type differentiation. However, from the time that Dobzhansky stated his creationist perspective in the terms of evolutionary theory, it has become clearer that amino acids substitutions differentiate cell types in all species. In Nothing in Biology Makes Any Sense Except in the Light of Evolution, Dobzhanksy 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.”
No experimental evidence of biologically-based cause and effect suggests the single amino acids substitutions that differentiate the cell types of these primates or the cell types of any other species can arise via a mutation or the accumulation of mutations. All experimental evidence and all model organisms that sexually reproduce via ligand-specific receptor-mediated fertilization exemplifies the fact that … exosomes are the carriers of a flow of information from somatic cells to gametes…That fact, like all other facts about sex differences in cell types indicates …that somatic RNA is transferred to sperm cells, which can therefore act as the final recipients of somatic cell-derived information.
Carl Zimmer is one of two people I know about who has written a book about viruses, see A Planet of Viruses. I’m not sure what planet his information came from, since it does not appear to include anything pertinent to links between the epigenetic landscape and the physical landscape of DNA in the organized genomes of species from microbes to man. However, a book published 2 years earlier by Luis Villarreal, see Origin of group identity: viruses, addiction and cooperation, includes the mention of pheromones 79 times.
Pheromones control the physiology of nutrient-dependent reproduction in living organisms via nutrient-dependent RNA-directed DNA methylation and RNA-mediated events that link amino acid substitutions to cell type differentiation via chromosomal rearrangements in all organisms. That’s why Zimmer’s book is of much less interest to me than Villarreal’s book.
Like his articles, Zimmer seems to be stuck touting evolutionary theory at a time when others have moved forward by providing experimental evidence of biologically based facts that link microbes to man via conserved molecular mechanisms, not via mutations and natural selection that Zimmer thinks is the basis for the evolution of biodiversity. Like Villarreal’s articles, those written by other serious scientists continue to attest to that fact that Carl Zimmer’s pseudoscientific nonsense will be exposed each time new experimental evidence is published that links RNA-mediated events to increasing organismal complexity with no mention of evolutionary events whatsoever.
See also: Body Cells Transfer Genetic Info Directly Into Sperm Cells, Amazing Study Finds.
Also, on July 31, 2013 Sayer Ji wrote: “Hereditary trauma: Inheritance of traumas and how they may be mediated”
Excerpt: “Mansuy and her team have succeeded in identifying a key component of these processes: short RNA molecules. These RNAs are synthetized from genetic information (DNA) by enzymes that read specific sections of the DNA (genes) and use them as template to produce corresponding RNAs. Other enzymes then trim these RNAs into mature forms. Cells naturally contain a large number of different short RNA molecules called microRNAs. They have regulatory functions, such as controlling how many copies of a particular protein are made.
See my comments on: Scientists unmask a piece in the puzzle of how the inheritance of traumas is mediated
1) “…traumatic stress alters the amount of several microRNAs in the blood, brain and sperm – while some microRNAs were produced in excess, others were lower than in the corresponding tissues or cells of control animals. These alterations resulted in misregulation of cellular processes normally controlled by these microRNAs.”
Nutrient stress and social stress act on the same central neuronal system that links epigenetic effects of food odors and social odors called pheromones on the microRNA/messenger RNA balance and cell type differentiation to mammalian behavior.
For details, see: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
The review follows from detailed representations with cross species examples of cause and effect in my 2013 published review and it adds the required details on the physics and chemistry of protein folding.
2) Kohl’s Laws of Biology: “The ecological origin of all biological laws is apparent 1) in the context of systems biology [91]; 2) in the context of the metabolism of nutrients by microbes [157]; and 3) in the context of how the metabolism of nutrients results in species-specific pheromones that control the physiology of reproduction [158]. Taken together, the systems biology of nutrient metabolism to species-specific pheromones, which control the physiology of reproduction, can be expressed in a summary of Kohl’s Laws of Biology: 1) Life is nutrient-dependent. See for review [2, 31]. The physiology of reproduction is pheromone-controlled. See for review [30]. In the context of nutrient-dependent epigenetically-effected human reproduction, it is clearer that the epigenetic effects of human pheromones integrate neuroendocrinology and behavior [104], which includes the neuroendocrinology of mammalian behavior associated with the development of sexual preferences [159].”
RNA-sequencing / exome sequencing now link RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of all organisms. Today’s news stresses the importance of RNA-mediated events to the understanding of differences between undifferentiated cancerous cell types and controlled cell type differentiation. New genome-editing technique enables rapid analysis of genes mutated in tumors. Simply put, researchers have applied what is known about RNA-mediated gene editing to help determine what goes wrong with cell metabolism processes in cancer cells. Why aren’t the theromodynamic cycles of protein biosynthesis and degradation limited by the biophysical constraints on protein folding that enable typical cell type differentiation via conserved molecular mechanisms in species from microbes to man? This rapid analysis of RNA-mediated genome editing eliminates the need for mouse models of what happens when genes are knocked out or knocked in. No need to wait for the mice to grow and manifest differences in their morphological and behavioral phenotypes as if mutations caused typical and atypical cell type differentiation as evolutionary theorist have told us occurs in the context of natural selection and the evolution of biodiversity.
 

poster-from-jesse

Biophysically constrained beginnings of RNA and DNA

Any anonymous participant in the discussion of: DNA may have had humble beginnings as nutrient carrier (Sep 01, 2014 by Adam Hadhazy) asks:
“when are you going to keep quiet?”
In a series of responses, I have explained the problem I have with honoring his request.
The following excerpts from Wikipedia and other sources are loosely strung together because there is no point to providing more extensive details of biologically-based cause and effect until others accept the fact that mutations and natural selection cannot lead to the evolution of biodiversity. Even without accepting the fact that nutrient-dependent amino acid substitutions differentiate the cell types of all individuals in all species, it should be clear that mutations do not. Until that fact becomes clear, nothing known about physics, chemistry, and molecular biology can be used to refute ridiculous theories. Here are examples of what cannot be used.
1) In mammals, phosphatidylserine is produced by base-exchange reactions with phosphatidylcholine and phosphatidylethanolamine. The products of this reaction are novel dinucleotides. Nicotinamide adenine dinucleotide (NAD) is a coenzyme found in all living cells. (The compound is a dinucleotide, since it consists of two nucleotides joined through their phosphate groups.)
The flipping of one base pair appears to result in Fragile X Syndrome, which is the most common form of mental retardation. It may represent what happens when an atomic-level change in nutrient-dependent energy perturbs protein folding.
For comparison, the nutrient-dependent flipping of a base pair associated with vitamin C uptake in mammals links frugivory in bats via morphological and behavioral phenotypes to their adaptive radiations. Their phenotypes link nutrient-dependent pheromone-controlled reproduction in all vertebrates and invertebrates to morphological and behavioral changes during the development of human preferences for food odors and pheromones.
2) Rather than be quieted by the pseudoscientific nonsense of evolutionary theorists who want others to believe that mutations and natural selection lead to the evolution of biodiversity, ecologists and other serious scientists continue to link biologically-based cause and effect from atoms to ecosystems via the conserved molecular mechanisms of amino acid substitutions that I detailed in my model.
Serious scientists know that models will lead to atomic level (nutrient-dependent) cures for diseases and disorders that evolutionary theorists claim are due to the same molecular mechanisms they think must link mutations to increasing organismal complexity manifested in morphological and behavioral phenotypes of species from microbes to man.
The difference between a serious scientist and a theorist (or any other idiot) is recognized by differences in their beliefs about biologically-based cause and effect. Theorists have no understanding of links between atoms and ecosystems; serious scientists attempt to understand the experimental evidence.
3) In metabolism, nicotinamide adenine dinucleotide is involved in redox reactions, carrying electrons from one reaction to another.
Most organisms synthesize NAD+ from simple components.[2] The specific set of reactions differs among organisms, but a common feature is the generation of quinolinic acid (QA) from an amino acid—either tryptophan (Trp) in animals and some bacteria, or aspartic acid in some bacteria and plants.[21][22] Besides assembling NAD+ de novo from simple amino acid precursors, cells also salvage preformed compounds containing nicotinamide. Despite the presence of the de novo pathway, the salvage reactions are essential in humans; a lack of niacin in the diet causes the vitamin deficiency disease pellagra.[28] This high requirement for NAD+ results from the constant consumption of the coenzyme in reactions such as posttranslational modifications, since the cycling of NAD+ between oxidized and reduced forms in redox reactions does not change the overall levels…
4) Rather than continue to examine facts that link the thermodynamic cycles of protein biosynthesis and degradation from atoms to ecosystems via organism-level thermoregulation, others may want to consider the alternative.
In “Mutation-Driven Evolution” for example, the claim is made that “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.”
That claim is not supported by any experimental evidence of biologically-based cause and effect, but many evolutionary theorists are convinced that the differences in morphology and behavior they can see are due to mutations that perturb protein folding at the level detailed in the Laws of Physics, which lead to everything known about chemistry and Kohl’s Laws of Biology, which are linked to the de novo Creation of olfactory receptor genes via the de novo Creation of RNA and DNA.
Addendum: Anyone willing to accept the fact that RNA and DNA somehow ‘evolved’ or that what’s known about the biophysical constraints that link ecological variation to ecological adaptations via conserved molecular mechanisms in species from microbes to man is not likely to lead to cures for diseases and disorders associated with mutations should participate in discussions on blog sites run by atheistic biology teachers like PZ Myers. For example see: One crank dies, another rises to take his place. Anyone willing to accept the fact that RNA and DNA were Created should examine the content of articles that represent what is known about the Laws of Physics; what is known about chemistry; and what is known about molecular biology. See for example: Darwin vs. Genetics: Surprises and Snags in the Science of Common Ancestry
In the context of biophysically-contrained ecological adaptations it may interest others to learn what is obviously missing from what’s being billed as the Theory of Everything. A theory of everything should have some explanatory power in the context of biologically-based cause and effect that does not link perturbed protein and nutrient-dependent ecological variation to pheromone-controlled ecological adaptations via the same molecular mechanisms. What if Hawkings’ disabled body could be linked from epigenetically-effected RNA and DNA to his highly functional mind? Would others be more interested in biological facts about the de novo Creation of proteins that can be compared to his theory of everything?
What if a nutrient-dependent flip in a single base pair led to amino acid substitutions that differentiate all the cell types of all individuals of all species via conserved molecular mechanisms? Could the link from Fragile X Syndrome and mental retardation be the same as the link to hemoglobin S and nutrient-dependent brain development in someone like you, or like Hawkings? If so, the link is likely to be nutrient-dependent amino acid substitutions that differentiate all cell types in all tissues of all organs in all organ systems of invertebrates and vertebrates via conserved molecular mechanisms of pheromone-controlled reproduction.
We can see the origins of that perspective on autophagy, which was the basis for my works in these two published works.
Effects of Carnitine on Fatty-Acid Oxidation by Muscle (1959)
DEPENDENCE OF RNA SYNTHESIS IN ISOLATED THYMUS NUCLEI ON GLYCOLYSIS, OXIDATIVE CARBOHYDRATE CATABOLISM AND A TYPE OF “OXIDATIVE PHOSPHORYLATION” (1964)
My comment: Both were co-authored by Bruce McEwen. He told me in 1991 that I would need to start with energy-dependent gene activation before my model of cell type differentiation could be completely validated. I did that in the following year with the help of Robert L. Moss and his co-authors in a series of published works that linked pheromones to gene activation in GnRH neurosecretory neurons of the mammalian hypothalamus.

neuronal-plasticity

The quantum biology of consciousness

Everything known about quantum biology “…suggests conscious experience is intrinsically connected to the fine-scale structure of space–time geometry, and that consciousness could be deeply related to the operation of the laws of the universe.” See for review: Consciousness in the universe: A review of the ‘Orch OR’ theory.
These laws of the universe might lead others to think in terms of “laws of biology” (biological laws). Indeed, many informed scientists could expect that ecological, social, and neurogenic niche construction would result in socio-cognitive niche construction, which appears to be a manifestation of increasing complexity in ecologically adapted organisms. For constrast, nothing known about mutations and natural selection leads to any informative explanation of biologically based cause and effect that involves any laws of biology. Evolutionary theory is useless because only biological laws link sensory input from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. Thus, the problem for evolutionary theorists is that cause and effect occur outside the context of the evolution of biodiversity.
In addition, we now know that cause and effect occur within the context of Darwin’s ‘conditions of life.’ See: Quantum biology: Algae evolved to switch quantum coherence on and off. The  news article reports that mutations perturb the function of  amino acid substitutions that link photosynthesis in algae to the laws of biology in other organisms via nutrient-dependent amino acid substitutions. In this report, light is the nutrient.
In other organisms, amino acid substitutions enable ecological adaptations that result from ecological variation, which includes variation in light linked to ecological adaptations manifested in eyes and in eye regression in blind cave fish. However,  these ecological adaptations are perturbed by mutations. Thus, attributing either the evolution of eyes or eye regression to mutations is a false attribution.
In the context of the quantum biology of consciousness, “They found that in two species a genetic mutation has led to the insertion of an extra amino acid that changes the structure of the protein complex, disrupting coherence.” This suggests that in all animals, the amino acid substitutions appear to link cell type differentiation via nutrient uptake and metabolism to species specific pheromones that control the physiology of reproduction.
Everything known about the photosynthetic, micronutrient, and macronutrient pathways that link ecological variation via base pair changes to ecological adaptations shows that mutations perturb the protein folding that is required for niche construction to result in increasing organismal complexity via amino acid substitutions. Mutations simply cannot result in the organismal complexity manifested in organisms with eyes.
For contrast, see: Evolution of the first genetic cells and the universal genetic code: A hypothesis based on macromolecular coevolution of RNA and proteins “The origin of homochiral amino acids and sugars is assessed. The integrated development of the Universal Genetic Code in shown in eight steps. Mutation rates limited the sizes of early nucleic acid genomes to about 200 bases.”
In the context of Kohl’s Laws of Biology, achiral glycine links the nutrient-dependent pheromone-controlled stabilized genomes of yeasts and mammals via the conserved molecular mechanisms of RNA-mediated amino acid substitutions. See:  Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems. Perhaps it will shed light on how the nutrient-dependent pheromone-controlled physiology of reproduction in algae is connected across species via amino acid substitutions in organisms from microbes to man. But, even if you are unable to see the light, there is still no experimental evidence that links it (e.g., the light) as a nutrient source to nutrient-dependent pheromone-controlled ecological adaptations.
As I said once before: “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.”
See also: ‘Quantum smell’ idea gains ground” Let there be light as a nutrient source for life and cell type differentiation via amino acid substitutions — as noted by Dobzhansky (1973): Nothing in Biology Makes Any Sense Except in the Light of Evolution. As it turned out, nothing about evolution makes sense except in the light of what’s known about light as the first nutrient source for ecological variation and ecological adaptations. For comparison, mutation-driven evolution is pseudoscientific nonsense. Sunlight, for example, alters levels of the steroid hormone vitamin D, which stabilizes the genome of human populations in areas where malarial parasites forced the nutrient-dependent ecological adaptation of lactose persistence.