Plenty of Room at the Bottom

Environmental selection is natural selection (2)

I believe that if you put enough biologically uniformed theorists in the same room, they will invent more theories to support the pseudoscientific nonsense they have touted in the past. See for example:

Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk

Acknowledgments

The synthesis presented here is a product of the American Association for the Advancement of Science’s 2017 annual meeting, as the ideas came together in the session entitled “Beringia and the Dispersal of Modern Humans to the Americas.”
 

Every aspect of every level of biophysically constrained food energy-dependent biologically-based cause and effect is placed back into the context of a ridiculous theory of human migration and evolution. The theory accurately attests to the link from one food energy-dependent base pair change to biodiversity in human populations via fixation of one amino acid substitution. But then, something goes horribly wrong.

The theory requires the fixation of the amino acid substitution to automagically occur in the context of the sun’s anti-entropic virucidal energy. The theory fails to mention the fact that the physiology of pheromone-controlled reproduction and the microRNA-mediated creation of all cell types in all living genera is required.

See for comparison: Anything published since the time I learned about the importance of microRNAs during the 2012 Society for Neuroscience annual meeting in New Orleans, LA.

From 2000/10/15 to 2012/10/15 microRNA Items: 1 to 20 of 19910

From 2012/10/15 to 2018/04/26 microRNA Items: 1 to 20 of 53458

The number of biologically informed serious scientists who have linked the energy-dependent creation of microRNAs to biophysically constrained viral latency and all biodiversity via the pheromone-controlled physiology of reproduction in bacteria continues to rapidly increase.

This begs the question: When will biologically uninformed science idiots stop attending meetings that facilitate their attempts to invent more ridiculous theories?

Biology to a Physicist

Abiogenesis vs microRNA biogenesis

Summary: The pseudoscientific nonsense about abiogenesis that has been touted by Karo Michaelian and others like him has caused the unnecessary suffering and premature death of millions to billions of people by placing the pathogenic consequences of deregulated miRNAs into the context of ridiculous theories.
See for comparison: Structural diversity of supercoiled DNA and the parody from the same research group:
——————————-
Abiogenesis (2017)
Microscopic dissipative structuring and proliferation at the origin of life (Oct 13, 2017)

Some fundamental molecules of life are suggested to have been formed, proliferated, and evolved through photochemical microscopic dissipative structuring and autocatalytic proliferation under the UV-C/UV-B solar environment prevalent at Earth’s surface throughout the Archean. Evidence is given in the numerous salient characteristics of these, including their strong absorption in this spectral region and their rapid non-radiative excited state decay through inherent conical intersections. The examples of the dissipative structuring and dissipative proliferation of the purines and of single strand DNA are given. UV-C and UV-B-induced stationary state isomerizations and tautomerizations are shown to be crucial to the formation of the purines from hydrogen cyanide in an aqueous environment under UV-C light, while UV-C induced phosphorylation of nucleosides and denaturing of double helix RNA and DNA are similarly important to the production and proliferation of single strand DNA. This thermodynamic dissipation perspective provides a physical-chemical foundation for understanding the origin and evolution of life.

The suggestion is ridiculous. No serious scientist would claim that some fundamental molecules of life formed, proliferated, and evolved in the context of thermodynamic dissipation after the UV-C induced phosphorylation of nucleosides and denaturing of double helix RNA and DNA.
The functional structure of supercoiled DNA is energy-dependent.
All serious scientists start with the link from the sun’s anti-entropic virucidal energy on contact with water to the creation of ATP synthase; the creation of microRNAs; the creation of all other enzymes; the creation of all receptors; the creation of all hormones. That’s how serious scientists link microRNA biogenesis to all biophysically constrained food energy-dependent pheromone-controlled morphological and behavioral diversity on Earth.
MicroRNA biogenesis (2018)

The tipping point of 72,000 indexed published works that mention microRNAs was reached on 4/18/18
See: microRNA
Example: Arthropod viruses and small RNAs (2013)

Understanding the role of small RNAs in arthropod host-virus molecular interactions will facilitate manipulation of these pathways for both management of arthropod pests of agricultural and medical importance, and for protection of beneficial arthropods such as honey bees and shrimp. This review highlights recent research on the role of small RNAs in arthropod host-virus interactions with reference to other host-pathogen systems.

Example: MicroRNAs as mediators of insect host-pathogen interactions and immunity (2014)

In this review, we will discuss the latest developments in regards to the role of microRNA in insect host-pathogen interactions and provide some insights into this rapidly developing area of research.

Example: miRNA regulation of innate immunity (2018)

MicroRNAs (miRNAs) are small noncoding RNA and are pivotal posttranscriptional regulators of both innate and adaptive immunity. They act by regulating the expression of multiple immune genes, thus, are the important elements to the complex immune regulatory network. Deregulated expression of specific miRNAs can lead to potential autoimmunity, immune tolerance, hyper-inflammatory phenotype, and cancer initiation and progression. In this review, we discuss the contributory pathways and mechanisms by which several miRNAs influence the development of innate immunity and fine-tune immune response. Moreover, we discuss the consequence of deregulated miRNAs and their pathogenic implications.

The pseudoscientific nonsense touted by Karo Michaelian and others like him has caused the unnecessary suffering and premature death of millions to billions of people by placing the pathogenic consequences of deregulated miRNAs into the context of ridiculous theories.
See for comparison: Structural diversity of supercoiled DNA and the parody from the same research group:

See also: Michaelian K
and Retraction: Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication (Nov 23, 2017)
The life’s works of all those who have ever touted their ridiculous claims about abiogenesis can now be placed into the context of the eternal significance of microRNAs. The energy dependent de novo creation of microRNA flanking sequences has repeatedly been linked from the physiology of pheromone-controlled reproduction to biophysically constrained viral latency and sympatric speciation in all living genera.
See: 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.

See also: Long-range coherence and energy storage in biological systems (1968)
See also: Cytosis (for ages 10+)

Players take turns placing workers on available organelles within a human cell in order to collect resources (such as Carbohydrates or ATP!) or take actions (such as purchasing Cell Component cards or translating mRNA into Proteins!)

Players use their resources to build Enzymes, Hormones, and Hormone Receptors and also to help detoxify the cell – all of which score health points. The player with the most health points at the end of the game wins!

See for comparison: DNA Denaturing through UV-C Photon Dissipation: A Possible Route to Archean Non-enzymatic Replication (2014)

Many of the fundamental molecules of life, those common to all three domains; bacteria, eukaryote, and archea, including RNA and DNA, amino acids, enzymes, vitamins, cofactors, and protoporphyrins, absorb photons in the UV-C 1. RNA or DNA in complexes with these molecules act as acceptor quenchers, providing the electronically excited pigment donor molecule with an extremely rapid (sub picosecond) non-radiative dexcitation channel, through internal conversion into vibrational energy of the nucleic acid and surrounding water molecules2.

On January 15, 2016 John Hewitt commented:  You have just described the founding principle and thermodynamic function of life
On April 17, 2018, I commented on the ridiculous claim this so-called science journalist made because he blocked me from seeing his tweets a few months ago.

Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

Sympatric Speciation vs Pseudoscientific Nonsense (1)

Summary: The “Science Behind the Game” from the cell biology game “Cytosis” supports all claims that clearly link energy-dependent alternative splicings of pre-mRNAs (aka microRNAs) to biophysically constrained viral latency. Game play by ages 10+ establishes the requirement for viral latency in the context of ecological variation and ecological adaptation outside the context of neo-Darwinian pseudoscientific nonsense. Simply put, Darwin presciently placed his “conditions of life” into the current perspective on ecological niche construction and sympatric speciation, which exemplifies ecological adaptation in all living genera.
For a historical perspective, see:
1996 From Fertilization to Adult Sexual Behavior

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.

For obfuscation of our claims about cause and effect, which have since been linked to all biodiveristy, see: Altered microRNA expression and pre-mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infection (2016)
Simply put, no new mechanisms were revealed. The well-known mechanisms of energy-dependent pheromone-controlled biophysically constrained RNA-mediated cell type differentiation were simply placed into the context of more unintelligible rhetoric.
See for comparison: 2013 Alternative splicings and amino acid substitutions (redux)
Tracking niche variation over millennial timescales in sympatric killer whale lineages

Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].

The differences in amino acid composition among different tissues can lead to large differences in trophic discrimination [38].

For more information on the current perspective, which is the same as the historical perspective, see:
2018 Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

…speciation of rorqual evolution occurred under gene flow, which is best depicted by evolutionary networks. Especially in marine environments, sympatric speciation might be common; our results raise questions about how genetic divergence can be established.

Reported as: Baleen Whale Genomes Point to Evolution With Gene Flow

Large baleen whales in the Balaenopteridae family (commonly known as rorqual whales) have undergone sympatric speciation — speciation without clear geographic barriers between them — despite ongoing hybridization…

See also: May, 2015 Riding the Evolution Paradigm Shift With Eugene Koonin

The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…

See also: August, 2015 Eibi Nevo: Evolution, Let’s Get It Right, It’s the “Basis of Everything”

Viruses are the dynamo of change that we see in the modern genome. . . .

Cytosis_Booklet_Science.pdf (63 KB) (Log in or Register [for free] to download.) The “Science Behind the Game” from the cell biology game “Cytosis” supports all claims that clearly link energy-dependent alternative splicings of pre-mRNAs (aka microRNAs) to biophysically constrained viral latency. Game play by ages 10+ establishes the requirement for viral latency in the context of ecological variation and ecological adaptation outside the context of neo-Darwinian pseudoscientific nonsense. Simply put, Darwin presciently placed his “conditions of life” into the current perspective on ecological niche construction and sympatric speciation, which exemplifies ecological adaptation in all living genera.
Cytosis is described as: A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!
The collaborative efforts of 20 serious scientists who validated the details in the game include the mention of Stephen J. Bush. See: Bush, SJ et al., (2017) Alternative splicing and the evolution of phenotypic novelty

Alternative splicing, a mechanism of post-transcriptional RNA processing whereby a single gene can encode multiple distinct transcripts, has been proposed to underlie morphological innovations in multicellular organisms. Genes with developmental functions are enriched for alternative splicing events, suggestive of a contribution of alternative splicing to developmental programmes. The role of alternative splicing as a source of transcript diversification has previously been compared to that of gene duplication, with the relationship between the two extensively explored. Alternative splicing is reduced following gene duplication with the retention of duplicate copies higher for genes which were alternatively spliced prior to duplication. Furthermore, and unlike the case for overall gene number, the proportion of alternatively spliced genes has also increased in line with the evolutionary diversification of cell types, suggesting alternative splicing may contribute to the complexity of developmental programmes. Together these observations suggest a prominent role for alternative splicing as a source of functional innovation. However, it is unknown whether the proliferation of alternative splicing events indeed reflects a functional expansion of the transcriptome or instead results from weaker selection acting on larger species, which tend to have a higher number of cell types and lower population sizes.

This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
See for comparison: Retraction: Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication
Reported as: RNA Replication Paper Retracted 
Szostak and others got busted for their pseudoscientific nonsense about non-enzymatic emergence by someone who understands quantized energy as information-dependent RNA-mediated top-down causation. People over age 10+ who play the cell biology game “Cytosis” may now force all biologically uninformed theorists to retract their claims, which typically have been placed into the context of mutation-driven evolution.

http://nnjournal.net/article/viewFile/2354/1850/10234

The MicroRNAome Strikes Back: A Sokalian hoax (5)

Premise: Sunlight is the quantized energy as information that is required to link endogenous RNA interference to healthy longevity (The energy-dependent creation of microRNAs links the physiology of reproduction from changes in electrons to ecosystems in all living genera via the creation of ATP, RNA, and supercoiled DNA in organized genomes.)
Counter claim:  The Quantum Thermodynamics Revolution: Information theory
Understanding entropy as a subjective measure allows the universe as a whole to evolve without ever losing information.
See, for comparison: On causal roles and selected effects: our genome is mostly junk 

The title is misleading, but this claim is not.

Selection is involved in such a story, but it is purifying selection against the loss of a component or activity (the chaperone), not positive selection for its presence.

Natural selection for food energy-dependent reproduction is purifying selection. I’ve already cited Frohlich (1968) in that regard. his proposals are no longer speculative. Purifying selection links the speed of light on contact with water to the creation of microRNAs that biophysically constrain the epigenetic effects of  food odors and pheromones via the creation of enzymes.

The epigenetic effects of food odor and pheromones on the creation of energy-dependent microRNAs and enzymes prevent the virus-driven degradation of messenger RNA in all living genera. The virus-driven theft of quantized energy degrades the enzymes linked to the degradation of messenger RNA and gene losses.

I am not the only one who knows that, but few others seem willing to admit that energy is required to create new genes. For example, here the authors make a claim about de novo assemblies of genomes.

See: The phylogenetic utility and functional constraint of microRNA flanking sequences

Both miRNAs and their flanking sequences provide phylogenetic signals suitable for the inference of phylogeny with high levels of accuracy, when sufficient numbers of this type are concatenated. As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.

De novo assemblies of geneomes and inferred phylogeny are linked to the slow evolution of microRNAs and microRNA flanking sequences. If I thought the authors were not serious about that ridiculous claim, I would have reported their work in the context of another Sokalian hoax. They eliminated the need for the energy-dependent creation of the microRNAs and the biophysical constraints on viral latency, but I think they seriously considered the de novo assembly of genomes to be possible. Indeed, to some theorists, the creation of new genes is like the magic of evolution.

Instead, I wrote: My comment to Science published at 2:54 pm on 1/29/15 

The 2015 Society for Integrative and Comparative Biology (SICB) presenters may not recognize how much progress has been made since the 2013 ecological epigenetics symposium. For example, since then authors claimed “…ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.” 

Six months later, other authors traced signaling factors found in vertebrates to the origin of nerve cell centralization via the diffuse nerve net of animals like the sea anemone.  That fact suggests ecological variation is linked to ecological adaptations in morphological and behavioral phenotypes via signaling protein concentrations that differentiate various cell types in body axes and the central nervous system.

Links across species from the epigenetic landscape to the physical landscape of DNA in organized genomes appear to have their origins in the conserved molecular mechanisms of RNA-directed DNA methylation and RNA-mediated protein folding. Two weeks after the publication that refuted ideas about independently evolved neural systems or muscle specification — and perhaps refuted the independent evolution of anything else, SICB presenters linked crustaceans to insects.

Apparently, they’ve learned that the same set of microRNAs controls expression of the genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans.

Why were they left with any questions about how crustaceans and insects could all be part of one big family? They linked RNA-mediated cell type differentiation to what we described in our section on molecular epigenetics in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior 

Instead of natural selection for the food energy-dependent protection of RNA and supercoiled DNA, this gene-centric pseudoscientific nonsense emerged on January 25, 2018, from the depths of theorist’s ignorance. (At times it seems that a conspiracy theory is linked from the insane ignorance of biologically uninformed theorists, to my insane obsession with disseminating facts.)

The new findings are in agreement with recent genetic studies that show changes in genes related to brain development in our lineage since the population split between Homo sapiens and Neandertals. They add to the accumulating archeological and paleoanthropological evidence demonstrating that Homo sapiens is an evolving species with deep African roots and long-lasting gradual changes in behavioral modernity, brain organization, and potentially brain function.

For comparison to experimentally established fact about selection for energy-dependent reproduction, archeological and paleoanthropological evidence suggests that genes emerged and that they automagically led to “…long-lasting gradual changes in behavioral modernity, brain organization, and potentially brain function.”

I have consistently failed to grasp the logic of  claims that fail to link what is known to serious scientists about the microRNAome to food energy-dependent “…long-lasting gradual changes in behavioral modernity, brain organization…” and biophysically constrained viral latency linked to brain function.

For instance, all organisms can find food without the energy-dependent creation of G protein-coupled photoreceptors. But the energy as information-dependent de novo creation of microRNAs, enzymes and  G protein-coupled receptors is required to linke for food odors and pheromones from pH-taxis to chemotaxis in all species that must forage to find food and reproduce.
All individuals of all species must also enzymatically metabolize the food to species-specific pheromones, which have consistently been linked, since the time of our 1996 review: From Fertilization to Adult Sexual Behavior, to epigenetically-effected sex differences in behavior in species from yeasts to mammals via the conserved molecular mechanisms of chromosomal rearrangements and the transgenerational epigenetic inheritance of all morphological and behavioral phenotypes.
It is time to watch very closely for more Sokalian hoaxes as the Inter-kingdom communication mechanisms mediated by non-coding RNAs (e.g, pre-mRNAs or microRNAs) are placed back into the context of claims about what supposedly has not been known to all serious scientists for more than 25 years.

The Expressed MicroRNA—mRNA Interactions of Toxoplasma gondii 4 Jan 2018

MicroRNAs-Based Inter-Domain Communication between the Host and Members of the Gut Microbiome 27 Sep 2017

Microbiota-Derived Extracellular Vesicles as New Systemic Regulators 24 Aug 2017

HIV-1 Nef Signaling in Intestinal Mucosa Epithelium Suggests the Existence of an Active Inter-kingdom Crosstalk Mediated by Exosomes 08 June 2017

Viruses and miRNAs: More Friends than Foes 15 May 2017

In summary, we are far from fully understanding the molecular mechanisms underlying the complex crosstalks between miRNA pathways and viral infections.

New Insight into Inter-kingdom Communication: Horizontal Transfer of Mobile Small RNAs 01 May 2017

The Role of HCMV and HIV-1 MicroRNAs: Processing, and Mechanisms of Action during Viral Infection 21 April 2017

Gut Microbiota as a Trigger of Accelerated Directional Adaptive Evolution: Acquisition of Herbivory in the Context of Extracellular Vesicles, MicroRNAs and Inter-Kingdom Crosstalk 20 April 2017

Linking Diet to Colorectal Cancer: The Emerging Role of MicroRNA in the Communication between Plant and Animal Kingdoms 05 April 2017

Non-coding RNAs in Host–Pathogen Interactions: Subversion of Mammalian Cell Functions by Protozoan Parasites 21 March 2017

Small Luggage for a Long Journey: Transfer of Vesicle-Enclosed Small RNA in Interspecies Communication 16 March 2017

Exo-miRExplorer: A Comprehensive Resource for Exploring and Comparatively Analyzing Exogenous MicroRNAs 01 February 2017

The Development of Our Organ of Other Kinds—The Gut Microbiota 23 Dec 16

See for comparison: Big Strides in Cellular MicroRNA Expression

A lack of knowledge of the cellular origin of miRNAs has greatly confounded functional and biomarkers studies. Recently, three studies characterized miRNA expression patterns across >78 human cell types. These combined data expand our knowledge of miRNA expression localization and confirm that many miRNAs show cell type-specific expression patterns.

There is no lack of knowledge about the quantized energy-dependent creation of microRNAs, which are now used as biomarkers of healthy longevity for comparison the the number of viral microRNAs, which is linked to pathology in species from bacteria that become archaea and humans that become non-human primates in the context of one or more base pair changes and fixation, or not, of one RNA-mediated amino acid substitution.
Here’s the problem: 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
See for comparison: Energy as information and constrained endogenous RNA interference (4)
Watch what happens when so-called science journalists wake up and recognize the Sokalian hoax.

For God and Country

The "walking fish" walks straight from quantum physics to quantum souls

Happy New Year! In 2018, serious scientists are prepared to help you prevent or effectively treat all pathology. We have nearly stopped the pseudoscientific nonsense touted by theorists — although some of them didn’t get the memo from 1968, which is when Frohlich published: Long-range coherence and energy storage in biological systems.
He linked certain processes in living systems from the creation of energy to hydrogen bonds in cell membranes and to dipolar oscillations that link the creation of the sense of smell in bacteria from the physiology of pheromone-controlled reproduction to all biodiversity via the creation of ATP; the creation of RNA, and fixation of energy-dependent RNA-mediated amino acid substitutions.
See: The vibrational theory of olfaction for the win
Historical perspective, based on Frohlich’s “speculation.”
From Fertilization to Adult Sexual Behavior (1996)

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation…

The sexual differentiation of cell types protects them from the virus-driven theft of quantized energy, which Frohlich linked to the degradation of the cell wall and what is now known about how unicellular bacteria become archaea before they become L-forms.
See: 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!

Food energy-dependent pheromone-controlled biophysically constrained viral latency keeps egg cells fresh in the context of autophagy and sexual differentiation. Biophysical constraints prevent the transgenerational epigenetic inheritance of virus-driven pathology, which is caused by the virus-driven theft of quantized energy that links the degradation of messenger RNA to all pathology.
See for comparison: Keeping egg cells fresh with epigenetics (2017)
As soon as the Medical Xpress news source realized that they had destroyed neo-Darwinian pseudoscientific nonsense with their report on epigenetics, the post went missing.

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Sorry, the page you were looking for could not be found.

The page might have been removed, had its name changed, or become temporarily unavailable.

They cited: Courtney W. Hanna et al, MLL2 conveys transcription-independent H3K4 trimethylation in oocytes, Nature Structural & Molecular Biology (2017). DOI: 10.1038/s41594-017-0013-5
The cited work is not yet available at the DOI: I attempted to add this comment:
The speed of light on contact with water links food energy to the physiology of pheromone-controlled reproduction and all biophysically constrained biodiversity. Now, there is a mathematical model that refutes neo-Darwinism and “Big Bang” cosmology. Use it to make all biologically uninformed theorists recognize their foolishness. Quantum Vacuum Dynamics, Coherence, Superluminal Photons and Hypercomputation in Brain Microtubules
The human idiocy exposed by Courtney W. Hanna et al (2017?) was also exposed at least twice in September. See: Striking a balance: regulation of transposable elements by Zfp281 and Mll2 in mouse embryonic stem cells Published online 2017 Sep 25

Transposable elements pervading mammalian genomes mostly originate from retrotransposons, including long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), and endogenous retroviruses (ERVs) (,). Retrotransposons shape host genome landscape and evolution through introducing, deleting or modifying cis-regulatory elements or genes (,). However, they can also induce detrimental genome instability and numerous human diseases (,).

The claim that retrotransposons shape host genome landscape and evolution is a ridiculous claim. Food energy links ecological variation to ecological adaptations via the pheromone-controlled physiology of reproduction in all living genera. Nothing links retrotransposons to evolution because viral latency must be biophysically constrained in the context of increasing organismal complexity.
See also: Genomic imprinting beyond DNA methylation: a role for maternal histones 2017 Sep 19

Sperm and oocytes exhibit different patterns of chromatin organisation: the sperm DNA is highly methylated and tightly packaged, with protamines replacing most canonical histones, while the oocyte genome has a bimodal methylation pattern, an extensively open chromatin conformation and atypical patterns of histone modifications [].Methylation and chromatin organization are food energy-dependent and biophysically constrained in the context of the physiology of pheromone-controlled reproduction and the space-time continuum.

See why Feynman was forced to comment on the facts about food energy, years before this information became generally known: Trinucleotide Repeats: Fragile X Syndrome

DNA (deoxyribonucleic acid)… contains a “code” of 3-letter words known as “codons” or “trinucleotides.” Many genes normally contain trinucleotide sequences that can be repetitive. These are called “trinucleotide repeats.” But when the number of trinucleotide repeats increases to a larger than normal number of copies, the DNA is changed. The gene may not function as it should, or may not work at all.

…extra trinucleotide repeats cause the DNA to become unstable, the repeats within that gene expand even more. The result is that the child has a gene that is not functioning properly (if at all), and the child is said to have the “full mutation.” An example of a trinucleotide repeat disorder is Fragile X syndrome.

See also: Researchers discover how cells remember infections decades later

On the surface and through the actions of their genes, they look like cells that have never been exposed to an infection, but on their DNA the researchers found a fingerprint, called a methylation pattern, that identifies them as having been through battle as an infection-fighting cell, which are called effector cells.

Thanks to passive-aggressive antagonist Jon Lieff for repeatedly bringing the difference between pseudoscientists and serious scientists to my attention. Pseudoscientists refer to “effector cells” so that the obvious link from food energy to autophagy to healthy longevity is obfuscated.
See for instance: Ancient Mutation may Help Explain Origin of Human Organs

1) Researchers have reported that a neutral mutation having no real purpose and occurring randomly over 700 million years ago may help to explain the origins of complex structures like organs in humans and other vertebrates.

The pseudoscientific nonsense reported by Labroots may have reached its peak.

2) The same gene can give rise to different proteins that can act in entirely different ways by editing those genes a little differently, in a phenomenon called alternative splicing…

A link to a video about alternative splicing is included; See: Alternative Splicing
Conclusion: 

“The new discovery confirms how versatile biological evolution is: the same foundation and gene tools can be used to build a wood cabin or a skyscraper,” concluded Garcia-Fernàndez.

There is no such thing as versatile biological evolution. It is long past time for serious scientists to stop the pseudoscientific nonsense touted by theorists.
For a reminder of how long serious scientists have known the facts about alternative splicing, see again:
From Fertilization to Adult Sexual Behavior (1996)

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation…

Alternative splicing is food energy-dependent and RNA-mediated in the context of the physiology of pheromone-controlled biophysically constrained viral latency.
All niche construction is food energy-dependent and controlled by the physiology of reproduction.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

This model details how chemical ecology drives adaptive evolution via: (1) ecological niche construction, (2) social niche construction, (3) neurogenic niche construction, and (4) socio-cognitive niche construction.

This model organism exemplifies how ecological variation must be linked to ecological adaptation in species from microbes to humans. See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

Under strong selection for motility, these bacteria consistently regained flagella within 96 hours via a two-step evolutionary pathway. Step 1 mutations increase intracellular levels of phosphorylated NtrC, a distant homolog of FleQ, which begins to commandeer control of the fleQ regulon at the cost of disrupting nitrogen uptake and assimilation. Step 2 is a switch-of-function mutation that redirects NtrC away from nitrogen uptake and toward its novel function as a flagellar regulator. Our results demonstrate that natural selection can rapidly rewire regulatory networks in very few, repeatable mutational steps.

This was reported in the context of the classic phrase from the Jurrasic Park series of movies: Life finds a way (video)
The claim that life finds a way to resurrect the bacterial flagellum over the weekend via mutations can be compared in the context of this model organism. See: The Axolotl Limb Regeneration Model as a Discovery Tool for Engineering the Stem Cell Niche

…this model has identified a number of proregenerative signals, including growth factor signaling associated with nerves, and signals associated with the extracellular matrix (ECM) that induce pattern formation.

Educational video: Meet the creature that can regenerate its brain and resist cancer.
At the end of the video, the yin yang symbol from Chinese philosophy is superimposed over the electron cloud, which links the anti-entropic virucidal energy of sunlight to the physiology of pheromone-controlled reproduction and the viral latency that protects all organized genomes from the degradation of messenger RNA.
The virus-driven degradation of messenger RNA is clearly the link from mutations to all pathology, and all pathology can be examined in the context of the axolotyl model organism (aka: The “walking fish.”)
The portrayals of the “walking fish” as an example of neo-Darwinian evolution is a ridiculous example of what Feynman called human idiocy. Darwin place his “conditions of life” before natural selection because he knew that organisms must eat and reproduce. Neo-Darwinists assumed that the 2nd Law of Thermodynamics did not need to include any aspect of quantum entanglement.
Energy-dependent changes have since been linked from electrons to ecosystems by autophagy — the innate antiphage defense mechanism.
The defense mechanism protects the cell types of axolotyl and all other living genera from the virus-driven energy theft that links the destruction of the cell wall from bacteria to archaea and to L-forms, the last example on Earth of virus-driven energy theft and failed autophagy.

 
Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

A null mutation and healthy longevity?

Summary: Food odors and pheromones biophysically constrain all pathology in species from microbes to humans. What kind of biologically uninformed science idiot leaves out everything known to serious scientists about the virus-driven degradation of messenger RNA and tells others they must falsify the neutral null theory that led to claims about a biophysically constrained beneficial “null mutation” in the Amish population of Berne, Indiana?
Glutamylation Regulates Transport, Specializes Function, and Sculpts the Structure of Cilia
Reported as: How to Control Traffic on Cellular Highways

Intracellular and extracellular traffic control

Reported in: How to control traffic on cellular highways http://neurosciencenews.com/enzyme-transportation-7915/

See for comparison: A null mutation in SERPINE1 protects against biological aging in humans
Reported as: Amish gene can make them live 10 years longer and avoid diabetes

A gene variant that arose decades ago in an Amish group…

All gene variants are quantized energy-dependent and the pheromone-controlled physiology of reproduction protects all organized genomes from the virus-driven degradation of messenger RNA. The degradation of messenger RNA links mutations to all pathology. Any claim that “a gene variant arose” is a claim made by a biologically uninformed science idiot. Gene variants in humans are biophysically constrained by the availability of food energy. Other humans may not know that.
Watch and listen to Richard P. Feynman presciently claim that the “null mutation” theory of healthy longevity is an example of “human idiocy.”

Help others to find any experimental evidence that suggests a “null mutation” can be beneficial and/or protect them from biological aging. See for alternative representations of biologically-based facts: Best matches for “null mutation“: and others.
If you cannot find experimental evidence of a beneficial “null mutation” see: Consciousness in the universe: A review of the ‘Orch OR’ theory They inadvertently linked quantum physics from consciousness to quantum souls.
Reported as: Anesthesia Points to Deeper Level ‘Quantum Channels’ as Origins of Consciousness subtitle “Electron resonance pervades the brain”

“Using molecular modeling, the US-Canadian team of Travis Craddock, Stuart Hameroff and Jack Tuszynski had previously shown anesthetic binding in ‘quantum channels’, non-polar arrays of amino acid pi resonance clouds, winding through microtubules.”

See also: The vibrational theory of olfaction for the win

The same kinds of amino acid substitutions that control the separations and interactions of side chains in fluorescent proteins also play an essential role in tuning the proposed mechanism for vibration detection—inelastic electron tunneling. Life literally runs on electron tunneling through the respiratory chain complexes in mitochondria.

For comparison, see the conclusion to: Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 2
Beneficial “null mutations” can now be placed into the context of the creation of a universe that — with or without us — is always watching, like Santa Claus.
For a historical perspective on that pseudoscientific nonsense, see:
Splendor and misery of adaptation, or the importance of neutral null for understanding evolution

To claim adaptation, the neutral null has to be falsified.

A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis… — Eugene Koonin
What kind of biologically uninformed science idiot leaves out everything known to serious scientists about the virus-driven degradation of messenger RNA and tells others they must falsify the neutral null theory that led to claims about a biophysically constrained beneficial “null mutation” in the Amish population of Berne, Indiana?
Food odors and pheromones biophysically constrain all pathology in species from microbes to humans.
See for comparison: Chemosignals from isolated females have antimutagenic effect in dividing the cells of bone marrow from male mice of the CBA strain

…specific, volatile, and zoosocial important chemosignals are a promising approach both to modeling posttraumatic stress disorders in humans [36] and to searching for mehods of their treatment.

Humans also have various pheromone-induced physiological effects, especially those associated with reproduction [46, 47]. This suggests that the human olfactory system is still an effective pathway for influencing environmental factors on the human nervous
system.

[46] is Kohl, J.V., Atzmueller, M., Fink, B., and Grammer, K., Human pheromones: integrating neuroendocrinology and ethology, Neuroendocrinol. Lett., 2001, vol. 22, pp. 309–321.
See also: Cytogenetic approaches for determining ecological stress in aquatic and terrestrial biosystems

The assessment of genomes’ integrity plays the key role in the studies of mutagenicity in a polluted environment. We present a step-by-step recommendations for the analysis of the cytogenetic data and discuss the prospects of applying genetic tests for ecological monitoring, based on the example of analysis using crustacean species.

I suspect that the manufacturer of my human pheromone-enhanced fragrance products asked to speak with me next week due to the all-to-obvious link from human pheromones to biophysically constrained viral latency and the prevention of all pathology, which was detailed in the context of the creation of sunlight, which was subsequently linked from the creation of ATP to the creation of RNA.
Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis
The last time I spoke with him, he asked how to monetize the facts. Bergdhal’s pathology may have prompted renewed interest. Attempts to discuss that fact with other veterans have failed. I think that some of them would rather see him crucified rather than link the energy-dependent weekend resurrection of the bacterial flagellum in P. fluorescens to the the energy-dependent Resurrection of Christ.
Bergdhal’s pathology can also be placed into the context of the problematic transitions from adolescence to adulthood that are altered by fixation of one energy-dependent RNA-mediated amino acid substitution.
See: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
The A or Met allele is associated with lower enzymatic activity and the polymorphism is associated with many different personality traits. The USAF is leading the way forward towards effective treatment of mental disorders in veterans, which is something the psychiatrists who evaluated Bergdhal know about.  See for instance: US Air Force Studying Impact of Exome Sequencing in Routine Care
 

Alternative splicing of pre-mRNA

The billion dollar baby (revisited)

Summary: All energy-dependent differences in the microRNA/messenger RNA balance have now been linked from the physiology of pheromone-controlled reproduction to all morphological and behavioral phenotypes by the conserved molecular mechanisms of RNA-mediated cell type differentiation.

FDA Approves Treatment That Modifies Patient’s Own Genes To Fight Cancer

It costs $475,000 and the treatment could kill you.
Discussion attempt 

Keep in mind that you could have stopped this. Now, you either continue to play their game, or play the cell biology game “Cytosis” when it becomes available next month.

All pathology, including all cancer is caused by the virus-driven degradation of messenger RNA. If you can’t afford the $475,000 treatment, learn how to prevent all pathology.

See: Cytosis: A Cell Biology Board Game

Biologically uninformed science idiots cannot link CAR-T from microRNAs to the cure for John McCain’s glioblastoma. Only serious scientists and those who play the game “Cytosis” can do that.

See for example: Regression of Glioblastoma after Chimeric Antigen Receptor T-Cell Therapy

See also: Expression of miR-17-92 enhances anti-tumor activity of T-cells transduced with the anti-EGFRvIII chimeric antigen receptor in mice bearing human GBM xenografts

It will become obvious to all serious scientist that microRNA therapy is the treatment that will control or cure John McCain’s glioblastoma and that the effective treatment must be placed into the context of the unaffordable CAR-T cell treatment. Otherwise too many people would recognize the fact that all pathology is caused by the virus-driven degradation of messenger RNA.

I’m sure the obfuscation is due to the plan to deliver this billion dollar baby “RNAi has targeted exogenous genes in models of viral infection…” Naturally occurring endogenous RNAi prevents the virus-driven degradation of messenger RNA, which links mutations to all pathology. That fact confirms claims that the “billion dollar baby” is a repackaged CAR-T version of microRNA-mediated treatments. Those treatments clearly link food energy from what organisms eat to all healthy longevity via the physiology of reproduction — not via mutations and evolution.

That fact is a problem for medical professionals who make more money from ineffective treatments than from prevention or from effective treatments based on the practice of Precision Medicine. But, it isn’t their fault. They were taught to believe in ridiculous neo-Darwinian theories and can’t accept the facts about Darwin’s “conditions of life” or Schrodinger’s claims in “What is Life?” (1944).

See also:

See also: Viral effects on the content and function of extracellular vesicles

Search Results for “”billion dollar baby””

The transgenerational epigenetic inheritance of all morphological and behavioral phenotypes is energy-dependent and RNA-mediated. Endogenous RNA inference (RNAi) protects all organized genomes from virus-driven entropy.
See also:

See also: Threonine and Methionine Are Limiting Amino Acids for Protein Synthesis in Patients with AIDS
From 1998:

Understanding the changes in protein and amino acid metabolism in HIV infection is crucial because they underlie the loss of protein (i.e., of lean tissue). Measurements of amino acid kinetics in AIDS patients have shown the characteristic features of a hypermetabolic response with increased protein turnover (Lieberman et al. 1994, Macallan et al. 1995, Stein et al. 1990). In addition, the degradation of tryptophan via the kynurenine pathway is stimulated (Werner et al. 1988), and sulfur amino acids and glutathione metabolism are altered (Buhl et al. 1989, Eck et al. 1989, Hortin et al. 1994).

Stop the nonsense. Serious scientists have known for at least two decades that the prevention of all virus-driven messenger RNA degradation and all pathology is nutrient energy-dependent in the context of RNA-mediated pheromone-controlled epigenetic inheritance.

From 1996 From Fertilization to Adult Sexual Behavior see our section on molecular epigenetics.

Molecular epigenetics. It is now understood that certain genes undergo a process called “genomic or parental imprinting.” Early in embryonic development attached methyl groups become removed from most genes. Several days later, methyl groups are reattached in appropriate sites. Fascinatingly, some such genes reestablish methylation patterns based upon whether the chromosomal segment carrying the gene came from maternal or paternal chromosomes.

Only biologically uninformed science idiots continue to tout the pseudoscientific nonsense of neo-Darwinian evolution to help others continue to suck the life out of you and profit by doing so.
For example, see: 7/25/13
Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.
See for comparison: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
All energy-dependent differences in the microRNA/messenger RNA balance have now been linked from the physiology of pheromone-controlled reproduction to all morphological and behavioral phenotypes by the conserved molecular mechanisms of RNA-mediated cell type differentiation.
But see also the “bad luck” theory of cancer:

 

Alternative splicing of pre-mRNA

The Origin of Information (4)

Summary: Others have learned that the energy in a hydrogen atom must be linked to all biodiversity on Earth.
The question is: “Where did the energy in the hydrogen atom come from?
See: The Origin of Information (3)
Finally, someone is asking questions that can be summarized in one question (see below). Until now, on the International Society for Human Ethology’s Yahoo group, and elsewhere, the moderator: Jay R. Feierman has prevented the dissemination of accurate information on this topic. Now others have learned that the energy in a hydrogen atom must be linked to all biodiversity on Earth.
The question is: “Where did the energy in the hydrogen atom come from?
See the discussion attempt at: 88233 Re: DNA Begins As a Quantum Wave, According to New Science

Excerpt: Much of the information in this article came from The Synchronicity Key: The Hidden Intelligence Guiding The Universe and You

Conclusion: Clearly though, our view of the universe and life itself is changing as these concepts are understood by more people each day.

The fact that DNA begins as a quantum wave linked to biophysically constrained amino acid substitutions was addressed in the context of: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
Natural selection for quantized energy-dependent codon optimality and the stability of messenger RNA during transgenerational epigenetic inheritance has since been placed into the context of experimental evidence reported as Olfaction Warps Visual Time Perception.
See also the series of presentations at virtual conferences that began with: The Origin of Information: How to Solve It.
When I realized that people might not understand that the origin of information must be linked from quantum waves to RNA-mediated healthy longevity and from virus-driven energy theft to all pathology, I split the original presentation submission into two parts. The revised title was RNA mediated molecular epigenetics and virus driven entropy.
From hydrogen atom transfer in DNA base pairs to ecosystems was presented during the same virtual conference.
Several more presentations added information about top-down energy-dependent RNA-mediated biologically-based biodiversity. For example, this may be my final presentation at Labroots virtual conferences Energy as Information and Constrained Endogenous RNA Interference
The journalists from Labroots have ignored my presentations despite a series of my comments on their attempt to continue touting pseudoscientific nonsense about neo-Darwinian theories.  It seems unlikely that any science journalist will admit to their overwhelming ignorance.
See for comparison:168949 From the evolutionary psychology Yahoo group. Re: DNA Begins As a Quantum Wave, According to New Science
Jay R. Feierman admits:

This claim is above my level of expertise to refute. It comes from a peer reviewed article in The American Chemical Society’s Journal of Physical Chemistry B. See below, which is taken from https://phys.org/news/2008-01-genetic-telepathy-bizarre-property-dna.html.
“Scientists are reporting evidence that intact, double-stranded DNA has the “amazing” ability to recognize similarities in other DNA strands from a distance. And then like friends with similar interests, the bits of genetic material hangout or congregate together. The recognition — of similar sequences in DNA’s chemical subunits — occurs in a way once regarded as impossible, the researchers suggest in a study scheduled for the Jan. 31 issue of ACS’ Journal of Physical Chemistry B”.
Read more at: https://phys.org/news/2008-01-genetic-telepathy-bizarre-property-dna.html#jCp

There are many things in physics and physical chemistry that seem incredulous to me. That includes some of the claims of quantum mechanics. What about the Penrose Hameroff Theory of Quantum Consciousness. See http://www.quantumconsciousness.org/sites/default/files/1998%20Hameroff%20Quantum%20Computation%20in%20Brain%20Microtubules%20The%20Penrose%20Hameroff%20Orch%20OR%20model%20of%20consciousness%20-%20Royal%20Society_0.pdf.

On several occasions, Feierman has threatened to ban me from the Human Ethology Yahoo Group. Then, he simply fails to post my comments when they do not support his nonsense.
I’ve added some comments to this discussion because it seems to be progressing nicely at a time after Feierman has admitted he knows virtually nothing about biophysically constrained biologically based RNA-mediated cell type differentiation.
See: Discus for discussion of

How to teach evolution when students hold creationist views


Feierman, and others like him, have been teaching neo-Darwinian theories either directly or indirectly. But Feierman’s nonsense has consistently been the most offensive to me personally. After publication of my 2013 review, I attempted to discuss the refutation of neo-Darwinian nonsense he had been touting since I first met him at a conference in 1995.
His responses to Nutrient-dependent/pheromone-controlled adaptive evolution: a model include:
7/25/13
Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.
7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
Now, he admits, albeit elsewhere, that he knows nothing about how food energy as quantized information must be linked to healthy longevity via the pheromone-controlled physiology of reproduction, or be linked from the virus-driven degradation of messenger RNA to mutations and all pathology.
See also this example of a false dichotomy: Scholars who believe nurture trumps nature also tend to doubt the scientific method

One group, made up of psychologists, economists, philosophers and political scientists believes more strongly in the genetic influences on behaviour, beliefs and culture. The other group, consisting sociologists, non-evolutionary anthropologists, women’s and gender studies scholars and all humanities scholars (except philosophy), believes in the primacy of environmental influences.

No Genetics without Epigenetics? No Biology without Systems Biology?

…there has never been a genetics without an epigenetics.

Energy-dependent changes link the epigenetic landscape to the physical landscape of supercoiled DNA, which protects all organized genomes from the virus-driven degradation of messenger RNA that all serious scientists have linked from mutations to all pathology in all living genera.
See: microRNA  for more than 63,000 examples of that fact.

Cytosis

New Testament Book Cover Refutes Theistic Evolution

Goats, bookworms, a monk’s kiss: Biologists reveal the hidden history of ancient gospels

Collins already had developed a method to identify ancient species by differences in the amino acid sequences of collagen and other proteins preserved in fossils.

See: Protein power by Robert F. Service

…methods to sequence amino acids lag behind DNA sequencing.

The report of 300 million year old proteins is based on ridiculous theories that failed to include what was known about food energy-dependent RNA-mediated fixation of amino acid substitutions.
Natural selection for energy-dependent codon optimality links the pheromone-controlled fixation of the substitutions to cell type differentiation in all individuals of all living genera.
Collins has since used the method he developed to recover amino acid sequences that reveal which animal skin was used for the leather cover for the Gospel of Luke.

Collins so-called revelation about the species-specificity of amino acid sequences was reported in Dobzhansky (1964) and again in 1973.

Pseudoscientists have ignored this fact:

…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 (p. 127).” — Dobzhansky (1973)

The sequences of amino acids link what animals eat to the food energy-dependent pheromone-controlled morphological and behavioral biodiversity manifested in every species on Earth. See: Feedback loops link odor and pheromone signaling with reproduction

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.The species-specific link from food energy-dependent changes in base pairs to the fixation of amino acid substitutions in supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA.

See also:  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!

See also: Olfaction Warps Visual Time Perception reported as: Odors Alter Subjective Time Experience 

The energy-dependent de novo creation of the sense of smell links food odors and natural selection for codon optimality to the physiology of reproduction. Feedback loops link the sense of smell in bacteria to all biodiversity via the pheromone-controlled physiology of reproduction.

Metaphorically, the sense of smell is like a time machine that links our experiences from the past to our behaviors throughout life. Experimental evidence of biologically-based cause and effect links the creation of the sense of smell to representations of food energy-dependent pheromone-controlled biodiversity in invertebrates to vertebrates. The fact that bookworms are invertebrates has aroused interest in the context of the Gospel of Luke.

Goats, bookworms, a monk’s kiss: Biologists reveal the hidden history of ancient gospels (revisited)

Others were more interested in the bookworms. Hedges announced that the wormholes he measured in the Gospel of Luke were 1.3 millimeters in diameter, suggesting that they were made by Anobium punctatum, a northern European beetle. That would confirm that the book was made in the United Kingdom or northern Europe, rather than in southern Europe. The DNA of bookworms “can provide clues as to when and where objects such as books originated and were transported,” Hedges says.

The energy-dependent creation of RNA-mediated amino acid substitutions in different species links experimental evidence of creation to the Dawn of Creation.

The New Testament Book Cover provides experimental evidence of how our visual perception of mass and energy is linked to the space-time continuum via olfaction and representations in Biblical Genesis that link energy as information at the “Dawn of Creation” for comparison to claims and theories about the emergence of energy and the evolution of all biodiversity.

See also: Researchers may have solved origin-of-life conundrum by Robert F. Service

… a pair of simple compounds, which would have been abundant on early Earth, can give rise to a network of simple reactions that produce the three major classes of biomolecules—nucleic acids, amino acids, and lipids—needed for the earliest form of life to get its start.

The origin of life is energy-dependent and RNA-mediated. Robert F. Service seems to be perfectly poised to prevent the dissemination of accurate information about how the virus-driven degradation of messenger RNA is linked from mutations to all pathology.
He has failed to link the energy-dependent creation of nucleic acids, amino acids, and lipids to the creation of the innate immune system and the pheromone-controlled physiology of reproduction in all living genera, which protects all organized genomes from the virus-driven energy theft that links mutations to all pathology.
Simply put, in the context of the Gospel of Luke, Robert F. Service has failed to link any aspect of biologically-based cause and effect from amino acid substitutions to biodiversity via supercoiled DNA.

That may explain why on 2/17/16, I received a message from Bob Grant who claimed to moderate reader comments on posts at www.the-scientist.com.

He claimed that many of my posts were off-topic and excessively long, and asked me to limit both the length and the focus of my comments in the future. He warned “If you continue to post long, rambling, or incoherent comments, I’ll be forced to bar you from our discussion board, something I do not want to do.”

I’ve been banned from many discussions, and consistently see why I am banned. Discussions of pseudoscientific nonsense prevails. For example, see:

First Support for a Physics Theory of Life Thanks to Oleksander Savsunenko for bringing this to my attention.

Take chemistry, add energy, get life. The first tests of Jeremy England’s provocative origin-of-life hypothesis are in, and they appear to show how order can arise from nothing.

My comment to Quanta Magazine

See for comparison: Olfaction Warps Visual Time Perception https://www.ncbi.nlm.nih.gov/pubmed/28334302

They link the energy-dependent creation of the sense of smell in bacteria to our visual perception of mass and energy in the context of the space-time continuum and everything known to serious scientists about RNA-mediated cell type differentiation via the physiology of reproduction.

Compared to the claims of Jeremy England, they start with Darwin’s food energy-dependent “conditions of life.”

Richard Feynman commented on the “conditions of life” and linked Jeremy England’s claims to examples of “human idiocy.” No one will complain that Jeremy England is an idiot (i.e., someone with no professional expertise), but everyone should remember that he has no professional expertise that can be linked to biologically-based top-down causation.

See: Food energy https://www.youtube.com/watch?v=roX2NXDUTsM
Richard Feynman, complains about all the different units that are used to measure the single concept of Energy.

Re: “Take chemistry, add energy, get life.” But do not tell a serious scientist about your theory.
And, do not expect those who moderate discussions to understand anything a serious scientist claims.
My follow-up to Bob Grant, who did not reply:

I am left with this impression.
I could respond to Roy Niles’ comment by linking virus-perturbed protein folding chemistry from loss of olfactory receptor genes to pathology in species from nematodes to humans. But, you might ban me.
The information comes from Cori Bargmann’s group, and she married Richard Axel, who shared the 2004 Nobel prize in Medicine with Linda Buck. Linda Buck extended our 1996 Hormones and Behavior review of RNA-mediated cell type differentiation across species from microbes to man when she co-authored: Feedback loops link odor and pheromone signaling with reproduction
I know a few others who have since linked viruses to perturbed thermodynamic cycles of RNA-mediated protein folding chemistry via amino acid substitutions but you’re not likely to be hearing from them, either. Eugene Daev and Anna Di Cosmo are among those who people like Roy Niles are indirectly responsible for censoring. Simply put anyone who understood our claims in the section on molecular epigenetics from our 1996 review, has made progress akin to the progress of my mentor, Bruce McEwen, whose group just linked a single nutrient-dependent RNA-mediated amino acid substitution from stress to life history transitions in human behavior via the mouse model and BDNF Val66Met. Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity

From Fertilization to Adult Sexual Behavior

Most polymaths live in a world of their own because others don’t want to learn enough to catch up, and the polymaths are too far ahead to explain what they have known for several decades.
A 6-hour long conversation with Bruce McEwen in 1991 led to my breakfast conversation in 1995 with Gene Garfield, which is when he learned enough about cell type differentiation from me and his octogenarian friend “Bill” Turner, to comment on my book in the year it was published. Greg Bear linked the information from my works to his stories about the evolution of a new human sub-species. Evolution rising from the grave; Living with the Neanderthals
I’m not sure if “The Scientist” will help others continue to move forward if you think my comments are off topic — and ban me when I try to elaborate on the link to the topic of RNA-mediated cell type differentiation for comparison to the thoughts of others about mutation-driven evolution.  I lost any linear thinking skills I might have had before writing the book, and without the help of my co-author — it wouldn’t have made sense even to Gene.
Thanks for the opportunity to vent my frustrations,
James V. Kohl

Medical laboratory scientist (ASCP)
Independent researcher

http://rna-mediated.com/

 

achiral-glycine

Energy-dependent microRNA biogenesis

Published May 3, 2017 Genetic variation and RNA structure regulate microRNA biogenesis

…primary sequence determinants and RNA structure are key regulators of miRNA biogenesis.

Genetic variation aka primary sequence determinants are energy-dependent and RNA-mediated. Energy-dependent RNA methylation is an experience-dependent link from natural selection for energy-dependent codon optimality. Natural selection for energy-dependent codon optimality links ATP-dependent microRNA biogenesis to RNA biosynthesis.
Ridiculous attempts to portray energy-dependent top-down causation as if genetic variation came first may continue for another 52 years. But see this report from 1964 to help you recognize how much pseudoscientific nonsense has been touted since then.
See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

Isolated thymus nuclei transport amino acids into an intranuclear pool by a process which seems to depend on energy from nuclear ATP synthesis (20).

If any experimental evidence of biophysically constrained RNA-mediated cell type differentiation was not linked from an anti-entropic energy source to nuclear ATP synthesis that experimental evidence might support the claims of pseudoscientists who think that mutations link natural selection to evolution of different species.
See for comparison: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The bias between codons or amino acids, and mRNA expression levels has been previously recognized across species and is thought to result from selection for efficient, accurate translation, and folding of highly expressed genes…

My translation: Natural selection for energy-dependent and energy-efficient protein folding chemistry links what organisms eat to the energy that they require for reproduction via the accurate translation and folding of highly expressed genes.
Alternatively, virus-driven energy theft links the degradation of messenger RNA to all pathology via conserved molecular mechanisms in all living genera. Simply put, the molecular mechanisms of healthy longevity and biodiversity are nutrient energy-dependent and pheromone-controlled.

The fact that population geneticists have ignored what us known to all serious scientists about the controlled molecular mechanisms that link metabolic networks to genetic networks has led to the unnecessary suffering and premature death of millions to billions of people. If you are not willing to join those who are Combating Evolution to Fight Disease, you probably will be asked why you decide to ignore everything known about the energy-dependent de novo creation of genes. If you did not recognize your ignorance, try to find experimental evidence in the works of evolutionary theorists who did not start after the energy-dependent de novo creation of genes.

So far as I know, all pseudoscientists still consistently place the facts about de novo gene creation, which refute their nonsense about mutation-driven evolution, into the context of their published works. Those works will continue to cause the unnecessary suffering and premature death of millions to billions of people.

The fact that experience-dependent genetic variation does not create itself is a thorn in the side of all theorists who now recognize and must ignore the facts about RNA-mediated cell type differentiation. The facts link the energy-dependent RNA-mediated fixation of amino acid substitutions to all biodiversity.

The facts also link mutations to all pathology, which means the facts have always been evolutionary theory killers. The facts haven’t changed since Thomas Hunt Morgan presciently linked them to chromosomal inheritance and Schrodinger presciently linked the anti-entropic virucidal energy of sunlight to RNA-mediated DNA repair.

See also: Exiqon “Genome Web” This link opens the pdf for microRNA target identification by RNA pull down with biotinylated microRNA mimics

Approximately one in five microRNA interactions with mRNAs occur through non-canonical binding sites. Although of functional relevance these microRNA targets are not predicted by bioinformatics tools. Improved RNA pull-down techniques with biotinylated microRNA mimics open new possibilities to identify microRNA targets experimentally.

Download the tech note

My  comment: Although I have repeatedly mentioned works that link energy-dependent changes in the microRNA/messenger RNA balance to cell type differentiation and healthy longevity, I had not seen any mention of biotinylation, until today.

In biochemistry, biotinylation is the process of covalently attaching biotin to a protein, nucleic acid or other molecule. Biotinylation is rapid, specific and is unlikely to perturb the natural function of the molecule…

I do not know any theorists who are biochemists and suspect that all the ridiculous theories of pseudoscientists include nothing that is known about biotinylation. That may be why I did not hear the term mentioned, until today. What would happen if I heard it and failed to learn what it meant? God forbid, I might still be a biologically uninformed theorist
See for example: The landscape of sex-differential transcriptome and its consequent selection in human adults

This work provides a comprehensive overview of the sex-differential transcriptome and its importance to human evolution and human physiology in health and in disease.

Reported as: Researchers identify 6,500 genes that are expressed differently in men and women

The detailed map of these genes, reported in BMC Biology, provides evidence that males and females undergo a sort of separate, but interconnected evolution.

I thank God, for not allowing me to believe that males and females are different mutants of the same species.
See for comparison: We are all mutants

Darwin is a god in evolution, so you can’t criticize Darwin. If you do, you’re branded as arrogant.

But any time a scientific theory is treated like dogma, you have to question it. The dogma of natural selection has existed a long time. Most people have not questioned it. Most textbooks still state this is so. Most students are educated with these books.

You have to question dogma. Use common sense. You have to think for yourself, without preconceptions. That is what’s important in science.

Common sense? Masatoshi Nei’s textbook Mutation-Driven Evolution was published on the same day as my 2013 review: Nutrient-dependent/pheromone-controlled adaptive evolution: a model, which is a refutation of mutation-driven evolution.

Excerpt:

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution.

Conclusion:

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

See for comparison: John Deely, from the Point of View of Biosemiotics

Conclusion:

….his unlimited but judiciously applied enthusiasm, his sterling example as  a scholar, and his inspirational support of semiotic colleagues, institutions, and the ongoing investigation into the reality of sign process at every level of life have been and will remain a force that both inspires and that sets the standard by which our colleagues continue with their important work.

My comment: The reality of sign process at every level of life is that it is energy-dependent, RNA-mediated, and biophysically constrained by the physiology of reproduction in species from archaea to humans.