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?

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.

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.

Two retractions of human idiocy

Excerpt: …she was interested in the PNAS research because it identified a potential inhibitor of the hepatitis C virus…

”Definitely embarrassing:” Nobel Laureate retracts non-reproducible paper in Nature journal

1)

This retraction marks the second in six months for Nature Chemistry after having none for eight years.

2)

In 2009, Szostak also retracted a 2008 paper in Proceedings of the National Academy of Sciences after an outside researcher could not replicate the results. The retraction notice credited Katherine Berry, then a doctoral student at the University of California, Berkeley, for bringing the issues to their attention. (Full disclosure: RW’s Victoria Stern and Berry were roommates freshman year of college).

Berry, who’s now an assistant professor of biochemistry at Mount Holyoke in South Hadley, Mass., told us that she was interested in the PNAS research because it identified a potential inhibitor of the hepatitis C virus…

Comment awaiting moderation

James V. Kohl December 7, 2017 at 4:35 am

The Science Behind the Game “Cytosis,” pits the collaborative efforts of 20 serious scientists against the pseudoscientific nonsense touted by theorists. The serious scientists know how energy-dependent RNA-mediated cell type differentiation occurs.

Resources (e.g., mRNA, ATP) are used to build enzymes, hormones, and/or receptors. Health points accumulate to show why food energy must be linked from the physiology of pheromone-controlled reproduction to biophysically constrained viral latency.

For comparison, Szostak and other theorists have been stuck with their ridiculous misrepresentations of emergence and neo-Darwinian evolution, which failed to consider Darwin’s “conditions of life.”

“Conditions of life” are energy-dependent. The energy is Schrodinger’s anti-entropic virucidal energy. It comes from sunlight and is epigenetically “trapped” in food via the physiology of reproduction.

Board Game:
Cytosis: A Cell Biology Game
Title:
Cytosis – The Science Behind the Game https://boardgamegeek.com/filepage/155090/cytosis-science-behind-game

Addendum: Naturally occurring base editing, microRNA editing, and RNA editing link the energy-dependent creation of microRNAs from natural selection for energy-dependent codon optimality to the physiology of pheromone-controlled reproduction, which biophysically constrains viral latency. Constraint breaking mutations have been linked to all pathology. The misrepresentations of Szostak and others like him have contributed to a history of unnecessary suffering and premature death. Richard Feynman helped to place their claims into this perspective:

 

 

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/

 

Cytosis

God's shrinking role in salvation

God’s shrinking role in salvation can temporarily be placed into the context of what serious scientists are reporting for comparison to the claims of pseudoscientists.
See: Quantum Simulation (free download)

It presents several examples of experiments using both density and momentum imaging and quantum gas microscopy to study the motion of atoms in optical lattices.

The energy-dependent motion of atoms must be linked to ecosystems by the physiology of pheromone-controlled reproduction in all living genera. That fact requires extended consideration of helicity, chirality, autophagy, and hydrophobicity in supercoiled DNA
Helicity – the projection of the spin onto the direction of momentum. ie. spin direction depends on direction of motion;
Chirality – not identical to its mirror image, ie. left-handed vs right-handed;
Cool animation of a particle where the Helicity matches the Chirality.

I’m not sure how to start an attempt to finalize ongoing comments on what has been learned during the past century about  energy-dependent RNA-mediated cell type differentiation, which is manifested in the complexity of the animation. I would like to move forward without the redundancy of explaining everything each time a new finding links quantized energy from physics to chemistry and the facts link molecular epigenetics to the biologically-based energy-dependent creation of microRNAs and RNA-mediated cause and effect.
The energy-dependent creation of microRNAs is missing in this representation of energy-dependent internal motion in DNA.
DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid

The internal motions of DNA appear to be governed by strong internal forces arising from being crowded into the small space of the nucleoid.

God’s shrinking role in salvation can be placed into the context of works published by those who fail to link the creation of energy as information to the packed nucleoid via DNA internal motion in the context of the creation of microRNAs.
See for example: microRNA
Everything known to serious scientists about the creation of microRNAs links the sun’s anti-entropic virucidal energy from the solar analemma to representations of the time-space continuum in a Mobius strip and to this solution to the grandfather paradox, which is based on quantum entanglement, which includes quantum entanglement in DNA.
The solution to the grandfather paradox links quantized energy from quantum entanglement to energy-dependent changes in the structure and function of supercoiled DNA, which helps to ensure the survival of individuals and species, but only if the anti-entropic virucidal energy of sunlight was created before anything else.
The creation of quantized energy also must be biophysically constrained by the physiology of reproduction in all living genera.
See: Light Modulates the Biosynthesis and Organization of Cyanobacterial Carbon Fixation Machinery through Photosynthetic Electron Flow, which was reported as: Illuminating the inner ‘machines’ that give bacteria an energy boost
See also: Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes, which was reported as: Nanotechnology reveals hidden depths of bacterial ‘machines’ and subsequently placed into the context of the nonsense touted by theorists on June 8, 2017 as  Revealing the Structure of Bacterial Machines
The structure and function of the bacterial machines depends on the innate ability of the species to find enough food. If an organism fails to find food, it cannot adapt to ecological variation and reproduce in the context of the pheromone-controlled physiology of reproduction. For example, this species finds food that it metabolizes to create a uranium isotope.
See: A new twist on uranium’s origin story, by CSU scientists

…using new techniques including synchrotron radiation-based spectroscopy and isotope fingerprinting. They found that up to 89 percent of the uranium from their 650-foot-deep samples wasn’t crystalline uraninite at all, but rather, a non-crystalline uranium that was bound to organic matter or inorganic carbonate. Most of the uranium they found in that unmined site is estimated to be 3 million years old, and formed via reduction by microorganisms – microbes that respire not on oxygen, but on uranium.

The energy-dependent creation of the isotope exemplifies how the energy of sunlight is biophysically constrained in the context of quantum physics and the physiology of energy-dependent reproduction, which Richard Feynman linked to the creation of the atomic bomb — even though he did not know where the energy in a hydrogen atom came from. I have asked others where the energy came from, but the question has not been answered.
The estimate that the uranium was formed by bacteria 3 million years ago is based on pseudoscientific nonsense touted by neo-Darwinian theorists and “Big Bang” cosmologists. Taken together those who are biologically uninformed are now attempting to separate everything known to serious scientists about the energy-dependent creation of all life on Earth from the quantized energy required for creation and the physiology of reproduction.
If quantized energy is not information, the loss of energy from the sun via thermal entropy could create life and all biodiversity, at least in theory. But who believes in theories that are this ridiculous?
See: Information entropy and thermal entropy: apples and oranges

…the change of information entropy and the related change of thermal entropy can be separated in space and time leading to the break of Brillouin’s negentropy principle. iv) The information entropy can increase without triggering any change of the thermal entropy indicating that information erasure does not necessarily require energy dissipation.
v) There is no case where Landauer’s principle of erasure dissipation is even seemingly valid because erasing of the memory does not yield change in the information entropy. vi) The information entropy can violate the Third Law of Thermodynamics.

When theorists are allowed by others who are biologically uninformed to tout the amount of pseudoscientific nonsense contained in this excerpt (above), everyone who believes that the Laws of Thermodynamics can be violated is an example of what Feynman claimed is a form of human idiocy.

See also, from 2-3 years ago in the science news:

The first ever photograph of light as both a particle and wave 3/2/15

Scientists see ripples of a particle-separating wave in primordial plasma 6/10/15

Scientists find genetic basis of brain networks seen in imaging studies 6/11/15
Cell density remains constant as brain shrinks with age 6/12/15
This Nifty Infographic Is a Great Introduction to Neuroplasticity and Cognitive Therapy
New immunoregulation and biomarker 6/12/15

Cell type stability is receptor-mediated and biophysically constrained.

DNA data explosion lights up the Bronze Age 6/10/15

Quantized energy-dependent amino acid substitutions are still being reported as if they are mutations.

See for comparison: The Molecular Nutrition of Amino Acids and Proteins, 1st Edition

See also: The Ancient Origins of Consciousness: How the Brain Created Experience 3/25/16
See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model 6/14/13 My review is cited in the context of:

12. Plotnick, Dornbos, and Chen (2010). Others who advocate smell-first are Lucia Jacobs (Jacobs, 2012), who says the building of smell maps of environmental space came first and James Kohl (Kohl, 2013), whose model says chemical ecology is the main driver of adaptive evolution.  — p. 263

The concept of smell-first was linked from energy-dependent changes in angstroms to ecosystems in all living genera.
Scientists investigate how the sense of smell works in bacteria

…the signaling and inactive states differ only very slightly at the nitrate-binding site – by 0.5-1 angstroms, which is approximately one fifth of the size of the ion itself (1 angstrom is 10-10 meters). However, when this ion binds to the sensor, it causes huge changes in the protein: The helices of different monomers begin to move in different directions, like pistons. These “pistons” transmit the small change of 0.5-1 angstroms through the membrane, and their outer ends shift by approximately 2.5 angstroms in different directions. Inside the cell, in the HAMP domain, these shifts are converted into the rotation of two parts of NarQ relative to each other. Ultimately, the positions of the output helices change by as much as 7 angstroms, thus completing the signal transmission.

The signal transmission was linked from the physiology of reproduction in soil bacteria to fertility in mammals via changes in the bull sperm microRNAome. See: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
Outside the context of the creation of quantized energy and the de novo creation of genes linked to increasing organismal complexity, there is no need to discuss God’s shrinking role in salvation. You can, instead, link the Stepwise Evolution of a Buried Inhibitor Peptide over 45 My from the de novo evolution of genes and the novel proteins they encode to the innovations that automagically contribute to the diversity of life via The evolution of social behavior in microorganisms.
See also: Metabolism and the evolution of social behavior

…using experimental evolution, we followed the joint evolution of the genome, the metabolome and the social behavior as swarming re-evolved. New variants emerged spontaneously with mutations that reorganized the metabolome and compensated in distinct ways for the disrupted metabolic prudence. These experiments with a unicellular organism provide a detailed view of how metabolism—currency of all physiological processes—can determine the costs and benefits of a social behavior and ultimately influence how an organism behaves towards other organisms of the same species.

Simply put, the quantized energy of the smell-first model of energy-dependent ecological adaptation in species from microbes to humans can be compared to the metabolism-first theory of de novo gene evolution. Both can be compared in the context of the joint evolution of the genome, the metabolome and the evolution of social behavior, which is portrayed as swarming in the bacterium Pseudomonas aeruginosa. The swarming behavior re-evolved in an evolution experiment.
The re-evolved ability to swarm can be compared to the report on the weekend resurrection of the bacterial flagellum in Pseudomonas fluorescens.
See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
The weekend resurrection of the bacterial flagellum suggests that virtually any change in an organized genome can be linked to the pheromone-controlled the physiology of reproduction. If not, the claims about evolution can be linked from the wrong choice of food to the virus-driven degradation of messenger RNA, which links mutations to all pathology. But claims about the virus-driven degradation of messenger RNA are rarely made by theorists.
When the missing information about the virus-driven degradation of messenger RNA is placed into the context of the the solar analemma, a Mobius strip, and the solution to the grandfather paradox, quantum entanglement appears to link all changes in the amount of quantized energy that comes from sunlight to biophysically constrained energy theft and viral latency, which prevents pathology.
For comparison, see: A New RNA Synthesis of Cells: A Possible End of Birth Defects

…an estimation of these two above elements [nitrogen and phosphorus] as a chemical compound leads a human’s birth defect to have the correct amino acid sequence as previously mentioned and then become a normal trait. With the correct calculation of the compound of nitrogen and phosphorous for an unstable RNA messenger, which is traced to a birth defect, a researcher can discover the ideal growth rate for its stability as an RNA messenger and then its end as a birth defect.

The quantized energy-dependent biosynthesis of RNA is food energy-dependent and pheromone-controlled in species from microbes to humans and virus-driven energy theft appears to cause the degradation of messenger RNA, which has been linked to all pathology. The report of the evolutionary resurrection of flagellar motility clearly exemplifies how energy-dependent changes in RNA-mediated amino acid substitutions are linked to survival of the species outside the context of the “magic traits.” The “magic traits” do not link nutrient-dependent pheromone-controlled cell type differentiation to all biodiversity in reports like this one: Magic traits in speciation: ‘magic’ but not rare?
The “magic traits” have been linked to rapid speciation in bacteria and vertebrates
See: Extraordinarily rapid speciation in a marine fish

We evaluated different possible evolutionary scenarios under the approximate Bayesian computation framework and estimate that the speciation process started in allopatry ∼2,400 generations ago, following the colonization of the Baltic by the demersal lineage. This is faster than most known cases of ecological speciation and represents the most rapid event of speciation ever reported for any marine vertebrate.

Reported as:“Evolution on the fast lane—One flounder species became two” May 30, 2017

“The answer may lay in so called magic traits, meaning traits that are under selection which at the same time cause reproductive isolation as a byproduct. In theory, selection on such traits could play a central role in rapid speciation events. The mating strategies and reproductive traits of the two flounder species could act as magic traits,” clarifies Momigliano.

Quantum Physics News (see for discussion on this group)
The Quantum Physics News was created by Robert Karl Stonjek, whose atheistic pseudoscientific nonsense is pervasively distributed among several other Facebook groups and yahoo groups. His influence has caused the unnecessary suffering and premature death of millions of people who think God’s shrinking role in salvation can best be viewed in the context of the “magic traits” of neo-Darwinian theorists.
 

Alternative splicing of pre-mRNA

RNA-mediated adult learning, memory, and neurogenesis

Here is a way to assess the power of the media-industrial complex to suppress accurate representations of biophysically constrained biologically-based cause and effect.
Wait to see whether this experimental evidence is reported in the science news, or how it is reported.
Enriched Environment Increases PCNA and PARP1 Levels in Octopus vulgaris Central Nervous System: First Evidence of Adult Neurogenesis in Lophotrochozoa

The experimental data obtained by immunohistochemistry and western blot assay using proliferating cell nuclear antigen and poli (ADP-ribose) polymerase 1 as marker of cell proliferation and synaptogenesis, respectively, reviled cell proliferation in areas of brain involved in learning, memory, and sensory stimuli integration. Furthermore, we showed how enriched environmental conditions affect adult neurogenesis.

See also: Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice.

The link from energy-dependent RNA methylation and endogenous RNA interference to fixation of amino acid substitutions in supercoiled DNA has again become an important consideration to serious scientists who understand the facts about how viral latency is established.

In this report, the differential effects of m6A appear to depend on natural selection for energy-dependent codon optimality and distinct cis-acting elements such as microRNAs that link the energy-dependent stability of organized genomes from the physiology of pheromone-controlled reproduction in bacteria to invertebrates and all vertebrates via interactions among the RNA molecule, m6A, and microRNAs.

For comparison, see: Evolutionarily conserved serum microRNAs predict radiation-induced fatality in nonhuman primates

…the same seven transcription factors are predicted to regulate the radiation-responsive serum miRNAs in humans, macaques, and mice. However, these results need to be experimentally validated, and our ability to do so has been limited for the following reasons. First, we do not know the source (cell type) of the serum miRNAs…

Anyone who does not know that the energy-dependent creation of serum miRNAs is biophysically constrained by what organisms eat might be a member of a High IQ Society. Some of them are like other biologically uninformed science idiots and atheistic magicians.

Clearly, magicians, most Mensans, and all neo-Darwinian theorists are likely to share the claim that energy automagically emerged before energy-dependent changes in the microRNA/messenger RNA balance led to the evolution of all nutrient-dependent pheromone-controlled biodiversity.

See for instance: FROM THE DESK OF THE EXECUTIVE DIRECTOR of Mensa:

Finally, planning is under way for a great Annual Gathering and Colloquium in Hollywood, Fla. this July. The 5-star Diplomat Beach Resort has stunning waterfront views, and I can’t wait to see the Gala Dinner speaker, Penn Jillette of Penn & Teller fame.

See also: Famous Atheist Magician Penn Jillette Cites Bible as a Favorite Book

Penn Jillette, of the Penn and Teller comedy magic duo, named the Bible as one of his six favorite books in a column for “The Week.” Anyone who reads all of it will become an atheist, Jillette asserts.

Anyone who attends the 2017 Annual Gathering presentation and listens to this atheistic magician can compare his claims to those I made during my 2010 Annual Gathering presentation.
 

My claims are supported in their entirety by the claims in the Holy Bible that begin in Genesis with “Let there be light!” Light energy as information is the link to the Word of God in John 1:1.”In the beginning was the word.”

But, please keep in mind that Penn Jillette is a professional comedian, and I am not. I do not get paid to make fun of people and/or religions during presentations at Mensa Annual Gatherings.

I did include some humorous comments about those who have failed to link anything known about biologically-based cause and effect to their ridiculous behaviors, but no one seemed to be offended. I’ve already been too offended by the nonsense touted by other members of Mensa. Although I became a member in 1982, I will not renew this year. The insults of other Mensans are too much to bear, and now we see that the organization is promoting an atheistic agenda at the time when creationism is being linked to Americanism by the current President and his administration.
See for comparison:

 

 
Physics

Young earth creationists refute theistic evolution

Every great scientific truth goes through three stages. First, people say it conflicts with the Bible. Next they say it has been discovered before. Lastly they say they always believed it. –Louis Agassiz

The series about refutations of theistic evolution continues. Creationists and two publications in “Nature” support the claims of young earth creationists who cited: Holmes (1996)  Who rules the waves? – Viruses might just be bit players in the drama of the seas. Then again, they could be major actors

See: Holmes E. C. 2003. Molecular Clocks and the Puzzle of RNA Virus Origins. Journal of Virology. 77 (7): 3893–3897.

Excerpt:

“Viruses tend to keep nutrients away from the big stuff and keep them going around in the little stuff,” says Fuhrman. If so, viruses have shaped the entire structure of the ecosystem.”

Are all evolutionists atheists?

As we point out in our article about peer-review, scientists are human beings, complete with the motivations and conflicts of interest all of us have. And it seems the secularization of the sciences has made things worse, as there is currently an epidemic of fraud in science.

My comment: Re: Richard Dawkins called theistic evolutionists ‘deluded’.
I agree. All serious scientists have linked the anti-entropic virucidal energy of sunlight on contact with water from chirality and autophagy to supercoiled DNA via the innate immune system and the physiology of reproduction. Serious scientists also have linked virus-driven energy theft to all pathology.
The accurate representations in Biblical Genesis of what is known about energy-dependent RNA-mediated cell type differentiation have forced pseudoscientists to finally admit to the facts about RNA, which refute their DNA-centric theories.
See for example: An epigenetics gold rush: new controls for gene expression
Excerpt:

“We are only in the beginning of the story,” Rechavi says.

See also: The RNA code comes into focus

…in October 2016, the US National Institutes of Health awarded He and Pan a 5-year, US$10.6-million grant to establish a centre to develop methods for identifying and mapping RNA modifications.

See for comparison:
Chronic treatment of non-small-cell lung cancer cells with gefitinib leads to an epigenetic loss of epithelial properties associated with reductions in microRNA-155 and -200c.
Combined small RNA and degradome sequencing reveals complex microRNA regulation of catechin biosynthesis in tea (Camellia sinensis).
More than 58,000 published works link nutrient energy-dependent changes in the microRNA/messenger RNA balance to healthy longevity or they link virus-driven energy theft to all pathology in all living genera.
Young earth creationists have called attention to the facts about sunlight as the link from energy as information to biophysically constrained viral latency for ~15 years. Evolutionary theorists waited too long to admit to the facts. It is not only the theistic evolutionists who were ‘deluded.’ It was anyone who was taught to believe in mutation-driven evolution. The biologically uniformed masses in the United States do not know that the US National Institutes of Health award millions of dollars in grants to establish nothing that is not already known to serious scientists about energy-dependent RNA-mediated cell type differentiation.
If the US National Institutes of Health did not spend millions, no one could attempt to deliver a “billion dollar baby” like this one: Get Well in the RNAi Way-RNAi, A Billion Dollar Baby in Therapy
Excerpt: RNAi has targeted exogenous genes in models of viral infection…
Instead, millions of dollars will be spent to “…develop methods for identifying and mapping RNA modifications…” before the biologically uniformed masses are told that the modifications are nutrient energy-dependent and pheromone-controlled via the physiology of reproduction in species from microbes to humans.
Ecological variation must be linked to energy-dependent ecological adaptations via RNA-mediated protein folding chemistry and amino acid substitutions that differentiate all cell types in all individuals of all living genera. The differences in bacteria and archaea can be compared to the transgenerational epigenetic inheritance of Zika virus-damaged DNA as examples of the continuum of energy-dependent creation and maintenance of all organized genomes in all living genera.
If unethical researchers continue to misrepresent what is know to young earth creationists and to all serious scientists, they can continue to steal millions of dollars to fund their ridiculous claims about mutations and evolution. Money is the motivator. Do not expect those who are motivated by it to tell the Truth. That’s what young earth creationists do.

See also: Researchers uncover a role for HSP90 in gene-environment interactions in humans

Excerpt:

By helping proteins fold and function, HSP90 influences a range of characteristics in simple organisms on which natural selection can act, and thus alters the course of evolution,” says Georgios Karras, lead author of the study and a post-doctoral researcher at Whitehead Institute.

My comment: He claims a Heat Shock Protein can be linked from natural selection to evolution.

Natural selection for energy-dependent codon optimality links pH-taxis, thermotaxis, chemotaxis, and phototaxis to the creation of the Heat Shock Protein, which helps to protect organized genomes from virus-driven energy theft and genomic entropy in the context of the pheromone-controlled physiology of reproduction in species from microbes to humans.
fruit-dove

Happy Darwin Day (2017)

My series of blog posts about the refutation of theistic evolution by George Church led him to contact me via email.

  1. He asked why he would get credit for or against the refutations
  2. He claimed he was trained in quantum physics.
  3. He claimed that he has authored peer reviewed papers on protein folding, biodiversity, supercoiling, etc.
  4. He wanted to know more but did not know enough about my target audience to realize why I included information about the viral hecatomb.
  5. He also claimed to have written more on what is known about endogenous RNA interference than on exogenous RNA interference.

I invited him to discuss this further on my FB group, or on this domain. He declined. That was a great end to my 2017 Darwin Day.
See Evolution-guided optimization of biosynthetic pathways, which was co-authored by George Church and published December 1, 2014.
There is no such thing as evolution-guided optimization. Natural selection for energy dependent codon optimality is the only link from ecological variation to ecological adaptation in all living genera. That means we can move forward without George Church and still place his comments into the context of “Trust me, I’m a biologist.
I think that most serious scientists agree that you can’t trust evolutionary theorists For comparison, you can trust Darwin’s “conditions of life.”
Darwin’s “conditions of life” link the anti-entropic virucidal energy of sunlight to the physiology of reproduction in all living genera. Can you trust anyone who claims evolution did that?
See: RNA-Guided Human Genome Engineering 

Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).

Nutrient energy-dependent microRNAs link natural selection for energy-dependent codon optimality to viral latency and protection of organized genomes from endogenous viral elements. Targeting endogenous viral elements with RNA-mediated amino acid substitutions is the key to biophysically constrained cell type differentiation. Fixation of amino acid substitutions prevents problematic nearly identical copies. There is no need for uncontrolled copies if there is no need to find another energy source. Uncontrolled copies link virus-driven energy theft from mutations to all pathology in all genera.
For example, energy theft from bacteria links messenger RNA degradation to morphological and behavioral phenotypes of archaea. Similarly, messenger RNA degradation in humans links the transgenerational epigenetic inheritance of Zika virus-damaged DNA to craniofacial morphology and brain development in infants.
Taken together with what is known about differences in energy-dependent endogenous RNA interference in nematodes, all ridiculous misrepresentations of Darwin’s works must be reversed to show the truth about what virus-driven energy theft does. It links RNA-mediated cell type differentiation from the energy-dependent creation of bacteria to the energy-dependent creation of humans and it links virus-driven energy theft to all pathology.
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… 

Is Eugene Koonin joking about what was left out? If not, big bang cosmologists and neo-Darwinian theorists have never tried to support their ridiculous theories with any experimental evidence of biologically based cause and effect. They never examined the role of energy-dependent microRNAs or virus-driven energy theft. Instead, they invented gene-centric theories of mutation-driven evolution.

See for comparison: Membrane Patterns Carry Ontogenetic Information that is Specified Independently of DNA
Reported as: Peer-Reviewed Paper: Development Needs Ontogenetic Information that Cannot Arise from Neo-Darwinian Mechanisms

With over 400 citations to the technical literature, this well-researched and well-documented article shows that embryogenesis depends on crucial sources of information that exist outside of the DNA.

A 16 page monograph with 12 pages of citations is an unparalleled achievement for anyone who is not a polymath or someone who has not already linked physics and chemistry from molecular epigenetics to all biophysically constrained cell type differentiation in all living genera via fixation of nutrient energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA.
None of the cited works appear to link what is known about virus-driven energy theft to all pathology. Again, it is time to move forward.
See: Charles Darwin’s Ocean Upwelling

It’s hard to overstate how vital Darwin’s coral reef theory was in developing his career and thinking. It paved the way, conceptually and methodologically, for everything to come — particularly his transmutation theory [natural selection]. The likenesses startle. Like the transmutation theory, the coral reef theory described how small, virtually unnoticeable changes could create differences of essential type in seemingly immutable forms — and in doing so, account for broad patterns of development and difference.

Changes in coral reefs are nutrient energy-dependent and controlled by the physiology of reproduction. De vries defined “mutation” in 1902, which means that Darwin could not have had a transmutation theory. Also, Darwin repeatedly asserted the claim that his “conditions of life” must come before any claims about natural selection.
Darwin Day 2017 may become known as the day George Church refused to publicly discuss evolution or to admit there is no such thing as evolution outside the context of virus-driven energy theft and the evolution of  pathology. On the same day, The Smithsonian National Museum of Natural History blog site published a post that misrepresented everything known to serious scientists about biophysically constrained energy-dependent RNA-mediated cell type differentiation and healthy longevity.  Who could ask for a better Darwin Day than one during which Darwin’s “conditions of life” clearly triumphed over the ridiculous claims made by neo-Darwinian theorists and others who refuse to admit to the facts that link energy-dependent changes in chirality from autophagy to endogenous RNA interference and to supercoiled DNA, which prevents virus-driven energy theft from causing the mutations that all serious scientists have linked to all pathology?
 

Alternative splicing of pre-mRNA

Energy-dependent hydrogen bonds in supercoiled DNA

Chirality Check

Most biological macromolecules are homochiral, and enzymes help to maintain this state of affairs; for example, checkpoints ensure that only l-amino acids are incorporated into proteins during translation.

The fixation of the only achiral amino acid, glycine in position 6 of the gonadotropin releasing hormone decapeptide protein links the nutrient energy-dependent pheromone-controlled physiology of reproduction from yeasts to humans. That fact about RNA-mediated protein folding chemistry is missing from the chirality check, It also is missing from representations of the anti-entropic virucidal force that biophysically constrains all biodiversity by protecting all organized genomes from virus-driven energy theft and genomic entropy.
That’s why theories of evolution have no explanatory power. An unknown force of nature must be included the theories for comparison to Schrodinger’s claims in What is Life? (pp. 73 and 74)

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: Force of nature gave life its asymmetry

…even demonstrating how a common physical phenomenon would have favoured left-handed amino acids over right-handed ones would not tell us that this was how life evolved…

The fact that there is no explanation for how life evolved outside the context of an unknown force of nature can be placed into the context of the energy-dependent creation of all differentiated cell types in all living genera.
See: RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria (2016) by Junjie U. Guo and David P. Bartel,

Owing to the extensive hydrogen-bonding and base-stacking interactions, RG4 structures can be very stable, with in vitro melting temperatures well exceeding physiological temperatures. This stability typically depends on the presence of K+, which is the optimal size to bind at the center of two stacked G-quartets…

They fail to mention that energy-dependent hydrogen-atom transfer in DNA base pairs in solution must be linked to the stability of supercoiled DNA. Instead, the unfolding of the RNA G-quadruplexes was reported as: RNA Sequences Don’t Predict In Vivo Transcript Structure

Interactions between nucleotides can turn sections of transcripts into loops, bends, and knots, some of which have regulatory functions in the cell.

See for comparison: Electrolytes induce long-range orientational order and free energy changes in the H-bond network of bulk water.  K+ is an important electrolyte in the context of interactions in solutions. That fact was reported as:  A single ion impacts a million water molecules. The fact that the interactions between nucleotides are pH-dependent makes it important to consider what happens when slight changes in the cell types of species-specific tissues occur in the context of nutrient stress or social stress.
The stress causes changes in protein folding that predictably links energy-dependent interactions between nucleotides from natural selection for codon optimaility to fixation of RNA-mediated amino acid substitutions and healthy longevity? If pH does not facilitate energy-dependent codon optimality, a change in pH may predict a change in the structure of functional proteins, which can effect biophysically constrained cell type differentiation.
See for instance: 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.

Unfortunately, the nutrient energy-dependent interactions between nucleotides and amino acids, which are the building blocks of proteins, are typically not considered in the context of virus-driven energy theft, which has been linked from viral latency to all pathology via transgenerational epigenetic inheritance in species from archaea to humans.
See for instance: Epigenetics and Genetics of Viral Latency
… viral latency is responsible for life-long pathogenesis and mortality risk…
My comment to The Scientist on RNA Sequences Don’t Predict In Vivo Transcript Structure :

See also: MicroRNAs: Genomics, Biogenesis, Mechanism, and Function (2004) by David P. Bartel

…about a quarter of the human miRNA genes) are in the introns of pre-mRNAs. These are preferentially in the same orientation as the predicted mRNAs…

For comparison, see: From Fertilization to Adult Sexual Behavior

… epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans…  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.

Hydrogen-atom energy-dependent changes in base pairs have since been linked from RNA-mediated protein folding chemistry to all biophysically constrained cell type differentiation in all living genera via amino acid substitutions.

The RNA-mediated fixation of amino acids links autophagy from the innate immune system to supercoiled DNA. Virus-driven energy theft has been linked to all pathology via changes in the microRNA/messenger RNA balance. The changes link fertilization to adult sexual behavior.  See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems.
See also, the other publications by David P. Bartel
2016 Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression
Excerpt:

…we assumed that (1) molecular species are well mixed within the cytosol and their concentrations are not influenced by cell growth and division; (2) each mRNA and miRNA is produced at a constant rate, and unbound mRNAs and miRNAs undergo constant first-order decay; (3) upon association with a miRNA, the mRNA degradation rate increases, regardless of the site type; and (4) miRNA binding is reversible, and upon miRNA dissociation the mRNA degradation rate reverts to its original value. We also assumed that the Michaelis constant (KM) describing mRNA degradation with respect to the miRNA-mRNA complex is well approximated by the complex dissociation constant (KD), and that both bound and unbound mRNA are translated.

Simply put, they seem to have assumed that energy-dependent changes in the microRNA/messenger RNA balance need not be considered in the context of any model of biologically-based cause and effect.
See for comparison: 2014 Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Abstract excerpt:

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 clear difference between the assumptions made by Bartel (and others like him) and the facts about energy-dependent biophysically constrained RNA-mediated protein folding chemistry make it pointless for serious scientists to discuss experimental evidence of biologically-based cause and effect with anyone who does not agree that it is energy-dependent and biophysically constrained by the physiology of energy-dependent reproduction in all living genera.
See also: How the elite control the masses
Control involves giving the masses partial information, which is what Bartel and others appear to be doing in attempts to promote evolutionary theories.

See for comparison ( December 30, 2016 at 5:37pm):

Peter Berean wrote:

James, I have no problem with “energy-dependent RNA-mediated amino acid substitutions” … however, that does not show that energy = information.

And, neither does the article about “construction of phylogenetic trees”…

My recommendation is DO take the advice of your brothers in Christ… And correct your views and models accordingly.

IF you do so, you could actually have more people believe what you have to say about your models.

The comment about taking advice from my “brothers in Christ” is a classic. It comes from someone who may never understand anything about energy-dependent hydrogen bonds in supercoiled DNA, or how energy as information must be linked to all biodiversity.

Peter Berean is only one among many who are biologically uninformed. Their masses are not told that virus-driven energy theft can be linked to all pathology in the context of conserved molecular mechanisms, which have been detailed by all serious scientists. Peter Berean may think that his faith in God and/or his brothers in Christ will save him from his ignorance.

That may be true, but it may also not apply to those who have been told the truth and continue to ignore it. People like that encourage others to ignore the truth about energy-dependent hydrogen bonds in supercoiled DNA. The truth is that if you don’t know where that energy came from, you are no better off than any other theorist or atheist.

That makes this Chirality Check a reality check, and makes this a lie: “…checkpoints ensure that only l-amino acids are incorporated into proteins during translation.”

See: Evolution of constrained gonadotropin-releasing hormone ligand conformation and receptor selectivity as cited in Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor

When the chiral amino acid (Ala) in position six of Ciona I GnRH was substituted with the achiral glycine or with d-Ala, which enhances the type II’ β-turn conformation, there was a marked increase in the binding affinity of the peptides at the vertebrate GnRH receptor (Barran et al., 2005).

The substitution of achiral glycine and the increased binding affinity were placed into the following context in the Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor:

The discovery of the fact that one decapeptide molecule, among the GnRHs, was constructed perfectly at the beginning of 400 million years evolution and that it is not possible to improve its physiological potency using the any natural amino acid is, in my opinion, important, fascinating and beautiful.

The claim about 400 million years of evolution has not been substantiated by experimental evidence of biologically-based cause and effect and virus-driven energy theft was not considered in the context of the invention of neo-Darwinian theory.
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…
[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another…. Assumptions, made but not verified, were taught as fact.
See also: Spectrum of Antimatter Observed for First Time

The Standard Model predicts that there should have been equal amounts of matter and antimatter in the primordial Universe after the Big Bang, but today’s Universe is observed to consist almost entirely of ordinary matter. This motivates physicists to carefully study antimatter, to see if there is a small asymmetry in the laws of physics that govern the two types of matter.

Without the anti-entropic energy of the sun, the laws of physics could not be linked from chemistry to molecular epigenetics, which must link energy-dependent autophagy from the innate immune system to supercoiled DNA. If not, you are left with the magic of emergence and evolution instead of the fact that Life is physics and chemistry and communication in the context of energy as information.
In 2016, scientists collectively failed to link the anti-entropic virucidal energy of the sun to autophagy and all biophysically constrained biodiversity via the physiology of reproduction in all living genera. They also failed to link virus-driven energy theft from the negative supercoiling of DNA to all pathology.
Instead, most scientific successes are examples of politicized science. Congratulations to those who are willing to place politicized science into the context of their theories.  The theories make their World a better place for other theorists to live in. Serious scientists, for comparison, will remember the theorists who failed to make the Chirality Check a reality check.

Biology to a Physicist

From Precis to Proof in 6000 years

Religious texts, such as The Holy Bible appear to be like a Precis of works from God. He seems to be explaining energy-dependent creation in the context of what is currently known to serious scientists about biophysically constrained RNA-mediated protein folding chemistry, healthy longevity and RNA-mediated biodiversity.
God made it perfectly clear, in advance, that all miraculous biodiversity is energy-dependent. Energy as information is the theme that extends to the weekend resurrection of the bacterial flagellum in P. fluorscens. Biologically uninformed theorists are beginning to realize the importance of a simplistic version of biologically-based systems complexity.
Energy as information can be understood by non-scientists whether or not they are interested in further examination of top-down causation at every level of subsequent interactions among subatomic particles and macroscopic biodiversity.
See for instance: Protein Folding Using Quantum Topology which is linked to this video as a part of a series from “Serious Science
Description:

Matematician Jørgen Andersen on local geometry of hydrogen bonds, quantum states of proteins and future methods of predicting the macromolecules structure.

Excerpt:

There are about 2000 local patterns that we’ve seen popping out now and we are trying to understand what is the correlation between the primary sequence of these patterns. Some of them have a clear significance. We’re trying to devise energy contributions for each of such patterns and then trying to see if we can create algorithms that generate all structures with a certain sequence of patterns. And this is a combinatorial problem that we’ve actually solved very recently.

My comment: Does he realize he is giving the bird to all pseudoscientists with both fingers?

See also: Jørgen Ellegaard Andersen publications

See for comparison: Precis: The Scent of Eros: Mysteries of Odor in Human Sexuality

The book was written for the general readership (as  indicated by the Table of Contents). This precis is  designed to elicit responses from the scientific readership.

This Precis provides an overview of the book “The Scent of Eros: Mysteries of Odor in Human Sexuality,” which details for a general audience a five-step biological pathway that allows the social environment to influence the genetic nature of mammalian behavior. This pathway is: gene-cell-tissue-organ-organ system. Moreover, though there are many environmental influences on genes, mammalian pheromones are the only known social-environmental stimuli that appear to activate gene expression in neurosecretory cells of tissue in the brain, an organ that is essential to any organ system involved in behavior. Human pheromones appear both to elicit a homologous “neuroendocrine” response and to influence behavior. Thus, human pheromones may fulfill the biological criteria required to link at least one aspect of a sensory-based, nurturing, social environment: olfaction, to the genetic nature of human behavior through a five-step pathway common to all terrestrial mammals and to many other vertebrates.

Full text:

1. This book incorporates both non-human animal and human models of reciprocity among odors, olfaction, neuroendocrinology, and behavior. It details the likely influences both of human chemical communication and of olfaction on genes in neurosecretory neurons. These neurons are found in brain tissue responsible for integrating, coordinating, and directing reproductive endocrine function in organs that comprise the organ systems known to influence mammalian reproductive sexual behavior and human sexuality. Though this book is not written to meet any requirements of a “hard scientific” approach to interdisciplinary topics, it is fully referenced for the knowledgeable scientist and for those interested either in further study or in support for any conclusions. Also included are chapter notes, a glossary, and an index.

2. After a Foreward by William E. Hartman and Marilyn A. Fithian and an Introduction by the co-author, Chapter 1 begins with commentary on previously published works by various scientific authorities who have offered their insights into the importance of human chemical communication. Among these authorities are Havelock Ellis, Irving Bieber, and Lewis Thomas, who offered the following statement: “I should think we might fairly gauge the future of biological science, centuries ahead, by estimating the time it will take to reach a complete, comprehensive understanding of odor. It may not seem a profound enough problem to dominate all the life sciences, but it contains, piece by piece all the mysteries.” (Thomas, 1980)

3. In Chapter 1, there are fourteen examples of the many questions that may be answered when one considers the likelihood of odorous human communication. Most of these questions concern different aspects of human sexuality. Briefly deliberated are concerns about an ineffective “language of olfaction” and errors in the logic that has been used in the past to deny the importance of odor in human sexuality. The introductory focus then turns to biological consistency among species; the common basis for scientific advancements; and the development of the working hypothesis that odors are a primary influence on human sexuality.

4. Chemical communication and its importance in other species from insects to mammals is more fully detailed in Chapter 2. The term pheromone is defined, with added emphasis of one basic causal relationship, namely, that mammalian pheromones appear to influence the secretion of gonadotropin releasing hormone (GnRH), a hormone with both short-term and long-term effects on neurotransmission. Distinguishing characteristics of pheromones like species-specificity, and the differences between signalling and releasing pheromones are added to the definition. After a brief discussion of mammalian pheromones, the natural production of human odors is discussed and anecdotal evidence of some of their effects are offered as support for the concept of human pheromones.

5. Chapter 3 alludes to Greek mythology; the story of Ariadne’s thread, which metaphorically addresses the issue of biological consistency among species. The development of the mammalian sense of smell is detailed from its beginnings in single-celled organisms. Olfactory transduction is briefly discussed. Four crucial turning points in the development of mammalian chemical communication systems, which contribute to species survival, are: (1) the release of pheromones to attract another organism, which occurs in single-celled non-motile organisms, (2) the ability to detect and respond to chemical messengers with movement, which occurs in motile single-celled organisms (3) the development of neural networks devoted to processing chemical signals, which occurs in brainless invertebrates, and (4) phylogenetic advances in the development of these neural networks to include development of the vertebrate brain. Species-specific comparisons and contrasts in structure and function are provided.

6. Chapter 4 offers an ontogenetic perspective on development, both of the mammalian olfactory systems and of the GnRH neuronal system. The ontogenetic connection between the structure and function of olfactory sensory systems and brain development ascends in its significance because it allows the odorous social environment to directly and indirectly influence brain function by acting on GnRH, which in turn has short-term effects on neurotransmission and long-term effects on the hypothalamic-pituitary-gonadal (HPG) axis.

7. Kallmann’s syndrome represents a failure of GnRH neuronal migration. Correlates with anosmia and the inability to fall in love are noted, as are correlates with the GnRH neuronal system and brain development in other species. Additional aspects of olfactory transduction and signal processing are discussed. There are differences between the main olfactory system and the accessory olfactory system. The importance of the vomeronasal organ (VNO) for pheromone detection in other species and renewed interest in the recently confirmed presence of the human VNO add to the argument for the influence of odors on human sexuality.

8. Chapter 5 begins with anthropological folklore associated with odor and human behavior and progresses to a discussion of empirical evidence for this link. The metabolism of hormones into pheromones is noted. Specifically addressed are experiments with putative human pheromones and the likelihood of causal physiological and behavioral relationships. Comparisons and contrasts among species again are offered in this regard. The use of mammalian pheromones in fragrances designed to enhance the sexual appeal of humans is examined. The naturally occurring fragrance of musk, present in the secretions of many species, is held in high regard for its universal sex-attractant properties.

9. Chapter 6 reports on experiments with consciously processed human odors, beginning with the classically-conditioned response of infants to their mothers’ naturally-scented or artificially-scented breasts. Olfactory imprinting and the importance of the mother-infant bond are linked through non-human animal models to the development of neural templates and the human “love map”. Aspects of odor hedonics are detailed.

10. Children can determine the genetic sex of adults, and adults can distinguish between different people using their sense of smell. The importance of mammalian odors in aggression and in other contexts besides the mother-infant bond suggests human correlates. Similarly, clinical and anecdotal evidence that humans are culturally aware of odor-associated customs enhances a more scientific approach to the link between sex and the human sense of smell. Odors and fetishism are linked. The natural superiority of women’s olfactory acuity and specificity is linked to estrogen levels and to an important role in female choice: What human beings lack in acuity they make up for in powers of discrimination, which rival those of any other mammal.

11. Chapter 7 is a simplistic overview of prenatal GnRH neuronal system development. Included are genetic predisposition and the importance of GnRH pulsatility in the regulation of the HPG axis. This chapter begins, however, with the importance of chemical communication between ovum and spermatozoa and progresses through basic genetics, neuroanatomy, endocrinology, and endocrine aspects of neurotransmission. Postnatally, odor input is linked to human HPG axis function. Pheromone input appears to be indirectly measurable in assays of luteinizing hormone.

12. Beginning with the “nature” versus “nurture” controversy, Chapter 8 proceeds to the important issue of finding a link between the social environment and genes. The likelihood that genes are involved both in physiological and in behavioral cause and effect relationships is detailed. The influence of pheromones on genes and on concurrent neuroendocrine, reproductive system, and central nervous system development is proposed.

13. Twin studies are discussed, as is recent evidence of master genes that may allow chemical communication at the cellular level to play a primary role in behavioral development and in sexual orientation. Genetic conservation among species, specifically with regard to chemical communication, is addressed. Enzymes and chemical responses are linked with human behavior, as are genes and G protein-coupled receptors through an example of familial precocious puberty. Correlates between adrenal androgen metabolism, pheromone production, sexual dimorphism in the human hypothalamus, and human sexual orientation are offered.

14. Chapter 9 details aspects of human consciousness and of limbic learning and memory. Olfaction plays a key role by providing input to the medial preoptic area of the hypothalamus. Comparisons and contrasts among species and among theories of consciousness are offered.

15. The importance of linking specialized research in diverse disciplines is made known, namely, how a “gay gene” might influence both human neuroanatomy and human sexuality. Dean Hamer has proposed the following: “The most simple hypothesis would be that the Xq28 makes a protein that is directly involved in the growth or death of neurons in the INAH-3. Alternatively, the gene could encode a protein that influences the regulation of this region by hormones.” (Hamer & Copeland 1994).

16. Effects of pheromones on other species are favorably compared to the effects of putative human pheromones. A consciously-processed odor stimulus has been used as an adjunct to classically condition the human immune response, thereby adding clinical significance to the effects of odors.

17. Chapter 10 reveals evidence of odor-driven hormonal effects on human behavior and on sexuality, again using cross-species comparisons that link information provided in earlier chapters. Examples supporting a link between pheromones and human sexuality are discussed. The “Law of Propinquity” appears to be invalidated by experience with pheromones that create more of a friendship or kinship bond, perhaps also creating an antibond effect on love. There is evidence that humans mate for genetic diversity on the basis of unconscious odor associations, and that odors may be involved in the Coolidge effect.

18. The sources of human pheromones are detailed in Chapter 11, with a discussion of the role of glandular secretions, fatty acids, bacteria, skin cells, and the relationship between levels or ratios of sex hormones and pheromone production. Important aspects of pheromone distribution are then linked to intimate behavioral associations. Androgenization appears to stimulate secretion of a more masculine pheromone signature. Odors can be used in clinical diagnostics. The inherent difficulties of human pheromone research are briefly discussed.

19. Chapter 12 links human pheromones to various courtship behaviors (e.g., dancing, kissing, et al.,) that appear to become progressively more intimate with increasing exposure to pheromones. Stereotypic attractive qualities (e.g., large breasts or hair color and distribution) with anecdotal evidence of causal relationships between pheromones, attraction, and intimacy are represented both positively and negatively. Culturally, negative representations often appear to correlate well with sexual repression. Racial differences in odor production that may contribute to racial prejudice are briefly addressed.

20. Included in Chapter 13 is a discussion of results from the National Geographic Smell Survey. Data was collected from approximately one and a half million people worldwide. Causes of anosmia and its link both to genetics and to the GnRH neuronal systems are detailed, as are links between damage to the VNO, age-related disorders, olfactory deficits, and behavior.

21. Chapter 14 provides both a historical and a modern-day overview of aromatherapy. Cultural differences in odor hedonics are explained by odor-associated classical conditioning. The roles of chemicals now known to function as human pheromones and of putative human pheromones in fragrances for commercial use is discussed. A brief summation of current research supporting the hypothesis that human pheromones are a primary influence on human sexuality is provided.

22. I believe that “the pheromones of other mammals are the only social-environmental stimuli to influence genes [in GnRH neurons].” Accordingly, human pheromones are the most likely link between the “nature” and the “nurture” of human sexuality. However, a typographical error: insertion of “not” on page 189, in paragraph 2, line 4 (intended to read as above) detracts from the concluding paragraphs.

REFERENCES

Thomas, L. (1980) Notes of a biology-watcher: on smell. New England Journal of Medicine 302: 731-733.

Hamer, D. & Copeland, P. (1994) The Science of Desire, Simon & Schuster: 163.

My comment: Claims that my Precis is linked to proof of biophysically constrained energy-dependent causd and effect can be viewed in the context of the video representation by Jorgen Anderson for comparison to this detailed representation of my model and/or this video:

See the discussion attempt here before it is removed via suggestion by an unfriendly administrator who claims he is my friend. I’ve already given him the bird (in the cartoon representation from this blog post).