5th-6th Sept 2018 Dublin, Ireland

2018 March for Science vs microRNAs

Summary: Only biologically uninformed theorists and other pseudoscientists do not seem to know that all carbon-based life is quantized energy-dependent and that biophotonic energy as information comes from the sun. It is obvious to all serious scientists that proton gradients link photons from quantized energy as information to the proton motive force, which is how the potential of hydrogen (pH) is linked to changes in the microRNA/messenger RNA balance that biophysically constrain viral latency in the context of hydrogen-atom transfer in DNA base pairs in solution that must be linked to supercoiled DNA.
The Second March for Science a Smaller Affair

…the events are not devoid of politics—either on signs or in rhetoric.

“It is a remarkable outpouring of scientists to talk about the marvelous accomplishments of science, the amazing relevance of science, and a call for defending the conditions under which science can thrive.” — Rush Holt, the CEO of the American Association for the Advancement of Science
Science is not thriving. See for comparison: All in the (bigger) family (2015)

…at a special symposium of the annual meeting of the Society for Integrative and Comparative Biology, researchers reported new parallels between these two very successful groups of animals and new insights about what it took for an ancient crustacean to give rise to insects.

Energy-dependent microRNA-mediated biophysically constrained viral latency was required. The scientific facts about food energy-dependent pheromone-controlled biophysically constrained viral latency and microRNA-mediated sympatric speciation probably contributed most to the reduced turnout at the ridiculous Marches for Science. All serious scientists know that science is not thriving, and pseudoscientists are finding out.
This is serious science: miRNA regulation of innate immunity

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.

Who needs more proof that neo-Darwinian theorists and Big Bang cosmologists are biologically uninformed science idiots?
When George Church reported in this interview that cyanobacteria fix light, he left no room for ridiculous claims about the emergence of energy or claims about mutation-driven evolution. Two months later, most theorists skipped the Marches.
I believe they probably stayed home and attempted to rewrite their grant proposals. But what I believe doesn’t matter. I can’t prove that they’ve been forced by serious scientists to eliminate “evolution” and/or their automagical “evolutionary processes” from the content/context.
But see at 15:10

“…the cyanobacteria turn out that they fix light ah as well or better than land plants…”

See for comparison, from the transcript:

The cyanobacteria fix [carbon via] light as well or better than land plants. Under ideal circumstances, they can be maybe seven to ten times more productive per photon.

Only biologically uninformed theorists and other pseudoscientists do not seem to know that all carbon-based life is quantized energy dependent and that biophotonic energy as information comes from the sun. It is obvious to all serious scientists that proton gradients link photons from quantized energy as information to the proton motive force, which is how the potential of hydrogen (pH) is linked to changes in the microRNA/messenger RNA balance that biophysically constrain viral latency in the context of hydrogen-atom transfer in DNA base pairs in solution that must be linked to supercoiled DNA.
Theorists have been left behind and anyone who participated in the 2018 March for Science has revealed their overwhelming ignorance. Why didn’t George Church warn them? Richard Feynman did:
See: Food energy  for Feynman’s claim about human idiocy.
Alternatively, see: Energy as information and constrained endogenous RNA interference
See also: A 360 degrees view of circular RNAs: From biogenesis to functions

The pre-mRNA splicing machinery generates circRNAs via backsplicing reactions, which are often facilitated by intronic repeat sequences that base pair to one another and bring the intervening splice sites into close proximity.

See also: Dr. Gene Nelson wrote:  “This year, I printed 500 copies of the handout that I wrote regarding CGNP’s battle with the CPUC and the plant’s owner. I returned with about 490 handouts.”
On April 19, 2018 “From Layout to Multi-Physics: Integrating Thermal and Photonics Simulation into the PIC Design Flow” will link the creation of the sun’s anti-entropic virucidal energy to thermal cycling.
The thermal cycles have been linked to cracks in the Vietnam Memorial Wall. This free Webinar will almost undoubtedly place the eternal significance of “The Wall” into the context of the eternal significance of microRNAs, which repair DNA damage in carbon-based life forms. Damage repair via the food energy-dependent creation of microRNAs is linked to the eternal significance of differences between organic and inorganic chemistry.
For instance, quantum physics can be linked to the biophysically constrained production of uranium isotopes by the physiology of reproduction in bacteria. And, the use of uranium isotopes in therapy attests to the fact that the unconstrained energy causes cracks in the human genome. The “cracks” are manifested in radiation-induced pathologies.
Treating glioblastoma with radiation may be ill-advised. For comparison, microRNA-mediated therapy has emerged as an effective treatment regimen based on naturally occurring prevention of all pathology.

Pseudoscientists are willing to let Vietnam Veterans and others with glioblastoma suffer unnecessarily and die prematurely. The pseudoscientists won’t admit that food energy-dependent changes in microRNAs have been linked to the stability of all organized genomes via sympatric speciation in all living genera.
 
 
 
There is no such thing as a de novo mutation. The virus-driven degradation of messenger RNA has been linked from mutations to all pathology via the death gene, which was discovered during the early 1990s by researchers who worked for Abcam.
See: Epigenetic modifications poster
See for comparison: A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution

Why is Jennifer Doudna still touting controlled evolution at a time when other serious scientists have linked every aspect of the quantized energy-dependent creation of microRNAs to the epigenetically modified physiology of reproduction and all ecological adaptations? What hasn’t she learned about biophysically constrained microRNA-mediated cell type differentiation in species from microbes to humans?
See: When the Most Potent Combination of Antibiotics Selects for the Greatest Bacterial Load: The Smile-Frown Transition (April 23, 2013)

Finding the most potent combinations of antibiotics in the lab can be a challenge if antibiotic interactions are not robust to evolutionary adaptation.

For nearly 5 years serious scientists have watched theorists try to escape from the traps that were set by their predecessors. All intelligent people now realize that there is no such thing as evolution of a new species. There is only ecological variation and quantized energy-dependent ecological adaptations to the virus-driven theft of quantized energy that comes from sunlight and sustains the physiology of pheromone-controlled reproduction in all living genera.
Reported as: The XV Collection: What Happens when the Antibiotic 1-2 Punch Backfires? (April 13, 2018)

Antibiotic-resistant mutants readily arise within almost any population of bacteria. If a population containing both susceptible and resistant mutants is treated with two antibiotics, the susceptible majority is, as expected, rapidly wiped out. But this also removes any competition for the resistant minority, enabling them to quickly grow and proliferate.

The food energy-dependent pheromone-controlled physiology of reproduction in bacteria biophysically constrains the virus-driven degradation of messenger RNA that links antibiotic resistance from mutations to all pathology.
Reported on June 14, 2013 as: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

That extension of the vertebrate/mammalian model to invertebrates occurred as researchers integrated what was known about human pheromones and their effects on neuroendocrine systems during the development of human behavior (Kohl et al., ). Invertebrate research rapidly progressed to include the epigenetic effects of nutrients and pheromones on gene expression and on hormone-organized and hormone-activated behavioral transitions throughout life (Elekonich & Roberts, ), which is consistent with their epigenetic effects throughout the life of vertebrates, including mammals.

The honeybee model organism exemplifies what has been learned from the study of invertebrates (De Loof, Lindemans, Liu, De Groef, & Schoofs, ). This includes what has been learned about the epigenetic effects of nutrients and pheromones on juvenile hormone (JH).

See also: Pursuing Preprints, Preventing Pandemics: How pre-peer review posting can accelerate outbreak science

Preprints are scientific manuscripts posted online prior to or concurrent with submission for peer review and publication in a scientific journal. They offer opportunities to share data and findings sooner and to get broader community feedback before publication. During outbreaks, decisions that can save lives must often be made quickly and with little information. The fast, open nature of preprint posting can help address these needs.

The posting of most preprints on the bioRxiv server obfuscates what is known to serious scientists about biophysically constrained energy-dependent microRNA-mediated sympatric speciation. The consistent focus of most preprints places the findings into the context of evolution because that is what biologically uninformed theorists have been taught to believe in.

Until everyone admits that the creation of microRNAs is food energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction, the ability to respond to urgent and complex health challenges will be placed into the ridiculous context of evolutionary processes.

See for exception:  A transmissible RNA pathway in honey bees

…RNA extracted from worker and royal jellies harbor differential naturally occurring RNA populations. Some of these RNAs corresponded to honey bee protein-coding genes, transposable elements, non-coding RNA and exogenous viruses. These results reveal an inherent property of honey bees to share RNA among individuals and generations. Thus, our findings suggest a transmissible RNA pathway, playing a role in social immunity and epigenetic dynamics among honey bees and potentially other closely interacting organisms.

See for comparison: SLC6A4 binding site and acute prosocial effects of (+/-)-3,4-methylendioxymethamphetamine (MDMA) are evolutionarily conserved in Octopus bimaculoides

Human and octopus lineages are separated by over 500 million years of evolution, and show divergent anatomical patterns of brain organization.

No experimental evidence of top-down causation or energy-dependent RNA interference suggests separation of the lineages by 500 million years of evolution.

See for comparison: Role of olfaction in Octopus vulgaris reproduction

From the concluding paragraph:

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

See also: See Diamond et al., 1996: From Fertilization to Adult Sexual Behavior

Elekonich and Robinson (2000) linked our 1996 Hormones and Behavior review of RNA-mediated cell type differentiation to the honeybee model of food energy-dependent biophysically constrained biodiversity.

Effects of hormones on brain and behavior occur through three mechanisms: (1) behaviors both organized and activated by hormones, (2) behaviors only organized by hormones, and (3) behaviors only activated by hormones (reviewed in Arnold and Breedlove, 1985; Diamond et al., 1996).”

See also: Honey bees as a model for understanding mechanisms of life history transitions

In this review we discuss the physiological and genetic mechanisms of this behavioral transition, which include large scale changes in hormonal activity, metabolism, flight ability, circadian rhythms, sensory perception and processing, neural architecture, learning ability, memory and gene expression.

See also: IAPV, a bee-affecting virus associated with Colony Collapse Disorder can be silenced by dsRNA ingestion (2009)

Here we report on RNAi-silencing of IAPV infection by feeding bees with double-stranded RNA, as an efficient and feasible way of controlling this viral disease. The association of CCD with IAPV is discussed, as well as the potential of controlling CCD.

Amino acid modification FA_Epigenetics_Table1

Predicting who wins the 2017 Nobel Prizes (6)

I failed to correctly predict who would win this year’s Nobel Prize in Chemistry, but there is still hope for my prediction of who will win the Nobel Peace Prize. I thought Lynn Zechiedrich would win for linking cryo-EM to the Structural diversity of supercoiled DNA

Our cryo-ET, biochemical, and computational studies show the astounding versatility and dynamism of DNA depending on the degree of supercoiling. DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases. Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

“Electron cryo-tomography (ECT, also called cryo-electron tomography, cryo-ET or CET) is an imaging technique used to produce high-resolution (~4 nm) three-dimensional views of samples, typically biological macromolecules and cells.[1] ECT is a specialized application of transmission electron microscopy (TEM) in which samples are imaged as they are tilted, resulting in a series of 2D images that can be combined to produce a 3D reconstruction, similar to a CT scan of the human body. In contrast to other electron tomography techniques, samples are immobilized in non-crystalline (“vitreous”) ice and imaged under cryogenic conditions (< −150 °C), allowing them to be imaged without dehydration or chemical fixation, which could otherwise disrupt or distort biological structures.[2]
See for comparison: Cryo-electron microscopy (cryo-EM), or electron cryomicroscopy, is a form of transmission electron microscopy (TEM) where the sample is studied at cryogenic temperatures (generally liquid-nitrogen temperatures).[1] Cryo-EM is gaining popularity in structural biology.[2]
The Zechiedrich group used cryo-ET to link the energy-dependent transfer of hydrogen atoms in DNA base pairs in solution from quantum physics to chemistry and the functional structure of DNA via RNA-directed DNA methylation. For example, fixation of amino acid substitutions differentiates all cell types in all living genera in the context of their pheromone-controlled physiology of reproduction.
I apologize for being wrong about this award. Obviously,  I do not know the diffference between cryo-EM and cryo-ET Instead, see:  Scientists Who Developed Cryo-Electron Microscopy Win Nobel Prize

The Nobel Prize in Chemistry was awarded this morning (October 4) to three scientists who developed cryo-electron microscopy, a method that allows scientists to freeze biomolecules and view them at atomic resolution. Using this technique, researchers have been able to study the structure of a variety of biological molecules, from proteins involved in circadian rhythms to the Zika virus.

This is the first of the three Prizes awarded to researchers this year who have linked quantum physics from chemistry to biology via the claims of Richard Feynman about food energy, which can now be placed into the context of links from cryo-EM and possibly also from cryo-ET to all biodiversity — especially if there are unremarkable differences between cryo-ET and cryo-EM.
In any case, Feynman knew that observation at the level of atomic resolution would be required to link food energy-dependent changes in electrons to ecosystems in all living genera (via hydrogen-atom transfer in DNA base pairs in solution) and the physiology of reproduction. Bruce McEwen also knew at the time he co-authored: 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.

Those who have failed to link quantized energy as information to ATP dependent life and all biodiversity via the synthesis of RNA have also failed to link the virus-driven degradation of messenger RNA from mutations to all pathology. For comparison, see: All About that Base (Meghan Trainor Parody).
Perhaps the Nobel Prize Committee does not value the use of parodies to ridicule pseudoscientists who have failed to link energy-dependent changes from the epigenetic landscape to the physical landscape of supercoiled DNA via RNA-mediated amino acid substitutions and the biophysically constrained physiology of pheromone-controlled reproduction in species form microbes to humans.
For comparison, this parody is about what “Chemists Know” about how to link energy-dependent changes in electrons to ecosystems.
See also: Celebrate Your Inner Virus 10/3/17

Viruses are amazingly complex and beautiful machines. They exhibit all the hallmarks of being designed, though we often fail to recognize them as such. Therefore, we seek to highlight the strengths of what makes a virus on this Virus Appreciation Day.1 The design in viruses is highlighted in many different ways, from being essential during normal developmental processes to being used as novel therapy for treating brain cancer. It is important that we understand the design present in viruses because God made them. All creatures of our God demonstrate his handiwork, and viruses are no different.

I was shocked to see the claim that God created viruses come from “…an apologetics ministry, dedicated to helping Christians defend their faith and proclaim the gospel of Jesus Christ.” The claims that viruses are like “All creatures of our God…” is even more amazing given the publication history of “Answers in Genesis.”
This was also reported in the same publication:  Did God Make Pathogenic Viruses? 4/1/1999

…viruses are not living, and in order to reproduce and to make ATP, they require all of the complex cellular machinery present in bacterial cells. Other scientists speculate that a reverse symbiosis occurred, and that viruses arose out of cell parts such as bacterial plasmids and other organelles, and eventually evolved into separate forms of life.18

See also: Research is showing that viruses are a critical part of life. Holmes has noted:

‘For sheer numbers, no other ocean beings can match viruses. Thousands, sometimes even millions of these molecular parasites inhabit every drop of surface seawater, outnumbering even bacteria by 10 to 1 … evidence that suggests that viruses are a powerful force in the sea, and one that determines how many plankton and ultimately how many fish, and even humans, an ocean ecosystem can support … viruses must have a profound influence on the entire oceanic ecosystem. When protozoans eat bacteria, energy passes along the food chain leading from protozoa to other zooplankton to larger predators, including fish. But when virus-infected bacterial cells burst, their energy-rich cell contents spill into the water for other bacteria to scavenge. “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.’62

Eugene Koonin admitted that  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…
Kalevi Kull wrote: 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.
It has become obvious that the virus-driven energy theft of quantized energy as information causes the mutations that all serious scientists have linked to all pathology in species from microbes to humans. In a twist of fate, an apologetics ministry appear to support claims linked to the Modern Synthesis. At the same time, the cutting edge research of all serious scientists and the cell biology game “Cytosis” have linked the creation of the sun’s anti-entropic virucidal energy to the creation of ATP and the creation of RNA. Energy-dependent RNA-mediated DNA repair has been linked to all biophysically constrained biodiversity via the physiology of pheromone-controlled reproduction.
Thank God, as we wait for more information to come from apologetics ministries and from biologically uninformed neo-Darwinian theorists, some of us can begin to learn how to protect ourselves from viruses, just in case that is what God intended us to be able to do.

Cytosis Shipping Update  

The fulfillment centers in the UK and Australia started shipping Cytosis out to backers last week, and the fulfillment centers in the US and Germany are planning to start shipping packages out this week (Let’s keep our fingers crossed). Shipments to Canada will be 3-4 days behind US shipments since those games got delivered to the US and then split off to Canada

 
 

Alternative splicing of pre-mRNA

Sexual communication signals: New Insights!

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

New insights in the evolution of sexual communication signals

Abstract excerpt:

Our research focuses on identifying a) the genes underlying sexual signals and responses in both sexes2-4, and b) ecological factors that may cause divergence in sexual communication. Factors that we found to affect sexual communication are closely related species with similar mating signals5, low nutritional quality, (toxic) secondary plant metabolites and pathogens6.

Elizabeth Pennisi reported on this 2017 conference presentation and claimed:

The results “demonstrate the importance of the social environment,” Halfwerk says. “One form does not attract males on its own, only in close proximity of the other form.” That result also parallels what’s been found in humans: that an attractive woman in a crowd of less attractive women also seems to attract more attention. But pinning down exactly why this happens should be much easier in moths than people, she notes. “That’s the nice thing about insects.”

See: Sexy females help ‘Plain Jane’ moths snag their mates

No experimental evidence of biologically-based sexual communication suggests that sex signals evolved. The fine-tuned systems of communication among individuals and species pose an evolutionary dilemma because they are food energy-dependent. Ecological variation must be linked from food energy to biophysically constrained ecological adaptations by the pheromone-controlled physiology of reproduction in all living genera. Also, everything known to serious scientists about energy-dependent top-down creation links the anti-entropic virucidal energy of sunlight from the creation of ATP to the creation of messenger RNA. That fact does not appear to be coincidental.

See: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

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

Detailed experimental evidence also links the virus-driven degradation of messenger RNA from mutations to all pathology. That fact leaves neo-Darwinian theorists and “Big Bang” cosmologists without any acceptable theory of anything or any theory of everything.

See for comparison: A New Physics Theory of Life and Jeremy England’s idea that “You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant.” 

Theorists and philosophers cannot link energy as information or “big bang” cosmology to biodiversity without the creation of energy. Most of them ignore the fact that they do not know where the energy in a hydrogen atom came from.

Without the de novo creation of energy, they cannot link hydrogen-atom transfer in DNA base pairs in solution from microRNA flanking sequences to SNPs, and they cannot link food energy as information to fixation of RNA-mediated amino acid substitutions in organized genomes. For comparison, all serious scientists have linked what is known about the food energy-dependent fixation of amino acid substitutions to the structure and function of supercoiled DNA, and all serious scientists have linked energy-dependent RNA-mediated cause and effect to all biodiversity via the physiology of pheromone-controlled reproduction.

That fact helps to explain why Richard Feynman referred to some theoretical physicists as examples of human idiocy.

See: Food energy

That suggests Elizabeth Pennisi is a biologically uninformed. She reported: “That’s the nice thing about insects.” If she was not a biologically uninformed science idiot, she would have linked food energy to the physiology of reproduction in all invertebrates and vertebrates. That is how the pheromone-controlled physiology of reproduction is linked from ecological variation to all biodiversity via what is known to all serious scientists about ecological adaptation.
See: Feedback loops link odor and pheromone signaling with reproduction and Olfaction Warps Visual Time Perception

For comparison to the science reporting by Elizabeth Pennisi,  J.A. Parker is the only person besides me, who has reported on this 2017 conference presentation:

See also: All in the (bigger) family by Elizabeth Pennisi with my comment:

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.” http://dx.doi.org/10.1038/nature13400

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. http://dx.doi.org/10.1038/ncomms6536 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 http://www.hawaii.edu/PCSS/biblio/articles/1961to1999/1996-from-fertilization.html

See also: Sex differences in microRNA-mRNA networks: examination of novel epigenetic programming mechanisms in the sexually dimorphic neonatal hypothalamus

Integrating miRNAs and their broad actions on gene function into our conceptualization of the factors directing sexual differentiation of the brain could be a highly informative next step in efforts to understand the complexities behind these processes.

They linked sex differences in microRNAs to the sexual differentiation of all cell types in all living genera that sexually reproduce via microRNA-mRNA networks.
See also: The phylogenetic utility and functional constraint of microRNA flanking sequences

…miRNAs can be employed as both qualitative [9] and quantitative markers, with the latter demonstrated clearly here. Our investigation demonstrates the utility of miRNA sequences as classical phylogenetic markers, and shows this usage is robust to different algorithms of phylogenetic analysis and the analysis of fast-evolving lineages. Such a method provides novel characters for assessing phylogenetic relationships that will be of use in a range of contexts for resolving branches across the tree of life.

See also: Role of olfaction in Octopus vulgaris reproduction

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

Kohl (2013) is: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (June 14, 2013)

…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. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, ; Duvarci, Nader, & LeDoux, ; Griggs et al., ; Monahan & Lomvardas, ) in adaptive evolution will certainly be discussed in published works that will follow.

Elekonich and Robinson (2000) cited:  From Fertilization to Adult Sexual Behavior (1996)
At the time of our 1996 Hormones and Behavior review, microRNAs were called pre-mRNAs. See our section on molecular epigenetics:

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

Social odors are still called pheromones and we linked the food energy-dependent pheromone-controlled physiology of reproduction to all biophysically constrained biodiversity on Earth via sex differences in microRNAs (pre-mRNAs).
The sex differences in microRNAs will soon be linked to sex differences in healthy longevity and to sex differences in diseases in the context of the cell biology game: “Cytosis.” Next, the game “Subatomic” will teach others how to build an atom.
The fact that this invited review linked energy-dependent changes in atoms to ecosystems may still go unnoticed, since the invited review was returned without review.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
But, for God’s sake, see for comparison: 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.”

Do not ignore the fact that Jay R. Feierman has no understanding of how ecological variation must be linked to energy-dependent ecological adaptation via the pheromone-controlled physiology of reproduction.
See also: December 5, 2016

[MODERATOR NOTE: I’m not going to post more from Kohl until he answers the very direct and simple question posed to him by anon, which is whether he (Kohl) believes that RNA splicing can change DNA.]

What I believe about RNA splicing is irrelevant unless someone else links the creation of energy to ATP and the creation of RNA outside the context of energy-dependent alternative splicings of pre-mRNA and the link from energy to the creation of the pre-mRNAs and to energy-dependent biophysical constraints on supercoiled DNA in all living genera.

As Heyn points out, “we still do not fully understand the mechanisms that drive epigenetic variation in populations.”

Natural selection for energy-dependent codon optimality links RNA-directed DNA methylation to all biophysically constrained biodiversity via the pheromone-controlled physiology of reproduction. That fact seems to be missing from this representation of a failed paradigm (neo-Darwinian evolution).
Claims that facts about natural selection and epigenetic variation in populations are not fully understood can be viewed in the context of reports by those who understand the facts about Darwin’s “conditions of life.” They are energy-dependent and RNA-mediated
See for example: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition and Olfaction Warps Visual Time Perception
It has become obvious to all serious scientists that the sense of smell in bacteria must be linked from mRNA stability to our visual perception of mass and energy in the context of natural selection across the time-space continuum via the pheromone-controlled physiology of reproduction. The complexity of that fact may not be understood by biologically uninformed theorists, but no theorist should claim that the mechanisms of food energy-dependent pheromone-controlled biophysically constrained cell type differentiation are not understood by all serious scientists.
Re: …a strong link between population-specific DNA methylation, mRNA levels, and genotypes.
See also: Methylation Variation Documented Between Human Populations

“Our analysis of five worldwide populations revealed a strong correspondence between population-specific DNA methylation, [messenger RNA] levels, and genotypes,” the authors wrote. “The correlation with genetic divergence was stronger for DNA methylation, and, consistent with this, our results suggest stronger local genetic control of population-specific DNA methylation levels than of mRNA expression levels.”

The strong link and/or strong correspondence between food energy-dependent DNA methylation, messenger RNA levels and genotypes is biophysically constained by the pheromone-controlled physiology of reproduction in all livng genera. See for example: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

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

Glycolysis and the citric acid cycle appear to provide the free energy for nuclear ATP synthesis and the food-energy-depenent biosynthesis of messenger RNA. If so, all pathology is caused by the virus-driven degradation of messenger RNA, which links mutations but not from ecological variation to ecological adaptations.
See also: Back to Basics: Next-generation sequencing methods and applications (with my emphasis)

…another common NGS application (although one currently more of a research application than a front-line clinical tool) is to examine the transcriptome of a sample—that is, the identity and relative abundance of mRNA transcripts present. Sometimes referred to as “exome sequencing,” this approach is efficient in that it applies resources only to that small portion of the genome which is functionally expressed. Of course, not all significant genetic aberrations occur within coding regions; but by observing levels (or even presence/absence) of transcripts in comparison to reference “normal” conditions, important mutations in non-coding regions such as gene promoters or splice site regulators can be inferred. When such findings are plausibly related to a disease condition, more directed studies to confirm the root cause can then be undertaken as or if needed.

See also: microRNA “exome sequencing Items: 1 to 20 of 55 There is no need to infer that splice site regulators are not food energy-dependent and yet that is what biologically uninformed neo-Darwinian theorists have consistently done with their claims about Mutation-driven evolution. For comparison, all serious scientists are Combating Evolution to Fight Disease.
See also: Global Epigenomic Reconfiguration During Mammalian Brain Development July 4, 2013

DNA methylation is implicated in mammalian brain development and plasticity underlying learning and memory. We report the genome-wide composition, patterning, cell specificity, and dynamics of DNA methylation at single-base resolution in human and mouse frontal cortex throughout their lifespan. Widespread methylome reconfiguration occurs during fetal to young adult development, coincident with synaptogenesis. During this period, highly conserved non-CG methylation (mCH) accumulates in neurons, but not glia, to become the dominant form of methylation in the human neuronal genome. Moreover, we found an mCH signature that identifies genes escaping X-chromosome inactivation. Finally, whole-genome single-base resolution 5-hydroxymethylcytosine (hmC) maps revealed that hmC marks fetal brain cell genomes at putative regulatory regions that are CG-demethylated and activated in the adult brain, and that CG demethylation at these hmC-poised loci depends on Tet2 activity.

See also: Inherited chromosomally integrated human herpesvirus 6 genomes are ancient, intact and potentially able to reactivate from telomeres, which was reported as: “Study of inherited herpes virus finds links to ancient humans” August 30, 2017

We used molecular dating methods to compare, for example, the inherited HHV-6B genomes in five individuals from Sardinia, Orkney and England, and estimated that the most recent common ancestor with the inherited HHV-6B existed 24,500 ±10,600 years ago.

The molecular dating methods are evaluated outside the context of what is known about energy-dependent pheromone-controlled feedback loops, which have been linked from the sense of smell in bacteria to our visual perception of mass and energy in the context of the space-time continuum. But, rather than repeat myself, I will simple support my claims with a link to: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants, which was reported in January, 2013, as: Past 5,000 years prolific for changes to human genome. The changes can be place into the context of exome sequencing, but not mutation-driven evolution.
The recent origin of most human protein-coding variants can be linked from food energy-dependent changes in exomes that are biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera. The recent origin of the variant can also be linked from the virus-driven degradation of messenger RNA to all pathology.

Of 1.15 million single-nucleotide variants found among more than 15,000 protein-encoding genes, 73% in arose the past 5,000 years, the researchers report. 164,688 of the variants — roughly 14% — were potentially harmful, and of those, 86% arose in the past 5,000 years.

See also: Whole-Exome Sequencing Reveals a Rapid Change in the Frequency of Rare Functional Variants in a Founding Population of Humans (2013)
I repeat:

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
diseases-disorders

Your indifference is killing you and others

Summary: Coherence-inducing mechanisms is double-speak for mechanisms that are nutrient-dependent and pheromone-controlled.
Feedback loops link odor and pheromone signaling with reproduction has been presented in double-speak as Looplessness in networks is linked to trophic coherence

We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

Feedback loops link the sun’s anti-entropic virucidal energy from the food that organisms eat to the physiology of pheromone-controlled reproduction in all living genera. The virucidal effect of ultraviolet light biophysically constrains viral latency. Energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA are fixed in organized genomes via the physiology of reproduction and supercoiled DNA protects all organized genomes from the virus-driven degradation of messenger RNA that links mutations to all pathology.
Coherence-inducing mechanisms is double-speak for nutrient-dependent and pheromone-controlled in the context of Nutrient-dependent/pheromone-controlled adaptive evolution: a model. 
Despite the validity of the model, it has not been accepted by neo-Darwinian theorists or “Big Bang” cosmologists. Ridiculous beliefs about emergence and evolution are pervasive and the pseudoscientific nonsense of their theories leads to claims about coherence-inducing mechanisms.
That is why I changed the FB page description at RNA-mediated after a series of posts (see below).

It took 20 years for others to realize that all life on Earth is food energy-dependent. Now, most people are indifferent to that fact. They refuse to learn anything about where the food energy comes from.

Differences in the energy of photons have been linked to quantized energy-dependent fixation of RNA-mediated amino acid substitutions. The substitutions biophysically constrain supercoiled DNA via the physiology of pheromone-controlled reproduction.

Virus-driven energy theft links the degradation of messenger RNA to mutations via amino acid substitutions in viruses. The substitutions in the viruses have been linked to all pathology via changes in the energy-dependent microRNA/messenger RNA balance.

For comparison, the pseudoscientific nonsense of neo-Darwinian theories links mutations from natural selection to the evolution of new species. In reality, light energy is quantized information. The information links physics, chemistry, and molecular epigenetics from the speed of light on contact with water and hydrogen-atom transfer in DNA base pairs in solution to learning, memory, and behavior via RNA-mediated events such as the energy-dependent creation of enzymes and the the de novo creation of G protein-coupled receptors such as olfactory receptor genes.

Top-down causation and de novo gene creation are exemplified by energy-dependent differences in the microRNA/messenger RNA balance that link natural selection for codon optimality to amino acid substitutions that link the physiology of reproduction to supercoiled DNA. Supercoiled DNA protects all organized genomes from virus-driven energy theft. That fact supports the beliefs of young earth creationists, which may be the only existing basis for discussion of quantum biology and refutations of neo-Darwinian theories that have linked olfaction to quantum souls. If there is another basis for the link from quantum physics to quantum souls, no one has detailed in in the context of top-down causation, which must include information about the creation of genes.

Most people seem unwilling to accept experimental evidence that attests to how genes are created or information that shows how virus-driven energy theft is linked to all pathology. Discussion of the energy-dependent paradigm shift would lead others away from pseudoscientific nonsense about emergence and/or beneficial mutations and evolution.

Only via discussion of facts about the paradigm shift will others learn what is currently known to serious scientists about the biophysically constrained nutrient energy-dependent chemistry of RNA-methylation and all biophysically constrained RNA-mediated protein folding chemistry. Simply put, the protein folding chemistry must be linked to all biodiversity by the physiology of energy-dependent pheromone-controlled reproduction in all living genera.

Your indifference to that fact is killing people.

See for comparison: Looplessness in networks is linked to trophic coherence (May 16, 2017)

Our theory correctly classifies a variety of networks-including those derived from genes, metabolites, species, neurons, words, computers, and trading nations-into two distinct regimes of high and low feedback and provides a null model to gauge the significance of related magnitudes. Because trophic coherence suppresses feedback, whereas an absence of feedback alone does not lead to coherence, our work suggests that the reasons for “looplessness” in nature should be sought in coherence-inducing mechanisms.

Reported August 14, 2017 as Trophic coherence explains why networks have few feedback loops and high stability

The researchers are also investigating whether negentropy – the opposite of entropy, and in which a physical, thermodynamic or biological process creates order – are affected by trophic coherence. “The modern concept of entropy,” Johnson points out, “comes from statistical physics and is a property of ensembles, as described above – that is, the entropy of an ensemble is simply a function of the number of elements it contains.” Moreover, he adds, graph ensemble entropy has proven to be a powerful tool for understanding various network properties. We are currently studying the entropy of the coherence ensemble we defined for this work. “In general, higher trophic coherence would be associated with lower entropy states, which means that if networks are more coherent than the random expectation there must indeed be some kind of negentropic process at work.” Johnson notes that the impact in this case relative to trophic coherence would be found in quantifying the extent to which different empirical networks have been driven from their maximum entropy state. “This might be the best way of discovering when there are coherence-inducing mechanisms at work, how much energy must be involved, and ultimately identifying the nature of such processes.”

See for comparison: Feedback loops link odor and pheromone signaling with reproduction

These studies also indicate that GnRH neurons are likely to influence numerous brain functions. They appear to transmit signals to as many as 30,000 or more neurons in 34 brain areas, consistent with previous studies showing GnRH+ fibers and GnRH receptors in multiple brain regions (Badr and Pelletier, 1987; Jennes et al., 1988; Jennes et al., 1997). BL+ neurons likely to receive synaptic input from GnRH neurons were seen in areas associated with numerous different functions, including odor and pheromone processing, sexual behavior, appetite, defensive behavior, motor programs, and the relay of information to higher cortical areas. These results may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.

See my posts on Discovering Vismodegib in the Fight Against Skin Cancer: The First Approved Inhibitor of the Hedgehog Pathway
No one I know is likely to understand this link from the anti-entropic virucidal energy of sunlight to prevention of all pathology because they must first understand the fact that proteins do not create themselves. There is no need for this inhibitor of the Hedgehog pathway or inhibition of any other pathway if cancer is prevented. But most people are not willing to learn about prevention because they think they can rely on medical practitioners to effectively treat their diseases. Do you think that your physician knows anything about light scattering characterization of glycoproteins and their interactions with other proteins and antibodies?
Absolute Characterization of Glycoproteins and their Interactions with Proteins and Antibodies by Light Scattering
Light scattering can now be linked to the characterization of glycoproteins and their immune system interactions in all species on Earth. That suggests the speed of light on contact with water links energy as information to the de novo creation of the glycoproteins,
If so, the physiology of reproduction links pheromones to biophysical constraints on the creation of more glycoproteins in the context of morphological and behavioral differences in species from microbes to humans. That suggests the refutation of neo-Darwinism is complete, since the virus-driven degradation of messenger RNA has been linked to all pathology in bacteria that become archaea before virus-driven energy theft causes them to become L-forms.
Simply put, Carl Woese was wrong. There is only one domain of life and virus-driven energy theft is what destroys all life on Earth.

 

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:

 

 
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

Chromatin: The structure of DNA (2)

A Genetically Encoded Probe for Live-Cell Imaging of H4K20 Monomethylation
Excerpt (with my emphasis):

Highlights
•    A histone H4K20me1-specific live-cell probe, H4K20me1-mintbody, was developed.
•    Dynamics and replication timing of Xi were visualized.
•    Critical amino acids for the stability and/or folding of the mintbody were revealed.

Reported as: Catching histones by the tail: A new probe to track histone modifications in living cells

Excerpt:

H4K20me1 is most likely associated with the tight packing of a redundant (inactivated) female X chromosome (Xi) into heterochromatin. In a roundworm Caenorhabditis elegans model, Prof. Kimura and colleagues showed that the H4K20me1-mintbody could be used to monitor changes in H4K20me1 over the cell cycle and localization of dosage-compensated X chromosomes without disrupting cell function.

Also reported as: New Probe Detects Histone Modifications in Live Cells

Excerpt:

Using genetic analysis and X-ray crystallography, the new work has also identified amino acids that are critical to the solubility and conformational stability of the H4K20me1-mintbody. Aberrant folding of the antibody fragments in the cellular cytoplasm usually causes solubility problems…

My comment: The nutrient-dependent pheromone-controlled cell cycle and localization of dosage-compensated X chromosomes links  Max Tegmark’s claims about reorganized food and consciousness via the physiology of reproduction in Caenorhabditis elegans and other model organisms. The research results reported above link RNA methylation, learning and memory to RNA-directed DNA methylation via the addition of a methyl group or groups to histone H4 at the lysine 20 position (H4K20).

That energy-dependent change in methylation links biophysically constrained biologically-based cause and effect from yeast to humans. For instance, X-inactivation is closely linked from chromosomal rearrangements to sex differences in morphological and behavioral phenotypes in humans.

In the most recent report, they did not jump to humans from sex differences in the cell types of yeasts. Instead, they used the nematode, Caenorhabditis elegans as a link between the H4K20me1-mintbody and changes in methylation (i.e., H4K20me1) during the cell cycle at the cellular location of X-inactivated chromosomes. That’s how increasing orgaanismal complexity from yeasts to humans was again placed into the context of fixed RNA-mediated amino acid substitutions. I will reiterate this claim:

•    Critical amino acids for the stability and/or folding of the mintbody were revealed.

They identifies the amino acids that are critical to the solubility and conformational stability of the H4K20me1-mintbody and critical to cell type differentiation in all cell types of all individuals of all species. They linked X-inactivation and chromosomal rearrangements from aberrant RNA-mediated protein folding biochemistry to the solubility problems caused by antibody fragments in the cellular cytoplasm and found a potential solution to the problem.

The problem they are trying to solve is different than mine.  I gave up trying to solve the problem of how to explain the origin of sex differences in cell types in species from yeasts to humans by putting the explanation in terms that educated laypersons might understand. Even other scientists won’t admit to knowing anything about amino acid substitutions and cell type differentiation. Meanwhile, neo-Darwinian theorists are trying to bury any explanation for the origin of sex difference in cell types so that evolution via mutations and evolution can continue to be used as an explanation for all biodiversity, including the diversity in male and female gametes.

However, no experimental evidence of biologically-based cause and effect suggests that X-inactivation “evolved” via mutations and natural selection. And no experimental evidence of biologically-based cause and effect suggests that sex difference in cell types “evolved.”

These researchers overcame the challenges involved in explaining that fact to biologically uninformed theorists by evaluating the performance of antibody fragments in live cells. Unfortunately, explaining the complexity of X-inactivation to an educated layperson may not be possible — especially if that person thinks that sex differences “evolved” via mutations and natural selection.

Until many others accept the fact that nutrient energy-dependent fixation of RNA-mediated amino acid substitutions in the context of the physiology of reproduction is the link to all biodiversity and all cell type, most theorists will not be encouraged to learn more about how virus-driven energy theft is linked to all pathology. If they don’t understand biologically-based cause and effect, they are not likely to understand the need to link thermodynamic cycles of protein biosynthesis and degradation to the molecular mechanisms of biodiversity.

See also:

My comment: The epigenetic effects of nutrients on intracellular signaling and stochastic gene expression appear to enable ecological adaptations in the context of tightly controlled organism-level thermoregulation in mammals. Nutrient-dependent single amino acid substitutions and de novo protein biosynthesis exemplify the involvement of the seemingly futile thermodynamic control of intracellular and intermolecular interactions in microbes that result in stochastic gene expression.
Thermodynamically “futile” cycles of RNA transcription and degradation also are responsible for changes in pheromone production that enable accelerated changes in nutrient-dependent adaptive evolution controlled by the microRNA/messenger RNA (miRNA/mRNA) balance. Environmental cues, like those that signal the availability of glucose, appear to cause changes in the miRNA/mRNA balance that enable gene expression during developmental transitions required for successful nutrient-dependent reproduction in species from microbes to humans.
The facts about protein biosynthesis and degradation show that the thermodynamic cycles are nutrient energy-dependent and the facts link virus-driven energy theft to all pathology via conserved molecular mechanisms of biophysically constrained RNA-mediated protein folding chemistry that prevent one species from evolving into another via mutations and natural selection.
See for comparison: Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition

Abstract excerpt:

Active removal of broad H3K4me3 domains by the lysine demethylases KDM5A and KDM5B is required for normal zygotic genome activation and is essential for early embryo development. Our results provide insight into the onset of the developmental program in mouse embryos and demonstrate a role for broad H3K4me3 domains in MZT.

My comment: They must think everyone knows the importance of amino acid substitutions that link lysine to biophysically constrained energy-dependent cell type differention or from mutations to pathogy. There is no mention of lysine demethylases outside the context of nutrient energy-dependent RNA-mediated amino acid substitutions and no mention of lysine in the context of virus-driven energy theft. The only indication that they know how important the difference may be is their citation to: Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).

The isoform switching is energy-dependent and RNA-mediated.

That fact was missing from this report of their work: Breakthrough genomics technique can be used to map epigenetic marks across the genome using fewer cells

Excerpt:

Very soon after fertilization, the control of embryonic development shifts from pre-existing maternal gene products to the products of genes encoded by the early embryo (or zygote). This passing of the genetic baton, called the maternal-to-zygotic transition (MZT), is poorly understood because existing technologies have generally been too insensitive to capture the full scale of the epigenetic changes it entails across the zygotic genome.

See for comparison: From Fertilization to Adult Sexual Behavior
Excerpt:

The Genome, positioning, timings. There are major structural differences between the X and Y chromosomes; e.g., centromeric aiphoid repeats sequences and distribution of heterochromatin (Graves, 1995; Wolfe et al., 1985). These structural differences correlate with sexually dimorphic chromosomal positioning within the nucleus and with male/female differences in replication timing of the active X, the inactive X, and the Y chromosomes, e.g., Boggs and Chinault (1994), Clemson and Lawrence (1996); Hansen, Canfield, and Gartler (1995). Increasingly the structure and timings within the nucleus are realized as contributing to gene expression regulation (Manders, Stap, Strackee, van Driel, and Aten, 1996; Stein, Stein, Lian, van Wijnen, and Montecino, 1996).

My comment: Our next section title was Molecular distance and the one after that was Molecular epigenetics. In the section on molecular epigenetics, we wrote:

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.

We did not link any aspect of RNA-mediated cell type differentiation from natural selection and evolution to sex differences in cell types or differences in somatic cell types. Why not? Because no experimental evidence suggests ecological variation can be linked to ecological adaptation via anything except energy-dependent fixation of RNA-amino acid substitutions in the context of the physiology of energy-dependent reproduction. All aspects of nutrient-dependent pheromone-controlled reproduction have been repeatedly linked from feedback loops to all biodiversity in all living genera. See: Feedback loops link odor and pheromone signaling with reproduction

See for comparison: Evolutionary learning of adaptation to varying environments through a transgenerational feedback

Excerpt:

The molecular basis of this learning mechanism could be searched for in model organisms showing epigenetic inheritance.

My comment: The transgenerational epigenetic inheritance of molecular mechanisms of learning is energy-dependent and transgenerational epigenetic inheritance is linked from RNA methylation to supercoiled DNA via the innate immune system in all model organisms. Simply put, transgenerational epigenetic inheritance is energy-dependent and controlled by the physiology of reproduction.
 
If individuals of a species cannot find food, or if virus-driven energy theft steals the energy they need to support biophysically constrained protein folding chemistry and error-free reproduction, the species is on its way to becoming extinct.

Zika virus damaged DNA is an example of how quickly one insect species can ecologically adapt to a virus that is transmitted to the humans with unrepaired DNA . The damage is manifested as changes in craniofacial morphology and brain development in the context of one base pair change and one amino acid substitution in the virus compared to failed ecological adaptation in primates.

Dobzhansky (1973) tried to put that fact into the context of primate ecological adaptation.

See: Nothing in Biology Makes Any Sense Except in the Light of Evolution

Excerpt:

…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).

See also: Combating Evolution to Fight Disease

Excerpt:

The evolutionary biologist Theodosius Dobzhansky famously noted that “nothing in biology makes sense except in the light of evolution,” but perhaps, too, “nothing in evolution makes sense except in the light of biology.” Although the latter might be an exaggeration, an important gap is being filled by molecular understanding of the genesis of variation that confers the ability to evolve.

My comment: RNA-mediated learning and memory link ecological variation to ecological adaptation. Nothing links the energy-dependent RNA-mediated genesis of variation to the ability to evolve. Ecological adaptation is energy-dependent and biophysically constrained. Neo-Darwinian theories were invented by people who did not know that, or refused to admit it. Why hasn’t everyone complained that their theories are ridiculous so that people do not keep adding to the pseudoscientific nonsense?

See also: Paul Allen’s Latest Surprising Revelation About The Human Brain

See also: The nexus of vitamin homeostasis and DNA synthesis and modification in mammalian brain

See also: Sex-biased chromatin and regulatory cross-talk between sex chromosomes, autosomes, and mitochondria

Excerpt:

Crudely defined molecular mechanisms, however, have prevented a better understanding of genetic variants mediating sexually dimorphic expression.

My comment: All definitions of molecular mechanisms are useless to serious scientists who have linked energy-dependent changes from angstroms to ecosystems by starting with the sun’s biological energy.

See also: Plant RNAs Found in Mammals

My September 20, 2011 comment to the Scientist about this fact now appears to be attributed to an anonymous source

This important finding in mammals is predicted by an insect model in which the diet of the honeybee queen and her pheromones determine everything about the success of the hive including the neuroanatomy of worker bee brains.

The honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, development, mental health, longevity, and diseases of the X chromosome. Included among these different aspects of eusocial species survival are learning and memory as well as conditioned responses to sensory stimuli, like food odors, and the social odors called pheromones. Thus, the honeybee model also predicts that the behavior of mammals will be influenced by food odors, nutrition, and pheromones to the same degree that chemical stimuli influence the behavior of every other species on the planet.

In mammals, of course, the epigenetic effects of pheromones in the mother’s milk are clearer, perhaps even to non-biologists.

See also: Sequencing Reveals Genomic Diversity of the Human Brain
Excerpt:

Researchers examine the role of long interspersed element-1 retrotransposition in neuronal mosaicism.

My comment: Somatic mosaicism is nutrient energy-dependent and controlled by the physiology of reproduction in plants and animals.
 Plant RNAs Found in Mammals (revisited)

MicroRNAs from plants accumulate in mammalian blood and tissues, where they can regulate gene expression.

Today’s comment: Energy-dependent changes in the microRNA/messenger RNA balance are linked to healthy longevity, and virus-driven energy theft is linked to all pathology via conserved molecular mechanisms.
See also: Abiogenesis: A Theory on The Origins of Life
My comment from last year:
See: Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism

Didn’t Sutherland’s group link the speed of light on contact with water to the de novo creation of nucleic acids and the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding in accord with Schrodinger’s claim about the anti-entropic epigenetic effect of the sun?

See also: Study shows lack of interest in sex successfully treated by exposure to bright light

Excerpt:

The researchers also found that testosterone levels increased in men who had been given active light treatment. The average testosterone levels in the control group showed no significant change over the course of the treatment – it was around 2.3 ng/ml at both the beginning and the end of the experiment. However, the group given active treatment showed an increase from around 2.1 ng/ml to 3.6 ng/ml after two weeks.

See also: Chromatin: The structure of DNA (3)

rp_tumblr_ngykp0yfND1r5gzz6o1_500.jpg

Major transition ends use of silly theories

Major transitions in human evolution

This theme issue focuses on key evolutionary transitions to understand the interaction of biology, behaviour, culture and environment. This issue is dedicated to Richard Leakey, whose critical discoveries have provided evidence for many of the key phases, and who has inspired much of the work discussed here.
This issue is based on a joint Royal Society and British Academy discussion meeting held in October 2015.
This issue is now available to read online.

Reported as: No giant leap for mankind: why we’ve been looking at human evolution in the wrong way

Excerpts:

…most of the credible models tend to take something that is unique to humans – such as language – and show how all the other bits of being human derive from that.

My comment: The Conversation  claims to be “…an independent, not-for-profit, news and information service… on current or relevant issues, as well as the latest research and breakthroughs.

Excerpt:

1) …most of the credible models tend to take something that is unique to humans – such as language – and show how all the other bits of being human derive from that.

2) The problem with these theories is that they depend on evolution being a sort of one-step game, where one change produces a great leap forward, one from which other changes cascade. But the record does not support this. We split from our last common ancestor with the chimpanzees 5-6m years ago.

See for comparison: Morphological variation in Homo erectus and the origins of developmental plasticity
Conclusion:

Our results so far suggest that comparisons of CVs across species should yield insignificant results when sufficiently large samples are available and single measures are compared and that CV seems not to be the way to look at the inherent ability of a species to vary.

My comment: Despite the lack of credible models, they claim “We split from our last common ancestor with the chimpanzees 5-6m years ago.” But they conclude that coefficients of variation (CVs) in morphological phenotypes are not the way to examine “…the inherent ability of a species to vary.”
For comparison, see: Biology, Molecular and Organismic (1964)
Excerpt 1)

The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists! I have heard a man whose official title happens to be Professor of Zoology declare to an assembly of his colleagues that “a good man cannot teach zoology. A good man can teach, of course, only molecular biology.

Excerpt 2)

Ingram and others found that hemoglobin S differs from A in the substitution of just a single amino acid, valine in place of glutamic acid in the beta chain of the hemoglobin molecule.

See also: Nothing in Biology Makes Any Sense Except in the Light of Evolution
Excerpt:

…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.

More than 1180 hemoglobin variants in human populations have been referred to as mutations, because that’s what population geneticists called the hemoblogin S variant that protects modern human populations from malaria.  See also: HbVar: A database of Human Hemoglobin Variants and Thalassemias
Excerpt 1)

Hemoglobinopathies are the commonest single-gene genetic disorders in humans, resulting from pathogenic genome variants in the human α-like and β-like globin gene clusters (reviewed in 1). Single nucleotide substitutions or indels [INsertions/DELetionS] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects in either regulatory or coding regions of the human HBA2, HBA1, HBB or HBD genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.

Even when all serious scientists know the difference a single nucleotide substitution and an amino acid substitution can make to the ability of a human population to adapt, pseudoscientists report that the variants are mutations.
Excerpt 2)

To identify new hemoglobin variants and thalassemia mutations not previously documented in the database, we continued to manually scan articles from the specialized journal ‘Hemoglobin’, which frequently publishes new hemoglobin variants and thalassemia mutations, and where applicable, previously undocumented variants have been entered into HbVar.

My comment: If you look for variants you will find all of them are nutrient-dependent and RNA-mediated. If you look for mutations, you will find theories that link virus-driven energy theft from perturbed protein folding biochemistry to the magic of evolution via natural selection. Re: “Richard Leakey, whose critical discoveries have provided evidence for many of the key phases…” They dedicated the issue to the man whose ridiculous claims led many people to look at human evolution in the wrong way.

Excerpt 3)

As far as we can tell, human evolution is like a mosaic of change, made up of many small steps, each of which adds a piece to what it is to be human. Only at the end do we see the full configuration, but had we stopped the clock at any point along that continuum, we would have seen a different mosaic. Human evolution is not one great transition, therefore, but many smaller ones.

My comment: That fact explains why all serious scientists are Combating Evolution to Fight Disease. Each small step requires ecological variation to lead

  1. from RNA methylation to ecological adaptation via the conserved molecular mechanisms…
  2. that link the nutrient-dependent pheromone-controlled physiology of reproduction in bacteria…
  3. to the supercoiled DNA in organized human genomes that protect us from virus-driven energy theft…
  4. and all pathology in the absence of stress.

    The fact that neo-Darwinian theorists failed to link viruses and stress to all pathology is the fact that has led all serious scientists to link energy-dependent changes from angstroms to ecosystems in all living genera via RNA-mediated amino acid substitutions in the context of the physiology of reproduction — three years post publication of Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

New partnership to study link between olfaction and neurodegenerative disease

Excerpt:

“Declines in olfactory function have been shown to be among the earliest signs of brain-related , but we need more data to better understand this connection,” said Monell olfactory scientist Pamela Dalton, PhD, MPH. “Adding an olfactory assessment to the BHR’s large existing database may yield the best information yet on the predictive relationship of olfactory function to neurodegenerative disease.”

See also:  CD36 is expressed in a defined subpopulation of neurons in the olfactory epithelium and Farnesol-Detecting Olfactory Neurons in Drosophila and The phylogenetic utility and functional constraint of microRNA flanking sequences

My comment:  Energy-dependent RNA methylation seems likely to be the link from hydrogen-atom transfer in DNA base pairs in solution to microRNA flanking sequences and the de novo creation of G protein-coupled receptors that link the innate immune system from receptor-mediated cell type differentiation and behavior to experience-dependent life history transitions that can be perturbed by virus-driven energy theft.  If so, the facts about biophysically constrained energy-dependent RNA-mediated cell type differentiation, healthy longevity, and virus-driven pathology will be very difficult to put back into the context of any ridiculous theories about top-down causation.
See also: my review of this book by George Ellis How Can Physics Underlie the Mind? Top-Down Causation in the Human Context
human-evolution

A bumper crop of virus-infected weeds and people

A Zika Catastrophe Could Rival Hurricane Katrina

Excerpt:

Looking more broadly, Zika may be representative of the kind of disease that increasingly characterizes the modern era—an illness that thrives, in large part, because of how human activity has affected the planet.

My comment: Neo-Darwinian theory has the largest impact on Earth. It causes researchers to ignore how ecological variation must be linked to energy-dependent ecological adaptation via thermodynamic cycles of protein biosynthesis and degradation.
The energy-dependent innate immune system must link nutritional epigenetics from metabolic networks to genetic networks in the context of the physiology of reproduction. Darwin put that fact into the context of his “conditions of life.”
Neo-Darwinian theorists removed Darwin’s “conditions of life” from their claims and substituted mutations and natural selection. Each spring, Darwin’s “conditions of life” are linked to another bumper crop of virus-infected weeds that grow in my yard. There is always at least one type of weed that I have never seen before. Growth occurs in the context of viruses in soil bacteria, which have been linked from thermodynamic cycles of protein biosynthesis and degradation to changes in the microRNAome of bull sperm and nutrient-dependent microRNAs in the milk of mammalian mothers. The complexity of the links includes epigenetic effects on protein biosynthesis and degradation, which link the nutrient-dependent RNA-mediated innate immune system of all living genera to supercoiled DNA via the physiology of reproduction. The physiology of reproduction links supercoiled DNA to protection of all organized genomes from virus-driven entropy.
Viruses in soil bacteria are linked from the growth or inhibited growth of grasses and other plant life to microRNA in sperm cells of mammals.
The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
Human milk miRNAs primarily originate from the mammary gland resulting in unique miRNA profiles of fractionated milk
Schrodinger linked cause and effect from viruses in soil bacteria to the development of the human brain in What is Life?
Excerpt:

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)

My comment: Neo-Darwinists refuse to acknowledge that sunlight is the virucidal anti-entropic force that prevents virus-driven entropy in organized genomes. Neo-Darwinists have over-populated Earth with their ridiculous theorists because serious scientists have not weeded out the pseudoscientists. The pseudoscientists are like the weeds in my yard. Any that are not effectively treated will choke out the growth of other life that has already adapted to the viruses that infect it.

See also: Neglected Tropical Diseases in the Anthropocene: The Cases of Zika, Ebola, and Other Infections

My comment: Obviously, this will force everyone to learn how nutrient-dependent RNA-mediated cell type differentiation occurs — even if it is too late to stop the last stages of virus-driven entropy.
In the end, the neo-Darwinian theorists will have killed us all — except perhaps for the very wealthy. Perhaps that is their plan.

Physics

Hydrogen-Atom Transfer in DNA Base Pairs

I requested a reprint of this article from the senior author on 10/29/15 and received it on 12/18/15.  Scientific progress moves fast, and Hydrogen-Atom Transfer in DNA Base Pairs (2) appears before the continuation of this post is linked to Hydrogen-Atom Transfer in DNA Base Pairs (3) and others in this series.
Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution [subscription required] It was reported as:

Researchers observe one of the world’s fastest chemical reactions for the first time

My comment: I will try to explain what they claim to have observed in the context of an atoms to ecosystems model of RNA-mediated cell type differentiation. The explanation will invite attacks by biologically uninformed science idiots, because it becomes obvious that RNA-mediated cell type differentiation is biophysically constrained by epigenetic effects on the structure and function of DNA that begin with epigenetically trapped light. I have not found anyplace else to discuss the links from UV light to energy-dependent base pair substitutions without the interference of those who cannot comprehend why physics and chemistry must be linked from top-down causation to the conserved molecular mechanisms of biologically-based cause and effect.
I encourage discussion of the claims in the news report in the context of the reports that follow:

New NASA study reveals origin of organic matter in Apollo lunar samples

Re: Amino acids from four sources.
1) contamination from terrestrial sources 2) rocket exhaust precursor molecules contamination 3) solar wind 4) chemical reactions inside asteroids
Sutherland’s group “…created nucleic acid precursors starting with just hydrogen cyanide (HCN), hydrogen sulfide (H2S), and ultraviolet (UV) light.”
The virucidal property of UV light links the sun’s biological energy to the de novo creation of RNA and the de novo creation of all cell types in all individuals of all species via the prevention of virus-driven genomic entropy.
Simply put, this links atoms to ecosystems via everything currently known to serious scientists about biophysically constrained protein folding chemistry and all biomass, which does not appear to have its origins in outer space — except perhaps when viewed from the perspective of biologically uninformed science idiots.

New Video: Quantum Annealing Explained

Quantum annealing appears to link assumptions about the evolution of quantum states to the evolution of biomass and the evolution of biodiversity outside the context of an atoms to ecosystems model. It could be an example of the one miracle that must be given to theorists so that they can place their ridiculous theories about evolution into the context of big bang cosmology and support for the evolution industry.
The immediate impression I got from the explanation of quantum annealing was that something must be happening at the sub-atomic level that links the anti-entropic energy of the sun from the virucidal effects of UV light to supercoiled DNA, which appears to protects the organized genomes of all living genera from virus-driven genomic entropy.
The alternative would be random optimization of quantum states that somehow became organized in the context of links from the epigenetic landscape to the physical landscape of DNA that appear to be nutrient-dependent and controlled by the physiology of reproduction.  In other words, if an energy source is a secondary consideration, quantum annealing might act as adaptive selection for an energy source. That could be the explanation for how all biodiversity on Earth evolved from nothing, including no source of energy. Indeed, neo-Darwinian theorists might still claim that de Vries 1904 definition of mutation is all that is required to link sudden energy jumps from no energy at all to all biodiversity with or without natural selection.
For example, without natural selection, evolution might “just happen.” See: The Surprising Origins of Evolutionary Complexity
Excerpt: 

Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed “the blind watchmaker.” To some extent, it just happens.

My comment to the Scientific American site on 7/21/13

Darwin’s ‘conditions of life’ are nutrient-dependent. Nutrients metabolize to species specific pheromones that control reproduction in species from microbes to man via the same molecular mechanisms.
The epigenetic effects of food odors associated with nutrition and pheromones associated with socialization and with sexual reproduction are clearly responsible for linking the sensory environment directly to adaptive evolution sans consideration of mutation-driven evolution.
See for details: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Socioaffective Neuroscience & Psychology 2013, 3: 20553 – http://dx.doi.org/10.3402/snp.v3i0.20553
The model includes examples of how a change in a single base pair results in an amino acid substitution that clearly links adaptive evolution, which has occurred during the past ~30,000 years in a human population in what is now central China, to the same molecular mechanisms in mice, other mammals, insects, nematodes, and microbes.

My comment to the Scientific American site on 4/19/14
Ecological variation in nutrient availability and epigenetically-effected methylation is clearly the driver of ecological adaptations manifested in species diversity. If this had not already become clear to serious scientists, methylation would not be reported in the context of ‘Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan‘  (Instead, methylation is substituted for mutations and linked to epigenetic cause and effect.)
If nutrient-dependent pheromone-controlled ecological adaptations were not clearly responsible for species diversity, serious scientists might still claim that mutations somehow caused it, as they have claimed until recently. See: ‘A functional test of Neandertal and modern human mitochondrial targeting sequences. However, as serious scientists realized that there is no such thing as a fixed beneficial mutation, only evolutionary theorists continue to make claims based on the pseudoscience of population genetics.
It is unfortunate that pseudoscientists have influenced the ridiculous beliefs of so many people, because most of them can no longer grasp the scientific truth that life is nutrient-dependent and that the physiology of reproduction is controlled by pheromones in species from microbes to man. However, the fact that scientists like Svante Paabo have finally recognized the role of methylation is a sign that the next generation will be the one that dismisses mutation-initiated natural selection and/or mutation-driven evolution from any further consideration whatsoever.
Thus, there is still hope for scientific progress to be made by those who are not stuck with their opinions, while others examine the facts. See, for example, “Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems.”
See also:

Entanglement at heart of ‘two-for-one’ fission in next-generation solar cells

Excerpt:

…developed a model which showed that when the molecules are vibrating, they possess new quantum states that simultaneously have the properties of both the light-absorbing singlet exciton and the dark triplet pairs. These quantum ‘super positions’, which are the basis of Schrödinger’s famous thought experiment in which a cat is — according to quantum theory — in a state of being both alive and dead at the same time, not only make the triplet pairs visible, they also allow fission to occur directly from the moment light is absorbed.

My comment: The model also appears to link Schrödinger’s claims about the anti-entropic energy of sunlight to nutrient-dependent base pair changes in bioluminescent microbes and to RNA-mediated cell type differentiation in all individuals of all living genera via their physiology of reproduction and the supercoiled DNA that prevents virus-driven genomic entropy.
The viruses pirate the nutrient-dependent energy (e.g., light energy) that bacteria and plants need to reproduce. Their reproduction provides an ecological foundation for the food chain that links all life on Earth to the sun’s biological energy via top-down causation in the context of quantum physics, quantum chemistry, quantum smell, quantum biology, and quantum consciousness as demonstrated in works by Luca Turin’s group and by Anna Di Cosmo​’s group.

The Most Astounding Bioluminescent Wonders on Planet Earth

Excerpt:

Through evolution, or at least the act of it, creatures in the animal kingdom have gained abilities that far exceed those of you and I. One of those characteristics is bioluminescence.

My comment: The attribution of bioluminescence to evolution fails to link it from the biological energy of the sun to the de novo creation of nucleic acids and fails to link the virucidal effect of UV light to the biophysically constrained RNA-mediated cell type differentiation of all living genera in the context of their physiology of reproduction.

Instead, like magic, the claim that bioluminescence “evolved’ is a way to direct your attention away from the fact that no experimental evidence of biologically-based cause and effect suggests that any morphological phenotype or behavioral phenotype has ever evolved because phenotypes must be linked to nutrient-dependent RNA-mediated amino acid substitutions and chromosomal rearrangements to the physiology of reproduction in species from microbes to humans.

Chemistry in evolution

Excerpt:
First there was inorganic chemistry (the solar system, the elements and minerals – about 4 to 5 billion years ago, 4–5Ga). Then there was life, the crucial role of photochemistry, emergence of cells, of DNA, blue-green algae (circa 2Ga) and the production of oxygen, followed by animals (circa 1Ga).
My comment: First, there was nothing and there would never have been anything if not for the light-induced de novo creation of nucleic acids and RNA-mediated events that link the de novo creation of G protein-coupled receptors from nutrient uptake to the physiology of reproduction via the innate ability described as DNA sensing.
DNA sensing limits virus-driven DNA damage and typically ensures healthy longevity via nutrient-dependent RNA-mediated amino acid substitutions that enable the supercoiling of DNA.
Nothing has ever evolved outside the context of nutrient-dependent base pair substitutions and RNA-mediated DNA repair, which is why some evolutionary theorists have changed their claims to claims about co-evolution.
Co-evolution is ecological adaptation in the context of ecological variation and the physiology of reproduction in all living genera. Their knowledge of ecological speciation is why the 2015 Nobel Laureates in Chemistry were criticized for including too much biology — in the context of DNA repair. Many chemists ignored the fact that DNA repair is required for ecological speciation to occur because, like many theoretical physicists, they never learned to think about the requirement to link physics and chemistry to biology via conserved molecular mechanisms that link atoms to ecosystems.
See for example:

Photochemical genetics

Excerpt:

We have developed ‘photochemical genetic’ methods to rapidly control the activity of proteins in living cells, providing insight into the dynamics of elementary steps in biological processes, as well as insight into the regulation of intracellular network connectivity in space and time; with these methods, we hope to understand molecular processes inside cells and organisms with the level of precision more commonly associated with in vitro biochemistry or biophysics.

See also:

Research offers new insight into light detection in vertebrates

Excerpt:
“Some of the photopigments discovered were found to be UV-sensitive and have the potential to assist with functions such as cell DNA repair,” he said.
My comment: Unfortunately, he said nothing about the virucidal properties of UV light, which means we cannot link the sun’s biological energy to the de novo creation of nucleic acids. It also means we can’t link the anti-entropic energy from the sun from RNA-mediated DNA repair of damage to organized genomes that is caused by virus perturbed energy-dependent protein folding.  If any explanation of how UV light has the potential to assist with DNA repair were provided, we might link nutrient energy-dependent ecological adaptations to RNA-mediated gene duplication and RNA-mediated DNA repair via nutrient-dependent amino acid substitutions and what was learned about microRNAs and adhesion proteins via the sequencing of the octopus genome.
See also:

Control of Protein Activity and Cell Fate Specification via Light-Mediated Nuclear Translocation

Excerpt:
Deiters and co-workers controlled protein localization by incorporating a photoactive amino acid in a nuclear localization signal so that it could only interact with the nuclear import machinery when the chemical moiety was removed via irradiation with UV light [10, 11]. This approach is not reversible and requires the bioavailability of a non-natural amino acid.
My comment: They link light-activated control of what would typically occur in the context of a nutrient-dependent RNA-mediated amino acid substitutions to what is represented as “…a powerful and potentially general way of controlling multiple cellular functions.” In the context of the other reports in this post, UV light is linked from its virucidal property to RNA-mediated DNA repair via amino acid substitutions that must be fixed in the organized genomes of all living genera to protect them from virus-driven genomic entropy.
All serious scientists have learned that the speed of light must be linked from the sun’s biological energy to cell type differentiation in all living genera. Why is there no evidence that science journalists, like Carl Zimmer, are going to learn how to link atoms to ecosystems.
On 12/3/15, in A radically simple idea may open the door to a new world of antibiotics, Zimmer claimed: “Epstein is using ichips to understand the ecology of bacteria in the natural world.”
On 12/3/15, in Parents May Pass Down More Than Just Genes, Study Suggests Zimmer claimed that: “…pinning down the epigenetic effects that fathers pass to their children will take much more work.”
Zimmer’s claims represent the epic failure of all science journalists to learn about how epigenetically-effected RNA-mediated cell type differentiation occurs in all living genera. All reports by serious scientists have linked nutrient energy-dependent microRNAs and cell adhesion proteins to protection from virus-driven genomic entropy via the conserved molecular mechanisms of pheromone-controlled reproduction in species from microbes to humans. The only work that is still required to pin down the epigenetic effects of nutrient-dependent pheromone-controlled cell type differentiation, which is linked to morphological and behavioral diversity in all individuals of all species, is the work that will be required for science journalists to accurately portray what is known at the same time they quit touting the pseudoscientific nonsense about mutations and evolution.

Natural Selection Unfriends Darwin

Excerpt:

Biological evolution exists only as a philosophical fact, not as a scientific fact.

Viral Genome Junk Is Bunk

Excerpt:

Perhaps the evolutionists have placed the cart before the horse on this issue, as proposed by several creationist scientists.4,6 In fact, in an ironic twist, the evidence mentioned above indicates that viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, “The most parsimonious answer is: the RNA viruses got their genes from their hosts.”6

My comment: The time has come to ask neo-Darwinian theorists and theoretical physicists what they think they got right about the role of mutations and/or natural selection and how what they got right links atoms to ecosystems in the context of what is known to serious scientists about biologically-based cause and effect.