Cytosis

God vs host-derived creation of virus-driven pathology (2)

When you next see someone claim that “…there is very little knowledge about the gut microbiome” you may associate that claim with the ignorance touted by neo-Darwinian theorists and compare it to what anyone 10 years-old or older will learn when they play the cell biology game “Cystosis.” A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!
Moving forward: Food energy is required to build enzymes, hormones and receptors and fend off attacking viruses. The metabolism of food to species-specific pheromones that control the physiology of reproduction in species from microbes to humans is represented in this presentation from 2009 by Eshel Ben-Jacob.
 

At 39:10, he declares that the link from food energy to pheromones and behavior is “epigenetic.”‘
See also: Energy as information and constrained endogenous RNA interference (video)

Published on 15 Feb 2017

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy.
The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.
This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes.
For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

See for comparison: Preprocessing of emotional visual information in the human piriform cortex

To conclude, our findings support the specific role of the piriform cortex beyond a mere sensory relay up to a higher-order associative brain area. We are the first to demonstrate that the human piriform cortex processes emotional visual information before odor perception. Moreover, we found a common activation pattern in regions of the olfactory network such as piriform cortex, orbitofrontal cortex, amygdala and hippocampus for the subsequent integration of the emotional visual information while processing the actual odor. Matching behavioral results reveal that the emotion of a facial expression influences the valence rating of an odor. Thus, the behavioral observation as well as brain activation data jointly point towards a preprocessed integration of emotional visual information that modulates olfactory processing.

Their ridiculous conclusion, which is based on brain imaging linked to behavior, makes it appear that humans are primarily visual creatures.For comparison, see: Olfaction Warps Visual Time Perception

Our perception of the world builds upon dynamic inputs from multiple senses with different temporal resolutions, and is threaded with the passing of subjective time. How time is extracted from multisensory inputs is scantly known. Utilizing psychophysical testing and electroencephalography, we show in healthy human adults that odors modulate object visibility around critical flicker-fusion frequency (CFF)-the limit at which chromatic flickers become perceived as a stable color-and effectively alter CFF in a congruency-based manner, despite that they afford no clear environmental temporal information. The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity. These findings point to a neuronal network in the right temporal cortex that executes flexible temporal filtering of upstream visual inputs based on olfactory information. Moreover, they collectively indicate that the very process of sensory integration at the stage of object processing twists time perception, hence casting new insights into the neural timing of multisensory events.
They linked what is known about natural information processing in bacteria: Learning from Bacteria about Natural Information Processing to what is known about how Feedback loops link odor and pheromone signaling with reproduction in all living genera.
The feedback loops typically prevent virus-driven energy theft from causing the mutations that have been linked to all pathology by all serious scientists.For comparison, see: Finding what fuels the ‘runaway train’ of autoimmune disease

It has been a long-standing observation in the clinic that autoimmune diseases evolve over time, attacking an ever-expanding array of organs and tissues – a phenomenon known as ‘epitope spreading…

The observation fails to link the virus-driven degradation of messenger RNA to all pathology via energy-dependent changes in the microRNA/messenger RNA balance. See for comparison: microRNA  Items: 1 to 20 of 63935

 
“It’s truly natural selection on a microcosm,” says van der Poel. “Once activated, there are ten different possible colors to represent different B cell clones. Over a week or two, the color diversity begins to shift—eventually one color dominates, representing a single clone winning out.”
 
It’s energy-dependent RNA-mediated autophagy. Activation is energy-dependent and RNA-mediated. Natural selection for energy-dependent codon optimality must be linked from ecological variation to ecological adaptation via the physiology of reproduction in all living genera. These researchers are making unsubstantiated claims about the “evolution” of pathology at a time when all serious scientists know that all pathology is caused by virus-driven energy theft.
Alternative splicing of pre-mRNA

Pseudoscientists hate what science explains! (3)

See also: Pseudoscientists hate what science explains (2)
Summary: In addition to germline silencing via information transfer to the physical landscape of supercoiled DNA, multicopy transgene arrays are linked from changes in the microRNA/messenger RNA balance to variation in their somatic expression level. That fact helps to establish the difference between healthy longevity and pathology across generations.
Problems with DNA replication can cause epigenetic changes that may be inherited for several generations
My summary: The polycomb repressive complex 2, additional chromatin- and small RNA–related pathways carry quantized energy as information from the epigenetic landscape. The information causes changes in microRNAs that modify histones, which links the energy to the transgenerational epigenetic inheritance of morphological and behavioral phentypes in the nematode model organism.
In addition to germline silencing via information transfer to the physical landscape of supercoiled DNA, multicopy transgene arrays are linked from changes in the microRNA/messenger RNA balance to variation in their somatic expression level. That fact helps to establish the difference between healthy longevity and pathology across generations.
The difference is food energy-dependent, RNA-mediated, and biophysically constrained by the pheromone-controlled physiology of reproduction in all living genera.
See for comparison: From Fertilization to Adult Sexual Behavior (1996)

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…. 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… That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans

We propose that CNEs [conserved non-coding elements] represent the ‘hard-wired’ sequence traces of these core animal group-specific GRNs [gene regulatory networks]. The alternative core GRNs of different animal lineages are reflected in their having alternative CNEs. However, because of their co-evolution from a common metazoan ancestor, the core GRNs of different animal groups often utilize the same regulatory genes. As a result, distinct yet parallel sets of CNEs have become irreversibly associated with the same genes that coordinate core developmental networks in diverse animal groups. Indeed, this evolution of regulatory elements may underlie the astounding diversification of animal body plans that was seen during the Cambrian period approximately 550 million years ago.

No experimental evidence suggests that regulatory elements evolved.
Predicting phenotypic variation in yeast from individual genome sequences
No experimental evidence predicts a link from gain of function mutations to evolution
Differential DNA mismatch repair underlies mutation rate variation across the human genome
All experimental evidence links natural selection for energy-dependent codon optimality to mutation rate variation across species and to individual differences in the human genome via the pheromone-controlled physiology of reproduction.

3D structures of individual mammalian genomes studied by single-cell Hi-C

Reported as: Scientists have determined the 3D structures of intact mammalian genomes from individual cells, showing how the DNA from all the chromosomes intricately folds to fit together inside the cell nuclei. The research is published in Nature this week. http://go.nature.com/2n6psaw

My comments:

See also: 3D RNA and Functional Interactions from Evolutionary Couplings “…the ongoing explosion of available sequence data means that the outlook for elucidating functional interactions in mRNAs, lncRNAs, and viral genomes, as well as their protein-binding partners, is promising.” http://dx.doi.org/10.1016/j.cell.2016.03.030

Virus-driven energy theft causes the degradation of messenger RNA in all organized genomes. That fact threatens anyone who has ever reported results in the context of mutations, natural selection and evolution because natural selection occurs only for energy-dependent codon optimality.

It would be even more amazing if they told the truth about energy-dependent amino acid substitutions that stabilize supercoiled DNA, which links chromosomal rearrangement to all biodiversity via the physiology of reproduction in species from microbes to humans. See: http://science.sciencemag.org/content/355/6328/910

See other comments to this Nature Facebook page
Addendum: Say goodbye to mutation-driven evolution. Everything known to serious scientists about biophysically constrained endogenous RNA interference and the pheromone-controlled physiology of reproduction has been linked from the de novo creation of nucleic acids to energy-dependent amino acid substitutions that differentiate all cell types in all living genera via fixation in organized genomes.
See: Transgenerational transmission of environmental information in C. elegans
They link diet- and stress-induced changes in heterochromatin from repressed repetitive elements that escape epigenetic reprogramming to phenotypic variation in mammals. It is obvious that heterochromatin provides the link from the molecular mechanisms of biophysically constrained protein folding chemistry to the epigenetic transmission of information between generations. But they speculate that the transgenerational epigenetic inheritance of environmentally triggered changes in expression from repressed chromatin may be linked to ecological adaptations.
See for comparison: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

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

Ben Lehner and his co-authors have consistently tried to sneak up from behind and link explanations of energy-dependent top-down causation from mutations to evolution.
Others are also ignoring the experimental evidence that links energy-dependent changes in microRNAs to healthy longevity or from virus-driven energy theft to all stress-linked pathology.
See: Stress-induced changes in miRNA biogenesis and functioning
See for comparison: I am not a story

Reported as: Life is not a neat narrative, it’s a patchwork of competing, even contradictory, forces. Sensations are too spurious and memory too fickle for the formation of reliable storylines. Reject the impulse to narrativise. Summer Reads from the Aeon archive: http://ow.ly/bLd430ekoJn

Re: Sensations are too spurious and memory too fickle for the formation of reliable storylines.

My comment: Too late for more of this nonsense. See: Olfaction Warps Visual Time Perception

 

The sense of smell in bacteria has been linked from the physiology of pheromone-controlled reproduction to our visual perception of mass and energy in the context of the space-time continuum via food energy.

See for comparison: Quantum common sense

We don’t need a conscious mind to measure or look. With or without us, the Universe is always looking

My comment: No, it’s Santa Claus who sees you when your sleeping; He knows when you’re awake. And he knows if you’ve been bad or good, so be good for goodness sake.

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.

 

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

Energy-dependent physical and biophysical constraints (7)

See first: Energy-dependent physical and biophysical constraints (6)
Stems Cells in the Hypothalamus Slow Aging in Mice
My comment to The Scientist

Cai says microRNAs could be a potential mechanism by which hypothalamic neural stem cells have such wide-ranging effects on aging, yet he believes that neurogenesis may also be involved.

See also: Feedback loops link odor and pheromone signaling with reproduction

At least 10,000 neurons in 26 different brain areas appear to transmit signals directly to GnRH neurons.  GnRH neurons 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. 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 also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

…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, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.

More than 63,000 indexed articles on PubMed link energy-dependent changes in the microRNA/messenger RNA balance to healthy longevity. Many of them also link the virus-driven theft of quantized energy from mutations to pathology such as John McCain’s glioblastoma. He will probably be treated with microRNAs, but that fact may not be reported because the effective treatment is a refutation of neo-Darwinian pseudoscientific nonsense about mutations, natural selection, and evolution.

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

Energy-dependent physical and biophysical constraints (6)

Conclusion: Like Richard Dawkins, Magnus S. Magnusson is a pseudoscientist.

A light-induced change in an endogenous substrate found in all cell types of all living genera links femtosecond blasts of UV light from the de novo creation of the innate immune system to RNA-mediated DNA repair in species from microbes to humans. The theft of quantized energy by viruses has been linked to all pathology.

The speed at which quantum decoherence occurs makes it difficult for virus-driven energy theft to be carried from one generation to the next via chromosomal inheritance, which is the only way that nutrient-dependent pheromone-controlled transgenerational epigenetic inheritance occurs — if it does not occur automagically in the small minds of theorists.

See first: Energy-dependent physical and biophysical constraints (5)
See next: Design of a synthetic yeast genome
They use what occurs in the context of natural selection for quantized energy-dependent changes in base pairs and link RNA-mediated amino acid substitutions from changes in enzymes and feedback loops. The feedback loops link the pheromone-controlled de novo creation of more receptors via the physiology of reproduction, which biophysically constrains viral latency in all organized genomes.
Their work was reported today, July 26, 2017 in the context of Scientists build DNA from scratch to alter life’s blueprint with my emphasis

Boeke, a researcher at New York University, directs an international team of 11 labs on four continents working to “rewrite” the yeast genome, following a detailed plan they published in March.

The research may reveal basic, hidden rules that govern the structure and functioning of genomes.

All serious scientists known that the structure and function of all organized genomes is energy-dependent and RNA-mediated. For example, in all animals the functional structure of supercoiled DNA is controlled by food odors and pheromones in the context of the physiology of energy-dependent reproduction that links food energy-dependent changes in the microRNA/messenger RNA balance to healthy longevity. Alternatively, virus-driven energy theft links the degradation of messenger RNA from mutations to all pathology.

See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

The question arises: Does Boeke or anyone like him know that the organized genome of yeast is rewritten only in the context of the food energy-dependent pheromone-controlled biophysical constraints on viral latency? I ask because he may be hiding something. Anyone who does not know how chirality and autophagy biophysically constrain viral latency is not likely to have written a book chapter like this, which was co-authored by J.D. Boeke in 1988.

See: Yeast Ty Elements as Retroviruses in  Viruses of Fungi and Simple Eukaryotes

The title of J.D. Boeke’s latest effort: Design of a synthetic yeast genome, would make any young earth creationist proud of his Boeke’s accomplishment. It attests to facts about “design” that atheistic hate mongers like Richard Dawkins and other pseudoscientists have linked from mutations and natural selection to evolution.

See: Mutation-Driven Evolution

See also for example: Magnus S. Magnusson’s comments on Richard Dawkins event cancelled over his ‘abusive speech against Islam’ Magunsson started removing my responses a few hours ago.

I attempted to discuss the fact that Boeke and others use base substitutions within ORFs to introduce or remove enzyme recognition sites. That is how they facilitate the energy-dependent assembly of synthetic chromosomes.

But there’s more! Boeke’s history of publications links nearly 30 years of pseudoscientific nonsense to an impressive refutation of neo-Darwinian theory. The design of the synthetic yeast genome via the energy-dependent assembly of synthetic chromosomes attests to the fact that natural selection for energy-dependent codon optimality is the link to the design of all biophysically constrained biodiversity.

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

Some people might think that pseudoscientists can recover from refutation linked to the stability of messenger RNA (mRNA), but the recovery time ended two decades ago with publication of From Fertilization to Adult Sexual Behavior

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…

The proteins do not automagically create themselves. Energy-dependent changes in chirality must be linked from autophagy to biophysically constrained viral latency. In that context, this report is another clear refutation of mutation-driven evolution.

See: Lipophilic siRNA targets albumin in situ and promotes bioavailability, tumor penetration, and carrier-free gene silencing

These data reveal the immense promise of in situ albumin targeting for development of translational, carrier-free RNAi-based cancer therapies.

The increased amount of information on naturally occurring energy-dependent RNA interference (RNAi) linked to cancer treatment was reported as: Molecular hitchhiker on human protein signals tumors to self-destruct

“What fascinates and excites me most about this approach, in addition to improved tumor penetration, is lack of toxicity at a relatively high dose,” she said. “We could potentially use our siRNA delivery system to target several genes simultaneously or sequentially. Most cancers are driven by multiple abnormal genes, so targeting one often leads to activation of others as the tumor adapts.”

Tumors do not adapt. Viruses quickly adapt via energy theft and the substitutions of amino acids in their genomes. The amino acid substitutions in the tumors cause the tumors to adapt to the lack of energy-dependent microRNAs carried by albumin. That is how virus-driven energy theft is linked to the proliferation of undifferentiated cell types in all tissues of all organisms.

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

As detailed here, the clear identity and easy alignment of these sequences makes them good candidates for estimating phylogeny, and they can reliably be found and identified across all members of a clade of interest. Their relatively slow evolution [3] also means that they can easily be identified in de novo assemblies of genomes.

The energy-dependent microRNA flanking sequences do not evolve and genes do not assemble themselves.  Quantized energy as information biophysically constrains virus-driven energy theft, which would otherwise link mutations to all pathology.

Young earth creationists recently placed the virus-driven theft of quantized energy into the context of Cancer Research Confirms the Curse.

…the cancer-suppressing molecule NAD+ diminishes with age appeared in the same Science issue.3Harvard Medical School News summarized the findings. As NAD+ lessens, “DNA breaks go unrepaired and, as these breaks accumulate over time, precipitate cell damage, cell mutations, cell death and loss of organ function.”4 It seems the only way to cure cancer would be to somehow reach into and constantly correct every cell’s mutations.

Carrier-free gene silencing links femtosecond blasts of UV light from the anti-entropic virucidal effects of sunlight on contact with water to everything serious scientists know about food energy-dependent top-down causation and changes in the microRNA/messenger RNA balance, which have been linked to all biophysically constrained biodiversity via what organisms eat and the physiology of their pheromone-controlled reproduction.

See: UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

The sequences have been selected according special charge distributions and lifetimes of excimer states previously characterized by femtosecond infrared spectroscopy.(3a, 3c, 3d) With these selected sequences we demonstrate that repair occurs when the intrastrand charge transfer leads to a suitably charged nucleotide adjacent to the lesion.

A femtosecond is the SI unit of time equal to 10−15 or 1/1,000,000,000,000,000 of a second; that is, one quadrillionth, or one millionth of one billionth, of a second.[1] For context, a femtosecond is to a second as a second is to about 31.71 million years; a ray of light travels approximately 0.3 µm (micrometers) in 1 femtosecond, a distance comparable to the diameter of a virus.[2]

For comparison: One picosecond is equal to 1000 femtoseconds (fs). Theoretical physicists who thought they knew something about the nature of quantum coherence based their theories on measurements of timescales up to 1.5 picoseconds (ps), but they have since learned that decoherence occurs within 60 fs. The transfer of energy in the context of photosynthesis clearly links the anti-entropic virucidal energy of UV light to RNA-mediated DNA repair in much less time than theorists realized.

See: Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer

Given the relatively well-defined structure of the FMO protein, and comparative couplings between chlorophylls to other photosynthetic systems, the observed extremely fast decoherence should be viewed as general, bringing to question any significant quantum coherent transport contributions to photosynthesis.

See also: OLYMPUS experiment sheds light on structure of protons

…unlike the theoretical predictions, analysis of the OLYMPUS measurements suggests that, most of the time, only one of the photons has high energy, while the other must carry very little energy indeed…

The differences in the energy of photons and the amount of time it takes for energy-dependent RNA-mediated DNA repair link displays of ignorance by Magnus S. Magnusson and other atheistic hate-mongers that can be compared to any display by anyone who has ever been involved in linking pattern recognition to biophysically constrained life on Earth.

For comparison, that is what young earth creationists have done with the information about energy as information from Biblical Genesis.

See also: One billion suns: World’s brightest laser sparks new behavior in light

The light’s coming off at different angles, with different colors, depending on how bright it is.

That phenomenon stemmed partly from a change in the electron, which abandoned its usual up-and-down motion in favor of a figure-8 flight pattern. As it would under normal conditions, the electron also ejected its own photon, which was jarred loose by the energy of the incoming photons. But the researchers found that the ejected photon absorbed the collective energy of all the scattered photons, granting it the energy and wavelength of an X-ray.

See: The Reality of Color Is Perception

Color is one of the longstanding puzzles in philosophy, raising doubts about the truthfulness of our sensory grasp on things, and provoking concerns as to the metaphysical compatibility of scientific, perceptual, and common sense representations of the world. Most philosophers have argued that colors are either real or not real, physical or psychological. The greater challenge is to theorize the subtle way that color stands between our understanding of the physical and the psychological.

See for comparison: Olfaction Warps Visual Time Perception

The fact that olfaction warps visual time perception links the speed of light on contact with water from the visual appeal of a rainbow to the integration of all sensory input and our appreciation of how energy and mass are linked across the time-space continuum via what is known about the sense of smell in bacteria and the food energy-dependent pheromone-controlled physiology of reproduction in all living genera.

For comparison, Magnus S. Magnusson co-authored “Complex spike patterns in olfactory bulb neuronal networks”  He and his colleagues failed to link fast decoherence from the anti-entropic virucidal energy of sunlight to all biodiversity via the physiology of reproduction and RNA-mediated DNA repair.

In the world of those who have consistently linked olfaction to our visual perception of energy and mass in the context of the space-time continuum, Magnusson can be referred to as a biologically uninformed science idiot — if only because he has no expertise in any scientific discipline.

Conclusion: Like Richard Dawkins, Magnus S. Magnusson is a pseudoscientist.

A light-induced change in an endogenous substrate found in all cell types of all living genera links femtosecond blasts of UV light from the de novo creation of the innate immune system to RNA-mediated DNA repair in species from microbes to humans. The theft of quantized energy by viruses has been linked to all pathology via the difference between “Nature” and God’s perfect “Creation.”

The speed at which quantum decoherence occurs makes it difficult for virus-driven energy theft to be carried from one generation to the next via chromosomal inheritance, which is the only way that nutrient-dependent pheromone-controlled transgenerational epigenetic inheritance occurs — if it does not occur automagically in the small minds of theorists.

Although that fact has been repeatedly revealed in the extant scientific literature, which includes texts like the Holy Bible, atheistic hate-mongers refuse to read anything that challenges their beliefs at the same time they either claim to believe in nothing or attack the beliefs of intelligent scientists.

See for examples of what pseudoscientists are likely to believe.

This New Equation Could Unite The Two Biggest Theories in Physics

Quantum entanglement… describes the way that two particles can interact in such a way that they become inexorably linked, and essentially ‘share’ an existence.

The Universe According to Emmy Noethe

…energy may not be conserved “locally” — that is, in an arbitrarily small patch of space — but everything works out when the space is sufficiently large.

That claim forced others to make their ridiculous theories fit into the context of “…the idea that the Universe expanded just like a balloon shortly after the Big Bang.”

Stephen Hawking And 32 Top Physicists Just Signed a Heated Letter on The Universe’s Origin

…three physicists heavily criticised inflation theory – the idea that the Universe expanded just like a balloon shortly after the Big Bang. The article went as far as claiming that the model “cannot be evaluated using the scientific method” – the academic equivalent of saying it isn’t even real science.

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

Energy-dependent physical and biophysical constraints (2)

Summary: The mind does not exist in nature. It is a manifestation of how ecological variation must be linked to the creation of food energy-dependent pheromone-controlled ecological adaptations.
Energy-dependent physical and biophysical constraints (1)
The energy-dependent de novo creation of all receptors is biophysically constrained.
See: Channel opening and gating mechanism in AMPA-subtype glutamate receptors
This was reported as: Scientists capture first image of major brain receptor in action

Defects in glutamate receptors, or the processes they mediate, are implicated in neurodegenerative disorders such as Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, multiple sclerosis and glaucoma; psychiatric disorders such as anxiety, depression, schizophrenia, and drug use disorders; as well as in acute disorders such as brain trauma and stroke. The new structure of an active AMPA receptor and understanding of the activating mechanism create a solid platform for developing therapeutics to treat neurological disorders that are associated with glutamate receptor dysfunction.

The activating mechanism is energy-dependent and virus-driven energy theft is linked to all pathology via changes in the microRNA/messenger RNA balance. Search the PubMed database for “microRNA” and “glutamate receptor,” “Alzheimer’s,” “Parkinson’s,” “Huntington’s,” “multiple sclerosis,” “glaucoma,” “anxiety,” “depression,” “schizophrenia” and any other disorders.
For example: microRNA+glutamate+receptor 

MicroRNA in glutamate receptor-dependent neurological diseases

But wait… There’s more.
“Alzheimer’s,”
“Parkinson’s,”
“Huntington’s,”
“multiple sclerosis,”
“glaucoma,”
“anxiety,”
“depression,”
“schizophrenia”

See also:  Cytosis: A Cell Biology Board Game

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses! Energy is required to build the enzymes, hormones and receptors that protect organized genomes from the virus-driven degradation of messenger RNA, which links mutations to all pathology.

See also: Excerpt from update #16

We’ve had a ton more of you volunteer to playtest the Subatomic PnP than we expected, which is terrific.

I did have the PnP ready to send out… or so I thought. Somehow every time we’ve played Subatomic the past several weeks I’ve made significant changes. We’ll integrate a change into the rulebook, player mat, cards… and then we play again, and make another set of significant changes all over again.

I want to get a good handle on which of these changes will stay and which don’t work well over the long term before I send the PnP to you all. All that being said, I’m planning to get the link out to you in the next week or so.

As all serious scientists know, the changes that stay will link quantized energy from the subatomic particles to our visual perception of energy and mass in the context of Olfaction Warps Visual Time Perception and a series of articles that were published by young earth creationists.
See: Researchers identify ‘tipping point’ between quantum and classical worlds
The “tipping point” between quantum and classical worlds is energy-dependent and biophysically constrained via the anti-entropic virucidal effect of sunlight, which is linked to the physiology of food energy-dependent reproduction in all living genera.
See also: Subatomic Particles, Part 1: Leptons
Subatomic Particles, Part 2: Baryons, the Substance of the Cosmos
Subatomic Particles, Part 3: Mesons
Subatomic Particles, Part 4: Gauge Bosons, the Glue That Holds the Universe Together

We have seen the delicate balance between the four forces; each is perfectly designed to make life possible. We have explored the fleeting nature of so many subatomic particles. Yet the ones needed for atomic chemistry and life are stable. The masses and forces are precisely tuned. If the up quark were just slightly heavier than the down quark, all matter would decay into neutrons. Slightly change the charge of an electron or a quark and atoms could never form larger structures due to electric repulsion. It’s clear the universe is perfectly designed for life.

What then can be said about the virus-driven degradation of messenger RNA that links mutations to all pathology? What challenges to perfectly designed life would theorists like serious scientists to consider outside the context of food energy and human idiocy?
For example, this claim was reasserted in the June 2017 issue of Discover Magazine:

…energy may not be conserved “locally” — that is, in an arbitrarily small patch of space — but everything works out when the space is sufficiently large.

See for comparison: Food energy

Richard Feynman was a Nobel prize winning Theoretical Physicist who popularized physics… This snippet is taken from one of his lectures in the series “The character of Physical Law” where he complains about all the different units that are used to measure the single concept of Energy.
Claims that the local conservation of energy do not require conservation in the context of an ever-expanding time-space continuum are additional examples of human idiocy. The fact that theoretical physicists must return to the examination of a early 1900’s theory set forth by an uneducated layperson attests to the reason why even Richard Feynman ridiculed those from his discipline.
See also: A Neuroscientist Just Tricked 4 Dodgy Journals Into Accepting a Fake Paper on ‘Midi-Chlorians’

…a prominent neuroscientist has tricked four publications into accepting a totally fake paper about midi-chlorians – the entirely fictional life forms in Star Wars that make ‘the force’ possible.

See also: Dear Readers – Hiatus From Blog

For five years, I have written summaries of current scientific literature in subjects related to how mind exists in nature.

The mind does not exist in nature. It is a manifestation of how ecological variation must be linked to the creation of food energy-dependent pheromone-controlled ecological adaptations.
My comment to Jon Lieff.

Finally. By the time the “Cytosis” becomes available, everyone else will learn how much confusion you have contributed via your failure to integrate what is known about energy-dependent RNA-mediated cell type differentiation into a cohesive representation of biophysically constrained top-down causation that exists outside the context of your nonsense about evolution.

Cytosis: A Cell Biology Board Game A board game taking place inside a human cell! Players compete to build
enzymes, hormones and receptors and fend off attacking Viruses!

I look forward to reviewing your book at the earliest opportunity to do so. See for example of a recent review: “How Can Physics Underlie the Mind?: Top-Down Causation in the Human Context (The Frontiers Collection)”

Big Bang

Richard P. Feynman refuted theistic evolution

Summary: Among other delightful examples of his expertise in physics, Feynman presciently linked natural selection for energy-dependent codon optimality from food energy-dependent pheromone-controlled biophysically constrained chromosomal rearrangements to healthy longevity. He also linked the radiation-induced theft of quantized energy to mutations in phages via amino acids that increase the virulence of the viruses. Updated information is presented in the context of refutations by many others who might otherwise claim to believe in theistic evolution.
The miR-23a~27a~24-2 microRNA cluster buffers transcription and signaling pathways during hematopoiesis
This is an uncorrected proof.
They link food energy-dependent changes in the microRNA/messenger RNA balance from amino acid substitutions to cell type differentiation via the physiology of pheromone-controlled reproduction in species from microbes to humans in the context of this claim from Dobzhansky (1973) Nothing in Biology Makes Any Sense Except in the Light of Evolution.

…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).

Cell type differentiation during hematopoiesis links the amino acid substitution that differentiates the alpha chains of hemoglobin to the differentiation of all other cell types in all other individuals of all vertebrate species via the conserved molecular mechanisms of energy-dependent pheromone-controlled cell type differentiation in all invertebrates.

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

This is my invited review of nutritional epigenetics that was returned without review by the guest editors of a special edition of the journal “Nutrients.”

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.

See for comparison: Surely You’re Joking, Mr. Feynman! (Adventures of a Curious Character)

Chapter 10: A Map of the Cat?

My summary: Among other delightful examples of his expertise in physics, Feynman presciently linked natural selection for energy-dependent codon optimality from food energy-dependent pheromone-controlled biophysically constrained chromosomal rearrangements to healthy longevity. He also linked the radiation-induced theft of quantized energy to mutations in phages via amino acids that increase the virulence of the viruses.

The delayed dissemination of accurate information about biophysically constrained biologically-based cause and effect has already contributed to the unnecessary suffering and premature deaths of thousands to millions of people since the time that Richard Feynman reported on mutations in bacteriophages. He realized that the mutations link the theft of quantized energy from living organisms to the amino acid substitutions in viruses that cause the degradation of messenger RNA, which links mutations to all pathology. If not for his love of physics and the pseudoscientific nonsense of neo-Darwinian theorists, all serious scientists would have linked quantum physics to quantum souls.

See for example: Olfaction Warps Visual Time Perception

Our perception of the world builds upon dynamic inputs from multiple senses with different temporal resolutions, and is threaded with the passing of subjective time. How time is extracted from multisensory inputs is scantly known. Utilizing psychophysical testing and electroencephalography, we show in healthy human adults that odors modulate object visibility around critical flicker-fusion frequency (CFF)-the limit at which chromatic flickers become perceived as a stable color-and effectively alter CFF in a congruency-based manner, despite that they afford no clear environmental temporal information. The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity. These findings point to a neuronal network in the right temporal cortex that executes flexible temporal filtering of upstream visual inputs based on olfactory information. Moreover, they collectively indicate that the very process of sensory integration at the stage of object processing twists time perception, hence casting new insights into the neural timing of multisensory events.

See also: The Sense of Smell Impacts Metabolic Health and Obesity

A PubMed search for microRNA and the disease you wish to prevent or effectively treat will help you to eliminate the foolishness of theorists who have failed to link the de novo creation of microRNAs to all biodiversity via the physiology of reproduction and biophysically constrained viral latency.

For example: microRNA alzheimers

To place your searches into the proper context, see: Germ line–inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition

Biologically uniformed theorists invented the term “enhancer” for ambiguous use in the context of energy-dependent changes in the microRNA/messenger RNA balance. They obfuscate facts about food energy and feedback loops that link pheromones to the biophysically constrained viral latency the enables ecological adaptations via use of “enhancer function.”

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

Natural selection for energy-dependent codon optimality links food energy-dependent changes in the microRNA/messenger RNA balance to protection from the virus-driven degradation of messenger RNA, which links mutations to all pathology unless terms such as enhancers and enhancer function are used to obfuscate facts about The phylogenetic utility and functional constraint of microRNA flanking sequences

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

There is no such thing as de novo assemblies of genomes. Food energy must be linked to the pheromone-controlled physiology of reproduction to link ecological variation to ecological adaptation via feedback loops.

See: Feedback loops link odor and pheromone signaling with reproduction

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.

7/26/13

Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.

See also: Researchers find new mechanism for genome regulation

Interestingly, this type of liquid-liquid phase separation is very sensitive to changes in temperature, protein concentration, and pH levels.

The sensitivity is food energy-dependent and RNA-mediated. Pseudosciedntists should stop their foolishness long enough to realize there is nothing new about the mechanisms of genome regulation. The mechanisms controlled by pheromones link the physiology of reproduction and chromosomal inheritance to healthy longevity unless they link virus-driven energy theft to all pathology via changes in the microRNA/messenger RNA balance.

See also: CSmiRTar: Condition-Specific microRNA targets database

…(Condition-Specific miRNA Targets). CSmiRTar collects computationally predicted targets of 2588 human miRNAs and 1945 mouse miRNAs from four most widely used miRNA target prediction databases (miRDB, TargetScan, microRNA.org and DIANA-microT) and implements functional filters which allows users to search (i) a miRNA’s targets expressed in a specific tissue or/and related to a specific disease…

See for comparison: Creationism support is at a new low. The reason should give us hope.

Stuart Kauffman refutes theistic evolution

God's shrinking role in salvation (2)

Conclusion: There is no such thing as a blind dance of atoms. Quantized energy-dependent changes link angstroms to ecosystems in all living genera via the physiology of reproduction. Serious scientists do not link “high-level cause and purposes” to anything that does not link what organisms eat from food energy to the physiology of reproduction. Only pseudoscientists claim that ideas about “emergence” are “…a remarkable synthesis across fields and levels.”
See: God’s shrinking role in salvation

These 6 Common Vegetables Are Actually All The Same Plant Species
The morphological traits are quantized energy-dependent, They link the de novo creation of plant microRNAs from the anti-entropic virucidal energy of sunlight to the physiology of reproduction in all living genera via the energy-dependent creation of microRNAs in animals.
See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

The interactions of these small noncoding RNAs in such primitive species have wide-reaching effects, from increasing viral and bacterial proliferation, better responses to stress, increased virulence, to manipulation of host immune responses to provide a more ideal environment for these pathogens to thrive. Here, we explore those roles to obtain a better grasp of just how complicated disease truly is.

Disease is much more complicated when it cannot be linked from top-down causation via physics, chemistry, and molecular biology. See for comparison; ‘Liquid Light’ Can Bend Around Objects in a Frictionless Flow
Thanks to Fiona Myrglwitz for calling attention to this claim that they can:

…conceive and design future photonic superfluid-based devices where losses are completely suppressed.

That suggests they may link the metabolism of bacteria from the creation of uranium isotopes to the errors made in mathematical models of evolved traits. The errors in mathematical models fail to link quantized energy-dependent changes in the microRNA/messenger RNA balance to the biophysically constrained by the physiology of reproduction.The errors are magnified by the fact that they fail to link incompletely suppressed energy losses to all pathology via the virus-driven degradation of messenger RNA.

For comparison, the physiology of reproduction links the solar analemma to the biophysically constrained energy in uranium, which is the reason that radiation therapy is used to treat cancer. Everything known about the link from sunlight to radiation therapy can be placed into context via use of the Mobius strip.
It is an example of how nutrient energy-dependent pheromone-controlled choices made by all living genera must link feedback loops to the biophysically constrained virucidal energy of sunlight. Any loss of energy can potentially be linked to the proliferation of viruses via a slight drop in the potential of hydrogen (pH).

That fact makes it more be obvious that God’s shrinking role in salvation can be viewed in the context of medical practices that appear to make physicians and/or other medical professionals your savior(s). They will warn you to avoid too much sun exposure and treat your cancer with radiation because you did not get enough sun exposure to protect you via the increased production of Vitamin D.
They will tell you to use a chemical “sun-screen” and treat your cancer with chemotherapy that was caused by the chemical imbalance your body could no longer cope with.
See also: Electrolytes induce long-range orientational order and free energy changes in the H-bond network of bulk water
This was reported as: A single ion impacts a million water molecules
So far as I know there has been no discussion of the link from free energy changes in the H-bond network to the hydrophobicity of supercoiled DNA, which links quantum physics to the protection of all organized genomes from the virus-driven degradation of messenger RNA and genomic entropy.
Could the lack of discussion be attributed to the claim that no one understands quantum mechanics in an age where the speed of light on contact with water has been linked to all biodiversity via energy-dependent changes in angstroms to ecosystems in all living genera?
From last year: How Can Physics Underlie the Mind? Top-Down Causation in the Human Context

My review on Amazon (6/12/16)

Others linked the sun’s anti-entropic virucidal energy from energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.

Ellis comments on at least one of Schrodinger’s claims from “What is Life?” but he largely ignores the energy-dependent links from ecological variation to ecological adaptation that also were reported in two recent publications. See: “Structural diversity of supercoiled DNA” and “Epigenetics and Genetics of Viral Latency.”

Ellis cannot be held accountable for not knowing the most recent work (May 11, 2016) reported that “…viral latency is responsible for life-long pathogenesis and mortality risk…”

However, it seems inappropriate for anyone whose opinions are held in high regard to ignore everything else that is known about energy-dependent RNA methylation and the biophysically constrained morphological and behavioral diversity of all living genera. Experimental evidence has established facts that are being used to link the Precision Medicine Initiative to the National Microbiome Initiative via attempts to crack the olfactory code.

When researchers report the direct link from energy-dependent RNA methylation to differences in behavior, this book will be compared to Masatoshi Nei’s “Mutation-driven evolution.” The biggest difference between the two seems to be that Ellis tries to link emergence to evolution via Darwin’s “conditions of life.”

But he now bears the burden of the report in “Science” of nutrient energy-dependent pheromone-controlled weekend evolution of the bacterial flagellum: “Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system.”

The “resurrection” is obviously energy-dependent and it also links the innate immune system to biophysically constrained biologically-based cause and effect in species from microbes to humans via RNA-mediated amino acid substitutions. Resurrecting Darwin’s “conditions of life” after they were ignored by neo-Darwinists for many decades should not be attempted by physicists, cosmologists, or biologically uninformed theorists from any other discipline without first learning more about what is known about the RNA-mediated links from physics and chemistry to molecular epigenetics.

See for comparison, this review by

An admirable, systematic approach to the issue of emergence from physics to sociology, of great originality, broad scope, and deep understanding. George Ellis argues with admirable clarity of thought that much of the world we live in is governed not by the blind dance of atoms, but by high-level causes and purposes. This is a much needed book and a remarkable synthesis across fields and levels. I know of no other book where the evidence for emergence is presented so thoroughly and with as much insight.

There is no such thing as a blind dance of atoms. Quantized energy-dependent changes link angstroms to ecosystems in all living genera via the physiology of reproduction. Serious scientists do not link “high-level cause and purposes” to anything that does not link what organisms eat from food energy to the physiology of reproduction. Only pseudoscientists claim that ideas about “emergence” are “…a remarkable synthesis across fields and levels.”

See: God’s shrinking role in salvation (3)
Amino acid modification FA_Epigenetics_Table1

Food energy-dependent cell type differentiation (2)

Summary: The concept of “faster-evolving DNA” regions in the context of nucleotide variation in both the 16S and 12S sequences is not consistent with any accurate representation of how the functional structure of supercoiled DNA must be linked from energy-dependent changes in angstroms to ecosystems in all living genera. Conserved molecular mechanisms link the sense of smell in bacteria from the de novo creation of olfactory receptor genes to the physiology of reproduction via the microRNA/messenger RNA balance and Feynman’s claim about the human idiocy of theoretical physicists who use different terms for their measurements of food energy.
See first: Food energy-dependent cell type differentiation
See also: Bacterial Communication And Relevance Of Quantum Theory
Thanks to antagonist Jay R. Feierman for calling this to my attention, See: Fwd: Bacterial Communication And Relevance Of Quantum Theory

The recent findings confirm that bacteria communicate each other through chemical and electrical signals. Bacteria use chemical signaling molecules which are called as quorum sensing molecules (QSMs) or autoinducers. Moreover, the ion channels in bacteria conduct a long-range electrical signaling within biofilm communities through propagated waves of potassium ions and biofilms attracts other bacterial species too. Both communication process are used by bacteria to make their own survival strategies. In this article, we model this bacterial communication mechanism by complex Ginzburg-Landau equation and discuss the formation of patterns depending on kinematic viscosity associated with internal noise. Again, the potassium wave propagation is described by the non-linear Schrodinger equation in a dissipative environment. By adding perturbation to non-linear Schrodinger equation one arrives at Complex Ginzburg-Landau equation. In this paper we emphasize that at the cellular level (bacteria) we use Complex Ginzburg-Landau equation as a perturbed Non-linear Schrodinger equation to understand the bacterial communication as well as pattern formation in biofilms for certain range of kinematic viscosity which can be tested in laboratory experiment. Here, the perturbation is due to the existence of nonthermal fluctuations associated to the finite size of the bacteria. It sheds new light on the relevance of quantum formalism in understanding the cell to cell communication.

For everyone who does not follow my posts on groups and in forums where they are not commonly edited or fail to appear because the moderators and administrators are biologically uninformed theorists, I reiterate:
Natural selection for energy-dependent codon optimality and nutrient energy-dependent quorum sensing have been linked from the pheromone-controlled physiology of reproduction in bacteria that naturally produce a uranium isotope to all morphological and behavioral biodiversity via an atoms to ecosystems model that refutes every aspect of neo-Darwinian theory and all theories linked to the claims of “Big Bang” cosmologists.
Clearly, Feedback loops link odor and pheromone signaling with reproduction (2005) in all living genera can be compared in the context of two claims, which were made by the moderator of the ISHE’s human ethology group, soon after I published Nutrient-dependent/pheromone-controlled adaptive evolution: a model (6/14/13)
7/25/13
Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.
7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
See for comparison: Quantum Souls

The sun’s energy flows to Earth as information that is absorbed by energy-dependent organisms. Along with nutrient-dependency and pheromones, it effects all living genera and ensures reproduction. God’s “conditions of life,” described in part by Darwin, come before natural selection.

For additional evidence that links the anti-entropic virucidal energy of sunlight to all biodiversity and the concept of quantum souls, I reiterate:
Figure 4: Conceptual model of uranium roll-front deposit formation. — from Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits (open access)

Precursors and conditions favouring the formation of uraninite, biogenic uraninite and non-crystalline U(IV) are illustrated.

The nutrient energy-dependent pheromone-controlled physiology of reproduction of bacteria that live underground was linked from thermodynamic cycles of RNA-mediated protein folding chemistry to the production of uranium isotopes. The obvious link from the quantized energy of sunlight to the de novo creation of all biodiversity also was reported in the context of 16S rRNA microbial community analysis in fish. Most authors report this in the context of a “DNA-based” analysis. That way, there is no need to differentiate between abiogeneis and biophysically constrained biogenesis. Start with genes and you do not need to explain how DNA was created.

See for comparison: Evaluation of the 16S and 12S rRNA genes as universal markers for the identification of commercial fish species in South Africa

The nucleotide variation in both the 16S and 12S sequences was suitable for identifying the large majority of the examined fish specimens to at least the level of genus, but was found to be less useful for the explicit differentiation of certain congeneric fish species. It is recommended that one or more faster-evolving DNA regions be analysed to confirm the identities of closely-related fish species in South Africa.

The concept of “faster-evolving DNA” regions in the context of nucleotide variation in both the 16S and 12S sequences is not consistent with any accurate representation of how the functional structure of supercoiled DNA must be linked from energy-dependent changes in angstroms to ecosystems in all living genera. Conserved molecular mechanisms link the sense of smell in bacteria from the de novo creation of olfactory receptor genes to the physiology of reproduction via the microRNA/messenger RNA balance and Feynman’s claim about the human idiocy of theoretical physicists who use different terms for their measurements of food energy.
The amount of food energy, measured in calories, is linked to whether or not the organism starves to death before it reproduces. That’s how ecological variation in the supply of nutrients may lead to extinction of any species that fails to evolve into another species. So far, no experimental evidence of biologically-based cause and effect suggests that any species has ever evolved into another species.
Claims about the need for energy-dependent changes in supercoiled DNA to protect all organized genomes from the virus-driven degradation of messenger RNA, which is linked to mutations and all pathology may have have peaked with this publication:
Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs (5/25/17)

Over the last decade, it has become increasingly apparent that miRNAs have many important roles in the development of disease and cancer. Recently, however, their role in viral and bacterial gene regulation as well as host gene regulation during disease progression has become a field of interest.

More than 61,000 works published peer-reviewed works show why differences in the types of microRNAs are the most important consideration to energy-dependent healthy longevity or to virus-driven pathology.
MicroRNA Items: 1 to 20 of 61426
See for comparison: It’s Time to Start Calling Evangelicals What They Are: The American Taliban

Atheistic hate-mongers like Magnus S. Magnusson continue to disseminate this nonsense and encourage attacks on any views that link Creationism to Americanism. The hate-mongers don’t know who created energy or how energy-dependent ecological adaptation is linked from changes in base pairs to all biodiversity, but they will claim that American evangelicals are like the Taliban.

See for comparison:  The in vivo structure of biological membranes and evidence for lipid domains

The structure and organization of the cell membrane are central to many biological functions, and although they have been extensively studied, there is still much that we don’t understand. A wealth of detailed information has been obtained from studies of model lipid membranes. However, these systems are often highly simplified in composition and always lack the active processes found in cells. The major obstacle to studying membranes in vivo in living cells has been that high-resolution physical methods used to investigate membrane structure are not compatible with living organisms. To overcome this obstacle, we employed a new in vivo approach that allows membrane structure to be observed directly in the gram-positive bacterium B. subtilis. This approach relies on tuning the isotopic content of hydrogen within the membrane, and other parts of the bacterium, to generate neutron scattering spectra exclusively from the membrane. Using this approach, we confirmed that the structure of the B. subtilis membrane is lamellar and has an average hydrophobic thickness of 23.9 ± 0.9 Ångstroms (Å). We were also able to observe nanoscopic lateral membrane structures, consistent with the notion of lipid rafts. This experimental approach will allow for a wide range of future structural studies of the cell membrane (and possibly other classes of biomolecules) without the need for extrinsic probes or labels. In this way, it fundamentally changes the scope of nanoscale structural questions that can be addressed in vivo.

Reported as: This Is The First Ever Nanoscale Image of a Living Cell Membrane 

They link the energy-dependent de novo creation of the cell wall in Bacillus subtilus, a Gram-positive, catalase-positive bacterium, found in soil and the gastrointestinal tract of ruminants and humans, to all biodiversity on Earth via differences in hydrogen ions, hydrogen atom transfer in DNA base pairs in solution, and the pheromone-controlled physiology of reproduction.

Hydrogen ions are made by the removal of one electron from atomic hydrogen. That fact supports the the claims of those who have linked energy-dependent changes from atoms to ecosystems in all living genera via what occurs at the level of changes in angstroms. The changes in angstroms are linked to the innate ability of all cell types to signal other cell types via changes in the membrane that biophysically constrains the contents of the cell.
Although it is important that these researchers showed how the role of quantized energy from the sun is linked to biophysically constrained hydrophobicity in supercoiled DNA, anyone who has ever performed a “catalase” test to distinguish between pathogenic and non-pathogenic strains of Staphlococcus and Streptococcus before testing for beta-lactamase and resistance to oxacillin/methicillin has observed the release of hydrogen caused by the breakdown of the cell membrane.

Catalase is a common enzyme found in nearly all living organisms exposed to oxygen (such as bacteria, plants, and animals). It catalyzes the decomposition of hydrogen peroxide to water and oxygen.[3]”

Beta-lactamase provides antibiotic resistance by breaking the antibiotics’ structure. These antibiotics all have a common element in their molecular structure: a four-atom ring known as a β-lactam. Through hydrolysis, the lactamase enzyme breaks the β-lactam ring open, deactivating the molecule’s antibacterial properties.”

Congratulate the researchers who have just refuted every aspect of neo-Darwinian theory as was predicted by any intelligent microbiologist who has ever needed to identify and perform susceptibility testing on a pathogen to help a physician keep the pathogen from killing the patient.

And, remember the Hippocratic Oath. First, do no harm. If you are a physician who thinks that people evolved from bacteria, learn something about cell type differentiation via a visit to the microbiology lab at a local hospital. Most medical laboratory scientists will be happy to help you stop killing people with your ignorance.

Serious scientists have forced theorists to change their claims about the gene editing technology called CRISPR Cas9 to reflect the fact that the reason the technology failed miserably. The technology was based on naturally occurring endogenous RNA interference. It is now being reported as CRISPRi in the context of identifying new genes but outside the context of their energy-dependent de novo creation.

See: High-throughput CRISPRi phenotyping identifies new essential genes in Streptococcus pneumoniae

Genome‐wide screens have discovered a large set of essential genes in the opportunistic human pathogen Streptococcus pneumoniae. However, the functions of many essential genes are still unknown, hampering vaccine development and drug discovery. Based on results from transposon sequencing (Tn‐seq), we refined the list of essential genes in S. pneumoniae serotype 2 strain D39. Next, we created a knockdown library targeting 348 potentially essential genes by CRISPR interference (CRISPRi) and show a growth phenotype for 254 of them (73%). Using high‐content microscopy screening, we searched for essential genes of unknown function with clear phenotypes in cell morphology upon CRISPRi‐based depletion. We show that SPD_1416 and SPD_1417 (renamed to MurT and GatD, respectively) are essential for peptidoglycan synthesis, and that SPD_1198 and SPD_1197 (renamed to TarP and TarQ, respectively) are responsible for the polymerization of teichoic acid (TA) precursors. This knowledge enabled us to reconstruct the unique pneumococcal TA biosynthetic pathway. CRISPRi was also employed to unravel the role of the essential Clp‐proteolytic system in regulation of competence development, and we show that ClpX is the essential ATPase responsible for ClpP‐dependent repression of competence. The CRISPRi library provides a valuable tool for characterization of pneumococcal genes and pathways and revealed several promising antibiotic targets.

The de novo creation of essential genes has been placed into the context of a problem with antibiotic sensitivity testing.

 
The problem was introduced into susceptibility testing by biologically uninformed theorists who still may not know the difference between energy-dependent ecological adaptation and mutation-driven evolution.

Cell-type-specific genome editing with a microRNA-responsive CRISPR-Cas9 switch

The transient and conditional expression of our system using synthetic RNA could provide genome editing as a potentially ‘one-shot therapy’ to treat numerous genetic diseases. In conclusion, our miR-Cas9 switch combined with a RNA-delivery approach can selectively engineer genomes of target cells by detecting an endogenous miRNA signature, with potential benefits for synthetic biology, genome editing field and future therapeutic applications.

The conditional expression of genes is linked from food energy-dependent pheromone-controlled biophysically constrained viral latency to healthy longevity or from virus-driven energy theft to constraint breaking mutations and all pathology.

People like Jay R. Feierman and Magnus S. Magnusson tout the pseudoscienitific nonsense of theories in books such as this one. The Biology of Religious Behavior: The Evolutionary Origins of Faith and Religion
Their atheistic agenda is the antithesis of any factual representation of anything known to serious scientists about biophysically constrained energy-dependent biologically-based cause and effect.
See for comparison:  Mechanism of transmembrane signaling by sensor histidine kinases reported as:Scientists investigate how the sense of smell works in bacteria

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

See also: Eros is a novel transmembrane protein that controls the phagocyte respiratory burst and is essential for innate immunity
For a non-technical representation of everything currently known to serious scientists about the energy-dependent biophysically constrained physiology of pheromone-controlled biodiversity in all living genera see: The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002)
Could any serious scientist fail to link the novel transmembrane protein “Eros” from what organism eat to innate immunity via the non-technical representations in The Scent of Eros? If you know someone who you think is a serious scientist ask them about the representations made in The Biology of Religious Behavior: The Evolutionary Origins of Faith and Religion. If you learn that they think Faith and Religion “evolved,” I will add them to my growing list of pseudoscientists who continue to tout ridiculous theories.
 

Hard Science vs the neo-Darwinian "magic box"

Summary: Identical nucleotide sequences link energy-dependent changes in binding sites to different amino acids in different proteins. The binding sites are conserved in the orthologous mammalian genes.

  1. The in vivo structure of biological membranes and evidence for lipid domains
  2. Scientists investigate how the sense of smell works in bacteria
  3. Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits

As presciently predicted in the works of Richard Feynman and Bruce McEwen, bacteria feed on something that allows them to produce uranium isotopes in the context of their food energy-dependent biophysically constrained pheromone-controlled physiology of reproduction. The link from a light-activated endogenous substrate in all cell types must be viewed in the context of energy-dependent feedback loops that link sunlight to the anti-entropic constraint of atomic energy in uranium isotopes. Chromosomal inheritance prevents the evolution of one species into another.


at futurism.com

See:  Scientists Have an Experiment to See If the Human Mind Is Bound to the Physical World

What it could mean is this: that the human mind (consciousness) isn’t made up of the same matter governed by physics. Furthermore, it could suggest that the mind is capable of overcoming physics with free will. This could potentially be the first time scientists gain a firm grasp on the problem of consciousness. “It wouldn’t settle the question, but it would certainly have a strong bearing on the issue of free will,” said Hardy.

The idea that the mind isn’t made up of matter, which is governed by the Laws of Physics is ridiculous. You cannot take such a ridiculous idea and make it meaningful via experiments. The experiment would be meaningless. All experiments must start with a rational hypothesis or something that is known. Then you must attempt to add scientific support for extending what is known to something that becomes known via your experiment. Otherwise, you start with a theory and add nothing more than another theory. You don’t get answers to any questions.
See for example: Did humans evolve in Europe rather than Africa? We don’t have the answer just yet

Charles Darwin believed that humans evolved in Africa, because that’s where our closest ape relatives the chimpanzees and gorillas live. And during the twentieth century he was vindicated through a combination of fossil and genetic discoveries.

Darwin placed his energy-dependent “conditions of life” first. .

While our place in the tree of life is now well established – chimpanzees being our closest relatives – the beginning of the human line millions of years ago continues to be shrouded in mystery.

Charles Darwin had a theory about how his “conditions of life” might be linked to biodiversity via natural selection. Others thought that his theory could be linked from natural selection to the evolution of humans from ape relatives. They claimed that Darwin thought humans evolved during millions of years of natural selection for small changes. De Vries (1902) defined the small changes as mutations. Biologically uninformed neo-Darwinian theorists still claim that mutation-driven evolution is supported by the fossil record and genetic discoveries.
See for comparison: Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees
Svante Paabo is one of the paleoanthropologists who has a grasp of cell biology, which links energy to RNA-mediated biodiversity via the sense of smell. When someone with his level of expertise refutes all neo-Darwinian nonsense with experimental evidence of biologically-based cause and effect, how can others justify their lack of acceptance for the facts? Paabo’s facts link natural selection for energy-dependent codon optimality to all biodiversity via the claims in Feedback loops link odor and pheromone signaling with reproduction.

See also: Engineering RGB color vision into Escherichia coli reported as: Bacterial Photography Goes Technicolor

Genetically engineered “disco bacteria” sense and respond to different colors of light, creating both stunning art in the culture dish and new possibilities for synthetic biology.

See for comparison:Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates
Who engineered the energy-dependent acquisition of RGB color vision in E. coli and full trichromatic RGB color vision in primates? What prevents the biophysically constrained loss of the engineered receptors for RGB color vision in E. coli that are linked from the de novo creation of olfactory receptor genes to the loss of the genes that coincides with the advent of RGB (Trichromatic) color vision in primates?
Pseudoscientists might claim that evolution engineers the acquisition of all morphological and behavioral traits, but they won’t make verifiable claims about biophysical constraints or loss of the genes after the genes are created. Instead, see: Mutation-Driven Evolution.
Theorists start with genes that were somehow created and then claim:

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations…

After the energy-dependent de novo creation of genes, genomic conservation continues to be nutrient energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction in all living genera. Chromosomal inheritance prevents the evolution of one species into another — unless it occurs via magic traits. In the context of mutation-driven evolution species must have magic traits.
See for example: Evolution on the fast lane—One flounder species became two

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

See for comparison: Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain

Reported as: Living fossil challenges thinking on brain evolution

Despite its appearance, amphioxus is not a fish. It has a primitive spinal cord which runs down its back, but no clearly defined face, no bones or jaws and a small brain with a single light-sensing “frontal eye”. It has changed so little for hundreds of millions of years that it has been described as a “living fossil”.

See for comparison to the report of a hundreds of million years-old “living fossil:” Bacteria evolve over a weekend  (video)
Serious scientists know that the bacteria that reportedly “evolved” adapted to ecological variation in their food supply. Adaptation is nutrient energy-dependent and pheromone controlled via the physiology of reproduction in all living genera. It occurs over-the-weekend in P. fluorescens, but it is still reported to be mutation-driven evolution by biologically uninformed theorists.
Biologically uniformed theorists also make claims like those found here: The Physics of Everything

For comparison: This is the Physics of Everything, outside the context of the magic of evolution in the context of magic traits.

See: The in vivo structure of biological membranes and evidence for lipid domains

This approach relies on tuning the isotopic content of hydrogen within the membrane, and other parts of the bacterium, to generate neutron scattering spectra exclusively from the membrane. Using this approach, we confirmed that the structure of the B. subtilis membrane is lamellar and has an average hydrophobic thickness of 23.9 ± 0.9 Ångstroms (Å).

Average hydrophobic thickness cannot be linked from energy-dependent changes in the cell membrane to biophysically constrained cause and effect via the pheromone-controlled physiology of reproduction in any organism.
See for comparison: Scientists investigate how the sense of smell works in bacteria

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

Serious scientists do not link average hydrophobic thickness from the sense of smell in bacteria to all biophysically constrained energy-dependent biodiversity via the physiology of reproduction in species from microbes to humans. Serious scientists link the energy-dependent changes from angstroms to ecosystems in the context of RNA-mediated amino acid substitutions in supercoiled DNA.
See: Structural diversity of supercoiled DNA

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.

The metabolic processes are energy-dependent and biophysically constrained.

For another example of biogenic metabolic processes, see: Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits

This was reported as: A new twist on uranium’s origin story, by CSU scientists

In recent years, scientists had uncovered new evidence that bacteria – living microorganisms – could generate a different kind of reduced uranium that is non-crystalline and has very different physical and chemical properties.

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

They linked the nutrient energy-dependent pheromone-controlled physiology of reproduction in bacteria and all other living genera to the creation of differences in the 238U to 235U isotope ratio. The differences in the 238U to 235U isotope ratio discriminate between the abiotic and biotic transformation of uranium. But, they placed their findings on abiogenesis into the context of ridiculous theories of evolution and ignored everything  known to serious scientists about the energy-dependent biotic transformation of uranium and all energy-dependent biogenesis.

For any example of how placing their results into the context of abiogenesis supports ridiculous theories about emergence and evolution, see: Uranium–lead dating

The method relies on two separate decay chains, the uranium series from 238U to 206Pb, with a half-life of 4.47 billion years and the actinium series from 235U to 207Pb, with a half-life of 710 million years.

For comparison, see: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

This was reported as: Evolutionary Rewiring: Strong selective pressure can lead to rapid and reproducible evolution in bacteria

NtrC shares 30 percent amino acid identity with FleQ… the re-evolved flagella enabled the bacteria to access food supplies…

Natural selection for food energy-dependent codon optimality links ultraviolet light (UV) to the nutrient energy-dependent pheromone-controlled physiology of reproduction in P. fluorescens, which links UV light to the weekend resurrection of the flagellum because P. fluorescens fluoresces with exposure to UV light.

Differences in the nutrient energy-dependent RNA-mediated amino acid substitutions link differences in supercoiled DNA to the protection of all organized genomes from viruses. Virus-driven energy theft causes the degradation of messenger RNA, which links mutations to all pathology.

See Feynman’s comments about food energy:

Could any other physicist but Feynman have guessed that bacteria feed on something that allows them to produce uranium isotopes in the context of their food energy-dependent biophysically constrained pheromone-controlled physiology of reproduction?

Could any other molecular biologist but Bruce McEwen have linked an endogenous substrate from the energy-dependent biophysically constrained pheromone controlled physiology of reproduction to all biodiversity in all living genera?

See also: The Binding Sites of miR-619-5p in the mRNAs of Human and Orthologous Genes

Binding sites of miR-619-5p in the 3’UTRs of all human target genes are also present in the 3’UTRs of orthologous genes of mammals. The completely complementary binding sites for miR-619-5p are conservative in the orthologous mammalian genes.

CONCLUSIONS:(with my emphasis)

The majority of miR-619-5p binding sites are located in the 3’UTRs but some genes have miRNA binding sites in the 5’UTRs of mRNAs. Several genes have binding sites for miRNAs in the CDSs that are read in different open reading frames. Identical nucleotide sequences of binding sites encode different amino acids in different proteins. The binding sites of miR-619-5p in 3’UTRs, 5’UTRs and CDSs are conservative in the orthologous mammalian genes.

To help differentiate between evolution and adaptation in the context of natural selection for food energy-dependent codon optimality in the context of the physiology of pheromone-controlled reproduciton, see: Metrics of assay accuracy

Neo-Darwinian evolution occurs only in the context of this “Magic Box” example. Each time you look at the “+” sign on the box, you are taught to believe in evolution.

For comparison, see: The Emerging View of Aging as a Reversible Epigenetic Process

This evidence supports the idea that progressive epigenetic dysregulation may be the key driver of organismal aging and challenges the conventional view of aging as an irreversible process. The model of aging as an epigenetic process provides an elegant explanation of a number of age-related processes difficult to explain by conventional theories of aging.

Conventional theories of aging have failed to link the nutrient energy-dependent pheromone-controlled physiology of RNA-mediated protein folding chemistry to all biodiversity via biophysically constrained chromosomal inheritance. That’s how conventional theories left all of humanity waiting for cures that will never become available. Biologically uninformed theorists still do not know how protein folding chemistry is linked from changes in the microRNA/messenger RNA balance to healthy longevity via cell type differentiation or from the virus-driven degradation of messenger RNA to mutations and all pathology.
See: Genome editing: That’s the way the CRISPR crumbles
Review of A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution This title will be released on June 13, 2017.

Not since the atomic bomb has a technology so alarmed its inventors that they warned the world about its use.

June 14, 2013 Nutrient-dependent/pheromone-controlled adaptive evolution: a model

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

 June 14, 2013 Mutation-Driven Evolution

(1) Mutation is the source of all genetic variation on which any form of evolution is dependent. Mutation is the change of genomic structure and includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc. (2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation. It does not have any creative power in contrast to the statements made by some authors.