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

MicroRNA-mediated denuclearization (4)

Summary: Christ’s lab showed that in vivo formation of I-motif structures is pH dependent and helped to put the “fear of God” into atheistic communists.

I-motif DNA structures are formed in the nuclei of human cells (4/23/18)

Reported as: In human cells, scientists find DNA that looks like a twisted knot instead of a double helix (4/23/18)

Also reported as: New Twisted ‘Knot’ Human DNA Structure Discovered—and It Looks Nothing Like the Double Helix (4/23/18)

Christ’s lab showed that in vivo formation of I-motif structures is pH dependent. Clearly, the potential of hydrogen (pH) and pH-dependent cell cycles link the quantized energy of virucidal sunlight to protection from the degradation of messenger RNA that links mutations to all pathology.
In that context, denuclearization has been forced on North Korea and other communist countries by scientific creationists in South Korea. The creationists have indirectly revealed that they could decimate human populations in China via the creation of a virus with one base pair change linked to one amino acid substitution.
See also: Virus-mediated archaeal hecatomb in the deep seafloor

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

Until recently, the pseudoscientific nonsense about vaccines that could protect human populations from the forthcoming viral apocalypse was tightly linked from communism to atheism. For comparison, Christ’s lab appears to have put the fear of God into its proper context; the 1918 Spanish flu.
Previously reported as: Structural diversity of supercoiled DNA (2015) and parodied in:

See also: The Pharmacology of Regenerative Medicine (2013)
See also: Energy as information and constrained endogenous RNA interference (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.

An evolutionary theory killer

How to create biologically uninformed theorists

Summary: On March 2, 2018, Philip C. Ball and Nick Lane started making claims about proton gradients. Their claims are based on my model of quantized energy as information. This post includes added support for what is known to all serious scientists about the light-activated endogenous substrates that link molecular epigenetics to RNA-mediated autophagy.
See first: Energy as information and constrained endogenous RNA interference (audio/visual aid 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.

Added support for the light-activated molecular epigenetics of autophagy:
Light-powering Escherichia coli with proteorhodopsin (2007)

…we quantify the coupling between light-driven and respiratory proton currents… and show that light-driven pumping by PR can fully replace respiration as a cellular energy source in some environmental conditions.

Structure of the Deactive State of Mammalian Respiratory Complex I (2018)

…the deactive state arises when critical structural elements that form the ubiquinone-binding site become disordered, and we propose reactivation is induced when substrate binding to the NADH-reduced enzyme templates their reordering. Our structure both rationalizes biochemical data on the deactive state and offers new insights into its physiological and cellular roles.

Global collective motions in the mammalian and bacterial respiratory complex I (2018)

…we identify here transitions between experimentally resolved structures of the mammalian complex I as low-frequency collective motions of the enzyme, highlighting similarities and differences between the bacterial and mammalian enzymes. Despite the reduced complexity of the smaller bacterial enzyme, our results suggest that the global dynamics of complex I is overall conserved.

The conservation of light-powered functional structures and energy-dependent proton gradients link the deactive state in critical structures to the active state via the creation of enzymes in species from bacteria to mammals. The energy-dependent creation of the enzymes links metabolism of the energy (e.g., food energy) from pheromones to biophysically constrained viral latency in the context of the physiology of reproduction.
The pheromone-controlled physiology of reproduction in species from microbes to humans links our visual perception of energy and mass in the context of how ecological variation must be linked to energy-dependent ecological adaptations in all living genera.
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.

See also: Odors Alter Subjective Time Experience Author: Dr. ZHOU Wen’s Research Group Update time: 2017/05/15

The brain is not a timepiece. Whereas it is equipped with senses like vision, audition, touch, smell, and taste, it has no direct access to or measure of the physical time (unless you read from a clock). Rather, it constructs the subjective “time” of an event from the dynamic multisensory inputs associated with that event. Yet different senses come with different temporal precisions. For instance, when standing near an apple tree, you can detect the falling of an apple much better with your eyes or ears than the nose. How does the brain coordinate multisensory signals entering different brain regions with different temporal resolutions, and come up with the subjective time?

A team at the Institute of Psychology at Chinese Academy of Sciences tackled this issue using odors and images. Specifically, Dr. Bin Zhou, the study’s lead author, and his colleagues examined whether odors could modulate one’s temporal sampling and subjective duration of visual objects. In their study, participants viewed two series of flickering isoluminant images in red and green (Figure 1A). One of the series contained opposite images of an apple or bananas; the other contained only images of red and green fields. When the images alternated at a frequency beyond 20 Hz, the participants started to have difficulty reporting which series contained an object. Indeed, for most people, chromatic flicker fusion frequency (CFF), the limit at which alternating colors become perceived as a stable fused color, falls somewhere between 20 and 25 Hz. Interestingly, the participants’ object detection accuracies around CFF were improved under the exposure of a congruent, as opposed to an incongruent, odor. In other words, the participants detected a rapidly flickering apple better when they smelled an apple odor rather than a banana odor, and vice versa (Figure 1B, left panel). In effect, the presence of a congruent odor facilitated the brain’s temporal sampling of a visual object and elevated its CFF (Figure 1B, right panel). Based on electrical activities recorded from the participants’ scalp, the researchers found that the integration between smell and vision strengthened the signals of the corresponding object in a brain region heavily implicated in object representations called the right temporal cortex, about 150-300 ms after object onset. They further showed that such integration lengthened one’s subjective duration of the corresponding object in a duration comparison task. The researchers concluded that subjective time is warped by the neural energy involved in representing multisensory inputs at subsecond scales.

Until Philip C. Ball mentioned that Nick Lane believed proton gradients came before the energy-dependent creation of RNA, I did not realize how little they knew about this link from differences in the energy of photons to consciousness.
See: What Affective Neuroscience Means for Science Of Consciousness (2013)

The coupling of the two circuits promotes an endogenous feedback that supports conscious processes. Within this framework, we present the defence that detailed study of both affective and cognitive processes, their interactions, as well of their respective brain networks, is necessary for a science of consciousness.

The coupling of the two circuits links differences in the energy of photons from the proton motive force to the light-activated endogenous feedback loops and Feedback loops link odor and pheromone signaling with reproduction.
It is extremely difficult for intelligent people to not link this experimental evidence to biophysically constrained viral latency in the context of reports that claim “Creatures’ Adaptability Begins with Their Sensors.”
But, see for comparison: David Attenborough on creationsim May, 2015

My comment on his nonsense: First steps to neutralizing Zika: How highly potent antibody neutralizes Zika infection discovered

This is framed within the context of energy-dependent changes in pH, which facilitate receptor-mediated entry of nutrients or viruses into specific cell types of species-specific tissues via stress-linked changes in hydrogen-atom transfer in DNA base pairs.

Virus-driven energy theft has been linked to all pathology in all living genera via the conserved molecular mechanisms of RNA-mediated polycombic protein folding chemistry compared to the hecatombic evolution of pathology manifested first in the differences between archaea and bacteria. Admitting that Carl Woese was wrong about the different domains of life is the first step towards understanding the difference between healthy longevity and the evolution of all virus-driven pathology.

Carl Woese was wrong

God did not create the viruses. He created the anti-entropic virucidal energy of sunlight, which protects all organized genomes from virus-driven entropy. Only the choices of our ancestors could have led to the increasing amout of virus-driven pathology during the past ~6000 years that pseudoscientists place into the context of millions of years of evolution. Then, they blame God, like these two pseudoscientists do. Darwin knew they would do that, which is why he insisted that others put conditions of life before natural selection. But they bastardized his theory anyway and taught their revision to anyone who was foolish enough to believe in it. It’s called the “Modern Synthesis” and was based on de Vries 1902 definition of “mutation.”

Celebrate Your Inner Virus

It is important that we understand the design present in viruses because God made them.

It is no wonder that Sir David Attenborough and many others like Philip C. Ball and Nick Lane are confused about the energy-dependent creation of healthy longevity and consciousness. Even some young earth creationists have failed to link the creation of the sun’s anti-entropic virucidal energy from changes in electrons to ecosystems via the proton motive force. That leaves every aspect of creation to be placed back into the context of ridiculous theories. The theories start with the virus-driven theft of quantized energy as information. The energy theft links mutations to all virus-driven pathology. The theft of quantized energy as information cannot be linked by serious scientists from beneficial mutations to the evolution of one species from another.
For comparison, pseudoscientists have no problem touting this confusing nonsense:
Sign of selection on mutation rate modifiers depends on population size (
1)  Genetic variation—the raw material for evolution—is ultimately generated by mutation.
2). …beneficial alleles never become deleterious and deleterious alleles never become beneficial.
Conclusion:

Whether these phenomena can be united in a single theoretical framework remains an open question that we are actively exploring. In any case, our results add to a growing appreciation of nonclassical population size dependence in evolution by natural selection (41, 42).

Funding for research that attempts to link natural selection to evolution via mutation-driven genetic variation should be used to link food odors and pheromones from the physiology of reproduction to biophysically constrained viral latency and ecological adaptations. It is time to stop creating more biologically uninformed theorists.

diseases-disorders

RNA-mediated "repurposing" is nutrient-dependent and pheromone-controlled

 Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Excerpt: The fast-spreading strain AR2F had acquired an additional point mutation in the σ54-dependent EBP gene ntrC, which alters an amino acid (R442C) within the DNA binding domain (Table 1 and table S2).

Reported as: Evolutionary Rewiring

Strong selective pressure can lead to rapid and reproducible evolution in bacteria.

By Ruth Williams | February 26, 2015

Excerpt: NtrC shares 30 percent amino acid identity with FleQ, suggesting the proteins may be able to minimally cross-react with each other’s target genes. Sure enough, the researchers determined that the initial mutations, which ramped up NtrC levels, enabled a minor upregulation of FleQ’s target genes. The second mutations to NtrC itself then improved the protein’s interaction with the FleQ targets, boosting their expression, and the bacteria’s ability to swim.

My summary: Researchers still seem to be very confused about the difference between amino acid substitutions, which stabilize RNA-mediated protein folding and mutations. Mutations perturb protein folding, which is why they are consistently linked to physiopathology and not linked from ecological variation to nutrient-dependent pheromone-controlled ecological adaptations via the physiology of reproduction in species from microbes to humans.
My comments on “Evolutionary Rewiring”:
Re: “…repurposing of a distantly related protein.”
1) The “repurposing” is nutrient-dependent and pheromone-controlled.
2) The repurposing exemplifies how ecological variation leads to nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions that stabilize DNA in the organized genomes of species from microbes to man.
See how important it is to understand genomic stability in the context of “repurposing.” Biocontainment of genetically modified organisms by synthetic protein design. See also the importance of Combating Evolution to Fight Disease.
Richard Lenski and many others have been on the wrong side of this fight for several decades. See, for example: A single amino acid substitution differentiates cell types of E. coli
Re: “The results highlight the importance of gene duplication…”
Gene duplication is nutrient-dependent. Fixation of amino acid substitutions that stabilize the genome is controlled by the physiology of reproduction, which is controlled by the metabolism of nutrients to species-specific pheromones.
The RNA-mediated fixation of amino acid substitutions links metabolic networks to genetic networks. That fact explains why Church’s group has taken great care to address other facts that link physics, chemistry, and conserved molecular mechanisms to cell type proliferation, which theorists tend to attribute to mutations and evolution.
For constast to the claims of theorists, Christ and others: The Pharmacology of Regenerative Medicine are also attempting to link “… the salient features of diverse fields of research—ranging from materials chemistry and functionalized biomaterials to stem cells, organ/tissue regeneration, wound healing, and development biology…”
Accurate representations of nutrient-dependent biologically-based cause and effect during life history transistions also can be viewed in the context of heterochronic parabiosis, which links fixed amino acid substitutions in red blood cells to the delivery of nutrients to every cell in organisms with a circulatory system.
Mutations perturb the molecular mechanisms of the delivery system, which typically prevent sepsis caused by E. coli or other microbes that ecologically adapt to higher body temperatures than can be maintained by immunocompromised mammals (e.g., like your grandmother who may have died from complications of a urinary tract infection in the context of evolutionary theory).
The journal article reports the de novo origination of new functions via the nutrient-dependent creation and rewiring of gene networks linked to metabolic networks by the pheromone-controlled fixation of an amino acid substitution in the DNA of the organized genome of a microbe with a flagellum that enables it to find food. In their example of a starving microbe, the flagellum is first evolved then lost. A few days later it has re-evolved, and they place evolution and re-evolution of the structure and its function into the context of mutations and evolution via “…a highly repeatable two-step evolutionary pathway with the same point mutations often recurring in independent lineages.”

See also: Bacteria ‘hotwire their genes’ to fix a faulty motor.
Watch for more pseudoscientific nonsense as evolutionary theorists try to explain the nutrient-dependent breaking of Mendel’s “Law of Segregation” reported here R2d2 beats Mendel: Scientists find selfish gene that breaks long-held law of inheritance and why additions must be made to the second Law of thermodynamics, reported here: On quantum scales, there are many second laws of thermodynamics.
Obviously, they will keep trying to get others to believe that they have accurately represented biologically-based cause and effect that may or may not lead to evolution in 4 days or 2 billion years. See: Scientists discover organism that hasn’t evolved in more than 2 billion years. There only other choice is to join the serious scientists who are Combating Evolution to Fight Disease. However, recruits may now be required to pass an intelligence test, since nearly everyone will want to join serious scientists in combat. Those who have published papers about mutations and evolution during the past decade may be automatically excluded unless they can explain why they thought that evolution via mutations automagically occurred.

diseases-disorders

RNA-mediated "repurposing" is nutrient-dependent and pheromone-controlled

 Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Excerpt: The fast-spreading strain AR2F had acquired an additional point mutation in the σ54-dependent EBP gene ntrC, which alters an amino acid (R442C) within the DNA binding domain (Table 1 and table S2).

Reported as: Evolutionary Rewiring

Strong selective pressure can lead to rapid and reproducible evolution in bacteria.

By Ruth Williams | February 26, 2015

Excerpt: NtrC shares 30 percent amino acid identity with FleQ, suggesting the proteins may be able to minimally cross-react with each other’s target genes. Sure enough, the researchers determined that the initial mutations, which ramped up NtrC levels, enabled a minor upregulation of FleQ’s target genes. The second mutations to NtrC itself then improved the protein’s interaction with the FleQ targets, boosting their expression, and the bacteria’s ability to swim.

My summary: Researchers still seem to be very confused about the difference between amino acid substitutions, which stabilize RNA-mediated protein folding and mutations. Mutations perturb protein folding, which is why they are consistently linked to physiopathology and not linked from ecological variation to nutrient-dependent pheromone-controlled ecological adaptations via the physiology of reproduction in species from microbes to humans.
My comments on “Evolutionary Rewiring”:
Re: “…repurposing of a distantly related protein.”
1) The “repurposing” is nutrient-dependent and pheromone-controlled.
2) The repurposing exemplifies how ecological variation leads to nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions that stabilize DNA in the organized genomes of species from microbes to man.
See how important it is to understand genomic stability in the context of “repurposing.” Biocontainment of genetically modified organisms by synthetic protein design. See also the importance of Combating Evolution to Fight Disease.
Richard Lenski and many others have been on the wrong side of this fight for several decades. See, for example: A single amino acid substitution differentiates cell types of E. coli
Re: “The results highlight the importance of gene duplication…”
Gene duplication is nutrient-dependent. Fixation of amino acid substitutions that stabilize the genome is controlled by the physiology of reproduction, which is controlled by the metabolism of nutrients to species-specific pheromones.
The RNA-mediated fixation of amino acid substitutions links metabolic networks to genetic networks. That fact explains why Church’s group has taken great care to address other facts that link physics, chemistry, and conserved molecular mechanisms to cell type proliferation, which theorists tend to attribute to mutations and evolution.
For constast to the claims of theorists, Christ and others: The Pharmacology of Regenerative Medicine are also attempting to link “… the salient features of diverse fields of research—ranging from materials chemistry and functionalized biomaterials to stem cells, organ/tissue regeneration, wound healing, and development biology…”
Accurate representations of nutrient-dependent biologically-based cause and effect during life history transistions also can be viewed in the context of heterochronic parabiosis, which links fixed amino acid substitutions in red blood cells to the delivery of nutrients to every cell in organisms with a circulatory system.
Mutations perturb the molecular mechanisms of the delivery system, which typically prevent sepsis caused by E. coli or other microbes that ecologically adapt to higher body temperatures than can be maintained by immunocompromised mammals (e.g., like your grandmother who may have died from complications of a urinary tract infection in the context of evolutionary theory).
The journal article reports the de novo origination of new functions via the nutrient-dependent creation and rewiring of gene networks linked to metabolic networks by the pheromone-controlled fixation of an amino acid substitution in the DNA of the organized genome of a microbe with a flagellum that enables it to find food. In their example of a starving microbe, the flagellum is first evolved then lost. A few days later it has re-evolved, and they place evolution and re-evolution of the structure and its function into the context of mutations and evolution via “…a highly repeatable two-step evolutionary pathway with the same point mutations often recurring in independent lineages.”

See also: Bacteria ‘hotwire their genes’ to fix a faulty motor.
Watch for more pseudoscientific nonsense as evolutionary theorists try to explain the nutrient-dependent breaking of Mendel’s “Law of Segregation” reported here R2d2 beats Mendel: Scientists find selfish gene that breaks long-held law of inheritance and why additions must be made to the second Law of thermodynamics, reported here: On quantum scales, there are many second laws of thermodynamics.
Obviously, they will keep trying to get others to believe that they have accurately represented biologically-based cause and effect that may or may not lead to evolution in 4 days or 2 billion years. See: Scientists discover organism that hasn’t evolved in more than 2 billion years. There only other choice is to join the serious scientists who are Combating Evolution to Fight Disease. However, recruits may now be required to pass an intelligence test, since nearly everyone will want to join serious scientists in combat. Those who have published papers about mutations and evolution during the past decade may be automatically excluded unless they can explain why they thought that evolution via mutations automagically occurred.