Filtering light through a prism to identify tissue type

Phenols: Laws of physics meet biology

Can the second law of thermodynamics hold in cell cultures?

Excerpt:

…for in vivo systems, the rules for self-organization require further investigations (Stuart, 1995), especially for multi-cellular organisms considering the exchange of matter between different cell types. Knowing this will allow us to better predict the emergent properties of the “real” living systems.

My comment: When Jay R. Feierman realizes how ridiculous his comments about mutations and evolution have become, he posts  links to articles like this one to the ISHE’s yahoo group. It addresses the obvious need to link the Laws of Physics to Kohl’s “Laws of Biology.”
See also:

Phenols

…sometimes called phenolics, are a class of chemical compounds consisting of a hydroxyl group (—OH) bonded directly to an aromatic hydrocarbon group. The simplest of the class is phenol, which is also called carbolic acid C6H5OH. Phenolic compounds are classified as simple phenols or polyphenols based on the number of phenol units in the molecule.[1][2][3]

Phenol – the simplest of the phenols.

Quercetin, a typical flavonoid, is a polyphenol

Synonyms are arenols[4] or aryl alcohols.[5]
Phenolic compounds are synthesized industrially; they also are produced by plants and microorganisms, with variation between and within species.[6]

My comment: Phenols appear to link the sun’s anti-entropic energy to the prevention of pathology via the Laws of Physics and Kohl’s Laws of Biology via nutrient energy dependent base pair changes and RNA-mediated events that clearly link mutations to pathology.
See also: Antioxidant Activity, Total Phenolics and Taxol Contents Response of Hazel (Corylus avellana L.) Cells to Benzoic Acid and Cinnamic Acid:
Excerpt:

Complementary investigations may suggest remedy of human cancers by the extract of BA- and CA-fed hazel cells which meanwhile provides the body with the advantage of decrease of detrimental effect of free radicals in non cancerous cells.

My comment: Anyone who is interested in linking what is currently known about the “Laws of Physics” to “Kohl’s Laws of Biology,” which link biophysically constrained nutrient-dependent protein folding chemistry from the sun’s anti-entropic energy to RNA-mediated cell type differentiation in all living genera, may also want to see:
The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
Conclusion:

…the miRNA profile of mature ejaculated sperm may in fact have downstream consequences upon embryonic development. The potential for sperm miRNA affecting zygote development has recently been reported in the literature [18] and has interesting implications for the use of sperm miRNA profiles as indicators of potential male fertility.

Physics

Plasma created by sunlight and RNA–mediated epigenetic heredity

Australian student confirms that giant plasma tubes are floating above Earth
Excerpt: The region of space around the Earth occupied by its magnetic field, called the magnetosphere, is filled with plasma created by the atmosphere being ionised by sunlight.
My comment: Scientists have believed in the creation of these structures for more than 60 years. Now visual evidence confirms structures exist that are created by sunlight on contact with the Earth’s atmosphere.
This reminds me of what someone who was born blind might claim if scientists claimed that rainbows exist. If scientists enabled sight in a congenitally blind person, would the sight of the rainbow confirm the belief that all life on Earth was created? If not, could the congenitally blind person still be considered to be blind to an obvious example of creation?
See also:
Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism

“…precursors of amino acids glycine, serine, alanine and threonine, are inevitable by-products of this RNA assembly chemistry9”

See also:
Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins
reported as: Researchers identify ‘tipping point’ between quantum and classical worlds
See also:
RNA–Mediated Epigenetic Heredity Requires the Cytosine Methyltransferase Dnmt2
My comment: Taken outside the context of everything currently known to serious scientists about the de novo creation of nucleic acids such as RNA and what is known about nutrient-dependent biophysically constrained RNA-mediated cell type differentiation in the context of the physiology of reproduction in all living, these authors make the following claim:
Excerpt:

Our data show that at least two tRNAs are methylated in mouse sperm in a Dnmt2-dependent manner (Figure S4), which raises the possibility that methylation-dependent processing of tRNAs [17] could result in the generation of paramutation-inducing sncRNAs.

My comment: Their data can be interpreted in the context of neo-Darwinian claims about mutations that somehow link the creation of life on Earth to biodiversity via natural selection. This eliminates the need for sunlight as the anti-entropic force that enabled all aspects of creation whether or not any aspect of creation has yet been seen by blind or sighted researchers.
As is typical, anything interpreted in the light of neo-Darwinism appears to be a misrepresentation of facts that link the creation of the sun to the creation of all biomass and all biodiversity that ever existed or that may continue to exist.
See also: Periodic Scarred States in Open Quantum Dots as Evidence of Quantum Darwinism, which was reported as: New evidence for quantum Darwinism found in quantum dots
and also reported as: Bridge to the quantum world: Darwinian concept of natural selection figures into theory about core of physical reality
Excerpt: 

It describes the transition from quantum to classical world as a “decoherence” process that involves a kind of evolutionary progression somewhat analogous to Charles Darwin’s concept of natural selection.

My comment: Darwin’s concept of natural selection was place after first consideration for “conditions of life.” Neo-Darwinian theorists are biologically uninformed science idiots who have failed to grasp the facts known to all serious scientists about the biophysically constrained creation of life and RNA-mediated cell type differentiation in all living genera. Life is all about that base and the sun’s biological energy is the biological basis of life’s diversity.

The sun’s biological energy effects the base pairs and the RNA-mediated events that link the sun to differences in morphological and behavioral phenotypes via the physiology of reproduction in all living genera.

rp_levels-of-organization.jpg

Positive feedback loops and epigenetic traps

Transcription factor trapping by RNA in gene regulatory elements

Conclusion:

…bidirectional transcription of active enhancers and promoters evolved, in part, to facilitate trapping of TFs at specific regulatory elements. The model also suggests that transcription of regulatory elements produces a positive-feedback loop that may contribute to the stability of gene expression programs in cells. The contribution of this TF trapping mechanism to cellular regulation has yet to be established but will be important to elucidate in future studies because much disease-associated sequence variation occurs in enhancers (20, 22) and may thus affect both DNA and RNA sequences that interact with gene regulators.

My comment: Bidirectional transcription did not evolve. It is nutrient-dependent and controlled by the physiology of reproduction. Feedback loops link odor and pheromone signaling with reproduction in species from microbes to humans. That fact links RNA-mediated gene duplication and RNA-mediated amino acid substitutions to the stability of organized genomes via what is known about supercoiled DNA. Supercoiled DNA protects the organized genomes of all living genera from virus-driven entropy.
Researchers who consistently fail to recognize the fact that supercoiled DNA is an epigenetic trap also seem reluctant to acknowledge the epigenetic trap that Schrodinger claimed linked the anti-entropic effect of the sun’s biological energy life on Earth in What is Life?
Excerpt:

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight)

My comment: By ignoring the epigenetic trap that links sunlight on contact with water to the energy spectrum manifested in the range from ultraviolet to infrared light, researchers become like theorists who must link the nutrient-dependent biophysically constrained chemistry of RNA-mediated protein folding in their ridiculous claims about mutations and evolution. For example: “…bidirectional transcription of active enhancers and promoters evolved…”
Stop the nonsense! Force all researchers to report their findings in terms of how ecological variation is linked to ecological adaptations via what is currently known about the stability of nutrient-dependent genome organization in all living genera.
See also: Nonparadoxical evolutionary stability of the recombination initiation landscape in yeast and Stable recombination hotspots in birds
reported as: Putting the breaks on meiosis and predicted in Combating Evolution to Fight Disease
Conclusion:

“…an important gap is being filled by molecular understanding of the genesis of variation that confers the ability to evolve.”

My comment: The genesis of variation is nutrient-dependent and nothing evolves from anything else. All living genera exemplify links between ecological variation and ecological speciation that is nutrient-dependent and controlled by the physiology of reproduction.
See also: Long non-coding RNAs as a source of new peptides, but stop claiming that there is any such thing as de novo protein evolution. Claims that proteins or species evolve are made only by the biologically uninformed.

Filtering light through a prism to identify tissue type

Let there be anti-entropic light (3)

See also: Let there be anti-entropic light (1) and Let there be anti-entropic light (2)
NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program and Putting chromatin in its place: the pioneer factor NeuroD1 modulates chromatin state to drive cell fate decisions
were reported as:

Master switch for brain development found

Excerpts:

1)  …the brain is also one of the most complex organs in the body, and very little is understood about the molecular pathways that guide its development.

2) “This is a significant step towards understanding the relationship between DNA sequence, epigenetic changes and cell fate. It not only sheds new light on the formation of the brain during embryonic development but also opens up novel avenues for regenerative therapy.”

My comment: Significant steps towards understanding how the anti-entropic energy of the sun links epigenetic changes to cell fate in the context of an atoms to ecosystems model have led serious scientists to conclusions that were predicted by Schrodinger in What is Life?
Excerpts:

1) We know definitely, today, that Darwin was mistaken in regarding the small, continuous, accidental variations, that are bound to occur even in the most homogeneous population, as the material on which natural selection works. For it has been proved that they are not inherited.
2) What then is that precious something contained in our food which keeps us from death?
3) Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight)

My comment: Anti-entropic nutrient energy-dependent epigenetic effects link the speed of ultraviolet (UV) light on contact with water to the creation of nucleic acids and the speed of infrared (IR) light to virucidal effects that promote RNA-mediated DNA repair in all living genera. Nutrient-dependent DNA repair links top-down causation from ecological variation and the sun’s biological energy to the physiology of reproduction and ecological adaptations.
Serious scientists have learned that the DNA double helix is not static, which is why only pseudoscientists continue to report vague links between mutations and/or natural selection that they claim somehow lead to the creation of all morphological phenotypes and behavioral phenotypes, which are manifested in biodiversity.
See: 42Evolution, which was reported as Evolution website sets out to tackle great scientific unknowns
Excerpt (with my emphasis):

The site was created by a team led by Simon Conway Morris…. “Evolution is true, and if it didn’t happen, we wouldn’t be here,” he said. “Like all the sciences, evolution is constantly, well, evolving. New insights and unexpected discoveries combine with seeing old things in a completely new light. It is active, dynamic, changing and unpredictable. We wanted to create a website that captures the excitement and thrill of that exploration.”

My comment: They are fighting desperately to avoid being accurately described as biologically uninformed science idiots.
See for comparison (with my emphasis):

IF under changing conditions of life organic beings present individual differences in almost every part of their structure, and this cannot be disputed; if there be, owing to their geometrical rate of increase, a severe struggle for life at some age, season, or year, and this certainly cannot be disputed; then, considering the infinite complexity of the relations of all organic beings to each other and to their conditions of life, causing an infinite diversity in structure, constitution, and habits, to be advantageous to them, it would be a most extraordinary fact if no variations had ever occurred useful to each being’s own welfare, in the same manner as so many variations have occurred useful to man. But if variations useful to any organic being ever do occur, assuredly individuals thus characterised will have the best chance of being preserved in the struggle for life; and from the strong principle of inheritance, these will tend to produce offspring similarly characterised. This principle of preservation, or the survival of the fittest, I have called Natural Selection. — Charles Darwin
…the greater variability of species having wider ranges than of those with restricted ranges, lead to the conclusion that variability is generally related to the conditions of life to which each species has been exposed during several successive generations. — Charles Darwin
When a variation is of the slightest use to any being, we cannot tell how much to attribute to the accumulative action of natural selection, and how much to the definite action of the conditions of life. — Charles Darwin
Instances could be given of similar varieties being produced from the same species under external conditions of life as different as can well be conceived; and, on the other hand, of dissimilar varieties being produced under apparently the same external conditions. Again, innumerable instances are known to every naturalist, of species keeping true, or not varying at all, although living under the most opposite climates. Such considerations as these incline me to lay less weight on the direct action of the surrounding conditions, than on a tendency to vary, due to causes of which we are quite ignorant. — Charles Darwin
By my theory these allied species are descended from a common parent; and during the process of modification, each has become adapted to the conditions of life of its own region, and has supplanted and exterminated its original parent-form and all the transitional varieties between its past and present states. — Charles Darwin

Summary: Darwin attributed all variation to unknown “conditions of life.” Only after the “conditions of life” were met could natural selection occur. He knew nothing of DNA, which means he knew nothing about the mutations that pseudoscientists still claim lead to the evolution of one species from a different species via natural selection. The pseudoscientists bastardized the entirety of Darwin’s works and turned his observations into the “Modern Synthesis” based on de Vries 1904 definition of mutation.
See for comparison: 

The atoms to ecosystems dynamics of supercoiled DNA

Researchers develop the first platform for DNA simulations
Excerpt:

“Advances in simulation are bringing us closer to the definition of a theoretical model that will allows us to simulate key aspects of cell life, therefore approaching the dream of describing the behaviour of organisms only based on the basic rules of physics and chemistry,” says Modesto Orozco…

See also: Understanding molecular origin of epigenetic markers
Excerpt:

This is the first mechanical explanation at the atomic level of an epigenetic effect, one of the most important, that connects an epigenetic modification with a phenotypic effect,” assures Orozco. “This leads us to believe that there is a similar explanation for other epigenetic modifications. There may be a very basic mechanism that accounts for the effect that they have on gene structure and expression,” he concludes.

My comment: The “first mechanical explanation” links epigenetic effects from atoms to ecosystems via what is currently known to other serious scientists. Nutrient-dependent biophysically constrained protein folding chemistry links microRNAs to protection against virus-driven genomic entropy. Protection against entropy arises only in the context of RNA-mediated events linked to supercoiled DNA via the speed of UV light on contact with water and the speed of IR light, which is linked to penetration of cells in different tissues of different organs in different organ systems via penetration of human skin, which is the largest organ of any human organ system.
Photobiomodulation: Laser Therapy for the Nervous System (free registration required)
Description:

The use of “low level” light applications, termed photobiomodulation (PBM), as a noninvasive, neuro-restorative therapy has potential to revolutionize repair of the injured nervous system. Experiments on the use of PBM to repair injured spinal cords and peripheral nerves will be discussed, along with the scientific basis for this improvement.
Light applied transcutaneously penetrates to the level of the spinal cord. Transmission spectra revealed that peak transmission through all tissue layers overlying the spinal cord was at 810 nm, with minimal absorption by blood and water. Axonal regeneration and functional recovery in various models of spinal cord injury was supported by 810 nm wavelength light. Genes involved in the immune response, cellular proliferation and growth factor receptors were significantly altered by PBM after spinal cord injury.

My comment: Given what is known to serious scientists about the obvious links from the sun’s biological energy to the physics, chemistry, and conserved molecular mechanisms that are the basis of what is known about biologically-based cause and effect, how much longer should we expect the pseudoscientific nonsense about mutations and evolution to be touted. Did that nonsense ever make sense to anyone who was not biologically uninformed?

terrarium-eco-system

Theorists can't understand biology

See also: Neuroplasticity
Thanks to Teresa Binstock for calling my attention to this:
 

Biology is imposssible

Optimizing neuroplasticity by linking atoms to ecosystems

Thanks to Anna Di Cosmo for calling the attention of others to this:

My comment: Attempts to explain the “binding problem” of integration in the context of ecoimmunology and disease ecology compared to emergence and evolution are examples of how much pseudoscientific nonsense has been accepted and touted in the context of the neo-Darwinian “Modern Synthesis.” For comparison, serious scientists have detailed a model of top-down causation that links the design of the brain from the bottom up in an atoms to ecosystems model of cell type differentiation. The model links our experiences from our first breath to our behavior during life history transitions via biophysically constrained protein folding.
Re: “Man is the measure of all things.” Intelligent scientists understand that their measurements from physics, chemistry, and the molecular mechanisms of biologically-based cause and effect must link all other scientific disciplines to biology.
See for example: Oxygen regulation of breathing through an olfactory receptor activated by lactate
Conclusion:

Although ORs [olfactory receptors] were first identified for their role in smell, they may be involved in myriad chemosensory pathways detecting endogenous and exogenous ligands throughout the body.

For comparison to what is known to serious scientists about receptor-mediated cause and effect in the context of chemosensory pathways, evolutionary theorists and theoretical physicists continue to misrepresent all measures of all things. For example, they refuse to explain how “re-evolution” of the bacterial flagellum occurred in four days but claim that an example of no evolution in ~2 billion years supports the claims included in the “Modern Synthesis.”
See: Scientists discover organism that hasn’t evolved in more than 2 billion years
See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
My comment: Try to place the evolutionary resurrection of flagellar motility into the context of the binding problem that must link receptor-mediated events to chemosensory pathways after watching this video.

The bacteria that “re-evolved” their flagella over a weekend exemplify how the nutrient-dependent pheromone-controlled physiology of reproduction links ecological variation to ecological adaptation in all living genera via receptor-mediated events that link food odors and pheromones to the physiology of reproduction in all living genera.
For comparison, Simon LeVay challenged my model of ecological adaptation, which resolved issues of the “binding problem” that links receptor-mediated behaviors in the context of sex differences in cell types and differences in sexual orientation.
See: Gay, Straight, and the Reason Why: The Science of Sexual Orientation
Excerpts:

That the odor of gay men is recognizably different from the odor of other people is believable, although the claim hasn’t been independently verified and its chemical basis hasn’t been studied. (p. 209)
It seems unlikely to me, though, that gay men have an innate preference for the odor of gay men over that of straight men because many gay men are attracted to straight men and, given the opportunity, will have sex with them even in preference to gay partners. Thus this finding, if replicable, is more likely to represent a learned association resulting from gay men’s prior history of intimacy with other gay men. (p. 210)
James Kohl, an independent researcher who also markets “human pheromones” to the general public, believes that pheromones may have a primary influence in setting up a person’s basic sexual orientation. Other, more consciously perceived aspects of attractiveness, such as facial appearance, are attached to a person’s basic orientation through a process of association during early postnatal life, according to Kohl. 35 (p. 210)
This model is attractive in that it solves the “binding problem” of sexual attraction. By that I mean the problem of why all the different features of men or women (visual appearance and feel of face, body, and genitals; voice quality, smell; personality and behavior, etc.) attract people as a more or less coherent package representing one sex, rather than as an arbitrary collage of male and female characteristics. If all these characteristics come to be attractive because they were experienced in association with a male- or female-specific pheromone, then they will naturally go together even in the absence of complex genetically coded instructions. (p. 210)
Still, even in fruit flies, other sensory input besides pheromones — acoustic, tactile, and visual stimuli — play a role in sexual attraction, and sex specific responses to these stimuli appear to be innate rather than learned by association [36.]. We simply don’t know where the boundary between prespecified attraction and learned association lie in our own species, nor do we have compelling evidence for the primacy of one sense over another. (p. 210 – 211)

The chapter 8 notes entry number 36 attempts to show there is “…no compelling evidence for the primacy of one sense over another.” LeVay tries to support that ridiculous claim by citing Spieth (1974) “Courtship behavior in Drosophilia” and Stockinger et al (2005) “Neural circuitry that governs Drosophilia male courtship
Excerpt:

Anatomical differences in this circuit that might account for the dramatic differences in male and female sexual behavior are not apparent.

My comment: In our 1996 Hormones and Beahavior review, From Fertilization to Adult Sexual Behavior, we placed anatomical differences and sex differences in behavior into the context of RNA-mediated cell type differention. The conserved molecular mechanisms we detailed in our section on molecular epigenetics extend across species, regardless of whether LeVay or anyone else can find sex differences in neuroanatomy that correlate with differences in the behaviors of flies and humans.
See for comparison: Courtship behavior in Drosophila melanogaster: towards a ‘courtship connectome’

Excerpt: 

The construction of a comprehensive structural, and importantly functional map of the network of elements and connections forming the brain represents the Holy Grail for research groups working in disparate disciplines.

My comment: None of my former colleagues from the Society for the Scientific Study of Sexuality has since made any attempt to challenge LeVay’s claims about my model. However, LeVay’s claims can be compared in the context of two recent reports from serious scientists:
1) Feedback loops link odor and pheromone signaling with reproduction
Excerpt:

Compelling evidence that links the feedback loops from microbes to humans

2) MicroRNA-encoded behavior in Drosophila
Conclusion:

The results of this study contribute to the understanding of how complex innate behaviors are represented in the genetic program. Our data lead us to propose that other miRNAs might also be involved in the control of behavior in Drosophila and other species.

See also: The protein arginine methyltransferase PRMT5 promotes D2-like dopamine receptor signaling, which was reported as: Receptor methylation controls behavior 
Excerpt:

Likhite et al. found putative arginine methylation motifs in some human G protein–coupled receptors (GPCRs), including the D2 dopamine receptor, and in homologs in the worm Caenorhabditis elegans.

My comment: Nutrient-dependent RNA-directed DNA methylation of GPCRs in nematodes and humans, links the pheromone-controlled physiology of reproduction to the nutrient-dependent pheromone-controlled physiology of reproduction in yeasts and other microbes via the conserved molecular mechanisms of cell type differentiation we detailed in our 1996 review. Serious scientists have linked the facts from our review from the epigenetic landscape to the physical landscape of DNA in the organized genomes of all living genera.
See: DNA twist as a transcriptional sensor for environmental changes (1992) and DNA supercoiling and bacterial gene expression (2006) and Flagellar and global gene regulation in Helicobacter pylori modulated by changes in DNA supercoiling (2007).
Addendum: Only pseudoscientists and other who are among the biologically uninformed have failed to accept the scientific progress that led to publication of Structural diversity of supercoiled DNA (2015).
This parody links what is known to serious scientists about biologically-based cause and effect to the ridiculous claims of theorists in an amusing musical rendition of insults to the theorists that is unlike any other collection of polite insults that you may ever see.

See also: Combating Evolution to Fight Disease
My comment: Help serious scientists to force pseudoscientists to learn about biologically-based cause and effect. Join the fight to stop the pseudoscience and preventable diseases!

Compare what is known to serious scientist to the claims of these pseudoscientists in the context of the most recent attempt to convince others that evolution is true.

Evolution website sets out to tackle great scientific unknowns

Excerpt: 

The site was created by a team led by Simon Conway Morris, Professor of Evolutionary Palaeobiology and a Fellow of St John’s College at the University of Cambridge. “Evolution is true, and if it didn’t happen, we wouldn’t be here,” he said.

My comment: Are you willing to accept that circular logic rather than examine life in the context of Schrodinger’s claims from “What is Life?
Excerpt:

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight)

My comment: The anti-entropic epigenetic effect of the sun’s virucidal energy on DNA repair links ecological variation to nutrient-dependent ecological adaptation via the physiology of reproduction or to virus-driven pathology in all living genera. That is not circular logic, and molecular mechanisms linked to the physiology of nutrient-dependent reproduction exemplify how the differences between life and death arose.
See also: Consciousness Mechanics: The Movie for more philosophical nonsense than most people have seen integrated into something to entertain the masses.
 

Light-induced-conformer-intercoversion-of-hydrogen-bond

Physicists: Desperate Acts

Participation on the FB group Thinking Allowed Original led to an invite by Ulla Mattfolk to participate on her secret group  Quantum Biology, coherence and decoherence.
On January 22 at 11:45pm, discussion led me to ask whether biophotonic energy differences could be recognized by the photons at the quantum level of their interactions/energies. I thought the answer might explain biodiversity via a link from quantum level self – other recognition to immune system recognition and to macromolecular self – other recognition.
My focus has been on well-established macromolecular links from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via conserved molecular mechanisms. For example, conserved molecular mechanisms link the sun’s biological energy via physical and chemical constraints to the ‘conditions of life’ that Darwin placed before consideration of natural selection.
The ‘conditions of life’ on earth require earthly biogenic origins that link immune system recognition at the quantum level of self – other recognition. For example, George F.R. Ellis posted a link to this article, which suggests that quantum physics may not extend to macromolecular interactions. Do Quantum Superpositions Have a Size Limit? That’s the type of question that I think leads physicists to unnecessary speculation about biologically-based cause and effect.
Their speculation supports the Big Bang cosmology industry but it has nothing do with what currently known about life. For example, serious scientists know that Life is physics and chemistry and communication. What serious scientists know can be traced back to what Charles Darwin learned by observations. What Darwin learned can be compared to what physicists have since learned about the chemistry of protein folding and biology of behavior. What some physicists have learned about biology may be simply stated in a picture that is worth 10,000 words.

See also:

 
This differences in these representations of birds appear to link quantum superpositions to macromolecular interactions. The difference also are linked to similarities in the interactions that link RNA-mediated cell type differentiation from quantum physics to cell type differentiation and all biodiversity.
Darwin’s ‘conditions of life’ require cell type differentiation. For example, cell types are different in different tissues of the bird and in different cell types of all other living organisms. Clearly, Darwin’s ‘condition of life’ were ignored when population geneticists bastardized his theory. Theorists used de Vries definition of mutation to make incomprehensible representations of biologically-based cause and effect that sometimes begin with abiogenesis in deep space.
For example, in this brief video, Brian Cox explains that cosmic rays and mutations and selection made him who he is, and what we are. Keep in mind that this is the type of experiment that many physicists may believe links deleterious mutations and beneficial mutations to the biodiversity of life on earth, which is manifested in morphological and behavioral phenotypes in species from microbes to man. Cox admits: “We don’t know but we can dream.” Serious scientists build their explanations of cause and effect on experimental evidence, not their dreams.

This experiment links cosmic rays and mutations to biodiversity but fails to link what is known about links from light perception to nutrient-dependent amino acid substitutions and self – other recognition differentiation of photo receptors and odor receptors that convert light energy and nutrient energy to chemical energy. Linking what is currently known about physics to what is known about biolgically-based cause and effect requires a link to the chemistry of RNA-mediated protein folding.
On January 24, 2015, I learned that one of the discussants in the secret group already had plagiarized my discussion comments as well as my Pheromones Reseach FB page comments and everything I have detailed during 20 years of published works on RNA-mediated cell type differentiation in blog posts here, like this one from January 10. Mutagenesis: Replacing facts with theories
Apparently, Matti Pitkänen  decided to take my details and add his pseudoscientific nonsense to them. It would have been ethical for him to tell others where his information came from, but ethics are not required to move theoretical physics forward. The problem is that, until now, theoretical physicists have not attempted to link light-induced changes in amino acid substitutions to the creation of life on earth via direct links from the sun’s biological energy to RNA-mediated events.
To me, linking the sun’s biological energy to life makes more sense that anything I’ve heard from biophysicists. Theoretical physicists seem to not recognize the need to link metabolic networks to genetic networks in species from microbes to man.
Indeed, Pitkänen claims to have spent the last 37 years on a noble, but failed, attempt to use Topological Geometrodynamics (TGD) to construct a theory of everything, not forgetting consciousness. Could anyone blame him for his desperate attempt to use my model of RNA-mediated amino acid substitutions in plants and animals — without attribution?
I think he will do whatever it takes in attempts to salvage what he can from physics and stake his claim to knowing something about chemistry and biology —  after learning about cell type differentiation from me. I also think others can recognize the material he plagiarized from my post here on January 10, 2015 Mutagenesis: Replacing facts with theories
He included it in a blog post linked to a pdf on January 11, 2015. A link to the pdf of the article opens here: Was ribosome the first self-replicator? 
Unfortunately, what I thought would be open discussion among professionals has led to representations of my ideas by others. Some people without original ideas secretly steal ideas from others and claim the ideas as their own. Credit for the ideas does not matter. After his representations of my details about RNA-mediated events, all that matters whether or not he contributes to scientific progress.
In this case, however, Matti Pitkänen does not add any intelligible thoughts to discussion of light-induced amino acid substitutions and cell type differentiation. I’ve included his attempt to extend my model via its incorporation in TGD, to show that physicists understand virtually nothing about chemistry and biology. After an incoherent review of what I detailed on RNA-mediated cell type differentiation in, Was ribosome the first self-replicator? he adds more theory — with my emphasis below:

How the pre-ribosome as first replicator relates to TGD approach?

TGD framework predicts that replication as a splitting of 3-surfaces to two copies is a fundamental mechanism of quantum TGD analogous to the 1→ 2 decay of elementary particle and the replication of DNA, cells, etc… should reduce to a hierarchy of replications starting from long length scales and proceeding as replications at shorter length scales with master slave relationship between the subsequent levels of the scale hierarchy. This identification of replication as a mere splitting of 3-surfaces saying nothing about what happens for the quantum states associated with them is too general to allow to talk about unique primary replicator. If one however restricts the consideration to systems consisting of RNA and amino-acid sequences the idea about ribosome as primary replicator becomes highly non-trivial. In TGD framework it is possible that pre-biopolymers were not bio-polymers but their dark counterparts formed from dark protons sequences at magnetic flux tubes with states of dark proton in 1-1 corresponds with DNA ,RNA, amino-acids and tRNA. If so pre-ribosome was realized at the level of dark matter as dark ribosome – a complex formed by dark analogs of bio-polymers. If so, then pre-ribosome consisting of dark matter at flux quanta could be the primary replicator and the formation of its bio-molecular counterpart would be induced from that of dark pre-ribosome like the dynamics of slave in master slave hierarchy. This raises questions. How does this replication proceed? Does ribosome still replicate as all other biological structures do and induce replication of low ever level structures in the dark matter hierarchy? Does the ordinary biomatter induced at the lowest level of hierarchy would only make visible this replication? In the following I briefly summarize the basic TGD based notions involved in attempt to answer these questions.

[Note: a series of caveats that attest to what is not known are now linked to more theory that attempts to what’s known about the sun’s biological energy and nutrient-dependent self organization to quantum jump sequence that somehow leads to the emergence of self organization. The jumps were defined by Hugo de Vries as “mutations”. Matti Pitkänen tries to link the quantum jumps (i.e., the mutations) to 4-D behavioral patterns via quantum self-organization, instead of nutrient-dependent self-organization.]

4-D self-organization and magnetic body One class of questions concerns the roles of self-organization and genetices. Even the definition of the notion of self-organization is poorly defined. In TGD zero energy ontology (ZEO) forms the basic framework of both quantum TGD proper and its applications to consciousness and biology. In zero energy ontology (ZEO) self-organization is replaced with self-organization by quantum jump sequence leading to the emergence of not only 3-D spatial patters but also of 4-D behavioral patterns: one can say that living system is 4-dimensional and also its geometric past changes in quantum jumps (Libet’s findings).

Various motor actions of magnetic body appear as basic processes of the quantum self-organization. This includes braiding and knotting, heff changing phase transitions changing the lengths fo flux tubes, reconnections allowing to build connections between different system consisting of flux tube pairs, and also replication. Also signalling by dark photons is an essential part of the picture and the general hypothesis is that dark photons have same universal energy spectrum as bio-photons and thus in the energy range of molecular transition energies.

Replication in TGD framework occurs at the fundamental level as a replications of 3-surface and is completely analogous to 1→ 2 decay for point elementary particle. This replication could take place for the magnetic flux quanta representing various biopolymers and higher level structures and induced the replication at the level of visible matter. As noticed, this replication is not enough in biology and must be accompanied by the replication of the quantum states associated with 3-surfaces.

One key question is how the bio-molecular processes arranged into a functional network. Here the hypothesis that magnetic flux tubes form a 3-D grid analogous to coordinate grid with points of grid at intersections of 3 flux tubes and flux tubes as coordinate lines is very attractive. This Indra’s web would be behind the gel like structure of cellular water and make it single coherent unit. Behavioral modes would be time evolutions of this grid: motor actions of the magnetic body – or hierarchy of them.

[Next:Matti Pitkänen  takes the discussion contributions on the biogenesis of achiral amino acid glycine by Joseph Klover and represents them as his own. Again, see my emphasis on the claim below: “I have proposed the identification of dark counterparts of RNAs and amino-acids as complex braided and knotted structures with braiding carrying information…” ]

Does dark matter induced the dynamics of visible biomatter?

The idea that dark matter induces the dynamics of biomatter is extremely attractive since the enormous complexity of biochemistry would be only adaptation to the dynamics of the much simple almost topological dynamics of the master represented as flux tubes carrying dark matter.

In TGD framework there are good reasons to believe that water contained the prebiotic life forms as dark analogs of various biomolecules consisting of dark proton sequences at magnetic flux tubes with the states of dark proton in 1-1 correspondence with various bio-polymers (DNA,RNA, amino-acids, tRNA). These string like objects would be dark nuclei but with a large value of Planck heff=n× h constant and with same size scale as biopolymers. The proposal is that they are present also in living matter and that is interaction between various levels based on dark photons which give bio-photons as decay products.

All the basic processes such as transcription, translation, and replication would be realized already at this level. The analogs of these processes assigning to dark analogs of biopolymers the biopolymers themselves would have evolved later. (ORP) suggests that ordinary biopolymers are accompanied by parallel flux tubes carrying dark protons sequences representing them. Ordinary manner would condense around dark matter. The strongest assumption is that dark processes induce their bio-chemical counterparts as biomolecules attach to the magnetic flux tubes for which they form images at the level of visible matter. This might explain why strong dehydration leads to denaturation of biomolecules and why denatured biomolecules are not biologically active. Dark DNA would represent the “soul” of DNA not present in denatured DNA! Same of course would apply to other biopolymers: the loss of dark matter would induce the in vivo → in vitro transformation. I have proposed the identification of dark counterparts of RNAs and amino-acids as complex braided and knotted structures with braiding carrying information making possible topological quantum computation like processes and topological realization of memory. DNA would provide a symbolic representation coding also the braiding characteristics of the dark amino-acid sequence. Dark amino-acid sequence would represent the braiding physically ad dark DNA as a sequence of symbols. Cyclotron frequencies are crucial for communication and the strength of magnetic field on flux tubes emanating transversally from dark amino-acid sequence would be determined by the state of dark proton. The correspondence between dark RNA and amino-acid would be determined by the condition that cyclotron frequencies are identical for the corresponding dark proton states (DNA and mRNA, RNA and amino-acid) so that resonant interaction is possible.

This picture conforms with the chemical properties of DNA, RNA and proteins.

RNA does not appear as double strands and in unfolded form is much less stable than DNA. This conforms with the fact that DNA serves as an information storage providing symbolic representation of RNA and amino-acids including their folding or at least braiding. RNA in turn would provide the concrete representation for braiding and folding.

DNA double strand is stable against hydrolysis but only inside cell – this could be due to the fact that the phase of water is ordered and ice-like so that it cannot induce hydrolysis by providing water molecules – perhaps the fourth phase of water discovered by Pollack and leading to the formation of dark proton sequences in TGD framework is in question.

The braiding structure of DNA is repetitive and carries no information. This conforms with the idea that DNA and its dark variant provide a purely symbolic representations in terms of genetic code for the corresponding amino-acid – and RNA polymers including also their braiding.

One can invent objections against the hypothesis that the dynamics of biopolymers is induced from that for their dark variants.

RNA is not stable against hydrolysis but it can gain stability by folding. Thus the shape of RNA molecule would not be determined by its dark variant in conflict with induction hypothesis. One can however consider the much weaker possibility that dark sector determines only topological dynamics. Only the braiding of the fold RNA molecules would determined by the braiding of dark variant.

DNA double strand is stable and braided in repetitive and very simple manner. If chemistry determines the stability of the DNA double strand then DNA double strand would induce the braiding of dark DNA strand rather than vice versa. Now one can argue that if dark DNA appears as double strand this forces the repetitive braiding.

[Next: Matti Pitkänen claims to resolve the chicken versus the egg problem in the context of their simultaneous emergence: “Hens and eggs emerged simultaneously.” I asked whether quantum level interactions were limited in scale, which they obviously cannot be when placed into the context of quantum biology.]

To how high level can one continue this parallelism. For instance, does it make sense to talk about dark variants of cell and cell membrane? Can one tell whether it was pro-cell or bio-molecules that emerged first? It seems that all these structures could have emerged simultaneously. What emerged was dark matter and its emergence involved the emergence of all the others. Hens and eggs emerged simultaneously.

Here the findings of Pollack about the generation of exclusion zones, which are negatively charged regions of water obeying exotic stoichiometry H1.5O, are suggestive. The TGD based model assumes that a phase transition generating dark protons sequences at flux tubes of magnetic body outside the EZ takes place. The self-organization at the level of ordinary matter would generate dark matter at quantum criticality – a basic aspect of self-organization process leading to higher hierarchy levels taking the role of master. Dark matter would be the master or rather – there would be entire hierarchy of masters labelled by the values of heff. I have also considered the possibility that the generation of large heff phases happens at criticality quite universally so that life would be universal phenomenon rather than random thermodynamical fluctuation.

EZs with sizes about 200 microns (size of cell) could have been the prebiotic cells. There is also evidence that EZs consist of structures with size of order micron called coherent regions (CDs to be not confused with Causal Diamonds!). Could they have been the predecessors of the cell nuclei inside which dark DNA would be stable? The TGD model for the formation of EZs assumes that they are formed from CDs under irradiation. This picture leads also to a view about metabolism predict that UV radiation with energies about 12.6 eV must play a key role in metabolism. The proposal is that this radiation arrives as dark photons along magnetic flux tubes of the magnetic body and excites water molecules inside CDs so that they are energetically at distance of about .5 eV from the splitting of OH bond. The excitation of water molecules inside CDs by metabolic energy quantum of nominal value .5 eV transforms this phase to EZs of Pollack.

Next:Matti Pitkänen places everything currently known about the physics, chemistry and conserved molecular mechanisms that link nutrigenomics to pharmacogenomics via metabolic networks and genetic networks into the context of his theory about the simultaneous emergence of chickens and their eggs.] Emergence of life as emergence of dark matter?
Many basic questions of biology seem to be hen-egg questions such as “genetics or metabolism?”, “cell membrane or biomolecules?”, “DNA or RNA?”, “RNA or amino-acids?”, etc.. This suggests that there exists a deeper level and emergence at this level induced the emergence at the level of biochemistry and cell biology. In TGD the emergence of living systems would reduce to the emergence of dark matter as large heff phases of ordinary matter taking place at quantum critical and perhaps even critical systems.

  1. The question whether genetics or metabolism emerged first ceases to be relevant in this framework, where basic physics provides candidates for the fundamental mechanisms of metabolism (for instance liberation of zero point kinetic energy when the p-adic length scale of space-time sheet (magnetic flux tube) increases). Also genetic code would have been realized already before biochemistry if dark proton sequences provided the counterparts for the fundamental biomolecules. The dark biology as dark nuclear physics would make itself visible via biochemistry induced by it. We would see directly the dynamics of dark matter just by looking living systems!
  2. If one takes this picture seriously, then also pre-RNA and various other pre-biopolymers could have been realized in terms dark proton sequences associated with dark magnetic flux tubes. The dark replication process could have been the arrangement of RNA and amino-acid flux tube portions in parallel and replication of the dark proton sequences with the help of the analog of tRNA attaching to the corresponding amino-acid. In this framework the notion of dark ribosome makes sense. It would however replicate only in cell replication.
  3. In the biochemical scenarios also the emergence of DNA looks like mystery. In TGD framework dark DNA could have emerged at the same time as dark RNA and dark amino-acids as CDs and EZs emerged and make the stable presence of also ordinary DNA inside CDs and EZs. All basic biomolecules and prebiotic cell and metabolism would have accompanied the emergence of CDs and EZs under the irradiation of water feeding metabolic energy and giving rise to prebiotic photosynthesis (note that the negative net charge of DNAs could be due to the fact that part of protons is at dark flux tubes). Dark DNA could be interpreted as an information storage representing the braiding patterns of dark RNA and dark amino-acids symbolically.
  4. In this framework the basic step of the replication is the generation of flux tube parallel to the flux tube from which one forms copy or map (say in DNA replication and and transcription). How this happens? A possible answer to the question relies on the earlier proposal that living system involves kind of coordinate grid formed from magnetic flux tubes serving as coordinate lines and meeting each other at the points of the grid. The replication process would involved translation of nearby flux parallel flux tube of the grid near to a given flux tube assignable to say DNA strand as a first step – maybe by heff reducing phase transition for flux tubes orthogonal the flux tube. After this the building bricks of the new biomolecule would be brought along either of the remaining locally orthogonal flux tubes – perhaps by heff reducing phase transition. The basic structure would be this Indras web containing visible matter at its nodes with dynamics consisting of magnetic motor actions.

This vision involves of course considerable challenges. One should model the dark ribosome counterparts of the replication process for dark DNA, transcription of dark DNA to dark mRNA, translation of dark mRNA to dark amino-acids, and also possible self-replication of dark ribosome.For background see the chapter Quantum gravity, dark matter, and prebiotic evolution of “Genes and Memes”. See also the article Was ribosome the first self-replicator?.

Here is the synopsis of Matti Pitkänen’s ridiculous claim:
Excerpt: “All basic biomolecules and prebiotic cell and metabolism would have accompanied the emergence of CDs and EZs under the irradiation of water feeding metabolic energy and giving rise to prebiotic photosynthesis (note that the negative net charge of DNAs could be due to the fact that part of protons is at dark flux tubes). Dark DNA could be interpreted as an information storage representing the braiding patterns of dark RNA and dark amino-acids symbolically.”
Matti Pitkänen’s answer to my question about water, which Joseph Klover linked to information about how it slows the speed of light. Joseph Klover seems to understand the fact that slowing the speed of light enable the transfer of information from the sun’s biological energy to the chemistry of protein folding via light-induced amino acid substitutions. In my model, the substitutions are linked to RNA-mediated cell type differentiation in plants and nutrient-dependent pheromone-controlled cell type differentiation in animals.
In Matti Pitkänen’s theory, information transfer from light to chemistry supports his claim that hens and their eggs simultaneously emerged. I think he has clarified the thoughts of most theoretical physicists and their ideas of how abiogenesis can be linked to mutations and the evolution of biodiversity, which is also clarified in this picture. Physicists seem to think that the bird and its eggs simultaneously emerged.

Ideas about cosmic rays with origins outside our solar system (Brian Cox) and ideas about beneficial mutations (Brian Cox) can now be compared to Matti Pitkänen‘s claims about the emergence of life in the context of the emergence of dark matter. Unfortunately, Matti Pitkänen took too much information from my model without learning what I had detailed and why I provided examples.
The examples established how the epigenetic landscape is linked to the physical landscape of DNA in the organized genomes of species from microbes to man via RNA-directed DNA methylation and amino acid substitutions. The substitutions differentiate the cell types of all individuals of all species. I provided details and examples so people like Brian Cox and Matti Pitkänen would continue to look like the the biologically uninformed physicists that they are. Clearly, anyone who tries to link deep space or simultaneous emergence of hens (female chickens) and their eggs to biologically-based cause and effect is wasting time and whatever money is funding their work.
The link must be from the sun’s biological energy to biologically-based cause and effect via the biophysically constrained chemistry of protein folding and differentiation of cell types that included the RNA-mediated sex differences in cell types that we explained in our 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior.
Physicists should stop making stuff up and start to learn about chemistry and biology. We wrote:
The Genome, positioning, timings. There are major structural differences between the X and Y chromosomes; e.g., centromeric aiphoid repeats sequences and distribution of heterochromatin (Graves, 1995; Wolfe et al., 1985). These structural differences correlate with sexually dimorphic chromosomal positioning within the nucleus and with male/female differences in replication timing of the active X, the inactive X, and the Y chromosomes, e.g., Boggs and Chinault (1994), Clemson and Lawrence (1996); Hansen, Canfield, and Gartler (1995). Increasingly the structure and timings within the nucleus are realized as contributing to gene expression regulation (Manders, Stap, Strackee, van Driel, and Aten, 1996; Stein, Stein, Lian, van Wijnen, and Montecino, 1996).”
The importance of that fact has since been placed into the context of cell type differentiaion and rejuvenative medicine.  See Making sense of amino acid sensing and Young blood reverses age-related impairments in cognitive function and synaptic plasticity in mice. 
The work of Christ et al (2013) extends these concepts to what is currently known about nutrigenomics and pharmacogenomics, which links metabolic networks to genetic networks via amino acid substitutions without the pseudoscientific nonsense of theories like Matti Pitkänen‘s that link the simultaneous emergence of birds and their eggs, which also links the the evolution of dinosaurs to birds.
See also: Experimental verification of Landauer’s principle linking information and thermodynamics and A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution
“In the fields of observation chance favors only the prepared mind.” — Louis Pasteur
Those who believe that abiogenesis and mutations can be linked to the evolution of biodiversty are not prepared to acknowledge that fact that “Life is physics and chemistry and communication.” Although Louis Pasteur could not explain the chicken and egg conundrum: “which came first, the chicken or the egg?” — there can be little doubt that he would never have thought that they simultaneously emerged.  Thank God, he was not a physicist like Matti Pitkänen.
 

The Nobel Prize in Physiology or Medicine 2004 was awarded jointly to Richard Axel and Linda B. Buck “for their discoveries of odorant receptors and the organization of the olfactory system”
They resolved the hen-egg conundrum by placing it into the context of what is known by serious scientists about biologically-based cause and effect.
They also showed how unimportant the ridiculous opinions of theoretical physicists are when it comes to discussions of biology. Matti Pitkänen reaffirmed how unimportant those opinions are and also he attested to how ridiculous the opinions of physicists are — at the same time.

 

poster-from-jesse

Biophysically constrained beginnings of RNA and DNA

Any anonymous participant in the discussion of: DNA may have had humble beginnings as nutrient carrier (Sep 01, 2014 by Adam Hadhazy) asks:
“when are you going to keep quiet?”
In a series of responses, I have explained the problem I have with honoring his request.
The following excerpts from Wikipedia and other sources are loosely strung together because there is no point to providing more extensive details of biologically-based cause and effect until others accept the fact that mutations and natural selection cannot lead to the evolution of biodiversity. Even without accepting the fact that nutrient-dependent amino acid substitutions differentiate the cell types of all individuals in all species, it should be clear that mutations do not. Until that fact becomes clear, nothing known about physics, chemistry, and molecular biology can be used to refute ridiculous theories. Here are examples of what cannot be used.
1) In mammals, phosphatidylserine is produced by base-exchange reactions with phosphatidylcholine and phosphatidylethanolamine. The products of this reaction are novel dinucleotides. Nicotinamide adenine dinucleotide (NAD) is a coenzyme found in all living cells. (The compound is a dinucleotide, since it consists of two nucleotides joined through their phosphate groups.)
The flipping of one base pair appears to result in Fragile X Syndrome, which is the most common form of mental retardation. It may represent what happens when an atomic-level change in nutrient-dependent energy perturbs protein folding.
For comparison, the nutrient-dependent flipping of a base pair associated with vitamin C uptake in mammals links frugivory in bats via morphological and behavioral phenotypes to their adaptive radiations. Their phenotypes link nutrient-dependent pheromone-controlled reproduction in all vertebrates and invertebrates to morphological and behavioral changes during the development of human preferences for food odors and pheromones.
2) Rather than be quieted by the pseudoscientific nonsense of evolutionary theorists who want others to believe that mutations and natural selection lead to the evolution of biodiversity, ecologists and other serious scientists continue to link biologically-based cause and effect from atoms to ecosystems via the conserved molecular mechanisms of amino acid substitutions that I detailed in my model.
Serious scientists know that models will lead to atomic level (nutrient-dependent) cures for diseases and disorders that evolutionary theorists claim are due to the same molecular mechanisms they think must link mutations to increasing organismal complexity manifested in morphological and behavioral phenotypes of species from microbes to man.
The difference between a serious scientist and a theorist (or any other idiot) is recognized by differences in their beliefs about biologically-based cause and effect. Theorists have no understanding of links between atoms and ecosystems; serious scientists attempt to understand the experimental evidence.
3) In metabolism, nicotinamide adenine dinucleotide is involved in redox reactions, carrying electrons from one reaction to another.
Most organisms synthesize NAD+ from simple components.[2] The specific set of reactions differs among organisms, but a common feature is the generation of quinolinic acid (QA) from an amino acid—either tryptophan (Trp) in animals and some bacteria, or aspartic acid in some bacteria and plants.[21][22] Besides assembling NAD+ de novo from simple amino acid precursors, cells also salvage preformed compounds containing nicotinamide. Despite the presence of the de novo pathway, the salvage reactions are essential in humans; a lack of niacin in the diet causes the vitamin deficiency disease pellagra.[28] This high requirement for NAD+ results from the constant consumption of the coenzyme in reactions such as posttranslational modifications, since the cycling of NAD+ between oxidized and reduced forms in redox reactions does not change the overall levels…
4) Rather than continue to examine facts that link the thermodynamic cycles of protein biosynthesis and degradation from atoms to ecosystems via organism-level thermoregulation, others may want to consider the alternative.
In “Mutation-Driven Evolution” for example, the claim is made that “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.”
That claim is not supported by any experimental evidence of biologically-based cause and effect, but many evolutionary theorists are convinced that the differences in morphology and behavior they can see are due to mutations that perturb protein folding at the level detailed in the Laws of Physics, which lead to everything known about chemistry and Kohl’s Laws of Biology, which are linked to the de novo Creation of olfactory receptor genes via the de novo Creation of RNA and DNA.
Addendum: Anyone willing to accept the fact that RNA and DNA somehow ‘evolved’ or that what’s known about the biophysical constraints that link ecological variation to ecological adaptations via conserved molecular mechanisms in species from microbes to man is not likely to lead to cures for diseases and disorders associated with mutations should participate in discussions on blog sites run by atheistic biology teachers like PZ Myers. For example see: One crank dies, another rises to take his place. Anyone willing to accept the fact that RNA and DNA were Created should examine the content of articles that represent what is known about the Laws of Physics; what is known about chemistry; and what is known about molecular biology. See for example: Darwin vs. Genetics: Surprises and Snags in the Science of Common Ancestry
In the context of biophysically-contrained ecological adaptations it may interest others to learn what is obviously missing from what’s being billed as the Theory of Everything. A theory of everything should have some explanatory power in the context of biologically-based cause and effect that does not link perturbed protein and nutrient-dependent ecological variation to pheromone-controlled ecological adaptations via the same molecular mechanisms. What if Hawkings’ disabled body could be linked from epigenetically-effected RNA and DNA to his highly functional mind? Would others be more interested in biological facts about the de novo Creation of proteins that can be compared to his theory of everything?
What if a nutrient-dependent flip in a single base pair led to amino acid substitutions that differentiate all the cell types of all individuals of all species via conserved molecular mechanisms? Could the link from Fragile X Syndrome and mental retardation be the same as the link to hemoglobin S and nutrient-dependent brain development in someone like you, or like Hawkings? If so, the link is likely to be nutrient-dependent amino acid substitutions that differentiate all cell types in all tissues of all organs in all organ systems of invertebrates and vertebrates via conserved molecular mechanisms of pheromone-controlled reproduction.
We can see the origins of that perspective on autophagy, which was the basis for my works in these two published works.
Effects of Carnitine on Fatty-Acid Oxidation by Muscle (1959)
DEPENDENCE OF RNA SYNTHESIS IN ISOLATED THYMUS NUCLEI ON GLYCOLYSIS, OXIDATIVE CARBOHYDRATE CATABOLISM AND A TYPE OF “OXIDATIVE PHOSPHORYLATION” (1964)
My comment: Both were co-authored by Bruce McEwen. He told me in 1991 that I would need to start with energy-dependent gene activation before my model of cell type differentiation could be completely validated. I did that in the following year with the help of Robert L. Moss and his co-authors in a series of published works that linked pheromones to gene activation in GnRH neurosecretory neurons of the mammalian hypothalamus.