5th-6th Sept 2018 Dublin, Ireland

Light-controlled cell biology (revisited)

See Sci-Bay Scholar for citations and downloads of more than 3300 published works that link viruses to microRNAs
Summary: …either the organized genomes of all cell types use the energy source, or viruses use the biophysically constrained energy of the cell types. No extant species can be used as an example of how the virus-driven theft of quantized energy can be linked from natural selection to the evolution of a new species.
See also, with my emphasis:

Light Offers New Way to Control Cell Biology (3/16/17)

…the power of light-sensitive proteins is that they can be used to study the inner workings of any living cell.

Archaea:

Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon; however, unlike plants and cyanobacteria, no known species of archaea does both.

George Church At 15:10

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

From the transcript:

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

The difference between the fixation of light and the fixation of carbon is that (see above)  no known species of archaea does both. That fact supports the claim that the ability to fix light is an ecological adaptation that links the quantized energy of sunlight to all biophysically constrained biodiversity in the context of energy-dependent viral latency.

Archaea that do not use sunlight as their energy source probably become L-forms in the context of the virus-driven degradation of their messenger RNA, which has been linked from mutations to all pathology in the context of one-carbon metabolism. Quantized energy is the obvious link from the fixation of light to the fixation of carbon in all carbon-based life forms on Earth.

Simply put, either the organized genomes of all cell types use the energy source that fixes carbon, or the viruses use the biophysically constrained energy of the cell types. For comparison, no extant species can be used as an example of how the virus-driven theft of quantized energy can be used in the context of natural selection and evolution.

See also:L-form bacteria

The cell wall is important for cell division, which, in most bacteria, occurs by binary fission. This process usually requires a cell wall and components of the bacterial cytoskeleton such as FtsZ. The ability of L-form bacteria to grow and divide in the absence of both of these structures is highly unusual, and may represent a form of cell division that was important in early forms of life.[1]
 
If the claim that L-forms are an early form of life was placed into the perspective of claims by Carl Woese about the different domains of life, theorists would need to explain how the cell wall “evolved” before all life on Earth evolved from archaea to bacteria and every other species.
 

For comparison, I claim that quantized energy as information carried by light is the link from the creation of the cell wall to all epigenetically-effected biophysically constrained food energy-dependent pheromone-controlled biodiversity. However, Carl Zimmer seems to want someone to redefine “heredity” to make the definition fit back into the context of evolution outside the context of Dobzhansky (1973) Nothing in Biology Makes Any Sense Except in the Light of Evolution

(quotes)

I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation.

For example, the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.

See also: Clinically Actionable Genotypes Among 10,000 Patients With Preemptive Pharmacogenomic Testing

…different SNPs may be present and confer risk for inefficacy or toxicity among AAs, as well as Asians, Hispanics, or other populations.

The light energy-dependent differences in the SNPs confer the diversity of morphological and behavioral phenotypes in all living genera. The SNPs also are linked to healthy longevity or pathology via the fixation of RNA-mediated amino acid substitutions. That fact must be placed into the context of pheromone-controlled reproduction and transgenerational epigenetic inheritance. That is why Carl Zimmer wants people to think that we need a new definition of heredity.
See the book description for: She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity

We need a new definition of what heredity is…

See for comparison: 6 Bacteria with Awesome Superpowers (Excerpt)

Chemolithoautotrophic, which means they get their energy from inorganic compounds in their environment

SARCASM ALERT: If neo-Darwinian evolutionary theorists make claims about chemolithoautotrophic heredity, will you still believe them?

See also: March for Science: How Democracy Kills Expertise (3/20/17)

“People don’t care how much you know until they know how much you care.”

Until the public is convinced that scientists and journalists care about truth and society, then I fear all of our labors will be in vain.

Serious scientists care about the truth and about society. Many so-called science journalists want the efforts of people who care to be viewed in the context of their pseudoscientific nonsense about heredity via evolution.
See: Changes in the vascular system may trigger Alzheimer’s disease (3/21/17)

The plasma protein, called Factor XII, is part of a cascade of enzymes that induces blood coagulation and inflammation.

If Alzheimer’s disease evolved, you do not need to know about the energy-dependent cascade of enzymes that starts with the creation of ATP synthase. What if you had become a so-called science journalist who did not know that proteins do not create themselves? For example, that’s how energy-dependent changes in the microRNA/messenger RNA balance can be linked to all healthy longevity. You wouldn’t know that.
Virus-driven energy theft causes Alzheimer’s and all other pathology. All serious scientists know that. All pseudoscientists, atheists, and theorists do not want you to know it. For example, viruses cause antibiotic resistance.

This antibiotic will ruin you (3/18/17)

It gets worse. There is no cure. No treatment. No relief. No specialist even.

2011 Researchers to study positive genetic contributions of viruses (3/18/11)

  1. The two-year, $550,000 grant has been awarded to K. Eric Wommack…
  2. These discoveries come from the study of marine ecosystems but allow researchers to learn more about the predominant biological features of viruses overall, which can affect how human conditions – such as cancer – are diagnosed and treated. “Within some of the samples we’ve collected, we found genes critical to protein folding,” says Polson. “In many cases, protein has to be directed to fold in the proper way. Protein misfolding is a component in the cause of some diseases, so this knowledge can be very important in our understanding of viral infection processes.”

Reported as: Social selection: genetic contribution of viruses to life on earth

… science fiction author Greg Bear successfully predicted the involvement of specific viruses in speciation (read Darwin’s Radio and Darwin’s Children). This new report attests to the likelihood that the mechanisms may someday be found. Bear’s concept of viral induction of species evolution — with further consideration given after reading this article — also sheds light on differences between what most people call “natural” selection and what some people are beginning to call “social” selection. There may be no evidence of transitionary species in the fossil record because viruses elicited comparatively sudden and dramatic changes in the genotype and phenotype of extant organisms as other organisms became extinct. One of the mechanisms involved in speciation, as indicated by Bear, is likely to be pheromones that signal similarities and differences in species that occupy similar social niches. I’m now suggesting that transfer of genetic material between species — not just single genes, but large segments of genetic code – could rather suddenly result in what might at first appear to be a newly evolved organism. If ever a newly evolved organism is found, it might be a good idea to look around its neighborhood for genetic clues that provide evidence of parenthood, or of Creation.

Virus-mediated archaeal hecatomb in the deep seafloor (2015)

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.

See for updates: Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory (2017)

While information from aquatic systems and medical microbiology suggests the potential for viral influences on nutrient cycles, food web interactions, gene transfer, and other key processes in soils, very few empirical data are available. To understand the soil virome, much work remains.

Re-examination of the relationship between marine virus and microbial cell abundances (2017)

…viral effect sizes derived from ‘representative’ abundances require substantial refinement to be extrapolated to regional or global scales.

If you let them, researchers like these will spend millions of dollars and never learn that viral latency is biophysically constrained in the context of the sun’s anti-entropic energy and the physiology of food energy-dependent pheromone-controlled feedback loops.
See for comparison: What is life? (1944)

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.)

What is life when it is not protected from virus driven entropy (2016)

See also: MicroRNA and autophagy

Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

Autophagy in health and disease (1)

Novel Treatment Strategies for the Nervous System: Circadian Clock Genes, Non-coding RNAs, and Forkhead Transcription Factors

Each of these pathways have an intimate relationship with the programmed death pathways of autophagy and apoptosis and share a common link to the silent mating type information regulation 2 homolog 1 (Saccharomyces cerevisiae) (SIRT1) and the mechanistic target of rapamycin (mTOR). Circadian clock genes are necessary to modulate autophagy, limit cognitive loss, and prevent neuronal injury. Non-coding RNAs can control neuronal stem cell development and neuronal differentiation and offer protection against vascular disease…

The author includes what is known about the links from biophysically constrained RNA-mediated energy-dependent pheromone-controlled reproduction in yeasts to mammals.
See also this comment by Frank Xavier on Eat Yourself to Live: Autophagy’s Role in Health and Disease

Amino acids are not all the same, EAA and NEAA messages epigenetically control sometimes univocal responses, but more often they rule opposing effects.

I wrote:

Thanks for mentioning that. In a recent interview about his forthcoming book, Carl Zimmer claimed

…we need to be much more skeptical about other forms of heredity, like epigenetics.

(edited) Food energy-dependent biophysically constrained viral latency has been linked to healthy longevity in all living genera via autophagy, in the context of fixation of RNA-mediated amino acid substitutions and game play in Cytosis, for ages 10+.

In that context, we included a section on molecular epigenetics in this 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior

Our claims have since been supported at every level of examination that now links the sun’s anti-entropic virucidal energy from electrons to ecosystems via cryo-EM technology and the creation of microRNAs.

See: Regulation of Luteinizing Hormone Receptor mRNA Expression in the Ovary: The Role of miR-122 and Regulation of FSH expression by differentially expressed miR-186-5p in rat anterior adenohypophyseal cells and Modulation of miRNAs by Vitamin C in Human Bone Marrow Stromal Cells
The microRNA-mediated link from Vitamin C to ecological adaptations in a modern human population in China established the facts about alternative splicings of pre-mRNA that we included in our 1996 review. See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
See also:  Reproductive role of miRNA in the hypothalamic-pituitary axis
See also: Chemistry at the nexus of water and energy

Our ability to harness reactions that absorb or release energy is often contingent on water as a mediator. We can appreciate this simply by considering the steam that drives our electricity-generating turbines, the rivers that flow through our hydroelectric plants, and the freshwater–saltwater interface from which we can harvest blue energy. Whether we split water (as plants do), make it (as a product of combustion) or just drink it, this compound is inexorably tied to energy. Chemistry is at the heart of these topics and this collection brings together content from across Nature Research that focuses on the chemistry of energy production and water treatment.

Philip C. Ball and Carl Zimmer continue to display their overwhelming ignorance of cell biology in two books:
Beyond Weird

We now realise that quantum mechanics is less about particles and waves, uncertainty and fuzziness, than a theory about information…

See for comparison: Life is physics and chemistry and communication and What is life when it is not protected from virus driven entropy
See also: She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity

We need a new definition of what heredity is…

Both so-called science journalists have ignored everything known to serious scientists about biophysically constrained viral latency. They reach a very large target audience of others who are biologically uninformed.
In the context of those who are equally uninformed, so-called science journalists have the power to contribute to increasing amounts of  unnecessary suffering and premature deaths. Only the emergence of Timothy J. Cunningham as director of the CDC is likely to stop them. May God help us all if Timothy J. Cunningham has somehow vanished without a trace and fails to return to put pseudoscientists and their idiot minions into their proper place.

Alternative splicing of pre-mRNA

Do not refute cherished theories

Synopsis:
All serious scientist know that pre-mRNAs (now known as microRNAs in more than 70,000 published works) do not create themselves.
For comparison, Ricki Lewis fails to mention how fertility is biophysically constrained by by the creation of the sun’s anti-entropic virucidal energy, the creation of enzymes (e.g, ATP synthase), the creation of ATP, the creation of microRNAs, and the RNA-mediated creation of hormones and receptors that link achiral glycine in position 6 of the GnRH decapeptide to all experience-dependent receptor mediated structures and function in all vertebrates with jaws.

8 Simple mistakes that can delay peer review (and how to avoid them) (2018)

Add: Do not refute neo-Darwinian pseudoscientific nonsense or Big Bang cosmology. If we publish your work, we will retract it.
See for instance: Biomechanical Characteristics of Hand Coordination in Grasping Activities of Daily Living (2016) [retracted]

Following publication, readers raised concerns about language in the article that makes references to a ‘Creator’, and about the overall rationale and findings of the study.

For comparison, there was no need to mention a “Creator’ in  From Fertilization to Adult Sexual Behavior (1996)

Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans…

All serious scientist know that pre-mRNAs (now known as microRNAs in more than 70,000 published works) do not create themselves.
For comparison, Ricki Lewis fails to mention how fertility is biophysically constrained by by the creation of the sun’s anti-entropic virucidal energy, the creation of enzymes (e.g, ATP synthase), the creation of ATP, the creation of microRNAs, and the RNA-mediated creation of hormones and receptors that link achiral glycine in position 6 of the GnRH decapeptide to all experience-dependent receptor mediated structures and function in all vertebrates with jaws.
See: The Biology Behind the Fertility Clinic Meltdown

The spindle apparatus is among the most elegant structures in a cell, quickly self-assembling from microtubules and grabbing and aligning chromosomes so that equal sets separate into the two daughter cells that result from a division.

Self-assembling is a term often used by biologically uninformed theorists who do not understand what is known to serious scientists about cell type differentiation. See for an accurate representation of how fertility in all mammals is naturally biophysically constrained by FSH.
Regulation of FSH expression by differentially expressed miR-186-5p in rat anterior adenohypophyseal cells

Our results demonstrate that miR-186-5p regulates FSH secretion by directly targeting the FSHb 3′ UTR, providing additional functional evidence for the importance of miRNAs in the regulation of animal reproduction.

For more information about the virus-driven fertility meltdown that alters the structure and function of all mammalian genomes in every generation, see:
The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
and
Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
 

Biology to a Physicist

MicroRNA-activated / RNA-mediated gene expression

Summary:
All patterns exist only in the context of the de novo creation of  enzymes and energy-dependent microRNAs that link light-activated endogenous substrates from what is known about particle physics to biophysically constrained viral latency in the cell biology game: Cytosis.
See also: miRNA activation is an endogenous gene expression pathway
Moving forward:
Few people are likely to ask about the origin (i.e., the de novo creation) of energy-dependent microRNAs. Fewer still will link the creation of quantized energy as information from the physiology of pheromone-controlled reproduction to viral latency via autophagy, which biophysically constrains the diversity of  ecologically adapted life.
That fact provides the opportunity for Philip C. Ball, a British science writer, to take the information from my blog posts and present it in his book: “Beyond Weird.”
Excerpt from the description:

Over the past decade it has become clear that quantum physics is less a theory about particles and waves, uncertainty and fuzziness, than a theory about information and knowledge—about what can be known, and how we know it. Discoveries and experiments over the past few decades have called into question the meanings and limits of space and time, cause and effect, and, ultimately, of knowledge itself.

Kindle edition
Historical Perspective:
In the summer of 2017, I reported this claim from Philip C. Ball, and placed it into the context of childish beliefs about Santa Claus (video):  To turn quantum to classical…

…we don’t need a conscious mind to measure or look; we just need an environment full of stuff. With or without us, the Universe is always looking.

By plagiarizing my life’s works on biophysically constrained energy-dependent RNA-mediated cell type differentiation, Philip C. Ball may now appear to have suddenly become a serious scientist. But he has already shown the world an unparalleled level of human idiocy. (See Feynman’s claim about Philip Ball’s idiocy).
See for comparison: Patterns in Nature: Why the Natural World Looks the Way It Does 1st Edition

By exploring similarities such as those between a snail shell and the swirling stars of a galaxy, or the branches of a tree and those of a river network, this spectacular visual tour conveys the wonder, beauty, and richness of natural pattern formation.

All patterns exist only in the context of the de novo creation of  enzymes and energy-dependent microRNAs that link light-activated endogenous substrates from what is known about particle physics to biophysically constrained viral latency in the cell biology game: Cytosis.
See also: miRNA activation is an endogenous gene expression pathway

Transfection of small non-coding RNAs (sncRNAs) molecules has become a routine technique widely used for silencing gene expression by triggering post-transcriptional and transcriptional RNA interference (RNAi) pathways. Moreover, in the past decade, small activating (saRNA) sequences targeting promoter regions were also reported, thereby a RNA-based gene activation (RNAa) mechanism has been proposed. In this regard, Turner and colleagues recently discovered an endogenous microRNA (miRNA) which binds its promoter in order to upregulate its own expression. Interestingly, several miRNA-induced RNA activation (miRNAa) phenomena have since then been identified. My objective here is to introduce the reader into the emergent miRNAa research field, as well as bring together important discoveries about this unexplored transcriptional activation pathway.

The claim that this is an unexplored transcriptional activation pathway can be placed into the context of how the pathway links light-activated endogenous substrates in all cell types to biophysically constrained energy-dependent changes that link atoms to ecosystems.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

See: Energy as information and constrained endogenous RNA interference (figshare, 2017) (video) (audio/visual narrative with citations to published works)
Abstract:

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.

The facts about the viral hecatomb link the virus-driven theft of quantized energy as information to all pathology. Science writers like Philip C. Ball have ignored that fact for several decades. Their ignorance has been the cause of unnecessary suffering and premature death, which could have been prevented if they had learned about the energy-dependent biophysically constrained ecological adaptations that link what is known about species from bacteria to humans. Simply put, food energy and the pheromone-controlled physiology of reproduction link what is known about microbes to all biodiversity on Earth.
That fact is not “Beyond Weird.” It is simply beyond the ability of Philip C. Ball to grasp.
See my book (with co-author, the late Robert T. Francoeur): The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002)

See his books for comparison:
  • Designing the Molecular World: Chemistry at the Frontier (1994)
  • Made to Measure: New Materials for the 21st Century (1997)
  • The Self-made Tapestry: Pattern Formation in Nature (1999)
  • H2O: A Biography of Water (1999) (published in the U.S. as Life’s Matrix)
  • Stories of the Invisible: A Guided Tour of Molecules (2001), (republished as Molecules: A Very Short Introduction (2003)
  • Bright Earth: The Invention of Colour (2001)
  • The Ingredients: A Guided Tour of the Elements (2002) (republished as The Elements: A Very Short Introduction (2004)
  • Critical Mass: How One Thing Leads to Another (2004)
  • Elegant Solutions: Ten Beautiful Experiments in Chemistry (2005)
  • The Devil’s Doctor: Paracelsus and the World of Renaissance Magic and Science (2006)
  • The Sun and Moon Corrupted, a novel, Portobello Books Ltd, (2008)
  • Universe of Stone: A Biography of Chartres Cathedral (2008)
  • Shapes, Nature’s Patterns, a Tapestry in three Parts (2009)
  • Flow, Nature’s Patterns, a Tapestry in three Parts (2009)
  • Branches, Nature’s Patterns, a Tapestry in three Parts (2009)
  • The Music Instinct (2010)
  • Unnatural, The Heretical Idea of Making People (2011)
  • Why Society is a Complex Matter: Meeting Twenty-first Century Challenges with a New Kind of Science (2012)
  • Curiosity: How Science Became Interested in Everything (2013)
  • Serving the Reich: The Struggle for the Soul of Physics under Hitler (2014)
  • Invisible: The Dangerous Allure of the Unseen (2015), University of Chicago Press (2014), Random House
  • Patterns in Nature: Why the Natural World Looks the Way It Does (2016)
  • The Water Kingdom: A Secret History of China (2017)

Remember: Philip C. Ball and others like him failed to link the speed of light on contact with water to all biodiversity on Earth in the context of the energy-dependent creation of the enzyme ATP synthase, the creation of ATP, and the biophysically constrained creation of RNA, which links autophagy to the protection from the virus-driven degradation of messenger RNA in all living genera. Watch for reviews of his book by others who know nothing about biophysically constrained viral latency.
See for comparison: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

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

See also: Subatomic: An Atom Building Board Game (September, 2018)

A deck-building game where particle physics & chemistry collide! Use quarks to build subatomic particles & particles to build Atoms!

Witzhany2018

Polymaths and paradigm shifts: From Asimov to Bear (5)

Summary: Neil deGrasse Tyson and Lawrence Krauss are among those who have continued to substitute pseudoscientific nonsense for legitimate facts, which is what Hawking did in every book he ever wrote, and each time he made a spurious claim based on his abilities as a conniving theorist whose works still have not been confirmed-and-validated. Now that he is gone, others may proclaim the greatness of his intellect and lionize the magnitude of his influence because they also are biologically uninformed science idiots. Like Hawking, they refused to learn how Darwin’s “conditions of life” have been linked to the prevention of all virus-driven pathology.

Renowned Physicist Stephen Hawking Dies

The comments by Neil deGrasse Tyson and Lawrence Krauss can be linked to this discussion: 2013 Isaac Asimov Memorial Debate: The Existence of Nothing and to the 2017 representation of biomolecules in On the Difference between Physics and Biology: Logical Branching and Biomolecules.
The food energy-dependent pheromone-controlled creation of the biomolecules will be discussed during Schrödinger at 75 – The Future of Biology – September 2018 after the virus-driven degradation of messenger RNA and all pathology is discussed during Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses
For comparison, Stephen Hawking gained fame by collaborating with Roger Penrose and with George FR Ellis, who co-authored The Large Scale Structure of Space-Time.
In the forward to the reprint edition of What is Life?, Roger Penrose wrote

How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy? (8 August 1991)

In the cell biology game Cytosis, anyone age 10+ can learn that the creation of energy as ATP protects all organized genomes from the virus-driven degradation of messenger RNA, which all serious scientists since Schrödinger have linked from mutations to all pathology.That’s all you need to know about Roger Penrose.
George FR Ellis is the co-author of On the Difference between Physics and Biology: Logical Branching and Biomolecules. He helped to link the food energy-dependent creation of microRNAs to biophysically constrained viral latency, but is determined to undermine the works of other serious scientists with his use of the ambiguous term biomolecules.
Taken together, Stephen Hawking, Roger Penrose, and George FR Ellis have done more than most to bastardize Darwin’s claims about the need to start with food energy-dependent  “conditions of life.” Their unproven ideas from physics should never have been substituted for experimental evidence.
The evidence links the premise of the game “Subatomic” from what is known about particle physics to biophysically constrained viral latency and healthy longevity via this claim, which was made by Schrödinger.

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.)

Neil deGrasse Tyson and Lawrence Krauss are among those who have continued to substitute pseudoscientific nonsense for legitimate facts, which is what Hawking did in every book he ever wrote, and each time he made a spurious claim based on his abilities as a conniving theorist whose works still have not been confirmed-and-validated. Now that he is gone, others may proclaim the greatness of his intellect and lionize the magnitude of his influence because they also are biologically uninformed science idiots. Like Hawking, they refused to learn how Darwin’s “conditions of life” have been linked to the prevention of all virus-driven pathology.
See: DNA Tumor Virus Regulation of Host DNA Methylation and Its Implications for Immune Evasion and Oncogenesis
Reported as: Here’s How Viruses Inactivate the Immune System, Causing Cancer

“Ultimately viruses are causing these tumors to form and are further manipulating the immune system to allow tumors to keep growing,” Kuss-Duerkop says. “But these same mechanisms may be key in combating tumors with immune-based therapies or in keeping cancer from developing in the first place.”

If not for the bastardization of Darwin’s claims by theorists, Kuss-Duerkop and others like her probably would have learned that sunlight is the source of energy for the growth of food that links food energy to the pheromone-controlled physiology of reproduction in species from microbes to humans. The energy links changes in the microRNA/messenger RNA balance from virus-driven energy theft to all unnecessary suffering and premature death.The fact that Stephen Hawking suffered throughout his life with a neurodegenerative disease may be fitting in the context of his ignorance.
The 4 Scientific Lessons Stephen Hawking Never Learned

  1. We have a tendency, when we turn people into heroes, to lionize their achievements and ignore their failings, but to do so cheats humanity out of recognizing all the facets of a complicated character.
  2. May we memorialize him in the best way possible: by increasing our own knowledge and curiosity to live better lives.

Until then, see: Prominent Neuroscientist Fired by Columbia, HHMI
This is the first clear indicator of how the Trump administration will drain the academic swamp.
Jessell is the serior author of: Activity Regulates the Incidence of Heteronymous Sensory-Motor Connections

The positioning of newly born neurons is a tightly regulated process that is critical for the assembly of the nervous system. In the spinal cord, nuclear organization of motor neurons into pools is an elaborated morphogenetic feature at the basis of the wiring of spinal sensory motor circuits (Sürmeli et al., 2011, Hinckley et al., 2015, Bikoff et al., 2016). The events controlling motor neuron positioning during development have yet to be clearly defined.

The activity is food energy-dependent and RNA-mediated in the context of sensory input and the physiology of pheromone-controlled reproduction, which biophysically constrains viral latency in species from microbes to humans.
See for example: Meet the creature that can regenerate its brain and resist cancer.(video) The superimposed electron cloud over the yin yang symbol of Chinese philosophy and medicine is a clear representation of the complexity. If neuroscientists cannot link energy-dependent changes in electrons to ecosystems in all living genera, they will be dismissed and replaced with serious scientists.
For example, the facts about regenerating the brain and resisting cancer suggests Jessell’s termination occurred due to his ongoing failure to link the virus-driven degradation of messenger RNA to loss of motor control in all neurodegenerative diseases.
See for comparison: “Blood Music” (1985) by Greg Bear, who presciently linked energy-dependent changes in the microRNA/messenger RNA balance to the creation of an advanced human species via naturally occurring biophysically constrained viral latency.
See also: Actor Steven Kearney reads excerpts from Greg Bear’s 1985 novel Blood Music.

Bear was one of the first sci-fi authors to delve deep into the possibilities of synthetic biology. In this section, a biologist named Michael Bernard is infected with a killer virus that has wiped out most of North America. The virus is made up of tiny biological computers called “noocytes,” where were intended to improve the human body — giving it routine maintenance and maximizing human potential. Instead, it wiped out most of North America.

Remember, without the food energy-dependent pheromone-controlled RNA-mediated DNA repair that biophysically constrains viral latency:
Image may contain: text

Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

Polymaths and paradigm shifts: from Asimov to Bear (3)

Polymaths and paradigm shifts: from Asimov to Bear (2)

Teilhardism And The New Religion: A Thorough Analysis of the Teachings of Pierre Teilhard de Chardin”, p.18, TAN Books

The evolutionist thesis has become more stringently unthinkable than ever before. — Dr. Wolfgang Smith (2015).

A Chat with Information Scientist Pedro Marijuán (2017)

I’ve based my informational scheme of the cell on this thinking of “distinction on the adjacent” — where molecular recognition is the essential phenomenon over which biological complexity has been developed.

Biological complexity develops in the context of the olfactory code. Molecular recognition of food odors and pheromones biophysically constrains viral latency.

See: Fundamental principles of the olfactory code  Volume 164, February 2018, Pages 94-101 open access

Sensory coding represents a basic principle of all phyla in nature: species attempt to perceive their natural surroundings and to make sense of them. Ultimately, sensory coding is the only way to allow a species to make the kinds of crucial decisions that lead to a behavioral response.

Alternative splicing of microRNAs (aka pre-mRNAs) are required for a behavior response.

The splicing code  Volume 164, February 2018, Pages 39-48

…the splicing code depends on a myriad of different factors that in part are influenced by the background in which they are read such as different cells, tissues or developmental stages. Given the complexity of the splicing process, the construction of an algorithm that can define exons or their fate with certainty has not yet been achieved.

Algorithms define nothing. The availability of quantized energy as information must be linked to biophysically constrained viral latency and all biologically based cause and effect.

What is code biology?  Volume 164, February 2018, Pages 1-10

The great discontinuities of the history of life, in other words, can be explained as the result of the appearance of new codes.

New codes do not automagically occur. The new codes are energy-dependent and RNA-mediated in the context of the fixation of amino acid substitutions that differentiate the cell types of all living genera.

On universal coding events in protein biogenesis  Volume 164, February 2018, Pages 16-25

The complete ribosomal protein synthesis cycle and codon-amino acids associations are universally preserved in all life taxa on Earth. This process is accompanied by a set of hierarchically organized recognition and controlling events at different complexity levels. It starts with amino acid activation by aminoacyl tRNA synthetases…

The energy-dependent creation of the tRNA synthetases links hydrogen-atom transfer in DNA base pairs in solution to all energy-dependent biodiversity.

How prokaryotes ‘encode’ their environment: Systemic tools for organizing the information flow  Volume 164, February 2018, Pages 26-38

An important issue related to code biology concerns the cell’s informational relationships with the environment. As an open self-producing system, a great variety of inputs and outputs are necessary for the living cell, not only consisting of matter and energy but also involving information flows.

Quantized energy is the information that flows through every cell type in all prokaryotes.

Causation, constructors and codes  Volume 164, February 2018, Pages 121-127

A formal definition of codes in general, and organic codes in particular, allows the relational diagram to be extended so as to capture this translation of formal cause into process. The extended relational diagram is used to exemplify causal entailment in a diverse range of processes, such as enzyme action, construction of automata, communication through the Morse code, and ribosomal polypeptide synthesis through the genetic code.

The diverse range of processes starts with the creation of energy-dependent enzyme action. The anti-entropic virucidal energy of sunlight was first linked to the creation of all biodiversity on Earth in 1944: What is Life?

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.) (pp. 73 and 74)

If you think you can link anything except sunlight to all biodiversity on Earth, see: Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses
If you know that serious scientists do not link viruses to the evolution of anything except pathology, see:
Schrödinger at 75 – The Future of Biology – September 2018
The future of biology will not be left in the hands of biologically uninformed theorists.

Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

Polymaths and paradigm shifts: from Asimov to Bear (2)

Polymaths and paradigm shifts: from Asimov to Bear (1)
See also: Search results for virus-driven energy theft
Summary: The creation of enzymes, such as ATP synthase is energy-dependent. The energy biophysically constrains viral latency via the creation of microRNAs and RNA-mediated amino acid substitutions that differentiate the cell types of all living genera.
Modifying Other’s Originality without Quote is an Act of Piracy

A writer who does not cite the sources in h/h feature article is committing piracy. Piracy is plagiarism… high level quality requires originality and creativity… these inattentions…should be strongly condemned… Accordingly, the originally contributing author may preserve the honor worthily and endeavor to further contribution in scientific study.

See for comparison: Here’s how viruses inactivate the immune system, causing cancer

It’s no new news that viruses cause cancer.

The full text of the article is free: DNA Tumor Virus Regulation of Host DNA Methylation and Its Implications for Immune Evasion and Oncogenesis

…virus-associated cancers show highly increased levels of DNMT expression [75,76,77,85,94,95,96,97,98,99]. In HBV-associated hepatocellular carcinoma (HCC), DNMT expression is inversely correlated with levels of tumor suppressor microRNAs (miRNAs), including miR-152 targeting DNMT1 [97] and miR-101 targeting DNMT3A [99]. Virus-induced DNA hypermethylation is commonly found on several tumor suppressor genes…

RNA-directed DNA methylation links the energy-dependent microRNA-mediated creation of tumor suppressor genes to biophysically constrained viral latency via the proton motive force. The proton motive force links differences in the energy of photons from hydrogen-atom transfer in DNA base pairs in solution to the light-activated endogenous substrates of RNA-mediated DNA repair.
See also: “There is no honor among thieves” is a pithy saying that captures Solomon’s observation concerning the wicked and those who choose their company.
A Twitter search returned several interesting comments related to what is known to serious scientists about the proton motive force and the claim that “There is no honor among thieves.” For instance, writers who modify the claims and questions about the proton motive force are plagiarists and/or thieves. See:

  1. 12 Sep 2010

What do proton motive force driven multidrug resistance transporters have in common?

2. 19 Jun 2010

The H+ gradient is called the proton-motive force. This force drives the H+ back across the membrane through H+ channels. ATP synthases aids

The creation of enzymes, such as ATP synthase is energy-dependent. The energy biophysically constrains viral latency via the creation of microRNAs and RNA-mediated amino acid substitutions that differentiate the cell types of all living genera.

 Philip Ball @philipcball Mar 2

This was filmed tonight, so you’ll soon get to see why Nick Lane thinks the key to the origin of life is not amino acids or RNA but proton gradients. (I think he may be right.)

See for comparison: snippet from our June 24, 2017 conversation about the claims of Philip C. Ball.

See also: The legacy of Frankenstein: A series of events celebrating 200 years of Frankenstein

The origin of life

Dr Frankenstein aimed to create new life from inanimate parts. But how did life first arise on Earth? Join Nick Lane in conversation with Phil Ball as they discuss the latest ideas, from warm ponds to space rocks and hydrothermal vents.

Ask when Nick Lane and/or Philip C. Ball first learned about proton gradients. See how much longer it takes them to link the creation of sunlight  from differences in the energy of photons to biophysically constrained viral latency and all biodiversity via the physiology of reproduction and this model: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013)

Conclusion:

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

See also: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

Abstract:

This angstroms to ecosystems model of ecological adaptation links nutrient energy-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements via the physiology of reproduction in species from microbes to humans. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity. Species-specific pheromones link quorum-sensing in microbes from chemical ecology to the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection for codon optimality links nutritional epigenetics to the behaviors that enable ecological adaptations. All biodiversity is an ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. Simply put, olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of supercoiled DNA in the organized genomes of species from microbes to man during their development.

See for comparison: On the Difference between Physics and Biology: Logical Branching and Biomolecules

In my model, microRNAs are the biomolecules that link the creation of sunlight to all energy-dependent biophysically constrained viral latency. Viral latency is required to link the physiology of reproduction to all biologically-based diversity in all species.

Claims about proton gradients that link physics to biology without starting with the creation of sunlight are made by biologically uninformed theorists.

An evolutionary theory killer

Polymaths and paradigm shifts: from Asimov to Bear (1)

Summary: In the context of what is known about how top-down causation must be linked to all biodiversity on Earth, the anti-entropic virucidal energy of sunlight links differences in the energy of two photons from the proton motive force to the creation of microRNAs. The link from the proton motive force to the creation of microRNAs is endogenous RNA interference (RNAi). Endogenous RNAi is manifested as energy-dependent differences in biophysically constrained viral latency.
Biophysically constrained viral latency has been linked to healthy longevity in all living genera from what appears to be the “dawn of creation.”
See: Conceptual Insights, Energy Transformations in Oxidative Phosphorylation (2002)

View this media module for an animated, interactive summary of how electron transfer potential is converted into proton-motive force and, finally, phosphoryl transfer potential in oxidative phosphorylation.

See: Section 18.4A Proton Gradient Powers the Synthesis of ATP
Place what is known to all serious scientists about the proton motive force into the context of energy-dependent electron transfer potential.
See also: Chemiosmosis

…the term proton-motive force (PMF)… can be described as the measure of the potential energy stored as a combination of proton and voltage (electrical potential) gradients across a membrane. The electrical gradient is a consequence of the charge separation across the membrane (when the protons H+ move without a counterion, such as chloride Cl).

See: Search results for proton motive force
On February 2, 2018 and on February 26, 2018 I linked the claim that Permeability transition in human mitochondria persists in the absence of peripheral stalk subunits of ATP synthase (2017) to findings on RNA-RNA interactions in The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14  (1993) This link opens the to free pdf

Two small lin-4 transcripts of approximately 22 and 61 nt were identified in C. elegans and found to contain sequences complementary to a repeated sequence element in the 3′ untranslated region (UTR) of lin-14 mRNA, suggesting that lin-4 regulates lin-14 translation via an antisense RNA-RNA interaction.

The small lin-4 transcripts of approximately 22 and 61 nt were subsequently referred to as pre-mRNAs before the term pre-mRNA became microRNA as the number of nucleotides (nt) was reduced to 22 in the context of more than 70,000 published works on microRNAs. See: microRNA
In the context of what is known about how top-down causation must be linked to all biodiversity on Earth, the anti-entropic virucidal energy of sunlight links differences in the energy of two photons from the proton motive force to the creation of microRNAs. The link from the proton motive force to the creation of microRNAs is endogenous RNA interference (RNAi). Endogenous RNAi is manifested as energy-dependent differences in biophysically constrained viral latency. Biophysically constrained viral latency has been linked to healthy longevity in all living genera from what appears to be the “dawn of creation.”
For instance see: Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants (2012) and Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes (2012)
Reported May 17, 2012 as: Humans riddled with rare genetic variants
See also: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants (2013)
Reported November 28, 2012 Past 5,000 years prolific for changes to human genome
See also: The splicing code (Feb 2018)

…except for very few and marginal variations, it is the same from bacteria to man, the RNA stretch: 5′ GUGUUC 3′ reads as the dipeptide: Val-Phe in bacteria, in yeast, in Arabidopsis, in zebra fish, in mouse and in human. A degree of ambiguity is possible if mutations are introduced in the tRNAs in a way that the anticodon reads one amino acid but the aminoacyl-transferase attaches a different one onto the tRNA.

See also: Creatures’ Adaptability Begins with Their Sensors
Sensory input must be linked to energy-dependent RNA-mediated biophysically constrained viral latency.
See: OLYMPUS experiment sheds light on structure of protons

…most of the time, only one of the photons has high energy, while the other must carry very little energy indeed…

In 2013 Isaac Asimov Memorial Debate:The Existence of Nothing, Neil deGrasse Tyson made this spurious claim:

Isaac Asimov, “…perhaps, the last polymath of our civilization.”

A polymath should be required to link quantum physics from quantum chemistry to biophysically constrained viral latency and all biodiversity. Wide-ranging knowledge should include what is known about the conserved molecular mechanisms that link the food energy-dependent physiology of reproduction to ecological adaptations in species from microbes to humans.
Eshel Ben-Jacob and Greg Bear are polymaths. Isaac Asimov was not.
Eshel Ben-Jacob presciently linked Learning from Bacteria about Natural Information Processing (2009)  to the biophysically constrained viral latency Greg Bear placed into the context of the creation of a new human species in two books reviewed in Nature:
Evolution rising from the grave (2000)
Living with the Neanderthals (2003)
See also: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)
Polymaths should be able to recognize patterns that link photophosphorylation and oxidative phosphorylation from the creation of enzymes to biophysically constrained RNA-mediated DNA repair, which links ecological variation from phytoremediation to ecological adaptations in all living genera. Anyone who fails to do that in the context of the weekend resurrection of the bacterial flagellum in P. fluorescens should be called a biologically uninformed theorist or a science journalist who has no excuse for reporting pseudoscientific nonsense.
The only way to resurrect the bacterial flagellum over-the-weekend involves what is known as the proton motive force. Fro example: A twitter search for “proton motive force” led me to this claim, thanks to Nigel Ten Fleming

Enzyme-bound ATP forms readily in the absence of a proton-motive force.

In the context of Energy Transformations in Oxidative Phosphorylation (2002), that claim was followed by this claim:

…the role of the proton gradient is not to form ATP but to release it from the synthase.

See also:

If the aspartate residue is protonated to its neutral form, the c ring can now rotate, but only in a clockwise direction. Such a rotation moves the newly protonated aspartic acid residue into contact with the membrane, moves the charged aspartate residue from contact with the matrix half-channel to the cytosolic half-channel, and moves a different protonated aspartic acid residue from contact with the membrane to the matrix half-channel. The proton can then dissociate from aspartic acid and move through the half-channel into the proton-poor matrix to restore the initial state. This dissociation is favored by the positive charge on a conserved arginine residue ( 210) in the a subunit.

The difference in the energy of photons was linked from protons to hydrogen-atom transfer in DNA base pairs in solution. The energy-dependent biophysically constraints link microRNA-mediated cell type differentiation from the RNA-mediated amino acid substitutions to the differences in all cell types in all individuals of all living genera.
See also: 18.4.5. ATP Synthase and G Proteins Have Several Common Features (with my emphasis)

In Chapter 15, we learned that the signaling properties of other members of this family, the proteins, depend on their ability to bind nucleoside triphosphates and nucleoside diphosphates with great kinetic tenacity. They do not exchange nucleotides unless they are stimulated to do so by interaction with other proteins. The binding-change mechanism of ATP synthase is a variation on this theme. The three different faces of the γ subunit of ATP synthase interact with the P-loop regions of the β subunits to favor the structures of either the NDP- or NTP-binding forms or to facilitate nucleotide release. The conformational changes take place in an orderly way, driven by the rotation of the γ subunit.

See for comparison:Jay R. Feierman:

Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.

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.

Cytosis can be used to teach everything from base editing to RNA editing to everyone over age 10. They will learn how to link the creation of energy to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction.

Carl Zimmer refutes theistic evolution (1)

Primers: From photons to the proton motive force (1) and From photons to the proton motive force (2)
George Church, Feng Zhang, Francis S. Collins, Stuart Kauffman, Emily Witkin, and Bill Gates are joined by Carl Zimmer. All have now refuted theistic evolution via their failed attempts to link photons from mutations to the proton motive force, or their ridiculous claims linked to the magic of evolution.
Carl Zimmer may be the only so-called science journalist to have published a thinly disguised refutation of neo-Darwinian pseudoscientific nonsense..
See: Whole-Genome-Sequence-Based Haplotypes Reveal Single Origin of the Sickle Allele during the Holocene Wet Phase

Starting from first principles of population genetics, we defined haplotypes on the basis of phased sequence data. In contrast, the classical haplotypes were based on patterns of restriction sites seen in individuals with sickle cell anemia.3, 4

The  haplotypes are not defined. They are energy-dependent ecological adaptations.

A haplotype has been identified among Sudanese individuals that was classified as atypical but might be a fifth African haplotype.54 It is possible that sampling additional populations could provide more evidence regarding when, where, and in whom the sickle mutation arose.

Therein lies the problem for Carl Zimmer and others like him. When they find “…more evidence of when, where, and in whom the sickle mutation arose,” that evidence will be linked from the mutation to energy-dependent ecological adaptations by changes in the microRNA/messenger RNA balance and alterrnative splicings linked to amino acid substitutions and more than 1700 other hemoglobin variants.
See: Updates of the HbVar database of human hemoglobin variants and thalassemia mutations

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

Clearly, the hemoglobin variants are food energy-dependent ecological adaptations and the adaptations can be compared to mutation-driven molecular defects manifested as the differences in the thallassemias.
See also:  How One Child’s Sickle Cell Mutation Helped Protect the World From Malaria by Carl Zimmer

…the protection afforded by a single copy of the sickle cell mutation against malaria kept fueling its spread.

Adaptations protect organized genomes from the virus-driven degradation of messenger RNA. Mutations link the virus-driven theft of quantized energy to all pathology.
See: Cytosis

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

Carl Zimmer may pretend not to know anything about biophysically constrained viral latency, but he recently announced the forthcoming publication of his book: She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity
Excerpt from the book description:

We need a new definition of what heredity is and, through Carl Zimmer’s lucid exposition and storytelling, this resounding tour de force delivers it.

No one delivers a new definition of heredity without risking the attacks that will come from serious scientists. Serious scientists do not need to define haplotypes in the context of population genetics. So-called science journalists have been caught in their misrepresentations of how viral latency is biophysically constrained by what organisms eat and the physiology of pheromone-controlled reproduction in species from microbes to humans.
Any intelligent person who places the facts that Carl Zimmer placed into the context of the past 7300 years of evolution will arrive at the same conclusions that young earth creationists have touted about the difference between evolution and engineered energy-dependent adaptability.
See for instance: Engineered Adaptability: Creatures’ Adaptability Begins with Their Sensors
See also: Feedback loops link odor and pheromone signaling with reproduction
See also: Carl Zimmer refutes theistic evolution (2) (in prep)