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

Evolutionary congruence (losers) vs ecological adaptation (winners)

by with No Comment AdaptationsAlternative SplicingsAutophagybase editingbiophotonicsCytosisDiseases & DisordersEcologyLight EnergyModel OrganismsPhysicsRNA DirectedRNA editingRNA-directed DNA methylationRNA-mediated epigenetic regulation of gene expressionRNA–Mediated Epigenetic HeredityVariations
This is the first DNA-sequence based phylogeographic assessment of Salvadora in the world. Sequence based phylogeographic assessment of tropical tree species is a relative rarity and in India, such investigations are almost non-existent.
 

Kalevi Kull: Censorship & Royal Society Evo Event

Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge.

In a rapidly changing world of post-censorship, the losers tout “DNA-sequence based phylogeographic assessment.” All serious scientists have linked energy-dependent RNA-mediated protein folding chemistry from changes in angstroms to ecosystems via supercoiled DNA, which protects all organized genomes from the virus-driven degradation of messenger RNA.

Each time you see a term like evolutionary congruence, ask for a definition that links it to what is currently known to all serious scientists about biophysically constrained energy-dependent RNA-mediated biologically based cause and effect.

You will learn There is no such thing as an evolutionary congruence. Molecular Phylogeography is not examined (e.g., by serious scientists) outside the context of the anti-entropic virucidal energy of the sun.

The virucidal energy links the creation of microRNAs in plants to the food energy-dependent creation of microRNAs in animals and all biophysically constrained biologically-based cause and effect on Earth via the physiology of pheromone-controlled reproduction in bacteria.
See: The phylogenetic utility and functional constraint of microRNA flanking sequences

See also: Cystosis

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

Food energy links the de novo creation of microRNA flanking sequences to the creation of enzymes, hormones and receptors that link ecological variation to ecological adaptation via the physiology of pheromone-controlled reproduction in species from microbes to humans. The pheromone-controlled physiology of reproduction biophysically constrains the transgenerational epigenetic inheritance of virus-driven energy theft, which has been linked from mutations to all pathology –except by Greg Bear, who linked biophysically constrained viral latency to the pheromone-controlled creation of a new human subspecies.

See: The Darwin Code by Greg Bear

Bacteriophages–phages for short–can either kill large numbers of host bacteria, reproducing rapidly, or lie dormant in the bacterial chromosome until the time is right for expression and release. Lytic phages almost invariably kill their hosts. But these latter types–known as lysogenic phages–can actually transport useful genes between hosts, and not just randomly, but in a targeted fashion.

See for comparison: A Crack in Creation review – Jennifer Doudna, Crispr and a great scientific breakthrough

Jennifer Doudna’s work began with organisms even further out on the Palin scale: bacteriophages, tiny viruses that prey on bacteria.

Conclusion: The difference between the works of science fiction novelist Greg Bear, and people like Jennifer Doudna, is clear. Greg Bear’s works (and the works of the late Eshel Ben-Jacob) predicted that, if viral latency was not biophysically constrained, the virus-driven degradation of messenger RNA would be linked to all pathology.
The works of biologically uninformed researchers tout the benefits of the virus-driven degradation of messenger RNA, which is used in their gene-editing technology, as if the concept of gene-editing exemplified a “Crack in Creation.” For comparison, natural selection for energy-dependent codon optimality links the pheromone-controlled physiology of reproduction from energy-dependent changes in chirality to autophagy, which protects all organized genomes from the virus-driven degradation of messenger RNA that Doudna and others have linked to all pathology.
See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The bias between codons or amino acids, and mRNA expression levels has been previously recognized across species and is thought to result from selection for efficient, accurate translation, and folding of highly expressed genes (Ikemura,
1982; Akashi, 1994; Akashi & Gojobori, 2002; Drummond & Wilke, 2008; Kudla et al, 2009; Novoa & Ribas de Pouplana, 2012). The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

See also:
The Origin of Information (3) If they do not know where the quantized energy in a hydrogen atom came from, they cannot discuss a Crack in Creation in the context of the virus-driven degradation of messenger RNA that is their key to gene editing.
See also: NgAgo Paper Retracted

[W]hen it comes to biology, answers are often not definitive. And when it comes to replication studies, the one thing we know is that it takes time,” it says. “In the case of NgAgo, the time has come and the data have spoken.

Next we will learn that “Nothing in Biology Makes Sense…” outside the context of food energy-dependent pheromone-controlled RNA-mediated ecological adaptations.

Biology to a Physicist

Sal Giardina: apologetics revisited

by with No Comment AdaptationsAlternative SplicingsAutophagybiophotonicsDiseases & DisordersEcologyHuman BrainHuman PheromonesLight EnergyModel OrganismsNeuronal PlasticityNutrigenomicsPharmacogenomicsPhysicsRNA DirectedRNA methylationRNA-directed DNA methylationRNA-mediated epigenetic regulation of gene expressionRNA-mediated gene silencingRNA-mediated toxicityRNA–Mediated Epigenetic HeredityVariations

March 26, 2017 Sal Giardina wrote:

“James, I appreciate your responding to my posts but I would prefer that your input would be related to the content of the post.”

My reply: If you do not want people to learn how my claims are linked to yours, please tell me that you intend to continue with apologetics rather the concept of energy as information.

Apologetics:

… the religious discipline of defending or proving the truth of religious doctrines through systematic argumentation and discourse.[1][2][3] Early Christian writers (c. 120–220) who defended their beliefs against critics and recommended their faith to outsiders were called Christian apologists.[4] In 21st century usage, ‘apologetics’ is often identified with debates over religion and theology.

In the context of debates over religion and theology, Sal Giardina opened discussion of physics, chemistry, and the conserved molecular epigenetics of RNA-mediated cell type differentiation. Secular humanists are scared by the ghosts of their biologically uninformed past and their ongoing ignorance. Fortunately for them, Sal Giardina and others like him cannot prove anything via the use of apologetics. So far as I know, the apologeticists have never convinced anyone to believe in any of their claims.
See for example: What does DNA have to do with the Origin of Life ?
Unfortunately, you must join this “false flag” group go find this post: https://www.facebook.com/groups/231023426993207/permalink/1119981528097388/?comment_id=1120290524733155&reply_comment_id=1120913471337527&notif_t=group_comment&notif_id=1477870268849582 I’ve been banned from the group twice, but just submitted a request to re-join.
My comments: Secular humanists seem willing to believe that the origin of life could somehow lead to consciousness as a side effect.
See for example: Consciousness could be a side effect of ‘entropy’, say researchers
My comment: Serious scientists do not make such ridiculous claims. These researchers are theorists who tout meaningless pseudoscientific nonsense. Their ridiculous claims makes news when biologically uninformed journalists, like Fiona Macdonald pass the unsupported claims on to others who do not know that the theorists are touting meaningless pseudoscientific nonsense.
See also: Virus evolution and this special issue on Orgasms:  Introductory editorial to ‘Orgasm: Neurophysiological, Psychological, and Evolutionary Perspectives’
My comment: Who are the people trying to convince others that virus evolution links prairie vole monogamy to the evolution of human love via organsm? One of them is James Pfaus.
Excerpt:

In ‘The Role of Orgasm in the Development and Shaping of Partner Preferences’, Coria-Avila, Herrera-Covarrubias, Ismail, and Pfaus (2016) explore the relationship between orgasm and sexual preference-formation in animals. Of particular significance with respect to human orgasm, Coria-Avila et al. describe the pre- and post-ejaculatory factors contributing to male rats forming conditioned sexual preferences.

See this article by Rachel Feltman, who placed the ridiculous claims of Pfaus before my detailed model of nutrient-dependent pheromone-controlled biologically-based cause and effect.
What Do We Actually Know About Pheromones?
Excerpt:

But Kohl’s products, which he likens to food spices (“They give you an extra kick!”), make some researchers roll their eyes. Dr. Jim Pfaus, professor of psychology at Concordia University in Montreal, is one of them.

See for comparison: Ecologically relevant neurobehavioral assessment of the development of threat learning
Summary: “Informed Conditioning” is linked to the differences between wolves and dogs and biophysically constrained cell type differentiation in all living genera.
See for example: A Comparison of the Sensory Development of Wolves (Canis lupus lupus) and Dogs (Canis lupus familiaris)
See also (link opens pdf): Early life experiences: enduring behavioral, neurological and endocrinological consequences

See also: Sexual Differentiation of the Brain: A Fresh Look at Mode, Mechanisms, and Meaning

…no study has yet shown an effect of manipulating the expression of a particular microRNA on a behavioral or brain sex difference. In other words, we are still awaiting the demonstration that microRNAs contribute to sexual differentiation of the brain.

Olfaction is important to humans as well, but visual stimuli are far more potent and the arousal potential of same-sex versus opposite-sex images depends on the partner preference of the observer (see for review Baum, 2006).

Michael Baum and others still make ridiculous claims about visual input compared to the epigenetic effect of food odors and pheromones on energy-dependent microRNA-mediated cell type differentiation in species from microbes to humans. That fact supports my claim that people like him are biologically uninformed.

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

See also: Crosstalk between epigenetics and metabolism—Yin and Yang of histone demethylases and methyltransferases in cancer

Pioneering experiments by Allfrey and Mirsky >50 years ago identified methylation and acetylation of histones by isotope incorporation and showed that histone modification can influence whether RNA synthesis of genes is switched on or off [3].

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

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

If you knew nothing about the energy-dependent de novo creation of nucleic acid precursors, you still could start from the energy-dependent creation of RNA and link RNA-directed DNA methylation to all biophysically constrained biologically-based cause and effect in all living genera to their physiology of pheromone-controlled reproduction in the context of learning and memory at the cellular level of intracellular and extracellular communications.

See also: Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice
My comment: The conserved molecular mechanisms of experience-dependent learning and memory have been linked from energy-dependent RNA-mediated cell type differentiation to all biodiversity via quantised energy and all subsequent levels of examination the must begin with the origins of information, the sun’s anti-entropic virucidal energy.

See for comparison:  Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution

My comment: Femtosecond blasts of UV light link the sun’s virucidal energy to RNA-mediated DNA repair in all living genera. People who do not know that should simply admit that they biologically uninformed. Most of them are theorists who know nothing about anything that must be linked from angstroms to ecosystems. They should not antagonize those who are biologically informed serious scientists. Serious scientists publish experimental evidence in reports such as this one.

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

Excerpt:

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

My comment: The sequences cannot be selected outside the context of natural selection for energy-dependent codon optimality, which is the basis for the control of hydrogen-atom transfer in DNA base pairs in solution. Control is manifested in the measurement of pH.

See: Control of pH responsive peptide self-association during endocytosis is required for effective gene transfer

Excerpt:

Coulombic interactions between the histidine residues modulate protonation and subsequent conformational transitions required for peptide mediated gene transfer activity and are an important factor to consider in future peptide design.

My comment: Coulomb barrier:The Coulomb repulsion which tends to keep positively charged bombarding particles out of the nucleus. Specifically, the Coulomb potential associated with this force.

Energy-dependent Coulombic interactions link autophagy to polycombic ecological adaptations for comparison to what happens when virus-driven energy theft is linked to the hecatombic evolution of all pathology.

See also: Coulombic interactions between partially charged main-chain atoms not hydrogen-bonded to each other influence the conformations of alpha-helices and antiparallel beta-sheet. A new method for analysing the forces between hydrogen bonding groups in proteins includes all the Coulombic interactions (published in 1995)

See for comparison: Jonas Edward Salk (October 28, 1914 – June 23, 1995) was an American medical researcher and virologist. He discovered and developed one of the first successful polio vaccines.

My comment: The fact that Jonas Edward Salk died in the same year that information about Coulombic interactions was published exemplifies the fact that we still need people like Salk to lead the way towards more scientific progress.

Is everyone who could do that already dead? Have people like Sal Giardina and other apologeticists replaced them. Will any of the works from the early 1990s to 1964 be resurrected before all of humanity is irreversibly impacted?

See for example: Biology, molecular and organismic (1964)

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

Such pronunciamentos can be dismissed as merely ridiculous. They are, however, caricatures of opinions entertained by some intelligent and reasonable people, whose views deserve an honest and careful consideration and analysis. Science must cope with new problems that arise and devise new approaches to old problems. Some lines of research become less profitable and less exciting and others more so.

Links from the creation of nucleic acid precursors to entropy and mutation-driven evolution are still being addressed by apologeticists who know nothing about physics, chemistry, or molecular epigenetics.
See also:  Biblical Creation / Entropy
http://godordirt.com/wp-content/uploads/2013/11/hsz-biblical-entropy.jpg
See for comparison: What is life when it is not protected from virus driven entropy (6 minutes)
I think most people can understand the concept of Creation by God of all biophysically constrained life on Earth. If not, they should be told about the examples, since all examples show that all organisms must eat or die. If they die, they do not reproduce, which means they never became an extant species. Instead, the individuals and/or species became part of the fossil record or they became nothing recognizable to serious scientists as anything more than dirt.
See also: godordirt.org
See also: Virus Documentary | Discovering & Understanding Viruses || How Viruses Work ? (60 minutes)

My comment: Terra Firma is the battlefield mentioned in the video (a village in central Brazil). Stephen Morse, virologist at Rockefeller is fighting on the side of virus-driven entropy, which he attributes to emergence and evolution. For example, His book, Emerging Viruses (Oxford University Press) was selected by “American Scientist” for its list of “100 Top Science Books of the 20th Century”.

My comment: According to the book, our innate immune system emerged and evolved to become the source of all pathology. If the innate immune system is referred to as our “immune system” the word innate changes to evolved, and mutations are linked to evolution in the context of ridiculous neo-Darwinian theories. That is how emerging viruses are automagically linked to all healthy longevity via polycombic ecocological adaptation and to all pathology via hecatombic evolution.
We have come full circle back to the definitions that are used and discussed in Polycombic ecological adaptation as a science, not a theory (2):
See also:  The Human Virome

For comparison, see: Mutation-Driven Evolution

Excerpt:

Mutation… includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc.

My comment: The definition above links mutations to any change in any genome. It does not link virus-driven energy theft toi mutations and all pathology.

Excerpt:

Single nucleotide substitutions or indels [insertions/deletions] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects [mutations] 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.

My comment: The facts about nutrient energy-dependent single nucleotide substitutions and RNA-mediated amino acid substitutions link hemoglobin variants to healthy longevity and the facts link molecular defects to the pathology of α-, β- or δ-thalassemia, respectively.

See for comparison: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

See also: Peptides design based on transmembrane Escherichia coli’s OmpA protein through molecular dynamics simulations in water-dodecane interfaces
See for comparison: Understanding abundance and diversity using ghosts and goblins: a spooky ecology lesson!
Conclusion:

If we wanted to compare the diversity of two forests, we would want to look at climate, elevation, drainage, available nutrients, proximity to human disturbance, soils, etc. Diversity can be impacted by a slew of factors. While this is a fun and rather ridiculous example of how species counts and diversity works, the leap to how this can inform ecology, management, and conservation is clear.

My comment: The fact that nothing known about virus-driven energy theft is included in their comparisons makes the most important of all comparisons irrelevant to their claims about how climate, elevation, drainage, available nutrients, proximity to human disturbance, soils, etc. link ecological variation to polycombic ecological adaptation via the physiology of reproduction in all living genera.
See for comparison: An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells

G540A supports virus replication in mammalian cells while retaining replication ability in avian cells. Host splicing regulator, SF2, interacts with this ESE to regulate splicing of NEP/NS1 mRNA and G540A substitution affects SF2–ESE interaction. The NS1 protein directly interacts with SF2 in the nucleus and modulates splicing of NS mRNAs during virus replication.

Reported as: Single nucleotide change responsible for allowing H7N9 flu to jump from birds to humans found
The identification of the G540A links the single nucleotide polymorphism (SNP) from a biomarker in fowl infected with a flu variant to what was reported as mutation.
Researchers assumed that “…the mutation played a role in allowing the virus to spread between humans once it made the leap from an avian source.”
As usual, they found no evidence to support that ridiculous claim. That ridiculous claim is among many others that theorists thought could be used to link mutations to evolution via mathematical models instead of facts about nutrient energy-dependent pheromone-controlled biophysically constrained RNA-mediated cell type differentiation.

terrarium-eco-system

George Church refutes theistic evolution (3)

by with No Comment AdaptationsAlternative SplicingsAutophagybiophotonicsDiseases & DisordersEcologyHuman BrainHuman PheromonesLight EnergyModel OrganismsNutrigenomicsPhysicsRNA DirectedRNA interferenceRNA methylationRNA-directed DNA methylationRNA-mediated epigenetic regulation of gene expressionRNA-mediated gene silencingRNA-mediated toxicityRNA–Mediated Epigenetic HeredityVariations

Fifty years of illumination about the natural levels of adaptation

… George C. Williams developed in his 1966 book Adaptation and Natural Selection the essentials of a unifying theory of adaptation that remains robust today and has inspired immense progress in understanding how natural selection works.

Light Could Propel Nanorobots on a “Fantastic Voyage” Through the Human Body

“Light is a more effective option to communicate between the microscopic world and the macroscopic world,” said Tang.

See also: George Church refutes theistic evolution and George Church refutes theistic evolution (2)
Why did so many pseudoscientists fail to link ecological variation to ecological adaptation via natural selection for energy-dependent changes in supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy? Why have they continued to tout ridiculous theories for comparison to what is being reported about adaptation by serious scientists. Almost every day there is something old reported as if it was new information to be considered before it is again ignored by theorists.
See for examples from this past week:
Optokinetically encoded nanoprobe-based multiplexing strategy for microRNA profiling
Interplay between miRNAs and Human Diseases: A Review
400 pilot whales stranded on New Zealand’s ‘whale trap’ beach

Other factors include whales’ incredibly tight social bonding, which is especially strong within groups of pilot whales.
 
Social bonding is nutrient energy-dependent and controlled by the physiology of reproduction. In species from microbes to humans, the physiology of reproduction is controlled by the metabolism of nutrients to species-specific pheromones.
 

Rather than tout theories about solar storms and geographical traps, serious scientists investigate the facts that link the sun’s anti-entropic virucidal energy to endogenous RNA interference via olfaction and the innate immune system. Serious scientists link food odors and pheromones to behavior in all living genera.

2005 Feedback loops link odor and pheromone signaling with reproduction

2015 Role of olfaction in Octopus vulgaris reproduction

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

Ecological variation that is not manifested in ecological adaptation links virus-driven energy theft to the stranded whales. The energy theft prevents nutrient energy-dependent ecological adaptation. Unfortunately, theorists do not understand any aspect of natural selection for energy-dependent codon optimality.The prefer to use definitions and assumptions for comparison to the experimental evidence of biologically-based cause and effect that serious scientists must use in the context of their religion.

Pseudoscientists claim that atheism is not a religion. Atheism is a religion by definition.

See: atheism

  1. 1a :  a lack of belief or a strong disbelief in the existence of a god or any godsb :  a philosophical or religious position characterized by disbelief in the existence of a god or any gods

See for comparison:  How an obscure oriental cult in a corner of Roman Palestine grew to become the dominant religion of the Western world
Even historians know that the history of a religion can influence the faith of believers today. For example, atheism today arose in the context of de Vries 1902 definition of “mutation” and acceptance of assumptions that accumulated mutations could lead from natural selection to the evolution of one species from another species.

Christianity can clearly be linked from events that start from the creation of energy as information in Biblical Genesis to the weekend resurrection of the bacterial flagellum in P. fluorescens, which fluoresces with exposure to UV light.

Atheism as a religion cannot stand up to the overwhelming amount of experimental evidence that supports claims in the Old Testament, which were linked to claims in the New Testament. There is nothing that appears to link the emergence of everything from nothing or the evolution of one species from another. That fact links three more definitions to all biodiversity on Earth.

The emergence of atheism as a world religion can now be placed into the context of definitions that recently were added to the Merriam-Webster dictionary.

Phytoremediation

the treatment of pollutants or waste (as in contaminated soil or groundwater) by the use of green plants that remove, degrade, or stabilize the undesirable substances (such as toxic metals)

CRISPR

The CRISPR segment encodes, via transcription, short RNA sequences that pair with complementary sequences of viral DNA. The pairing is used to guide an enzyme to cleave the viral DNA and prevent further infection.

 Microbiome

  1. 1 :  a community of microorganisms (such as bacteria, fungi, and viruses) that inhabit a particular environment and especially the collection of microorganisms living in or on the human body <Your body is home to about 100 trillion bacteria and other microbes, collectively known as your microbiome. — Carl Zimmer> < … what’s arguably become the hottest area of medicine: microbiome research, an emerging field that’s investigating how the bacteria that live in and on our bodies affect our health. — Sunny Sea Gold>
    1. 2 :  the collective genomes of microorganisms inhabiting a particular environment and especially the human body <They form one community among the many that make up the human microbiome: the full genetic complement of bacteria and other organisms at home on your skin, gums, and teeth, in your genital tract, and especially in your gut. — Nathan Wolfe>

The definitions that were recently added to the Merriam-Webster dictionary link the energy-dependent pheromone-controlled physiology of reproduction in bacteria from the National Microbiome Initiative to the Precision Medicine Initiative via endogenous RNA interference, which prevents the virus-driven energy theft that links mutations to all pathology.

For comparison, see: How algorithms (secretly) run the world

“Algorithms are not inherently fair, because the person who builds the model defines success,” she said.
See also: Digital Star Chamber

Following the advice of Jeff Jarvis’s What Would Google Do, they are collecting data from both workers and customers, using algorithmic tools to make decisions, to sort the desirable from the disposable.

What would Jesus do about the use of algorithms to predict outcomes?

Algorithms can be made more accountable, respecting rights of fairness and dignity for which generations have fought. The challenge is not technical, but political, and the first step is law that empowers people to see and challenge what the algorithms are saying about us.

Did Jesus know the creation of energy and virus-driven energy theft are predictable links to outcomes that pseudoscientists think can be linked via algorithms? Did He ever mention the fact that pseudoscientists might be called theorists by serious scientists who have linked energy-dependent changes from angstroms to ecosystems in all living genera via what is known about the physiology of reproduction and the functional structure of supercoiled DNA.

See for example: Structural diversity of supercoiled DNA
The functional structure of supercoiled DNA links what organisms eat to endogenous RNA interference and the physiology of reproduction, which links chromosomal inheritance from chirality to autophagy and all biodiversity on Earth. That cannot be done with definitions and/or algorithms.

See also: microRNA
How will you continue to avoid discussing the energy-dependent link from nutrient-dependent changes in the microRNA/messenger RNA balance to all healthy longevity, as everything known about virus-driven energy theft continues to be linked to all pathology?

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

Dobzhansky 1973 and precision medicine (5)

by with 2 Comments AdaptationsbiophotonicsDiseases & DisordersEcologyLight EnergyModel OrganismsNutrigenomicsPhysicsRNA DirectedRNA methylationRNA-directed DNA methylationRNA-mediated epigenetic regulation of gene expressionRNA-mediated gene silencingRNA-mediated toxicityRNA–Mediated Epigenetic HeredityVariations

See: Dobzhansky 1973 and precision medicine (4)

Microenvironmental autophagy promotes tumour growth

…non-cell-autonomous autophagy is induced both in the tumour microenvironment and systemically… transformed cells engage surrounding normal cells as active and essential microenvironmental contributors to early tumour growth through nutrient-generating autophagy.

Non-cell autonomous autophagy links non-random natural selection for codon optimality from the nutrient energy-dependent pherormone-controlled physiology of reproduction to biophysically constrained RNA-mediated protein folding chemistry via fixation of amino acid substitutions in supercoiled DNA.

The supercoiled DNA links metabolic networks to genetic networks and chromosomal rearrangements to the transgenerational epigenetic inheritance of morphological phenotypes and behavioral phenotypes. Chromosomal inheritance links the 1933 Nobel Prize winning works of Thomas Hunt Morgan and Erwin Schrodinger to the works of 2016 Nobel Laureates Ben Feringa and Yoshinori Ohsumi.  Collectively, their Nobel Prizes explain why Richard Axel and Linda Buck won the Nobel Prize in Physiology or Medicine in 2004 for detailing how the de novo creation of G protein-coupled receptors was linked to healthy longevity in all living genera.

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

It has become obvious that light induced changes in chirality must be linked from chemotaxis and phototaxis to all biodiversity via the pheromone-controlled physiology of reproduction.

Serious scientists start with the anti-entropic virucidal energy of UV light, and link energy to behavior.

See: CRYPTOCHROME mediates behavioral executive choice in response to UV light 

See also: Fast Evolution Confirms Creationist Theory

Up-to-date research shows that they may employ dozens of mechanisms including epigenetic, hybridization, cryptic variation, behavioral changes, unreduced gametes, directed crossover, regulated micro-RNAs or RNA splicing, horizontal gene transfer, and even modulation of an organism’s microbiota. None of these mechanisms require a struggle for life and death!

See also this easy to read accurate representation of facts about healthy longevity compared to virus-driven pathology. Jeffrey P. Tomkins, Ph.D. 2015. Viral Genome Junk Is Bunk. Acts & Facts. 44 (4).
See also: Nothing in Biology Makes Any Sense Except in the Light of Evolution

Cytochrome C is an enzyme that plays an important role in the metabolism of aerobic cells. It is found in the most diverse organisms, from man to molds.

E. Margoliash, W. M. Fitch, and others have compared the amino acid sequences in cytochrome C in different branches of the living world. Most significant similarities as well as differences have been brought to light. The cytochrome C of different orders of mammals and birds differ in 2 to 17 amino acids, classes of vertebrates in 7 to 38, and vertebrates and insects in 23 to 41; and animals differ from yeasts and molds in 56 to 72 amino acids. Fitch and Margoliash prefer to express their findings in what are called “minimal mutational distances.” It has been mentioned above that different amino acids are coded by different triplets of nucleotides in DNA of the genes; this code is now known.

See also:Combating Evolution to Fight Disease
For comparison see: Scientists planning their own march in Washington

There are certain things that we accept as facts with no alternatives,” according to the site. “The Earth is becoming warmer due to human action. The diversity of life arose by evolution. … An American government that ignores science to pursue ideological agendas endangers the world.

Anyone who accepts the claim that the diversity of life arose by evolution is not a serious scientist. Pseudoscientists who sign up for the march should repeatedly march themselves into a corner for a “time-out” until they learn not to throw temper tantrums or make claims that cannot be supported by experimental evidence of biologically-based facts. All serious scientists know that their claims must link chirality and autophagy to all biodiversity via the physiology of reproduction and supercoiled DNA.
See: Dobzhansky 1973 and precision medicine (6) in prep

Alternative splicing of pre-mRNA

Autophagy is the antiphage defense strategy

by with No Comment AutophagyEcologyLight EnergyModel OrganismsPhysicsRNA DirectedRNA-directed DNA methylationRNA-mediated epigenetic regulation of gene expressionRNA-mediated gene silencingRNA-mediated toxicityRNA–Mediated Epigenetic Heredity

The “Antiphage Defense Strategy” in Vibrio anguillarum is called autophagy by many serious scientists. It links nutrient energy-dependent pheromone-controlled quorum sensing to viral latency, healthy longevity, symbiosis, reproduction, and biodiversity from microbial species to humans.

For an evolutionary approach to energy-dependent autophagy that fails to address any aspect of how virus-driven energy theft causes all pathology see: (12/7/16) Part I: Living together: The symbiosis of host-microbial interactions (12/7/16)
See also: 12/7/16

….McFall-Ngai tells the story of a symbiosis between the Hawaiian bobtail squid and Vibrio fischeri (V. fischeri), a type of luminescent bacteria that enables the squid to hunt at night. McFall-Ngai and collaborators have identified the molecular mechanism by which nascent Hawaiian bobtail squid select V. fischeri from the thousands of other bacteria in their habitat. V. fischeri induces developmental changes in the squid that drive daily rhythms of gene expression, which are necessary to control bacterial growth, a crucial cycle in this symbiotic partnership.


Bobtail squid select bacteria that become luminescent. The squid do not not select archaea. That fact exemplifies how natural selection for energy-dependent codon optimality links top-down causation from the sun’s anti-entropic biological energy to ecological adaptation.
Whether or not you accept this fact, energy-dependent natural selection continues in the context of symbiosis among the most ecologically adapted species.
“The four stages of acceptance: ― J.B.S. Haldane
1. This is worthless nonsense.
2. This is an interesting, but perverse, point of view.
3. This is true, but quite unimportant.
4. I always said so.”
Natural selection cannot link mutations to evolution in the context of symbiosis because the interactions among species are far too complex.

See also: Komodo dragons provide insights into microbial health in captive animals

…the pattern of microbial exchange is “likely circular in nature.” That means that captive dragons contribute microbes to their environment, and they reacquire these same microbes from their environment, repeating this exchange in an ongoing cycle without other external sources of microbial diversity.

Pattern recognition is essential to the understanding of how the microbiome of bobtail squid is linked to symbiosis via the microbiome in all other living genera via the anti-entropic virucidal energy of sunlight.

Search Results for “McFall-Ngai”

Beneficial microbes kill beneficial mutations
1/15/15 Excerpt: McFall-Ngai, Bonnie Bassler, Anna Di Cosmo and others, continue to show that Darwin’s ‘conditions of life’ are nutrient-dependent and pheromone-controlled by linking:
1) metabolic networks,
2) genetic networks,
3) reproduction in microbes,
and
4) reproduction in their model organisms.
Environment epigenetically shapes the immune system
1/15/15 Excerpt: 1) –with my emphasis Re: “There’s nothing here that is revolutionary or requires rethinking of our assumptions about how the immune system functions…”
Quantum physics, quantum biology, and quantum consciousness
2/15/15 Excerpt: One would think that the representations of McFall-Ngai that appear to link light-induced amino acid substitutions from the stability of DNA in luminescent microbes to the stability of DNA in squid would invite more attention to details than attempts to pirate ideas about epigenetic links from Turin’s links and my links from quantum physics to Gunther Witzany’s Life is physics and chemistry and communication.

8/25/15 Excerpt: See also my invited review of nutritional epigenetics. I submitted it by request for a special issue of “Nutrients” and posted the submission to Figshare.com on April 11, 2014, after the submission was returned without review.

See also:  Quorum Sensing Determines the Choice of Antiphage Defense Strategy in Vibrio anguillarum

6/25/16 Excerpt: Quorum sensing links the physiology of energy-dependent reproduction and virus-driven energy theft from the microRNAome of and light organ of bobtail squid to the bull sperm microbiome, which links microRNAs in breast milk to human brain development. The bacteria that populate the light organ have already been linked by Bonnie Bassler’s group and Margaret McFall-Ngai’s group to everything known about the physiology of energy-dependent reproduction in all living genera.

Alternative splicing of pre-mRNA

Energy-dependent de novo creation and neurogenesis (2)

by with No Comment AdaptationsAlternative SplicingsAutophagybiophotonicsDiseases & DisordersEcologyLight EnergyModel OrganismsNutrigenomicsPhysicsRNA DirectedRNA methylationRNA-directed DNA methylationRNA-mediated epigenetic regulation of gene expressionRNA-mediated gene silencingRNA-mediated toxicityRNA–Mediated Epigenetic HeredityVariationsWhat's in the News

See also: Energy-dependent de novo creation and neurogenesis
12/7/16 Atlas of the RNA universe takes shape
Excerpt:

MicroRNA are very mysterious. They are really relics of the RNA world—pieces of RNA that are highly reactive, very small and which pair and bind other RNA and facilitate catalytic reactions,” Mangone says. “We don’t know much about them—where they come from or how they regulate gene expression, but they are very misregulated in many diseases.

See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model Published 14 Jun 2013
Excerpt:

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow.

My comment: Only if you lived among wolves or among theorists for the past 10 years would you not know that more than 55,000 indexed publications link energy-dependent changes in the microRNA/messenger RNA balance to healthy longevity. For comparison, all serious scientists also know that virus-driven energy theft links viral microRNAs from mutations to all pathology.
You need only search for “RNA mediated” to find information on how cellular and viral microRNAs are linked from energy-dependent changes to RNA-mediated amino acid substitutions and biophysically constrained protein folding chemistry. For example, this is all it takes to recognize the amount of pseudoscience that is packaged in claims that we don’t know much about microRNAs.
See also: Published to Figshare 10 April 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.

See also: MicroRNAs: the future of genomic science?
Excerpt:

The ubiquity of miRNA occurrence is reflected in the current literature, which reports a wide range of potential biomarker applications for this highly conserved molecule.

My comment: MicroRNAs are biomarkers that clearly link energy-dependent biophysically constrained changes in base pairs from RNA-mediated amino acid substitutions to cell type differentiation in all living genera. The energy-dependent links from the innate immune system to the physiology of reproduction also link all metabolic networks to all genetic networks in species from microbes to humans.
See for comparison: A single splice site mutation in human-specific ARHGAP11B causes basal progenitor amplification

…we hypothesize that the novel, human-specific C-terminal sequence of modern ARHGAP11B has a key role in the mechanism by which this protein promotes BP amplification. In this regard, the present data show that this sequence is due to a single C→G base substitution, which creates a novel splice donor site that results in the replacement of the ancestral C-terminal sequence of the ARHGAP11B GAP domain. The present data also demonstrate that this single C→G base substitution underlies the ARHGAP11B-mediated BP amplification implicated in neocortex expansion.

Reported as: Small Mutation Contributed to Evolution of Bigger Human Brains
Excerpt:

A single base change in a human gene likely played an important role in evolutionary expansion of the human brain, researchers say.

My comment: They claim that a single cytosine to guanine substitution created a novel splice site. They failed to mention that base pair (BP) amplification is nutrient energy-dependent. They also failed to mention that the de novo creation of a novel splice donor site must be linked from the energy-dependent fixation of an RNA-mediated amino acid substitution to the physical landscape of supercoiled DNA via the physiology of reproduction.

Svante Paabo is one of the co-authors who reported this:

Hence, it is not the ARHGAP11 partial gene duplication event ~5 million years ago, as such, that impacted human neocortex evolution. Presumably, ARHGAP11A and ancestral ARHGAP11B coexisted as functionally similar proteins for some time after the gene duplication event. The ability of ARHGAP11B to amplify BPs likely arose more recently from a change that is tiny on a genomic scale but substantial in its functional and evolutionary consequences.

My comment: No experimental evidence of biologically-based cause and effect suggests that any partial gene duplication event ~5 million years ago could have linked a mutation and the altered de novo creation of genes that Svante Paabo (and co-authors) placed into the context  of biophysically constrained biodiversity in:

Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees

My comment: Natural selection for energy-dependent codon optimality is the only way to link the de novo creation of genes from autophagy to RNA-mediated amino acid substitutions and nutrient-dependent polycombic ecological adaptation.
See: From Fertilization to Adult Sexual Behavior

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

See also: PTBP1 and PTBP2 Serve Both Specific and Redundant Functions in Neuronal Pre-mRNA Splicing
Excerpt:

…the two paralogs displayed similar RNA binding across the transcriptome, indicating that their differential targeting does not derive from their RNA interactions, but from possible different cofactor interactions.

My comment: The cofactors are nutrient energy-dependent microRNAs, which are linked to healthy longevity and all biodiversity and viral microRNAs, which are linked from mutations to all pathology.
See also: Viral and cellular messenger RNA targets of viral microRNAs

…viral miRNAs may be particularly important for regulating the transition from latent to lytic replication and for attenuating potentially inhibitory host antiviral immune responses.

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

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).”

See also: Light- and Carbon-Signaling Pathways. Modeling Circuits of Interactions

…carbon either attenuated or potentiated light repression of ASN1 in light-grown plants. These studies indicate the interaction of carbon with blue, red, and far-red-light signaling and set the stage for further investigation into modeling this complex web of interacting pathways using systems biology approaches.

My comment: When did theorists decide to take the light as information and energy out of systems biology and ecological adaptations? Who decided to replace the anti-entropic virucidal energy of light with mutations and evolution?

Alternative splicing of pre-mRNA

Epigenetics and autophagy vs mutations and evolution (7)

by with No Comment AdaptationsAlternative SplicingsAutophagyDiseases & DisordersEcologyLight EnergyModel OrganismsPhysicsRNA DirectedRNA-directed DNA methylationVariations
rp_levels-of-organization.jpg

Innate immunity and multiplexing

by with No Comment AdaptationsAlternative SplicingsbiophotonicsDiseases & DisordersEcologyHuman BrainHuman PheromonesLight EnergyModel OrganismsNeuronal PlasticityNutrigenomicsPharmacogenomicsPhysicsRNA DirectedRNA methylationRNA-directed DNA methylationRNA-mediated epigenetic regulation of gene expressionRNA-mediated gene silencingRNA-mediated toxicityRNA–Mediated Epigenetic HeredityVariationsWhat's in the News

Scientists Hope to Cultivate an Immune System for Crops

by Carl Zimmer
Excerpt: The complex microbial world in the soil may protect plants much like our immune system protects our bodies.
My comment: The speed of light on contact with water links the sun’s quantized anti-antropic virucidal energy from the de novo creation of nucleic acid precursors to biophysically constrained RNA-mediated protein folding chemistry and supercoiled DNA, which protects all living genera from virus-driven energy theft and genomic entropy.
See “What is Life? (1944)
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)

See also: Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B
Reported as:
1) Virus uses ‘stolen’ CRISPR to hack its host’s immune system;
2) Virus uses ‘stolen’ CRISPR to hack its host’s immune system
3) Virus Hacks Host Genome, Steals CRISPR to Protect Itself
4) Viruses Hack Their Host’s Genome with CRISPR
5) Virus uses ‘stolen’ CRISPR to hack its host’s immune system
6) Virus uses ‘stolen’ CRISPR to hack its host’s immune system
This ridiculous claim is found in all reports:

“Bacteria and their viruses have a shared evolutionary history stretching for billions of years,” says Suttle. “So at some point along the way N1 stole a defensive CRISPR array from Nostoc or a close relative.”

Someone at the LABROOTS Genetics & Genomics site is removing my posts about this attempt to include viruses in neo-Darwinian theory, which links them to billions of years of co-evolution.
On June 15, 2016 the Genetics & Genomics site reported this:

In the past decade, humans have adopted CRISPR as a genetic editing system, derived from a mechanism bacteria use to remember the pathogens they come across. It turns out that humans are not the only ones who want to “steal” the CRISPR idea – a new study uncovered a virus with a CRISPR DNA sequence.
“This is the first evidence we’ve seen that a virus can donate an immunity system via CRISPR. This is like a hacker compromising a computer system, and then immediately patching it to ensure other hackers can’t break in.”

My comment: Everything in their report is a ridiculous misrepresenation of what is known to serious scientists about biophysically contrained protein folding chemistry and RNA-mediated cause and effect, which links the energy-dependent creation and maintenance of all innate immune systems in all cell types of all living genera to ecological adaptation, or from virus-driven energy theft to all pathology.
Epigenetics and Genetics of Viral Latency
Excerpt:

…viral latency is responsible for life-long pathogenesis and mortality risk…

My comment: The innate immune system biophysically constrains cell type differentiation by forcing viruses to wait for stress-induced changes in pH to enable the energy theft that facilitates viral replication. The systems complexity is beyond the grasp of most science journalists and all neo-Darwinian theorists. “Big Bang” cosmologists must learn something about biochemistry and RNA-mediated cell type differentiation before adding more pseudoscientific nonsense for the biologically uninformed masses to regurgitate.
See for example:  How Can Physics Underlie the Mind? Top-Down Causation in the Human Context
See for comparison: Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic
Excerpt:

we identified a core set of more than 1000 responsive enhancers in the human genome. This TP53 cistrome is invariably used between cell types and experimental conditions, whereas differences among experiments can be attributed to indirect nonfunctional binding events.

Reported as: Cancer-preventing protein finds its own way in our DNA
Excerpt:

It’s a known fact that genes are activated when a protein binds to a specific sequence on our DNA. But how does this protein find its way in our extraordinarily complex DNA? Scientists have thus far been assuming that one protein could never locate the exact DNA sequence to activate a specific gene all by itself – at least not in human beings. However, Professor Aerts and his colleagues from the Department of Human Genetics at KU Leuven, Belgium, have now shown that some of these proteins are in fact capable of locating their targets autonomously. Furthermore, the composition of some DNA switches turns out to be unexpectedly simple.

My comment: The simplicity can be compared in the context of the forward by Roger Penrose to the reprint edition of Schrodinger (1944) What is Life?

“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?”

My comment: The energy links hydrogen-atom transfer in DNA base pairs in solution to RNA methylation and supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.

See for example: One Tiny RNA Could Break the Cycle of Arterial Thrombosis  (Labroots)
Excerpt:

…a specific type of microRNA called miR-181b regularly balances the impact of both acute and vascular inflammation.

See also:  Color vision helps birds find good food and the right partner

Excerpt:

The researchers have established that chickens — just like people — have colour constancy. For birds, this means that they, in different environments and under different lighting conditions, recognise the colour of, for instance, berries and can thereby distinguish those that are ripe from those that are not. Without colour constancy, they would not be able to rely on their colour vision — they would simply see the berries in different colours as the light changed. They would certainly also not be able to recognise their own kind of species.

My comment: Species recognition is nutrient-dependent and the pheromone-controlled physiology of species specific reprodution in all vertebrates has been link linked to chromosomal rearrangements in birds and to morphological as well as behavioral diversity.  See: Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes

See also: DNA in ‘unbiased’ model curls both ways

Excerpt:

“Think of the chromosome at mitosis as a bit like what would happen to a piece of sewing thread if you doubled it up and rolled it between your finger and your thumb,” he said. “Depending on how you rolled your fingers, you would get right- or left-turning structures.”
The thread itself has a helical arrangement of even smaller fibers, though the twist at one scale doesn’t necessarily determine the twist at the larger scales. “But bundles of threads usually get twisted somehow,” Wolynes said.
That “somehow” remains one of the mysteries, he said.

My comment: The fact that someone like Wolynes thinks that details of biophysically constrained RNA-mediated protein folding, supercoiled DNA, and energy-dependent chromosomal rearrangements have left us with any mysteries is a mystery. It’s as if he cannot link physics to chemistry, and stalls before linking protein folding chemistry from RNA methylation to supercoiled DNA. If he were not attempting to explain biologically-based cause and effect, he might readily explain why there is no mystery to how energy is created in physical systems.
See:Scientists using sunlight, water to produce renewable hydrogen power
Excerpt:

Hydrogen also can be made using electrolysis, which requires electricity and highly purified water to split water molecules into hydrogen and oxygen. Although this is a sustainable process (assuming the electricity is produced from a renewable energy source), the cost of materials associated with the system are expensive—a major barrier to the affordable production of renewable hydrogen.

My comment: All life on earth is hydrogen powered. Hydrogen-atom transfer in DNA base pairs in solution links the sun’s anti-entropic virucidal force to the de novo creation of receptors that link olfaction from the innate immune system to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. What prevents serious scientists from grasping the facts that must link quantized energy to physical systems or to biophysically constrained cell type differentiation?

See: Engineers discover light can stamp out defects in semiconductors for better solar panels and LED bulbs
Excerpt:

The team discovered that if you add light while firing the material in a furnace at high temperatures, the light generates extra electrons that can change the composition of the material.

My comment: The energy-changing properties of light and its effects on the composition of materials is linked from the speed of light on contact with water to the de novo creation of nucleic acid precursors and all biodiversity via supercoiled DNA.
See also: Biosensor Chip Flawlessly Detects Genetic Mutations
Excerpt:

The future of this technology is as vast as scientists’ understanding of the genetic mutations that cause certain diseases. If they know the SNP that causes a certain autoimmune disease, they can create the complementary strand and attach it to a biosensor chip to be sent into a patient suspected to have the disease or has a family history of the disease.

My comment: If they know how biophysically constrained energy-dependent RNA-mediated cell type differentiation occurs, they can link viruses from energy theft to the changes in SNPs that are link mutations to all pathology. But, even people who know that are not going to tell anyone until after their plans to make money from potent cures are secured by patents like this one.

RNA-Guided Human Genome Engineering

Excerpt:

Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).

My comment: They know that energy-dependent RNA-mediated protein folding chemistry is the cure for all virus-driven energy theft and pathology. When do you think they’re going to tell you that?

See also: Pregnant women’s high-fat, high-sugar diets may affect future generations
Excerpt:

“Our data are the first to show that pregnant mouse mothers with metabolic syndrome can transmit dysfunctional mitochondria through the female bloodline to three generations,” Moley said. “Importantly, our study indicates oocytes – or mothers’ eggs – may carry information that programs mitochondrial dysfunction throughout the entire organism.”

My comment: That fact has been known to all serious scientists for at least two decades. See our section on molecular epigenetics in From Fertilization to Adult Sexual Behavior
See also: Alzheimer’s Disease: The Role of Presenilin 2
Excerpt:

Why exactly this is the case is unclear, but Ralph Nixon at NYU (who was unaffiliated with this study in Cell), suggests that it might be because the aggregation-prone Aβ42 is more resistant to the acidic environment in the lysosomes so it accumulates instead of being degraded like Aβ40.

My comment: Nutrient stress and social stress cause the pH changes the favor viral replication in specific tissue types.

rp_levels-of-organization.jpg

Millions of water molecules vs years of evolution

by with No Comment AdaptationsbiophotonicsDiseases & DisordersEcologyLight EnergyModel OrganismsPhysicsRNA-mediated toxicityVariations

Electrolytes induce long-range orientational order and free energy changes in the H-bond network of bulk water

Reported as: A single ion impacts a million water molecules

See also:  Remembering Evolution Visionary Mae-Wan Ho

Excerpt:  

Mae-Wan Ho believed that “water is the medium of life,” that “[q]uantum coherent water underlies the quantum coherence of organisms.”

My comment 1) It saddens me to think about how many intelligent visionaries have been lost during the time that neo-Darwinists continued to tout the pseudoscientific nonsense of their well-funded claims about beneficial mutations.

Thank you for continuing to help show how what started with definitions and assumptions has become an almost insurmountable force for virus-driven pathology. Many scientists appreciate the works of journalists who are willing to learn about biologically-based cause and effect. I’m sure that Mae-Won Ho appreciated your efforts.
For example, you may help put a stop to claims about weekend evolution of the bacterial flagellum, which was attributed to two mutations instead of two RNA-mediated amino acid substitutions.
The nutrient-dependent substitutions link the energy-dependent physiology of reproduction to biophysically constrained cell type differentiation in all livng genera. But see the forward by Roger Penrose to: “What is Life?: The Intellectual Pertinence of Erwin Schrödinger.”
Excerpt: “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?”
Similarly, how often does anyone link the anti-entropic virucidal energy of sunlight on contact with water from Mae-Won Ho’s works to healthy longevity compared to virus-driven pathology?

My comment 2)

I suspect that someday soon everyone will place this fact into the context of the fact that there is no boundary between genetic and epigenetic (per Mae-Wan Ho and all other serious scientists).

A single ion impacts a million water molecules http://phys.org/news/2016-04-ion-impacts-million-molecules.html
SARCASM ALERT: Contextualization of facts must wait until after the upcoming Royal Society meeting on the evolution paradigm shift.
Apparently, they are not going to allow anyone to address the effects of virus-driven energy theft, which are linked to all cell type differentiation in all living genera by those damned viruses in the water. The viruses cause the mutations that some people still want to link to evolution across millions of years.
But then, what about the nutrient-dependent pheromone-controlled weekend resurrection of the bacterial flagellum?
Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system http://www.sciencemag.org/content/347/6225/1014.abstract
I don’t think anyone invited to the meeting is ready to talk about that, either.

See also: The pressing need to link physics and chemistry to biologically-based cause and effect, which is what Mae-Wan Ho tried to do, can be viewed in the context of findings from cryoelectron tomography (cryo-ET) and links from angstroms to ecosystems in the context of cryo-EM.

See:

  1. Architecture of the symmetric core of the nuclear pore
  2. The 3.8 Å resolution cryo-EM structure of Zika virus
  3. Structural diversity of supercoiled DNA