Watering Young Plant - Vintage Effect

The eternal significance of microRNAs (1)

Common Allele Linked to Sugar Consumption Leads to Lower Body Fat, Higher Blood Pressure
One energy-dependent change in a base pair is linked from the FGF21 rs838133 variant to microRNA-mediated changes in morphology and behavior. The quantized energy as information link from microRNAs to morphology and behavior is common to my mouse-to-human model of sympatric speciation.

By linking the common allele to sugar consumption, the authors attest to the fact that sympatric speciation is quantized energy-dependent. Energy as information biophysically constrains viral latency in the context of the game Cytosis for ages 10+.
See also: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Theorists have been reluctant to comment on this invited review of nutritional epigenetics, which I posted to Figshare.com on 4/10/14. As of today, the model of food energy-dependent pheromone-controlled ecological adaptations / sympatric speciation has been available for 4 years.
In my mouse-to-human model, the variant is rs3827760, aka 1540T/C, 370A or Val370Ala. It is a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2.
Summary: The energy-dependent creation of ATP synthase, ATP, microRNAs, messenger RNA, and supercoiled DNA biophysically constrains viral latency in the context of the “Levels of Biological Organization” I included in this presentation from 2010: Human Pheromones: Linking Neuroendocrinology and Ethology (revisited) See slide # 6.
See also, our award-winning 2001 review: Human pheromones: integrating neuroendocrinology and ethology

Watering Young Plant - Vintage Effect

What happened to Timothy J. Cunningham?

Missing CDC scientist: What happened to Tim Cunningham? Police release new details (video)

My comment:
He linked racial/ethnic disparities from epigenetically-effected RNA-mediated sex differences to all virus-driven pathology before anyone else did it.
His published works clearly refute all neo-Darwinian pseudoscientific nonsense and he also refuted all the claims made by Big Bang cosmologists.
See:
1) Racial/ethnic disparities in self-reported short sleep duration among US-born and foreign-born adults
2) Sex-specific relationships between adverse childhood experiences and chronic obstructive pulmonary disease in five states
3) miRNA-mediated ‘tug-of-war’ model reveals ceRNA propensity of genes in cancers
4) SRARP and HSPB7 are epigenetically-regulated gene pairs that function as tumor suppressors and predict clinical outcome in malignancies 
5) STAT1 is a sex-specific tumor suppressor in colitis-associated colorectal cancer
 
 

5th-6th Sept 2018 Dublin, Ireland

NSF's parrot and other parrots

Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

“Isolated thymus nuclei transport amino acids into an intranuclear pool by a process which seems to depend on energy from nuclear ATP synthesis (20).”

The energy must be biophysically constrained: Long-range coherence and energy storage in biological systems (1968)
Human Pheromones: Linking Neuroendocrinology and Ethology (revisited) (2010)
Slide # 6 attests to the fact that the levels of biological organization have been known to all serious scientists for more than 50 years.
See for comparison: NSF’s Big Ideas: Understanding the Rules of Life and The Quantum Leap

Thursday, April 12, 2018 at 2-3 pm ET

Recently the National Science Foundation unveiled a set of “Big Ideas” that are bold, long-term research and process ideas that all scientists should be aware of if they seek funding opportunities for their research.

For instance, a half-century after the discovery of the double helix, new DNA sequencing methods began our feverish race towards more and more data on the linear sequences of genomes, from microorganisms to humans. In 2018 there is potential uncover deeper codes embedded in DNA—those involving non-Watson-Crick bases like the epigenome and non-Watson-Crick folding like G-quadruplexes—in order to fully translate the code into a cellular symphony.

In addition to the former research opportunity, many of today’s technologies like lasers, computers, GPS, and LEDs rely on the interaction of matter and energy at extremely small and discrete dimensions. That said how do we control the behavior of particles and energy at dimensions at least a million times smaller than the width of a human hair? There could be great impact with a new approach toward spectroscopic investigations with non classical light, where a new view of electronic states may be possible with the consideration of entangled states of light.

Join Angela Wilson of NSF, Cynthia Burrows of the University of Utah, Theodore Goodson of the University of Michigan, and Glenn Ruskin of ACS for an introduction of two of the most impactful “Big Ideas” as well as an overview of this innovative NSF program that will advance prosperity, security, health, and well-being in the United States.

What You Will Learn

  • What are the National Science Foundation’s “Big Ideas” and how to learn more about funding opportunities
  • How a combination of methylation and oxidation of DNA bases can ‘write’ markers onto the genome that are later ‘read’ and ‘erased’
  • Why oxidative stress, a normal process in cells responding to their environment, sets up a DNA response that can be considered not just as ‘DNA damage’ but also as a form of epigenetics
  • How guanine-rich sequences may be positioned in the genome to act as sensors of oxidative stress by impacting the folding of G-quadruplexes
  • What are entangled states of light and why they can be used to probe electronic processes in molecules
  • Why Quantum entangled processes may play a role in our understanding of biological processes
  • What are some of the new spectroscopic methods being developed to probe molecules with non classical states of light

 

5th-6th Sept 2018 Dublin, Ireland

Let there be anti-entropic virucidal light

Summary: This is a lie!

…theories are too detailed to be included in models that study host-phage interactions in the long term, which hinders our understanding of systems that range from pathogens infecting gut bacteria to marine phage shaping present and future oceans.

Fuelling the future

In his short story ‘Let There Be Light’, the science-fiction author Robert A Heinlein introduced the energy source that would power his Future History series of stories and novels.

In The Darwin Code, Greg Bear helped to explain how he linked biophysically constrained light energy to the creation of a superior human species in “Darwin’s Radio” (1999) and “Darwin’s Children” (2003).
On June 21, 2017, Philip C. Ball ignored the science fiction and all facts that link the quantized energy of sunlight to biophysically constrained viral latency.
See: Quantum common sense

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.

His pseudoscientific nonsense led me to ridicule him on June 24, 2017.
See:

See for comparison: Genesis 1:3

And God said, “Let there be light,” and there was light.

For a historical perspective on the creation of anti-entropic virucidal light see Schrodinger’s claims in “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.) (pp. 73 and 74)

See for comparison: Ecological and evolutionary consequences of viral plasticity 3/27/18

For bacteriophages, this host-viral performance link has been characterized empirically and with intracellular theories. Such theories are too detailed to be included in models that study host-phage interactions in the long term, which hinders our understanding of systems that range from pathogens infecting gut bacteria to marine phage shaping present and future oceans.

My comment on the preprint:

The “importance of viral plasticity to unravel host-phage interactions” has been modeled in the context of everything known about the creation of anti-entropic virucidal light (e.g., ultraviolet light), and how sunlight is linked from the creation of ATP synthase to the creation of ATP and to the creation of RNA and fixation of RNA-mediated amino acid substitutions that biophysically constrain viral latency in all cell types of all living genera.

A google search for “virus-driven energy theft” would be a good place to start looking for information that you appear to have missed in its entirety.

See also, for example: Virus-mediated archaeal hecatomb in the deep seafloor http://advances.sciencemag.org/content/2/10/e1600492.full

“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 comparison: Riding the Evolution Paradigm Shift With Eugene Koonin May 7, 2015

…the new understanding of evolution needs to integrate what we now know about viruses and virus-host interactions which, from my own perspective, has been absolutely one of the key factors of all evolution since the emergence of cells — well, actually even before the emergence of cells.

Israeli Middle Schools School to Include Theory of Evolution

…learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.

To learn more about ecology and dismiss the pseudoscientific nonsense touted by neo-Darwinian theorists and Big Bang cosmologists, see:
Phase Transitions in the Assembly and Function of Human miRISC March 16, 2018

…may explain how miRISC silences mRNAs … and provide[s] experimental evidence that protein-mediated phase separation…

Probably facilitates biophysically constrained RNA-mediated achiral glycine-controlled energy processing in all jawless vertebrates.

Alternative splicing of pre-mRNA

Psychophysical Laws of Biology: RNA-mediated nutritional psychiatry (3)

Psychophysical Laws and the Superorganism  (open access)

…superorganisms may also exhibit such behaviour, suggesting that these laws arise from fundamental mechanisms of information processing and decision-making.

Reported on Jun 14, 2013 as Nutrient-dependent/pheromone-controlled adaptive evolution: a model

and again on: Mar 27, 2018 as Honeybees may unlock the secrets of how the human brain works

The study… found that superorganisms may obey the same laws as the human brain.

Kohl’s “Laws of Biology” and Darwin’s “conditions of life” can now be compared in the context of how quantized energy as information was linked to biodiversity in this invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)
See also for review:

Functional and evolutionary aspects of chemoreceptors (2012)
Sensory receptors—design principles revisited (2013)
Moving forward: See: Tuning Insect Odorant Receptors (in press)

Among the insect olfactory receptors the odorant receptors (ORs) evolved in parallel to the onset of insect flight. A special property of this receptor type is the capability to adjust sensitivity of odor detection according to previous odor contacts. This article presents a current view on regulatory processes affecting the performance of ORs and proposes a model of mechanisms contributing to OR sensitization.

Future attempts to place psychophysical laws of biology back into the context of neo-Darwinian pseudoscientific nonsense will continue to pit ridiculous theories about experience-dependent tuning of odor receptors against everything known to serious scientists about RNA-mediated biophysically constrained viral latency and supercoiled DNA.
See for comparison:
Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment (2003)
Seeking the foundations of cognition in bacteria: From Schrödinger’s negative entropy to latent information (2006)
Learning from Bacteria about Natural Information Processing (2009)
Stability of the hybrid epithelial/mesenchymal phenotype (2016)

Epithelial-to-Mesenchymal Transition (EMT) and its reverse – Mesenchymal to Epithelial Transition (MET) – are hallmarks of cellular plasticity during embryonic development and cancer metastasis.

Cellular plasticity was linked from the energy-dependent pheromone-controlled physiology of reproduction in bacteria to our visual perception of energy and mass in the context of the space-time continuum.
See: Olfaction Warps Visual Time Perception (2017)

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.

See also: Schrödinger at 75 – The Future of Biology – September 2018
The scheduled speakers will undoubtedly link the Science Behind the Game “Cytosis” to the Science Behind the Game “Subatomic” via everything known to all serious scientists based on Schrodinger’s prescient claims in What is Life? (1944).
See also: What is life when it is not protected from virus driven entropy

The anti-entropic force of virucidal ultraviolet light links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

See also: Energy as information and constrained endogenous RNA interference

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.

This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

See also “Outer Membrane Vesicles” microRNA (4 of 4 from a 3/27/18 search)

How Our Other Genome Controls Our Epi-Genome (2016)

Secretable Small RNAs via Outer Membrane Vesicles in Periodontal Pathogens (2017)

Tiny RNAs and their voyage via extracellular vesicles: Secretion of bacterial small RNA and eukaryotic microRNA (2017)

Molecular Paths Linking Metabolic Diseases, Gut Microbiota Dysbiosis and Enterobacteria Infections (2018)

See also: March 28, 2018 sponsored by System Biosciences
Webinar: Deciphering how bacteria utilize outer membrane vesicles (OMVs) to communicate and infect
 
Outer Membrane Vesicles (OMVs) are membrane vesicles secreted by bacteria that contain DNA, RNA, proteins and endotoxins. Bacteria respond to many environmental factors by secreting specifically-enriched OMVs, which makes these bacteria more fit for their environment. For example, OMVs may be enriched with invasion proteins at the host-pathogen interface. OMVs have recently gained attention as a novel mechanism for transmission of molecular information within bacteria as well as between bacteria and mammalian cells. Owing to their similarities to well-studied extracellular vesicles (EVs), OMVs are being utilized by researchers to study host-bacterial interactions in pathogenesis, cancer therapy, host immune response modulation, as well as bacterial OMV engineering for use as vaccines. This webinar will give an overview of recent studies on the role of OMVs in host-pathogen interactions and discuss their bioengineering potential as vehicles for cargo delivery. We will also introduce our new & revolutionary ExoBacteria™ OMV Isolation Kit, which will enable you to achieve faster, simpler & better OMV isolation.
Learn how OMVs are being utilized by researchers to study host-bacterial interactions in pathogenesis, cancer therapy, host immune response modulation, as well as bacterial OMV engineering for use as vaccines.
5th-6th Sept 2018 Dublin, Ireland

Part 3: Light-controlled cell biology (revisited)

Your cells are constantly being shed and replaced—so is your body ever completely refreshed? Does anything remain of the body that existed on Jan. 1, 2017? 2007? The day you were born? (video)

Out of Order: Undaunted 

…as I prepared for this issue’s Special Report on Microbiomics (starting on page 19), I am stunned by what I am only starting to understand. That our individual existence as humans may only be 10 percent of what we see in the mirror—and that perhaps only 1 percent of our personal ecological genome is a human genome…

When you understand the concept of biophysically constrained energy-dependent ecology (Frohlich, 1968), you may begin to understand the difference between ecological adaptation and evolution. Each cell type represents biophysically constrained viral latency, not mutation-driven evolution.

Outside the context of energy-dependent RNA-mediated DNA repair (aka autophagy), no cell types exist. Bacteria become archaea and archaea become L-forms and the L-forms become non-cells. The energy for cell type differentiation comes from sunlight or from food. It is biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans.

See also: This Compound Can Reverse Aging in Mice. Will It Work in People? and Mitotic progression, arrest, exit or death is determined by centromere integrity and independent of de novo transcription

Theorists used the term “de novo” in the context of de novo transcription and other aspects of energy-dependent cell type differentiation that they cannot explain with their ridiculous theories. For instance, David Sinclair has touted pseudoscientific nonsense until now.

He knows that the cell biology game, “Cytosis” for ages 10+ has exposed him to ridicule, and obviously won’t go away without a fight to maintain some scientific credibility.

See also: PhD title: Fibrillation of proteins involved in neurodegenerative diseases: influence of mRNA

State of art:
TDP-43 and FUS, two RNA-binding proteins (RBPs), have been recently the subject of increased attention due to their role in Amyotrophic Lateral Sclerosis (ALS) and FrontoTemporal Lobar Degeneration (FTLD). In non-pathological conditions, these proteins are mostly found in the nucleus where they participate to mRNA biogenesis and regulation of alternative splicing. However, TDP-43 and FUS are also present in the cytoplasm and they are able to shuttle from one compartment to another. TDP-43 and FUS notably participate in cytoplasmic functions such as mRNA transport and localized translation, which are of critical importance for neuron physiology. In neurons of ALS and FTLD patients, TDP-43 and FUS form insoluble cytoplasmic aggregates with fibrillar structure that can further spread the disease to other areas of the brain.

If this is the state of the art, was the information used to treat the late Stephen Hawking, or was he left to suffer unnecessarily until he died?

See also:

 More germane to DDNews, the most recent pattern I cannot seem to shake is discussion of the microbiome.

Neo-Darwinian theorists and Big Bang cosmologists seem to have no sense of pattern recognition in the context of Olfaction Warps Visual Time Perception

See for comparison: What Stephen Hawking’s Final Paper Says (And Doesn’t Say)

The claims in “Olfaction Warps Visual Time Perception” link the sense of smell in bacteria to our visual perception of energy and mass in the context of the space time continuum and biophysically constrained viral latency. Everything known to Hawking’s co-authors Roger Penrose and George FR Ellis has since been linked from what organisms eat to the physiology of reproduction via the creation of sunlight and biomolecules.

The difference between Hawking’s ridiculous theories and biologically-based facts will place the claims about his intelligence and insight into the historical context of how celebrity scientists have led to our unnecessary suffering and premature death. It’s ironic that Hawking could have been effectively treated with food energy-dependent microRNAs, but instead got stuck with a useless theoretical approach to life. I would not want that to happen to my children or grandchildren (if I had any). What are your children being taught to believe in: theories or experimentally established facts?.

Witzhany2018

Part 2: Light-controlled cell biology (revisited)

Greg Bear took the lead with this approach in his novel Quantico (2006). A genetically engineered virus was used to erase the memory of a specifically targeted human population to reduce inter-ethnic conflict.

[Greg Bear] …served as a consultant for NASA, the U.S. Army, the State Department, the International Food Protection Association, and Homeland Security on matters ranging from privatizing space to food safety, the frontiers of microbiology and genetics, and biological security.

Greg Bear is a likely candidate for work with Robert Redfield, who is currently the director of the CDC. Predictably, Timothy J. Cunningham will reappear as second in command at the CDC — when the Trump administration is ready to finish draining the academic swamp.

Until then, see: Three dimensional two-photon imaging of neuronal activity in freely moving mice using a miniature fiber coupled microscope with active axial-scanning

The ability to link two-photon imaging from the proton motive force to social behavior in the mouse model can be linked from food energy-dependent pheromone-controlled feedback loops to all vertebrate behavior via changes in the potential of hydrogen (pH) and RNA-mediated cell type differentiation.

See also: New Blood Test For Alzheimer’s Is So Precise It Could Predict It 30 Years Ahead

This was reported in this video  — with the mention of this published work. High performance plasma amyloid-β biomarkers for Alzheimer’s disease

There is no mention of microRNAs in the published work. See for comparison: MicroRNA+ Alzheimer’s+amyloid-β biomarkers

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

5th-6th Sept 2018 Dublin, Ireland

Nick Lane refutes theistic evolution (1)

Neo-Darwinian theorists and others who are biologically uninformed will learn this in September (2018).
Synopsis: The difference in two photons has been linked to the Proton motive force. It drives the activity of the enzyme, ATP synthase, which makes ATP. All energy-dependent biophysically constrained viral latency has since been linked from the creation of ATP synthase and the creaton of ATP to changes in the microRNA/messenger RNA balance and healthy longevity. For comparison, the virus-driven degradation of messenger RNA has been linked to all pathology.
There is no such thing as an intrinsic biogeochemical cycle of energy-dependent protein biosynthesis. Light activated endogenous substrates are required for energy-dependent protein biosynthesis. Energy-dependent biophysical constraints on protein biosynthesis link the intrinsic biogeochemical cycle to biophysical constraints on the virus-driven degradation of messenger RNA.
After the presentations during Schrödinger at 75 – The Future of Biology – September 2018, some theorists may need to be placed on a suicide watch due to the availability of “Cytosis” and the ability of students aged 10+ to learn more about cell biology than theorists have learned during the past 75 years.
See for example: Hard Two-Photon Contribution to Elastic Lepton-Proton Scattering Determined by the OLYMPUS Experiment (2017)
Reported as: OLYMPUS experiment sheds light on structure of protons

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

The link from differences in the energy of photons to the amount of ATP that must be be biophysically constrained has been largely ignored since the time that McEwen et al., (1964) linked the creation of ATP to the creation of RNA via oxidative phosphorylation.
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.

The difference in two photons have been linked to the Proton motive force. It drives the activity of the enzyme, ATP synthase, which makes ATP. All energy-dependent biophysically constrained viral latency has since been linked from the creation of ATP synthase and the creaton of ATP to changes in the microRNA/messenger RNA balance and healthy longevity. For comparison, the virus-driven degradation of messenger RNA has been linked to all pathology.
See for instance this 6-7 minute-long video: Energy as information and constrained endogenous RNA interference (February 15, 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.

See for comparison: The energy expansions of evolution (April 28, 2017) with my emphasis.

Sunlight is a consequence of the planet’s position in the Solar System, whereas geochemical energy is an intrinsic property of the Earth. Geochemical energy arises when water reacts with basalts and other rocks…

Although sources of geochemical energy can be at or near Earth’s surface, they need not be: many are deep within the planet, out of reach of sunlight.

That fact became clear in the context of bacteria that eat electrons and the physiology of their reproduction, which was linked to the creation of uranium isotopes.
See: Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits

Many low-temperature ores display similar isotopic fractionation59,60 as found here suggesting an under-recognized importance of biological processes in roll-front ore formation.

The origin of microbial life and the creation of uranium ores via the energy-dependent pheromone-controlled physiology of reproduction in bacteria appears to have gone missing in the context of pseudoscientific nonsense touted by theorists who are already scheduled to present during: Schrödinger at 75 – The Future of Biology – September 2018
 
See also: Proton gradients at the origin of life (May 16, 2017) by Nick Lane
People like Nick Lane still claim that biochemistry emerged from geochemistry. They link the origins of biochemistry to the emergence of genetically encoded catalysts, such as ribozymes, ATP synthase and other enzymes. Then they proceed to tell others about naturally occurring evolutionary processes. The evolutionary processes supposedly link the automagical creation of ATP sythase in some geochemical settings to the biochemistry of our last universal common ancestor (LUCA).
See: Evolution of ATP Synthase (Video) Jackson Wheat claims that ATP and ATP synthase might link the Last Universal Common Ancestor to the evolution of all biodiversity on Earth.
See for comparison the claim from A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

The magic and logic of evolution now start with the evolution of an enzyme (ATP synthase) linked from ATP to the creation of RNA and RNA-mediated amino acid substitutions that differentiate all cell types in all living genera only in the context of the physiology of energy-dependent biophysically constrained reproduction.
See for comparison: Virus-mediated archaeal hecatomb in the deep seafloor

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

Unfortunately, Nick Lane and others appear to initially missed the connection from the virus-driven theft of quantized energy to the creation of archaea from bacteria. He reported the bioenergetic basis for divergence as if DNA replication somehow arose in LUCA outside the context of everything known to serious scientists about the biophysically constrained top-down energy-dependent creation of membranes.
See: A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria (2014)

Because the bacterial replicon is attached to the plasma membrane during cell division [58]–[60], this complex presumably arose after (or coevolved with) the bacterial membrane, which must have driven a deep phylogenetic disparity, even if DNA replication had arisen in LUCA.

Anyone who still touts claims of emergence or pretends to think that the complexity of the plasma membrane in bacterial replicons automagically arose or coevolved in the context of phylogenetic disparities, may want to attend Schrödinger at 75 and laugh at the nonsense touted by Nick Lane and other neo-Darwinian theorists who are scheduled to present.
See: Schrödinger at 75 – The Future of Biology – September 2018
Nick Lane is an evolutionary biochemist
Beth Shapiro is an evolutionary biologist
Svante Pääbo is a Swedish biologist specialising in evolutionary genetics.
In 2012, I attended a conference presentation on microRNAs and the speaker confirmed the fact that every aspect of cell type differentiation occurs downstream from changes in microRNAs. He claimed that is what had been learned during the past 10 years. I confirmed that others who attended his presentation also knew the facts about biophysically constrained RNA-mediated cell type differentiation before publishing a refutation of neo-Darwinian nonsense in 2013.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
After the presentations during Schrödinger at 75, all neo-Darwinian theorists and most big bang cosmologists who have no valid model for comparison may need to be placed on a “suicide watch” for losers.
Kalevi Kull: Censorship & Royal Society Evo Event (2016)

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.

Published works by people like Nick Lane, Beth Shapiro, and Svante Pääbo have not been at the cutting edge since 1964.
See: Biology, molecular and organismic

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.

Ingram and others found that hemoglobin S differs from A in the substitution of just a single amino acid, valine in place of glutamic acid in the beta chain of the hemoglobin molecule.

See also: Patterns of shared signatures of recent positive selection across human populations

…we present a catalogue of selective sweeps in humans, and identify those that overlap and share a sweeping haplotype. We connect these sweep overlaps with potential biological mechanisms at several loci, including potential new sites of adaptive introgression, the glycophorin locus associated with malarial resistance and the alcohol dehydrogenase cluster associated with alcohol dependency.

The failed pattern recognition of biologically uninformed theorists has led serious scientists to proclaim that the pseudoscientists have no way out. Every aspect of life on Earth is energy-dependent, RNA-mediated and biophysically constrained in the context of viral latency.
See: No way out: when RNA elements promote nuclear retention

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:
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