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

Sympatric Speciation vs Pseudoscientific Nonsense (1)

Summary: The “Science Behind the Game” from the cell biology game “Cytosis” supports all claims that clearly link energy-dependent alternative splicings of pre-mRNAs (aka microRNAs) to biophysically constrained viral latency. Game play by ages 10+ establishes the requirement for viral latency in the context of ecological variation and ecological adaptation outside the context of neo-Darwinian pseudoscientific nonsense. Simply put, Darwin presciently placed his “conditions of life” into the current perspective on ecological niche construction and sympatric speciation, which exemplifies ecological adaptation in all living genera.
For a historical perspective, see:
1996 From Fertilization to Adult Sexual Behavior

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.

For obfuscation of our claims about cause and effect, which have since been linked to all biodiveristy, see: Altered microRNA expression and pre-mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infection (2016)
Simply put, no new mechanisms were revealed. The well-known mechanisms of energy-dependent pheromone-controlled biophysically constrained RNA-mediated cell type differentiation were simply placed into the context of more unintelligible rhetoric.
See for comparison: 2013 Alternative splicings and amino acid substitutions (redux)
Tracking niche variation over millennial timescales in sympatric killer whale lineages

Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].

The differences in amino acid composition among different tissues can lead to large differences in trophic discrimination [38].

For more information on the current perspective, which is the same as the historical perspective, see:
2018 Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

…speciation of rorqual evolution occurred under gene flow, which is best depicted by evolutionary networks. Especially in marine environments, sympatric speciation might be common; our results raise questions about how genetic divergence can be established.

Reported as: Baleen Whale Genomes Point to Evolution With Gene Flow

Large baleen whales in the Balaenopteridae family (commonly known as rorqual whales) have undergone sympatric speciation — speciation without clear geographic barriers between them — despite ongoing hybridization…

See also: May, 2015 Riding the Evolution Paradigm Shift With Eugene Koonin

The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…

See also: August, 2015 Eibi Nevo: Evolution, Let’s Get It Right, It’s the “Basis of Everything”

Viruses are the dynamo of change that we see in the modern genome. . . .

Cytosis_Booklet_Science.pdf (63 KB) (Log in or Register [for free] to download.) The “Science Behind the Game” from the cell biology game “Cytosis” supports all claims that clearly link energy-dependent alternative splicings of pre-mRNAs (aka microRNAs) to biophysically constrained viral latency. Game play by ages 10+ establishes the requirement for viral latency in the context of ecological variation and ecological adaptation outside the context of neo-Darwinian pseudoscientific nonsense. Simply put, Darwin presciently placed his “conditions of life” into the current perspective on ecological niche construction and sympatric speciation, which exemplifies ecological adaptation in all living genera.
Cytosis is described as: A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!
The collaborative efforts of 20 serious scientists who validated the details in the game include the mention of Stephen J. Bush. See: Bush, SJ et al., (2017) Alternative splicing and the evolution of phenotypic novelty

Alternative splicing, a mechanism of post-transcriptional RNA processing whereby a single gene can encode multiple distinct transcripts, has been proposed to underlie morphological innovations in multicellular organisms. Genes with developmental functions are enriched for alternative splicing events, suggestive of a contribution of alternative splicing to developmental programmes. The role of alternative splicing as a source of transcript diversification has previously been compared to that of gene duplication, with the relationship between the two extensively explored. Alternative splicing is reduced following gene duplication with the retention of duplicate copies higher for genes which were alternatively spliced prior to duplication. Furthermore, and unlike the case for overall gene number, the proportion of alternatively spliced genes has also increased in line with the evolutionary diversification of cell types, suggesting alternative splicing may contribute to the complexity of developmental programmes. Together these observations suggest a prominent role for alternative splicing as a source of functional innovation. However, it is unknown whether the proliferation of alternative splicing events indeed reflects a functional expansion of the transcriptome or instead results from weaker selection acting on larger species, which tend to have a higher number of cell types and lower population sizes.

This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
See for comparison: Retraction: Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication
Reported as: RNA Replication Paper Retracted 
Szostak and others got busted for their pseudoscientific nonsense about non-enzymatic emergence by someone who understands quantized energy as information-dependent RNA-mediated top-down causation. People over age 10+ who play the cell biology game “Cytosis” may now force all biologically uninformed theorists to retract their claims, which typically have been placed into the context of mutation-driven evolution.

5th-6th Sept 2018 Dublin, Ireland

Is meat protein unhealthy? (1)

Patterns of plant and animal protein intake are strongly associated with cardiovascular mortality
Reported as: Meat protein is unhealthy, but protein from nuts and seeds is heart smart

In the context of everything known about how the creation of anti-entropic virucidal light must be linked to all biodiversity on Earth, watch this ridiculous misrepresentation of the honeybee model organism. Food energy-dependent microRNA-mediated pheromone-controlled biophysically constrained viral latency is portrayed as if visual input was most important.

Bee swarms work like giant brains

See instead:

RNA-mediated nutritional psychiatry

RNA-mediated nutritional psychiatry (2)

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

Learn how to prevent more school shootings via what is known about how the “Psychophysical Laws” of Biology are linked to food energy-dependent biophysically constrained behaviors via microRNA-mediated cell type differentiation and the fixation of RNA-mediated amino acid substitutions like COMT Val158Met during the transition from adolescence to adulthood.

Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults (Epub Oct 16 2014)

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

Less evolvable RNA-mediated ecological adaptations

No experimental evidence of biophysically constrained RNA-mediated cell type differentiation supports the claim about “…the evolutionary plasticity of the regulatory regions involved in transcriptional regulation…” The overwhelming systems complexity of energy-dependent RNA-mediated cause and effect can no longer be placed into the context of the pseudoscientific nonsense touted by theorists. Watch Andrea Wagner’s group try to escape from the claims made by losers.
But first see: 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. — Kalevi Kull

RNA-mediated gene regulation is less evolvable than transcriptional regulation

…nucleic acid binding sites of RNA-mediated gene regulation are less evolvable than those of transcriptional regulation. This observation is consistent with the high levels of mRNA target conservation for RBPs (10, 82, 83) and the evolutionary plasticity of the regulatory regions involved in transcriptional regulation (84⇓–86) as well as their role in the evolution of myriad adaptations and innovations (11, 87, 88).

It is obvious to anyone who has followed the works of Andreas Wagner that his group has reached an impasse.
See: Evolution of Viral Proteins Originated De Novo by Overprinting (2012)

We found that young de novo genes have a different codon usage from the rest of the genome.

There is no such thing as a de novo gene.
See: From de novo to “de nono”: most novel protein coding genes identified with phylostratigraphy represent old genes or recent duplicates

I collectively refer to the putative de novo genes that failed to pass the validation criteria as the ‘de nono’ genes.

See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

Natural selection for energy-dependent codon optimality links what organisms eat to their pheromone-controlled physiology of reproduction in species from microbes to humans. Ecological variation is linked to ecological adaptations only in the context of biophysically constrained viral latency. That fact is now perfectly clear in the context of more than 71,000 indexed published works that link the energy-dependent creation of ATP synthase to the creation of ATP and the creation of RNA in the context of McEwen et al., (1964) and Frohlich (1968).
People like Andreas Wagner are stuck with their ridiculous claims about evolution, when all serious scientists know that only the hecatombic evolution of virus-driven pathology is possible. Healthy longevity requires food energy-dependent biophysically constrained polycombic ecological adaptations. The metabolism of food to species-specific pheromones links RNA-mediated autophagy to all biodiversity. The virus-driven degradation of messenger RNA is linked to all pathology.
Andreas Wagner reversed every aspect of what is known in: Arrival of the Fittest: Solving Evolution’s Greatest Puzzle (2014)

…he has found that adaptations are not just driven by chance, but by a set of laws that allow nature to discover new molecules and mechanisms in a fraction of the time that random variation would take.

See for comparison: Kohl’s Laws of Biology in Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)

Life is nutrient-dependent. That is a Biological Law. The ecological origin of all biological laws is apparent 1) in the context of systems biology (P. Kohl, et al., 2010); 2) in the context of the metabolism of nutrients by microbes (K. D. Kohl, 2012); and 3) in the context of how the metabolism of nutrients results in species-specific pheromones that control the physiology of reproduction (J. Kohl, Ostrovsky, Frechter, & Jefferis, 2013). Taken together, the systems biology of nutrient metabolism to species-specific pheromones, which control the physiology of reproduction, can be expressed in a summary of Kohl’s Laws of Biology: 1) Life is nutrient-dependent. See for review (J. V. Kohl, 2012; M. Lynch, 2007). The physiology of reproduction is pheromone-controlled. See for review (J. V. Kohl, 2013). In the context of nutrient-dependent epigenetically-effected human reproduction, it is clearer that the epigenetic effects of human pheromones integrate neuroendocrinology and behavior (J. V. Kohl, et al., 2001), which includes the neuroendocrinology of mammalian behavior associated with the development of sexual preferences (J.V. Kohl, 2007).

Andreas Wagner, and others like him, will probably continue to misrepresent what is known about how the creation of sunlight must be linked to food energy-dependent pheromone-controlled reproduction by natural selection for codon optimality. But the facts about how energy must be linked to increasing organismal complexity are not going to change.
See: Schrödinger at 75 – The Future of Biology – September 2018
and/or Cytosis: A Cell Biology Board Game

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

 
 
 

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

RNA-mediated nutritional psychiatry (2)

Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

Neo-Darwinian theorists dispense with Darwin’s food energy-dependent  “conditions of life.” They link mutations and disease to evolution via mathematical models. They exemplify human idiocy.
See for example: Neopterygian phylogeny: the merger assay
Reported as: Adaptive radiations in the Mesozoic

Bony fishes are the most diverse of all extant vertebrate groups. A comprehensive phylogenetic analysis of the group now provides new insights into its 250-million-year evolutionary history.

The claim about the 250-million-year evolutionary history can be compared to what happens when food energy-dependent fixation of a single RNA-mediated amino acid substitution occurs across a vertebrate lineage.
See: Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor

It is very surprising and fascinating that the coordinated evolutionary selection of amino acids participating in binding GnRH has resulted in such perfection, that no substitution with a natural amino acid in any position improves binding potency.

Evolution does not select amino acids. Natural selection for food energy-dependent pheromone-constrained viral latency links the substitution of achiral glycine in position 6 of the GnRH decapeptide to the biodiversity of all morphological and all behavioral phenotypes in all vertebrates.
See also: Handbook of Biologically Active Peptides (2013) Chapter 106 GnRH (LHRH)
Page 794 Figure 2 shows that food energy-dependent substitution of achiral glycine at position 6 stabilizes the folded conformation; increases binding affinity; and decreases metabolic clearance.

This feature is incorporated in all agonist and antagonist analogs.

Simply put, the substitution of achiral glycine in the GnRH decapeptide biophysically constrains viral latency in the context of ligand-receptor interactions and the physiology of pheromone-controlled reproduction.
See also: Role of olfaction in Octopus vulgaris reproduction
From the concluding paragraph:

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).

Kohl (2013) is Nutrient-dependent/pheromone-controlled adaptive evolution: a model
The facts that link vertebrates to invertebrates via olfaction and the 2013 model will almost undoubtedly be restated when Tuning Insect Odorant Receptors is published.
Until then, see:Evolution of Constrained Gonadotropin-releasing Hormone Ligand Conformation and Receptor Selectivity (2005)
Biophysical constraints link feedback loops from odors and pheromones to the functional structure of the GnRH decapepetide via achiral glycine in position 6. The link from food to the de novo creation of energy-dependent receptors is required in all organisms. They must select the right food, which helps to ensure their ability to reproduce.

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?.

5th-6th Sept 2018 Dublin, Ireland

Light-controlled cell biology (revisited)

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

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

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

Archaea:

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

George Church At 15:10

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

From the transcript:

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

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

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

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

See also:L-form bacteria

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

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

(quotes)

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

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

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

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

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

We need a new definition of what heredity is…

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See also: MicroRNA and autophagy

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

Autophagy in health and disease (1)

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

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

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

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

I wrote:

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

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

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

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

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

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

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

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

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

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

We need a new definition of what heredity is…

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

Biology to a Physicist

MicroRNA-activated / RNA-mediated gene expression

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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