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.

Achromobacter and killer theories

A pan-genomic approach to understand the basis of host adaptation in Achromobacter 

Ecological variation is linked to food energy-dependent biophysically constrained viral latency by the pheromone-controlled physiology of reproduction in species from microbes to humans.

For comparison, these authors claim:

This study provides strong phylogenetic and pan-genomic bases to motivate further research on Achromobacter, and contributes to the understanding of opportunistic pathogen evolution.

Their claim exemplifies how teaching neo-Darwinian theory causes unnecessary suffering and how it may cause the premature death of our loved ones. Physicians who do not know the difference between the human idiocy of claims about pathogen evolution and the facts about pathogen adaptation to a host are not likely to ever link the conserved molecular mechanisms of energy-dependent RNA-mediated cell type differentiation to healthy longevity.

That means they are not likely to link the virus-driven degradation of messenger RNA from mutations to all pathology. They will never look for the results of a search like this:

bacteriophage achromobacter For example: (1974) Bacteriophages and cryptic lysogeny in Achromobacter

See this explanation of energy-dependent viral latency: Viral replication: lytic vs lysogenic (video 5:10) Instead of accurately representing the anti-entropic virucidal effect of UV light, as explained here: Energy as information and constrained endogenous RNA interference (video 6:46)

How much longer will it be until everyone realizes that teaching students to believe in mutation-driven evolution leads them to become professors who are the biologically uninformed science idiots? The professors teach medical professionals to believe in the “bad luck” theories of pathology. See for comparison to the “Bad Luck” theory of random mutations.

In the world of serious scientists, bacteria become archaea and humans become non-human primates in the context of the viral hecatomb (i.e., the virus-driven degradation of messenger RNA). In the world of pseudoscientists who teach physicians to believe in “bad luck” theories, the only hope that most people have is the fact that energy-dependent polycombic ecological adaptations typically biophysically constrain viral latency.

Clearly, bacteriophages (viruses in bacteria) can steal quantized energy to proliferate and kill. Evolutionary theorists are willing to let that continue to happen. Are you?

If not, see: Cytosis

See also: To save a young woman besieged by superbugs, scientists hunt a killer virus

Part of the issue is that phages [viruses] are alive, and continue evolving inside the body.

Viruses are not “alive” and nothing alive evolves inside or outside the body. Organisms adapt to the virus-driven degradation of messenger RNA, or species become extinct.

See also: Episode 10: A giant Petri dish chock-full of superbugs shows evolution as it happens  by Carl Zimmer

…you can observe the evolution of antibiotic resistance in a series of bursting waves. It’s so eminently viewable, in fact, that the MEGA plate video has been watched almost 25 million times since it was posted online in September.

The pseudoscientific nonsense touted by journalists like Carl Zimmer will continue to cause unnecessary suffering and premature deaths. The pathology will be attributed to antibiotic resistance, instead of the failure to teach intelligent students about food energy-dependent pheromone-controlled ecological adaptations.

Amino acid modification FA_Epigenetics_Table1

Eutrophication and phosphorylated biodiversity

In Chinese philosophy, yin and yang (also yinyang or yin yang, 陰陽 yīnyáng “dark–bright”) describe how seemingly opposite or contrary forces may actually be complementary, interconnected, and interdependent in the natural world, and how they may give rise to each other as they interrelate to one another.

Last night I dreamed that someone added color to this symbol and represented it as a spinning disk (in a publication from the Nature publishing group).  The specifics of the dream helped me to complete this accurate representation of biophysically constrained viral latency.
See for comparison: Phosphorylation, oligomerization and self-assembly in water under potential prebiotic conditions
Reported as: Scientists find potential ‘missing link’ in chemistry that led to life on Earth

“It reminds me of the Fairy Godmother in Cinderella, who waves a wand and ‘poof,’ ‘poof,’ ‘poof,’ everything simple is transformed into something more complex and interesting,” Krishnamurthy said.

In the context of energy-dependent Biblical Creation or Chinese philosophy, the speed of light on contact with water links the Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism to a cleansing Flood of Biblical proportions. After-the-Flood, eutrophication probably stimulated the growth of aquatic plant life.
That speculation helps to explain the rapid re-population of the Earth via the “the process by which a body of water becomes enriched in dissolved nutrients (such as phosphates)…
For comparison, Krishnamurthy’s ‘poof,’ ‘poof,’ ‘poof’ theory of how increasing complexity initially arose twice — before and after the extinction of many different species, will always be placed into the context of a “Fairy Tales.”  Serious scientists can use what is known about biophysically constrained viral latency to link eutrophication from phosphorylation and oligomerization to what has been referred to as the Cambrian Explosion — the rapid diversification of most major living animal body plans (phyla) in the fossil record.
However, serious scientists can also link the facts about eutrophication, phosphorylation and oligomerization to all food energy-dependent pheromone-controlled biodiversity on Earth via the weekend resurrection of the bacterial flagellum.
See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
See also: A communal catalogue reveals Earth’s multiscale microbial diversity reported as: Mapping the Microbiome of…Everything
The funding includes money from the John Templeton Foundation, which in the past seems to have ensured that all results would be reported in the context of randomness and evolution. But, even with millions of dollars spent trying to support that dogma, efforts are doomed to fail.
Eugene Koonin said it best: 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…
That fact is readily linked to the ‘poof,’ ‘poof,’ ‘poof’ theory of how increasing complexity arose, because the theory does not include any information on how the virus-driven degradation of messenger RNA has since been linked to all pathology.
Indeed, the fossil record may be the best example of how the viral hecatomb links the virus-driven degradation of messenger RNA to calcification of tissues and to ossification of the tissue that neo-Darwinian theorists claim is evidence that our ancestors evolved into us. Their ridiculous claims have not been supported by any experimental evidence of biophysically constrained biologically-based top-down causation.
If serious scientists allow the ‘poof,’ ‘poof,’ ‘poof’ theory, the pseudoscientists may continue to prevail against all odds. In the world of science, their theories would never be considered. Instead, it seems that biologically uninformed science idiots can suggest anything.When they continue to repeat their suggestions, the uninformed masses may believe them — rather than attempt to learn anything about eutrophication, phosphorylation, or food energy-dependent pheromone-controlled feedback loops, ecological adaptations, and biodiversity.
For instance, in the context of energy-dependent top-down causation, physics and chemistry can be linked from molecular epigenetics to supercoiled DNA in organized genomes via Histone methylation and amino acid substitutions.​​

Lysine methylation of H3 and H4 is implicated in both transcriptional activation and repression depending on the methylation site, while arginine methylation promotes transcriptional activation1.

Methylation is food energy-dependent and RNA-mediated in species from microbes to humans. That fact and all facts about supercoiled DNA, which prevents the virus-driven degradation of messenger RNA, can be placed into the following two representations of cause and effect — or represented as a spinning yin-yang symbol.
The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.
…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 this black and white representation of energy-dependent biodiversity.
See for comparison, this 3-D imagery:

My comment on Inching toward the 3D genome has not been removed.

Re: “…the nucleome structure changes as cells age, differentiate, and divide, and researchers want to understand how and why.”
Cell type differentiation is nutrient-dependent. RNA-directed DNA methylation links RNA-mediated amino acid substitutions to cell type differentiation via protein folding during life history transitions. Amino acid substitutions stabilize protein folding; mutations perturb it, during nutrient-dependent theromodynamic cycles of protein biosynthesis and degradation.
Life is physics and chemistry and communication — http://dx.doi.org/10.1111/nyas.12570
The metabolism of nutrients links metabolic networks to genetic networks via species-specific pheromones that control the physiology of reproduction. Simply put, pheromones link nutrient-dependent life via physics, chemistry, and the conserved molecular mechanisms of communication in species from microbes to man.
Until nutrient-dependent protein folding is linked via the conserved molecular mechanisms of amino acid substitutions and pheromone-controlled DNA stability in organized genomes, which links the epigenetic landscape to the physical landscape of DNA, researchers must take a piece-meal approach to integrating the requirements for life and successful life history transitions — despite the fact that life history transitions have been detailed in the context of the honeybee model organism. See: Honey bees as a model for understanding mechanisms of life history transitions http://www.ncbi.nlm.nih.gov/pubmed/15925525

Gene Robinson is the senior author of this report on phosphorylation in the honeybee model organism. See: Socially responsive effects of brain oxidative metabolism on aggression

Despite ongoing high energetic demands, brains do not always use glucose and oxygen in a ratio that produces maximal ATP through oxidative phosphorylation. In some cases glucose consumption exceeds oxygen use despite adequate oxygen availability, a phenomenon known as aerobic glycolysis. Although metabolic plasticity seems essential for normal cognition, studying its functional significance has been challenging because few experimental systems link brain metabolic patterns to distinct behavioral states. Our recent transcriptomic analysis established a correlation between aggression and decreased whole-brain oxidative phosphorylation activity in the honey bee (Apis mellifera), suggesting that brain metabolic plasticity may modulate this naturally occurring behavior.

Elekonich and Robinson (2000) cited our 1996 Hormones and Behavior review:

The development of species-typical and sex-specific adult behaviors in vertebrate animals is influenced by gonadal steroid hormones, non-gonadal hormones, and non-hormonal factors working on the underlying neural circuitry (reviewed in Diamond et al., 1996; Kawata, 1995; Schlinger, 1998).

The facts that link the creation of sunlight from the creation of ATP to the creation of RNA have been known since 1964.
See: 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 facts about Honey bees as a model for understanding mechanisms of life history transitions have been ignored.
See also: Feedback loops link odor and pheromone signaling with reproduction
What can be said about the amount of willful ignorance that has been displayed by theorists, since “What is Life?” was published in 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)

In the reprint edition, Roger Penrose (8 August 1991) 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?

See also my comments on: Methyldynamics behind virtually all pathologies?

Vast Complexity of Chromatin 3D Shapes
http://jonlieffmd.com/blog/vast-complexity-of-chromatin-3d-shapes
N6-methyladenosine marks primary microRNAs for processing http://dx.doi.org/10.1038/nature14281
Our 1996 Hormones and Behavior review linked pre-mRNAs (microRNAs) to RNA-mediated cell type differentiation in species from yeasts to mammals via what was known about the conserved molecular mechanisms of nutrient-dependent RNA-mediated protein folding and the pheromone-controlled physiology of reproduction.
From Fertilization to Adult Sexual Behavior http://www.hawaii.edu/PCSS/biblio/articles/1961to1999/1996-from-fertilization.html
See also:
Unraveling the secrets of RNA-mediated events http://rna-mediated.com/unraveling-the-secrets-of-rna-mediated-events/

It is difficult for me, as a medical laboratory scientist, to understand how others who are involved in diagnostic medicine seem to have accepted ridiculous theories that cannot be linked to results reported from testing in the medical laboratory.
See: Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels

Mutations in the period (per) gene of Drosophila melanogaster affect both circadian and ultradian rhythms. Levels of per gene product undergo circadian oscillation, and it is now shown that there is an underlying oscillation in the level of per RNA. The observations indicate that the cycling of per-encoded protein could result from per RNA cycling, and that there is a feedback loop through which the activity of per-encoded protein causes cycling of its own RNA.

What have other medical laboratory scientists and medical professionals been taught to believe about the underlying oscillation that have since been linked from cryo-EM to all energy-dependent biophysically constrained viral latency? Is there any model of biologically-based cause and effect that links anything except food energy-dependent feedback loops from the physiology of pheromone-controlled reproduction to all biodiversity? If not, help stop the nonsense.
Play the cell biology game: 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!

Stop playing the games of theorists.

Cytosis

Long-term adaptation replaces evolution (2)

The food energy-dependent “doubling up” on ‘junk DNA’ is biophysically constrained by the physiology of pheromone-controlled reproduction. The metabolism of food to species-specific pheromones links the conserved molecular mechanisms of RNA-mediated cell type differentiation in all individuals of all living genera to healthy longevity via what is known about amino acid substitutions in supercoiled DNA, which link energy-dependent changes in chirality to autophagy.

See: It’s all about that base

The virus-driven degradation of messenger RNA in bacteria links top-down causation to what happens to archaea and L-forms in the context of the viral hecatomb, which links the destruction of G protein-coupled receptors to all pathology because the de novo creation of G protein-coupled receptors links the creation of the sense of smell to all biodiversity.

Our ability to detect differences in amino acid substitutions in the blood has been linked to the ability of flies to find food and to reproduce via the physiology of food-energy-dependent pheromone-controlled reproduction.

See: A mammalian blood odor component serves as an approach-avoidance cue across phylum border – from flies to humans
See also:

Adaptive evolution by spontaneous domain fusion and protein relocalization

Phenotypic heterogeneity promotes adaptive evolution

My 2013 model of energy-dependent ecological adaptations: Nutrient-dependent/pheromone-controlled adaptive evolution: a model refuted neo-Darwinian pseudoscientific nonsense. That that model is being revisited each day that another publication is added to those that link the energy-dependent de novo creation of microRNAs to all biodiversity via hydrogen-atom transfer in DNA base pairs in solution. See: microRNA

For example:Recent advances in signal amplification strategy based on oligonucleotide and nanomaterials for microRNA detection-a review.

See also:

Overview of microRNA biology. Mohr AM et al. Semin Liver Dis. (2015)

MicroRNA Therapeutics: the Next Magic Bullet? Simonson B et al. Mini Rev Med Chem. (2015)

MicroRNAs in cancer: biomarkers, functions and therapy. Hayes J et al. Trends Mol Med. (2014)

Lethal virus kills 5 billion people?

Entertaining yourself to death

Summary: Food energy is required for the creation of enzymes that metabolize the food, which links the metabolism to the pheromone-controlled physiology of reproduction in species from microbes to humans via alternative splicings of pre-mRNAs, which are now called microRNAs in more than 65,000 published works. The horrid tradjedy of of yet another preventable death by suicide extends those works to preventing the cause of death of those killed by Stephen Paddock.
Vegas gunman transferred $100K, set up cameras at hotel room
Excerpts with my emphasis:

Lombardo said he is “absolutely” confident authorities will find out what set off Paddock, a 64-year-old high-stakes gambler and retired accountant who killed himself….

…speculated that there was “some sort of major trigger in his life — a great loss, a breakup, or maybe he just found out he has a terminal disease.”

…a “psychological autopsy” may be necessary to try to establish the motive. If the suicide didn’t destroy Paddock’s brain, experts may even find a neurological disorder or malformation

He said there could be a genetic component to the slaughter…

“The genetics load the gun, personality and psychology aim it, and experiences pull the trigger, typically,” Clemente said.

He later worked for a defense contractor.

“No affiliation, no religion, no politics. He never cared about any of that…

Two former facebook friends are among those who claim that “nobody cares” that I have detailed the facts about the virus-driven cause of death for Stephen Paddock and his victims. When will others learn why there was no obvious motive to his madness?
The excerpts above clearly indicate that virus-driven epigenetic drift led to the deadly constraint-breaking mutations via everything known to serious scientists about epitranscriptomics and biophysically constrained viral latency.
Simply put, like most people, Stephen Paddock failed to protect himself from the virus-driven degradation of messenger RNA that serious scientists have linked to all pathology in all living genera. Psychiatrist/antagonist Jay R. Feierman put that fact into the context of this post to the “Evolutionary Psychology” Yahoo Group.

168958 Origin and Evolution of RNA-Dependent RNA Polymerase OPEN ACCESS

I find this article interesting because of the “object of study.” We are used to thinking about evolution at hierarchical levels above that of protein enzymes. Yet, protein enzymes are “structural design features” and follow the same principles of evolution by natural selection as structural design features at higher hierarchical levels, such as certain kinds of behaviors and even species. Compared to other kinds of evolution, protein enzyme evolution is very conservative in that it does not change much through phylogeny. We essentially have the same enzymes for metabolizing glucose as do bacteria and other single cell animals.

The death of Stephen Paddock and his victims can now be attributed to medical professionals, like Jay R. Feierman, and anyone else who claims: “We are used to thinking about evolution at hierarchical levels above that of protein enzymes.”
The creation of protein enzymes requires an energy source. That fact refutes every aspect of the pseudoscientific nonsense touted by biologically uninformed science idiots. [An idiot is someone with no professional expertise: A biologically uninformed science idiot is someone like Feierman, who has professional expertise but no common sense.] Feierman linked to this article: Origin and Evolution of RNA-Dependent RNA Polymerase (with my emphasis)

With the emergence of a variant with properties of reverse transcriptase, and subsequently a DNA polymerase, a fundamental step occurred to originate the first genomes based in DNA, being the bridge to move from a RNA/Protein World to a DNA/RNA/Protein World (Gilbert, 1986; Müller, 2006). When DNA molecules emerged, by variation, other classes of polymerases appeared. With the complexification of the biological system, functions such as replication, repair, and recombination emerged, very high error rates were selected against, and the new variants arose to work in specific processes.

My summary: The authors eliminate the energy-dependent creation of enzymes (1) reverse transcriptase and (2) a DNA polymerase. In the second act of their tragic comedy routine, they eliminate the biophysical constraints that link the physiology of pheromone-controlled reproduction from natural selection for energy-dependent codon optimality to the creation of enzymes and food energy-dependent RNA-mediated DNA repair via feedback loops.
See: Feedback loops link odor and pheromone signaling with reproduction
The feedback loops link the sense of smell in bacteria from the physiology of their pheromone-controlled reproduction to our visual perception of energy and mass in the context of the space-time continuum.
See: Olfaction Warps Visual Time Perception

The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity. These findings point to a neuronal network in the right temporal cortex that executes flexible temporal filtering of upstream visual inputs based on olfactory information. Moreover, they collectively indicate that the very process of sensory integration at the stage of object processing twists time perception, hence casting new insights into the neural timing of multisensory events.

Virus-driven degradation of messenger RNA links alterations in the timing of multisensory events to the suicide of Stephen Paddock and to the unnecessary suffering and premature death of his victims. That fact was placed into the context of Feierman’s thinly veiled attack on the practice of Precision Medicine.
See: Energy as information and constrained endogenous RNA interference, which was presented during the Labroots: Precision Medicine Virtual Conference February 22-23. 2017
Description:

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

Stephen Paddock killed 59 people and more than 500 people were injured. On 10/4/17, there were only 637 views of my 7 minute-long presentation. With release of the cell biology game “Cytosis,” which is scheduled to be available later this month, everyone who is not dead yet will be able to learn how to protect themselves from the cause of death by suicide: viruses. The virus-driven degradation of messenger RNA will also be the cause of death for people who have not learned the difference between energy-dependent healthy longevity and the virus-driven energy theft that will kill them either directly or indirectly.

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

See also this comment to the human-ethology Yahoo group (reproduced below)

See for comparison: Transcription factor clusters regulate genes in eukaryotic cells

Attempts continue to link epigenetic drift and epitranscriptomics to RNA-mediated cell type differentiation outside the context of natural selection for energy-dependent codon optimality and the biophysically constrained pheromone-controlled physiology of reproduction. All past attempts have failed.

The reason for those attempts and the reason all past attempts have failed may require more clarification from people like Jay R. Feierman. Others realize that the enzymes linked from metabolism to survival of all species did not create themselves and did not evolve, which means that no species evolved via natural selection for beneficial mutations. Pseudoscientists have been left behind with their hypothetical scenarios.’

See for example: Origin and Evolution of RNA-Dependent RNA Polymerase

“Based in the present results, we suggest a hypothetical scenario where initially a ribozyme with polymerase activity could have enhanced its activity by the binding of a simple cofactor, as magnesium (Shechner et al., 2009; Horning and Joyce, 2017), thus, exerting the functions of replication of some information stored on RNA molecules (Kim and Higgs, 2016; Tagami et al., 2017).”

See for comparison: Lipid Encapsulation of Self Replicating Ribozymes

“Despite their challenges, ribozymes have made an interesting niche for themselves in the field of abiogenesis. The evolution of a successful RNA polymerase ribozyme is a lofty goal. While its discovery would not be the be-all and end-all of abiogenesis research, it would represent an important stepping stone between prebiotic chemistry and life. The encapsulation of such a ribozyme is also an important step, as it would enable a system of heredity and evolution through natural selection. Based on progress in current research, it is only a matter of time before that ribozyme is discovered.”

I have discussed the claims about abiogenesis and ribozymes in the context of “…a system of heredity and evolution through natural selection…” with scientists who have repeatedly assured me that the claims are nothing more than examples of what Richard Feynman placed into the context of “human idiocy.” Food energy is required for the creation of enzymes that metabolize the food, which links the metabolism to the pheromone-controlled physiology of reproduction in species from microbes to humans via alternative splicings of pre-mRNAs, which are now called microRNAs in more than 65,000 published works.

See for example: miRNA as viral transcription tuners in HPV-mediated cervical carcinogenesis

Discovery of microRNAs (miRs) in recent years and differential expression of a set of specific miRs in HPV infection and cervical lesions indicate that among various regulatory mechanisms, role of these differentially expressed miRs in the post-transcriptional control is pivotal.

When will people like Feierman and Jones begin to examine the extant literature that links energy-dependent biophysically constrained biologically-based cause and effect as detailed in the molecular epigenetics section of our 1996 review:
From Fertilization to Adult Sexual Behavior
How many more people will needlessly suffer and/or die prematurely due to the ignorance and arrogance of biologically uninformed science idiots?

fruit-dove

Happy Darwin Day (2017)

My series of blog posts about the refutation of theistic evolution by George Church led him to contact me via email.

  1. He asked why he would get credit for or against the refutations
  2. He claimed he was trained in quantum physics.
  3. He claimed that he has authored peer reviewed papers on protein folding, biodiversity, supercoiling, etc.
  4. He wanted to know more but did not know enough about my target audience to realize why I included information about the viral hecatomb.
  5. He also claimed to have written more on what is known about endogenous RNA interference than on exogenous RNA interference.

I invited him to discuss this further on my FB group, or on this domain. He declined. That was a great end to my 2017 Darwin Day.
See Evolution-guided optimization of biosynthetic pathways, which was co-authored by George Church and published December 1, 2014.
There is no such thing as evolution-guided optimization. Natural selection for energy dependent codon optimality is the only link from ecological variation to ecological adaptation in all living genera. That means we can move forward without George Church and still place his comments into the context of “Trust me, I’m a biologist.
I think that most serious scientists agree that you can’t trust evolutionary theorists For comparison, you can trust Darwin’s “conditions of life.”
Darwin’s “conditions of life” link the anti-entropic virucidal energy of sunlight to the physiology of reproduction in all living genera. Can you trust anyone who claims evolution did that?
See: RNA-Guided Human Genome Engineering 

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

Nutrient energy-dependent microRNAs link natural selection for energy-dependent codon optimality to viral latency and protection of organized genomes from endogenous viral elements. Targeting endogenous viral elements with RNA-mediated amino acid substitutions is the key to biophysically constrained cell type differentiation. Fixation of amino acid substitutions prevents problematic nearly identical copies. There is no need for uncontrolled copies if there is no need to find another energy source. Uncontrolled copies link virus-driven energy theft from mutations to all pathology in all genera.
For example, energy theft from bacteria links messenger RNA degradation to morphological and behavioral phenotypes of archaea. Similarly, messenger RNA degradation in humans links the transgenerational epigenetic inheritance of Zika virus-damaged DNA to craniofacial morphology and brain development in infants.
Taken together with what is known about differences in energy-dependent endogenous RNA interference in nematodes, all ridiculous misrepresentations of Darwin’s works must be reversed to show the truth about what virus-driven energy theft does. It links RNA-mediated cell type differentiation from the energy-dependent creation of bacteria to the energy-dependent creation of humans and it links virus-driven energy theft to all pathology.
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… 

Is Eugene Koonin joking about what was left out? If not, big bang cosmologists and neo-Darwinian theorists have never tried to support their ridiculous theories with any experimental evidence of biologically based cause and effect. They never examined the role of energy-dependent microRNAs or virus-driven energy theft. Instead, they invented gene-centric theories of mutation-driven evolution.

See for comparison: Membrane Patterns Carry Ontogenetic Information that is Specified Independently of DNA
Reported as: Peer-Reviewed Paper: Development Needs Ontogenetic Information that Cannot Arise from Neo-Darwinian Mechanisms

With over 400 citations to the technical literature, this well-researched and well-documented article shows that embryogenesis depends on crucial sources of information that exist outside of the DNA.

A 16 page monograph with 12 pages of citations is an unparalleled achievement for anyone who is not a polymath or someone who has not already linked physics and chemistry from molecular epigenetics to all biophysically constrained cell type differentiation in all living genera via fixation of nutrient energy-dependent RNA-mediated amino acid substitutions in supercoiled DNA.
None of the cited works appear to link what is known about virus-driven energy theft to all pathology. Again, it is time to move forward.
See: Charles Darwin’s Ocean Upwelling

It’s hard to overstate how vital Darwin’s coral reef theory was in developing his career and thinking. It paved the way, conceptually and methodologically, for everything to come — particularly his transmutation theory [natural selection]. The likenesses startle. Like the transmutation theory, the coral reef theory described how small, virtually unnoticeable changes could create differences of essential type in seemingly immutable forms — and in doing so, account for broad patterns of development and difference.

Changes in coral reefs are nutrient energy-dependent and controlled by the physiology of reproduction. De vries defined “mutation” in 1902, which means that Darwin could not have had a transmutation theory. Also, Darwin repeatedly asserted the claim that his “conditions of life” must come before any claims about natural selection.
Darwin Day 2017 may become known as the day George Church refused to publicly discuss evolution or to admit there is no such thing as evolution outside the context of virus-driven energy theft and the evolution of  pathology. On the same day, The Smithsonian National Museum of Natural History blog site published a post that misrepresented everything known to serious scientists about biophysically constrained energy-dependent RNA-mediated cell type differentiation and healthy longevity.  Who could ask for a better Darwin Day than one during which Darwin’s “conditions of life” clearly triumphed over the ridiculous claims made by neo-Darwinian theorists and others who refuse to admit to the facts that link energy-dependent changes in chirality from autophagy to endogenous RNA interference and to supercoiled DNA, which prevents virus-driven energy theft from causing the mutations that all serious scientists have linked to all pathology?
 

Alternative splicing of pre-mRNA

George Church refutes theistic evolution (2)

See: George Church refutes theistic evolution

George Church may not know that he refuted every aspect of theistic evolution in his presentation on February 8, 2017. Hopefully, someone will tell him how he linked quantum physics from chemistry to biophysically constrained protein folding and all biodiversity, or explain to others how he did that. Here is my explanation of his admissions. I placed the explanation into the context of this poster session submission.

Title: Energy as information and constrained endogenous RNA interference
Abstract:

Sunlight-induces energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution. Changes in the potential of hydrogen (pH) link quantum physics to classical physics via chirality (manifested in chemistry). Energy-dependent biophysically constrained protein folding chemistry links what is known about molecular epigenetics to what is known about autophagy.  For instance, energy-dependent changes in pH link ecological variation from angstroms to ecosystems via base pair changes and RNA-directed DNA methylation (endogenous RNA interference).  That is how the sun’s anti-entropic virucidal energy is linked from the physiology of reproduction to all life on Earth.

Base pair changes link microbial quorum sensing from the nutrient energy-dependent pheromone-controlled physiology of reproduction to the National Microbiome Initiative. Endogenous RNA interference (RNAi) links the base pair changes from the innate immune system to supercoiled DNA and chromosomal inheritance. Sunlight is linked from the National Microbiome Initiative to the Precision Medicine Initiative via genome wide inferences of natural selection for nutrients and the pheromone-controlled energy-dependent fixation of amino acid substitutions in all organized genomes.

This presentation explains how natural selection for energy-dependent codon optimality links biologically-based cause and effect from the de novo creation of G protein-coupled receptors (GPCRs) to fixation of RNA-mediated amino acid substitutions. GPCRs link metabolic networks and genetic networks to the amino acid substitutions that differentiate all cell types in all individuals of all species.

Ecological variation is linked to energy-dependent metabolic networks and genetic networks, which link alternative RNA splicings from supercoiled DNA to polycombic ecological adaptations.  Ecological adaptations, which are manifested in morphology, are linked from supercoiled DNA and chromosomal inheritance to healthy longevity via energy-dependent differences in behavior.

For contrast, virus-driven energy theft links messenger RNA degradation to negative supercoiling and constraint-breaking mutations. Virus-driven hecatombic evolution links energy theft from biophysical constraint-breaking mutations to all pathology. For example, the viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA in human infants, which typically is repaired by energy-dependent endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

A link to the poster session and narrative summary should be available within the next two weeks.

Biology to a Physicist

2016 obfuscated facts about energy as information

Zika infection may affect adult brain cells

Illumination of the fluorescent biomarker in green revealed that the adult mouse brain could be infected by Zika in a region called the subgranular zone of the hippocampus. Full of neural progenitor cells, this part of the brain is important in learning and memory. Credit: Laboratory of Pediatric Brain Disease at The Rockefeller University/Cell Stem Cell

As reported by Bob Yirka in: Best of Last Year – The top Medical Xpress articles of 2016

a team of MIT biologists reported that amino acids, not sugar, supplied most of the building blocks for tumor cells—cell mass was not mostly glucose, as they had expected.
In other news, at team at Duke University found a key protein for spinal cord repair

Most of the pseudoscientific nonsense reported in the top Medical Xpress articles from the past can be compared to the facts about how energy-dependent viral latency is required for ecological adaptation in the context of RNA-mediated amino acid substitutions.

The facts were reported as “New CRISPR–Cas systems from uncultivated microbes

See also: More refutations of neo-Darwinian nonsense and Dietary lutein and pheromone-controlled brain development

All serious scientists have learned there is no “new CRISPR–Cas” system. The de novo creation of the innate immune system links nutrient energy-dependent changes from angstroms to ecosystems via hydrogen-atom transfer in DNA base pairs in solution. The energy-dependent changes in base pairs are the obvious links to the development of morphological and behavioral phenotypes in all living genera. All phenotypic expression is energy-dependent, and it must link autophagy to the physiology of reproduction. For example, in species from microbes to humans Feedback loops link odor and pheromone signaling with reproduction

The pheromone-controlled physiology of reproduction links the energy-dependent creation of supercoiled DNA to protection from virus-driven energy theft and all pathology. Simply put, supercoiled DNA prevents the genomic entropy that is linked to all pathology.
 

For comparison, the link from the anti-entropic virucidal energy of sunlight to supercoiled DNA via the viral hecatomb in archaea is the link to the transgenerational epigenetic inheritance of Zika virus-damaged DNA in human infants. Facts about energy-dependent polycombic ecological adaptations will put an end to ridiculous theories about mutations and evolution. That will become perfectly clear if Gunter Witzany allows others to help present  what is known about energy-dependent changes in the microRNA/messenger RNA balance at the 2018 conference he reportedly is organizing.

See: Royal Society: The Public Evolution Summit (p. 12)

 … evolution of genome invading RNA networks that edit host g… Witzany is organizing a conference symposium for July 2018 “Evolution-genetic innovations without error replication”

Until everyone learns how energy-dependent autophagy and supercoiled DNA prevent error replication, pseudoscientists may continue to tout their ridiculous theories. Many more people will suffer and die prematurely due to biased reporting that supports the evolution industry and “big bang” cosmology industry.

But wait, 2016 is not over yet, is it?

See: Spatiotemporal antagonism in mesenchymal-epithelial signaling in sweat versus hair fate decision

This was reported by Bob Yirka as: Researchers identify signals during embryonic development that control the fate of skin cells to be sweaty or hairy

See also: Royal Society’s Sir Venki Ramakrishnan Agrees to Post Public Evo Audio

…public discussion from the recent “new trends” in evolution conference will be posted shortly online on the Royal Society event webpage.

The public discussion may help to reveal that the fate of all cell types is energy-dependent and RNA-mediated via natural selection for codon optimality linked to autophagy and to supercoiled DNA.
See for example: rs3827760, also known as 1540T/C, 370A or Val370Ala, is a SNP in the ectodysplasin A receptor EDAR gene on chromosome 2.
This SNP and everything known about how chromosomal rearrangements are linked to energy-dependent  pheromone-controlled biodiversity, which links the mouse model of cell type differentiation to humans via what is known about energy-dependent RNA-mediated amino acid substitutions such as Val370Ala. The facts about the Val370Ala and other amino acid substitutions have been known since 1973 and four more decades of facts were detailed in the context of this 2013 review.
See for other examples: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

These two reports (Grossman et al., 2013; Kamberov et al., 2013) tell a new short story of adaptive evolution. The story begins with what was probably a nutrient-dependent variant allele that arose in central China approximately 30,000 years ago. The effect of the allele is adaptive and it is manifested in the context of an effect on sweat, skin, hair, and teeth. In other mammals, like the mouse, the effect on sweat, skin, hair, and teeth is due to an epigenetic effect of nutrients on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones control the nutrient-dependent hormone-dependent organization and activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates as previously indicated. That means the adaptive evolution of the human population, which is detailed in these two reports, is also likely to be nutrient-dependent and pheromone-controlled, since there is no other model for that.

Each week’s science news brings additional representations of facts that refute all neo-Darwinian pseudoscientific nonsense by linking Darwin’s “conditions of life” to all biodiversity. Most science news outlets still report and/or tout pseudoscientific nonsense because the reporters missed the fact that life is nutrient-dependent and the physiology of reproduction is controlled by pheromones in species from microbes to humans.
Can you imagine how embarrassed you would be if you had not learned to include the fact that all organisms must eat or they cannot reproduce in your reports. That fact means organisms cannot become part of a species if they can’t find food. What’s worst about having to explain that fact to reporters and/or pseudoscientists is that no experimental evidence of biologically-based cause and effect supports claims that one species ever evolved into another.
“The Battlefield”
I may have mentioned this before.  I’ve been banned from participation on this group, twice. Most recently, I complained that two other admins support Peter Berean’s attempts to denigrate my life’s works on energy as information-dependent changes in the microRNA/messenger RNA balance and denigrate me personally with his claims about “bio-functional information.”
By default, Larry Kisner Sr., and John L Leonard support the ignorant representations made by Peter Berean, and there is rarely any accurate representation of energy-dependent biologically-based cause and effect.

I’ve suggested several times that the group may be another “False Flag” group. Others can evaluate the claims made there for comparisons to the accurate claims of serious scientists who have linked hydrogen-atom transfer in DNA base pairs in solution to energy-dependent changes in microRNA flanking sequences and all biodiversity via natural selection for energy-as-information-dependent codon optimality.
You’ll be learning more about the facts as others try to obfuscate them in the weeks to come. Until then, see this conclusion from my 2013 review:

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