5th-6th Sept 2018 Dublin, Ireland

Complexity: Routes and Patterns (1)

Physical foundations of biological complexity

 “Routes and patterns of the evolution of complexity are poorly understood.”

Serious scientists have linked differences in the competing energy of two photons from the proton motive force to biophysically constrained viral latency via the physiology of pheromone-controlled reproduction in species from microbes to humans. Ages 10+ can learn how serious scientists did this by playing the cell biology game “Cytosis.” It starts from the creation of the sun’s anti-entropic virucidal energy and links it to all biodiversity.
The game “Subatomic” is scheduled for September, 2018 release and in the same month conference presentations during “Schrodinger at 75: The future of biology” will eliminate the pseudoscientific nonsense touted by Eugene Koonin and others like him. See for instance.

“We propose a general conceptual framework for emergence of complexity through competing interactions and frustrated states similar to those that yield patterns in stripe glasses and cause self-organized criticality.”

Koonin knows he is touting pseudoscientific nonsense.
See: 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…”

 

An evolutionary theory killer

How to create biologically uninformed theorists

Summary: On March 2, 2018, Philip C. Ball and Nick Lane started making claims about proton gradients. Their claims are based on my model of quantized energy as information. This post includes added support for what is known to all serious scientists about the light-activated endogenous substrates that link molecular epigenetics to RNA-mediated autophagy.
See first: Energy as information and constrained endogenous RNA interference (audio/visual aid 2017)

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy.

The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.

This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes.

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

Added support for the light-activated molecular epigenetics of autophagy:
Light-powering Escherichia coli with proteorhodopsin (2007)

…we quantify the coupling between light-driven and respiratory proton currents… and show that light-driven pumping by PR can fully replace respiration as a cellular energy source in some environmental conditions.

Structure of the Deactive State of Mammalian Respiratory Complex I (2018)

…the deactive state arises when critical structural elements that form the ubiquinone-binding site become disordered, and we propose reactivation is induced when substrate binding to the NADH-reduced enzyme templates their reordering. Our structure both rationalizes biochemical data on the deactive state and offers new insights into its physiological and cellular roles.

Global collective motions in the mammalian and bacterial respiratory complex I (2018)

…we identify here transitions between experimentally resolved structures of the mammalian complex I as low-frequency collective motions of the enzyme, highlighting similarities and differences between the bacterial and mammalian enzymes. Despite the reduced complexity of the smaller bacterial enzyme, our results suggest that the global dynamics of complex I is overall conserved.

The conservation of light-powered functional structures and energy-dependent proton gradients link the deactive state in critical structures to the active state via the creation of enzymes in species from bacteria to mammals. The energy-dependent creation of the enzymes links metabolism of the energy (e.g., food energy) from pheromones to biophysically constrained viral latency in the context of the physiology of reproduction.
The pheromone-controlled physiology of reproduction in species from microbes to humans links our visual perception of energy and mass in the context of how ecological variation must be linked to energy-dependent ecological adaptations in all living genera.
See: Olfaction Warps Visual Time Perception

Our perception of the world builds upon dynamic inputs from multiple senses with different temporal resolutions, and is threaded with the passing of subjective time. How time is extracted from multisensory inputs is scantly known. Utilizing psychophysical testing and electroencephalography, we show in healthy human adults that odors modulate object visibility around critical flicker-fusion frequency (CFF)-the limit at which chromatic flickers become perceived as a stable color-and effectively alter CFF in a congruency-based manner, despite that they afford no clear environmental temporal information. The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity. These findings point to a neuronal network in the right temporal cortex that executes flexible temporal filtering of upstream visual inputs based on olfactory information. Moreover, they collectively indicate that the very process of sensory integration at the stage of object processing twists time perception, hence casting new insights into the neural timing of multisensory events.

See also: Odors Alter Subjective Time Experience Author: Dr. ZHOU Wen’s Research Group Update time: 2017/05/15

The brain is not a timepiece. Whereas it is equipped with senses like vision, audition, touch, smell, and taste, it has no direct access to or measure of the physical time (unless you read from a clock). Rather, it constructs the subjective “time” of an event from the dynamic multisensory inputs associated with that event. Yet different senses come with different temporal precisions. For instance, when standing near an apple tree, you can detect the falling of an apple much better with your eyes or ears than the nose. How does the brain coordinate multisensory signals entering different brain regions with different temporal resolutions, and come up with the subjective time?

A team at the Institute of Psychology at Chinese Academy of Sciences tackled this issue using odors and images. Specifically, Dr. Bin Zhou, the study’s lead author, and his colleagues examined whether odors could modulate one’s temporal sampling and subjective duration of visual objects. In their study, participants viewed two series of flickering isoluminant images in red and green (Figure 1A). One of the series contained opposite images of an apple or bananas; the other contained only images of red and green fields. When the images alternated at a frequency beyond 20 Hz, the participants started to have difficulty reporting which series contained an object. Indeed, for most people, chromatic flicker fusion frequency (CFF), the limit at which alternating colors become perceived as a stable fused color, falls somewhere between 20 and 25 Hz. Interestingly, the participants’ object detection accuracies around CFF were improved under the exposure of a congruent, as opposed to an incongruent, odor. In other words, the participants detected a rapidly flickering apple better when they smelled an apple odor rather than a banana odor, and vice versa (Figure 1B, left panel). In effect, the presence of a congruent odor facilitated the brain’s temporal sampling of a visual object and elevated its CFF (Figure 1B, right panel). Based on electrical activities recorded from the participants’ scalp, the researchers found that the integration between smell and vision strengthened the signals of the corresponding object in a brain region heavily implicated in object representations called the right temporal cortex, about 150-300 ms after object onset. They further showed that such integration lengthened one’s subjective duration of the corresponding object in a duration comparison task. The researchers concluded that subjective time is warped by the neural energy involved in representing multisensory inputs at subsecond scales.

Until Philip C. Ball mentioned that Nick Lane believed proton gradients came before the energy-dependent creation of RNA, I did not realize how little they knew about this link from differences in the energy of photons to consciousness.
See: What Affective Neuroscience Means for Science Of Consciousness (2013)

The coupling of the two circuits promotes an endogenous feedback that supports conscious processes. Within this framework, we present the defence that detailed study of both affective and cognitive processes, their interactions, as well of their respective brain networks, is necessary for a science of consciousness.

The coupling of the two circuits links differences in the energy of photons from the proton motive force to the light-activated endogenous feedback loops and Feedback loops link odor and pheromone signaling with reproduction.
It is extremely difficult for intelligent people to not link this experimental evidence to biophysically constrained viral latency in the context of reports that claim “Creatures’ Adaptability Begins with Their Sensors.”
But, see for comparison: David Attenborough on creationsim May, 2015

My comment on his nonsense: First steps to neutralizing Zika: How highly potent antibody neutralizes Zika infection discovered

This is framed within the context of energy-dependent changes in pH, which facilitate receptor-mediated entry of nutrients or viruses into specific cell types of species-specific tissues via stress-linked changes in hydrogen-atom transfer in DNA base pairs.

Virus-driven energy theft has been linked to all pathology in all living genera via the conserved molecular mechanisms of RNA-mediated polycombic protein folding chemistry compared to the hecatombic evolution of pathology manifested first in the differences between archaea and bacteria. Admitting that Carl Woese was wrong about the different domains of life is the first step towards understanding the difference between healthy longevity and the evolution of all virus-driven pathology.

Carl Woese was wrong

God did not create the viruses. He created the anti-entropic virucidal energy of sunlight, which protects all organized genomes from virus-driven entropy. Only the choices of our ancestors could have led to the increasing amout of virus-driven pathology during the past ~6000 years that pseudoscientists place into the context of millions of years of evolution. Then, they blame God, like these two pseudoscientists do. Darwin knew they would do that, which is why he insisted that others put conditions of life before natural selection. But they bastardized his theory anyway and taught their revision to anyone who was foolish enough to believe in it. It’s called the “Modern Synthesis” and was based on de Vries 1902 definition of “mutation.”

Celebrate Your Inner Virus

It is important that we understand the design present in viruses because God made them.

It is no wonder that Sir David Attenborough and many others like Philip C. Ball and Nick Lane are confused about the energy-dependent creation of healthy longevity and consciousness. Even some young earth creationists have failed to link the creation of the sun’s anti-entropic virucidal energy from changes in electrons to ecosystems via the proton motive force. That leaves every aspect of creation to be placed back into the context of ridiculous theories. The theories start with the virus-driven theft of quantized energy as information. The energy theft links mutations to all virus-driven pathology. The theft of quantized energy as information cannot be linked by serious scientists from beneficial mutations to the evolution of one species from another.
For comparison, pseudoscientists have no problem touting this confusing nonsense:
Sign of selection on mutation rate modifiers depends on population size (
1)  Genetic variation—the raw material for evolution—is ultimately generated by mutation.
2). …beneficial alleles never become deleterious and deleterious alleles never become beneficial.
Conclusion:

Whether these phenomena can be united in a single theoretical framework remains an open question that we are actively exploring. In any case, our results add to a growing appreciation of nonclassical population size dependence in evolution by natural selection (41, 42).

Funding for research that attempts to link natural selection to evolution via mutation-driven genetic variation should be used to link food odors and pheromones from the physiology of reproduction to biophysically constrained viral latency and ecological adaptations. It is time to stop creating more biologically uninformed theorists.

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

A null mutation and healthy longevity?

Summary: Food odors and pheromones biophysically constrain all pathology in species from microbes to humans. What kind of biologically uninformed science idiot leaves out everything known to serious scientists about the virus-driven degradation of messenger RNA and tells others they must falsify the neutral null theory that led to claims about a biophysically constrained beneficial “null mutation” in the Amish population of Berne, Indiana?
Glutamylation Regulates Transport, Specializes Function, and Sculpts the Structure of Cilia
Reported as: How to Control Traffic on Cellular Highways

Intracellular and extracellular traffic control

Reported in: How to control traffic on cellular highways http://neurosciencenews.com/enzyme-transportation-7915/

See for comparison: A null mutation in SERPINE1 protects against biological aging in humans
Reported as: Amish gene can make them live 10 years longer and avoid diabetes

A gene variant that arose decades ago in an Amish group…

All gene variants are quantized energy-dependent and the pheromone-controlled physiology of reproduction protects all organized genomes from the virus-driven degradation of messenger RNA. The degradation of messenger RNA links mutations to all pathology. Any claim that “a gene variant arose” is a claim made by a biologically uninformed science idiot. Gene variants in humans are biophysically constrained by the availability of food energy. Other humans may not know that.
Watch and listen to Richard P. Feynman presciently claim that the “null mutation” theory of healthy longevity is an example of “human idiocy.”

Help others to find any experimental evidence that suggests a “null mutation” can be beneficial and/or protect them from biological aging. See for alternative representations of biologically-based facts: Best matches for “null mutation“: and others.
If you cannot find experimental evidence of a beneficial “null mutation” see: Consciousness in the universe: A review of the ‘Orch OR’ theory They inadvertently linked quantum physics from consciousness to quantum souls.
Reported as: Anesthesia Points to Deeper Level ‘Quantum Channels’ as Origins of Consciousness subtitle “Electron resonance pervades the brain”

“Using molecular modeling, the US-Canadian team of Travis Craddock, Stuart Hameroff and Jack Tuszynski had previously shown anesthetic binding in ‘quantum channels’, non-polar arrays of amino acid pi resonance clouds, winding through microtubules.”

See also: The vibrational theory of olfaction for the win

The same kinds of amino acid substitutions that control the separations and interactions of side chains in fluorescent proteins also play an essential role in tuning the proposed mechanism for vibration detection—inelastic electron tunneling. Life literally runs on electron tunneling through the respiratory chain complexes in mitochondria.

For comparison, see the conclusion to: Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 2
Beneficial “null mutations” can now be placed into the context of the creation of a universe that — with or without us — is always watching, like Santa Claus.
For a historical perspective on that pseudoscientific nonsense, see:
Splendor and misery of adaptation, or the importance of neutral null for understanding evolution

To claim adaptation, the neutral null has to be falsified.

A universal trend of amino acid gain and loss in protein evolution

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

The 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… — Eugene Koonin
What kind of biologically uninformed science idiot leaves out everything known to serious scientists about the virus-driven degradation of messenger RNA and tells others they must falsify the neutral null theory that led to claims about a biophysically constrained beneficial “null mutation” in the Amish population of Berne, Indiana?
Food odors and pheromones biophysically constrain all pathology in species from microbes to humans.
See for comparison: Chemosignals from isolated females have antimutagenic effect in dividing the cells of bone marrow from male mice of the CBA strain

…specific, volatile, and zoosocial important chemosignals are a promising approach both to modeling posttraumatic stress disorders in humans [36] and to searching for mehods of their treatment.

Humans also have various pheromone-induced physiological effects, especially those associated with reproduction [46, 47]. This suggests that the human olfactory system is still an effective pathway for influencing environmental factors on the human nervous
system.

[46] is Kohl, J.V., Atzmueller, M., Fink, B., and Grammer, K., Human pheromones: integrating neuroendocrinology and ethology, Neuroendocrinol. Lett., 2001, vol. 22, pp. 309–321.
See also: Cytogenetic approaches for determining ecological stress in aquatic and terrestrial biosystems

The assessment of genomes’ integrity plays the key role in the studies of mutagenicity in a polluted environment. We present a step-by-step recommendations for the analysis of the cytogenetic data and discuss the prospects of applying genetic tests for ecological monitoring, based on the example of analysis using crustacean species.

I suspect that the manufacturer of my human pheromone-enhanced fragrance products asked to speak with me next week due to the all-to-obvious link from human pheromones to biophysically constrained viral latency and the prevention of all pathology, which was detailed in the context of the creation of sunlight, which was subsequently linked from the creation of ATP to the creation of RNA.
Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis
The last time I spoke with him, he asked how to monetize the facts. Bergdhal’s pathology may have prompted renewed interest. Attempts to discuss that fact with other veterans have failed. I think that some of them would rather see him crucified rather than link the energy-dependent weekend resurrection of the bacterial flagellum in P. fluorescens to the the energy-dependent Resurrection of Christ.
Bergdhal’s pathology can also be placed into the context of the problematic transitions from adolescence to adulthood that are altered by fixation of one energy-dependent RNA-mediated amino acid substitution.
See: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
The A or Met allele is associated with lower enzymatic activity and the polymorphism is associated with many different personality traits. The USAF is leading the way forward towards effective treatment of mental disorders in veterans, which is something the psychiatrists who evaluated Bergdhal know about.  See for instance: US Air Force Studying Impact of Exome Sequencing in Routine Care
 

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.

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?
 

rp_levels-of-organization.jpg

Light ‘drives’ adaptation; nothing ‘drives’ evolution (2)

See: Light ‘drives’ adaptation; nothing ‘drives’ evolution

See also: Who rules the waves? – Viruses might just be bit players in the drama of the seas. Then again, they could be major actors

Excerpt (from 1996): 

Most consider viruses to be a legion of cripples, sterilised by ultraviolet radiation and rendered impotent by hosts that are largely immune to their threat. But a few researchers take the opposite view. And if they turn out to be right, viruses could radically alter the balance of life in the oceans, ripping away huge parts of the food web that supports whales, sea birds and the fisheries on which many people rely.

See also: Riding the Evolution Paradigm Shift With Eugene Koonin

Excerpt: 

This is a good point to make. 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…

From 1996: From Fertilization to Adult Sexual Behavior

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

Forthcoming, two decades later: New trends in evolutionary biology: biological, philosophical and social science perspectives
Excerpt:

Developments in evolutionary biology and adjacent fields have produced calls for revision of the standard theory of evolution…

My comment: Topics mentioned in the abstracts (my categories):

Science

The physics of organisms

multilevel and reciprocal causation

adaptability could influence the inherited characteristics of an organism’s descendants
phenotypic traits have complementary rather than antagonistic functions
‘second inheritance system’, built on the shoulders of the primary genetic inheritance system
adaptive design at the level of genes, individuals and societies
…niche construction co-directs adaptive evolution
integrated symbioses
‘developmental niche construction’ as a framework to integrate findings from fields ranging from molecular biology to developmental psychology
epigenetic inheritance
the involvement of epigenetic inheritance in adaptive evolutionary change
inherited yet non-genetic adaptation.
somatic inheritance, maternal effects and DNA methylation.
processes that sustain persisting lineages.
understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations

Pseudoscientific nonsense

a distinction between epigenetic and exogenetic inheritance

different narratives as to exactly what such an evolutionary approach entails.
how different mechanisms of inheritance contributes to evolution.
understanding of how important the process has been in shaping the evolution of animal form.
a closely allied distinction between ‘organic’ and ‘cultural’ evolution?
domestication to serve once again as a model system
‘human like’ modes of behaviour (and presumably more biocultural evolution)

See for comparison to everything currently known to serious scientists about biophysically constrained energy-dependent RNA-mediated protein folding chemistry.

A niche for the genome

Excerpt:

…the study of phenotypic plasticity, epigenetic and exogenetic inheritance, have not yet demonstrated the need for any revolutionary change in evolutionary thought. For us they highlight the extent to which proximate developmental mechanisms can inform ultimate biology.

My comment: Twenty years after our review of energy-dependent RNA-mediated molecular epigenetics and cell type differentiation, this exemplifies the overwhelming foolishness of theorists who seem to think that not all developmental mechanisms are energy-dependent and biophysically constrained by the physiology of reproduction.

See also the discussion attempt at: What does DNA have to do with the Origin of Life ?

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Hecatombic evolution VS polycombic ecological adaptation

Hecatombic evolution can be compared to polycombic ecological adaptation in the context of facts that do not support the Demoncrat’s agenda.

Demoncrat: A biologically uninformed politician acting on behalf of ignorance to promote virus-driven pathology as a source of all biodiversity.

Alt: “A member of the Democratic Party (with a demonic implication).”

How many people think that this report of what Dr. Ben Carson said is an accurate representation of what he said? Is “ugly surrogacy” suggestive of biased reporting?

Ben Carson Said It Doesn’t Matter Whether or Not Donald Trump Committed Sexual Assault

My comment: I remember when biologically uninformed science idiots claimed that Dr. Ben Carson was a fool to believe in young earth creationism. Since then, the idiots have invented hecatombic evolution as a replacement for the Modern Synthesis, because no serious scientist has ever believed in the pseudoscientific nonsense of neo-Darwinian theory.

Daniel Orloski wrote: No one is listening James · 46 mins

My comment: People seem to underestimate the intelligence of those who are not Demoncrats. They have been listening for many years. Republicans intuitively know the difference between hecatombic evolution and polycombic ecological adaptation and so do all young earth creationists.
All are listening but they can’t explain the difference between what theorists claim happens during millions of years of hecatombic evolution and what serious scientists have shown happens in 6000 years of nutrient-dependent pheromone-controlled RNA-mediated polycombic ecological adaptation.
See: From Fertilization to Adult Sexual Behavior

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

I reiterate: Small DNA-binding chromo domain proteins are called polycomb in the context of the polycomb repressive complex. These proteins alter chromatin structure in the context of energy-dependent effects on the transcription and silencing of various genes. The polycomb repressive complex links energy to polycombic ecological adaptation. Virus-driven energy theft links hectombic “evolution” to all pathology.
What’s worst is that the theorists explain millions of years of evolution and weekend evolution of the bacterial flagellum with the same ridiculous theories that were invented in the first part of the 20th century

See for example: Biologists Use Genomics to Identify Evolving New Bird Species in Southern Idaho
Excerpt:

This may be a fleeting instance of coevolution influencing speciation, but we have observed enough of it to see that it can happen and may happen in other similar situations.

Excerpt:

The birds counter-evolved against those defenses as evolution favored deeper-beaked crossbills, resulting in a coevolutionary arms race that has driven evolutionary divergence of this unique bird population.

My comment: All serious scientists who have linked the claims of Thomas Hunt Morgan about chromosomal rearrangements to the claims of Yoshinori Ohsumi via nutrient energy-dependent biophysically constrained RNA-mediated protein folding and the physiology of reproduction in species from microbes to humans, will enjoy this recent misrepresentation of everything known about supercoiled DNA and biodiversity that arose during the past 6000 years.

See also: Genome divergence and diversification within a geographic mosaic of coevolution
Excerpt:

…clear examples of reciprocal selection and adaptation driving speciation (the link between coevolution as a micro- and macroevolutionary process) are largely lacking (Althoff et al. 2014; Hembry et al. 2014).

My comments: All clear examples of biophysically constrained RNA-mediated cell type differentiation which are clearly linked from the physiology of reproduction to all biodiversity are ignored in statements like the one above.
See for comparison: Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes
Excerpt:

Thus, our results illustrate a detailed chain of events linking a chromosomal rearrangement to changes in overt social behavior.

The chain of events they detailed links the Nobel Prize Winning works of serious scientists from representations of how chromosomal rearrangements are linked to all biodiversity (1933) to how the energy-dependent creation of amino acids  links nutrient-dependent pheromone-controlled physiology of reproduction (2004) to autophagy (2016). Look at the reports of the works presented by the Nobel Laureates in Physiology or Medicine and help serious scientists stop the killing spree of biologically uninformed politicians.

Alternative splicing of pre-mRNA

DNA repair via junk DNA (2)

See also: DNA repair via junk DNA (1)

Recently Evolved Genes Identified From Drosophila yakuba and D. erecta Accessory Gland Expressed Sequence Tags (2006)

Reported in Singer (2015) as:

In 2006, Begun found some of the first evidence that genes could indeed pop into existence from noncoding DNA.

Singer’s claim that genes automagically pop into existence is consistent with Masatoshi Nei’s conclusion in: Mutation-Driven Evolution

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements. (p. 199)

See also: Viral Proteins Originated De Novo by Overprinting Can Be Identified by Codon Usage: Application to the “Gene Nursery” of Deltaretroviruses

Diethard Tautz suggested that this representation was a “…fact that is often used as additional evidence for the power of de novo evolution.” Apparently, Tautz believes that the magic of gene evolution in viruses can be linked to his claims about the magic of evolution in Evolution: Dynamics of De Novo Gene Emergence

See my August 20, 2015 comment on Singer (2015):

Re: Viruses are certainly not ignored, but can be excluded in most cases.

In a recent interview, Eugene Koonin made the opposite claim. See: http://www.huffingtonpost.com/suzan-mazur/riding-the-evolution-paradigm-shift-with-eugene-koonin_b_7217216.html

Excerpt: “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…”

Begun is the senior author of: Origin and Spread of de Novo Genes in Drosophila melanogaster Populations (2014)

Conclusion:

…important details of such processes remain obscure and much additional work is required to clarify the dynamics, biochemical and genetic properties, and phenotypic effects of young de novo genes and the processes underlying gene loss in natural populations.

The works by Begun, Tautz, and others who have claimed that the de novo origin of genes that pop into existence can lead to evolution were reported by Carl Zimmer in The Continuing Evolution of Genes

Excerpt:

As genes duplicate over millions of years, they can grow into so-called gene families, each containing hundreds of similar genes.

One family, for example, is essential for our sense of smell. These genes encode 390 different kinds of proteins produced in our noses, called olfactory receptors. Each olfactory receptor has a slightly different structure, allowing it to capture a different set of molecules.

My comment: Gene duplication is energy-dependent. The energy-dependent de novo creation of olfactory receptor genes links hydrogen-atom transfer in DNA base pairs in solution from changes in the microRNA/messenger RNA balance to alternative RNA splicings that link natural selection for energy-dependent codon usage from the innate immune system to supercoiled DNA via the physiology of reproduction in all living genera.

Why have some science journalists continued to place the pseudoscientific nonsense touted by theorists into the context of emergence and evolution?  Do they ever wonder how gene duplication occurs in the absence of nutrient-energy dependent changes in organized genomes, or where the organized genomes came from?

See also: Combinatorial epigenetics, “junk DNA”, and the evolution of complex organisms (2007)

Inheritable epigenetic changes (“epimutations”) with effects at a distance would then perdure over the number of generations required for “assimilation” of the several regulatory novelties through the occurrence and selection, gene by gene, of specific classical mutations. These mutations would have effects similar to the epigenetic effects, yet would provide stability and penetrance. The described epigenetic/genetic partnership may well at times have opened the way toward certain complex new functions. Thus, the presence of “junk DNA”, through co-determining the (higher or lower) order and the variants of chromatin structure with regulatory effects at a distance, might make an important contribution to the evolution of complex organisms.

See for comparison:  ENCODE Project Writes Eulogy for Junk DNA September 7, 2012.
See also The Case for Junk DNA (2014) reported by Carl Zimmer
Excerpt:

Even if ninety percent of the genome does prove to be junk, that doesn’t mean the junk hasn’t played a role in our evolution. As I wrote last week in the New York Times, it’s from these non-coding regions that many new protein-coding genes evolve. What’s more, much of our genome is made up of viruses, and every now and then evolution has, in effect, harnessed those viral genes to carry out a job for our own bodies. The junk is a part of us, and it, too, helps to make us what we are.

*I mean functional in terms of its sequence. The DNA might still do something important structurally–helping the molecule bend in a particular way, for example.

[Update: Fixed caption. Tweaked the last paragraph to clarify that it’s not a case of teleology.]

Look again at Singer (2015) A Surprise Source of Life’s Code: Emerging data suggests the seemingly impossible — that mysterious new genes arise from “junk” DNA (2015)

“How does novel gene become functional? How does it get incorporated into actual cellular processes?” McLysaght said. “To me, that’s the most important question at the moment.”

My comment: Claims that genes pop into existence do not address how the genes are created or how they are incorporated into actual cellular processes. There is only one way for incorporation into cellular processes to occur. The innate immune system must link RNA-mediated cell type differentiation from amino acid substitutions to supercoiled DNA via the nutrient energy-dependent creation of G protein-coupled receptors that link receptor-mediated behavior from natural selection for codon optimality to supercoiled DNA. The supercoiled DNA is the link from non-coding DNA to the epigenetically-effected organized genomes of all living genera.
See for instance:
Junk DNA: A Journey Through the Dark Matter of the Genome (2015) reviewed by Casey Luskin in New Book on “Junk DNA” Surveys the Functions of Non-Coding DNA

The bits of gobbledygook between the parts of a gene that code for amino acids were originally considered to be nothing but nonsense or rubbish. They were referred to as junk or garbage DNA, and pretty much dismissed as irrelevant. … But we now know that they can have a very big impact. (pp. 17-18)

The impact of the amino acids links everything known about molecular epigenetics to RNA-mediated DNA repair. The epigenetically-effected RNA-mediated amino acid substitutions in organized genomes must link the initiation of DNA repair to the maintenance of organized genomes throughout the life history transitions of all living genera. Simply put, the energy-dependent RNA-mediated amino acid substitutions are linked to healthy longevity.
Codon optimality controls differential mRNA translation during amino acid starvation

Our data reveal a previously unappreciated mechanism underlying cellular adaptation to amino acid shortage at the level of mRNA translation.

A chemical-inducible CRISPR-Cas9 system for rapid control of genome editing

For spatial control, one may apply photocaged tamoxifen or 4-HT and use ultraviolet light to target a subset of cells within a mixed population34. Hence, our ERT2-based iCas technology expands the toolkit for precise genome engineering in mammalian cells.

ADAR-Mediated RNA Editing Predicts Progression and Prognosis of Gastric Cancer
Abstract:

Gastric cancer (GC) is the third leading cause of global cancer mortality. Adenosine-to-inosine RNA editing is a recently described novel epigenetic mechanism involving sequence alterations at the RNA but not DNA level, primarily mediated by ADAR (adenosine deaminase that act on RNA) enzymes. Emerging evidence suggests a role for RNA editing and ADARs in cancer, however, the relationship between RNA editing and GC development and progression remains unknown.

My comment: ADAR is Adenosine-to-inosine RNA editing. They fooled you, didn’t they? If you did not think it was something new, you probably are a serious scientist, or more biologically informed than any theorist.
L1-associated genomic regions are deleted in somatic cells of the healthy human brain
My comment: They cite Needleman, S.B. & Wunsch, C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443–453 (1970).
A Fear of Pheromones (1971)

What on earth would we be doing with such things? With the richness of speech, and all our new devices for communication, why would we want to release odors into the air to convey information about anything?

On Smell (1980)

I should think we might fairly gauge the future of biological science, centuries ahead by estimating the time it will take to reach a complete comprehensive understanding of odor. It may not seem a profound enough problem to dominate all the life sciences, but it contains, piece by piece, all the mysteries (p. 732).

— Lewis Thomas as cited in The Scent of Eros: Mysteries of Odor in Human Sexuality (1995/2002)

 

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Neuroplasticity

Can You Think Yourself Into a Different Person?

Excerpt 1)

Those who over-evangelise emerging disciplines like neuroplasticity or epigenetics can sometimes be guilty of talking as if the influence of our genes no longer matters.

Excerpt 2)

Of course, it’s our malleable brains that have moulded themselves to these rhythms.

See also: Nature and nurture: Human brains evolved to be more responsive to environmental influences
See for comparison: Mae-Wan Ho: No Boundary Really Between Genetic and Epigenetic
My comment: Everything known to serious scientists about RNA-mediated cell type differentiation links atoms to ecosystems in the context of biophysically constrained nutrient-dependent protein folding chemistry linked to supercoiled DNA, which protects organized genomes from virus-driven entropy.
Nothing known to serious scientists suggests our brains have moulded themselves. Only pseudoscientists continue to report neuroplasticity as if it automagically evolved to link the epigenetic landscape to the physical landscape of DNA via epigenetically-effected metabolic networks and metabolic networks.
The networks link the orgins of the nervous system in nematodes from ecological variation to ecological adaptation in primates via the conserved molecular mechanisms that link nutrient-dependent microRNAs in flies to behavior, which is linked from RNA-directed DNA methylation to receptor-mediated cell type differentiation and to behavior via energy-dependent base pair changes and amino acid substitutions that differentiate all cell types in all individuals of all living genera.
What is known about neuroplasticity to serious scientists links single amino acid substitutions from nutritional epigenetics to pharmacogenomics in the context of the Precision Medicine Initiative, which attests to the foolishness of neo-Darwinian theories. Watch as those who believe in pseudoscientific nonsense continue to try to make others believe in it — until finally everyone learns how ridiculous the “Modern Synthesis” actually is, and how outdated it has become.
See also: Researchers sequence genomes of parasite that is actually a ‘micro jellyfish’
Excerpt: 

…a diverse group of microscopic parasites that infect invertebrate and vertebrate hosts, are actually “highly reduced” cnidarians — the phylum that includes jellyfish, corals and sea anemones.

My comment: Genome sequencing of the octopus genome has already linked microRNAs to cell adhesion proteins via what is known about how supercoiled DNA protects organized genomes from virus-driven genomic entropy.
See: The octopus genome and the evolution of cephalopod neural and morphological novelties
Excerpt: Taken together, these novel genes, the expansion of C2H2 ZNFs, genome rearrangements, and extensive transposable element activity yield a new landscape for both trans- and cis-regulatory elements in the octopus genome, resulting in changes in an otherwise ‘typical’ lophotrochozoan gene complement that contributed to the evolution of cephalopod neural complexity and morphological innovations.
My comment: Everything they claim is linked to evolution of neural complexity and morphological innovations is linked from virus-driven genomic entropy to pathology via mutations. It is linked from nutrient-dependent supercoiled DNA to healthy longevity.
There is no new mechanism of cell type differentiation. Protection against virus-induced genomic entropy in all cell types of all individuals is nutrient-dependent. Protection of all cell types is controlled by the physiology of reproduction in all living genera.
Claims of a new mechanism tell other pseudoscientists that they never learned anything important about how cell type differentiation occurs. It occurs in the context of an atoms to ecosystems model of epigenetically effected biophysically constrained RNA-mediated protein folding chemistry. Protein folding chemistry explains how metabolic networks and genetic networks link RNA-mediated events to supercoiled DNA to healthy longevity. Perturbed protein folding chemistry links viruses to all pathology.
See:

See also: Repairing Neurons With Light
Excerpt:

… our results show for the first time how the repair of a complex neural circuit in a whole animal can be promoted remotely by the use of light

My comment: The virucidal properties of UV light have been virtually ignored since the time that Schrodinger first linked them to cell type differentiation in all living genera. Pseudoscientists decided to continue linking beneficial mutations to evolution via natural selection even after Schrodinger exposed their fraud in “What is Life.”
Excerpt: Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight)
The fraud that Schrodinger exposed more than 70 years ago is still accepted as mainstream science by all pseudoscientists. A textbook example of the fraud is the conclusion from Mutation-Driven Evolution.
Conclusion:

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements (p. 199).

In the real world of biologically-based cause and effect, serious scientists link atom to ecosystems via the sun’s biological energy and RNA-mediated cell type differentiation.
See also: Scientists discover new mechanism that protects brain stem cells against aging-induced damage
Excerpt:

This is an exciting new mechanism involved in stem cell division and aging. But as of now we are only just beginning to understand the molecular constituents and the true meaning of the barrier for stem cell division in the brain. One key question to be answered is whether the barrier is established in all somatic stem cells of the body.

My comment: There is no new mechanism of cell type differentiation. Protection against virus-induced genomic entropy in all cell types of all individuals is nutrient-dependent. Protection of all cell types is controlled by the physiology of reproduction in all living genera.
Claims of a new mechanism tell other pseudoscientists that they never learned anything important about how cell type differentiation occurs. It occurs in the context of an atoms to ecosystems model of epigenetically effected biophysically constrained RNA-mediated protein folding chemistry. Protein folding chemistry explains how metabolic networks and genetic networks link RNA-mediated events to supercoiled DNA to healthy longevity. Perturbed protein folding chemistry links viruses to all pathology.
See also: Theorists can’t understand biology

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Do young neurons in the brain evolve?

Brain Gain

Young neurons in the adult human brain are likely critical to its function.

By Jef Akst | October 1, 2015

Excerpt

“The rate at which [new neurons] incorporate is dependent upon experience,” Gage says.

My comment: The experience-dependent de novo creation of olfactory receptor genes is the basis for the following representation of biologically-based cause and effect:
Feedback loops link odor and pheromone signaling with reproduction
Virus-perturbed nutrient-dependent RNA-mediated protein folding biochemistry is the clearest link from nutrient-stress and social stress to brain pathology and other pathology. The pathology is linked to viral microRNAs that steal the energy provided by nutrient-dependent microRNAs, which is essential for RNA-mediated DNA repair during the life history transitions of all living genera.
Neo-Darwinian theorists tend not to comment on that fact. Perhaps the problem is Eugene Koonin’s admission that:  “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…”