5th-6th Sept 2018 Dublin, Ireland

Nick Lane refutes theistic evolution (1)

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

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

The link from differences in the energy of photons to the amount of ATP that must be be biophysically constrained has been largely ignored since the time that McEwen et al., (1964) linked the creation of ATP to the creation of RNA via oxidative phosphorylation.
Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

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

The difference in two photons have been linked to the Proton motive force. It drives the activity of the enzyme, ATP synthase, which makes ATP. All energy-dependent biophysically constrained viral latency has since been linked from the creation of ATP synthase and the creaton of ATP to changes in the microRNA/messenger RNA balance and healthy longevity. For comparison, the virus-driven degradation of messenger RNA has been linked to all pathology.
See for instance this 6-7 minute-long video: Energy as information and constrained endogenous RNA interference (February 15, 2017)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

5th-6th Sept 2018 Dublin, Ireland

Anti-entropic sunlight: Schrödinger’s Creationist Secret? (5)

Anti-entropic sunlight: Schrödinger’s Creationist Secret? (3)


The list of those scheduled to present has changed. Michael Rosbash has been added. John E. Walker is not scheduled, which suggests that everyone else already knows that the creation of the sun’s anti-entropic virucidal energy is the link from the creation of ATP to the creation of RNA and all biophysically constrained viral latency via feedback loops and the physiology of reproduction.
Rosbash, as all serious scientists know,  started with energy-dependent changes in cycles of RNA biosynthesis. Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels (1990). Pseudoscientists failed to link the energy from feedback to biophysically constrained viral latency.
But see: Permeability transition in human mitochondria persists in the absence of peripheral stalk subunits of ATP synthase

Production of ATP depends on the oxidation of energy-rich compounds to produce a chemical potential difference for hydrogen ions, the proton motive force (pmf), across the inner mitochondrial membrane (IMM).

Other serious scientists have consistently linked photophosphorylation from oxidative phosphorylation to all biodiversity via the physiology of pheromone-controlled reproduction in species from soil bacteria to humans
Speakers (new copy-protected list)
Speakers (old list)
See also: Viral Resistance Project
The differences in innate immunity and ecological adaptation are obviously nutrient energy-dependent and transgenerationally inherited in the context of the epigenetically-effected physiology of pheromone-controlled reproduction and the affects of hormones on behavior. For instance, pheromones biophysically constrain viral latency via the fixation of amino acid substitutions.
See for comparison: Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses
There are several neo-Darwinian theorists who are scheduled to present, which means they may be ready to accept the ridicule from serious scientists.
See for example: 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.

See also: Why I got rid of my friends
Some of my former friends kept dumping their garbage about evolution on others in the same way that I. King Jordan and Eugene Koonin did it with their comment about the evolution of the amino acid composition of proteins. See for comparison: All About that Base (Meghan Trainor Parody) 12/10/14 and Energy as information and constrained endogenous RNA interference 2/15/17
Help others who are Combating Evolution to Fight Disease

Redox sensing controls DNA replication!

Observing energy-dependent intelligence and human idiocy

Conclusion: “Absolutely no information is provided about the sensory systems that enabled predators to detect their single-celled prey. No explanation is offered of how the sensory systems came into being that permitted single-celled organisms to detect their enemies’ scents and thus survive. Neither are we told what “evolutionary” mechanisms entered the equation during the construction of this extraordinarily complex mechanism.”

Seeing the Beautiful Intelligence of Microbes

…slime molds have evolved a system for essentially mapping their terrain and memorizing where not to go…

The weekend resurrection of the bacterial flagellum in P. fluorescens showed that energy as information is the source of intelligence. For example, the quantized energy from sunlight links the physiology of pheromone-controlled reproduction from two food energy-dependent RNA-mediated amino acid substitutions to the ability of the fluorescent organism to move and find more food.
See: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Foraging behavior is important to all organisms and so is the biophysically constrained quantized virucidal energy of sunlight. Without the energy-dependent ability to find more food, the virus-driven activation of a death gene awaits. But, eventually, organisms must find the “right” food source, to prevent the unnecessary suffering and/or premature death of people like John McCain.
See for example: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene
The phylogenetic utility and functional constraint of microRNA flanking sequences links energy-dependent base editing from microRNA editing to RNA editing and the pheromone-controlled fixation of RNA-mediated amino acid substitutions in the organized genomes of all living genera. Autophagy is the term used to link the quantized energy-dependent activation of endogenous substrates in all cell types from the creation of enzymes to the function of the innate immune system, which prevents the virus-driven degradation of messenger RNA.
The alternative to the energy-dependent error-free polycombic de novo creation of replacement RNA and healthy longevity is the hecatombic evolution of pathology.
See: Virus-mediated archaeal hecatomb in the deep seafloor

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

The virus-driven degradation of messenger RNA in bacteria is linked to the creation of archaea and L-forms. Similarly, it links the virus-driven degradation of messenger RNA in humans to the creation of non-human primates via one amino acid.

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

For comparison to the ridiculous opposite scenario, see: 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.

See also: A null mutation in SERPINE1 protects against biological aging in humans
Reported as: Genetic mutation in extended Amish family in Indiana protects against aging and increases longevity (Update)

“The findings astonished us because of the consistency of the anti-aging benefits across multiple body systems,” said Dr. Douglas Vaughan, the lead author of the paper who has been studying PAI-1 for almost 30 years.

During the past 30 years, all serious scientists have learned how important it is to link the sun’s anti-entropic virucidal energy from the physiology of reproduction in bacteria to fixation of RNA-mediated amino acid substitutions in organized genomes via the physiology of pheromone-controlled reproduction. The astonishing claim(s) of Eugene Koonin and others like him attest to facts about why others are astonished. Pseudoscientists are astonished by the the fact that serious scientists have linked what organisms eat to protection from the virus-driven degradation of messenger RNA.

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 (2015)

See for comparison: Splendor and misery of adaptation, or the importance of neutral null for understanding evolution

The proper question is: how has this sequence evolved? And the proper null hypothesis posits that it is a result of neutral evolution: that is, it survives by sheer chance provided that it is not deleterious enough to be efficiently purged by purifying selection. To claim adaptation, the neutral null has to be falsified.

Energy-dependent sequences do not evolve. That fact has not been considered by biologically uninformed science idiots. That is why they continue to insist that serious scientists falsify the statistical “neutral null,” which is an example of human idiocy.

If you ask an intelligent person like the late Richard P. Feynman where the energy comes from that supports the representation below, you are probably not an example of human idiocy.
———————————-
High magnification of the slime mold Physarum polycephalum shows the cytoplasm pumping furiously through its huge single cell (left). This cytoplasmic streaming allows the slime mold to push forward toward nutrients and potentially carpet a surface (right).

Credit to the open access source: Seeing the Beautiful Intelligence of Microbes
See also: Neuroscience research provides evidence the brain is strobing, not constant

3. oscillations are a general feature of perception, not specific to vision.

“This strobing approach to attention would bind together relevant information at regular time points and allow new groupings of information to reassemble at other moments.”

See also: Celebrate Your Inner Virus

See for comparison: Evolutionists Cannot Account for the Origin of the Sense of Smell

…what Caprio, an evolutionist researcher, wants to say is that single-celled organisms unknowingly released chemical substances; that predators detected these and hunted them. In addition to being exceptionally illogical, his conjecture fails to answer how the sense of smell came into existence. Absolutely no information is provided about the sensory systems that enabled predators to detect their single-celled prey. No explanation is offered of how the sensory systems came into being that permitted single-celled organisms to detect their enemies’ scents and thus survive. Neither are we told what “evolutionary” mechanisms entered the equation during the construction of this extraordinarily complex mechanism.

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

Dobzhansky 1973 and precision medicine (3)

Dobzhansky 1973 and precision medicine
Dobzhansky 1973 and Precision Medicine (2)
How Do Bacteria Help Cancer

Studying bacterial effects on cancer are very complex, because there is no one clear mechanism

Jon LIeff has again obfuscated the clarity of facts about energy-dependent conserved molecular mechanisms. These are the facts:
1) Closed feedback loops link nutrient energy-dependent pheromone-controlled quorum sensing in bacteria to supercoiled DNA in all living genera.
2) Virus-driven energy theft causes the degradation of messenger RNA in bacteria that is manifested in the morphology and behavior of so-called archaea.
3) Archaea are bacteria with less supercoiling in their DNA. (For comparison to bacteria the so-called archaea are less well-adapted. They must struggle harder to avoid extinction.)
4) Negative supercoiling in the organaized genomes of bacteria has been linked to communication among viruses.
5) Viral signaling pits energy theft against the nutrient energy- dependent signaling that links quorum sensing from ecological variation to ecological adaption in all cell types of all individuals of all species on Earth.
Healthy longevity is linked from the nutrient-dependent pheromone-controlled physiology of reproduction in bacteria to supercoiled DNA, which prevents the transgenerational epigenetic inheritance of Zika virus-damaged DNA.
To his credit, this is the first time I have seen Jon Lieff attempt to distance himself from ridiculous theories about evolution.
He concludes:

All of these interactions are based on the natural communications between bacteria and human cells.

See also: Scientists have caught viruses talking to each other—and that could be the key to a new age of anti-viral drugs

…Sorek reports in the journal Nature that his team has found the protein that viruses used to communicate. His team has called the protein arbitrium, which is Latin for “decision.”

They conclude with this ridiculous claim about viruses as a primitive life form instead of realistically linking virus-driven energy theft from mutations to all pathology.

Even though viruses are the most primitive form of life, they infect and harm millions of people every year. The possibility of tapping into viral communication has many scientists excited, because it offers new ways to build drugs that could defeat viruses.

Quorum sensing in bacteria is the nutrient energy-dependent pheromone-controlled link from the innate immune system of all living genera to the physiology of reproduction. Ecological variation must be linked to ecological adaptation via conserved molecular mechanisms of RNA-mediated protein folding chemistry in the context of the physiology of reproduction. If the physiology of reproduction is not biophysically constrained by the availability of nutrients, you are left with a ridiculous theory about mutation-driven evolution.
See also: Alternative RNA Splicing in Evolution (2012)
On 10/27/13 Jon Lieff wrote:

I very much appreciate your comments on pheromone communication and its rapid and critical link to the olfactory brain. I look forward to any current references and future work to help understand the immune brain connection as well as communication in general.

That comment was edited, and now appears as:

Thanks for the current article and information. I very much appreciate your important information and will try to learn more about it.

Another pertinent current article was published in May 2016
See: Spliceosomal intronogenesis
Unfortunately, Jon Lieff and many others have tried to link alternative RNA splicings to the evolution of morphological and behavioral phenotypes outside the context of the energy-dependent physiology of reproduction. Attempts to make viruses the cause of evolution are even more ridiculous, since virus-driven energy theft is the cause of all pathology.
See for comparison: Stromal cues regulate the pancreatic cancer epigenome and metabolome

…these studies raise the possibility that microenvironmental context broadly influences the epigenetic state of tissue-resident cell types under physiological and pathological conditions.

They refuse to admit that the epigenetic state is energy-dependent and RNA-mediated. They must not reveal that virus-driven energy theft is the cause of all pathology. Instread, they claim that  “…the mechanistic underpinning of this crosstalk remains poorly understood.”
See for comparison: Communication between viruses guides lysis–lysogeny decisions
Reported as: Do you speak virus? Phages caught sending chemical messages

If you had a molecule that could drive viruses into complete latency, it would be a good drug.

Viral latency is nutrient energy-dependent and it is controlled by the physiology of reproduction. There is no need for a good drug until virus-driven energy theft causes the accumulated mutations that all serious scientists have linked to all pathology. For comparison, all pseudoscientists have linked the mutations to evolution.
Pseudoscientists abandoned every aspect of nutrient energy-dependent healthy longevity and focused on drug development. For a track record of pseudoscientific nonsense, see:
Masatoshi Nei and Naruya Saitou (1986) Genetic relationship of human populations and ethnic differences in reaction to drugs and food

…variant alleles at the pseudocholinesterase locus seem to be maintained by the balance between mutation and weak selection.

Naruya Saitou, JC Stephens and Masatoshi Nei (1985) Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from humans and apes

The DNA sequence data suggested that the chimpanzee is the closest and that the gorilla is the next closest to the human species.

Naruya Saitou and Masatoshi Nei (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees

A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data.

29 years later we have:
IA Babarinde and Naruya Saitou (2016) Genomic locations of conserved noncoding sequences and their proximal protein-coding genes in mammalian expression dynamics

CNS-flanking genes were often found in evolutionarily conserved genomic neighborhoods. ChIP-Seq signal and gene expression patterns also suggested that CNSs regulate nearby genes. Interestingly, genes with more CNSs have more evolutionarily conserved expression than those with fewer CNSs. These computationally obtained results suggest that the genomic locations of CNSs are important for their regulatory functions. In fact, various kinds of evolutionary constraints may be acting to maintain the genomic locations of CNSs and protein-coding genes in mammals to ensure proper regulation.

Conserved non-coding sequences, which are typically reported as microRNA flanking sequences, are reported as CNS-flanking genes. Two decades after we reported how alternative splicings of pre-mRNA were linked from RNA-mediated cell type differentiation to biodiversity via sexual differentiation of cell type in species from yeasts to mammals, the experimental evidence forced Masatoshi Nei’s 1985 co-author to admit that the statistical evidence matches the facts. At first glance, it mght appear that Saitou and Nei never heard about virus-driven energy theft in the context of neo-Darwinian evolution. But wait, instead, they chose to ignore what they knew.
See: Naruya Saitou and Masatoshi Nei (1986) Polymorphism and evolution of influenza A virus genes
See also: Naruya Saitou and Masatoshi Nei (1986) The number of nucleotides required to determine the branching order of three species, with special reference to the human-chimpanzee-gorilla divergence

When these five different tree-making methods, as well as Fitch and Margoliash’s method, are applied to the mitochondrial DNA data (1834 bp) obtained by Brown et al. and by Hixson and Brown, they all give the same phylogenetic tree, in which human and chimpanzee are most closely related. However, the trees considered here are “gene trees,” and to obtain the correct “species tree,” sequence data for several independent loci must be used.

Simply put, they admitted that the nonsense about minimal mutational difference could not be used for comparison to the data from sequencing which now links natural selection for energy-dependent codon optimality to all biodiversity.
See also: Switching off the brain: Study implements an optogenetic tool that inhibits neural activity

In optogenetics, neurons are genetically modified to express light-sensitive ion channels (proteins that conduct electricity), such that light exposure may be used to activate or inhibit electrical activity.

The fact that femotosecond blasts of virucidal UV light have been linked from quorum-sensing in bacteria to repair of virus-driven DNA damage in species from archaea to humans, suggests the understanding of optogenetics has moved far beyond what was specific to neuronal activation.

See for example: Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein 

By varying the time between two pulses of light, serious scientists saw how the structure of the protein morphed over time. They did not extend the time to millions of years and suggest that protein evolution had occurred during that time because they are serious scientists, not pseudoscientists.

See: Dobzhansky 1973 and precision medicine (4) in prep

Physics

Origin and evolution of the genetic code

Origin and evolution of the genetic code: the universal enigma

Excerpt:

…it appears essentially certain that the evolution of the code involved some combination of frozen accident with selection for error minimization.

My comment: This claim from 2009 failed to address anything currently known to serious scientists about the Schrodinger’s claim from 1944, in What is Life?

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)

My comment: The claim from 2009 also failed to address anything currently known to serious scientists about the Dobzhansky’s claim from 1973, in Nothing in Biology Makes Any Sense Except in the Light of Evolution.
Excerpt:

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

My comment: The claim from 2009 also failed to address anything currently known to serious scientists about supercoiled DNA in the context of the Structural diversity of supercoiled DNA.
Conclusion:

Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

My comment: In the forward to What is Life?: With Mind and Matter and Autobiographical Sketches (Canto Classics) Reprint Edition by Roger Penrose, who co-authored with George F.R. Ellis and Stephen Hawking, Penrose asks:

How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?

My comment: How much longer will the serious scientists who have linked nutrient uptake to hydrogen-atom transfer in DNA base pairs allow teleophobic pseudoscientists to claim that:

…it appears essentially certain that the evolution of the code involved some combination of frozen accident with selection for error minimization.

See also: A universal trend of amino acid gain and loss in protein evolution
Excerpt:

We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.

See also:
On origin of genetic code and tRNA before translation
RNA-amino acid binding: a stereochemical era for the genetic code
Absolute binding-free energies between standard RNA/DNA nucleobases and amino-acid sidechain analogs in different environments
Cross-species conservation of complementary amino acid-ribonucleobase interactions and their potential for ribosome-free encoding
My comment: How much longer will teleophobic theorists continue to ignore everything known to serious scientists about ecological variation and nutrient-dependent ecological adaptation, which is controlled by the physiology of reproduction in all living genera?

achiral-glycine

Deeply ingrained thoughts

A universal trend of amino acid gain and loss in protein evolution
Excerpt: “We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.”
Excerpt: There is a Corrigendum (26 May 2005) associated with this document. We have since discovered that a similar scenario for protein evolution was proposed by Zuckerkandl and colleagues more than thirty years ago1.
Excerpt: There is a Brief Communications Arising (24 August 2006) associated with this document. ‘recent’ amino acids are becoming more common. They argue that this process has been going on since the genetic code first evolved to encompass all 20 amino acids. Here we provide evidence that the patterns observed conform with standard, nearly neutral theoretical expectations3 and require no new explanation.

Everything known about links from physics and the chemistry of RNA-mediated protein folding suggests that the de novo creation of light-induced amino acid substitutions leads to the differentiation of all cell types in all individuals of all genera. Obviously, it is long past time for evolutionary biologists to support their ridiculous claims with experimental evidence of biologically-based cause and effect. Let’s start with Masatoshi Nei, who concluded that: “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world” (p. 199).

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

Understanding cell type differentiation

The Wisdom of the Fly Crowds

IMG_2329-e1413855233208-958x718

Thermodynamic constraints and ecological adaptations sans evolution

Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites

Excerpt: “…a two-variable model that combines stability and stress signi ficantly improves predictions. Therefore, both the overall stability [symbol] and the stress [symbol] seem to capture distinct thermodynamic constraints on protein evolution.”
My comment: Proteins do not evolve. Nutrients are required. Metabolism of nutrients to species-specific pheromones controls the physiology of reproduction in species from microbes to man. The nutrient-dependent pheromone-controlled physiology of reproduction enables epistasis via nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate cell types in the context of thermodynamic cycles of protein biosynthesis and degradation.
Species-specific pheromones control the physiology of reproduction and “fix” the amino acid substitutions in populations. The substitutions stabilize the DNA in organized genomes and the substitutions prevent most of the damage that would otherwise result from accumulated mutations.
Nutrient-dependent DNA repair mechanisms also typically prevent the accumulation of damage that might otherwise occur during life history transitions. For example, vitamin D uptake or natural production links ecological adaptations in populations where malaria is endemic via substitution of the amino acid associated with the hemoglobin S (sickle cell) variant.
The idea of protein evolution is foreign to me because protein evolution is not exemplified in model organisms. The universal trend of amino acid gain and loss in proteins occurs when nutrient-dependent substitutions stabilize the DNA in organized genomes. Accumulated mutations that cause too much dysfunction are typically eliminated — until nutrient stress and/or social stress overwhelm the ability of organisms that might otherwise continue to ecologically adapt as if they were immortal.
Two external factors cause changes in amino acid compositions of proteins in all genera that lead to biodiversity via mortality of individuals. The external factors are nutrient uptake and the pheromone-controlled physiology of reproduction. Together, they link the epigenetic landscape to the physical landscape of DNA in organized genomes via the bio-physically constrained chemistry of protein folding. That is how protein folding can be linked to the conserved molecular mechanisms of ecological adaptations in all species via amino acid substitutions.
biomolbioandco My comment about the Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites was posted at this site after it was blocked by the moderator at the BioRxiv article site.
The stability model they detail is a model in which mutations are either neutral or completely deleterious. However, their evolutionary inferences link the mutations to biodiversity.
The same thing is done in Biophysics of protein evolution and evolutionary protein biophysics.
My comment: These are people who “…expect to witness increasing collaboration between the fields of biophysics and evolution as well as between theory/computation and experiment to decipher many aspects of the evolutionary forces that have been shaping the biological roles of proteins.”
I expect them to be humiliated by serious scientists who are less likely to think that mutations link perturbed protein folding to the increasing organismal complexity manifested in nutrient-dependent pheromone-controlled biodiversity.
See for example, a 5.5 minute video representation of: Nutrient-dependent / Pheromone-controlled adaptive evolution: (a mammalian model of thermodynamics and organism-level thermoregulation)
This model refutes a book-length revision of a comparable theory: ‘Mutation-driven evolution’ [1] Chemical ecology drives adaptive evolution via ecological, social, neurogenic, and socio-cognitive niche construction. Nutrients are metabolized to pheromones that epigenetically effect hormones that affect behavior in the same way food odors classically condition behavior associated with food preferences. In mammals, the epigenetic effects of olfactory/pheromonal input are on gonadotropin releasing hormone (GnRH) neurosecretory neurons of brain tissue. For example: glucose and pheromones alter the secretion of GnRH and luteinizing hormone (LH). Secretion of LH is the measurable proxy for genetically predisposed differences in hypothalamic GnRH pulse frequency and amplitude and the downstream effects of GnRH, which is the central regulator of genetically predisposed nutrient-dependent individual survival and pheromone-controlled species survival.
This model of systems biology represents the conservation of bottom-up organization and top-down activation via the 1) thermodynamics of nutrient stress-induced and social stress-induced intracellular changes in the microRNA / messenger RNA  (miRNA/mRNA) balance; 2)  intermolecular changes in DNA (genes) and alternative splicing; 3) non-random experience-dependent stochastic variations in de novo gene expression and biosynthesis of odor receptors; 4) the required gene-cell-tissue-organ-organ system pathway that links sensory input directly to gene activation in neurosecretory cells and to miRNA-facilitated learning and memory in the amygdala of the adaptively evolved mammalian brain; and 5) the reciprocity that links the thermodynamics of gene expression to behavior and altered organism-level thermoregulation in species from microbes to man.
Examples of nutrient-dependent amino acid substitutions clarify the involvement of seemingly futile thermodynamic control of intracellular and intermolecular interactions, which result in de novo creation of olfactory receptor genes. Thermodynamically controlled cycles of RNA transcription and protein degradation are responsible for organism-level changes in pheromone production, which enable accelerated changes in the miRNA/mRNA balance and thermoregulation of controlled nutrient-dependent adaptive evolution.
In this mammalian model, food odors associated with nutrient uptake and species-specific social odors cause changes in the miRNA/mRNA balance. Those changes enable differential gene expression in GnRH neurons during developmental transitions required for successful nutrient-dependent pheromone-controlled reproduction, which occurs in species from microbes to man. Recent data extend this mammalian model of conserved molecular mechanisms across the continuum of adaptive evolution to selection for phenotypic expression associated with pheromones in a human population.
Across species comparisons of epigenetic effects on pangenomic microbial nutrient-dependent reproduction and on hormone-controlled invertebrate and vertebrate social and sexual behavior indicate that human pheromones alter the development of the brain and behavior via the molecular mechanisms conserved across all species.
It is now clear how an environmental drive evolved from that of nutrient uptake in unicellular organisms to that of pheromone-controlled socialization in insects. This makes it clearer that, in mammals, nutrients associated with food odors and pheromones associated with body odors cause controlled changes in hormones, which have developmental affects on the control of behavior in nutrient-dependent reproductively fit individuals that signal their fitness via pheromones. For contrast, in theory, mutations are not physiologically controlled, but control is required for adaptive evolution to occur [2].
An epigenetic continuum of nutrient-dependent pheromone-controlled adaptive evolution
Nematodes: Species incompatibilities are associated with cysteine-to-alanine substitutions [3]. Differences in behavior are determined by nutrient-dependent rewiring of their primitive nervous system [4].
Insects: Neurogenic niche construction in nematodes [4] is also exemplified in the honeybee model organism of nutrient-dependent pheromone-controlled adaptive evolution of the brain and behavior[5]. In flies, nutrient-dependent changes in mitochondrial tRNA and a nuclear-encoded tRNA synthetase enable the attachment an amino acid that facilitates the reaction required for efficient and accurate protein synthesis [6]. In wasps, the change in a pre-existing signaling molecule triggered by a glucose-dependent [7] stereochemical inversion [8] leads to species-specific pheromone production. In Ostrinia moth species, substitution of a critical amino acid, is sufficient to create a new pheromone blend [9].
Mammals: The association of the nutrient choline in humans and its metabolism to trimethylamine odor in different species of mice was the best example of how a change in diet becomes associated with the presence of mammalian conspecifics whose androgen estrogen ratio-associated odor distinguishes them sexually, and also as nutrient-dependent physically fit mates [10].  The mouse model makes it clearer that glucose uptake changes cellular thermodynamic equilibrium [11] and differential pathway regulation that results in adaptively evolved fitness in species from microbes [12] to mammals.
Humans: Two reports link substitution of the amino acid alanine for the amino acid valine [13] to nutrient-dependent pheromone-controlled adaptive evolution. Cause and effect was established in mice [14]. These two reports [13, 14] tell a new short story of nutrient-dependent pheromone-controlled adaptive evolution. The story begins with what was probably a nutrient-dependent variant allele that arose in central China ~ 30,000 years ago. In other mammals, like the mouse, the effect of the allele is manifested in sweat, skin, hair, and teeth, and the effect is clearly due to the epigenetic effect of nutrients on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. In the model here, the pheromones control the nutrient-dependent hormone-dependent organization and activation of reproductive sexual behavior in mammals such as mice and humans, and also in invertebrates as previously indicated [5]. Therefore, the adaptive evolution of the human population, which is detailed in these two reports, is also likely to be nutrient-dependent and pheromone-controlled sans mutations theory. See also [15] 1.     Nei, M., Mutation-Driven Evolution. 2013, Oxford, UK: Oxford Univesity Press.
2.     Noble, D., Physiology is rocking the foundations of evolutionary biology. Experimental Physiology, 2013: 10.1113/expphysiol.2012.071134.
3.     Wilson, L., et al., Fertilization in C. elegans requires an intact C-terminal RING finger in sperm protein SPE-42. BMC Dev Biol 2011. 11(1): 10.
4.     Bumbarger, Daniel J., et al., System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes. Cell, 2013. 152(1): 109-119.
5.     Kohl, J.V., Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2012. 2(17338).
6.     Meiklejohn, C.D., et al., An Incompatibility between a Mitochondrial tRNA and Its Nuclear-Encoded tRNA Synthetase Compromises Development and Fitness in Drosophila. PLoS Genet, 2013. 9(1): e1003238.
7.     Yadav, J.S., B.V. Joshi, and M.K. Gurjar, An enantiospecific synthesis of (4R,5R)-5-hydroxy-4-decanolide from d-glucose. Carbohydr Res, 1987. 165(1): 116-119.
8.     Niehuis, O., et al., Behavioural and genetic analyses of Nasonia shed light on the evolution of sex pheromones. Nature, 2013. 494: 345–348.
9.     Lassance, J.-M., et al., Functional consequences of sequence variation in the pheromone biosynthetic gene pgFAR for Ostrinia moths. Proceedings of the National Academy of Sciences, 2013. in press.
10.    Stensmyr, M. and F. Maderspacher, Olfactory Evolution: Mice Rethink Stink. Curr Biol, 2013. 23(2): R59-R61.
11.    Kohl, J.V., Nutrient-dependent / Pheromone-controlled thermodynamics and thermoregulation. http://dx.doi.org/10.6084/m9.figshare.643393, 2013.
12.    Kondrashov, F.A., Gene duplication as a mechanism of genomic adaptation to a changing environment. Proc Biol Sci, 2012. 279 (1749): 5048-5057.
13.    Grossman, Sharon R., et al., Identifying Recent Adaptations in Large-Scale Genomic Data. Cell, 2013. 152(4): 703-713.
14.    Kamberov, Yana G., et al., Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant. Cell, 2013. 152(4): 691-702.
15.    Kohl, J.V., Nutrient–dependent / pheromone–controlled adaptive evolution: a model. Socioaffective Neuroscience & Psychology, 2013. 3(20553).