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The virome, microbiome, replisome and supercoiled DNA

Excerpt:

This architecture could also potentially play an important role in developmental biology by providing a pathway for treating the two daughter strands differently. Many modifications to DNA, including how it is packaged with other proteins, control which of the many genes in the sequence are eventually expressed in cells. An asymmetric replisome may result in asymmetric treatment of the two daughter strands during cell division—an essential step for making different tissues within a multicellular organism.

As the paper concludes, “Clearly, further studies will be required to understand the functional implications of the unexpected replisome architecture reported here.”

My comment: This replisome architecture would have been expected by anyone who understands what is currently known about biophysically constrained RNA-mediated cell type differentiation.  For example, this parody puts nutrient-dependent base pair changes and RNA-mediated gene duplication into the context of the RNA-mediated amino acid substitutions in histones that protect organized genomes from virus-driven genomic entropy.

See also: Scientists reveal 90 percent of skin-based viruses represent viral ‘dark matter’

Excerpt: 

The findings also clearly linked the skin virome to the skin microbiome: Most of the detected viral DNA appeared to belong to phage viruses, which infect and often take up long-term residence within bacteria. And when Grice and colleagues sequenced skin bacterial DNA from the same 16 subjects, they found that it often contained tell-tale marks—called CRISPR spacers—of prior invasion by the same phage viruses.

My comment: Finding viruses and retroviruses in the bacteria of the largest organ of the human body links them from nutrient-dependent metabolic networks to genetic networks via the effects of viruses in gut bacteria on RNA-mediated gene duplication and RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all living genera via the controlled physiology of reproduction.
See also:
Pineapple genome offers insight into photosynthesis in drought-tolerant plants
Protecting plants from stealthy diseases
Evolution on the inside track: Study shows how viruses in gut bacteria change over time
Genetic variation in human gut viruses could be raw material for inner evolution
Study: Vitamin B3 may help prevent certain skin cancers
Eventually, someone will get the Nobel Prize that Rosalind Franklin probably would have received had she lived to link the tobacco mosaic virus and poliovirus from pathology in plants to all pathology in mammals via an atoms to ecosystems model of epigenetically-effected non-static DNA structure and function.
The works reported in the links above inadvertently link viruses in gut microbes from metabolic networks to genetic networks that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to human via the physiology of reproduction, which links RNA-mediated amino acid substitutions in histones to supercoiled DNA and protection from virus-driven DNA damage.
The link from viruses in gut microbes to viruses in skin cells and pathology also may have secured the US Presidency for a candidate who is wiling to tout his creationist beliefs. I suspect that others, will now begin to follow Ben Carson’s lead even though the others know nothing about cell type differentiation compared to Ben Carson.

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Controled Stem Cell Expansion

Serine … is one of the proteinogenic amino acids. [It]… is classified as a polar amino acid.
My comment: Serine synthesis in the body is linked to glycine, which also may be naturally produced when UV light illuminates simple ices (e.g., combinations of water, methanol, hydrogen cyanide, and ammonia). That suggested to some people that glycine and other amino acids may be easily produced in cold regions of space, and the suggestion, like virtually all suggestions, seems to be believable to theorists.  For contrast, Sutherland’s group linked UV light to the creation of glycine on Earth.
Their research was reported as: Researchers may have solved origin-of-life conundrum
Excerpt:

…a pair of simple compounds, which would have been abundant on early Earth, can give rise to a network of simple reactions that produce the three major classes of biomolecules—nucleic acids, amino acids, and lipids—needed for the earliest form of life to get its start.

My comment: That claim may link the UV light-induced de novo creation of glycine on Earth to the RNA-mediated cell type differentiation of all vertebrates.  Claims about RNA-mediated cell type differentiation have been made for more than 30 years, and the molecular mechanisms that link cell type differentiation in all species have been detailed. See: RNA mediated
See for comparison: Atypical PKC-iota Controls Stem Cell Expansion via Regulation of the Notch Pathway
Excerpt 1)

These studies, together with data presented here, provide genetic evidence that evolutionarily conserved polarity pathways may play a central role in NOTCH1 activation and stem cell self-renewal in mammals. Further genetic studies using Cre transgenes that are specific for progenitors in the neural plate, primitive erythrocytes, cardiomyocytes, and other progenitors to ablate aPKC function will be needed to determine how generally this mechanism is used in diverse tissues.

Excerpt 2)

…a complete picture for the requirement of aPKCs at different stages of mammalian development has not yet emerged.
Excerpt:

…the Notch pathway produces a protein that signals to stem cells to make more stem cells. In the presence of Prkci, the Notch pathway remains silent, and stem cells differentiate into specific cell types.

My comment:  Cell type differentiation is nutrient-dependent and RNA-mediated in the context of biophysically constrained protein folding chemistry. The chemistry links atoms to ecosystems via everything known about thermodynamic cycles of protein biosynthesis and degradation. The cycles lead to successful organism thermoregulation when the cycles are not perturbed by viruses. Perturbed cycles of protein biosynthesis and degradation link viruses to mutations to all pathology.
Arguably, further studies of controlled stem cell expansion will eventually link everything currently known From Fertilization to Adult Sexual Behavior in all mammals via what is currently known about nutrient-dependent RNA-mediated cell type differentiation in all vertebrates.
For example, substitution of achiral glycine in the GnRH decapeptide links food odors and pheromones from atoms to ecosystems via the physiology of reproduction.  Predictably, the complete picture that will emerge in mammals will link conserved polarity pathways to the stability of organized genomes in all vertebrates outside the context of theoretical physics and neo-Darwinian theories about mutations and evolution.
Indeed, it seems likely theorists will learn that all RNA-mediated cell type differentiation in all vertebrates is nutrient-dependent and that Feedback loops link odor and pheromone signaling with reproduction, from microbes to humans, since serious scientists have known that for more than a decade.
As we wait for the complete picture to be seen by those who continue to frame their experimental evidence of biologically-based cause and effect in the context of ridiculous theories about evolutionarily conserved polarity pathways, we should remember that many theorists will continue to believe whatever they are taught to believe.
Most of them may never learn anything about how nutrient-dependent RNA-mediated cell type differentiation occurs, which means they may never link species-specific pheromones to morphological and behavioral phenotypes in species from microbes to humans. Indeed, most theorists will never become serious scientists who frame their experimental evidence in the context of biologically-based facts that others have established.
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700 million years of evolution?

Analysis of 5′ gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals
Conclusion:

It is our hope that each and every one of these regions will make interesting candidates for experimental analysis, helping to increase our understanding of regulation of gene expression, and particularly our understanding of regulatory elements in RNA.

My comment: In other words, they hope what has already been detailed in the context of how nutrient-dependent microRNAs link the epigenetic landscape to the physical landscape of DNA via RNA-mediated events will help others to understand what is known about biophysically constrained cell type differentiation in all living genera. Their hope can be placed into the context of two published works from 2013.
1) Human expression QTLs are enriched in signals of environmental adaptation
Excerpt:

Environmental correlation is a way of detecting adaptation by testing whether the spatial distribution of the frequency of an allele could be explained by an environmental factor.

2) Nutrient-dependent/pheromone-controlled adaptive evolution: a model
Conclusion:

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

My comment: Others have since established the validity of 2) the model, which links 1) environmental correlation to the detection of ecological adaptations. For example, ecological variation is consistently linked from nutrient-dependent microRNAs to the pheromone-controlled physiology of reproduction via feedback loops. The feedback loops were placed into the context of ecological adaptations across species in

All in the (bigger) family

Excerpt:

…last week at a special symposium of the annual meeting of the Society for Integrative and Comparative Biology, researchers reported new parallels between these two very successful groups of animals and new insights about what it took for an ancient crustacean to give rise to insects.

My comment: (Submitted on Mon, 01/19/2015 – 11:51 and published to the “Science Magazine” site)

The 2015 Society for Integrative and Comparative Biology (SICB) presenters may not recognize how much progress has been made since the 2013 ecological epigenetics symposium. For example, since then authors claimed “…ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.” http://dx.doi.org/10.1038/nature13400
Six months later, other authors traced signaling factors found in vertebrates to the origin of nerve cell centralization via the diffuse nerve net of animals like the sea anemone. http://dx.doi.org/10.1038/ncomms6536 That fact suggests ecological variation is linked to ecological adaptations in morphological and behavioral phenotypes via signaling protein concentrations that differentiate various cell types in body axes and the central nervous system.
Links across species from the epigenetic landscape to the physical landscape of DNA in organized genomes appear to have their origins in the conserved molecular mechanisms of RNA-directed DNA methylation and RNA-mediated protein folding. Two weeks after the publication that refuted ideas about independently evolved neural systems or muscle specification — and perhaps refuted the independent evolution of anything else, SICB presenters linked crustaceans to insects.
Apparently, they’ve learned that the same set of microRNAs controls expression of the genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans.
Why were they left with any questions about how crustaceans and insects could all be part of one big family? They linked RNA-mediated cell type differentiation to what we described in our section on molecular epigenetics in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior http://www.hawaii.edu/PCSS/biblio/articles/1961to1999/1996-from-fertilization.html

See also: Oldest DNA sequences may reveal secrets of ancient animal ancestors
This report on the findings from Analysis of 5′ gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals places everything currently known to serious scientists about how nutrient-dependent microRNAs link ecological variation to ecological adaptation into the context of neo-Darwian evolutionary.
The report begins with this ridiculous claim:

700 million year-old DNA sequences from ancient animals have been unearthed by researchers at the Universities of Leicester and Warwick, shedding new light on our earliest animal ancestors and how they influenced modern species – including the sponge.

My comment: How did they determine that the DNA sequences are from 700 million year old animals? That is the first question every serious scientist I know would ask if they saw this report.
Here’s the answer (with my emphasis):

Among the CNEs that we identified were previously-studied regulatory elements, as well as many unidentified novel putative regulatory elements. As the majority of CNEs overlap 5’ UTRs, we calculated the likelihood of there being a conserved secondary structure in each CNE.

My comment: No serious scientist calculates the likelihood that a conserved secondary structure in any extant or extinct species could be linked to 700 million years of evolution.
I will have more to say on this later. I wanted to report it here, in case the “Science Magazine” site removes my comment as they did at least once before. The comment they removed was replaced with the author’s comment here: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

Here’s the comment that was removed:

The idea of biophysical constraints seems antithetical to the idea of nature somehow selecting mutations that cause amino acid substitutions. However, I am not a biophysicist or evolutionary theorist.
The problem may be my focus on nutrient-dependent receptor-mediated amino acid substitutions in species from bacteria to humans (non-viral organisms). Since I am not a virologist or physicist, I’m not sure that the laws of physics apply to viruses and their replication.
If they do, natural selection for random mutations is not likely to result in amino acid substitutions because the thermodynamics of changes in organism-level thermoregulation preclude such randomness. Stability of protein biosynthesis and degradation that probably depends on protein folding must somehow be controlled. Besides, I don’t know how random mutations in viruses could be naturally selected for inclusion in the human virome (or in the virome of any organism capable of thermoregulating its thermodynamic intercellular signaling).
If the Second Law of Thermodynamics does not apply to viruses, which means the chemical bonds that enable the amino acid substitutions can form at random and somehow be naturally selected, the details of biophysical constraints in this article seems out of place, since I do not think in terms of constrained random mutations and natural selection in mutation-driven evolution.
Hopefully, someone with a background in biophysics will address my confusion in case others are confused. In addition, I wonder if the consequences of understanding the evolutionary mechanisms that govern viruses extend to consequences important to understanding the evolution of species from bacteria to humans via constrained random mutations and natural selection?

The fact that a single amino acid substitution in a virus can lead to changes across species that occur via amino acid substitutions in bacteria that re-evolved their flagellum in as few as four days is something that I have repeatedly addressed in blog posts here. I will continue to do so.
See FREE* SAMPLE Histone Modification Antibodies

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RNA-mediated retrotransposon-mediated biodiversity

Retrotransposons (also called transposons via RNA intermediates) are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms.

See also: A Single Amino Acid Change in the Yeast Retrotransposon Ty5 Abolishes Targeting to Silent Chromatin

Excerpt:

Target site biases observed among retroviruses and retrotransposons are thought to be the consequence of interactions between the retroelement integration complex and chromosome-localized proteins.

My comment: Clearly, the way to make scientific progress is to examine the consequences of these interactions. It is past time to abandon claims about mutations and evolution that have failed to be supported by experimental evidence of biologically-based cause and effect in the context of the nutrient-dependent physiology of reproduction and ecological adaptations in all living genera. The balance of nutrient-dependent microRNAs and viral microRNAs can be linked to nutrient-dependent healthy longevity or to virus-driven pathology. But the contribution of microRNAs to the microRNA/messenger RNA balance and nutrient-dependent DNA repair or virus-driven pathology is missing in everything presented below.

Primate-Specific ORF0 Contributes to Retrotransposon-Mediated Diversity

Abstract conclusion: “Capped and polyadenylated ORF0 mRNAs are present in the cytoplasm, and endogenous ORF0 peptides are identified upon proteomic analysis. Finally, ORF0 enhances LINE-1 mobility. Taken together, these results suggest a role for ORF0 in retrotransposon-mediated diversity.”
My comment: Retrotransposon-mediated diversity.is nutrient-dependent and biophysically constrained. The diversity is constrained by the RNA-mediated amino acid substitutions that differentiate cell types in the context of the physiology of vertebrate and invertebrate reproduction.
Note: The Gage lab concentrates on the adult central nervous system, and unexpected plasticity and adaptability to environmental stimulation that remains throughout the life of all mammals.
Rusty Gage may be the best person to ask about RNA-mediated retrotransposon-mediated diversity in the context of what is currently known about the honeybee model organism and the links from its life history transitions to humans. For example: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults.
If nutrient energy-dependent base pair changes and RNA-mediated amino acid substitutions do not link RNA-directed DNA methylation to cell type differentiation in species from microbes to human via chromosomal rearrangement and the physiology of reproduction, there may be another model for comparison to mine. If there is, Dr. Gage probably knows where to find information on the comparable model of biologically-based cause and effect.

Scientists discover protein factories hidden in human jumping genes

Excerpt:

Evolutionarily speaking, this represents a way to generate entirely new molecules that could be beneficial to a species. On the other hand, the reshuffling of an existing ORF0 sequence during a jump could result in a disease-causing mutation.

My comment: It is not surprising to me that they claim this link from the epigenetic landscape to the nutrient-dependent physical landscape of primate DNA exemplifies a form of evolution that must be placed into the context of disease-causing mutations. Serious scientists learned only recently that the generation of any new molecules must be linked from base pair changes to their function without the pseudoscientific nonsense about the evolution of new proteins and/or new genes.

But see for comparison from Dobzhansky (1973)

…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 link from base pair changes to RNA-mediated amino acid substitutions in the cell types of 3 primate species appears to require just one amino acid substitution in the hemoglobin molecule of three primate species.

See also: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

Conclusion:

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

See also: Speedy evolution affects more than one species
Excerpt: 

The fruit flies in question evolved into new species when they began laying their eggs and mating on apple trees, as opposed to their native hawthorn tree hosts. Three different kinds of parasitoid wasps were collected from a number of different fly host plant environments in the wild.
Analyses in the lab showed that all three of the different kinds of wasps had diverged from others of the same kind, both genetically and with respect to host-associated physiology and behavior.
“In a sense,” Smith said, “they have caught an entire community of parasitoids actively ecologically diverging in response to a historically documented host plant shift of their fly host.”

My comment: They report ecological variation and nutrient-dependent adaptations controlled by the physiology of reproduction in all living genera, in the context of fruit fly evolution. To the biologically uninformed this links the evolution of the flies to the evolution of other species.  To anyone who understands anything about the biophysically constrained chemistry of nutrient-dependent protein folding, they place ecological divergence into the context of a magic trick.

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Supercoiled DNA constrains virus-driven genomic entropy

1) Genes linked with malaria’s virulence shared by apes, humans and
2) Supercoiled DNA is far more dynamic than the ‘Watson-Crick’ double helix were reported today.
One report (1) links viruses to the evolution of biodiversity in chimpanzees and humans compared to gorillas.
The other report (2) links nutrient energy-dependent base pair changes to RNA-mediated amino acid substitutions and DNA repair.

Both reports are linked to open access publications:

See 1)  Ape parasite origins of human malaria virulence genes
Excerpt:

This Laverania species diversity provides an unprecedented opportunity to study the origins of genomic features that previously seemed unique to P. falciparum, such as the var gene family encoding erythrocyte membrane proteins. Here we show that various aspects of the multi-scale modularity of these loci can be recognized in diverse Laverania species, with the implication that a var or var-like gene family already existed in their last common ancestor.

My comment: The implication that gene families already existed in a last common ancestor are linked to the theoretical ghosts of the evolution industry. Despite a century of scientific progress, the ghosts are still linked to the gene-centric views of population geneticists. They used de Vries (1904) definition of “mutation” as the basis for assumptions about how long it would take for all extant or extinct biomass to automagically arise from a primodial soup. Sometime during that time apes evolved from microbes and became modern humans.
See also 2): 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: The data that links small molecules, such as microRNAs, from metabolic networks to genetic networks, makes the claims of neo-Darwinian theorists the theme of this parody. It is an accurate representation of how nutrient-dependent base pair changes link ecological variation to ecological adaptation and all biomass on earth via what is currently known to serious scientists about base pair changes and RNA-mediated DNA repair.

Last week, I recorded a less technical representation of biologically-based cause and effect that placed squirrel-centric evolution into the context of current philosophy (we don’t know how species evolved) and claims of evolutionary theorists (random mutations and natural selection led to the theoretical basis of the “walnut crush” phenomenon). Sarcasm alert: Creationist claims are vaguely presented with no experimental evidence to support the idea that the walnuts grew on and fell from trees.

Obviously, no one can be perfectly sure that what is known about RNA-mediated epigenetic regulation of gene expression and RNA-mediated gene silencing link base pair changes to all extant biodiversity, or if de Vries definition of “mutation” and theories are the best approach to understanding the pathology of malaria. However, the 2015 Nobel Prize winners in Physics, Chemistry, and Physiology and/or Medicine have linked neutrinos to mass and the speed of light on contact with water from the light’s virucidal properties to the effective treatment of malaria via a water-based chemical extraction procedure described 1600 years ago.
 

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Let there be anti-entropic light (2)

Predicted Inactivation of Viruses of Relevance to Biodefense by Solar Radiation (2005)Excerpt:

Sunlight or, more specifically, solar UV radiation (UV) acts as the principal natural virucide in the environment. UV radiation kills viruses by chemically modifying their genetic material, DNA and RNA.

See also: Let there be anti-entropic light (1)
Excerpt:

Nutrient-stress and social stress contribute to the accumulation of viral miRNAs that would typically be prevented by nutrient-dependent pheromone-controlled feeback loops that link food odors and social odors to the nutrient-dependent physiology of reproduction via controlled changes in the miRNA/mRNA balance.

A Model of Extracellular Enzymes in Free-Living Microbes: Which Strategy Pays Off?
Conclusion:

The combination of an enzyme threshold concentration and the dilute nature of individual compounds could explain the persistence and apparent refractory state of some compounds in oceanic DOM. This aligns with the hypothesis that a large fraction of DOM in the oceans persists primarily due to dilute concentrations (61–63) and calls for further experiments and methodological developments to further investigate this. Extracellular enzymes and how microbes  utilize them in response to ambient DOM carry important implications for microbial ecology and the microbial impact on carbon sequestration in the ocean as DOM.

My comment: In the context of nutrient-dependent metabolic networks and dissolved organic matter (DOM), the authors linked the pheromone-controlled physiology of microbes to genetic networks via extracellular enzymes and thermodynamic cycles of protein biosynthesis and degradation.
In other words, they linked what is known about physics and chemistry to the conserved molecular mechanisms of biophysically constrained RNA-mediated gene duplication and RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all living genera.
There representation is consistent with works by other serious scientists who are examining ecological variation and nutrient-dependent biodiversity. For example, these researchers do not mention “mutations,” “natural selection,” or “evolution” in the body of their text.
Also, they do not mention anything about the role that viruses might play in links between entropic elasticity and genomic entropy manifested in pathology.  Indeed, this article, which was coauthored by Sachia J. Traving, is about “living” organisms.
An earlier article co-authored by Sachia J. Traving, linked the role of viruses to bacterial growth in the context of  the complexity of what is known about microbial ecosystems. No experimental evidence of biologically-based cause and effect suggests that microbial ecosystems “evolve.”
See also: Increased acidification has a profound effect on the interactions between the cyanobacterium Synechococcus sp. WH7803 and its viruses (2014)
Conclusion: 

The present study demonstrates that the role of viruses in the regulation of cyanobacterial growth may be significantly altered in future climate scenarios, thus emphasizing the need for including viruses in ecosystem modelling.

See also: Viral Genome Junk Is Bunk
Excerpt:

Perhaps the evolutionists have placed the cart before the horse on this issue, as proposed by several creationist scientists.4,6 In fact, in an ironic twist, the evidence mentioned above indicates that viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, “The most parsimonious answer is: the RNA viruses got their genes from their hosts.”6

My comment: In the excerpt above, young earth creationists linked viruses to all pathology. They did not address the complexity of  links from atoms to ecosystems, but their findings are consistent with what appears to be known about ecosystem modeling to the 2015 Nobel Laureates whose works linked the disciplines of Physics, Chemistry, and Physiology and/or Medicine. For contrast, the likely role of viruses and their threat to ecosystems in the context of global warming has remained virtually unknown to theoretical physicists or to the evolutionary theorists who invented the neo-Darwinian “Modern Synthesis.” As you know, this links the creationist literature to a threat to neo-Darwinian theory. However if you don’t trust the representations of creationists, or simply do not want to read any of their literature…
see The Promise and Pitfalls of Extracellular Biochemistry.

Excerpt:

…free enzymes can make up significant portions of the total enzyme activity.” Some have argued that such enzymes are nonspecific leftovers from burst cells, but an alternative option is that a certain density of like-minded microbes flips the switch, making the production of free enzymes more useful to the whole community than the surface-attached approach. What that density is for marine heterotrophs remains a mystery, but it points to a common goods strategy of ocean living.

My comment: The “common goods strategy of ocean living” links the anti-entropic force of the sun’s biological energy from neutrinos to the de novo creation of nucleic acids and RNA-mediated events that differentiate all cell types in all individuals of all living genera. Cell type differentiation is required to protect organisms from virus-induced DNA damage in the context of the physiology of nutrient-dependent RNA-mediated gene duplication and RNA-mediated amino acid substitutions. The amino acid substitutions link metabolic networks to genetic networks in all organaized genomes via RNA-mediated DNA repair. Nutrient-dependent RNA-mediated events appear to degrade viral microRNAs and prevent DNA damage that is caused by the proliferation of viruses, which links entropic elasticity to genomic entropy.
See also: RNA-mediated degradation of microRNAs: A widespread viral strategy?
My comment: The nature of this widespread viral strategy appears to link marine microbes to viral infections in flies via RNA-mediated events
See for example: The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster
Excerpt 1)

Viral infections are universal, and virus-mediated selection may play a unique role in evolution [1].

Excerpt 2)

Our results provide an unprecedented insight into the virus community of Drosophila, and thereby provide the evolutionary and ecological context needed to develop Drosophila as a model for virus research.

My comment: It is important to notice the misrepresentation in these two excerpts. Virus research has failed to link viruses in marine microbes to viruses in Drosophila in the context of evolution. The link from marine microbes to flies is biophysically constrained by the nutrient-dependent pheromone-controlled physiology of reproduction, which is linked to the nutrient-dependent pheromone-controlled physiology of reproduction outside the context of neo-Darwinian theory, but within the context of Darwin’s nutrient-dependent “conditions of life” and the physiology of reproduction.
That means future claims about evolution must address the claims of creationists who linked viruses to all pathology. Some creationists probably also agree that the sun’s biological energy should be linked from the de novo creation of nucleic acids to its virus-killing anti-entropic effects on RNA-directed DNA methylation and epigenetically-effected biophysically constrained protein folding chemistry.
For contrast, see: A virocentric perspective on the evolution of life.
Koonin’s virocentric perspective on evolution can be compared to the gene-centric perspectives on evolution which are no longer considered in the context of biologically-based cause and effect that links atoms to ecosystems.  All living organisms require nutrients and viruses steal the nutrient-energy that is required for RNA-mediated cell type differentiation.
See also: Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter
 

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Foundamentals of theory

There are foundations of epigenetics and fundamentals of molecular mechanisms. They have been detailed in this atoms to ecosystems model of RNA-mediated cell type differentiation. Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems.

I have never seen anyone mention the “foundamentals” of epigenetics. It appears the word has been invented. Similarly, the word “mutation” was invented in 1904 by de Vries.

Inventing words and defining them to fit ridiculous theories about neo-Darwinian evolution is required to continue convincing theorists that they are something more than biologically uninformed science idiots.

See for comparison:

Absence of canonical marks of active chromatin in developmentally regulated genes

Excerpt:

…strong chromatin marking is related to transcriptional and post-transcriptional stability, an association that we also observe in mammals. Our results support a model in which chromatin marking is associated with the stable production of RNA…

Reported as:

Shaking up the foundamentals of epigenetics

Excerpt:

The results of this study contrast sharply with the generally accepted view of the key roles that these epigenetic marks play in regulating gene expression.

My comment: If true, this should have been reported before the top three 2015 Nobel Prizes for science were awarded to researchers who linked physics, chemistry, and conserved molecular mechanisms of epigenetically effected RNA-mediated cell type differentiation in species from microbes to man via DNA repair in the context of the physiology of reproduction. See: DNA Repair Pioneers Win Nobel
Pretending there is any contrast to the accurate representations of what experimental evidence has clearly detailed in the context of an atoms to ecosystems model is like returning to the 20th century definition of “mutation” and trying to link it to evolution while all serious scientists are linking nutrient-dependent RNA-mediated amino acid substitutions from ecological variation to ecological adaptation via DNA repair.
See also: A Nutrient-Driven tRNA Modification Alters Translational Fidelity and Genome-wide Protein Coding across an Animal Genus
Excerpt:

These results reveal a strikingly direct mechanism by which recoding of entire genomes results from changes in utilization of a nutrient.

Reported as: 

Nutrient availability can cause whole-genome recoding

Excerpt:

“When queuine is abundant, organisms naturally recode its codons to favor the use of ones that are more efficiently translated by Q-modification,” Drummond said. “In this way, a single nutrient causes a snowballing effect that leads to wide-spread changes in how proteins are encoded

The “snowballing effect” was manifested as “re-evolution” of the bacterial flagellum over-the-weekend. See: Evolutionary Rewiring
The epigenetic effect of nutrient stress can also be placed into the context of the anti-entropic epigenetic effects that link heat shock proteins to nutrient-dependent ecological adaptations or compared to virus-driven genomic entropy during thermodynamic cycles of protein biosynthesis and degradation.
In the model organisms that reportedly are Shaking up the foundamentals of epigenetics, ecological variation is linked to ecological adaptation via the anti-entropic effects of food and the pheromone-controlled physiology of reproduction that link the biodiversity of all species from atoms to ecosystems as shown in the collective works of this year’s Nobel Laureates in Physics, Chemistryand Physiology and/or Medicine.
See also: Reversible, Specific, Active Aggregates of Endogenous Proteins Assemble upon Heat Stress
Excerpt:

Proteins synthesized in response to heat shock, such as the chaperone Hsp104, show an increase in both pre- and post-shock ratios, indicating new synthesis; increased signal in both channels reflects incorporation of imported post-shock amino acids and residual or recycled pre-shock amino acids (Figure 6B).

My comment: The synthesis of proteins links nutrient-dependent thermodynamioc cycles of protein biosynthesis and degradation to RNA-mediated cell type differentiation in the context of feedback loops.  See: Feedback loops link odor and pheromone signaling with reproduction
See also: Mechanisms of stress in the brain
Abstract excerpt:

…continually changing pattern of gene expression mediated by epigenetic mechanisms involving histone modifications and CpG methylation and hydroxymethylation as well as … the activity of retrotransposons … may alter genomic stability.

The continually changing patterns of epigenetically effected gene expression linked to genomic stability are perturbed by viruses, which steal the nutrient energy that is required for proper RNA-mediated protein folding chemistry that is mediated by amino acid substitutions.
Journal article excerpt:

Glucocorticoids are not the sole mediators of these effects, in which excitatory amino acids and many other cellular mediators also play important parts (Box 1). These mediators span influences from extracellular adhesion molecules to cytoskeletal elements and at least one nuclear pore complex protein.

My comment: The role of RNA-mediated events that link amino acid substitutions to cell type differentiation in all cells of all tissues of all organs and all organ systems attests to the amount of pseudoscientific nonsense touted by evolutionary theorists who still can’t seem to stop making claims that are unsupported by any experimental evidence of biologically-based cause and effect.

See also: Archaeal ancestors of eukaryotes: not so elusive any more
Conclusion:

The challenge lies in the investigation of the biology of these organisms. Although we can never know what precisely happened more than a billion years ago, to me, demonstration of the archaeal–bacterial endosymbiosis in the laboratory would mean the completion of the bridge. This is an extremely tall order but then again, who would have predicted 25 years ago that complete genome sequencing of microbes that do not grow in culture would become a near routine exercise?

My comment: Who would have predicted that Koonin would continue making unsupported claims about the origin of endosymbiosis after he admitted “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…
Why hasn’t he searched for information about RNA-mediated epigenetic regulation of gene expression or RNA-mediated gene silencing. What is know about cell type differentiation in species from microbes to man should be considered in the context of how viruses perturb protein folding before any more unsubstantiated claims are made by Koonin or anyone else.

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Viruses come alive: Tree of life pseudoscience

This comment was removed from a “tree of life” discussion site by the “site staff.” In the context of anonymous “peer” review, the comment was removed for the following reason: PSEUDOSCIENCE, with an added threat that my account might be suspended in case of regular violations of the guidelines that led the “site staff” to remove this comment.

Young earth creationists addressed the “Tree of life” nonsense in: “Evolutionary Predictions Fail the Reality Test.”

Excerpt:
Evolutionary developmental biologist Sean Carroll describes the implications of the stunning details:
When the sequence of these homeoboxes were examined in detail, the similarities among species were astounding. Over the 60 amino acids of the homeodomain, some mice and frog proteins were identical to the fly sequences at up to 59 out of 60 positions. In Dobzhansky’s (1973) claim, a single amino acid substitution differentiates cell types of chimpanzees and humans from gorillas. One “Tree” expert claims:
…this first tree of life is also important in revealing what we don’t know…
Compared to the creationists, these tree experts appear to know nothing about RNA-mediated amino acid substitutions and cell type differentiation.

My summary: Comments that someone considers to include pseudoscience auto-magically include non-mainstream theories. No matter how ridiculous the mainstream theories have become in the light of experimental evidence that links top-down causation to biologically-based cause and effect, non-mainstream facts are dismissed.
That explains why “Pseudoscientific beliefs are widespread, even among state school science teachers and newspaper reporters.[5]”
My comment: Every aspect of the ‘Tree of life’ for 2.3 million species released nonsense is probably considered by serious scientists to be based on pseudoscience.
Excerpt 1) 

A first draft of the “tree of life” for the roughly 2.3 million named species of animals, plants, fungi and microbes—from platypuses to puffballs—has been released.

My comment: Serious scientists now use genome wide sequencing to differentiate species that pseudoscientists simply names.
Excerpt 2)

The initial draft is based on nearly 500 smaller trees from previously published studies.

My comment: The previously published studies probably did not include contributions from serious scientists who perform genome wide sequencing to differentiate species.
Excerpt 3)

As a result, the relationships depicted in some parts of the tree, such as the branches representing the pea and sunflower families, don’t always agree with expert opinion.
Other parts of the tree, particularly insects and microbes, remain elusive.
My comment: The opinions of experts are based on genome wide sequencing that differentiate species from microbes to humans. Experts do not exclude insects and microbes.
Excerpt 4 with my emphasis)

“As important as showing what we do know about relationships, this first tree of life is also important in revealing what we don’t know,” said co-author Douglas Soltis of the University of Florida.

My comment: The “Tree of Life” researchers appear to know nothing about nutrient-dependent RNA-mediated gene duplication and RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all species via their physiology of reproduction. What’s missing from this first “tree of life” is everything currently known to serious scientists about physics, chemistry, and the conserved molecular mechanisms of biophysically constrained protein folding. What’s missing reveals that fact that they know nothing about viruses and cell type differentiation.
See for comparison:

Researchers discover contenders in molecular arms race of major plant disease

Excerpt: Researchers have discovered how a tiny viral protein enables the infection of a complex plant, and the finding could lead to understanding viral diseases in other plants, animals and humans.
My comment: Understanding the role that viruses play in perturbed protein folding links viral microRNAs to all pathology, which has typically been prevented by nutrient-dependent microRNAs.
See: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants
Excerpt:

In summary, the spectrum of protein-coding variation is considerably different today compared to what existed as recently as 200 to 400 generations ago. Of the putatively deleterious protein-coding SNVs, 86.4% arose in the last 5,000 to 10,000 years, and they are enriched for mutations of large effect (Supplementary Fig. 14) as selection has not had sufficient time to purge them from the population.

See also: The palaeolithic diet and the unprovable links to our past

Excerpt:

…genetics play a pretty minor role in determining the specifics of our diet. Our physical and cultural environment mostly determines what we eat. Textbook examples include genes associated with lactose tolerance, starch digestion, alcohol metabolism, detoxification of plant food compounds and the metabolism of protein and carbohydrates: all mutations associated with a change in diet.

My comment: That claim was linked to this claim in Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants
Excerpt:

Of the putatively deleterious protein-coding SNVs, 86.4% arose in the last 5,000 to 10,000 years, and they are enriched for mutations of large effect (Supplementary Fig. 14) as selection has not had sufficient time to purge them from the population.

My comment: The claim that selection has not had sufficient time to purge the mutations from the population was placed into the context of beneficial mutations via this report: The palaeolithic diet and the unprovable links to our past.
Excerpt:

Textbook examples include genes associated with lactose tolerance, starch digestion, alcohol metabolism, detoxification of plant food compounds and the metabolism of protein and carbohydrates: all mutations associated with a change in diet.

My comment: Theorists have not yet realized that they can not link virus perturbed protein folding to our past via mutations, natural selection, or evolution. Changes in diet must be linked from our past to ~5-10K years of ecological variation and ecological adaptations via biophysically constrained nutrient-dependent RNA-mediated protein folding and the amino acid substitutions that differentiate all cell types in all individuals of all living genera.

On August 21st, the research team led by Prof. Yigong Shi from School of Life Sciences, Tsinghua University in China published two side-by-side research articles in Science, reporting the long-sought-after structure of a yeast spliceosome at 3.6 angstrom resolution determined by single particle cryo-electron microscopy (cryo-EM), and the molecular mechanism of pre-messenger RNA splicing. Until now, decades of genetic and biochemical experiments have identified almost all proteins in spliceosome and uncovered some functions. Yet, the structure remained a mystery for a long time. The works, primarily performed by Dr. Chuangye Yan, and Ph.D students Jing Hang and Ruixue Wan under Prof. Yigong Shi’s supervision, settled this Holy Grail question and established the structural basis for the related area. This work was supported by funds from the Ministry of Science and Technology and the National Natural Science Foundation of China.

My comment: Re: the settled “Holy Grail” question:
Excerpt 1)

The involved proteins and RNAs assemble into and dissociate from spliceosome in a strict order during splicing, endowing extreme dynamics and flexibility of the spliceosome. These features guarantee the accomplishment of the complex splicing reaction, but at the same time tangling the structural investigations of spliceosome.

Excerpt 2)

…[this] group provided the first structural insight into the molecular mechanism for pre-mRNA splicing: the spliceosome is in essence a protein-directed ribozyme, with the protein components essential for the delivery of critical RNA molecules into close proximity of one another at the right time for the splicing reaction (shown in Figure 2).

Summary of their findings: Linking physics to chemistry and the conserved molecular mechanism of cell type differentiation via alternative splicings of pre-mRNA and the nutrient-dependent de novo creation of olfactory receptor genes is not an easy task. Nevertheless, the links from atoms to ecosystems were predicted by co-author Teresa Binstock in our 1996 review of RNA-mediated cell type differentiation.

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.

My comment: Attempts to move forward from our accurate representations of biologically-based cause and effect have been stalled by evolutionary theorists for nearly 2 decades. The theorists seem to want mutations to be the cause of cell type differentiation via natural selection and evolution. It has not been possible to convince them to not put natural selection for anything except food in the primary position that must be considered in the context of Darwin’s “conditions of life.”

Darwin’s conditions of life are linked across generations by RNA-mediated DNA mechanisms.
See also:

Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH

New Research Surfaces Spelling Bad News For Tylenol: It Doesn’t Just Kill Pain…
My comment: The effect on glucose is readily linked to affects on behavior via metabolic networks and genetic networks in all living genera.
 
amino acid homeostasis

Gene creation (revisited)

New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation

Abstract:

The origin of novel protein-coding genes de novo was once considered so improbable as to be impossible. In less than a decade, and especially in the last five years, this view has been overturned by extensive evidence from diverse eukaryotic lineages. There is now evidence that this mechanism has contributed a significant number of genes to genomes of organisms as diverse as Saccharomyces, Drosophila, Plasmodium, Arabidopisis and human. From simple beginnings, these genes have in some instances acquired complex structure, regulated expression and important functional roles. New genes are often thought of as dispensable late additions; however, some recent de novo genes in human can play a role in disease. Rather than an extremely rare occurrence, it is now evident that there is a relatively constant trickle of proto-genes released into the testing ground of natural selection. It is currently unknown whether de novo genes arise primarily through an ‘RNA-first’ or ‘ORF-first’ pathway. Either way, evolutionary tinkering with this pool of genetic potential may have been a significant player in the origins of lineage-specific traits and adaptations.

Excerpt: 

De novo genes are usually defined as protein-coding genes that have evolved from scratch from previously non-coding DNA.

Conclusion:

De novo genes are not only important for their functional and biological contribution to the lineages in which they originate; they are also very informative in terms of our growing understanding of the evolution the genome and of new gene functions. Evolution continues to tinker.

My comment: If you define de novo genes in the context of their evolution from scratch, you have no choice but to tout the pseudoscientific nonsense about neo-Darwinism that you were taught to believe in.
For contrast: The de novo creation of experience-dependent olfactory receptor genes links atoms to ecosystems via the conserved molecular mechanisms of nutrient-dependent RNA-mediated protein folding chemistry.
See also: Search Results for ‘de novo creation’

Big Bang

Theorists have not seen the light

2015 Physiologists uncover a new code at the heart of biology

Excerpt:

It was long known that almost every amino acid can be encoded by multiple synonymous codons and that every organism, from humans to fungi, has a preference for certain codons.

My comment:
That fact underlies our representation of RNA-mediated cell type differentiation from our 1996 review From Fertilization to Adult Sexual BehaviorSee our section on molecular epigenetics. Our representation was subsequently linked to organization of genomes in insects and to life history transitions in honeybees and humans via single nutrient-dependent amino acid substitutions. Those links were fully established before microRNAs and adhesion proteins were linked via the octopus genome sequence from microbes to humans. All serious scientists now realize that the conserved molecular mechanisms of biophysically constrained RNA-mediated protein folding link the epigenetic landscape to the physical landscape of DNA in all living genera.

See also:

2011 We are not only eating ‘materials’, we are also eating ‘information’
Excerpt:

The finding is obviously very thought-provoking; for instance, it would indicate that in addition to eating “materials” (in the form of carbohydrates, proteins, etc), you are also eating “information” (as different miRNAs from distinct food sources could well bear different consequences on the regulation of host physiology once taken by the host due to potential regulation of different target genes as determined by the “information” contained within the miRNA sequence), thus providing a whole new dimension to “You are what you eat”.

Re: 1) Genes can adapt to different environmental changes by choosing the most optimal codon, which is counterintuitive to natural selection
My comment:  Ecological variation leads to ecological adaptation via nutrient-dependent RNA-mediated protein biosynthesis and degradation in the context of biophysically constrained thermodynamic cycles of protein biosynthesis and degradation that link the physiology of reproduction to biodiversity via organism-level thermoregulation.Genes cannot adapt outside that context, which helps to explain why Darwin insisted his “conditions of life” be placed before “natural selection.” If Darwin had known about genes he probably would have linked epigenetic effects of food to ecological adaptation even without knowing about nutrient-dependent RNA-mediated gene duplication and RNA-mediated amino acid substitutions that stabilize the organized genomes of all living genera.His book title might have been “Life is RNA-mediated.”
See also: Life is physics and chemistry and communication and Life as physics and chemistry: A system view of biology and Top-down causation: an integrating theme within and across the sciences? and Physiology is rocking the foundations of evolutionary biology
If life is not RNA-mediated in the context of what is known to serious scientists about physics, chemistry, communication, biology, top-down causation, and the physiology of nutrient dependent reproduction, life may have somehow evolved to link metabolic networks to genetic networks in all cells of all individuals of all living genera. However, no evidence of biologically-based cause and effect links anything encoded by multiple synonymous codons to RNA-mediated  gene duplications and the RNA-mediated amino acid substitutions that differentiate all cell types of all individuals of all species.
Re: 2) Genes can adapt to different environmental changes by choosing the most optimal codon, which is counterintuitive to natural selection
This statement can be placed into the context of what others have claimed about natural selection compared to ecological speciation July 2013 Carl Zimmer: “Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed “the blind watchmaker.” To some extent, it just happens.”June 2013 James Kohl “…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.”

Re: “…compared to any other factual representations of epigenesis and epistasis…”

June 2013 Masatoshi Nei

“…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 for comparison: Understanding faith, teaching evolution not mutually exclusive

My comment: “In… the New York Times (3/8, MM60, Zimmer, …) reports on the developing view among scientists about the status of “junk” DNA, also known as non-coding DNA. Though previously it was thought to be nonessential, in January, Dr. Francis Collins… made a comment that revealed just how far the consensus has moved.” Asked about junk DNA at a healthcare conference Collins said, “We don’t use that term anymore. It was pretty much a case of hubris to imagine that we could dispense with any part of the genome — as if we knew enough to say it wasn’t functional.” He added that “most of the DNA that scientists once thought was just taking up space in the genome…’turns out to be doing stuff.'” The Times notes that some biologists reject this hypothesis.”

See also: Is Most of Our DNA Garbage?

Excerpt:

Scientists estimate that the first eukaryotes evolved about 2 billion years ago, in one of the greatest transitions in the history of life. But there is little evidence of this momentous event, no missing link…

My comment: Some of the uninformed biologists are interviewed by Zimmer.

See also: Under the Sea, a Missing Link in the Evolution of Complex Cells
Excerpt: 

This is a genuine breakthrough,” said Eugene Koonin, an evolutionary biologist at the National Center for Biotechnology Information who was not involved in the research. “It’s almost too good to be true.”

See also:  Riding the Evolution Paradigm Shift With Eugene Koonin
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…” — Eugene Koonin

My comment: The question arises: Can anything taught to today’s students about evolution be useful without ridiculous ideas about mutations and natural selection?
See also: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
This was reported as: Evolutionary Rewiring
The “re-evolution” of the bacterial flagellum in 4 days makes sense if it was driven by viruses. It does not make sense to put it into the context of evolution either with or without mutations and natural selection.
See my additional comments to The Scientist.