Watering Young Plant - Vintage Effect

A single base change refutes theistic evolution

Everyone who failed to learn how light-activated endogenous substrates biophysically constrain viral latency is playing “catch up” to serious scientists. The serious scientists know how quantized energy-dependent RNA-mediated cell type differentiation occurs in the context of the physiology of reproduction in all living genera. Rather than accept the fact that the innate immune system of bacteria (CRISPR) linked the pheromone-controlled physiology of reproduction from autophagy to biophysically constrained viral latency, theorists decided to waste money on virus-assisted gene-editing attempts to repair virus-damaged DNA.

Mammoth Biosciences launches a CRISPR-powered search engine for disease detection

Jennifer Doudna, George Church and many others still refuse to admit that they have refuted theistic evolution. They are just beginning to accurately portray the how detection of changes in the microRNA/messenger RNA balance links virus-driven energy theft to the degradation of messenger RNA. Clearly, however, they know how the degradation of messenger RNA is linked to all pathology.

Had they followed the works of Christ et al. (2013), The Pharmacology of Regenerative Medicine and Christ et al., (2018) Western Diet Triggers NLRP3-Dependent Innate Immune Reprogramming, they could intelligently interact with those who are scheduled to present during Schrödinger at 75 – The Future of Biology – September 2018.

(Nick Lane excepted.) He appears to be a biologically uninformed theorist who does not realize that Fast food makes the immune system more aggressive in the long term

Unhealthy eating causes some of these normally hidden pieces of DNA to unwind, similar to a loop hanging out of a ball of wool. This area of the genetic material can then be read much easier as long as this temporary unwrapping remains active. Scientists call these phenomena epigenetic changes. “The inflammasome triggers such epigenetic changes,” explains Dr. Latz. “The immune system consequently reacts even to small stimuli with stronger inflammatory responses.”

The immune system reacts to the proliferation of viruses. The viruses cause the inflammation, which has been linked to all pathology in more than 72,500 published works. See microRNA.

See also: Field-deployable viral diagnostics using CRISPR-Cas13

…the Cas13-based SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) platform can detect Zika virus (ZIKV) and dengue virus (DENV) in patient samples at concentrations as low as 1 copy per microliter. We developed HUDSON (heating unextracted diagnostic samples to obliterate nucleases), a protocol that pairs with SHERLOCK for viral detection directly from bodily fluids, enabling instrument-free DENV detection directly from patient samples in <2 hours. We further demonstrate that SHERLOCK can distinguish the four DENV serotypes, as well as region-specific strains of ZIKV from the 2015–2016 pandemic. Finally, we report the rapid (<1 week) design and testing of instrument-free assays to detect clinically relevant viral single-nucleotide polymorphisms.

Pardis C. Sabeti’s group already linked the anti-entropic virucidal energy of sunlight from the creation of enzymes to natural selection for energy-dependent codon optimality via the pheromone-controlled stability of organized genomes in a human population in what is now Central China.
See this report from 2013 on fixation of the EDAR V370A substitution.
Following the footprints of positive selection February 15th, 2013.
For comparison to positive selection for food and fixation of the EDAR V370A amino acid substitution, the pseudoscientific nonsense about evolution touted by Pardis C. Sabeti’s group appears in this YouTube video report: 2 Cell Studies Reveal Genetic Variation Driving Human Evolution
In the mouse model of food energy-dependent pheromone-controlled ecological adaptations, they replaced the valine normally found in mouse EDAR with the alanine that’s under selection in humans. They got mice with thicker hair, changes in mammary tissue, and and increased  number of eccrine sweat glands. Those changes parallel phenotypic changes in humans. The phenotypic changes in humans link the quantized energy-dependent creation of microRNAs to biophysically constrained viral latency in all living genera.
In humans, the changes are linked to visual perception of mass and energy and the perception of physical features that are sexually selected.
See: Olfaction Warps Visual Time Perception
A single base change results in the valine to alanine substitution, which changes the ancient mammalian gene EDAR and the EDAR encoded protein.
That fact was reported in the context of links from subatomic particles and all levels of biophysically constrained viral latency and biological organization in my 2014 invited review of nutritional epigenetics.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (unpublished)
Conclusion:

The ecological adaptations, which appear to be manifested in the human population are detailed in these two reports [162-163]. The ecological adaptations are likely to be nutrient-dependent and pheromone-controlled. If so, ecological variation probably leads to ecological, social, neurogenic, and socio-cognitive niche construction, which is manifested in increasing organismal complexity and species diversity. If not, there may be something as yet unknown about mutations and evolution that makes sense in the light of what is known about nutritional epigenetics and the molecular biology of species from microbes to man

162. Kamberov, Yana G.; Wang, S.; Tan, J.; Gerbault, P.; Wark, A.; Tan, L.; Yang, Y.; Li, S.; Tang, K.; Chen, H., et al., Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant. Cell 2013, 152 (4), 691-702. doi: 10.1016/j.cell.2013.01.016
163. Grossman, Sharon R.; Andersen, Kristian G.; Shlyakhter, I.; Tabrizi, S.; Winnicki, S.; Yen, A.; Park, Daniel J.; Griesemer, D.; Karlsson, Elinor K.; Wong, Sunny H., et al., Identifying Recent Adaptations in Large-Scale Genomic Data. Cell 2013, 152 (4), 703-713. doi: 10.1016/j.cell.2013.01.035
See also:
161. Rosenberg, S. M.; Queitsch, C., Combating Evolution to Fight Disease. Science 2014, 343 (6175), 1088-1089. doi: 10.1126/science.1247472
Kalevi Kull: Censorship & Royal Society Evo Event

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

Serious scientists from South Korea are the winners. Two recent publications forced the denuclearization of North Korea.
Emergence of Human G2P[4] Rotaviruses in the Post-vaccination Era in South Korea: Footprints of Multiple Interspecies Re-assortment Events

Compared to the G2 RotaTeq vaccine strain, 17-24 amino acid changes, specifically A87T, D96N, S213D, and S242N substitutions in G2 epitopes, were observed. These results suggest that multiple interspecies re-assortment events might have contributed to the emergence of G2P[4] rotaviruses in the post-vaccination era in South Korea.

A Single Amino Acid at the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses

When analyzed using reverse-genetically rescued viruses, it was shown that PA K338R alone could increase the pathogenicity of both IBVs in mice and viral replication property in the respiratory tracts of ferrets. In a subsequent mini-replicon assay, the effect of PA K338R was highlighted by the enhancement of viral polymerase complex activity of both Vc_BR60 and Ym_WI01 viruses. These results suggest that the PA K338R mutation may be a molecular determinant of IBV pathogenicity via modulating the viral polymerase function of IBVs.

Mutations are known to be the molecular determinants of all pathology in species from microbes to humans. See:  Virus-mediated archaeal hecatomb in the deep seafloor
Watch as Hashem Al-Ghaili puts everything known to serious scientists about the virus-mediated archaeal hecatomb back into the context of neo-Darwinian evolution.

See also: Study offers new approach to starve p53 deficient tumors

One major hallmark of cancer cells is their ability to adapt to stressful conditions such as nutrient deprivation. Rapidly growing tumor cells must compete for the ever-diminishing supply of nutrients in the surrounding environment to survive and proliferate. Targeting these adaptive mechanisms represents a promising approach for cancer therapeutics.

It’s a little late to claim that the virus-driven theft of quantized energy is linked from autophagy to adaptations in viruses. All serious scientists know that food energy-dependent pheromone-controlled biophysically constrained autophagy has been linked to viral latency and to ecological adaptations in all living genera. Intelligent people know that viruses have been linked to all pathology.
See also: From Istanbul, Turkey. Respect for all human life has been placed into the context of the energy-dependent de novo creation of microRNAs and the works of an Islamic creationist in Turkey.

Autophagy-Regulating microRNAs and Cancer
Cancer researchers in other countries clearly are approaching the cure for all pathology from a scientific creationist perspective despite being forced to place their claims into the context of evolution to get their works past peer review.
The Trump administration has been working towards world peace with other leaders for more than a year. See for example:
May 3, 2017
LIVE: President Donald J. Trump and Palestinian President Mahmoud Abbas make a joint statement at the White House.
Who does not want World Peace? Why The End of the Korean War Is Bad News for the United States
Caption: Contemporary analyses of cell metabolism have called out three metabolites: ATP, NADH, and acetyl-CoA, as sentinel molecules whose accumulation represent much of the purpose of the catabolic arms of metabolism and then drive many anabolic pathways. Such analyses largely leave out how and why ATP, NADH, and acetyl-CoA (Figure 1) at the molecular level play such central roles. Yet, without those insights into why cells accumulate them and how the enabling properties of these key metabolites power much of cell metabolism, the underlying molecular logic remains mysterious. Four other metabolites, S-adenosylmethionine, carbamoyl phosphate, UDP-glucose, and Δ2-isopentenyl-PP play similar roles in using group transfer chemistry to drive otherwise unfavorable biosynthetic equilibria. This review provides the underlying chemical logic to remind how these seven key molecules function as mobile packets of cellular currencies for phosphoryl transfers (ATP), acyl transfers (acetyl-CoA, carbamoyl-P), methyl transfers (SAM), prenyl transfers (IPP), glucosyl transfers (UDP-glucose), and electron and ADP-ribosyl transfers (NAD(P)H/NAD(P)+) to drive metabolic transformations in and across most primary pathways. The eighth key metabolite is molecular oxygen (O2), thermodynamically activated for reduction by one electron path, leaving it kinetically stable to the vast majority of organic cellular metabolites

MicroRNA-mediated denuclearization (4)

Summary: Christ’s lab showed that in vivo formation of I-motif structures is pH dependent and helped to put the “fear of God” into atheistic communists.

I-motif DNA structures are formed in the nuclei of human cells (4/23/18)

Reported as: In human cells, scientists find DNA that looks like a twisted knot instead of a double helix (4/23/18)

Also reported as: New Twisted ‘Knot’ Human DNA Structure Discovered—and It Looks Nothing Like the Double Helix (4/23/18)

Christ’s lab showed that in vivo formation of I-motif structures is pH dependent. Clearly, the potential of hydrogen (pH) and pH-dependent cell cycles link the quantized energy of virucidal sunlight to protection from the degradation of messenger RNA that links mutations to all pathology.
In that context, denuclearization has been forced on North Korea and other communist countries by scientific creationists in South Korea. The creationists have indirectly revealed that they could decimate human populations in China via the creation of a virus with one base pair change linked to one amino acid substitution.
See also: 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.

Until recently, the pseudoscientific nonsense about vaccines that could protect human populations from the forthcoming viral apocalypse was tightly linked from communism to atheism. For comparison, Christ’s lab appears to have put the fear of God into its proper context; the 1918 Spanish flu.
Previously reported as: Structural diversity of supercoiled DNA (2015) and parodied in:

See also: The Pharmacology of Regenerative Medicine (2013)
See also: Energy as information and constrained endogenous RNA interference (2017)

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

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

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

Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution.

The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

diseases-disorders

RNA-mediated "repurposing" is nutrient-dependent and pheromone-controlled

 Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Excerpt: The fast-spreading strain AR2F had acquired an additional point mutation in the σ54-dependent EBP gene ntrC, which alters an amino acid (R442C) within the DNA binding domain (Table 1 and table S2).

Reported as: Evolutionary Rewiring

Strong selective pressure can lead to rapid and reproducible evolution in bacteria.

By Ruth Williams | February 26, 2015

Excerpt: NtrC shares 30 percent amino acid identity with FleQ, suggesting the proteins may be able to minimally cross-react with each other’s target genes. Sure enough, the researchers determined that the initial mutations, which ramped up NtrC levels, enabled a minor upregulation of FleQ’s target genes. The second mutations to NtrC itself then improved the protein’s interaction with the FleQ targets, boosting their expression, and the bacteria’s ability to swim.

My summary: Researchers still seem to be very confused about the difference between amino acid substitutions, which stabilize RNA-mediated protein folding and mutations. Mutations perturb protein folding, which is why they are consistently linked to physiopathology and not linked from ecological variation to nutrient-dependent pheromone-controlled ecological adaptations via the physiology of reproduction in species from microbes to humans.
My comments on “Evolutionary Rewiring”:
Re: “…repurposing of a distantly related protein.”
1) The “repurposing” is nutrient-dependent and pheromone-controlled.
2) The repurposing exemplifies how ecological variation leads to nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions that stabilize DNA in the organized genomes of species from microbes to man.
See how important it is to understand genomic stability in the context of “repurposing.” Biocontainment of genetically modified organisms by synthetic protein design. See also the importance of Combating Evolution to Fight Disease.
Richard Lenski and many others have been on the wrong side of this fight for several decades. See, for example: A single amino acid substitution differentiates cell types of E. coli
Re: “The results highlight the importance of gene duplication…”
Gene duplication is nutrient-dependent. Fixation of amino acid substitutions that stabilize the genome is controlled by the physiology of reproduction, which is controlled by the metabolism of nutrients to species-specific pheromones.
The RNA-mediated fixation of amino acid substitutions links metabolic networks to genetic networks. That fact explains why Church’s group has taken great care to address other facts that link physics, chemistry, and conserved molecular mechanisms to cell type proliferation, which theorists tend to attribute to mutations and evolution.
For constast to the claims of theorists, Christ and others: The Pharmacology of Regenerative Medicine are also attempting to link “… the salient features of diverse fields of research—ranging from materials chemistry and functionalized biomaterials to stem cells, organ/tissue regeneration, wound healing, and development biology…”
Accurate representations of nutrient-dependent biologically-based cause and effect during life history transistions also can be viewed in the context of heterochronic parabiosis, which links fixed amino acid substitutions in red blood cells to the delivery of nutrients to every cell in organisms with a circulatory system.
Mutations perturb the molecular mechanisms of the delivery system, which typically prevent sepsis caused by E. coli or other microbes that ecologically adapt to higher body temperatures than can be maintained by immunocompromised mammals (e.g., like your grandmother who may have died from complications of a urinary tract infection in the context of evolutionary theory).
The journal article reports the de novo origination of new functions via the nutrient-dependent creation and rewiring of gene networks linked to metabolic networks by the pheromone-controlled fixation of an amino acid substitution in the DNA of the organized genome of a microbe with a flagellum that enables it to find food. In their example of a starving microbe, the flagellum is first evolved then lost. A few days later it has re-evolved, and they place evolution and re-evolution of the structure and its function into the context of mutations and evolution via “…a highly repeatable two-step evolutionary pathway with the same point mutations often recurring in independent lineages.”

See also: Bacteria ‘hotwire their genes’ to fix a faulty motor.
Watch for more pseudoscientific nonsense as evolutionary theorists try to explain the nutrient-dependent breaking of Mendel’s “Law of Segregation” reported here R2d2 beats Mendel: Scientists find selfish gene that breaks long-held law of inheritance and why additions must be made to the second Law of thermodynamics, reported here: On quantum scales, there are many second laws of thermodynamics.
Obviously, they will keep trying to get others to believe that they have accurately represented biologically-based cause and effect that may or may not lead to evolution in 4 days or 2 billion years. See: Scientists discover organism that hasn’t evolved in more than 2 billion years. There only other choice is to join the serious scientists who are Combating Evolution to Fight Disease. However, recruits may now be required to pass an intelligence test, since nearly everyone will want to join serious scientists in combat. Those who have published papers about mutations and evolution during the past decade may be automatically excluded unless they can explain why they thought that evolution via mutations automagically occurred.

diseases-disorders

RNA-mediated "repurposing" is nutrient-dependent and pheromone-controlled

 Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Excerpt: The fast-spreading strain AR2F had acquired an additional point mutation in the σ54-dependent EBP gene ntrC, which alters an amino acid (R442C) within the DNA binding domain (Table 1 and table S2).

Reported as: Evolutionary Rewiring

Strong selective pressure can lead to rapid and reproducible evolution in bacteria.

By Ruth Williams | February 26, 2015

Excerpt: NtrC shares 30 percent amino acid identity with FleQ, suggesting the proteins may be able to minimally cross-react with each other’s target genes. Sure enough, the researchers determined that the initial mutations, which ramped up NtrC levels, enabled a minor upregulation of FleQ’s target genes. The second mutations to NtrC itself then improved the protein’s interaction with the FleQ targets, boosting their expression, and the bacteria’s ability to swim.

My summary: Researchers still seem to be very confused about the difference between amino acid substitutions, which stabilize RNA-mediated protein folding and mutations. Mutations perturb protein folding, which is why they are consistently linked to physiopathology and not linked from ecological variation to nutrient-dependent pheromone-controlled ecological adaptations via the physiology of reproduction in species from microbes to humans.
My comments on “Evolutionary Rewiring”:
Re: “…repurposing of a distantly related protein.”
1) The “repurposing” is nutrient-dependent and pheromone-controlled.
2) The repurposing exemplifies how ecological variation leads to nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions that stabilize DNA in the organized genomes of species from microbes to man.
See how important it is to understand genomic stability in the context of “repurposing.” Biocontainment of genetically modified organisms by synthetic protein design. See also the importance of Combating Evolution to Fight Disease.
Richard Lenski and many others have been on the wrong side of this fight for several decades. See, for example: A single amino acid substitution differentiates cell types of E. coli
Re: “The results highlight the importance of gene duplication…”
Gene duplication is nutrient-dependent. Fixation of amino acid substitutions that stabilize the genome is controlled by the physiology of reproduction, which is controlled by the metabolism of nutrients to species-specific pheromones.
The RNA-mediated fixation of amino acid substitutions links metabolic networks to genetic networks. That fact explains why Church’s group has taken great care to address other facts that link physics, chemistry, and conserved molecular mechanisms to cell type proliferation, which theorists tend to attribute to mutations and evolution.
For constast to the claims of theorists, Christ and others: The Pharmacology of Regenerative Medicine are also attempting to link “… the salient features of diverse fields of research—ranging from materials chemistry and functionalized biomaterials to stem cells, organ/tissue regeneration, wound healing, and development biology…”
Accurate representations of nutrient-dependent biologically-based cause and effect during life history transistions also can be viewed in the context of heterochronic parabiosis, which links fixed amino acid substitutions in red blood cells to the delivery of nutrients to every cell in organisms with a circulatory system.
Mutations perturb the molecular mechanisms of the delivery system, which typically prevent sepsis caused by E. coli or other microbes that ecologically adapt to higher body temperatures than can be maintained by immunocompromised mammals (e.g., like your grandmother who may have died from complications of a urinary tract infection in the context of evolutionary theory).
The journal article reports the de novo origination of new functions via the nutrient-dependent creation and rewiring of gene networks linked to metabolic networks by the pheromone-controlled fixation of an amino acid substitution in the DNA of the organized genome of a microbe with a flagellum that enables it to find food. In their example of a starving microbe, the flagellum is first evolved then lost. A few days later it has re-evolved, and they place evolution and re-evolution of the structure and its function into the context of mutations and evolution via “…a highly repeatable two-step evolutionary pathway with the same point mutations often recurring in independent lineages.”

See also: Bacteria ‘hotwire their genes’ to fix a faulty motor.
Watch for more pseudoscientific nonsense as evolutionary theorists try to explain the nutrient-dependent breaking of Mendel’s “Law of Segregation” reported here R2d2 beats Mendel: Scientists find selfish gene that breaks long-held law of inheritance and why additions must be made to the second Law of thermodynamics, reported here: On quantum scales, there are many second laws of thermodynamics.
Obviously, they will keep trying to get others to believe that they have accurately represented biologically-based cause and effect that may or may not lead to evolution in 4 days or 2 billion years. See: Scientists discover organism that hasn’t evolved in more than 2 billion years. There only other choice is to join the serious scientists who are Combating Evolution to Fight Disease. However, recruits may now be required to pass an intelligence test, since nearly everyone will want to join serious scientists in combat. Those who have published papers about mutations and evolution during the past decade may be automatically excluded unless they can explain why they thought that evolution via mutations automagically occurred.