New class of DNA repair enzyme discovered

New class of DNA repair enzyme discovered
The new type of DNA repair enzyme, AlkD on the left, can identify and remove a damaged DNA base without forcing it to physically "flip" to the outside of the DNA backbone, which is how all the other DNA repair enzymes in its family work, as illustrated by the human AAG enzyme on the right. The enzymes are shown in grey, the DNA backbone is orange, normal DNA base pairs are yellow, the damaged base is blue and its pair base is green. Credit: Brandt Eichman, Vanderbilt University

This year's Nobel Prize in chemistry was given to three scientists who each focused on one piece of the DNA repair puzzle. Now a new study, reported online Oct. 28 in the journal Nature, reports the discovery of a new class of DNA repair enzyme.

When the structure of DNA was first discovered, scientists imagined it to be extremely chemically stable, which allowed it to act as a blueprint for passing the basic traits of parents along to their offspring. Although this view has remained prevalent among the public, biologists have since learned that the double helix is in fact a highly reactive molecule that is constantly being damaged and that cells must make unceasing repair efforts to protect the genetic information that it contains.

"It's a double-edged sword," said Brandt Eichman, associate professor of biological sciences and biochemistry at Vanderbilt University, who headed the research team that made the new discovery. "If DNA were too reactive then it wouldn't be capable of storing genetic information. But, if it were too stable, then it wouldn't allow organisms to evolve."

The DNA double-helix has a spiral staircase structure with the outer edges made from sugar and phosphate molecules joined by stair steps composed of pairs of four nucleotide bases (adenine, cytosine, guanine and thymine) that serve as the basic letters in the genetic code.

There are two basic sources of DNA damage or lesions: environmental sources including ultraviolet light, toxic chemicals and ionizing radiation and internal sources, including a number of the cell's own metabolites (the chemicals it produces during normal metabolism), reactive oxygen species and even water.

"More than 10,000 DNA damage events occur each day in every cell in the human body that must be repaired for DNA to function properly," said first author Elwood Mullins, a postdoctoral research associate in the Eichman lab.

The newly discovered DNA repair enzyme is a DNA glycosylase, a family of enzymes discovered by Tomas Lindahl, who received this year's Nobel prize for recognizing that these enzymes removed damaged DNA bases through a process called base-excision repair. It was the first of about 10 different DNA repair pathways that biologists have identified to date.

In base-excision repair, a specific glycosylase molecule binds to DNA at the location of a lesion and bends the double-helix in a way that causes the damaged base to flip from the inside of the helix to the outside. The enzyme fits around the flipped out base and holds it in a position that exposes its link to the DNA's sugar backbone, allowing the enzyme to detach it. After the damaged base has been removed, additional DNA-repair proteins move in to replace it with a pristine base.

Eichman and his collaborators discovered that a glycosylase called AlkD found in Bacillus cereus - a soil-dwelling bacterium responsible for a type of food poisoning called the "fried rice syndrome" - works in a totally different fashion. It does not require base flipping to recognize damaged DNA or repair it.

Seven years ago, Eichman's group discovered that AlkD had a structure unlike any of the other glycosylases. The researchers determined that the enzyme was able to locate damaged DNA that has a positive electrical charge. This is the signature of alkylation, attaching chains of carbon and hydrogen atoms of varying lengths (methyl, ethyl etc.), to specific positions on the damaged base. Positively charged alkylated bases are among the most abundant and detrimental forms of DNA damage. However, they are highly unstable, which has made them very difficult to study.

New class of DNA repair enzyme discovered
Top and side view showing the difference in the way that a normal DNA repair glycosylase enzyme (AAG) and the new enzyme (AlkD) recognize a damaged DNA base. The AAG enzyme bends the DNA in way that forces the damaged base to rotate from its normal position inside the double helix to an outside position where the enzyme binds to it and removes it. In contrast, the AlkD enzyme senses the chemical features of the damaged base through the DNA backbone, without physically contacting the damaged base itself. The enzymes are shown in grey, the DNA backbone is orange, normal DNA base pairs are yellow, the damaged base is purple and its pair base is green. Credit: Brandt Eichman / Vanderbilt

Now the researchers have captured crystallographic snapshots of AlkD in the act of excising alkylation damage and have shown that the enzyme doesn't use base flipping. Instead, they have determined that AlkD forms a series of interactions with the DNA backbone at and around the lesion while the lesion is still stacked in the double helix. Several of these interactions are contributed by three amino acids in the enzyme that catalyze excision of the damaged base.

According to the researchers, the AlkD mechanism has some remarkable properties:

  • It can recognize damaged bases indirectly. AlkD identifies lesions by interacting with the DNA backbone without contacting the damaged base itself.
  • It can repair many different types of lesions as long as they are positively charged. By contrast, the base-flipping mechanism used by other glycosylases relies on a relatively tight binding pocket in the enzyme, so each glycosylase is designed to work with a limited number of lesions. AlkD doesn't have the same type of pocket so it isn't restricted in the same way. Instead, the catalytic mechanism that AlkD uses is limited to removing positively charged lesions.
  • It can excise much bulkier lesions than other glycosylases. Base excision repair is generally limited to relatively small lesions. A different pathway, called nucleotide excision repair, handles larger lesions like those caused by UV radiation damage. However, Eichman's team discovered that AlkD could excise extremely bulky lesions, such as the one caused by the antibiotic yatakemycin, which is beyond the capability of other glycosylases.

"Our discovery shows that we still have a lot to learn about DNA repair, and that there may be alternative repair pathways yet to be discovered. It certainly shows us that a much broader range of DNA damage can be removed in ways that we didn't think were possible," said Eichman. "Bacteria are using this to their advantage to protect themselves against the antibacterial agents they produce. Humans may even have DNA-repair enzymes that operate in a similar fashion to remove complex types of DNA damage. This could have clinical relevance because these enzymes, if they exist, could be reducing the effectiveness of drugs designed to kill cancer cells by shutting down their ability to replicate."


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Newly discovered DNA repair mechanism

More information: The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions, Nature, DOI: 10.1038/nature15728
Journal information: Nature

Citation: New class of DNA repair enzyme discovered (2015, October 29) retrieved 23 August 2019 from https://phys.org/news/2015-10-class-dna-enzyme.html
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JVK
Oct 29, 2015
Nutrient-dependent RNA-mediated DNA repair links the epigenetic landscape to the physical landscape of supercoiled DNA during life history transitions that link ecological variation to ecological adaptations via metabolic and genetic networks.

Nutrient-dependent microRNAs link atoms to ecosystems via biophysically constrained protein folding that is perturbed by the accumulation of viruses, which are linked via viral microRNAs to all pathology. Nutrient-dependent microRNAs are linked to healthy longevity via the cell adhesion proteins that protect genome organization from nutrient stress and/or social stress during thermodynamic cycles of protein biosynthesis and degradation.

See my invited review of nutritional epigenetics:
Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
http://figshare.c...s/994281

Oct 29, 2015
See my invited review of nutritional epigenetics


JVK-Skippy if nobody wanted any of your stinky love potions, why you think they are going to take you up on your invitation for some nutritional gobbledygook? Man that sounds nasty, and probably illegal too. You should lay off that stuffs before it's too late,,,, well it's probably too late already, but you should still try to cut back some.

JVK
Oct 29, 2015
Re: "The enzyme fits around the flipped out base and holds it in a position that exposes its link to the DNA's sugar backbone, allowing the enzyme to detach it. After the damaged base has been removed, additional DNA-repair proteins move in to replace it with a pristine base."

Viruses steal the energy that cells need to maintain the positions of the base pairs. Without the nutrient-dependent energy supplied by nutrient-dependent microRNAs, the proliferation of virsuses links viral microRNAs to age-related immune system changes and to pathology.

That pathology can extend across generations via transgenerational epigenetic inheritance of the morphological and behavioral phenotypes that are typically fine-tuned for species-specific survival via fixation of RNA-mediated amino acid substitutions in the context of the physiology of reproduction in all living genera.

One amino acid substitution is all that is required to differentiate an individual or a species.

JVK
Oct 29, 2015
Re: "Bacteria are using this to their advantage to protect themselves against the antibacterial agents they produce."

Isn't it more likely that they are using nutrient-dependent RNA-mediated DNA repair to protect their organized genomes from virus-driven genomic entropy and using the metabolism of nutrients to species-specific pheromones to control their physiology of reproduction?

There's model for that! Nutrient-dependent/pheromone-controlled adaptive evolution: a model http://www.ncbi.n...24693353

Excerpt: THIS MODEL DETAILS HOW CHEMICAL ECOLOGY DRIVES ADAPTIVE EVOLUTION VIA: (1) ecological niche construction, (2) social niche construction, (3) neurogenic niche construction, and (4) socio-cognitive niche construction.

The required link from quantum mechanics to RNA-mediated cell type differentiation in the brain tissue of some individuals of some species appears to be docosahexanoic acid. See: http://www.ncbi.n...23206328

JVK
Oct 29, 2015
Re: "The required link from quantum mechanics to RNA-mediated cell type differentiation in the brain tissue of some individuals of some species appears to be docosahexanoic acid."

It seems obvious that people like "Uncle Ira" did not get enough docosahexanoic acid during brain development to enable fixation of the amino acid substitutions that lead to intelligent thought processes. In theory, the docosahexanoic acid-deprived are the people who become neo-Darwinian theorists.

Oct 29, 2015


There's model for that! Nutrient-dependent/pheromone-controlled adaptive evolution: a model http://www.ncbi.n...24693353


JVK's model destroyed:
http://www.ncbi.n...4049134/

JVK
Oct 29, 2015
My model is supported by everything currently known about nutrient-dependent base pair flipping and RNA-mediated DNA repair in the context of links from quantum physics, quantum chemistry, quantum smell, and quantum biology to quantum consciousness -- as detailed in the context of the sequencing of the octopus genome, which links microRNAs to adhesion proteins across species, and what is presented in this parody:

https://www.youtu...youtu.be All About that Base (Meghan Trainor Parody)

Oct 30, 2015
Isn't it more likely that they are using nutrient-dependent RNA-mediated DNA repair to protect their organized genomes from virus-driven genomic entropy and using the metabolism of nutrients to species-specific pheromones to control their physiology of reproduction?

Sorry to bust your self-love fest but - prob'ly not...


Oct 30, 2015
"My model is supported by blah blah blah--"

Only in JVK's deluded mind is his model supported.

JVK
Oct 30, 2015
Sorry to bust your self-love fest but - prob'ly not...


What is the basis for your assessment of that probability (you moron)?

https://www.faceb...2583907/

Has the energy link from the speed of light on contact with water
to the colors of the rainbow and the structure of supercoiled DNA been placed into the context of nutrient-dependent thermodynamics and organism-level thermoregulation?

For example, could Phi be the link from quantum mechanics to the conserved molecular mechanisms of RNA-mediated protein folding chemistry that links RNA-mediated amino acid substitutions to the stability of organized genomes in all living genera?

Visible light spectrum range
~ 650nm to ~400nm
650/400 = 1.625

DNA molecule
34Å long by 21Å wide (for each full cycle of its double helix spiral)
34/21=1.619

Oct 30, 2015
It seems obvious that people like "Uncle Ira" did not get enough docosahexanoic acid during brain development to enable fixation of the amino acid substitutions that lead to intelligent thought processes. In theory, the docosahexanoic acid-deprived are the people who become neo-Darwinian theorists.


Well Skippy, it should be obvious by now if you want to insult me or hurt my feelings you are going to need to say something that makes a whole lot more sense than that.

And if the stuff you are talking about is what caused you to turn out like you did, I am glad I missed out on those drugs.

JVK
Oct 30, 2015
I am glad I missed out on those drugs.


Your problem is the drugs. They have caused horrid deficits in the development of your brain.

In an invited review of nutritional epigenetics I mentioned that experimental evidence from studies of amino acid substitutions and cell type differentiation suggests that a cascade of changes in protein structure and function may begin with a single vitamin-dependent base pair change.

This research report attests to that fact in the context of the musical parody that attests to the ignorance of all theorists. https://www.youtu...youtu.be

Everything about cell type differentiation starts with atoms and is linked at every level of examination from base pairs to ecosystems in all living genera. The obvious links are from RNA-mediated amino acid substitutions during life history transitions -- as noted here:
http://link.sprin...4-0895-5

Oct 30, 2015
I am glad I missed out on those drugs.


Your problem is the drugs. They have caused horrid deficits in the development of your brain.


Well that is a really good theory Skippy. Except I do not take drugs, and never have either. You are the one who is pushing drugs all the time, not me. I am not sure those stinky love potions are even legal, eh? What goes into them anyway?

JVK
Oct 30, 2015
Re: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

I asked
...could Phi be the link from quantum mechanics to the conserved molecular mechanisms of RNA-mediated protein folding chemistry that links RNA-mediated amino acid substitutions to the stability of organized genomes in all living genera?


A serious scientist would attempt to answer that question because the Val158Met amino acid substitution is epigenetically effected by a functional single nucleotide polymorphism in COMT. The G-to-A base-pair substitution leads to the methionine (Met) valine (Val) substitution at codons 108/158.

That fact can be placed into the context of claims about the new DNA repair enzyme. For example, carriers of the Met allele display a fourfold decrease in enzymatic activity compared to Val allele carriers, and that fact is linked to an increase of prefrontal dopamine activity.

Oct 30, 2015
Jvk provides a link to : "Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults" that has nothing to do with cell type differentiation but some how he finds a link.

That is to be expected since JVK is so stupid he doesn't know the age of the Earth.

JVK
Oct 30, 2015
Re: prefrontal dopamine activity

Food odors and pheromones are linked via changes in GnRH to prefrontal dopamine activity and the reward mechanisms associated with classically conditioned epigenetically effected experience-based de novo creation of receptors in cell types during maturation of the brain, which is linked to successful reproduction.

What goes into [human pheromone-enhanced] fragrance products?


Thanks for asking. We used a mixture of androstenol and androsterone to elicit effects on women's flirtatious behaviors because that is the mixture in the product I developed for use by men, and also by women -- if they are interested in a potential mood increase / potential head-ache remedy or potential help with symptoms of menstrual cycle distress.

But enough about me and that product. What about you? What kind of biologically uniformed science idiot repeatedly displays his ignorance here? Why do you do that -- if you are not taking mind-altering drugs?

JVK
Oct 30, 2015
"Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults" ... has nothing to do with cell type differentiation


What kind of biologically uninformed science idiot makes such a ridiculous claim about an article that links a single amino acid substitution to changes in behavior during life history transitions, which are directly comparable to the changes that occur in the honeybee model organism?

See: Honey bees as a model for understanding mechanisms of life history transitions http://www.ncbi.n...15925525

See also: Feedback loops link odor and pheromone signaling with reproduction
http://www.ncbi.n...16290036

... JVK is so stupid he doesn't know the age of the Earth.


Obviously, I am not as stupid as the person who asks such a stupid question in the context of what could be intelligent discussion about RNA-mediated DNA repair.

JVK
Oct 30, 2015
The entirety of the current focus on personalized/precision medicine is based on what has been learned about RNA-mediated DNA repair during the past 15-30 years.

Simply put, DNA repair is nutrient dependent. At the level of quantum mechanics, that fact links food odors -- via Schrodinger's claims about the anti-entropic energy of sunlight -- to the de novo creation of cell type receptors that enable nutrient energy to cause species-specific changes that increase the stability of organized genomes in all living genera.

Viruses perturb that stability by stealing the nutrient-dependent energy, which is how viruses are linked from perturbed protein folding to all pathology. The fact that prevention of all pathology appears to be in reach and that cures will refute all claims ever made by neo-Darwinian theory explains why my antagonists continue their desperate attempts to discredit me, while insulting the intelligence of all other serious scientists.

Oct 30, 2015
But enough about me and that product.


Oh Cher, if only really meant that true.

What about you?


What about me? I said I do not take drugs like you mistake I did.

What kind of biologically uniformed science idiot repeatedly displays his ignorance here?


I do not wear the uniform, why you think I should? And I don't mind repeating my displays, most of the time, if I am not really busy.

Why do you do that --


Just for something to do. Why you do want you do?

if you are not taking mind-altering drugs?


I told you I do not take drugs. You sure do make a lot noise about about drugs and such-like,,, are you trying to camouflage something Cher?

Oct 30, 2015
The fact that prevention of all pathology appears to be in reach and that cures will refute all claims ever made by neo-Darwinian theory explains why my antagonists continue their desperate attempts to discredit me, while insulting the intelligence of all other serious scientists.


Skippy, do you work hard to say really stupid stuffs? Or does it just come natural to you? Cher, read that one again over, careful like, and try to explain why that means something. It sounds like something a crankpot with the mental conditions would write.

JVK
Oct 30, 2015
Only in JVK's deluded mind is his model supported.


See: Methyl-H3K9-binding protein MPP8 mediates E-cadherin gene silencing and promotes tumour cell motility and invasion http://www.ncbi.n...2982762/

See: Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity http://dx.doi.org.../ncb3227

See: The octopus genome and the evolution of cephalopod neural and morphological novelties http://dx.doi.org...ure14668

Excerpt: "Protocadherins have high expression in neural tissues. Cadherins generally show a similar expression pattern..."

Similar expression patterns link nutrient-dependent microRNAs to the stability of organized genomes in all living genera via the physiology of reproduction, which enables the fixation of RNA-mediated amino acid substitutions that protect organized genomes from virus-driven genomic entropy. Top-down causation is energy, not mutations.

JVK
Oct 30, 2015
Re: Top-down causation is energy, not mutations.

...try to explain why that means something. It sounds like something a crankpot with the mental conditions would write.


It was Darwin's claim before de Vries defined "mutation." Are you claiming that Darwin's claims about "conditions of life" and his insistence that "conditions of life" be considered before natural selection were made by a crackpot?

If so, we can compare my claims to yours and to the claims of all other crackpots who invented or continue to tout neo-Darwinism based on their assumptions of how long it might take for mutations to lead to the creation of a new species.

I repeat:
The fact that prevention of all pathology appears to be in reach and that cures will refute all claims ever made by neo-Darwinian theory explains why my antagonists continue their desperate attempts to discredit me, while insulting the intelligence of all other serious scientists.


Keep trying, you morons!


Oct 30, 2015
"Jvk provides a link ... that has nothing to do with cell type differentiation..."

That is what the crank does. Observations from a _real_ biologist:

"The regulars here may recall John A. Davison, who died in 2012. He was notoriously persistent and repetitive, and rather clueless ...

... you knew another had to emerge, and he has come. I was asked to look at a string of comments left on a science article by a fellow going by the pseudonym JVK, and all the Davison traits were there. Pretentious phrasing. Repetition: if the audience didn't get it the first time, just say the same thing again, twice. A kind of sneering anger that people don't understand how smart he is. An obsession with one narrow idea, which is his, which explains all of evolution and proves that everyone else is wrong.

Behold James Vaughn Kohl."

[ http://freethough...s-place/ ]

A pheromone has more ability than JVK has.

JVK
Oct 30, 2015
Keep trying, you morons!


"That is what the crank does. Observations from a _real_ biologist" -- Torbjorn_Larsson_OM (a real crank)

Thanks "Torbjorn_Larsson_OM" -- every serious scientist knows that PZ Myers is a crank, who is typically supported by idiot minions who are, like you, are biologically uninformed science idiots. The question is why -- after I linked to the article that showed chromosomal rearrangements are the source for differences in the morphological and behavioral phenotypes of the same species -- you would again bring up the attack by Myers for my correct claim:

Excerpt: "Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction."

JVK
Oct 30, 2015
Have any of PZ Myers idiot minions ever defended the ridiculous claims made by neo-Darwinian theorists by providing experimental evidence of biologically-based cause and effect that could, for example, explain how the bacterial flagellum "re-evolved" in four days?

See: Bacteria 'hotwire their genes' to fix a faulty motor http://phys.org/n...tor.html

The anonymous fool (Andrew Jones) wrote: There was no new functional structure or gene created. There were merely two mutations altering existing regulatory elements:

Like all other anonymous fools or self-identified fools, Jones obviously does not know the difference between a nutrient-dependent RNA-mediated amino acid substitution and a mutation.

He links perturbed protein folding from atoms to ecosystems via the mutation, instead of the required nutrient-dependent microRNAs and cell adhesion proteins that stabilize organized genomes.

JVK
Oct 30, 2015
Re: "He links perturbed protein folding from atoms to ecosystems via the mutation, instead of the required nutrient-dependent microRNAs and cell adhesion proteins that stabilize organized genomes."

See: Criticisms of the nutrient-dependent pheromone-controlled evolutionary model http://www.ncbi.n...4049134/

It is an unparalleled example of what happens when you let a biologically uninformed science idiot criticize accurate representations of biologically-based cause and effect with across species examples -- as in Nutrient-dependent/pheromone-controlled adaptive evolution: a model http://www.ncbi.n...24693353

Simply put, other biologically uninformed science idiots are led to attack the model, instead of other idiots, like Masatoshi Nei (2013) who wrote: "...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world." [cont]

JVK
Oct 30, 2015
[cont] "In this view of evolution there is no need of considering teleological elements" (p. 199). http://www.amazon...99661731

Nei's textbook was published on the same day as my review article. His claim that teleological elements can be ignored echoes through the extant literature published by biologically uninformed science idiots who will never quite grasp the fact that the enzymes that repair DNA, and the DNA, did not create themselves from nothing and there would have been no need for the enzymes to facilitate DNA repair if the DNA was not damaged by the excess proliferation of viruses.

The fact that young earth creationists were among the first to call this to the attention of neo-Darwinian theorists and theoretical physicists attests to a huge problem with what some people consider to be mainstream science.

Much of it is pseudoscientific nonsense, as serious scientists who understand the need for DNA repair already know.

JVK
Oct 30, 2015
See also: Molecular Clocks and the Puzzle of RNA Virus Origins http://jvi.asm.or...93.short

Excerpt: "...families of RNA viruses circulating today could only have appeared very recently, probably not more than about 50,000 years ago. Hence, if evolutionary rates are accurate and relatively constant, present-day RNA viruses may have originated more recently than our own species."

See also: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants http://dx.doi.org...ure11690

Excerpt: "We estimate that approximately 73% of all protein-coding SNVs and approximately 86% of SNVs predicted to be deleterious arose in the past 5,000–10,000 years."

This pattern recognition is examined in the context of atoms to ecosystems by serious scientists, and the pattern is ignored by pseudoscientists who ignore the fact that final causes, design, and purpose exist in nature in the context of creation, not neo-Darwinism.

Oct 30, 2015
Like all other anonymous fools or self-identified fools, Jones obviously does not know the difference between a nutrient-dependent RNA-mediated amino acid substitution and a mutation.


A mutation is a change in the DNA sequence. The name alone does not determine whether it's beneficial or detrimental.

You're the one hung up on definitions. If you want to call beneficial DNA changes substitutions and negative ones mutations, go right ahead. It doesn't change what happens at the molecular level though.

Oct 30, 2015
Sorry to bust your self-love fest but - prob'ly not...


What is the basis for your assessment of that probability (you moron)?

https://www.faceb...2583907/


Simply because you misunderstand Phi.
And - who is Jamie Janover?

JVK
Oct 30, 2015
you misunderstand Phi


Thanks. That does not surprise me given my knowledge of biology compared to math.

Are you claiming the 360 degree rotation of the DNA molecule does not link 34 angstroms divided by 21 angstroms to the number 1.619 instead of 1.618?

Or, are you claiming that every angstrom is not dynamically effected by the sun's biological energy as indicated by the use of the visible light spectrum in the representation?

JVK
Oct 30, 2015
If you want to call beneficial DNA changes substitutions and negative ones mutations, go right ahead. It doesn't change what happens at the molecular level though.


What happens at the molecular level links nutrient-dependent RNA-mediated amino acid substitutions to the stability of organized genomes in all living genera and it also links viruses from perturbed protein folding to genomic entropy.

You claim that the difference doesn't matter because you are a biologically uninformed science idiot. The difference matters to serious scientists who do not call RNA-mediated amino acid substitutions "mutations" because they don't want other serious scientists to think they are biologically uninformed science idiots.

Oct 30, 2015

Visible light spectrum range
~ 650nm to ~400nm
650/400 = 1.625

DNA molecule
34Å long by 21Å wide (for each full cycle of its double helix spiral)
34/21=1.619

The ratio of visible light wavelengths has nothing to do with the DNA length/width ratio.
First, the ratio of visible wavelength is not a constant, but is species dependent. Second, even in humans the average human visual range is more like 390 nm to 700 nm, or a ~1.8x ratio. So not only is the ratio you quote as being near phi only coincidentally near phi, but it isn't constant and the value you use is wrong.

DNA also varies from ~18Å to ~26Å, so the ratio ranges from ~1.3 to ~1.9. Even the most common B-DNA form is 23.7, so the ratio is closer to pi/2 or to the square root of two, for example, than it is to phi.

LMAO.

Oct 30, 2015
The ratio of visible light wavelengths has nothing to do with the DNA length/width ratio.
First, the ratio of visible wavelength is not a constant, but is species dependent. Second, even in humans the average human visual range is more like 390 nm to 700 nm, or a ~1.8x ratio. So not only is the ratio you quote as being near phi only coincidentally near phi, but it isn't constant and the value you use is wrong.

DNA also varies from ~18Å to ~26Å, so the ratio ranges from ~1.3 to ~1.9. Even the most common B-DNA form is 23.7, so the ratio is closer to pi/2 or to the square root of two, for example, than it is to phi.

LMAO.


Well they didn't say anything about all that stuffs on the "Art-Bell-Skippy's-What-If-Show" so none of that counts, eh?

JVK
Oct 30, 2015
The ratio of visible light wavelengths has nothing to do with the DNA length/width ratio.


Thanks. I still find it difficult to believe that all this is a misrepresentation of mathematically based cause and effect.

https://www.faceb...2583907/

It's as if they were neo-evolutionary theorists who invented a theory and then used mathematical models from population genetics to support their assumptions and reach a consensus based on the definition of mutation.

Even the most common B-DNA form is 23.7


What does that tell us about supercoiled DNA? Is it better represented in three dimensions that link RNA-mediated events to gene duplication and link RNA-mediated amino acid substitutions to the stability of organized genomes in all living genera?

JVK
Oct 30, 2015
not only is the ratio you quote as being near phi only coincidentally near phi, but it isn't constant and the value you use is wrong.


Thanks again. How is the speed of light mathematically linked to its virucidal effects and anti-entropic effects on cell type differentiation per Schrodinger in "What is LIfe?" -- and others since then who claim that "Life is physics and chemistry and communication" http://dx.doi.org...as.12570 and/or tout Life as physics and chemistry: A system view of biology http://www.scienc...12000922

Have you ever tried to explain what is right in the context of what you claim is wrong -- like a serious scientist would do?

Oct 31, 2015
He links perturbed protein folding from atoms to ecosystems via the mutation, instead of blah blah kohlslaw full of sh*t blah
@jk
well, if you are saying that you link using your model, then, by definition, you ALSO link "perturbed protein folding from atoms to ecosystems via the mutation" because your model uses adn requires MUTATIONS (which you call perturbed protein folding as well as pathological)... and you ADMITTED this more than once. shall i re-quote you again on that, mrs-jeenyious?
you really should re-read ANON's post and tattoo it to your head, creationist-girl
A mutation is a change in the DNA sequence. The name alone does not determine whether it's beneficial or detrimental.
You're the one hung up on definitions. If you want to call beneficial DNA changes substitutions and negative ones mutations, go right ahead. It doesn't change what happens at the molecular level though.


Oct 31, 2015
@jk cont'd
Thanks. That does not surprise me given my knowledge of biology compared to math
i hate to burst your bubble yet again, but as for your comprehension of biology:
to date, you have a 100% FAIL rate interpreting biology/medical studies, and that is per the feedback of the authors, NIH, REAL biologists and medical personnel
as for math... considering your comments re: speed of light- i would recommend taking some basic courses and at least attempting long division, as you've demonstrated a complete failure of any higher math and physics
just sayin'
Are you claiming...
you are the one with the voodoo religious claims, bubbette: saying the aramaic alphabet is linked to "20 amino acids and 2 stop codons"???? on Sep 20 here:
http://phys.org/n...ane.html

then you link a x-tian link? on a science site? WTF?

reported

Oct 31, 2015
@jk cont'd
The difference matters to serious scientists who do not call RNA-mediated amino acid substitutions "mutations" because they don't want other serious scientists to think they are biologically uninformed science idiots
Epic fail: see this link
http://myxo.css.m...dex.html

Lenski is not only a HIGHLY RESPECTED scientist, but a great experimental researcher
Then there is DR. Extavour:
http://www.extavourlab.com/

exceptional scientists using the word mutation WRT actual validated proven science... not smelly perfume like you, jk, but PROVEN VALIDATED science. something you have YET to produce!

this is your legacy: failure and religion over science with a fanatical overtone which doesn't allow you to comprehend the science

want to know what the number one feedback WRT you and your comments on SciMag/Biology/Medical studies when i queried the authors with your comments?

"I don't reply to pseudoscience or religious nuts. there is no point."

Oct 31, 2015
@jk cont'd
Thanks. I still find it difficult to believe that all this is a misrepresentation of mathematically based cause and effect
so... basically you are saying: "Ok. i am proven wrong but i will still believe in what i said because...????"
WTF?
.faceb...2583907/
It's as if they were neo-evolutionary theorists who invented... mathematical models
1- facebook is not a journal nor valid scientific reference
2- the profile linked is an ARTIST
3- arguing semantics while being illiterate is like trying to claim you can fly because you once watched peter pan do it
How is the speed of light mathematically linked to...
but you still haven't actually proven your other previous claims WRT the speed of light (nor pheromones, nor about anything else)

your argument is the god of the gaps argument
https://www.youtu...kg4hMRjs

reported for continually spamming & trolling with youtube, facebook and religious dogma
epic failure for jk

JVK
Oct 31, 2015
"I don't reply to pseudoscience or religious nuts. there is no point."


Tell us again who you are quoting.

Lenski is not only a HIGHLY RESPECTED scientist, but a great experimental researcher


Like most biologically uninformed science idiots, he was taught to believe that the structure of the DNA double helix was static. He may never have considered the role of viruses. They cause genomic entropy in the absence of nutrient-dependent pheromone-controlled physiology of reproduction. He exemplified that in experiments. He clearly showed the innate ability of the E. coli to respond to ecological variation with ecological adaptations.

https://www.youtu...youtu.be

See also: Nuclear membrane repairs the 'dark matter' of DNA http://phys.org/n...dna.html

Ecological variation is not linked by mutations to "evolved" ecological adaptations. Nutrient-dependent DNA repair is required.

JVK
Oct 31, 2015
Re: Ecological variation is not linked by mutations to "evolved" ecological adaptations. Nutrient-dependent DNA repair is required.

See also: DNA twist as a transcriptional sensor for environmental changes (1992)
http://www.ncbi.n.../1508037

Any claims linked to Lenski's experiments can now be viewed in the context of what serious scientists have shown about how ecological variation is linked from metabolic networks and genetic networks to ecological adaption.

Anyone who still claims that mutations and evolution are the links between metabolic networks and genetic networks has been exposed. They are fools.

They cannot explain how the bacterial flagellum "re-evolved" over-the-weekend, which means they must ignore the fact that it did and continue to let their idiot minions tout the pseudoscientific nonsense they were taught by fools to believe in.

Thank you, Captain Stumpy, for continuing to represent the idiot minions.

Oct 31, 2015
He clearly showed the innate ability of the E. coli to respond to ecological variation with ecological adaptations.


If you understood his experimental protocol, you would know that's a faulty statement. All of his E. coli were in identical environments. There was no ecological variation.

JVK
Oct 31, 2015
All of his E. coli were in identical environments. There was no ecological variation.


I wrote: He clearly showed the innate ability of the E. coli to respond to ecological variation with ecological adaptations.

The anonymous fool (aka Andrew Jones) does not seem to know how the innate ability of the E. coli to respond links ecological variation in what the organisms eat from the physiology of their pheromone-controlled reproduction to the ecological adaptations that Lenski placed into the ridiculous context of mutations and evolution.

Obviously, Andrew Jones needs the support of other idiot minions who will reassert this claim: "...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."

JVK
Oct 31, 2015
Re: "...it just happens."

See: The Surprising Origins of Evolutionary Complexity by Carl Zimmer in "Scientific American"
http://www.scient...plexity/

Some serious scientists may be attempting to get "Scientific American" to change the name of publication to "Un-Scientific American" so that other serious scientists will not be encouraged to try to find any accurate reporting of biologically-based cause and effect.

Complexity that emerges in the context of something that "just happens" may seem like mainstream science to theorists, but it exemplifies the pseudoscientific nonsense that they have been taught to believe in when serious scientists read such ridiculous claims.

Oct 31, 2015
Tell us again who you are quoting
@jk
so far, it is the bulk of those who respond to my inquiries to their studies using your direct quotes. they clarify the subject for me but also note that they refuse to engagte idiots like you. they also request to be left out of the argument becuase the evidence speaks for itself and directly refutes your claims
unlike you, they let the evidence talk rather than try to "interpret it" with religious or other pseudoscience delusions
Like most biologically uninformed science idiots, he was taught to believe
so... when directly refuted with empirical evidence your tactic is to libelously attack something you could never attain: respected experimental scientists with education?
and then you misinterpret the study by adding in your religion and FAILING to actually comprehend the science? (Anon called you out: you just proved you were the only idiot here!)

reported

Oct 31, 2015
Thank you, Captain Stumpy, for continuing to represent the idiot minions
@jk
i do not represent you: so therefore your comment is fallacious
doesn't all that chronic lying and intentional fraud make you tired?
I wrote: He clearly showed
you have written a LOT of things... problem is: most are wrong
especially your posts on PO

just because you don't understand Lenski's experiment doesn't mean no one else does, mensa-waif...

perhaps you should read up on it?
http://myxo.css.m...dex.html

and then, perhaps you should read this: it discusses you
http://www.ploson...tion=PDF

Conspiracist ideation, by contrast, is associated with the rejection of all scientific propositions tested
this is also true of FANATICAL religious zealots like yourself

JVK
Oct 31, 2015
just because you don't understand Lenski's experiment doesn't mean no one else does


I don't understand how it can be linked to re-evolution of the bacterial flagellum over-the-weekend, and neither does any other serious scientist.

See: Evolutionary Rewiring http://www.the-sc...ewiring/


Oct 31, 2015
On 30 Oct. 2015 JVK wrote: " the fact that final causes, design, and purpose exist in nature in the context of creation, not neo-Darwinism."

Read more at: http://phys.org/n...html#jCp

So creation is a fact, a statement completely free of any evidence, hence a religious declaration
and not the least bit scientific.


JVK
Oct 31, 2015
creation is a fact, a statement completely free of any evidence


http://www.cam.ac...proteins

There is no experimental evidence from physics, chemistry, or biology that does not attest to the facts that link conserved molecular mechanisms from RNA-mediated protein folding chemistry to cell type differentiation in all living genera without claiming that mutations and evolution can be automagically linked to all biomass on Earth in the context of neo-Darwinian theory.

Oct 31, 2015
@JVK

Where is the evidence for creation being a "fact"?

That's right, it doesn't exist.

JVK
Oct 31, 2015
"Gene expression is the process by which the information encoded in a gene is used to direct the assembly of a protein molecule. The cell reads the sequence of the gene in groups of three bases. Each group of three bases (codon) corresponds to one of 20 different amino acids used to build the protein." http://ghr.nlm.ni...pression

No experimental evidence of biologically-based cause and effect suggests that the information encoded in genes created itself.

See: "What is Life?" http://www.google...;cad=rja

See: Life is physics and chemistry and communication http://dx.doi.org...as.12570

See: Akt Kinase-Mediated Checkpoint of cGAS DNA Sensing Pathway http://dx.doi.org...5.09.007

JVK
Oct 31, 2015
Now that everything known to serious scientists links the light-induced de novo creation of nucleic acids to RNA-mediated cell type differentiation via the physiology of reproduction in the context of RNA-mediated events that link physics and chemistry from atoms to ecosystems via the conserved molecular mechanisms of biophysically constrained metabolic networks and genetic networks, is there anyone who does not feel sorry for people like Vietvet (aka Steven Taylor) and others who are biologically uninformed science idiots who refuse to inform themselves?

If you do not feel sorry for people who refuse to inform themselves, are you one of them?

If you do feel sorry for people who refuse to inform themselves, do you know a way to help anyone who cannot help theirself? Think about that. Maybe a group intervention is all it would take. Shall I start a "help Steven Taylor et al" FB group?

Meanwhile, see: http://rna-mediated.com/

Nov 01, 2015
I don't understand ...bacterial flagellum
@jk
you should read the freaking article and study instead of crying about it here... or maybe talk to those who know, like Lenski or the author?
The ability to adapt to changes in the function of gene regulators, as opposed to structural genes, is a crucial aspect of evolutionary change. Taylor et al. mutated a central regulator for the formation of flagella in the bacterium Pseudomonas fluorescens. They then put the mutated flagella-free bacteria under strong selection pressure to regain mobility. The mutated bacteria regained the lost flagella, and motility, within 4 days. Two stereotypical mutations diverted an evolutionarily related regulator that normally controls nitrogen uptake to control flagella biosynthesis. The mutations increased the levels of the co-opted regulator, then altered its specificity for the flagella pathway
http://www.scienc...full.pdf


Nov 01, 2015
//rna-mediated
PSEUDOSCIENCE PHISHING SITE
this is not only a site that contains creationist pseudoscience but it is also personally owned and used for PHISHING and acquiring personal data of the visitors

reported for pseudoscience and phishing

if you had ANY ability to present factual reputable peer reviewed data, you should be linking a reputable journal, not your personal pseudoscience site and creationist sites

the fact that you continue to link this garbage means you have NO reputable or scientific evidence for your claims

epic fail

your week is almost up, little jimmie

JVK
Nov 01, 2015
Two stereotypical mutations diverted an evolutionarily related regulator that normally controls nitrogen uptake to control flagella biosynthesis.


Mutations perturb protein biosynthesis and degradation.

In their study "Genome resequencing revealed a single-nucleotide point mutation in ntrB in strain AR2S, causing an amino acid substitution within the PAS domain of the histidine kinase sensor NtrB [Thr97→Pro97 (T97P)] (13). 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)."
http://www.scienc...abstract

They reported the nutrient-dependent amino acid substitutions as if they were mutations instead of placing them into the context of the physiology of reproduction, which is nutrient-dependent and pheromone-controlled.


Nov 01, 2015
All I got was a word salad. Never could grasp the nub of what the fellow was saying. I have to admire his passion though. Unless of cause the salad was computer generated. The IT boys and girls are getting very good at that sort of stuff.

My own understanding derives from the highly improbable complexity of the necessary conditions that must prevail in order for us to be making these observations.

My model (which I plagiarised or synthesized from many sources) is coherent. All that it requires is the sacrifice of Time.
There is no past. It is a necessary illusion, generated as a binding narrative to support the observed reality.
These incredibly complex molecules never existed before we investigated them. They were invented as a necessary support for our reality. Expect exponentially growing complexity as we investigate the fidelity of the folding of these molecules.
In essence we exist in a model.

JVK
Nov 01, 2015
All I got was a word salad. Never could grasp the nub of what the fellow was saying.


I get that a lot. I include a link, and biologically uniformed science idiots cannot grasp the basis of the claims about the amino acid substitutions so they claim I am putting together a "word salad."

For comparison to my model, we now have
There is no past. It is a necessary illusion, generated as a binding narrative to support the observed reality.


No word salad, just more pseudoscientific nonsense that can be understood
All that it requires is the sacrifice of Time.



Nov 01, 2015
And the basis for assuming that time is real?

Nov 01, 2015
Mutations perturb protein biosynthesis and degradation
1- so, according to you, all mutations are pathological... therefore, per your own words, your model is pathological as well as FALSE, thus, logically, we can see that you are intentionally perpetrating a FRAUD
(do i really need to quote where you said your own model requires mutations?)

2- this statement is also factually incorrect, and you know it. mutations can be beneficial, as demonstrated by experimental evidence from Lenski (see: http://myxo.css.m...dex.html ) and validated by experimental evidence from biologists like Dr. Extavour (see studies & lab linked here: http://www.oeb.ha...oeb.html )

the only conclusion you can reach by the evidence?
jk is a pseudoscience fraud attempting to fanatically defend a religion and acquire acolytes

JVK
Nov 01, 2015
(do i really need to quote where you said your own model requires mutations?)


You need to quote me within the context of your question AND my answer.

My model is: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

Only a biologically uniformed science idiot would repeatedly take a quote out of context and continue to claim that my model links mutations to pathology in the context of reports on the requirement for nutrient-dependent DNA repair and cell type differentiation in the context of the physiology of reproduction in species from microbes to humans.

See also: Bactericidal Antibiotics Induce Toxic Metabolic Perturbations that Lead to Cellular Damage http://www.cell.c...901101-8

Only a biologically uninformed science idiot would link cellular damage to the evolution of anything. RNA-mediated amino acid substitutions and DNA repair are required.

Nov 01, 2015
You need to quote me
Ok
remember when I asked
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
(this is the DEFINITION of mutation) to which you answered
YES!
--Thanks for asking
this is your wording and as such it means, specifically, that your model REQUIRES mutations to work

however, you also state
Mutations perturb protein folding
http://medicalxpr...mic.html

so, if you claim all mutations perturb protein folding (& thus are deleterious or pathological) then, PER YOUR OWN WORDS, you are saying your model is CRAP

these are your quoted words!

it appears that either you don't know what you are talking about (as noted here: http://www.socioa...ew/24367 )

OR
You're a religious zealot
OR
a chronic liar

which is it?

Nov 02, 2015
(do i really need to quote where you said your own model requires mutations?)


You need to quote me within the context of your question AND my answer.

My model is: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

Only a biologically uninformed science idiot would link cellular damage to the evolution of anything. RNA-mediated amino acid substitutions and DNA repair are required.


Are you a chemist or are you just pretending to be one?

JVK
Nov 02, 2015
You're a religious zealot OR a chronic liar which is it?

Are you a chemist...


I am a medical laboratory scientist who claims that anyone incapable of a executing a google search for "RNA mediated" is doomed to remain a biologically uninformed science idiot.

One click is required to see what is currently known about physics, chemistry, and biology, which are linked by the conserved molecular mechanisms we detailed in the "molecular epigenetics" section of our 1996 Hormones and Behavior review.

https://www.googl...mediated

See also: http://www.psmag....es-64616 Robinson had not expected that. "The pheromone just lit up the gene expression, and it kept leaving it higher." The reason soon became apparent: Some of the genes affected were transcription factors—genes that regulate other genes. This created a cascading gene-expression response, with scores of genes responding.

JVK
Nov 02, 2015
Re:
Some of the genes affected were transcription factors—genes that regulate other genes. This created a cascading gene-expression response, with scores of genes responding.


That cascade links the epigenetic effects of food odors and pheromones from RNA-mediated gene duplication and RNA-mediated amino acid substitutions to nutrient-dependent DNA repair in species from microbes to man via the conserved molecular mechanisms that link supercoiled DNA to protection from virus-driven genomic entropy.

But, as Captain Stumpy continue to suggest, see "Criticisms of the nutrient-dependent pheromone-controlled evolutionary model." http://www.ncbi.n...24959329

If you do not, you will never recognize how much ignorance biologically uninformed science idiots continue to display compared to what I detailed in: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.http://www.ncbi.n...24693353

JVK
Nov 02, 2015
See also: A Prkci gene keeps stem cells in check http://phys.org/n...tml#nRlv

The idea that any gene keeps anything in check is one that is left-over from ridiculous gene-centric theories that cannot link what is currently know to serious scientists about how atoms and ecosystems interact at the level of nutrient energy-dependent base pair flipping because the pseudoscientific nonsense of neo-Darwinian evolutionary theory starts with sudden jumps in energy that de Vries defined as "mutations" in 1904.

The fact that the "Modern Synthesis" adopted and kept de Vries definition after Schrodinger claimed that the anti-entropic energy of the sun was required to link the stability of all organized genomes across all species embarasses neo-Darwinists because it makes all of them appear to be as ignorant of biologically-based cause and effect as PZ Myers and his idiot minions, like Captain Stumpy.

So, the idiots and idiot minions attack!

Nov 02, 2015
I am a medical laboratory scientist
Translation: i am a lab tech trying to inflate my authority based upon no evidence and false claims (some of which are felonious)
this is called argument from authority and is irrelevant to the subject: you can't actually provide empirical evidence supporting your religious claims, therefore you argue from self-perceived authority which is highly influenced by your Dunning-Kruger (see: https://en.wikipe...r_effect )
the idiots and idiot minions attack!
this is a demonstration of your brittle ego
https://www.psych...ttle-ego

googl...mediated blah blah
as Captain Stumpy continue to suggest
you really should learn basic English as well as what constitutes evidence in science
https://en.wikipe...evidence

Google also has millions of "hits" for fairies... doesn't make them real or true though


JVK
Nov 02, 2015
Google also has millions of "hits" for fairies... doesn't make them real or true though


Are you claiming that all the links to what is known about RNA-mediated events in the context of a google search contain questionable content?

If so, do you think your comments could be any less specific when you condemn the entirety of what is known to serious scientists about biologically-based cause and effect because you were taught to believe in ridiculous theories?

https://www.googl...mediated+dna+repair]https://www.googl...a+repair[/url]
https://www.googl...mediated
https://www.googl...directed
https://www.googl...mediated+gene+silencing
https://www.googl...mediated+control+of+virulence+gene+expression+in+bacterial+pathogens
https://www.googl...mediated+gene+expression

Nov 03, 2015
Are you claiming that all the links to what is known about RNA-mediated events in the context of a google search contain questionable content?
Nope, and you know it.

I am stating, however, that if you are searching for ACTUAL scientific content, then you would be better off using Google Scholar, for starters

also note: as long as you link sites that contain BOTH reputable science as well as RELIGION and pseudoscience, like your own site does, then it is PSEUDOSCIENCE

https://en.wikipe...oscience

A field, practice, or body of knowledge might reasonably be called pseudoscientific when it is presented as consistent with the norms of scientific research, but it demonstrably fails to meet these norms
Cover JA, Curd M (Eds, 1998) Philosophy of Science: The Central Issues, 1–82

you flood with links (called Gish Gallop) when it is not only irrelevant but you are trying to establish yourself as LEGIT

you're NOT
2Bcont'd

Nov 03, 2015
@jk cont'd
do you think your comments could be any less specific when you condemn the entirety of what is known to serious scientists about biologically-based cause and effect because you were taught to believe in ridiculous theories?
i never condemn REAL scientists, like you
This is the reason i support fundamental science and scientists
I follow the evidence: PERIOD

so far, your "evidence" has only demonstrated that you:
- want to be taken seriously, but can't because of your religious fanaticism

- can't comprehend the science

- are a religious fanatic attempting to pass off pseudoscience as actual science

- are having problems with your ego and intellect, combining Dunning-Kruger with a fragile ego
https://www.psych...ttle-ego

if you were to post validated science, or JUST SCIENCE, people would take you more seriously
(maybe...as long as you left out the religion and prejudice)

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