MicroRNA biogenesis vs Abiogenesis (1)

See first: MicroRNA-constrained human endogenous retroviruses vs pathology

Yesterday was RNA Day

See also:  Expanding the horizons of microRNA bioinformatics  “…over 500 microRNAs… and over 2400 experimentally validated microRNA:target interactions… can be used to create microRNA-focused interaction networks with a biological context using the known biological role of microRNAs and the mRNAs they regulate, enabling discovery of associations between gene products, biological pathways and, ultimately, diseases.”

More than 75,000 publications link the quantized energy (light-activated) creation of microRNAs to biophysically constrained viral latency and all biodiversity

See: The tipping point (revisited): 75,000 publications

Based on what is known to all serious scientists about light-activated microRNA biogenesis in plants, biophysically constrained viral latency has been linked from plants to naturally occurring RNA interference and treatment for human enterovirus infections.
 

“Human enterovirus 71 (EV-A71) infections cause a wide array of diseases ranging from diarrhoea and rashes to hand-foot-and-mouth disease and, in rare cases, severe neurological disorders. No specific antiviral drug therapy is currently available.

Fukinolic acid and cimicifugic acid A and J, were identified as active anti-EV-A71 compounds for Cimicifuga heracleifolia, whereas for Arnebia euchroma, two caffeic acid derivatives were tentatively deduced. Commercially available fukinolic acid analogues like L-chicoric acid and D-chicoric also showed in vitro micromolar activity against EV-A71 lab-strain and clinical isolates.”

See for comparison this thesis by Andrew Jones: Lipid Encapsulation of Self-Replicating Ribozymes

In light of the prior research demonstrating that the necessary prebiotic reactions can occur under hypothesized early Earth conditions, the emergence of a self-sustaining, encapsulated ribozymesystem is both possible and would comply with the current, most widely accepted abiogenesis hypothesis- the RNA world hypothesis; it would represent an important stepping stone between prebiotic chemistry and what many believe to be the first life form.

Andrew Jones also wrote: Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

James V. Kohl overextends his expertise in trying to overthrow established evolutionary theory.

See also: The neural basis of ‘being in the mood’ 2/12/15

Leslie Vosshall@pollyp1 supposedly wrote:

Thanks for being our advocate! I now do remember glancing at some of [Kohl’s claims] a few years ago, and it is ridiculous. My approach is just to ignore rather than engage pseudoscience.

There’s been no debate since then, despite the claim that @JacksonWheat1 wants to debate a creationist. Can anyone guess why those who tout abiogenesis do not enter debates with scientific creationists, but claim that the creationists engage in…?

I reiterate with the examples of my tweets from earlier today. Watch for responses from people who want to enter debate about the quantized energy-dependent microRNA-mediated neural basis of ‘being in the mood.’ See the discussion comments from The neural basis of ‘being in the mood’ 2/12/15, for comparison.

See also the discussion attempt on The neural basis of ‘being in the mood’ 2/12/15
JVK
1 / 5 (3) Feb 13, 2015

“…there is in fact a brain region where hormonal state and social interaction are integrated.”

Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. https://www.ncbi.n…24693349

Human pheromones: integrating neuroendocrinology and ethology https://www.nel.ed…view.htm

https://perfumingt…t-sense/

Excerpt: “Smell is the dominant sense in many animals, including humans, and meetings between individuals usually begin with a period of intense mutual sniffing.”

JVK

1 / 5 (3) Feb 13, 2015

General audience:

How Pheromones Work in Human Courtship https://www.youtu…cyr898rY

Science-oriented audience:
Nutrient-dependent / Pheromone-controlled adaptive evolution: (a mammalian model of thermodynamics and organism-level thermoregulation) https://www.youtu…youtu.be

Captain Stumpy

3.7 / 5 (3) Feb 13, 2015

youtube is NOT a scientific reference to support your “conclusions” about sniffing

it isn’t a reputable scientific publication, either

epic fail, jk

JVK

1 / 5 (3) Feb 13, 2015

https://time.com/3…ve-life/

Excerpt 1) “…there’s some preliminary evidence that pheromones might be a potential X factor for attraction and fertility.”

Excerpt 2) “…no two people experience the olfactory world in exactly the same way. Add in all of the other complexities of attraction…”

Human pheromones, epigenetics, physiology, and the development of animal behavior https://f1000.com/…ary/1387

Main conclusion:
When he was wearing the mixture compared to when he wore the diluent, women were more likely to make eye contact (t (12) = 3.43, p = 0.01; IRR: r = 0.964, p = 0.01). They also laughed more (t (12) = 5.20, p < 0.01; IRR: r = 0.810, p = 0.01), and they subsequently rated themselves as being more attracted to him (t (12) = 2.786, p = 0.016). Our results combine the known effects of androstenol on LH and on mood with a likely behavioral affect of androsterone.

JVK

1 / 5 (3) Feb 13, 2015

it isn’t a reputable scientific publication, either

Details of the conserved molecular mechanisms were included in the section on molecular genetics in our 1996 Hormones and Behavior review article: From Fertilization to Adult Sexual Behavior

https://www.hawaii…ion.html

Elekonich and Robinson (2000) linked our model to hormone-organized and hormone-activated insect behaviors. Elekonich and Roberts (2005) linked it to life history transitions in the honeybee. The honeybee is one of the model organisms I used to link nutrient-dependent pheromone-controlled ecological adaptation from ecological variation to the RNA-mediated differentiation of all cell types in all individuals of all species.

Nutrient-dependent/pheromone-controlled adaptive evolution: a model. https://www.ncbi.n…24693353

anonymous_9001

5 / 5 (3) Feb 13, 2015

Citing a publication from 2000? Whenever I do that, you claim it’s outdated and falsified based on the year alone.
JVK

1 / 5 (3) Feb 14, 2015

None of the biological facts represented in the series of works that built on our accurate representation of RNA-mediated cell type differentiation in species from yeasts to mammals have changed.

For comparison to your pseudoscientific nonsense, I’ve mentioned this before:

If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based. (p 1014)

https://jp.physoc….abstract

You learned how to perform mutagenesis experiments and meaningfully interpret meaningless results. You learned nothing of importance to biologically-based cause and effect. Your citations to outdated articles attests to that fact.

My citations build on biological facts that you could have learned by now if you were not a science idiot.

JVK

1 / 5 (3) Feb 14, 2015

2002 Zdenek Klein award for Human Ethology: Panksepp’s group
Comparative approaches in evolutionary psychology: molecular neuroscience meets the mind
https://www.ncbi.n…12496741“…homologous brain systems in humans and other animals can be studied with the same neurochemical techniques, and the underlying neurochemical systems can be linked directly to genetic issues.”2001 Zdenek Klein award for Human Ethology (my group)
Human pheromones: integrating neuroendocrinology and ethology https://www.nel.ed…view.htm“Affective reactions can occur without extensive perceptual and cognitive encoding. They are made with greater confidence than cognitive judgments, and can be made sooner [5, 7]. Olfactory input from the social environment is well adapted to fit such assertions. For example, chemical cues allow humans to select for, and to mate for, traits of reproductive fitness that cannot be assessed simply from visual cues.”

JVK

1 / 5 (3) Feb 14, 2015

https://phys.org/n…fly.html

Excerpt 1) “The principle of adaptation—the gradual modification of a species’ structures and features—is one of the pillars of evolution. While there exists ample evidence to support the slow, ongoing process that alters the genetic makeup of a species, scientists could only suspect that there were also organisms capable of transforming themselves ad hoc to adjust to changing conditions.”

Excerpt 2) “Does the squid have some mechanism we can learn from?”

Evolutionary theorists can learn nothing about the molecular mechanisms of adaptation from mutagenesis experiments. Theoretical physicists can learn nothing about molecular biology without first linking the sun’s biological energy to the chemistry of RNA-mediated protein folding.

Andrew Jones (aka anonymous_9001) knows nothing about anything because he is a biologically uninformed science idiot.

RealScience

5 / 5 (3) Feb 14, 2015

From https://phys.org/n…ize.html

The messenger RNAs are produced by RNA polymerase, which transcribes the sequence of base pairs in a gene into an RNA version thereof. So the sequence of the DNA base pairs in the DNA gene determines the sequence of bases in the messenger RNA.

Do you agree that this is PART of the way in which most proteins are synthesized?

Of course I do not agree.

The squid study you linked (https://phys.org/n…ly.html) illustrates the point well. These squid have the most substitutional editing of any species yet studied, yet EVEN HERE most of the sequence of bases in the mRNA is determined from the sequence of bases in the DNA.

This can be seen by looking at the study data itself.
(See https://datadryad….how=full and download EisenbergSI_Table1.xlsx )

– continued –

RealScience

5 / 5 (3) Feb 14, 2015

-continued –

In this study:

the researchers extracted both DNA and RNA from squid. Harnessing DNA sequencing and computational analyses at TAU, the team compared the RNA and DNA sequences to observe differences. The sequences in which the RNA and DNA did not match up were identified as “edited.”

While that headline is that 60% of the mRNAs had their base sequences edited (in addition to splicing edits), a look at the data shows that most are only edited a handful of sites and each site is edited only a few percent to a few tens of percent of the time.

Even a highly-edited mRNA transcript like TPC13 is only edited at 17 out of ~1200 sites, or ~1.5%, and only one of those sites is edited more than a few percent of the time in more than one of the tissue types. It AVERAGES only one such edit out of 1200 sites, or less than 0.1%.

– continued –

RealScience

5 / 5 (3) Feb 14, 2015

– continued –

So looking at the data on which the squid article that YOU LINKED shows that even in the species with the MOST such edits known to date, and even picking a HIGHLY-EDITED mRNA, the sequence of RNA bases in that mRNA is roughly 99.9% determined by the sequence of DNA bases in the DNA from which the mRNA was transcribed.

So regarding:

The messenger RNAs are produced by RNA polymerase, which transcribes the sequence of base pairs in a gene into an RNA version thereof. So the sequence of the DNA base pairs in the DNA gene determines the sequence of bases in the messenger RNA.

A study finding a species in which the DNA sequence only accounts for ~99.9% of the mRNA sequence is headline-making news, and this study that you linked CLEARLY shows that this process is PART of the way in which most proteins are synthesized.

Checkmate again, JVK!

JVK

1 / 5 (3) Feb 14, 2015

This was YOUR claim.

So the sequence of the DNA base pairs in the DNA gene determines the sequence of bases in the messenger RNA.

What are you claiming now?

How can whatever pseudoscientific nonsense you’re touting be linked to cell type differentiation in species from microbes to man?

How is the stability of DNA maintained in the differentiated cells of all tissues in all organs of all organisms like the cephalopods?

How can you remain completely uniformed about the basics of biology that link cause and effect via the epigenetic effects of sensory input?

anonymous_9001

5 / 5 (4) Feb 14, 2015

How can you remain completely uniformed about the basics of biology

Ironic coming from the person that’s repeatedly proved he doesn’t understand the sequence of events leading from DNA to RNA to protein.

You learned how to perform mutagenesis experiments and meaningfully interpret meaningless results.

I was hoping that those experiments would be easy enough for even you to understand, but I overestimated your critical thinking skills again. When mutations are made to DNA templates through mutagenic PCR or chemicals, it changes the amino acid chain the template codes for. These experiments are direct evidence of beneficial mutations because they specifically cause mutations and observe better enzymes as a result. It can’t be any clearer than that. What part of that process do you dispute? Do you dispute they’re mutations or do you dispute that they observe improved enzymes? Those are the only two steps involved.

RealScience

5 / 5 (3) Feb 14, 2015

@JVK, I said:

OK, since you haven’t disagreed with MOST of the amino acids in most proteins being specified in the sequences of RNA bases in exons of the messenger RNA, I will continue explaining clearly to you the most common relationship between mutations and amino acid substitutions.

The messenger RNAs are produced by RNA polymerase, which transcribes the sequence of base pairs in a gene into an RNA version thereof. So the sequence of the DNA base pairs in the DNA gene determines the sequence of bases in the messenger RNA.

Do you agree that this is PART of the way in which most proteins are synthesized?

You disagreed.

However the study that you cited checked the mRNA sequence against the DNA sequence and showed that EVEN AFTER EDITING, the sequence of DNA bases determined over 99.9% of the sequence of the mRNA bases.

Do you STILL disagree that DNA bases being transcribed into RNA bases is PART of the way in which most proteins are synthesized?

JVK

1 / 5 (3) Feb 14, 2015

I’m disputing the intellectual capacity of anyone who does not yet understand that the link between metabolic networks and genetic networks is NOT beneficial mutations.

Anonymous fools who claim I do not understand results from mutagenesis experiments should put those results into the context of cell type differentiation instead of uncontrolled cell type proliferation. But first, the science idiots need to understand the basics of nutrient-dependent metabolism.

Clinically Actionable Genotypes Among 10,000 Patients With Preemptive Pharmacogenomic Testing https://www.medsca…24253661

Video representation of the results: https://www.youtu…G_9EEeeA

Does anyone know how science idiots link beneficial mutations to the fixed amino acid substitutions that vary in the different cell types of different individuals of different species? Are they still using natural selection against mutated cells to explain the nutrient-dependent substitutions?

JVK

1 / 5 (3) Feb 14, 2015

Do you STILL disagree that DNA bases being transcribed into RNA bases is PART of the way in which most proteins are synthesized?

Have you stopped beating your dog? I’ve never understood any part of the process that leads to people beating their dogs or leads them to stop it. I would be grateful if you can explain to me what part of the process leads you to ask me questions like

Do you STILL disagree that DNA bases being transcribed into RNA bases is PART of the way in which most proteins are synthesized?

Captain Stumpy

4 / 5 (4) Feb 14, 2015

I’m disputing the intellectual capacity of anyone who does not yet understand that the link between metabolic networks and genetic networks is NOT beneficial mutations.

@jk
so you are disputing your own intellectual capacity?
WOW
thanks for that quote!

fools who claim I do not understand results from mutagenesis experiments \

he’s not anonymous if you know who he is, moron
also, you don’t even comprehend the WORD mutation, nor that your own model causes mutation, so why would we take ANY science advice from you?

if you knew half as much as you claimed, you would comprehend what ANON and RealScience were telling you, and you wouldn’t continually confuse yourself

Like Anon says

Ironic coming from the person that’s repeatedly proved he doesn’t understand the sequence of events leading from DNA to RNA to protein.

And that has been PROVEN time and again in these comment threads in PO!

nice to see you haven’t learned Anything at all!

JVK

1 / 5 (3) Feb 14, 2015

don’t even comprehend the WORD mutation

Use of the WORD mutation by science idiots makes no sense.

See: Stability-mediated epistasis constrains the evolution of an influenza protein https://elife.elif…2/e00631

1) “How does epistasis arise from an evolutionary process that is conceived as proceeding through the incremental accumulation of mutations? And is it possible to coherently understand epistasis in terms of the underlying protein biophysics?”

2) “…WORD→WORE→GORE→GONE→GENE.”

3) “Implicit in this analogy is the idea that epistasis constrains evolution—for example, the original parent sequence does not tolerate three of the four eventual changes, as GORD, WERD and WOND are not words.”

With no language of DNA, information about the epigenetic landscape is not transferred to the physical landscape of DNA in organized genomes. The only way for evolution to occur is via magic.

RealScience

5 / 5 (3) Feb 14, 2015

I would be grateful if you can explain to me what part of the process leads you to ask me questions like

Do you STILL disagree that DNA bases being transcribed into RNA bases is PART of the way in which most proteins are synthesized?

JVK, I asked if you need the most common relationship between mutations and amino acid substitutions explained more clearly, and you replied

Yes.

So I started explaining:

1) Ribosomes produce proteins by translating messenger RNAs (mRNAs) into the sequences of amino acids that form the proteins.

The mRNAs are likely to be extensively edited in this process before they get to the ribosome, such as by removing introns and splicing together the remaining exons, but MOST of the amino acids in most proteins are specified in the sequences of RNA bases in exons of the messenger RNA.

– continued –

RealScience

5 / 5 (3) Feb 14, 2015

– continued –

To see if you understood so far and find out if you agreed so far, I asked:

Do you agree that this is PART of the way in which most proteins are synthesized?

If you do NOT agree with this, please state which part you disagree with.

If you do NOT understand this, please state which part you do not understand and I will explain that part in more detail.

(Note that this is just one of several steps the explanation of the most common relationship between mutations and amino acid substitutions).

You did not agree, but you did not state any disagreement so I went on to the next part:

OK, since you haven’t disagreed with MOST of the amino acids in most proteins being specified in the sequences of RNA bases in exons of the messenger RNA, I will continue explaining clearly to you the most common relationship between mutations and amino acid substitutions.

– continued –

RealScience

5 / 5 (3) Feb 14, 2015

– continued –

The messenger RNAs are produced by RNA polymerase, which transcribes the sequence of base pairs in a gene into an RNA version thereof. So the sequence of the DNA base pairs in the DNA gene determines the sequence of bases in the messenger RNA.

Do you agree that this is PART of the way in which most proteins are synthesized?

If you do NOT agree with this, please state which part you disagree with.

If you do NOT understand this, please state which part you do not understand and I will explain that part in more detail.

You replied:

Of course I do not agree.

I then asked:

So which part do you disagree with?

Do you disagree that DNA contains genes whose sequence of DNA base pairs gets transcribed into RNA bases?
Do you disagree the sequence of RNA bases depends in part on the sequence of DNA bases in the gene?

– continued –

RealScience

5 / 5 (3) Feb 14, 2015

– continued –

(Note that I am not asking whether this is the complete process or that all proteins are made this way, but whether you agree that this is PART of the process in which most proteins are made.)

“The messenger RNAs are produced by RNA polymerase, which transcribes the sequence of base pairs in a gene into an RNA version thereof” IS TRANSCRIPTION, and it results in the sequence of the DNA base pairs in the DNA gene determining the sequence of bases in the messenger RNA.

You previously disagreed that this is even PART of the way that MOST proteins are synthesized, so after the data behind the squid mRNA editing article showed that even in the species with the most RNA editing found so far, over 99.9% of the mRNA sequences match the DNA sequence that they are transcribed from, I was curious whether even after having the data explained to you that you STILL disagreed that this is PART of the way that most proteins are synthesized.

– continued –

RealScience

5 / 5 (3) Feb 14, 2015

– continued –

So THAT’s the process that led me to ask you

Do you STILL disagree that DNA bases being transcribed into RNA bases is PART of the way in which most proteins are synthesized?

Now that I’m not right at a 1000-character comment limit, I’ll ask without relying on you understanding what ‘transcription’ is:

The mRNAs are likely to be extensively edited before they get to the ribosome, such as by removing introns and splicing together the remaining exons, but MOST of the amino acids in most proteins are specified in the sequences of RNA bases in exons of the messenger RNA.

The messenger RNAs are produced by RNA polymerase, which transcribes the sequence of base pairs in a gene into an RNA version thereof. So the sequence of the DNA base pairs in the DNA gene determines the sequence of bases in the messenger RNA.

Do you STILL disagree that this is PART of the way in which most proteins are synthesized?

If so, what part(s) do you disagree with?

JVK

1 / 5 (3) Feb 14, 2015

Please change your name to RealScienceIDIOT and I will consider addressing your questions.

Until then, as everyone knows, I have a detailed model of how RNA-mediated cell type differentiation occurs in species from microbes to man. My publication history spans two decades. https://www.ncbi.n…24693353

If you want to compare models, tell me what model you think can be compared in the context of “Life is physics and chemistry and communication” https://dx.doi.org…as.12570

Vietvet

3.4 / 5 (5) Feb 15, 2015

Please change your name to RealScienceIDIOT and I will consider addressing your questions.

@Jvk isn’t competent enough to answer the questions.

anonymous_9001

4.8 / 5 (4) Feb 15, 2015

Please change your name to RealScienceIDIOT and I will consider addressing your questions.

More deflecting because you don’t know what transcription and translation involve.

RealScience

5 / 5 (3) Feb 15, 2015

Regarding JVK not being competent enough to answer the questions, or deflecting because he doesn’t know what transcription and translation involve, JVK hasn’t let EITHER ignorance or a lack of competence stop him before…

I think that he DOES understand that the sequence of DNA bases in a gene is transcribed to a sequence of RNA bases in mRNA, and that even after editing, most of the sequence of amino acids a protein comes from the transcribed sequence in the mRNA.

And he understands that if he thinks it through he will no longer be able to deny that a single change to the DNA sequence of base pairs (the canonical point mutation) will thus often cause an amino acid substitution in the resulting protein. He has acknowledged that amino acid substitutions can be selected FOR, so this would show that mutations can be selected for, and his whole anti-mutations rant would fall apart.

Since he can’t admit this, he refuses to answer and tries to changes the subject.

Captain Stumpy

4 / 5 (4) Feb 15, 2015

Use of the WORD mutation by science idiots makes no sense

@jk
so, because something doesn’t make any sense to you, due likely to your failing out of college, then it must be wrong?
or is it that it doesn’t make sense in light of your religious beliefs so it must be wrong?

That is the problem with you, jk… YOU don’t understand where YOU are wrong because you don’t understand the lexicon, NOR do you understand all the biology, chemistry and physics behind what is happening, but you think you are an AUTHORITY on the subject, which Anon, Real and everyone else has proven wrong time and again, even with your own posts!

again, i point out: just because you THINK it is wrong doesn’t mean it is… take Quantum Mechanics, for instance. it is NOT intuitive, but happens to be the single most successful theory to date: EVER
it is the physics behind every computer, cell phone, EVERYTHING… but it is not something you understand at all…

so is that wrong too?

Captain Stumpy

4 / 5 (4) Feb 15, 2015

Since he can’t admit this, he refuses to answer and tries to changes the subject.

@RealScience

That is how pseudoscientists work
Take his announcement above

Use of the WORD mutation by science idiots makes no sense

because you (and everyone else educated beyond high school, and most high school students to) comprehend the term, how it is used, etc… he thinks you (and everyone else) is a “science idiot”

He cannot answer your questions because he is NOT educated (nor experienced) enough to comprehend the actual biology or anything else behind it… but instead of learning something, he simply denigrates you and changes the subject

and the biggest reason is because he is presenting everything IN LIGHT OF A RELIGIOUS BELIEF!
as a creationist, he is promoting his pseudoscience as the final word because, in church, he CAN do that… but in science, we need evidence, which he cannot provide!

@ANON & REAL
KEEP POSTING and spreading REAL SCIENCE
WE APPRECIATE IT

JVK

1 / 5 (3) Feb 15, 2015

take Quantum Mechanics, for instance.

I have. A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution https://www.ncbi.n…23206328

as a creationist, he is promoting his pseudoscience

“…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.” https://www.jstor…./4444260 Nothing in Biology Makes Any Sense Except in the Light of Evolution (1973)

See also: More Evidence That Mammals Coexisted With Dinosaurs https://www.nytime…amp;_r=0

No experimental evidence of biologically based cause and effect links mutations to the evolution of increasing organismal complexity. Only science idiots still believe in ridiculous theories. They always will.

Captain Stumpy

3.7 / 5 (3) Feb 15, 2015

No experimental evidence of biologically based cause and effect links mutations to the evolution of increasing organismal complexity. Only science idiots still believe in ridiculous theories. They always will.

So what you are saying is that, the following link (found here: https://www.ncbi.n…24693353 ) is NOTHING but HOGWASH because it uses MUTATIONS and tries to link them to biodiversity?

WOW
THANKS for that little quote jk!

you are saying that you are a HUGE SCIENCE IDIOT

Only science idiots still believe in ridiculous theories. They always will.

because you are specifically linking mutations to biodiversity in your “model” published for everyone to see

for any sane biologist: please read the REFUTE
https://www.ncbi.n…4049134/

This is from a man who KNOWS what he is talking about and is educated enough to show WHY jk is wrong

thanks

JVK

1 / 5 (3) Feb 15, 2015

Ahuja, A. and Extavour, C.G. Patterns of molecular evolution of the germ line specification gene oskar suggest that a novel domain may contribute to functional divergence in Drosophila. Development, Genes and Evolution 224(2): 65-77 (2014)

“oskar is not highly conserved across animals. It is instead a novel gene that evolved in the lineage leading to insects (Ewen-Campen et al. 2012), and may have facilitated the evolution of germ plasm in holometabolous insects (those that undergo true metamorphosis) (Lynch et al. 2011). oskar orthologs have been identified to date only from flies and mosquitoes…”

Vosshall’s group has linked experience-dependent de novo creation of olfactory receptor genes across species to the differences in morphological and behavioral phenotypes.

Her group has linked mutations to to failed ecological adaptations. I’ve repeatedly cited and linked to the published works that confirm these facts.

Captain Stumpy

3.7 / 5 (3) Feb 15, 2015

I’ve repeatedly cited

yeah, you used to repeatedly tell LIES about Dr. Extavour’s work when you misunderstood it in the PAST too!

we in no way claim that mutations in the heritable genome play no role in evolution. Indeed, as you [Cpt Stumpy] correctly state, just because we provide evidence that nutritional conditions play a role, this does not negate a role for mutations. Indeed, in that very same paper, we provide evidence that heritable differences in the genome sequences between Drosophila species, in other words, mutations, ALSO play a role in the evolution of the trait we are studying.

So Kohl is mistaken if he is claiming that my study (or Rich Lenski’s work) provide evidence AGAINST the role of mutations in evolution.

WHOOPS!
creationists are dying of embarrassment over jk’s post NOW!
because you EPICALLY FAILED AGAIN

Captain Stumpy

3.7 / 5 (3) Feb 15, 2015

Lets REVIEW the pertinent parts of that comment which completely DEBUNKS jk’s claims about the role of MUTATIONS

in that very same paper, we provide evidence that heritable differences in the genome sequences between Drosophila species, in other words, mutations, ALSO play a role in the evolution of the trait we are studying.

Yes, jk either CANNOT READ or cannot comprehend the science in the paper

i would say a little of BOTH
especially considering his subsequent failure to provide ANY scientific REFUTE to Dr. Extavour’s study… OR to Lenski’s study!

jk USED to use Extavour as prof he was right… till she outed his misinterpretations of her work! Now he denigrates her in the comments…. shall i post those as well, jk?

EPIC FAIL, for jk!

I will close with the DR’s words, which STILL ring true

Kohl is mistaken if he is claiming that my study (or Rich Lenski’s work) provide evidence AGAINST the role of mutations in evolution.

JVK

1 / 5 (3) Feb 15, 2015

Vosshall’s work and the works of many others provide evidence AGAINST the role of mutations in evolution.

orco mutant mosquitoes lose strong preference for humans and are not repelled by volatile DEET https://www.ncbi.n…3696029/

Evolution of mosquito preference for humans linked to an odorant receptor
https://www.nature…964.html

JVK

1 / 5 (3) Feb 15, 2015

Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. https://www.ncbi.n…24693349

Excerpt: “Socioaffective neuroscience and psychology may progress more quickly by keeping these apparent facts in mind: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).”

anonymous_9001

5 / 5 (3) Feb 15, 2015

The devil’s in the details when you praise Vosshall’s work, Kohl, and here’s why. The same techniques they use to perform knockout studies like that (site-directed mutagenesis and general mutagenesis) are also used to produce beneficial mutants.

Here’s a paper citing a couple models that utilizes the SOS response I’ve told you about before to produce adaptive mutations in E. coli:

https://www.ncbi.n…C240707/

Here’s one describing the techniques in detail:

https://aem.asm.or…258.full

Alteration of GFP color through mutagenesis:

https://nar.oxford…78.short

Brand new papers about in vitro evolution applications just so you can’t complain about me citing old ones:

https://www.scienc…14001446
https://www.scienc…14002002
https://scholar.go…sdt=0,14

JVK

1.3 / 5 (3) Feb 16, 2015

Our model of RNA-mediated hormone-organized and hormone-activated behavior detailed an across-species continuum of molecular epigenetics from yeasts to humans. The model was subsequently extended to hormone-organized and hormone-activated behavior in insects (Elekonich & Robinson, 2000) and to the honeybee model of life-history transitions (Elekonich & Roberts, 2005).
See: https://www.hawaii…ion.html“…there is increasing evidence that individual ants, bees, and termites are very intelligent…”
https://jonlieffmd…e-updateThat evidence continues to invalidate anything you or anyone else has ever claimed about mutations and evolution.”Life is physics and chemistry and communication” https://dx.doi.org…as.12570 Communication is nutrient-dependent and pheromone-controlled.

See also: https://jonlieffmd…volution

JVK

1 / 5 (3) Feb 16, 2015

When Second Best Is Good Enough: Another Probabilistic Look at Saturation Mutagenesis
https://aem.asm.or…abstract“…given the randomization scheme, the amino acid probabilities are induced by the genetic code…”What kind of science idiot starts with randomization of what must obviously be selection for food, which is based on the odor of the food, and links the nutrient-dependent RNA-mediated fixation of amino acid substitutions via the pheromone-controlled physiology of reproduction to mutations and evolution?That was a rhetorical question.

RealScience

5 / 5 (3) Feb 16, 2015

“…given the randomization scheme, the amino acid probabilities are induced by the genetic code…”
What kind of science idiot starts with randomization of what must obviously be selection for food, which is based on the odor of the food…

How are thee mistaken, JVK? Let me count the ways…

First, you are once again confusing GENERATING the variants (mutagenesis) with SELECTION for variants (which in nature often does include selection for food, etc.).
This is clearly described in the paper you refer to ( https://aem.asm.or…258.full ):

… a large number of random variants, which together constitute a library, are produced and then screened in an attempt to discover a highly active variant among them

.
– continued –

RealScience

5 / 5 (3) Feb 16, 2015

– continued –

Second, the paper EXPLAINS that randomization can explore a large variant space efficiently. There are 400 possible variations even if only two amino acids are varied (n = 20 • 20 = 400 variants in variant space), and to create each of these individually would take 400 separate custom productions of a variant. However one can get almost as good a result with a single randomization process that produces hundreds of variants:

when randomizing two positions, only 875 variants are required to ensure a 0.95 probability of discovering any of the top two variants in variant space …

So you are calling people ‘science idiots’ for using a relatively simple randomization procedure at two sites rather than 400 separate custom procedures (and this advantage grows exponentially as the number of sites is increased).

– continued –

RealScience

5 / 5 (4) Feb 16, 2015

– continued –

Third, as the paper says:

Saturation mutagenesis (also called oligonucleotide-directed randomization) is a protein-engineering technique that has been used WIDELY and SUCCESSFULLY to IMPROVE protein properties such as catalytic activity, enantioselectivity, thermostability, … [emphasis added]

So you are calling people ‘science idiots’ for using a SUCCESSFUL process!

Fourth, the properties that have been SUCCESSFULLY improved by creating mutations (mutagenesis) include THERMOSTABILITY, so you cited a paper that DISPROVES your claim that mutations can never be selected for because they destabilize proteins.

Fifth, the basis for this widely and successfully used protein engineering technique is that a point mutation to a DNA sequence can cause one amino acid to be substituted for another in a protein, so you just cited a paper which shows that what I was explaining to you is used ‘widely and successfully’ in science.

– continued –

JVK

1 / 5 (3) Feb 16, 2015

https://www.scienc…3747.htm

The across-kingdom link obviously is the microRNA/messenger RNA balance. It is perturbed by viral microRNAs when it is not maintained by nutrient uptake and RNA-directed DNA methylation.

Methylation is linked to RNA-mediated amino acid substitutions that stabilize DNA in the organized genomes of species from microbes to man via the physiology of their nutrient-dependent reproduction. https://www.faceb…5911912/

Nutrient-dependent / pheromone-controlled thermodynamics and thermoregulation
https://www.youtu…youtu.be

anonymous_9001

5 / 5 (4) Feb 16, 2015

Methylation is linked to RNA-mediated amino acid substitutions that stabilize DNA

Can you explain this in more detail? A cytosine is methylated, then what happens? How is it then turned into a different nucleotide?

Edit: Oh yeah, and I contacted Vosshall. Guess what? You’re misinterpreting.

Thanks for being our advocate! I now do remember glancing at some of [Kohl’s claims] a few years ago, and it is ridiculous. My approach is just to ignore rather than engage pseudoscience.

RealScience

5 / 5 (3) Feb 16, 2015

– continued –

I’m sure that there are more ways in which this paper you cite shows your mistakes, JVK, but I prefer variety. So do you have MORE papers on SUCCESSFUL techniques that use selection FOR mutations to IMPROVE protein properties such as thermostability that you need a ‘science idiot’ to EXPLAIN to you?

(This is NOT a rhetorical question – you come up with interesting papers, and explaining how they go AGAINST your claims on mutations is fun!)

JVK

1 / 5 (3) Feb 16, 2015

Thanks for being our advocate! I now do remember glancing at some of [Kohl’s claims] a few years ago, and it is ridiculous. My approach is just to ignore rather than engage pseudoscience.

She didn’t like Luca Turin’s 1996 claims, either. They have since been linked from quantum physics to quantum biology and quantum consciousness in the context of Vosshall’s works and mine. Too bad she didn’t do more than glance at my claims. She might have avoided some embarrassment.

A Spectroscopic Mechanism for Primary Olfactory Reception

Molecular Vibration-Sensing Component in Human Olfaction

A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution

Electron spin changes during general anesthesia in Drosophila

Dose-Dependent Effects of the Clinical Anesthetic Isoflurane on Octopus vulgaris: A Contribution to Cephalopod Welfare

Role of olfaction in Octopus vulgaris reproduction

RealScience

5 / 5 (3) Feb 16, 2015

from quantum physics to quantum biology and quantum consciousness

Repeating ‘quantum’ won’t make what you say sound intelligent, JVK.

My favorite example is when you were asked ( https://phys.org/n…ars.html ):

Do you understand the difference between changing a gene’s nucleotide sequence and changing how often it is expressed?

and you answered:

Yes. I do, albeit only starting at the level of quantum physics …

I’m still laughing that in an attempt to sound smart you ADMITTED that you don’t understand the difference between changing HOW a gene is SPELLED and WHEN a gene is ‘READ’ without ‘starting at the level of quantum physics’.

Still ROTFLMAO!

Captain Stumpy

4 / 5 (4) Feb 16, 2015

I’m still laughing that in an attempt to sound smart you ADMITTED that you don’t understand the difference between changing HOW a gene is SPELLED and WHEN a gene is ‘READ’ without ‘starting at the level of quantum physics’.

Still ROTFLMAO!

@RealScience
MAN
I must have missed that one!
ROTFLMFAO

i wish i could give you 100Stars for that one!
that is HILARIOUS!

i’ll bet he doesn’t even know what “quantum” means!
let alone “quantum Physics”

@jk
so tell us: which theory will you be using with regard to explaining the above “starting at the level of quantum physics”?
Q Mechanics?
Q ElectroDynamics?
are you using Q Field Theory?

Tell us a little more about the Quantum theory being used to establish the link between the quanta and the biological processes,
because obviously we are talking macro effects RIGHT?

THANKS

JVK

1 / 5 (3) Feb 16, 2015

Starting from base pair flipping at the level of hydrogen energies is the only way I know to get to “A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution” or to quantum consciousness.

What are you science idiots trying to say about how that is done? Ask Leslie Vosshall for help if necessary.

Amino Acid Residues Contributing to Function of the Heteromeric Insect Olfactory Receptor Complex https://www.ploson….0032372]https://www.ploson….0032372[/url]

Tell her I would be happy to explain to her what her works mean in the context of physics, chemistry, and conserved molecular mechanisms.

See also: https://www.ploson….0032372]https://www.ploson….0032372[/url]
It’s an open access review, which means that no one needs to be a science idiot who doesn’t prefer being one.

RealScience

5 / 5 (4) Feb 16, 2015

Starting from base pair flipping at the level of hydrogen energies is the only way I know to get to “A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution” or to quantum consciousness.

You sure are wide of the mark, JVK!

Base pair flipping is something that happens to DNA (for example during DNA repair).

In contrast, the docosahexaenoic acid paper’s reference to ‘quantum’ is to a property of the docosahexaenoic acid (DHA) molecule itself (rather than of the DNA that encodes for it).

As the paper says:

The unique molecular structure of DHA allows for quantum transfer and communication of π-electrons…

It looks like you saw ‘quantum’ in an article on nutrient-dependent brain development and get so excited that you confused DNA and DHA. (These acronyms do look rather similar so that would be understandable.)

JVK

1 / 5 (3) Feb 16, 2015

It looks like you do not understand the fact that the sun’s biological energy must be epigenetically linked to cell type differentiation in the context of the biophysically constrained RNA-mediated chemistry of protein folding. That would be understandable since you are a science idiot — except for what the abstract clearly states, which makes you a moron.

“Docosahexaenoic acid (DHA) provided the core for the development of the photoreceptor, and conversion of photons into electricity stimulated the evolution of the nervous system and brain. Since then, DHA has been conserved as the principle acyl component of photoreceptor synaptic and neuronal signalling membranes in the cephalopods, fish, amphibian, reptiles, birds, mammals and humans. This extreme conservation in electrical signalling membranes despite great genomic change suggests it was DHA dictating to DNA rather than the generally accepted other way around.”

RealScience

5 / 5 (3) Feb 16, 2015

So that’s your best answer, JVK, to it being pointed out that you confused base pair flipping in DNA with quantum conduction effects in DHA?

Do you need me to explain the DHA paper’s abstract to you?

JVK

1 / 5 (3) Feb 17, 2015

you confused base pair flipping in DNA with quantum conduction effects

What causes base pair flipping in DNA in your model of biologically-based cause and effect?

anonymous_9001

5 / 5 (3) Feb 17, 2015

It’s not base pair flipping, it’s just base flipping. We know how this process works at the atomic level.

https://en.wikiped…echanism

JVK

1 / 5 (3) Feb 17, 2015

Thanks. Sorry, I was not aware that there are “grammar queens” here. I thought there were only science idiots.

At the atomic level, what causes the “base flipping” to occur in one of the base “pairs” in which the “flipping” occurs, which I referred to as “base pair flipping”?

In my model, for example, it is RNA-directed DNA methylation. How does the process work at the atomic level in your mutagenesis experiments or in a realistic model of biologically-based cause and effect that can be compared to my model?

What causes the “base flipping” that others report as “base pair flipping”?
[you FLIPPING science idiot]
https://search.ya…=yhs-001

JVK

1 / 5 (3) Feb 17, 2015

https://en.wikiped…echanism
DNA methylation is the process in which a methyl group is added to either a cytosine or adenine.[22]The anonymous fool (aka Andrew Jones, the science idiot, wrote:)

A cytosine is methylated, then what happens? How is it then turned into a different nucleotide?

Edit: Oh yeah, and I contacted Vosshall. Guess what? You’re misinterpreting.

Now Jones claims:

It’s not base pair flipping, it’s just base flipping. We know how this process works at the atomic level.

This is typical of those who know nothing. They wait until what’s known is perfectly clear and then claim that they’ve known it all along. See for comparison, his thesis.

https://www.scribd…s#scribd “The encapsulation of such a ribozyme is also an important step, as it would enable a system of heredity and evolution through natural selection.”

JVK

1 / 5 (3) Feb 17, 2015

See also: https://www.brainf…e-brain/

“No longer should humans be considered poor smellers. In fact, new research suggests that your nose can outperform your eyes and ears, which can discriminate between several million colors and about half a million tones. “It’s time to give our sense of smell the recognition it deserves,” said Vosshall.”

What kind of self-serving biologically uninformed researcher says:

Thanks for being our advocate! I now do remember glancing at some of [Kohl’s claims] a few years ago, and it is ridiculous. My approach is just to ignore rather than engage pseudoscience.

—-

and then claims “It’s time to give our sense of smell the recognition it deserves” — 20 years after my book was published.

The Scent of Eros: Mysteries of Odor in Human Sexuality https://books.goog…AAAAIAAJ

Captain Stumpy

5 / 5 (3) Feb 17, 2015

Thanks. Sorry, I was not aware that there are “grammar queens” here. I thought there were only science idiots.

@jk
you got it wrong
there are idiots (like you making your pseudoscience claims, religious beliefs and misinterpretations of everyone’s work and studies)

and there are educated people trying to show you where you are making a big mistake with your reasoning process, like :
RealScience
Anonymous9001

The Scent of Eros: Mysteries of Odor in Human Sexuality https://books.goog…AAAAIAAJ

this is called PSEUDOSCIENCE

it is also called TROLLING and SPAM
go advertise your stupid perfume elsewhere, this is a SCIENCE SITE

I contacted Vosshall. Guess what? You’re misinterpreting.

and AGAIN you are proven to lie about interpretations of another study!
this is becoming embarrassing for you jk
at least it SHOULD be

your Dunning-Kruger is showing

anonymous_9001

5 / 5 (3) Feb 17, 2015

Base flipping can occur through Brownian motion or induced by a few different enzymes, as the wiki points out. Here’s a study on the biophysics behind spontaneous flipping of mismatched pairs:

https://www.ncbi.n…4050552/

In my model, for example, it is RNA-directed DNA methylation.

Flipping occurs during the process of methylation so methyltransferases have access to the base. Is that what you’re referring to? That’s not the only process that flipping is involved in though. Where in your model do you discuss flipping? I don’t recall seeing it mentioned in any of your papers

JVK

1 / 5 (3) Feb 17, 2015

I didn’t ask whether base flipping occurs. Claims that it spontaneously occurs or that it occurs through Brownian motion or via different enzymes fail to address the change in energy that is required.

The energy “jumps” are what de Vries defined as “mutations” more than a century ago.

Spontaneous base flipping is another way to say that evolution occurs via mutations without saying what causes the mutations or the evolution. Simply put it is more pseudoscientific nonsense that fails to address biologically-based cause and effect in the context of what is currently known about physics and the chemistry of protein folding, which enables the de novo creation of olfactory receptor genes and cell type differentiation in all cells of all individuals of all species via RNA-mediated amino acid substitutions.

Where in your model do you discuss flipping?

What difference does that make if you do not know how it occurs or want to argue about my grammar?

JVK

1 / 5 (3) Feb 17, 2015

Where in your model do you discuss flipping? I don’t recall seeing it mentioned in any of your papers

As I recall, Leslie Vosshall did not discuss base pair flipping in her reports on amino acid substitutions that differentiate the cell types of mosquitoes. But you invited her to comment on my published works.

Perhaps you should ask her if mutations cause the base pair flipping or if the amino acid substitutions automagically occur.

If she cannot explain how mutations cause the amino acid substitutions, it might make her work appear to be pseudoscienctific nonsense to anyone who knows that the base pair flipping must occur for cell type differentiation via amino acid substitutions to occur.

https://www.nature…964.html

anonymous_9001

5 / 5 (3) Feb 17, 2015

Claims that it spontaneously occurs or that it occurs through Brownian motion or via different enzymes fail to address the change in energy that is required.

The study I linked specifically concerns the kinetics:

We measured the rate and equilibrium constants at different temperatures, from which the thermodynamic and dynamic parameters (i.e., the reaction free energy, enthalpy, entropy, out- and inward flipping activation energy, and preexponential factor of the rate constant) of the investigated mismatched base pairs can be derived. We also applied enhanced sampling molecular simulations (36) to characterize the mechanistic and molecular details of the single-base flipping. Our computational and experimental results are in good agreement. These data have offered fundamental understanding on the dynamics of the spontaneous single-base flipping.

anonymous_9001

5 / 5 (3) Feb 17, 2015

One of the papers they cite:

Free energy and structural pathways of base flipping in a DNA GCGC containing sequence
https://www.ncbi.n…12051942

Let’s go back almost a year:

https://phys.org/n…ion.html

You insist there that flips are substitutions/SNPs. Are you still under that impression?

JVK

1 / 5 (3) Feb 17, 2015

Where does free energy come from?

I cited “Large Numbers of Novel miRNAs Originate from DNA Transposons and Are Coincident with a Large Species Radiation in Bats”

Now I’m saying that “Spontaneous base flipping is another way to say that evolution occurs via mutations without saying what causes the mutations or the evolution. Simply put it is more pseudoscientific nonsense that fails to address biologically-based cause and effect in the context of what is currently known about physics and the chemistry of protein folding, which enables the de novo creation of olfactory receptor genes and cell type differentiation in all cells of all individuals of all species via RNA-mediated amino acid substitutions.”

I would like to find the free energy that you seem to think is responsible for the biodiversity and bat radiation that I claim is nutrient-dependent and pheromone-controlled. Is the free energy found in something you can eat, or use to heat your house?

anonymous_9001

5 / 5 (3) Feb 17, 2015

The fact that you say a paper I provide fails to address the change in energy when it’s an in-depth look at the physics (study of matter and energy) tells us that you have absolutely no idea what you’re talking abut.

Where does free energy come from?

The energy organisms get comes from a variety of sources, including solar energy, chemical energy, etc. Radiotrophic organisms are another story entirely. The harness the energy given off by radioactive elements within the Earth.

JVK

1 / 5 (3) Feb 17, 2015

https://www.ncbi.n…12051942 “During flipping, the target base tracks along the respective grooves, leading to hydrogen-bonding interactions with neighboring base-pairs. Such hydrogen-bonding interactions with the neighboring sequence suggest a novel mechanism of sequence dependence in DNA dynamics.”

Where is the free energy found that suggests “…a novel mechanism of sequence dependence in DNA dynamics.” ?

You insist there that flips are substitutions/SNPs. Are you still under that impression?

Why do you ask more questions, without answering mine? Why are you bringing up what I said before in whatever context I said it — without placing it into the context you wish to discuss? Do you think the flips are substitutions/SNPs?

I think you’re a science idiot. Do you?

JVK

1 / 5 (3) Feb 17, 2015

The energy organisms get comes from a variety of sources, including solar energy

Is that what you call “free energy?”

Solar energy is the source of the biological energy that links amino acid substitutions from plants to animals via the conserved molecular mechanisms of the biophysically constrained nutrient-dependent RNA-mediated chemistry of protein folding.

Where does chemical energy come from? Do the radiographic elements within the earth cause its biodiversity? I’m having difficulty following your train of thoughts; it’s like sifting through a train wreck caused by pseudoscientific nonsense.

Have you asked Leslie Vosshall for help, yet?

Amino Acid Residues Contributing to Function of the Heteromeric Insect Olfactory Receptor Complex https://www.ploson….0032372

“the biophysical properties of the channel vary according to subunit composition”

Ask her where biophysical properties come from.

anonymous_9001

5 / 5 (3) Feb 17, 2015

Where is the free energy found that suggests “…a novel mechanism of sequence dependence in DNA dynamics.” ?

I’m not sure what you mean by that.

Why do you ask more questions, without answering mine?

It’s a gauge of whether you learned anything last time or if you’re going to bring up the same questions that were answered 10 months ago.

Do you think the flips are substitutions/SNPs?

If you can’t answer that on your own, then you really need help.

JVK

1 / 5 (3) Feb 17, 2015

No, wait. I think I found where she thinks the biophysical properties came from. Ask her if she thinks they arose from “…constraint-breaking mutation” and became “…the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.” https://www.amazon…99661731

anonymous_9001

5 / 5 (3) Feb 17, 2015

Is that what you call “free energy?

https://en.wikiped…e_energy

Where does chemical energy come from?

From energetic chemical bonds. ATP, for example, utilizes the favorable decomposition of its triphosphate bonds to store and release energy.

I’m having difficulty following your train of thoughts

That’s ironic coming from somebody who changes topics with almost every post.

Ask her where biophysical properties come from

As the part you quoted says, the properties depend on the subunit composition. Physical properties vary with chemical properties and structure. Look up isomers. Molecules with the same composition can have drastically different properties by being arranged differently.

JVK

1 / 5 (3) Feb 17, 2015

I wrote:

Solar energy is the source of the biological energy that links amino acid substitutions from plants to animals via the conserved molecular mechanisms of the biophysically constrained nutrient-dependent RNA-mediated chemistry of protein folding.

What other energy source links physics and chemistry to the conserved molecular mechanisms of cell type differentiation, and how does any other energy source lead to biodiversity? Where does the “other” energy source come from?

RealScience

5 / 5 (3) Feb 17, 2015

As I recall, Leslie Vosshall did not discuss base pair flipping in her reports on amino acid substitutions that differentiate the cell types of mosquitoes. But you invited her to comment on my published works.

The sequence of comments in this thread CLEARLY shows, JVK, that YOU cited Vosshall’s work, and made the claim that it provides evidence AGAINST the role of mutations in evolution, and Anon_9001 contacted her, and posted her reply that calls your claims ridiculous, all before base pair flipping was even mentioned.

So what does base pair flipping have to do with Anon_9001 contacting Vosshall?
It only entered the comments when you confused quantum properties of DHA with base pair flipping in DNA…

– continued –

RealScience

5 / 5 (3) Feb 17, 2015

– continued –

And it sure is funny how your attitude changed when Vosshall disagreed with you. You cited her work at least 30 times in 16 different comment threads (including three times in this one), with never a bad thing to say about Vosshall until Anon_9001 got a reply from her.

But now that everyone can see that she think that your claims are ‘ridiculous’, suddenly it is

Too bad she didn’t do more than glance at my claims. She might have avoided some embarrassment

and calling her a

self-serving biologically uninformed researcher

and saying

If she cannot explain how mutations cause the amino acid substitutions, it might make her work appear to be pseudoscienctific nonsense…

And this is far from the first case where you go from claiming that a researcher’s work supports your model to insulting the researcher after that researcher replies that you are misinterpreting his or her work!

LMAO

– continued –

RealScience

5 / 5 (3) Feb 17, 2015

– continued –

But let’s get back to the ongoing discussions of amino acid substitutions and then base pair flipping and then DHA.

I’m sure Vosshall knows how most of the possible point mutations in the protein-coding regions of a gene cause one amino acid to be substituted for another if when that protein is produced. It is well known and well-accepted by experts in the field.

I have explained the most common link between mutations and amino acid substitutions to you twice already in considerable detail, and I’ll explain it again if you tell me what part you still fail to grasp (although it seems to be a case of “you can explain JVK the details but you can’t make him think”).

Do you want me to explain it again?
(And, if so, what part do you fail to understand so that I can concentrate on that part?)

– continued –

RealScience

5 / 5 (3) Feb 17, 2015

– continued –

Regarding your base pair flipping comment:

… the base pair flipping must occur for cell type differentiation via amino acid substitutions to occur.

It seems as if you are still using base pair flipping in a non-standard manner. As Anon points out, base flipping (also but less commonly called base pair flipping), is normally used to mean a DNA base pair being decoupled and at least one of the bases rotated outward so that it is more accessible.

But the main link of this meaning of flipping to amino acid substitutions is that some DNA repair enzymes use this to detect mispaired bases that are then repaired to PREVENT mutations that would otherwise cause amino acid substitutions.

Base pair flipping is also used by enzymes that epigenetically modify DNA (e.g., DNA methyltransferases and alkyltransferase), but this is also linked to PREVENTING amino acid substitutions. (Alkylguanine-DNA alkyltransferase, or AGT, repairs DNA)

– continued –

RealScience

5 / 5 (3) Feb 17, 2015

– continued –

Since the standard meaning of ‘base pair flipping’ is more strongly connected to preventing amino acid substitutions than to causing them, it seems likely that you are still referring to single nucleotide polymorphisms as ‘base pair flipping’

This would fit with your earlier comment:

… in my model, which links SNPs (base pair flipping) to amino acid substitutions.

While Anon_9001 already explained that this doesn’t match the standard way ‘base pair flipping’ is used, I known that you have an aversion to definitions and standard terminology, so if you are still using ‘base pair flipping’ to means SNPs I’d be happy to explain ‘base pair flipping’ in that context (in which it would indeed be related to amino acid substitutions…)

Would you like me to explain the link ‘base pair flipping’-meaning-SNPs to amino-acid substitutions?

Or should I move on to explaining the quantum-properties-of-DHA article to you?

JVK

1 / 5 (3) Feb 17, 2015

Tell me where the energy that causes the base pair flipping comes from and what switches it on and off.
RealScience

5 / 5 (3) Feb 18, 2015

Tell me where the energy that causes the base pair flipping comes from and what switches it on and off.

Is that addressed to me or to Anon_9001?

If to me, then are you equating ‘base pair flipping’ to SNPs as you did previously, or are you using it in the most common way to mean rotation of DNA bases?
(The energy sources are the same in in either case, but what switches it on and off depends on which meaning you are using for ‘base pair flipping’…)

JVK

1 / 5 (3) Feb 18, 2015

What are the two meanings of base pair flipping that would be different in the context of the energy source that flips the switch from on to off or vice versa?

How does the energy source link the base pair flipping to anti-entropic epigenesis and epistasis?

RealScience

5 / 5 (3) Feb 18, 2015

What are the two meanings of base pair flipping that would be different in the context of the energy source that flips the switch from on to off or vice versa?

I already described the two different meanings of base pair flipping that have been used in phys.org discussions involving you: the most common meaning in the field (decoupling a DNA base from its paired base and rotating its position to expose the base), and the meaning you have used previously of SNPs.

I also commented that the energy sources were the same – but that is the underlying sources, not the proximate energy carrier.

If you are referring to the proximate energy carrier, then there IS a difference: the energy for the standard meaning of base pair flipping can be either thermal energy (spontaneous base flipping), or can be ATP (flipping by RNAs or enzymes such as transferases to access the base), while for SNPs the energy is almost never thermal and the carrier is often a free radical.

JVK

1 / 5 (3) Feb 18, 2015

Isn’t the origin of thermal energy and of ATP the biological energy of the sun?

I asked: “How does the energy source link the base pair flipping to anti-entropic epigenesis and epistasis?”

I asked: “What are the two meanings of base pair flipping that would be different in the context of the energy source that flips the switch from on to off or vice versa?”

How does a free radical flip the switch from on to off or vice versa?

Captain Stumpy

5 / 5 (2) Feb 18, 2015

Isn’t the origin of thermal energy and of ATP the biological energy of the sun?

@jk
WTF?
i thought you knew something about physics?

after all you are quoting QM and stating you know it all when it comes to biology…. but now all of the sudden you don’t know SQUAT about chemical energy or basic chemistry?
you don’t know that thermal energy can come from chemical or radiation sources?

really?

this is something you can find in a 2 second search on Google…

Here is a 7th grade Physical science class paper on it: https://thinktankc…mal.html

i am going to QUOTE your own words back at you

I think you’re a science idiot. Do you?

i am not even going to ASK about what the “biological energy of the sun” means in your world

you are likely referring to biological processes deriving energy from the sun, but too stupid to articulate it in anything but PSEUDOSCIENCE talk

EPIC FAILURE for jk
AGAIN

JVK

1 / 5 (3) Feb 18, 2015

i am not even going to ASK about what the “biological energy of the sun” means in your world

It links light-induced amino acid substitutions in plants and animals to nutrient-dependent RNA-mediated cell type differentiation in species from microbes to man via what is currently known about physics, chemistry, and molecular biology.

Obviously, I know how the switches are flipped in my model.

But, I have no idea how they are flipped on and off by energy in the ridiculous theories that science idiots, like you, have been taught to believe in.

That’s why I want someone to tell me how the energy they think flips the on/off switches leads to cell type differentiation.

JVK

1 / 5 (3) Feb 18, 2015

Speaking of science idiots. Here’s the latest from PZ Myers who other science idiots supported when he attacked me for my position on chromosomal rearrangements and cell type differentiation.

“… biology verifies the existence of a continuum of sexual differentiation. Drag this article out next time someone tries to argue that biology supports their simplistic version of a discrete sexual dichotomy.” https://freethough…an-that/

“…the existence of a continuum of sexual differentiation” is what we detailed in our 1996 Hormones and Behavior review, after I extended my model to sexual orientation in my 1995 book and in an award winning book chapter/journal article.

The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences
https://www.sexarc…kohl.htm

You can’t get across the continuum without chromosomal rearrangements.

RealScience

5 / 5 (3) Feb 18, 2015

Isn’t the origin of thermal energy and of ATP the biological energy of the sun?

Usually, but not always.

For thermal energy: At the earth’s surface 99.97% of the thermal energy is from the sun, but 0.03% is geothermal. However many microbes live in geothermal hot springs, hydrothermal vents, or simply deep enough in the earth’s crust that geothermal energy is a major contributor.

For the energy of ATP, again at the surface of the earth it is almost all from the sun. However there are hot springs and especially under-water hydro-thermal vents where the energy of ATP is geochemically driven, and there are even microbes in underground mines whose energy for ATP comes more directly from radioactivity.

But why do you ask? – I haven’t seen anyone on this thread claim otherwise.

-continued-

NOTE: comment made before reading the last two JVK posts…

RealScience

5 / 5 (3) Feb 18, 2015

-continued-

I asked: “How does the energy source link the base pair flipping to anti-entropic epigenesis and epistasis?”

For thermal energy the link is pretty indirect, with the strongest link being that some creatures regulate their temperature and hence indirectly regulate the thermal energy available for ALL events, including spontaneous base flipping.

However for ATP-carried energy the link depends on whether by ‘base pair flipping’ you mean the commonly used definition of rotation of a DNA base (which, as explained previously, is used by DNA repair enzyme and so largely PREVENTS amino acid substitutions), or whether by base pair flipping you mean an SNP, which IS related to amino acid substitutions.

You still haven’t said which of these meanings for you are using for ‘base pair flipping’. DO you understand the difference, and, if so, which are you using ‘base pair flipping’ to mean?

-continued-

RealScience

5 / 5 (3) Feb 18, 2015

-continued-

I asked: “What are the two meanings of base pair flipping that would be different in the context of the energy source that flips the switch from on to off or vice versa?”

I ALREADY told you:

equating ‘base pair flipping’ to SNPs as you did previously
or the most common meaning of rotation of DNA bases

Do you fail to understand the difference between these?

How does a free radical flip the switch from on to off or vice versa?

Base pair flipping in the sense of rotating a base can indeed be switched on and off (e.g., DNA repair enzymes can switch it on to recognize a mispaired base to repair the DNA, but I already explained to you that this is ATP-DRIVEN.

FREE RADICALS are an energy carrier for the SNP meaning you have used for ‘base pair flipping’, but SNPs are in general not switched on and off.

Again, do you fail to understand the difference between these?
If you do understand the difference, which do you mean?

anonymous_9001

5 / 5 (4) Feb 18, 2015

Isn’t the origin of thermal energy and of ATP the biological energy of the sun?

Thermal energy can have many origins. The sun is one of them. Latent heat from the planet’s formation, radioactive decay, lightning, etc.

How does the energy source link the base pair flipping to anti-entropic epigenesis and epistasis?

As far as anti-entropic processes, base flipping is involved in excision repair, but it doesn’t really have a direct connection to epigenesis (morphogenesis) or epistasis.

What are the two meanings of base pair flipping that would be different in the context of the energy source that flips the switch from on to off or vice versa?

Base flipping is a conformational change which changes a base from being inside the helix to being exposed outside the helix so that enzymes can interact with it. Being inside is more thermodynamically stable, so that’s where they are most of the time. Think of it like a resonance structure.

Captain Stumpy

5 / 5 (2) Feb 18, 2015

Speaking of science idiots.

@jk
wait… i think you should go back and learn a little something about BASIC -chemistry, biology, physics and QM- first!

you made a fallacious claim and now not even a correction of your statement?
can’t admit when you are wrong?

your Dunning-Kruger is showing, pheromone-stinky-boy

You can’t get across the continuum without chromosomal rearrangements

WOW
another fallacious comment

care to specify WHICH continuum before you start to REALLY look stupid?

the reality of jk: https://freethough…s-place/

his model DEBUNKED: https://www.socioa…ew/24367

his religion DEBUNKED: https://rationalwi…_science
proven to be NON science: https://en.wikipe…Arkansas

another epic fail for you, jk

JVK

1 / 5 (3) Feb 18, 2015

Captain Stumpy

I cannot remember anytime you have made an intelligent comment on any topic. Your links to the ignorant comments by others are increasingly annoying. Either address the experimental evidence from what you know, or admit you know nothing and are being led to believe in pseudoscientific nonsense by others who know nothing.

JVK

1 / 5 (3) Feb 18, 2015

Think of it like a resonance structure.

I do.
Electron spin changes during general anesthesia in Drosophila https://www.ncbi.n…4151765/

Dose-Dependent Effects of the Clinical Anesthetic Isoflurane on Octopus vulgaris: A Contribution to Cephalopod Welfare https://www.tandfo…uMckXI6I

Those two article link my model from insects to octopuses and quantum consciousness in humans via epigenesis and epistasis.

See also: Role of olfaction in Octopus vulgaris reproduction https://www.scienc…14004006 ” …peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).”

Nutrient-dependent base pair flipping is the most obvious key to DNA repair in my model.

You can’t even begin to link it to epistasis, you flipping science idiot.

RealScience

5 / 5 (3) Feb 18, 2015

JVK, first your model EQUATED base pair flipping with SNPs (which do cause amino acid substitutions).

… in my model, which links SNPs (base pair flipping) to amino acid substitutions.

Now, AFTER the link between base pair flipping and DNA repair has been pointed out to you, you are linking ‘base pair flipping’ to to DNA repair:

Nutrient-dependent base pair flipping is the most obvious key to DNA repair in my model.

However DNA repair is part of a process that PREVENTS new SNPs and their resulting amino acid substitutions.

SO WHICH IS IT?

Are you standing by your earlier claim in which your model EQUATES base flipping to SNPs?

Or, AFTER others have pointed out to you that the standard definitiuon of base pair flipping is something that is part of DNA repair that PREVENTS new SNPs and amino acid substitutions, are you switching what you mean by base pair flipping?

Make up your flipping mind!

anonymous_9001

5 / 5 (4) Feb 19, 2015

Nutrient-dependent base pair flipping is the most obvious key to DNA repair in my model.

Considering there’s no mention of it in any of your publications…

You can’t even begin to link it to epistasis

https://www.ndsu.e…del6.htm

Epistasis – the interaction between two or more genes to control a single phenotype

What does base flipping have to do with epistasis?

Captain Stumpy

5 / 5 (2) Feb 19, 2015

@jk

I cannot remember anytime you have made an intelligent comment on any topic

Except to point out that you know nothing about physics, chemistry and you fail epically with regard to biology and the nomenclature used from medicine to biological research, right? or to point out that your fallacious belief system is actually nothing more than creationist diatribe wrapped in pheromone double-talk and word salads

Your links to the ignorant comments by others are increasingly annoying

Why, because they prove you are an idiot? or because they prove you are wrong?

Either address the experimental evidence from what you know, or admit you know nothing and are being led to believe in pseudoscientific nonsense by others who know nothing.

let me start out by saying:
I FULLY ADMIT you know nothing and are being led to believe in pseudoscientific nonsense by others who know nothing

and you can quote me on that
you really DONT know anything

Captain Stumpy

5 / 5 (2) Feb 19, 2015

Electron ….Drosophila

Ok, i’ll see your Drosophila and raise you a statement that LIKELY applies to any link and study that you post on here, including your own work

in that very same paper, we provide evidence that heritable differences in the genome sequences between Drosophila species, in other words, mutations, ALSO play a role in the evolution of the trait we are studying.

So Kohl is mistaken if he is claiming that my study (or Rich Lenski’s work) provide evidence AGAINST the role of mutations in evolution

Dr. Extavour feedback regarding your “interpretation” of her work

which leaves us with your continual failure to comprehend the terminology you work with and claim to know
it proves that you are nowhere near as intelligent as you think you are
and that you are likely misinterpreting every link you suppl as “defense” of your religious creationist BS that you post

to you i say

you flipping science idiot

at least Anon and Real post LEGIT science

RealScience

5 / 5 (2) Feb 19, 2015

Nutrient-dependent base pair flipping is the most obvious key to DNA repair in my model.

Considering there’s no mention of it in any of your publications…

Nor did JVK mention it in any comments, either, until after you pointed it out to him in https://phys.org/n…ion.html

Base flipping is the transition of the base from the interior of the double helix to the outside. It’s utilized by DNA glycolyases as part of the DNA repair process. …

Flipping in and of itself, however, is not substitution.

Even then he didn’t get it until it was REPEATEDLY pointed it out to him in this thread!

And now he has been caught red-handed learning from what he calls ‘science idiots’…

ROTFLMAO!

(I’m surprised that he didn’t just rely on his usual cop-out of refusing to use definitions, and insisting on using flipping it to mean SNPs. That would at least have been consistent.)

JVK

1 / 5 (2) Feb 19, 2015

The anonymous fool (aka Andrew Jones) asked…

What does base flipping have to do with epistasis?

… after he linked to a site about Mendelian genetics: https://www.ndsu.e…del6.htm

See my comments at
https://phys.org/n…ene.html — breaks Gregor Mendel’s century-old “law of segregation,” which states that you have an equal probability of inheriting each of two copies of every gene from both parents.

If the “law of segregation” was an accurate representation of biologically based cause and effect, we could not have cited extant literature on epigenetic imprinting in our 1996 review.

Now, 18 years later we read that Female mice pass on one copy of the R2d2 gene more frequently than the other copy — and that

at least Anon and Real post LEGIT science.

RealScience

5 / 5 (2) Feb 19, 2015

Quit trying to change the subject, JVK.Do you equate base pair flipping with SNPs, as you CLEARLY did before Anon_9001 pointed out how the term is commonly used in genetics?

… in my model, which links SNPs (base pair flipping) to amino acid substitutions.

… you want others to believe that Flipping =/= substitution …

or do you show that you actually learned something from ‘science idiots’ by using it as part of the DNA repair process, after Anon and I have repeatedly pointed that out to you?

(Anon) Base flipping is … utilized by DNA glycolyases as part of the DNA repair process.

(Anon) base flipping used in the excision repair pathway,

(Anon) a base flips from its usual conformation inside the helix to being outside the helix, which makes it accessible to enzymes involved in DNA repair pathways.

(RS) Base pair flipping is something that happens to DNA (for example during DNA repair).

-continued-

JVK

1 / 5 (2) Feb 19, 2015

… you actually learned something from ‘science idiots’ by using it as part of the DNA repair process”

In my invited review of nutritional epigenetics, I wrote:

Do enzymes such as glucose dehydrogenase allow organisms from microbes to man to incorporate nucleotides from other organisms into new structures associated with glucose uptake and amino acid substitutions? There is still a lack of conclusive proof that links DNA uptake among different bacterial species existing in similar environments (Palchevskiy & Finkel, 2009) to nutrient-dependent epigenetic effects on interspecies changes in the physical landscape of DNA and speciation via conjugation in bacteria (Fall et al., 2007; Finkel & Kolter, 2001; Friso & Choi, 2002).

There is no longer a lack of conclusive proof, and the proof attests to the fact that most participants here are biologically uninformed science idiots who believe in mutation-driven evolution.

JVK

1 / 5 (2) Feb 19, 2015

https://www.amazon…99661731 Mutation-Driven Evolution
Conclusion: “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements.” (p. 199)Nutrient-dependent/pheromone-controlled adaptive evolution: a model. https://www.ncbi.n…24693353
Conclusion: “… this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.”Criticisms of the nutrient-dependent pheromone-controlled evolutionary model.
https://www.ncbi.n…4049134/
James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research.1) Andrew Jones
2) RealScience
3) Captain Stumpy
—————
SCIENCE IDIOTS

RealScience

5 / 5 (2) Feb 19, 2015

Sorry about the delay…

-continued-

(RS) some DNA repair enzymes use this to detect mispaired bases that are then repaired

(RS) base pair flipping … (which, as explained previously, is used by DNA repair enzyme …

(Anon) base flipping is involved in excision repair

Only AFTER we had drummed it through your thick skull did you suddenly proclaim:

Nutrient-dependent base pair flipping is the most obvious key to DNA repair in my model.

So which is it, JVK, do you go back to your earlier mistake of equating base pair flipping with SNPs? or do you ADMIT that you learned something from ‘anonymous fools’ and ‘science idiots’?

RealScience

5 / 5 (2) Feb 19, 2015

In my invited review of nutritional epigenetics, I wrote:

Do enzymes such as glucose dehydrogenase allow organisms from microbes to man to incorporate nucleotides from other organisms into new structures associated with glucose uptake and amino acid substitutions?

Ah, JVK, now you are trying to claim that you knew it all along.

This goes so well with your earlier quote:

This is typical of those who know nothing. They wait until what’s known is perfectly clear and then claim that they’ve known it all along. (JVK, Feb 17 2015).

So this sentence that mentions some enzyme and amino acid substitutions in the same sentence is your best evidence that you really did know it all along? OK, let’s chick it out!!!

-continued-

RealScience

5 / 5 (2) Feb 19, 2015

-continued-

Glucose dehydrogenase is NOT a DNA repair enzyme. As its name would suggest, it is an enzyme that removes a hydrogen from a glucose molecule.

It looks like you made a similar mistake before, and claimed that glucose dehydrogenase introduces SNPs (which is funny because creating an SNP is a DNA sequence change and hence a mutation by the standard definition).

As Anon_9001 told you then:

They, as the name implies, dehydrogenate glucose. That’s all they do. They don’t flip base pairs. They don’t interact with DNA at all. As I said before, if you name something that’s well documented, it’s not hard to see if they do what you say they do. As it turns out, glucose dehydrogenases are well characterized and you’re flat out lying in saying that they make DNA changes.

So, JVK, are you going to compound your error by claiming that glucose dehydrogenase is now a DNA repair enzyme?

JVK

1 / 5 (2) Feb 20, 2015

No. I’m going to quit responding to science idiots and focus on presenting what is known to serious scientists about RNA-mediated cell type differentiation.

See my Facebook Group: RNA-mediated

https://www.faceb…5911912/

RealScience

5 / 5 (2) Feb 20, 2015

I’m going to quit responding to science idiots

So you are not even going to TRY to defend your attempt to represent glucose dehydrogenase as a DNA repair enzyme?

I’ll give you another chance: do you have anything ELSE to present to try to show that your model had base pair flipping as the most obvious key to DNA repair BEFORE Anon pointed out to you that base pair flipping is associated with DNA repair enzymes?

You have given us so many legitimate reasons to laugh that I would really hate to laugh at how well your quote:

This is typical of those who know nothing. They wait until what’s known is perfectly clear and then claim that they’ve known it all along. (JVK, Feb 17 2015)

applies to you if it actually doesn’t apply in this case.

JVK

1 / 5 (2) Feb 20, 2015

do you have anything ELSE to present to try to show that your model had base pair flipping as the most obvious key to DNA repair BEFORE Anon pointed out to you that base pair flipping is associated with DNA repair enzymes?

I can’t resist responding to one more claim by a science idiot that suggests another science idiot has informed me about what I have thoroughly detailed.

“… calcitriol is the active form of vitamin D. Its effects on the microRNA(miRNA)/messenger RNA (mRNA) balance appear to protect against perturbed protein folding, which is associated with colorectal cancer. MiRNA-627 targets the mRNA that encodes an enzyme linked to histone demethylation and amino acid substitutions that increase stability of hydrogen bonds in DNA, which are important to protein folding (Padi, Zhang, Rustum, Morrison, & Guo, 2013).”

anonymous_9001

5 / 5 (2) Feb 20, 2015

That calcitriol excerpt says nothing about and has nothing to do with base flipping. What was posting an excerpt irrelevant to the topic at hand supposed to achieve?
JVK

1 / 5 (2) Feb 20, 2015

Vitamin D stabilizes the DNA in the organized genomes of human populations in areas where malaria is endemic via the conserved molecular mechanisms of biophysically constrained protein folding, which is RNA-mediated by nutrient-dependent amino acid substitutions, e.g., in red blood cells. (See Dobzhansky, 1973 and Combating Evolution to Fight Disease https://www.scienc…8.short)

How can you continue to be a biologically uninformed science idiot? It has been more than a decade since Greg Bear included everything known about RNA-directed DNA methylation and nutrient-dependent RNA-mediated amino acid substitutions in two different books that set the Sci-Fi standard of excellence in fact-checking.

Theorists have continued to ignore all the facts. Your claim that my “…calcitriol excerpt says nothing about and has nothing to do with base flipping” exemplifies the claims of science idiots. https://www.youtu…NcMR_-RU

anonymous_9001

5 / 5 (2) Feb 20, 2015

Again, you make another post that has nothing to do with base flipping.
RealScience

5 / 5 (2) Feb 20, 2015

… calcitriol is the active form of vitamin D. Its effects on the microRNA(miRNA)/messenger RNA (mRNA) balance appear to protect against perturbed protein folding, which is associated with colorectal cancer. MiRNA-627 targets the mRNA that encodes an enzyme linked to histone demethylation and amino acid substitutions that increase stability of hydrogen bonds in DNA, which are important to protein folding (Padi, Zhang, Rustum, Morrison, & Guo, 2013).”

JVK, that is a big improvement, and this quote is actually somewhat relevant. While the KDM2A enzyme that MiRNA-627 targets is NOT a DNA repair enzyme, at least histone demethylation through KDM2A does trigger DNA base excision repair, and hydrogen bond stability in DNA is at least related to base pair flipping, so at least that quote is in the right ballpark.

-continued-

RealScience

5 / 5 (2) Feb 20, 2015

-continued-

However although it is in the ballpark, this quote doesn’t really show that you understood the link before Anon_9001 pointed it out to you. Amino acid substitutions are changes in proteins and in general don’t affect the stability of hydrogen bonds in DNA, and hydrogen bonds in DNA don’t in general have an impact on protein folding (although amino acid substitutions certainly can), and neither your quote nor the Padi et al. paper it refers to even mentions either base pair flipping or DNA repair.

If your model truly had ‘base pair flipping’ as ‘the most obvious key to DNA repair’, and you have ‘thoroughly detailed’ this, surely you at least have ONE pre-Anon_9001 reference that used ‘base pair flipping’ and ‘DNA repair’ in the same sentence, or at least the same paragraph?

JVK

1 / 5 (2) Feb 20, 2015

For those of you who have not yet realized it, RealScience wants me to do his homework for him. He’s worse than the typical biologically uninformed science idiot; he’s too lazy to learn and would rather simply steal material from others.

See also: https://matpitka.b…tor.html

Any idea that’s good enough is good enough to be pirated by those who have never had a good idea.

anonymous_9001

5 / 5 (3) Feb 20, 2015

neither your quote nor the Padi et al. paper it refers to even mentions either base pair flipping or DNA repair.

Exactly. How can you claim to have included base flipping and repair in your model if they’re nowhere to be found in any of your publications? Do you know what “included” means?

RealScience

5 / 5 (2) Feb 21, 2015

He’s worse than the typical biologically uninformed science idiot; he’s too lazy to learn and would rather simply steal material from others.

See also: https://matpitka.b…tor.html

Any idea that’s good enough is good enough to be pirated by those who have never had a good idea.

I’m puzzled – are you saying that I copied the article that you just linked and then claimed it as my own work?

If so, let’s see what you claim is evidence.

If not, then explain what it is that you are trying to saying.

RealScience

5 / 5 (2) Feb 21, 2015

RealScience wants me to do his homework for him.

MY homework?

When you claimed that Anon had waited until base pair flipping was understood at the atomic level and then claimed that he had known it all along, I recalled that I hadn’t seen a single case where you had used ‘base pair flipping’ and ‘DNA repair’ together BEFORE Anon_9001 repeatedly pointed the connection out to you.

Yet you were now claiming that “base pair flipping is the most obvious key to DNA repair” in your model, and since even a Google search didn’t find any use by you of base pair flipping and DNA repair together, I quoted your own ‘wait until what’s known is perfectly clear’ comment back at you.

I have asked THREE TIMES and you STILL haven’t presented any evidence that shows that you understood the link before it was drummed into your head.

Your first attempt was laughable – confusing glucose dehydrogenase with a DNA repair enzyme!

-continued-

RealScience

5 / 5 (2) Feb 21, 2015

-continued-

Your second try still didn’t show that you understood, but since it wasn’t as bad I did YOUR HOMEWORK and made a case for leaving the door open for you.

However since you are now being even more of a jerk than usual, I’ll point out that there is EVIDENCE that you in fact DID NOT understand:

The text you quoted in your second attempt was uploaded to figshare on April 10th, and the very next day your comments on phys.org show that you were still mistakenly equating base flipping to SNPs rather than associating it with DNA repair.

… in my model, which links SNPs (base pair flipping) to amino acid substitutions.

And worse, three days later when Anon SPECIFICALLY asked you if you were referring to excision repair, you replied:

Start providing citations for your imaginary support of pseudoscientific nonsense

Both of these are in https://phys.org/n…ion.html

-continued-

RealScience

5 / 5 (2) Feb 21, 2015

-continued-

So the HARD EVIDENCE FROM YOUR PHYS.ORG COMMENTS shows that when Anon first explained base pair flipping to you, you incorrectly equated it to SNPs and called Anon’s correct explanation PSEUDO_SCIENTIFIC NONSENSE.

This leaves three possibilities:

1) You find some evidence that you knew about it before Anon told you. Since you have claimed that you have ‘thoroughly detailed’ it, it should be EASY for you to find conclusive evidence.

2) You failed to learn it even when it was repeatedly and explicitly pointed it out to you, yet what you called pseudo-science nonsense is now part of your own model.

3) You learned it from Anon, and now claim you didn’t.

So do YOUR HOMEWORK and show that you were merely confused and wrong back in April, because in EITHER possibility 2 or 3 your own ‘this is typical of those who know nothing’ words apply to you.

RealScience

5 / 5 (2) Feb 21, 2015

Your transference is acting up again, JVK.

When Anon correctly linked flipping and DNA repair you called it ‘pseudoscience nonsense’. You then got caught red-handed copying this into your model.
So your transference caused you to claim to have caught ME copying..

However I check out the link you provided in your accusation.
It is on RNA replicators and the origin of life, and since the only extensive comments I have made on this subject recently were to Maggnus on replicators in a comments thread you were also on, it seems that you are referring to my comments there:
https://phys.org/n…ton.html

But the article that you linked bears so little resemblance to my comments that claiming the one is copied from the other is LAUGHABLE.
Furthermore the article was written a week AFTER I made my comments, so I would have needed a time machine to have copied it.

You lose again, JVK!

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Author: James Kohl

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