Scientists identify patterns of RNA regulation in the nuclei of plants

Penn scientists identify patterns of RNA regulation in the nuclei of plants
In a new study done in plants, University of Pennsylvania biologists give a global view of the patterns that can affect the various RNA regulatory processes that occur before these molecules move into the cytoplasm, where they are translated into the proteins that make up a living organism. Credit: University of Pennsylvania

When the human genome was first sequenced, experts predicted they would find about 100,000 genes. The actual number has turned out to be closer to 20,000, just a few thousand more than fruit flies have. The question logically arose: how can a relatively small number of genes lay the blueprint for the complexities of the human body?

The explanation is that genes are subject to many and varied forms of regulation that can alter the form of that protein and can determine whether and how much of a is made. Much of this regulation occurs during and just after DNA is transcribed into RNA.

In a new study done in plants, University of Pennsylvania biologists built on earlier work in which they cataloged all the interactions that occur between RNA and the proteins that bind to it. This time, they looked exclusively at these interactions in the nuclei, and simultaneously obtained data about the nuclear RNA molecules' structure. By combining these datasets, their findings give a global view of the patterns that can affect the various RNA regulatory processes that occur before these molecules move into the cytoplasm, where they are translated into the proteins that make up a living organism.

In addition, the researchers have provided a vast, publically available set of data that other scientists can use to address questions about any genes and regulatory mechanisms that interest them, gaining a better understanding of the dynamics of the journey from DNA to protein.

Brian D. Gregory, an assistant professor in Penn's School of Arts & Sciences' Department of Biology, was senior author on the work, which will appear in the journal Molecular Cell. Sager J. Gosai, a research specialist, and Shawn W. Foley, a graduate student, both members of Gregory's lab, were co-first authors. Additional contributors from Penn included Ian M. Silverman, a graduate student in the Gregory lab, along with Fevzi Daldal, a professor in the Department of Biology and Nur Selamoglu of the Daldal lab. The Penn researchers teamed with Emory University's Dongxue Wang and Roger B. Deal and University of Arizona's Andrew D. L. Nelson and Mark A. Beilstein to conduct the study.

Earlier this year in Genome Biology, Gregory's team reported on a method they developed to obtain a complete catalog of the interactions in live organisms between RNA and RNA-binding proteins, or RBPs, which interact with RNA transcripts to repress, enhance or otherwise alter gene expression in a cell-type specific manner. The technique is called PIP-seq, for protein interaction profile sequencing. Their initial demonstration of PIP-seq identified the full complement of RBP interaction sites in a human cell line.

In the current work, they used the commonly studied plant Arabidopsis thaliana to map out all of the RBP interaction sites as well as compile a full look at the secondary structure of the RNA transcripts. Unlike the first study, which looked at all the RNA in the cell, a set of material known as the transcriptome, this study looked only in the nucleus.

"By focusing specifically on the nucleus we can get away from all of the features on RNA molecules that are associated with the process of translation into proteins, which occurs in the cytoplasm," Gregory said.

The researchers extracted nuclei from 10-day-old Arabidopsis seedlings. They performed PIP-seq and also obtained information on the secondary structure of the RNA—how the strands of RNA fold, loop or bind together.

Focusing on sections of RNA that bind to RBPs, the team found that these sequences have been conserved over evolutionary time and are likely playing an important function in gene regulatory mechanisms.

The scientists also found a strong inverse relationship between patterns of RBP binding and secondary structure.

"When structure is low, proteins tend to bind those regions and when structure is high, RBPs tend to not bind those regions," Gregory said. "Time and time again, we've seen that the structural context, and not just the RNA sequence, is a selective force in RBP binding."

Another significant finding was unique patterns of RBP binding and structure present around the start codon of each messenger RNA transcript, which is where a cell's protein-making machinery begins the process of making RNA in proteins.

"This is suggesting that there is a regulatory event happening here even before the RNA comes out of the nucleus and engages with the translation machinery," Gosai said. "It's an exciting place for future studies to start with and figure out what regulation events are happening in the nucleus."

Two key forms of transcript regulation are , in which pieces of RNA undergo a cut-and-paste process to generate new sequences that can code for various proteins, and alternative polyadenylation, which alters where a transcript ends and an adenine "tail" is added, a process that can enhance either stabilization or degradation of the RNA molecule.

In their analysis, the Penn biologists found that RBP-binding sites and certain patterns of secondary structure were much more common at sites where alternative splicing and alternative polyadenylation occur.

"In humans, almost 95 percent of genes are alternatively spliced, and the number is at least 60 percent in plants," said Foley. "To see high levels of RBP binding and an interplay with secondary structure at sites of alternative splicing and polyadenylation in plants is good indication of where and how regulation is occurring to produce different proteins from one RNA sequence."

As in their previous study using PIP-seq, Gregory and his colleagues identified recurring patterns, known as "motifs," of RNA sequences at sites that tended to be bound by certain RBPs. It's possible, the researchers noted, that these groups of RBPs could bind functionally-related to coordinate their regulation.

Finally, the team zoomed in on one RBP-bound sequence motif that was particularly abundant and found that it interacted with an RBP called CP29A.

"This protein was known to bind RNA in the chloroplast, but we were able to identify it as a nuclear RBP for the first time," Foley said, suggesting CP29A may be an important regulatory factor in both organelles.

To follow up on this work, the Penn scientists will examine how RNA regulation differs in plant tissues at different developmental stages. They also plan to use PIP-seq and structural analyses to study other types of organisms.

"Now that we've found beautiful patterns that mark alternative splicing and other events that shape the protein-coding capacity of plants, we're going to go in and identify the proteins that lead to those," Gregory said. "And eventually we'd like to go into humans and other organisms and ask if we see similar patterns."


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Biologists establish new method for studying RNA's regulatory 'footprint'

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Citation: Scientists identify patterns of RNA regulation in the nuclei of plants (2014, December 31) retrieved 20 August 2019 from https://phys.org/news/2014-12-scientists-patterns-rna-nuclei.html
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JVK
Dec 31, 2014
Excerpt: "... we've found beautiful patterns that mark alternative splicing and other events that shape the protein-coding capacity... eventually we'd like to go into humans and other organisms and ask if we see similar patterns."

See also: http://medicalxpr...tml#nRlv

"Gene expression involves transcription of DNA to messenger RNA (mRNA) followed by translation of mRNA into proteins. ...a mechanism known as alternative splicing makes it possible for mRNA to be translated into any number of different proteins"

http://medicalxpr...l#inlRlv "... our work is the first structural explanation for the cooperation between splicing regulatory factors at atomic resolution..."

"Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism..." http://www.ncbi.n.../9047261

JVK
Dec 31, 2014
Our 1996 review (see above) contained a section on the molecular epigenetics of RNA-mediated cell type differentiation that I extended to RNA-mediated cell type differentiation via amino acid substitutions in all cells of all individuals of all species in a subsequent series of published reviews.

The title of the last invited review I submitted is: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

See: http://figshare.c...s/994281

It extends my last published work to the works above via what is known about cell type differentiation in the context of an atoms to ecosystem model of RNA-directed DNA methylation and RNA-mediated amino acid substitutions.

The model refutes all aspects of mutation-driven evolution.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

Dec 31, 2014
@jvk

The model refutes all aspects of mutation-driven evolution.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

Your model is a study in the hubris of ignoring all evidence to the contrary. Typical of a creationist.

JVK
Dec 31, 2014
2011 "...the relatively small genetic divergence between the human and chimpanzee genomes includes ~50,000 amino acid changes along with ~30,000,000 point mutations in noncoding sequences, as well as millions of insertions, deletions, inversions, genomic rearrangements, transposable element movements, and others33." http://dx.doi.org.../nrn3372

If an evolutionary theorist would simply explain how natural selection occurred for any of these differences in cell types during any length of time, we could compare the explanation with claims about dinosaurs evolving into birds during the time that coelacanths did not evolve into anything except other coelacanths.

Instead, we have this: 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." -- Carl Zimmer (July 2013)

JVK
Dec 31, 2014
Typical of a creationist.


Dobzhansky was a creationist. He wrote: Nothing in Biology Makes Any Sense Except in the Light of Evolution http://www.jstor..../4444260

In it, he wrote: "...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."

I've detailed the fact that amino acid substitutions differentiate all cell types of all individuals of all species and provided examples.What kind of science idiot claims my "model is a study in the hubris of ignoring all evidence to the contrary." ?

That was a rhetorical question.

What kind of science idiot claims my model is "Typical of a creationist." ? -- unless the creationist the idiot refers to was Dobzhansky?

Dec 31, 2014
to ANYONE who can read, the following is what is known as a blatant lie, fallacy and stupid
The model refutes all aspects of mutation-driven evolution.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353
Especially given that the mentioned model CAUSES MUTATIONS

then there is the FACT that the author or the model admitted that it causes mutations
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
Take all of that into consideration, PLUS the author shows that the model actually describes a BENEFICIAL MUTATION

we can conclude that the author jk is not only NOT a honest person
but is also completely ignorant/STUPID of a great many scientific things

especially clear concise communications

Dec 31, 2014
The model refutes all aspects of mutation-driven evolution.
@jk specifically
your model does not IN ANY WAY refute Evolution Theory
NOR does your model in any way refute all aspects of mutation-driven evolution

one major reason that your model CANNOT refute mutation-driven evolution is because your "model" actually describes beneficial mutations and demonstrates beneficial mutations for the SAKE of mutation driven evolution

this means, logically and by definition, that your "model" is simply part of the Theory of Evolution
as well as demonstrates your complete stupidity regarding the differences between epigenetics and genetics

you've FAILED to refute mutation-driven evolution with your link SPECIFICALLY because your link, to YOUR MODEL, demonstrates the plausibility of mutation-driven evolution by demonstrating MUTATIONS that can be beneficial

whether you like it or not
YOUR MODEL CAUSES MUTATIONS
your admittance proves it
therefore it CANNOT refute it
LMFAO

Jan 01, 2015
@ Captain Stumpy

Anyone with any intelligence and a minimum of education knows Jamie is a delusional fool. She deflects questions with off topic links that not only don't support her model but actually refute it it.

Referring to Jamie as a she is not a sexist comment but her salivating over supporting comments from John Hewitt shows her desperation for a suitor. She sure wont get it from any one who respects science.

Happy New Year!


Jan 01, 2015
@jvk

Typical of a creationist.


Dobzhansky was a creationist. He wrote: Nothing in Biology Makes Any Sense Except in the Light of Evolution http://www.jstor..../4444260

Dobzhansky also believed in mutations and natural selection. The difference between him and you (besides your religion based ignorance) is that he may have thought there might have been a designer but it in no way directed evolution.

You, on the other hand you believe god popped species into existence, to hell with all other evidence to the contrary.

Science and james v kohl don't belong in the same sentence unless you're comparing astronomy to astrology.




Jan 01, 2015
@ JVK-Skippy. How you are Cher? I'm good thanks. Let me ask you a serious question from me. Please don't answer with the gobbledygook because I am not the real scientist-Skippy, I am just the amateur-not-the-scientist-Skippy. Just something simple please.

This article is about the nuclei stuffs in plants as best I can tell by reading it. So what I want to know is, how does the smelly stinky stuffs work in the plant nuclei stuffs? Plants do not have the nose like us so how they smell it?

That's about it from me today. So I'll check in later to see if you can write me the answer that I can understand. Thanks and Happy New Year for you.

Jan 01, 2015
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

Which was cited (more accurately, pilloried) here:

http://www.socioa...ew/24367

Jan 01, 2015
Which was cited (more accurately, pilloried) here:

http://www.socioa...ew/24367


It looks like that Andrew-Jones-Skippy has JVK-Skippy's number real good. We should sign him up on the physorg because JVK-Skippy does not listen to anybody here when they try to set him straight. I like the list of other peoples who also got his number because it shows that the physorg is not the only place where he spreads his stinky love potion gobbledygook stuffs.

JVK
Jan 01, 2015
http://www.scienc...14010407

The article links nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions from ecological variation to ecological adaptations. The link requires knowledge of bio-physically constrained protein folding and recognition of the fact that mutations perturb protein folding.

That fact links RNA-mediated sex differences in cell types to their origins in the yeast model. The yeast model links sex differences in cell types to the pheromone-controlled physiology of reproduction in species from microbes to man via conserved molecular mechanisms of protein folding during the development of species-specific foraging and reproductive sexual behaviors required for survival in multicellular organisms.

http://www.pnas.o...abstract Conclusion "Morph thus interacts with sex, and we should expect that the neural mechanisms meditating the behavioral effects..."

JVK
Jan 01, 2015
My thesis, advised by an ecologist and a biochemist, concerned the evolution of RNA enzymes.


http://www.cartha...ademics/

Andrew Jones appears to now recognize that he has brought disgrace to Carthage via his review of my published work. If he graduated, we can be rather certain that his diploma will be revoked -- if only because educational facilities do not want to become linked to the teaching of science idiots who are biologically uniformed.

2015 is the year in which 'heads will role' across academia. Those who continue to teach the pseudoscientific nonsense of evolution via mutations will be removed or relocated. They will be found in closets or storage areas in the basement -- until they willingly retire themselves and make way for those who understand the reason why physics, chemistry, and molecular mechanisms must be integrated into their lesson plans.

Thanks to the efforts of Andrew Jones in 2014, serious scientists will have a Happy New Year!

Jan 01, 2015
If he graduated, we can be rather certain that his diploma will be revoked
ROTFLMFAO
really?

this anger you have towards educated people who try to help you and teach you is stunning in how widespread it is and how acerbic it has made you towards actual science
NO ONE is going to mess with his diploma, and the reason is simple:
HE IS 100% CORRECT

Those who continue to teach the pseudoscientific nonsense of evolution via mutations will be removed or relocated.
Then you had better go RUN and HIDE
because your own model CAUSES MUTATIONS
therefore YOU are teaching Evolution Via Mutations by example
ROTFLMFAO

Jan 01, 2015
The link requires knowledge of bio-physically constrained protein folding and recognition of the fact that mutations perturb protein folding.


Should read - environmental change affects nutrient intake, thusly impacting protein folding, creating a variety of mutated protein folds in subsequent cellular generations (passed on through RNA).
The ones that survive are now beneficially mutated, which is then passed on to further generations until something else happens to further impact nutrient intake.
Thusly starting the process all over, again.
That, my stubborn friend, is called the process of evolving - evolution...

JVK
Jan 01, 2015
That, my stubborn friend, is called the process of evolving - evolution...


You're describing perturbed protein folding and the evolution of cancer for other science idiots as if cancer was beneficial.

'Bad luck' of random mutations plays predominant role in cancer, study shows
http://medicalxpr...ant.html

For comparison, in my model ecological variation links nutrient availability to cell type differentiation via RNA-mediated amino acid substitutions that stabilize DNA in organized genomes. Conserved molecular mechanisms link physics and the chemistry of protein folding to molecular biology, which helps serious scientists to avoid making ridiculous claims like this:

"...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world." (p 199) http://www.amazon...99661731

Jan 01, 2015
I'll try to post again three times. Maybe it take this time. I sure hope the nice peoples at physorg have not cut me off.

@JVK-Skippy. How you are again Cher? I'm still fine thanks. Are you going to help with me with question or not help me? The question down there I ask about smelling things without a nose.

Late add in: Hooyeei, that is the relief. They have not cut me off.

Jan 01, 2015
If he graduated, we can be rather certain that his diploma will be revoked


Hahaha what?

physics, chemistry, and molecular mechanisms must be integrated into their lesson plans


I can see why you would be under the impression that they're not already integrated. It's probably because you didn't take enough classes at that level. I have my transcripts right in front of me and I can assure you that all of those topics were covered in extreme detail.

It looks like that Andrew-Jones-Skippy has JVK-Skippy's number real good. We should sign him up on the physorg


Already here.

Jan 01, 2015
Already here.


Well I did not know that, that you are him I mean. Good for us and good for you. You are the one who sounds like he went to the real science school. JVK-Skippy sounds like he went to the gobbledygook school. Even if he might know what he's talking about, he sure does have big trouble trying explain it to peoples so they can understand him.

JVK
Jan 01, 2015
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping http://www.cell.c...)01497-4

The article above links physics, chemistry, and conserved molecular mechanisms from cell type differentiation in yeasts to cell type differentiation in mammals.

Yeasts: Signaling Crosstalk: Integrating Nutrient Availability and Sex
http://www.ncbi.n...3932994/

Mammals: Feedback loops link odor and pheromone signaling with reproduction
http://www.scienc...05009815

Who taught you to believe that cell type differentiation occurs in any other way than via nutrient-dependent pheromone-controlled ecological adaptations?

How does it occur in any other way?

How does that way lead to the evolution of increasing organismal complexity?

I doubt that anyone at Carthage will say they taught you to believe in pseudoscientific nonsense, so tell us what you believe.

JVK
Jan 01, 2015
he sure does have big trouble trying explain it to peoples so they can understand him.


Science cannot be understood by science idiots. They are biologically uniformed and can't grasp anything about physics or chemistry. That's why they are science idiots. That's why they accept what their taught about evolution.

If they were not biologically uninformed they would realize the need to learn about physics and chemistry -- not expect someone in a discussion forum to teach them. Besides, as we've seen here, science idiots are perfectly content to be science idiots. They will believe anything another science idiot tells them, which is what they have always done.

Jan 01, 2015
I can see why you would be under the impression that they're not already integrated. It's probably because you didn't take enough classes at that level.
@ANON
actually, he's already admitted to failing out of college... when i find the reference in my documents i will link it to you via e-mail

this is one of the reasons that he refuses to learn the basic terminology of the field
Apparently there is the ingrained fear that it will somehow make him less intelligent as it is his assertions (judging by posts and content) that anyone with an education must be a complete idiot unless they are also creatinoists or religious because they were taught wrong, in his words

Hope you had/have a great New Years!

glad to see you showing us the REAL info and biology and not letting kohlslaw get away with his stupidity!


Jan 01, 2015
Science cannot be understood by science idiots. They are biologically uniformed and can't grasp anything about physics or chemistry
THIS would explain why jk cannot comprehend that his own model causes mutations!

the only science idiot around here is YOU, jk
here is PROOF of that claim:
You state
You're describing perturbed protein folding
when people talk about mutations (especially with Evolution)
but there is experimental and empirical evidence proving mutations CAN BE BENEFICIAL
http://www.oeb.ha...oeb.html
http://myxo.css.m...dex.html

Plus, if MUTATIONS are NEVER beneficial (as you've stated)

THEN YOUR OWN MODEL CANNOT BE BENEFICIAL
PERIOD

Jan 01, 2015
If he graduated, we can be rather certain that his diploma will be revoked -- if only because educational facilities do not want to become linked to the teaching of science idiots who are biologically uniformed.


ROTFLMAO, JVK. That's funny, coming from you whose university refused to give you a diploma because they did not want to be linked to a pseudo-scientist like you.

Jan 01, 2015
If he graduated, we can be rather certain that his diploma will be revoked -- if only because educational facilities do not want to become linked to the teaching of science idiots who are biologically uniformed.


ROTFLMAO, JVK. That's funny, coming from you whose university refused to give you a diploma because they did not want to be linked to a pseudo-scientist like you.


You ought to ask him to tell you about the one he tried to buy off the interweb.

Jan 01, 2015
Science cannot be understood by science idiots. They are biologically uniformed and can't grasp anything about physics or chemistry.


Even funnier, JVK!

You have admitted that you have no experimental evidence to support your theory that mutations are never selected for, and you have also admitted that you ignore experimental results that show that mutations are sometimes selected for. You also ignores that (as the Captain points out) your own model produces DNA sequence changes that meet the standard definition mutations. And you have admitted that you can't grasp the difference between a change in gene expression and a change in gene sequence without starting from quantum mechanics

You stay biologically uninformed so that you can pretend that your failed hypothesis is valid, and can't even grasp the basics of a field that you pretend to be an expert in.

Thank you for starting my new year with such a good laugh!

JVK
Jan 01, 2015
I asked
Who taught you to believe that cell type differentiation occurs in any other way than via nutrient-dependent pheromone-controlled ecological adaptations?

How does it occur in any other way?

How does that way lead to the evolution of increasing organismal complexity?


Why hasn't anyone answered any of those questions?

you have admitted that you can't grasp the difference between a change in gene expression and a change in gene sequence without starting from quantum mechanics


Tell us what the difference is when you start with de Vries definition of mutation and assume that "... genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world." (p. 199) http://www.amazon...99661731

I think the difference can be compared in the context of pseudoscientific nonsense to facts in my model of biologically-based cause and effect.

JVK
Jan 01, 2015
university refused to give you a diploma because they did not want to be linked to a pseudo-scientist like you.


http://www.nel.ed...ward.htm My diploma and medal were concurrently issued by Charles University in Prague; Society for Integrated Sciences; and Neuroendocrinology Letters.


JVK
Jan 01, 2015
no experimental evidence to support your theory that mutations are never selected for


http://www.scienc...abstract

Excerpt: "Rqc2p then catalyzes the addition of these amino acids onto the unfinished protein, in the absence of both the fully assembled ribosome and mRNA. These so-called CAT tails may promote the heat shock response, which helps buffer against malformed proteins."

The malformed proteins exemplify mutations linked to pathology via perturbed protein folding, which is stabilized by nutrient-dependent amino acid substitutions in my model. I have no
theory that mutations are never selected for


My model shows that amino acid substitutions that stabilize DNA in organized genomes are fixed via the species-specific metabolism of nutrients to pheromones that control the physiology of reproduction.

Others who tout ridiculous theories about selection and mutations should explain how that is possible, but they won't.

Jan 01, 2015
university refused to give you a diploma because they did not want to be linked to a pseudo-scientist like you.


http://www.nel.ed...ward.htm My diploma and medal were concurrently issued by Charles University in Prague; Society for Integrated Sciences; and Neuroendocrinology Letters.


Well excuse me. I took you at your word when you said:

"On the other hand, since I don't have a degree, this may mean (to you and some others) that I have nothing of value to say, with or without peer review. Perhaps, I have no peers in academia."
James V. Kohl, May 27, 2004


So your diploma is not associated with a degree?


Jan 01, 2015
Waitaminit....
Wasn't James Kohl, the name of the character played by Bruce Willis in "12 Monkeys"?

JVK
Jan 01, 2015
So your diploma is not associated with a degree?


What does that have to do with the topic of patterns of RNA regulation?

Jan 01, 2015
So your diploma is not associated with a degree?


What does that have to do with the topic of patterns of RNA regulation?


Gosh, JVK, you are the one who introduces diplomas to this thread (and in a manner usually associated with getting a degree):
... If he graduated, we can be rather certain that his diploma will be revoked ...


And you also said that you got a diploma, with a link to a 2001 medal:
http://www.nel.ed...ward.htm My diploma and medal were concurrently issued by Charles University in Prague; Society for Integrated Sciences; and Neuroendocrinology Letters.

Yet subsequent to 2001 you proclaimed that you do not have a degree:
... since I don't have a degree...
James V. Kohl, May 27, 2004

So that raises the question: what kind of a 'diploma' did you get it 2001 that is consistent with your 2004 statement that you don't have a degree?

Jan 02, 2015
So that raises the question: what kind of a 'diploma' did you get it 2001 that is consistent with your 2004 statement that you don't have a degree?


Zing...

Jan 02, 2015
Waitaminit....
Wasn't James Kohl, the name of the character played by Bruce Willis in "12 Monkeys"?

This one appears to be more like the Brad Pitt character...

JVK
Jan 02, 2015
what kind of a 'diploma' did you get it 2001 that is consistent with your 2004 statement that you don't have a degree?


Thanks for asking. I got a piece of paper, like the one science idiots can get if they endure several years of studies taught by other science idiots. I skipped the "science idiot" part and published an award-winning review. Saved the tuition and cost of books, too!

I think that's part of the problem here. People spend money to become science idiots, and they are annoyed when others don't waste money getting a degree.

diploma refers to a level of academic award.
http://en.wikiped.../Diploma


Jan 02, 2015
my Aunty Natalie just got red Mercedes-Benz CLA-Class CLA45 AMG from only workin part time on a computer... hop over to this site,.,,,,, paygazette.c�m


Tell Aunty-Natalie-Skippette that JVK-Skippy already has this corner staked out for pushing his stinky love potions.

Jan 02, 2015
@JVK - to include more of that quote:
A diploma ... is a certificate or deed issued by an educational institution, such as a college or university, that testifies that the recipient has successfully completed a particular course of study or confers an academic degree. In countries such as the United Kingdom and Australia, the word diploma refers to a level of academic award.

So did you complete a particular course of study, or receive an academic degree?
That would be "like the one science idiots can get if they endure several years of studies".

(I have nothing against your early review papers - they were actually decent compilations of interesting articles, many of which would have been new to someone outside of biology. Too bad you devolved into pseudo-science and started pushing conclusions that are not supported by experimental evidence or even by the articles that you cite.)

JVK
Jan 02, 2015
Thanks for asking.

So did you complete a particular course of study...


Obviously I did, or I could not have had a career as a medical laboratory scientist (ASCP).

or receive an academic degree?


Obviously not. I was afraid I would be taught to be a science idiot. After I by-pass tested through all the prerequisite courses, the dean of the UNLV biology department tried, but failed, to force me into a degree program.

After book publication in 1995 -- the dean invited me to audit any courses that interested me. When Elekonich (at UNLV) and Robinson (in 2000) extended our 1996 work on cell type differentiation to insects, I moved forward without further coursework.

How were you forced to become a science idiot? Or, is that all you ever wanted to become? if so, why do you use "RealScience" when all you know about is pseudoscientific nonsense?


JVK
Jan 02, 2015
Too bad you devolved into pseudo-science and started pushing conclusions that are not supported by experimental evidence or even by the articles that you cite.)


Too bad you're a science idiot who has no idea how much experimental evidence supports the conclusions in my model, which includes examples of biologically-based cause and effect across species that link RNA-mediated metabolic networks to genetic networks via the conserved molecular mechanisms of bio-physically constrained chemistry of protein folding.

Jan 02, 2015
Thanks for asking.

So did you complete a particular course of study...


Obviously I did, or I could not have had a career as a medical laboratory scientist (ASCP).

or receive an academic degree?


Obviously not.


Good timing - you got the MLS certification before the requirements to have a degree go into effect. But you took the question out of context, so I'll be more specific: was the DIPLOMA that you were issued conferred for a completing a particular course of study?

Jan 02, 2015
Too bad you're a science idiot who has no idea how much experimental evidence supports the conclusions in my model, which includes ...


I am well aware of experimental evidence on many factors that modulate or in some cases even override the effect of gene sequences - that's well known to anyone versed in modern biology.

However NONE of that supports your conclusion that mutations are NEVER selected for. After you demanded experimental evidence from others (and then ignored it), I pointed out that you have never presented any experimental evidence to support that conclusion.

So do you have any experimental evidence to support mutations NEVER being selected for? Or do you ADMIT (again) that there is no such evidence? Then maybe you won't have to "throw out results that appear to attest to mutations as the cause of adaptive evolution", and can look at what nature ACTUALLY does rather than pretending that your MODEL trumps reality.

JVK
Jan 02, 2015
NONE of that supports your conclusion that mutations are NEVER selected for.


No experimental evidence suggest mutations, which perturb protein function, are beneficial. Only a science idiot would twist what I am saying into a ridiculous conclusion because the science idiot cannot support the conclusion that mutations ARE selected.

Amino acid substitutions are selected, you idiot! They stabilize protein folding.

Defying textbook science, study finds new role for proteins
http://www.scienc...2314.htm another protein specifies which amino acids are added. Results from a study published on Jan. 2 in Science defy textbook science, showing for the first time that the building blocks of a protein, called amino acids, can be assembled without blueprints -- DNA and an intermediate template called messenger RNA (mRNA). A team of researchers has observed a case in which another protein specifies which amino acids are added....

Jan 02, 2015
No experimental evidence suggest mutations, which perturb protein function, are beneficial.


As has been pointed out to you many times Lenski shows clear experimental evidence of mutations being selected for. As was pointed out by several commenters, 1) If the changes were nutrient-dependent/pheromone-controlled, than many in each generation would have had the changes, whereas it took thousands of generations of numerous bacteria for a change to occur in a single bacterium, and 2) Some of the changes selected for are DNA base sequence changes, and hence would meet the definition of MUTATIONS even if they were controlled.

Only a science idiot would twist what I am saying into a ridiculous conclusion ...
So that's why you twisted evidence that adaptation involved many things in addition to mutations into a conclusion that it doesn't involve mutations!

But seriously - are you now withdrawing your conclusion that mutations are NEVER selected for?

Jan 02, 2015
Amino acid substitutions are selected, you idiot! .


Are you claiming that mutations are not selected for because mutations don't cause amino acid substitutions?

JVK
Jan 02, 2015
I've published a series of papers that detail all aspects of the "...molecular mechanisms by which a single genotype gives rise to diverse..." morphological and behavioral phenotypes in species from microbes to man via the bio-physically constrained chemistry of RNA-mediated cell type differentiation. Cell type differentiation links conserved molecular mechanisms to amino acid substitutions via links from the epigenetic landscape to the physical landscape of DNA in organized genomes.

Others have helped to complete the model. See:
http://www.the-sc...Society/

No serious scientists link mutations to increasing organismal complexity because mutations perturb protein folding.

Jan 02, 2015
@JVK - That doesn't answer the question:

Are you claiming that mutations are not selected for because mutations don't cause amino acid substitutions?


Jan 03, 2015
@Real, you know he will never answer a direct challenge like that... it would prove he is wrong! LOL
keep him reeling!
No serious scientists link mutations to increasing organismal complexity because mutations perturb protein folding
but kohlslaw, YOU link mutations to "increasing organismal complexity" [sic] with your own model!
because, as you've already admitted, your model causes Mutations!

Also, if Lenski's experimental evidence was working under your model assumptions, there would be a markedly higher number of altered generations mutated whereas the evidence demonstrates that there are very few selected, thus Lenski's experiments disproves your contention that your model type mutations MUST be "nutrient dependent..." blah blah blah

[cont'd]

Jan 03, 2015
Then we get to Dr. Extavour's work which, in her own words...
I can clarify that although our work does, we hope, provide an example of how nutrition/ecology could affect the evolution of potentially adaptive traits, you [Captain] are right that we in no way claim that mutations in the heritable genome play no role in evolution. Indeed, as you [Captain] 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.
THIS per the Dr who ran the experiment

PROVING YOU WRONG JK

epic fail for jk and creationists


JVK
Jan 03, 2015
http://phys.org/n...firstCmt

Conclusion: "The anonymous fools and idiot minions of biology teachers like PZ Myers continue to ignore everything known about the bio-physically chemistry of protein folding and tout pseudoscientific nonsense about mutations.

Attempts to discuss facts on phys.org is futile."

Jan 03, 2015
@Real, you know he will never answer a direct challenge like that... it would prove he is wrong! LOL
keep him reeling!


Captain, "never" is a dangerous word that it takes only one counter example to prove wrong. That's like JVK's mistake saying the natural selection NEVER elects for mutations.

While that odds are in your favor, JVK could for a change actually answer a direct question (he actually has on a few rare occasions) to show that you are not ALWAYS right.

But you are pretty safe - attempts to discuss facts with JVK on phys.org are typically futile because he so rarely actually answers a direct question whose answer would clarify his position.

So how about it JVK - care to have a civil discussion (and prove the Captain wrong) by actually answering the question? Here it is again:

You state "Amino acid substitutions are selected..."
Are you claiming that mutations are not selected for because mutations don't cause amino acid substitutions?

Jan 03, 2015
I see that I missed a question from you, so in the interest of civil discussion:

you have admitted that you can't grasp the difference between a change in gene expression and a change in gene sequence without starting from quantum mechanics


Tell us what the difference is when you start with de Vries definition of mutation and assume that "... genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world."


First, why would I assume Nei's position? I have already told you that I disagree with Nei on many points, and you have also disagreed with Nei, so why ask me to assume a position that neither of us agrees with?

-continued-

Jan 03, 2015
-continued-

Second, de Vries work is roughly 100 years old, as is his work on mutations in pangenes. Do you base your statement that 'mutations are never selected for" on a 100-year-old definition and a mutation model that was shown to be wrong 90 years ago?

That could explain both your conclusion and your reluctance to state the definition of 'mutation' that you are using. If you would be so kind as to clearly state exactly the de Vries definition you are using (or whatever definition you are using), I will be happy to re-evaluate your statement using that definition.

- continued -

Jan 03, 2015
- continued -

But regardless of assuming or not assuming Nei's statement, the difference between a change in gene expression and a change in gene sequence is pretty simple.

As explained to you in http://phys.org/n...rs.html:

Gene expression is reading a gene, so reading 'pray' three times instead of reading it twice would be a change in how often it is expressed.

Changing a gene's nucleotide sequence changes the way a gene is spelled, like changing the 'r' to an 'l' so that 'pray' gets changed to 'play'.

So the difference between the difference between changing a gene's nucleotide sequence and changing how often it is expressed is the same as the difference between changing 'pray' to 'play' and reading 'pray' three times instead of twice.


Do you understand this difference?

Jan 03, 2015
@jvk

http://phys.org/news/2014-12-eukaryotic-cell-ii-cytoskeleton.html#firstCmt

Conclusion: "The anonymous fools and idiot minions of biology teachers like PZ Myers continue to ignore everything known about the bio-physically chemistry of protein folding and tout pseudoscientific nonsense about mutations.

Attempts to discuss facts on phys.org is futile."


That's because you hand-wave away known facts about evolution. You deflect , obsticate and ignore questions. You quote out of context and mis-interpret the work of others. Your willful ignorance of paleontology, geology, zoology, and cladistics is driven by your stubborn creation beliefs.

You are the only one failing to discuss facts.

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

Jan 03, 2015
No serious scientists link mutations to increasing organismal complexity because mutations perturb protein folding.

Perturbed folding which cause mutations - some beneficial, most not. The majority are "selected" away... What's so hard to get about that?

Jan 04, 2015
Tell us what the difference is when you start with de Vries definition of mutation and assume that "... genomic conservation


That's even funnier for you to ask, since as the good Captain has pointed out, in http://phys.org/n...rge.html you said:

I refuse to accept definitions and assumptions about mutations!


The Captain shows that you are a hypocrite, asking others to accept that which you refuse!

So how about it JVK - care to score a point against the Captain, who says that you won't give me a direct answer? You can prove him wrong by actually answering the question:

You state "Amino acid substitutions are selected..."
Are you claiming that mutations are not selected for because mutations don't cause amino acid substitutions?

Jan 08, 2015
You can run, but you can't hide, JVK.

No experimental evidence suggest mutations, which perturb protein function, are beneficial ... Only a science idiot would twist what I am saying into a ridiculous conclusion because the science idiot cannot support the conclusion that mutations ARE selected.

Amino acid substitutions are selected, you idiot! They stabilize protein folding.


@JVK - the archetypical mutation is a single nucleotide change in the DNA sequence of the coding portion of a gene. And what effect does this have? Looking at the 9 possible single changes for each of the 64 codons, 138 out of 576 are synonymous (no change to the protein sequence coded), 50 change to or from stop codons and change the length of the protein, and 388, or 67% CAUSE AN AMINO ACID SUBSTITUTION in the resulting protein.

So if amino acid substitutions are selected because they stabilize proteins, so too are mutations that cause them.

Checkmate again, JVK!

JVK
Jan 08, 2015
This is not a game for science idiots to play. Inform yourself by reading the current extant literature and quit coming at me with claims based on ridiculous theories.

"Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes" http://www.nature...880.html

The bio-physically constrained chemistry of protein folding links ecological variation to nutrient-dependent pheromone-controlled ecological adaptations in species from microbes to man.

There has never been any scientific support for a biological basis of this claim.

"...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world." (p. 199) http://www.amazon...99661731

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

Jan 08, 2015
"Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes" http://www.nature...880.html


Without copying and pasting your little nonsense catchphrases and in your own words, explain how this refutes evolutionary theory.

Jan 08, 2015
Nutrient-dependent/pheromone-controlled adaptive evolution: a model.


@ JVK-Skippy. How you are Cher? I'm still really good thanks.

I tried to give you some advice about that Nutrient-dependent/pheromone-controlled thing you are so proud of bandying about. I begin to think you use him too much because it will show up on the Google-Skippy's answers a gazillion times if you write him a gazillion times. Is that why you use him so much?

Well Skippy, that is working against you in a big way. I just Google-Skippyed Nutrient-dependent/pheromone-controlled and guess what he shows? It shows a gazillion places where peoples are calling you a couyon and proving it at the same time.

Oh yeah,I almost forget, Google-Skippy also shows more than just the few with a picture of you wearing your silly looking pointy cap, with your really silly looking picture where it looks like somebody is tickling your toes while you were getting your picture made.

JVK
Jan 08, 2015
It links the bio-physically constrained chemistry of protein folding from atoms to ecosystems. The link clearly is from biological energy to nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all species.

What do you think it means? What do you think this abstract excerpt means?

"...intermolecular tethering of RNA to DNA. Studying the MS2 coat protein, we decompose the binding energy contributions from primary and secondary RNA structure, and observe that differences in affinity are often driven by sequence-specific changes in both association and dissociation rates."

They linked thermodynamic cycles of protein biosynthesis and degradation to the RNA-mediated amino acid substitutions that differentiate cell types in the model organisms I used as examples of biologically-based cause and effect. That's how it refutes theories about mutations and evolution.

JVK
Jan 08, 2015
I just Google-Skippyed Nutrient-dependent/pheromone-controlled and guess what he shows? It shows a gazillion places where peoples are calling you a couyon and proving it at the same time.


I'm surprised that others haven't done that. I'm not surprised when they have and are unwilling to admit it. Only a science idiot would claim that other science idiots have proved I'm a couyon.

https://www.googl...ntrolled

See also: RNA-mediated https://www.googl...mediated

Jan 08, 2015
The bio-physically constrained chemistry of protein folding links ecological variation to nutrient-dependent pheromone-controlled ecological adaptations in species from microbes to man.

There has never been any scientific support for a biological basis of this claim.


There has never been any scientific support for a biological basis of WHICH claim?

As shown in the direct quote above, the claim right above your comment is one of your own claims. Are you seriously saying that there is no scientific support for your own claim?

I'll give you the benefit of the doubt - you were probably referring to some other claim, so WHICH CLAIM were you referring to?

JVK
Jan 08, 2015
There has never been any scientific support for a biological basis of this claim.

"...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world." (p. 199) http://www.amazon...99661731

My review was published on the same day as his book. Since then, my model has been supported by everything published by serious scientists who understand biologically based cause and effect.

Jan 08, 2015
Ah, the claim that follows your comment. Thank you for clarifying that (using a colon instead of a period would have made that clear initially).

I've already told you on several occasions that I don't agree with Nei on many things, so in responding to my comment why would you introduce a Nei quote and say that there is no support for it?

quit coming at me with claims based on ridiculous theories


Are you calling it a 'ridiculous theory' that a mutation consisting of a single nucleotide change in a DNA sequence in a coding region of a gene will cause an amino acid substitution in the protein resulting from that gene?

Please answer clearly and without changing the subject.

JVK
Jan 08, 2015
Please tell me how the "mutation" you introduce above leads to anything except pathology.

In my review I detailed how amino acid substitution link ecological variation to ecological adaptations via conserved molecular mechanisms in species from microbes to man.

Jan 09, 2015
Please tell me how the "mutation" you introduce above leads to anything except pathology.

Roughly 2/3 of all possible mutations of the type I introduced above will cause an amino acid substitution in the resulting protein. To use your substitution of alanine for valine example, substitution of the amino acid alanine for the amino acid valine can be caused by a mutation that changes the second base in ANY of the valine codons from a T to a C (i.e. GTT, GTC, GTA or GTG to a GCT, GCC, GCA or GCG).

In a case where such an amino substitution stabilized a protein that it was beneficial to have stabilized, the result would not be pathology.

- continued -

Jan 09, 2015
- continued -

Whether a given mutation is pathological or beneficial can also depend on the circumstances.

For example, one sickle cell mutation is the single nucleotide change of a glutamate codon (GAG) to a Valine codon (GTG) in the beta hemoglobin gene. While two copies of this mutation DO cause pathology (sickle cell disease), one copy of this mutation does NOT cause pathology.

One copy of this mutation does, however provide malarial resistance, and so is beneficial in malaria-prone areas.

Checkmate again!

JVK
Jan 09, 2015
The hemoglobin S variant is directly attributed to nutrient uptake in the context of RNA-mediated links between metabolic networks and genetic networks. Vitamin D production, for example, from fermented grains and milk products and naturally occurring exposure to the biological energy from the sun, is linked via nutrient-dependent amino acid substitutions to genomic stability in populations where malaria is endemic.

There are ~1180 other hemoglobin variants that obviously have arisen in different human populations due to ecological variation. All of them, like hemoglobin S, are linked to ecological adaptations -- most recently in the context of rejuvenation via heterochronic parabiosis, but also in the context of everything known by serious scientists about nutrigenomics and pharmacogenomics (they link metabolic networks and genetic networks without the nonsense of beneficial mutations, because there is no evidence that mutations are beneficial to physiology).

JVK
Jan 09, 2015
In a case where such an amino substitution stabilized a protein that it was beneficial to have stabilized, the result would not be pathology.


Amino acid substitutions stabilize protein folding that is perturbed by mutations. Amino acid substitutions that are beneficial are fixed in the DNA of organized genomes via the physiology of nutrient-dependent pheromone-controlled reproduction.

Mutations are not fixed in human populations or other populations. They are eliminated by the physiology of reproduction except in cases of transgenerational epigenetic inheritance in which they show up as genetic predispositions for disease and disorders linked from nutrient-stress and social stress to their manifestations across generations in some offspring but not others.

If mutations were fixed in human populations, humans would already have mutated to extinction due to perturbed protein folding. We're on our way due to science idiots who think mutations are beneficial!

Jan 09, 2015
Amino acid substitutions that are beneficial are fixed in the DNA of organized genomes.


Great – so you agree that amino acid substitutions that are beneficial are fixed in the DNA of organized genomes!

Do you agree that the amino acid substitution is made by modifying the DNA nucleotide sequence such as the CAG to CTG modification in the hemoglobin example above?


JVK
Jan 09, 2015
I agree that only a science idiot would think I cannot see where this is leading. My model linked nutrient-dependent amino acid substitutions to their pheromone-controlled fixation.

http://www.scienc...14006778 "The evolution of independently replicating ribosomes assumes that the necessary precursor molecules (sugars, bases, nucleosides, nucleotides, amino acids, etc.) were either readily available in the environment through inorganic, prebiotic reactions or that these are being provided by the simultaneous evolution of other hyperstructures capable of catalyzing these prebiotic reactions (Hunding et al., 2006, Norris et al., 2007, Norris et al., 2012 and Root-Bernstein and Dillon, 1997)."

The assumptions of science idiots who think "...the necessary precursor molecules (sugars, bases, nucleosides, nucleotides, amino acids, etc.)" arose via mutations establishes the fact that they are science idiots.

Jan 09, 2015
I agree that only a science idiot would think I cannot see where this is leading.


Skippy please sign me up as the science-idiot-Skippy because I think you have the very serious mental condition or two of them.

The nice peoples at physorg is the only place you can play out at your "I-am-the-scientist-Skippy" game. Cher you have fell into the deep water still don't see that you are wet.

JVK
Jan 09, 2015
Note: We first detailed the molecular epigenetics of RNA-mediated cell type differentiation in our 1996 review: From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html

The fact that science idiots still try to put cell type differentiation in the context of mutations and the evolution of biodiversity attests to how pseudoscience works.

The nonsense convinces science idiots to ignore experimental evidence of biologically-based facts, and focus only on definitions and assumptions that appear to support ridiculous theories. Science idiots are easy to convince, since they know nothing about physics, chemistry, or molecular biology and they don't want to learn.

They don't want others to learn, either. When others learn about physics, chemistry, and molecular biology -- as many people have during the past 50 years, they learn who the science idiots are who have taught them to be science idiots.

Jan 09, 2015
The assumptions of science idiots who think "...the necessary precursor molecules (sugars, bases, nucleosides, nucleotides, amino acids, etc.)" arose via mutations


You have absolutely no idea what you're talking about. Precursor molecules are produced through a variety of chemical reactions. It doesn't make any sense to say they arose via mutations. These reactions are very well studied and I covered them in my thesis on pages 7 and 8 starting beneath Figure 2:

http://www.scribd...s#scribd

Jan 09, 2015

Great – so you agree that amino acid substitutions that are beneficial are fixed in the DNA of organized genomes!

Do you agree that the amino acid substitution is made by modifying the DNA nucleotide sequence such as the CAG to CTG modification in the hemoglobin example above?


So you respond:
I agree that only a science idiot would think I cannot see where this is leading.

(Followed by statements that do not answer the question.)

I think that you CAN see where the question is leading, JVK, and that you are refusing to answer because you would either have to make a false answer (and then be shown to be wrong), or to admit that single-nucleotide changes, which are an archetypical mutation, cause amino acid substitutions (which you have acknowledged can be beneficial and can be selected for).

The fact that you still refuse to admit that mutations can be selected for attests to how pseudo-science works - ignoring evidence and evading questions.

JVK
Jan 09, 2015
It doesn't make any sense to say they arose via mutations.


It doesn't make any sense to claim that amino acid substitutions are mutations.

JVK
Jan 09, 2015
you still refuse to admit that mutations can be selected for


Mutations perturb protein folding. Organisms do not naturally select for perturbed protein structures or perturbed cell functions manifested in the morphological phenotypes or the behavioral phenotypes of another organism, unless they are going to eat the least "fit" from a population of heterospecifics.

Jan 09, 2015
Mutations perturb protein folding
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
so i guess that means that YOUR MODEL causes perturbed protein folding and thus you are pushing pseudoscience

PER YOUR OWN WORDS

I still think Real summed it up the best of us, so i will simply quote it here again
The fact that you still refuse to admit that mutations can be selected for attests to how pseudo-science works - ignoring evidence and evading questions.


jk = PSEUDOSCIENCE TROLL

JVK
Jan 09, 2015
Andrew Jones seems to have ignored what is currently known about bio-physically constrained thermodynamic cycles of protein biosynthesis and degradation in species from microbes to man. That should surprise no one. However, it makes his advisers look like science idiots, too. http://www.scribd...s#scribd

"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 ribozyme system 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. Between the synthesis routes outlined and the discovery of an RNA polymerase ribozyme, the literature satisfies Orgel's four problems."


JVK
Jan 09, 2015
A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution
http://www.ncbi.n...23206328

Excerpt 1)
Whilst the view that nutritional conditions had a role in directing evolution seems contrary to the gene-centric view of evolution, it is consistent with pure Darwinism.


Excerpt 2)
Again classical biophysics has no ready explanation for this [32]. In this theory, the energy released in the signalling would be absolutely and precisely quantised by tunnelling, giving us the clear vision, high acuity necessary for reading, fine motor skills, and three-dimensional vision; together with smooth mental processing of our external environment upon which we depend. A similar process might take place in the synapse where the DHA is also densely packed. There DHA might act as a quantum gate controlling the signal in a fashion reminiscent of semi-conduction.

Jan 09, 2015

It doesn't make any sense to claim that amino acid substitutions are mutations.

No one is claiming that amino acid substitutions ARE mutations.
Amino acid substitutions are the change from one amino acid to another amino acid in a PROTEIN. In contrast a mutation is a nucleotide change in a DNA sequence.

However most (~67%) of the possible single-nucleotide changes in a DNA sequence that codes for a protein will CAUSE a change from one amino acid to another amino acid in a PROTEIN.

And a single-nucleotide changes in a DNA sequence that codes for a protein is an archetypical mutation.

So some mutations CAUSE amino acid substitutions in proteins.

The beta globin single nucleotide DNA sequence change described above (GAG to GTG) is an EXAMPLE of just such a mutation, and it does indeed produce an amino acid substitution (Valine for Glutamate) the resulting protein.

Is that clear enough for you?

JVK
Jan 09, 2015
Molecular Vibration-Sensing Component in Human Olfaction http://dx.doi.org....0055780

Reported as: http://www.bbc.co...21150047

See also: Life as physics and chemistry: A system view of biology http://www.scienc...12000922

The role of information in cell regulation http://www.scienc...1200106X

These articles show how magical thinking arises from theories about evolution. First, exclude everything known to physicists and chemists. Then you invent a theory. Finally, you proclaim that "...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world."

Other science idiots believe you and they graduate after wasting time preparing a thesis that ignores facts known to serious scientists. And that's where science idiots like Andrew Jones come from.

JVK
Jan 09, 2015
No one is claiming that amino acid substitutions ARE mutations.


http://ghr.nlm.ni...titution Definition from: Human Genome Project...

Substitution is a type of mutation where one base pair is replaced by a different base pair. The term also refers to the replacement of one amino acid in a protein with a different amino acid.


Is that clear enough for you?

I'm not going to keep trying to hit the moving targets you put up --as if anything you might have to say would ever make sense. I've already differentiated mutations and amino acid substitutions in the context of health and disease and so have many others. Only science idiots, like you are living in the past. Real scientists understand reports like this:

http://dx.doi.org...4-0895-5
The A or Met allele is associated with lower enzymatic activity (due to thermoinstability), and with exploratory behaviour.

Life is physics, chemistry, and thermoregulation.

JVK
Jan 09, 2015
Re: Andrew Jones thesis.
http://www.scribd...s#scribd

A few years ago I was asked to act as an external examiner for an undergraduate's Honors Thesis. I mention this because I suspect no external examiner was present when Jones attempted to defend his thesis. (no external adviser is credited on the manuscript)

If I had been there, or if any other serious scientist from outside his institution would have been there -- he probably would not have graduated.

Jan 09, 2015
A few years ago I was asked to act as an external examiner for an undergraduate's Honors Thesis.


Of course you were Cher. We all believe that without any doubt.

I mention this because I suspect no external examiner was present when Jones attempted to defend his thesis. (no external adviser is credited on the manuscript)


Well I suspect that if it is already written it would be hard to add anything or credits on it after the examining starts.

If I had been there,


But you were not there. Were you Skippy?

he probably would not have graduated.


Well that just goes to show you, why don't let drop-outs and flunk-outs do the external or internal examining.

Skippy you are getting stupider and stupider, I can see how you could not cut it in the science school.

Jan 09, 2015
What "facts" did I ignore in my thesis? Enlighten us. Be specific.

Jan 09, 2015
Oh, and as a reminder again, I'll bring back something you still haven't addressed: The SOS response. The entire point of that system is to deliberately create more mutations under stressful conditions in order to increase genotype variability and aid survival.

Jan 09, 2015
Be specific.


Good luck with that Andrew-Skippy.

If you can get a straight answer out of that couyon you should get the Nobel Prize for something. (But don't get your hopes up, a lot of really smart-scientist-Skippys have been trying to do that for a long time.)

JVK
Jan 09, 2015
What "facts" did I ignore in my thesis? Enlighten us. Be specific.


I already told you. You ignored nutrient-dependent thermodynamic cycles of protein biosynthesis and degradation. Simply put, you ignored all of physics, which includes bio-physical constraints on the chemistry of protein folding.

The SOS response. The entire point of that system is to deliberately create more mutations under stressful conditions in order to increase genotype variability and aid survival.

The point of the seemingly futile thermodynamic cycles of protein biosynthesis and degradation is to use any available nutrient source to avoid starvation and establish organism-level thermoregulation that facilitates reproduction, which is nutrient-dependent and pheromone-controlled via RNA-mediated events that link amino acid substitutions to cell type differentiation in microbes to man.

Please tell your advisers that when you request your tuition refund.

Jan 09, 2015
Can you even read? I'm being completely serious when I say you should see an optometrist.

My thesis has NOTHING to do with protein biosynthesis. It doesn't involve proteins AT ALL. It's about RNA enzyme replication. It's a review of ribozyme biochemistry and lipid biophysics. I can't be ignoring biochemistry or biophysics when that's precisely what my thesis is about.

Read. Use your eyes. It's not hard.

JVK
Jan 09, 2015
What are enzymes made of?

JVK
Jan 09, 2015
The seemingly futile thermodynamic cycles of protein biosynthesis and degradation in yeasts establish their RNA-mediated cell type differences at the advent of sexual reproduction.

We wrote: "Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus (Runge and Zakian, 1996; Wu and Haber, 1995)."
http://www.hawaii...ion.html

Others have since realized that nutrient-dependent RNA-mediated amino acid substitutions differentiate cell types linked to human sexual orientation. http://www.scienc...2133.htm

They're just not going to tell anyone because it makes too many people appear to be like the science idiots who participate here (and their teachers).

Jan 09, 2015
What are enzymes made of?


I see what you're trying to do here and it's not going to work. You're in over your head.

RNA enzymes, which my thesis is about, are made of RNA, oddly enough. So is the ribosome, DNase-P, and a handful of others. As I said, no protein.

Jan 09, 2015
@Anon -
From thesis:
self-replicating ribozymes ... a couple variations. One is a single ribozyme ... and the other is a cross-catalytic system of two ribozymes

RNA evolution can start even before a 'replicator' RNA – a process that strings together random bases suffices. Some generated RNAs will be selective-aggressor RNAs that preferentially chop up RNA chains not matching themselves; these will increase as other RNAs are 'recycled'. Chopping is easier than copying, and Aggressors readily evolve improved self-recognition.

The simplest 'copier' RNA will with some chance and low fidelity copy ANY RNA that it encounters – no self-recognition needed. Copiers readily evolve improved fidelity.

Regions with Aggressors that don't chop Copiers accumulate both faster than other regions do (and diffusion spreads this around the RNA world), creating ample opportunities for the two to merge to create a true Replicator (life 1.0), but self-cross-catalytic.

JVK
Jan 09, 2015
A paper co-authored by Petrov in 2012 was the most recent reference included in the thesis by the science idiot Andrew Jones. Petrov is first author on the paper linked below.

http://www.pnas.o...abstract

Excerpt 1) "We infer distinct phases of ribosomal evolution through which ribosomal particles evolve, acquiring coding and translocation, and extending and elaborating the exit tunnel."

Excerpt 2) " We construct a molecular model of ribosomal evolution starting from primordial biological systems near the dawn of life, culminating with relatively recent changes specific to metazoans."

The difference between evolutionary inferences in molecular models and integrating Laws of Physics; the chemistry of proteins folding; and the molecular epigenetics of RNA-mediated cell type differentiation via amino acid substitutions that stabilize protein folding in DNA is the difference between serious scientists and evolutionary theorists/science idiots.

Jan 09, 2015
No one is claiming that amino acid substitutions ARE mutations.


Definition from: Human Genome Project...
Substitution is a type of mutation where one base pair is replaced by a different base pair. The term also refers to the replacement of one amino acid in a protein with a different amino acid.

Is that clear enough for you?


I CLEARLY and specifically said that no is claiming that AMINO ACID substitutions are mutations.

The definition you quote for the MORE GENERAL TERM "substitution" covers both NUCLEOTIDE substitutions (where one base pair in DNA is replaced by a different base pair) and AMINO ACID substitutions, (the replacement of one amino acid in a protein with a different amino acid.

Do you REALLY not understand the difference, JVK?

Jan 10, 2015
However, it makes his advisers look like science idiots, too. http://www.scribd...s#scribd
@jk
i would ask you to point out the flaws but i can already see that you don't understand the paper
A few years ago I was asked to act as an external examiner for an undergraduate's Honors Thesis
i highly doubt this, especially considering the obvious stupidity you've demonstrated which is reinforced by you running from the conversation with Real et al above

when they try to teach you something (your Dunning-Kruger kicks in)
magical thinking arises from theories about evolution
and yet, again, you fail to prove your points
You ignored nutrient-dependent thermodynamic cycles of protein biosynthesis and degradation
AGAIN you prove your own stupidity with your own words/links/posts!

You didn't understand his Thesis at all, did you?

you are nothing more than a wanna-be scientist TROLLING with pseudoscience here on PO

Jan 10, 2015
These articles show how magical thinking arises from theories about evolution. First, exclude everything known to physicists and chemists. Then you invent a theory. Finally, you proclaim that "...genomic conservation and constraint-breaking mutation ..."


Your comments show wishful thinking from a theorist who don't understand genetics. First, you invent a model (not even a theory). Then you excludes all evidence that contradicts your model. Then you touts terms physics and chemistry terms that you fail to understand. Finally, you repetitiously proclaims that "The model refutes all aspects of mutation-driven evolution" on thread after thread in phys-org comments, in spite of evidence to the contrary.

But at least you have a great sense of humor, commenting:
The biologically uninformed continue to yell: MUTATIONS!

when it is YOU, JVK, who first yells that term in thread after thread (including the one in which you posted that comment).

LMAO!

JVK
Jan 10, 2015
...physics and chemistry terms that you fail to understand.


The energy of molecular epigenetics that differentiates cell types via amino acid substitutions come from the sun, which is the source of all biological energy.

The idea that physics and chemistry could be included in a ridiculous theory of mutations and evolution has now shown that merely mentioning the fact that physics and the chemistry of protein folding MUST BE included in cell type differentiation strikes terror in the mindless brains and hardened hearts of science idiots like you. However, your ignorance costs others more than it does you.

Science idiots won't even try to address the experimental evidence of biologically-based cause and effect. They cannot be expected to address the experimental evidence from physics or from the chemistry of protein folding in any genera.

Jan 10, 2015
You are in no position to lecture people on physics. You had to ask if a cell is a closed system. Remember that? That's like asking what 2 plus 2 is and then trying to teach somebody calculus.

JVK
Jan 10, 2015
Remember that?


No.

Please place your answer into the context of what you were taught to believe about thermodynamic cycles of protein biosynthesis and degradation that must lead to organism-level thermoregulation for epigenesis to lead to epistasis.

Jan 10, 2015
Here's you not knowing anything about DNA binding entropy:

http://phys.org/n...ife.html

Here's you thinking a cell is a closed system:

http://medicalxpr...sis.html

It seems you haven't learned anything about physics since then.

Jan 10, 2015
JVK
You have been schooled by your betters, take your lumps like a man and stop your incessant whining. These people have written actual published theses not just self-congratulatory articles on their own websites. What's that, I can hear you ranting "No but yeah but no ..." , Vicky Pollard style.

You have plenty of your own websites where you can go play "Mirror mirror on the wall" games to stroke your ego, don't expect to play that game here and enjoy the outcome.

JVK
Feb 15, 2015
Where would serious scientists be without their ability to recognize patterns that link physics, chemistry, and molecular biology in all genera?

http://phys.org/n...fly.html

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