Never mind the selfish gene – ribosomes are the missing link

January 7, 2015 by Robert Root-Bernstein And Meredith Root-Bernstein, The Conversation
Ribosomes: squiggly and yummy. Credit: crobin, CC BY

Since the discovery that DNA encodes genetic information, research on the evolution of life has focused on its genetic origins. Following this "genes-first" approach, Oxford University evolutionary biologist Richard Dawkins has argued in his book The Selfish Gene that cells and organisms evolved simply as packages to ever-more efficiently protect and transmit genes.

But this genes-first point of view ignores much. All cells share three organelles, or internal structures, besides gene-containing chromosomes: ribosomes which contain the machinery for translating into the proteins that perform the cell's work; a cell membrane that selectively permits materials in and out; and acidocalcisomes, which store and regulate the ions that drive the chemical reactions of life.

We challenge the "selfish gene" concept, proposing instead that if a cellular component is "selfish" it must be ribosomes. Cells – and DNA itself – evolved, we argue, to optimise the functioning of ribosomes. That upends everything we think we know about the evolution of cellular life and ribosomes themselves.

What does DNA want?

We came to this idea through a father-daughter collaboration that began when Meredith was re-reading Robert's 1989 book Discovering. Half-way through, Meredith looked up and asked: "What does DNA want?"

Though it may sound strange to anthropomorphise a molecule, in fact this is a discovery strategy suggested in Robert's book. What's more, scientists often express the selfish gene theory in scientific short-hand as: "DNA wants to replicate itself."

Chemists use a different metaphor when they anthropomorphise molecules. They say that molecules "want to be in their lowest energy conformation". This means that, like people, energetic molecules move through many positions, but they always return to a resting position.

The resting position of DNA is very tightly curled up with its genes inaccessible. Resting DNA is so stable that it can protect its genes for 10,000 years or more, allowing scientists to recover DNA from frozen mammoths. This is not a molecule yearning to disperse its genes, but one that wants to conserve them by remaining curled up in a knot.

We reasoned that the cellular structure that wants to copy genes and turn them into the proteins that make up functioning cells is ribosomes. The resting state of a is: "I'm ready to translate DNA into proteins." Ribosomes "want" to convert genes into working molecules.

What do ribosomes want?

The big question, by analogy to the "selfish gene" theory, then became: Might ribosomes "want" to make copies of themselves? If ribosomes wanted to copy themselves, then they would harbour the means to do so.

To understand what would be required for ribosomes to copy themselves, a bit of information about ribosome structure and function is necessary. Ribosomes are composed of proteins and RNA, which is structurally similar to DNA and exists in three distinct forms. One is ribosomal RNA, or rRNA, which forms a structural scaffold upon which proteins arrange themselves to form a functional ribosome "machine". This "machine" uses the other two types of RNA to make proteins. Messenger RNA, or mRNA, transcribes the genetic information from DNA and carries it to the ribosome. Transfer RNA, or tRNA, translates the mRNA message into amino acids, which are strung together on the ribosome to make a protein.

If a ribosome "wants" to makes copies of itself, the rRNA forming the structure at the core of the ribosome machine would have to be functional. For this to be true, the rRNA must contain three things. First, it must contain the "genes" encoding its own ribosomal proteins so as to be able to form a working "machine". Second, it must contain the mRNAs needed to carry its own genetic information to the "machine". Finally, it had to encode the tRNAs necessary to translate the mRNAs into proteins.

In a recent paper in the Journal of Theoretical Biology, we have shown that rRNA does contain vestiges of the mRNAs, tRNAs and "genes" that encode its own structure and function. Ribosomes are not simply the passive translators of as described in textbooks. We believe they are the missing link between simple pre-biotic molecules and the single-celled LUCA, the Last Universal Common Ancestor, considered to be the first living thing on Earth.

DNA evolved to conserve and protect the information originally encoded in rRNA. Cells and organisms have evolved to optimise the replication of ribosomes, and ribosomes are almost the same across all species. Maybe the selfish ribosome puts a new spin on feeling kinship with other creatures. We are all just different kinds of homes to ribosomes.

Explore further: Evolution of life's operating system revealed in detail

More information: Meredith Root-Bernstein, Robert Root-Bernstein, "The ribosome as a missing link in the evolution of life," Journal of Theoretical Biology, Volume 367, 21 February 2015, Pages 130-158, ISSN 0022-5193, dx.doi.org/10.1016/j.jtbi.2014.11.025.

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Torbjorn_Larsson_OM
5 / 5 (5) Jan 07, 2015
No one denies that RNA preceded DNA. But that doesn't attack the selfish gene concept, and in fact what is claimed here would serve to support it.

And no one denies that the preserved RNA core of the ribosome is still catalytic, like tRNA is. It is in fact its present function, but it is also a generic catalyst in early Earth conditions (no oxygen, lots of iron) which mRNA isn't. This is consistent with rRNA phylogenies. ["Evolution if the ribosome at atomic resolution", Petrov et al, PNAS EE 2014]

I'm not an expert on BLAST genome alignments. But I note that:
- matches are used that else wouldn't be accepted, by adjusting the program until it gives such
- matches are out of frame or reverse read
- matches are small string fragments
- matches include genes that arose late (DNA and murein genes).

The paper also claims that mitochondria, a late simplified endosymbiont, has the same type of matches which is inexplicable in their model.
antialias_physorg
4.2 / 5 (5) Jan 07, 2015
No one denies that RNA preceded DNA. But that doesn't attack the selfish gene concept, and in fact what is claimed here would serve to support it.

I think they are not really attacking it - merely relegating DNA to a helper-role in a "selfish RNA" concept. And since RNA was likely first that does make some sense.
nickmaxell
5 / 5 (2) Jan 07, 2015
And what exactly is new about this theory? - all of it was taught to me 25 years ago - autocatalytic RNA is a bit younger but the stuff in the article can be found in 20 year old textbooks
baudrunner
1 / 5 (3) Jan 07, 2015
What's fascinating about this type of research is that it attempts to establish the driving force behind evolution. "What does DNA want?" is the million dollar question. We used to think that the nucleus was the CPU of the cell. It now appears that DNA is merely the hard drive that contains the periodically upgraded source code snippets which ribosomes process through the magic of intracellular communication. If this research is extended then some day they might find the RNA "seed" that got that evolutionary process started.
nickmaxell
4 / 5 (2) Jan 07, 2015
baudrunner - pretty simple just go what came first - RNA which can self replicate - rRNAs are integral parts of ribosomes (which would not work without them) - DNA is just more stable because it is double stranded so every error can be mended other than in the mostly single stranded RNA - also the repair mechanisms are better so you get fewer mutations - don t forget that the only difference between RNA and DNA is one single base - Uracil instead of Thymine - and that difference is so minor that DNA - RNA hybrids occor in nature everytime
RobertKarlStonjek
5 / 5 (1) Jan 07, 2015
Another way of asking the "what do genes want?" question is to consider ultimate success: what would happen if a gene was 100% successful?

The answer is that without diversity, the species will become extinct. Preservation of diversity is essential for the genome of a species and sexual reproduction ensures this. The genes that are passed on, say, by the father are not necessarily those that made the father unique.

This is because meiosis scrambles the Genes to a degree (through 'crossovers', humans having the most) and then is combined with the female contribution to produce the offspring.

Consider, for instance, that peahens also have genes for the male's elaborate tail (females, and not males, have unique genes in birds, the opposite of mammals).
JVK
1 / 5 (8) Jan 07, 2015
Consider... that peahens...

Also, consider... my attempt to discuss "The ribosome as a missing link in the evolution of life" in the context of nutrient-dependent pheromone-controlled feedback loops linked to chromatin loops and protein folding via RNA-mediated events. See: "DNA Loop-the-Loops"
http://www.the-sc...e-Loops/

I wrote:
What about The ribosome as a missing link in the evolution of life
In theory, it links nutrient-dependent RNA-mediated events to cell type differentiation across all genera, and that takes us back to this claim: "We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins..."

--
But that doesn't attack the selfish gene concept...

says Torbjorn_Larsson_OM as if there was anything left of that ridiculous concept in the context of nutrient-dependent RNA-mediated protein folding.
JVK
1 / 5 (8) Jan 07, 2015
Re: Torbjorn_Larsson_OM

How many others are biologically uninformed enough to claim that evolution occurs outside the context of biological energy from the sun? Check out his link to Petrov: http://www.pnas.o...abstract

"We construct a molecular model of ribosomal evolution starting from primordial biological systems near the dawn of life..."


Is Torbjorn_Larsson_OM a creationist? If not, perhaps light doesn't enter the picture at the dawn of life.

How could ribosomes evolve in the absence of biological energy that links light-induced amino acid substitutions in plants and animals to nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation in all cells of all individuals of all species via conserved molecular mechanisms in my model? That's ecological adaptation, not ribosomal evolution.

Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353
barakn
4.5 / 5 (6) Jan 07, 2015
don t forget that the only difference between RNA and DNA is one single base - Uracil instead of Thymine - and that difference is so minor that DNA - RNA hybrids occor in nature everytime -nickmaxell

No. You've forgotten the R vs the D. As in RNA and DNA. The sugar attached to each and every base is ribose in one and deoxyribose in other. RNA and DNA have different backbones.
nickmaxell
not rated yet Jan 07, 2015
wrong as in context with chromosome mixtures - as soon as you get to plants things get difficult^^
Uncle Ira
3.9 / 5 (7) Jan 07, 2015
nutrient-dependent pheromone-controlled


@JVK-Skippy. How you are Cher? I'm good and good, thanks.

Skippy, I know you are really proud of that. I can tell because you put it in every article on the physorg. Most of the articles get it seven or six times. But maybe you would could tidy it up a little bit. Why you don't do like the Zephir-Skippy and make into the NDPC theory like his AWT theory. That's what all the real scientist-Skippys do when they are talking about their theories. What you write sounds like made up gobbledygook after you read him about more than the first couple of times.

Anyhoo, carry on with your tutoring the science idiots. Don't forget to leave your silly looking pointy cap at the door so the next couyon gets to wear one while he's helping the science idiots along.
nickmaxell
not rated yet Jan 07, 2015
bararin - my point was that they are cloesely enough chemically to form functional hybrids and dimeric "pseudohelices" for a lack of a better word - not only during "reading" the DNA to form RNA but also later where some RNAs have a functional control on gene expression
Uncle Ira
3.9 / 5 (7) Jan 07, 2015
P.S. for you JVK-Skippy. I just counted em Skippy. You got the nutrient-dependent pheromone-controlled thing in there five or four times in just the two postums.

Do you get some kind of payment if nutrient-dependent pheromone-controlled shows up a bunch of times in the google-Skippy thing? Just curious me.
nickmaxell
5 / 5 (1) Jan 07, 2015
don t forget that the only difference between RNA and DNA is one single base - Uracil instead of Thymine - and that difference is so minor that DNA - RNA hybrids occor in nature everytime -nickmaxell

No. You've forgotten the R vs the D. As in RNA and DNA. The sugar attached to each and every base is ribose in one and deoxyribose in other. RNA and DNA have different backbones.

barakin - if it is a pentasugar or a hexasugar makes astounishing litte difference - but of course you are right
Whydening Gyre
5 / 5 (3) Jan 08, 2015
P.S. for you JVK-Skippy. I just counted em Skippy. You got the nutrient-dependent pheromone-controlled thing in there five or four times in just the two postums.

Do you get some kind of payment if nutrient-dependent pheromone-controlled shows up a bunch of times in the google-Skippy thing? Just curious me.

Ira - he just gets more hits...
Don't feed the bears (by quoting them)...
Whydening Gyre
5 / 5 (3) Jan 08, 2015
don t forget that the only difference between RNA and DNA is one single base - Uracil instead of Thymine - and that difference is so minor that DNA - RNA hybrids occor in nature everytime -nickmaxell

No. You've forgotten the R vs the D. As in RNA and DNA. The sugar attached to each and every base is ribose in one and deoxyribose in other. RNA and DNA have different backbones.

barakin - if it is a pentasugar or a hexasugar makes astounishing litte difference - but of course you are right

Barakn n Nick - really good informative exchange (and pleasant..:-)
antialias_physorg
5 / 5 (5) Jan 08, 2015
Another way of asking the "what do genes want?" question is to consider ultimate success: what would happen if a gene was 100% successful?

The answer is that without diversity, the species will become extinct.

Not really - because if DNA replication were perfect for every species then no species would evolve to attack another species. The only way to become extinct would be through radical environmental changes for a localized species.
anonymous_9001
5 / 5 (7) Jan 08, 2015
How many others are biologically uninformed enough to claim that evolution occurs outside the context of biological energy from the sun?


Every chemosynthetic organism ever.

light-induced amino acid substitutions


What evidence suggests light CAUSED the substitution in that study? You have yet to demonstrate that, just like you've yet to demonstrate nutrient- and pheromone-induced causation of things like peppered moth color change and E. coli citrate promoter transposition.
Torbjorn_Larsson_OM
5 / 5 (5) Jan 08, 2015
@antialias: "I think they are not really attacking it - merely relegating DNA to a helper-role in a "selfish RNA" concept. And since RNA was likely first that does make some sense."

The second would follow from the first. However it seemed to me, and even more so from the inital comments from the authors over at The Conversation, that they mean a whole self-replicating package of tRNA, riboproteins et cetera.

Dawkins didn't call his book "The Selfish Cell". Presumably because he had reasons. (Such as understanding why the gene (including the first self-replicating RNA) is the target for selection.)

@nickmaxell: RNA can be doublestranded too, and RNA cells likely used that later, as demonstrated by dsRNA viruses. But strand comparisons have RNA as having a half life of 4 years against hydrolysis when DNA has 1 million years or so.

The driver for evolving DNA was likely the first parasitism. Dividing transcription from translation makes the system more robust and defensible.
JVK
1 / 5 (7) Jan 08, 2015
http://www.scienc...1405.htm

Excerpt: "This new hypothesis was tested by Robert, comparing ribosomal RNA to databases of all the RNAs, DNA and proteins of the bacteria E. coli."

Comparing experimental evidence in the context of the ridiculous untested "null hypothesis" that mutated genes lead to biodiversity differentiates pseudoscientific nonsense from facts based on differences between what perturbed proteins do and what nutrient-dependent RNA-mediated amino acid substitutions do.

Mutations perturb protein folding and cause pathology. Nutrient-dependent amino acid substitutions link the epigenetic landscape to the physical landscape of DNA in organized genomes via RNA-mediated events and the pheromone-controlled fixation of substitutions that stabilize DNA.

In my model feedback loops link nutrient uptake to pheromone-controlled reproduction via bio-physically-constrained protein folding, not ridiculous theories.
JVK
1 / 5 (7) Jan 08, 2015
"you've yet to demonstrate nutrient- and pheromone-induced causation of things like peppered moth color change and E. coli citrate promoter transposition."


That nonsense was linked to the untested "null hypothesis." It's been replaced because people like Meredith and Robert Root-Bernstein also found it to be one of the most ridiculous assumptions ever to remain untested. In 2013, others reported that mutations are not fixed in the DNA of organized genomes in nematodes. As you know they eliminated natural selection from the ridiculous theory of mutation-driven evolution. http://www.nature...417.html

Now, mutated genes have been eliminated from the "null hypothesis." That eliminates the entirety of the ridiculous theory.

The link to biodiversity from the nutrient-dependent pheromone-controlled physiology of reproduction needs no more proof than I've provided. It only requires science idiots to accept common sense.
JVK
1 / 5 (8) Jan 08, 2015
... didn't call his book "The Selfish Cell". Presumably because he had reasons.


Everything he has ever done is based on the fact he is a science idiot who seems incapable of understanding the fact that life is bio-physically constrained by the chemistry of protein folding. It links biological energy to nutrient-dependent metabolic networks and genetic networks in the context of what these researchers have reported.

Like other science idiots, Dawkins is not capable of reason.

... he had reasons.


No, he had the same unreasonable ideas about evolution that have been touted by other science idiots since the time de Vries definition of "mutation" was used in their assumptions about how mutations led to the evolution of biodiversity.

Example: "...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
anonymous_9001
5 / 5 (6) Jan 08, 2015
As you know they eliminated natural selection from the ridiculous theory of mutation-driven evolution. http://www.nature...417.html


Remember that time I contacted Chelo and he told me how you were wrong? Do you still not know how to interpret data? They found out that fixation probability is proportional to the percentage of individuals with a given allele in the population. Everything needed to refute you is in the abstract. You don't even have to look at the actual data.

extinction rates decrease with increasing initial numbers of beneficial alleles, as expected... We further show that the extinction rates of deleterious alleles are higher than those of beneficial alleles ... we also find that for these inbred lines ... the fate of invaders might not result in their ultimate fixation or loss but on their maintenance. Our study confirms the key results from classical population genetics...


What null hypothesis? Do you even know what a null hypothesis is?
Captain Stumpy
4.2 / 5 (5) Jan 08, 2015
Mutations perturb protein folding and cause pathology
well that means, by definition, that your model "Nutrient-dependent/pheromone-controlled adaptive evolution: a model" perturbs protein folding causing pathology and should also be considered, in YOUR words, PSEUDOSCIENCE
In my model
there is also the FACT that you've still not been able to answer ANON's questions or prove causation in some of your comments, as proven here:
http://phys.org/n...firstCmt
http://phys.org/n...firstCmt
http://phys.org/n...firstCmt
http://phys.org/n...firstCmt

when are you going to answer those questions and give some legitimate science proving you know what you are talking about so that we can move forward to explanations?
Captain Stumpy
4.2 / 5 (5) Jan 08, 2015
since the time de Vries definition of "mutation" was used
but jk, you've said yourself that
Serious scientists do not include definitions in their models
and since we've already seen that you are WRONG about that...

but you must clarify something for us all, you stated
I refuse to accept definitions and assumptions about mutations!
but you also stated
I use [the word idiot] to accurately describe people who who won't learn about biologically-based cause and effect
Now, considering that Anon and AA_P are both degree'd professionals regarding "biologically based cause and effect" then does that mean that you are the only IDIOT here, per your own words?
because you are ignoring all the cause and effect, as well as the empirical evidence that proves you wrong posted by Real, Anon and AA_P !

Plus, you've never answered their questions in the links i posted above (or here)

WHY is that?
don't you know the answers?
Captain Stumpy
4.3 / 5 (6) Jan 08, 2015
the most confusing part about all this hype you continually publish, jk is the following
It only requires science idiots to accept common sense.
Common sense says that when you post a model
Nutrient-dependent/pheromone-controlled adaptive evolution: a model
then you state that, with no exceptions
Mutations perturb protein folding and cause pathology
then anyone with common sense, reading your model and already knowing that it causes mutations, in your own words ...(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
) then you are saying that your own model causes pathology and perturbed protein folding meaning that, common sense prevailing, your own model cannot by definition be used for biodiversity

YOUR WORDS
not mine
anonymous_9001
5 / 5 (7) Jan 08, 2015
I got this email from a graduate student at Cornell yesterday:

Hello Andrew,

I just stumbled across your letter to the editor, regarding a publication by James Kohl. I was reading an article in The Scientist about a recently published work regarding genome architecture and when I got to the bottom happened to notice a series of VERY unusual comments by Mr. Kohl. Intrigued I Googled him and quickly realized he was either disturbed or a charlatan selling pheromones.

Any way in the process I came across your criticism of his "article". You did a very thorough and professional job debunking whatever it was he was trying to get across in that manuscript.
anonymous_9001
5 / 5 (7) Jan 08, 2015
cont.

Regardless of the stature of the journal, if it's contents are available online, putting something like that out there and passing it off as peer reviewed (as the editor commented in his response) is at the very least irresponsible. There is enough obfuscation and pseudoscientific controversy around evolution already. At least you've done something to counter it's presence. I just wanted to say thank you and congratulate you for taking the time to do it.

Best,

--------

Dept. of Molecular Medicine
College of Veterinary Medicine
C4-163 VMC
Cornell University


Yes, the blog posts are certainly self-promoting and inflammatory, but even more so, just gibberish. He's just stringing together scientific jargon in a way that someone with any scientific background would immediately view as nonsensical but lay people would likely just accept as a sign of expertise.
Uncle Ira
3.9 / 5 (7) Jan 08, 2015
Yes, the blog posts are certainly self-promoting and inflammatory, but even more so, just gibberish. He's just stringing together scientific jargon in a way that someone with any scientific background would immediately view as nonsensical but lay people would likely just accept as a sign of expertise.


Well I'm about as lay and not science background as you can get. When I read stuff on the physorg comments by the scientist-Skippy-posters their jargon makes sense even if I don't understand the deep science in the subjects. When I read stuffs by the JVK-Skippy it sounds like gobbledygook.

He wrote a paper in a contest for students and won a ribbon or something for it. He thought that meant he didn't really need to finish the school stuffs and he was ready to be the real scientist. He even found a club to join that lets people who run the machine that tests blood in the hospital call them self scientists without ever finishing the science schools.
JVK
1 / 5 (7) Jan 08, 2015
There is enough obfuscation and pseudoscientific controversy around evolution already.


Let's discuss what there isn't. There is not another model for comparison to mine. No matter how many science idiots recognize that fact, all they can do is what this anonymous graduate student did.

They cannot tether the epigenetic landscape via RNA-mediated amino acid substitutions to the physical landscape of DNA in organized genomes of species from microbes to man via what is currently known about the bio-physically constrained chemistry of protein folding.

Their inability to do that should be discussed now that Robert and Meredith Root-Berstein have done it.

Anything else is simply a continuation of the pseudoscientific nonsense about mutations and evolution that has been taught to science idiots by generations of other science idiots.

http://www.nature...880.html Quantitative analysis of RNA-protein interactions...
anonymous_9001
4.7 / 5 (10) Jan 08, 2015
JVK
1 / 5 (7) Jan 08, 2015
You and the graduate student at Cornell should team up with any other science idiots from Cornell and compare whatever you think is a model of biologically-based cause and effect to the model I detailed.

Examples of model organisms, such as those I included, would help to support your claims -- if you could show how the model organisms exemplified biologically-based cause and effect by linking mutations to increasing organismal complexity via bio-physically constrained chemistry and the conserved molecular mechanisms of protein folding in species from microbes to man.

Otherwise, all you have is definitions and assumptions to work with, and that's what makes science idiots the science idiots they are. Tell the science idiot at Cornell I said to request a tuition refund. If he's in grad school, tell him to contact Warren D. Allmon, who may help him respond to my claims. See for example: http://dx.doi.org...la.12054
anonymous_9001
5 / 5 (7) Jan 08, 2015
Did you just Google "Cornell" and "ecology", see the mention of ecology on his page, and figured he supports you? I don't see what the relevance of Allmon is otherwise.

You want a comparison between your "model" and those I linked? Here it is: They actually study this stuff at the molecular level. They're doing the primary research. They're the ones directly doing experiments and studies and getting results. All you're doing is throwing together irrelevant citations and making vague claims that those citations don't support and that's been demonstrated over and over in extreme detail. Then you make grave misinterpretations of their research and other works and say that the evidence they've gathered doesn't support their claims, all the while, being unable to provide more details about your own "model" and repeating nonsense catchphrases over and over.
JVK
1 / 5 (7) Jan 08, 2015
Warren D. Allmon "... the roles of selection and isolation in the origin of species are likely diverse and complex." I've addressed that complexity in my model and provided examples of cause and effect.

...make grave misinterpretations of their research


Anyone attempting to support a ridiculous theory of mutations and the evolution of increasing organismal complexity has led many people to their grave.

Anyone doing primary research who has not yet realized that I correctly detailed everything currently known about how the epigenetic landscape becomes the physical landscape of DNA in the organized genome of species from microbes to man need only try to provide an alternative model.

I'm claiming that not only you can't do that, but that no one else can. Not just the science idiot you contacted at Cornell, but no one else at Cornell either individually or collectively. If they could have, they would have. That's why I cited Allmon!
jsdarkdestruction
4.5 / 5 (11) Jan 09, 2015
jvk, if you are so sure your "ideas" are correct and you've got enough free time to spam like crazy here and other sites and think you are smarter than everyone and that's why they cant understand your ideas then why not spend this time writing to experts in the field and convincing them? what are you expecting to gain here? not a one of us takes you seriously, you are just wasting your time. a lot of it, wouldn't the time also be better spent testing and further researching into your ideas and then convincing people in the field you are discussing.
MandoZink
5 / 5 (7) Jan 09, 2015
@jsdarkdestruction

My sincerest apologies. My excited trigger finger prematurely fired off a 1 star when I really wanted to give you a couple of 5's for posting such a reasonable inquiry.
JVK
1 / 5 (7) Jan 09, 2015
why not spend this time writing to experts in the field and convincing them?


Thanks for asking.

This is where the ignorance is. That's why others who publish their works aren't here. They don't care about the ignorance. Serious scientists have incorporated every aspect of the RNA-mediated cell type differentiation we detailed into their works. Only pseudoscientists have not realized the importance of feedback loops and chromatin loops to the bio-physically constrained chemistry of protein folding. They attribute cell type differentiation to mutations.

See: http://www.the-sc...Society/

Why aren't any science idiots commenting on the representation of Gene Robinson's work, which took flight after he extended what we detailed in our 1996 review (section on molecular epigenetics) to insects? For example, attack this: "...identified a histone-regulating protein as a key ingredient in royal jelly..."
JVK
1 / 5 (7) Jan 09, 2015
I was reading an article in The Scientist about a recently published work regarding genome architecture and when I got to the bottom happened to notice a series of VERY unusual comments by Mr. Kohl.


After reading an article that linked nutrient-dependent pheromone-controlled cell type differentiation to every aspect of honeybee brain organization and behavior via the conserved molecular mechanisms we detailed in our 1996 review, this led one science idiot to contact another science idiot (aka anonymous_9001 / Andrew Jones) and offer his congratulations on the criticism of my model. http://www.ncbi.n...24693353

Excerpt: "The honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, diseases of the X chromosome, learning and memory, as well as conditioned responses to sensory stimuli..."
Uncle Ira
4.1 / 5 (9) Jan 09, 2015
Well how you are this morning JVK-Skippy? I am just fine thanks. But to answer your question there,,

Why aren't any science idiots commenting on the representation of Gene Robinson's work


You just did Cher. May be you are alone in the idiot-scientist-Skippy category so don't be expecting too much.

Hooyeei Skippy. Guess what I did just did? I put James V. Kohl into the ask Google about it box. Did you know if you put that in there it has a gazillion articles about James V. Kohl being a science idiot? You should change your name Cher, someone might mistake you for being the James V. Kohl science idiot and not the James V. Kohl who is the guy who runs the blood testing machine in the hospital basement.
JVK
1 / 5 (6) Jan 09, 2015
"The Stagnation of the Genetic and Evolutionary Research Programs" can be directly attributed to the science idiots who have been taught to believe in beneficial mutations and/or evolutionary theory. See: http://dx.doi.org...4-9273-5

They can't understand how bio-physical constraints limit the chemistry of RNA-mediated protein folding, which leads to sex differences in cell types. That means they can't understand anything else about cell type differentiation or that they report what they think they understand in the context of definitions and assumptions about mutations.

Ultimately, we have people like Andrew Jones and the unnamed science idiot from Cornell who continue to regurgitate the pseudoscientific nonsense they were taught to believe in -- and it shows up here in the context of comments by others who are equally incapable of intelligent thought that enables others to discuss the importance of ribosomes to cell type differentiation.
JVK
1 / 5 (5) Jan 09, 2015
I put James V. Kohl into the ask Google about it box. Did you know if you put that in there it has a gazillion articles about James V. Kohl being a science idiot?


Others could do the same thing. See how easy it is....

https://www.googl...+Kohl%22
Example: "James V. Kohl received the Ira and Harriet Reiss Theory Award for 2007 from the Foundation for the Scientific Study of Sexuality (FSSS)."

Search Results for: RNA-mediated http://perfumingt...mit.y=14

See also: https://www.faceb...Research
jsdarkdestruction
5 / 5 (11) Jan 09, 2015
They don't care about the ignorance.

That is completely untrue. scientists are always taking steps to reduce their and our collective ignorance of the subject being studied. that is what science and research is all about.
That's why others who publish their works aren't here.

Or more likely they have better things to do than visit a science reporting site and having to deal with people like you. like you know, research and stuff. what you should be doing if you wish to be taken seriously.
Uncle Ira
4.1 / 5 (9) Jan 09, 2015
I put James V. Kohl into the ask Google about it box. Did you know if you put that in there it has a gazillion articles about James V. Kohl being a science idiot?


Others could do the same thing. See how easy it is....

https://www.googl...+Kohl%22


Skippy, I would not be so very proud of those two linkums if I was you. They are not very much flattering to your stature as a scientist-Skippy and they makes you look like a weirdo-Skippy. (And those funny looking pictures with the goofy grins don't help none.)

Oh yeah, I almost forget, the silly looking pointy cap does look good though but please try to work on the grinning that makes you look like someone it tickling your toes while you are getting your picture took.
cjn
4.7 / 5 (3) Jan 09, 2015
I get where the authors are coming from in their stance, as the ribosomes are constructed of the most fundamental cellular units (RNA) and translate transcription products to functional proteins.

My counter-argument would be that since the ribosomes do not contain or replicate the RNA necessary to create DNA Polymerase and Sigma factors, that they cannot be the initiators of the process. As these actors are necessary for transcription (and transcription necessary for translation), I'm still on the DNA-centric model. That said, I wouldn't be surprised if there is evidence to support Ribosomal action which initiates or facilitates transcription of Polymerase and sigma factor sites.
JVK
1 / 5 (6) Jan 09, 2015
scientists are always taking steps to reduce their and our collective ignorance of the subject being studied. that is what science and research is all about.


Indeed. Just look at where the latest findings about the importance of the ribosome have led.

The display of collective ignorance and avoidance of any discussion about the facts they published proves that science idiots have effectively convinced most people that their pseudoscientific nonsense is based in biological facts.

... if a cellular component is "selfish" it must be ribosomes. Cells – and DNA itself – evolved, we argue, to optimise the functioning of ribosomes. That upends everything we think we know about the evolution of cellular life and ribosomes themselves.


The anonymous fool writes:
How about we discuss your inability to read?

http://www.ncbi.n...6211/...


Discuss the facts on the ribosome and RNA-mediated cell type differentiation?
JVK
1 / 5 (6) Jan 09, 2015
...since the ribosomes do not contain or replicate the RNA necessary to create DNA Polymerase and Sigma factors, that they cannot be the initiators of the process.


Why not simply state what every serious scientist already knows? Nutrient-dependent pheromone-controlled feedback loops link RNA-mediated events to chromatin-modifying
activities via the conserved molecular mechanisms of bio-physically constrained cell type specificity in all cells of all individuals of all species. There's a model for that!

Nutrient-dependent/pheromone-controlled adaptive evolution: a model
http://www.ncbi.n...3960065/

The model includes what is currently known about physics, chemistry, and molecular biology.

So does their representation of the role of ribosomes. What's missing is a model of Mutation-Driven Evolution http://www.amazon...99661731

"...constraint-breaking mutation is the ultimate source of all biological innovations..."
JVK
1 / 5 (5) Jan 09, 2015
http://www.scienc...14006778
Excerpt 1)
RNA-world models cannot explain the evolution of metabolism and generally fail to take into account the fact that amino acids (and therefore peptides and proteins) almost certainly were synthesized along with polynucleotides under prebiotic conditions, making it almost certain that these classes of molecules co-evolved (Caetano-Anolles and Seufferheld, 2013 and Galadino et al., 2012).


Science idiots assume that the amino acids are mutations based on NIH definitions. All pseudoscientific nonsense progresses from there.

Excerpt 2)
LUCA models provide insight (with much disagreement) into the minimum complexity required for cellularity but reveal little about the preceding evolutionary steps.


http://phys.org/n...firstCmt
My Dec 17th comment: "Those who think self-replication arose in the context of mutations should will not like..."
JVK
1 / 5 (6) Jan 09, 2015
The comments by science idiots here merely extended the idiocy expressed from December 17th until now in the context of what should have been discussion of John Hewitt's book review and the fact that Koonin also co-authored a paper in 2005 that stated:

"We cannot conceive of a global external factor that could cause... parallel evolution of amino acid compositions of proteins in 15 diverse taxa that... span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms."

There is one way to link the biological energy of life to the origins of amino acid substitutions and nutrient-dependent cell type differentiation in all cells of all individuals of all genera. That way links physics, chemistry, and molecular biology. Whose way is that? Obviously, it is not the way that science idiots suggest.
Captain Stumpy
4.5 / 5 (8) Jan 09, 2015
There is not another model for comparison to mine
where do you get this idea? your own model causes mutations and therefore your model is nothing more than a subset for the Theory of Evolution as it complies with the Theory as well as supports aspects
what part of that don't you understand?
how many science idiots
please note that the so-called "idiots" you are referring to are all FAR MORE EDUCATED than you are, and understand the processes far better than you do, and that is evidenced by the posts and the supporting links as well as your inability to comprehend what they are asking as proven by your inability to answer their questions directly.

here is one question that i think needs answering as well... IF you are working in a hospital and IF you are the important researcher that you tell everyone you are...

WHY do you have so much time to TROLL with PSEUDOSCIENCE and WHY can't you answer Anon, Real, et al above and in other threads?

Checkmate AGAIN
Captain Stumpy
4.5 / 5 (8) Jan 09, 2015
They attribute cell type differentiation to mutations
but jk, so do YOU!
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 that means you fully admit to suporting mutations as well by continuing to advocate your model!
That's why others who publish their works aren't here
the reason they are not here is:
-they are doing research and pushing our knowledge boundries
-they have better things to do than argue with a TROLL PSEUDOSCIENCE joke (jk) who doesn't comprehend why he is so stupid
-because there is NO REASON with Real, Anon, AA_P, JSDark and other degree'd pro's here posting legit science for the beginners to learn CORRECTLY

that is why you are ultimately bound to fail
because you have ZERO evidence to support your lies, jk
Whydening Gyre
5 / 5 (7) Jan 09, 2015
Hmm. protein folding...
While a majority of incorrect folds may indeed cause cell failure, one or two small variances can sneak through and be selected for. This creates diversity (no two are exactly alike anyway).
All changes can be called mutation. Some survive, most don't.
Captain Stumpy
4.3 / 5 (6) Jan 09, 2015
If he's in grad school, tell him to contact Warren D. Allmon, who may help him respond to my claims. See for example: http://dx.doi.org...la.12054
well, although i am not the grad student who contacted Jones with the e-mail regarding the published refute of your model, i decided to accept your advice and sent a "Request for clarification" to Warren D. Allmon at Cornell, including your exact quoted above and also linking your study, and Andrew Jones refute as well

I also took the time to include the entire text quoted above from the Grad student who contacted Jones

I am hoping to get clarification directly from the author regarding your claims, jk
just like all the other authors you continually mention support your work (except the dead ones... but i CAN get the other authors to clarify, so there is hope yet)

Uncle Ira
4 / 5 (8) Jan 09, 2015
WHY do you have so much time to TROLL with PSEUDOSCIENCE and WHY can't you answer Anon, Real, et al above and in other threads?


Because all he has do to at his job is to put the little blood tube on a rack that they ride through the testing machine and take them off after the machine tests the blood. The machine does all the real work and even tells the computer to tell the doctor-Skippy's computer what the machine found out.

A monkey could be trained to do that, but the hospitals thought it would be the bad idea if it got out that they were using monkeys to do something in the hospital. Also they can jack up the prices on if they say "clinical laboratory scientist" is doing him.

That's the only reason that club he joined will let them use the word "scientist" on them selfs even though they didn't finish the science school, so they can bamboozle the peoples on the bills. JVK-Skippy doesn't realize that out here we check on what they are really saying.
JVK
1 / 5 (5) Jan 09, 2015
see Andrew Jones (aka anonymous_9001) thesis at http://www.scribd...s#scribd

Instead of adding it to discussion of ribosomes here, he wants to discuss it elsewhere.

http://phys.org/n...firstCmt
http://phys.org/n...firstCmt

Obviously, I'm not going to follow his scattered comments all over the place. In any case, the result will be the same.

He has exposed his ignorance of physics, chemistry, and molecular epigenetics in his thesis, which is based on mutagenesis experiments, not on the integration of any facts about the bio-physically constrained chemistry of protein folding and conserved molecular mechanisms that link ribosomes via protein biosynthesis and degradation to cell type differentiation in species from microbes to man.

He's going to ignore the work detailed here. I will try to ignore him.
Uncle Ira
4.1 / 5 (9) Jan 09, 2015
I will try to ignore him.


This ought to be good. When you going to start that show Cher?
anonymous_9001
5 / 5 (7) Jan 09, 2015
He has exposed his ignorance of physics, chemistry, and molecular epigenetics in his thesis


Considering biochemistry and biophysics are the basis of my thesis, no.

which is based on mutagenesis experiments


What's the issue with mutagenesis experiments? Be specific.

Obviously, I'm not going to follow his scattered comments all over the place.


3 links you have to read! What a tragedy! How do you think we feel about you posting on every article you come across?

not on the integration of any facts about the bio-physically constrained chemistry of protein folding


It doesn't involve proteins, so of course it doesn't involve protein folding. RNA folding, however, it does.

He's going to ignore the work detailed here.


The work you detail rarely has anything to do with the claims you make.
JVK
1 / 5 (5) Jan 10, 2015
What's the issue with mutagenesis experiments? Be specific.


They fail to link atoms to ecosystems by starting with a definition of "mutation." They assume that everything downstream from the definition is relevant to what is currently known about thermodynamic cycles of protein biosynthesis and degradation. Controlled thermodynamic cycles are required for organism-level thermoregulation.

Organism-level thermoregulation exemplifies what is currently known about the bio-physically constrained chemistry of protein folding and molecular epigenetics. What is known links the epigenetic landscape to the physical landscape of DNA in organized genomes via nutrient-dependent RNA-mediated DNA methylation and RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all species via their pheromone-controlled physiology of reproduction.

See for examples: http://www.ncbi.n...24693353
JVK
1 / 5 (5) Jan 10, 2015
The work you detail rarely has anything to do with the claims you make.


The work you did for your thesis supports the ridiculous claims you make. You could have included a reference to it, or to other works on mutagenesis for comparison to my model.

See: Criticisms of the nutrient-dependent pheromone-controlled evolutionary model. http://www.ncbi.n...24959329 Your conclusion
James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others' research. It was a mistake to let such a sloppy review through to be published.


My conclusion http://www.ncbi.n...24693353
Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific 'fit'.


Why didn't you try to compare your ideas from mutagenesis experiments to my facts about RNA-mediated cell type differentiation?
anonymous_9001
5 / 5 (7) Jan 10, 2015
Since you still don't seem to understand, I should probably start by summarizing the experiment for you:

1. QB replicase is translated from viral RNA
2. The replicase produces plus and minus strands from that RNA and introduces mutations along the way
3. New QB replicases are translated from those genes after being serially transferred

After doing this many times, they found they had produced a much faster version. The mutations were introduced during replication and the selective process was merely the result of the faster versions replicating more quickly and becoming more represented in the population.

This is mutation and selection at its most basic level. None of your above nonsense is relevant.

In vitro evolution of beta-lactamase resistance mimicking nature:

http://www.geneti...full.pdf
JVK
1 / 5 (5) Jan 10, 2015
I asked:
Why didn't you try to compare your ideas from mutagenesis experiments to my facts about RNA-mediated cell type differentiation?


The anonymous fool (aka Andrew Jones) links to a 2002 journal article

See for comparison: Penicillin tactics revealed by scientists http://www.scienc...4011.htm

"An enzyme called Soluble Lytic Transglycosylase (Slt) has been a suspect in recruiting beta lactamases to the struggle. Now it has been directly shown to cause the futile cycle of building and degrading new cell-wall material, creating the alarm signal the bacterium uses to start the production of beta-lactamases."

The science idiot thinks I don't understand that he is claiming the enzyme arises as a mutation in the context of nutrient-dependent thermodynamic cycles of protein biosynthesis and degradation.

The science idiot claims
None of your above nonsense is relevant.
because he knows his nonsense is irrelevant.
Uncle Ira
4.1 / 5 (9) Jan 10, 2015
They fail to link atoms to ecosystems by starting with a definition of "mutation."


Well help us science idiots out Skippy.

1) What is JVK-Skippy's approved definition of "atom"?

2) What is the JVK-Skippy's approved definition of "ecosystems"?

3) What is the JVK-Skippy's approved definition of "mutation"?

Now while you are helping us science idiots be sure to give us the proper definitions, do not just tell us we are science idiots because we do not already know. This is your BIG chance un-idiot-ate us here on the physorg.

I give you three easy ones to get the show on the road. If you can not write something smart for those three I'm going to give you a really bright sparkly florescent pink extra tall silly looking pointy cap for being the Couyon Of The Year and you can call him the Nobel Prize if you want, but you got to wear him.
Uncle Ira
4 / 5 (8) Jan 10, 2015
P.S. For you JVK-Skippy.

How is this experiment going with you Cher?

I will try to ignore him


Maybe you can help with JVK-Skippy's definition for "ignore"?
JVK
1 / 5 (5) Jan 10, 2015
If the science idiot did not know his nonsense is irrelevant, he would have compared what he learned from mutagenesis experiments to my portrayal of what is currently known about the physics, chemistry, and conserved molecular mechanisms of RNA-mediated cell type differentiation.

For example, beta-lactamase testing typically identifies differences between the cell types of pathogenic and less pathogenic bacteria of the same species. The test is simple to perform and it determines what other tests are required in the context of antibiotic resistance that could kill an infected patient. Antibiotic resistance kills, in part, because organisms have adapted to higher temperatures than infected patients can maintain.

Evolutionary theory kills via portrayals of ecological variation and ecological adaptations as if mutations linked physics, chemistry, and molecular biology to patient outcomes.

Science idiots kill people by touting their ridiculous theories.
JVK
1 / 5 (5) Jan 10, 2015
Maybe you can help with JVK-Skippy's definition for "ignore"?


It's very difficult for me to ignore science idiots, like you and like Andrew Jones, who are killing people.

Call me a fool for trying to stop your foolishness, but after 40 years as a medical laboratory scientist, I got fed up with the loss of life and health that can be directly linked from evolutionary theory to patient outcomes.

Do not call me a science idiot, because that is a term used to describe the biologically uninformed.

Have you ever known anyone who died from "natural" causes? How many others do you know who died from evolutionary theory? What do you, as a science idiot, understand about the cause of death? If you were responsible for telling a patient's family about the cause of death, would you claim it was people like "Uncle Ira"?

I do. As we both know, that's why you hide behind your anonymity. Otherwise, there would be consequences, like there will be for Andrew Jones.
Uncle Ira
4 / 5 (8) Jan 10, 2015
Science idiots kill people by touting their ridiculous theories.


Does this mean you can not do the three easy definitions? Four if you include "ignore".

Oh yeah, I might be the science idiot but I have never killed any peoples. You are starting to sound like the Really-Skippy now.
JVK
1 / 5 (5) Jan 10, 2015
I have never killed any peoples.


Of course you have. Science idiots are silent killers. They are just too ignorant to realize it.
Uncle Ira
4 / 5 (8) Jan 10, 2015
but after 40 years as a medical laboratory scientist,


Skippy putting the blood tubes into one end of the machine and taking them out of the other end of the machine is not science. A monkey could to that.

The machine does all the good stuff. Choot, the machine even tells the computer what he found and tells the computer to go tell the Doctor-Skippy's computer what to tell the Doctor-Skippy.

The only reason they don't use monkeys to load and unload the machine is because it would be bad for business and they could not charge as much. The hospital basement blood testing place is the only place that hires drop-outs and flunk-outs from the science schools and lets them go around calling them selfs scientists.
JVK
1 / 5 (5) Jan 10, 2015
See for comparison to Andrew Jones ridiculous thesis: "Life as physics and chemistry: A system view of biology" -- linked for free: http://www.kbaver...ge9.html

In the context of ribosomes as the missing link...
"Cellular life can be viewed as one of many physical natural systems that extract free energy from their environments in the most efficient way, according to fundamental physical laws, and grow until limited by inherent physical constraints. Thus, it can be inferred that it is the efficiency of this process that natural selection acts upon. The consequent emphasis on metabolism, rather than replication, points to a metabolism-first origin of life with the adoption of DNA template replication as a second stage development. This order of events implies a cellular regulatory system that pre-dates the involvement of DNA and might, therefore, be based on the information acquired as peptides fold into proteins, rather than on genetic regulatory networks...
JVK
1 / 5 (5) Jan 10, 2015
The hospital basement blood testing place is the only place that hires drop-outs and flunk-outs from the science schools and lets them go around calling them selfs scientists.


You are one of the most obviously ignorant and offensive anonymous participants in discussion that I have ever encountered. You also present a threat to the life of anyone who encounters your nonsense. Thanks for exemplifying the kind of ignorance that kills others. Is that your purpose in life, or just here?

Rarely have I encountered a science idiot that would denigrate an entire profession. How did you become so incredibly ignorant before deciding to bring your ignorance to the attention of others in the context of what should be a discussion of ribosomes?

http://ascp.org/L...ssionals
Uncle Ira
3.7 / 5 (6) Jan 10, 2015
You are one of the most obviously ignorant and offensive anonymous participants in discussion that I have ever encountered.


Sheltered life, eh Cher?

You also present a threat to the life of anyone who encounters your nonsense.


I am not the one pushing stinky love potions pretending to be the scientist-Skippy.

Rarely have I encountered a science idiot that would denigrate an entire profession.


Well Cher, you come to the right place, we are not so rare around here it seems.

How did you become so incredibly ignorant before deciding to bring your ignorance to the attention of others in the context of what should be a discussion of ribosomes?


If you can make everything about stinky love potions then I can have fun with how incredibility ignorant you are.

http://ascp.org/Laboratory-Professionals


Yep that's where I found out about peoples calling them scientists just to jack up the prices on the tests that the machine does.
Captain Stumpy
4.4 / 5 (7) Jan 10, 2015
Obviously, I'm not going to follow his scattered comments all over the place. In any case, the result will be the same
this is true
he will demonstrate that you are a complete idiot and ignorant of basic biology
you will ignore it and argue about pheromones, mutations that your own model makes and stinky love potions
links to a 2002 journal article
are you stating said article to be fallacious? please point out the specific science that is fallacious so we can direct this to the author
Science idiots are silent killers
you're right... you are killing a lot of people with your continual spread of stupidity and pseudoscience

in this we can actually agree, jk
you are a science idiot and you will kill people with your ignorance and pseudoscience religious double talk kohlslaw word salads that obfuscate and distort the science

-rather than clarify with clear concise communication like A.Jones, Real and others do
anonymous_9001
5 / 5 (7) Jan 10, 2015
because he knows his nonsense is irrelevant.


It's perfectly relevant. It's experimental demonstration of Darwinian mutation and selection. You, on the other hand, can't refute them and continue to copy and paste your little catchphrases.

BE SPECIFIC and tell us what invalidates the studies I've posted.
JVK
1 / 5 (5) Jan 10, 2015
RNA Sociology: Group Behavioral Motifs of RNA Consortia http://www.mdpi.c.../4/4/800

Why Biocommunication of Animals? http://dx.doi.org...7414-8_1

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

Inching toward the 3D genome http://comments.s....6217.10

Mitochondrial Genome Acquisition Restores Respiratory Function and Tumorigenic Potential of Cancer Cells without Mitochondrial DNA http://www.cell.c...)00554-3

"Among different bacterial species existing in similar environments, DNA uptake... appears to have epigenetically 'fed' interspecies methylation and speciation via conjugation.... This indicates that reproduction began with an active nutrient uptake mechanism in heterospecifics and that the mechanism evolved to become symbiogenesis in the conspecifics of asexual organisms..." -- http://www.ncbi.n...24693349
JVK
1 / 5 (5) Jan 10, 2015
BE SPECIFIC and tell us what invalidates the studies I've posted.


I should have simply said: EVERYTHING PUBLISHED BY SERIOUS SCIENTISTS DURING THAT PAST 80+ YEARS SINCE THE RIDICULOUS THEORIES OF THE MODERN SYNTHESIS WERE INVENTED based on de Vries definition of mutation.

"[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent.... Evolution was defined as "changes in gene frequencies in natural populations." The accumulation of genetic mutations was touted to be enough to change one species to another.... Assumptions, made but not verified, were taught as fact."
http://www.huffin...211.html
anonymous_9001
5 / 5 (7) Jan 10, 2015
Mutations introduced to the replicase genes caused increases in replication speed. Once again, be specific in how that's a false conclusion. What else could have happened in those experiments?
JVK
1 / 5 (5) Jan 10, 2015
My model is very specific.

You be specific.

How do mutations lead to the evolution of diversity via what's known about ribosomes and protein folding?

Ask your advisers for extra credit or the science idiot from Cornell, or anyone in the biology department there or anywhere else.

The Surprising Origins of Evolutionary Complexity http://www.scient...plexity/

"Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed "the blind watchmaker." To some extent, it just happens."
anonymous_9001
5 / 5 (7) Jan 10, 2015
As always, you're exceedingly good at avoiding clarification. You said they ignored the biophysics of protein biosynthesis and degradation. That's an extremely vague statement. What do you mean by that?

My model is very specific.


The only molecular mechanism mentioned is splicing, so no, it is not.
nickmaxell
not rated yet Jan 10, 2015
Another way of asking the "what do genes want?" question is to consider ultimate success: what would happen if a gene was 100% successful?

The answer is that without diversity, the species will become extinct.

Not really - because if DNA replication were perfect for every species then no species would evolve to attack another species. The only way to become extinct would be through radical environmental changes for a localized species.

Well RNA alone is too much suspect to mutations (thats why some viruses change every year) - DNA is more stable and can fix mistakes by "proofreading" - in higher organisms these systems can repair upwards 95% of damage - in humans with a lack of these repairsystems the cancer probability shoots upward (usually a "two hit system" - first the proofreading is disabled than the mistakes accummulate - which can lead to cancer depending where the mistakes happen
nickmaxell
not rated yet Jan 10, 2015
How many others are biologically uninformed enough to claim that evolution occurs outside the context of biological energy from the sun?


Every chemosynthetic organism ever.

light-induced amino acid substitutions


best answer against this - kudos from me
JVK
1 / 5 (5) Jan 10, 2015
mutations (thats why some viruses change every year)


Which viruses mutate? I'd like to compare them to those that adapt via amino acid substitutions.

"Biological and Structural Characterization of a Host-Adapting Amino Acid in Influenza Virus"
http://dx.doi.org....1001034

Help me to stop the Ebola viruses before they kill us all. Tell me how they are mutating given what is known about bio-physically constrained protein folding.
JVK
1 / 5 (5) Jan 10, 2015
you're exceedingly good at avoiding clarification.


I've published a series of works, including two that won awards. All of my works attest to the fact that RNA-mediated events link the epigenetic landscape to the physical landscape of DNA in the organized genomes of microbes to man via conserved molecular mechanisms.

Claiming that I've avoided clarification, is a deliberate ploy to get the lawyers off your back, isn't it? Why are you only now trying to protect yourself and Carthage College? Did you finally realize there are others like me who will be happy to provide their services as expert witnesses?

Clearly, as the death toll mounts, the school bell tolls for thee (and for the school, of course).
JVK
1 / 5 (5) Jan 10, 2015
The only molecular mechanism mentioned is splicing


How many conserved molecular mechanisms do you think are needed to link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man?

Alternative RNA Splicing in Evolution http://jonlieffmd...volution

"...alternative splicing may be the critical source of evolutionary changes differentiating primates and humans from other creatures such as worms and flies with a similar number of genes."

From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html (our 1996 review)

"Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans. That similar proteins perform functions in humans..."
anonymous_9001
5 / 5 (6) Jan 10, 2015
How many conserved molecular mechanisms do you think are needed to link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man?


Considering that splicing does not make changes to DNA and we observe intergenerational DNA changes, more than just that.
JVK
1 / 5 (5) Jan 10, 2015
RNA-protein interactions influence gene expression1, viral assembly2 and a wide variety of other critical biological processes.


http://www.nature...880.html

The idea that viruses mutate to become more virulent or to jump from one species to another has not been supported by any experimental evidence I know about. Hopefully, one of the theorists most concerned about the danger that viruses pose to human existence will explain why they think the existence of different viruses is mutation-driven.

So far as I know, there's no model for that, either.
nickmaxell
not rated yet Jan 10, 2015


@nickmaxell: RNA can be doublestranded too, and RNA cells likely used that later, as demonstrated by dsRNA viruses. But strand comparisons have RNA as having a half life of 4 years against hydrolysis when DNA has 1 million years or so.

The driver for evolving DNA was likely the first parasitism. Dividing transcription from translation makes the system more robust and defensible.

I never contested the existance of doublestranded RNA - that is prooven but it is much less stable even than DNA RNA hybrids in nature - I dont get your comparison with hydrolysis - both of them are gone very soon when in contact with enzymes or sunlight - keeping both of them in a dark fridge at 4 C - after two weeks most of it will be degraded - translation has nothing to do with the DNA/RNA concept as it is the reading of the information on a mRNA by a ribosome into a protein
JVK
1 / 5 (5) Jan 10, 2015
The driver for evolving DNA was likely the first parasitism.


Thanks, I'm familiar with the extant literature on viruses and self vs other recognition.

I dont get your comparison with hydrolysis - both of them are gone very soon when in contact with enzymes or sunlight


I am not familiar with theories involving biophotonics / hydrolysis. (Mae Won Ho?) I'm learning about quantum biology as suggested by Schrodinger (physics) and by Luca Turin (olfaction).

translation has nothing to do with the DNA/RNA concept as it is the reading of the information on a mRNA by a ribosome into a protein


We could also discuss RNA editing in the context of RNA-mediated events.

It would be great if you could comment on the likelihood that mutations lead to evolution via any means known to serious scientists who understand physics, chemistry, and molecular mechanisms.

That could move discussion forward by eliminating the science idiots.
anonymous_9001
5 / 5 (5) Jan 10, 2015
The idea that viruses mutate to become more virulent or to jump from one species to another has not been supported by any experimental evidence I know about


A key part of viral polymerases and replicases is their high mutation rate.
JVK
1 / 5 (5) Jan 10, 2015
Considering that splicing does not make changes to DNA and we observe intergenerational DNA changes, more than just that.


What are you claiming is the alternative that links everything attributed to transgenerational epigeneitic inheritance?

Why don't you simply admit you struck out with your idea that mutagenesis experiments could be meaningfully interpreted and that you understand your advisers let you become a science idiot? Everyone else can see that, and will continue to see it until either the Carthage College lawyers shut you up, or the College is shut down due to lack of enrollment.

In any case, not one thing you have ever written makes sense to those who understand physics, chemistry, and the conserved molecular epigenetics of RNA-mediated cell type differentiation. You should start a discussion group for science idiots or find where Captain Stumpy and others contribute the most ridiculous of their thoughts.
JVK
1 / 5 (5) Jan 10, 2015
A key part of viral polymerases and replicases is their high mutation rate.


How is that relevant? There's not even a citation that might be used to make sense of what you are trying to say. I'm betting that's because the citation would be to literature on mutagenesis, but only because I know what you're capable of -- now that I've seen your thesis.
anonymous_9001
5 / 5 (7) Jan 10, 2015
You're deflecting. You won't even admit that you were under the impression splicing makes changes to DNA. You don't know the most basic details about the only molecular mechanism you mention.

What are you claiming is the alternative that links everything attributed to transgenerational epigeneitic inheritance?


Changes in DNA sequence are the complete OPPOSITE of epigenetic. You still don't know the difference between genetics and epigenetics. Are you willfully ignorant of this difference? Genetics governs the base sequence (TCGATTCA...) of a gene. Epigenetics governs how often that gene is transcribed into mRNA. Splicing alters the mRNA, not the DNA.

How is that relevant?


Their high mutation rate causes substitutions to occur quickly. HIV and the common cold replicative machineries have very high mutation rates and thus, antibody targets change rapidly and outpace our efforts to produce vaccines.
anonymous_9001
5 / 5 (7) Jan 10, 2015
There's not even a citation that might be used to make sense of what you are trying to say.


Viruses don't have exonuclease proofreading. This causes them to accrue mutations orders of magnitude more often than other organisms. This is the reason they have such high sequence variability.

http://jvi.asm.or...733.full
http://www.nature...BX1.html
http://www.virolo...nthesis/
http://www.plospa....1002881
http://www.pnas.o...910.full
JVK
1 / 5 (5) Jan 10, 2015
You still don't know the difference between genetics and epigenetics.


You still don't know when to simply admit you are a science idiots. See my two monographs and our 1996 review article from Hormones and Behavior (with a section on molecular epigentics).

"An epigenetic continuum from microbes to humans: from theory to facts" -- Kohl (2012) http://www.ncbi.n...3960071/

Epigenetics: "An essential mechanism for pruning down the wide range of possible behaviors permitted by genes, selecting those that fit an individual's environment (Berreby, 2011)." -- Kohl (2013) http://www.ncbi.n...24693353

Molecular epigenetics -- Diamond, Binstock & Kohl (1996) http://www.hawaii...ion.html

Others. The science idiot wrote: http://www.ncbi.n...24959329 "Despite his valid publications involving endocrinology, sexuality, and epigenetically induced..."
JVK
1 / 5 (5) Jan 10, 2015
Their high mutation rate causes substitutions to occur quickly.


Science idiots do not know the difference between mutations and amino acid substitutions. Anything further that Andrew Jones (aka anonymous_9001) claims about viruses is based on ridiculous theories that do not include anything currently known about physics, the chemistry of protein folding, or molecular mechanisms of RNA-mediated cell type differentiation.
JVK
1 / 5 (5) Jan 10, 2015
You don't know the most basic details about the only molecular mechanism you mention.


http://www.hawaii...ion.html

I think we were the first to detail the molecular mechanisms of RNA-mediated cell type differentiation in our section on molecular epigenetics:

"Molecular epigenetics.
It is now understood that certain genes undergo a process called "genomic or parental imprinting." Early in embryonic development attached methyl groups become removed from most genes. Several days later, methyl groups are reattached in appropriate sites. Fascinatingly, some such genes reestablish methylation patterns based upon whether the chromosomal segment carrying the gene came from maternal or paternal chromosomes. These sexually dimorphic patterns are labeled genomic or parental imprinting, and these imprintings are inheritable but non-genetic modifications of specific genes..."
JVK
1 / 5 (4) Jan 10, 2015
Viruses don't have exonuclease proofreading. This causes them to accrue mutations orders of magnitude more often than other organisms


This is the kind of nonsense that led to the Ebola crises.

Science idiots don't understand thermodynamic cycles of protein biosynthesis and organism level thermoregulation, which means they think viruses mutate and cross species from vertebrates that fly (including frugivorous bats) -- all of which have higher body temperatures -- to humans.

They don't know that amino acid substitutions stabilize protein folding in the viruses, which enables them to adapt to different ecologies in different hosts. Indeed, evolutionary theorists are probably some of the most ignorant people on the planet when it comes to biologically-based cause and effect. What they can't understand, they attribute to mutations and evolution.
anonymous_9001
5 / 5 (6) Jan 10, 2015
Science idiots do not know the difference between mutations and amino acid substitutions.


Viral enzymes don't have the ability to make deliberate changes to their genome. No polymerases do. If you have research demonstrating otherwise, present it. How do viruses direct changes to their genes and how do they know what effects they will have?

Anything further that Andrew Jones (aka anonymous_9001) claims about viruses is based on ridiculous theories that do not include anything currently known about physics, the chemistry of protein folding, or molecular mechanisms of RNA-mediated cell type differentiation.


A biophysical study of adaptive mutations:

http://www.scienc...14001800

http://faculty.ch...-effects
Captain Stumpy
4.2 / 5 (5) Jan 11, 2015
@Anonymous et al
Thank you for spreading real, ACTUAL science and facts so that the idiot pseudoscience trolls like jk are spotted for the stupidity they spread

you've done a great job refuting the stupidity he posted above, even if he IS threatening to sue Dr. Extavour and your school in another thread! LOL
http://phys.org/n...firstCmt

You still don't know when to simply admit you are a science idiots
@jk
now THAT is pure religion logic there... YOU can't asnwer the questions because you don't know, so instead you simply claim that we're idiots! WOW
Science idiots do not know the difference between mutations and amino acid substitutions
well, apparent;y neither do you, because you've already admitted your own model makes mutations
Jones is giving legitimate science and you're sticking your finger in your ears yelling "LALALALA"
like i said... per your OWN WORDS, you are an IDIOT
anonymous_9001
5 / 5 (5) Jan 11, 2015
I don't pay any mind to idle threats. I can't find it at the moment, but I recall him a while ago saying that we should be publicly hanged.
JVK
1 / 5 (4) Jan 11, 2015
Inching toward the 3D genome
My comment to the Science site: http://comments.s....6217.10

Re: "...the nucleome structure changes as cells age, differentiate, and divide, and researchers want to understand how and why."

Cell type differentiation is nutrient-dependent. RNA-directed DNA methylation links RNA-mediated amino acid substitutions to cell type differentiation via protein folding during life history transitions. Amino acid substitutions stabilize protein folding; mutations perturb it, during nutrient-dependent theromodynamic cycles of protein biosynthesis and degradation.

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

The metabolism of nutrients links metabolic networks to genetic networks via species-specific pheromones that control the physiology of reproduction. Simply put, pheromones link nutrient-dependent life via physics, chemistry, and ..."
Captain Stumpy
3.7 / 5 (3) Jan 11, 2015
My comment to
just because you can post a reply in ScienceMag doesn't mean it is CORRECT, nor does it mean that you are relevant to the article

in fact, it only means that you have paid a subscription fee that allows you to post whatever pseudoscience you want and look as stupid to a professional community of scientists as you do here

Also note, per the site
Science does not endorse any User Submission or any opinion, recommendation, or advice expressed therein, and Science expressly disclaims any and all liability in connection with User Submissions
just because you can post there, doesn't mean they ENDORSE your bullsh*t

your pseudoscience has been noted by others as well

most just ignore you because they think you are just another silly ignorant religious troll, not a legit scientist in ANY way

and that is what ScienceMag will tell you when you report the trolls, too
"Ignore it!
they're being publicly stupid- let them"

JVK
1 / 5 (3) Jan 11, 2015
I don't pay any mind to idle threats. I can't find it at the moment, but I recall him a while ago saying that we should be publicly hanged.


Ignorance is not a capital offense, and lawyers make more money on class action suits. The reason I think that Carthage College will be targeted is because Andrew Jones publicly proclaimed his ignorance in his review of my published work, before revealing his inability to understand anything about the basic principles of biology or levels of biologically-based cause and effect required to link sensory input to hormones and hormones to behavior.

The review of his thesis reveals that he graduated with a degree in biology after linking results from mutagenesis experiments to his theories that link nothing to the gene-cell-tissue-organ-organ system pathway that links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via conserved molecular mechanisms.
Captain Stumpy
3.7 / 5 (3) Jan 11, 2015
Andrew Jones publicly proclaimed his ignorance in his review of my published work
and yet we can see from repeated posts as well as from actual degreed professionals and intelligent people who are well versed in the area that not only is he CORRECT, but it actually points out your own delusions of grandeur and ignorance

why else would you still be crying about it?
the ONLY person here who demonstrated
his inability to understand anything about the basic principles of biology or levels of biologically-based cause and effect
is you, kohlslaw

and you repeatedly demonstrate that with every post that you denigrate the respected scientists/biologists like Myers, Lenski and Extavour

I hope you actually try to make good on your threat here: http://phys.org/n...firstCmt

likely they will have free legal as well, considering the outcome and counter-suit & your subsequent loss of finances
better get insurance while you can
nickmaxell
5 / 5 (1) Jan 11, 2015


Thanks for asking.

This is where the ignorance is. That's why others who publish their works aren't here. They don't care about the ignorance. Serious scientists have incorporated every aspect of the RNA-mediated cell type differentiation we detailed into their works. Only pseudoscientists have not realized the importance of feedback loops and chromatin loops to the bio-physically constrained chemistry of protein folding. They attribute cell type differentiation to mutations.

Well - we "science idiots" simply stick to proofable science or at least fundated theories - the garbage you are writing how chromatin structure influences proteins as it is exactly the other way round as proteins (eg histones) are responsible and regulating chromatin structure in the first place
JVK
1 / 5 (3) Jan 11, 2015
Ch.16 Language and Communication as Universal Requirements for Life http://www.crcpre...66584617

Conclusion: "The biocommunication and natural genome-editing approach on processual reality of living agents brings some advantages to traditional scholarly conviction:

Clear distinction between life and nonlife.
• Empirical nonmechanistic and nonreductionistic description method of biotic interactional
patterns throughout all organismic kingdoms.
• Any observed coordination within and between organisms can be deciphered by
research that identifies signaling molecules and syntactic, pragmatic, and semantic
rules underlying the mode of signal use.
• Biological research must not concentrate any longer on experimental setups and theoretical
approaches that want to elucidate language and communication in nonhuman
living nature by mathematical (algorithm-based) modeling."

If you're a science idiot who disagrees with these conclusions, explain why.
JVK
1 / 5 (3) Jan 11, 2015
proteins (eg histones) are responsible and regulating chromatin structure in the first place


Thanks. I made the mistake of believing you might not be a science idiot.

the garbage you are writing how chromatin structure influences proteins


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

Excerpt: "•Contact domains (∼185 kb) segregate into six subcompartments with distinct histone marks
•Loop anchors occur at domain boundaries and bind CTCF in a convergent orientation
•Loops correlate with gene activation and are conserved across cell types and species
•The inactive X chromosome contains large loops anchored at CTCF-binding repeats"
Captain Stumpy
3.7 / 5 (3) Jan 11, 2015
Ch.16 Language and Communication as Universal Requirements for Life http://www.crcpre...66584617

you do realize you are quoting from an astrobiology book, right?
Astrobiology: An Evolutionary Approach provides a full course in astrobiology with an emphasis on abiogenesis and evolution. The book presents astrobiology both as a developing science and as the science of the future.
This is like trying to build a house in the US but trying to quote from the German Gov't building codes as proof of your legitimacy or legality of code compliance

Which is NOT surprising considering you have no idea about how similar jobs or specialties might have a different focus

thanks for pointing that out
it makes a LOT more sense now...

so, what are you going to quote next?
Quantum Field theory to support your inability to comprehend technical nomenclature?
nickmaxell
5 / 5 (1) Jan 11, 2015
So you believe its the chromatin directing the DNA to wrap around histones and not the helper proteins? - well I hope you take a science class soon
JVK
1 / 5 (3) Jan 11, 2015
you do realize you are quoting from an astrobiology book, right?


Ideas about top-down cause come from serious scientists who refute ridiculous theories.

http://en.wikiped...R._Ellis
"George Francis Rayner Ellis, FRS, Hon. FRSSAf, (born 11 August 1939), is the Emeritus Distinguished Professor of Complex Systems in the Department of Mathematics and Applied Mathematics at the University of Cape Town in South Africa. He co-authored The Large Scale Structure of Space-Time with University of Cambridge physicist Stephen Hawking, published in 1973, and is considered one of the world's leading theorists in cosmology.[1]"

Top-down causation: an integrating theme within and across the sciences? http://rsfs.royal...abstract full text is free This is one article from the Top-down causation Organized by George F. R. Ellis, Denis Noble and Timothy O'Connor http://rsfs.royal.../2/1.toc
JVK
1 / 5 (3) Jan 11, 2015
Re: Organized by George F. R. Ellis, Denis Noble and Timothy O'Connor...

Neo-Darwinism, the Modern Synthesis and selfish genes: are they of use in physiology? http://jp.physoc....007.full

"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)

George F. R. Ellis, who also co-authored with Stephen Hawking, and Denis Noble have one thing in common -- despite their different disciplines. They are serious scientists who examine what's known about physics, chemistry, and the molecular biology of life, instead of attributing its diversity to mutations and evolution. Only science idiots attribute the diversity of morphological and behavioral phenotypes to mutations and evolution. That's how you know a science idiot when you encounter one.
JVK
1 / 5 (3) Jan 11, 2015
So you believe its the chromatin directing the DNA to wrap around histones and not the helper proteins? - well I hope you take a science class soon


Like the other science idiots here, you fail to tell us what you believe. If you do not believe that serious scientists are accurately representing biologically-based cause and effect, address the evidence and provide your alternative. Try to not keep acting like other science idiots. No one cares what they think, because they can't think about anything except mutations and evolution.

Captain Stumpy
3.7 / 5 (3) Jan 11, 2015
Like the other science idiots here, you fail to tell us what you believe
this is your tactic as well... when pressed into attempting to find where your knowledge base is by intelligent professionals, you retreat and refuse to answer (mostly because acknowledging the science would mean retreating from your religion and pseudoscience)

so you are simply saying that someone is using YOUR OWN TECHNIQUE here, which is nothing we aren't used to reading, jk

see above or any other thread where you are pressed for clarifying information by RealScience, Anonymous or anyone else
Try to not keep acting like other science idiots. No one cares what they think, because they can't think about anything except mutations and evolution.
but kohlslaw, YOU obviously care a great deal about being outed as a pseudoscience troll

just like you care a great deal about what we say about you (although you should be used to being outed as a Pseudoscience TROLL by now)
JVK
1 / 5 (3) Jan 11, 2015
...you believe its the chromatin directing the DNA to wrap around histones


"Current research spanning and uniting diverse fields and exploring the physical and chemical nature of organisms across temporal, spatial, and organizational scales is replacing the model of evolution as a passive filter selecting for random changes at the nucleotide level with a paradigm in which evolution is a dynamic process both constrained and driven by the informational architecture of organisms across scales, from DNA and chromatin regulation to interactions within and between species and the environment."
http://dx.doi.org...as.12140

See also: Combating Evolution to Fight Disease http://comments.s....1247472

But, enough about what serious scientists believe. What do science idiots believe, and why do they believe it? We know who taught Andrew Jones to be a science idiot.

Who taught you?
JVK
1 / 5 (3) Jan 11, 2015
YOU obviously care a great deal about being outed as a pseudoscience troll...


That's not going to happen.

I'm taking this opportunity to again show how much pseudoscientific nonsense the science idiots of the world have been taught to accept, and how they regurgitate it when anyone challenges them by providing evidence -- like the Root-Berstein's have done -- that refutes their ridiculous theories about mutations and evolution.
anonymous_9001
5 / 5 (3) Jan 11, 2015
Ideas about top-down cause come from serious scientists who refute ridiculous theories.


Nope. Remember that time I contacted Ellis and he told me you were misinterpreting him?

Captain Stumpy
4 / 5 (4) Jan 11, 2015
That's not going to happen.
it already HAS
see above

see also: http://phys.org/n...firstCmt
or read most ANY other thread here on PO where you argue with Anon, AA_P and Real (all degreed professionals whereas all you are is a glorified lab tech who tried to illegally claim the ability to diagnose without a license)
I'm taking this opportunity to again show how much pseudoscientific nonsense the science idiots of the world have been taught to accept
well, you ARE a huge living example of someone being scientifically illiterate
But in order to teach anyone, you would first have to be educated yourself, and you are NOT... (self admitted)
Nor are you able to teach WHY you are correct
Anon et al have been making you look QUITE foolish...
plus, you attack anyone who disagrees with you on ANY point
that is why Dr. Extavour is not in your link "repertoire" any longer - she proved you WRONG
and that you LIED
JVK
1 / 5 (3) Jan 11, 2015
Remember that time I contacted Ellis and he told me you were misinterpreting him?


There was no need for interpretation. What he said is linked here via the comments on the article: http://journal.fr...127/full

I concluded my post with: 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)."

George F R Ellis wrote: This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: http://rsfs.royal.../2/1.toc

The only way to misinterpret that, is to try to place it into the ridiculous context of mutagenesis experiments because you were taught to be a science idiot.
JVK
1 / 5 (3) Jan 11, 2015
...here on PO where you argue with Anon, AA_P and Real (all degreed professionals...


There is no argument. They simply claim I'm wrong. They provide no alternative to my model, which links physics and chemistry to conserved molecular mechanisms.

Yet they will not claim how the three are linked to whatever they were taught to believe in -- because they know they were taught to believe in something so ridiculous as to not ever again be mentioned.

For all anyone knows, they all performed mutagenesis experiments and believed their results could be meaningfully interpreted.

Who cares? No matter how many science idiots try to convince others that perturbed protein folding leads to increasing organismal complexity, only other science idiots will believe it.

As we can see here, I'm the only serious scientist who has any interest in teaching science idiots about anything. Most already know it is impossible to teach anything to a science idiot.
JVK
1 / 5 (3) Jan 11, 2015
Just for fun, let's see how much longer the science idiots can ignore this May 2013 statement:

"Current research spanning and uniting diverse fields and exploring the physical and chemical nature of organisms across temporal, spatial, and organizational scales is replacing the model of evolution as a passive filter selecting for random changes at the nucleotide level with a paradigm in which evolution is a dynamic process both constrained and driven by the informational architecture of organisms across scales, from DNA and chromatin regulation to interactions within and between species and the environment."
http://dx.doi.org...as.12140

In June 2013 Nei concluded: "...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world." http://www.amazon...99661731

Even other science idiots will not claim to believe in that.

anonymous_9001
5 / 5 (3) Jan 11, 2015
What he said is linked here via the comments on the article


What he said directly in my inbox:

Natural selection as usually envisaged is a form of top down causation (because the environment is a major causal factor in the outcomes). Selection is a key process in the rise of complexity. That is quite clear in what I have written. Indeed I claim that multilevel selection is a key to complexity


They provide no alternative to my model, which links physics and chemistry to conserved molecular mechanisms.


http://www.scienc...14001800

Models:

http://faculty.ch...-effects
http://www.nature...672.html
http://www.cell.c...901268-8
http://rsif.royal...19?rss=1
JVK
1 / 5 (3) Jan 11, 2015
In the June 2013 publication of my model, I linked the nutrient-dependent "...informational architecture of organisms across scales, from DNA and chromatin regulation to interactions within and between species and the environment" via their species-specific physiology of nutrient-dependent reproduction -- and cell type differentiation via RNA-mediated amino acid substitutions in all cells of all individuals of all species.

Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
http://www.ncbi.n...24693353
anonymous_9001
5 / 5 (3) Jan 11, 2015
Just for fun, let's see how much longer the science idiots can ignore this May 2013 statement:


Reading comprehension fails you again. That's the same thing Noble talks about- SUPPLEMENTING traditional theory with modern methods, not an outright refutation.

For emphasis:

a paradigm in which evolution is a dynamic process both constrained and driven by the informational architecture of organisms across scales, from DNA and chromatin regulation to interactions within and between species and the environment


Interactions between species and the environment = selective processes
JVK
1 / 5 (3) Jan 11, 2015
Natural selection as usually envisaged is a form of top down causation (because the environment is a major causal factor in the outcomes). Selection is a key process in the rise of complexity. That is quite clear in what I have written. Indeed I claim that multilevel selection is a key to complexity


Selection of nutrients is selection for reproduction, which links nutrient-dependent pheromone-controlled ecological adaptations in species from microbes to man via multilevel selection across life history transitions. Plant life and animal life are linked via light-induced amino-acid substitutions in the context of biophotonics, without trying to make the term "mutations" fit.
http://discoverma...tum-life
nickmaxell
not rated yet Jan 11, 2015
BLAST is a pretty old program you could align DNA or predict mRNA - still very useful but outdated - in principle it was never more than a seachrable database - there are newer programs based on it which allow more functions
nickmaxell
5 / 5 (2) Jan 11, 2015
JVK you are quoting not a scientific journal with your link the "quantum effects" they claim to be found 8 years ago have never been verified - a search for the main authors on several databases came up blank - just a huge pile of bs you are propagating
JVK
1 / 5 (3) Jan 11, 2015
... a huge pile of bs...


I wrote:
[q Just for fun, let's see how much longer the science idiots can ignore this May 2013 statement:

"Current research spanning and uniting diverse fields and exploring the physical and chemical nature of organisms across temporal, spatial, and organizational scales is replacing the model of evolution as a passive filter selecting for random changes at the nucleotide level with a paradigm in which evolution is a dynamic process both constrained and driven by the informational architecture of organisms across scales, from DNA and chromatin regulation to interactions within and between species and the environment."
http://dx.doi.org...as.12140

In June 2013 Nei concluded: "...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world." http://www.amazon...99661731

Even other science idiots will not claim to believe in that.
Captain Stumpy
3.7 / 5 (3) Jan 12, 2015
There was no need for interpretation. What he said is linked here via the comments on the article:
Actually, what happened was you made a series of claims with regard to the article and then tried to use the article as validation for your claims

Then your claims were refuted and proven false by the author

This also happend with regard to Dr. Extavour's work, where you made a series of claims and then tried to say that the work linked validated your claims

and AGAIN, Dr. Extavour plainly stated that not only were you WRONG, but you were WAY OFF BASE with your "interpretation"

when you choose to create a kohlslaw word salad of obfuscation which, when broken down to constituent parts, does not truthfully interpret the claims or experiments published, then it is called an "interpretation" of the work, not a factual representation of the work

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