59,000 generations of bacteria, plus freezer, yield startling results

Feb 14, 2014 by Alvin Powell
Since 1988, Richard Lenski has watched E. coli bacteria multiply through 59,000 generations, a span that has allowed him to observe evolution in real time. He also found that one of the 12 bacterial lines he has maintained has developed into what he believes is a new species. Credit: Melanie Rieders

After 26 years of workdays spent watching bacteria multiply, Richard Lenski has learned a thing or two.

He's learned that naturalist Charles Darwin was wrong about some things. For one, evolution doesn't always occur in steps so slow and steady that changes can't be observed.

Lenski also learned that a laboratory freezer can function as a .

A professor at Michigan State University, Lenski has watched E. coli bacteria multiply through 59,000 generations, a span that has allowed him to observe evolution in . Since his Long-Term Experimental Evolution Project began in 1988, the bacteria have doubled in size, begun to mutate more quickly, and become more efficient at using the glucose in the solution where they're grown.

More strikingly, however, he found that one of the 12 bacterial lines he has maintained has developed into what he believes is a new species, able to use a compound in the solution called citrate—a derivative of , like that found in some fruit—for food.

Lenski described his groundbreaking work at Harvard's Mineralogical and Geological Museum on Wednesday during a talk sponsored by the Harvard Museum of Natural History, one of the Harvard Museums of Science & Culture (HMSC).

His presentation, "Time Travel in Experimental Evolution," was introduced by HMSC executive director Jane Pickering and by Jonathan Losos, the Monique and Philip Lehner Professor for the Study of Latin America and curator of herpetology in the Museum of Comparative Zoology.

Losos, who studies the behavior and evolution of Anolis lizards on Caribbean islands, called Lenski's long-running work "simply extraordinary" and said that his approach has been adopted by other researchers around the world.

Losos said Lenski's talk was particularly appropriate because it occurred on the 205th anniversary of Darwin's birth. In the spirit of the ongoing Olympics, Losos said that if there were ever an all-star team of evolutionary biologists, Lenski would be its captain.

While the ability to observe creatures with short reproductive times over thousands of generations has brought insights, Lenski said it was the use of the laboratory freezer that allowed the work to cross from observation into experimentation.

Researchers periodically froze samples of E. coli, and because the frozen bacteria remained viable, scientists interested in particular evolutionary developments could directly compare modern populations against their ancestors. In addition, the development of cheap, accurate ways to analyze the genome has given researchers better analytical tools.

One of the central questions Lenski has explored is the tension between evolution's opposing forces: the random mutations that initiate genetic change and the natural selection that shapes which mutations survive. Those forces, Lenski said, provide evolutionary pressure in different directions.

Random genetic mutation pushes organisms to diversify, while natural selection is a homogenizing force, favoring characteristics that enhance survival under specific conditions.

The experiment has run according to the same protocol since it began. E. coli bacteria are grown in the solution of glucose, a kind of sugar. The glucose is carefully measured so it eventually runs out and creates a period of scarcity and starvation before the bacteria are propagated the next day and transferred into a fresh solution. Every 75 days, roughly 500 generations, a portion of the cultures is frozen.

Though the bacteria were originally genetically identical, they have evolved. Today's populations grow roughly 80 percent faster than the original lines, a development that Lenski called "a beautiful example of adaptation by natural selection."

An analysis of the 12 lines after 20,000 generations showed 45 mutations from the ancestral population among the bacteria's roughly 4,000 genes. Many of the same genes were mutated in all lines, but it was rarely exactly the same mutation within the genes, Lenski said. He equated the bacteria's evolutionary feats in the glucose-limited "flask world" with those of mountain climbers finding other routes to the peak.

"Populations are climbing Mount Glucose in similar, though not identical, ways," Lenski said.

After 30,000 generations, researchers noticed something strange. One population had evolved the ability to use a different carbon-based molecule in the solution, called citrate, as a power source.

Researchers wondered whether it was the result of a rare, single mutation, or a more complex change involving a series of mutations over generations. To find out, one of Lenski's postdocs, Zachary Blount, took some of the frozen cells and grew them in a culture lacking glucose, with citrate as the only potential food source.

After testing 10 trillion ancestral cells from early generations, he got no growth. But when he tested cells from the 20,000th generation on, he began to get results, eventually finding 19 mutants that could use citrate as a power source. The results showed that the citrate-eating mutation was most likely not the result of a single mutation, but one enabled by multiple changes over 20,000 generations.

In further testing to determine if the new bacteria were different enough to qualify as a new species, Lenski's researchers found that beyond changes to the genes responsible for glucose and citrate consumption, other changes had occurred in the organism that had made it less fit to survive in a glucose-only environment,

"We find they are getting less fit in the ancestral niche over time," Lenski said. "I would argue that citrate users are—or are becoming—a ."

Lenski said he'd like to see the experiment continue in the future, even after he has retired, because the bacteria continue to surprise.

"I call this the experiment that keeps on giving, because the bacteria continue to do interesting things," Lenski said. "I'd like this experiment to continue long after I'm gone."

Explore further: Unpacking the past: Identifying a key evolutionary step in E. coli metabolism

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JVK
1 / 5 (6) Feb 15, 2014
"...begun to mutate more quickly, and become more efficient at using the glucose in the solution where they're grown."

Isn't glucose dehydrogenase required for the use of glucose by E. coli? If so, what is the mutation that is supposedly responsible for organisms becoming more efficient at using glucose in the ecological environment where they are grown?

Nestle
2.1 / 5 (7) Feb 15, 2014
It could be switching of sleeping genes or similar stuff. Also, the asexual replication of procaryots makes the verification of species formation problematic. The Darwin's theory was about formation of NEW species with SEXUAL selection, not about adaptation of single strain. Such an experiments would rather prove the theory of Lamarck, who has been Darwin opponent in his time and Darwin wouldn't be probably very happy about it.
Nestle
2.3 / 5 (9) Feb 15, 2014
Also many creationists are claiming, that the number of species is constant (they can only die out) and the richness of our world is in capacity of their adaptation. Which is exactly the outcome of the above experiment.

The hidden trick of this hypothesis is, the bacteria can exchange portion of their genomes through viruses or another mechanism, so that the reservoir of their adaptability is pretty larger, than one could expect from single organism.
Nestle
2.1 / 5 (7) Feb 15, 2014
Now, if we consider the hypothesis of Hoyle and Wickramasinghe's, in which viral infections spread with cosmic dust, then we have infinite reservoir of such a variability. Also, the oceans are reservoir of surprisingly huge number of viruses of all possible kinds. The solar flares may not bring the viruses from cosmic space - they just affect the nucleation of atmospheric watter. When the water condenses in tiny droplets, it doesn't rain, which would help in spreading of marine viruses at distance.

Maybe the core of fight between evolutionists and creationists is just in misunderstanding of evolutionary mechanisms and the role of horizontal gene transfer in it.
JVK
1.6 / 5 (8) Feb 15, 2014
I asked:
Isn't glucose dehydrogenase required for the use of glucose by E. coli? If so, what is the mutation that is supposedly responsible for organisms becoming more efficient at using glucose in the ecological environment where they are grown?


Who cares what the creationists claim, unless they claim that glucose dehydrogenase is not required for the use of glucose by E. coli? That would make them pseudoscientists unless glucose dehydrogenase is not required.

Darwin would probably be happy to learn that someone finally accepted the fact that his 'conditions of life' must be the primary consideration in the context of his theory. Lenski seems to have ignored Darwin's 'conditions of life' and is touting mutation-driven evolution instead of what is now known about the conserved molecular mechanisms in species from microbes to man that enable ecological adaptations.

Why continue to celebrate Darwin week by continuing to ignore what Darwin wrote?
Nestle
2.3 / 5 (6) Feb 15, 2014
Who cares what the creationists claim, unless they claim that glucose dehydrogenase is not required for the use of glucose by E. coli
Why they should claim it? I don't see any reason for it.
Why continue to celebrate Darwin week by continuing to ignore
At first, I don't ignore it, at second, Darwin was a scientist and the science is not based on celebrations of personality cults, but in systematical reconciliation of ideas and theories.
the fact that his 'conditions of life' must be the primary consideration
This is what the Lamarck or even Lysenko have said too. Actually these guys adhered on driving effects of conditions of life way too much. Lysenko in particular tried to evolve the better cows with their feeding of butter. Of course, such a cows got a fatter milk quite soon and his model seemed to be vindicated. My point rather is, Darwin unappreciated the creationist aspects of evolution in the same way, like his opponents did the same for the opposite.
Nestle
2.3 / 5 (6) Feb 15, 2014
When we compare the Lysenko's experiments with the above experiments of bacteria, we may get into surprising similarities. The bacteria got sugar - and they started to utilize it. The cows got butter and they started to utilize it. No new species were formed during this in both cases. But Trofim Lysenko was indeed a Darwin denying crackpot - whereas Richard Lenski is a genius supporting Darwin. Maybe I've just missed something...
Maggnus
3.9 / 5 (11) Feb 15, 2014

Isn't glucose dehydrogenase required for the use of glucose by E. coli? If so, what is the mutation that is supposedly responsible for organisms becoming more efficient at using glucose in the ecological environment where they are grown?
Yep, puts a giant hole in your "theory" doesn't it? The mutation allowed more efficient use of a nutrient it was already using. Can you now admit your theory was wrong?
Maggnus
4 / 5 (12) Feb 15, 2014
Lenski seems to have ignored Darwin's 'conditions of life' and is touting mutation-driven evolution instead of what is now known about the conserved molecular mechanisms in species from microbes to man that enable ecological adaptations.
How do you reach this conclusion? He has shown, experimentally (which you claimed could not be done) that mutationally driven genome changes can result in changes in the behavior of a species, and then taken that a step further by proving mutational changes can result in the rise of a new species. This is exactly the mutationally driven evolution you were claiming could not occur.

Can you now admit that you were wrong?
Maggnus
3.4 / 5 (5) Feb 15, 2014
Zephyr, can you be a little more specific in what you are saying? Your stilted English is a bit confusing at times, and this is one of them. Are you claiming the creationists were right?
Nestle
2.6 / 5 (5) Feb 15, 2014
that mutationally driven genome changes can result in changes in the behavior of a species
Were these genome changes really caused with mutations? Maybe just some already existing sleeping genes from "Junk DNA" were activated. Recently we all have read about pluripotent STAP cells prepared with controlled starvation. What the bacteria will do inside of environment full of sugar, which they cannot otherwise utilize under normal circumstances? They will starve.

Can you now admit that you were a bit fast in conclusions?

Are you claiming the creationists were right?
IMO nope - in general. But could they have a bit of truth, especially regarding the evolution of protozoa? You may guess...
big_hairy_jimbo
5 / 5 (1) Feb 15, 2014
Now I have no idea at HOW the glucose is being used more efficiently, but I will suggest that perhaps uptake, and expulsion of metabolites have been increased, therefore allowing a more efficient utilsation of glucose dehydrogenase. ie, follow equilibrium and kinematic rules at how to make something more efficient. Or perhaps the enzyme had a small change which improved it.
JVK
1 / 5 (7) Feb 15, 2014
Thanks,

It is natural genetic engineering that allows enzymatic change in DNMT paralogues, which enables more efficient use of glucose and stabilizes the thermodynamics of intercellular signaling and protein biosynthesis/degradation that leads to additional amino acid substitutions, organismal complexity and eventually to chromosomal rearrangements in eukaryotes that manifest the changes in beneficial organism-level thermoregulation.

The idiot minions of evolutionary theorists and biology teachers like PZ Myers cannot comprehend the fact that biophysical constraints on protein folding prevent mutation-driven evolution, which is why they claim amino acid substitutions that stabilize the genome are mutations that can only perturb it. Simply put, they are like all pseudoscientists who simply accept theories rather than attempt to find experimental evidence that supports the theories. That's why I put pseudoscientists, like PZ Myers, and his idiot minions in the same class.
JVK
1 / 5 (7) Feb 15, 2014
Lenski may be in another class. Perhaps he lets people misrepresent the results of his experiments, which helps to ensure additional funding. I'm not sure what he has claimed, but doubt that he has claimed that the E. coli became two different species via mutation-driven evolution.

It would be almost impossible for any biologist except PZ Myers to not realize that ecological adaptations are nutrient-dependent and pheromone-controlled in microbes and that the molecular mechanisms for the nutrient-dependent pheromone-controlled physiology of reproduction don't change with speciation that exemplifies ecological adaptation (not mutation-driven evolution).
anonymous_9001
5 / 5 (8) Feb 15, 2014
Many of the same genes were mutated in all lines, but it was rarely exactly the same mutation within the genes, Lenski said


Your model has yet to account for this, Kohl. If glucose CAUSED the gene changes, as you claim, why wouldn't they all accumulate the same mutations? There can't be a causal link if there are multiple outcomes from the same input.
JVK
1 / 5 (6) Feb 15, 2014
Your model has yet to account for this, Kohl.


Of course it does. But the biophysical constraints on perturbations of protein folding that prevent fixation of beneficial mutations in the DNA of organized genomes in any species form microbes to man are too far beyond your intellectual grasp to understand. Thus, you will no doubt plague me here as is typical of anonymous fools and idiot minions of biology teachers like PZ Myers.

Other idiot minions will soon be joining us here and also tell me what can or can't be a causal link in different circumstances that they have been taught by pseudoscientists to believe result from mutation-initiated natural selection.

Maggnus wrote:
This is exactly the mutationally driven evolution you were claiming could not occur.
Captain Stumpy
4.4 / 5 (14) Feb 16, 2014
A professor at Michigan State University, Lenski has watched E. coli bacteria multiply through 59,000 generations, a span that has allowed him to observe evolution in real time. Since his Long-Term Experimental Evolution Project began in 1988, the bacteria have doubled in size, begun to mutate more quickly, and become more efficient at using the glucose in the solution where they're grown.

More strikingly, however, he found that one of the 12 bacterial lines he has maintained has developed into what he believes is a new species, able to use a compound in the solution called citrate—a derivative of citric acid, like that found in some fruit—for food

@jvk
if your theory was correct, ALL the generations would have developed the ability to use citrate
IOW- this is PROOF that YOU ARE WRONG and pushing a PSEUDOSCIENCE HYPOTHESIS
actually, you cannot even rate Hypothesis, as you have already been publicly proven WRONG
anonymous_9001
5 / 5 (8) Feb 16, 2014
Of course it does.


No it doesn't. It's clear the base changes were random. If the nutrients CAUSED them, the same changes would be seen in all the populations, because they all have the same environment.
evolution3
5 / 5 (3) Feb 16, 2014
It could be switching of sleeping genes or similar stuff. Also, the asexual replication of procaryots makes the verification of species formation problematic. The Darwin's theory was about formation of NEW species with SEXUAL selection, not about adaptation of single strain. Such an experiments would rather prove the theory of Lamarck, who has been Darwin opponent in his time and Darwin wouldn't be probably very happy about it.


don't you think they map the genomes to test, if that gene was there before? And its not about sexual selection, there are many types of selection. I think you mean sexually reproducing organisms, but even asexually reproducing organisms evolve by selection and mutation. And no...Lamarckian evolution wouldn't work better because of that, although its to a degree working, when the only thing done is asexual reproduction.
JVK
1.6 / 5 (7) Feb 16, 2014
perhaps uptake, and expulsion of metabolites have been increased, therefore allowing a more efficient utilsation of glucose dehydrogenase. ie, follow equilibrium and kinematic rules at how to make something more efficient. Or perhaps the enzyme had a small change which improved it.


That was an intelligent comment.

If you start to pay attention to other intelligent discussants, or provide information on what you think causes the organisms to mutate into different species, we could proceed.

Simply saying "Nuh-uh" as you've done in the past, exemplifies ignorance of heterogeneity in base pairs in organisms that reproduce.
Torbjorn_Larsson_OM
5 / 5 (8) Feb 16, 2014
"he found that one of the 12 bacterial lines he has maintained has developed into what he believes is a new species".

Finally. I was starting to wonder when someone should take a bat at the ecological species concept of prokaryotes. Glad it was Lenski himself.

Actually some of the clustering, multicellular eukaryotes that people had evolve from unicellulars (at least 2 times now) in less of a year could be another example of rapid ecological speciation. It's a new trait suited to the new environment (usually promoting slow settling in a liquid), and maybe they too are less fit in the original environment.
Torbjorn_Larsson_OM
5 / 5 (9) Feb 16, 2014
Hilarious how creationists and pheromonists are happily trolling science threads. We have fun, and they are inadvertently making ever more converts to atheism and biology, see Dawkins's Convert's Corner.

@bhj: "it was rarely exactly the same mutation within the genes", so it is hard to sum up the science. I read some earlier papers, and IIRC some mutants simply express the enzymes for glucose metabolism more since it was the only game in town. That could be mutations giving more copies, amped up promotors that activate transcription, et cetera. I have forgotten, and obviously Lenski has been able to make a lot of work on this through the years.

Maybe you should look for a recent review?
JVK
1 / 5 (8) Feb 16, 2014
Ecological variation in nutrient availability alters genetically predisposed differences in nutrient uptake in my model of species diversification and increased organismal complexity in prokaryotes and eukaryotes via ecological, social, neurogenic, and socio-cognitive niche construction.

Torbjorn_Larsson_OM seems to think that Lenski has examined the ecological species concept of prokaryotes, which I don't think is what he did. I think what Lenski did was claim that mutations might be somehow driving species diversity in prokaryotes as if their diversity was not controlled by the metabolism of nutrients to species-specific pheromones that control the physiology of reproduction in species from microbes to man.

I mentioned this before. The physiology of reproduction controls nutrient-dependent speciation, which means that mutations do not. You can pretend that they do, but Creationists will not take you seriously. They know organisms must eat and reproduce to speciate. Atheists don't?
RealScience
5 / 5 (4) Feb 17, 2014
Ecological variation in nutrient availability alters genetically predisposed differences in nutrient uptake in my model ...


So you have a model that genetic changes can be made under nutrient/pheromone control. Even if that can happen (which is actually not unreasonable if epigenetic control is included), it does not mean that ALL genetic changes are made that way.

Lenski started with genetically identical (although not necessarily epigenetically identical) bateris and now has 45 mutations, many of which improve glucose metabolism and some of which enable citrate metabolism. That the changes happened on the timescale of mutations and were not consistent across bacterial populations is experimental evidence of selection for mutations.

You don't even present experimental evidence that that part of your model is ever correct, let alone that it is the only source of genetic changes.
JVK
1 / 5 (5) Feb 17, 2014
Which of the 45 mutations resulted in speciation? What part of that ridiculous theory is correct?

If you find one part that is supported by experimental evidence of cause and effect in the context of mutation-driven evolution, we can compare that part of the ridiculous theory to what I have detailed in my model.

Then we can compare the evidence of conserved molecular mechanisms in species from microbes to man to whatever part of the ridiculous theory of mutation-driven evolution you have found experimental evidence to support.

Sooner or later we might agree on how ridiculous the idea of mutation-driven evolution actually is. Meanwhile, see: http://dx.doi.org...rep04088 for experimental evidence of nutrient-dependent sex determination and see http://dx.doi.org...rep03932 for the link from the gut bacteria of mosquitoes to a human hemoglobin variant attributed to accumulated mutations by racist evolutionary theorists who think that species mutate into other species.
JVK
1 / 5 (5) Feb 17, 2014
First evidence that the genome can adapt to temperature changes
http://www.eureka...0513.php

"Today's flies are more heat-tolerant than those of the 70's"

Why haven't they mutated into another species? If that's what is happening in bacteria, how many generations of flies are required before someone shows evidence of mutation-driven evolution?
Osteta
Feb 18, 2014
This comment has been removed by a moderator.
JVK
1 / 5 (4) Feb 18, 2014
Why haven't they mutated into another species?
After all, aren't the black people adapted to tropical conditions with their skin color? Are do they form a new species just because of it?


All instances of a gene mutation that contributes to light skin color in Europeans came from the same chromosome of one person who most likely lived at least 10,000 years ago, according to Penn State College of Medicine researchers.

http://medicalxpr...eal.html
RealScience
5 / 5 (6) Feb 18, 2014
If you find one part that is supported by experimental evidence of cause and effect in the context of mutation-driven evolution, we can compare that part of the ridiculous theory to what I have detailed in my model.


As pointed out, this article IS evidence of selection FOR mutations, which is part of the process that you say can never happen. So your response to a comment pointing out the evidence you ask for is to ignore the evidence.

You have said:
I can throw out results that appear to attest to mutations as the cause of adaptive evolution because no evidence suggests that is possible.


So you ignore any results that are evidence because you say that there is no evidence, and you don't see any evidence because you ignore the results.

Open your eyes, open your mind, and looks at what actually happens.
If your model doesn't include reality, your model is incomplete, so improve your model rather than ignoring reality.

JVK
1 / 5 (5) Feb 18, 2014
A Single Gene Affects Both Ecological Divergence and Mate Choice in Drosophila

Excerpt: "Evolutionary changes in traits involved in both ecological divergence and mate choice may produce reproductive isolation and speciation."

See my comment on the Science Magazine article site:
http://comments.s....1249998

Intelligent discussion of Science is welcomed. Comments from uninformed pseudoscientists are not likely to appear. But try telling intelligent people that you believe the effect of the single gene on ecological divergence via mate choice is evidence of selection FOR mutations -- just for laughs

Note: the senior author of this article is Sean B. Carroll, and he appears to have dismissed mutation-driven evolution in flies and now attributes ecological adaptations and speciation to a single gene. He will not be the only atheistic biology teacher to begin to acknowledge the reality of what is currently known. Watch for others to quickly distance themselves from nonsensical theory.
cjn
5 / 5 (5) Feb 18, 2014
That fact that mutation occurs is indicative of it being a desirable process over the long term. If variation in a genome was not desired, then more effective polymerases would exist.
JVK
1 / 5 (5) Feb 18, 2014
That fact that mutation occurs is indicative of it being a desirable process over the long term.


Mutations perturb protein folding which is the basis of ecological adaptations. They are not desirable and are not part of any desirable process that I know about. What makes mutations desirable to you? Do you you desire to have cancer, for example?

I should have been clearer and said: Watch for others with enough intelligence to quickly distance themselves from nonsensical theory, while those who display no signs of intelligent life try to defend how different species mutated into existence.
RealScience
5 / 5 (5) Feb 18, 2014

But try telling intelligent people that you believe the effect of the single gene on ecological divergence via mate choice is evidence of selection FOR mutations -- just for laughs


You are still ignoring the evidence of mutations being selected FOR in Lenski's experiments, as pointed out in several comments above.

Try publishing an article, in a well-respected peer-reviewed genetics journal, in which you state that mutations are NEVER selected for by natural selection -- just for laughs!
JVK
1.8 / 5 (5) Feb 18, 2014
It makes no sense to publish a refutation of mutation-initiated natural selection in a genetics journal until experimental evidence suggests that mutation-initiated natural selection is biologically plausible. Serious scientists would simply laugh at anything I used to refute, Lenski's claims, since only pseudoscientists think that mutation-driven evolution is somehow exemplified in organisms from microbes to man that have obviously ecologically adapted via the conserved molecular mechanisms I have detailed in a series of published works.

Nutrient-dependent/pheromone-controlled adaptive evolution: a model
http://www.socioa...53/27989

Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors
http://www.socioa...38/20758

It makes sense to publish in "Nutrients" since ecological adaptations are nutrient-dependent.
RealScience
5 / 5 (4) Feb 18, 2014
It makes no sense to publish a refutation of mutation-initiated natural selection in a genetics journal until experimental evidence suggests that mutation-initiated natural selection is biologically plausible.


Are you deliberately confusing the wording, or do you not even understand the theory you are arguing against?
As has been explained to you many times, mutations create variety on which natural selection acts (as it also acts on variety from other causes), so it is natural selection of acting on mutation-initiated variety, not mutation-initiated natural selection.

Both in this thread and in others you have been presented evidence that it happens, and if something happens then it is plausible (and any model that says that it is implausible is wrong).

So stop making excuses and submit your claims on genetics to a genetics journal.

Whydening Gyre
1 / 5 (1) Feb 18, 2014
Of course it does.


No it doesn't. It's clear the base changes were random. If the nutrients CAUSED them, the same changes would be seen in all the populations, because they all have the same environment.

No such thing as random....
JVK
1 / 5 (5) Feb 18, 2014
not mutation-initiated natural selection.


"...natural selection is an evolutionary process initiated by mutation." Nei, M (2013)

No such thing as random....


Do you think that anyone else understands the concept of biophysical constraints on mutation-initiated natural selection that begin at the atomic level of sodium-coordinating amino acids?

I think that there is no one else here besides you who has more than the minimal intelligence exhibited by evolutionary theorists who know nothing about biology and nothing about physics.

What they do know is that people have claimed Lenski's experiments exemplify mutation-driven evolution, so they will argue against evidence that it's not biologically plausible -- as if it were.

Biophysical constraints makes no difference to them. Someone told them something and they believed it.
RealScience
5 / 5 (4) Feb 18, 2014
"...natural selection is an evolutionary process initiated by mutation." Nei, M (2013)


Natural selection is an ongoing process that mutations provide variety for. The difference is mostly, but not entirely, picky semantics.

Do you think that anyone else understands the concept of biophysical constraints on mutation-initiated natural selection that begin at the atomic level of sodium-coordinating amino acids?


There are no such constrains on natural selection for some mutations within the STANDARD meaning of the term.

However since you have indicated that you don't define mutation the same way most scientists do (such as excluding amino-acid substitutions from mutations), no one can know if there are biophysical constraints on what YOU call mutations.

Please define mutations as YOU use the term.

Captain Stumpy
4 / 5 (8) Feb 18, 2014
Try publishing an article, in a well-respected peer-reviewed genetics journal, in which you state that mutations are NEVER selected for by natural selection -- just for laughs!

@RealScience
jvk will not do the above. He is a PSEUDOSCIENCE crackpot who prefers to enter into comment sections of blogs, on-line sites etc and throw around jargon heavy word salads to try to impress.
By his own admissions, he could not hack college and didnt get a degree because he could not accomplish the basics
One basic reason that he is here, not arguing publicly or in studies with learned educated professors... even though he DID try it here:
http://freethough...s-place/
he sells perfumes and is a lab tech. Thats it. And he has a serious issue with anyone who is educated that refutes his hypothesis (which, by the way, causes MUTATIONS and is a small subset of current evolution theory)
he doesnt understand standard meanings either
Captain Stumpy
4 / 5 (8) Feb 18, 2014
Please define mutations as YOU use the term.

@RealScience
get ready to go down the rabbit hole...

we already went through this once.
Even though he gave a definition, his definition caused mutation
he disagrees with the definition of mutation (he actually said this in another argument... I can post the comment if you like, but it takes time to find)

Good luck with your fight... as all you are likely to get is called an idiot minion because you are intelligent

he really, REALLY doesn't like to be proven wrong!

P.S.
Are you deliberately confusing the wording, or do you not even understand the theory you are arguing against?

no, he doesn't.
JVK
1.8 / 5 (4) Feb 18, 2014
From Fertilization to Adult Sexual Behavior (1996) Hormones and Behavior was my first co-authored review.
JVK
1 / 5 (5) Feb 18, 2014
From Fertilization to Adult Sexual Behavior (1996) Hormones and Behavior was my first co-authored review.
http://www.hawaii...ion.html

My second, was the award winning (2001) review: Human pheromones: integrating neuroendocrinology and ethology
http://www.nel.ed...view.htm

The odds against any evolutionary theorist, biology teacher, or idiot minion proving I'm wrong about anything that involves biophysics, chemistry, or biology are astronomical and can be compared to the likelihood that any experimental evidence will ever be found that supports the ridiculous theory of mutation-driven evolution.

Clearly, if no experimental evidence has been found since 1996 to support anything except our accurate representation of molecular epigenetics, the mental midgets here aren't going to provide anything but more ridiculous commentary.
JVK
1 / 5 (5) Feb 18, 2014
it is natural selection of acting on mutation-initiated variety, not mutation-initiated natural selection.


"...natural selection is an evolutionary process initiated by mutation." Nei, M (2013)

Natural selection is an ongoing process that mutations provide variety for. The difference is mostly, but not entirely, picky semantics.


No, it is not mostly picky semantics. It's science. Either you support your ridiculous claims, or it's pseudoscience, where you argue about definitions because you can't support your claims with anything but more nonsense. If you continue to claim that natural selection is involved or that mutation-driven evolution occurs, you will need to provide experimental evidence.

I've had all the pseudoscientific nonsense I can take from people who know so little about biologically based cause and effect that they come into discussion like this to argue anonymously with people like me who have established their expertise.

Educate yourself!

Captain Stumpy
3.9 / 5 (7) Feb 19, 2014
where you argue about definitions because you can't support your claims with anything but more nonsense

@jvk
I noticed you DIDNT ANSWER THE QUESTION
maybe it is because you dont have an education and that is why you dont like vocabulary?
There is a REASON that there is a common vocabulary among scientists in a field... it is so that everyone talks the SAME LANGUAGE
its called COMPREHENSION
they dont make crap up like you do!
mutation-driven evolution occurs, you will need to provide experimental evidence

not only does the ABOVE study show it occurs, but YOUR STUDIES SHOW IT TOO
you are just trying to CALL IT SOMETHING ELSE
your studies show mutations
just because you want to call it something else doesnt mean it IS something else
this is the mark of PSEUDOSCIENCE
making up a new vocabulary for the acolytes to adhere to
does that kind of control make you feel big?
Educate yourself!

hilarious coming from the college failure!
we could say the same to YOU
cjn
5 / 5 (3) Feb 19, 2014
That fact that mutation occurs is indicative of it being a desirable process over the long term.


Mutations perturb protein folding which is the basis of ecological adaptations. They are not desirable and are not part of any desirable process that I know about. What makes mutations desirable to you? Do you you desire to have cancer, for example?

I should have been clearer and said: Watch for others with enough intelligence to quickly distance themselves from nonsensical theory, while those who display no signs of intelligent life try to defend how different species mutated into existence.


You absolutely missed the point. The fact that cancer persists, and has not been selected against (which one would assume would happen since it is critically negative to the individual) directly implies that mutation has a benefit to the population. A benefit which outweighs the cost to the individuals lost to adverse mutations. Mutation and variation equal resilience to a species
JVK
1 / 5 (5) Feb 19, 2014
You missed my point, which is that anyone who attributes evolution to mutations instead of thinking in terms of ecological adaptations is simply approaching what is currently known about conserved molecular mechanisms in species from microbes to man via what they have been taught to believe.

What you have been taught to believe about cancer has nothing to do with what is known about adaptations. But what is known is too difficult for your teachers to understand, so what choice do they have. They're not ever going to try to educate you using tools like this:

http://figshare.c...a/938190

or models like this one:

http://figshare.c..._/643393

That's why I wrote: Educate yourself! Alternatively, you can remain an idiot minion of the biology teacher PZ Myers, as Captain Stumpy and many others have decided is best to do.
RealScience
5 / 5 (4) Feb 19, 2014

@RealScience
get ready to go down the rabbit hole...

Even though he gave a definition, his definition caused mutation
he disagrees with the definition of mutation (he actually said this in another argument...

Good luck with your fight... as all you are likely to get is called an idiot minion because you are intelligent

I know the rabbit hole well - I have pointed out the shortcomings of his theory and evidence against it in quite a few threads.

I haven't seen JVK's definition - I'll look for it.

Good luck with your fight... as all you are likely to get is called an idiot minion


Thanks. I know the childish insults well - they show up when JVK runs out of arguments.
And after he has been shown to be wrong enough times, he stops responding. But then he starts again on another thread with a slightly different argument.

he really, REALLY doesn't like to be proven wrong!
He should be used to it by now.

RealScience
5 / 5 (5) Feb 19, 2014

Either you support your ridiculous claims, or it's pseudoscience, where you argue about definitions because you can't support your claims with anything but more nonsense.

That's funny coming from you who fails to support your ridiculous claims and then redefines terms like mutations because the standard definition make it obvious that you are wrong.

If you continue to claim that natural selection is involved or that mutation-driven evolution occurs, you will need to provide experimental evidence.


The article that this thread discusses IS experimental evidence that some mutations are selected FOR. And other evidence has been pointed out in other threads, which you also ignored, including showing the some of your own citations disagree with you.

You even admit that you "throw out results that appear to attest to mutations as the cause of adaptive evolution".

When results disagree with your theory, open your mind instead of throwing out the results.
JVK
1 / 5 (5) Feb 19, 2014
Roles of Mutation and Selection in Speciation: From Hugo de Vries to the Modern Genomic Era

http://gbe.oxford...abstract

"...we will not consider geographical and ecological factors because of space limitation. Our primary purpose is to clarify the roles of mutation and selection..."

Mutation-driven evolution can only be touted after throwing out the ecological factors that enable adaptations. That applies in Lenski's experiments and in any other experiments that claim mutation-initiated natural selection is somehow involved. No experimental evidence shows how mutations can be selected. Thus, you are stuck with a belief in population genetics and your refusal to belief in biological facts.

JVK
1 / 5 (6) Feb 19, 2014
Scientists identify 'long distance scanner' for DNA damage: http://medx.cc/312013846

Mutations are eliminated.

http://www.the-sc...Moments/

Eventually, the nonsensical theory of mutation-driven evolution will also be eliminated. Students will be taught to believe in experimental evidence, not ridiculous theories based on statistics.

The problem with the pseudoscientific theory of mutation-driven evolution is that there is no experimental evidence that can be refuted.No papers were published with examples of how mutations caused species diversity, so none could be retracted when it became clear that ecological adaptations are exemplified in species diversity.
russell_russell
not rated yet Feb 19, 2014
Viruses mutate. Of course the definition or label 'life' is not applicable here.

Too bad.

To test for 'life' (our definition) on a planet other than our own planet, place a virus there.
If the virus remains dormant and mutates, then you are forced by definition to conclude
the factors involved are not the components belonging to a label called 'life'.

Did this non life form 'evolve'? through mutation anyway?
RealScience
5 / 5 (4) Feb 19, 2014
The odds against any evolutionary theorist, biology teacher, or idiot minion proving I'm wrong about anything that involves biophysics, chemistry, or biology are astronomical and can be compared to the likelihood that any experimental evidence will ever be found that supports the ridiculous theory of mutation-driven evolution.


You are correct that the odds can be compared!
Since you have repeatedly been shown to be misinterpreting articles, the odds of you being proven to be wrong are 100%.
Since this article is on an experiment that provides experimental evidence that supports mutation-driven evolution, the odds of that are also 100%.
RealScience
5 / 5 (4) Feb 19, 2014
Scientists identify 'long distance scanner' for DNA damage: http://medx.cc/312013846


When presented with antibiotic resistance experiments that show antibiotic resistance mutations being selected for, you disputed that an adaptive trait (like antibiotic resistance) can arise through mutations. Yet you now cite an article that says:

"Mutations ... can enable pathogens such as bacteria to acquire new and dangerous characteristics such as antibiotic resistance."

Once again an article that you cite disagrees with you.
JVK
1 / 5 (5) Feb 19, 2014
Articles that continue to mention mutations will continue to plague those who will never understand the difference between a mutation and an ecological adaptation. They will not provide experimental evidence of mutation-initiated natural selection because there is none, yet they will continue to claim that

"Mutations ... can enable pathogens such as bacteria to acquire new and dangerous characteristics such as antibiotic resistance."


When asked for experimental evidence to support such ridiculous claims, the claim of the pseudoscientists again echo across the internet.

That's what I was taught to believe, so I believe it. My teacher didn't require any experimental evidence of cause and effect, and neither will I.

Better yet:
Viruses mutate.
-- as if their antigenic changes were not glucose-dependent -- as in every other organism on the planet. The level of intelligence displayed here continues to decline.
RealScience
5 / 5 (5) Feb 19, 2014
When asked for experimental evidence to support such claims those who understand understand that mutations play a role in evolution provide experimental evidence, INCLUDING THE ARTICLE that these comments are on.

In contrast, you ignore the presented experimental evidence while failing to present experimental evidence that mutations are never selected for.

All you do is repeat your theory that it never happens and your theory that there are constraints preventing it from happening, while ignoring experimental evidence that shows that at least this aspect of your theory is wrong.

When reality disagrees with your theory, change your theory instead of ignoring reality.
So present EXPERIMENTAL EVIDENCE that the gene sequence changes that Lenski observed were not mutations as the term is commonly used in genetic science.
JVK
1 / 5 (5) Feb 19, 2014
Please continue to use the term as it has been commonly used for the rest of your life, as those before you have done. Nothing I can provide to you will convince you that scientific progress has been made, and you will make none because you've been stuck with a ridiculous theory.
Captain Stumpy
4 / 5 (8) Feb 19, 2014
Please continue to use the term as it has been commonly used for the rest of your life, as those before you have done

@RealScience
arguing with jvk about the definitions is getting nowhere because he does not understand them
it is a comprehension issue
this is why he failed out of college
he cannot comprehend basic vocabulary that is used in the field
instead offering his own brand of jargon and expecting everyone else to jump on the bandwagon
(and he wonders why there are comprehension issues?)

had his theory had ANY power or experimental evidence, it would be used to alter the definitions used by geneticists/biologists etc already
however, it does NOT contain the requisite evidence
and the studies that he HAS been part of STILL SHOW MUTATIONS
which... according to the definition, places it firmly under evolution theory

one more sign of proof that jvk pushes PSEUDOSCIENCE rather than science
JVK
1 / 5 (5) Feb 19, 2014
Tools like this represent the level of comprehension that allows me to dismiss mutation-driven evolution and definitions.

http://figshare.c...a/938190


That's why I wrote: Educate yourself!

As always Captain Stumpy comes back to tell us all I'M NOT GOING TO DO THAT, AND YOU CAN'T MAKE ME!
Captain Stumpy
3.9 / 5 (7) Feb 19, 2014
As always Captain Stumpy comes back to tell us all I'M NOT GOING TO DO THAT, AND YOU CAN'T MAKE ME!

@jvk
again with comprehension problems?

Here is a question:
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

I know you will most likely post some long drawn out explanation of WHY YOU THINK that your changes are not considered mutations... BUT...
PER THE DEFINITION it is a mutation
PER YOUR DEFINITION that you've posed in other threads, there is a change, therefore, MUTATION

IOW- it is YOU who cannot understand or learn
nice try mensa boy
JVK
2.5 / 5 (4) Feb 19, 2014
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


YES!

--Thanks for asking. If it didn't, there could be no increased organismal-level thermoregulation in species from microbes to man via alterations in hydrogen bonds (glucose & glucose dehydrogenase interactions). Obviously, you must first break the bonds before they can be strengthened.

http://figshare.c..._/643393
anonymous_9001
5 / 5 (4) Feb 19, 2014
Now the million dollar question, Kohl. I'll give you another chance since you utterly failed to answer it on Myers' blog:

What, specifically, makes those changes to the genome? I'm looking for an enzyme or pathway here. Last time, you answered with "pre-mRNA", which I found absolutely hilarious because mRNA does not have the capacity to alter the genome, so that makes no sense at all.
JVK
1 / 5 (5) Feb 19, 2014
Stop telling me what you think can or cannot happen and give me a model of mutation-driven evolution for comparison. I don't care what you think makes sense since you are an anonymous fool.

Others may want to try to make sense of your foolishness so they can compare your deluge of nonsense to my model of biologically based cause and effect. Look at my track record here and everywhere else I participate.

I consistently provide links to works that support the model I have detailed in a series of published works. You and PZ Myers other idiot minions consistently say "Nuh-uh" then ask: "What about this?"

You have nothing for comparison, which attests to the fact that even when you think that Lenski's experiments exemplify mutation-driven evolution, you think that way because you cannot think for yourself.

Address the details in my pre-pub post to Figshare; come up with an alternative that tells us how mutation-driven evolution works or stop annoying intelligent people.
RealScience
5 / 5 (4) Feb 19, 2014
Look at my track record here and everywhere else I participate.

I consistently provide links to works that support the model I have detailed in a series of published works.


Your track record is that you consistently confuse there being more than just mutations in evolution with mutations not playing a role, you consistently confuse epigenetics with genetics, you consistently dodge questions rather than answering them, you consistently ask for evidence and then ignore evidence presented and/or fail to explain how it is not evidence, you consistently cite studies that don't support what you say or even actively disagree with what you say, and you consistently lose the arguments and stoop to insulting people who disagree with you.

Your track record here is pretty dismal.
anonymous_9001
5 / 5 (5) Feb 19, 2014
I don't care what you think makes sense since you are an anonymous fool.


If your explanation of how it works is false, then your model is false. You claimed pre-mRNA makes changes to the genome in your model. pre-mRNA does no such thing. There are no two ways about it.
JVK
1 / 5 (5) Feb 19, 2014
I did not claim that pre-mRNA makes changes to the genome, and my model is published so that others can see what I did claim.

Nutrient-dependent/pheromone-controlled adaptive evolution: a model
http://www.socioa...53/27989

"This model details how chemical ecology drives adaptive evolution via: (1) ecological niche construction, (2) social niche construction, (3) neurogenic niche construction, and (4) socio-cognitive niche construction. This model exemplifies the epigenetic effects of olfactory/pheromonal conditioning, which alters genetically predisposed, nutrient-dependent, hormone-driven mammalian behavior and choices for pheromones that control reproduction via their effects on luteinizing hormone (LH) and systems biology."

"Thus, the epigenetic 'tweaking' of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance...."
RealScience
5 / 5 (5) Feb 19, 2014
my model is published so that others can see what I did claim.


That's all you have?

No one here has argued against factors in addition to mutations being involved in adaptation.
That other factors are sometimes involved does NOT mean that mutations are never involved.

Furthermore your paper's model does NOT detail a mechanism for making changes to genetic sequences, and so does NOT answer 9001's challenge. And even if, as I would expect, our genomes have evolved feedback mechanisms that influence genetic sequences in far-from-random ways, that also would NOT exclude a role for mutations.
Your paper also doesn't offer any experimental evidence of ANY controlled amino-acid substitutions, so it falls laughably short of showing that such substitutions are NEVER caused by mutations, or even showing that the substitutions that Lenski found are not mutations.

- continued –
RealScience
5 / 5 (4) Feb 19, 2014
- continued -

The closest that your paper comes to addressing any of this is to mention the nutrient-dependent substitution of alanine for valine, citing Grossman et al. and Kamberov et al.

So do these papers you cite support your position?

The Grossman paper you cite says:
"Over the last decade, genome-wide scans for selection have been frequently reported, finding several hundred loci that show patterns of variation characteristic of new beneficial mutations that have spread quickly through the population…"

"For example, a study of diversity and differentiation in 1000 Genomes (1000G) Project data estimated that _0.5% of nonsynonymous substitutions in the past 250,000 years have been subject to positive selection…"

"We use this database to identify a nonsynonymous mutation in TLR5 with strong evidence for selection"


So the Grossman paper that you cite clearly disagrees with your position that mutations are NEVER selected for.

- continued –
RealScience
5 / 5 (6) Feb 19, 2014
- continued -

And the Khamberov paper you cite?

Khamberov clearly thinks that the genetic change of 370 SMP is a MUTATION:
"Using both newly generated and publicly available data, we examined 280 SNPs flanking the 370A SNP in 51 worldwide populations in order to assess the origin of 370A. Haplotype analysis supports a single origin of the derived allele (Figure 1A), with the mutation lying on a unique, nearly unbroken haplotype extending more than 100 kb"


And Khamberov clearly think that this mutation is SELECTED FOR:
"The estimated selection coefficient has a 95% CI between 0.030 and 0.186, with a mode of 0.122, and a median of 0.114."


And Khamberov clearly think that such strongly-selected mutations can BECOME FIXED:

"However, in a case of rapid local fixation, as is likely for a strongly selected and semi-dominant like 370A allele"


And all of these are things that you have said can never happen.

And that's just from papers that YOU cite!
anonymous_9001
5 / 5 (4) Feb 19, 2014
Good catches RealScience.
JVK
1 / 5 (5) Feb 19, 2014
"These two reports (Grossman et al., 2013; Kamberov et al., 2013) tell a new short story of adaptive evolution. The story begins with what was probably a nutrient-dependent variant allele that arose in central China approximately 30,000 years ago. The effect of the allele is adaptive and it is manifested in the context of an effect on sweat, skin, hair, and teeth. In other mammals, like the mouse, the effect on sweat, skin, hair, and teeth is due to an epigenetic effect of nutrients on hormones responsible for the tweaking of immense gene networks that metabolize nutrients to pheromones. The pheromones control the nutrient-dependent hormone-dependent organization and activation of reproductive sexual behavior in mammals such as mice and humans, but also in invertebrates as previously indicated. That means the adaptive evolution of the human population, which is detailed in these two reports, is also likely to be nutrient-dependent and pheromone-controlled..."
Captain Stumpy
3.9 / 5 (7) Feb 20, 2014
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


YES!

--Thanks for asking

@jvk
I edited here because there should be a FULL STOP
THERE IS NO REASON TO GO ANY FURTHER!

IF your models show changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element

THEN they show MUTATION

this is not debatable
you have just proven that YOUR MODELS ARE PART OF EVOLUTION THEORY
there is no need for explanations
there is simply the fact that your model, BY YOUR OWN ADMISSION causes MUTATION
which means that you are supporting mutations with EVIDENCE
which means that you provide EVIDENCE FOR EVOLUTION

THIS IS BASIC grade school comprehension
I HOPE that you finally get it...
anonymous_9001
5 / 5 (4) Feb 20, 2014
I did not claim that pre-mRNA makes changes to the genome


Need I bring up what you said on Myers' blog?

The spliceosome is to splicing, as pre-mRNA is to nutrient-dependent, pheromone-controlled, specifically directed base substitutions.


I asked what mechanism made genomic changes and you said that, followed by G protein cascades. Neither of them alter DNA base sequences.

I asked for further clarification -where genomic changes come from- and you answered with alternative splicing.

http://freethough...comments

comment #652

Splicing does nothing to the genome. Absolutely nothing. Splicing does not involve genomic material and has no effect on the genome at all.
JVK
1 / 5 (4) Feb 20, 2014
THERE IS NO REASON TO GO ANY FURTHER!

IF your models show changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element

THEN they show MUTATION


My model details how nutrient-dependent epigenetic effects on DNA are controlled by the metabolism of nutrients to species-specific pheromones that control the physiology of reproduction. This would not be possible if the epigenetic effects were not biophysically constrained (e.g., by the laws of physics).

I think what you are telling others is that the laws of physics don't apply when it comes to mutation-driven evolution, and that you are telling others that because you are one of PZ Myers idiot minions.

I think that if you were not an idiot minion you might be able to understand what I have detailed in my model, but I can't be sure. Please try to contribute something that requires intelligence to this discussion before I make my final determination.

JVK
1 / 5 (6) Feb 20, 2014
Splicing does nothing to the genome. Absolutely nothing. Splicing does not involve genomic material and has no effect on the genome at all.


Alternative RNA Splicing in Evolution
"...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."

http://jonlieffmd...AXd.dpuf

However, if an anonymous fool tells you "Splicing does nothing to the genome." -- you should probably ignore all the evidence of biologically based cause and effect that I have detailed and listen to what the anonymous fool has to say --- shouldn't you?
anonymous_9001
5 / 5 (6) Feb 20, 2014
You clearly don't understand what splicing does. That quote means that alternative splicing can differentiate species in the sense that, although they may have the same genomic sequence, they produce different translation products. It doesn't mean splicing alters the genome.
RealScience
5 / 5 (5) Feb 20, 2014
"...alternative splicing may be the critical source of evolutionary changes"

... if an anonymous fool tells you "Splicing does nothing to the genome." -- you should probably ignore all the evidence of biologically based cause and effect that I have detailed and listen to what the anonymous fool has to say --- shouldn't you?

You are confusing genetic changes affecting splicing with splicing effecting genetic changes.

Here is a high-school-level summary for you:
A gene gets copied into an RNA-equivalent called mRNA.
This does not change the gene.

Regions of the mRNA copy are cut and spliced
There are many alternate splicings possible.
They affect the mRNA COPY, not original the gene.

So splicing itself does not affect the genome.

Since you repeatedly make such BASIC mistakes, people SHOULD IGNORE WHAT YOU SAY about the papers that you cite, and read those papers for themselves.
Captain Stumpy
3.9 / 5 (7) Feb 20, 2014
I think what you are telling others is

@jvk
no
BY YOUR OWN ADMISSION, YOUR MODEL CAUSES MUTATION
YOUR MODEL IS A PART OF EVOLUTION
PERIOD
you might be able to understand what I have detailed in my model

I understand
but apparently YOU STILL DONT
please re-read my post and TRY to comprehend what I wrote
Please try to contribute something that requires intelligence

you IGNORE logic so if I WERE to post, you would only deny it, regardless of the contents
so I will offer this
IF mutation=changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element
THEN your model has mutations
and THEREFORE your model is a part of evolution theory

you will now argue against mutation driven evolution
but you still dont understand, apparently, that YOUR OWN MODELS only reinforce the current theory of evolution, WHICH INCLUDES BUT IS NOT LIMITED TO mutation driven evolution
Captain Stumpy
3.9 / 5 (7) Feb 20, 2014
@jvk
one last thing that you cannot seem to comprehend that I will reiterate
RealScience said it best, so I will use his quote:
No one here has argued against factors in addition to mutations being involved in adaptation.
That other factors are sometimes involved does NOT mean that mutations are never involved.

This is also the same thing that Myers said
this is the same thing that you tried to argue against with Myers
I know you dont like hearing that, but it is true
Myers gave you credit for the knowledge you DID bring, but you are so wrapped up in your little world that you couldnt see it for yourself
THAT is why I have used the same argument over and over...
your models cause mutations
your models are just more empirical data supporting evolution

PERIOD
there is NO NEED for discussion past this point because all it does is make it look like you cant comprehend basic English!
it also makes it look like you cant comprehend the basic jargon of your own field...
JVK
1 / 5 (5) Feb 20, 2014
You are confusing genetic changes affecting splicing with splicing effecting genetic changes.


I think you meant to say that Jon Lieff MD, is confused, since I linked to his article.

So splicing itself does not affect the genome.


Please substantiate that ridiculous opinion with a citation to any current published work.

Since you repeatedly make such BASIC mistakes, people SHOULD IGNORE WHAT YOU SAY about the papers that you cite, and read those papers for themselves.


I've always thought people should ignore what people like you say, since people like you have no knowledge of the basic principles of biology and levels of biologically-based cause and effect that are required to link nutrient-dependent pheromone-controlled epigenetic effects to ecological adaptations in E. coli and every other organism on this planet via alternative splicings in prokaryotes and via alternative splicings and chromosomal rearrangements in eukaryotes.
JVK
1 / 5 (5) Feb 20, 2014
your models cause mutations
your models are just more empirical data supporting evolution


There is one model: MINE, that refutes the ridiculous idea of mutation-driven evolution with examples of epigenetic cause and effect, which are based on Kohl's Laws of Biology.

Kohl's Laws of Biology are based on biophysical constraints included in the Laws of Physics.

PZ Myers opinions of biologically-based cause and effect are so far outdated that he should be removed from his teaching position before his students do physical harm to him and his university because he has ignored the laws of physics and biology and taught them to be his idiot minions.
anonymous_9001
5 / 5 (6) Feb 20, 2014
Splicing takes place at the mRNA level. It has no effect on the genome itself. That's not how it works. That is not an opinion.

For the love of God, learn how it works. It doesn't do what you think it does.

http://en.m.wikip...splicing
JVK
1 / 5 (5) Feb 20, 2014
"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..." Diamond, Binstock & Kohl (1996) http://www.hawaii...ion.html

"It now appears that alternative splicing is, perhaps, the most critical evolutionary factor determining the differences between human beings and other creatures." -- Jon Lieff, already cited.

See how to use experimental evidence in published works to support your assertions? Why not try it? Is it because attempts to do that make you look as foolish as you obviously are?
anonymous_9001
5 / 5 (5) Feb 20, 2014
None of that says splicing alters the genome.
cjn
5 / 5 (6) Feb 20, 2014
Dr Lieff's (and JVK's) is based upon a journal article which does not indicate nutrient/pheromone factors as a method for variable protein expression or alternative splicing.
Abstract:
"Most mammalian genes produce multiple distinct messenger RNAs through alternative splicing, but the extent of splicing conservation is not clear. To assess tissue-specific transcriptome variation across mammals, we sequenced complementary DNA from nine tissues from four mammals and one bird in biological triplicate, at unprecedented depth. We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific." (cont)
cjn
5 / 5 (4) Feb 20, 2014
^^(cont)
"Thousands of previously unknown, lineage-specific, and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR, and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators. Our data also indicate that alternative splicing often alters protein phosphorylatability, delimiting the scope of kinase signaling. "
Science 21 December 2012:
Vol. 338 no. 6114 pp. 1593-1599
DOI: 10.1126/science.1228186
cjn
5 / 5 (4) Feb 20, 2014
Dr Lieff's work only illustrates something that is well known in biology. Many genes are highly conserved with a multitude of structures. Mutation in these genes is quite often deleterious, and terminal to the individual -thus it takes longer for genome mutations to accumulate in a population (with the exception of punctuated-equilibrium style events or bottlenecks). Since these are conserved, much phenotypic variation is predicated on mRNA splicing and expression regulation. These are selected-for chemical behaviors with a biological product. None of that indicates an external, non-selective influence such as pheromones or nutrient influence.
JVK
1 / 5 (5) Feb 20, 2014
Thanks cjn.

How long do you think you can continue to ignore the role of ecological variation and microRNA's and pretend that mutations are sometimes beneficial?

http://www.scienc...abstract
"...changes in splicing patterns often contribute to evolutionary rewiring of signaling networks."

What is the cause of the benefical mutations and how are they naturally selected or fixed in the DNA of any organized genome?

Is there a model that links mutations to evolutionary rewiring of signaling networks, or are you just making stuff up like other theorists? You appear to be better informed but still a decade or more behind the experimental evidence.

"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..." http://jp.physoc....abstract
JVK
1 / 5 (5) Feb 20, 2014
These are selected-for chemical behaviors with a biological product. None of that indicates an external, non-selective influence such as pheromones or nutrient influence.


Selected-for chemical behaviors???? How does selection occur in E. coli that appear to some idiot minions and uniformed theorists to be mutating into another species?
RealScience
5 / 5 (3) Feb 20, 2014
There is one model: MINE, that refutes the ridiculous idea of mutation-driven evolution with examples of epigenetic cause and effect, which are based on Kohl's Laws of Biology.

As has already been pointed out, epigenetic cause and effect can coexist with mutations, and it would CAUSE what experts in the field call mutations.

That no genetics experts have signed on to your mutation-free model should be a clue to you that your model is flawed.
That you have to publish it in a journal that doesn't have a single genetics expert on its board or its editorial staff should be another clue.
While you could think those are a conspiracy, that you have to ignore evidence that disagrees with your model should be a clue even to you.
And that you have to make up your own meaning for terms like mutation should be yet another clue.

- continued -
RealScience
5 / 5 (4) Feb 20, 2014
- continued -

You are entitled to have your own model, even if you are its only adherent.
Where you go to far is in repeatedly spamming Phys.org comments with claims that have been shown to be wrong.
Even there you aren't the only one - cantdrive, for example spams with his EU beliefs even when many of his examples are shown to be wrong.

But where you really go wrong is to claim that other papers support your model when those papers actually go against your model.
At first it could just have been you misunderstanding the basics, but it has been pointed out too many times for that to be an excuse any more.
So if it continues, it will clearly be dishonesty - it will be fraud.

JVK
2 / 5 (4) Feb 20, 2014
You are entitled to have your own model, even if you are its only adherent.


Two award-winning publications later, and that is all you can come back with?

http://www.amazon...99737673

p. 210 "This model is attractive in that it solves the "binding problem" of sexual attraction. By that I mean the problem of why all the different features of men or women (visual appearance and feel of face, body, and genitals; voice quality, smell; personality and behavior, etc.) attract people as a more or less coherent package representing one sex, rather than as an arbitrary collage of male and female characteristics. If all these characteristics come to be attractive because they were experienced in association with a male- or female-specific pheromone, then they will naturally go together even in the absence of complex genetically coded instructions."
JVK
1 / 5 (4) Feb 20, 2014
Insect pheromone in elephants. http://www.ncbi.n.../8602213

https://fbcdn-sph...98_n.jpg

Can you imagine the mother elephant thinking she merely had a bug up her rear, only to learn after a long gestation what had actually happened.

If not for the fact that an elephant never forgets, she probably wouldn't even remember who the father was. But at least she wouldn't attribute cause and effect to mutation-driven evolution like some theorists do.

Even if this picture does not accurately represent across-species conservation of molecular mechanisms, it certainly doesn't represent mutation-driven evolution.

Does it? Are there any examples of one species mutating into another, for comparison?
cjn
5 / 5 (4) Feb 20, 2014
Selected-for chemical behaviors???? How does selection occur in E. coli that appear to some idiot minions and uniformed theorists to be mutating into another species?


You are aware, as am I, that all biology is an aggregate of chemical behaviors, and ultimately physics-based interactions. For instance: pH changes altering the rate of protein folding, or changes in concentration of protein "x" increase the rate of binding or expression. Thus, organisms with a mutation which arises in an increase in concentration of "x", which results in an increase in "y", which is a favorable expression, increases the general fitness of the individual in the population. On average, this will increase the rate of occurrence of this mutation in the population.
cjn
5 / 5 (5) Feb 20, 2014
What is the cause of the benefical mutations and how are they naturally selected or fixed in the DNA of any organized genome?


The preponderance of mutations are neutral or not phenotypically expressed (same-codon/silent mutations, per se), and thus are not selected against. It is only when expression of a mutation creates a physical reduction in fitness, or requires an unsustainable energy obligation. Ultimately, its only after a selection event or under selective pressure, where aggregated neutral mutations or explicitly beneficial mutations (citrate metabolism from the article) are selected-for and increase in the population -vice merely not being selected against.
cjn
5 / 5 (5) Feb 20, 2014
Does it? Are there any examples of one species mutating into another, for comparison?


Please don't be one of those people. This statement is acutely intellectually-dishonest. In sexually-reproducing organisms, Speciation occurs when two populations cannot interbreed, as a result of mechanical, behavioral, or genetic (polyploidy, chromosomal, etc...) changes. Since it involves entire populations, it takes many generations -hence why Lenski chose E. Coli over elephants to demonstrate genome changes.
JVK
1 / 5 (4) Feb 20, 2014
So, what has Lenski showed is selected and how was it selected to "demonstrate" genome changes?

I say the natural selection of a novel nutrient source occurred via natural genetic engineering that is manifested in every individual of every species that must eat and reproduce because feeding chemotaxis is nutrient-dependent and mating chemotaxis is obviously pheromone-controlled.

Please don't be one of those people who tells me mutations were naturally selected without telling me how -- and please don't hide behind definitions and rhetoric. Instead, explain how mutation-driven evolution is biologically plausible in microbes or is an ecologically valid approach to species diversity, which I say cannot occur due to biophysical constraints on protein folding that ensure mutations are not beneficial.

Tell me about those "constraint-breaking mutations" for example. How do they do their magic act and defy the laws of physics and biology? Is there a model for that?
anonymous_9001
5 / 5 (4) Feb 20, 2014
What constraints do mutations break? What laws of physics and biology do they break? I've seen you say this many times, but I've never seen any further explanation.
anonymous_9001
5 / 5 (4) Feb 20, 2014
Just stumbled upon this-

http://www.educat...nicorns/

This demonstrates another huge misinterpretation by Kohl. I see you never bothered to respond after Sean so clearly told you what actually occurred in the E. coli.
JVK
1 / 5 (5) Feb 20, 2014
Thanks

As did PZ Myers, Pittman blocked my posts when he realized he could not support the ridiculous theory of mutation-driven evolution with anything more than mathematical models.
Neither can anyone else, and serious scientists know that.

http://www.biomed...007/12/2
"...pictures of cells frozen in time can be useful, but also misleading with respect to each one's ultimate behavior as well as that of the population to which they belong. We need to tell the roses from the daffodils, but also be careful not to call two roses a rose and a lily."

The atheistic bloggers are the worst in this regard. They jumped at the opportunity to explain away species diversity with an untested idea that has only recently received scrutiny. Some people now wonder how they could have so blindly accepted a silly proposal. Others, like anonymous fools, want to continue to accept it with no experimental evidence whatsoever to support it.
JVK
1 / 5 (5) Feb 20, 2014
Mutation-driven evolution?
Evidence for Mito-Nuclear and Sex-Linked Reproductive Barriers between the Hybrid Italian Sparrow and Its Parent Species
http://dx.doi.org....1004075

Or nutrient-dependent pheromone-controlled ecological adaptation?
Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes
http://www.pnas.o...abstract

Experimental evidence across species from microbes to man supports only the biologically plausible ecologically validated approach to species diversification.
Jaeherys
5 / 5 (6) Feb 21, 2014
explain how mutation-driven evolution is biologically plausible in microbes


Two bacterium have share an essential gene. One has a random mutation that abolishes function of said gene. That bacterium dies and the other proliferates. It gets no simpler than that. Well......

Bacterium-1, Bacterium-2.
Bacterium-2 dies.
Bacterium-1, Bacterium-1
Bacterium-1, Bacterium-1, Bacterium-1, Bacterium-1
Bacterium-1, Bacterium-1, Bacterium-1, Bacterium-1, Bacterium-1, Bacterium-1, Bacterium-1, Bacterium-1...

Thus the only thing of real importance here is ratio of the probability of death between bacterium 1 and 2.
cjn
4 / 5 (4) Feb 21, 2014
Just stumbled upon this-

http://www.educat...nicorns/


This article is really bad. Any article claiming to be about genetics and spouting off the line "random mutation" or "Darwinian mechanism" cannot be taken seriously.
JVK
1 / 5 (4) Feb 21, 2014
Just stumbled upon this-

http://www.educat...nicorns/


This article is really bad. Any article claiming to be about genetics and spouting off the line "random mutation" or "Darwinian mechanism" cannot be taken seriously.


anonymous_9001 took it seriously and claimed it demonstrated "another huge misinterpretation by Kohl"

This demonstrates another huge misinterpretation by Kohl. I see you never bothered to respond after Sean so clearly told you what actually occurred in the E. coli.


It's very amusing when anonymous fools ignore all experimental "Evidence for Ecological Speciation and Its Alternative" http://www.scienc...abstract
What's even more amusing is when they claim that I have somehow misinterpreted something that many others have accepted for many years.
anonymous_9001
5 / 5 (3) Feb 21, 2014
anonymous_9001 took it seriously and claimed it demonstrated "another huge misinterpretation by Kohl"


He was being sarcastic. How did you not catch that?

"Evidence for Ecological Speciation and Its Alternative" http://www.scienc...abstract


Discusses both mutations and Darwinian natural selection. You must be completely deluded to think that's evidence AGAINST those.
RealScience
5 / 5 (3) Feb 21, 2014
Two award-winning publications later, and that is all you can come back with?

http://www.amazon...99737673

p. 210 "This model is attractive in that it solves the "binding problem" of sexual attraction.


The paper of yours that the book cites and complements is a pheromone-related paper. As I told you in our first exchange a year ago:
@JVK - by the way, I happen to agree that humans sense pheromones and that the older medical thinking that they don't is flawed.


The paper that the book cites makes NO MENTION of mutations or putative constraints against them, it does not redefine standard terms, or, as far as I can see misrepresent what papers that it cites say.

You model has several parts:
1) Humans and Pheromones
2) Conserved Nutrient/Pheromone pathways
3) Epigenetically/RNA-controlled DNA-sequence changes
4) Redefining 'mutations' to exclude controlled DNA-sequence changes)
5) Constraints against spontaneous mutations ever being beneficial

-continued –
RealScience
5 / 5 (3) Feb 21, 2014
-continued –
As noted above, I agree with you on the first part.
I also agree on the second part, and even complemented you cy-P450 paper.
(And I haven't seen anyone in these threads argue with either of these.)

For the third part, unlike many in the field I agree that this SHOULD happen, with varying degrees of control. I have encouraged you on this, stating that
if you have any experimental evidence to support that it would be a significant contribution to the field

For the fourth part, I agree that there are problems with lumping all DNA changes into a
single category, and have said that this is especially problematic since 'mutations' were historically called 'random'.

Here we start to diverge. REDEFINING a standard term like mutations makes communication harder. It would be much better to QUALIFY mutations (e.g., spontaneous, encouraged, controlled, deterministic), or create new terms (e.g., 'genomic edits' for highly-controlled or deterministic changes).

-cont
RealScience
5 / 5 (3) Feb 21, 2014
-continued -
The problem with redefining a standard term is that unless you constantly state your redefinition, people don't think that you mean what you mean.

For example, although you apparently somewhere stated your definition for mutations, I have not seen it. My decoding of your responses leads me to believe that you definition of "mutations" is something like what I would call "spontaneous mutations", but you also APPEAR to exclude ALL amino-acid substitutions from mutations, as well as duplications and inversion.

However when I asked for your definition you refused to give it.

-continued –
Captain Stumpy
3 / 5 (4) Feb 21, 2014
What's even more amusing is when they claim that I have somehow misinterpreted something that many others have accepted for many years

@jvk
this claim is not so hard to believe given that you dont accept or comprehend the basic jargon used in biology and genetics. You have already admitted that yourself, and proved it by consistently denying the fact that your own model causes mutations.

this jargon is normally taught in college when you take the basics, though, so i can understand that you never learned it...

you are getting destroyed by anonymous_9001 and cjn ... could it be because you have comprehension issues?
I rather think Anon_9001 has it right... you must be completely deluded...

sorry for interrupting RealScience
RealScience
5 / 5 (3) Feb 21, 2014
-continued -
But the fifth part of your model is wrong. Spontaneous mutations happen (although even those are not truly random and are corrected in a highly non-random pattern), and natural selection makes use of them. Initially you dismissed this saying that there was no model for it, then when it was pointed out that there were well-established models, you asked for evidence that it happens. After evidence was provided that it happens in actual natural selection, you asked for experimental evidence, and when that was provided you said that you could ignore the evidence because there was no evidence that it was possible.

Then in addition to ignoring evidence presented, you started citing papers and claiming that they were evidence against mutations being selected for, when in reality those papers supports a role for mutations. That is MISREPRESENTING other authors' works.

Stick to the parts of you model where you don't have to ignore evidence or misrepresent what you cite!
Captain Stumpy
3.4 / 5 (5) Feb 21, 2014
REDEFINING a standard term like mutations makes communication harder. It would be much better to QUALIFY mutations (e.g., spontaneous, encouraged, controlled, deterministic), or create new terms (e.g., 'genomic edits' for highly-controlled or deterministic changes)

NOW THIS SOUNDS COMPLETELY LOGICAL!!!!
thanks RealScience!
The problem with redefining a standard term is that unless you constantly state your redefinition, people don't think that you mean what you mean

I have been telling jvk this for a YEAR
I think Myers also said something about this too...
you started citing papers and claiming that they were evidence against mutations being selected for, when in reality those papers supports a role for mutations. That is MISREPRESENTING other authors' works

its part of his delusion and quest to alter the definition of mutation, rather than qualify his definition!
where you don't have to ignore evidence or misrepresent what you cite!

VERY WELL SAID
thank you
JVK
1 / 5 (4) Feb 21, 2014
anonymous_9001 took it seriously and claimed it demonstrated "another huge misinterpretation by Kohl"


He was being sarcastic. How did you not catch that?


Use of sarcasm ensures confusion about the intended meaning. What makes you think he was being sarcastic? Do you think he's just trying to confuse you more than you already are? I don't think that's possible.
JVK
1 / 5 (4) Feb 21, 2014
-continued -
The problem with redefining a standard term is that unless you constantly state your redefinition, people don't think that you mean what you mean.


Do you understand what I mean when I say that mutations perturb protein folding? If not, you're not going to understand anything else, since perturbed protein folding does not lead to mutation-driven evolution.

Instead, biophysically constrained protein folding leads to ecological adaptations.
anonymous_9001
5 / 5 (3) Feb 21, 2014
What makes you think he was being sarcastic?


More reading comprehension issues. This is to be expected from Kohl. Reread cjn's triplet post (as of right now, made 19 hours ago), where he ended by saying "don't be one of those people".
RealScience
5 / 5 (2) Feb 21, 2014
sorry for interrupting RealScience


No problem - a mutli-part post deserves to be interrupted.

RealScience
5 / 5 (3) Feb 21, 2014
-continued -
The problem with redefining a standard term is that unless you constantly state your redefinition, people don't think that you mean what you mean.


Do you understand what I mean when I say that mutations perturb protein folding? If not, you're not going to understand anything else


You illustrate my point.

While I understand what "mutations perturb protein folding" would mean with the standard definition of mutations as used in genetics, if YOU assign a DIFFERENT meaning to the term mutations and then refuse to define what YOU mean by mutations, there is no way to understand what YOU mean by "mutations perturb protein folding".

Define "mutations" as YOU use the term.
Captain Stumpy
3.4 / 5 (5) Feb 21, 2014
No problem - a mutli-part post deserves to be interrupted.

@RealScience
actually, it is my fault
I am working off of dial-up speed over public airwaves so... there is a huge time lag between when I DL something and when I post (can be 9-13 minutes)...

I never saw your posts till I posted...
More reading comprehension issues

I think this is the whole issue with jvk, to tell the truth
like you said: he is trying to REDEFINE the term rather than just qualify his statements

in all honesty, had he taken the time/consideration/discipline to put his nose to the grindstone and learn the basics, he would be doing amazing things today.
instead he is selling perfume and arguing comprehension/definitions out of a position of ignorance
sad, really, as there is much potential there.

instead, he is fighting a losing battle trying to force the world into a delusional mindset to assuage his hurt ego from his past failures

RealScience
5 / 5 (4) Feb 21, 2014
... anonymous fools ignore all experimental "Evidence for Ecological Speciation and Its Alternative" http://www.scienc...abstract


Did you again fail to comprehend a paper you cite, or delude yourself into thinking that it supports your position that mutations are never selected for and thus can't contribute to evolution?

The paper you cite supports not just that mutations can be selected FOR, but that their accumulation can even lead to speciation:

"Evidence for mutation-order speciation comes from instances in which reproductive isolation apparently evolved as a by-product of conflict resolution between genetic elements..."

"Laboratory experiments on various microbes maintained under homogeneous conditions for many generations have detected genetic divergence consistent with the mutation-order process..."


Its Fig 1 (B) is even an "Example of reproductive isolation evolving under the mutation-order mechanism."
RealScience
5 / 5 (3) Feb 21, 2014
I never saw your posts till I posted...


@Captain:
And I didn't see your most recent post until I clicked "submit" on my post recent post.
Even on a mid-speed connection it happens because updates don't show up while typing up a comment.

Huh - Captain - low-speed internet connection over public airwaves - are you on a boat?
anonymous_9001
5 / 5 (4) Feb 21, 2014
"Laboratory experiments on various microbes maintained under homogeneous conditions for many generations have detected genetic divergence consistent with the mutation-order process..."

Its Fig 1 (B) is even an "Example of reproductive isolation evolving under the mutation-order mechanism."


Another nail in the coffin. At this point, it's starting to look like more of a pincushion than a coffin.
JVK
1 / 5 (4) Feb 21, 2014
Open questions: A rose is a rose is a rose - or not?
http://www.biomed...007/12/2

"... pictures of cells frozen in time can be useful, but also misleading with respect to each one's ultimate behavior as well as that of the population to which they belong. We need to tell the roses from the daffodils, but also be careful not to call two roses a rose and a lily."

I probably mentioned that before, but it attests to how little credibility the interpretation of Lenski's experiments have in the context of what is known about biologically based cause and effect.
Captain Stumpy
3 / 5 (4) Feb 22, 2014
Huh - Captain - low-speed internet connection over public airwaves - are you on a boat?

@RealScience
No, just very remote. There is no electricity out my way. Solar panels running a shortwave rigged for CB bouncing a signal on to what is called the "missionary net"... I use radio signals to log into a remote server to the internet... some boats use this method. That is where I got my equipment from, anyway.
JVK
1 / 5 (4) Feb 22, 2014
Lifelong Neuronal Rebirth: Neuronal regeneration in the human adult brain is more widespread than previously thought.

http://www.the-sc...Rebirth/

The molecular mechanisms that enable the differentiation of cell types in all individuals of all species are conserved, which is why serious scientists know Lenski's experiments do not represent mutation-driven evolution, except to biology teachers like PZ Myers and their idiot minions. Like other idiot minions, Captain Stumpy cannot seem to grasp the difference between mutations that perturb protein folding and epigenetically-effected changes in intercellular signaling that stabilize protein folding.

Experimental evidence causes serious scientists to change their opinions about cause and effect. It causes pseudoscientists and idiot minions to claim that the experimental evidence supports their ridiculous opinions about mutation-driven evolution.
RealScience
5 / 5 (2) Feb 22, 2014
... just very remote. There is no electricity out my way. Solar panels running a shortwave rigged for CB bouncing a signal on to what is called the "missionary net"...


That is indeed remote!
Up here people complain that we don't have fiber and that the power goes out a few times a winter...
RealScience
5 / 5 (3) Feb 22, 2014
@JVK -
You have said:
I can throw out results that appear to attest to mutations as the cause of adaptive evolution …


Now you say:

Experimental evidence causes serious scientists to change their opinions about cause and effect.


So by your own comments you are not a serious scientist (at least when mutations are involved).

Some parts of your model are valid, but some parts are not.
Where you have to ignore evidence, those parts of your model are wrong.

Serious scientists look at what the results say, and when results show that reality disagrees with their models, they change their models rather than denying reality and throwing out those results.
Captain Stumpy
3.4 / 5 (5) Feb 22, 2014
Like other idiot minions, Captain Stumpy cannot seem to grasp the difference between mutations that perturb protein folding and epigenetically-effected changes in intercellular signaling that stabilize protein folding

@jvk
actually, I understand fine, it is YOU who has comprehension issues
heck, you cannot even define your own model with a single statement: one minute you admit it causes mutation, the next you stupidly assert that it does not.
Experimental evidence causes serious scientists to change their opinions about cause and effect

and your comments here alone PROVE that you are NOT a serious scientist
see any comment about MUTATIONS for proof!
YOU DONT EVEN UNDERSTAND THE DEFINITION even though I have given it to you at least 50 times over the past year!
you are trying to manipulate REALITY to fit your model!
That is indeed remote!

@RealScience
The nearest power lines to my house are miles away LOL
it goes to a hunting camp
Captain Stumpy
3 / 5 (4) Feb 22, 2014
@jvk
do you want to know WHY people consider you a crackpot? Especially REAL scientists in the field whom have taken the time to TRY to enlighten you... I give you a comment by RealScience:
Serious scientists look at what the results say, and when results show that reality disagrees with their models, they change their models rather than denying reality and throwing out those results

THIS is why YOU are considered a PSEUDOSCIENTIST !
THIS IS WHAT MYERS was trying to tell you
THIS IS WHAT YOU CONTINUALLY IGNORE

you assume that your mensa membership is going to get you props in the real world where DATA and EMPIRICAL evidence count... it will NOT
(and you give the rest of us a bad name)
you have tenacity, I will admit, but it is misplaced.
You continually hold onto a bad model because you have a gut feeling that you MUST be right... even though it has been proven that YOU are WRONG

disagree all you like
deep down you know it is true
your type a just doesnt like to lose
JVK
1 / 5 (4) Feb 22, 2014
No one but PZ Myers, an ignorant biology teacher, and his idiot minions has ever referred to me as a crackpot. Ask yourself why. Then look at the latest evidence from a human study that links the epigenetic effects of nutrients to our pheromone-controlled physiology of reproduction via the conserved molecular mechanisms of microbes to man -- not via mutations, you idiot.

Change in paternal grandmothers´ early food supply influenced cardiovascular mortality of the female grandchildren http://www.biomed...56/15/12
JVK
1 / 5 (3) Feb 22, 2014
Clearly, there will be no end to the experimental evidence that refutes the ridiculous idea of mutation-driven evolution, and there will be no end to the comments from idiot minions that claim ecological adaptations MUST involve mutations.

What we've seen here is merely the rantings of pseudoscientists who cannot grasp or will not accept the biological basis of morphological and behavioral phenotypes in species from microbes to man.

The pseudoscientists cannot support their claims with experimental evidence, so all they can do is claim that serious scientists who challenge their ridiculous ideas are pseudoscientists or "crackpots" like me and John A. Davison, who insist that ecoloigcal adaptations are manifested in chromosomal rearrangements and species diversity without the involvement of mutations, as they obviously are.
Captain Stumpy
3 / 5 (4) Feb 22, 2014
an ignorant biology teacher, and his idiot minions has ever referred to me as a crackpot

@jvk
wrong again
you ASSUMED that I am a follower of Myers
I just liked his explanations and how he showed everyone what an idiot you could be
The pseudoscientists cannot support their claims with experimental evidence

WRONG AGAIN!
YOU are IN the article/study commenting with YOUR PSEUDOSCIENCE
it is YOU who needs to bring proof!
and so far you have ONLY SUPPORTED THE CLAIMS OF THE AUTHOR ABOVE AND LENSKI

shall we go over the definition of Mutation again?
Given that you cannot comprehend basic English
I recommend remedial training and language classes

I will help you understand:
Answer RealScience
Define "mutations" as YOU use the term

use multiple posts
regale us with your knowledge
RealScience
4.7 / 5 (3) Feb 22, 2014
Clearly, there will be no end to the experimental evidence that refutes the ridiculous idea of mutation-driven evolution


Clearly if you delusionally CLAIM that evidence for mutations having a role is evidence that refutes mutations having a role, there will be no end to your delusional claims of evidence that refutes a role for mutations in evolution.

and there will be no end to the comments from idiot minions that claim ecological adaptations MUST involve mutations.


I have not seen a single claim on this thread that ecological adaptations MUST involve mutations. There are many other factors involved, including those that you detail in your papers.

It is you who has the narrow-minded thinking that evolution can NEVER involve mutations.

It has been repeatedly pointed out that many papers that you cite, and even your model, involve what are standardly called mutations. If you are using some non-standard definition, STATE WHAT IT IS.
JVK
1 / 5 (4) Feb 22, 2014
It is you who has the narrow-minded thinking that evolution can NEVER involve mutations.


No, it is you who now claims that is what I've been claiming, after realizing that what I've been claiming about mutations is unequivocally correct.

Mutations perturb protein folding. No matter how you define "mutation," perturbed protein-folding cannot contribute to mutation-driven evolution.

That's what I've been saying, which is why you again are insisting that I state my definition. You have finally learned what makes the comments here seem to be those that come from ignorant biology teachers like PZ Myers or their idiot minions.

The biophysical constraints on protein folding ensure that mutations are not beneficial, and that natural selection for nutrients enables genomic stability via olfactory/pheromonal input that links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes, like E.coli, to man. No definitions required!
JVK
1 / 5 (4) Feb 22, 2014
It has been repeatedly pointed out that many papers that you cite, and even your model, involve what are standardly called mutations.


It has been repeatedly pointed out that all the papers I cite, especially in the context of my published works and detailed model, what others like to call mutations cannot possibly be involved in what they like to call mutation-initiated natural selection. Thus, now Masatoshi Nei and others must claim "We are mutants" without explaining how that could be possible since mutations perturb protein folding and he claims natural selection is not the driving force of evolution.

Even an idiot minion of an ignorant biology teacher should realize that Nei and others have realized ecological variation is the driving force of adaptations and that, unlike what evolutionary theorists have been claiming, there are no mutants that arise in the context of my model. Thus, all mutants must arise in the context of their model, so "We are all mutants."
RealScience
5 / 5 (3) Feb 22, 2014
what others like to call mutations cannot possibly be involved in what they like to call mutation-initiated natural selection


The standard definition of a mutation is a change to the DNA sequence.
So "what others like to call mutations" includes everything from relatively random changes to completely controlled changes.

Since apparently in your model DNA sequences are changed under highly-non-random epigenetic/nutrient/pheromone control, your model involves "what others like to call mutations".

So even your model involves "what others like to call mutations".

Since you say that your models does not involve mutations, you apparently mean something different by 'mutations' than what others mean. This is why you need to DEFINE WHAT YOU MEAN by mutations if you want to communicate your ideas on mutations to others.
Jaeherys
5 / 5 (5) Feb 22, 2014
Mutations perturb protein folding. No matter how you define "mutation," perturbed protein-folding cannot contribute to mutation-driven evolution


Silent mutations do not perturb protein folding. Perturbed protein-folding can contribute to mutation-driven evolution in MANY ways. Perhaps the simplest example would be mutations in regulatory domains of proteins in pro-survival pathways, e.g. RTKs, PKB, mTOR, etc. When an organism and subsequently the cells are stressed and this stress induces apoptosis, these mutations that block binding to negative regulatory elements may be beneficial to the survivability in this stressed environment. This is common in cancers but when you have single hits to these pathways, this can be an overall positive change, especially if they are not at a much greater risk for developing tumors.
JVK
1 / 5 (4) Feb 22, 2014
Mutations perturb protein folding. No matter how you define "mutation," perturbed protein-folding cannot contribute to mutation-driven evolution


Silent mutations do not perturb protein folding. Perturbed protein-folding can contribute to mutation-driven evolution in MANY ways.


Thanks.

If I had defined "mutations" we could discuss the difference between silent mutations and those that perturb protein folding, like those common in cancers, which you seem to think may effect an overall positive change.

Instead, I'll ask: How do silent mutations or accumulated "silent" mutations in E. coli, which perturb protein folding when they accumulate, result in mutation-driven evolution? You seem to think that nutrient stress and social stress have beneficial effects on pro-survival pathways, e.g. RTKs, PKB, mTOR, etc. that involve mutations.

Is there a model for that, or model organism that exemplifies cause and effect? The honeybee, perhaps. No! -- any other model organism?
JVK
2 / 5 (4) Feb 22, 2014
what others like to call mutations cannot possibly be involved in what they like to call mutation-initiated natural selection


The standard definition of a mutation is a change to the DNA sequence.

So "what others like to call mutations" includes everything from relatively random changes to completely controlled changes.


What controls what others like to call mutations so that they can cause mutation-driven evolution?

(1) A permanent, heritable change in the nucleotide sequence in a gene or a chromosome; the process in which such a change occurs in a gene or in a chromosome.

http://www.biolog...Mutation

Please cite your source for your "standard definition of a mutation." Masatoshi Nei just redefined the term outside the context of ecological and geographical factors that obviously contribute to adaptations and speciation sans mutations. But his 2013 definition is not the standard, is it?
JVK
2 / 5 (4) Feb 22, 2014
This is where the discussion typically degrades. If the definition doesn't fit, it must be changed to appear that it may fit, or that it can still be used in some form that appears to fit the nonsensical misrepresentations of cause and effect made by ignorant biology teachers and their idiot minions for more than 80 years.

Whatever it takes to limit discussion of biologically based cause and effect is what will be entered into the discussion of mutation-driven evolution, which is not biologically plausible and has not been ecologically validated by any experimental evidence from any model organism or non-model organism. That's because there is no such thing as mutation-driven evolution, but we will continue to see how badly the ignorant and the idiotic need us to believe in something that cannot happen due to biophysical constraints.

Nei eliminated ecological factors and at the same time removed what was left of any common sense approach. What's left is common nonsense.
Jaeherys
5 / 5 (2) Feb 22, 2014
How do silent mutations or accumulated "silent" mutations in E. coli, which perturb protein folding when they accumulate, result in mutation-driven evolution?


Well, I remember reading about codon usage on the rate of translation in E. coli a few years ago. The researchers found that under different environments, I think they were changing pH and temperature, different codon usage could not only effect the rate of amino acid insertion but also halt its entry. I don't need to tell you about how that can have massive effects on phenotype!

But either way, this is a possible mechanism that can create selective pressure for or against these silent mutations. If you slow down the rate of ribosome biogenesis, for example, then those organisms would probably be less fit, but perhaps in its environment could be beneficial. Thus, you may see a change in allele frequency over time, initiated by a change in nucleotide sequence, which is the definition of evolution.
RealScience
5 / 5 (3) Feb 22, 2014
Thank you JVK.

A permanent, heritable change in the nucleotide sequence in a gene or a chromosome; the process in which such a change occurs in a gene or in a chromosome.


This is a reasonable general definition for a mutation.

A minor flaw is that it emphasizes genes - while some mutations do affect genes (translated into proteins via mRNA), many more affect regulatory regions or regions transcribed into RNAs other than mRNA.

As for what causes such mutations, Biology Online lists:
may arise from faulty deletions, insertions, or exchanges of nucleotides in the genetic material, as caused by exposure to ultraviolet or ionizing radiation, chemical mutagens, viruses, etc.

While these can indeed cause mutations, the list makes it sound as if all such changes are accidental. This ignores encouraged changes such amplification of changes to some regions (known), and probable epigentically-controlled or RNA-controlled changes (but it does not exclude them).

-cont-
Jaeherys
5 / 5 (2) Feb 22, 2014
mutation-driven evolution


I still don't quite understand what your model really is nor do I have the time to understand it completely. That being said, I think it would be a fair statement to say that evolution is not driven by mutation, evolution is initiated by mutation as it gives some difference in survivability to be acted upon. I would say that evolution is environmentally driven, e.g. nutrient levels, toxins, radiation, predation, intrinsic error (e.g. DNA damage), etc. Coincidentally enough, the factors that drive evolution forward also initiate it. To include non-mutation forms of evolution, any change in the environment that affects phenotype over time can affect allele frequencies and therefore evolution of the species.

Out of curiosity could you answer this? Viruses have very high mutation rates and have been observed to adapt quickly. We have evidence of high error rates in viral polymerases. Is mutation causative or correlative to adaptation here?
RealScience
5 / 5 (3) Feb 22, 2014
-continued-

It also ignores epigenetics, and some epigenetic changes have been shown to be heritable even if they don't change the nucleotide sequence itself.

And I am not too fond of permanent as an unqualified term – it appears that they use this to refer to a change that the cell does not restore (since almost all 'faulty' changes are very quickly repaired), rather than to a change that hangs around for the life of the universe.

But it does include all sequence changes to a chromosome, and it doesn't exclude other sources of such changes, so its faults are sins of omission, rather than commission (and of a lack of clarity on 'permanent').

So if you wish to use this as an example of "what other people call mutations", it is acceptable.

Now in your model, do permanent (unrestored), heritable change in the nucleotide sequence in a gene or a chromosome occur, regardless of what controls them?
JVK
1 / 5 (4) Feb 22, 2014
Thus, you may see a change in allele frequency over time, initiated by a change in nucleotide sequence, which is the definition of evolution.


That's an interesting definition of evolution. Has anyone ever asked their biology teacher what caused the change in the nucleotide sequence that might be somehow involved in increasing organismal complexity via speciation that is associated with ecological variation?

I'm beginning to wonder if any biology teachers actually teach biology as opposed to teaching evolutionary theory.
JVK
1 / 5 (4) Feb 22, 2014
Thank you JVK.

A permanent, heritable change in the nucleotide sequence in a gene or a chromosome; the process in which such a change occurs in a gene or in a chromosome.


This is a reasonable general definition for a mutation.


You jerk! I tried to refuse discussion of definitions and that's all you want to do. Finish writing your thesis on your own. Ask your biology teacher if anything you're being taught still makes sense in the context of what's been published during the past decade.

As for me, cite your sources and discuss biological facts or leave me out of your nonsense.
anonymous_9001
5 / 5 (3) Feb 22, 2014
Has anyone ever asked their biology teacher what caused the change in the nucleotide sequence...?


It's certainly not splicing.
JVK
1 / 5 (4) Feb 22, 2014
I still don't quite understand what your model really is nor do I have the time to understand it completely... I would say that evolution is environmentally driven, e.g. nutrient levels...


Of course you would say that, because evolution is the only thing that makes sense to you.

To include non-mutation forms of evolution, any change in the environment that affects phenotype over time can affect allele frequencies and therefore evolution of the species.


That's not evolution, that's ecological adaptation.

Out of curiosity could you answer this? Viruses have very high mutation rates and have been observed to adapt quickly. We have evidence of high error rates in viral polymerases. Is mutation causative or correlative to adaptation here?


Viruses ecologically adapt via the same molecular mechanisms conserved in living organisms.
JVK
1 / 5 (4) Feb 22, 2014
Has anyone ever asked their biology teacher what caused the change in the nucleotide sequence...?


It's certainly not splicing.


Has anyone who is not an anonymous fool ever asked their biology teacher what caused the change in the nucleotide sequence...?
RealScience
5 / 5 (3) Feb 22, 2014
You jerk! I tried to refuse discussion of definitions and that's all you want to do. …
As for me, cite your sources and discuss biological facts or leave me out of your nonsense.

You started discussing "what others like to call mutations", and then gave a standard definition of mutations, along with a reference for it.
What controls what others like to call mutations so that they can cause mutation-driven evolution?

(1) A permanent, heritable change in the nucleotide sequence in a gene or a chromosome; the process in which such a change occurs in a gene or in a chromosome.
http://www.biolog...Mutation

How is that you trying to "refuse discussion of definitions"?

I assumed that this was you engaging in a civil discourse on definitions, and I AGREED TO USE YOUR REFERENCE.
So if you wish to use this as an example of "what other people call mutations", it is acceptable.

How the heck is that being a jerk?

JVK
1 / 5 (4) Feb 22, 2014
I asked: WHAT CONTROLS what others like to call mutations so that they can cause mutation-driven evolution?

I asked you to cite your source to see if your definition source mentioned controlled evolution.

So "what others like to call mutations" includes everything from relatively random changes to completely controlled changes.


You didn't cite your source and didn't mention anything about how evolution was controlled, but launched a discussion of definitions, instead. That's being a jerk. The fact that you don't seem to realize that you are a jerk, makes you a bigger jerk whose nonsense is intolerable.

Please continue discussion with an anonymous fool or one of PZ Myers idiot minions, or anyone else but me.
Captain Stumpy
3.4 / 5 (5) Feb 22, 2014
It is you who has the narrow-minded thinking that evolution can NEVER involve mutations.

No, it is you who now claims that is what I've been claiming, after realizing that what I've been claiming about mutations is unequivocally correct.

@jvk
erm. no... you specifically said your model causes mutations.
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

I used the basic definition of mutation that is used by biologists and geneticists
THEN YOU ANSWERED
YES!
--Thanks for asking

https://www.genom...m?id=134
https://en.wikipe...Mutation
http://dx.doi.org...900007-8
http://dx.doi.org....1112699
http://dx.doi.org...4.01.012
Captain Stumpy
3.7 / 5 (6) Feb 22, 2014
I tried to refuse discussion of definitions and that's all you want to do

@jvk
in order for comprehension for both parties in communication, there must be ground rules, as well as acceptable jargon usage.
What RealScience is using is the acceptable jargon of the biological sciences, which you should be aware of.
What you are arguing against is the acceptable use of jargon in the biological sciences which means that you are unaware of its use, you are attempting to arbitrarily change its use, and you are wrong.

You have comprehension issues and you fail to realise that you are stupidly arguing against the standard definition!
RealScience
5 / 5 (4) Feb 22, 2014
It is you who has the narrow-minded thinking that evolution can NEVER involve mutations.


No, it is you who now claims that is what I've been claiming


@JVK - Here are some quotes from you:

mutations … no evidence suggests they are ever fixed in the genome.

mutations are not fixed in the organized genome of any species

I'm not willing to believe that natural selection ever selects for a mutation

The biophysical constraints on mutations is why they cannot be selected.

what others like to call mutations cannot possibly be involved


Do you or do you not think that mutations are EVER selected for in natural selection?
RealScience
5 / 5 (3) Feb 23, 2014

Mutations perturb protein folding. No matter how you define "mutation," perturbed protein-folding cannot contribute to mutation-driven evolution.


Several definitions for mutations have been presented in this thread. Under none of these, nor under the top ten definitions Google finds, do mutations violate biophysical constraints on protein folding or perturb protein folding ways that prevents all mutations from being selected for. So under ALL of these definitions your claims are wrong.

Papers that you cite against mutations actually support mutations, and that is true with ANY of the definitions of mutations presented in this thread. Even you own model uses mutations as ANY of these defines mutations.

Now you may have some secret definition of mutations that somehow automagically limits mutations to sequence changes that violate biophysical constraints. If so, define it!

And if not, admit that you were wrong (or at least stop REPEATING your error).
Captain Stumpy
3 / 5 (4) Feb 24, 2014
nutrient-dependent pheromone-controlled ecological adaptation

@jvk
per the NIH
"In the most literal sense, polymorphism means multiple forms. So a DNA polymorphism, simply put, is a difference between sequences. Mutation is the process by which changes are made. So, yes, you can think of mutation and polymorphism as equivalent. Genome changes due to "nutrient-dependent pheromone-controlled ecological adaptation" would have evolved because of natural selection acting on differences that original arose because of mutation.  So, 'yes' again. Regarding "amino acid substitutions lead to chromosomal rearrangements and different morphological and behavioral phenotypes" –amino acid substitutions or chromosomal rearrangements could both be the ultimate cause of phenotype changes (behavioral or otherwise). The substitutions or rearrangements being genetic variation that natural selection could act on."
cont'd
Captain Stumpy
3 / 5 (4) Feb 24, 2014
@jvk cont'd
"Lenski et al  were able to map out the genetic changes (multiple changes at different times) that enabled a population of E coli to ingest citrate. Mutations occurred, the E coli that got the mutations could ingest citrate, grow and reproduce more that the E coli that couldn't. So, over subsequent generations more and more of the population of E coli could ingest citrate. "
also
"I think [this conversation] is a debate about what is most important in explaining evolutionary change – mutation or natural selection. Keep in mind they are BOTH important."
THEREFORE
per NIH
your claims that your model does not make mutations is WRONG
which only re-verifies what you already admitted in the first place

Captain Stumpy
3.4 / 5 (5) Feb 24, 2014
@RealScience
One of the biggest problems with jvk is that his arguments are actually against single mutation speciation and the methodology of speciation, NOT mutation itself, if you view all his links/studies and read them.
his argument is predominantly against single mutation species, which, if IIRC, is an outdated perspective (at least to me). Nei argues this same point: from a brief synopsis by another biologist:
if there is anything in evolutionary biology, is the insight that evolutionary change is a two-step process: mutation and some form of fixation of mutants in the population, be it by selection, drift, or meiotic drive. What is debatable, however, is the question what the explanatory power of each of these processes/mechanisms is

not realising that his argument is about methods of speciation rather than mutation itself, jvk argues the wrong argument out of linguistic ignorance, inhibiting communication

saddest thing is: I doubt that he sees it
JVK
1 / 5 (4) Feb 24, 2014
The biological basis of nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction is a scientifically established fact that excludes the pseudoscience of mutation-driven evolution. Scientific facts exclude Captain Stumpy from arguments.

http://www.socioa...53/27989
Captain Stumpy
3.4 / 5 (5) Feb 25, 2014
blah Scientific facts exclude Captain Stumpy from arguments

@jvk
mad because NIH made you look stupid?
you REALLY CANT see it!

you are arguing against single mutation speciation with arguments that support your preferred methodology.

You are unaware of the prescription grammatical lexicon which governs your field/studies. This is normally taught during college in order to facilitate communication.
(see posts above)

This observation (reinforced by your continued diatribe against mutation) validates the fact that you are unable to grasp lingual concepts needed

You are arguing out of linguistic ignorance, inhibiting communication, and therefore you are not capable of understanding the basis of the argument

therefore it is imperative that you seek education & elucidation to clarify your arguments insuring that you can functionally communicate without tangential irrelevant denunciation before returning to debate
otherwise you are nothing but a troll
JVK
1 / 5 (4) Feb 25, 2014
My model acknowledges the unequivocal fact that biophysical constraints prevent mutation-driven evolution and it details how epigenetic effects -- from atoms to ecosystems -- enable ecological adaptations. There is no debate here. You simply continue to make unsupported claims as idiot minions always do.
cjn
5 / 5 (3) Feb 25, 2014
In a world without genomic mutations, how do you account for the difference in genomic sizes between humans (21,000 genes) and E. Coli (4200 genes)? If it was simply epigenetic factors influencing expression and speciation, then we'd have whatever the minimum genes required for life... just expressed as differently as the gene would support.

As an actor, these pheromones you propose would be unnecessary with the known, measurable occurrence of bp mutations. Since it is a redundant process, it would not have evolved along with genetic mutation as a means to increase fitness in the earliest cells. If it did not evolve at the earliest point of divergence, it would not exist -as you insist- across ALL species, kingdoms, and phyla.
JVK
1 / 5 (4) Feb 25, 2014
The known, measurable occurrence of bp mutations can be placed into the context of what is currently known about organismal complexity, which is that it does not result from the absolutely nonsensical chaos of mutation-driven evolution in any species. See, for example:

Bidirectional developmental potential in reprogrammed cells with acquired pluripotency.

http://www.nature...969.html

If you still cannot comprehend what I have been saying here for many days, ask questions that are not based on the ridiculous idea of genetic mutation as a means to increase fitness in the earliest cells.

Mutations perturb protein folding, which does not increase the fitness of any cell type of any individual in any species from microbes to man. Thus, when you start with a biologically improbable null hypothesis that has never been substantiated with experimental evidence, you simply continue to stack the deck with your nonsense, like Captain Stupid (Stumpy).
cjn
5 / 5 (3) Feb 25, 2014
Mutations perturb protein folding, which does not increase the fitness of any cell type of any individual in any species from microbes to man.


This is wrong on numerous levels. DNA codes for many things, not just amino acids. If mutations were always bad, then genes would only code for a single protein, and would contain the minimum number of bp's required to express said gene. The fact is, that a single gene often codes for numerous proteins, predicated on mRNA and tRNA instructions -which are derived from non-gene segments of the genome.

Further, this "x to y" claim is bogus. The point of divergence between extant species and single cellular organisms is so ancient that only the most conserved of structures is preserved. This pheromone-based mutation mechanism would not be one of them since its evolution would have been unnecessary. The fact that there are bp mutations indicate that it has been selected-for; if it was the redundant element, it would not exist.
cjn
5 / 5 (3) Feb 25, 2014
I understand that this is a really poor attempt at mental-gymnastics to justify some Intelligent Design mechanism, but it simply does not exist. Not only does it not exist, it has no need to exist. Redundant mechanisms for adaptation would not exist, especially if one of them was predicated on benevolent environmental interactions (which is insane by itself, as no organism would evolve to explicitly support the sustainment of an unrelated, non-interdependent species), and the other [genome mutations] are so often harmful to the individual.

Stick to Irreducible Complexity or other ID mechanisms that people are scientifically-illiterate enough to believe, the logic simply isn't there with this one.
JVK
1 / 5 (4) Feb 25, 2014
The fact that there are bp mutations indicate that it has been selected-for; if it was the redundant element, it would not exist.


Thanks. Your version of reality is interesting nonsense.

The fact that people don't know the difference between an epigenetically-effected bp change and a mutation makes them appear to be scientifically illiterate evolutionary theorists who would rather believe in mutation-driven evolution than attempt to learn what they must learn to become serious scientists.

Serious scientists are not likely to believe that
The point of divergence between extant species and single cellular organisms is so ancient that only the most conserved of structures is preserved. [/q/]

Serious scientists already know the molecular mechanisms that link the epigenetic landscape to the physical landscape must be conserved across all species from microbes to man -- or, minimally, all of them that must acquire food and reproduce.

JVK
1 / 5 (4) Feb 25, 2014
Stick to Irreducible Complexity or other ID mechanisms that people are scientifically-illiterate enough to believe, the logic simply isn't there with this one.


I noticed that you did not respond to the logic of this one:

Bidirectional developmental potential in reprogrammed cells with acquired pluripotency.

http://www.nature...969.html

Please describe the role you think mutations play in the bidirectional developmental potential of cell types in individuals of different species. Do you know how cell types of E.coli mutate into the cell types of Klebsiella, for example, and how they might change back to the cell types of E. coli?
cjn
5 / 5 (4) Feb 25, 2014
I noticed that you did not respond to the logic of this one:

Bidirectional developmental potential in reprogrammed cells with acquired pluripotency.

http://www.nature...969.html

Please describe the role you think mutations play in the bidirectional developmental potential of cell types in individuals of different species. Do you know how cell types of E.coli mutate into the cell types of Klebsiella, for example, and how they might change back to the cell types of E. coli?


All this article indicates is that in the mouse cells tested, differentiated cells can be "shocked" back into pluripotent cells. They're still mouse cells. This does nothing to support your argument. If they turned into capybara cells, then maybe this would support you in some way.

I don't understand your second statement? Are you asking how one extant species turns into another extant species? If that's what you think speciation is, then you are certainly not a "serious scientist".
JVK
1 / 5 (4) Feb 25, 2014
I don't understand your second statement? Are you asking how one extant species turns into another extant species? If that's what you think speciation is, then you are certainly not a "serious scientist".


Thanks. Do you understand this question?

HOW DOES SPECIES DIVERSITY ASSOCIATED WITH MUTATIONS IN E. COLI OR ANY OTHER SPECIES OCCUR? That's what I had hoped you would address when I said: Please describe the role you think mutations play in the bidirectional developmental potential of cell types in individuals of different species.

You chose to address the nonsense: Do you know how cell types of E.coli mutate into the cell types of Klebsiella, for example, and how they might change back to the cell types of E. coli? -- as if I were the one touting mutation-driven evolution.

How did the mouse cells become mouse cells via accumulated mutations?

cjn
5 / 5 (5) Feb 25, 2014
HOW DOES SPECIES DIVERSITY ASSOCIATED WITH MUTATIONS IN E. COLI OR ANY OTHER SPECIES OCCUR?... How did the mouse cells become mouse cells via accumulated mutations?


Diversity within a species occurs with genotypic mutations which allow for a varied expression of traits (eye color, ear size, etc...), while not diminishing the fitness of the individual or preventing it from reproducing. In multi-cellular species, these mutations occur through errors in gene copying, splicing, or "editing" during meiosis. Since these gametes ultimately form the genome for the entire organism, deleterious omissions which significantly impact the fitness of the organisms result in the mutation not being passed on. Mutations which are generally silent, or not overtly negative tend to accumulate in the population since they are not selected-against. Speciation occurs when selective pressure on the species results in certain traits being favored.
cjn
5 / 5 (5) Feb 25, 2014
^^^(Cont)

Individuals which are more fit in this new environment (due to a natural variation in trait expression which was within the natural tolerance before the selection event) will increase the presence of these previously-neutral mutations in the new population. Over time, the accumulation of these new genes will result in a new species. A perfect example is population competition selecting-for individuals which could utilize food in a new/different niche.

As for your concerns with the mouse. A "mouse" became a "mouse" when the population could no longer breed with the previous species. This is divergence.

Further, this process does not go "backwards" between species. One species cannot turn into another, and that new species revert to the previous. No one is arguing that, and it does not happen. This is a red herring argument. The cells in the article you cite are all not only of one species, but one individual within the species moving from one state to another.
Captain Stumpy
3.4 / 5 (5) Feb 25, 2014
There is no debate here

@JVK
well, not between us... we already established that you were an idiot pushing known delusional interpretations of real science that is effectively nothing more than your attempt to justify intelligent design.
The debate was whether or not you were intelligent enough to realise it and admit it, or whether you would continue to troll.
You simply continue to make unsupported claims as idiot minions always do

actually, NIH supported my assertions that:
1- your model makes mutations
2- your argument predominantly is against single mutation speciation
3- You are arguing out of linguistic ignorance, inhibiting communication because you cannot understand the lexicon which governs your field/studies

therefore, you are correct. There is NO DEBATE
you are a PSEUDOSCIENCE SPAMMING TROLL

please also note that cjn et al (above) has completely destroyed your arguments
JVK
1 / 5 (4) Feb 25, 2014
Today's support for my claims.

Oral glycotoxins are a modifiable cause of dementia and the metabolic syndrome in mice and humans http://www.pnas.o...abstract

http://medicalxpr...ets.html

Glycotoxins form when sugars react with fats, proteins and nucleic acids.

The nutrient-dependent link from glucose to glucose dehydrogenase typically enables ecological adaptations. The difference between an adaptation and a toxic mutation should be clear.

The difference between a base pair mutation that perturbs protein folding and a nutrient-dependent base pair adaptation that stabilizes protein folding establishes the fact that nutrient-dependent pheromone-controlled reproduction enables species diversity in the absence of nutrient-stress, social stress, and mutations.

Too much stress perturbs adaptations in mammals and all other species because they cannot mutate quickly enough.
Captain Stumpy
2.3 / 5 (3) Feb 26, 2014
Today's support for my claims. blah blah blah they cannot mutate quickly enough

@jvk
nice irrelevant topic change while attempting to utilise convoluted delusional logic to support a hypothesis which cannot legitimately succeed Evolution because it is based upon a fallacy due to your ignorance and comprehension issues
your model still creates a mutation per the definition used by Biologists, Geneticists and others in the field in which you keep referring to for support.
BUT DONT WORRY jvk!
There is hope for you yet!

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

PERHAPS if you could find a way to comprehend the lexicon used by your field, you can actually open your eyes and see that you are continuing to offer evidence FOR mutation and evolution!
cjn
5 / 5 (3) Feb 26, 2014
Oral glycotoxins are a modifiable cause of dementia and the metabolic syndrome in mice and humans http://www.pnas.o...abstract

Glycotoxins form when sugars react with fats, proteins and nucleic acids.


This is irrelevant and doesn't support your claims. "Glycotoxins" are the end-product of metabolic cycle which begins with the unregulated (no enzyme) interactions between sugars and proteins, lipids, and carbohydrates. These metabolic processes result in the release of H202 and other oxidizing products, which then may degenerate certain cellular structures (which is bad). This is a chemical process, it is not controlled or designed -it is chemistry. It is fairly obvious to conclude that NOT introducing these oxidative products into an organism would be beneficial to them, while introducing them might encourage these neuro-degenerative conditions. This is not indicative of any specific behavior which supports any argument you have.
cjn
5 / 5 (2) Feb 26, 2014
The difference between a base pair mutation that perturbs protein folding and a nutrient-dependent base pair adaptation that stabilizes protein folding establishes the fact that nutrient-dependent pheromone-controlled reproduction enables species diversity in the absence of nutrient-stress, social stress, and mutations.


I'm not sure how many times I have to say it, but base pair mutations DO NOT have to have an impact on "protein folding". There is more to nuclear transcription than simply coding for amino acids. Additionally, not all mis-folded proteins result in a negative product.

There is no such thing as "base pair adaptation" - it is an entirely fictional process.
cjn
5 / 5 (3) Feb 26, 2014
One of us went to a professional academic institution to study cellular biology, molecular biology, and population genetics; the other apparently found a cool pamphlet at the creation museum.
JVK
1 / 5 (3) Feb 26, 2014
HOW DOES SPECIES DIVERSITY ASSOCIATED WITH MUTATIONS IN E. COLI OR ANY OTHER SPECIES OCCUR?... How did the mouse cells become mouse cells via accumulated mutations?


Speciation occurs when selective pressure on the species results in certain traits being favored.


Is there a model for that, or any experimental evidence that supports the ridiculous theory that mutation-driven evolution "just happens?"
JVK
1 / 5 (3) Feb 26, 2014
One of us was biased by teachers who taught their ridiculous belief in automagical mutation-driven evolution; the other worked as a medical laboratory scientist for 38 years and learned how to link the conserved molecular mechanisms of ethanol-producing yeasts to nutrient-dependent pheromone-controlled neuronal copy number mosaicism in the human brain.

"I'm not sure how many times I have to say it, but base pair mutations DO NOT have to have an impact on "protein folding".


Quit saying it, and explain how Kamberov et al and Grossman et al linked a SNP in mice to an amino acid substitution and differences in morphology that clearly extend to differences in behavioral phenotypes via the same molecular mechanisms in species from microbes to man.

What caused the bp mutation? What enabled the amino acid substitution to be manifested in morphology. What was selected? How was the mutation fixed in the populations of mice and man?

How can you be such an educated fool?

cjn
5 / 5 (4) Feb 26, 2014
Is there a model for that, or any experimental evidence that supports the ridiculous theory that mutation-driven evolution "just happens?"


Of course there are:
http://gbe.oxford...812.full

http://www.nature...26230527

http://rspb.royal...399.full

JVK
1 / 5 (3) Feb 26, 2014
JVK: Glycotoxins form when sugars react with fats, proteins and nucleic acids.

This is irrelevant and doesn't support your claims. "Glycotoxins" are the end-product of metabolic cycle which begins with the unregulated (no enzyme) interactions between sugars and proteins, lipids, and carbohydrates


You really know nothing about this, right?

Regulation of DNA methylation by ethanol induces tissue plasminogen activator expression in astrocytes http://dx.doi.org...nc.12465

If you do know anything, tell us why you think glycotoxins produced by yeasts that kill bacteria and also alter the molecular mechanisms of brain development in mammals are irrelevant.
JVK
1 / 5 (3) Feb 26, 2014
http://gbe.oxford...812.full -- eliminates ecological and geographical factors from their "model"

http://www.nature...26230527 -- ideas about the introduction of new genetic material via mutation are ridiculous ideas. Mutations perturb protein folding, they don't create new functional genes.

http://rspb.royal...399.full -- is about correlations between natural selection, ecological divergence, reproductive isolation. Correlations do not lead to models of biologically based cause and effect.

You just showed your educated ass to anyone who has attempted to follow this thread by attempting to reintroduce regurgitated nonsense that I already eliminated because it is all based on population genetics, which has no explanatory power, unless it can be supported by experimental evidence of cause and effect.

http://www.socioa...53/27989
cjn
5 / 5 (3) Feb 26, 2014
Regulation of DNA methylation by ethanol induces tissue plasminogen activator expression in astrocytes http://dx.doi.org...nc.12465

If you do know anything, tell us why you think glycotoxins produced by yeasts that kill bacteria and also alter the molecular mechanisms of brain development in mammals are irrelevant.


That article is not about "the regulation" of DNA methylation by ethanol, it is about the adverse impact of ethanol on DNA methylation. There are two completely different things. One is controlled, the other is an adverse effect.

The production of ethanol in fermentation by yeast is facilitated by cellular mechanisms means it IS NOT a glycotoxin -it is a byproduct of ADP production.

In summation: Not a glycotoxin in yeast, not a regulatory mechanism, and the article clearly doesn't support your stance.
cjn
5 / 5 (2) Feb 26, 2014
You just showed your educated ass to anyone who has attempted to follow this thread by attempting to reintroduce regurgitated nonsense that I already eliminated because it is all based on population genetics, which has no explanatory power, unless it can be supported by experimental evidence of cause and effect.


Population genetics is the evidence.
JVK
1 / 5 (3) Feb 26, 2014
Population genetics is the evidence.


It is NOT experimental evidence, which means it is 'evidence' only for people who do not understand the need for experimental evidence to support their ridiculous theories, especially the theories that are based on population genetics.

If anything can be derived from the continuation of this thread for 12 days since I began the discussion, it is the fact that many evolutionary biologists and evolutionists do not understand the concept of experimental evidence.

Experimental evidence links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via conserved molecular mechanisms, which is what I did with my model. Until evidence from population genetics is linked to experimental evidence of conserved molecular mechanisms, evolutionists have nothing more than a ridiculous theory of cause and effect that includes no biophysical constraints, which means it has no biological basis.
cjn
5 / 5 (3) Feb 26, 2014
Evolution, selection, and speciation are all population-level processes. To say that observation of a single instance with a single individual is the evidence required to "prove" the theories behind these processes indicates that you don't understand how species-level genetics operates.

I always appreciate engaging in discourse over new ideas, especially if they are ideas that I have not been exposed-to in the past. Unfortunately (for both of us), the evidence provided does not support your claimed mechanism; it would have been very interesting if it did. On the other hand, there is a wide body of empirical evidence -and most importantly, logic - which supports what I have been taught, believe, and operate-upon.

I do believe this is where we part ways in this discussion. Thank you.
JVK
1 / 5 (3) Feb 26, 2014
Evolution, selection, and speciation are all population-level processes.


None occur in the absence of nutrient-dependent pheromone-controlled reproduction.

To say that observation of a single instance with a single individual is the evidence required to "prove" the theories behind these processes indicates that you don't understand how species-level genetics operates.


I understand that evolution, selection, and speciation are all nutrient-dependent pheromone-controlled population-level processes that result in ecological adaptations based on conserved molecular mechanisms and nutrient availability.

Unfortunately (for both of us), the evidence provided does not support your claimed mechanism...


I detailed the experimental evidence of conserved molecular mechanism of alternative splicings of pre-mRNA that determine cells types in individuals of all species.

I do believe this is where we part ways...


YES! Experimental evidence always causes that.
JVK
1 / 5 (3) Feb 26, 2014
Mathematical models vs. biological facts excerpted from Kohl (2013)

"Random mutations that somehow cause one or more amino acid substitutions are not likely to simultaneously cause adaptive evolution from the bottom up via the thermodynamics of chromatin remodeling and control of adaptive evolution from the top down via organism-level thermoregulation. However the nutrient-dependent substitution of alanine for valine (Grossman et al., 2013; Kamberov et al., 2013) appears to result in species-specific organism-level changes in skin, glands, and hair, through pheromone-controlled reproduction."

http://www.socioa...53/27989

"If this genes-to-behavior-and-back model of systems biology is correct, it shows what has gone missing from cause and effect in the context of adaptive evolution of the human brain and behavior. What is missing is the complex interplay of intrinsic properties, sensory drive, and the feedback activity..."
JVK
1 / 5 (3) Feb 26, 2014
Moving forward http://www.socioa...53/27989
"Evidence from genome-wide analysis suggests that polymorphisms cause alterations in neural connections and signaling in olfactory pathways, which contribute to natural variation in olfactory perception in flies (Swarup et al., 2013). That evidence links olfactory/pheromonal input to genetically predisposed species-specific behavior via previously unmodeled epistatic interactions that must occur throughout the lifecycle transitions of all organisms. Thus, the epigenetic 'tweaking' of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance..." [in ecological adaptations sans mutations THEORY will be discussed in a published work that follows].
Captain Stumpy
2.3 / 5 (3) Feb 26, 2014
One of us was biased by teachers who taught their ridiculous belief in automagical mutation-driven evolution

@jvk
and so because jvk was not intelligent enough to pass the basics in college, he must condemn those who have taken the time to learn = PSEUDOSCIENCE
the other worked as a medical laboratory scientist for 38 years

you would have THOUGHT that in that 38yrs he would have AT LEAST learned to use the jargon correctly, however, as proven time and again, he cannot even understand the basics = PSEUDOSCIENCE
If anything can be derived from the continuation of this thread for 12 days since I began the discussion, it is the fact that...

you are ignorant and trying to prove creation!
You have FAILED and you are too stupid to see the truth, and the SCIENCE in front of you!

GOOD JOB cjn! Keep it up!
RealScience
5 / 5 (2) Feb 27, 2014
"Random mutations that somehow cause one or more amino acid substitutions are not likely to simultaneously cause adaptive evolution from the bottom up via the thermodynamics of chromatin remodeling and control of adaptive evolution from the top down via organism-level thermoregulation. However the nutrient-dependent substitution of alanine for valine (Grossman et al., 2013; Kamberov et al., 2013) appears to result in …species-specific organism-level changes in skin, glands, and hair, through pheromone-controlled reproduction."

"…. and explain how Kamberov et al and Grossman et al linked a SNP in mice to an amino acid substitution and differences in morphology"


On SNP EDAR 370A, Grossman merely references Kamberov, and Kamberov call the allele 370A a mutation:
…to assess the origin of 370A. Haplotype analysis supports a single origin of the derived allele (Figure 1A), with the mutation lying on a unique, nearly unbroken haplotype…


-continued-
RealScience
5 / 5 (3) Feb 27, 2014
-continued-
Kamberov linked it the mutation to differences in morphology by mutating mice similarly:
We generated a knock-in mouse model and find that, as in humans, hair thickness is increased in EDAR370A mice. We identify novel biological targets affected by the mutation…

So again your reference SUPPORTS mutations, as the term is used by experts in the field, contributing to adaptive evolution.
As to your claim that this is not likely for 'random mutations':
There are four DNA codons for valine (GTA,GTC, GTG, and GTT), and from any of them 1/9 of the possible single substitutions codes for alanine (GCA,GCC, GCG, and GCT). Therefore even a random change to a valine codon would stand an 11% chance of coding for alanine.
Since the alanine-for-valanine substitution didn't violate the rules of thermodynamics, and since even a random mutation could make the same substitution, your claim of constraints that prevent mutations from contributing to evolution are SHOWN TO BE WRONG.
JVK
1 / 5 (2) Feb 27, 2014
Let's have it your way for a moment. You seem to be saying that racial differences like those I say are ecological adaptations are due to mutations. Which race has the superior mutations that enable "those people" to claim to be more highly evolved?

Let's have it Nei's way: We're all mutants (but some of us may be more highly evolved).

Now, let's look at it from a perspective of ecological variation and nutrient-dependent pheromone-controlled ecological adaptations in species from microbes to man. NO, YOU CAN'T DO THAT.

Back to you. Which sex is the mutant sex? Does homosexual orientation result from a mutation in males and females?

You're not very bright, are you?

Vitamin D hormone regulates serotonin synthesis. Part 1: relevance for autism
http://www.fasebj...abstract

Three brain hormones that affect social behavior, are all activated by vitamin D hormone. Which behaviors are due to mutations?
Captain Stumpy
3 / 5 (4) Feb 27, 2014
So again your reference SUPPORTS mutations, as the term is used by experts in the field, contributing to adaptive evolution.

@RealScience
yeah... I've been trying to tell him that, but he is stupidly ignoring the data in front of him... in fact, I posed the question directly to NIH (using his words quoted verbatim) and it was pretty much confirmed.
At best, he is arguing against single mutation speciation (of which I am skeptical also, but so are many others)
but in reality, his arguments only SUPPORT mutation (as you said so well above AGAIN)

KEEP IT UP RealScience... and know that NIH pretty much confirmed it all already

oh yeah.... almost forgot. Yet ANOTHER biologist also stated that some of his assessments are nothing but gobbledy-goop word salad attempting to sound smart, but instead make him look really stupid, especially given his interpretation of studies
Captain Stumpy
3 / 5 (4) Feb 27, 2014
We're all mutants (but some of us may be more highly evolved)

@jvk
those would be the ones capable of educating themselves into degree's and furthering the cause of SCIENCE
from a perspective of ecological variation and nutrient-dependent pheromone-controlled ecological adaptations in species from microbes to man

why? Its already included in evolution as it causes mutation
Which sex is the mutant sex?

depends on what they find out about you
Does homosexual orientation result from a mutation in males and females

this is a wiring issue in the brain, maybe, not a mutation
it is also irrelevant to the topic
unless you are pushing creationist beliefs, which are based upon a fallacy
and governed by a religion which is proven to be full of fallacies
forcing data to fit a bible is PSEUDOSCIENCE
and also STUPID
You're not very bright

you know... every biologist/geneticist etc that I send your quotes too say the same thing about you, too

jvk=PSEUDOSCIENCE
JVK
1 / 5 (3) Feb 27, 2014
Signaling Crosstalk: Integrating Nutrient Availability and Sex
http://stke.scien...291/pe28

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

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

"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)"
Captain Stumpy
4 / 5 (4) Feb 28, 2014
"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)"

@jvk
throwing quotes now?
Ok then!
Uncontroversial, if there is anything in evolutionary biology, is the insight that evolutionary change is a two-step process: mutation and some form of fixation of mutants in the population, be it by selection, drift, or meiotic drive.

Wagner GP.(Alison Richard Professor of Ecology and Evolutionary biology at Yale University, and head of the Wagner Lab)- Reviewing "Mutation-Driven Evolution" by  Masatoshi Nei.
JVK
1 / 5 (3) Feb 28, 2014
Thanks. I've followed his published works for several years and I suspect he is familiar with some of mine. He wrote:

"...evolutionary transitions in ligand specificity depend on coincidental presence of certain amino acid residues, enabling the functionally adaptive amino acid substitutions."
http://gbe.oxford...06.short

He may not realize that my model details HOW non-random experience-dependent amino acid substitutions occur in the context of the conserved molecular mechanisms that link nutrient-dependent pheromone-controlled ecological adaptations in species from microbes to man.

I wrote: "Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific 'fit'."
http://www.socioa...53/27989
JVK
1 / 5 (3) Feb 28, 2014
"... tissue-specific splicing might contribute to the functional versatility of proteins and shape the interaction networks in different tissues in multicellular organisms. This plasticity may lead to the emergence of novel phenotypes and increased complexity during organismal evolution." http://www.ncbi.n...3437557/

This was the approach I started from in the early 90's. It led to our 1996 review, which placed what was known about alternative splicings into the context of molecular epigenetics.

http://www.hawaii...ion.html full text 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..."

If not for people like PZ Myers and his idiot minions, many others would understand how ecological variation leads to everything else.
RealScience
5 / 5 (3) Feb 28, 2014
Thanks. I've followed his published works for several years and I suspect he is familiar with some of mine. He wrote:
"...evolutionary transitions in ligand specificity depend on coincidental presence of certain amino acid residues, enabling the functionally adaptive amino acid substitutions."

@JVK - The Wagner paper you cited DISAGREES with your claim that mutations are never fixed in populations:
Uncontroversial, if there is anything in evolutionary biology, is the insight that evolutionary change is a two-step process: mutation and some form of fixation of mutants in the population...

The passage that you quote on amino acid substitutions also is in a section that SUPPORTS genome evolution through mutational change:
… three bodies of knowledge support the notion of mutation-driven evolution … evolution of large-scale genomic features as explained by Michale Lynch's model of genome evolution, experimental studies of protein function evolution…

-continued-
RealScience
5 / 5 (3) Feb 28, 2014
-continued-
"Lynch shows that large-scale patterns of genome evolution can, to a surprising extent, be explained by the interplay of random genetic drift and the molecular biases of mutational change… evolutionary transitions in ligand specificity depend on coincidental presence of certain amino acid residues, enabling the functionally adaptive amino acid substitutions. Hence, the outcome of evolution depends on mutational events not "seen" by natural selection because they seem to be neutral and only enabling rather than functionally important themselves.

So yet again a paper that you cite supports mutations contributing to evolution.

Furthermore Wagner generally SUPPORTS Nei, as can be seen from his concluding sentence:
Nei's perspective is broadly consistent with those of developmental evolution, the functional synthesis and the mutationist view of genome evolution, and is one that is greatly expanding the scope and nature of evolutionary thinking.

JVK
1 / 5 (4) Feb 28, 2014
You seem unable or unwilling to address Nei's concept of constraint-breaking mutations. What constraints are broken. How? You could have stopped touting a ridiculous theory several days ago. Instead, you can now answer this question.

If biophysical constraints are broken, is evolution merely the process of mutations that break hydrogen bonds, which then automagically results in benefits to the organism that are naturally selected by a conspecific?

You're not very bright, are you?

http://www.abc.ne...raction/
RealScience
5 / 5 (2) Feb 28, 2014
@Captain - I missed that it was you who initially introduced the Wagner paper the JVK re-cited. Nice paper.

Regarding your low-bandwidth connection and being miles from the grid, are your latitude and longitude both 20-something? (South and East)
JVK
1 / 5 (2) Feb 28, 2014
Experts like Gunter Wagner speak in terms of mutations despite the lack of experimental evidence. Only recently have others begun to address their audiences using the terms based on experimental evidence of ecological variation that results in ecological adaptations. Even then, like Gunter, they risk attack for what others -- especially the idiot minions of atheists like PZ Myers -- will claim are Creationist views.

As we've seen here, experimental evidence does not fit the mutation-driven evolution theory, but academics cannot yet fully support my model of nutrient-dependent pheromone-controlled ecological adaptations. Most people, think that I must prove mutations do not cause evolution, which makes even serious scientists hesitate to support a new perspective --even when they know that the idea of constraint-breaking mutations is even more ridiculous than the theory the idea is supposed to support.

http://www.youtub...9CcrOuas
RealScience
5 / 5 (3) Feb 28, 2014
You seem unable or unwilling to address Nei's concept of constraint-breaking mutations. ...


HUH??? This is the first I've seen you mention "Nei's concept of constraint-breaking mutations", so HOW COULD I have addressed it?

And unless you claim that it supports a part of your model that I disagree with, WHY WOULD I address it?
I don't agree with everything that Nei says (I have already pointed out that I disagree with Nei's blanket statement that "natural selection is an evolutionary process initiated by mutations."*), but I don't go around correcting people unless they cross my path of their own accord.

* While natural selection can be initiated by a mutation, many neutral or positive-only-at-low-frequency mutations exist and are stable. A change in environment can then initiate natural selection from this pre-existing pool of variety (and I haven't seen anyone here argue against that).
RealScience
5 / 5 (4) Feb 28, 2014
Experts like Gunter Wagner speak in terms of mutations despite the lack of experimental evidence. Only recently have others begun to address their audiences using the terms based on experimental evidence of ecological variation that results in ecological adaptations.


Ecological variation that results in ecological adaptions was a cornerstone of Darwin's work -- it says nothing about the source of the variety that natural selection acts on.

Experimental evidence that the source of the variety is mutations (as the term is commonly used in the field) has been pointed out to you in this and other threads (including that the article that this thread is about is such evidence). And as also pointed out, even papers that you cite agree that mutations contribute to evolution by providing variety.

You just keep ignoring the evidence because it doesn't fit part of your model.
If part of your model requires you to ignore evidence, that part of your model is WRONG.
JVK
2.3 / 5 (3) Feb 28, 2014
Experimental evidence that the source of the variety is mutations...


Again, you are unable to differentiate between evidence from population genetics, which falsely attests to the likelihood of mutation-driven evolution, and experimental evidence that unequivocally shows HOW ecological variation results in ecological adaptation via ecological, social, neurogenic and socio-cognitive niche construction that is manifested in the biophysically-constrained increasing organismal complexity of species from microbes to man.

You have been taught to believe in "mutation for dummies" and should demand a tuition refund. Perhaps even ask for damages since you appear to have suffered brain damage associated with the amount of nonsensical theory you accepted, all the while you thought it made sense.

Darwin would have laughed at you and your kind more than I have after crying about what you did to his theory by not testing it with experiments and moving forward.
JVK
1 / 5 (2) Feb 28, 2014
[Ecological variation that results in ecological adaptions was a cornerstone of Darwin's work -- it says nothing about the source of the variety that natural selection acts on.


It must have been obvious to Darwin that ecological variation was the availability of food and that it must be selected, which is why he repeatedly stated that 'conditions of life' must be the first consideration. Only someone with no knowledge of his works, or someone who set out to deliberately bastardize his theory could have come up with the claims about mutations that were subsequently incorporated into his theory. No matter how much work had already been done by him to avoid the ridiculous claims by others that he knew would follow, others with their ignorant agendas managed to convince generations of students that mutation-initiated natural selection was biologically plausible despite no experimental evidence that validated the idea added on after-the-fact.
Captain Stumpy
2.3 / 5 (3) Feb 28, 2014
@Captain - I missed that it was you who initially introduced the Wagner paper the JVK re-cited. Nice paper.

Regarding your low-bandwidth connection and being miles from the grid, are your latitude and longitude both 20-something? (South and East)

@RealScience
thanks
read this link (Wagner reviews Nei) http://www.ncbi.n...3814208/

Lets see... 20 degrees south and 20 degrees east would put me... erm, about southern Africa, if I am right... no, sorry, not there.

In the US, just WAY out in the middle of nowhere :-)
JVK
1 / 5 (3) Feb 28, 2014
* While natural selection can be initiated by a mutation, many neutral or positive-only-at-low-frequency mutations exist and are stable. A change in environment can then initiate natural selection from this pre-existing pool of variety (and I haven't seen anyone here argue against that).


Have you seen anyone develop a model that incorporates experimental evidence of biologically-based cause and effect to detail how a change in environment can initiate natural selection from a pre-existing pool of variety? If so, I'd like to compare their model to my model of ecological variation and ecological adaptation in species from microbes to man via conservered molecular mechanisms that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of all species that have obviously not mutated into existence.
RealScience
5 / 5 (2) Feb 28, 2014

Have you seen anyone develop a model that incorporates experimental evidence of biologically-based cause and effect to detail how a change in environment can initiate natural selection from a pre-existing pool of variety?


Are you SERIOUSLY saying that you HAVEN'T seen such a model?

JVK
1 / 5 (3) Feb 28, 2014
Of course that's what I'm saying.

All you have done is continue with the same nonsensical approach seen everywhere that people believe in a ridiculous theory. If there was such a model "...that incorporates experimental evidence of biologically-based cause and effect to detail how a change in environment can initiate natural selection from a pre-existing pool of variety" you would have mentioned it.

Instead you have been stuck with no model of experimental evidence and only a useless idea from population genetics that is not even biologically plausible.

Two weeks after I started this discussion, and several months after my comment on Lenski's paper in Science to The Scientist, here we are again. No experimental evidence of mutation-driven evolution exists except in your mind.

http://www.the-sc...E--coli/

http://www.the-sc...ost96884
JVK
1 / 5 (3) Feb 28, 2014
"There also was significant correlation between nucleotide composition and amino acid composition."

The significant correlation, which also shows up in experimental evidence of biologically plausible ecological adaptations in plants, extends from algae to animals via conserved molecular mechanisms, which is why you find no mention of mutations in this article.

https://www.acade..._genomes

If they did attribute increasing organismal complexity to mutations, it would indicate they were too ignorant to publish. They could still become biology teachers, however. Good luck in your teaching career. (I pity your students.)
Whydening Gyre
not rated yet Feb 28, 2014
In the US, just WAY out in the middle of nowhere :-)

Wisconsin? here, hold my beer, I wanna try something....
Whydening Gyre
5 / 5 (2) Feb 28, 2014
. No experimental evidence of mutation-driven evolution exists except in your mind.

How bout - mutation as a result?
RealScience
5 / 5 (2) Feb 28, 2014
@JVK: So you have NEVER SEEN a model that incorporates experimental evidence of biologically-based cause and effect to detail how a change in environment can initiate natural selection from a pre-existing pool of variety?

It's a standard model, so you must have skipped basic biology (antibiotic resistance arises when low doses of antibiotics are given, sickle-cell variants are selected for in malarial regions but are selected against n non-malarial regions, etc.).

You have even cited, in this thread, papers containing examples:

http://www.eureka...513.php:
… during the heatwave, flies carrying genomic variants tolerant to the temperature increase left on average five times more descendents than those with variants that were sensitive to these changes.


Evidence for Ecological Speciation and Its Alternative:
Under ecological speciation, divergence is driven by divergent natural selection between environments
RealScience
5 / 5 (2) Feb 28, 2014
No experimental evidence of mutation-driven evolution exists except in your mind.


Given all of the evidence presented in this and other threads, it is obvious that experimental evidence of mutations contributing to evolution exists EXCEPT in your mind.

JVK
1 / 5 (3) Feb 28, 2014
Is there anyone else following this discussion who cannot grasp the difference between:

1) EXPERIMENTAL evidence that links ecological variation to ecological adaptation via conserved molecular mechanisms in species from microbes to man and

2) evidence from population genetics?

Is inclusion of the word EXPERIMENTAL in the context of evidence -- as in EXPERIMENTAL evidence -- meaningless to everyone else?

If not, will someone else try to explain why evidence from population genetics is not EXPERIMENTAL evidence like the EXPERIMENTAL evidence that links the fact that organisms must eat and reproduce to species diversity?

Antibiotic resistance, the hemoglobin S and 1181 other hemoglobin variants, and the industrial melanism of peppered moths exemplify the nutrient-dependent thermodynamics of organism-level thermoregulation that is clearly linked to all morphological and behavioral phenotypes in all species by the epigenetic effects of food odors and social odors called pheromones.
JVK
1 / 5 (3) Feb 28, 2014
Mutation-initiated natural selection and/or mutation-driven evolution is not biologically plausible, which explains why it has never been ecologically validated.

That's also why -- no matter what you've been taught to believe:THERE IS NO SUCH THING AS MUTATION-DRIVEN EVOLUTION.

If you were taught to believe there was such a thing, it was probably because you were too stupid to learn about the biological basis of cause and effect. Other kids in biology class who actually learned about biology, were laughing at you behind your back, and they still are laughing at anyone like you who managed to graduate from college.

Cause and effect requires conserved molecular mechanisms that link what every organism of every species must do 1) EAT to the physiology of organisms that 2) REPRODUCE, which enables nutrient-dependent pheromone-controlled species diversity.

Listen for the laughter, stop believing in nonsense, and get on with your ecologically adapted life.
JVK
1 / 5 (3) Mar 01, 2014
Theoretical models assuming equal phenotypes (e.g. simple diffusion) for all individuals fail to accurately describe the commonly observed population-level variation in dispersal.


http://www.academ...n_nature

Again, this make theoretical models of population genetics useless, and statements like this in the current extant literature attest to the ignorance of theorists that has been consistently shown since the time of our 1996 review article that included a section on molecular epigenetics.

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

I mention this to show how futile it is to continue presenting experimental evidence across decades during which biology teachers like PZ Myers and his idiot minions refuse to look at it, so that they can continue touting their nonsensical theories -- as RealScience has done.

"Evolution for dummies prevails."
JVK
1 / 5 (3) Mar 01, 2014
Palmitoylation of [delta]-catenin by DHHC5 mediates activity-induced synapse plasticity
http://dx.doi.org.../nn.3657

This is the type of article that should drive the students being taught "evolution for dummies" (based on Lenski's experiments) out of the classroom -- never to return, until they actually learn something about biologically based cause and effect.

The molecular mechanisms of learning and memory, for example, must have their origins in microbes. In this article, we see the importance of the only achiral amino acid: glycine, to the stability of synapses, and can trace the substitution of glycine in the decapeptide GnRH (the central feature of my model) to its conserved role across what is reported to be 400 million years of vertebrate evolution. Then, we can find mention of the origins of the GnRH molecule in yeast cells -- as the nutrient-dependent alpha-mating pheromone (in the 1996 review article I mentioned).
Captain Stumpy
3 / 5 (4) Mar 01, 2014
you must have skipped basic biology

@RealScience
actually, he already admitted that he failed out of college, so..... not skipped, failed out of

not only has he NOT seen it, he has built a wall around any experimental evidence that would prove that he is wrong, this is the blinder system that he uses. Admission of knowledge of this would be admitting he is wrong, therefore ignoring it (or assigning some arbitrary delusional definition as well as including derogatory comments) would insure that his self-delusional state is kept intact and there is no evidence to rock his personal beliefs see comments like: "who cannot grasp the difference between" etc
in order to maintain the self-delusion, there must be a paradigm used to interpret all evidential production that refutes his analysis and interpretations, and that where we get these continual posts from.
This is argument from delusion and there is no evidence that can be provided that will break the chain
it is his RELIGION
RealScience
5 / 5 (3) Mar 01, 2014
How bout - mutation as a result?


Yes.
It has been known for decades that bacteria under stress increase their mutation rates.

Recently even selective amplification of mutation rates have been found. For example, in dms4-mutants of A. thaliana Sasaki et al document 35x to 150x amplification of mutations of the dms4 gene that restore its function, without a higher mutation rate in the rest of the genome (http://www.ncbi.n...023006).
RealScience
5 / 5 (2) Mar 01, 2014
Is there anyone else following this discussion who cannot grasp the difference between:

1) EXPERIMENTAL evidence that links ecological variation to ecological adaptation via conserved molecular mechanisms in species from microbes to man and

2) evidence from population genetics?

Is inclusion of the word EXPERIMENTAL in the context of evidence -- as in EXPERIMENTAL evidence -- meaningless to everyone else?


It has repeatedly been pointed out to you that:

1) NO ONE on this thread has DISAGREED with ecological variation causing ecological adaptation via conserved molecular mechanisms in species from microbes to man.

2) That this does not exclude a role for mutations in evolution

3) That the article that this discussion started with is EXPERIMENTAL evidence that mutations are sometimes selected for.

YOU are the one who has a problem with experimental evidence - whenever experimental evidence disagrees with you, you ignore it.
RealScience
5 / 5 (4) Mar 01, 2014
you must have skipped basic biology


actually, he already admitted that he failed out of college, so..... not skipped, failed out of


Yes, but selection from existing variety is taught in HIGH SCHOOL biology ;-)

And what's really funny is that creationists often use selection from pre-existing variety to try to explain away results showing natural selection for mutations ("those aren't mutations, those variants already existed in the gene pool"), which is why Lenski and others now go to great lengths to start with identical-sequence bacteria.

However not only does jvk deny evidence that mutations are sometimes selected for, he is now denying that natural selection acts on pre-existing variety regardless of where that variety comes from!
Captain Stumpy
3.4 / 5 (5) Mar 01, 2014
Yes, but selection from existing variety is taught in HIGH SCHOOL biology ;-)

@RealScience
was it taught back then? In HIS day?
I know I learned it, but apparently his school was substandard... especially given some of the arguments used, either that or it was a religious school.
However not only does jvk deny evidence ....!

yeah...
like I said... his pre-existing bias fueled by intentional ignorance is a defense mechanism relating to his personal religion (and I make a clear distinction between religion and faith)
in his case, he will not be able to recognize any evidence that challenges his preconceived notions that rule his religion, as that would upset the delusion and force compliance with reality
you see this most often in cults, addicts (including alcoholics), and the mentally disabled (including the conspiracy paranoia etc)
evidence that supports is used, no matter the instability or source
refuting is considered ignorant/biased/unfactual/misinterpreted etc etc
russell_russell
not rated yet Mar 01, 2014
Physicists have a wave which 'evolves' while in limbo. Or a wave with everything in limbo.
Just as the rest of science needs "conditions" so too the physicist.
This condition for the physicist is called "collapse" for lack of a better understanding.
The "conditions" for life lack just as much understanding as the "condition" for the physicists' wave.
Be patient.
A solution to the protein folding problem will contribute to understanding.
Synthesizing new and all existing proteins will be a new dilemma for humans.
JVK
1 / 5 (3) Mar 01, 2014
... not only does jvk deny evidence that mutations are sometimes selected for, he is now denying that natural selection acts on pre-existing variety regardless of where that variety comes from!


Is there a model supported by EXPERIMENTAL evidence for that? I would not be so quick to deny that natural selection for SOMETHING acts on pre-existing variety if you or anyone else could tell me how the pre-existing variety somehow happens to "pre-exist" or how natural selection "acts" on SOMETHING so that it continues to "pre-exist" in species from microbes to man with their increasing nutrient-dependent pheromone-controlled organismal complexity.

If the pre-existing variety is nutrient-dependent and pheromone-controlled, however, there's a model for that! What you're denying is the entirety of the model while you continue to tell me there is a theory that explains how mutation-driven evolution occurs. I've been aware of that ridicuLous theory for several decades. IT'S NONSENSE!
JVK
1 / 5 (3) Mar 01, 2014
Synthesizing new and all existing proteins will be a new dilemma for humans.


Biophysically constrained protein biosynthesis and degradation are nutrient-dependent and pheromone-controlled via epigenetic effects on the microRNA/messenger RNA balance. Why do you think there's some dilemma associated with that biological fact now or in the future?
RealScience
5 / 5 (3) Mar 01, 2014
I would not be so quick to deny that natural selection for SOMETHING acts on pre-existing variety if you or anyone else could tell me how the pre-existing variety somehow happens to "pre-exist" or how natural selection "acts" on SOMETHING


We have sequenced numerous human genomes, and they are not identical so variety exists in the 'gene pool'. When the environment changes (such as by people from malaria-prone areas moving to non-malarial areas, or alcohol being introduced to new groups of people, or food becoming more plentiful, or new diseases being introduced, etc.), that variety existed before the change, and is thus 'pre-existing variety'.

As for natural selection acting on this pre-existing variety, some people die before having kids or have surviving kids - for example, sickle-cell disease can lead to sudden death of young adults.

Step away from your model, and look at what happens in the real world.
If the real world disagrees with your model, YOUR MODEL IS WRONG!
JVK
1 / 5 (3) Mar 01, 2014
If the real world disagrees with your model, YOUR MODEL IS WRONG!


Is Earth still flat? The sickle-cell variant and 1181 other hemoglobin variants are nutrient-dependent. That fact attests to the difference between SCIENTIFIC evidence and what you call evidence, which is derived from the pseudoscience of population genetics, and applied to prevent you from learning anything but nonsense about skin pigmentation and hemoglobin variants that supposedly arise from mutation-initiated natural selection.

"if natural selection is driving lactase persistence evolution in a place where people have no problems making vitamin D in their skin, then clearly the vitamin D and calcium explanation (known as the calcium assimilation hypothesis) isn't cutting it."

The link from fermented milk products to sickle cell AND skin pigmentation incorporates scientific evidence that isn't accepted on your planet.

http://phys.org/n...ans.html
RealScience
5 / 5 (3) Mar 01, 2014
If the real world disagrees with your model, YOUR MODEL IS WRONG!


Is Earth still flat?


No. The real world disagreed with the model so the model was wrong, just as your model is wrong where it disagrees with the real world.

I am sure that there were flat-earthers who ignored the evidence that the earth was round, just as you ignore evidence that mutations contribute to evolution.

A better comparison is Guilio Libri refusing to look through Galileo's telescope to see evidence that the heavens didn't match his model of perfection. While this may be apocryphal, it certainly would be similar to the way you refuse to see the evidence for mutations contributing to evolution.
Whydening Gyre
not rated yet Mar 01, 2014
Be patient.
A solution to the protein folding problem will contribute to understanding.
Synthesizing new and all existing proteins will be a new dilemma for humans.

The use of the word dilemma is misinformation. More like - new playground for learning.
Any folding issues must always consider chirality. Any subsequent observations must consider "mirror effect".
If you cannot wrap your head around these statements, then common-sense has left the building.
JVK
1 / 5 (4) Mar 01, 2014
If you cannot wrap your head around these statements, then common-sense has left the building.


I've seen no indication that common sense was ever here.

The substitution of achiral glycine in the GnRH decapeptide links nutrient-dependent pheromone-controlled reproduction in yeasts to what is supposedly 400 million years of ecological adaptations in vertebrates, which theorists think is mutation-driven evolution.

Do you know any theorists with enough common sense to incorporate what is known about the biophysical constraints on protein folding or fact that the earth probably has a spherical shape and may even orbit the sun?
JVK
1 / 5 (4) Mar 01, 2014
...you refuse to see the evidence for mutations contributing to evolution.


No, I've seen the evidence from population genetics and dismissed it because it is not experimental evidence. I keep telling you that scientific evidence is experimental evidence and that the absence of experimental evidence makes what you call evidence pseudoscientific evidence. The trouble here is your inability to make pseudoscientific evidence appear to be scientific evidence, when everyone else but Captain Stupid knows the difference. I included a link to alert you once again to the difference, and you ignored it.

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

Do you think that lactase persistence and skin pigmentation are due to mutations associated with monoallelic hemoglobin variants and sickle cell disease and mutation-driven evolution? Is there a model for that?
RealScience
5 / 5 (3) Mar 01, 2014
if natural selection is driving lactase persistence evolution in a place where people have no problems making vitamin D in their skin, then clearly the vitamin D and calcium explanation (known as the calcium assimilation hypothesis) isn't cutting it.

From the article you cite:
But in famine conditions, such as when crops fail, they are likely to have eaten all the fermented milk foods, leaving only the more high-lactose products. This would have caused the usual lactose intolerance symptoms such as diarrhea. Diarrhea in in healthy people is not usually life-threatening, but in severely malnourished individuals it certainly can be. So famine could have led to episodes of very strong natural selection favoring lactase persistence.

So the article you cite supports natural selection acting on pre-existing variety!

-continued-
RealScience
5 / 5 (3) Mar 01, 2014
-continued-

If the lactose tolerance variant were created directly by nutrients and pheromones, drinking milk would make one lactose tolerant. If it were produced by nutrient-dependent pheromone-controlled editing of genes, then milk drinkers' children would be lactose tolerant. Yet many people suffer from lactose intolerance in spite of parents who tried to drink milk.

So where does YOUR CITATION say the variation comes from? A MUTATION.
the mutation that causes lactase persistence in Europeans (LCT -13910*T

The article also support natural selection for this mutation:
… how much natural selection was needed to drive lactase persistence up to today's frequencies… they found that the answer was, "a lot"!

So AGAIN an article that YOU CITE supports natural selection FOR a mutation.

Open your eyes – the evidence you keep asking for is in the links that you cite!
Whydening Gyre
5 / 5 (2) Mar 01, 2014
No, I've seen the evidence from population genetics and dismissed it because it is not experimental evidence.

JVK
Not refuting what you see in your research (I've no doubt you are deeply schooled in it). But, isn't what you see in the population genetics evidence experimental - by nature/evolution/The Universe? Maybe you could try and step back and see relative to the bigger picture.
RealScience
5 / 5 (4) Mar 01, 2014
No, I've seen the evidence from population genetics and dismissed it because it is not experimental evidence...

As repeatedly pointed out, you ignore the experimental evidence, too, even in articles and papers that YOU cite.
I included a link to alert you once again to the difference, and you ignored it.

Contrary to what you seem to think, the entire universe does not revolve around you. My reply was delayed by DINNER. As you can see (or more likely as anyone who isn't blind can see), my reply shows that your link supports natural selection of pre-existing variety as well as once again supporting selection for mutation.
JVK
1 / 5 (3) Mar 01, 2014
...isn't what you see in the population genetics evidence experimental - by nature/evolution/The Universe?


Thanks for asking. No! Biophysical constraints prevent nature/evolution/The Universe from experimenting with mutations to see if perturbed protein folding can somehow be beneficial. Think of it this way. If you fry or boil an egg, is it still viable? Of course not. The perturbed protein folding does not allow that egg to contribute to evolution.

Maybe you could try and step back and see relative to the bigger picture.


Is there a big picture you see where you don't see any biophysical constraints on species diversity? Is there a model for that?

What do you think it means when I state in my most recent published work that "Members of the Society for Integrative and Comparative Biology (SICB) recently organized and held an ecological epigenetics symposium (January, 2013)."

Do you think I am the only researcher who understands cause and effect?
Whydening Gyre
not rated yet Mar 01, 2014
Is there a big picture you see where you don't see any biophysical constraints on species diversity? Is there a model for that?

Yes I do. And the model for it is us. And will happen according to a certain ratio - Phi. The only constraint is - time.
JVK
1 / 5 (3) Mar 01, 2014
Symposium: Ecological Epigenetics

http://www.sicb.o...tics.php

I'm convinced. No one else here realizes how ignorant they seem to be to anyone who has attended any scientific meeting in the past decade.

There is no evidence of intelligent life in this discussion and clear evidence that others cannot understand the basic principles of biology and levels of biological organization that enable the conserved molecular mechanisms of species from microbes to man to result in the diversity of species.

http://www.youtub...youtu.be
Whydening Gyre
5 / 5 (2) Mar 01, 2014
I'm convinced. No one else here realizes how ignorant they seem to be to anyone who has attended any scientific meeting in the past decade.

There is no evidence of intelligent life in this discussion and clear evidence that others cannot understand the basic principles of biology and levels of biological organization that enable the conserved molecular mechanisms of species from microbes to man to result in the diversity of species.


Haven't attended anything but funerals, weddings and art shows in the last decade. oh and a trip or two to the courthouse...
You are right. I'm just an under-educated simpleton who has no idea of the value of your immense conceptualizations. Please accept my apologies for intruding on your illusion.

Shall I try the Spicolli quote here?


JVK
1 / 5 (4) Mar 02, 2014
Please accept my apologies for intruding on your illusion.


Sarcastic apology accepted. What illusion? You obviously realized it is not MY illusion, since I linked to the SICB symposium and a video from my ISHE presentation, which was very similar to my June 2013 presentation to the Society for Behavioral Neuroendcrinology and November 2012 presentation at the Society for Social Neuroscience.

Clearly I have integrated and presented a large body of work to other scientists and challenged the current views of theorists with experimental evidence like the 100 or so cited works from my 2012 publication: Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors

http://www.socioa...38/20758

Cited works:
http://scholar.go...sdt=0,43

The reactions to experimental evidence here are typical of theorists.
JVK
1 / 5 (4) Mar 02, 2014
The importance of protein folding

http://www.youtub...st-vrecs

Protein folding is so important to function, that perturbations prevent mutation-driven evolution. However, there are biology teachers and there idiot minions who do not understand the importance of biophysical constraints on protein folding or anything else except the importance to them of continuing to believe in a ridiculous theory that has never been substantiated by experimental evidence; is not biologically plausible, and simply put is the most idiotic thing that serious scientists have ever considered.
JVK
1 / 5 (4) Mar 02, 2014
Nutrient-dependent pheromone-controlled ecological adaptations, for comparison, occur via epigenetic effects of odors on alternative splicings, which can be reported in terms of evolution -- when people are not familiar with the concept of ecological variation as the condition of life from which pheromone-controlled ecological adaptations arise.

http://jonlieffmd...volution
anonymous_9001
5 / 5 (4) Mar 02, 2014
The sickle cell hemoglobin is caused by one base alteration in the gene.

"Sickle-cell anaemia is caused by a point mutation in the β-globin chain of haemoglobin, causing the hydrophilic amino acid glutamic acid to be replaced with the hydrophobic amino acid valine at the sixth position"

What prevents a mutation from occurring in the same place as your alleged "nutrient-dependent phermone-controlled" base alteration?

You have not shown a causal link between whatever nutrient you claim caused sickle cell and the disease itself. If it were possible, you could take a sample population, feed them whatever you claim it is, and see the resulting change in all of them. This is the same logic as Lenski's experiment. If the presence of citrate caused the promoter movement, all of his populations would have shown the same change and it wouldn't have taken as long as it did. Why did only one of his populations evolve to use citrate if they were all identical? It can't be causal in that case.
JVK
1 / 5 (4) Mar 02, 2014
If it were possible, you could take a sample population, feed them whatever you claim it is, and see the resulting change in all of them.


Are you referring to the works that have demonstrated this in C. elegans, the honeybee model organism, or in mice?

Why do you think it's necessary to demonstrate it in every species on the planet? Is there an alternative model for species diversification? If not, why doesn't the model of conserved molecular mechanisms in species from microbes to man make sense to you.

Is it perhaps, no wait... let me guess.... Could it be that it doesn't make sense to you because YOU ARE an ANONYMOUS FOOL?
anonymous_9001
5 / 5 (4) Mar 02, 2014
If it's so apparent, it should be simple to answer. What nutrient caused the hemoglobin change and could you reliably repeat it in any given human? Why wasn't the citrate pathway evolution reliably repeatable in Lenski's populations?

There can't be a causal link if you don't get the same result with the same inputs in multiple trials when everything else is the same.
JVK
1 / 5 (3) Mar 02, 2014
There can't be a causal link if you don't get the same result with the same inputs in multiple trials when everything else is the same.


Then how did someone come up with the idea of mutation-driven evolution and get people to think that mutations cause the same result (e.g., species diversity) when everything else is the same?

RealScience
5 / 5 (3) Mar 02, 2014
If it were possible, you could take a sample population, feed them whatever you claim it is, and see the resulting change in all of them.


Are you referring to the works that have demonstrated this in C. elegans, the honeybee model organism, or in mice?


@JVK - are you confusing genetics and epigenetics YET AGAIN?

While many works have shown this for gene EXPRESSION changes, you have yet to cite any evidence that this happens for gene SEQUENCE changes. Which, to anyone not trying to be obstinate, is what 9001 is obviously referring to.

Then how did someone come up with the idea of mutation-driven evolution and get people to think that mutations cause the same result (e.g., species diversity) when everything else is the same?
Because that's what EXPERIMENTAL EVIDENCE shows. Lenski had to wait thousands of generations with billions of bacteria for a key mutation to occur once, but that mutation was selected FOR and spread.

-continued-
RealScience
5 / 5 (3) Mar 02, 2014
- continued -

That EXPERIMENTAL EVIDENCE matches the model.
Such events are individually rare, but because beneficial mutations are selected for, they accumulate. And this is ONE WAY that new species form (there are others, such as ecological speciation).

That's pretty basic genetics, and while it is valid it is only a small part of the evolutionary picture. In the short run epigentics, nutrients and pheromones play a bigger role (you used to do good work in that area until you started wasting your time denying reality and ignoring experimental evidence in your vain quest to banish mutations).

The experimental evidence shows that Natural Selection use mutations as ONE of its tools. Quit trying to pretend that it doesn't and go back to doing something useful. Find some experimental evidence that RNA/epigenetics sometimes predictably edit gene sequences - it should exist, and finding it would shake up the field and make a name for you.
JVK
1 / 5 (4) Mar 02, 2014
You continue to pretend that evidence from population genetics is experimental evidence.

This is experimental evidence:
Tra is a female-determinant protein that is translated only in females and stimulates splicing near its binding site on the primary RNA transcript (also known as precursor mRNA or pre-mRNA) (Nagoshi et al. 1988). Due to the presence or absence of Tra, the fru primary transcript derived from the most distal promoter is subjected to sexually dimorphic splicing...
http://dx.doi.org...4-0891-5

Experimental evidence shows that mutations and knock down of any genes currently known to effect male courtship activities reduce male courtship activities toward a female. I modeled the conserved molecular mechanisms that link nutrient-dependent pheromone-controlled ecological adaptations to sex differences in behaviors, which are negatively effected by mutations.

What experimental evidence suggests to you that mutations are beneficial?

RealScience
5 / 5 (4) Mar 03, 2014
What experimental evidence suggests to you that mutations are beneficial?

Most aren't, but some are.

As has been pointed out repeatedly, the experiment described in THE ARTICLE THAT WE ARE COMMENTING ON shows that some mutations are beneficial and were selected for.

I don't agree with everything in the article - for example, the mutations are characterized as 'random'. Even C14-decay-induced mutations (the subclass of mutations closest to random) are not truly random in either location or in genetic effect, and especially in how often they remain unrestored. 'Non-deterministic' would be a much more accurate term than 'random'.

But that doesn't change that after 59,000 generations of billions of bacteria, 45 de novo mutations had been incorporated into the genomes of Lenski's bacteria. And those mutations led to roughly 80% faster growth, confirming that at least some of the mutations are BENEFICIAL as well as SELECTED FOR.

And that, JVK, is EXPERIMENTAL EVIDENCE.
JVK
1 / 5 (4) Mar 03, 2014
...the mutations are characterized as 'random'... 'Non-deterministic'... after 59,000 generations... 45 de novo mutations had [automagically] been incorporated into the genomes... those mutations [automagically] led to roughly 80% faster growth, confirming that at least some of the mutations are [automagically] BENEFICIAL as well as [automagically] SELECTED FOR....that is EXPERIMENTAL EVIDENCE.


What null hypothesis was automagically refuted? Please ask someone slightly more intelligent that you (e.g., anyone) and continue up the ladder of increasing intelligence until someone tells you what explanation was refuted. You seem to imply that increasing organismal complexity and increasing intelligence are not due to nutrient-dependent pheromone-controlled ecological adaptations like those that obviously occur in every other species on the planet, which makes your ideas about experimental evidence based on something that automagically occurs in E.coli seem quite typically foolish.
RealScience
5 / 5 (3) Mar 03, 2014
What null hypothesis was automagically refuted?

YOUR hypotheses that mutations are NEVER beneficial, mutations are NEVER for, and that there are biophysical constrainst that prevent mutations from EVER being beneficial or selected for are all REFUTED by the EXPERIMENTAL EVIDENCE.

All it takes is one counter example to disprove such exclusive claims.

You seem to imply that increasing organismal complexity and increasing intelligence are not due to nutrient-dependent pheromone-controlled ecological adaptations


I imply nothing of the kind.

YOU are the person who seems to think that nature only uses ONE tool - that evolution using mutations would mean that it doesn't uses nutrient-dependent pheromone-controlled adaptations, and that evolution using nutrient-dependent pheromone-controlled adaptations would mean that it doesn't use mutation.
RealScience
5 / 5 (3) Mar 03, 2014
... experimental evidence based on something that automagically occurs in E.coli...

So you agree that selection for mutations occurs in E. coli?

(Or are you STILL ignoring the EXPERIMENTAL EVIDENCE from the experiment that this article is on?)
anonymous_9001
5 / 5 (4) Mar 03, 2014
45 de novo mutations had [automagically] been incorporated into the genomes


There's nothing "automagical" about replicative processes we know to be error prone.

those mutations [automagically] led to roughly 80% faster growth


In vitro evolution can be demonstrated with a wide variety of enzymes. For example- http://www.che.ca...1997.pdf

This shows an improvement in enzyme activity through purely random means. The same random sequence changes occur in vivo (although mutagenesis is designed to do it at a much faster rate).
JVK
1 / 5 (4) Mar 03, 2014
Biochemistry reveals the missing link in a pathway that archaea and some bacteria use to generate essential compounds.
http://www.the-sc...ost96983

The enzyme catalyzing the step preceding this event...


Does the fact that there MUST be an enzyme also attest to the likelihood that nutrient uptake links ecological factors to ecological adaptations sans mutations in all genera?

It seems to me that the complexity of conserved molecular mechanisms involved in the atoms to ecosystems biophysically constrained rate-limiting epigenetic effects of phosphate ions and elemental phosphorus are perhaps best exemplified when phosphate-contaminated water drains into lakes and causes problems with algal blooms that reportedly may kill dogs and cause illnesses in people.

Is there evidence of cause and effect that involves mutation-driven evolution across genera? If so, we might be able to save some dogs.
JVK
1 / 5 (4) Mar 03, 2014
This shows an improvement in enzyme activity through purely random means. The same random sequence changes occur in vivo (although mutagenesis is designed to do it at a much faster rate).


Sorry, I didn't see your post until after I posted on the clearly stated need for an enzyme (but not a mutation). Had I looked at your post first, I would have commented again on the fact that you are an anonymous fool who knows nothing about biologically based cause and effect because you have been taught to believe in a ridiculous theory.

But thanks again for trying to explain what automagically happens in your world.
JVK
1 / 5 (4) Mar 03, 2014
All it takes is one counter example to disprove such exclusive claims.


The gene, cell, tissue, organ, organ system model of nutrient-dependent pheromone-controlled increasing organismal complexity shows that whatever you think is a counter example in a unicellular organism is based on theoretical nonsense, not biological facts. Only an idiot would choose one level of investigation and proceed with thoughts that null hypothesis testing supported the ridiculous idea of mutation-driven evolution.
RealScience
5 / 5 (4) Mar 03, 2014
... experimental evidence based on something that automagically occurs in E.coli...


Is there evidence of cause and effect that involves mutation-driven evolution across genera?


So you agree that selection for mutations occurs in E. coli, and you are asking if this happens in general rather than just in E. coli?

(Or are you STILL ignoring the EXPERIMENTAL EVIDENCE from the experiment that this article is on?).

anonymous_9001
5 / 5 (4) Mar 03, 2014
This shows an improvement in enzyme activity through purely random means. The same random sequence changes occur in vivo (although mutagenesis is designed to do it at a much faster rate).


Sorry, I didn't see your post until after I posted on the clearly stated need for an enzyme (but not a mutation). Had I looked at your post first, I would have commented again on the fact that you are an anonymous fool who knows nothing about biologically based cause and effect because you have been taught to believe in a ridiculous theory.

But thanks again for trying to explain what automagically happens in your world.


Your refutation of the paper I posted is where, exactly?
JVK
1 / 5 (4) Mar 03, 2014
This shows an improvement in enzyme activity through purely random means. The same random sequence changes occur in vivo (although mutagenesis is designed to do it at a much faster rate).


Your refutation of the paper I posted is where, exactly?


Do not trouble me with the posting of papers published before the turn of the century. The refutations of such nonsense have been reported everywhere. You're not even living in the 21st century, are you? It's no wonder everything seems automagical to you and others. You probably haven't been taught anything new since the 1920's.

http://www.the-sc...ion-Age/

Another taxonomically broad comparison study, focused on amino acid metabolism, uncovered conserved biosynthetic pathways for 8 of the 20 canonical amino acids, and conserved enzymes from pathways for another eight (Genome Biology, 9:R95, 2008).
anonymous_9001
5 / 5 (4) Mar 03, 2014
The refutations of such nonsense have been reported everywhere.


Obviously not, or you would be able to offer references.

Do not trouble me with the posting of papers published before the turn of the century.


Evidence would invalidate it, not age in and of itself.
JVK
1 / 5 (4) Mar 03, 2014
I have cited an average of approximately 100 articles in my last 6 published works (1995, 1996, 2001, 2006, 2012, 2013).

If I did nothing else for the rest of my life, what I've already done is sufficient proof that you will never be more than an anonymous fool.

http://scholar.go...sdt=0,43

http://scholar.go...sdt=0,43

http://scholar.go...sdt=0,43

http://scholar.go...sdt=0,43
anonymous_9001
5 / 5 (4) Mar 03, 2014
I ask you for direct evidence and you throw your shoddily thrown-together papers at me that I've read multiple times that don't address what's being asked of you which contain citations that CERTAINLY don't mesh with your assertions.

Which ones support your assertions that mutations are not fixed and not utilized by natural selection? I want specifics.

While you're at it, take another try at telling us what makes directed changes to the genome (hint: it's not pre-mRNA).
RealScience
5 / 5 (3) Mar 03, 2014
I have cited an average of approximately 100 articles in my last 6 published works

Your papers are on nutrients pheromones and epigenetics rather than genetics, and none are in genetics journals - are you confusing genetics and epigenetics again?

Do even your own papers support your claim that mutations don't contribute to evolution because they are never selected for?

Which of your papers best shows experimental evidence that mutations don't contribute to evolution because they are never selected for?

Which of your papers best shows experimental evidence that there are biophysical constraints that prevent mutations from ever being selected for?

Which 3 of your 100 references best offer experimental evidence that mutations don't contribute to evolution because they are NEVER selected for?

Which 3 of your 100 references best show experimental evidence that there are biophysical constraints that prevent mutations from ever being selected for?

Give it your 8 best shots!
JVK
1 / 5 (4) Mar 03, 2014
http://medicalxpr...cer.html

"Carbohydrates aren't just telling you the type of cell they came from, but also by which process they were created," explains Mahal. "Our results showed that there are regulatory networks of miRNAs and that they are associated with specific carbohydrate codes."
RealScience
5 / 5 (3) Mar 03, 2014
"Our results showed that there are regulatory networks of miRNAs and that they are associated with specific carbohydrate codes."


No one on this thread has argued against RNAs, nutrients or even pheromones playing a role in adaptive evolution, so you appear to be confusing genetics and epigenetics YET again, JVK.

Or are you trying to change the subject so no one will notice that you have failed to provide any experimental evidence to support your position that mutations are never selected for?
Captain Stumpy
3.4 / 5 (5) Mar 03, 2014
Or are you trying to change the subject so no one will notice that you have failed to provide any experimental evidence to support your position that mutations are never selected for?

@RealScience
that is pretty much it...
IF he avoids giving you the specific ammunition to directly refute him and sink his pet theory, then he gets to stand and preach a little while longer about how we are all "fools" etc...
This is the work of PSEUDOSCIENCE
IF he actually gives you what you (and Anon) ask for, then he will also have to confront the knowledge that he is wrong, and this directly contradicts his world view... his psyche cannot handle it.
he is unstable as it is
he believes that he is intelligent (watch his wording/posturing)
when confronted with intellectual superiors, he must either back off or start throwing out jargon that is nonsensical again, or distract from the main argument

good luck... we are all watching yall destroy his argument
too bad he CANNOT LEARN
he had potential
anonymous_9001
5 / 5 (3) Mar 04, 2014
http://medicalxpress.com/news/2014-03-carbohydrates-coal-cancer.html

"Carbohydrates aren't just telling you the type of cell they came from, but also by which process they were created," explains Mahal. "Our results showed that there are regulatory networks of miRNAs and that they are associated with specific carbohydrate codes."


That has what to do with anything being discussed?
JVK
1 / 5 (4) Mar 04, 2014
http://medicalxpr...cer.html
"Carbohydrates aren't just telling you the type of cell they came from, but also by which process they were created," explains Mahal. "Our results showed that there are regulatory networks of miRNAs and that they are associated with specific carbohydrate codes."


That has what to do with anything being discussed?


It's about the nutrient-dependent de novo creation of different cell types in individuals of different species that anonymous fools, PZ Myers, and idiot minions like Captain Stupid and RealScience seem to think mutated into existence based on what they know about Lenski's experiments.

In my last published work, for example, I wrote: "..the epigenetic 'tweaking' of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the..."
JVK
1 / 5 (4) Mar 04, 2014
@RealScience
that is pretty much it...
IF he avoids giving you the specific ammunition to directly refute him and sink his pet theory, then he gets to stand and preach a little while longer about how we are all "fools" etc...


@Captain Stumpy:
Perhaps I failed to clarify the conditions of your participation here. You obviously are not a fool, like the anonymous fool. You are brain-damaged.

http://medicalxpr...oms.html

You should remind people of that from time to time, so that they understand why you can't understand anything about the biology of behavior.
JVK
1 / 5 (4) Mar 04, 2014
...you have failed to provide any experimental evidence to support your position that mutations are never selected for?


You've mentioned that before. It's beyond ignorant! No one can provide experimental evidence that something never happens. Experimental evidence shows what happens, not what doesn't.
Maggnus
3 / 5 (4) Mar 04, 2014
I can't get over the fact this thread is still going! I have to say how entertaining it is to read JVK's twists and weaves and dodges! He makes the most convoluted, back-tracking, circular arguments of any pseudo-scientist out there! I have to say, as snake oil love potion salesmen go, you have raised the bar!

Guys, you have to understand that there is nothing you can say that will sink into his delusional world, because he walks with God! He has his theory, and it explains how His hand guides the creation of species, so any evidence given in counter is blasphemy and not worthy of consideration.

You're all arguing against belief here, nothing you say will matter to him.
RealScience
5 / 5 (3) Mar 04, 2014
You've mentioned that before. It's beyond ignorant! No one can provide experimental evidence that something never happens. Experimental evidence shows what happens, not what doesn't.

So you ADMIT that you have no experimental evidence that mutations are never selected for.
In contrast to your ADMITTED LACK of experimental evidence to support your claim, you have repeatedly been presented experimental evidence that mutations ARE sometimes selected for (including the article that this comments thread is on).

And yet you, who INSISTS on experimental evidence elsewhere, are so convinced that this cannot happen that you WILLFULLY ignore any evidence that it does happen.
I can throw out results that appear to attest to mutations ...


Now that your lack of EXPERIMENTAL evidence has been established, do you have any non-experimental evidence that mutations are NEVER selected for by natural selection?
JVK
1 / 5 (4) Mar 04, 2014
He makes the most convoluted, back-tracking, circular arguments of any pseudo-scientist out there!


Convoluted?

Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors
http://www.socioa...38/20758

"The gene, cell, tissue, organ, organ-system pathway is a neuroscientifically established link between sensory input and behavior. Marts and Resnick (2007) stress the importance of this pathway in the context of a systems biology approach to pharmacogenomics. Naftolin (1981) stressed its importance to the understanding of sex differences. This pathway is sensitive to conditioning. Sensory input from an organism's environment activates and reactivates the pathway and causes changes in hormone secretion that condition hormone-driven behavior."

In my model, It doesn't get less convoluted than that. How do mutations cause behavior to change?
Captain Stumpy
3.4 / 5 (5) Mar 04, 2014
You are brain-damaged

@jvk
it never ceases to amaze me how you can argue that someone else is brain damaged because you are too stupid to understand your own lexicon
especially given that I learned most of it in high school!
As the article about Pseudoscience mentioned, it is the PSEUDOSCIENCE TROLL that uses language like
so that they understand why you can't understand anything about the biology of behavior
&
It's beyond ignorant!
&
and idiot minions like

it is apparent that you cannot LEARN from current information
it is apparent that you cannot UNDERSTAND your own lexicon
it is apparent that you cannot fathom the complexities involved (and this is probably due to failing out of college where you SHOULD have learned the basics)

Please, continue to attack anyone who disputes you...(YOU are the one not able to understand!)
I have predicted your responses and made over $400 dollars in the past month betting... I dont mind your BS at all

Maggnus
3.7 / 5 (3) Mar 04, 2014
In my model, It doesn't get less convoluted than that.
I know, and that's why it is hilarious that you just wrote this, and even more hilarious that you probably don't understand why it's hilarious!!!!!

PS I'll accept that $10.00 now Stumpy :D
Captain Stumpy
3.4 / 5 (5) Mar 04, 2014
Or are you trying to change the subject so no one will notice that you have failed to provide any experimental evidence to support your position that mutations are never selected for?

@RealScience
@Maggnus
@Anonymous_9001
please continue with the posts!
Not only are you teaching OTHERS how to deal with PSEUDOSCIENCE CRACKPOTS like jvk, but you are teaching anyone who comes to this thread (and others) about how to use LOGIC and SCIENCE to support the argument, instead of (like jvk) using personal conjecture and misplaced delusional hysteria to interpret studies in order to see exactly what they want regardless of the reality in front of them...

it might seem frustrating, guys, but it is beneficial to those who watch and read!

But mostly, I am making a KILLING betting on the stupidity of jvk

@Mag
about that $10...
erm... the check is in the mail? LMFAO
RealScience
5 / 5 (4) Mar 04, 2014
How do mutations cause behavior to change?


Since you need even the basics explained to you:

By changing the genetic sequence, which sometimes changes a regulatory region (and thus interacts with epigentics and the expression of a gene or even a whole genetic network) and sometimes changes the way a protein folds (and sometimes in doing so changes its interaction with nutrients and even your beloved pheromones).

Many of these changes are neutral, and most of the remained are detrimental.
Some of the changes affect behavior - for example, mutations in the FMR1 can cause hyperactive behavior.

With that settled, let's get back to the questions you appear to be trying to dodge:

Now that your lack of EXPERIMENTAL evidence (that mutations are never selected for by natural selection) has been established, do you have any non-experimental evidence that mutations are NEVER selected for by natural selection? If so, present your evidence.
JVK
1 / 5 (5) Mar 04, 2014
How do mutations cause behavior to change?


By changing the genetic sequence, which sometimes changes a regulatory region (and thus interacts with epigentics and the expression of a gene or even a whole genetic network) and sometimes changes the way a protein folds (and sometimes in doing so changes its interaction with nutrients and even your beloved pheromones).

Many of these changes are neutral, and most of the remained are detrimental.
Some of the changes affect behavior - for example, mutations in the FMR1 can cause hyperactive behavior.


Is there a model for that?

With that settled, let's get back to the questions you appear to be trying to dodge:


Nothing is settled until a biologically plausible model is ecologically validated by experimental evidence of biologically based cause and effect in species from microbes to man. You don't even have a biologically plausible model, since mutations perturb protein folding.
Captain Stumpy
3.7 / 5 (6) Mar 04, 2014
Nothing is settled until a blah blah blah folding

@jvk
so, what you are saying is:
you CANT PROVE that mutations are never selected for by natural selection
(BECAUSE THERE IS NO PROOF)
and you CANT PROVE that mutations are NEVER selected for by natural selection
(BECAUSE THERE IS NO PROOF)

so your reply is instead to babble and try to change the subject?

GOOD ONE!
that will REALLY TEACH US how smart you are!

if only there was a way to show us you were right...
OH YEAH! HOW ABOUT PRODUCING EVIDENCE!

Oh, wait... NEVER MIND!
YOU CANT!

Maybe it is because you dont understand WHY you are wrong?
we already KNOW that you dont understand the definition of Mutation, because you have already admitted that much...
what is next?

Try answering RealScience and Anon... maybe they can finally explain to you why your religious attempts to alter reality are wrong in the light of Science and proof

3...
2...
1...
RealScience
5 / 5 (5) Mar 04, 2014
Nothing is settled until a biologically plausible model is ecologically validated by experimental evidence of biologically based cause and effect in species from microbes to man.

Bull. To disprove a claim that something NEVER happens only requires ONE counter-example.
Similarly to prove that something CAN happen only requires ONE example.

Regarding FMR1 and:
Is there a model for that?

That it DOES happen is all the proof that is needed, but are you SERIOUSLY telling me that, with all your supposed expertise and your papers in NEUROSCIENCE journals you don't even know whether there is a model for how fragile-X mutations affect the brain?

-continued-
RealScience
5 / 5 (5) Mar 04, 2014
-continued-

You don't even have a biologically plausible model, since mutations perturb protein folding.

You keep saying that, but even leaving aside synonymous mutations that don't affect protein folding, you have not presented experimental evidence that perturbed protein folding prevents all mutations from being selected for.

So now that your lack of EXPERIMENTAL evidence (that mutations are never selected for by natural selection) has been established, do you have any non-experimental evidence that mutations are NEVER selected for by natural selection? If so, present your evidence.
RealScience
5 / 5 (5) Mar 05, 2014
JVK, you should learn from this.

You valued your MODEL more than the REALITY it is attempting to model, and ignored evidence from the real world when it conflicted with your model.

When this was pointed out, you demanded experimental evidence from people, yet when that was provided you ignored that too, claiming that such things can't happen and insulting those who provided the evidence.

And when asked for evidence to support your contention, you admitted that there could be no experimental evidence and you FAILED to provide ANY evidence.

Meanwhile you cited papers to support your contention, but when these were analyzed not a single one support you and many actively contradicted you.

Here's what you should learn:
1) Don't throw away evidence just because it conflicts with what you think you know.
2) When reality conflicts with your model, don't try to change reality!
3) A child-like curiosity is good, childish behavior is not
JVK
1 / 5 (5) Mar 05, 2014
What I've learned is that no matter how much experimental evidence is offered to refute a biologically implausible and ridiculous theory that has no ecological validity, the anonymous discussants here will refuse to believe anything they have not already learned to believe in.

Common sense dictates that ecological variation results in nutrient-dependent pheromone-controlled ecological adaptations that are manifested in species diversity in species from microbes to man.

Common sense, if you had any, would tell you to forget that you've been taught mutations somehow cause something and move forward as many others have done who are not idiots.
RealScience
5 / 5 (4) Mar 05, 2014
What I've learned is that no matter how much experimental evidence is offered to refute a biologically implausible and ridiculous theory that has no ecological validity.

No matter how much evidence? You have offer NO EVIDENCE AT ALL.
No one on this thread has argued against epigenetics, nutrients or pheromones playing a role, but that does not mean the mutations do not ALSO play a role.

And in spite of being asked repeatedly, you have offered NO EVIDENCE, experimental or otherwise, that mutations do not play a role. NONE.

the anonymous discussants here will refuse to believe anything they have not already learned to believe in.

It is you, JVK, who has refused to learn anything, even when presented with both experimental evidence AND evidence of natural selection in the real world.

Common sense, if you had any,would tell you that when evidence contradicts your model, you should update your model rather than denying the evidence.

-continued-
RealScience
5 / 5 (4) Mar 05, 2014
-continued-

But I am a very patient person, JVK, so I'll give you another chance.

Now that your lack of EXPERIMENTAL evidence, for your claim that mutations are never selected for by natural selection, has been established, do you even have any non-experimental evidence that mutations are NEVER selected for by natural selection?
If so, present your evidence.
anonymous_9001
5 / 5 (5) Mar 05, 2014
On the topic of second chances, I'll give James another chance as well (although this is probably the 20th chance he's gotten) to tell us what makes non-random, directed changes to the genome.

He insists deliberate nucleotide-resolution changes are made to the genome (despite it not being covered in his article, which I have read multiple times), but has refused to tell us what enzymatic pathway makes those changes. When I asked him this question on Myers' blog, he said that pre-mRNA makes those changes, which makes absolutely no sense, as mRNA is not an enzyme and does no such thing.
JVK
1 / 5 (5) Mar 05, 2014
The anonymous fool writes:
mRNA is not an enzyme and does no such thing.


I started this discussion with the following comment.

"...begun to mutate more quickly, and become more efficient at using the glucose in the solution where they're grown."

Isn't glucose dehydrogenase required for the use of glucose by E. coli? If so, what is the mutation that is supposedly responsible for organisms becoming more efficient at using glucose in the ecological environment where they are grown?


Glucose dehydrogenase is an enzyme. Participants here are idiots and the biggest idiots of all came here from PZ Myers blog. Clearly, his idiot minions will never become more than idiot minions.
RealScience
5 / 5 (4) Mar 05, 2014
@anon - I expect that there is a whole range of changes between almost random and deterministically directed. I've pushed JVK to look for this, but so far he hasn't provided anything. I even provided him a starter example (the link no longer seems to work, but Google will find it):

For example, in dms4-mutants of A. thaliana Sasaki et al document 35x to 150x amplification of mutations of the dms4 gene that restore its function, without a higher mutation rate in the rest of the genome.

A 150x specific acceleration in a restorative mutation is FAR from random, but it is still EVEN FARTHER from deterministic.

(But you are, of course, correct about mRNA splicing not changing gene sequences - that's just JVK confusing gene sequences and gene products again).
JVK
1 / 5 (5) Mar 06, 2014
"The intricate disguise of the swallowtail butterfly, which mimics the wing patterns of some toxic butterfly species, is controlled by a single gene, finds a study published1 in Nature today."

http://www.nature...-1.14820

"They couldn't fathom the idea that a single gene could do all of this," says Marcus Kronforst, an evolutionary biologist at the University of Chicago in Illinois, who led the latest study."
Captain Stumpy
3.7 / 5 (6) Mar 06, 2014
another chance

@RealScience
@Anonymous_9001
I enjoy your patience and persistence
Watch jvk's wording carefully. Note that there is a lack of comprehension of basic terminology as well as an inability to fully comprehend the implications of the studies that he/you post
this creates an anger feedback which manifests in lashing out with derogatory remarks like "idiot minion" or "fool" or "any idiot can see"
this is directly because he is being challenged on his own percieved "turf"
it is also because of his lack of comprehension issues as well as his known failures in the past
his identity is being attacked and he makes it personal- this also points to a religious styled system as he has a fixed belief that, even when challenged with empirical data, remains unaltered
what you are dealing with is a fanatical believer in a fringe idea
no matter HOW much empirical data/proof you throw at him
HE CANNOT COMPREHEND WHY HE IS WRONG
only that he is being attacked (in his mind)
Captain Stumpy
3.7 / 5 (6) Mar 06, 2014
cont'd
@RealScience
@Anonymous_9001
notice that he writes
The anonymous fool writes

&
Participants here are idiots and the biggest idiots of all came here from PZ Myers blog. Clearly, his idiot minions will never become more than idiot minions

This is the BEST EXAMPLE of a PSEUDOSCIENCE poster that I have ever found, really
the pseudoscience poster has a fanatical belief and reality is irrelevant, and given jvk's posts, you can see that he actually can't see the proof right in front of him
this intentional blindness is caused by the challenges to his belief
in a (perceived) threat, he resorts to name calling, attacks, & spamming posts
there may be NO REAL RELEVANCE to the post... he could link pics of fairy farts, but he actually believes that he is supported by the links he leaves
we are talking a complete inability to see/comprehend what is reality

this is his personal Jihad, as well
NO empirical data will convince him that his view is wrong
Captain Stumpy
3.7 / 5 (6) Mar 06, 2014
cont'd
@RealScience
@Anonymous_9001
lastly – given his functional ability to post, read, and that he actually does have some skill, it is most likely that his skewed perceptions are centered mostly around his inability to acquire an education in the past (a likely motivating factor) as well as his (apparent) mental problems
he truly believes that he is more intelligent than anyone else here
this is proven by his comments like
That's why I wrote: Educate yourself
&
I think that if you were not an idiot minion you might be able to understand what I have detailed in my model

notice how, when he perceives an attack, he tries to transfer his lack of education onto others?
The need to remain and prove his failed system is likely due to several causes, from mental disorder (diagnosed or not) and his fanatical belief, which his religion is now replaced with his model
Captain Stumpy
3.7 / 5 (6) Mar 06, 2014
cont'd
@RealScience
@Anonymous_9001
oops... this is the last post. Sorry...
There is no debate here. You simply continue to make unsupported claims as idiot minions always do

&
all the evidence of biologically based cause and effect that I have detailed

His justification for his fanaticism comes from the continued refute that you/others give, in that he likely believes that, because you are arguing against him, he must be right
it shows that he is aware of some science HOWEVER there is no real way to show him how he is wrong as it is already predetermined in his mind that he cannot be wrong
although he really is doing nothing but TROLLING it is hard to ignore really bad science, especially when it is so obviously wrong, like jvk's idiocy.
Just keep posting the FACTS and let jvk cry and pout. For every factual refute others can see/learn how to deal with TROLLS like him
THANKS GUYS
anonymous_9001
4.8 / 5 (4) Mar 06, 2014
The anonymous fool writes:
mRNA is not an enzyme and does no such thing.


I started this discussion with the following comment.

"...begun to mutate more quickly, and become more efficient at using the glucose in the solution where they're grown."

Isn't glucose dehydrogenase required for the use of glucose by E. coli? If so, what is the mutation that is supposedly responsible for organisms becoming more efficient at using glucose in the ecological environment where they are grown?


Glucose dehydrogenase is an enzyme. Participants here are idiots and the biggest idiots of all came here from PZ Myers blog. Clearly, his idiot minions will never become more than idiot minions.


Does glucose dehydrogenase make alterations to the genome? NO, it does not, so bringing that up is completely irrelevant. That has NOTHING to do with what I asked you. It's an extremely simple question.
JVK
1 / 5 (5) Mar 06, 2014
Does glucose dehydrogenase make alterations to the genome? NO...


Are you implying that your opinion about this matters? At what point does any anonymous fool begin to think their opinion about anything is important? You might just as well be a Captain Stumply clone. But wait.... maybe all of PZ Myers idiot minions are clones of PZ Myers. That would explain why they have no "real" names and no opinions that matter.

http://www.microb...citation

The effect of the N-terminal amino acids on the expression levels of a fungal FAD-dependent GDH in E. coli was shown in the US patent 7,741,100 [15]. Expression levels could be increased approximately 10-fold by deletion of the signal sequence of A. oryzae GDH.
RealScience
5 / 5 (4) Mar 06, 2014
Expression levels could be increased approximately 10-fold by deletion of the signal sequence of A. oryzae GDH.


@JVK:
The text you quote clearly says "levels could be increased ... by deletion of the signal sequence". So you are confusing a gene sequence change causing changes in enzyme levels with enzyme levels causing a gene sequence change.

@Anon - please be more specific in your wording.
I am sure that what you meant is "Does glucose dehydrogenase make alterations to the DNA SEQUENCE?" rather than the more general "genome", because even an epigenetic alteration would be an alteration to the genome under many definitions (and enzyme-to-epigenetic-alterations are well known).

JVK could have picked on your wording and found a counter-example, and could have used that to make it look like he knew what he was talking about. However JVK confused genetics and epigenetics again and answered what you meant to ask (and his answer also confused cause and effect).
anonymous_9001
5 / 5 (5) Mar 06, 2014
Are you implying that your opinion about this matters?


Not an opinion. These are facts.

I am sure that what you meant is "Does glucose dehydrogenase make alterations to the DNA SEQUENCE?"


Correct.
JVK
1 / 5 (5) Mar 06, 2014
Supergene Discovered in Lookalike Butterflies

A butterfly's varied disguises are controlled by variants of a single gene...

http://www.the-sc...erflies/

"Maybe this particular gene family, involved in sex determination throughout the animal kingdom, is also involved in making deer antlers or peacock tails."

That is not something that seems biologically plausible for constraint-breaking mutations to do. However, the idea that one gene family and biophysically constrained chromosomal rearrangements might be involved at the advent of sexual reproduction in unicellular organisms and also in the morphological and behavioral phenotypes of all species that sexually reproduce -- from microbes to man -- was unknowingly suggested in the context of Darwin's "conditions of life."

Dobzhanksy (1972) extended the idea to unbuttered flies http://www.scienc...64.short
anonymous_9001
5 / 5 (4) Mar 06, 2014
constraint-breaking mutations


What constraints do mutations supposedly break? Is there something that prevents them from happening even though we can watch them happen in vitro?
RealScience
5 / 5 (6) Mar 06, 2014
@JVK, you have said:
The biophysical constraints on protein folding ensure that mutations are not beneficial

However the butterfly article you just cited shows you to be wrong YET AGAIN:
These mutations change the way the doublesex protein folds. However, they do not affect the parts of the gene involved in separating the sexes, allowing it to retain its usual function while picking up a new role as a wing-pattern controller.

So your citation provides an example of mutations that perturbed protein folding, yet this does not stop them from having a benefit: picking up a new role as a wing-pattern controller.

So yet again YOUR OWN CITATION is evidence that you are wrong.
JVK
1 / 5 (6) Mar 06, 2014
So yet again YOUR OWN CITATION is evidence that you are wrong.


Your inability to understand the basic principles of biology and levels of biological organization required to link sensory cause to behavioral affect make it impossible for you to look beyond the mention of the word "mutations." I've repeatedly told you that's the problem with you and with PZ Myers' idiot minions.

Please feel free to continue this discussion in "The Scientist" comments section so that your nonsense can become globally known. I don't think you're reaching a wide enough audience or anyone who knows anything about cause and effect. Simply put, you're drawing too many annoying flies after the discussion has changed from being about E. coli to butterflies.

http://www.the-sc...ost97165
russell_russell
5 / 5 (1) Mar 08, 2014
@WB/JVK
The dilemma:
Synthetic protein will bypass "biophysical constraints" that naturally made protein succumb to during the time proteins carry out their function through folding.

This is independent of what "biophysical constraints" means to anyone defending or dismissing evolutionary "conditions" from any standpoint of genetics, epigentics, etc.

"Protein folding is so important to function, that perturbations prevent mutation-driven evolution. - JVC"

Whatever "perturbations" means here, synthetic protein will be "perturbation" insensitive - allowing "mutation-driven" evolution.

All commentators here are "mutation-driven" proponents.
Except JVC. Synthetic protein makes his assertion moot.

JVK
1 / 5 (4) Mar 08, 2014
http://freethough...-page-1/

see: "nothing in evolution makes sense except in the light of biology." Although the latter might be an exaggeration, an important gap is being filled by molecular understanding of the genesis of variation that confers the ability to evolve."

That leaves only PZ Myers and his idiot minions to champion their ridiculous theories when everyone else knows that ecological variation confers the ability to adapt -- not to mutate and "evolve" into another species.
JVK
1 / 5 (4) Mar 08, 2014
"nothing in evolution makes sense except in the light of biology."
excerpted from http://www.scienc...88.short

"nothing about evolution makes sense in the absence of the conserved molecular mechanisms of amino acid substitutions."
Excerpted from my response to PZ Myer's defamation of my character (see #15) http://freethough...-page-1/

Citations to support my claim, which is now the claim by otheres in the lastest issue of Science Magazine

Nutrient-dependent/pheromone-controlled adaptive evolution: a model http://www.socioa...53/27989

See also: Physiology is rocking the foundations of evolutionary biology http://ep.physoc....abstract
RealScience
5 / 5 (3) Mar 08, 2014
Your inability to understand the basic principles of biology ... make it impossible for you to look beyond the mention of the word "mutations"


Your inability to understand the basic principles of science, that what nature actually does trumps what your model says it should do, makes it impossible for you to even see that the articles you cite support that mutations contribute to evolution and thus conflict with your statements.

Since you have failed to show that anything I have said is wrong, yet multiple commenters in this thread have repeatedly shown that you are wrong, it is easy to see that it is you who is spouting nonsense.

To return to a question that you keep trying to dodge:
Now that your lack of EXPERIMENTAL evidence, for your claim that mutations are never selected for by natural selection, has been established, do you even have any NON-experimental evidence that mutations are NEVER selected for by natural selection?
JVK
1 / 5 (4) Mar 08, 2014
Does anyone else understand what this means? "Molecular biology and evolutionary biology have been separate disciplines and scientific cultures: The former is mechanistic and focused on molecules; the latter is theoretical and focused on populations."
http://www.scienc...88.short

RealScience thinks that I should be able to provide NON-experimental evidence that mutations are NEVER selected for by natural selection, because no one has provided experimental evidence that mutations are selected (or that it's even biologically plausible given what is known about biophysical constraints on ecological adaptations). For me, and most serious scientists, there has never been a question of whether you begin with what you observe in the context of population genetics and then do your best to explain it without experimental evidence to support your claims.

Serious scientists call that nonsense. RealScience thinks pseudoscientific nonsense is real science.
RealScience
5 / 5 (3) Mar 09, 2014
because no one has provided experimental evidence that mutations are selected


As has been pointed out many times, the experiment that article that we are commenting on is about provides experimental evidence that some mutations are selected for, and numerous other examples have been pointed out to you as well. So your statement above is WRONG.

In contrast, you have provided no evidence, experimental or otherwise, that mutations are never selected for.

So you make a claim that not only do you admit has no experimental evidence to support it up, but you have failed to produce ANY evidence to support it.
Furthermore both examples from nature and experimental evidence refute your claim.

You have said
Experimental evidence causes serious scientists to change their opinions

and
I can throw out results that appear to attest to mutations as the cause of adaptive evolution


So by your own admissions you are not a serious scientist.
JVK
1 / 5 (4) Mar 09, 2014
So by your own admissions you are not a serious scientist.


Thank you. When someone like you -- or any anonymous fool or idiot minion -- makes claims that I have admitted something, it attests only to their ignorance. What I have done is publish a series of papers that remove mutations from consideration and replace mutation-driven evolution with experimental evidence that ecological variation causes ecological adaptations in species from microbes to man via conserved molecular mechanisms.

Others, like me, claim that "nothing in evolution makes sense except in the light of biology." -- and they understand the need to address all aspects of molecular biology rather than simply arrive at the simple-minded conclusion that mutations are somehow selected.

You continue to attest to the power that people like PZ Myers hold over others who remain too ignorant of biology to ask questions during times when they are taught "evolution for dummies."
JVK
1 / 5 (4) Mar 09, 2014
http://dx.doi.org...35080556
"...mutations stimulated by stress, some of which allow adaptation to the stress. The emerging mechanisms of adaptive genetic change cast evolution, development and heredity into a new perspective, indicating new models for the genetic changes that fuel these processes."

Replace the word "mutations" with ecological adaptations, which are obviously induced by nutrient stress and social stress via conserved molecular mechanisms that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. Attempt to move forward based on what is currently known since Rosenberg wrote the above in 2001, which is the same year I co-authored the award-winning review Human pheromones: integrating neuroendocrinology and ethology http://www.nel.ed...view.htm -- required to exemplify "...new models for the genetic changes that fuel..." the processes of ecological adaptations.
RealScience
5 / 5 (4) Mar 09, 2014
When someone ... makes claims that I have admitted something, it attests only to their ignorance.

You said:
Experimental evidence causes serious scientists to change their opinions about cause and effect

You have also admitted that you throw our result (experimental evidence). To Aroc's presenting experimental results:
Together, these mutations result in dramatic increase in cell surface hydrophobicity, which in turn confers these yeasts the ability to float by surface tension

...
I'm just wondering how you can throw these results out...

On Jan. 25 2013 you replied:
I can throw out results that appear to attest to mutations as the cause of adaptive evolution because no evidence suggests that is possible.

So you admit that you throw out experimental evidence that something happens (which is experimental evidence that it must be possible) because you THINK that it is not possible.

So by your own statements you are not a serious scientist.
RealScience
5 / 5 (1) Mar 09, 2014
JVK - I see that your second post may lead to civil and productive discussion!

I will respond to it later today when I have time to give it the attention that civil discussion deserves.

JVK
1 / 5 (4) Mar 09, 2014
Sexy Science: Neanderthals, Svante Pääbo and the story of how sex shaped modern humans Tabitha M. Powledge | March 6, 2014 | Genetic Literacy Project

http://www.geneti...zSYVniSo

Lust must be in the genes. If not, ecological variation and ecological adaptations that led to nutrient-dependent pheromone-controlled differences in cell types at the advent of sexual reproduction in yeasts could be linked directly via conserved molecular mechanisms to sex differences in our response to human pheromones.
Captain Stumpy
3.4 / 5 (5) Mar 09, 2014
When someone like you -- or any anonymous fool or idiot minion -- makes claims that I have admitted something, it attests only to their ignorance

@jvk
are you illiterate or stupid?
He didnt make a claim, he provided your own words for you to see
What I have done is publish a series of papers

your papers do NOT do as you CLAIM
mostly because you cannot understand the definition of mutation, apparently
You continue to attest to the power that people like PZ Myers hold over others

and again... you cannot understand the basic lexicon of your field that you "publish" in and therefore you draw unwarranted conclusions based upon your ignorance, which, given the time you've had to "brush up" on the jargon, should be considered stupidity
Your own admission your model caused mutation (see your own Feb 19 post)
was this because you failed out of college?
Your comments are like saying we cant say what our own eye color is because we cant see it directly so only YOU can say
JVK
1 / 5 (4) Mar 09, 2014
I wrote:
Others, like me, claim that "nothing in evolution makes sense except in the light of biology." -- and they understand the need to address all aspects of molecular biology rather than simply arrive at the simple-minded conclusion that mutations are somehow selected.


That should not have been interpreted as an invitation issued to idiot minions like Captain Stumply to rejoin the discussion. Most others will recognize it is an invitation to discuss biological facts, which is what I've been trying to do. Staff sergeant Stumply, and others who are among PZ Myers' idiot minions may continue their attempts to disrupt intelligent discussion. Hopefully, others will join the discussion if only to help discourage the idiot minions. However, retired professional bowlers, and other retired professionals like them, may want to discuss nonsense with Sergeant Stumply elsewhere.

JVK
1 / 5 (4) Mar 09, 2014
unwarranted conclusions based upon your ignorance


" James Kohl...believes that pheromones may have a primary influence in setting up a person's basic sexual orientation. Other, more consciously perceived aspects of attractiveness, such as facial appearance, are attached to a person's basic orientation through a process of association during early postnatal life, according to Kohl. 35"

This model is attractive in that it solves the "binding problem" of sexual attraction. By that I mean the problem of why all the different features of men or women (visual appearance and feel of face, body, and genitals; voice quality, smell; personality and behavior, etc.) attract people as a more or less coherent package representing one sex, rather than as an arbitrary collage of male and female characteristics.

Gay, Straight, and the Reason Why: The Science of Sexual Orientation (p. 210)
http://www.amazon.com
Captain Stumpy
3.9 / 5 (7) Mar 09, 2014
That should not have been interpreted as an invitation issued

@jvk
then I guess its lucky for me that I dont care
given that you made a claim
When someone like you -- or any anonymous fool or idiot minion -- makes claims that I have admitted something, it attests only to their ignorance

that is DIRECTLY REFUTED by just reading the above posts
then it is my PEROGATIVE to point out your stupidity
especially when it is VERY RELEVANT to the conversation and to the thread
(given that you cannot fathom how your own posts only supported RealScience's arguments)
invitation to discuss biological facts, which is what I've been trying to do

THAT would be GREAT if you could only UNDERSTAND that you are not interpreting the results of said "biological facts" with anything coming close to accuracy
AS PROVEN ABOVE IN MULTIPLE POSTS
Captain Stumpy
3.7 / 5 (6) Mar 09, 2014
Staff sergeant Stumply, and others who are among PZ Myers' idiot minions may continue their attempts to disrupt intelligent discussion

@jvk
how did you know I was a SSG? Wow...musta been those pheromones
to continue: this is NOT an attempt to DISRUPT the discussion
but to point out that:
1- you lied
2- you still cannot comprehend the basic lexicon used by biologists
WHICH THEN TRANSLATES TO
how can you intelligently discuss the results of ANY biological study/paper/publication if you are talking apples to everyone else's oranges?
You are making claims based upon your faith/religion which is attempting to manipulate the data/proof and argue a point which is NOT proven, as well as change the definitions of words in order to make them more palatable/ amenable to your philosophy/religion
Captain Stumpy
4.2 / 5 (5) Mar 09, 2014
Hopefully, others will join the discussion if only to help discourage the idiot minions

@jvk
appeal to creationists will only get you more of the same, as they are the ones most likely to support your known claims given that they are, like you, attempting to discredit known science and cannot understand the basic science that is proven EVEN IN THE ARTICLE ABOVE YOU which you state BY REASON OF IGNORANCE is evidence is something that only exists in your fractured mind
However, retired professional bowlers, and other retired professionals like them, may want to discuss nonsense with Sergeant Stumply elsewhere

no nonsense here, ONLY SCIENCE
and observations of your promotions of PSEUDOSCIENCE as well as BULL

perhaps it is YOU who should go elsewhere, as you are trying to prove pseudoscience
given that your links only REINFORCE the current evolution theory, and you cannot understand them, perhaps you should visit creationists sites and push your beliefs there?
JVK
1 / 5 (3) Mar 09, 2014
The Science and Religion Dialogue
http://www.youtub...re=watch

Are any of the people featured in this series of videos among the creationists whose opinions you think are invalid when compared to your experimentally unsupported biologically implausible opinions?

See also: "The Changing Face of Evolutionary Thinking"
http://gbe.oxford...06.short

Again, however, as I suggested before, substitute ecological adaptation each time you read or hear the word "mutation" since there is no such thing as mutation-driven evolution -- except in the minds of people like PZ Myers and his idiot minions who have been taught to believe in a theory and ignore everything known about the basic principles of biology and levels of biological organization required to link sensory cause to behavioral affects in species from microbes to man.
RealScience
5 / 5 (3) Mar 09, 2014
JVK - the article that you linked in your second post this morning is a good article in an area of shared interest (the non-randomness of DNA sequence changes). It shows a ~100-fold increase in sequence changes, some of which are beneficial changes to the lac gene, in stressed bacteria.
However that increase in changes was spread throughout the genome rather than being targeted to the lac gene, so it is a non-random rate but still non-specific locations.

Stronger on-randomness is shown in http://www.ncbi.n...512138/, in which the increase in changes is restricted to the gene that can help the plant.

Another example would be:www.ncbi.nlm.nih....MC21821/
JVK
1 / 5 (5) Mar 09, 2014
RealScience

My published works detail how non-random epigenetic effects of nutrient stress and social stress on ecological adaptations occur via conserved molecular mechanisms. Please cite or link to anything in the current extant literature that suggests how mutation-driven evolution is biologically plausible in any species from microbes to man.

One of your links doesn't work, and the other is to an article published in 1999.
anonymous_9001
5 / 5 (5) Mar 10, 2014
One of your links doesn't work


Fixed by anyone who knows how to use the backspace key.

the other is to an article published in 1999


Irrelevant. Time alone does not nullify results.

My published works detail how non-random epigenetic effects of nutrient stress and social stress on ecological adaptations occur via conserved molecular mechanisms.


For emphasis:

EPIGENETIC effects


This isn't about epigenetic changes; this is about genetic changes, something your model does not address in any appreciable detail. Your paper does not cover how genetic sequence changes occur. The closest it comes is in the "An epigenetic continuum..." section where you say "The story begins with what was probably a nutrient-dependent variant allele..."

What suggests the variant was the result of a nutrient? What nutrient was it? By what mechanism did it cause the allele change? Your paper goes into no further detail about it.
JVK
1 / 5 (4) Mar 10, 2014
What suggests the variant was the result of a nutrient? What nutrient was it?


Thanks for asking. The variant was unequivocally the result of glucose and its metabolism since the molecular mechanisms of glucose metabolism are conserved across species from microbes to man.

By asking the question, which IS a stupid question -- no matter who tells you there is no such thing as a stupid question -- you offer everyone evidence that anonymous fools should not participate in any discussions of biological fact.

You cannot place anything into an epigenetic continuum because you believe in constraint-breaking mutations -- a theory that could only be accepted by biology teachers like PZ Myers and his idiot minions.

Anyone who is more intelligent that a nematode would have already realized they did not mutate into existence and that glucose is the nutrient that epigenetically effects morphological and behavioral phenotypes in species from microbes to man.

Again, thanks for asking.
anonymous_9001
5 / 5 (4) Mar 10, 2014
If glucose caused it, differentiation would be impossible because everything gets glucose, so every organism would have the same sequence change.

Same thing as the citrate metabolism evolution. If citrate *caused* the movement of the promoter, then all of Lenski's populations would have evolved the ability to use it. If it doesn't do it every time, then you can't link cause and effect.
JVK
1 / 5 (4) Mar 10, 2014
If glucose caused it, differentiation would be impossible...


Thanks for confirming that you are less intelligent than the grazing nematodes that become predatory nematodes with teeth based on what they eat.

My comment on Evolutionary Duality has been approved and is now live at
http://comments.s....1055-f,

Has anyone seen experimental evidence that suggests that the molecular mechanisms that enable species diversity are different in flies and butterflies?
JVK
1 / 5 (4) Mar 10, 2014
If citrate *caused* the movement of the promoter, then all of Lenski's populations would have evolved the ability to use it. If it doesn't do it every time, then you can't link cause and effect.


Thanks again for demonstrating less intelligence than a nematode.

What causes mutation-driven evolution? You seem to think that the same mutation is required ever time.

My comment on Combating Evolution to Fight Disease has been approved and is
now live at http://comments.s...1247472,

"Darwin probably anticipated the insemination of population genetics that led to the bastardization of his detailed observations in the "Modern Synthesis." He politely insisted that 'conditions of life' be considered before natural selection.

There are two 'conditions of life.' It is nutrient-dependent and pheromone-controlled. Rosenberg and Queitsch now note the work with Dobzhansky's rarely acknowledged claim: "I am a creationist and an evolutionist." ..."
RealScience
5 / 5 (3) Mar 10, 2014
Please cite or link to anything in the current extant literature that suggests how mutation-driven evolution is biologically plausible in any species from microbes to man.

One of your links doesn't work, and the other is to an article published in 1999.

Links to "Unusual Case of Apparent Hypermutation in Arabidopsis thaliana" seem unreliable, so I simply Google it and get a new link each time. The 1999 article is one of the first to show specific amplification of sequence change rates, and is still well worth reading.

As for mutation-driven evolution, I have repeatedly pointed out that I do not think that mutations typically drive evolution. Most creatures are quite well evolved to suit their current environments and so environmental changes drive most current evolution. However what are standardly defined as mutations do play a role, by contributing variety for natural selection to act on.

-continued-
RealScience
5 / 5 (3) Mar 10, 2014
-continued-

As for citations to show that selection for mutations is biologically plausible:

Plausibility is a matter of theory/models, and reality trumps models of reality so if something can be shown to happen, then any model that says that it is implausible is invalid or at best incomplete.

I cannot provide links or citations regarding the plausibility of what you refer to as mutations without knowing what you refer to as mutations.

Since you have not defined what you mean by mutations I can only go by the standard definition of DNA sequence changes, which I think is NOT what you refer to. And numerous studies, such as Lenski's, show that what are standardly called mutations are indeed sometimes selected for.
JVK
1 / 5 (4) Mar 10, 2014
As for citations to show that selection for mutations is biologically plausible:

Plausibility is a matter of theory/models


Enough of your nonsense! You change "biologically plausible" to plausibility, which makes biological facts irrelevant because plausibility becomes a matter of theory.

Either you're not bright enough to understand the difference between theory and biological facts or you're intellectually dishonest.
russell_russell
not rated yet Mar 11, 2014
http://phys.org/n...ion.html

Here are your mentors. Their approach is beyond reproach.
JVK
1 / 5 (3) Mar 11, 2014
@russell_russell

Thanks.

@WB/JVK All commentators here are "mutation-driven" proponents.
Except JVC. Synthetic protein makes his assertion moot.


Whose assertion does synthetic protein make moot?

Whose approach is beyond reproach?

What does biologically plausible mean to YOU? Does it mean that if you can either induce a mutation or synthesize a protein then that's obviously the way that mutation-driven works?

If so, you can comfortable contribute virtually any comment to this discussion and claim that your opinions are supported by experimental evidence, which is precisely what people like PZ Myers and his idiot minions have done despite the experimental evidence in my published works and evidence like this.

RealScience
5 / 5 (3) Mar 11, 2014
As for citations to show that selection for mutations is biologically plausible:

Plausibility is a matter of theory/models


Enough of your nonsense! You change "biologically plausible" to plausibility, which makes biological facts irrelevant because plausibility becomes a matter of theory.

Either you're not bright enough to understand the difference between theory and biological facts or you're intellectually dishonest.


Or YOU are not bright enough to realize that 'plausibility' includes 'biologically plausible'.

Since you seem to have trouble with understanding written English, I'll spell it out:

I cannot provide links or citations regarding whether what you refer to as mutations are biologically plausible without knowing what you refer to as mutations.

However numerous studies, such as Lenski's, show that what are standardly called mutations are indeed sometimes selected for.

(I even politely left the door open for your non-standard definition of mutations.)
JVK
1 / 5 (4) Mar 11, 2014
What mutations are selected for in these flies or in any other species on this planet?

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

"...the first hint that a heritable trait—differences in ovariole number—might be linked with phenotypic plasticity came when they put flies on a starvation diet. some flies seemed to notice the change in their food supply virtually overnight, while others responded far more slowly."

http://rspb.royal...abstract

"This demonstrates that a plastic response conserved across animals can underlie the evolution of morphological diversity, underscoring the potential pervasiveness of plasticity as an evolutionary mechanism."

If you continue to suggest to anyone more intelligent than a nematode that mutations somehow lead to species diversity, you will look less like an idiot minion if you can supply any experimental evidence to support your ridiculous claim.
Maggnus
5 / 5 (3) Mar 11, 2014
What mutations are selected for in these flies or in any other species on this planet?


http://www.scienc...13004674

JVK
1 / 5 (4) Mar 11, 2014
Pretending to know something about this again, aren't you. Why not stay out of it until you learn what's pertinent. I established the context for my question:

What mutations are selected for in these flies or in any other species on this planet?


This idiot minion responds with a meaningless reference and no context as if ....

"One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering"

...could be meaningfully interpreted in the context of this discussion.

When all else fails, and you have no more intelligence than a nematode -- toss garbage into the discussion (to see if others will think you are an intelligent being instead of just another worm).
RealScience
5 / 5 (3) Mar 11, 2014
What mutations are selected for in these flies or in any other species on this planet?

A model that says that something NEVER happens only needs a single counter example to prove it wrong.

The article that this comments thread is on shows multiple mutations being selected for in E. coli, and E. coli is a species on this planet. Therefore the part of your model that says that mutations are never selected for IS WRONG.

I've left the door open on several occasions for you to have a non-standard definition of mutations that somehow includes only mutations that cannot be selected for (in which case you could possibly be guilty merely of linguistic error rather than scientific error), but since you haven't presented such a definition by now, it is pretty obvious that you don't have a reasonable definition to present.

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