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

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


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JVK
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?


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.

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.

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
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?

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.

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...

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?

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?

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?

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...

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
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
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).

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
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.

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

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.

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
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.

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.

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
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?

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
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
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?

Feb 18, 2014
This comment has been removed by a moderator.

JVK
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

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
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
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
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.

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
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.

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.


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
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.

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.


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

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
Feb 18, 2014
From Fertilization to Adult Sexual Behavior (1996) Hormones and Behavior was my first co-authored review.

JVK
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
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!


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
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
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.

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.


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
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
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.

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?

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%.

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
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.

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
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.

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
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!

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
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

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
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.

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.

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
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...."

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 –

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 –

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!

Feb 19, 2014
Good catches RealScience.

JVK
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..."

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...

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
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
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?

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.

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.

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

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
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
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.

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
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?

Feb 20, 2014
None of that says splicing alters the genome.

cjn
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
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
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
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
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?

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 -

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
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
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
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
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
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
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?

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.

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
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
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.

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
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
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.

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.

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 –

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

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 –

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

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!

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
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
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.

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".

Feb 21, 2014
sorry for interrupting RealScience


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


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.

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


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."

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?

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
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.

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
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.

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...

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.

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

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
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
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.

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

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
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
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."

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.

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
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
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
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.

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.

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-

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?

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
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
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.

Feb 22, 2014
Has anyone ever asked their biology teacher what caused the change in the nucleotide sequence...?


It's certainly not splicing.

JVK
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
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...?

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
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.

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

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!

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?

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).

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

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


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
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

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
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
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
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
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
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
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
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
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
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
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
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.

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
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.

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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].

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!

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-

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
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?

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

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
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)"

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
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
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.

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-

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
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/

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
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

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).