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Genetic evidence for punctuated equilibrium
The Scientist ^ | 06 October 2006 | Melissa Lee Phillips

Posted on 10/07/2006 9:08:18 AM PDT by PatrickHenry

Evidence for punctuated equilibrium lies in the genetic sequences of many organisms, according to a study in this week's Science. Researchers report that about a third of reconstructed phylogenetic trees of animals, plants, and fungi reveal periods of rapid molecular evolution.

"We've never really known to what extent punctuated equilibrium is a general phenomenon in speciation," said Douglas Erwin of the National Museum of Natural History in Washington, D.C., who was not involved in the study. Since its introduction by Stephen Jay Gould and Niles Eldredge in the 1970s, the theory of punctuated equilibrium -- that evolution usually proceeds slowly but is punctuated by short bursts of rapid evolution associated with speciation -- has been extremely contentious among paleontologists and evolutionary biologists.

While most studies of punctuated equilibrium have come from analyses of the fossil record, Mark Pagel and his colleagues at the University of Reading, UK, instead examined phylogenetic trees generated from genetic sequences of closely related organisms.

Based on the number of speciation events and the nucleotide differences between species in each tree, the researchers used a statistical test to measure the amount of nucleotide divergence likely due to gradual evolution and the amount likely due to rapid changes around the time of speciation.

They found statistically significant evidence of punctuated evolution in 30% to 35% of the phylogenetic trees they examined. The remaining trees showed only evidence of gradual evolution.

Among the trees showing some evidence of punctuated equilibrium, the authors performed further tests to determine the size of the effect. They found that punctuated evolution could account for about 22% of nucleotide changes in the trees, leaving gradual evolution responsible for the other 78% of divergence between species.

Pagel and his colleagues were surprised that rapid evolution appears to contribute so much in some lineages, he said. "I would have maybe expected it to be half that much," he told The Scientist.

The researchers also found that rapid bursts of evolution appear to have occurred in many more plants and fungi than animals. Genetic alterations such as hybridization or changes in ploidy could allow rapid speciation, Pagel said, and these mechanisms are much more common in plants and fungi than in animals.

"Their result is pretty interesting, particularly the fact that they got so much more from plants and fungi than they did from animals, which I don't think most people would expect," Erwin told The Scientist.

However, it's possible that the analysis could be flawed, because the authors didn't take into account extinction rates in different phylogenetic trees when they determined the total number of speciation events, according to Douglas Futuyma of the State University of New York at Stony Brook, who was not involved in the study. But "they've got a very interesting case," he added. "I certainly think that this warrants more attention."

According to Pagel, the results suggest that other studies may have misdated some evolutionary events. Dates derived from molecular clocks assumed to have a slow, even tempo will place species divergences too far in the past, he said, since genetic change assumed to take place gradually may have happened very quickly.

"These kinds of events could really undo any notion of a molecular clock -- or at least one would have to be very careful about it," Futuyma told The Scientist.

Well known evolutionary mechanisms could account for rapid genetic change at speciation, Pagel said. Speciation often takes place when a population of organisms is isolated, which means that genetic drift in a small population or fast adaptation to a new niche could induce rapid evolutionary change.

=======
[Lots of links are in the original article, but not reproduced above.]


TOPICS: Culture/Society; Philosophy
KEYWORDS: crevolist; junkscience; ntsa; obsession; punctuatedidiocy; speculation
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To: Professor Kill

" believe the scientific theory of evolution explains how human beings came to have their current form. I'm not going to explain the entire theory to you, but the very short version states that natural selection forces a change in the frequency of alleles within a population from one generation to the next. These changes give rise to all the biological diversity we see around us, including human beings. "

Perhaps you can't explain the theory . Your statement is a simple illusion. I call it inventive natural selection. It's certainly not science: it makes no predictions and is untestable. So, let's play and not shift back and forth between naive and inventive natural selection. If you can demonstrate that Natural selection makes predictions..please share. It does not predict that adaptations are inevitable, nor even possible.

You've drank the lemonade and are content with a lie.

If you are going to confuse population genetics with natural selection. I must tell you that they are distinctly separate bodies of theory. Survival of the fittest is intended as a general theory of survival. It claims to predict the magnitude of differential survival based on biological design. Population genetics does not claim to make that prediction. Population genetics does not tell which alleles will survive until you first tell population genetics about the differential survival of the allele pairs.
Just for your information....


441 posted on 10/12/2006 10:57:11 AM PDT by caffe (W)
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To: caffe
It's certainly not science: it makes no predictions and is untestable

Actually, it has had stupendous success in predicting genetic distribution.

It does not predict that adaptations are inevitable, nor even possible.

Really? Do you know anyone that has been treated for tuberculosis?

Population genetics does not tell which alleles will survive until you first tell population genetics about the differential survival of the allele pairs.

Perhaps you *think* that sentence imparts some type of useful information, but it does not. It is nonsense, and carries no meaning whatsoever.

Sir, I'm not going to try to explain a scientific theory to someone that is willfully ignorant of what the theory actually states. You choose to ignore the evidence, misstate the science, and draw specious conclusions based on arguments no one is making. All of that is your choice, of course, and you remain free to believe in whatever creation myth you choose. If your belief system is so fragile, however, that it depends on the willful ignorance of science, I feel very sorry for you.

You didn't answer my question, by the way. How do *you* think human beings came to have their present form?

442 posted on 10/12/2006 11:51:05 AM PDT by Professor Kill
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To: Professor Kill

again, your confusing population genetics with natural selection theory. Population genetics predicts the genetic consequence of differential survival. It does not tell which alleles will survive until you first tell population genetics about the differential survival of the allele pairs. Must I continue to give you elementary lessons on the difference between population genetics and natural selection?

Survival of the fittest is not within population genetics. Survival of the fittest is intended as a general theory of survival. It claims to predict the magnitude of differential survival based on biological design. Population genetics does not claim to make that prediction.

One is a science, the other sir, is NOT!!
Now , let's keep it simple.......do you or do you not agree with what i've said? If not...then why?

Once you understand that population genetics is not natural selection, it will eliminate alot of problems. If you don't, I can continue and show you , in population genetics own scientists words, that they understand the difference.

I'm a woman.......

If you don't understand the relevance, then you frankly don't understand whatever discussion we're trying to have.


443 posted on 10/12/2006 1:03:54 PM PDT by caffe (W)
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To: caffe
Here is small piece of advice, madam. If you are going to remain willfully ignorant about a basic scientific theory that is supported by the overwhelming bulk of data and is accepted by the overwhelming bulk of scientists around the world, it is not particularly convincing to give lectures on your misinterpretation of science, particularly when that lecture is woefully inaccurate.

Population genetics

The study of both experimental and theoretical consequences of mendelian heredity on the population level, in contradistinction to classical genetics which deals with the offspring of specified parents on the familial level. The genetics of populations studies the frequencies of genes, genotypes, and phenotypes, and the mating systems. It also studies the forces that may alter the genetic composition of a population in time, such as recurrent mutation, migration, and intermixture between groups, selection resulting from genotypic differential fertility, and the random changes incurred by the sampling process in reproduction from generation to generation. This type of study contributes to an understanding of the elementary step in biological evolution. The principles of population genetics may be applied to plants and to other animals as well as humans.

McGraw-Hill Encyclopedia of Science and Technology. Copyright © 2005 by The McGraw-Hill Companies, Inc. All rights reserved.

Now, I believe you *still* have not answered my question. Would you care to do so now, madam?

444 posted on 10/12/2006 1:18:50 PM PDT by Professor Kill
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To: Professor Kill

It is quite obvious you have no concept of what i've attempted to share with you. You give me a dictionary definition? I'm addressing your post that confuses population genetics and natural selection. Do you not understand the difference?
Population genetics uses a parameter called fitness - defined in terms of suvival. It has no relationship to 'survival of the fittest'
population genetics is about 'differential survival of genotypes' and evolutionists call this 'natural selection.
this gives the erroneous impression that natural selection is within the machinery of population genetics. Differential survival is lame because it does not try to explain adaptation.
population genetics uses the term selection as a shorthand for either natural selection or differential survival. so this one word, selection, can lead to a tautology or lame formulations.
If we exclude this misuse of terminology, then population genetics is scientific and its findings do not contradict ID or creationists.

I can tell you have no understanding of this issue...so perhaps you could just share one macro evolutionary fact that would contradict ID or creationists. Let's keep it simple.
You should be able to come up with something. One fact that supports natural selection? survival of the fittest?
You get the idea? More of man's cousins? LOL Also, could you support this fact with the research?


445 posted on 10/12/2006 3:32:36 PM PDT by caffe (W)
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To: caffe
Who is confusing population genetics with natural selection!? One is an area of study, and the other is the mechanism by which successful adaptations are selected. The only one confused here is you, madam. No one, least of all me, is claiming that these terms are interchangeable.

And by the way, natural selection isn't a "theory"--it is an observed mechanism by which evolution occurs. You need to stop throwing around significant terms if you don't know their actual meaning.

Once again, madam, you have avoided answering a very direct question. How do you think human beings came to have their present form? I answered your question directly, but for some reason you haven't extended the same courtesy.
446 posted on 10/12/2006 6:05:47 PM PDT by Professor Kill
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To: Professor Kill

Courteous placemarker


447 posted on 10/12/2006 6:42:20 PM PDT by Jaguarbhzrd
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To: Professor Kill

you are the one who is deeply confused. i'm rather bored talking to someone who does'nt say anything. I'm tired of dealing with people like you who throw around terms and have no understanding of the definitions or the science. You simply have a little formula and rely on that without knowing how shallow is your understanding.

I refuse to even try and have another conversation with you. Your name should be changed to Professor Dead because you really have nothing of substance to say.


448 posted on 10/12/2006 9:18:58 PM PDT by caffe (W)
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To: caffe

Madam, you again failed to answer the question.

I answered your question directly and honestly, yet for some reason you won't even attempt to answer the same question.

How do you think human beings came to have their current form?


449 posted on 10/12/2006 9:30:20 PM PDT by Professor Kill
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To: caffe

From the Dover transcript, Behe being examined by a friendly lawyer.

It is hard to format this so I'll put it in a post on its own.

1 Q. I want to return to Ernst Mayr and ask you
2 are the parts of Darwin's theory as he's listed
3 here well tested?
4 A. No, they are not. If you look at the
5 top ones, evolution as such, common descent,
6 multiplication of species, those are all well
7 tested. The claim of gradualism is in my
8 opinion rather mixed. There's evidence for,
9 and some people argue against it. But the
10 component of Darwin's theory natural selection
11 which is sometimes viewed as the mechanism that
12 Darwin proposed for evolution is very poorly
13 tested and has very little evidence to back
14 it up.
24 15 Q. I want to go through in a little bit more
16 detail on some of these claims. Going back to
17 that first claim, and I believe you testified
18 probably akin to an empirical observation, is
19 that correct?
20 A. Yes, evolution as such that the world
21 is changed over time, and life as well.
25 22 Q. Does intelligent design refute the
23 occurrence of evolution?
24 A. No, it certainly has no argument with this
25 component of Darwin's theory. As a matter of
19
1 fact I think there is a, on the next slide
2 there's an excerpt from Of Pandas and People
3 where the authors write, "When the word is used
4 in this sense, that is the sense of change over
5 time, it is hard to disagree that evolution is a
6 fact. The authors of this volume certainly have
7 no dispute with that notion. Pandas clearly
8 teaches that life has a history, and that the
9 kinds of organisms present on earth have changed
10 over time." And let me make the point that
11 Ernst Mayr calls this component evolution as
12 such. That is the basic idea of evolution.
26 13 Q. So when you hear a claim that intelligent
14 design is anti-evolution, are those accurate?
15 A. No, they are completely inaccurate.


Here is another one:

Q. I'm sorry. I'm pointing to down here, and that's
-- you're not that good a mind reader. Now bacteria had
been on the Earth for billions of years, correct?
A. That's right.

And another one:

Q. Okay. And no human laboratory can duplicate all
of the selective pressures that have existed in the
billions of years that bacteria have been around?
A. That's correct. So we can't rule out all
explanations. We have to investigate to see what are
likely.



450 posted on 10/13/2006 12:18:30 AM PDT by Thatcherite (I'm PatHenry I'm the real PatHenry all the other PatHenrys are just imitators)
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To: caffe
From Behe's book, "Darwin's Black Box":

For the record, I have no reason to doubt that the universe is the billions of years old that physicists say it is. Further, I find the idea of common descent (that all organisms share a common ancestor) fairly convincing, and have no particular reason to doubt it.

Spin it how you like, despite his attempts to hand the age of the universe off to experts in other fields, Behe is a molecular biologist, and as such is aware of the mountains of bio-molecular evidence that clearly indicates common descent and the billion-year duration of life on earth (and the earth can hardly be younger than life on it is ;) ). He is an expert talking about his own field of expertise, and he is the foremost brilliant ID scientist. In his own work he repeatedly talks of the billions of years over which the bio-molecular processes he observes the modern results of have been operating.

Michael Denton is another case. He started by doubting evolution, and even wrote "Evolution, A Theory in Crisis" in 1986 in which he expounded many of the standard creationist arguments and clearly rejected evolution. By 1993 however as he learned more, and as the crushing genomic data came in he had reversed himself in his book, "Nature's Destiny" (added emphasis mine):

One of the most surprising discoveries which has arisen from DNA sequencing has been the remarkable finding that the genomes of all organisms are clustered very close together in a tiny region of DNA sequence space forming a tree of related sequences that can all be interconverted via a series of tiny incremental natural steps

That is the definition of evolutionary common descent! Denton's entire thrust by then had reversed itself. So convincing is the molecular data for common descent that he is now a total advocate, and says that evolution is an inevitable result of God's grander design of the universe.

So, do you agree with these brilliant ID scientists who have used their specific scientific knowledge to infer that evolution has occured, and that life on earth is an ancient phenomenon, or do you disagree with their scientific conclusions?

451 posted on 10/13/2006 12:34:23 AM PDT by Thatcherite (I'm PatHenry I'm the real PatHenry all the other PatHenrys are just imitators)
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To: caffe; Thatcherite
Again, I support all of the specific scientific research of ID scientists. Behe, for example, simply focused on specific biochemical "machines" and revealed design not chance.

No he didn't. He didn't do any "specific scientific research" which "revealed" any such thing.

He did however say that since he couldn't personally see how something might have evolved, he couldn't imagine any other possibility than design. But that shaky line of "reasoning" is a far different thing entirely from "specific scientific research" which "revealed design not chance". And by the way, evolutionary processes are not "chance", even though they do have a stochastic component.

452 posted on 10/13/2006 1:07:18 AM PDT by Ichneumon (Ignorance is curable, but the afflicted has to want to be cured.)
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To: Thatcherite

Your posting is as good as anybody elses with respect to the matter at hand. I'm fairly certain that you feel honored to have been "tapped" as you have been (and you have been).

The "punctuated equilibrium" theory of Niles Eldredge and Stephen Jay Gould was proposed as a criticism of the traditional Darwinian theory of evolution.

Eldredge and Gould observed that evolution tends to happen in fits and starts, sometimes moving very fast, sometimes moving very slowly or not at all (its unclear upon just what those conclusions were based upon though). Oh, I know, fossils are just like chemistry: you put two together and you get a new one.

On the other hand, typical variations that are infered from the fossil record tend to be quite small. Darwin saw evolution as a slow, continuous process, without sudden jumps. However, if you study the fossils of organisms found in subsequent geological layers, you will see long intervals in which nothing changed ("equilibrium"), "punctuated" by short, revolutionary transitions, in which species became extinct and replaced by wholly new forms. Instead of a slow, continous progression, the evolution of life on Earth seems more like the life of a soldier: long periods of boredom interrupted by rare moments of terror.

Clearly Darwin's theory is beyond reproach based on evidence infered to fit the theory.

FYI: my original target will also be "tapped". I just so happened to see you on my way "there".


453 posted on 10/13/2006 1:45:51 AM PDT by raygun (Whenever I see U.N. blue helmets I feel like laughing and puking at the same time.)
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To: Ichneumon

your comments only reinforce your total ignorance


454 posted on 10/13/2006 7:14:06 AM PDT by caffe (W)
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To: LibertarianSchmoe

You have poor reading comprehension skills. Or you're simply dishonest.

Nothing in my abbreviated quote of the founders alters their thought one iota.

You're like our current crop of lawyers and judges. You refuse to comprehend simple words, because those words blow away your humanistic myths.


455 posted on 10/13/2006 1:08:43 PM PDT by EternalVigilance ("We hold these truths to be self-evident, that all men are created..." - Thomas Jefferson et al)
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To: EternalVigilance

Revitalization bump.


456 posted on 10/13/2006 9:27:03 PM PDT by stultorum (dont hire illegal aliens)
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ID-is-ignorance placemarker.


457 posted on 10/14/2006 6:23:20 PM PDT by balrog666 (Ignorance is never better than knowledge. - Enrico Fermi)
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To: EternalVigilance
You have poor reading comprehension skills. Or you're simply dishonest.

What a model creationist you are. YOU dishonestly alter the words of one of the founders and then call ME dishonest for calling you on it. YOU believe that dropping words from sentences does NOT change their meaning and then accuse ME of having poor reading comprehension.

Nothing in my abbreviated quote of the founders alters their thought one iota.

More BS. MORE dishonesty. So, Thomas Jefferson included words that he didn't need to? Ol' TJ (and that shoddy wordsmith Ben Franklin) wasn't very precise in his wording? Gosh, if only he'd had the superior writing skills of EternalVigilance on hand when he was drafting the Declaraion...

458 posted on 10/16/2006 7:39:40 AM PDT by LibertarianSchmoe ("...yeah, but, that's different!" - mating call of the North American Ten-Toed Hypocrite)
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To: LibertarianSchmoe

Why are you ignoring the simple self-evident fact that if our rights come from the Creator, we had to have had one?


459 posted on 10/16/2006 10:29:33 AM PDT by EternalVigilance ("We hold these truths to be self-evident, that all men are created..." - Thomas Jefferson et al)
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To: EternalVigilance
I'm not. I'm addressing the more important issue of you twisting the words of Jefferson for your own selfish reasons. You know you're doing it. The word you chose to leave off, "equal", is the operative word in that sentence. "All men are created" has a completely different meaning than "All men are created equal". Jefferson was pointing out the equality of men. This was the self-evident truth to which he refered. You are fixated (as all zealots are) on pushing your agenda, and (again, like all good zealots) believe that you can do no wrong in the service of that agenda.

"Hi, my name is EternalVigilance, and I'm a quote-minaholic". Admit you have a problem, EV. It's the first step.

460 posted on 10/16/2006 10:52:21 AM PDT by LibertarianSchmoe ("...yeah, but, that's different!" - mating call of the North American Ten-Toed Hypocrite)
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