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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: SoldierDad
And this claim is based on . . .? What evidence? Conjecture yet again!

He was merely giving an example of the math involved, to demonstrate how the statements "A given life form is unlikely to be fossilized" and "an extensive fossil record exists" are not contradictory.

Try this: Any given person is very unlikely to be born with two differently-colored eyes. However, the fact that so many people have been born throughout history means that there is a huge pool of people who have, indeed, had such.

Makes sense? If you don't understand this example, say something other than "Conjecture!"
281 posted on 10/08/2006 9:55:44 PM PDT by aNYCguy
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To: aNYCguy

Okay. Old news. We've moved on to more important matters.


282 posted on 10/08/2006 10:09:10 PM PDT by SoldierDad (Proud Father of a 10th Mountain Division Soldier fighting in Mahmudiyah)
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To: caffe
"Well, I believe if you actually study all the evolutionary theories , for example, the specific topic of this post, punctuated equilibria, you will understand my assertion."

You didn't answer my question. Could you be please more specific?

Again, why do you believe that support for intelligent design is more scientific than that of evolution?
283 posted on 10/08/2006 10:14:49 PM PDT by Boxen (Branigan's law is like Branigan's love--Hard and fast.)
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To: Boxen

again, why don't you study how they support their evidence; it's junk science. If you want specific examples ...tell me. If you want me to pick examples of how unscientific their science is, I will . However, I know what will happen. You will then go into circular thinking and bring other issues into the one assertion i'm using as an example ....So why don't you give me a great example of their great scientific proofs?

I won't respond tonight as it's too late for scientific inquiry. lol


284 posted on 10/08/2006 10:35:11 PM PDT by caffe (W)
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To: caffe

Evidence, indeed.

/sarcasm


285 posted on 10/08/2006 10:37:23 PM PDT by unspun (What do you think? Please think, before you answer.)
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To: SoldierDad

Sorry. I must have missed the post where you understood.


286 posted on 10/08/2006 10:55:27 PM PDT by aNYCguy
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To: caffe
"again, why don't you study how they support their evidence; it's junk science."

This is a non-answer. It doesn't tell me why you believe that support for intelligent design is more scientific than that of the theory of evolution.

"If you want me to pick examples of how unscientific their science is, I will."

Please.

"However, I know what will happen. You will then go into circular thinking and bring other issues into the one assertion i'm using as an example"

It's good to know that I'm being judged for actions that I've yet to commit.

"So why don't you give me a great example of their great scientific proofs?"

Off the top of my head: EVIDENCE FOR INVERSION POLYMORPHISM RELATED TO SYMPATRIC HOST RACE FORMATION IN THE APPLE MAGGOT FLY, RHAGOLETIC POMONELLA, from the March 2003 issue of Genetics. If you'd like, I can obtain the full text PDF for you.
287 posted on 10/08/2006 11:32:11 PM PDT by Boxen (Branigan's law is like Branigan's love--Hard and fast.)
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To: aNYCguy; SoldierDad
orry. I must have missed the post where you understood.

It doesn't exist. Curiously SoldierDad claims to have studied evolution at college level, yet appears to have done so without learning anything about it, such is his manifest incomprehension of what the theory says. He has claimed that no evidence for the theory exists. When presented with an avalanche of such evidence, including lists of numerous successful predictions made using the theory he handwaves it away, as if it will cease to exist if he makes sure that he doesn't try to understand it.

Truly ignorance is curable, but the afflicted have to desire the cure.

288 posted on 10/08/2006 11:33:56 PM PDT by Thatcherite (I'm PatHenry I'm the real PatHenry all the other PatHenrys are just imitators)
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To: elmer fudd

Exactly. By default you almost have to believe in a higher being (God). Where did he come from? It makes me think that our brains cannot comprehend and gives even more credence to believe in God.


289 posted on 10/09/2006 4:32:21 AM PDT by ItisaReligionofPeace
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To: caffe
To compare Scientology to ID is well, just as ridiculous, as saying man evolved from apes.

Both are religious movements deceptively masquerading as something else. Don't believe me? Tell me this... who was the most vocal when Dover, PA, threw the school board out for pushing in ID? That is right, Pat Robertson. And what did he say? If God punishes you don't expect anyone to help. Now why would he think God would punish Dover, PA, for throwing out ID? Why would Pat Robertson even care about this if ID is just a "Science".

You are not fooling anyone, ID is Creationism re-packaged for public schools. Period.

ID has tons of brilliant scientists who support their evidence more scientifically than so called "evolutionary scientists."

With all due respect, you are either flat out lying or you believe all the propaganda that they feed you. There are a small handful of people, some claiming to be scientists and some that are, that support ID. But an exceptionally small number.

In addition, it is never scientific to say that an "Unknown Intelligence" did something. If you think that is science, then I sincerely have pity on you.

It's also true that most American people agree with me.

It's also true that most Americans cannot point out where Asia is on a map, or where Afghanistan is, or who is the Secretary of State. I am not surprised that "most Americans" agree with you.

As for a detailed discussion of the science, try reading all the other threads on these topics or perhaps go buy some ID books or books that go into huge detail about the evolving lies of evolution .

Oh I have read the online literature of the Discovery Institute and I am not about to support their cause by buying their books. Who exactly do you think you are fooling? ID is a religion backed way to push the teaching of Creationism into schools. Do you really expect me to believe that "an unknown intelligence" doesn't equal God? Is an "unknown intelligence" EVER a valid scientific answer? Guess what... the answer is "No".

290 posted on 10/09/2006 6:38:43 AM PDT by trashcanbred (Anti-social and anti-socialist)
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To: caffe
You appear to be an ID supporter and you claim that there are "brilliant scientists" who support ID. The most prominent credentialled biologists supporting ID are Behe, Denton, and Meyer. They are all on record endorsing the following in their published books and articles (and Behe endorsed the following under oath at the Dover trial):

Presumably as an enthusiastic supporter of the brilliant scientists who support ID you can fully endorse all of those positions. They reflect your views on the matter, don't they?

291 posted on 10/09/2006 6:56:18 AM PDT by Thatcherite (I'm PatHenry I'm the real PatHenry all the other PatHenrys are just imitators)
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To: Thatcherite
Is creationism really faith-based? Of course it is. There's nothing wrong with that, but there's nothing scientific about it either. Imagine a competent scientist from Japan or India or some other place where no one studied the creation account in Genesis (or its Islamic counterpart). If he were to honestly and systematically consider the objectively verifiable evidence in reaching scientific conclusions, then:

a. it would never occur to him that the world is only 6,000 years old [How Old is the Earth];

b. it would never occur to him that there had been a miles-deep global flood about 3,000 years ago [The Geologic Column and its Implications for the Flood];

c. it would never occur to him that all species lived at the same time [The Fossil Record: Evolution or "Scientific Creation"]; and

d. he would inevitably conclude that all species are related by common descent, and that the relationships are becoming more clear all the time [Tree of Life Web Project ].


292 posted on 10/09/2006 7:15:27 AM PDT by PatrickHenry (Unresponsive to trolls, lunatics, fanatics, retards, scolds, & incurable ignoramuses.)
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To: Thatcherite
Amazing how some seem able to put words into the mouths of others. When exactly did I make the "claim" that evidence for ToE doesn't exist? Uou said: He has claimed that no evidence for the theory exists.

Not exactly the same thing as saying that I find the evidence lacking in specificity regarding fossilized transitionals which would demonstrated conclusively that one species of animal "evolved" into another distinctly different species, now is it? I get what the theory is claiming, but don't buy all the huey. Please do not put your words in my mouth.

293 posted on 10/09/2006 7:34:51 AM PDT by SoldierDad (Proud Father of a 10th Mountain Division Soldier fighting in Mahmudiyah)
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To: PatrickHenry

After reading the article, my initial impression is that there is an underlying assumption built-in that MACRO-EVOLUTION has indeed happened.

Given this assumption, of course they are bound to find some data that can be used as evidence for this theory.

The question of course is this -- WHAT IF MACRO-EVOLUTION (speciation) DID NOT HAPPEN ? How would this result then be interpreted ?

My second thought is that there is STILL no credible mechanism for driving punctuated equilibrium. In the end, this theory maintains, in the face of all OTHER observations, that one sort of animal will rapidly change into another sort of animal ( or apes to men ), for no apparent reason and by means that are completely obscure.

It's bad enough trying to find a mechanism to drive
conventional evolution by microsteps; As of today, the fossil record completely contradicts evolution by microsteps. The myriads of transitional forms that there
ought to be according to the Darwinian theory simply do not exist. Hence Punctuated equilibrium was conceived ( foremost proponent being Stephen Jay Gould) to "explain" the evidence of STASIS in our fossil records.

I am at this point in time, not sure if punctuated equilibriun is an even more impossible theory that is used to replace it.

Now, regarding this :




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.



Of course these trees are CURRENT MODELS used to describe a theory. Some people would call it a nice idea or invention. This was constructed to show that life higher up the tree really did evolve from life further down it.
The theory was conceived, and then the tree built to support the theory. These trees are constructed on the assumption that macroevolution has happened.

Here is another assumption :



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.




So, we go to the crux of the matter --- ASSUMPTIONS AGAIN.
It's ALL assumption and maybe. This a very similar to the scholastic disputes about how many angels could dance on a pin head.

FINALLY, THIS STATEMENT




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.




Well what can I say ?

Here he has probably switched to talking about observable natural selection, which of course isn't the same thing as evolution of one kind of creature from another.

The nature of such changes IS NOT SPECIATION AT ALL but restriction of the gene pool, leading to a loss of genetic
information. This leads, for example, to cretinism in isolated human populations, or to the many different breeds of dog. In fact in all such cases observed, greater specialisation leads to a decreased overall ability to survive.

I'm not sure of this is as earth-shaking a discovery as some would want it to be.





294 posted on 10/09/2006 7:44:11 AM PDT by SirLinksalot
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To: EternalVigilance
It really isn't nice for you to put words in my mouth. Obviously, that isn't what I said. Is that sort of inaccurate portrayal of easily determined fact an example of your honesty in handling facts that aren't so easy to discern?

Given your post 49, you may want to revisit your feigned indignation here about "inaccurate portrayals."

295 posted on 10/09/2006 8:09:06 AM PDT by atlaw
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To: SoldierDad

I didn't say you were ignorant. I do think you are badly mistaken about what the theory of evolution actually states, and you attempted to make a point by mischaracterizing nature of evolutionary theory.

If you feel ignorant because you were shown to be mistaken, that's your business.


296 posted on 10/09/2006 8:11:18 AM PDT by Professor Kill
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To: SoldierDad
Amazing how some seem able to put words into the mouths of others. When exactly did I make the "claim" that evidence for ToE doesn't exist? Uou said: He has claimed that no evidence for the theory exists.

This is the internet, not some bar-room where you can shoot the breeze and deny you said stuff later and no-one can prove it.

Not exactly the same thing as saying that I find the evidence lacking in specificity regarding fossilized transitionals which would demonstrated conclusively that one species of animal "evolved" into another distinctly different species, now is it? I get what the theory is claiming, but don't buy all the huey. Please do not put your words in my mouth.

Your words, in that link, responding to a brief exposition of the theory of evolution: "Grand theory with absolutely no empirical evidence to support it." There is in fact an avalanche of such evidence. But you metaphorically shut your eyes, put your hands over your ears, and start chanting "La, La, La, I can't hear you." whenever it is presented. The molecular evidence and fossil evidence are crushing independently. If we just had either on its own it would be case closed (as indeed it was already regarded as case closed by biologists prior to the molecular data coming in over the last decade or so). But in fact we've got both; and they both say the same thing.

297 posted on 10/09/2006 8:17:48 AM PDT by Thatcherite (I'm PatHenry I'm the real PatHenry all the other PatHenrys are just imitators)
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To: Thatcherite
But in fact we've got both; and they both say the same thing.

That just proves the conspiracy. Besides, there isn't any evidence!
</creationism mode>

298 posted on 10/09/2006 8:20:36 AM PDT by PatrickHenry (Unresponsive to trolls, lunatics, fanatics, retards, scolds, & incurable ignoramuses.)
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To: PatrickHenry

What evidence have the biologists ever produced for us. They know nothing!

Well, there is the biogeographical distribution of the fossil record.

Yeah, Ok, but apart from that, what OTHER evidence have the biologists ever produced?

Yeah, pretty much nothing, apart from loads of startling predictions of the location of fossil finds, what strata they'd be found in, and subtle predictions of their morphology.

......

......

OK, apart from ERV predictions that precisely match the assumption of common descent, Linneous' observation that all life falls into a nested hierarchy, the continuing confirmation that the fossil record also falls into the same nested hierarchy with modern forms at the tips of the tree, the neatly arranged location of fossils in appropropriate strata so that they appear in sequences, numerous geographical predictions of fossil finds that match the assumption of modern descent and plate tectonics, the numerous successful predictions of modern species behaviour and distribution that bear out the idea of natural selection, the discovery of ring species in the actual act of speciation, startling detailed predictions like the baleen transitions and fresh-salt water transitions in the sequence leading to modern cetaceans, the marvellous sequences of recent fossil hominids, the correlation of numerous dating methods with all of the above, what evidence have the biologists ever presented that the theory of evolution is true?

I'll tell you. ABSOLUTELY NONE!


299 posted on 10/09/2006 8:30:10 AM PDT by Thatcherite (I'm PatHenry I'm the real PatHenry all the other PatHenrys are just imitators)
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To: Thatcherite

300


300 posted on 10/09/2006 8:31:44 AM PDT by PatrickHenry (Unresponsive to trolls, lunatics, fanatics, retards, scolds, & incurable ignoramuses.)
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