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Intelligent Design Theory: Science or Religion?

 
 
wandeljw
 
  1  
Wed 13 Jun, 2007 08:57 am
I apologize for double posting but I wanted to use this article to start off a new page.

Quote:
One Scientist's Junk Is a Creationist's Treasure
(Catherine Shaffer, Wired.com, 06.13.07)

Without your "junk DNA" you might be reading this article while hanging upside down by your tail.

That's one of the key findings of the opossum genome-sequencing project, and a surprising group is embracing the results: intelligent-design advocates. Since the early '70s, many scientists have believed that a large amount of many organisms' DNA is useless junk. But recently, genome researchers are finding that these "noncoding" genome regions are responsible for important biological functions.

The opossum data revealed that more than 95 percent of the evolutionary genetic changes in humans since the split with a common human-possum ancestor occurred in the "junk" regions of the genome. Creationists say it's also evidence that God created all life, because God does not create junk. Nothing in creation, they say, was left to chance.

"It is a confirmation of a natural empirical prediction or expectation of the theory of intelligent design, and it disconfirms the neo-Darwinian hypothesis," said Stephen Meyer, director of the Center for Science and Culture at the Discovery Institute in Seattle.

Advocates like Meyer are increasingly latching onto scientific evidence to support the theory of intelligent design, a modern arm of creationism that claims life is not the result of natural selection but of an intelligent creator. Most scientists believe that intelligent design is not science. But Meyer says the opossum data supports intelligent design's prediction that junk DNA sequences aren't random, but important genetic material. It's an argument Meyer makes in his yet-to-be-published manuscript, The DNA Enigma.

Scientists have made several discoveries about what some call the "dark matter of the genome" in recent years, but they say the research holds up the theory of natural selection rather than creationism.

In May 2007, Stanford scientists identified more than 10,000 "snippets" of DNA that are not genes but have been conserved across species throughout evolution.

When genes are conserved through natural selection, it's usually because they have important functions. In this case the researchers believe the DNA snippets are associated with early development.

"We are saying it's functional because we observe this trajectory of a hundred million years," said Gill Bejerano, an assistant professor of developmental biology and computer science at Stanford and co-author of the paper on the 10,000 DNA snippets. "If you disbelieve this process, then from your perspective, we haven't found anything interesting in the genome."

Geneticist Susumu Ohno coined the phrase "junk DNA" in his 1972 paper, "So Much 'Junk' DNA in our Genome." Four years later, Richard Dawkins published The Selfish Gene, which popularized the idea that genes are the basis of evolutionary selection. Any DNA that was not actively trying to get to the next generation -- namely junk DNA -- was slowly decaying away through mutation, Dawkins wrote.

With scientists increasingly believing that so-called junk DNA regulates other genes, among other functions, creationists like Michael Behe, a biochemistry professor at Lehigh University in Pennsylvania and author of the controversial new book on intelligent design, The Edge of Evolution, are more than happy to point out their errors.

"From the very beginning Darwinism thought whatever it didn't understand must be simple, must be nonfunctional," Behe said. "It's only in retrospect that Darwinists try to fit that into their theory."

Part of the difficulty in studying junk DNA is that it's impossible to prove a negative, i.e., that any particular DNA does not have a function.

That's why T. Ryan Gregory, an assistant professor in biology at the University of Guelph, believes that nonfunctional should be the default assumption. "Function at the organism level is something that requires evidence," he said.

Many scientists, including Francis Collins, author of The Language of God and director of the National Human Genome Research Institute, believe that "junk" may have been an overstatement from the beginning.

Collins is known for believing in both evolution and God, but he stops short of using junk DNA as proof of God as the master of creation.

"I've stopped using the term," Collins said. "Think about it the way you think about stuff you keep in your basement. Stuff you might need some time. Go down, rummage around, pull it out if you might need it."

"Obviously 'junk' is pretty much a colloquial term," said Stanford's Bejerano. "There's no scientific definition of what is junk."
0 Replies
 
spendius
 
  1  
Wed 13 Jun, 2007 02:13 pm
wande quoted-

Quote:
Since the early '70s, many scientists have believed that a large amount of many organisms' DNA is useless junk.


That's oxtail soup wande. No seasoning.

Stephen Hawking wrote-

Quote:
In effect, we have redefined the task of science to be the discovery of laws that will enable us to predict events up to the limits set by the uncertainty principle.


I presume he means that beyond those limits irreducible complexity kicks in.
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cicerone imposter
 
  1  
Wed 13 Jun, 2007 02:22 pm
No. It simply means scientists have not been able to produce enough evidence to support the ideas presented - for now. It's only uncertain for now. It's somewhat similar to trying to find a cure for cancer or alzheimer's.
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farmerman
 
  1  
Wed 13 Jun, 2007 03:05 pm
Thats the part of the genome that I quoted a paper that adopted the term "fossil DNA" for the sections that preserved these once functioning but now relict snippets.
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spendius
 
  1  
Wed 13 Jun, 2007 03:34 pm
c.i. wrote-

Quote:
It's somewhat similar to trying to find a cure for cancer or alzheimer's.


It's not only not similar it's nothing like it.
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cicerone imposter
 
  1  
Wed 13 Jun, 2007 03:58 pm
spendius wrote:
c.i. wrote-

Quote:
It's somewhat similar to trying to find a cure for cancer or alzheimer's.


It's not only not similar it's nothing like it.


Please explain why "it's not similar?"
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spendius
 
  1  
Wed 13 Jun, 2007 04:58 pm
You must be kidding c.i.

Read Spengler. Carefully. Slowly. Takes a few years. It's not a novel. It's not entertainment. Follow up the leads.

Tunisia is like going on another ride at the fairground.
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cicerone imposter
 
  1  
Wed 13 Jun, 2007 05:09 pm
spendi, I'm not here to read anything you suggest as reading matter. If you are unable to provide a summary of what he wrote that relates, why did you even bother to read it yourself? Do you even have a grasp of what he wrote? I doubt it.
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spendius
 
  1  
Wed 13 Jun, 2007 05:24 pm
Spengler wrote the summary old boy. He made it as short as he could. Surely you don't think I would recommend you reading a woffler. wande quotes enough of them.

Your problem seems to be that you think easy answers are available for your appraisal just like that.

You'll be asking for a summary of the Bible next. In 100 words of no more that three syllables.
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cicerone imposter
 
  1  
Wed 13 Jun, 2007 05:30 pm
spendi, I'd ask for a summary on a Archie comic book before I ask anyone to summarize the bible for me. You made the statement "It's not only not similar it's nothing like it." Now, explain it. Too tough for you? Quit making stupid statements if you're unable to back it up - yourself. Spengler surely didn't give the answer you did.
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wandeljw
 
  1  
Thu 14 Jun, 2007 09:33 am
NEW BOOK FROM MICHAEL BEHE

Quote:
Michael Behe's The Edge of Evolution: The Search for the Limits of Darwinism
(Book Review by Sean B. Carroll, Science Magazine, June 8, 2007)

"The Lord hath delivered him into mine hands."

Those are the words that Thomas Huxley, Darwin's confidant and staunchest ally, purportedly murmured to a colleague as he rose to turn Bishop Samuel Wilberforce's own words to his advantage and rebut the bishop's critique of Darwin's theory at their legendary 1860 Oxford debate. They are also the first words that popped into my head as I read Michael J. Behe's The Edge of Evolution: The Search for the Limits of Darwinism. In it, Behe makes a new set of explicit claims about the limits of Darwinian evolution, claims that are so poorly conceived and readily dispatched that he has unwittingly done his critics a great favor in stating them.

In Darwin's Black Box: The Biochemical Challenge to Evolution, Behe had forwarded the notion that certain biochemical systems were "irreducibly complex," could not have evolved stepwise by Darwinian mechanisms, and thus were intelligently designed. Since that earlier book, Behe has played a key role in the intelligent design (ID) movement, including a star turn as a defense witness in the 2005 Dover school board case. Despite his testimony--or, I should say, partly because of what he said -- ID was ruled to be a religious concept and its teaching in public schools unconstitutional.

Behe, a professor of biochemistry at Lehigh University, has found an audience among various flavors of creationists who find Darwinian evolution incompatible with their religious views and see scientific validation in Behe's claims. Clearly, this book's main audience would be that constituency, although they will find some parts very discomfiting. For instance, Behe explicitly accepts the ability of random mutation and selection to account for the variation within and differences between closely related species (but not higher taxa such as vertebrate classes). He also accepts (as he has before) the 4.5-billion-year age of Earth and that we share a common ancestor with chimpanzees. That certainly won't go over well in some camps.

Behe also explores some examples of Darwinian evolution at the molecular level, including an extensive treatment of the evolutionary "trench warfare" fought between humans and malarial parasites over the millennia--all in the context of what Darwinian evolution "can do." So what's the problem?

The problem is what Behe asserts Darwinian evolution can't do: produce more "complex" changes than those that have enabled humans to battle malaria or allowed malarial parasites to evade the drugs we throw at them. Behe's main argument rests on the assertion that two or more simultaneous mutations are required for increases in biochemical complexity and that such changes are, except in rare circumstances, beyond the limit of evolution. He concludes that "most mutations that built the great structures of life must have been nonrandom." In short, God is a genetic engineer, somehow designing changes in DNA to make biochemical machines and higher taxa.

But to arrive at this conclusion, Behe relies on invalid assertions about how genes and proteins evolve and how proteins interact, and he completely ignores a huge amount of experimental data that directly contradicts his faulty premises. Unfortunately, these errors are of a technical nature and will be difficult for lay readers, and even some scientists (those unfamiliar with molecular biology and evolutionary genetics), to detect. Some people will be hoodwinked. My goal here is to point out the critical flaws in Behe's key arguments and to guide readers toward some references that illustrate why what he alleges to be beyond the limits of Darwinian evolution falls well within its demonstrated powers.

Behe's chief error is minimizing the power of natural selection to act cumulatively as traits or molecules evolve stepwise from one state to another via intermediates. Behe states correctly that in most species two adaptive mutations occurring instantaneously at two specific sites in one gene are very unlikely and that functional changes in proteins often involve two or more sites. But it is a non sequitur to leap to the conclusion, as Behe does, that such multiple-amino acid replacements therefore can't happen. Multiple replacements can accumulate when each single amino acid replacement affects performance, however slightly, because selection can act on each replacement individually and the changes can be made sequentially.

Behe begrudgingly allows that only "rarely, several mutations can sequentially add to each other to improve an organism's chances of survival." Rarely? This, of course, is the everyday stuff of evolution. Examples of cumulative selection changing multiple sites in evolving proteins include tetrodotoxin resistance in snakes, the tuning of color vision in animals, cefotaxime antibiotic resistance in bacteria, and pyrimethamine resistance in malarial parasites--a notable omission given Behe's extensive discussion of malarial drugresistance.

Behe seems to lack any appreciation of the quantitative dimensions of molecular and trait evolution. He appears to think of the functional features of proteins in qualitative terms, as if binding or catalysis were all or nothing rather than a broad spectrum of affinities or rates. Therefore, he does not grasp the fundamental reality of a mutational path that proteins follow in evolving new properties.

This lack of quantitative thinking underlies a second, fatal blunder resulting from the mistaken assumptions Behe makes about protein interactions. The author has long been concerned about protein complexes and how they could or, rather, could not evolve. He argues that the generation of a single new protein-protein binding site is extremely improbable and that complexes of just three different proteins "are beyond the edge of evolution." But Behe bases his arguments on unfounded requirements for protein interactions. He insists, based on consideration of just one type of protein structure (the combining sites of antibodies), that five or six positions must change at once in order to make a good fit between proteins--and, therefore, good fits are impossible to evolve. An immense body of experimental data directly refutes this claim. There are dozens of well-studied families of cellular proteins (kinases, phosphatases, proteases, adaptor proteins, sumoylation enzymes, etc.) that recognize short linear peptide motifs in which only two or three amino acid residues are critical for functional activity. Thousands of such reversible interactions establish the protein networks that govern cellular physiology.

Very simple calculations indicate how easily such motifs evolve at random. If one assumes an average length of 400 amino acids for proteins and equal abundance of all amino acids, any given two-amino acid motif is likely to occur at random in every protein in a cell. (There are 399 dipeptide motifs in a 400-amino acid protein and 20 20 = 400 possible dipeptide motifs.) Any specific three-amino acid motif will occur once at random in every 20 proteins and any four-amino acid motif will occur once in every 400 proteins. That means that, without any new mutations or natural selection, many sequences that are identical or close matches to many interaction motifs already exist. New motifs can arise readily at random, and any weak interaction can easily evolve, via random mutation and natural selection, to become a strong interaction. Furthermore, any pair of interacting proteins can readily recruit a third protein, and so forth, to form larger complexes. Indeed, it has been demonstrated that new protein interactions and protein networks can evolve fairly rapidly and are thus well within the limits of evolution.

Is it possible that Behe does not know this body of data? Or does he just choose to ignore it? Behe has quite a record of declaring what is impossible and of disregarding the scientific literature, and he has clearly not learned any lessons from some earlier gaffes. He has again gone "public" with assertions without the benefit (or wisdom) of first testing their strength before qualified experts.

For instance, Behe once wrote, "if random evolution is true, there must have been a large number of transitional forms between the Mesonychid [a whale ancestor] and the ancient whale. Where are they?". He assumed such forms would not or could not be found, but three transitional species were identified by paleontologists within a year of that statement. In Darwin's Black Box, he posited that genes for modern complex biochemical systems, such as blood clotting, might have been "designed billions of years ago and have been passed down to the present … but not 'turned on'." This is known to be genetically impossible because genes that aren't used will degenerate, but there it was in print. And Behe's argument against the evolution of flagella and the immune system have been dismantled in detail and new evidence continues to emerge, yet the same old assertions for design reappear here as if they were uncontested.

The continuing futile attacks by evolution's opponents reminds me of another legendary confrontation, that between Arthur and the Black Knight in the movie Monty Python and the Holy Grail. The Black Knight, like evolution's challengers, continues to fight even as each of his limbs is hacked off, one by one. The "no transitional fossils" argument and the "designed genes" model have been cut clean off, the courts have debunked the "ID is science" claim, and the nonsense here about the edge of evolution is quickly sliced to pieces by well-established biochemistry. The knights of ID may profess these blows are "but a scratch" or "just a flesh wound," but the argument for design has no scientific leg to stand on.
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farmerman
 
  1  
Thu 14 Jun, 2007 11:30 am
Sean Carroll is himself an author of a topical bookTHE MAKING OF THE FITTEST, which is a perfect refutation of Behes hypothesis that multiple allele mutations are "rare"( and implies that it cant happen) . Thats where evolution lives. One of Carrolls genetic examples is the Antarctic "Ice Fish" the genome of which shows clearly that the genese for producing hemoglobin have been "shut down" and modified into "antifreeze producing " proteins. The proteins in an icefish are simple and unusual. They are made of up to 55 repeats of 3 amino acids, whereas most proteins contain all 20 of the type of amino acids seen in life. Since warm ater fish dont have any of this, the icefish had to invent it. The U of Illinois genomocs labs discovered that the antifreeze genes arose from part of another unrelated gene. The original gene encoded a digestive enzyme. A hunk of it broke off and relocated in another portion of the fish genome (such occurences happen all the time but are often non fitness improving , or are lethal) From this little hunk, when added onto theexisting genes in the place where the gene hunk reattached a new stretch of coding genes were cranking out a form of antifreeze. This all happened while the water temperature was slowly lowering since the Eocene. As the fishes blood thinned and became almost hemoglobin free. Its oxygen exchange was assisted by the fact that O2's solubility is much higher in freezing water. So insted of evolving a "thermal blanket", the icefish turned itself into an engine that could run in freezing water and at the same time make its respiration depend on directly translocating the O2 in the water by more efficient gills, hearts and capillaries. This fish evolved arespiration system that dispensed with hemoglobin entirely and turned its blood into antifreeze while growing direct respiratory parts that could slosh water through its sytem via a better pump and oxygen exchange mechanisms. ALl the genome still records the "fossil" nature of the hemoglobin forming genes that only exist as a ghost series of codons in their chromosome 11.
The "Use it or lose it" dictum of ken Miller is proven science as described by Sean Carroll.

Id like to see Carroll and Behe debate.
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cicerone imposter
 
  1  
Thu 14 Jun, 2007 11:36 am
Thank you, farmerman. That's something I have not heard of before, but seem to be somewhat related to other animals living in the cold such as penguins, seals, and polar bears.

I know I mentioned this before, but there are caves in Tennessee with insects in them that have learned to live in pitch darkness. They have evolved to a point where they can survive in the darkness against other predators.
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farmerman
 
  1  
Thu 14 Jun, 2007 11:41 am
These cave animals of the Mammoth Cave region, have evolved into blind animals with unique cave dwelling body plans (long legs, sensors in their skins and long feelers in insects) The interesting thing is that theyve evolved from their relative species who liove only near that particular cave.
Cave crickets in Indonesia are entirely different than crickets in the MAmmoth Caves or other major US caves. That evolution is derivative of the animals in the immediate biogeographical area is almost proof enough for the resonable mind to catch on that evolution is a real mechanism.
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wandeljw
 
  1  
Thu 14 Jun, 2007 11:54 am
farmerman wrote:
Sean Carroll is himself an author of a topical bookTHE MAKING OF THE FITTEST, which is a perfect refutation of Behes hypothesis that multiple allele mutations are "rare"( and implies that it cant happen).............

Id like to see Carroll and Behe debate.


I also would like to see the two of them debate. Carroll points out that Behe continues to behave as if his ideas have never been challenged. Behe even ignores data that is already out there (data that contradicts Behe's assertions).

Quote:
Is it possible that Behe does not know this body of data? Or does he just choose to ignore it? Behe has quite a record of declaring what is impossible and of disregarding the scientific literature, and he has clearly not learned any lessons from some earlier gaffes. He has again gone "public" with assertions without the benefit (or wisdom) of first testing their strength before qualified experts.
0 Replies
 
cicerone imposter
 
  1  
Thu 14 Jun, 2007 12:00 pm
Quote:
Is it possible that Behe does not know this body of data? Or does he just choose to ignore it? Behe has quite a record of declaring what is impossible and of disregarding the scientific literature, and he has clearly not learned any lessons from some earlier gaffes. He has again gone "public" with assertions without the benefit (or wisdom) of first testing their strength before qualified experts.


I find that an interesting phenomenon about those people of religion or in politics who refuse to acknowledge all the facts in front of them that shows that their "belief" is based on nothing more than "faith." They continue to challenge anything that doesn't fit into their mindset.
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stlstrike3
 
  1  
Fri 15 Jun, 2007 09:49 am
This article is a decisive dismantling of Behe and his support of ID.

I relished virtually every sentence. I urge you to do the same.

http://richarddawkins.net/article,1271,The-Great-Mutator,Jerry-Coyne-The-New-Republic
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spendius
 
  1  
Fri 15 Jun, 2007 05:11 pm
Yeah--The Selfish Gene.

The ineluctable modality of the human race before the Christian era.
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farmerman
 
  1  
Fri 15 Jun, 2007 05:21 pm
Yeh, Im sure the "Christian era" is responsible for the progress of science.
If that were even true, we in the USA are busy dismantling whatever advances weve made in the name of Christianity.

Meanwhile China and India are graduating Millions of scientists/ engineers. I cant wait till the pressures off this leadership gig.
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Coolwhip
 
  1  
Sat 16 Jun, 2007 05:12 pm
Just a side note; I think labelling everyone who does not support the ID crusade, anti-ID, is just as dumb as calling muslims anti-christians.
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