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Author Topic:   Meyer's Hopeless Monster
Percy
Member
Posts: 22359
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.8


Message 181 of 207 (147065)
10-03-2004 9:03 PM


Who is that Intelligent Designer behind the curtain?
After all his denials that the identity of the designer was a consideration for ID, I'd love to see John Paul's reaction to this quote from the Raelian Movement's statement about the Meyer paper:
"The Raelian Movement would like to underscore that The Theory of Intelligent Design does not lead to a supernatural designer but to an extraterrestrial human civilization designer..."
Of course, maybe Raelian Movement members aren't genuine IDists.
--Percy

  
Brad McFall
Member (Idle past 5023 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 182 of 207 (147197)
10-04-2004 1:36 PM
Reply to: Message 178 by Percy
10-01-2004 10:30 AM


Re: personalFact Check
Catmoose provided a link from which I extracted,
quote:
Sternberg said he was concerned that some in the science community have labeled him and Meyer as creationists. "It's fascinating how the 'creationist' label is falsely applied to anyone who raises any questions about neo-Darwinian evolutionary theory," he said. "The reaction to the paper by some [anti-creationist] extremists suggests that the thought police are alive and well in the scientific community."
Which made me wonder if in the cognition of origin of information if this rather than amount of info of/on taxogeny is the real problem (on either "side" of whatever is 'false'.)? When I made ALL THINGS ORDERED (my version of video format creationism/evolutionism trying to be fair to any 'side')I was very clear to indicate that my own ideas were DIFFERENT than ICR standards (which I was using as/for "talking" points"") and it IS the application of this false labeling that I have used here and elsewhere on the net to organize some of my responses. It also seems that because information is often taught biologically as being IN DNA that IF a creationist were to USE this notion (same thing as Price did with GEOLOGY in the past but interms of computers and society but not phones) to propose INTERVALS where information EXISTS and IS BOUND BY DNA then indeed one MIGHT NOT have said anything on taxonomy (see also old evolutionist issue of nonadaptive traits) but instead something indeterminant but real.
Analyzing this gets very difficult and it quickly becomes easier to simply synthesize some understanding than being able to recover any sense. So perhaps the issue IS ONLY the simple QUESTIONING of NEODARWINISM. The difficulty is that THE QUESTION matters IF the probability is GIVEN but the ANSWER matters if the sample space is put in question. This is how it can be that a "Debate" on EVC continues despite the needed use of different probabilities by creationists but part of THIS problem is the higher learning needed to reach this kind of Statistical Discussion as is in some ID and yet I know by my own history that this WAS stifled. I dont think it was because I was more a creationist but because I simply thought the collateralization of taxogeny differently than my teachers. I tried to show that it is true that fringe biology (panbiogeography, phenomenological thermodynamics, neophenogenics, topobiology) ALL SUFFER becuase of the negative climate/atmosphere that this IS. Even willing it to be other will not work. My lover STILL calls me lovingly (after decades) despite the absurdity of such a personal call given the illegality involved. That however involved designs, purpose, 4 ways around painting and things that are not obviously part of the sociology that gave rise to the barrier.

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markoo
Inactive Member


Message 183 of 207 (154121)
10-29-2004 11:35 AM


There's a passage in Meyer's paper that I have a question about:
quote:
Cassette mutagenesis experiments performed during the early 1990s suggest that the probability of attaining (at random) the correct sequencing for a short protein 100 amino acids long is about 1 in 1065 (Reidhaar-Olson & Sauer 1990, Behe 1992:65-69). This result agreed closely with earlier calculations that Yockey (1978) had performed based upon the known sequence variability of cytochrome c in different species and other theoretical considerations. More recent mutagenesis research has provided additional support for the conclusion that functional proteins are exceedingly rare among possible amino acid sequences (Axe 2000, 2004). Axe (2004) has performed site directed mutagenesis experiments on a 150-residue protein-folding domain within a B-lactamase enzyme. His experimental method improves upon earlier mutagenesis techniques and corrects for several sources of possible estimation error inherent in them. On the basis of these experiments, Axe has estimated the ratio of (a) proteins of typical size (150 residues) that perform a specified function via any folded structure to (b) the whole set of possible amino acids sequences of that size. Based on his experiments, Axe has estimated his ratio to be 1 to 1077. Thus, the probability of finding a functional protein among the possible amino acid sequences corresponding to a 150-residue protein is similarly 1 in 1077.
I did read Elsberry's response in regards to Axe's citation here - interesting to say the least.
But I still have a couple of questions:
1. What is cassette mutagenesis, and how does it differ from other mutagenesis techniques?
2. I seem to have come across an abstract or two that seems to show that cassette mutagenesis certainly has its limitations:
quote:
To achieve a non-biased random replacement on the amino acid level, oligonucleotide-directed mutagenesis (5) and cassette mutagenesis (6,7) have been carried out. These methods are limited to a defined region of the gene and can not introduce mutations at random positions
http://www.humanapress.com/ChapterDetail...
{Shortened display form of URL, to restore page width to normal - Adminnemooseus}
Am I incorrect on my assessment? If I am correct, wouldn't Meyer's analysis also be on a limited scope here?
3. Anything else in this passage that might be a bit off or misleading?
This message has been edited by Adminnemooseus, 02-03-2005 17:22 AM

  
Nic Tamzek
Inactive Member


Message 184 of 207 (154501)
10-30-2004 9:56 PM


Howdy,
quote:
There's a passage in Meyer's paper that I have a question about:
quote:
---------------------------------------------------------------------
Cassette mutagenesis experiments performed during the early 1990s suggest that the probability of attaining (at random) the correct sequencing for a short protein 100 amino acids long is about 1 in 1065 (Reidhaar-Olson & Sauer 1990, Behe 1992:65-69). This result agreed closely with earlier calculations that Yockey (1978) had performed based upon the known sequence variability of cytochrome c in different species and other theoretical considerations. More recent mutagenesis research has provided additional support for the conclusion that functional proteins are exceedingly rare among possible amino acid sequences (Axe 2000, 2004). Axe (2004) has performed site directed mutagenesis experiments on a 150-residue protein-folding domain within a B-lactamase enzyme. His experimental method improves upon earlier mutagenesis techniques and corrects for several sources of possible estimation error inherent in them. On the basis of these experiments, Axe has estimated the ratio of (a) proteins of typical size (150 residues) that perform a specified function via any folded structure to (b) the whole set of possible amino acids sequences of that size. Based on his experiments, Axe has estimated his ratio to be 1 to 1077. Thus, the probability of finding a functional protein among the possible amino acid sequences corresponding to a 150-residue protein is similarly 1 in 1077.
---------------------------------------------------------------------
I did read Elsberry's response in regards to Axe's citation here - interesting to say the least.
But I still have a couple of questions:
1. What is cassette mutagenesis, and how does it differ from other mutagenesis techniques?
Mutating a group of amino acids at once. E.g., in a 150 amino acid protein, you might mutated aas 1-10, then 11-20, then 21-30, etc. You might discover that positions 1-10 can be just about anything without destroying whatever function you are testing for, but that 11-20 are very important.
This is useful for certain purposes (figuring out how the protein works) but is not very close to any evolutionary process. In evolution, the main process, point mutation, is 1 mutation at a time, and with this kind of small change you can end up changing many more amino acids than if you blast whole chunks of the protein with cassette mutagenesis. IDists of course prefer the cassette mutagenesis studies and ignore the others.
quote:
2. I seem to have come across an abstract or two that seems to show that cassette mutagenesis certainly has its limitations:
quote:
---------------------------------------------------------------------
To achieve a non-biased random replacement on the amino acid level, oligonucleotide-directed mutagenesis (5) and cassette mutagenesis (6,7) have been carried out. These methods are limited to a defined region of the gene and can not introduce mutations at random positions
http://www.humanapress.com/ChapterDetail...
{Shortened display form of URL, to restore page width to normal - Adminnemooseus}
---------------------------------------------------------------------
Am I incorrect on my assessment? If I am correct, wouldn't Meyer's analysis also be on a limited scope here?
Yes, although the fact that experimental mutation techniques can be biased is not the biggest problem with Meyer's usage of these kinds of studies. The biggest problems are:
(1) Evolution usually doesn't mutate a whole bunch of aas at once (like cassette mutagenesis), typically it's one aa at a time. Selection eliminates the failures and keeps/allows the successes/neutrals.
(2) The studies that Meyer cites take the "reverse" approach to estimating the density of "functional sequences" -- they take a functional protein, mess it up, and see how many mutants retain function. "Forward" studies, which take random sequences and test for function, get much higher numbers, as Axe (2004) explicitly concedes.
(3) Axe (2004), at least, tests for one function, and a fairly specific mechanism for that function. This is a small target. Evolution, OTOH, "tests" for many functions at once, and cares not about mechanism, as long as it works. This is a much bigger target.
(4) The origin of new genes is well understood and there are many papers on the topic, all of which Meyer ignored.
(5) Lastly, cases of new functional proteins are known to have evolved from non-protein-coding sequences in recent history in the wild and in the lab (google on "nylonase evolution"). Therefore such things clearly are possible, and anyone who denies this just doesn't know what they're talking about. Unfortunately this conclusion must apply to Meyer, the editor Sternberg, and the reviewers Sternberg picked.
quote:
3. Anything else in this passage that might be a bit off or misleading?
Axe (2004) actually concluded that the range of density of functional sequences was between 1 in 10^53 (from a similar study) and 1 in 10^77 (from Axe's study). Meyer only cites the 1 in 10^77 figure, ignoring the uncertainty of about 1 million billion billion billion in the figure.
There are numerous other points, e.g. Axe's actual opinion on protein evolution based on his study (he thinks it's quite possible), and the fact that according to Dembski something is supposed to have odds of 1 in 10^150 in order to actually have "CSI." Like the critique says, the mistakes are many and layered. But that's probably enough for now...
This message has been edited by Adminnemooseus, 02-03-2005 17:15 AM

  
JonF
Member (Idle past 158 days)
Posts: 6174
Joined: 06-23-2003


Message 185 of 207 (182871)
02-03-2005 11:40 AM


A response to Sternberg's accusations against the Smithsonian
Well, the WSJ: The Branding of a Heretic isn't open for replies, so I guess this is the best place to put it.
Jonathan Coddington (Research Scientist and Curator at the National Museum of Natural History, and Richard Sternberg's sponsor/supervisor as a Research Associate at the Smithsonian) has posted a response to Richard Sternberg's complaint of discrimination (see The Branding of a Heretic) at The Panda's Thumb in this comment in the Sternberg vs. Smithsonian thread.
quote:
6. As for prejudice on the basis of beliefs or opinions, I repeatedly and consistently emphasized to staff (and to Dr. von Sternberg personally), verbally or in writing, that private beliefs and/or controversial editorial decisions were irrelevant in the workplace, that we would continue to provide full Research Associate benefits to Dr. von Sternberg, that he was an established and respected scientist, and that he would at all times be treated as such.
On behalf of all National Museum of Natural History staff, I would like to assert that we hold the freedoms of religion and belief as dearly as any one. The right to heterodox opinion is particularly important to scientists. Why Dr. von Sternberg chose to represent his interactions with me as he did is mystifying. I can’t speak to his interactions with anyone else.

Replies to this message:
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Percy
Member
Posts: 22359
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.8


Message 186 of 207 (182917)
02-03-2005 3:55 PM
Reply to: Message 185 by JonF
02-03-2005 11:40 AM


Re: A response to Sternberg's accusations against the Smithsonian
As evidence of my perspicacity, I quote myself in full from Message 179 of this thread a few months ago:
Percy writes:
Just as the cold fusion fiasco of Fleischman and Pons ruined their careers, Sternberg's ID fiasco will run his. I predict that Sternberg will not hold his current positions for more than another year. Those positions are:
  • Staff Scientist, National Center for Biotechnology Information
  • Research Associate, National Museum of Natural History
He'll probably join Discovery Institute or one of the related theological institutions.
I don't think this is an iffy prediction. Behe maintains his academic position by publishing legitimate scientific articles and by conducting himself with integrity and honesty in scientific arenas. He makes no secret of what he believes, but he's never tried to sneak his ID beliefs into his technical contributions. This is in stark contrast to Sternberg, who has really stuck his neck out professionally with his editorial misconduct and transparent defenses. We'll keep watch during the next year and see what happens to him.
Sternberg is making a ridiculous attempt to paint a picture of religious discrimination. The reality is that he's being systematically ostracized for letting his religious views influence his scientific judgement. He abused his editorial authority by rigging the peer-review process, and in defending his misconduct he was less than forthcoming about his views. This is transparently obvious from his defense of the Meyer paper as good science, from his attempts to justify the Meyer paper as an appropriate topic for the BSOW proceedings, and from his defense of ID as a worthy area for scientific investigation.
Naturally Sternberg's supervisors and colleagues are shocked and distrustful. It's one thing to disagree on scientific matters, but quite another to disagree on the nature of legitimate science. The transparently religious motivations of the ID movement are not overcome by the equally transparent denials. Sternberg is sorely confused if he believes that the same obfuscations and dissemblings that fool the public would work on the scientific community, and especially on those in his own fields. What's happening to him is the predictable outcome of violating the trust given scientists.
--Percy

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JonF
Member (Idle past 158 days)
Posts: 6174
Joined: 06-23-2003


Message 187 of 207 (182920)
02-03-2005 4:23 PM
Reply to: Message 186 by Percy
02-03-2005 3:55 PM


Re: A response to Sternberg's accusations against the Smithsonian
Sternberg's position and privileges have not been curtailed in any way (according to Coddington). Perhaps his peers are not as chummy as they used to be, but chumminess is not guaranteed by the Constitution or any law of which I'm aware.

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Brad McFall
Member (Idle past 5023 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 188 of 207 (182924)
02-03-2005 4:59 PM
Reply to: Message 186 by Percy
02-03-2005 3:55 PM


Re: A response to Sternberg's accusations against the Smithsonian
As far as I can tell ID can only be science if
Kant's "permissibleness" be true and the next paragraph IDONT type exist.(Critique of the Teleological Judgement) "Here it is permissible for the archeologist of nature to derive from the surviving traces of its oldest revoutions, accoording to all its mechanism known or supposed by him, that great family of creatures (for so we represent them if the said thotoughgoing relationship is to have any ground). He can suppose the bosom of mother earth, as she passed out of her chaotic state (like a great animal), to have given birth in the beginning to creatures of less purposive form, that these again gave birth to others which formed themselves with greater adaptation to their place of birth and their relations to each other, until the womb becoming torpid and ossified, limited its births to definite species not further modifiable, and the manifoldness remained as it was at the end of the operation of that fruitful formative power. Only he must still in the end ascribe to this universal mother an organization purposive in respect of all these creatures; otherwise it would not be possible to think of the possibility of the purposive form of the products of the animal an vegtable kingdoms."p 208 Hafner Publishing Co. NEw YOrk.
is univocally within a Darwinian individual. Evos only can doubt this as we have not seen evidence of a living creature taking physical advantage of its "mother" fossil form, ie has a Darwinian advantage by utilizing the "niche"(sic!) of its ancestors taphonomic death made solid geologically. Should we find this, man can construct the adaptibility ON PURPOSE for any comparable creature just as we should not make life just to take it. Adaptationism has NEVER hardened for this race as Gould proposed however. We dont have this data. It could exist in the creatures living in Rocks. And should life ever be found OFF EARTH, I would suspect even more that this could be found here."
We individually at evc have seen more diversity than that. So somewhat amazingly I agree pretty much with captial PeRcY.
I predict ID can not stand short of EVC and ALL OTHER websites like it NOT continuing. In other words we have *SOME* ground, we dont have the sky that goes with it. I pray it is our generations race that resolves this difference of opinion. Many evos proceed by not thinking on purpose. They should. Its easy to play defense that we. We have seen THAT since the 60s. Its a differnt game on offense. Computer forms should have given them the spur if the change did not already. I know that biologists' thought that by making an organicist teleomatic a new philosophy was supplied that need not fear being a state of ID where there is but this "pushing back" of said mother earth abstracted but it is not much materially to think that plants and animals are MORE seperated given the plethora of computer logic self replications being discussed WIHTOUT an older philosophy of science of the 18th century. We are stuck on the 19th but live in the 21st. The numbers dont match the letters.
This message has been edited by Brad McFall, 02-03-2005 17:06 AM

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Brad McFall
Member (Idle past 5023 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 189 of 207 (183967)
02-08-2005 2:36 PM
Reply to: Message 185 by JonF
02-03-2005 11:40 AM


Re: A response to Sternberg's accusations against the Smithsonian
Meyer is on Janet's just now
—app_—‘
over the whole Sternberg thing.
quote:
Tuesday, 2/8/2005
Hour 1
A new controversy has erupted in the ongoing debate over Darwin's theory of evolution and the idea that challenges it--Intelligent Design. We'll talk about this with the Director and Senior Fellow of the Center for Science and Culture at The Discovery Institute, based in Seattle, Stephen Meyer, and the President and Founder of The Discovery Institute, Bruce Chapman. These gentlemen offer a wealth of expertise in this area, and they'll help make the complex understandable. We'll give you straight answers about this new development in this ever-changing discusssion.

This message has been edited by Brad McFall, 02-08-2005 14:41 AM

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Percy
Member
Posts: 22359
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.8


Message 190 of 207 (184391)
02-10-2005 10:41 AM
Reply to: Message 185 by JonF
02-03-2005 11:40 AM


Re: A response to Sternberg's accusations against the Smithsonian
There were some letters to the editor responding to the WSJ Klinghoffer column: Intelligent Design Intrigues, but Is It Science?.
I'm not sure whether viewing this link requires a WSJ subscription. If others can't view it let me know and I'll post a copy of the page.
--Percy

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Replies to this message:
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NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 191 of 207 (184400)
02-10-2005 11:09 AM
Reply to: Message 190 by Percy
02-10-2005 10:41 AM


Re: A response to Sternberg's accusations against the Smithsonian
Needs a subscription.

This message is a reply to:
 Message 190 by Percy, posted 02-10-2005 10:41 AM Percy has not replied

  
PaulK
Member
Posts: 17815
Joined: 01-10-2003
Member Rating: 2.1


Message 192 of 207 (184401)
02-10-2005 11:10 AM
Reply to: Message 190 by Percy
02-10-2005 10:41 AM


Re: A response to Sternberg's accusations against the Smithsonian
It does require a subscription.
From my own reading around I've a strong suspicion that the WSJ article is highly misleading.

This message is a reply to:
 Message 190 by Percy, posted 02-10-2005 10:41 AM Percy has replied

Replies to this message:
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Percy
Member
Posts: 22359
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.8


Message 193 of 207 (184411)
02-10-2005 11:38 AM
Reply to: Message 192 by PaulK
02-10-2005 11:10 AM


Re: A response to Sternberg's accusations against the Smithsonian
Here's a link to a local copy: http:///DataDropsite/WSJ_ID_Letters.html
I used IE to create the copy, and I'm wondering if it is so complete that it even checks registration. Let me know if it's still not accessible and I'll post an image file instead.
--Percy

This message is a reply to:
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PaulK
Member
Posts: 17815
Joined: 01-10-2003
Member Rating: 2.1


Message 194 of 207 (184412)
02-10-2005 11:48 AM
Reply to: Message 193 by Percy
02-10-2005 11:38 AM


Re: A response to Sternberg's accusations against the Smithsonian
The page works perfectly well here.
The most significant letter is the one from the Smithsonian. I'd already seen it quoted on The Panda's Thumb - but it's nice to confirm the content for myself

This message is a reply to:
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Percy
Member
Posts: 22359
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.8


Message 195 of 207 (184425)
02-10-2005 2:02 PM
Reply to: Message 189 by Brad McFall
02-08-2005 2:36 PM


Interview with Meyer and Chapman of Discovery Institute
Janet Parshall archives previous programs of the week at . I've listened to the segment interviewing Steven Meyer and Bruce Chapman (president of Discovery Institute). Here are brief paraphrased excerpts:
  • Janet: One would think the Smithsonian would be a bastion of open thinking, but apparently not.
  • Janet: Discovery institute is a most prestigious organization, a public policy center on national and internation affairs, and has some of the greatest minds in history.
  • Meyer: The BSOW distanced itself from the article by citing the position of the AAAS which calls ID unscientific by definition, a sort of doctrinal declaration.
  • Commercial: Now you can set up your own on-line Christian bookstore from your own home. Make money and share the word of Jesus Christ at the same time.
  • Janet: One would think the Smithsonian would be a bastion of liberalism and openmindedness, but apparently when someone with two PhD's like Richard Sternberg dares question Darwinism he is sunk into the primordial ooze fighting for his job. If you touch Darwinism then you're going to have a shambles of your professional career. Sternberg is trying to save his career because he has been so vilified by the Smithsonian.
  • Chapman: Some of his colleagues are shunning him, some are afraid to work with him on projects. I don't understand how someone could be persecuted only for carrying out his duties as an editor. Scientists have always said that science should be discussed in peer-reviewed journals, then as soon as it appears in a peer-reviewed journal they make it a personal matter. There's been no response on the merits, they just attack the people.
  • Meyer: The media have been unable to get off the theme of religious motivations, and don't seem to perceive that there is a genuine scientific controversy here. Right across the subdisciplines of evolution are criticisms of Darwinism in the technical literature. The people like myself and Behe and Demski are scientists with good credentials making arguments based upon evidence. What we find in the media is the Scopes trial stereotype. When we try to get across that there is a serious evidential challenge to Darwinism, what we're confronted with is, "What's your religious angle."
  • Janet: Well, Stephen, in our conversations we've talked about the growing number of scientists who embrace the theory of intelligent design, because there are so many holes in Darwinism, and you've told me that many people who are moving closer to intelligent design are people who have not made a proclamation of faith of any kind.
  • Meyer: One of the biggest news items from last year was that the world's most famous atheists, Anthony Flew, had embraced some form of theism or belief in a creator on the basis, in part, on the arguments for design that he was reading from people in our movement, in particular the argument about information. Clearly his position is not based upon religion. I recently followed Flew on a BBC program where he'd just excoriated the Darwinists for not following the evidence where it leads.
  • Janet: In yesterday's New York Times Michael Behe had an OpEd piece where he wrote: "The strong appearance of design allows a disarmingly simple argument: if it looks, walks and quacks like a duck, then absent compelling evidence to the contrary, we have warrant to conclude it's a duck. Design should not be overlooked simply because it's so obvious." Yet you have scientists who say, "I don't want to believe, I want to know, therefore my belief is predicated upon the evidence."
  • Chapman: We have a topsy-turvy world where those advocating intelligent design want to talk about the evidence, while the scientists are saying all we want to talk about is our committment to Darwinism as an absolute given that you cannot challenge. They're acting in a kind of religous way. Darwinism *is* a religion.
  • Janet: It reminds of the people who believed the world was flat.
  • Chapman: They also make it hot for people who don't accept the theory. There are cases of real discrimination. It has a religiosity to it that just has everything turned upside-down.
  • Meyer: This is a very exciting debate, and one thing that has come from the intense interest in this is a lot of inquiries from younger scientists. Scientific revolutions take place in the younger generation.
  • Janet: Sternberg is saying he's spending all his time trying to salvage a scientific career. This is a man with two PhD's! What a tremendous loss for the scientific community if he gets marginalized for this. Where's the hue and cry from the public?
  • Meyer: Darwinism is a dying scientific theory. It is being propped up by bluff and by power. When you get into the evidence, as Jonathon Wells book does very well, all the most prominent most knock-down drag-out arguments for the theory, each one of them is flawed, overstated or just outright false. The theory was concocted in the 19th century during the era of the steam engine, and we're now in the era of nanotechnology and information technology, and when we look at the information technology in the cell it's hard for many of us to think that good old Darwin's theory is going to survive this, no matter the attempts to supress the dissent.
  • Meyer: Behe's OpEd piece was the 3rd most referenced piece in yesterday's New York Times.
  • Chapman: Behe is a highly respected microchemist in his field, and he has shown there are no Darwinian explanations for what he sees in the cell.
Here's a link to the Behe NYT OpEd piece. You need to register, but it's free: Opinion | Design for Living - The New York Times
--Percy

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