Francis Beckwith on ID

Intelligent Design and Me, Part IV: A Response to Some Critics by Francis Beckwith

Here’s the problem, as I see it: the ID advocate is assuming that an anomaly in the apparently seamless story of evolution is a necessary condition for a defeater to naturalism. But that assumption is mistaken, since it requires that we believe that efficient and material causality (not to mention evolution itself) are rivals to teleology in nature, which is the essence of the mechanistic view. This is why the ID advocate spends so much time protecting the non-seamlessness of nature by trying to find flaws in the works of thinkers like Margulis and Morris. Consider, for example, Dembski’s comments in his review of Morris’ book, Life’s Solution. In it Dembski lets the mechanistic cat out of the ID bag:

here

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225 Responses to “Francis Beckwith on ID”

Pez Says:
May 23rd, 2010 at 5:03 pm
Beckwith rocks!
But not on this subject.

Here’s the problem, as I see it: the ID advocate is assuming that an anomaly in the apparently seamless story of evolution is a necessary condition for a defeater to naturalism.

ID proponent do not think this is a necessary condition for a defeater of naturalism. Most ID proponents think naturalism is defeated long before anyone looks a evolution.
Beckwith continually mistakes the philosophy and principles with the science.
For instance he quotes Dembski on S. Conway-Morris:

By refusing to allow that teleology can be scientifically tractable, Conway Morris remains squarely within the scientific mainstream.

And says that this makes Dembski a slave to mechanism. This is not the case at all. What Dembski is complaining about is the metaphysical assumption of the atheist that design is illusory and , in Conway Morris' case, that design absolutely can not be detected.

Beckwith admits the failure of naturalism as argued for by ID advocates like Plantinga, Craig, Moreland, etc., in the first installment of his series. But he classifies these as being outside what he considers the crux of ID – irreducible complexity and specified complexity. But these theorists, some of whom advocate for ID very explicitly, know that naturalism is defeated in the same way Beckwith does, and long before the science origins is investigated.

Indeed, Beckwith defines ID this way in his second contribution:

Some of these arguments challenge aspects of neo-Darwinism. Others make a case for a universe designed at its outset, and thus do not challenge any theory of biological evolution.

But even ID advocates who criticize neo-Darwinism are technically not offering an alternative to evolution, if one means by evolution any account of biological change over time that claims that this change results from a species' power to accommodate itself to varying environments by adapting, surviving, and passing on these changes to its descendants. This is not inconsistent with a universe that has earmarks and evidence of intelligent design that rational minds may detect.1

Of course, he will soon tell us why he, Francis Beckwith, has decided these ID arguments are not to be called ID arguments.
As he goes it becomes more and more clear that what he is calling ID is merely the Behe/Dembski arguments. But he fails to allow them to speak for themselves with regard to mechanism and discontinuities.

This means that for Dembski as well as other ID advocates, nature’s order, including its laws and principles, need not require a mind behind it except for in the few instances where the explanatory filter allows one to detect design.

This is not the case at all. Dembski and Behe are clear that there is design which cannot be detected by their methods. This is such weak argumentation. If one claims there is no life in a sample of water and I can prove with a magnifying glass that there is then my case is closed. It doesn't matter whatsoever, nor am I saying anything, about life which might not be visible with my glass but would be with a microscope.

But whatever design we detect, it can always be overturned by future discoveries, and thus conceding yet another slice of nature to atheism.

Big deal. So future science shows they did not detect design with their methods. Future science threatens all scientific conclusions. This will not touch the design which is known through other means, means which Beckwith accepts along with the ID advocates he agrees with. And, alas, along with those with whom he disagrees.

On the other hand, Thomists and many other Christian philosophers do not accept this philosophy of nature. For them, design is immanent in the universe, and thus even an evolutionary account of the development of life requires a universe teeming with final causes. What is a final cause? It is a thing’s purpose or end.

As do design advocates. Some, like Behe and Dembski, also see it manifest in other ways.

Beckwith returns often to Final and Formal Causes against Material and Efficient Causes. For some reason he acts as though an ID advocate who sees design in the latter is denying it in the former. Obviously this does not follow.

This is why, for example, ID advocates analogize their project with the detection of the agent causes of artifacts in anthropology, computer science, and the Search for Extraterrestrial Intelligence (SETI). In each of these cases, the thing created is a result of a mind taking the material parts of other things and designing them for some end extrinsically imposed on the parts. Whether it is pottery, computer programs, or alien messages, each is the consequence of imposing form and finality on that which does not have them by nature.

Beckwith misses his own point here. Dembski does use the computer program as an analogy, but not as Beckwith says. Dembski shows that an entire program is designed (like nature) and that evidences of that design can be seen in a different manner from that encompassing the whole, at certain points in its running. But he uses the analogy to show that the design seen at that point was not imposed at that point – but was built into the program from the beginning. In the analogy Beckwith would create, this does make the design part of its "nature" just as he accepts in the life processes.

A reply on UD that Beckwith references.
http://www.uncommondescent.com...
I've just started to glance at it and see Beckwith responds immediately in the first comment.

Comment by Pez — May 23, 2010 @ 5:03 pm

Pez Says:
May 23rd, 2010 at 5:13 pm
Still can't edit. Sorry about the blockquote mishap.
And for the sentence that might appear to imply that Conway-Morris is an atheist. I was comparing his assumptions to those of atheists and showing how Dembski disagrees with both.

Comment by Pez — May 23, 2010 @ 5:13 pm

Pez Says:
May 23rd, 2010 at 5:18 pm
BTW, from that UD thread:

For example, Michael Denton, in Nature’s Destiny, combines “design” on the one level, with “purely natural causes” on the other. He affirms an evolutionary chain of development “from molecules to man” which involved no supernatural interventions, but was nonetheless planned from the outset to yield specific results, most notably, the emergence of man. And while Denton does not call himself an “ID proponent”, both Behe and Dembski have at various times acknowledged that the combination of naturalism and design is within the bounds of the definition of intelligent design.

Comment by Pez — May 23, 2010 @ 5:18 pm

Pez Says:
May 23rd, 2010 at 5:22 pm
and

ID as such does not depend on refuting naturalistic accounts of origins at all. It is compatible with a thoroughgoing naturalism from the moment of the Big Bang. ID depends on showing, not that the creation of life or species requires supernatural intervention, but that it requires design â€“ the rational adjustment of means to ends. Whether the design is implemented via purely natural means, via nothing but miracles, or via some combination, is irrelevant to ID as such. Whatever sharp disagreements might exist within the ID camp over miracles vs. naturalism, macroevolution vs. special creationism, etc., all ID proponents are united on what I have called the architectural level, where the question is design versus chance.

Comment by Pez — May 23, 2010 @ 5:22 pm

olegt Says:
May 23rd, 2010 at 5:31 pm
Can't catch a break, Pez? Everyone misrepresents ID. Everyone

Comment by olegt — May 23, 2010 @ 5:31 pm

Pez Says:
May 23rd, 2010 at 5:45 pm
I find it quite encouraging. If even good and thoughtful thinkers like Beckwith miss the point and fail to actually critique the real deal then the real deal stands that much stronger.

Keen comment, by the way, professor. I'm so glad you have time to add your thoughtful contributions.

Comment by Pez — May 23, 2010 @ 5:45 pm

olegt Says:
May 23rd, 2010 at 7:57 pm
Or maybe the real deal is how those thoughtful thinkers perceive it. Come on, Pez. With a possible exception of Behe, "ID theorists" are dyed-in-the-wool creationists. Dembski is on record saying "I personally don’t believe in common descent." Nelson is a YEC. Point me to one ID theorist apart from Behe whose views are not totally bonkers.

Comment by olegt — May 23, 2010 @ 7:57 pm

Pez Says:
May 23rd, 2010 at 8:07 pm
As always, Oleg, your culture warring has nothing to do with the point or ID.

Anyway, I came back to refer to another response to Beckwith:

Now, note that I have spoken only of “design”, not of “miracle”, “intervention”, “supernatural causes”, filling in “gaps” in naturalistic explanation, etc. In my view, ID, in its purest form, has nothing to do with these things. In my view, ID is a theory of design detection, applied to nature, especially to biological nature. It detects design, not how the design was implemented. And it detects present patterns, not past events which might account for those patterns. In other words, ID is (or at least in my view should be) an a-historical theory of design, not a historical theory of “origins”.

..

But neither an affirmation of a particular historical narrative nor an insistence upon divine interventions is essential to ID theory as I understand it.
So if Nelson believes that direct creation was necessary and that macroevolution did not occur, and if Behe accepts macroevolution and is open-minded about whether or not it needed to be executed or supplemented by divine intervention, and if Denton accepts macroevolution and utterly rejects intervention, this is not an inconsistency in ID theory as such; it is a difference of opinion about second-tier questions among ID proponents.

…
ID is completely compatible with naturalism of other sorts. For example, it is compatible with a naturalism in which the whole course of evolution is laid out by physical and biochemical necessities programmed into the universe from the moment of Creation.
…
But in the former sense, there is nothing in ID that rules out wholly naturalistic macroevolution. The design can be conceived of as built into the universe, to unfold or evolve over time.
…
if ID can conceive of evolution as the unfolding of a latent design rather than the constant imposition of an extrinsic design — is ID still necessarily incompatible with the view of final causation held by Thomas Aquinas or by modern Thomists? Is it only the miracles, the interventionism and the literal understanding of the clockmaker metaphor that are unacceptable to Thomism? Or is the idea of design detection itself, even in the context of a seamless naturalism, antithetical to Thomist thought? Is it simply wrong, from a Thomist point of view, for a Christian to think that the details of God’s creation might point decisively against chance and decisively in favor of design?

http://www.uncommondescent.com...

Keep it up, Oleg. It's not like you have any credibility left on this subject to further destroy.

Comment by Pez — May 23, 2010 @ 8:07 pm

Salvador T. Cordova Says:
May 23rd, 2010 at 8:56 pm
To the best of my knowledge, Non-creationists associated with ID:

1. David Berlinski
2. Robert Sheldon
3. Granville Sewell (not a YEC, not a literalist)

It would be worth confriming the list I just provided, however as I'm not 100% certain.

But even granting that all ID proponents are creationists, the compartmentalization of the disciplines of thought are sensible.

And even granting that the distinction between ID and Creationism was for nefarious political and cultural reasons, the question of the adequacy of Darwinian theory remains.

The questions raised of Behe Black Box have not be adequately answered by evolutionary biologists in a manner consistent with other disciplines like Chemistry, Physics and Engineering.

I suggested to Frank Beckwith not to be so quick to defend the mainstream evolutionary views, as they could still be proven wrong. He said he had no argument with that. See:

http://www.uncommondescent.com...

Comment by Salvador T. Cordova — May 23, 2010 @ 8:56 pm

Richardthughes Says:
May 23rd, 2010 at 10:04 pm
Only three, Sal? I see your name isn't up there..

Comment by Richardthughes — May 23, 2010 @ 10:04 pm

Pez Says:
May 23rd, 2010 at 10:55 pm
Speaking of Sheldon
http://rbsp.info/WTS/ST761-ii....

Comment by Pez — May 23, 2010 @ 10:55 pm

Salvador T. Cordova Says:
May 23rd, 2010 at 10:56 pm
Frank writes:

Biologist Lynn Margulis, for example, has offered endosymbiotic theory1 as a non-neo-Darwinian evolutionary account that may explain irreducible complexity without requiring a design inference (as understood by Behe and Dembski)

Endosymbothic theory is not a good explanation, the theory has a lot of holes.

It appears the irreducible nature of eukaryotes flies in the face of endosymbosis. Frank is not citing not up-to-date literature!!!

See:
http://www.nature.com/nrg/jour...

and

http://www.sciencemag.org/cgi/...

Seem's the biologos folks from Falk etc. are unwilling to acknowledge they're putting forward suspect and obsolete arguments.

Data from many sources give no direct evidence that eukaryotes evolved by genome fusion between archaea and bacteria.

Furthermore, even if endosymbosis is true, it doesn't solve the problem of Irreducible Complexity. It actually suggest pre-medititation that allows easy integration through endosymbiosis!

Comment by Salvador T. Cordova — May 23, 2010 @ 10:56 pm

Richardthughes Says:
May 23rd, 2010 at 11:04 pm
Geez Sal, there's no data that doesn't fit ID! 'This is clearly not well supported and full of holes, but if it WAS right it supports ID'.

Your lens is always 'How does this fit design'.

Comment by Richardthughes — May 23, 2010 @ 11:04 pm

Salvador T. Cordova Says:
May 23rd, 2010 at 11:07 pm
Richard Hughes,

Are you the Orthodentist in Herndon?

Sal

Comment by Salvador T. Cordova — May 23, 2010 @ 11:07 pm

olegt Says:
May 24th, 2010 at 12:13 am
Sal wrote:

To the best of my knowledge, Non-creationists associated with ID:

1. David Berlinski
2. Robert Sheldon
3. Granville Sewell (not a YEC, not a literalist)

It would be worth confriming the list I just provided, however as I'm not 100% certain.

You can cross out Berlinski: although he is a critic of evolution, he is not an ID theorist in any other sense. Here is an excerpt from an article in Slate describing his association with ID:

Unlike his colleagues at the Discovery Institute—a religious think tank that sponsors his work and promotes intelligent design—Berlinski refuses to theorize about the origin of life. He describes his attitude towards ID as "warm but distant. It's the same attitude that I display in public toward my ex-wives."

And what are, exactly, the contributions of Sheldon and Sewell? I hope you don't mean this.

Comment by olegt — May 24, 2010 @ 12:13 am

Salvador T. Cordova Says:
May 24th, 2010 at 12:34 am
I forgot to mention Richard Sternberg! He was not a creationist as of 2004, but identified himself as a "Process Structuralist".

Comment by Salvador T. Cordova — May 24, 2010 @ 12:34 am

Salvador T. Cordova Says:
May 24th, 2010 at 12:50 am
With a possible exception of Behe, "ID theorists" are dyed-in-the-wool creationists. Dembski is on record saying "I personally don’t believe in common descent." Nelson is a YEC. Point me to one ID theorist apart from Behe whose views are not totally bonkers.

If I may ask, what relevance does an ID theorist also being a creationist have to whether Darwinism is true or not? What relevance does that have to the correctness of Darwinism?

I'm a creationist, but I also think it appropriate that ID is conceptually a separate discipline.

ID asks if something is designed.

Assuming life and the universe are designed, Creationism asks: "who, what, where, when, how".

It seems the demarcations are fairly logical.

Point me to one ID theorist apart from Behe whose views are not totally bonkers.

Even if they are bonkers, they're still scoring points against their opposition. Case in point, Michael Behe vs. Ken Miller or Rick Sternberg vs. Darrell Falk: .

So it doesn't speak well of Miller and Falk that they are being sucessfully challenged by ID proponents who are supposedly "bonkers". Further, Behe was giving Miller some remedial lessons in biochemistry (Miller didn't know that hormones are not proteins but lipids). Kind of embarassing for Miller I'd say.

Comment by Salvador T. Cordova — May 24, 2010 @ 12:50 am

Richardthughes Says:
May 24th, 2010 at 1:18 am
Hi Sal, that's not me. Nor this one:

http://www.press.uillinois.edu...

Comment by Richardthughes — May 24, 2010 @ 1:18 am

Pez Says:
May 24th, 2010 at 1:49 am
Don't you see, Sal?
If they're creationists they're nuts.
If they're nuts design is falsified and Darwinism is true and Oleg will not be judged in the afterlife.
Easy as 1-2-3

Comment by Pez — May 24, 2010 @ 1:49 am

Richardthughes Says:
May 24th, 2010 at 2:01 am
Looks like projection to me, Pez. I doubt Oleg is trying to make reality conform to a book…

Comment by Richardthughes — May 24, 2010 @ 2:01 am

Pez Says:
May 24th, 2010 at 2:14 am
Good for you Richard.

Comment by Pez — May 24, 2010 @ 2:14 am

ID guy Says:
May 24th, 2010 at 7:35 am
olegt,

Some or even most IDists don't accept Common Descent because the premise is not science- it cannot be tested.

Every "hypothesis" for Common Descent can be used to support alternative scenarios.

And not one "hypothesis" for Common Descent includes a mechanism.

So perhaps instead of saying the people who do not accept Common Descent are "bonkers" you could actually present some scientific data that shows they are.

Comment by ID guy — May 24, 2010 @ 7:35 am

Salvador T. Cordova Says:
May 24th, 2010 at 8:32 am
Hi Sal, that's not me. Nor this one:

http://www.press.uillinois.edu... l

Thanks for you kind reply! At least I know now you weren't the guy who put braces on me once upon a time.

Comment by Salvador T. Cordova — May 24, 2010 @ 8:32 am

JOHN_A_DESIGNER Says:
May 24th, 2010 at 8:42 am
It appears to me that both olegt and Richard Hughes are operating on the assumption that empirical science has proven their metaphysical naturalistic worldview to be true.

Comment by JOHN_A_DESIGNER — May 24, 2010 @ 8:42 am

JOHN_A_DESIGNER Says:
May 24th, 2010 at 8:47 am
typo above: "there" should be "their." (when will we get the edit function back?)

Comment by JOHN_A_DESIGNER — May 24, 2010 @ 8:47 am

Salvador T. Cordova Says:
May 24th, 2010 at 8:49 am
The Richard Hughes I once knew was a nice as…hmm….Mister Rogers or Kaptain Kangaroo. The Richard Hughes I knew used to do magic tricks to entertain the kids he put braces on.

I'd hate to think he now keeps company with the likes of Lou moderator of ATBC (aka Janie Belle McKnight, the Darwinist Transvestite Cross Dresser) who say the nastiest things about me and my friends.

What a relief the Richard Hughes here isn't the Richard Hughes that put braces on me.

Comment by Salvador T. Cordova — May 24, 2010 @ 8:49 am

Salvador T. Cordova Says:
May 24th, 2010 at 9:08 am
Frank Beckwith writes:

Here’s the problem, as I see it: the ID advocate is assuming that an anomaly in the apparently seamless story of evolution is a necessary condition for a defeater to naturalism. But that assumption is mistaken, since it requires that we believe that efficient and material causality (not to mention evolution itself) are rivals to teleology in nature, which is the essence of the mechanistic view.

This is a philosophical distortion of what ID is. The discipline of ID is "the search for patterns that signify intelligence".

How one can get from "the search for patterns that signify intelligence" to :

the ID advocate is assuming that an anomaly in the apparently seamless story of evolution is a necessary condition for a defeater to naturalism

is beyond me.

We don't need such philosophical contortions to conclude stonehenge or mount rushmore are designs. It's only a minor extension to observe that living systems look like incredible information processing systems full of computation and signalling at every level, hall marks of engineering.

Comment by Salvador T. Cordova — May 24, 2010 @ 9:08 am

olegt Says:
May 24th, 2010 at 9:19 am
Good try, Pez, but I am not worried about afterlife. Back to the drawing board.

Comment by olegt — May 24, 2010 @ 9:19 am

Richardthughes Says:
May 24th, 2010 at 9:41 am
Any reason why you put "the Darwinist Transvestite Cross Dresser" out there, Sal? Don't make it hard to like you. If you're going get ID started / over the line it'll have to be by being honest and doing science, not telling everyone how Darwin beat puppies.

Comment by Richardthughes — May 24, 2010 @ 9:41 am

Salvador T. Cordova Says:
May 24th, 2010 at 9:45 am
Any reason why you put "the Darwinist Transvestite Cross Dresser" out there, Sal?

Thought it was funny to point out the company you keep. Kinda makes the company I keep (creationists) seem tame by comparison.

Comment by Salvador T. Cordova — May 24, 2010 @ 9:45 am

Salvador T. Cordova Says:
May 24th, 2010 at 9:47 am

Thought it was funny to point out the company you keep. Kinda makes the company I keep (creationists) seem tame by comparison.

Also, we were talking about creationist going bonkers. What do make of your friend Lou the Transvestite. In my humble opinion, that's bonkers time 10. Do you think that sort of behavior is bonkers? Isn't that more bonkers than thinking God created life?

Comment by Salvador T. Cordova — May 24, 2010 @ 9:47 am

Richardthughes Says:
May 24th, 2010 at 9:54 am
Well, let's examine your well-poisoning, if that's what you want to do.

1. I've never met Lou physically.
2. I don't think one instance of dressing in drag for humour qualifies as 'transvestite'. You may want to apologize to him.
3. Even if he was a cross dresser, you imply that I shouldn't hang out with him or there is something inherently wrong with that. Are you going to get ID into schools by causing outrage in the moral majority? Can't you keep it to science – or is that too hard?

Creationists can be perfectly nice people. They're just clueless about some aspects of science.

So I find your honest

Comment by Richardthughes — May 24, 2010 @ 9:54 am

Richardthughes Says:
May 24th, 2010 at 9:57 am
the "So I find your honest" above should have been edited out. I'll let readers judge Sal's honesty for themselves.

Comment by Richardthughes — May 24, 2010 @ 9:57 am

Salvador T. Cordova Says:
May 24th, 2010 at 10:13 am
I'll let readers judge Sal's honesty for themselves.

My honesty is not the issue, ID's correctness is.

ID's correctness does not hinge on my character (or lack thereof).

I don't think one instance of dressing in drag for humour qualifies as 'transvestite'. You may want to apologize to him.

And Lou has spent years pretending to be a lesbian (aka Janie Belle McKnight) on the internet. Not exactly "one instance".

Creationists can be perfectly nice people. They're just clueless about some aspects of science.

Creationist have been clueless about some aspects of science. That is true. It doesn't mean the top tier creationists (like John Sanford) are bonkers.

I view Lou (aka Janie Belle McKinght) the moderator of Elsberry's forum as bonkers.

For the record, Richard Hughes, you strike me as a nice guy.

Comment by Salvador T. Cordova — May 24, 2010 @ 10:13 am

Richardthughes Says:
May 24th, 2010 at 10:24 am
Sal – I understand if your position isn't well received initially it can be frustrating. But don't make it personal. I'm not a Christian, so I can kill babies like cross-dressing Auntie Hitler-Darwin told me, but you sir are expected to take some sort of moral high ground.

I don't think nom de plumes qualify as transvestism.

http://en.wikipedia.org/wiki/G...

Comment by Richardthughes — May 24, 2010 @ 10:24 am

ID guy Says:
May 24th, 2010 at 11:06 am
richtard:
They're just clueless about some aspects of science.

Unlike you who appears to be clueless in all aspects of science…

Comment by ID guy — May 24, 2010 @ 11:06 am

Richardthughes Says:
May 24th, 2010 at 11:20 am
Hey, joe! How old is the earth? I have a clue… do you?

Comment by Richardthughes — May 24, 2010 @ 11:20 am

JOHN_A_DESIGNER Says:
May 24th, 2010 at 1:32 pm
Beckwith: Here’s the problem, as I see it: the ID advocate is assuming that an anomaly in the apparently seamless story of evolution is a necessary condition for a defeater to naturalism. But that assumption is mistaken, since it requires that we believe that efficient and material causality (not to mention evolution itself) are rivals to teleology in nature, which is the essence of the mechanistic view. This is why the ID advocate spends so much time protecting the non-seamlessness of nature by trying to find flaws in the works of thinkers like Margulis and Morris.

But what is natural selection? It is a mechanism, is it not? Most modern evolutionist’s, continue to believe that it is the main creative force that drive evolutionary change. You can’t scientifically begin to understand evolution unless you have a mechanism.

It is the Darwinist and neo-Darwinist who claim that because of the way the mechanism of natural selection operates that evolution is non-teleological. Darwin thought this way; Ernst Haekel thought this way; and it is the way that modern neo-Darwinist think.

For example, Jerry Coyne a biologist from the University of Chicago writes:

“…any injection of teleology into evolutionary biology violates precisely the great advance of Darwin’s theory: to explain the appearance of design by a purely materialistic process — no deity required. In a letter to his mentor Charles Lyell, Darwin explicitly decried the idea of divine intervention in evolution:

‘I entirely reject, as in my judgment quite unnecessary, any subsequent addition ‘of new powers and attributes and forces,’ or of any ‘principle of improvement’, except in so far as every character which is naturally selected or preserved is in some way an advantage or improvement, otherwise it would not have been selected. If I were convinced that I required such additions to the theory of natural selection, I would reject it as rubbish. . . I would give absolutely nothing for the theory of Natural Selection, if it requires miraculous additions at any one stage of descent.’”

Comment by JOHN_A_DESIGNER — May 24, 2010 @ 1:32 pm

ID guy Says:
May 24th, 2010 at 5:50 pm
RichTard,

You only think you have a clue.

But in reality all you can do is to blindly and mindlessly parrot the party propaganda.

And when you do that you prove you don't know jack about science.

Comment by ID guy — May 24, 2010 @ 5:50 pm

ID guy Says:
May 24th, 2010 at 6:08 pm
Why RichTard is clueless:

If the solar system was brought about by an accidental collision, then the appearance of organic life on this planet was also an accident, and the whole evolution of Man was an accident too. If so, then all our present thoughts are mere accidents – the accidental by-product of the movement of atoms. And this holds for the thoughts of the materialists and astronomers as well as for anyone else's. But if their thoughts – i.e., of Materialism and Astronomy – are merely accidental by-products, why should we believe them to be true?

I see no reason for believing that one accident should be able to give me a correct account of all the other accidents.

It's like expecting that the accidental shape taken by the splash when you upset a milk-jug should give you a correct account of how the jug was made and why it was upset.–CS Lewis

And what CS Lewis said is backed up by Stphen Hawking- that our existence is an accident…

Comment by ID guy — May 24, 2010 @ 6:08 pm

Richardthughes Says:
May 24th, 2010 at 6:24 pm
Age of the universe = "party propaganda".

Oh Joe, why so embarrassed at being a YEC?

Just get with Sal, he's got a website that will bring you up to speed. You can show him AIG and Creation Safaris which you often link to.

Comment by Richardthughes — May 24, 2010 @ 6:24 pm

ID guy Says:
May 24th, 2010 at 7:14 pm
Richtardhughes:
Age of the universe = "party propaganda".

That is correct.

And this is why:

If the solar system was brought about by an accidental collision, then the appearance of organic life on this planet was also an accident, and the whole evolution of Man was an accident too. If so, then all our present thoughts are mere accidents – the accidental by-product of the movement of atoms. And this holds for the thoughts of the materialists and astronomers as well as for anyone else's. But if their thoughts – i.e., of Materialism and Astronomy – are merely accidental by-products, why should we believe them to be true?

I see no reason for believing that one accident should be able to give me a correct account of all the other accidents.

It's like expecting that the accidental shape taken by the splash when you upset a milk-jug should give you a correct account of how the jug was made and why it was upset.–CS Lewis

Not being to understand richtard is forced to spout false accusations:

why so embarrassed at being a YEC?

I am not a YEC- I do not accept the Bible as any authority.

I do not accept the divinity of Jesus of Nazareth.

And I have not seen any evidence that the Earth is only 6,000-12,000 years old.

Comment by ID guy — May 24, 2010 @ 7:14 pm

Richardthughes Says:
May 24th, 2010 at 7:24 pm
CS – bad analogy, but interesting you're into him, Joe.

Comment by Richardthughes — May 24, 2010 @ 7:24 pm

ID guy Says:
May 24th, 2010 at 7:51 pm
Why is a bad analogy Richtard?

It happens to be spot on.

Or do you know of any reasons why one set of accumulated accidents should eb able to give a correct accounting of other sets of accumulated accidents?

Or are unsupported one-liners the best you have?

Comment by ID guy — May 24, 2010 @ 7:51 pm

Richardthughes Says:
May 24th, 2010 at 9:48 pm
Oh well if you say that it's a bad analogy and then follow up with your cut-and-paste soundbite, it must be true.

We believe our thoughts and rationality to be 'true' because they can be checked against reality. you can use your senses to observe the universe, interact with other minds and assess the validity / utility of your thoughts temporarily.

Lewis is another who flails against materialism – yet he uses it every second of his life just like everyone else.

Comment by Richardthughes — May 24, 2010 @ 9:48 pm

olegt Says:
May 25th, 2010 at 12:28 am
Salvador T. Cordova wrote:

How one can get from "the search for patterns that signify intelligence" to :

the ID advocate is assuming that an anomaly in the apparently seamless story of evolution is a necessary condition for a defeater to naturalism

is beyond me.

Sal, why don't you read a discussion of Denton's Nature's Destiny by a panel of ID theorists and answer this simple question: why are Dembski, Nelson, Wells, Meyer, and even Behe are so vehemently opposed to Denton's newly found approach? My answer is because it does not include any discontinuities in the evolutionary scenario. What's yours?

Comment by olegt — May 25, 2010 @ 12:28 am

Pez Says:
May 25th, 2010 at 1:05 am
If there are discontinuities they are in nature, Oleg, not in "approaches".
Don't bother letting thm say for themselves what their problem is – the absence of directed contingency in his solution, the explication of what is implicit (that choices had to be made), the inability of law (alone) to make choices, etc.

Being wrong on two threads doesn't make you right.

Comment by Pez — May 25, 2010 @ 1:05 am

Salvador T. Cordova Says:
May 25th, 2010 at 2:16 am
Olegt asked:

Sal, why don't you read a discussion of Denton's Nature's Destiny by a panel of ID theorists and answer this simple question: why are Dembski, Nelson, Wells, Meyer, and even Behe are so vehemently opposed to Denton's newly found approach? My answer is because it does not include any discontinuities in the evolutionary scenario. What's yours?

First I would not characterize Dembski, Nelson, Wells, and Meyer and even Behe as "vehemently" opposed, but they are very critical with some elements of praise.

Second: "My answer is because it does not include any discontinuities in the evolutionary scenario." Is close to what I think. Denton wanted to connect physics directly to biology. This was expressed more clearly in his essay in "Uncommon Dissent".

Dembski (and others) think that the important features of biology transcend physics much like software transcends hardware. Dembski's view is identical to mine in that respect. Thus we disagree with Denton that one can seamlessly connect physics to biology (since software is not seamlessly connected to hardware in the conceptual sense, but rather detached in a conceptual sense).

Dembski articulates this critique:

Dembski: Having said this, I think there’s a serious confusion in Nature’s Destiny between necessary and sufficient conditions, a confusion related to Denton’s deeper goal of explaining life only in terms of natural regularities. “Creation by law,” or “design by law”–that’s what Denton is after. It reminds one of the ideas circulating in the early 19th century. God designed the world, to be sure, only he did so through natural laws. Denton cites the pre-Darwinian teleological evolutionist Robert Chambers favorably, and calls his idea of “directed evolution,” as elaborated in Chambers’s Vestiges of the Natural History of Creation (1844), “immensely attractive” (p. 272). The idea may be attractive, but I’m afraid it just doesn’t work. Natural regularities, or the necessary physical conditions which Denton discusses, by their very nature cannot generate the specified complexity required for life.

From computer science we see that computer hardware is not a sufficient description or explanation of computer software. There is a similar parallel between the software of life (symbols and genetic codes, etc.) and the hardware (chemistry and physics) of life. For an information processing system to work, there have to be dimensions not constrained by regularity or lawlike behavior.

Denton does not account for this distinction. He thinks that life can be sufficiently described by the laws of physics.

Now if one wishes to argue that Denton is crticized because he is not a creationist, I don't think that is a strong argument. His writings are valued especially because he is NOT a creationist. It is precisely because Denton and Sternberg are not creationists that there critique of Darwin holds more weight because they can't be accused of creationist bias in their critique of Darwin.

I do think there was a falling out of sorts between Denton and the DI and Denton and ARN. I don't know all the details.

One final note, Denton and Behe are the only evolutionists I know of whose books are sold by Answers in Genesis.

Comment by Salvador T. Cordova — May 25, 2010 @ 2:16 am

Salvador T. Cordova Says:
May 25th, 2010 at 2:42 am
I say again:

How one can get from "the search for patterns that signify intelligence" to :

the ID advocate is assuming that an anomaly in the apparently seamless story of evolution is a necessary condition for a defeater to naturalism

is beyond me.

The ID advocate does not need to assume any such thing. Dembski's essay, "The Last Magic" is a case in point.

See: The Last Magic and see if the is one shred of mention of "an anomaly in the apparently seamless story of evolution is a necessary condition for a defeater to naturalism"! Rather:

Equations that are factorable are much easier for us to deal with than those that are not. Factorability, however, has no physical significance. A world indifferent to us has no stake in rendering itself intelligible to us by making the equations that describe it factorable through some mathematical device (like the Clifford algebra). And yet precisely such idiosyncratic manipulations of humanly constructed notations result in genuine and previously unsuspected physical insights.

There really is a problem here for naturalism. As Steiner notes, in every other area where human constructions are manipulated according to human convenience, naturalism expects and indeed confirms no profound in sight into the structure of the world. The rules of chess, for instance, do not yield insight into the structure of the atom. The study of palindromes (sentences that read the same backward as forward; e.g., "Madam, I'm Adam") tells us nothing about the first three minutes after the Big Bang.

Indeed, the claim that human constructions manipulated according to human convenience supply insights into reality belongs to what traditionally has been called magic—the view that what humans do in the purely human world (i.e., the microcosm) mirrors the deep structure of the world at large (i.e., the macrocosm). Naturalism has no place for magic. And yet the applicability of mathematics to physics is magic. Ac cording to Steiner, mathematics is the last redoubt of magic, but one that stands se cure and is in no danger of naturalistic debunking. This is a user-friendly world where we humans are the users, and where the tool of discovery that renders the natural world friendly is mathematics.

In place of naturalism, Steiner therefore opts for an anthropocentrism which affirms that humans do have a privileged place in the scheme of things. Steiner's anthropocentrism falls short of a full-blown metaphysical position like Judeo-Christian theism, Platonism, or Pythagoreanism. But it stands sharply against the widely held evolutionary view that humans are mere accidents of natural history.

The Applicability of Mathematics As a Philosophical Problem is a technical contribution to analytic philosophy that presupposes not just a background in philosophy but also extensive exposure to mathematics and physics. Readers without the relevant technical background should be prepared to find no more than 20 percent of the book intelligible. Even so, Steiner's challenge to naturalism is accessible, powerful, and well worth pondering.

Thus this is an example of an argument against naturalism by Dembski that doesn't rely on "assuming that an anomaly in the apparently seamless story of evolution is a necessary condition for a defeater to naturalism".

Frank is way off target.

Comment by Salvador T. Cordova — May 25, 2010 @ 2:42 am

Salvador T. Cordova Says:
May 25th, 2010 at 2:43 am
Gasp! Where is the edit button. Can I have it back.

Comment by Salvador T. Cordova — May 25, 2010 @ 2:43 am

Salvador T. Cordova Says:
May 25th, 2010 at 2:53 am
By what I just wrote above regarding the last magic, it follows that although a sufficiently powerful anomaly in the evolutionary story is a sufficient condition to defeat naturalism, it is not a necessary condition.

But this does not preclude ID advocates from arguing for sufficient conditions.

The following mis-states confuses "necessary conditions" with "sufficient conditions"

the ID advocate is assuming that an anomaly in the apparently seamless story of evolution is a necessary condition for a defeater to naturalism

No.

Necessary conditions are not the same as sufficient conditions. Bad, bad, bad, logic!!!!

Better to re-write:

the ID advocate is assuming that an anomaly in the apparently seamless story of evolution is a sufficient condition for a defeater to naturalism

Even Jerry Coyne would agree with that!

Comment by Salvador T. Cordova — May 25, 2010 @ 2:53 am

ID guy Says:
May 25th, 2010 at 7:34 am
richtardhughes:
Oh well if you say that it's a bad analogy and then follow up with your cut-and-paste soundbite, it must be true.

What the hell is that supposed to mean?

We believe our thoughts and rationality to be 'true' because they can be checked against reality. you can use your senses to observe the universe, interact with other minds and assess the validity / utility of your thoughts temporarily.

But we wouldn't expect to be able to do such a thing if this was all a series of accidents.

And we sure as hell cannot your position against reality.

IOW rich is this was all an accident then you have no idea what is valid and what isn't.

Lewis is another who flails against materialism – yet he uses it every second of his life just like everyone else.

Any evidence for your slander?

Comment by ID guy — May 25, 2010 @ 7:34 am

ID guy Says:
May 25th, 2010 at 7:38 am
olegt-

Methinks you have no idea what Denton is saying.

Anyone who has read "Nature's Destiny" knows he is into front-loading.

He thinks that biological form is dictated by some yet to be discovered law.

However he is wrong- form is dictated by the software that not only controls development but also determines the outcome.

Comment by ID guy — May 25, 2010 @ 7:38 am

Richardthughes Says:
May 25th, 2010 at 9:55 am
But we wouldn't expect to be able to do such a thing if this was all a series of accidents.

Why not? I don't see anything past personal incredulity.

Comment by Richardthughes — May 25, 2010 @ 9:55 am

Richardthughes Says:
May 25th, 2010 at 10:01 am
Any evidence for your slander?

Yes. He never levitated to work, nor cooked his food by pyrokinesis. No one ever reported having a telepathic conversation with him and his teleportation was somewhat lacking.

Sadly, like everyone else everywhere else everywhen else, he had to move atoms to get stuff done. Or so the dark brotherhood of the materialist cabal would have us believe.

Slander, eh? Another word you don't understand.

Comment by Richardthughes — May 25, 2010 @ 10:01 am

ID guy Says:
May 25th, 2010 at 11:11 am
But we wouldn't expect to be able to do such a thing if this was all a series of accidents.

Richtardhughes:
Why not?

It's up to you to tell us why one series of accidents would be able to give a correct accounting of other series of accidents.

As for the slander:

Lewis is another who flails against materialism – yet he uses it every second of his life just like everyone else.

There isn't any evidence that CS Lewis "flails away at materialism"- just your slanderous droolage.

Also it is a safe to say that you don't understand what is meant by "materialism"- it is the ideology that everything can be reduced to matter and energy…

Comment by ID guy — May 25, 2010 @ 11:11 am

ID guy Says:
May 25th, 2010 at 11:13 am
slander

1 : the utterance of false charges or misrepresentations which defame and damage another's reputation
2 : a false and defamatory oral statement about a person

Excatly what richtard was attempting to do to CS Lewis.

Comment by ID guy — May 25, 2010 @ 11:13 am

Richardthughes Says:
May 25th, 2010 at 11:53 am
What does 'utterance' and 'oral' mean, Joe?

It is not incumbent for me to account for everything. That's why ID is such a crock – Son of god of the gaps.

Show me some things that aren't reduced to matter and energy, Joe.

Comment by Richardthughes — May 25, 2010 @ 11:53 am

Salvador T. Cordova Says:
May 25th, 2010 at 12:15 pm
Show me some things that aren't reduced to matter and energy

Mathematics.

Comment by Salvador T. Cordova — May 25, 2010 @ 12:15 pm

Richardthughes Says:
May 25th, 2010 at 12:16 pm
Is there any math without a contruct to do them?

Comment by Richardthughes — May 25, 2010 @ 12:16 pm

ID guy Says:
May 25th, 2010 at 5:32 pm
richtardhughes:
Show me some things that aren't reduced to matter and energy,

There isn't any evidence that living organisms are so reducible.

Then there are all the artifacts in the world- by definition they are not reducible to matter and energy.

The laws of nature are not reducible to matter and energy.

Also it is incumbent on you to be able to provide positive evidence for your position.

Yet you have failed to do so.

Comment by ID guy — May 25, 2010 @ 5:32 pm

ID guy Says:
May 25th, 2010 at 5:33 pm
utterance:

1 : something uttered; especially : an oral or written statement : a stated or published expression

IOW richtard, your ignorance is exposed yet again…

Comment by ID guy — May 25, 2010 @ 5:33 pm

ID guy Says:
May 25th, 2010 at 5:38 pm
As for the "oral" part, well that is taken care of because it is a given that you have to mouth the words as you type.

Comment by ID guy — May 25, 2010 @ 5:38 pm

Richardthughes Says:
May 25th, 2010 at 5:52 pm
Legal terminology – something *else* you don't understand. What's the difference between libel and slander, Joe? You're exposing someone's ignorance, Joe – that's for sure.

Laws of nature are constructs that need matter and energy to have foundation. I'm fairly sure matter and energy exist Joe. You're probably 'not sure' as this seems to be your line with widely accepted facts.

There is no evidence that living organisms are made up of matter and energy? really?

Comment by Richardthughes — May 25, 2010 @ 5:52 pm

Richardthughes Says:
May 25th, 2010 at 6:00 pm
Only 1 entry for "utterance", Joe?

Comment by Richardthughes — May 25, 2010 @ 6:00 pm

ID guy Says:
May 25th, 2010 at 6:03 pm
richtard:
Only 1 entry for "utterance"

All it takes is one to expose your ignorance, richtard.

Comment by ID guy — May 25, 2010 @ 6:03 pm

ID guy Says:
May 25th, 2010 at 6:07 pm
richtard:
Legal terminology – something *else* you don't understand. What's the difference between libel and slander,

You slandered CS Lewis richtard.

Laws of nature are constructs that need matter and energy to have foundation.

That does not mean that they are reducible to matter and energy- duh.

There is no evidence that living organisms are made up of matter and energy?

There isn't any evidence that living organisms are REDUCIBLE to matter and enery, richtard.

I take it that English is not your primary language.

Either that or you are just plain stupid/ dishonest.

Comment by ID guy — May 25, 2010 @ 6:07 pm

CharlieM Says:
May 25th, 2010 at 7:50 pm
richtardthughes:
Show me some things that aren't reduced to matter and energy

CharlieM:
To keep things simple; straight lines. (Not approximations of straight lines.)

I suppose to simplify things even further I could have said points in space.

Comment by CharlieM — May 25, 2010 @ 7:50 pm

CharlieM Says:
May 25th, 2010 at 8:26 pm
Francis Beckwith from article:
Biologist Lynn Margulis, for example, has offered endosymbiotic theory as a non-neo-Darwinian evolutionary account that may explain irreducible complexity without requiring a design inference.

CharlieM:
The consensus seems to be that mitochondria are captured bacteria. I was wondering if it could be the other way round and bacteria developed from escapee mitochondria or mitochondria like organelles? Are there any reasons why this couldn't be the case?

Comment by CharlieM — May 25, 2010 @ 8:26 pm

Richardthughes Says:
May 25th, 2010 at 9:08 pm
Answer the question Joe – what's the difference between slander and libel?

For a guy who pretends not to be ID guy, you've got no grounds to lecture on honesty. I don't go 'round the internet threatening people with in real life meetings like you.

Have a look at yourself sometime. Is this what your mother wanted for you?

Comment by Richardthughes — May 25, 2010 @ 9:08 pm

Richardthughes Says:
May 25th, 2010 at 9:10 pm
Charlie, what are these lines made of?

Comment by Richardthughes — May 25, 2010 @ 9:10 pm

CharlieM Says:
May 26th, 2010 at 5:35 am
Richardthughes Says:
Charlie, what are these lines made of?

CharlieM:
They are not made of matter that's for sure. Draw a 'straight line' on paper with pencil and look at it through a microscope. It is as much a straight line as the Rockies are. Because it has breadth its edge will be a meandering line, in other words nowhere near straight. What you will have is an approximation of a straight line.

Comment by CharlieM — May 26, 2010 @ 5:35 am

ID guy Says:
May 26th, 2010 at 7:20 am
richtard:
what's the difference between slander and libel?

They are pretty much the same richtard- both deal with defamation.

Are you trying to say that the accepted definition of "slander" I provided is wrong?

I don't go 'round the internet threatening people with in real life meetings like you.

How is meeting people a threat?

You just go around slanering people and spouting false accusations.

Now back to materialism- Thank you for proving your ignorance on that subject too.

Comment by ID guy — May 26, 2010 @ 7:20 am

ID guy Says:
May 26th, 2010 at 7:24 am
Information is not reducible to matter and energy:

Information is information, neither matter nor energy. Any materialism that disregards this will not survive one day–Norbert Weiner

So we have living organisms- there isn't any evidence they are reducible to matter and energy; artifacts, which by their definition are not reducible to matter and energy; and information.

Comment by ID guy — May 26, 2010 @ 7:24 am

ID guy Says:
May 26th, 2010 at 7:33 am
difference between libel and slander:

One of the main areas of controversy when determining whether something qualifies as libel or slander is online media. For example, online chats are broadcast through a mass medium and are written forms of communication, so one could consider any defamatory statements that take place online to be libelous. However, the mode of online chats is similar to a face-to-face conversation or phone call, which would qualify as slander if someone published or broadcast these communications. Generally speaking, courts usually decide whether online communication qualifies as libel or slander on a case-by-case basis.- (bold added)

You lose again richtard…

Comment by ID guy — May 26, 2010 @ 7:33 am

Richardthughes Says:
May 26th, 2010 at 9:44 am
Online chat are things like AIM,MSM, etc.

This is a messageboard / blog. oops.

How is meeting people a threat?

https://www.blogger.com/commen...

Rich, you silly man. You should know that when Joe says,

"And I am being very generous by saying that on this blog as opposed to driving a few miles to say it to your face,"

and

"I will do whatever it takes to stop it,"

plus,

"I was at the BC game yesterday. I think you know what that means… (think location),"

he really means

"I would like please to give you an old edition of a basic anatomy book."

H

Comment by Richardthughes — May 26, 2010 @ 9:44 am

ID guy Says:
May 26th, 2010 at 10:49 am
However, the mode of online chats is similar to a face-to-face conversation or phone call, which would qualify as slander if someone published or broadcast these communications.

Note the words "similar to". This forum is similar to a face-to-face conversation.

And:

Generally speaking, courts usually decide whether online communication qualifies as libel or slander on a case-by-case basis.

IOW Richtardhughes doesn't get to make that decision.

As for how is meeting people a threat, is that all you have to make your case?

You are a joke…

Comment by ID guy — May 26, 2010 @ 10:49 am

ID guy Says:
May 26th, 2010 at 10:53 am
The way evolutionists treat anyone who disagrees with them is a threat to all of those people.

Evolutionists are bullies and now that they have the internet they are cyber-bullies.

And cyber-bullies, as with all bullies, deserve what they get.

I would say if one person taunts and slanders another they too deserve what they get.

Comment by ID guy — May 26, 2010 @ 10:53 am

Richardthughes Says:
May 26th, 2010 at 11:17 am
And cyber-bullies, as with all bullies, deserve what they get.

I would say if one person taunts and slanders another they too deserve what they get.

What does that mean, Joe? If they get cancer, do they deserve that? Are you advocating that any retribution for perceived 'cyber bullying' is okay?

Comment by Richardthughes — May 26, 2010 @ 11:17 am

ID guy Says:
May 26th, 2010 at 11:27 am
If they get cancer, do they deserve that?

If the cancer is directly linked to their actions of bullying, yes.

Are you advocating that any retribution for perceived 'cyber bullying' is okay?

Nope.

I am saying that one's actions have consequences regardless of whether or not the consequences fit the "crime".

If you want to poke someone with a stick don't be surprised if that stick winds up being shoved up your…

Comment by ID guy — May 26, 2010 @ 11:27 am

Richardthughes Says:
May 26th, 2010 at 11:37 am
But Joe, "poking with a stick" is a metaphor. There is no real stick. Its imaginary.

If someone doesn't tie their shoelace and trips and dies, do they deserve that?

Comment by Richardthughes — May 26, 2010 @ 11:37 am

ID guy Says:
May 26th, 2010 at 12:01 pm
richtard:
"poking with a stick" is a metaphor

Not always.

Its imaginary.

Obviously so are the "threats" you said I have made.

If someone doesn't tie their shoelace and trips and dies, do they deserve that?

If that person is a bully who has never atoned for that, yes.

So are you trying to use this distraction to try to hide the fact that you don't know what you are talking about pertaining to science, ID and materialism?

Comment by ID guy — May 26, 2010 @ 12:01 pm

Richardthughes Says:
May 26th, 2010 at 12:02 pm
So a rightful punishment for 'unatoned bullying' is death? How hold testament!

Has anyone here ever poked you with a real stick?

Comment by Richardthughes — May 26, 2010 @ 12:02 pm

Richardthughes Says:
May 26th, 2010 at 12:03 pm
*hold / old. *sigh*

Comment by Richardthughes — May 26, 2010 @ 12:03 pm

ID guy Says:
May 26th, 2010 at 12:08 pm
richtard:
So a rightful punishment for 'unatoned bullying' is death?

Death by their own stupidity/ incompetence, why not?

Try to stay in context.

Has anyone here ever poked you with a real stick?

Yes.

So you are trying to distract fdrom the fact that you don't know what you are talking about.

How evolutionary of you…

Comment by ID guy — May 26, 2010 @ 12:08 pm

Richardthughes Says:
May 26th, 2010 at 12:11 pm
That is terrible! who here poked you with a real stick? Don't worry Joe – you have my full support in this frankly unacceptable episode.

Comment by Richardthughes — May 26, 2010 @ 12:11 pm

ID guy Says:
May 26th, 2010 at 12:31 pm
Yes it is pathetically terrible that you have to try to distract from the fact that you don't know what you are talking about and are forced to fart false accusations and slanderous comments.

Comment by ID guy — May 26, 2010 @ 12:31 pm

Richardthughes Says:
May 26th, 2010 at 12:36 pm
Joe, if someone here poked you with real, physical stick I think we all need to know who it was and when it happened. That sort of behaviour is just unacceptable – you should consider informing the police.

Comment by Richardthughes — May 26, 2010 @ 12:36 pm

ID guy Says:
May 26th, 2010 at 12:51 pm
The chimpish behaviour of evolutionists is unacceptable, yet it goes on unabated.

Your childish behaviour should be unacceptable, but seeing it is all you have it is tolerated.

Comment by ID guy — May 26, 2010 @ 12:51 pm

Richardthughes Says:
May 26th, 2010 at 1:00 pm
Joe, I don't think you understand how serious your claim is. It may be categorized as 'assault' and there is no place for that regardless of ideological difference. When and where did this happen?

Comment by Richardthughes — May 26, 2010 @ 1:00 pm

ID guy Says:
May 26th, 2010 at 1:04 pm
I know how serious my claim is-> Evolutionists are dirty little chimps and you are a dirty little child.

Now what?

Comment by ID guy — May 26, 2010 @ 1:04 pm

Richardthughes Says:
May 26th, 2010 at 1:56 pm
Joe. I know reliving the event may be hard, but you might have to address it for your long term good.

PTSD symptoms include "Intrusive symptoms might include daytime fantasies, traumatic nightmares, and even vivid breaks with reality. When such symptoms of "re-experiencing" occur, people naturally try to avoid or suppress them. In extreme cases, the individual refuse to leave the house out of fear of coming across reminders of the trauma. "

That's not healthy, and I feel the stick poker should be brought to justice, but not death as you seem to think is appropriate.

Comment by Richardthughes — May 26, 2010 @ 1:56 pm

Satolep Says:
May 26th, 2010 at 3:39 pm
Now when the absurd claim that somebody did something sometime without any clues about who did what when that is all that ID is about has grown so painfully boring, it is quite entertaining and refreshing to see a real issue being debated at TT. That should up the attendance thermometer a bit.

Now, can we learn who did what to ID guy when? I.e., who poked ID-guy with a stick (probably an atheistic evilutionist), where and when? That looks like a much more productive sort of debate than about ID itself; that one is as dead as the porcupines I see on the highway.

Comment by Satolep — May 26, 2010 @ 3:39 pm

Bradford Says:
May 26th, 2010 at 4:31 pm
I'll hole any more comments that are not related to the thread topic.

Comment by Bradford — May 26, 2010 @ 4:31 pm

Acipenser Says:
May 26th, 2010 at 9:05 pm
Sal: Case in point, Michael Behe vs. Ken Miller or Rick Sternberg vs. Darrell Falk: .

So it doesn't speak well of Miller and Falk that they are being sucessfully challenged by ID proponents who are supposedly "bonkers". Further, Behe was giving Miller some remedial lessons in biochemistry (Miller didn't know that hormones are not proteins but lipids). Kind of embarassing for Miller I'd say.

Remedial lessions? I don't think so, Sal.

The majority of hormones are peptides and proteins as any remedial book on endocrinology will demonstrate. For example calcitonin, vasopresson, insulin, and everything made by the pituitary and parathyroid glands We, of course, could also include the amine hormones, e.g., epinephrine, norepinephrine, thyroxine, melatonin. (none of those represent complete lists, FYI).

I wouldn't hang my hat or reputation on that quote since it is so obviously false.

Comment by Acipenser — May 26, 2010 @ 9:05 pm

Salvador T. Cordova Says:
May 27th, 2010 at 10:55 am
Remedial lessions? I don't think so, Sal.

The majority of hormones are peptides and proteins as any remedial book on endocrinology will demonstrate. For example calcitonin, vasopresson, insulin, and everything made by the pituitary and parathyroid glands We, of course, could also include the amine hormones, e.g., epinephrine, norepinephrine, thyroxine, melatonin. (none of those represent complete lists, FYI).

I wouldn't hang my hat or reputation on that quote since it is so obviously false.

I misquoted Behe, the word should be STEROID not HORMONE.

Now, dear reader, when Miller writes of “protein-to-protein” binding sites in one sentence, wouldn’t you expect the papers he cites in the next sentence would be about protein-to-protein binding sites? Well — although the casual reader wouldn’t be able to tell — they aren’t. None of the papers Miller cites involves protein-protein binding sites. The Science paper concerns protein-steroid-hormone binding;

So Miller needs remedial lessons in biochemistry as much as I do.

Still think well you Ken Miller Acipenser? That was a retarded mistake by and Ivy League professor, or better yet, a literature bluff that he didn't expect to get called on.

Comment by Salvador T. Cordova — May 27, 2010 @ 10:55 am

Acipenser Says:
May 27th, 2010 at 11:32 am
S

al: Still think well you Ken Miller Acipenser? That was a retarded mistake by and Ivy League professor, or better yet, a literature bluff that he didn't expect to get called on.

Given that you were mistaken once and have provided no link for independent verification I have no idea if Miller made a "retarded msitake" or not.

Do you have a link for the entire discourse so correct context, content, and perspective can be placed on whatever the original quote actually is?

Comment by Acipenser — May 27, 2010 @ 11:32 am

Salvador T. Cordova Says:
May 27th, 2010 at 8:56 pm
Given that you were mistaken once and have provided no link for independent verification I have no idea if Miller made a "retarded msitake" or not.

Do you have a link for the entire discourse so correct context, content, and perspective can be placed on whatever the original quote actually is?

A simple cut-and-paste and into google would have gotten you the link.

Comment by Salvador T. Cordova — May 27, 2010 @ 8:56 pm

Acipenser Says:
May 27th, 2010 at 9:39 pm
Sal: A simple cut-and-paste and into google would have gotten you the link.

Sometimes I feel like going on scavenging hunts and sometimes not so much.

Behe is trying (miserably at that) to make a mountain out of a molehill in trying to parse away the evolution of new binding sites….both STEROID hormone-protein and protein-protein binding sites. ERV (aka, Abbie Smith) handily called Behe on his mistaken belief that new protein-protein binding sites are beyond the edge of evolution.

http://pandasthumb.org/archive...

http://pandasthumb.org/archive...

As was pointed out to Behe this information was available since 1988 and ignoring this evidence in his book Edge of Evolution makes one wonder why he would do that in the first place.

Comment by Acipenser — May 27, 2010 @ 9:39 pm

ID guy Says:
May 28th, 2010 at 7:49 am
Acipenser,

The theory of evolution needs much, much more than just a new binding site in order to get the diversity of life from some population(s) of single-celled organisms.

And Abbie was only to provide one new binding site in a virus- a virus that remained virtually the same even given this new feature.

Do you really think that helps you?

Also doe Abbie have any data that supports the claim that this new binding site was the result of blind, undirected chemical processes?

Comment by ID guy — May 28, 2010 @ 7:49 am

Acipenser Says:
May 28th, 2010 at 12:41 pm
IDguy:The theory of evolution needs much, much more than just a new binding site in order to get the diversity of life from some population(s) of single-celled organisms.

You should jsut leave the goalposts where they are set instead of trying to move them around. In this case Behe drew the line in the sand at no new protein-protein binding sites have or will develop. This was clearly falsified.

ID guy:And Abbie was only to provide one new binding site in a virus- a virus that remained virtually the same even given this new feature.

Which was all that was necessary to refute Behe's claim. Sorry the virus didn't turn into a turnip for you but no one really expected in would. That is an old YEC canard that should be put to rest.

ID guy: Do you really think that helps you?

Helps me? I don't think it helps or hurts me in any fashion but it clearly refutes Behe's unfounded assertions which is the issue in this case after all.

Comment by Acipenser — May 28, 2010 @ 12:41 pm

Guts Says:
May 28th, 2010 at 2:15 pm
Acipenser, if Behe's claim is that no protein-protein binding sites have or will ever develop, then why does he himself give an example of one developing in his book?

Comment by Guts — May 28, 2010 @ 2:15 pm

Acipenser Says:
May 28th, 2010 at 3:15 pm
guts:Acipenser, if Behe's claim is that no protein-protein binding sites have or will ever develop, then why does he himself give an example of one developing in his book?

Perhaps the same sloppiness that led to his confusion of genomic RNA and proviral DNA in HIV.

Failing to cite the oligomerization of Vpu into a pentameric ion channel (as well as other novel functions, e.g., golgi bindingwhile citing sickel cell anemia is, IMO, a purposeful ommission. Hey to his credit (very little actually) it only took him 105 days to admit he was wrong after ERV pointed out his obviously erroneous claim.

Comment by Acipenser — May 28, 2010 @ 3:15 pm

CharlieM Says:
May 28th, 2010 at 4:37 pm
guts:Acipenser, if Behe's claim is that no protein-protein binding sites have or will ever develop, then why does he himself give an example of one developing in his book?

Acipenser:
Perhaps the same sloppiness that led to his confusion of genomic RNA and proviral DNA in HIV.

CharlieM:
I haven't read 'The Edge of Evolution' so maybe someone can clear up an inconsistency here.

Behe from his Amazon blog:
Miller is as subtly misleading when writing about the substantive points of The Edge of Evolution as he is when making supercilious offhand comments. Miller writes: “Telling his readers that the production of so much as a single new protein-to-protein binding site is ‘beyond the edge of evolution’, [Behe] proclaims darwinian evolution to be a hopeless failure.” But the book says plainly that it is two, not one, binding sites that marks the edge of evolution. That was not an obscure point. Chapter 7 is entitled “The Two-Binding-Sites Rule”; Figure 7.4 has a line at two binding sites, with a big arrow pointing to it labeled “Tentative molecular edge of evolution.” What’s more, the book goes out of its way to say that Darwinism is certainly not a “hopeless failure”, that there are important biological features it clearly can explain. That’s why one chapter is called “What Darwinism Can Do”.

Behe is drawing a 'tentative' line here at two binding sites. Someone is moving the goalposts and I'd like to know, who? Is there an instance where Behe says, 'no new protein-protein binding sites have or will develop'? And if so what was the context?

Comment by CharlieM — May 28, 2010 @ 4:37 pm

ID guy Says:
May 28th, 2010 at 4:59 pm
Acipenser:
In this case Behe drew the line in the sand at no new protein-protein binding sites have or will develop.

Not the Dr Behe I have read.

As Charlie M has pointed out the criterion is two protein-protein binding sites- that is in "The Edge of Evolution".

What Abbie was crying about is that he has 0 (zero) new protein binding sites for HIV and apparently there has been one (table on page 143).

Such is the "power" of blind, undirected chemical processes.

Comment by ID guy — May 28, 2010 @ 4:59 pm

Acipenser Says:
May 28th, 2010 at 5:28 pm
ChalireM: Behe is drawing a 'tentative' line here at two binding sites.

Behe ahs already admitted the error of his ways and basically ahs transitioned from: HIV has not (and implied cannot) develop any new biochemical pathways/mechanisms (paraphrased) to now it is HIV easily evolved new biochemical mechanisms pathways.

ID guy: What Abbie was crying about is that he has 0 (zero) new protein binding sites for HIV and apparently there has been one (table on page 143).

I don't think Abbie is/was crying at all but Behe probably is given he was bested by an undergrad and a woman undergrad at that.

There are more than one new protein-protein binding sites that have occurred in HIV that Abbie has pointed out to Behe…….CD4 binding with 2 CII-kinases and a novel golgi binding that facilitates removal of CD4 proteins. There are also others that are being investigated so the number is obviously higher than 0 and even greater than 1.

If you think the biochemical changes were not significant/powerful than the ID camp should have no problem popping out a vaccine for HIV.

The point being that Behe was so obviously worng and so reluctant to admit the error of his ways on this easily checkupable fact and to me this indicates the ommisions was purposeful and meant to pander to his followers. Or, conversely, he is just a really sloppy researcher (non-researcher for over 10 years now) and didn't find any mention of these research findings in the NY Times. Take your pick.

Comment by Acipenser — May 28, 2010 @ 5:28 pm

ID guy Says:
May 28th, 2010 at 6:17 pm
Acipenser,

It is obvious that you don't have any idea what Dr Behe has claimed and all you can do is blindly flail away in the hope of hitting something.

Comment by ID guy — May 28, 2010 @ 6:17 pm

Acipenser Says:
May 28th, 2010 at 7:18 pm
ID guy: It is obvious that you don't have any idea what Dr Behe has claimed and all you can do is blindly flail away in the hope of hitting something.

LOL…and whatever was hit was hit out-of-the-park with Behe's admission that he was indeed wrong and a woman undergrad was correct!

Comment by Acipenser — May 28, 2010 @ 7:18 pm

CharlieM Says:
May 28th, 2010 at 7:49 pm
Acipenser:
Behe ahs already admitted the error of his ways and basically ahs transitioned from: HIV has not (and implied cannot) develop any new biochemical pathways/mechanisms (paraphrased) to now it is HIV easily evolved new biochemical mechanisms pathways.

CharlieM:
Can you supply references?

Michael Behe from 'Edge'
Another, more important point to note is that I’m considering just cellular proteins binding to other cellular proteins, not to foreign proteins. Foreign proteins injected into a cell by an invading virus or bacterium make up a different category. [emphasis added here] The foreign proteins of pathogens almost always are intended to cripple a cell in any way possible. Since there are so many more ways to break a machine than to improve it, this is the kind of task at which Darwinism excels. Like throwing a wad of chewing gum into a finely tuned machine, it’s relatively easy to clog a system — much easier than making the system in the first place. Destructive protein-protein binding is much easier to achieve by chance.

Behe from Amazon blog:
The Edge of Evolution is concerned with how molecular machinery is constructed, not destroyed. One can’t ignore such critical distinctions and make progress.

Behe from Uncommondescent:
…Darwinian evolutionary scenarios where critical protein binding sites are assumed without justification to pop up when needed (such as, say, in the building of multiprotein structures like the cilium or flagellum).

CharlieM:
Can you supply any references to experiments or discoveries which relate to, or refute, Behe's main argument given above?

We know that critical protein binding sites occur in building structures but have any structural proteins with more than one critical binding site been observed to develop by Darwinian means?

Comment by CharlieM — May 28, 2010 @ 7:49 pm

olegt Says:
May 28th, 2010 at 8:28 pm
CharlieM wrote:

Behe is drawing a 'tentative' line here at two binding sites. Someone is moving the goalposts and I'd like to know, who? Is there an instance where Behe says, 'no new protein-protein binding sites have or will develop'? And if so what was the context?

Here is An Open Letter to Dr. Michael Behe written by Ian Musgrave. Here is the opening paragraph:

Dear Dr. Behe

I have recently read your response to Abbie Smith’s article on the HIV-1 protein VPU. Ms Smith showed how Vpu’s recently evolved viroporin activity directly contradicts your statement that HIV has evolved no new biding sites since it entered humans (Edge of Evolution, page 143 and figure 7.4, page 144 ). I was greatly disappointed in your response. I must admit to having a special involvement in this case. Firstly, I drew the illustrations for Ms Smith’s article, and its its follow up. But secondly, as a member of my professional association’s education committee, I am directly concerned with the support and nurturing of the new generations of enquiring minds, those that we will pass the torch of enquiry on to when we retire. It is in this regard that your response very disturbing. It is almost the exact opposite of what a concerned scientist and science communicator should have done.

From Behe's response, Part IV:

And now let’s talk about Dr. Musgrave’s “core argument,” that subsequent to the virus leaping to humans from chimps Vpu developed the ability to act as a viroporin, allowing the leakage of cations which helps release the virus from the cell membrane. Yes, I’m perfectly willing to concede that this does appear to be the development of a new viral protein-viral protein binding site, one which I overlooked when writing about HIV. So the square point in Figure 7.4 representing HIV should be placed on the Y axis at a value of one, instead of zero, and Table 7.1 should list one protein-binding site developed by HIV instead of zero.

Comment by olegt — May 28, 2010 @ 8:28 pm

Acipenser Says:
May 28th, 2010 at 8:28 pm
Charliem: Can you supply any references to experiments or discoveries which relate to, or refute, Behe's main argument given above?

If I were interested in taking on this side-task that would be something I would include in any refutation. But I'm not interested getting side-tracked off of this issue.

CharlieM: We know that critical protein binding sites occur in building structures but have any structural proteins with more than one critical binding site been observed to develop by Darwinian means?

You can put the goalposts down now so you don't wear yourself out.

What do you mean by structural? And how are 'we' going to define critical binding site? Or structures? Does protein folding and creation of an active site count as a structure, e.g., acetylcholinesterase? Would carbon dioxide binding to hemoglobin fit the bill or how about epoxide hydrolase and epoxide binding or any of the P450 isoforms and the multidude of substrates that bind to them? Would ion-channel formation count in your scenario? If not why not?

Proteins like to bind to each other, other molecules, peptides, sugars, ect. That you find so many binding sites (think active site of enzymes) should really come as no surprise.

CharlieM, Behe admitted his mistake years ago but I'm going to pull a Sal here and say a simple google search of the terms would get you the info you want. ERV posted on her blog (hint) so you might include that in yoru search.

Comment by Acipenser — May 28, 2010 @ 8:28 pm

Guts Says:
May 28th, 2010 at 9:42 pm
Acipencer that makes no sense. Consider the fact that your assertion is wrong instead.

Comment by Guts — May 28, 2010 @ 9:42 pm

Acipenser Says:
May 28th, 2010 at 9:52 pm
Guts: Acipencer that makes no sense. Consider the fact that your assertion is wrong instead.

Sure, whatever you say. Which one, i.e., assertion, would you like me to tackle first?

Comment by Acipenser — May 28, 2010 @ 9:52 pm

Guts Says:
May 28th, 2010 at 10:13 pm
It's rather odd to me that you don't think your assertion that"Behe drew the line in the sand at no new protein-protein binding sites have or will develop" is wrong. It's quite obviously wrong, since Behe discussed several examples of protein-protein binding sites developing, one of which by random mutation alone.

Comment by Guts — May 28, 2010 @ 10:13 pm

Acipenser Says:
May 28th, 2010 at 10:42 pm
Guts: It's rather odd to me that you don't think your assertion that"Behe drew the line in the sand at no new protein-protein binding sites have or will develop" is wrong. It's quite obviously wrong, since Behe discussed several examples of protein-protein binding sites developing, one of which by random mutation alone.

and yet we have Behe admitting to not mentioning the protein-protein binding which have evolved in HIV as he rightly should have in his book. Especially since the data were available for years prior to the writing of the book in the first place. Why would he admit to something he was wrong about if he wasn't wrong about it in the first place…even if it took 105 days to get to that point of acceptance for him.

Comment by Acipenser — May 28, 2010 @ 10:42 pm

Acipenser Says:
May 28th, 2010 at 10:46 pm
Guts, I meant to also include that I'll admit to incorrectly paraphrasing Behe but I don't see where that changes anything in relation to Behe's admission he was wrong or why he was wrong.

Comment by Acipenser — May 28, 2010 @ 10:46 pm

fifth monarchy man Says:
May 29th, 2010 at 12:52 am
Acipenser,

I hesitate to comment for fear that my lack of education will show but here goes.

In what way does Behe’s omission hurt his argument?

From my understanding of the book he never argued that protein-protein binding was impossible only that is was difficult. According to Behe the edge lies beyond this level of complexity

In fact it seems to me that this omited detail actually strengthens his case.

This example verifies that HIV is a proper subject of study. There is no quirk in the virus that makes it uniquely unable to develop a protein-protein binding .

At the same time that we apperently have only one example in HIV despite the unimaginable number of opportunities seems to support his contention that such things are difficult and rare.

If you’re only arguing that he made a mistake as to a certain fact, all I have to say is "after all this time is that all you got?"

peace

Comment by fifth monarchy man — May 29, 2010 @ 12:52 am

Bradford Says:
May 29th, 2010 at 1:22 am
fmm: From my understanding of the book he never argued that protein-protein binding was impossible only that is was difficult. According to Behe the edge lies beyond this level of complexity

That's also my understanding. Very unlikely but not impossible. Does anyone have references indicating otherwise?

Comment by Bradford — May 29, 2010 @ 1:22 am

Guts Says:
May 29th, 2010 at 2:18 am
Acipenser, now that you see that you were wrong in paraphrasing Behe, lets employ some more critical thinking.

Your initial thinking was that Behe said no protein-protein interactions ever did or ever will be developed.

ERV showed an example of a protein-protein interaction that developed.

Therefore Behe is wrong.

And yet we have Behe showing an example of a protein-protein interaction that developed by random mutation in his own book prior to ERV's demonstration.

Employ critical thinking and reason out why Behe didn't refute Behe (and neither did ERV).

Comment by Guts — May 29, 2010 @ 2:18 am

CharlieM Says:
May 29th, 2010 at 7:53 am
Hi Acipenser,

You talk about others moving goal posts but your goal seems to be to highlight an oversight by Behe that he has already admitted and explained why it doesn't affect his argument in any substantial way. If you wish to attack Behe, why not attack his stronger argument on Darwinian evolution's extremely poor ability to form new cellular structures. If the only evidence you have is what you've brought so far then I don't find it convincing in the least.

Abbie Smith said to Behe, from Pandasthumb:
There is no excuse for you to write an entire book on the premise of HIV not being able to do something, when it is clear that these impossible feats did happen.

Was that the premise of his entire book?

You said:
What do you mean by structural?

To give an example, the proteins that form a structure like the universal joint of the bacterial flagellum. These proteins need to bind to each other in such a way that a hollow tube is formed. They also need to be able to bind to the proteins at the rod and tail junctions.Not only that but if we take one single universal joint protein and think what it must do during one rotation of the flagellum. Whilst at the inside of the hook curve the protein is in the compressed position and half a revolution later at the outside of the curve it is fully expanded. The protein must be able to take up this change of shape while still remaining bound to the protein molecules surrounding it. If you think that this is an easy feat to accomplish try making yourself a tube of chain-mail (or similar) with a universal joint, support it at one end only and rotate it whilst keeping the other end pointing in the same direction. Unless it is supported at both ends its a nigh on impossible task, ask an engineer if you don't believe me. (Unless you are an engineer then you'll know for yourself).

How many steps would it take to achieve all this starting from the closest homologous protein available? Show me how all this is feasible by Darwinian means and I'll become a believer.

Comment by CharlieM — May 29, 2010 @ 7:53 am

Zachriel Says:
May 29th, 2010 at 8:44 am
fifth monarchy man: From my understanding of the book he never argued that protein-protein binding was impossible only that is was difficult. According to Behe the edge lies beyond this level of complexity

That is the basic contention. The odds of a single binding Behe figures is 10^-20, and the odds of two bindings he calculates as 10^-20 * 10^-20 = 10^-40. That constitutes his "Two Binding Site Rule." Of course, this presumes that both mutations have to occur in the same organism, which is a silly strawman, but that's the gist of it.

The 10^-20 number is flawed. There are so many proteins in a typical organism, that the problem isn't creating new bindings, but preventing them! Furthermore, many critical bindings in animals evolved deep in the Precambrian when populations and reproductive rates were much higher, and many of those are simply modified duplications. More importantly, if the first mutation confers a partial benefit, then it may become fixed in the population. (Indeed, it might become fixed even if it doesn't confer a benefit.) Hence, the assumption that each mutation is independent and must occur in the same cell (essentially simultaneously) means the calculation is bunk.

Comment by Zachriel — May 29, 2010 @ 8:44 am

Bradford Says:
May 29th, 2010 at 8:53 am
Zach, I've been away and admittedly have not even read all the preceding comments in my own thread but the protein binding discussion is limited by the malaria context is it not? If so that would relate to this comment of yours:

There are so many proteins in a typical organism, that the problem isn't creating new bindings, but preventing them!

Comment by Bradford — May 29, 2010 @ 8:53 am

ID guy Says:
May 29th, 2010 at 9:48 am
Dr Behe NEVER claimed that no new protein to protein binding sites will evolve.

Comment by ID guy — May 29, 2010 @ 9:48 am

ID guy Says:
May 29th, 2010 at 9:51 am
Zachriel:
Of course, this presumes that both mutations have to occur in the same organism, which is a silly strawman, but that's the gist of it.

How is that a strawman?

Of course they have to occur in the same organism- that is how they accumulate.

If an organism cannot even manage to "evolve" two new binding sites then transforming into some other type of organism is out of the question.

Furthermore, many critical bindings in animals evolved deep in the Precambrian when populations and reproductive rates were much higher, and many of those are simply modified duplications.

Unsupportable hearsay.

Comment by ID guy — May 29, 2010 @ 9:51 am

Zachriel Says:
May 29th, 2010 at 10:18 am
ID guy: How is that a strawman?

Premise: The Theory of Evolution requires specific, multiple, simultaneous mutations.
Fact: It is implausible for specific structures to have evolved by specific, multiple, simultaneous mutations.
Therefore: The Theory of Evolution is implausible.

The Premise is the strawman. The Theory of Evolution does not require specific, multiple, simultaneous mutations.

ID guy: Of course they have to occur in the same organism- that is how they accumulate.

No. The usual way they accumulate is through inheritance. Consider a structure that requires two mutations, A and B. Mutation A occurs in an organism. This mutation is passed down to its descendents, which may be numerous. It may even become fixed in the population, especially if it is beneficial. In any case, there may be a large number of organisms that are variant A. Later on, mutation B may occur in any of those descendents.

ID guy: Unsupportable hearsay.

Gossip from the deep Precambrian!

Comment by Zachriel — May 29, 2010 @ 10:18 am

Zachriel Says:
May 29th, 2010 at 10:27 am
Bradford: I've been away and admittedly have not even read all the preceding comments in my own thread but the protein binding discussion is limited by the malaria context is it not?

"Two Binding Site Rule" is meant to be a general rule, a barrier beyond which evolution can't surpass.

Bradford: If so that would relate to this comment of yours:

Zachriel: There are so many proteins in a typical organism, that the problem isn't creating new bindings, but preventing them!

Most bindings are concentrated in just a few amino acids, and most proteins are flexible in terms of amino acid sequence.

Comment by Zachriel — May 29, 2010 @ 10:27 am

fifth monarchy man Says:
May 29th, 2010 at 10:57 am
"Two Binding Site Rule" is meant to be a general rule, a barrier beyond which evolution can't surpass.

Not evolution unguided Darwinian evolution. Behe is not anti evolution.

There are so many proteins in a typical organism, that the problem isn't creating new bindings, but preventing them!

Do you know of any examples of violations to the "Two Binding Site Rule" that have been observed to occur in the lab or have been observed in the field in the last 50 years or so that we have been looking at this sort of thing?

peace

Comment by fifth monarchy man — May 29, 2010 @ 10:57 am

ID guy Says:
May 29th, 2010 at 11:03 am
Premise: The Theory of Evolution requires specific, multiple, simultaneous mutations.
Fact: It is implausible for specific structures to have evolved by specific, multiple, simultaneous mutations.
Therefore: The Theory of Evolution is implausible.

The Premise is the strawman. The Theory of Evolution does not require specific, multiple, simultaneous mutations.

That isn't what Dr Behe is saying.

IOW the strawman is all yours.

Of course they have to occur in the same organism- that is how they accumulate.

No. The usual way they accumulate is through inheritance.

They have to occur before they can accumulate.

And inheritance isn't any guarantee they will accumulate.

Later on, mutation B may occur in any of those descendents.

I don't think that Dr Behe denies that.

If you read "The Edge of Evolution"- I am sure you haven't read it yet- you will read what his position is.

As for what occurred in the precam- you don't have any idea.

"Two Binding Site Rule" is meant to be a general rule, a barrier beyond which evolution can't surpass.

That is incorrect.

The barrier pertains to blind, undirected chemical processes only and it is a tentative barrier at that.

Comment by ID guy — May 29, 2010 @ 11:03 am

Zachriel Says:
May 29th, 2010 at 11:10 am
ID guy: They have to occur before they can accumulate.

But the individual mutations are not posited to "occur in the same organism," as you had said.

ID guy: I don't think that Dr Behe denies that.

No, but his fallacious calculation depends on specific, multiple, simultaneous mutations.

Comment by Zachriel — May 29, 2010 @ 11:10 am

Guts Says:
May 29th, 2010 at 11:40 am
The problem is that a mutation that occured in the previous organism may be deleterious, but if the mutations happen together at once, they will be beneficial. This is one of the reasons why it is thought that highly resisitant malaria didn't arise in africa(some do but where the population is large), but is actually a lot older (it migrated from asia), despite strong selection pressure.

Comment by Guts — May 29, 2010 @ 11:40 am

ID guy Says:
May 29th, 2010 at 11:49 am
Zachriel:
No, but his fallacious calculation depends on specific, multiple, simultaneous mutations.

That is what you say- that it "depends on specific, nultiple, simultaneous mutations".

Can you provide a quote or quotes from "The Edge of Evolution" that would support your claim?

But the individual mutations are not posited to "occur in the same organism," as you had said.

Right, my bad. Should have been "appear" not "occur".

That is what Dr Behe is saying.

That once one appears it looks like it is too much to ask of blind, undirected chemical processes to produce a another.

IOW if a new binding site is required on a protein that already received one new binding site, then it appears that is out of the reach of blind, undirected chemical processes.

Comment by ID guy — May 29, 2010 @ 11:49 am

ID guy Says:
May 29th, 2010 at 11:52 am
Guts:
The problem is that a mutation that occured in the previous organism may be deleterious, but if the mutations happen together at once, they will be beneficial. This is one of the reasons why it is thought that highly resisitant malaria didn't arise in africa(some do but where the population is large), but is actually a lot older (it migrated from asia), despite strong selection pressure.

Absolutely.

Comment by ID guy — May 29, 2010 @ 11:52 am

Acipenser Says:
May 29th, 2010 at 12:58 pm
Guts: Employ critical thinking and reason out why Behe didn't refute Behe (and neither did ERV).

LOL. OK guts, how much critical thinking does it take to acknowledge that the man (Behe) admitted he was in error, why he admitted he was in error, and what data he was referring to when he made that admission of error.

Do you think he admitted he was wrong when he wasn't?

Comment by Acipenser — May 29, 2010 @ 12:58 pm

Acipenser Says:
May 29th, 2010 at 1:08 pm
CharlieM: These proteins need to bind to each other in such a way that a hollow tube is formed.

Like an ion-channel formed by a pentameric oligomerization of Vpu.

How is your example any different than oh say the cooperative binding of oxygen to tetrameric hemoglobin and how allosteric changes caused by the binding of carbon dioxide and/or protons affect oxygen affinity.

Or a G-coupled protein receptor and how this 7-transmembrane protein changes conformational shape upon binding its substrate (or mimic) to trigger phosphorylation cascades.

There are a multitude of examples that can be given and that changes occur in protein structure with binding to each other and other small and large molecules should not really be all that mysterious. Look at all of the variety in the sterochemistry within a single protein and decide what you think is possible.

How many steps would it take to achieve all this starting from the closest homologous protein available? Show me how all this is feasible by ~~Darwinian means~~ Intelligent design and I'll become a believer.

Comment by Acipenser — May 29, 2010 @ 1:08 pm

Acipenser Says:
May 29th, 2010 at 1:11 pm
Guts: The problem is that a mutation that occured in the previous organism may be deleterious, but if the mutations happen together at once, they will be beneficial.

Or it may be neutral or beneficial as well and could simple reside without consequences to the organism until another mutation event occurs.

Comment by Acipenser — May 29, 2010 @ 1:11 pm

ID guy Says:
May 29th, 2010 at 1:39 pm
Acipenser:
Show me how all this is feasible by Intelligent design and I'll become a believer.

A targeted search.

On another note- You didn't read "The Edge of Evolution", did you?

Comment by ID guy — May 29, 2010 @ 1:39 pm

Acipenser Says:
May 29th, 2010 at 2:38 pm
ID guy: A targeted search.

Which assumes the content already exists to search. You have some references that document this assertion? Or alternately you can outline all of the steps necessary for an intelligent agent to set all of this up so it works, i.e., provide the mechanism behind your assertion.

Comment by Acipenser — May 29, 2010 @ 2:38 pm

ID guy Says:
May 29th, 2010 at 3:11 pm
Acipenser,

What do you have?

Heck you can't even produce the methodology used to determine that living organisms are the result of blind, undirected chemical processes.

Show me how all of this is feasible by blind, undirected chemical processes and I will rail against ID.

Comment by ID guy — May 29, 2010 @ 3:11 pm

Guts Says:
May 29th, 2010 at 5:52 pm
Acipenser,

Do you think he admitted he was wrong when he wasn't?

Of course he admitted he was wrong. But you made it out like his error refuted his entire thesis. It didn't.

Comment by Guts — May 29, 2010 @ 5:52 pm

Zachriel Says:
May 29th, 2010 at 5:54 pm
fifth monarchy man: Not evolution unguided Darwinian evolution.

Thank you for the clarification, but it becomes rather cumbersome to constantly write "evolutionary processes as posited by the modern Theory of Evolution." Most everyone uses the term "evolution" to refers to the modern Theory, and it should be clear from context.

fifth monarchy man: Behe is not anti evolution.

As he is claiming a barrier to stepwise adaptation, it is contrary to evolutionary theory, at least with regards to protein interactions.

Guts: The problem is that a mutation that occured in the previous organism may be deleterious, but if the mutations happen together at once, they will be beneficial.

Then, that is a pathway evolution is unlikely to follow. (The vast majority of pathways will never be explored by evolutionary processes.) But Behe's argument depends on there being no selectable pathway, because if there is, then his math is bogus.

Comment by Zachriel — May 29, 2010 @ 5:54 pm

ID guy Says:
May 29th, 2010 at 8:51 pm
Zachriel:
Most everyone uses the term "evolution" to refers to the modern Theory, and it should be clear from context.

That is misleading and it makes it appear as if ID argues against any and all types of change.

As he is claiming a barrier to stepwise adaptation, it is contrary to evolutionary theory, at least with regards to protein interactions.

He is just making an observation.

And it is something that can be refuted just by more research.

However I don't like his "argument" because it seems to preclude targeted searches.

But Behe's argument depends on there being no selectable pathway, because if there is, then his math is bogus.

You haven't even read the book.

Comment by ID guy — May 29, 2010 @ 8:51 pm

ID guy Says:
May 29th, 2010 at 10:14 pm
Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution

Not exactly a glowing endorsement for the "power" of blind, undirected chemical processes…

Comment by ID guy — May 29, 2010 @ 10:14 pm

fifth monarchy man Says:
May 29th, 2010 at 10:26 pm
Thank you for the clarification, but it becomes rather cumbersome to constantly write "evolutionary processes as posited by the modern Theory of Evolution."

Why not just write Darwinism or Neo-Darwinism? We'll know what you mean and it will reduce the probability that observers will mistake your statement for an ad hominin attack on the good professor

As he is claiming a barrier to stepwise adaptation, it is contrary to evolutionary theory, at least with regards to protein interactions.

A particular evolutionary theory is not evolution.

No one called Einstein antigravity even though he thought the prevailing theory was inadequate to account for certain phenomenon.

peace

Comment by fifth monarchy man — May 29, 2010 @ 10:26 pm

Zachriel Says:
May 29th, 2010 at 11:07 pm
Zachriel: Most everyone uses the term "evolution" to refer to the modern Theory, and it should be clear from context.

ID guy: That is misleading and it makes it appear as if ID argues against any and all types of change.

In biology, the term "evolution" is associated with the processes and mechanisms described in the Theory of Evolution. As ID is the outlier, if ID wants to posit some other type of evolution, it should use a modifier or a neologism to avoid confusion.

Zachriel: As {Behe} is claiming a barrier to stepwise adaptation, it is contrary to evolutionary theory, at least with regards to protein interactions.

ID guy: He is just making an observation.

No. Behe is making an assertion based on a faulty premise.

fifth monarchy man: Why not just write Darwinism or Neo-Darwinism?

Because those terms already have other meanings, and the terms are not descriptive of the modern Theory of Evolution. Darwinism originally referred to Darwin's theory, and today it refers to theories of natural selection. Neodarwinism usually refers to the modern synthesis from the mid-twentieth century. Evolution is the proper term, and arguing semantics won't advance the discussion.

Comment by Zachriel — May 29, 2010 @ 11:07 pm

fifth monarchy man Says:
May 29th, 2010 at 11:33 pm
Me: Why not just write Darwinism or Neo-Darwinism?

Zach: Because those terms already have other meanings

ok

How about undirected evolution?

As long as you insist on calling it generic "evolution" you will be misunderstood. I would hope that would concern you.

peace

Comment by fifth monarchy man — May 29, 2010 @ 11:33 pm

ID guy Says:
May 30th, 2010 at 12:01 am
Zachriel:
In biology, the term "evolution" is associated with the processes and mechanisms described in the Theory of Evolution.

Then please reference an accepted definition of evolution that states that evolution is change associated only with blind, undirected chemical processes.

Zachriel: As {Behe} is claiming a barrier to stepwise adaptation, it is contrary to evolutionary theory, at least with regards to protein interactions.

ID guy: He is just making an observation.

No. Behe is making an assertion based on a faulty premise.

That is incorrect.

You haven't even read the book.

The table is based on observations.

And the peer-reviewed paper I linked to appears to support Dr Behe.

Comment by ID guy — May 30, 2010 @ 12:01 am

KC Says:
May 30th, 2010 at 7:48 am
And the peer-reviewed paper I linked to appears to support Dr Behe.

Hmmm… from that paper:

Arguing that (i) there are 1 trillion parasitic cells in an infected person, (ii) there are 1 billion infected persons on the planet, and (ii) chloroquine resistance has arisen only 10 times in the past 50 years, he concludes that the odds of one parasite developing resistance to chloroquine, an eventhe calls a chloroquine complexity cluster (CCC), are 1 in 1020. Ignoring the fact that humans and P. falciparum have different mutation rates, he then concludes that "On the average, for humans to achieve a mutation like this by chance, we would have to wait a hundred million times ten million years" (BEHE 2007, p. 61), which is 5 million times larger than the calculation we have just given.

Indeed his error is much worse. To further sensationalize his conclusion, he argues that "There are 5000 species of modern mammals. If each species had an average of a million members, and if a new generation appeared each year, and if this went on for two hundred million years, the likelihood of a single CCC appearing in the whole bunch over that entire time would only be about 1 in 100" (BEHE 2007, p. 61). Taking 2N = 106and µ1 = µ2 = 10–9, Theorem 1 predicts a waiting time of 31.6 million generations for one prespecified pair of mutations in one species, with [square root of u2--KC] having reduced the answer by a factor of 31,600

Comment by KC — May 30, 2010 @ 7:48 am

KC Says:
May 30th, 2010 at 7:51 am
Also, this:

Lynch M & A Abegg (2010). The Rate of Establishment of Complex Adaptations. Molecular Biology and Evolution 27(6):1404-1414

From the abstract (my emphasis):

A central problem in evolutionary theory concerns the mechanisms by which adaptations requiring multiple mutations emerge in natural populations. We develop a series of expressions that clarify the scaling of the time to establishment of complex adaptations with population size, mutation rate, magnitude of the selective disadvantage of intermediate-state alleles, and the complexity of the adaptation. In general, even in the face of deleterious intermediate steps, the time to establishment is minimized in populations with very large size. Under a broadrange of conditions, the time to establishment also scales by no more than the square of the mutation rate, regardless of the number of sites contributing to the adaptive change, demonstrating that the emergence of complex adaptations is only weakly constrained by the independent acquisition of mutations at the underlying sites. Mutator alleles with deleterious side effects have only moderate effects on the rate of adaptation in large populations but can cause a quantum decrease in the time to establishment of some adaptive alleles in small populations, although probably not at a high enough rate to offset the increased deleteriousmutation load. Transient hypermutability, whereby a subset of gamete-producing cells mutate at an elevated rate in a nonheritable manner, may also elevate the rate of adaptation, although the effect is modest and appears to result from a simple increase in the rate of transitions between intermediate states rather than from the saltational production of doublet mutations. Taken together, these results illustrate the plausibility of the relatively rapid emergence of specific complex adaptations by conventional population genetic mechanisms and provide insight into the relative incidences of various paths of allelic adaptation in organisms with different population genetic features.

Comment by KC — May 30, 2010 @ 7:51 am

Zachriel Says:
May 30th, 2010 at 8:00 am
fifth monarchy man: How about undirected evolution?

Unfortunately, some IDers have made a habit of conflating that with metaphysics.

fifth monarchy man: As long as you insist on calling it generic "evolution" you will be misunderstood. I would hope that would concern you.

Nearly everyone uses the term "evolution" to refer to the processes and mechanisms associated with the Theory of Evolution. No one is confused. Rather, you are arguing semantics. But we'll restate so as to avoid the diversion.

Zachriel: "Two Binding Site Rule" is meant to be a general rule, a barrier beyond which evolution {meaning the processes and mechanisms as detailed in the modern Theory of Evolution} can't surpass.

Behe doesn't propose an alternative theory of evolution, but puts forth a bogus argument based on a strawman version of evolutionary theory {i.e. the modern Theory of Evolution that nearly every working biologist accepts}.

Comment by Zachriel — May 30, 2010 @ 8:00 am

Zachriel Says:
May 30th, 2010 at 8:03 am
Zachriel: Behe is making an assertion based on a faulty premise.

ID guy: That is incorrect.

Premise: The Theory of Evolution requires specific, multiple, simultaneous mutations.
Fact: It is implausible for specific structures to have evolved by specific, multiple, simultaneous mutations.
Therefore: The Theory of Evolution is implausible.

The odds of a single binding Behe figures is 10^-20, and the odds of two bindings he calculates as 10^-20 * 10^-20 = 10^-40. That constitutes his "Two Binding Site Rule." Of course, this presumes that both mutations have to occur in the same organism, which is a silly strawman, but that's the gist of it.

Comment by Zachriel — May 30, 2010 @ 8:03 am

CharlieM Says:
May 30th, 2010 at 9:33 am
Zachriel:
The odds of a single binding Behe figures is 10^-20, and the odds of two bindings he calculates as 10^-20 * 10^-20 = 10^-40. That constitutes his "Two Binding Site Rule." Of course, this presumes that both mutations have to occur in the same organism, which is a silly strawman, but that's the gist of it.

CharlieM:
Consider the rod, hook (universal joint) and tail of the bacterial flagellum. Consensus is that their constituents are all homologous. Even so they all differ from each other by at least two binding sites.

How on earth can they have developed if the different binding sites never occur in the same organism? What makes you think that the odds of each developing in separate bacteria and then fortuitously appearing in a single bacterium are any less than the odds given by Behe?

Also you are equating 'binding sites' with 'mutations', but one change of binding site would normally involve several mutations.

Comment by CharlieM — May 30, 2010 @ 9:33 am

CharlieM Says:
May 30th, 2010 at 9:50 am
On protein homology.

At the start of the industrial revolution nothing was standard. Things such as the threads used on nuts and bolts varied as much as there were people manufacturing them. Then we began to realize that things would run much better if there was just one standard design that everyone used. If humans had had more foresight they would have preferred to do things this way from the beginning.

So for me homology is evidence for foresight in nature and not an unguided process.

Comment by CharlieM — May 30, 2010 @ 9:50 am

ID guy Says:
May 30th, 2010 at 10:28 am
And the peer-reviewed paper I linked to appears to support Dr Behe.

KC:
Hmmm… from that paper:

The authors misrepresent Dr Behe-

From Dr Behe:

Durrett and Schmidt (2008) compare the number they got in their model to my literature citation (1) that the probability of the development of chloroquine resistance in the malarial parasite is an event of order 1 in 10^20, and they remark that it “is 5 million times larger than the calculation we have just given.” The implied conclusion is that I have greatly overstated the difficulty of getting two necessary mutations. In the next several posts I will show that they are incorrect.

part 2 from Dr Behe

Interesting as it is, there are some pretty serious problems in the way they applied their model to my arguments, some of which they owned up to in their reply, and some of which they didn’t. When the problems are fixed, however, the resulting number is remarkably close to the empirical value of 1 in 10^20. I will go through the difficulties in turn.

The first problem was a simple oversight. They were modeling the mutation of a ten-nucleotide-long binding site for a regulatory protein in DNA, so they used a value for the mutation rate that was ten-times larger than the point mutation rate. However, in the chloroquine-resistance protein discussed in The Edge of Evolution, since particular amino acids have to be changed, the correct rate to use is the point mutation rate. That leads to an underestimate of a factor of about 30 in applying their model to the protein. As they wrote in their reply, “Behe is right on this point.” I appreciate their agreement here.

part 3 of Dr Behe's response

part 4

And part 5

KC then references another paper- is that paper all experiments or just theoretical musings?

Comment by ID guy — May 30, 2010 @ 10:28 am

ID guy Says:
May 30th, 2010 at 10:32 am
Zachriel:
Premise: The Theory of Evolution requires specific, multiple, simultaneous mutations.

That is not Dr Behe's premise.

I have already told you that and yet you persist.

You have already proven that you are dishonest and now you do this to make sure everyone knows just how dishonest you are.

You haven't even read the book Zach.

Of course, this presumes that both mutations have to occur in the same organism, which is a silly strawman, but that's the gist of it.

That is incorrect.

It is very noticeable that you have failed/ refused to provide quotes from "The Edge of Evolution" to support your BS.

I have also asked to to provide a valid definition of evolution:

Then please reference an accepted definition of evolution that states that evolution is change associated only with blind, undirected chemical processes.

You have failed/ refused to do that also.

IOW Zachriel you are a dishonest intellectual coward.

Comment by ID guy — May 30, 2010 @ 10:32 am

Zachriel Says:
May 30th, 2010 at 10:43 am
CharlieM: Consider the rod, hook (universal joint) and tail of the bacterial flagellum. Consensus is that their constituents are all homologous.

We don't have to know exactly how the flagellum evolved to know that Behe's argument is fallacious. His argument depends on a strawman, that is, specific, multiple, simultaneous mutations.

The flagellum evolved billions of years ago and left very scant evidence, but we have evidence of how complex and irreducible structures can evolve incrementally, so an a priori argument simply can't work.

CharlieM: How on earth can they have developed if the different binding sites never occur in the same organism?

Of course they exist in the same organism, typically through inheritance.

CharlieM: Also you are equating 'binding sites' with 'mutations', …

No. That's the whole point. We don't expect specific, multiple, simultaneous mutations, which is Behe's strawman, but we do expect that variants will become fixed and optimized in the population. That means we don't multiply the probabilities.

Comment by Zachriel — May 30, 2010 @ 10:43 am

ID guy Says:
May 30th, 2010 at 10:50 am
Zachriel:
His argument depends on a strawman, that is, specific, multiple, simultaneous mutations.

You are incorrect.

Dr Behe's argument does not depend on specific, multiple, simultaneous mutations.

IOW you are lying.

Zachriel, who has never read "The Edge of Evolution" feels like he can comment on it.

Typical troll but still pathetic.

Comment by ID guy — May 30, 2010 @ 10:50 am

Zachriel Says:
May 30th, 2010 at 11:05 am
ID guy: IOW Zachriel {blah, blah, blah}

Two entire posts of invective. Good work!

Behe: The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40.

Again, that assumes there is no fixation of any of the intermediate steps, yet he considers it a "reasonably firm judgment."

Comment by Zachriel — May 30, 2010 @ 11:05 am

CharlieM Says:
May 30th, 2010 at 12:20 pm
CharlieM: How on earth can they have developed if the different binding sites never occur in the same organism?

Zachriel:
Of course they exist in the same organism, typically through inheritance.

I want to be specific here, that's why I'm concentrating on the flagellum.

The hook protein is supposed to have developed from a protein that also produced the rod and the tail. It has very specialized properties, see below.

From © 2004 Nature PublishingGroup:
'Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism' when comparing the hook and the filament proteins:

'It is curious that these two molecules with completely different structures both form the tubular structures with basically the same architecture and helical symmetry.'

One difference is that the filament is built to be rigid axially while the hook is built to be flexible.

Now they say that these two structures are built of sequentially homologous proteins. And:

Mark Pallen Sunday, September 14, 2008:
…all the axial proteins. Interestingly, in every case, the structures show clear homology to one another and to flagellin, confirming earlier suggestions by myself and others that the flagellar axial filament has arisen by a process of successive gene duplications from a single progenitor protein. The way is now open to a detailed reconstruction of the steps leading to the evolution of the axial structures and even to resurrection and investigation of the original axial protein.

So I presume that Pallen is of the opinion that the hook protein evolved by gene duplication and then by point mutations on the duplicated gene.

I haven't even considered regulation at this stage, how the hook is made up of a precise number of protein molecules, how it is put in place in a precise order and sequence of flagellar development, that sort of thing.

Now a universal joint is not something that we would expect to just appear by chance. Without the flagellar tail it is a pointless construction. And we have no evidence of universal joints popping up anywhere else in the natural world just waiting to be used by some yet to be built drive system.

So you are saying that a bacterium with a hook but no tail combined with a bacterium with no hook but possibly a proto-tail to produce the flagellum we see before us today!

So where we are at today is: The hook and tail are genetically sequentially homologous, they are structurally homologous overall. But the proteins that they consist of are not structurally homologous.

And when they say they are sequentially homologous they are talking in the order of forty percent similarity at the most as far as I can tell, although I could be wrong on that.

Comment by CharlieM — May 30, 2010 @ 12:20 pm

Guts Says:
May 30th, 2010 at 4:32 pm
zach:

But Behe's argument depends on there being no selectable pathway, because if there is, then his math is bogus.

No Behe's argument is not that there is no selectable pathway to anything. It's quite obvious you never even read the book. Just that most molecular machines appear to be made of epistatic interactions, and so those likely require multiple simultaneous mutations, or they evolved through another pathway that is not Darwinian.

Comment by Guts — May 30, 2010 @ 4:32 pm

KC Says:
May 30th, 2010 at 8:36 pm
Durrett & Schmidt respond to Behe’s reply:

WE showed that the mean waiting time for two mutations to occur in the same individual, one with probability u1 and another with probability u2 (when the first mutation is neutral), is 1/2Nu1 . The square root on the second factor is an important insight from our calculation and is the main difference between our theory and Behe's naive calculations, which assume that the two mutations must occur almost simultaneously. Our results show that there are an order of [1/u2^1/2-- KC] individuals with the first mutation before the second one occurs (see the sketch of the proof of Theorem 1 on p. 1503 of DURRETT and SCHMIDT 2008).
In BEHE (2009), the accompanying Letter to the Editors in this issue, Michael Behe writes (here and in what follows italicized quotes are from his letter), "… their model is incomplete on its own terms because it does not take into account the probability of one of the nine matching nucleotides in the region that is envisioned to become the new transcription-factor-binding site mutating to an incorrect nucleotide before the 10th mismatched codon mutates to the correct one."This conclusion is simply wrong since it assumes that there is only one individual in the population with the first mutation. There are on the order of [1/u2^1/2-- KC ]individuals with the first mutation before the second one occurs, and since this event removes only one individual from the group with the first mutation, it has no effect on the waiting time.
Behe is not alone in making this type of mistake. When Evelyn Adams won the New Jersey lottery on October 23, 1985, and again on February 13, 1986, newspapers quoted odds of 17.1 trillion to 1. That assumes that the winning person and the two lottery dates are specified in advance, but at any point in time there is a population of individuals who have won the lottery and have a chance to win again, and there are many possible pairs of dates on which this event can happen. The probability that it happens in one lottery 1 year is 1 in 200 (DURRETT 2009).
"For the rate of the first mutation Durrett and Schmidt use a value estimated for the alteration of a transcription-factor-binding site, where any of 10 nucleotides could be changed. In the case of the protein, however, it is likely that a particular nucleotide of a particular amino acid residue's codon must be changed. This introduces a 30-fold underestimate of the waiting time." Behe is right on this point. This divides our previously computed overestimate of 5 million by 30.

In other words, Behe still overestimated by 166,667 times. LOL! Oh yeah, Durrett & Schmidt really support Behe’s calculation.

"They use the model that they developed for an initial neutral mutation, but it is likely that the initial protein point mutation is deleterious. If it is strongly deleterious, their calculation could be low by many orders of magnitude, as their own model for deleterious mutations shows." If the first mutation is mildly deleterious (a fitness loss of order [u2^1/2-- KC], then the waiting time is increased by a factor of 2 or 3. If the loss of fitness were 0.1, then the mean waiting time would be 1/(20Nu1u2). We leave it to biologists to debate whether the first PfCRT mutation is that strongly deleterious.
"My figure of 1020 [the odds of a malaria parasite developing resistance to chloroquine] is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model." </em? We disagree that Behe's result is an empirical fact. It is clearly impossible to know the number of times that the double mutation has occurred. Therefore, to infer that from the number of times the mutation has avoided extinction in an individual and risen to a frequency where it can be noted in a subpopulation requires a model, which we have provided.

.
Indeed, Behe’s “empirical statistic” was actually a speculative estimate. Behe got his numbers from a review paper . The actual paper that produced the estimate had this to say (in the notes for Table 1):

The estimates for chloroquine and artemisinin are speculative.

From:
White NJ & W Pongtavornpinyo (2003). The de novo selection of drugresistant malaria parasites. Proc. R. Soc. Lond. B 270: 545-554

Finally, Behe notes that for one prespecified pair of mutations in one gene in humans with the first one neutral, we obtain a "prohibitively long waiting time" of 216 million years. However, there are at least 20,000 genes in the human genome and for each gene tens if not hundreds of pairs of mutations that can occur in each one. Our results show that the waiting time for one pair of mutations is well approximated by an exponential distribution. If there are k nonoverlapping possibilities for double mutations, then by an elementary result in probability, the waiting time for the first occurrence is the minimum of k independent exponentials and hence has an exponential distribution with a mean that is divided by k. From this we see that, in the case in which the first mutant is neutral or mildy deleterious, double mutations can easily have caused a large number of changes in the human genome since our divergence from chimpanzees. Of course, if the first mutant already confers an advantage, then such changes are easier.

Durrett R & D Schmidt (2009). Reply to Michael Behe. Genetics 181: 821-822

Comment by KC — May 30, 2010 @ 8:36 pm

KC Says:
May 30th, 2010 at 8:40 pm
ID Guy asks:

KC then references another paper- is that paper all experiments or just theoretical musings?

As opposed to Behe trying to foist a speculative estimate on us as an "empirical statistic?" LOL.

Comment by KC — May 30, 2010 @ 8:40 pm

Guts Says:
May 30th, 2010 at 10:45 pm
KC Behe already responded to that:

I have shown above that, despite their assertion, my conclusion is right. But where do they get the idea that “it assumes that there is only one individual in the population with the first mutation”? I wrote no such thing in my letter about “one individual.” Furthermore, I “assumed” nothing. I merely cited empirical results from the literature. The figure of 1 in 10^20 is a citation from the literature on chloroquine resistance of malaria. Unlike their model, it is not a calculation on my part.

here

Comment by Guts — May 30, 2010 @ 10:45 pm

Zachriel Says:
May 31st, 2010 at 8:38 am
CharlieM: I want to be specific here, that's why I'm concentrating on the flagellum.

The flagellum originated billions of years ago, and left scant evidence of its historical origin. You can't understand the evidence for evolution by ignoring the vast bulk of the evidence. We have ample evidence of evolution, including complex, irreducible adaptations.

Let's assume we have no idea how the flagellum evolved. So?

Comment by Zachriel — May 31, 2010 @ 8:38 am

Zachriel Says:
May 31st, 2010 at 8:50 am
Zachriel: But Behe's argument depends on there being no selectable pathway, because if there is, then his math is bogus.

Guts: No Behe's argument is not that there is no selectable pathway to anything.

Yes, he does. But he claims there is a limit beyond which evolution {meaning the processes and mechanisms as detailed in the modern Theory of Evolution} can't go beyond. And if a structure *requires* specific, multiple, simultaneous mutations, then it is unlikely to evolve.

But that is not Behe's claim. He is claiming that *all* (or nearly all) complex, irreducible structures are out of reach of evolutionary processes; that they *require* specific, multiple, simultaneous mutations. And it is this claim that he can't support. Pointing out that many things are out of reach of evolution doesn't support his argument, because it is obvious that evolution will never explore the vast majority of possible structures.

Guts: Just that most molecular machines appear to be made of epistatic interactions, and so those likely require multiple simultaneous mutations, or they evolved through another pathway that is not Darwinian.

Yes, that is his "reasonably firm judgment" based on nothing more than conjecture. He is claiming evolution of molecular machines would require specific, multiple, simultaneous mutations. Not only do we have reason to believe that complex, irreducible structures can evolve, but even in the most ancient transitions, we can often find homologous relationships to support this view.

Comment by Zachriel — May 31, 2010 @ 8:50 am

ID guy Says:
May 31st, 2010 at 10:39 am
Behe: The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40.

Zachriel:
Again, that assumes there is no fixation of any of the intermediate steps, yet he considers it a "reasonably firm judgment."

That is incorrect.

It does not assume there isn't any fixation.

IOW once again Zach procves that he is clueless and forced to misrepresent Dr Behe.

Comment by ID guy — May 31, 2010 @ 10:39 am

ID guy Says:
May 31st, 2010 at 10:41 am
Zachriel:
The flagellum originated billions of years ago, and left scant evidence of its historical origin.

Unsupportable hearsay.

And if a structure *requires* specific, multiple, simultaneous mutations, then it is unlikely to evolve.

Dr Behe does not say that. He doesn't even imply it.

IOW Zachriel you are a liar as you have been corrected on this point several times and refuse to change.

Comment by ID guy — May 31, 2010 @ 10:41 am

ID guy Says:
May 31st, 2010 at 10:43 am
Zachriel:
Let's assume we have no idea how the flagellum evolved. So?

Then it ain't science.

As a matter of fact the bulk of the "theory" ain't science for that very reason.

Comment by ID guy — May 31, 2010 @ 10:43 am

Zachriel Says:
May 31st, 2010 at 11:42 am
Zachriel: Again, that assumes there is no fixation of any of the intermediate steps, yet he considers it a "reasonably firm judgment."

ID guy: That is incorrect. It does not assume there isn't any fixation.

If we don't make that assumption, then the math is wrong. Assume we need two variants, A and B, to achieve result AB. If A is beneficial, the odds of it being found in a cell will probably be much greater than 10^-20. Indeed, it may reach fixation, already have an existing function in the cell.

Zachriel: The flagellum originated billions of years ago, and left scant evidence of its historical origin.

ID guy: Unsupportable hearsay.

Whispers from the dawn of time.

Comment by Zachriel — May 31, 2010 @ 11:42 am

ID guy Says:
May 31st, 2010 at 12:58 pm
Zachriel,

Have you read "The Edge of Evolution"?

Yes or No.

Comment by ID guy — May 31, 2010 @ 12:58 pm

ID guy Says:
May 31st, 2010 at 12:59 pm
Zachriel:
Whispers from the dawn of time.

More like voices in your head…

Comment by ID guy — May 31, 2010 @ 12:59 pm

Guts Says:
May 31st, 2010 at 5:22 pm
zach:

He is claiming that *all* (or nearly all) complex, irreducible structures are out of reach of evolutionary processes; that they *require* specific, multiple, simultaneous mutations.

No he isn't.

zach:

Yes, that is his "reasonably firm judgment" based on nothing more than conjecture. He is claiming evolution of molecular machines would require specific, multiple, simultaneous mutations. Not only do we have reason to believe that complex, irreducible structures can evolve, but even in the most ancient transitions, we can often find homologous relationships to support this view.

This is more evidence that you never read the book, since Behe's problem isn't with evolution, it's with Darwinian evolution. He discusses other possible alternatives in the book. Also, his reasoning is not based on conjecture but on extrapolation of what he sees being accomplished in HIV and malaria, and in observations of complexity of molecular machines, and you would have known this if you had actually read the book. One more thing, the assertion that "we can 'often' find homologous relationships" has to be tested on a case by case basis. It may not be generally true, and it may not be indicative of a random step by step process even if it is generally true.

Comment by Guts — May 31, 2010 @ 5:22 pm

Zachriel Says:
May 31st, 2010 at 8:33 pm
Guts: Behe's problem isn't with evolution, it's with Darwinian evolution.

In the comment you quoted from:

evolution {meaning the processes and mechanisms as detailed in the modern Theory of Evolution}. Constantly harping on the semantics of well-established terms, even when those terms are explicitly defined, doesn't constitute an argument.

Comment by Zachriel — May 31, 2010 @ 8:33 pm

Zachriel Says:
May 31st, 2010 at 8:40 pm
Behe: The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40.

That assumes there is no fixation of any of the intermediate steps, yet he considers it a "reasonably firm judgment." Yes, improbable events are improbable. Most pathways will never be explored by evolutionary processes {meaning the processes and mechanisms as detailed in the modern Theory of Evolution}. That's not a novel insight, nor an argument against evolutionary theory.

Comment by Zachriel — May 31, 2010 @ 8:40 pm

Guts Says:
May 31st, 2010 at 8:57 pm
zach:

That assumes there is no fixation of any of the intermediate steps, yet he considers it a "reasonably firm judgment."

I already responded to this here and here.

Comment by Guts — May 31, 2010 @ 8:57 pm

Zachriel Says:
May 31st, 2010 at 9:27 pm
Guts: The problem is that a mutation that occured in the previous organism may be deleterious, but if the mutations happen together at once, they will be beneficial.

Yes, it could happen that way. And there are undoubtedly structures that are even farther from any plausible evolutionary pathway {meaning the processes and mechanisms as detailed in the modern Theory of Evolution}.

Guts: most molecular machines appear to be made of epistatic interactions, and so those likely require multiple simultaneous mutations, or they evolved through another pathway that is not Darwinian.

There is no reason why epistatic interactions can't evolve incrementally.

Behe's argument hinges on the 'fact' that rare events are rare. We can point to all sorts of rare events, or propose events that are so rare that evolution would never run across them. Some things will just never happen. So? That's not how evolution is posited to occur.

Behe is left trying to argue that because a particular pathway is beyond the "edge of evolution" {heh, consider Behe's use of the word evolution!} in that it requires specific, multiple, simultaneous mutations, and that this applies generally to every possible evolutionary pathway. But we know it doesn't apply to evolutionary processes as a mathematical class, and we have every reason to believe it doesn't apply to molecular evolution.

Comment by Zachriel — May 31, 2010 @ 9:27 pm

Guts Says:
May 31st, 2010 at 9:34 pm
zach:

There is no reason why epistatic interactions can't evolve incrementally.

I give a reason why here

zach:

Behe is left trying to argue that because a particular pathway is beyond the "edge of evolution" {heh, consider Behe's use of the word evolution!} in that it requires specific, multiple, simultaneous mutations, and that this applies generally to every possible evolutionary pathway.

Of course not, in his book, Behe gives several examples of very sophisticated interaction evolving by only 1 mutation.

zach:

But we know it doesn't apply to evolutionary processes as a mathematical class, and we have every reason to believe it doesn't apply to molecular evolution.

Please go into those reasons.

Comment by Guts — May 31, 2010 @ 9:34 pm

ID guy Says:
June 1st, 2010 at 7:31 am
Guts,

Zachriel is a troll- he hasn't even read "The Edge of Evolution".

Comment by ID guy — June 1, 2010 @ 7:31 am

ID guy Says:
June 1st, 2010 at 7:34 am
Behe: The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40.

Zachriel:
That assumes there is no fixation of any of the intermediate steps

It assumes no such thing.

IOW that "assumption" is all in your head.

You erected a strawman Zachriel- just as you always do.

And in the end all it takes is some real evidence/ scientific data, to refute Dr Behe.

One is is 100% sure- your strawman arguments are not going to refute anything…

Comment by ID guy — June 1, 2010 @ 7:34 am

Zachriel Says:
June 1st, 2010 at 7:57 am
Guts: I give a reason why here

You gave an example, one where it takes an enabling, but deleterious mutation. Some pathways will not be explored. Some great adaptationas may take numerous, specific, simultaneous mutations. Iraqi kids could use Kevlar® skin. Evolution may never go there. So?

Zachriel: Behe is left trying to argue that because a particular pathway is beyond the "edge of evolution" {heh, consider Behe's use of the word evolution!} in that it requires specific, multiple, simultaneous mutations, and that this applies generally to every possible evolutionary pathway.

Guts: Of course not, in his book, Behe gives several examples of very sophisticated interaction evolving by only 1 mutation.

Yes. Again, so?

Zachriel: But we know it doesn't apply to evolutionary processes as a mathematical class, and we have every reason to believe it doesn't apply to molecular evolution.

Guts: Please go into those reasons.

There are "very sophisticated interactions evolving by only 1 mutation."

Comment by Zachriel — June 1, 2010 @ 7:57 am

KC Says:
June 1st, 2010 at 10:49 am
Guts,

Behe's response to Durrett & Schmidt is weak. For example, he says he never explicitly made the assumption about simultaneous mutations, as if that somehow obviously gets him off the hook. But you and I both know that this isn't necessarily true– the assumption may just as well be implicit in his calculations. When he calculates the probability of a double CCC, he simply multiplies the probability of each (10^20). That calculation tells us exactly what assumption Behe is making, as Steve Matheson notes: :

Here is one of many places in EoE where Behe makes a very basic mistake in the presentation of probabilities:

Recall that the odds against getting two necessary, independent mutations are the multiplied odds for getting each mutation individually. What if a problem arose during the course of life on earth that required a cluster of mutations that was twice as complex as a CCC? (Let's call it a double CCC.) For example, what if instead of the several amino acid changes needed for chloroquine resistance in malaria, twice that number were needed? In that case the odds would be that for a CCC times itself. Instead of 1020 cells to solve the evolutionary problem, we would need 1040 cells. (pp. 62-63)

What Behe is saying is this: if event A has probability a, and event B has probability b, then the probability of both events happening is a times b. But that is only true if the events must happen simultaneously. That's the only time you multiply two probabilities. And to make matters worse, Behe is confusing two very different probabilities: the probability that the event will happen in any given attempt, and the probability that it will occur at all. Consider the following example to see how these mistakes (if that's what they are) are so tremendously misleading.

Suppose I hand you a pair of dice and ask you: "What is the probability that you will roll snake eyes?" You might immediately ask: "In how many rolls?" And that is quite an important question.

The probability that you will roll snake eyes on any given roll is 1/36, which is the probability of getting a 1 on the first die (1/6) times the probability that you will get a 1 on the second die. Because the two events must happen together, we multiply the probabilities of the separate events. And that probability, 1/36, is pretty small.

But what is the probability that you will get snake eyes in, say, 12 rolls? It is in considering the second question that you can begin to see how Behe went badly wrong in his arguments in EoE. When Behe reports on the likelihood of occurrence of a "double CCC," he reports its probability of occurring in a single attempt. That's what the simple multiplication assumes, and Behe knows that this is nonsense. The real question, then, is this one: what is the likelihood that a certain event will occur given a certain number of attempts? Behe is happy to calculate probabilities based on crude estimates of certain events in a certain organism, but he never takes a whack at the only interesting question: assuming a certain mutation rate, and a certain number of effective generations, what are the probabilities involved in particular mutational trajectories that have led to adaptation? What, for that matter, is the probability of a particular pair of mutations occurring in a human gene over a certain number of generations?

This is why Behe's critics, including Durrett and Schmidt, claim Behe is arguing for simultaneous mutations within one individual. The assumption is implicit in his calculation.

Comment by KC — June 1, 2010 @ 10:49 am

KC Says:
June 1st, 2010 at 10:52 am
What's up with the edit feature?

The link for the Matheson quote is:

Comment by KC — June 1, 2010 @ 10:52 am

KC Says:
June 1st, 2010 at 12:08 pm
Let's tray that again, this time not using the Quicktags

http://sfmatheson.blogspot.com...

Comment by KC — June 1, 2010 @ 12:08 pm

ID guy Says:
June 1st, 2010 at 5:36 pm
KC:
For example, he says he never explicitly made the assumption about simultaneous mutations, as if that somehow obviously gets him off the hook. But you and I both know that this isn't necessarily true– the assumption may just as well be implicit in his calculations.

IOW KC knows what Dr Behe was saying better than Dr Behe.

And again to refute what Dr Behe is saying all you have to do is show us more than one new binding site arising via blind, undirected chemical processes- take as many generations as you need.

IOW the heck with his calculations bring on your data and stop whining already…

Comment by ID guy — June 1, 2010 @ 5:36 pm

Guts Says:
June 1st, 2010 at 6:08 pm
Zachriel, it's quite obvious you never read the book and you don't understand Behe's argument, much less molecular evolution.

Comment by Guts — June 1, 2010 @ 6:08 pm

chunkdz Says:
June 1st, 2010 at 6:31 pm
Let's not forget Zachriel's stated purpose for visiting:

"Climbing down into the Tard-Pits."

Comment by chunkdz — June 1, 2010 @ 6:31 pm

Guts Says:
June 1st, 2010 at 6:47 pm
KC wrote:

This is why Behe's critics, including Durrett and Schmidt, claim Behe is arguing for simultaneous mutations within one individual. The assumption is implicit in his calculation.

Your link to Matheson is referring to the Behe's own 10^40 calculation, Behe was simply saying, with reference to his 10^20 calculation, that it was not his calculation, and that the calculation is referring to individuals in a population, it doesn't assume that there's only one individual in the entire universe. I don't think Behe is denying that he is calculating the probability of a cluster of mutations arising in an entire organism.

Comment by Guts — June 1, 2010 @ 6:47 pm

Zachriel Says:
June 1st, 2010 at 7:22 pm
Guts: it's quite obvious you never read the book and you don't understand Behe's argument, much less molecular evolution.

This is Behe's stated position:

Behe: The immediate, most important implication that complexes with more than two different binding sites—ones that require three or more different kinds of proteins—are beyond the edge of evolution, past what is biologically reasonable to expect Darwinian evolution to have accomplished in all of life in all of the billion-year history of the world. The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40.

You don't have to be bothered to defend it, because the claim is faulty for reasons given above.

Comment by Zachriel — June 1, 2010 @ 7:22 pm

Guts Says:
June 1st, 2010 at 7:24 pm
You didn't provide any reason above for the claim being faulty. You don't even understand his argument.

Comment by Guts — June 1, 2010 @ 7:24 pm

KC Says:
June 1st, 2010 at 7:24 pm
ID guy bleats:

IOW the heck with his calculations

Oh yeah, to heck with Behe's calculations. LOL.

Comment by KC — June 1, 2010 @ 7:24 pm

ID guy Says:
June 1st, 2010 at 7:30 pm
And again to refute what Dr Behe is saying all you have to do is show us more than one new binding site arising via blind, undirected chemical processes- take as many generations as you need.

IOW the heck with his calculations bring on your data and stop whining already…

KC farts-

Oh yeah, to heck with Behe's calculations.

I take it that means you do not have any evidence nor scientific data to support your position. Typical.

Can't even focus on one sentence-> you have to chop it up- pathetic.

Comment by ID guy — June 1, 2010 @ 7:30 pm

ID guy Says:
June 1st, 2010 at 7:32 pm
Zachriel:
You don't have to be bothered to defend it, because the claim is faulty for reasons given above.

Pretty much everything you said is faulty for all the reasons provided above.

Comment by ID guy — June 1, 2010 @ 7:32 pm

Zachriel Says:
June 1st, 2010 at 7:34 pm
Guts: You didn't provide any reason above for the claim being faulty. You don't even understand his argument.

The claim at issue is quoted above.

Guts: IOW the heck with his calculations

Behe's says the reasoning concerning the edge of evolution is straightforward, and then points to the calculations.

Comment by Zachriel — June 1, 2010 @ 7:34 pm

Zachriel Says:
June 1st, 2010 at 7:36 pm
IOW the heck with his calculations

should be attributed to ID guy.

Comment by Zachriel — June 1, 2010 @ 7:36 pm

ID guy Says:
June 1st, 2010 at 7:36 pm
Zachriel,

You didn't read the book so perhaps now is the time to stop commenting on it.

Or do you not care that people see how dishonest you are?

Comment by ID guy — June 1, 2010 @ 7:36 pm

ID guy Says:
June 1st, 2010 at 7:38 pm
Zachriel:
IOW the heck with his calculations

should be attributed to ID guy.

Nice of you to ignore the supporting statement and the rest of the sentence.

You really don't care if everyone knows that you are a prick.

Comment by ID guy — June 1, 2010 @ 7:38 pm

Zachriel Says:
June 1st, 2010 at 7:42 pm
ID guy: You didn't read the book so perhaps now is the time to stop commenting on it.

The quote is accurate. If you feel it is out of context, feel free to explain Behe's position and respond to the argument concerning his calculations.

Comment by Zachriel — June 1, 2010 @ 7:42 pm

ID guy Says:
June 1st, 2010 at 7:53 pm
Zachriel,

You didn't read the book so you shouldn't comment on it.

Also even if the calculation is wrong you still don't have any positive evidence for your position.

Comment by ID guy — June 1, 2010 @ 7:53 pm

ID guy Says:
June 1st, 2010 at 7:54 pm
And the quote could be accurate.

That does not mean what you are doing to it is accurate thiough…

Comment by ID guy — June 1, 2010 @ 7:54 pm

KC Says:
June 1st, 2010 at 10:36 pm
ID guy is desperately trying to divert attention from Behe's naive calculations by lamely demanding the other side produce its calculations. Of course, it already has: Durret & Schmidt, Lynch & Abegg. ID Guy apparently thought people weren't paying attention to his lame argument, and would fall for his "Hey look, it's Haley's Comet!" gambit. Frakking loser.

Comment by KC — June 1, 2010 @ 10:36 pm

Guts Says:
June 1st, 2010 at 10:41 pm
KC,

It's Durret's & Schmidt's calculation that is naive, since it assumes that the previous intermediates are neutral.

Comment by Guts — June 1, 2010 @ 10:41 pm

KC Says:
June 1st, 2010 at 11:40 pm
Guts writes:

It's Durret's & Schmidt's calculation that is naive, since it assumes that the previous intermediates are neutral.

Have you actually read the original paper, Guts? They assign relative fitnesses of 1 to wild type, r to the A mutant, and s to the B mutant (A being the intermediate). Then, on page 8 they consider the neutral case (i.e., r = 1). But you really need to read all the way to page 11, where they take up the deleterious case for the intermediate A mutant, i.e., r < 1.

Comment by KC — June 1, 2010 @ 11:40 pm

Guts Says:
June 2nd, 2010 at 1:24 am
KC, of course they consider a deleterious model, but that possibility brings the probability closer to Behe's calculation.

Comment by Guts — June 2, 2010 @ 1:24 am

KC Says:
June 2nd, 2010 at 6:39 am
KC, of course they consider a deleterious model, but that possibility brings the probability closer to Behe's calculation.

If they considered the deleterious case, then they weren't being naive by "assuming" the neutral case, as you asserted.

Comment by KC — June 2, 2010 @ 6:39 am

ID guy Says:
June 2nd, 2010 at 7:15 am
KC:
ID guy is desperately trying to divert attention from Behe's naive calculations by lamely demanding the other side produce its calculations.

I don't want calculations.

I am asking you to produce positive evidence for your position.

Something that shows two binding sites can arise would be a good start.

IOW KC I am asking you for something you have never produced- real scientific data that would support your claims.

I take it KC the moron didn't undersatnd the following even though it is spelled out:

Also even if the calculation is wrong you still don't have any positive evidence for your position.

Frakkin' loser…

Comment by ID guy — June 2, 2010 @ 7:15 am

ID guy Says:
June 2nd, 2010 at 8:26 am
Doug Axe weighs in on the paper"Waiting for two mutations":

Bold Biology for 2009

Comment by ID guy — June 2, 2010 @ 8:26 am

Guts Says:
June 2nd, 2010 at 9:58 am
KC:

If they considered the deleterious case, then they weren't being naive by "assuming" the neutral case, as you asserted.

LOL KC, if when they don't assume a neutral case the probability gets closer to Behe's, then saying that Behe's calculation is naive is simply false. It's not naive, it's simply correct. Furthermore, protein sequences are highly constrained, as an example, only about 50% of the residues in tubulin sequences do not vary across different insect species, so in fact Behe's calculation may be the one that is closer to reality.

Comment by Guts — June 2, 2010 @ 9:58 am

KC Says:
June 2nd, 2010 at 10:15 am
ID Guy:

IOW KC I am asking you for something you have never produced- real scientific data that would support your claims.

Like in ribonucleases? Ian Musgrave talked about it here:

http://pandasthumb.org/archive...

From the posting (my emphasis):

This paper was looking at the basis of the binding of bovine seminal ribonuclease. Ribonuclease is an enzyme that, as its name suggests, breaks down ribonucleaic acid. These enzymes are typically monomers, but bovine seminal ribonculease is a modified duplicate of standard ribonuclease which is a dimer. The question that researchers were interested in was which mutations were responsible for binding. At stake was a particular model of how proteins bind to each other. To explain this, I have to briefly diverge into a discussion of protein folding.
When proteins are synthesized in a cell, they have to fold up into their final, three dimensional shapes. In this process, loops on the protein chain fit into pockets in the protein chain. Sound familiar? It’s the same process the produces protein-protein binding. One of the simplest ways for two proteins to bind to each other is if the loop of one binds into the pocket of the other (see the diagram). You can see that it would be very simple to set this up. In the end the researchers found there were multiple ways to get ribonulcease to dimerise. One mutation was all it took. So we have evidence that in nature, single mutations are all it takes to produce important protein-protein complexes. And we have had this evidence for sometime. Why didn’t Behe address this?

Comment by KC — June 2, 2010 @ 10:15 am

KC Says:
June 2nd, 2010 at 10:24 am
Guts, Behe's "calculation": was based not on an "empirical statistic" as he claims, but on a speculative estimate that was not exclusively based on just two amino acid substituitions, but instead could involve possibly three or more. Yet Behe expects us to take this value as as an empirical fact for two substitutions. That is wishful, naive thinking on his part.

Comment by KC — June 2, 2010 @ 10:24 am

Guts Says:
June 2nd, 2010 at 11:10 am
So KC, did you read the book?

Comment by Guts — June 2, 2010 @ 11:10 am

Guts Says:
June 2nd, 2010 at 11:30 am
One mutation was all it took.

Assuming that Musgrave is correctly interpreting the data (which is doubtful given past experiences), it appears he has never read the book either.

Comment by Guts — June 2, 2010 @ 11:30 am

ID guy Says:
June 3rd, 2010 at 7:33 am
KC,

Methinks Ian didn't read the book.

He sure as heck mangles what Dr Behe wrote- was that by design?

Comment by ID guy — June 3, 2010 @ 7:33 am

KC Says:
June 3rd, 2010 at 9:27 am
He sure as heck mangles what Dr Behe wrote

Example? I have my copy of the book right here. Let's go through it together.

Comment by KC — June 3, 2010 @ 9:27 am

ID guy Says:
June 3rd, 2010 at 10:04 am
Great find where Dr Behe talks about simultaneous mutations.

Comment by ID guy — June 3, 2010 @ 10:04 am

ID guy Says:
June 3rd, 2010 at 1:33 pm
KC- did you go to work or are you reading the book looking for "simultaneous mutations"?

I looked and can't find it.

Perhaps you will have better luck…

Comment by ID guy — June 3, 2010 @ 1:33 pm

KC Says:
June 3rd, 2010 at 1:51 pm
As I said before, Behe doesn't have to specifically say he is assuming simultaneous mutations. His calculations already reveal the assumption. Let's consider his 10^20 figure for the cluster of mutations necessary for chloroquine resistance (CCC). On page 57 of the book he clearly states that two individual amino acid substitutions are required for rthe resistance to develop. Can we assume Behe means that one subsitution could appear in an individual first, then the second occur in another individual who carries the first later, rather than assuming they both must spontaneously in one individual? No. The reason for that is, Behe draws his figure from a population under the very harsh chloroquine regime (on page 57, note that Behe's description of White's calculatioin only applies only during the years chloroqine was used). Individuals who carry only one of the substitutions are eliminated and cannot pass it along to the next generation. Only an individual in which both substitiutions occur at the same time can pass resistance on to its offspring. It doesn't matter one whit whether or not one subsitution alone is neutral or deleterious on its own, either– chloroquine takes out both equally. So the 10^20 figure, in reality, depends on simultaneous mutations occurring. Since it comes from a population under a very harsh selection regime, and since selection coeffiecients in natural populations are rarely that high, it doesn't make sense for Behe to do what he does next, and calculate a "double CCC" on page 63 using the same probability without specifying what the selection coefficient is for the "double CCC". If the selection coefficient is significantly less than the chloroquine regime, then sequential mutations become a possibility, along with many other factors which could actually lower the probability further (bottlenecks, as just one example, bringing one required mutation up to a high frequency quickly).

Comment by KC — June 3, 2010 @ 1:51 pm

KC Says:
June 3rd, 2010 at 1:53 pm
(I was waiting for my lunch break)

Comment by KC — June 3, 2010 @ 1:53 pm

KC Says:
June 3rd, 2010 at 2:12 pm
KC- did you go to work or are you reading the book looking for "simultaneous mutations"?

I looked and can't find it.

ID Guy should check out page 109 (my emphasis):

In order to go straight from regular hemoglobin to C-Harlem, the right mutations would have to show up simultaneously in positions 6 and 73 of the beta chain of hemoglobin. Why is that so hard? Switching those two amino acids at the same time would be very difficult for teh same reason that developing resistance to cocktail drugs is difficult for malaria– teh odds aghainst getting two needed steps at once are the multiple of th eodds for each step haeppening on its own.

Comment by KC — June 3, 2010 @ 2:12 pm

Zachriel Says:
June 3rd, 2010 at 2:36 pm
Behe: That leaves three or four amino acid changes that might cause trouble if they occur singly. For the Darwinian step in question, they must occur together. Three or four simultaneous amino acid mutations is like skipping two or three steps of an evolutionary staircase.

The concept of multiplying two probabilities means that they are singular and independent events. When we acknowledge that a mutation can be inherited and spread through a population, then the odds change substantially. So, Behe's math implies they are specific, multiple, simultaneous mutations.

Comment by Zachriel — June 3, 2010 @ 2:36 pm

ID guy Says:
June 3rd, 2010 at 4:05 pm
Excuse me- I thought we were discussing protein-to-protein binding sites.

That chapter starts at page 123.

Comment by ID guy — June 3, 2010 @ 4:05 pm

KC Says:
June 3rd, 2010 at 4:19 pm
You're excused for asking me to read the "book" looking for the term "simultaneous mutations", when what you really meant was "read only after page 123".

Comment by KC — June 3, 2010 @ 4:19 pm

ID guy Says:
June 3rd, 2010 at 4:36 pm
KC,

It just so happens tat Dr Behe is correct when he said:

In order to go straight from regular hemoglobin to C-Harlem, the right mutations would have to show up simultaneously in positions 6 and 73 of the beta chain of hemoglobin.

So I don't understand why you even posted that.

Also we were talking about protein-to-protein binding sites and that is what Musgrat was referring to also.

Comment by ID guy — June 3, 2010 @ 4:36 pm

ID guy Says:
June 3rd, 2010 at 4:38 pm
Behe: That leaves three or four amino acid changes that might cause trouble if they occur singly. For the Darwinian step in question, they must occur together. Three or four simultaneous amino acid mutations is like skipping two or three steps of an evolutionary staircase.

In the contaxt he is speaking that happens to be true.

Comment by ID guy — June 3, 2010 @ 4:38 pm

KC Says:
June 3rd, 2010 at 5:43 pm
ID Guy, then when Matheson and others claim Behe is assuming simultaneous mutations, they are right. Besides, Musgrave points out that, for protein-protein binding, 5-6 amino acid changes are NOT necessary for protein binding as a general rule so Behe's context is bogus too.

Comment by KC — June 3, 2010 @ 5:43 pm

Guts Says:
June 3rd, 2010 at 8:37 pm
KC, bovine seminal Ribonuclease biological activity depends on dimerization and the swap of the two N-terminal a-helices (residues 1–15) between the two subunits generating two composite active sites consisting of residues that belong to different subunits. Two cysteine residues at positions 31 and 32 is the minimal determinant for dimerization and each of the residues at position 19,28,31 and 32 , Pro, Leu, and Cys respectively, contributes to the exchange of the N-terminal helices of the dimeric ribonucleases.

Comment by Guts — June 3, 2010 @ 8:37 pm

ID guy Says:
June 3rd, 2010 at 8:38 pm
Not only is that a lame and invalid “argument”, but do you mean this Steve Matheson?

Matheson’s intron fairy tale

And when Dr Behe says 5-6 amino acid changes he is talking about those existing protein complexes which would require such a thing.

IOW Dr Behe is talking about one thing and Muskrat is saying "Hey look Haley's comet".

Comment by ID guy — June 3, 2010 @ 8:38 pm

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