Coopting cooption

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Cooption

I think Dembski may now be exploring gradual, intelligence-guided cooption because cooption nuked Behe’s irreducible complexity argument. Unfortunately, Dembski’s specified complexity argument depended entirely on Behe’s irreducible complexity argument in order to succeed in biology. Dembski and Behe first said that irreducible complexity couldn’t evolve because any precursor missing a part was by definition nonfunctional. As a backup argument, they acknowledged that cooption could perhaps produce such systems, but they only addressed a fake, strawman version of cooption, namely all-the-parts-come-together-at-once, tornado-in-a-junkyard-type assembly. When that backup argument didn’t hold water, because of the commonality of functional subsystems (with some but not all of the parts of the “irreducible” system of interest), Dembski switched to a backup-backup argument: “The only well-documented examples that we have of successful co-option come from human engineering.” (“Unintelligent Evolution”, December 2004 – various versions of this same statement are found in several places in Dembski’s writing).

That was from the start a silly thing to assert, but unfortunately for Dembski, his colleague Scott Minnich torpedoed whatever vestiges of credibility Dembski’s backup-backup argument might have had, when he explained in his sworn testimony in Kitzmiller v. Dover that a degradation pathway for a toxic compound (2,4-DNT, a derivative of the explosive TNT), a pathway which requires a half-dozen different proteins, had in fact naturally evolved in microbes on a U.S. Air Force base within the last few decades.

The relevant Minnich testimony is here, and the exhibit they are discussing is this paper: Glenn R. Johnson and Jim C. Spain (2003). “Evolution of catabolic pathways for synthetic compounds: bacterial pathways for degradation of 2,4-dinitrotoluene and nitrobenzene.” Applied Microbiology and Biotechnology, 62(2-3), pp. 110-123. [PubMed] [DOI] [Journal]

Johnson and Spain (2003) is a review paper, based in part on this research paper: Glenn R. Johnson, Rakesh K. Jain, and Jim C. Spain (2003). “Origins of the 2,4-Dinitrotoluene Pathway.” Journal of Bacteriology, 184(15), pp. 4219-4232. [PubMed Central (free)] [DOI] [Journal]

As if Minnich’s testimony weren’t clear enough, the fact of natural cooption in the origin of this system was underscored by DI spokesperson Casey Luskin. In his review of Minnich’s testimony, Luskin wrote,

Minnich, who had previously read the paper, explained that to evolve this pathway required the modification of maybe 2 or 3 preexisting enzymes. There was really nothing new here, and certainly nothing approaching an irreducibly complex biomolecular machine. Minnich called this microevolution.

There you go, a multiple-proteins-required system evolving in an evolutionary eyeblink by a natural process of cooption, something which leading ID expert William Dembski said required intelligence, and we get the “it’s just microevolution” line!

But it’s just a metabolic pathway!

Clever ID advocates will pull out the old emergency defense, used only when convenient by Michael Behe, that “metabolic pathways are not irreducibly complex” (italics original). Unfortunately for this defense, at trial and elsewhere Michael Behe, William Dembski, and Casey Luskin have all made it very clear that metabolic pathways with multiple required parts are, in fact, irreducibly complex:

1. Dembski,Three Frequently Asked Questions about Intelligent Design (PDF)”, September 2003:

Strong Irreducible Complexity of Molecular Machines and Metabolic Pathways. For certain enzymes (which are themselves highly complicated molecular structures) and metabolic pathways (i.e., systems of enzymes where one enzyme passes off its product to the next, as in a production line), simplification leads not to different functions but to the complete absence of all function. (italics original)

2. Luskin favorably quotes this whole section of Dembski’s article on the IDEA center website.

3. Behe, discussing the lac operon (the lactose metabolism pathway of E. coli) Kitzmiller Trial Testimony Day 10, afternoon:

Q. Sir, have some scientists argued that there is experimental evidence that complex biochemical systems can arise by Darwinian processes?

A. Yes, there have been a total of two such arguments which I regard to be very important, because these were claims that there had been experimental demonstrations, not just speculations, not just stories, but experimental demonstrations that either irreducible complexity was incorrect or that complex systems could be built by Darwinian processes.

Q. And one of those claims was raised by Dr. Miller, is that correct?

A. That’s correct. I think on the next slide we see that he wrote in his book Finding Darwin’s God,which was published in 1998, he said, “A true acid test used the tools of molecular genetics to wipe out an existing multipart system and then see if evolution can come to the rescue with a system to replace it.”

So here he was making the point well, here one test of this claim of irreducible complexity and the ability of Darwinian processes to make complex systems, well, is to find a complex system in a cell, destroy it, and then see if random mutation and natural selection can come back and replace it. And I have to say I agree that’s an excellent test of that claim. However, I disagree with Professor Miller’s further comments and conclusions.

Q. What was the particular system that he was looking at?

A. Well, he was referring to what is shown in a little cartoon version on the next slide. This is a figure again taken from that biochemistry textbook by Voet and Voet discussing a system called the lac operon. Now, an operon is a little segment of DN A in a bacteria which codes for a couple of genes, and genes code for proteins, and the proteins usually have related functions or function as a group, and one of them is called the lac operon which is used to, the proteins of which are necessary for the bacterium Escherichia coli to metabolize a sugar called lactose, which is a milk sugar.

And it consists of a number of parts.

[…]

Q. So this was the system that Dr. Miller was talking about in –

A. Yes, I’m afraid this is the background for the system that he started to discuss in his book.

Q. Which he sees it as experimental evidence to refute the irreducible complexity claim?

A. Yes, that’s right, and if you look on the next slide you’ll see the part of his book where he discusses that. He says of the system, he says, “Think for a moment. If we were to happen upon the interlocking biochemical complexity of the re-evolved lactose system, wouldn’t we be impressed by the intelligence of its design. Lactose triggers a regulatory sequence that switches on the synthesis of an enzyme that then metabolizes lactose itself.

“The products of that successful lactose metabolism then activate the gene for the lac permease, which ensures a steady supply of lactose entering the cell. Irreducible complexity, what good would the permease be without the galactosidase? No good of course.” And he continues that same discussion on the next slide, he continues, “By the very same logic applied by Michael Behe to other systems, therefore, we can conclude that this system had been designed, except we know that it was not designed. “We know it evolved, because we watched it happen right in the laboratory. No doubt about it, the evolution of biochemical systems, even complex multipart ones, is explicable in terms of evolution. Behe is wrong.”

Q. Is Dr. Miller right?

A. No. Dr. Miller is wrong. Now, Professor Miller is always enthusiastic and he always writes and speaks with great excitement, but I say that when you examine his arguments closely, under close inspection they simply don’t hold up and this is enormously exaggerated, and the results of researcher Barry Hall that he is describing here I would happily have included as an example of irreducible complexity in Darwin’s Black Box.

(bolds added)

So, three prominent spokespeople for ID agree: metabolic pathways with multiple required parts actually are irreducibly complex. And yet Dr. Minnich admitted at trial that cooption had produced just such a system in a matter of decades. He has furthermore said that his colleagues at the University of Idaho have gotten similar results on other degradation-resistant, human manufactured chemicals, like TNT. And, in fact, the scientific literature is full of such examples.

So, to sum up, as a result of Kitzmiller v. Dover, we’ve not only established that ID really is creationism, and that the ID movement has been scandalously hiding this inconvenient fact – we have also established that both molecular cooption, and the natural evolution of irreducible complexity, have in fact occurred within a few decades. And not just once, but many times.

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Matzke on Cooption in Evolution from Dispatches from the Culture Wars on November 30, 2005 10:43 AM

Nick Matzke has an excellent post at the Panda's Thumb about cooption as an evolutionary mechanism for building up complex biochemical systems. Cooption is when a given feature - a protein, perhaps, or in some cases an entire organ -... Read More

35 Comments

How about the evolution of Behe’s IC from purportedly establishing the impossibility of these systems gradual evolution into a space-age argument from ignorance?

Bets on how long before we have the Theory of Intelligent Coopting?

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Luskin

Minnich, who had previously read the paper, explained that to evolve this pathway required the modification of maybe 2 or 3 preexisting enzymes. There was really nothing new here, and certainly nothing approaching an irreducibly complex biomolecular machine. Minnich called this microevolution.

…which is the work of micro-gods, right?

So Casey Luskin claims to know that this system with 2 or 3 preexisting enzymes is “certainly nothing approaching an irreducibly complex biomolecular machine.”

A reasonable person would conclude that Casey Luskin must know what an irreducibly complex biomolecular machine is. If Casey Luskin was unable to answer a couple of straightforward questions about irreducibly complex biomolecular machines, then a reasonable person could fairly conclude that Casey Luskin is being less than honest when he makes statements such as the statement above.

Here are two straightforward questions for Casey Luskin:

1) Of all the irreducibly complex biomolecular machines you are aware of, which is the simplest in terms of the total number of proteins? in terms of the total number of amino acids?

2) Of all the complex biomolecular machines that you are aware of, which is the most complex biomolecular machine that is not irreducibly complex?

“There you go, a multiple-proteins-required system evolving in an evolutionary eyeblink by a natural process of cooption, something which leading ID expert William Dembski said required intelligence, and we get the “it’s just microevolution” line!”

What is to stop an IDist from concluding the opposite? “By jove, you’re right! A Designer at work! It’s a miracle!” Why can’t it be a miracle? Do they not believe in an interventionist God^H^H^HDesigner? Isn’t this proof? “Aha, something that I just said is impossible to happen naturally has happened, ergo ID!” Makes as much sense as anything else they say.

BTW, I saw it on PT a while back but I can’t find it now–what’s the name of the law having to do with Engineers and evolution/creation debates? Sorry for the off-topic.

Stoffel Wrote:

BTW, I saw it on PT a while back but I can’t find it now—what’s the name of the law having to do with Engineers and evolution/creation debates? Sorry for the off-topic.

The Salem Hypothesis??

Dembski actually started this “contest” last September and, in my opinion, it was won by “Jeff Blogworthy”, the fourth commenter, on the evolution of a lawn edger into the Weed Whacker™:

———————————————————-

4. Don’t know if this comes anywhere close to fitting the bill for you, but here is a lurch at it :)

1. Lawn edger.

2. Lawn edger becomes weed whacker c. 1971. “In 1971, George Ballas sought a better way to trim around the trees in his yard. After visiting an automatic car wash and noticing how the bristles stood out straight as they swirled, Ballas had a brainstorm. He went home, found a tin popcorn can in the trash, punched holes in it and inserted knotted fishing line to simulate the car wash bristles. He then attached the string-and-can to his rotary electric edger and tried it. It worked.”

3. The weed whacker was first used for light duty trimming, but quickly evolved to heavy brush with the addition of a saw blade.

4. Users quickly realized the need for a shoulder harness, to avoid strain.

5. The rigid drive shaft was replaced with a flexible shaft by Echo in 1977, allowing the mower head to parallel the ground.

6. First trimmers used individual, short pieces of string.

7. Spool added to head, user still had to stop machine and manually pull string from head.

8. “Bump-N-Go” head introduced.

9. Automatic feed head introduced which relies on the centrifugal force of the string to initiate feed with no user intervention. (hah!)

10. Standard color coding introduced, corresponding with string diameter — blue, green, and orange.

11. The first weed whackers had few safety features. A guard was added to the part of the head facing the user to improve safety, and functionality (the guard doubles as a string cutter.)

12. Hose and bag added, allowing the cooler impellers to double as a vacuum.

13. By directing leaves and small brush through sharpened impellers, the weed whacker can also serve as a mulcher.

14. Wheels added to weed whacker, see picture here: http://www.popularmechanics.com/hom[…]ge=3&c=y

Comment by Jeff Blogworthy — September 19, 2005 @ 10:24 pm ———————————————– Doctor Dembski, pay the man his hundred dollars!

Or maybe comment #5 deserves it, for his book on the history of the steam engine, or comment #12 on the history of the gun or maybe some of the other 58 responses to this challenge.

I’m surprised that Dr. Dembski hasn’t tripped over the multiple fun TV series by James Burke – e.g. “The Day the Universe Changed”.

Amazon has many references, or check your local library.

(Hint… just ignore James Lee Burke; he’s someone else entirely)

The evolution in recent decades of the pentachlorophenol (PCP, a man made toxin) degradation pathway is another example. It involves four enzymes, or maybe more depending on where you draw the boundaries of the ‘system’. Are four enough? In Behe’s testimony, he says he is sure that a group of four enzymes within the blood clotting cascade is IC. How about just 1 protein? Proteins have hundreds of ‘parts’ (amino acids). One of the easy ways that Behe’s thesis goes wrong is that his ‘parts’ (generally whole proteins) themselves evolve. However, it is possible to think of a protein as having just two or three or four large parts. IDists have at times suggested that a single protein could be IC in terms of such parts.

Meanwhile back in reality, here is an overview of pathway evolution published in 2003.

Well, that’s how software in general tends to evolve. Perl is one nice example, so are Tcl, HTML (that is, the WWW), X windows, and word processors.

In fact, Microsoft is known for using this as a defensive tactic, timing subtle changes to fend off the potential compatibility of competitors.

The evolution of a motorcycle from a motor and a bicycle is not a good example in this regard because the motor and bicycle require extensive design-work to adapt them to each other.

I wonder if Dembski is even remotely familiar with the history of the motorcycle? The very first motorcycles were made by doing nothing more than taking an ordinary small motor from nearly anywhere, and bolting it to an ordinary bicycle so that the shaft of the motor pressed against one of the bicycle’s tires. The early adaptations consisted of adjusting the gearing, modifying the way the shaft contacted the wheel for better traction, and bolting a fuel tank to the bar.

Note also that the base used for building a motorcyle remained an ordinary, off-the-shelf bicycle for decades; it remained possible to remove the motor and pedal all motorcycles as essentially normal (though heavy) bicycles for 30 years!

If this transition doesn’t qualify, I don’t see how anything could. Apparently Dembski’s definition of “extensive redesign” is ANY AT ALL. Gee, “added clamp to attach motor to bicycle frame. Extensive redesign. Doesn’t count!”

possibilities:

1. the stone axe. sharp rock plus stick plus sinew.

2. the glass bottle. glass and cups evolved separately.

3. reese’s peanut butter cups. hey, you got chocolate in my peanut butter!

I vote for James Burke’s television shows as having good examples… (Connections, etc.)

One example, Jacquard Loom…

Next coal tar! (o.k. inside joke, but if you watch too much of the later connections sereies you become convinced everything is based on coal tar. :-) )

Is Dembski trying to hurt ID? By exposing his followers to series where incremental changes and repurposings resulted in significantly different systems, he is going to damage their belief in Irreducible Craplexity.

Easy. The photomultiplier tube led to the microwave oven via co-option of traits from older technologies. The original electron tubes (Crookes tubes and PMTs) were scientific curiosities. A few decades of fiddling with them led to the invention of the vacuum valve, basically a diode. Adding one element to the diode makes it a triode, an extremely useful object that eventually would lead to electronics and computers. Anyway, after vacuum tubes underwent a decade or two of refinement, in 1921 Hull put a vacuum tube diode into a magnetic field and discovered that he could regulate the current by changing the field. That was the first magnetron. Magnetrons evolved a little bit in their role as current regulators. Shortly before WWII, it was discovered that these tubes *just so happened* to emit strong radio waves, although noone knew what such a thing would be good for. They evolved a bit to improve their performance as radio emitters. During the war, Boot and Randall realized it could serve as the compact microwave source needed for airplane-mounted radar—i.e., they simply plugged it in to their existing radar technology in place of other functioning-but-unwieldy sources. Given that task, the magnetron evolved gradually to handle very high powers. In the course of *that* evolution, someone accidentally discovered that it could cook food—with no modification at all, actually, you could just put some food near any 300W, ~2 GHz magnetron. These “radar ranges” then evolved into the microwave ovens you have on your countertop today.

Note the cladogenesis: microwave ovens, radar, vacuum tubes, and photomultipliers all still exist today.

evolutionist, having read Ben M’s comment above: So it seems like the television and microwave oven have a common ancestor.

creationist: Oh yeah? Well where’s the missing link? A half-television, half microwave device?

evolutionist: Shut up Salvador.

I’m getting this feeling from all the comments that many of you are expecting Dembski to show more honesty about this “contest” than he does about anything else. It sounds like more “street theater” to me.

PaulC wrote

I’m getting this feeling from all the comments that many of you are expecting Dembski to show more honesty about this “contest” than he does about anything else. It sounds like more “street theater” to me.

Dembski has been pursuing a technology development analogy for at least three years, with his mention of TRIZ on ISCID here and elsewhere in 2002.

None of which speaks to the honesty (or lack thereof) of Dembski’s use of the analogy, of course.

RBH

Flint Wrote:

The evolution of a motorcycle from a motor and a bicycle is not a good example in this regard because the motor and bicycle require extensive design-work to adapt them to each other.

If this transition doesn’t qualify, I don’t see how anything could. Apparently Dembski’s definition of “extensive redesign” is ANY AT ALL. Gee, “added clamp to attach motor to bicycle frame. Extensive redesign. Doesn’t count!”

Flint, that’s exactly what I was thinking way back when I first saw the “contest”, how dumb. By the way, if a person were to scroll down the contest page to comment 22, they would see James Taylor taking Dembski to task about the all the comments disappearing only from public view. Suddenly, posts seem to reappear, although, quite a few other people seemed to have problems posting… and not a peep from “WmAD” is heard about it.

Evolutionist: HaHaHa HaHaHaHa HaHaHaHa Creationist: http://www.biblegateway.com/passage[…]p;version=31; Evolutionist:????? Creationist: http://www.ideacenter.org/contentmg[…].php/id/1207 Evolutionist: Oh boy. Creationist: http://msnbc.msn.com/id/10242549/ Evolutionist: Uh oh. Creationist: http://www.700club.com/spirituallif[…]tnessing.asp Evolutionist: Hmmmm.

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Dembski has been pursuing a technology development analogy for at least three years

Can someone explain in readable, unambiguous terms what he’s hoping to accomplish? (Yes, I followed the links.)

It seems that if cooption were demonstrated as an important driver of technology development (I think it is, by the way) that wouldn’t help the ID case. It would merely demonstrate that the human process of invention is analogous in certain ways to evolution and there’s no reason to believe that human inventiveness (*) can produce certain kinds of stuctures (e.g. CSI or IC) that evolution is supposedly incapable of producing.

On the other hand, if Dembski is presenting his “contest” as a challenge to demonstrate that cooption is not important in technology development, and therefore a red herring, then I could sort of see what he’s driving at. But he will clearly fail, as demonstrated above by the motorcycle example and any number of other instances in which people use whatever they have to perform a function for which there is no existing tool.

I doubt he wants to part with his money either, so we can expect him to keep redefining the meaning of his words every time someone claims to have won his “contest.”

(*) Humans can do some things that evolution does not, such as coopting a pattern from one substrate to an entirely new one in a single step, or simulating design improvements without building prototypes. This makes humans faster at doing certain things, but humans are also limited to optima that can be found using a series of exhaustive searches over a tractable search space, and incremental refinements. Inaccessible optima (which is roughly the idea of irreducible complexity) are no more accessible to humans than they are to evolution.

You know, even if someone did come up with a really good example of cooption in technology, one good enough to convince Dembksi, I’d bet ten bucks Dembski will just use it to say “COOPTION REQUIRES INTELLIGENT DESIGN!”

Any of a few thousand drug molecules would do. Try rapamycin for starters.

Well, that’s how software in general tends to evolve. Perl is one nice example, so are Tcl, HTML (that is, the WWW), X windows, and word processors.

You know, there is an interesting thought. Languages, both human and computer languages, evolve by a system of gradual random mutation, with some degree of exchange of material occurring with other languages. This process is not genetic, but it is in a sense natural.

Never mind cooption for a moment. I would be very curious to know: Do there exist any human languages with “irreducibly complex” features? It seems likely the answer would be yes.

I’m not sure that the systematic sound changes that human languages tend to undergo are best described as “random.”

My understanding is that certain phonemes are more likely to change to certain other phonemes, that some of these changes are more likely to proceed in one direction than the other, etc. Perhaps these are analogues of genetic mutations where some types of mutations are more likely than others…

Whether there are similar loose “rules” that apply to the grammatical infrastructure of the languages, I’m not sure.

Dembski has been pursuing a technology development analogy for at least three years

I say(one mans view) that’s because he thinks god is a machine a reflection of his own self view, a perpetual motion machine in his case, a case of tautological stasis of thought, not moving forward to a less mechanistic view of self. Perhaps because he was treated as a machine when he grew up with no room for dreaming and enjoying the innocent pleasures of growing up and of life. Projected as a privately held Myth, Give to God what is Caesar’s and give to Caesar what is God’s, to deceive himself for his rape of innocence and the noble Truth, a reflection of his own life. Pure Solipsism and tautological Obscurantism caused by a distrust of the subjective feelings and thoughts actions and motives in those around him and the hidden noble truth in his up bringing obscured in sacred text by fundamentalists and obscured in the natural world through an ignoble loss of innocence… a distrust of God (gods and antigods) in fact and a distrust in the natural/secular world and the actions of natural/secular world on him.He is unawre that heaven and hell are states of mind in the here and now not reflections of the devine and the secular, projected into the future through a remembered past. Lack of self awareness and the cause and effect of thought and action. Not unlike most fundamentalist religious world views everything is black and white to them because of perceived intolerance by those outside their horizon to themselves and expressed…projected as an intolerance for the world outside their own horizon. God with no room for the devil and the devil with no room for god …no appreciation or trust for true good and bad in themselves and the same distrust in others. The inability of the fundamentalist/literalist/obscurantist to forgive himself and the world beyond his horizon discounts the one noble Truth that all the great Mystics(Jesus,Gautama Buddha, Mohommed) gave to the world and those in it, us, as noble ideas… truths to be experienced and held as an ideal goal in the game of life, not dogma to be worshiped… but love and redemption, not self love/hate and projected “love”/hate supported by a private Myth obscuring the noble Truth(s) of the great Mystics. The concept that a noble truth exists as an infinite idea… the Mind at Large reflected in the thoughts, feelings, aspirations, creativity, desires a whole panoply of parts of the whole and at once a single “pinhead” the here and now, by me and by you projected by us towards each other as the players in the game of life with one rule the noble Truth, hidden by obscuartionists, but available to be experienced for those whose journey is in search of the knowable noble Truth by the *self* revealing the unknown. Is there a function, a method, a test, a way, a story, a new Mythology?

Back to the Master of Myth: J Campbell (“Myths to Live By” last sentence)

“ It is - and will forever be, as long as our human race exists- the old, everlasting, perennial mythology, in its “subjective sense”, poetically renewed in terms neither of remembered past nor of a projected future, but of now: addressed, that is to say, not to the flattery of “peoples,” but to the waking of individuals in the knowledge of themselves, not simply as egos fighting for place on the surface of this beautiful planet, but equally as centers of Mind at Large*- each in his own way at one with all and with no horizons “ *12th Century “The book of the twenty-four Philosophers”

The Book of 24 Philosophers is a work ascribed to Hermes Trismegistus, written in Europe around the year 1200. It consists of 24 definitions of God, the most famous of which is ‘God is an infinite sphere whose centre is everywhere and whose circumference is no where’, quoted by Meister Eckhart, Alan of Lille and Thomas Bradwardine, among others. A critical edition of this text has recently been published:

Is there a timeless story on Fundamentalism.? “Lolita” by Nabokov

The destruction of the noble truth by a self seducing lie.

An Ontology of private Myth making.Humbert’s solipsistic self created Myth purposefully designed as a tautology.. neither true nor false and… true and false at the same time; to support the rape of innocence and the noble Truth by a lie,

A story of the manipulation of love/hate by a Solipsistic/Obscurantist/Literalist/Fundamentalist/Tautologist(individual people with the aid of regimes, and religions) and finally redemption.

The Buddha is reported to have said ‘With our thoughts we make the world’ And if those thoughts are the broken noble Truth then those thoughts will be projected as un-redeeming evils by the unredeemable.

Jesus forgave them

I on ther other hand am going to kick their ass after I have had a good chat to a few devils and gods and then forgive them .…maybe.

Andrew McClure

Never mind cooption for a moment. I would be very curious to know: Do there exist any human languages with “irreducibly complex” features? It seems likely the answer would be yes.

The Basque language has no known “demonstrable genealogical (or “genetic”) relationship with other living languages”. Wikipedia also lists “Ainu, Burushaski, and Korean” as other examples of “language isolates”. I assume that these languages do derive from ancestral languages, but if I was a big time ID Theorist, I’d be claiming this particular piece of ignorance was clear evidence for an Intelligent (language) Designer.

Steviepinhead:

I’m not sure that the systematic sound changes that human languages tend to undergo are best described as “random.”

My understanding is that certain phonemes are more likely to change to certain other phonemes, that some of these changes are more likely to proceed in one direction than the other, etc. Perhaps these are analogues of genetic mutations where some types of mutations are more likely than others…

Sounds like evo-devo to me, where certain change are much more likely than others because of the underlying structure of the organism/language.

For people looking for a biological example of cooption, the Wnt pathway is great. Take the planar cell polarity pathway, add a cell adhesion molecule, borrow two kinases that regulate metabolism, throw in a transcriptional repressor.…

Paul C Wrote:

Can someone explain in readable, unambiguous terms what he’s hoping to accomplish?

Assuming he’s trying to accomplish the same thing as with his earlier TRIZ invocations…

The point is to demonstrate that human technological advancement, beyond some particular threshold, requires creative “redesign” and not mere successive modification of preexisting parts. In other words, there has to be true creativity rather than simple tinkering with what came before. By extending this idea to biology, he hopes to show that beyond some particular threshold (who knows what), the evolution of biological systems could not occur through cooption, but instead requires the input of some creative intelligence experiencing a Erueka moment of sorts.

But even if this is true about human technology (and I’m not sure how it could be shown true in any rigorous fashion), why we should automatically assume that it applies to biology is beyond me. This is a fallacy that they invoke often: trying to draw conclusions about biological objects through analogy to man-made artifacts. Unfortunately, there’s no reason to think that a given property of man-made artifacts will carry over to biology. In the case of cooption, I think it’s safe to say that multi-functionality, particulary on the molecular level, is far and away more common in biology than it is in human designs.

Dembski has a new contest (of sorts) now, he’s looking for our favorite contemptuous remarks by Darwinists.

http://www.uncommondescent.com/inde[…]archives/538

If you can still get on his site that might be fun to supply him with.

HOT NEWS!,

William Dembski responds to Nick Matzke.

Norman wrote:

“Dembski has a new contest (of sorts) now, he’s looking for our favorite contemptuous remarks by Darwinists.”

Ah yes, he posted an email I sent him and then proceeded to show that he can’t tell the difference between snootiness and sarcasm. It’s ironic that he talks about “Darwinists” showing contempt when his blog is populated by some acolytes who are far worse in that respect.

Erm… I’ve tried to map Dembski’s response onto the points that Matzke makes, but I haven’t got anywhere.

I know critical questions aren’t allowed on Uncommon Dissent, er, Descent so can anyone paraphrase what Dembski’s saying and show how it actually applies to Matzke’s original post? All I can make out is the final line - “Matzke… is as usual bluffing” - which is far too weak a response to merit a posting, and an ‘it’s just microevolution’ riposte. Such a reaction was one of Matzke’s original observations in the first place, so repeating it doesn’t get us anywhere.

R

LOL, I just looked at Dembski’s reply. Dembski isn’t even trying anymore. The contradictions between Behe, Minnich and Dembski are so clear and simple, there is really no way out except to concede that leading ID advocates made egregious errors on simple matters, which is something Dembski definitely won’t do. Either irreducible complexity has evolved in the last few decades, or these guys can’t even figure out amongst themselves what counts as “irreducibly complex.”

Various mistakes and absurdities in Dembski’s reply:

* Minnich’s deposition was in May 2005, not July 2005.

* At the deposition, I believe we actually showed Minnich the research paper on 2,4-DNT degradation, not the review paper, although I have to double-check.

* The DNT paper was in response to the claim of no phylogenetic histories for a “biochemical pathway”. The same claim for an “organelle” was rebutted with a different paper, on mitochondrial evolution.

* Dembski repeats Minnich’s handwaving about the DNT pathway being an “adaptational response.” Fine, but that’s the whole point! “Microevolutionary” processes of variation and natural selection, producing irreducible complexity in a few years!

* Dembski says that the DNT paper was published in a “second tier” journal. He doesn’t mention that the journal was the Journal of Bacteriology, probably the leading workhorse journal for microbiology. It wasn’t published in Nature because it wasn’t really novel – this kind of evolutionary assembly of a catabolic pathway has been documented numerous times! The problem is the ID movement’s complete ignorance of what the scientific literature says, not with the scientific literature.

* Regarding Lenski et al. not citing the DNT paper, Dembski assumes Minnich’s reading of Lenski et al. was vaguely lucid, which it wasn’t. Lenski et al. aren’t saying what Minnich/Dembski think they are saying. (see below)

Lenski and “lack of phylogenetic history”

Minnich relies heavily on something he says he gets from the Lenski, Pennock et al. paper to the effect that (paraphrase) “we lack a single phylogenetic history of a sub-cellular organelle or biochemical pathway.” Dembski cites this statement in his reply to me. But if you read the Lenski paper, the authors never say anything like this. In his expert report, Minnich’s logic runs as follows:

Minnich expert report Wrote:

Proponents of evolution recognize, as they must, the significant gaps and problems with the theory of evolution. For example, experts in the field acknowledge that we have no phylogenetic history (i.e., inability to historically trace the roots) of a single biochemical pathway or subcellular organelle. This is acknowledged in the introduction of a recent Nature paper attempting to account for the origin of new biological information in cells:

“From the outset, Darwin realized that ‘organs of extreme perfection and complication’ such as the eye posed a difficulty for his theory. Such features are much too complex to appear de novo, and he reasoned that they must evolve by incremental transitions through many intermediate states, sometimes undergoing changes in function. There now exists substantial evidence concerning the evolution qf complex features that supports Darwin’s general model. Nonetheless, it is difficult to provide a complete account of the origin of any complex feature owing to the extinction of intermediate forms, imperfection of the fossil record, and incomplete knowledge of the genetic and developmental mechanisms that produce such features.” [Lenski et al., The evolutionary origin of complex features. Nature. 2003 May 8;423(6936): 139-44.]

Thus, proponents of Darwin’s theory of evolution assume that evolution is true, even though we lack the intermediate structures, we lack fossils, and we do not have adequate knowledge of how natural selection can introduce novel genetic information.

(Minnich expert report, formatting original)

Minnich made exactly the same manuever in his slides and testimony at trial. I still have not figured how Minnich gets from the Lenski quote to “no phylogenetic history.” All Lenski et al. are saying is while we have “substantial evidence concerning the evolution qf complex features that supports Darwin’s general model,” we don’t have a complete account, i.e. every single mutation, for microscopic events that occurred millions of years ago. This is not a revolutionary observation, and it is not the same as saying that we have “no phylogenetic history,” a claim which appears to be Minnich’s invention. A “phylogenetic history” is a phylogeny, and we in fact have tons of those.

Basically, Minnich wildly overinterprets what Lenski et al. are actually saying on the page (you can see that he does it also with “fossils,” “intermediate structures,” and biological “information.”) With remarkable predictability, Minnich repeated the same manuever in his expert report, his deposition, and at trial.

So, in cross examination, we decided to punch a few holes in the rhetoric. Regarding “subcellular organelles”, we showed him the phylogenetic history of mitochondrion, published in 1999 in Science under the easy-to-miss title “Mitochondrial Evolution.” The paper has been cited by 299 other papers according to Google Scholar. We asked him to confirm his claim about no history phylogenetic history for subcellular organelles, and then showed Figure 1, which is a phylogenetic history showing that mitochondria emerged from a specific sub-subgroup of bacteria.

And regarding “biochemical pathway”, we showed the 2,4-DNT review paper. The pathway has a half-dozen steps, with a half-dozen enzymes or enzyme complexes involved. I believe we put up Figure 1, which shows the three ancestral groups of enzymes that the pathway was assembled from. The next figure has the phylogenies of the key proteins. What more could you want in terms of “phylogenetic history”?

(The point about irreducible complexity was a bonus, and requires the extra argument, in the original post above, about what counts as “irreducible complexity.” At his deposition, Minnich went for the “it’s just a metabolic pathway” defense, a point sadly undermined by Michael Behe at trial.)

(It may be that Minnich and Dembski simply have no idea what the term “phylogenetic history” actually means, and instead were referring to “You don’t have every single mutation.” But (a) this shows just how shockingly unfamiliar they are with the relevant field, which doesn’t help their case, and (b) “you need to give us every single mutation” is a preposterous argument against evolution, just like it would be preposterous to say that the Battle of Gettysburg didn’t occur because you couldn’t account for the exact actions of every single soldier.)

As for “bluffing” (Dembski’s term for when I do annoying things like back up my claims with references to the actual scientific literature), I guess we’ll just have to wait and see what the judge says about who made the most convincing case – the two leading actual scientists in the ID movement, or the plaintiffs’ experts and cross-examination team.

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This page contains a single entry by Nick Matzke published on November 28, 2005 9:14 PM.

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