Ahmad,
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Like I said, he thinks IC can evolve. Behe was wrong.
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Now where does Behe state the non-evolvability of metabolic pathways that are IC?
IC is IC, isn't it? Anything with multiple parts required can't (according to Behe) function without those multiple parts, therefore (according to Behe) the function cannot be reached gradually because you need all the parts. I don't see how being a metabolic pathway makes any difference, if it's an IC metabolic pathway.
Some metabolic pathways have only one required part (at least hypothetically) -- e.g., the AMP biosynthesis pathway is Behe's example in chapter 7 (p. 140 starting) -- and are therefore not technically IC according to Behe: "[t]hey do not necessarily require several parts to function" (p. 142). But
some metabolic pathways (particularly that break down toxins through several toxic intermediate steps, e.g. the PCP degradation pathway)
do require several parts to function and are therefore IC. But they can evolve anyway, apparently well within human lifetimes.
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His main arguments focuses around the examples of IC molecular machines which are very distinct, in function and nature, from metabolic pathways. So where exactly does Behe get it wrong, I wonder.
How is the blood clotting cascade so radically distinct from a metabolic pathway?
And of course, Behe includes the lactose metabolism pathway as IC -- note that it's a metabolic pathway -- as proven by the vociferous debate that Behe and Ken Miller had over it. Behe has since mentioned lactose metabolism in many speeches. At other times, to be sure, Behe has claimed that metabolic pathways aren't IC, but this seems to be an argument of convenience for him and he uses it only when confronted with evidence that this or that metabolic pathway has evolved.
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He then sets up a sub-category of IC which he thinks is impossible/very improbable to evolve, called IC machines. But this is clearly a retreat from Behe's position.
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How is it a retreat? Behe merely outlines the several problems with traditional explanations for the origin of metabolic pathways. He makes no such claim of that metabolic pathways can't evolve for him to be wrong. Gene elaborates it further.
No, Gene appears to concede the evolution of IC metabolic pathways -- as shown by the PCP degradation example, which has three required enzymes. This is different than Behe, who says basically IC = can't evolve (or IC = wildly unlikely to evolve, a pointless distinction often tediously insisted on by IDists).
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The PCP degradation has three required parts. Non-degradors only have two. Yet it evolved anyhow, and quite recently (PCP is an artifical pesticide).
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Interesting. What I got from Gene's webpage has this to say:
"What all of this means is that any evidence for the evolution of metabolic pathways does not translate as evidence for the evolution of IC machines. This is especially true if dealing with a sluggish pathway, composed of three enzymes, all borrowed from other pre-existing pathways, as with the PCP degradation pathway. There is a huge difference between molecular machines like the ribosome or flagellum and the PCP degradation pathway."
Mike Gene says there's a huge difference between the PCP degradation pathway and the flagellum etc., but then the PCP degradation pathway has had (at most) only about 60 years to evolve, as PCP was introduced as an artificial pesticide only in 1939 IIRC. It probably took rather less time than that, given that really only a few mutations were required (the key mutation was simply regulation). The point that the pathway makes is that "multiple parts required" is no barrier *at all* to evolution. Numerous similar examples, e.g. atrazine degradation, experimental studies of the evolution of multipart metabolic pathways in the lab, etc., support the point.
To back up: the main argument against IC is change-of-function, i.e. cooption. As you've been reading Mike Gene, you know that his response to this argument is (1) to concede that it works in certain cases but that (2) it is an appeal to chance and is therefore a very unlikely explanation.
But he admits that the PCP degradation pathway, with 3 required parts, was assembled from enzymes with
other original functions! (One of them is quite a radical switch, too) And if we look at evolution in general, we see that change-of-function is a ubiquitous event, not radically unlikely at all. Essentially every gene origin event is a cooption-of-function event. Your hands were not always functioning as tool-using hands, but in your ancestors were climbing hands, before that feet, and before that fins.
Here is some of the documentation backing up the above:
Topic: Co-option/change of function, literature citations on its long-recognized importance in evolution
The Origin of "Information" (new genes especially) via natural causes, Refuting a key ID claim (refs, webpages)
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And I am interested in knowking more about how this PCP is used as an insecticide as you claim. Any links?
On the evolution of PCP degradation:
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Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach.
Trends Biochem Sci 2000 Jun;25(6):261-5
Copley SD.
Dept of Chemistry and Biochemistry and Cooperative Institute for Research in Environmental Studies, University of Colorado at Boulder, Boulder, CO 80309, USA. copley@cires.colorado.edu
The pathway for degradation of the xenobiotic pesticide pentachlorophenol in Sphingomonas chlorophenolica probably evolved in the past few decades by the recruitment of enzymes from two other catabolic pathways. The first and third enzymes in the pathway, pentachlorophenol hydroxylase and 2,6-dichlorohydroquinone dioxygenase, may have originated from enzymes in a pathway for degradation of a naturally occurring chlorinated phenol. The second enzyme, a reductive dehalogenase, may have evolved from a maleylacetoacetate isomerase normally involved in degradation of tyrosine. This apparently recently assembled pathway does not function very well: pentachlorophenol hydroxylase is quite slow, and tetrachlorohydroquinone dehalogenase is subject to severe substrate inhibition.
[On the key step of the origin of PcpC, the central step in the origin of PCP degradation]
Recruitment of a double bond isomerase to serve as a reductive dehalogenase during biodegradation of pentachlorophenol.
Biochemistry 2000 May 9;39(18):5303-11
Anandarajah K, Kiefer PM Jr, Donohoe BS, Copley SD.
Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Campus Box 216, Boulder, Colorado 80309-0216, USA.
Tetrachlorohydroquinone dehalogenase catalyzes the replacement of chlorine atoms on tetrachlorohydroquinone and trichlorohydroquinone with hydrogen atoms during the biodegradation of pentachlorophenol by Sphingomonas chlorophenolica. The sequence of the active site region of tetrachlorohydroquinone dehalogenase is very similar to those of the corresponding regions of maleylacetoacetate isomerases, enzymes that catalyze the glutathione-dependent isomerization of a cis double bond in maleylacetoacetate to the trans configuration during the catabolism of phenylalanine and tyrosine. Furthermore, tetrachlorohydroquinone dehalogenase catalyzes the isomerization of maleylacetone (an analogue of maleylacetoacetate) at a rate nearly comparable to that of a bona fide bacterial maleylacetoacetate isomerase. Since maleylacetoacetate isomerase is involved in a common and presumably ancient pathway for catabolism of tyrosine, while tetrachlorohydroquinone dehalogenase catalyzes a more specialized reaction, it is likely that tetrachlorohydroquinone dehalogenase arose from a maleylacetoacetate isomerase. The substrates and overall transformations involved in the dehalogenation and isomerization reactions are strikingly different. This enzyme provides a remarkable example of Nature's ability to recruit an enzyme with a useful structural scaffold and elaborate upon its basic catalytic capabilities to generate a catalyst for a newly needed reaction.
[atrazine degradation, a similar case]
Melamine deaminase and atrazine chlorohydrolase: 98 percent identical but functionally different.
J Bacteriol 2001 Apr;183(8):2405-10
Seffernick JL, de Souza ML, Sadowsky MJ, Wackett LP.
Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, USA.
The gene encoding melamine deaminase (TriA) from Pseudomonas sp. strain NRRL B-12227 was identified, cloned into Escherichia coli, sequenced, and expressed for in vitro study of enzyme activity. Melamine deaminase displaced two of the three amino groups from melamine, producing ammeline and ammelide as sequential products. The first deamination reaction occurred more than 10 times faster than the second. Ammelide did not inhibit the first or second deamination reaction, suggesting that the lower rate of ammeline hydrolysis was due to differential substrate turnover rather than product inhibition. Remarkably, melamine deaminase is 98% identical to the enzyme atrazine chlorohydrolase (AtzA) from Pseudomonas sp. strain ADP. Each enzyme consists of 475 amino acids and differs by only 9 amino acids. AtzA was shown to exclusively catalyze dehalogenation of halo-substituted triazine ring compounds and had no activity with melamine and ammeline. Similarly, melamine deaminase had no detectable activity with the halo-triazine substrates. Melamine deaminase was active in deamination of a substrate that was structurally identical to atrazine, except for the substitution of an amino group for the chlorine atom. Moreover, melamine deaminase and AtzA are found in bacteria that grow on melamine and atrazine compounds, respectively. These data strongly suggest that the 9 amino acid differences between melamine deaminase and AtzA represent a short evolutionary pathway connecting enzymes catalyzing physiologically relevant deamination and dehalogenation reactions, respectively.
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Read that ISCID thread, I think that Mike Gene may have given us his position on the immune system again in the thread. He certainly didn't defend Behe, Dembski, Nelson et al., even though he is probably the person who knows more about it that any of them.
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How do you know how much he knows? Whatever it is, just because he didn't defend them does not at all favor your claim about him. I'll try to email him and hear it from the horse's mouth.
Regards,
Ahmad
I've had a number of online debates with Mike Gene, so everything I say about what he thinks is simply my interpretation based on that experience. You are free to ask him yourself. Unfortunately I don't keep a database of Mike Gene quotes on tab.
I am, however, sure he knows a lot -- in fact, he knows enough to know that (despite being tremendously complex and IC according to Behe) there is plenty of evidence and a thick stack of peer-reviewed literature indicating that the immune system did, in fact, originate via evolution. This, too, undermines Behe, Nelson, Dembski, et al.
My opinion is that arguments for ID based on biological complexity are rather badly undermined once the evolution of horrendously complex things like the vertebrate immune system is conceded.
Mike Gene thinks that the idea is still salvagable. He is written a lot on why but I for one still don't "get it". If you have better luck, please explain it to us...
Thanks, nic
[This message has been edited by Nic Tamzek, 12-01-2002]
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