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Author
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Topic: Data, interpretation and false positive inferences
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charlie d.
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Member # 159
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posted 07. November 2002 11:53
I am tentatively starting this as per Paul's suggestion in Dembski's "No False Positives and Lust for Certainty" thread.
The focus of this new thread is the possibility of erroneous design inferences due to lack of familiarity with published data, and a concrete suggestion for semi-formal (though not anonymous) scientific peer-review of such claims that might be acceptable to ID proponents.
It all started with this quote from Dembski's "Logical Underpinnings" article: quote:
But there is now mounting evidence of biological systems for which any slight modification does not merely destroy the system's existing function, but also destroys the possibility of any function of the system whatsoever (Axe, 2000). For such systems, neither direct nor indirect Darwinian pathways could account for them.
Rafe and myself pointed out that this is a misreading, or at best a large overinterpretation, of Axe's 2000 JMB paper findings (the following quote of myself is not literal, I made a few changes to make it more understandable in isolation): quote:
As I remember it, the central point of Axe’s paper was the existence of constraints posed by apparently “neutral” substitutions to protein evolution by genetic drift. That is, he challenged the probably somehow simplistic view that proteins are largely made up of “stuffer” sequences, with great tolerance for aa substitutions, that can freely mutate and “wander around” without much effect on protein function, which in turn is assumed to dependent only on a restricted subset of aa.
Thus, he took the TEM-1 beta-lactamase and (IIRC) barnase, and replaced a number of residues that on the basis of phylogenetic analysis were expected to be selectively neutral. He found that combining more than a certain number of such supposedly neutral mutations effectively severely reduced the mutants' fucntion, in the case of TEM-1 its ability to confer resistance to its known antibiotic targets, penicillin and ampicillin. Therefore, he concluded, proteins cannot just perform easy random walks at their non-essential positions during drift, without losing their primary function. Indeed, he said those two proteins appeared to exist in largely isolated peaks, each corresponding to the protein in a certain organism, and that transition form one peak to another, maintaining function intact, appeared highly unfavored.
This is an interesting finding regarding specifically neutral evolution of related proteins within a functional family, with the caveats of a need to understand what the function under selection is at given transitional stages, the fundamental difference between gradual evolution vs the one-shot multiple alterations Axe made, and of course the potential applicability of these findings to other proteins.
I also suggested that recently published data directly contradict the contention that a TEM-1 mutant that has lost penicillin resistance activity cannot posses, or evolve, a new function: quote:
J Mol Biol 2002 Jun 28;320(1):85-95
Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs.
Wang X, Minasov G, Shoichet BK.
Pressured by antibiotic use, resistance enzymes have been evolving new activities. Does such evolution have a cost? To investigate this question at the molecular level, clinically isolated mutants of the beta-lactamase TEM-1 were studied. When purified, mutant enzymes had increased activity against cephalosporin antibiotics but lost both thermodynamic stability and kinetic activity against their ancestral targets, penicillins. The X-ray crystallographic structures of three mutant enzymes were determined. These structures suggest that activity gain and stability loss is related to an enlarged active site cavity in the mutant enzymes. In several clinically isolated mutant enzymes, a secondary substitution is observed far from the active site (Met182-->Thr). This substitution had little effect on enzyme activity but restored stability lost by substitutions near the active site. This regained stability conferred an advantage in vivo. This pattern of stability loss and restoration may be common in the evolution of new enzyme activity. (c) 2002 Elsevier Science Ltd.
Again to para-quote myself: quote:
The Wang paper ... shows that new functions (in this case, a substrate specificity change) can evolve from an existing protein at the expense of other functions, if the selection pressures are appropriate. It also shows that to a certain extent adaptive “valleys” can be crossed in the transition from one peak to another (in this case, certain mutations allowed some level of cephalosporin resistance by sacrificing both penicillin resistance and protein stability, but that the latter could be regained by a successive mutation found in some highly resistant variants).
Therefore, Wang’s paper speaks more directly to the issue of direct vs indirect Darwinian evolution, co-option, functional shifts and so on. This paper of course does not stand in opposition to Axe’s results. Both findings are compatible.
In summary, we argued that Dembski's implicit design inference (as stated for instance in this sentence, following the one quoted above) quote:
we would be dealing with an in-principle argument not merely that no known material mechanism is capable of accounting for the system but also that any unknown material mechanism is incapable of accounting for it as well.
is not warranted by the literature referenced in its support (Axe 2000), and in fact may well be contradicted both on theoretical considerations, and directly by more recent literature.
Dr. Dembski replied to rafe that he has had a "preview of Axe's research for some time" and he's "anticipating where he's going". I do not doubt Demsbki's information on the matter, but of course any of these unpublished and future data will need to become accessible (or stated in more detail), before anybody can objectively evaluate whether the original design inference (or a new form thereof) is warranted.
In general, this stresses that a more formalized and critical approach to data analysis, presentation and interpretation, as opposed to the occasionally quasi-anecdotal style currently employed, is required for the necessary transition of design inferences from essentially "hunches" to properly supported scientific claims. In the "Lust" thread Dembski contends that design inferences (whether formalized mathematically or not) are provisional, and subject to being overturned by future data. However, some mechanism has to be put in place to guarantee proper justification for any such inference in the face of existing data as well.
While I understand the ID proponents' reluctance to undergo "mainstream" peer review (whether warranted or not), it seems to me that a small but sufficient number of properly trained ID-friendly molecular biologists exists (Behe, Macosko, Minnich, Axe himself perhaps, others?) to establish a review panel for specific biological evidence-based claims (indeed, multiple discipline-specific review panels could be implemented, in "Cosmology and Physics", for instance, or "Organismal Biology and Evolution", etc). This seems to be especially important given the wide variety of backgrounds of ID proponents, and the fact that they often cover, in individual publications, an equally wide range of subjects from philosophy to mathematics to molecular biology, for which it is absurd to expect sufficient expertise and scholarship in a single person. Perhaps, an acknowledgment sentence at the end of papers not otherwise peer-reviewed, such as "This manuscript was reviewed for accuracy of content by the ISCID Scientific Review Panel - Molecular Biology" would help guarantee scientific standards in this respect.
Any comment on the science or the proposal for formal review panels is appreciated.
[ 07. November 2002, 11:59: Message edited by: charlie d. ]
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rafe gutman
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Member # 134
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posted 08. November 2002 16:56
dr. dembski, in your original post from the lust for certainty thread, you suggest that there are cases where all unknown "material" mechanisms can be eliminated. your article discusses this in a little more detail, but you rely entirely on your interpretation of axe's results to make that assertion. however, as charlie and i have shown, you really cannot make such a claim based on axe's published research. do you have any other support for that idea?
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John Bracht
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Member # 5
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posted 08. November 2002 17:47
charlie d., rafe,
You guys are too quick to jump on Dembski, and to quote the Wang paper as proof that evolution can produce new enzymatic functions.
If you do some research into the structure of cephalosporins, you find that they are very similar to penicillin. (see here, for instance). Indeed, both antibiotics have the key beta-lactam ring, and it is actually possible to interconvert the two via some simple chemical manipulations (see here). Here is an image showing penicillin being transformed into cephalosporin:
1=penicillin
4=cephalosporin
Notice how similar they are. It is highly likely that a penicillinase enzyme would, with small changes, be able to destroy cephalosporins (as found in the Wang paper, a larger binding pocket allows the different side-groups of cephalosporin to fit). Indeed, Wang's fully functional cephalosporin enzyme had only a few mutations from a penicillinase, and probably the original enzyme (or a single point-mutated version of that original enzyme) has slight cephalosporinase activity that can be gradually improved, step-by-step. The implication, then, is that both penicillin and cephalosporin enzymes reside in the same functional "island" that Doug Axe is mapping out. Dembski, on the other hand, is talking about moving from one island to another across the sea of non-functional sequence (sequences that don't even fold into stable structures, much less have biological activity). You can't use the Wang paper to talk about bridging from one functional island to another--you're trying to use evidence from within-island evolution to support across-island evolution. You need to be more careful in your scholarship before accusing Dembski of misrepresenting the evidence. Be careful--if someone were not reading carefully (and not willing to do their own research) they would get a very wrong impression from you two--and thus the charge of misrepresenting the evidence could apply to you instead of Dembski.
John Bracht
[ 08. November 2002, 18:03: Message edited by: John Bracht ]
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charlie d.
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Member # 159
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posted 08. November 2002 20:48
John:
sorry, but you are mistaken. On two counts.
First, from Wang's paper, activity on penicilln and activity of cephalosporins appear reciprocally exclusive. Judging from their bar graphs, there is no mutant enzyme with significant activity on cephalosporins that also has not lost most (>95% or so) of their penicillase activity. Similarly, unlike what you say, TEM-1 has no detectable activity on cephalosporins. That the chemistry of the reaction is the same, you will agree, is irrelevant if both reactions can't be efficiently carried out by the same enzyme (in fact, thinking about it, even if they could it'd still mean that TEM-1 can evolve into something else by leaving the penicillase "island" for good, see below).
Second, and most importantly, it's still entirely arbitrary to take Axe's data to suggest in any way that TEM-1 sits in a completely isolated functional island, when the only functions he tests are against penicillin and ampicillin. That's the only function relevant to Axe's experiments, the only ones that apply. Indeed, looking back at his paper, that's the only conclusion he himself draws, and correctly so. Any extrapolation to any other function, as shown by Wang, is not warranted by the data.
Again, if Axe could comment, since he's the real expert, I am sure things would become more clear for everybody.
Besides this, though, what do you think about instituting internal peer-review panels?
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Mike Gene
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Member # 149
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posted 08. November 2002 21:27
From the other thread:
Charlie: Quite obviously, and unfortunately, we cannot check all inactive mutants against all the possible ranges of biological activities such mutants may have. Thus, it is impossible to assert with any reasonable degree of certainty that a mutant protein cannot have any function whatsoever, as claimed by you and others for TEM-1 mutants. The ability of evolution to co-opt the most unlikely candidates for the most disparate functions (enzymes for crystallins, or anti-freeze peptides, etc) should give anybody pause in this respect.
And
Rafe: a better experiment would be to amplify the gene via PCR with an error-prone polymerase, reintroduce it into bacteria, then select for function. after several rounds of this you might start to see some drift.
Well, it would seem to me that a few million years of bacterial evolution has already run Rafe's experiment, making it possible to look for these other functions. When I BLASTed with Pseudomonas aeruginosa TEM-1 sequence, I got a few hundred hits. Yet as I scanned by eye, they all appeared to be beta-lactamase. I then did a PubMed search using 'beta lactamase' as search words. With 11603 hits, this protein has clearly been the object of much study. But when I added "cooption" or "co-option" to the search, the number of hits dropped to zero. Perhaps something Bill said is instructive here:
Also, how do we individuate the functions? We're talking some sort of antibiotic/penicillin resistance in both cases. So depending on how we individuate function, it seems that you may well lose the evolvability you're after.
If beta-lactamase contains the potential to acquire all sorts of other biological functions (that stray modestly far from its observed function(s)), apparently evolution has yet to benefit from it.
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charlie d.
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Member # 159
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posted 08. November 2002 22:07
You may have missed some papers, Mike. There are a number of proteins with structural homology to beta-lactamases which have nothing to do with antibiotic resistance:
Here's a review: quote:
In Silico Biol 1999;1(2):69-91
An evolutionary classification of the metallo-beta-lactamase fold proteins.
Aravind L.
All the detectable metallo-beta-lactamase fold proteins were identified in the publicly available sequence databases and complete genome sequences using iterative profile searches with the PSI-BLAST program and motif searches with position specific weight matrices. The catalytic site/mechanism and the corresponding structural elements were characterized for these proteins based on the available structure of the Bacillus zinc-dependent beta-lactamase. Based on pair-wise sequence and phylogenetic analysis an evolutionary classification for enzymes of this fold was developed and discussed in terms of implications for substrate specificity. Finally, some predicted inactive members which have been recruited for non-enzymatic functions such as microtubule binding in a cytoskeletal MAP1 are described.
Here's another one: quote:
FEBS Lett 2001 Aug 10;503(1):1-6
Expansion of the zinc metallo-hydrolase family of the beta-lactamase fold.
Daiyasu H, Osaka K, Ishino Y, Toh H.
Recently, the zinc metallo-hydrolase family of the beta-lactamase fold has grown quite rapidly, accompanied by the accumulation of sequence and structure data. The variety of the biological functions of the family is higher than expected. In addition, the members often have mosaic structures with additional domains. The family includes class B beta-lactamase, glyoxalase II, arylsulfatase, flavoprotein, cyclase/dehydrase, an mRNA 3'-processing protein, a DNA cross-link repair enzyme, a DNA uptake-related protein, an alkylphosphonate uptake-related protein, CMP-N-acetylneuraminate hydroxylase, the romA gene product, alkylsulfatase, and insecticide hydrolases. In this minireview, the functional and structural varieties of the growing protein family are described.
And here's a more specific one: quote:
Protein Sci 2002 Mar;11(3):467-78
EstB from Burkholderia gladioli: a novel esterase with a beta-lactamase fold reveals steric factors to discriminate between esterolytic and beta-lactam cleaving activity.
Wagner UG, Petersen EI, Schwab H, Kratky C.
Esterases form a diverse class of enzymes of largely unknown physiological role. Because many drugs and pesticides carry ester functions, the hydrolysis of such compounds forms at least one potential biological function. Carboxylesterases catalyze the hydrolysis of short chain aliphatic and aromatic carboxylic ester compounds. Esterases, D-alanyl-D-alanine-peptidases (DD-peptidases) and beta-lactamases can be grouped into two distinct classes of hydrolases with different folds and topologically unrelated catalytic residues, the one class comprising of esterases, the other one of beta-lactamases and DD-peptidases. The chemical reactivities of esters and beta-lactams towards hydrolysis are quite similar, which raises the question of which factors prevent esterases from displaying beta-lactamase activity and vice versa. Here we describe the crystal structure of EstB, an esterase isolated from Burkholderia gladioli. It shows the protein to belong to a novel class of esterases with homology to Penicillin binding proteins, notably DD-peptidase and class C beta-lactamases. Site-directed mutagenesis and the crystal structure of the complex with diisopropyl-fluorophosphate suggest Ser75 within the "beta-lactamase" Ser-x-x-Lys motif to act as catalytic nucleophile. Despite its structural homology to beta-lactamases, EstB shows no beta-lactamase activity. Although the nature and arrangement of active-site residues is very similar between EstB and homologous beta-lactamases, there are considerable differences in the shape of the active site tunnel. Modeling studies suggest steric factors to account for the enzyme's selectivity for ester hydrolysis versus beta-lactam cleavage.
[ 08. November 2002, 22:09: Message edited by: charlie d. ]
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Mike Gene
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posted 08. November 2002 22:34
Charlie: You may have missed some papers, Mike.
It looks that way. More for the "to read" file. ![[Smile]](smile.gif)
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Paul A. Nelson
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Member # 26
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posted 09. November 2002 08:37
Charlie asked:
Besides this, though, what do you think about instituting internal peer-review panels?
I think it's a good idea. Something more informal than Charlie's suggestion -- in the way of critical peer review -- is already going on (e.g., at the recent RAPID meeting), but as the ID research community matures, it's going to need robust internal quality controls.
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rafe gutman
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posted 09. November 2002 23:27
quote:
john bracht:
You guys are too quick to jump on Dembski, and to quote the Wang paper as proof that evolution can produce new enzymatic functions.
john, i never claimed that the wang paper provided such a proof. i'm not really sure if the wang paper itself made such a claim, i only skimmed the paper. the paper does however, provide evidence that renders the following dembski quote totally false:
quote:
But there is now mounting evidence of biological systems for which any slight modification does not merely destroy the system's existing function, but also destroys the possibility of any function of the system whatsoever (Axe, 2000).
without the wang paper, dembski's claim is just an argument from ignorance. axe never tested his mutants for alternative function, nor did axe conclude from his research that his mutations "destroyed the possibility of any function of the system". i should note that the term "function of the system" is different from your term "new enzymatic function".
with the wang paper, dembski's claim is demonstrably false. there are "slight" modifications that can damage the system's existing function, but increase an alternative one. it doesn't really matter if you lump penicillin resistance along with cephalsporin resistance as a single functional "island" because of structural similarities. one activity went down while the other went up.
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Argon
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posted 10. November 2002 11:55
Mike Gene writes:
quote:
I then did a PubMed search using 'beta lactamase' as search words. With 11603 hits, this protein has clearly been the object of much study. But when I added "cooption" or "co-option" to the search, the number of hits dropped to zero.
Should've tried: "beta lactamase evolution" or "beta lactamase evolution structure". Keywords "motif" and "family" can be useful, too.
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Nel
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posted 24. September 2003 20:39
charlie d stated:
quote:
He found that combining more than a certain number of such supposedly neutral mutations effectively severely reduced the mutants' fucntion, in the case of TEM-1 its ability to
confer resistance to its known antibiotic targets, penicillin and ampicillin. Therefore, he
concluded, proteins cannot just perform easy random walks at their non-essential positions
during drift, without losing their primary function. Indeed, he said those two proteins
appeared to exist in largely isolated peaks, each corresponding to the protein in a certain
organism, and that transition form one peak to another, maintaining function intact,
appeared highly unfavored.
Rafe also stated:
quote:
with the wang paper, dembski's claim is demonstrably false. there are "slight" modifications that can damage the system's existing function, but increase an alternative one. it doesn't really matter if you lump penicillin resistance along with cephalsporin resistance as a single functional "island" because of structural similarities. one activity went down while the other went up.
Actually what charlie and rafe stated here is incorrect. Activity on penicilln and activity of cephalosporins do not appear reciprocally exclusive. In fact, a lot of the mutants (R164H, G238A, G238S, and E104K) actually retained considerable activity needed to resist penicillin. Even the mutants that lost 95% of the activity still had enough for resistance to the penicillins. So as they respond to the new constraint, they were actually able to stay within the same functional island. So you can't use this example, as Bracht stated, to argue against Dembski's discussion of bridging from one functional island to another, since the enzymes in this example while responding to having to hydrolyze cephalosporins, were able to retain penicillin activity such that they were still able to resist penicillin. I found this interesting considering all the talk about scholarship and peer review.
[ 24. September 2003, 22:25: Message edited by: Nelson-Alonso ]
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gedanken
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posted 25. September 2003 13:52
John Bracht said:
quote:
You guys are too quick to jump on Dembski, and to quote the Wang paper as proof that evolution can produce new enzymatic functions.
I don't know why this point I am about to make has to be presented over and over. And then the next time the issue comes up it is ignored.
But the "logical underpinnings" of ID are that there is a rejection region that is exceedingly small.
Thus the showing of an alternate explanation does not have to have high probability of applying. It only has to provide a probability distribution that is significantly above "alpha" significance factor in the explanatory filter (such as GCE procedure).
I discuss this fundamental problem further in my Does intelligence imply "motive"? thread.
[Added in edit -- I don't want to use up a lot of small posts]
The relevance of this to this thread is that the original basis of the thread is the question of "no false positives". The details of this thread are about particular causes in dispute. (I won't venture into the biology myself, only argument structure.)
Then John Bracht's request is about "proof" as though "proof" was an issue for the original basis of the thread, of "no false positives" of the EF. It is this basis in Dembski's "no false positives" issue that I am referring to. And the consequences of the specific causes being discussed affect that original argument. Also my thread discusses the effect of such "missed distributions" that the alternate causes discussed in this thread have for the Explanatory Filter.
Charlie D's OP discusses "the possibility of erroneous design inferences". Thus the possibility of erroneous design inferences as detailed in my thread by way of "missed distributions" is highly relevant. This thread is about a possibly "missed distribution". My thread is about the consequences in terms of "erroneoud design inferences". This ties them together.
[ 25. September 2003, 15:22: Message edited by: gedanken ]
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Nel
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posted 25. September 2003 14:46
Umm, Ged's post is completely irrelevant to not only this thread, but to what Bracht stated. I have no idea why he posted a link to his own thread in this one (and other unrelated threads).
Ged's edit seems to fail to explain the relevance of his post. It also seems obvious that he did not understand a lot of the posts in this thread. For example Ged writes:
quote:
Then John Bracht's request is about "proof" as though "proof" was an issue for the original basis of the thread, of "no false positives" of the EF.
However, what Ged was replying to was not a "request" from Bracht. Bracht was saying that the Wang paper does not supply an argument against what Dembski said about proteins. What does the significance factor have to do with this?
When Ged talks about missed distributions he is referring to an ambiguous future explanation which he hopes will explain away the complexity in Biology. What does this have to do with the Wang paper?
[ 25. September 2003, 15:33: Message edited by: Nelson-Alonso ]
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charlie d.
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posted 25. September 2003 20:40
Nelson:
I don't have the paper available right now, so I can't check. Anyway, regardless of whether there were any bi-functional mutants, the interpretation vis-a-vis Axe's paper (which was OK) and Dembski's interpretation of it (which was badly off target) does not change. As I said before in my reply to the same objection, when John raised it, Wang's data simply indicate that one cannot extrapolate Axe's data outside of the strict limits of the function he tested for, i.e. ampicillin/penicillin resistance. quote:
Second, and most importantly, it's still entirely arbitrary to take Axe's data to suggest in any way that TEM-1 sits in a completely isolated functional island, when the only functions he tests are against penicillin and ampicillin. That's the only function relevant to Axe's experiments, the only ones that apply. Indeed, looking back at his paper, that's the only conclusion he himself draws, and correctly so. Any extrapolation to any other function, as shown by Wang, is not warranted by the data.
That is, Axe's mutants could have lost amp/pen catalytic activity, but retained, or even improved (unbeknownst to him) their activity on cephalosporins, or God knows what else, that could have provided a selectable function in the appropriate context.
It's actually funny that you bring this up again now, because I just noticed that Dembski, despite having had this simple fact explained to him several times, still publicly mentions Axe's paper, with the same overinterpretation of it (most recently in his Texas FAQ). Unfortunately, Axe's new data, apparently forthcoming last year when this thread was started (in fact since 2000, at least according to Dembski), have yet to materialize, and he has not provided any input about this, so it's hard to know whether this is just another biology mistake on Dembski's part, or whether in fact there are some empirical reasons to argue otherwise. Personally, after the Wang paper, I cannot think of any experiment that would exhaustively demonstrate absolute lack of TEM functionality of the kind that Dembski still likes to talk about.
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Nel
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posted 26. September 2003 10:15
Charlie wrote:
quote:
It's actually funny that you bring this up again now, because I just noticed that Dembski, despite having had this simple fact explained to him several times, still publicly mentions Axe's paper, with the same overinterpretation of it (most recently in his Texas FAQ).
Thats because, as I showed, it's not an overinterpretation. I think you are even misinterpreting the Axe paper (Dembski probably knows this). Douglas Axe's paper shows that it's not necessarily true that proteins can obtain a new function after the stability of the folded structure is disrupted. If the folded structure is retained, then yes, a new function is likely.
In the Wang paper it is possible that the stability of the unfolded state was increased. Furthermore, that the tradeoff was not exclusive is very important, in that it wasn't really all that new.
All in all this example shows how ID can guide laboratory research.
[ 26. September 2003, 12:17: Message edited by: Nelson-Alonso ]
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