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Author
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Topic: ID and Peer Review
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Nel
Member
Member # 614
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posted 02. July 2003 21:21
Brauer,
We already have some results by Behe that show us that ID is being rejected without even looking at the substantial content of the presented works.
In
Correspondence with Science Journals Behe's submissions were rejected with the advice "Let us speak about it again in 1000 years."
This is consistent with the findings of the Cochrane review
quote:
Anonymous peers can reject or unfairly criticize papers from direct competitors.
http://www.biomedcentral.com/news/20030128/05/
[ 02. July 2003, 22:16: Message edited by: Nelson-Alonso ]
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Mike Gene
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Member # 149
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posted 02. July 2003 22:07
quote:
Given that the ID-identified scientists (Behe, Wells, "Mike Gene") do not seem to be doing active ID research, I suspect that the quantity of ID papers submitted is closer to the smaller number.
Let’s leave me out of the equation since I have not claimed to be a scientist. Wells doesn’t have a lab. Dembski could have had one, but various people made sure that did not materialize. Behe has one. But that would move the question from peer reviewed articles to obtaining grant funding. Tipler does address this, as the two are related. The dynamics that would prevent papers from being published also work to prevent research from being funded. No funds – no research.
There is also another angle. Behe chose his field of specialization prior to becoming focused on ID. Surely you realize that being competent in certain forms of inquiry does not automatically translate as the ability to pick up a project in a distantly related field. Someone making transgenic mice to genetically probe a transcription factor just doesn’t decide one day to redirect his lab’s attention to the structural properties of a flagellar component from B. subtilis. And grant reviewers aren’t likely to fund such a radical change in direction, especially if it is motivated by ID. I’m not sure how much of Behe’s original research focus becomes lends itself to his ID focus on IC. The key is the young IDers (like Jay and John), who are entering the research world with ID in mind.
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Mike Gene
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Member # 149
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posted 02. July 2003 22:16
andyg:
quote:
To date, I would expect that a referee faced with a paper by Behe or Dembski on, say, the bacterial flagellum, would respond using a paraphrase of Behe's own words:
“The peril of negative arguments is that they may rest on our lack of knowledge, rather than on positive results. The contention that {}intelligent processes can account for complex biological functions should, to the extent possible, be supported by positive results, rather than by intuitions of what [a] designer would do.”
Then that brings up an interesting question. Robin Holliday got this argument in BioEssays:
quote:
So how do the creationists explain why an all-powerful deity did not on any occasion design an animal incorporating the enormously advantageous rotary motion of wheels?
Creationists have no answer to that question. In complete contrast, Darwinian natural selection provides the perfect answer. The wheel is a manufactured object that can only function when it is complete. One cannot use a quarter or a half of the wheel; indeed they would be an impediment to any animal. Therefore one cannot evolve a wheel in multiple stages, in the way that one can evolve an eye, a brain or a limb. So there can be no selection of advantageous mutations in the case of the wheel, because they simply do not exist.
In other words, you can use a Behe-like argument to address something that does not exist, but you can’t use it to address something that does exist. If it applies to things that do not exist, how do we know it doesn’t also apply to some things that do exist? Shouldn’t this be explored, rather than assumed?
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RBH
Member
Member # 380
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posted 02. July 2003 22:19
Nelso-Alonso wrote quote:
First Behe et. al. are doing active ID research. At the debate at the Museum of Natural History Behe mentioned something about disulphide bonds.
There's no mention of disulphide bonds in the formal essays from the debate, nor is there any mention of disulphide bonds in the transcripts of the various verbal exchanges. Do you recall where that mention occurs, Nelson?
RBH
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Nel
Member
Member # 614
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posted 02. July 2003 22:43
Actually, the exchanges that RBH links to does mention disulphide bonds:
quote:
Finally, to show what specific research questions might be asked by a theory of Intelligent Design, I'd like to briefly describe a little bit of my own work. This is title slide of a seminar I gave six-weeks ago to the biotechnology group at Sandia National Laboratory. The title, "Modeling the Evolution of Protein Binding Sites: Probing the, the dividing line between Natural Selection and Intelligent Design", points to a question I'm very interested in exploring...I know it's hard to see, but this yellow link is called a disulfide bond. A disulfide bond requires two cystaine?? residues. Just one ?? residue can't form such a bond. Thus in order for a protein that did not have a disulfide bond to evolve one, several changes in the same gene have to occur. Thus in a sense, the disulfide bond is irreducibly complex, although not really to the same degree of complexity as systems made of multiple proteins. The problem of irreducibility, irreducibility in proteins is a general one.
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RBH
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Member # 380
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posted 02. July 2003 23:38
Yup, you're right - I missed that first time I searched. I must have misspelled (mispelled? Mis-spelled?) "disulphide" in the search. Sorry.
Given the defensiveness about the Lenski, et al., paper and the Nilsson and Pelger paper in the Literature Review thread, I'm entranced that what Behe's reporting are computer simulations, not wet lab work. ![[Smile]](smile.gif) quote:
One can then ask the question, how long would it take for two proteins that originally interact to evolve the ability to bind each other by random mutation and natural selection, if binding only occurs when all positions have the correct residue in place. Although it would be difficult to experimentally investigate the question, the process can be simulated on a computer.
Has he published this simulation work in a more complete form anywhere, in a journal or on a web site? I couldn't find one.
RBH
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charlie d.
Member
Member # 159
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posted 02. July 2003 23:39
And the research would be?
Behe starts by saying that's "an example of a research question that might be asked", and then... that's it. Disulfide bonds are a little IC, IC is inexplicable, a big problem, a "general one". Period. Some question. Some research.
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Nel
Member
Member # 614
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posted 02. July 2003 23:46
RBH,
I think that would be a great project to add to the computer stuff ISCID is doing. As for whether Behe is still working on this, I think Gene's comments become relevant. IDers aren't against computer simulations, IDers are complaining that the simulations you mention simply do not address the problem.
charlie d.,
I think Behe is offering an explanation for the IC system, he is obviously interested in how it can be better explained from a design view, so it's not inexplicable.
[ 02. July 2003, 23:57: Message edited by: Nelson-Alonso ]
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Pim van Meurs
Member
Member # 541
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posted 03. July 2003 00:18
Nelson about Behe:
quote:
We already have some results by Behe that show us that ID is being rejected without even looking at the substantial content of the presented works.
Or perhaps they did look at the content of the presented works and rejected in based on such?
Remember that Behe's work was not to provide evidence for intelligent design but rather to rebut criticism.
Or as the editor stated
quote:
So, your unorthodox theory would have to displace something that would be extending the current paradigm.
Behe was then asked to resubmit a shorter essay which was given for review to a senior journal advisor
quote:
As you will see, the accompanying review identifies many apparent flaws in your arguments, and also questions the basic premise of your arguments, that complex systems cannot be dissected to reveal individual components' roles.
Paul Nelson states that
quote:
Actually the precedent for such papers is long-standing. For instance, Tom Schneider's 2000 paper on the origin of biological information cites Behe by name (as I recall):
Indeed, how could I forget Tom Schneider's work which generated some interesting exchange between Schneider and Dembski. Schneider's work, without the additional work performed by Schneider to address Dembski's criticisms, made it into NFL.
I addressed some of the problems with Strahan's claims 'published' here at ISCID and I am sure that Schneider will have his say about the relevance of Iain's paper.
Of course much of Schneider's findings have been supported by for instance "evolution of complexity" by Adami and the recent Lenski et al paper.
As far as ID friendly research is concerned, what happened to the promising works by Axe? Was Axe not sponsored by the Discovery Institute for his work? Any direct mention of its relevance to ID? What about Axe himself? Is he a proponent of ID?
I am glad that the moderator is allowing for some discussion despite the original posting being somewhat borderline as to its relevance. Nevertheless it does liven up the boards a little bit.
Jack: Dembski clearly stated that no ID papers that explicitly affirms intelligent design or explicitly denies Darwinian and other forms of naturalistic evolution are are getting published in the peer-reviewed literature.
With the understanding of course that this is Dembski's opinion which may likely not be totally correct. Of course that still leaves the other possibility namely that little intelligent design research exists and/or is submitted to such publications. Even Behe's rejected letter was not research but rather a rebuttal of arguments made against his ideas.
Jack: The only articles that are getting published by ID theorists in the peer-reviewed literature are those articles where the author isn't identified as a design theorist and the article doesn't mention ID.
And often these papers are not even relevant to the issue of intelligent design may I add?
Nelson: Ussery's paper shows just that, that the scientific community not only takes it seriously, but is actually addressing it.
It takes it serious sofar as to reject it. Surely that is hardly that relevant...
Nelson then claims that: Direct evolutionary mechanisms cannot form IC structures
But indirect pathways such as found in Lenski et al for instance do seem to work despite initial assertions by Behe that such indirect pathways were unlikely (no supporting calculations were provided).
Nelson:
Being cited in a peer reviewed paper is a major achievment for ID in that it is now being taken seriously, whether it is in a laundry list or not is irrelevant.
You presume that ID is taken seriously in a scientific sense. Does this mean that a scientific paper rejecting a young age of the earth should be considered as evidence of taking YEC seriously? Surely you are kidding?
[ 03. July 2003, 00:31: Message edited by: Pim van Meurs ]
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RBH
Member
Member # 380
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posted 03. July 2003 00:47
Nelson-Alonso wrote quote:
I think that would be a great project to add to the computer stuff ISCID is doing.
That's the kind of allusive remark that one keeps hearing but is impossible to evaluate. What "computer stuff"??? In this thread alone there's "the computer stuff ISCID is doing" (whatever the heck it is), Behe's elusive disulphide bonds simulation (mentioned but not described in his own talk) and Dembski's unidentified ID theorists publishing ID-relevant but invisible research in peer-reviewed journals. Curiouser and curiouser.
RBH
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yersinia
Member
Member # 324
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posted 03. July 2003 02:48
Pim writes,
quote:
Nelson:
Being cited in a peer reviewed paper is a major achievment for ID in that it is now being taken seriously, whether it is in a laundry list or not is irrelevant.
You presume that ID is taken seriously in a scientific sense. Does this mean that a scientific paper rejecting a young age of the earth should be considered as evidence of taking YEC seriously? Surely you are kidding?
...my point exactly...
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fish
Member
Member # 213
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posted 03. July 2003 04:33
quote:
P.S. Just saw this link over at talk.design:
http://www.blackwell-synergy.com/links/doi/10.1046/j.1538-7836.2003.00062.x/abs/
Check it out. Now, in whose mill is this properly grist? If it's OK to criticize Behe, would it be OK to defend him in the same journal? Give your thoughts.
I think if you can find something constructive to say about blood clotting systems, as the authors of the article claim to, while replying to the points made in it, then good luck to you. You should be able to wangle it past the editors.
I think that the Lenski article was adjudged to be topical because it was written by Richard Lenski,...(sour grapes creeping in??) No, because the authors are developing a new take (digital organisms) on general biological problems.
If you adopt a similarly creative approach (and have something to say), then "ID friendly" as well as "ID hostile" science will be published in peer review journals.
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Paul A. Nelson
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Member # 26
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posted 03. July 2003 09:00
Pim wrote:
quote:
You presume that ID is taken seriously in a scientific sense.
Stephen Gould used to make a joke about his evolutionary biology critics dismissing his ideas as hardly worth a moment's reflection -- at the same time that they were publishing long and detailed treatises responding to those ideas.
This is simply a matter of intellectual symmetry. If evidence can be brought to bear against a theory, evidence can also support that theory. I agree with Fish: if IDers "adopt a similarly creative approach (and have something to say), then 'ID friendly' as well as 'ID hostile' science will be published in peer review journals." We just need a few ballsy editors and a handful of creative ID scientists and philosophers.
[ 03. July 2003, 09:29: Message edited by: Paul A. Nelson ]
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charlie d.
Member
Member # 159
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posted 03. July 2003 09:31
quote:
Behe:
One can then ask the question, how long would it take for two proteins that originally interact to evolve the ability to bind each other by random mutation and natural selection, if binding only occurs when all positions have the correct residue in place. Although it would be difficult to experimentally investigate the question, the process can be simulated on a computer.
quote:
RBH:
Nelson-Alonso wrote
----------------------------------------
I think that would be a great project to add to the computer stuff ISCID is doing.
--------------------------------------------
That's the kind of allusive remark that one keeps hearing but is impossible to evaluate. What "computer stuff"??? In this thread alone there's "the computer stuff ISCID is doing" (whatever the heck it is), Behe's elusive disulphide bonds simulation (mentioned but not described in his own talk) and Dembski's unidentified ID theorists publishing ID-relevant but invisible research in peer-reviewed journals. Curiouser and curiouser.
quote:
I think Behe is offering an explanation for the IC system, he is obviously interested in how it can be better explained from a design view, so it's not inexplicable.
Actually, Behe is saying he'd like to generate a computer simulation of some sort, to show how 2 proteins would evolve an interaction by mutation and selection, with the ID expectation being that this would not happen in a reasonable time frame. Of course, that's no explanation at all. Behe's only possible conclusion from such a negative result would be that the interaction is inexplicable according to his simulation. That's again confusing a negative result with a positive one.
As most scientists know, when one obtains a negative result, there are hundreds of alternative explanations that can account for it(that's why negative results are so hard to publish). In this case, one could wonder:
- did the simulation work as expected?
- were the initial assumptions about rate and site of mutations appropriate?
- where the evolutionary precursors correctly chosen?
- Are there potential intermediate selectable steps the simulation did not consider?
- Could other proteins have "chaperoned" the interaction in vivo, which were not included in the simulation?
- would alternative assumptions work?
all the way down to:
- did someone turn off the computer half way through the run, or input the data incorrectly?
This is not research, and it's not even based on ID. If working as expected, it's just a fancy computer formalization of the same old, theoretically flawed and now empirically disproven argument about IC unevolvability.
Furthermore, we currently know so little about the chemico-physical constraints of protein-protein interactions that it takes structural biologists an inordinate amount of work and computer power to figure out even how two simple domains, already known to interact, do so. To fantasize about a simulation in which two proteins are left to mutate randomly and we can calculate the chances of any two mutants to actually interact, is basically nothing more than pie-in-the-sky. I sincerely doubt that Behe has taken any practical or theoretical step forward on this idea, past what we just read. Basically,as RBH remarks, it is just "Hey, here's a great idea for research - "computer stuff"!"
But maybe there are better examples of ongoing ID research, by Behe or anybody else?
[ 03. July 2003, 09:31: Message edited by: charlie d. ]
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charlie d.
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Member # 159
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posted 03. July 2003 12:47
Not to go off on a tangent, but here's a nice paper, fresh off PNAS, that illustrates the issue of disulfide bonds, protein structure and function. A must-read for Behe ![[Wink]](wink.gif) . quote:
Engineering disulfide bridges to dissect antimicrobial and chemotactic activities of human -defensin
Zhibin Wu *, David M. Hoover , De Yang , Cyril Boulègue *, Fanny Santamaria *, Joost J. Oppenheim , Jacek Lubkowski , and Wuyuan Lu *
*Institute of Human Virology, University of Maryland Biotechnology Institute, Baltimore, MD 21201; and Macromolecular Assembly Structure and Cell Signaling Section, Laboratory of Immunoregulation, National Cancer Institute, Frederick, MD 21702
Human defensins form a family of small, cationic, and Cys-rich antimicrobial proteins that play important roles in innate immunity against invading microbes. They also function as effective immune modulators in adaptive immunity by selectively chemoattracting T lymphocytes and immature dendritic cells. On the basis of sequence homology and the connectivity of six conserved Cys residues, human defensins are classified into alpha and beta families. Structures of several beta-defensins have recently been characterized, confirming the disulfide connectivity conserved within the family, i.e., Cys1-Cys5, Cys2-Cys4, and Cys3-Cys6. We found that human beta-defensin 3 (hBD3), a recently described member of the growing beta family, did not fold preferentially into a native conformation in vitro under various oxidative conditions. Using the orthogonal protection of Cys1-Cys5 and of Cys1-Cys6, we chemically synthesized six topological analogs of hBD3 with predefined disulfide connectivities, including the (presumably) native beta pairing. Unexpectedly, all differently folded hBD3 species exhibited similar antimicrobial activity against Escherichia coli, whereas a wide range of chemotactic activities was observed with these analogs for monocytes and cells transfected by the chemokine receptor CCR6. Furthermore, whereas substitution of all Cys residues by alpha-aminobutyric acid completely abolished the chemotactic activity of hBD3, the bactericidal activity remained unaffected in the absence of any disulfide bridge. Our findings demonstrate that disulfide bonding in hBD3, although required for binding and activation of receptors for chemotaxis, is fully dispensable for its antimicrobial function, thus shedding light on the mechanisms of action for human beta-defensins and the design of novel peptide antibiotics.
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