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Author
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Topic: ID and Peer Review
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Jack
Member
Member # 265
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posted 02. July 2003 16:15
For those that claim the peer-reviewed literature contains no articles authored by ID theorists that strengthens the ID inference, I would like to ask a simple question. How do you know if you read such an article you would recognize it as such?
[ 02. July 2003, 16:32: Message edited by: Jack ]
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yersinia
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Member # 324
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posted 02. July 2003 16:16
Unfortunately, ID writers have a checkered history when it comes to citing peer-reviewed literature in their favor.
1. E.g., Dembski, in No Free Lunch, wrote (p. 270):
quote:
For the scientific community to take this concept [IC] seriously, the peer-reviewed scientific literature needs to address this concept explicitly and acknowledge it as a genuine problem for biology. That has happened. In 2000 Thornhill and Ussery published an article in the Journal of Theoretical Biology addressing "the accessibility by Darwinian evolution of irreducibly complex structures of functionally indivisible components." [61]
But ref. 61, if the reader happened to follow the footnote, look up the article, and read it, is:
quote:
J Theor Biol. 2000 Mar 21;203(2):111-6.
A classification of possible routes of Darwinian evolution.
Thornhill RH, Ussery DW.
2505 Tomin Tower, 3-10-1 Iidabashi, Chiyoda-ku, Tokyo, 102-0072, Japan.
A classification of four possible routes of Darwinian evolution is presented. These are serial direct evolution, parallel direct evolution, elimination of functional redundancy, and adoption from a different function. This classification provides a conceptual framework within which to investigate the accessibility by Darwinian evolution of complex biological structures. Copyright 2000 Academic Press.
...the whole article is online here:
http://www.cbs.dtu.dk/staff/dave/JTB.html
...and, upon reading it, one discovers that it is in fact a refutation of Behe. How can you cite papers that are refuting your position without mentioning that little fact?
2. In another vein, during the Ohio debate the DI put out a list of literature that supposedly questioned Darwinism, describing them as "publications represent dissenting viewpoints that challenge one or another aspect of neo-Darwinism (the prevailing theory of evolution taught in biology textbooks), discuss problems that evolutionary theory faces, or suggest important new lines of evidence that biology must consider when explaining origins" (quoted here):
DI list
...but NCSE contacted the authors and found that this wasn't the case:
NCSE response
3. The phrase "ID-relevant literature" seems to be tactically ambiguous, and in practice refers to:
(1) Standard biochemistry papers that happen to be published by ID supporters/sympathizers, but which have no obvious connection to the ID argument that intelligent design actually did something somewhere in biology (and certainly no such explicit connection is made). Various papers by Axe, Behe etc. sometimes appear in this category.
(2) Standard papers by lots of scientists that happen to discuss complex systems. In this mode of argumentation, ID advocates try to turn any paper on (say) the bacterial flagellum into a "paper supporting ID".
(3) Vague citations of Behe or Dembski, or even more obliquely, Denton, in what I might describe as "vaguely pro-teleology" review papers. As far as I've seen no external intervention is argued for, usually neodarwinism is questioned and some version of orthogenesis is suggested.
A case in point here is Dembski's seemingly strongest bit of evidence in his essay above, namely that he was cited in Annual Reviews in Genetics. This paper is almost certainly:
quote:
Annu Rev Genet. 2002;36:389-410.
Chromosome rearrangements and transposable elements.
Lonnig WE, Saedler H.
Max-Planck-Institut fur Zuchtungsforschung, Carl-von-Linne-Weg 10, D-50829 Koln, Germany; loennig@mpiz-koeln.mpg.de
There has been limited corroboration to date for McClintock's vision of gene regulation by transposable elements (TEs), although her proposition on the origin of species by TE-induced complex chromosome reorganizations in combination with gene mutations, i.e., the involvement of both factors in relatively sudden formations of species in many plant and animal genera, has been more promising. Moreover, resolution is in sight for several seemingly contradictory phenomena such as the endless reshuffling of chromosome structures and gene sequences versus synteny and the constancy of living fossils (or stasis in general). Recent wide-ranging investigations have confirmed and enlarged the number of earlier cases of TE target site selection (hot spots for TE integration), implying preestablished rather than accidental chromosome rearrangements for nonhomologous recombination of host DNA. The possibility of a partly predetermined generation of biodiversity and new species is discussed. The views of several leading transposon experts on the rather abrupt origin of new species have not been synthesized into the macroevolutionary theory of the punctuated equilibrium school of paleontology inferred from thoroughly consistent features of the fossil record.
Both Behe and Dembski are referenced in the paper, but the citations are less than impressive:
quote:
In regard to the question of species formation in muntjac deer and cyclops, McClintock (90) suggested, “it is difficult to resist concluding that some specific “genomic shock” was responsible for origins of new species” in these genera. Despite the reservations and open questions noted above, her hypothesis is intrinsically attractive and a promising possibilty that warrants further investigation. However, if all the proof that is still lacking to substantiate her view on the origin of species were available, would that also give us the mode of origin of the higher systematic categories and types of life referred to by Schindewolf? To be more specific: If so, to what extent can any of the TE-incited rearrangements contribute to the origin of novel genes and new gene reaction chains as well as the genesis of irreducibly complex structures? All three of these may be especially relevant for the origin of higher systematic categories (3–5, 33, 69, 80–85, 121, 122, 130).
[...]
The Darwinian centennial in 1959 (138) provided the occasion for many voices to declare that all the basic problems of the origin of species and higher systematic categories had fully been solved by the modern synthesis. The speakers and authors of the centennial were, of course, aware of some outstanding problems, but itwould be only a matter of time and effort before these were also resolved within the frame of the synthetic theory. In any case, there was nothing of substance to be really worried about. This was in stark contrast to the many opposing views advanced in 1909 at the 50th anniversary celebration of the publication of Darwin’s Origin of Species. TEs had no part in these discussions. Extrapolating from the wide range of current opinions (3–5, 14, 29, 30, 33, 38, 40, 55, 56, 64, 69, 71, 75–85, 89–93, 101, 109, 121, 122, 126–130, 132–138), we might safely predict that if similar meetings are held in 2009, the climate of opinion will be much closer to that of the 1909 semicentennial than to that of the 1959 centennial, and transposable elements will have played a special part in discussions on the origin of systematic species, from small to large chromosome rearrangements in muntjac deer to many different plant chromosome lines. However, in the face of the numerous scientific problems still unresolved in the context of the origin of species and higher systematic categories, we would probably be well advised to continue to welcome the plethora of different and diverging ideas and hypotheses on the origin of life in all its forms as well as to remain open-minded on real results of investigations, wherever they may lead.
Ref 5 is Darwin's Black Box and ref 33 is No Free Lunch. Being mentioned in a laundry list of various perspectives on the prospects of neodarwinism, in a paper that appears to be trying to reinvigorate macromutation/saltation via transposons and chromosome rearrangements (rather than endorsing ID), is not exactly a vindication of ID.
But Dembski is evidently stuck grasping at the few straws he has, apparently. This in itself says something about the record of ID in the literature.
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Grape Ape
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Member # 399
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posted 02. July 2003 16:22
Paul Nelson writes:
quote:
I agree, except that I would unpack "fecundity" into "fruitfulness for discovery and knowledge" (just churning out ID papers that lead nowhere won't do). But this business about peer review and the mainstream literature, which I also agree has great potential for tedium and pointlessness, is really a reply to a major criticism of ID.
I take the opposite position. The buisness about peer review, coming from ID critics, is itself a reaction to claims made by the ID movement. I don't know what Forrest and Gross argue, but pointing out the lack of peer-reviewed literature (or any other kind of scientific output, as opposed to mere polemics) becomes appropriate when ID advocates make bold claims regarding the scientific progess of their movement. In fact, Dembksi starts off his opening post with a familiar brag: he basically drops a bunch of names and numbers (which will probably impress the unwary) to try and show just how mighty ID has become. But has it really? That's why critics turn to the literature in order to assess the validity of the more general claim that ID is making major inroads. I'll repost a bit of what I posted on ARN:
quote:
But in my experience, pointing out the lack of papers is not so much a proactive stab at ID, but rather a reactive response to the bold claims that the ID movement makes in regards to its progress. We see frequent claims that the ID movement is engaging in scientific research, is a legitmate scientific movement, and is actively finding new discoveries that validate the ID position. Not surprisingly, these claims tend to raise eyebrows. That along with the "growing number of scientists supporting ID" claim -- which may or may not be technically true, but is misleading nonetheless -- form the basis for much of the ID movement's reasoning that ID deserves "equal time" or something similar in public school science classes. (Which oddly enough, seems to be a higher priority than building a research program.) This kind of argument resonates well with the public, because they figure intuitively that students should be exposed to "all sides" when there are legitimate scientific disputes. And if there were a lot of ID research and researchers, and that ID related research was making a signficant contribution to the body of scientific work, then this would indeed seem to be the case. But the lack of ID papers in the peer-reviewed literature shows that the scientific community as a whole is not taking ID seriously, there is no great rush among researchers to apply ID methods, and that there is no significant body of empirical research that lends support to ID. So it's not so much a matter of "ID can't be true because it hasn't published anywhere", but rather a matter of, "the ID movement's claim to be on near-equal footing with their opponents in terms of scientific output holds no water."
[My apologies to the mods if this runs afoul of the rules.]
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fish
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Member # 213
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posted 02. July 2003 16:26
Unkind thought:
If the development of ID is really being inhibited by the peer review process, then why, when Tipler [for example] gets the chance to publish in an uninhibited forum like ISCID, does he choose the subject of peer review, which is always going to be dangerously close to being aristocratic sour grapes? The fact that he so far has more to say on the habits of mainstream science than on ID speaks for itself.
In response to Paul Nelson (but in a similar vein). There are some of us who are evolutionary biologists but are still too sophisticated to believe in the wicked witch of the west (or that ID is identically equal to the wedge).
Nevertheless, the fact that leading members like Dembski spend a great deal of time apparently trying to defend ID as being ready for mainstream consumption (isnt this what the peer review issue is all about?), when it manifestly isnt, tends to suggest that politics do come high on the priority list.
Summary: this is an issue on which ID sympathises cannot win, and shouldnt bother to fight.
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RB
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Member # 263
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posted 02. July 2003 16:28
This is a fine and dandy discussion, but why is it a brainstorm, because Bill started it?
How does a whine about peer review make it as a start for a topic, why didn't Bill just post it under Tipler's topic?
Feel free to delete this mod.
I enjoy reading posts that make me think about evo and ID (though I haven't seen one that pulls me toward the ID side), but at least they are thought provoking, this topic is long been run through the ringer enough times making it flatter than Illinois (and anyone from the US know how boring that state is to drive through.)
I will now return to lurker status.
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Paul A. Nelson
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Member # 26
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posted 02. July 2003 16:44
Fish wrote:
quote:
There are some of us who are evolutionary biologists but are still too sophisticated to believe in the wicked witch of the west (or that ID is identically equal to the wedge).
Yes -- I meet you sophisticates when I lecture here and there around the country. Makes life fun, because we can engage the substantive questions and put aside the polemics.
I'm going to invite Paul Gross to drive up to Boston from Cape Cod, at the end of this month, to drop in at the Society for Developmental Biology meeting where Marcus Ross and I will be presenting a poster on ontogenetic depth. Who knows, he might make the trip and say hello.
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. ![[Cool]](cool.gif)
[ 02. July 2003, 16:52: Message edited by: Paul A. Nelson ]
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Jack
Member
Member # 265
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posted 02. July 2003 16:48
Fish<< Nevertheless, the fact that leading members like Dembski spend a great deal of time apparently trying to defend ID as being ready for mainstream consumption {isnt this what the peer review issue is all about?}, when it manifestly isnt, tends to suggest that politics do come high on the priority list. >>
What does ID need to do to become ready for mainstream consumption? Is abiogenesis ready for mainstream consumption? How does a non-teleological account of the origin of life explain the data better than a teleological approach?
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Moderator
Administrator
Member # 1
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posted 02. July 2003 16:49
Several have written in wondering why this post was made in Brainstorms (and perhaps even more important, why has it been allowed to stay open).
1. I'm assuming that Bill Dembski made this post, spurred on by the Frank J. Tipler paper. Otherwise, I can't speak for Bill Dembski's reasons for posting here.
2. Occasionally, at Brainstorms, we let discussions about scientific method proceed, especially when the discussion seems to be substantial and/or novel. Brainstorms was created to fascillitate scientific creativity, and it seems that the current "peer review" debate has a lot to do with, well, scientific creativity.
Do current "peer-review" methods fascillitate scientific creativity? That question alone gives me reason to let the discussion ride for a while.
Posting rules are lightened a bit (in these threads only) in case any lurkers want to jump into the fray.
[ 02. July 2003, 16:54: Message edited by: Moderator ]
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Evan
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Member # 164
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posted 02. July 2003 16:52
Dembski wrote,
" Readers may refer to the ISCID bibliography at www.iscid.org/bibliography/bibliography.php for works in the peer-reviewed literature by design theorists that support intelligent design (note that this is a bibliography of design-relevant literature and thus also includes references to work by scientists who are not design theorists). Rather than list a number of such works, ..."
But Micah wrote,
“1. The ISCID bibliography contains over 3 thousand entries. Not all of them fit Dr. Dembski's description. There is no pre-generated list at that URL that fits Dr. Dembski's description (as far as I know)
2. The ISCID bibliography is a members only service and will stay that way for practical purposes.”
Therefore, perhaps it would be reasonable for Dembski to prepare a short list from those 3000 entries and post them here. Since Dembski, I’m sure, knows that the ISCID bibliography is not open to the public, and yet his post is from a book he is writing, offering some subset of the bibliography to the public so they can judge his claim about the works for themselves would be reasonable, I think.
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andyg
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Member # 415
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posted 02. July 2003 17:33
It might set the minds of ID proponents at rest if they realize that *everyone* complains about peer-review of both manuscripts and grant proposals. Both Science and Nature regularly carry articles or op-ed pieces that discuss the peer-review process.
Bill seems to be saying that *some* ID papers are published in the peer-reviewed literature, but not enough for his liking. That may be true. I can certainly say the same for my own work too, and I am sure that most of my colleagues would concur about their work!
I would be very interested to see some data on the number of ID research papers that have been submitted to peer-reviewed journals and rejected, as well as the reasons for rejection. I suspect that the number is quite small, and the number of different reasons for rejection is also small. Would any authors of ID papers care to comment?
Since Paul and Bill are contributing to this thread, perhaps they might like to comment on some questions I raise in another thread:
What comes after detecting design?
They both make claims for the revolutionary nature of ID in science. I would like to hear where they think this revolution will lead us.
AndyG
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RBH
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Member # 380
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posted 02. July 2003 17:46
Micah wrote quote:
1. The ISCID bibliography contains over 3 thousand entries. Not all of them fit Dr. Dembski's description. There is no pre-generated list at that URL that fits Dr. Dembski's description (as far as I know)
and Dembski's description is quote:
... works in the peer-reviewed literature by design theorists that support intelligent design (note that this is a bibliography of design-relevant literature and thus also includes references to work by scientists who are not design theorists).
Can you tell us, Micah, just how many of the 3,000 papers are "works in the peer-reviewed literature by design theorists that support intelligent design," as distinguished from design-relevant (by some criterion or other) work by scientists who are not design theorists? If some of the papers are by already identified design theorists and if their papers support intelligent design, it makes little sense to suppose that keeping their identities behind a membership barrier would protect them from the inquisition Dembski fears on their behalf. Or is their secret research so subtle in its design (!) and interpretation that its support for intelligent design is not as unequivocal as Dembski would have us believe?
RBH
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Jack
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Member # 265
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posted 02. July 2003 20:15
AndyG<< Bill seems to be saying that *some* ID papers are published in the peer-reviewed literature, but not enough for his liking. That may be true. I can certainly say the same for my own work too, and I am sure that most of my colleagues would concur about their work!
I would be very interested to see some data on the number of ID research papers that have been submitted to peer-reviewed journals and rejected, as well as the reasons for rejection. I suspect that the number is quite small, and the number of different reasons for rejection is also small. Would any authors of ID papers care to comment?>>
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. This also agrees with what design critics like Eugenie Scott, Paul Gross, and Barbara Forrest say, namely, that design theorists have gotten exactly ZERO articles published in the peer-reviewed biological literature that support intelligent design. 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.
[ 02. July 2003, 20:28: Message edited by: Jack ]
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andyg
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Member # 415
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posted 02. July 2003 20:32
Jack wrote:
quote:
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. This also agrees with what design critics like Eugenie Scott, Paul Gross, and Barbara Forrest say, namely, that design theorists have published exactly ZERO articles in the peer-reviewed biological literature that support intelligent design.
Several points:
1. I am not at all clear how one can "explicitly affirm" ID. The best Dembski and others can do at the moment is offer a method that they claim can detect design reliably. To my knowledge, this method has not been rigorously tested. Others have critiqued the method for inferring design.
2. I am not clear how one can "explicitly deny" evolution. That would be rather like explicitly denying gravity. There are many papers that have described different ways in which evolution can occur.
3. 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:
quote:
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.
Taken from
Behe letter
AndyG
[ 02. July 2003, 20:33: Message edited by: andyg ]
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Nel
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posted 02. July 2003 20:44
Nic,
First, Dembksi's quote is consistent with the reference. His quote states that IC needs to be addressed and taken seriously by the scientific community, Ussery's paper shows just that, that the scientific community not only takes it seriously, but is actually addressing it.
quote:
For the scientific community to take this concept [IC] seriously, the peer-reviewed scientific literature needs to address this concept explicitly and acknowledge it as a genuine problem for biology.
You can see this in Ussery's paper when he writes:
quote:
However, the more theoretical question about the accessibility by Darwinian evolution of irreducibly complex structures of functionally indivisible components, if such exist, has not been thoroughly examined. One suggested mechanism for the evolution of such structures is the addition of advantageous but inessential components which become essential later as a result of the addition of further, interlocking, components (Orr, 1996). However, this could only produce a complex, rather than an irreducibly complex, structure.
Even so, the Ussery paper is not a refutation of Behe's thesis (or at least not a successful one). The paper, for the most part, is a restatement of Behe's thesis. Direct evolutionary mechanisms cannot form IC structures. Ussery refers to these as Serial direct Darwinian evolution and Parallel direct Darwinian evolution. Ussery states that these mechanisms cannot form IC systems. Behe also wrote in Darwin's Black Box that direct pathways cannot form IC systems. However, both Ussery and Behe say that indirect mechanisms can form an IC system. Ussery calls them Elimination of functional redundancy and Adoption from a different function. In Behe's book, Behe also agrees that Adoption from a different function could form an IC system. The difference however, is that Behe states that the more complex an IC system is the less likely that co-option can form it (because it's mostly just pure chance) and with elimination of functional redundancy there still remains an IC core that needs to be explained. So the paper isn't much of a refutation it's just repeating what Behe said in his book.
For more on this see:
http://www.idthink.net/back/ic/index.html
As for the list of papers that the DI cited, the NCSE response consisted of e-mailing the authors
of the papers, some of which did not reply, but others replied by either saying the same thing that the DI said (but making it sound as if they were saying something different), or simply brushing it off with a simple "they're wrong".
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.
I havn't seen the bibliography that Dembski points to but it is quite obvious that a lot of papers do support ID regardless of whether the authors agree with intelligent design or not. The data sometimes speaks louder than the current dominant paradigm. Data doesn't give a hoot what you believe. If the flagellum cannot function with any lower complexity, the data will show this, whether you are a Darwinist or not. If there is no evolutionary history, the data will show this whether you are Darwinist or not. If you can't get a monophyletic tree together showing a universal common ancestor because there was no universal common ancestor the data will show this whether you are a Darwinist or not. Of course I'm not saying that things are clear cut. My point is that as data that strains the framework of a dominant theory accumulates, it becomes more and more likely that an alternative theory will have more use out of research comming out of the field than the dominant theory.
[ 02. July 2003, 21:07: Message edited by: Nelson-Alonso ]
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brauer
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posted 02. July 2003 20:50
Jack wrote:
quote:
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. This also agrees with what design critics like Eugenie Scott, Paul Gross, and Barbara Forrest say, namely, that design theorists have gotten exactly ZERO articles published in the peer-reviewed biological literature that support intelligent design. 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.
Again, this is an interesting anecdote, but ignores the question that has been asked, namely "how many ID papers have been submitted?"
It's one thing if zero out of five (say) ID papers were accepted. It's quite another if zero out of 500 were accepted.
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.
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