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This year in "intelligent design"

This year, I haven't found a single paper in a scientific journal presenting new data and claiming to show a role for a supernatural "designer" in the origin or subsequent evolution of life. Readers are invited to call my attention to papers I missed. Any paper published in a journal with a citation impact of at least 1.0 and containing actual data will do. In your comment, please quote the text that invokes intelligent design. Comments not meeting these three basic requirements may be ridiculed or deleted.

If scientists ever find any actual evidence for intelligent design, it will modify our understanding of evolution rather than completely replacing what we already know. In biology, "evolution" refers to genetic changes in populations over generations, by any mechanism. The mechanisms for which there is evidence are mutation (direct changes to DNA by various means), selection (including sexual selection, kin selection, deliberate selection by humans, etc. ), gene flow (e.g., migration or blowing pollen), and the random genetic drift of small populations. If there were any evidence for supernatural intervention, we would add that to the list, but there isn't, so far. Whining doesn't constitute evidence.

"Intelligent design" never got off the ground as a scientific field and now it seems to be dead even as a religious movement.

Comments

Although I doubt anyone will provide evidence for intelligent design, your blog has this disclaimer:

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That might make ID supporters think that there's no point in responding since they might be censored. Maybe you should remove that requirement for a little while?

I don't have control of that wording. I added CAPCHA and hold-for-approval in response to lots of commercial spam and occasional random obscenity. My "Rules for Comments" notes that:
"Comments immune from deletion outside the Troll Refuge are either:
1) narrowly focused on the particular paper-of-the-week, or
2) suggestions for papers to discuss that meet the criteria in my first post."

In practice, I've been more liberal. The only creationist comment I remember deleting was a cut-and-paste copy of one already left on another post (where I responded) and unrelated to either post. For an example of a clueless comment I let stand, see last post.

For awhile now, the Discovery Institute has been taking about a laboratory they have been funding called "The Biologic Insitute", where ID scientists can do actual research, supposedly.

I looked at their website (http://biologicinstitute.org/research/)and found a few publications funded by them for 2008:

D’Andrea-Winslow L, Novitski AK (2008) Active bleb formation is abated in Lytechinus variegatus red spherule coelomocytes after disruption of acto-myosin contractility. Integrative Zoology 3: 106-113. doi:10.1111/j.1749-4877.2008.00086.x

Axe DD, Dixon BW, Lu P (2008) Stylus: A system for evolutionary experimentation based on a protein/proteome model with non-arbitrary functional constraints. PLoS ONE 3: e2246. doi:10.1371/journal.pone.0002246

Sternberg RV (2008) DNA codes and information: Formal structures and relational causes. Acta Biotheoretica doi:10.1007/s10441-008-9049-6. PMID: 18465197
Gonzalez G (2008) Parent stars of extrasolar planets - IX. Lithium abundances. Monthly Notices of the Royal Astronomical Society, Online Early Articles doi:10.1111/j.1365-2966.2008.13067.x

I took a look at the Axe et al paper (cuz it was in PLoS and easily accessible). Didn't find any ID-specific stuff, but there was this interesting note:

. In the protein world, functions are a direct consequence of physical structures. This, in combination with a highly many-to-one mapping of protein sequences to structures, allows sequences to change continually while meeting the structural constraints imposed by the original function (a phenomenon known as neutral drift [14]). In contrast, alphabetic strings function as raw sequences, with no physical structure mediating between them and their function (they are, of course, recorded and conveyed through physical media, but the only requirement for achieving this is accurate representation of sequence). Although alphabetic sequences show a many-to-one mapping to function, it is “many? in a sparse and highly discontinuous sense. Because these sequences are directly constrained by the rules of linguistic function (grammar, vocabulary and spelling) they cannot withstand the continual step-wise change seen in proteins.
The importance of structure in the protein world suggests that a structure-based system of writing would provide a better analogy. Many of the Asian languages use non-alphabetic writing based on the Chinese characters that became standardized during the Han Dynasty (206 BC–220 AD). Like alphabetic letters, the Han characters are recognized by their distinct structural forms. But unlike letters, the characters have word-like meanings as stand alone entities. In these written languages, then, basic linguistic meaning is rooted in structure rather than sequence. This suggests a new way of framing the linguistic analogy to proteins. Instead of viewing the letters in alphabetic strings as being analogous to the amino-acid residues in a protein chain, the new approach views the Han characters as being analogous to whole protein folds (Figure 1).

I'm not sure where this can lead in an ID context,but the approach might prove fruitful in general.

There was also a very weird paper published in 2008 by a reputable journal (I'll have to rummage around to find the reference, it escapes me at the moment) by some Korean researchers that was so bad it had to be retracted as it obviously had not undergone any kind of decent peer-review. I wouldn't be surprised if the ID community viwed its retraction with suspicion.

Ah. Here it is. PZ Myers, on his blog Pharyngula wrote about the strange Korean paper which was published (and withdrawn, for several reasons, including plagiarism) in the respected journal Proteomics:

http://scienceblogs.com/pharyngula/2008/02/a_baffling_failure_of_peer_rev.php

I know it doesn't fit your criteria, but had it not been withdrawn, it would have been a fun one to shred (just because it was so outrageously silly).

Dave,
Thanks for digging deeper. Can you tell whether any of these meet my three criteria?
PLoS One is only very lightly peer reviewed, as your excerpt shows. We already knew that sequence can change without changing structure. For example, Tony Dean, in my department, found that two enzymes, duplicated and diverged from a common ancestral enzyme way back in the good old days, retain almost identical structure, despite major changes in sequence.

Frankly, I don't see where any of them meet your criteria. Instead they illustrate where the ID movement has been stuck ever since it began: a vain attempt to try and argue for intelligent design by obsessing on finding limitations and constraints to evolution.

They cannot seem to get it out of their heads that you don't empirically support a theory by looking for problems in a competing theory. Not only that, they also fail miserably in their quest to show that evolutionary processes are inadequate to explain biological diversity. I'm no expert on ID, but one thing I've noticed in the antievolutionary arguments I have read (like Behe's books) is an almost congenital inability to comprehend just how much variation living organisms can generate. In my own limited experience (genetic variation in small mammals) the amount of variation a population can present to the environment makes me wonder if any of these ID 'scientists' ever really deal with real-world data. I certainly would have expected Behe,as a biochemist,to be aware of it, and yet he talks as if the actual amount of variation life can come up with is several orders of magnitude less than that.

Google Trends confirms too.

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