The Questionable Authority

Over at the Discovery Institute’s Media Complaints Division, Michael Behe seems to be a wee bit concerned by the attention that a recent Nature paper is getting, moaning that, “It seems some scientists have discovered that one way to hype otherwise-lackluster work is to claim that it discredits ID.”

OK. To start with, watching Michael Behe whine about someone else using ID to hype “otherwise-lackluster work” creates a concentration of irony so dense that four mining firms have put in bids for that post. Sorry, but I had to get that one out of my system. Now that I’ve more or less managed to get that minor issue out of the way, let’s look at what, for lack of a better term, we will have to call the “substance” of Behe’s complaints.

The January 25th issue of Nature carries a “Progress” paper by Poelwijk et al that’s touted on the cover as “Plugging Darwin’s Gaps,” and cited by its authors as addressing concerns raised by proponents of intelligent design. The gist of the paper is that some amino acid residues of several proteins can be altered in the lab to produce proteins with properties slightly different from those they started with.

. . .

Quite unsurprisingly, the current paper shows that microevolution can happen. Small changes in a protein may not destroy its activity. If you start out with a protein that does something, such as bind DNA or a hormone, it’s not surprising that you can sometimes find a sequence of changes that can allow the protein to do something closely similar, such as bind a second sequence of DNA or a second, structurally-similar hormone.

That’s Behe’s description of what the paper is doing. Now, let’s go for the reality-based summary:

Despite the plethora of modern genetic tools, something that is little changed since Darwin’s time is our reliance on evolutionary outcomes to unravel the process of evolution. The lack of evolutionary intermediates leaves the door ajar for the proponents of intelligent design. But a new technique could help fill the gaps. It involves the construction of evolutionary intermediates in the lab, and the search for viable paths between them. The resulting ‘fitness landscapes’ map viable routes between accessible evolutionary paths.

That’s the editor’s summary for that article. I realize that it isn’t quite as reader-friendly as Behe’s summary, so let me try to sum up the summary: scientists are using new lab techniques to take a step-by-step, mutation-by-mutation look at the various paths that evolution might have taken.

Looking at what I just wrote, I think an example might be called for. A good one can be found in a recent paper in Science that was referenced in this Nature article.

There are some bacteria that have a version of a particular enzyme that makes them 100,000 times more resistant to certain antibiotics (like penicillin). We know that there are five differences that separate this version of the enzyme from the basic version, and we know what those mutations are. In theory, if the mutations happened one at a time, there are 120 possible ways that the enzyme could go from the original form to the resistant form. (For example, mutation 1 could have happened first, mutation 2 second, mutation 3 third, mutation 4 fourth, and mutation 5 fifth, or mutation 2 could have happened first, mutation 1 second, mutation 3 third . . . or mutation three could have happened first . . . and so on until all the possibilities are exhausted. )

Scientists then were able to construct possible intermediate forms of the enzyme – varieties that contained some, but not all 5, of the mutations, and test their resistance to the antibiotic. What they found was that 12 of the 120 possible paths from the original form to the new form increased resistance with every additional mutation. That’s pretty cool – it shows that not only could natural selection drive the changes in this enzyme, but also that there are 12 different ways it could have happened.

The Nature article that Behe is bitching about looks at the ways in which that type of approach is being used to study evolution at the cellular level, mutation by mutation. That’s a bit different from Behe’s description of the article: “the gist of the paper is that some amino acid residues of several proteins can be altered in the lab to produce proteins with properties slightly different from those they started with.” Actually, we already know that proteins can be altered to slightly change their properties. What this paper is discussing is how we can study, in the lab, the mutation-by-mutation paths that natural selection can take in moving a protein from one form to another. That’s something that any scientist with even marginal reading comprehension skills could figure out from skimming the paper. So why is Behe trying to obfuscate what the paper is really about?

It might have something to do with statements like this:

Not only would I need a step-by-step, mutation by mutation analysis, I would also want to see relevant information such as what is the population size of the organism in which these mutations are occurring, what is the selective value for the mutation, are there any detrimental effects of the mutation, and many other such questions.

That quote was taken from Behe’s testimony during the Kitzmiller trial. Behe was talking about the immune system there. The current studies are a long way from systems like that, but they do show mutation-by-mutation paths, with selective values for each step, in the development of some new traits. (Like it or not, a 100,000-fold improvement in antibiotic resistance is a new trait.) Some of the other studies cited in the paper look at even more things, like the possible effects of taking paths that are longer than the shortest possible paths investigated in the bacterial resisitance study, by looking at things like the effect of a muation that is gained then lost along the way.

Under the circumstances, it’s really no surprise that Behe is trying to obfuscate these studies and minimize their significance. Our understanding of evolution keeps improving, and his complaints about the things we don’t yet understand sound weaker and weaker every day.

Reference

Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins
Daniel M. Weinreich, Nigel F. Delaney, Mark A. DePristo, and Daniel L. Hartl
Science 7 April 2006 312: 111-114 [DOI: 10.1126/science.1123539]

Comments

  1. #1 Foxy
    February 2, 2007

    Ignoring Behe, those results really are quite fascinating.

  2. #2 wright
    February 2, 2007

    Did he actually pass up the opportunity to trumpet this as another example of “peer-reviewed work” on ID? That’s the usual pattern…

  3. #3 afarensis
    February 2, 2007

    This paper of Zhang’s does something similar with pancreatic RNases. They were able to identify five amino acid substitutions and show the effect of those substitutions on the Rnases digestive function in colobines.

  4. #4 sparc
    February 2, 2007

    A major problem of Behe and Demski is that they are seemingly only following what appears in Nature and Science (of course Cordova, GilDogen and DaveScot are even more obsessed with quotemining articles from prestigious journals without much comprehension).

    Thus, they miss papers like this one from the January issue of Current Biology:
    Meier S, Jensen PR, David CN, Chapman J, Holstein TW, Grzesiek S, Ozbek S. (2007) Continuous molecular evolution of protein-domain structures by single amino acid changes. Curr Biol. 17(2):173-178
    In an editorial the same issue Todd Yeates comments:

    “Meier et al. [4] weigh in on this question by illuminating an evolutionary transition or ”bridge state” between two small protein domains whose folds are structurally dissimilar. (�) Working with a CRD called NW1 from a different protein (NOWA) of Hydra, they show that their CRD can be converted by single amino acid changes from a structure that resembles the amino-terminal CRD of minicollagen-1 to a structure that resembles the alternative conformation seen in the carboxyterminal CRD of minicollagen-1.

    (emphasis mine)
    I’ve already linked to the article in a comment of a recent post of Arthur Hunt at Panda’s Thumb (Axe (2004) and the evolution of enzyme function (http://www.pandasthumb.org/archives/2007/01/92_second_st_fa.html#new-comments) but I believe it fits to this thread as well.

  5. #5 Crudely Wrottc
    February 2, 2007

    All of these contortions and squirmings must be taking a toll on Behe. Watch for possible signs of further deterioration.

  6. #6 Jeremy Mohn
    February 3, 2007

    In the blog post you linked to, Behe also wrote:

    The authors remark, “The evolutionary puzzle becomes more complex at a higher level of cellular organization.” No kidding. Nonetheless, they, like most Darwinists, assume that larger changes involving more components are simple extrapolations of smaller changes.

    If you actually read the paper you will find that Poelwijk et al do not assume that what has been observed in the lab so far can be extrapolated to account for larger changes.

    In fact, earlier in the paper (available online here) the authors wrote:

    We note that the presented approach starts with naturally occurring sequences, which are themselves the product of evolution, and may therefore yield a biased sample of trajectories. Whether the conclusions are general or not, and whether they break down when the evolved feature becomes more complex, can only be determined through future studies. (p. 383-384)

    The fact that Behe must resort to this kind of misrepresentation in order to minimize the work of people who actually do research in molecular evolution only serves to magnify the desperation of his position.

  7. #7 Bryson Brown
    February 3, 2007

    The irony of Behe dismissing work that actually presents step-by-step selectable paths to new traits is nearly overwhelming. This work, though still on a small scale, is exactly what Behe’s been demanding from ‘Darwinists’ for years. Of course, nothing could be more threatening to him than that, and what’s a little intellectual dishonesty when you’ve got a religion to defend?

  8. #8 Torbjörn Larsson
    February 3, 2007

    So when having different rules for each team or moving the goalposts aren’t enough, Behe has to deny the goal altogether.

    Next time he will try to take the ball – at a guess, evolution isn’t science for Behe because it explains things the bible says it shouldn’t.

  9. #9 Michael Wells
    February 4, 2007

    Would the contents of this paper count as a “pathetic level of detail”?

  10. #10 boojieboy
    February 4, 2007

    If you want a ready analogy to explain what these guys have done, they’ve created a molecular version of the word transformation game doublets

    Cool.

  11. #11 Whatever
    February 4, 2007

    Behe and Dembski will remain certain beyond all doubt that a designer was at work until scientists can reconstruct the details of biological evolution in atom-by-atom detail. Of course, asking what, when, how, who or any details about the “designer” or its mode of operation will always remain off limits.

    No wonder Behe’s colleagues at Lehigh roll their eyes whenever he writes something…

  12. #12 rmr
    February 14, 2007

    You quote:

    “Despite the plethora of modern genetic tools, something that is little changed since Darwin’s time is our reliance on evolutionary outcomes to unravel the process of evolution. The lack of evolutionary intermediates leaves the door ajar for the proponents of intelligent design. But a new technique could help fill the gaps. It involves the construction of evolutionary intermediates in the lab, and the search for viable paths between them. The resulting ‘fitness landscapes’ map viable routes between accessible evolutionary paths.”

    This “construction of evolutionary intermediates in the lab” is exactly what Behe terms as intelligent design. The hand of man created the circumstances resulting in “accessible evolutionary paths.”

    This is like saying that because the possibility of time travel has been proven by Steven Hawking through mathematical analysis, then time travel readily exists on its own in nature. The problem is however, that it has not been observed and most likely is not a common occurance in nature as we know it.

    This also holds true for circumstances created in the lab. Just because you can open the door to possibilities of “viable paths” in the lab doesn’t mean that these paths are a common occurance in nature.

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