Posted by Steve Reuland on April 9, 2007 10:01 AM

Bill Dembski and company are having a self-congratulatory session about a new “pro-ID” paper published by Finnish researchers Matti Leisola and Ossi Turunen in Applied Microbiology and Biotechnology. Looking at the paper, you wouldn’t know that it’s a “pro-ID” paper at all because it contains not one shred of evidence in favor of ID, nor does it even try directly arguing for ID (compare this to the Meyer paper, which while riddled with errors, at least put forth pro-ID arguments). On what basis could it possibly be a pro-ID paper? If it weren’t for the fact that Matti Leisola is a creationist, there would be no reason to believe it was intended as such at all.

Nevertheless, Dembski apparently thinks that it’s a pro-ID paper on the basis of its content, presumably because he conflates rational design methodology as used in protein engineering with ID. Of course this is nonsense, and in reality the paper is merely a redundant review of the current state of protein engineering techniques, with most of the space dedicated to the very long list of successes enjoyed by evolutionary methods. There are much better reviews out there, but nevertheless Leisola and Turunen give a decent (if too limited) overview of directed evolution experiments. Then they proceed to argue that rational design methods will start working better once we have more detailed knowledge of the mechanism by which the primary sequence of a protein determines its structure and function. This is an obvious and noncontroversial conclusion, so one is still left wondering how this could possibly be spun as “pro-ID”. I’ll say more about that in a minute, but first let me give a quick overview of the state of protein engineering as it exists today.

There are generally two ways one can go about trying to engineer a protein. The first is to use what is commonly called “rational design”. As the name implies, this simply means taking what you know about the structure and function of a protein and trying to predict which changes you need to make in order to get a desired result. The problem with this approach is, first of all, that you need detailed knowledge of the protein’s structure and function. Not all proteins have had their structures solved, and many of their functions are either poorly characterized or not characterized at all. Obtaining this knowledge is an expensive and time consuming process. And secondly, no one really knows what the exact relationship is between sequence, structure, and function. Even if you know everything there is to know about a protein’s current structure and function, it is very difficult to predict what’s going to happen when you start changing things around.

So protein engineers employ a second technique known as “directed evolution”. Again, the name tells you essentially what the technique involves: you apply random mutagenesis to whole or part of your protein, you screen for the properties you’re looking for, and you repeat the process as necessary. In other words, you use the Darwinian mechanism, the very mechanism that ID advocates have spent the last decade fruitlessly arguing is incapable of doing the very things we see it doing in the lab. And as it turns out, directed evolution methods are generally superior to rational design methods, so much so that a number of successful biotech companies such as Diversa and Applied Molecular Evolution use directed evolution as their primary engineering tool. (Incidentally, creationists who argue that evolution has no practical applications – paging Michael Egnor! – should sit down and have a talk with the officers of these companies.) But in spite of the success of directed evolution techniques, they’re not without drawbacks. You need a means of screening large numbers of mutants quickly (known as high-throughput) in order to find the rose among thorns. This means using expensive automated equipment and/or a lot of researchers. Plus such screens often have to be developed independently for each individual protein, and lots of proteins just aren’t going to be easy to screen. So both rational design and directed evolution each have their advantages and disadvantages. Luckily, researchers are not limited in which approach they use, and when applicable, they will use both directed evolution and rational design approaches together.

Okay, now back to the paper. One of the central deceits of the ID movement is to claim that anytime a human being designs something, she is using the theory of “intelligent design”. Sorry, but no. Researchers who employ rational design techniques do not operate under the premise that natural proteins were “designed” by some unknown intelligence using unknown methods. And if for some reason they did, it would be entirely unhelpful. The paper does not argue directly that rational design methodology somehow supports “intelligent design”, but given Leisola’s creationist sympathies, this might be what he intended. And this is certainly what Bill Dembski is implying, going so far as to claim that it is “pro-ID article without the usual disclaimers…” But absent the glaringly illogical attempt to connect protein engineering with ID, there is no support for ID to be found anywhere in the paper. (In fact, the phrase “intelligent design” does not even appear in the article – how could it be a “pro-ID article without disclaimers” if ID never even gets mentioned?)

The only claim that might be relevant to the ID/evolution debate is in one small section titled “Obstacles in protein engineering” in which the authors argue that there is an “Overreliance on the Darwinian methodology”. But this argument is made very tepidly, and little if any support is provided for it. Leisola and Turunen are forced to conceded throughout the paper that Darwinian methods are not only highly successful, but are more successful than rational design approaches. They merely contend that as our knowledge of protein structure and function improves, rational design approaches will also improve. Well, yeah, that’s kind of obvious. If someday we obtain perfect knowledge of the relationship between protein sequence, structure, and function, then rational design methods will definitely be superior. How could they not? If you can make a precise prediction about which mutations will generate which functions, you can skip the messy high-throughput methods and just go straight to the desired result. It’s no secret that evolution is a slow and wasteful process requiring a lot of trial and error. That’s why life on Earth took billions of years to reach its present state; if the ID people were correct, one would imagine that the goals of the “designer” would have been reached instantaneously.

In the meantime however, directed evolutionary approaches are very powerful, and even rational design approaches are increasingly incorporating evolutionary methods. (This is one major weakness of the paper – rational design and evolutionary methods are presented as an either/or dichotomy, when in fact rational design approaches, particularly those derived from computational models, make extensive use of evolutionary theory.) Most importantly, directed evolution refutes one of the central tenets of ID argumentation, which is that the Darwinian mechanism — random mutation plus selection – cannot generate new “information”, protein functions, or whatever. We knew this was false long before the ID movement ever began. Now they’re reduced to arguing that just because directed evolution methods are less than perfect, or that researchers can design stuff directly, that this somehow supports ID. And of course there’s the annoying spectacle of pretending as if an ID advocate getting a paper of any kind published is some sort of coup. Dembski claims that “perhaps this is a sign of things to come.” Actually we’ve been seeing it for quite awhile now.