Posted by PvM on April 9, 2007 04:18 PM

On UcD, Dembski shows such a level of despair about the lack of fertility of the ID thesis that he is willing to claim anything which mentions the word Darwin(ism) and problem(atic) as ID friendly. While Dembski provides, as usual, little more than a snippet introduction and fails to formulate much of anything similar to what could be considered an argument, I argue that his claim that the paper is pro-ID is lacking in logic, supporting evidence and relevance.

It is helpful to remind ourselves of what Intelligent Design is, free from its rhetoric and equivocation: “The set theoretic complement of chance and regularity”. In other words, that which cannot be explained by chance and regularity is given the label ‘intelligent design’. In this case we notice that the authors are talking about science exploring a better understanding of proteins (in other words regularities) as well as Darwinian approaches to design proteins (regularity and chance).

Here’s a pro-ID article without the usual disclaimers (e.g., a ritualistic suck-up to Darwin, an obligatory sneer at ID). Perhaps this is a sign of things to come.

Protein engineering: opportunities and challenges
Matti Leisola and Ossi Turunen

Journal Applied Microbiology and Biotechnology

|Abstract: The extraordinary properties of natural proteins demonstrate that life-like protein engineering is both achievable and valuable. Rapid progress and impressive results have been made towards this goal using rational design and random techniques or a combination of both. However, we still do not have a general theory on how to specify a structure that is suited to a target function nor can we specify a sequence that folds to a target structure. There is also overreliance on the Darwinian blind search to obtain practical results. In the long run, random methods cannot replace insight in constructing life-like proteins. For the near future, however, in enzyme development, we need to rely on a combination of both.

Steve Reuland already defused much of the ‘claims’ made in a posting on PT called The Pro-ID Paper That Wasn’t. I intent to focus instead on the scientific irrelevance that is better known as “Intelligent Design”

I have already shown that the paper fails to have any relevance to the concept of Intelligent Design, so what about its weaker cousin “Teach the Controversy”, which is a thinly disguised attempt to introduce quote mining as ‘scientific evidence’, mostly against Darwinian theory? Again the paper fails to support this thesis, although it does make some arguments that indicate that Darwinian approaches may not be always successful when designing proteins. But that’s hardly a surprise.

Perhaps Dembski considers it ID friendly or pro-ID because at least one of the authors of the paper is a known creationist, strengthening the unavoidable link between religion and Intelligent design? Matti Leisola seems to be quite active in the creationist movement and was involved in inviting Paul Nelson and Richard von Sternberg to speak at the Helsinki University of Technology. And despite all this, we see little relevance to ID in this article. Is this the best ID has to offer I wonder? It should not come as a surprise that various people have argued convincingly that ID lacks scientific content, is scientifically vacuous and infertile?

Beyond the abstract

Since the paper is quite interesting, it may be helpful to venture beyond the abstract and see what the overall argument really is all about:

The argument is that there may be too much reliance on Darwinian approaches in designing new proteins, although the successes of Darwinian processes should not be ignored:

It is often said that random genetic methods to improve enzyme properties “rely on simple but powerful Darwinian principles of mutation and selection” (Johannes and Zhao 2006). We agree. It is also said that “every protein has become adapted by step-by-step improvement and refinement of its function over millions of years” (McLachlan 1987). The present theories, however, only partly explain the protein diversity, although a recent study (Poelwijk et al. 2007) shows that even the key-lock dilemma can be resolved by the Darwinian approach when the operation field for random search is within the same protein family, and the new key-lock pair closely resembles the original (ancestral).


In spite of the progress, we still do not have a general theory on how a sequence produces a specific structure and how a structure determines a function. Therefore, a blind Darwinian search within a known protein scaffold is often used to modify proteins. Unfortunately, blind searches have hard resource limits whereas insight has not. Therefore, in the long run, blind searches are of limited value in compensating our present ignorance. We still have a long way to go before we are able to design a suitable protein scaffold, position binding, and catalytic groups correctly into this scaffold and optimize the designed protein for life-like efficiency.

Indeed, the less ignorant we are, the less we have to depend on random search methods, and instead we can focus on more directed approaches. However, how this argument supports ID or can even be argued to be ID friendly is beyond me because ID depends on our ignorance to make its claims. Anytime science improves our understanding, Intelligent Design has lost another gap in which to hide.

Evolution’s intelligent designers

The article also touches on the concept of evolvability, another destroyer of ID gaps since evolvability itself can be shown to be under evolutionary control. In other words, while a simplistic argument based on the No Free Lunch theorems may argue that evolutionary mechanisms can never outperform a random search, reality is that evolvability makes the fitness landscape far from totally random. That evolution has been so successful can quickly be understood by understanding how evolutionary processes themselves can evolve.

Bloom et al. (2006) recently demonstrated that the stability of the protein scaffold improves its evolvability. In other words, when the stability of a protein scaffold is
increased, it may be possible to make mutations that create a truly novel property, which without increased stability would be too harmful for the protein. This approach can be very promising in finding novel enzymatic solutions that otherwise cannot be detected in the functional screening.

ID’s resident part-time ‘scientist’ and Friend Of Charles Darwin, Salvador Cordova (YEC) proudly proclaims the ‘good news’

Well by golly it seems there’s empirical evidence Darwinism doesn’t work so well in the very areas it hopes for vindication.

Amazing how abstract mining can lead to so much ignorance. What is even more amazing is how ID proponents seem to do anything but critically analyzing the arguments. To many of us that does not really come as a surprise.

As far as Dembski is concerned, he should really stick to what he knows best, or at last where his heart lies.