Tuesday, January 17, 2006

On Pattern and Process

PZ Myers has provided an excellent summary of West-Eberhard's ideas on what evolutionary theory is currently lacking (RPM offered a population geneticist's perspective). This is a topic close to my own interests -- I too dream of an extended evolutionary synthesis, one integrating population genetics, development and phenotypic evolution. This is a major problem, which will likely occupy evolutionary biologists for decades, if not centuries, to come.

Here I would like to consider a follow up question: will current trends in evolutionary developmental biology (evo-devo) finally lead to the solution of the problems raised by West-Eberhard and others? I would like to put forward a controversial view. Although there has been spectacular progress in evo-devo, I believe that most of it will leave evolutionary theory relatively untouched. The problem is that most of current evo-devo, concentrates on what might be called pattern evo-devo (from an evolutionary perspective): the study of what the developmental mechanisms underlying a given trait are, and how these mechanisms have changed in evolution. This work has enriched our understanding of evolution immensely. However, I believe that an overhaul of evolutionary theory will require progress in the more difficult questions of process evo-devo: how do evolutionary forces, such as mutation, environmental change and natural selection, operate on developmental mechanisms, and, conversely, how does development interact with these forces to direct, bias and constrain phenotypic evolution? Many such questions have been well articulated by, among others, Gould, Arthur, Raff, West-Eberhard and the "developmental systems theorists", but progress in answering them has been slow. These questions are hard to tackle using present techniques of developmental genetics, molecular evolution and experimental evolution, but ultimately they will have to be faced if we want to usher in a "new and general theory of evolution", to borrow Gould's phrase.

Read on

Monday, January 02, 2006

On Wolfram and Dembski

Jeffrey Shallit has written an interesting post in his new blog comparing Dembski and Wolfram in their "never retract, never explain, never apologize" approach to science. I've been meaning to say something about Wolfram's New Kind of Science (NKS) for a while. It is true that Wolfram, like Dembski, does have a very high opinion of himself. For example, while Dembski had someone compare him to Newton, Wolfram compares himself to Newton. This makes reading NKS (the main text) a much more irritating experience than it ought to be -- and no, I didn't find Wolfram's explanation for his Nietzschean "tone" convincing.

However, Wolfram is no Dembski, even when it comes to evolutionary biology: I believe Wolfram's work to be much more interesting and substantive. I have read most of NKS carefully, as well as many reviews of it (I quite like Weinberg's), and I have never seen any criticism that is nearly as damaging as, say, Shallit and Elsberry's critique of Dembski (see, for example, pp. 13-17). Although Wolfram is not as interested in biology as he is in computation, mathematics or physics, I still found what he had to say on complexity very interesting in the context of biological complexity and, therefore, don't agree with Shallit's conclusion that: "if he did use a more formal definition -- let's say Kolmogorov complexity -- then his claims become incoherent, trivial, or wrong." Also, Wolfram's work, unlike Dembski's, has stimulated a fair amount of research in several areas of science -- whether it will all turn out to be as "New" as Wolfram so passionately believes remains to be seen, but it should not be dismissed.

What I find most disturbing about Wolfram is his suggestion that just because some of the simplest programs imaginable can produce complexity, therefore it will be helpful to model complex systems using these simple programs even when there is no reason to believe that there is any correspondence between the mechanics of the models and that of the actual processes involved. As a biologist I have generally found this "model in search of a question" approach (common in other physical scientists, by the way) very unproductive. I also don't agree with some of Wolfram's ideas on evolution, but I think he got more flack on that from my colleagues than he deserved. I'm actually working on something which is relevant to this discussion, so I'll come back to it at some point.

Read on

Sunday, January 01, 2006

Brave New Year

Apologies for the long silence! Has it really been over two months? Oh well, I should say something about that. Initially I had to work on a paper, and that took all my time in between teaching. Eventually it got into Nature, so that was time well spent. I'll post about it when it comes out, probably sometime next month. Then my laptop had to be repaired, so I did not have a computer to blog from home and at work I had to actually, well, "work". Then, I kept waiting for a good opportunity to get back into it, and... here I am. I guess procrastination doesn't end in graduate school. Sadly I won't be able write much over the next couple of weeks because I have to work on a grant application (talk of procrastination).

There have been some interesting developments in the favorite topics of this blog. First, Science judged recent developments in Evolution to be the most important scientific breakthrough of the year. So maybe it wasn't such a bad idea to dedicate my scientific life to it... Maybe that will help in selling Evolutionary Biology to the next cohort of students. Second, Judge Jones ruled! In so doing he handed the first major legal defeat to Intelligent Design Creationism, one that should have far-reaching implications. I'm still reading the decision (that grant proposal again...) but I can already see that it's a thing of beauty. Hopefully it will help to keep creationism out of science classes in other places. Curiously, perhaps as a result of the Jones decision, Dembski, the Stephen Wolfram of Intelligent Design Creationism has decided to stop blogging. I suppose that means I should keep at it to even things out a little in the struggle against the army of the night.

I'll leave you with two reading suggestions. First, Neal Stephenson's Cryptonomicon, one of the best scientific novels I have ever read. If you have an interest in the history of computer science, cryptography and the Second World War, you should read it. It's great fun as well... Second, I've spent large chunks of the last few reading another great novel: the Shadow of the Wind by Carlos Ruiz Zafon. From the Borgesian opening I was hooked. Enjoy!

Read on