In a comment on my post about the book Compositional Evolution, William Bradford pointed out that the compositional operators which are supposed to enable greater evolutionary change are themselves embedded in and dependent upon complex cellular contexts. So, by themselves, they do not explain the problem of biological complexity.

This immediately suggests a few research problems. It seems that the problem of the origin of compositional variation methods must be described by a gradualist framework (unless we assume that the first reproducing organisms contained them, which seems unlikely). So, characterizations of these mechanisms as strongly interdependent and irreducibly complex would provide a greater problem to evolution than evolution with them does. This would be hard to do, because such mechanisms aren't easy to separate from the function of the rest of the cell. But then, perhaps that strengthens the point.

From a more formal perspective, can random-mutation genetic algorithms evolve different modes of variation which include compositional mechanisms? My hunch is that they can, but only by specifying the target ahead of time, that is front-loading the algorithm with everything it needs to know to reach the desired goal. Such a teleological search is not biologically plausible under Darwinian assumptions.

Just stumbled upon an interesting link: Arizona State University's Biodesign Institute (HT: CEH). Here is an overview of this institute:

Research in the Institute shares a common starting point. It explores the remarkable structure and function of living systems, which have been honed by thousands of years of evolution and natural selection. If man could duplicate what nature does routinely, all aspects of society would be transformed...

A major critique of Dembski's use of the No Free Lunch (NFL) theorems has centered around new results that they don't hold under coevolution – that is, when you factor in multiple agents competing against each other. This was based on new, then-unpublished results by Wolpert, who derived the original NFL theorems. Many people (including Wolpert himself) claimed that Dembski's use of the NFL theorems was flawed because coevolution could indeed provide a free lunch. Dembski wrote a short note claiming that coevolution could do nothing of the sort. That is where the matter stood the last time I checked.

Well, Wolpert's coevolution results were published in December '05. Guess what appears in the abstract? This sentence:

However, in the typical coevolutionary scenarios encountered in biology, where there is no champion, the NFL theorems still hold.

So, what happened to this particular critique of Dembski's work? It died a quite death, apparently. I'm almost disapointed. The coevolution objection I was so interested in examining turned out to be a big, overhyped non-event. It's hard to know exactly why. Maybe Wolpert discovered that his earlier comments were incorrect for the functions Dembski was interested in? Maybe Dembski's response convinced him he had been wrong? At any rate, it seems likely that his correspondence with Dembski is partly responsible for the disclaimer in his abstract.

Incidentally, Wolpert isn't as critical of Dembski as Darwinists want you to think. His oft-cited jello critique takes Dembski to task for a lack of mathematical precision, but not for his use of the NFL theorems.

HT: Uncommon Descent

I'm reading through a new book, Compositional Evolution by Richard Watson, and it is really interesting. Watson's thesis is that certain evolutionary methods of variation (sexual recombination, lateral gene transfer, symbiotic encapsulation, etc.) are fundamentally distinct in an algorithmic sense from the traditional gradualist framework (in which beneficial mutations are accumulated in a linear fashion). Gradualism operates as a hill-climbing search strategy, and is therefore prone to get stuck in local optima. Compositional mechanisms, on the other hand, are apparently able to escape them (in systems with a semi-modular relationship among their variables) by combining pre-adapted genetic data from two distinct lineages.

Watson is a computer scientist, and examines evolution from an algorithmic perspective. The admission and proof of the inability of gradualism to evolve systems with strong dependencies among its variables is refreshingly frank. He presents a substitute mechanism, of course, so the book is not supportive of ID. Still, it helps formalize and highlight the issues involved, in a way that makes them easier to talk about. Computational Evolution is definitely worth a read if you're interested in looking at evolution from an algorithmic perspective – especially if you'd like to critically evaluate the power of evolutionary search strategies.

Gil has an interesting post over at Uncommon Descent about evolving a simple "Hello World" c program. The idea, as he presents it, is to try evolving the simplest functional c program by randomly assembling the non-whitespace letters required. Of course this is impossible, you don't have to try it to know the universe will experience heat death before such a random search succeeds.

PvM's criticism at the Pandas Thumb, which cites a genetic algorithm (GA) that evolves software, misses Gil's point. I don't know the details of the GA involved, but I am sure that it either starts with a functioning piece of software or assigns positive fitness values to non-functional source code. Gil's point, though, was that the simplest functional (i.e. "selectable") c program is already highly specified. In other words, Gil was posing an origin-of-life analogy to evolution. Responding with a paper that shows what can evolve if you design the cost function with a pre-specified target in mind and start with replicating, functional pieces is an exercise in irrelevance.

All the same, I didn't find Gil's analogy very interesting. The primary biological question is not "did the first reproducing organism arise through inconceivable good luck?", but "do simpler intermediates exist which improve the odds?" This is the source of the disconnect between Gil and PvM. I also don't find origin-of-life arguments all that interesting because, well, they don't seem sporting. Demanding that evolutionists explain how life could have arisen in enough detail to prove that its emergence is reasonably probable is too easy; it doesn't give Darwinists a sporting chance.

I do, however, like the idea of comparing biological evolution with some sort of genetic algorithm for program evolution. Cells can be thought of as computers in a lot of ways. In fact, a few months ago there was a Nature article about the similarities and differences between computers and cells. The gist was that the computing modules aren't as distinct in the cell, but they are definitely there.

There would be a lot of details to work out, but I think it could be an interesting idea (I am, of course, almost certainly ignoring reams of prior work :-). Ultimately, though, the biological relevance of these models is going to be the controversial point. What criteria must be met for theoretical results to count as evidence for or against evolution?

ResearchID, a wiki devoted to intelligent design, has officially opened today.

In this article, Francis Collins, the director of the US National Human Genome Research Institute, makes this statement:

“When you have for the first time in front of you this 3.1 billion-letter instruction book that conveys all kinds of information and all kinds of mystery about humankind, you can’t survey that going through page after page without a sense of awe. I can’t help but look at those pages and have a vague sense that this is giving me a glimpse of God’s mind.”

The next question is asking whether this 3.1 billion-letter instruction book could have been produced by a blind stochastic evolutionary process or whether some intelligent input was needed to produce such a book.

This blog has been quiet for the past couple of weeks due to finals. But now we are done! To get back on track, here are some interesting blog links:

• At ID the Future, Paul Nelson provides an extended discussion of the origin of RNA (also see Wedge's colloquium notes).
• Pro-evolution Panda's Thumb discusses the origin of chirality and provides a link to a homochirality paper that I wrote a couple of years ago.