Saturday, May 26, 2007

Snakes and ladders

PZ Myers has just written an excellent essay on the evolution of complexity. He makes several interesting points with which I agree. For example, human scientists have long assumed that we (humans) are the most complex organisms in the biosphere. They used to think we had about 100,000 genes. (Kauffman was a bit out of date by 1995, but that number was kicking around. For example, I remember seeing it in the first edition of Jonathan Slack's From egg to embryo from 1983). In 2001, initial estimates from the draft sequence of the human genome put the number of protein-coding genes at 30,000-40,000. It has been shrinking ever since. By 2004, the estimates were down to 20,000-25,000. Of course, this is only the latest in a long series of slights to human delusions of grandeur: from being at the center of the Universe to being in one of many, many, many planets; from being the pinnacle of creation to being genealogically related to every organism on the planet (actually, I find this rather cool, and not demeaning at all, but that's just me...), from being a complexity champion among the metazoa, to being perilously close in genomic complexity to the nematode C. elegans, which has about 19,000 genes and 959 somatic cells.

Like PZ Myers (and Larry Moran), I find most of the current hypotheses that try to do away with the so called genomic paradoxes, unconvincing, bordering on wishful thinking. An understanding of the nearly neutral theory of molecular evolution should makes us intensely skeptical of any claims to deep significance in the non-coding portions of genomes of species with low effective population sizes like us (what counts is the historical population size during our evolution over the last few million years, not the explosion over the last few centuries, in case you're wondering). Just because our genome is crawling with small RNAs (I'll assume it, even though the estimates are not terribly reliable at the moment), and some of them can regulate gene expression, doesn't mean that these RNAs are doing anything terribly important or in any way related to our supposed complexity. Of course, this is no reason to stop looking -- don't take my word for it. I'm just giving you an evolutionary biologist's hunch as to the outcome of this flurry of activity.

Where I have to disagree with PZ (and with others before him, such as SJ Gould in Full House) is in dismissing the problem of increases in complexity.

[Continue reading below the fold.]

On this I'm with Wallace Arthur in his latest book Creatures of Accident (his defense of agnosticism is less persuasive). Just because increases in complexity are not the dominant theme in the evolution of life (more snakes and ladders, than just ladders), does not mean that we should ignore this important feature of the pattern. The fact remains that from simple molecules we got simple prokaryotic cells, then more complex eukaryotic cells, then simple multicellular organisms, ..., then exquisitely complex multicellular creatures like cephalopods, crocodiles and chimpanzees. There are even well-documented cases of generalized increases in complexity across whole groups of animals, such as in the complexity of septal sutures in ammonoids (cephalopods again). Finding out what evolutionary forces could possible drive such increases in complexity is a central problem in biology, and one that has not been adequately addressed yet. Sure, gene duplications are part of the story. But what are the selective pressures on complexity? What are the distributions of mutational effects on complexity?

I have actually been working on the evolution of complexity and have just written a theoretical paper on it. I've been promising to say something about it. Now, that I've started talking about it, I might just get around to doing so.