Saturday, June 16, 2007

Junk DNA

Junk DNA is the term given to long segments of DNA that scientists had assumed for many years simply had no function. It was believed to be vestigial, like an appendix, or the result of duplication of genetic material that subsequent mutations rendered inoperative.

At the same time intelligent design theorists predicted that it would one day be shown that junk DNA wasn't junk at all but rather had some function in the organism. This was a clear case of a prediction that could be verified and would lay to rest the claims of critics that ID can't be empirically tested.

Now it turns out that the predictions have indeed been verified. Junk DNA does appear to be operative during early development.

Darwinians are now retroactively asserting that this is to be expected as a result of natural selection, but the point is that ID theorists had been predicting this all along, whereas the Darwinians, including Ken Miller and Richard Dawkins, were saying the opposite.

There's a story on this at Wired which, despite its annoying tics (the author insists on calling Michael Behe a creationist), gives a good overview of recent developments in this matter.

The folks at Uncommon Descent are indulging themselves in a little understandable gloating.


Waving the Wand

Newsweek's Sharon Begley pens an article which includes some lamentably uninformed criticism of the concept of Irreducible Complexity. She writes, for instance, that:

The intelligent design camp also argues that some biological structures are just too darn sophisticated to have evolved through random mutation and natural selection. They must therefore have been designed by an intelligent agent. In particular, since complex structures have lots of components, how could the components have been just hanging around for eons waiting for the final component to emerge? Think of it this way: if you don't already have all the other components of a mousetrap, why would you keep a spring around? A spring is only useful if you also have the base, the bar and the rest. This is the argument called "irreducible complexity," and it has proved very persuasive to the public.

Which brings us to the latest discovery in evolution: DNA needed to make synapses, the sophisticated junctions between neurons, in none other than the lowly sea sponge. Considered among the most primitive and ancient of all animals, sea sponges have no nervous system (or internal organs of any kind, for that matter), notes Todd Oakley, assistant professor in the Department of Ecology, Evolution and Marine Biology at the University of California, Santa Barbara. But, he adds, they "have most of the genetic components of synapses."

He, Oakley and the rest of the team listed all the genes known to be operative in synapses in the human nervous system. They then examined the sponge genome. "That was when the surprise hit," said Kosik. "We found a lot of genes to make a nervous system present in the sponge."

What were genes for synapses doing in a sponge, which has no neurons and therefore no synapses? This is where the irreducible-complexity crowd makes a fatal error: they assume that whatever the function of a biological component (gene, protein, biochemical pathway . . . ) today must have been its function in the past. Maybe you noticed that my mouse trap example above wasn't very persuasive; even without a base and a bar, a spring can be a useful little device. So it goes with biological systems. For instance, of the 42 proteins known to make up the bacterial flagellum, 40 have been found to serve as ion channels or something else in bacteria. It is therefore perfectly plausible that they really were hanging around-serving some function that would have allowed evolution and natural selection to keep them around generation after generation-until they all got together and formed a flagellum.

This is called the wave of the wand method of scientific explanation. According to Begley all these proteins just happened to get together to make a flagellum, as if the fairy godmother waved her wand and magic happened. Begley omits mention, however, of the incredible obstacles the magic wand has to overcome in order for the proteins to find themselves located in just the right place, at just the right time, with just the right partner proteins with which to bind. She also neglects to tell us where the genetic plan came from which synchronizes the arrangement of these molecules in the flagellum, where the enzymes necessary for carrying the proteins to the assembly point came from, and what mechanism coordinated it all and how did it arise.

These and many more puzzles are supposed to be explained by just pointing out that some of the proteins found in a flagellum are also found elsewhere in the cell. It's like arguing that the construction of a jet plane in California can be explained in purely mechanistic terms without reference to any intelligent input by noting that many of the parts needed for the plane already exist and can be found in warehouses scattered around the state.

To watch a video of a flagellum being assembled and to get some idea of what Begley is leaving out when she says that the proteins just got together and assembled a flagellum, go here and click on movie #5. Note the timing necessary for the assembly and how the end cap protein constantly adjusts its shape to allow flagellar proteins to take their proper place.

I know incredulity is not an argument, but nevertheless - that such a system evolved by blind, random mutations of genes that established the production and placement of the proteins, the timing of their insertion into the developing flagellum, the precision of the amino acid sequence that allows the protein to take on precisely the correct shape and function, all strikes me as literally incredible. But perhaps I just lack imagination.

Begley continues:

So it seems to be with the genes for synapses. The sea sponge did not use them for their current purpose, but that doesn't mean the genes had no use. "We found this mysterious unknown structure in the sponge, and it is clear that evolution was able to take this entire structure and, with small modifications, direct its use toward a new function," said Kosik. "Evolution can take these 'off the shelf' components and put them together in new and interesting ways."

Sure. Just like parts scattered in warehouses around California, given enough time and enough tornados, floods, and other prodigies of nature to move them around, will eventually produce a fully assembled, fully functional fighter jet. People like Begley can keep waving the wand, but it just doesn't seem to a lot of us to have much magic left in it.