Scientists have noted for a long time that the Y chromosome has been shrinking for hundreds of millions of years. Its decline has to do with how it is copied each generation. Out of the 23 pairs of our chromosomes, 22 have the same structure, and as a result they swap some genes as they are put into sperm or egg cells. Y chromosomes do not, because their counterpart, the X, is almost completely incompatible. My Y chromosome is thus a nearly perfect clone of my father’s. Mutations can spread faster when genes are cloned than when they get mixed together during recombination. As a result, many pieces of the Y chromosome have disappeared over time, and many Y genes that once worked no longer do.

How can Carl write this? Or am I missing something? It sounds like something an ID supporter would write: "If there weren't ID the Y would self destruct - explain that!" Obviously, the new, smaller Y survived and thrived because it was superior to the old one. And the reason seems clear too: Genes on the Y don't get to enjoy sexual reproduction, therefore the less of them the better. If there is an equivalent gene on the X or elsewhere, chances are that it's superior, so the Y's gene should just get out of the way.

Actually, the major problem for studying gene expression changes is that it is done on arrays with probes based on human sequences. Now that we have the chimp genome, we can use this to igore array signals from probes that cover DNA where humans and chimps differ. Errors in the chimp sequence draft have little impact on this analysis.

thanks clint, i garbled it :)