Let me add one more comment concerning Avise’s PNAS paper. In the last entry, I focused on his argument that introns counts as evidence against intelligent design. We saw the whole argument fails if we envision design working through evolution. But I want to you to notice something else. In the paragraph preceding the discussion of introns, Avise wrote:
Approximately 1% of all known genes in the human genome encode molecular products that our cells employ to build spliceosomes and conduct splicing operations on premRNA. All this rigmarole has some advantages (e.g., opportunities for alternative splicing during ontogeny and exon shuffling during evolution, both of which can generate functional protein diversity), but such benefits do not come without major fitness costs.
Note that Avise describes alternative splicing as something that confers “some advantage.” Some advantage. As if alternative splicing is just a minor factor in evolution.
Now let’s contrast this to the abstract from a paper by Stephanie Boue, Ivica Letunic, and Peer Bork (Alternative splicing and evolution. BioEssays 2003 25:1031–1034):
Alternative splicing is a critical post-transcriptional event leading to an increase in the transcriptome diversity. Recent bioinformatics studies revealed a high frequency of alternative splicing. Although the extent of AS conservation among mammals is still being discussed, it has been argued that major forms of alternatively spliced transcripts are much better conserved than minor forms.(1) It suggests that alternative splicing plays a major role in genome evolution allowing new exons to evolve with less constraint.
“A major role in genome evolution” sounds a tad more than “some advantage “ to me. In fact, consider the conclusion of Boue et al.: