In science, a theory needs to explain the data. If ID/creationism is going to be considered a scientific theory, then it needs to explain the data.
The challenge for ID/creationists in this thread is to explain the divergence of exons and introns as measured by sequence comparisons between species.
Just for clarity, exons are segments of eukaryotic genes that are stitched together to make a mature mRNA molecule that is then translated into protein. The introns are clipped out of the immature RNA molecule and are not translated into protein. The vast majority of intron sequence lacks any known function.
Let's look at the human MMP9 gene. Homologues of the human gene can be found in almost all vertebrate genomes. When we compare the gene between vertebrate species and look for conserved sequence we find that there are strong signals of sequence conservation that line up with the exons.
click on image for larger format
If this image doesn't load, you may be able to load the page here at the UCSC genome browser.
The line with the boxes is the gene. The boxes represent the exons and the lines between the boxes are the introns. The spiky line below it is a measure of sequence conservation across the whole gene for 100 vertebrates ("Cons 100 Verts"). As you can see, there are strong signals of sequence conservation that line up with the exons.
How do ID/creationists explain this? Why is there more sequence conservation in the exons as compared to the introns?
The third group down is a comparison of the human sequence to specific species with the black bars representing sequence conservation. As we can see, there is a lot of similarity between human and rhesus introns, but as we get to frogs and fish towards the bottom of the group the only similarities we find are in the exons. How does ID/creationism explain this pattern where introns and exons diverge as we move through these species?