In this post, I will discuss what the theory of evolution predicts with respect to a comparison of homologous exons and introns between species, and also show what those comparisons actually look like.
As a nod to BioLogos, Dr. Francis Collins discusses this same evidence in his essay "Faith and the Human Genome," which I would recommend to all interested readers on this site.
So what does evolution predict, and why? Two mechanisms that drive evolution are random mutation and natural selection. Random mutations will produce harmful mutations, and this is especially so in functional DNA. Mutations that make harmful changes to functional sequences in exons will be selected against (i.e. negative selection). But what about introns? Since the majority of introns lack function then harmful mutations are much less common in introns, so there are fewer mutations that are selected against.
When you have stronger negative selection in exons as compared to introns you will see fewer changes in exons as compared to introns. Therefore, when you compare genes between species you should see more conserved sequence in exons than in introns, the very opposite of what creationism predicts. Also, the farther back in time two species share a common ancestor the more time there has been for the exons and introns to diverge from one another. Therefore, the more evolutionary distance there is between the two species the less conserved the introns will be compared to the exons.
Let's look at a specific example, the human gene MMP9 that is shared between all vertebrates. Here is what the comparison looks like when using the UCSC genome browser (click on pic for larger version):
(if the picture isn't working, click here
. Hopefully the formatting carries over)
Going from top to bottom, the top line with the blocks and dashed lines is the gene. The blocks represent the exons and the dashed lines between the blocks are the introns. The next line down with the spiky graph are areas of sequence conservation across 100 different and diverse vertebrate genomes. As you can see, the conserved sequences line up with the exons, exactly what we would expect from evolution and not what is predicted by creationism.
The next section down is the comparison between the human gene and specific vertebrate species with increased evolutionary distance as you go down the list. The closest relative to humans on the list is the rhesus monkey, and most of the sequence is conserved across the gene, including the introns. However, a closer examination would demonstrate that there is still more conserved DNA in the exons. As you move down the list from mammals to frogs to jawed fish and finally to jawless fish (lamprey) you see that you lose conserved sequence in the introns but keep conserved sequence in the introns. You see divergence of exons and introns with evolutionary distance. Again, this is exactly what the theory of evolution predicts, and the opposite of what creationism predicts.
This evidence is found throughout the human genome and throughout the eukaryote kingdom. Dr. Francis Collins describes it thusly, in the aforementioned essay:
Eric Green at the Genome Institute has looked at this same region in many other species and, in fact, you can find this same CAPZA2 gene in everything from chimps down to zebra fishes and a lot of things in between (see Figure 4). Notice the pattern. The chimpanzee is almost 100% identical to the human, except the chimp has a deletion just before exon 2 that we do not have. Otherwise the match-up, as in most cases of human and chimp comparison, is about 98.5% to 99%. You can see that the baboon is starting to diverge. The cat and the dog and the cow all look a lot alike, and again if you look at the CAPZA2 exons, you will see that every one of those species has a nice conserved little segment there. But as you get further away to rats, mouse, chicken, two different kinds of pufferfish and then a zebra fish, about the only thing you see is the protein encoding regions, while the rest of the scattered noise goes away. Again, this is a very compelling kind of pattern in terms of what one would expect from evolution.--Dr. Francis Collins, "Faith and the Human Genome"
This is an example of why evolution is "assumed" to be true. When there is volumes and volumes of genetic evidence pointing to evolution, scientists tentatively accept it as true and use it as a foundation for further research. That is how science works.