Could you please provide some examples of "broken" genes that humans and chimps share?
I believe it is called the GLO gene and it is not just that they are broken but that they are broken in the exact same way which is unique. The gene itself is what allows other mammals to synthesize their own absorbic acid (vitamin C). In primates if we don't eat enough vitamin C we get scurvy.
The gene is broken in primates due to a retro-viral insertion. A virus invates a gamete cell and tries to hijack the cell's copy mechanism like all good viruses do. In this case something terrible (for the virus) goes wrong and the cell copies just fine except that it includes some of the virus code in the cell's regular DNA. In this case the virus code interrupted the GLO gene causing the offspring to loose that feature. Since primates ate a lot of stuff that had Vitamin-C to begin with there was no survival disadvantage to this loss.
If God created humans, chimps, gorillas, etc seperatly then he also decided to break all of the GLO genes by sending the exact same virus to cause the exact same highly rare event to occur to each species in the exact same spot in the genome. Not a very good "design" for an ID to do when he simply could have designed those creatures without the GLO gene to begin with.
I may have butched that description so I hope someone who is not an armchair scientist will fix anything I said that was not quite on detail. The gist I believe is correct though.
How this fits into nested hierarchies is rather interesting. These type of genetic anomalies can be used as characteristics to construct a nested heirarchy. For example, there are other mammals that also have a broken GLO gene but they are broken in a different way. So we can take a number of these traits and create a different nested hierarchy then what we might create from other physical traits, genetic similarity, fossil progression, etc. Even though there is no reason for this particular hierarchy to match the other ones it does. Related creatures have similar quirky genetic sequences that make no sense in "design" because they are non-functional.
Also, instead of looking at cytochrome-C differences from the perspective of how different they are from some worm it makes more sense to look at the cross differences between all species. When we use this we get a measure of similarity between humans and chimps, humans and gorillas, humans and mice, humans and fish, etc. You use that difference to build a nested hierarchy and guess what it looks like. You got it, the same hierarchy we get from the physical characteristics, genetic similarity, fossil progression, sharing of non-functional sequences, etc.
There is no reason for a human and chimp to share the same cytochrome C unless they were related. This taking into account that it is slightly more different than other primates which is then slightly more different than other mammals, etc. There is an impossibly huge number of ways to make a functional cytochrome C and no reason a designer had to assign the sequences to animals in a way that exactly mimics common decent.
Of course, biblical creationists are committed to belief in God's written Word, the Bible, which forbids bearing false witness; --AIG (lest they forget)
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