I may be wrong in what fallacycop was trying to say, but if we were intelligently designed, why the heck would there be a non-functioning gene? And why would the creator make the break in the exact same point? There's no rhyme or reason then, no pattern that can be predicted. But, if evolution is true, which it is (scientifically true, that is), then it makes sense to say that chimps and us share an ancestor. And looking at this broken gene and making a cladistics chart with it leads to a similar chart as the one based off of other characteristics. Also, the broken gene isn't responsible for any phenotype. Again, you can't answer why the creator chose to make the exact same break in the exact same gene for two different species, but evolution has an answer to the problem.
Also, those however million base pairs that aren't found on the chimp genome, you have to remember, we've one (or is it two?) chromosomes more than them. And chromosomes have a huge number of genes (particularly ours, seeing as how they are so long).
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