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Add to this the fact that, frankly, science still doesn't have a decent grasp on how genetics actually works. There are many open questions, and what they have learned in recent years is that there's a hell of a lot more to how DNA operates than the simple idea that one gene controls one specific thing. "Junk" DNA may not be junk at all.
Tom, you gotta read Richard Dawkins' latest, and perhaps greatest, "The Ancestor's Tale". What is known will spin your head around about 720 degrees, particularly the new taxonomies (note the plural) of life based on DNA analysis. In the modern view, there are a couple of dozen kingdoms of life, not the three we were taught in school. And guess which species alive today is closest relative to the whale...I tell ya, the latest understandings are absolutely mind-blowing.