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Richard Dawkins in The Ancestor's Tale says the mystery isn't that there isn't enough time to evolve all the phenotypes we see around us, but that there is too much time to evolve all the phenotypes. IOW, he says it's a mystery why there aren't more species rather than how did all the species evolve in the time available.

It seems that most DNA changes are no longer present:
1. many changes do nothing or work negatively, so they fade away
2. most species have been terminated in mass extinction events
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