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The concept of evolution is as close to a 'perfect' theory as you'll get - beautiful and simple, and impossible to 'prove' to non-believers who don't want to take entropy as a given, etc.
We can produce (micro-)evolution in laboratory conditions . . . If we could extend the time frame a few thousand years, I have no doubts that macroevolution would be seen as well.
As far as that goes, I'll fit my personal religious beliefs into the framework of the natural world, rather than the other way around - no "deus ex machina" for me - however, scientific observation is an analog, continuous process; remember that just a few hundred years ago we talked about humours and bloodletting as "medicine"
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