In Darwin's time all of biology was a black box: not only the cell, or the eye, or digestion, or immunity, but every biological structure and function because, ultimately, no one could explain how biological processes occurred.
The question is: exactly how did life get here? Was it by natural selection and random mutation or was it by something else? Everybody - even Richard Dawkins - sees design in biology. You see this design when you see co-ordinated parts coming together to perform a function - like in a hand. And so it's the appearance of design that everybody's trying to explain. So that if Darwin's theory doesn't explain it we're left with no other explanation than maybe it really was designed. That's essentially the design argument.
Biology has progressed tremendously due to the model that Darwin put forth. But the black boxes Darwin accepted are now being opened, and our view of the world is again being shaken.
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