Context determines meaning. Miller's speculations about as-yet undiscovered indirect Darwinian pathways where a system evolves by also modifying its function is irrelevent to Behe's points concerning DIRECT Darwinian pathways. From that same exchange:
MB:
I said, I said that the function of the system is missing. I'm happy to admit that similar proteins can have other functions in the cell, but the system loses its function.
Cordially,
True enough.
MB: I said, I said that the function of the system is missing. I'm happy to admit that similar proteins can have other functions in the cell, but the system loses its function.
And the context was blood clotting.
Behe claims that all the 14 or so factors are required beforehand to create a blood clot, -- if any are missing the fuction fails (blood doesn't clot). That is "irreducibly complex" by his argument.
Miller points out that the Hagemann factor is absent in Cetaceans (Whales and dolphins), yet their blood clots just fine.
Thus blood clotting is not "irreducibly complex".