Kenneth Miller seems to assume that if a designer had anything to do with the origin of species, then we should see evidence in the fossil record that someone waved a magic wand.
As ENV readers may know, I wrote an article, "A Second Look at the Second Law," that was reviewed and accepted by Applied Mathematics Letters (AML) in 2011, then withdrawn at the last minute.
In my 2000 Mathematical Intelligencer article "A Mathematician's View of Evolution," I compared the development of the genetic code of life with the development of a computer program, such as my finite element code PDE2D.
If you want to show that evolution does not violate the second law, you cannot simply say, sure, evolution is astronomically improbable, but the Earth is an open system, so there is no problem.