Augustine contra Darwin

In a 1996 talk entitled "Truth Cannot Contradict Truth," Pope John Paul II announced to the Pontifical Academy of Sciences that evolution does not contradict Christianity. In this talk, the point of human kind's separateness and likeness to God is emphasized.
Of course, innate in this line of thinking is an idea that humankind, though not necessarily coming from two beings in the Garden of Eden whose names were "Adam" and "Eve," is the idea that we descended from some origin divinely set apart by God.
This contradicts a lot of evolutionary theory that depicts the mutations that caused evolution to be random and the selection of traits to be natural. In this case, God has fore-ordained which traits would be passed down to the human species that would make us in His likeness and image.
Now, this kind of thinking does not sit very well with traditional Biblical thinking. Pope John Paul II emphasized that the evolution theories don't depict well the innate spiritual qualities of man nor do they talk about our being the end of God's creation.
So we begin to see where the two don't function very well together. With an Augustinian view of natural sin, how can this correspond in a human history that has no root in the Garden? If we descended from Cro-Magnon and Neanderthals, how is it that we are the only creations created in God's image and likeness?
Furthermore, we begin to see problems like what John Paull II mentions. How do Athanasius' and Anselm's views on the Word made Flesh correspond to a human kind that does not derive its humanity from God? How can Christ take on our sins and become one of us if all we are is a process of random mutations?
I offer no solutions to this problem. I do offer this, however: in the Muslim Empire from the tenth through the thirteenth centuries, science was never seen to contradict faith. If one thought they were in opposition, then it was clear to that person that either his scientific discovery was off, or his faith was not correct. In this case, it is clear that this applies to us. If God is the God of nature and the cosmos, than no scientific law or truth can contradict what God has made so. Thus, if evolution is the way that scientists say it is, then this does not disprove God, only what we think of God.