Science is, just as John Paul II said, silent on the issue of ultimate purpose, an issue that lies outside the realm of scientific inquiry. This means that biological evolution, correctly understood, does not make the claim of purposelessness. It does not address what Simpson called the "deeper problem," leaving that problem, quite properly, to the realm of faith.The rest of the argument is, in many ways, a boiled down version of the one he proposed in Finding Darwin's God: A Scientist's Search for Common Ground Between God and Evolution, where he argued that contingency is built into the system. He writes:
The neo-creationists of intelligent design, unlike Popes Benedict and John Paul, argue against evolution on every level, claiming that a "designer" has repeatedly intervened to directly produce the complex forms of living things. This view stands in sharp contradiction to the words of a 2004 International Theological Commission document cited by the Cardinal. In reality, this document carries a ringing endorsement of the "widely accepted scientific account" of life's emergence and evolution, describes the descent of all forms of life from a common ancestor as "virtually certain," and echoes John Paul II's observation of the "mounting support" for evolution from many fields of study.Miller is coming at this from the back side. It is a common misunderstanding that evolution is a random process. This is argued by Cardinal Schönborn (who he quotes in the post as calling evolution an “unguided, unplanned process of random variation and natural selection” ) as well as quite a few Discovery Institute fellows like David Klinghoffer and David Berlinski. Here is the problem: natural selection is measurable and it is directional. Therefore, if you want to argue that evolution is an “unguided, unplanned process,” than the forces that act on plants and animals in nature are unplanned and unguided as well. I doubt any Christian wants to go down that road theologically. This is exactly contrary to what Miller is suggesting. He argues that the events in nature are not random, as is generally conceived by philosophical naturalism, but are, instead, contingent in ways that we, perhaps, cannot understand.
More important, the same document makes a critical statement on how we should interpret scientific studies of the complexity of life: "whether the available data support inferences of design or chance cannot be settled by theology. But it is important to note that, according to the Catholic understanding of divine causality, true contingency in the created order is not incompatible with a purposeful divine providence."
The point he is making is that the scientific enterprise cannot examine this problem. It is a theological one, not a scientific one. It is not just that at a gross level we cannot use science to prove or disprove God's existence, but that even at a subatomic level, there is no certainty. We act on faith, and, sometimes, that has to be enough.