Reacting to David Heddle's post (see my previous post), Rob commented that there was at best nothing to choose between the theist blind leap of faith regarding their presuppositions, and the atheist/naturalist blind leap of faith regarding theirs (namely that empirical observation will be a reliable guide to the universe).
In a sense, there is some mileage in this. I accept that it is the case that ultimately presuppositions are not provable, and indeed I've spent lots of time at least trying to get atheists to recognise that they have presuppositions as much as theists do.
And yet ....
I have quoted Schaeffer's essay on the difference between postmodern faith and Christian faith here. It is worth considering how this relates to science. I would argue that the atheist approach to science is effectively a postmodern leap. In effect, philosophically, they are saying, "I believe that the universe is rational, tractable and comprehensible," in the same way that a person lost in the fog on a mountain might say, "I believe that if I step off this ledge, I will drop onto another ledge a few feet below and there I'll be able to shelter for the night." The theist says, "I believe that the universe is rational, tractable and comprehensible, because it is the product of a creator who is able to express rationality and tractability. Furthermore, I believe in this creator because he has spoken." This isn't a "leap in the dark" in the same way - this is the acceptance of an external witness, one which the atheist claims doesn't exist.
How come the "leap in the dark" atheist approach to science is so effective? I would argue that it is because the atheists are "stepping off the ledge" following theists who have stepped off not with blind faith, but in confidence of the outcome, thanks to their theistic presuppositions. Many great feats of technology, engineering and philosophy were achieved in different cultures throughout human history. But as I have suggested before, modern science - which has incredible levels of abstraction, and has transformed the world in which we live - grew specifically out of the Reformation, where the scientists believed that it was possible to study the universe because God had made it comprehensible. They may have had kooky beliefs in many areas - but the key presupposition that underlay their beliefs concerning science was that the existence of a creator and sustainer God made the pursuit of knowledge about the universe reasonable.
Atheist scientists have continued to follow them onto the safety of the ledge below, even though they have forgotten what it was that led their antecedents to believe the ledge might be there.