Here Lynch is getting near my solution: we justify science rather than faith as a way of finding out stuff not on the basis of first principles, but on the basis of which method actually gives us reliable information about the universe. And by "reliable," I mean "methods that help us make verified predictions that advance our understanding of the world and produce practical consequences that aren't possible with other methods". Take a disease like smallpox. It was once regarded as manifestations of God's will or displeasure. Indeed, inoculation was once opposed on religious grounds: that to immunize people was to thwart God's will. You can't cure smallpox with such an attitude, or by praying for its disappearance. The disease was cured by scientific methods—the invention and testing of inoculations—and completely eradicated on this planet by the use of epidemiological methods. Science gets us to the Moon; religion can do no such thing.
Scientific understanding advances with time; religious "ways of knowing," even by the admission of theologians, don't bring us any closer to the "truth" about God. We know not one iota more about the nature or character of God than we did in 1300, nor are we any closer to proving that a god exists! In what sense, then, has religious epistemology brought us any closer to truth?
---SPSmith
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