A Tradition's Evolution: Is Darwin Kosher? - Wall Street Journal http://online.wsj.com/article/SB118308869790152666.html?mod=todays_us_weekend_journal
In a recent discussion with some of my chevra , we concluded that TRUE science and TRUE religion - since all of the above emanate from the same God - cannot be in any conflict.
However, in the human realm, we don't really understand the ultimate truths of science yet, as we probably do not really understand Torah or God - except on a superficial level. One day, there will live a Rambam and an Einstein all wrapped up in the same person who will get to the bottom of both realms. He will discover that when you really comprehend both Torah and science, their only conflict is semantic.
I believe it was R. Sa'adya Gaon who first posited that mitzvoth will gradually become more and more rational over time, and we will then grasp their meaning.
Here is an example: Most meforshim interpret "Taninim Gedolim" as sea monsters or whales... This is loosely based on RSR Hirsch on Parshat Vo'eira. He asserts, basing himself on the Haftorah, that we can interpret "Tanim" as crocodile and "Taninim g'dolim" as great lizards - Dinosaurs. A little bit of archaeology, some flexlible etymology, and you can point to dinosaurs within the Torah.
What is definitively true of the Torah well before Darwin is that it describes a creation proceeding from the simple and progressing to the complex. Thus we see the confluence of Torah and Mada as an evolving process. - pun most intended -