Namely, that the evolutionary scientist is commited to his philosophy of life. He isn't any more objectively neutral in his presupositions than the theistic scientists you feel have given up. This is why we must consider this issue of evolutionism and creationism on a different level. That is why refereed journal are necessary and why evidence is needed, not just conjecture. Again, just because Behe can't figure out how modern pathways evolved doesn't mean they didn't.
Biochemistry is an interesting field in biology in general.
It rarely, if ever, mentions evolution - it is a whole different field. He state very clearly about his observations that this is a system which if reduced would fail to work, a system which only functions when all its constituent elements are working together. Gradualistic evolutionism has not even begun to offer a counter example for how this could possibly work through gradual and fortuitious means. Which doesn't mean that the molecular pathways he described didin't evolve from simpler precursors. It just means evolutionary biologists haven't been able to solve the problem - yet.