I waffle on the topic, to be honest, and it's why I'm not entirely comfortable with Catholic doctrine. :P

The reasoning behind "life begins at conception but it's okay to abort under x, y, and z conditions" would be, I think, that the existing life of the mother must take precedence over the life-yet-to-be of the embryo. Sure, the embryo is alive, but it can't exist independently of the mother, and thus the independent life must be put first.

I think. Anyone out there who actually holds to this position, please correct me if I've understood this wrong.