Daniel Sulmasy, OFM MD PhD and a member of the new President’s Bioethics Commission discusses exactly what conscience is and is not … as well as proposing some boundaries for the mutual respect of conscience.
“Conscience thus arises from a fundamental commitment or intention to be moral … The acts of conscience, by contrast, are judgments. The judgments of conscience are judgments that what one has done or one is contemplating doing are in violation of this fundamental commitment to be moral. As such, conscience is the most fundamental of all moral duties—the duty to unite one’s powers of reason, emotion, and will into an integrated moral whole based upon one’s most fundamental moral principles and identity.”
Dr. Sulmasy discussed this in a talk (video) and radio interview.