The relationship between an individual's conscience and the authority of the magisterium is often easily confused and intentionally distorted.
Let's start with a definition: "Conscience is a judgment of reason whereby the human person recognizes the moral quality of a concrete act that he is going to perform, is in the process of performing, or has already completed. In all he says and does, man is obliged to follow faithfully what he knows to be just and right. It is by the judgment of his conscience that man perceives and recognizes the prescriptions of the divine law. . ."(CCC, no. 1778).
Let's start with a definition: "Conscience is a judgment of reason whereby the human person recognizes the moral quality of a concrete act that he is going to perform, is in the process of performing, or has already completed. In all he says and does, man is obliged to follow faithfully what he knows to be just and right. It is by the judgment of his conscience that man perceives and recognizes the prescriptions of the divine law. . ."(CCC, no. 1778).
Conscience "perceives and recognizes" moral truth. Contemporary Catholics often seem to believe that conscience is the ability to choose freely among available moral options. So long as I preface my choices with something like, "In good conscience, I believe. . .," I am safeguarded from error. This is false. Conscience is not the ability to magically turn an evil choice into a good choice. Conscience is what helps us to perceive the Good and recognize that Good in making moral choices.
When I walk into a bookstore, I perceive and recognize items that we call books. I do not walk into a bookstore and choose to perceive the books as squirrels and recognize them as squirrels. If I do this, I am in error. Announcing my erroneous judgment about the books with, "In good conscience, I perceive and recognize this collection of paper and cloth bound pages of printed material as squirrels," does not magically transform the books into squirrels.
Catholic teaching holds that the morality of human acts is as real as the books in a bookshop. Calling the intrinsically morally evil act of abortion "good" is the same error you make when you call a book a squirrel.* Conscience empowers you to perceive and recognize abortion as evil. If you do not perceive and recognize abortion as evil, then you are either ignorant and need to be instructed, or your conscience has been twisted into folly by sin and you need both instruction and confession.
The Church's role in conscience formation is to present the truth of the faith. Ideally, a Catholic will immediately perceive and recognize the truth and act accordingly. But because we have been mislead for a generation or two about the nature of conscience, many Catholics fail to perceive and recognize moral truth when they see it. Basically, we have been told for decades now that conscience makes truth, or that conscience assigns truth value to moral acts according to subjective, private standards of judgment. This is how we end up with pro-abortion Catholics, pro-same sex "marriage" Catholics, pro-torture Catholics, pro-women's "ordination" Catholics, ad. nau. These Catholics have falsely perceived and falsely recognized moral truth and misused "conscience" as a defense of their errors.
To repeat: conscience perceives and recognizes truth; it does NOT create truth.
Tom Krietzberg at Disputations has a very good post on how Aquinas' thoughts on conscience have been misunderstood and misused to push the Free Choice notion of conscience.
*Of course, the eternal consequences of these two errors are not the same.
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