But the more interesting puzzle is the second puzzle. Aquinas holds that it is wrong to violate conscience; he mentions in this context Romans 14:23, in which Paul says that everything that is not of faith is of sin. David then asks:
Remember that for Aquinas, conscience is an “act” arising out of the “disposition,” synderesis (ST I, Q 79, A. 13). This disposition is an universal ordering of all humans to the good. According to the glossary in LMP, conscience is “the dictate of reason that one should or should not do something.”
If that is true, then how can Aquinas equate an evil “conscience” with the Pauline phrase “everything not of faith?” If a human can know the dictate of reason, “I ought not commit suicide”, through reason–apart from faith–then how can an evil conscience be the absence of faith? The dictate of conscience (according to the Aquinas) does not arise either within faith or apart from faith. It arises from practical reason, determined by synderesis, the disposition (again quoting the glossary of LMP) that all humans “should seek the good proper to their human nature….” But the absence or presence of faith does not bear on this issue. I do not see how Aquinas can properly cite the apostolic text as authority for his claim.
In other words, “conscience” in Paul (and the entire New Testament canon) is a state of moral knowledge known in and through the living (in technical terms, “existential”) reality of a specific community that enacts and expresses a new experience of life and moral reasoning. Aquinas reappropriates this concept and redefines it as a state of moral knowledge known by, and accessible to all humans, apart from that new life.
But a little thought shows that this puzzle is unknotted easily enough. Just as reason, although universal, can be examined specifically in a Christian context, so can universal moral dispositions. That everyone has something in the way of conscience doesn't mean that it is formed in the same way for everyone. And in the Summa Theologiae, which David is considering, Aquinas is not considering conscience "apart from that new life"; the ST is a work of sacred doctrine, not ethical philosophy. Philosophy is a handmaid here, a queen attending on an empress. Thus he sets up the general framework solely in order to see how it works in the context of Christian life. Thus it is false in context to say that the absence or presence of faith has no bearing on the issue of these universal capacities of the mind; faith is not irrelevant to moral life, and the ST throughout presupposes faith. It explicitly says this, right at the beginning, in fact.
The point is actually generally important for interpreting much of Aquinas's moral theory in the Summa. The long, detailed discussion of virtue in the ST is a discussion of infused virtue. What reason says about acquired virtue comes up quite a bit, of course; but it comes up solely as a starting-point for understanding its infused and charity-formed counterpart. The Summa moves from God ruling over us to God working in us to God being with us; it is, as it says, a work of Christian theology.