"At any rate, in Aquinas's thought, "nature" refers to human nature as it concretely exists, that is, as already integrated within the context of grace but as formally considered independently of what revelation teaches of that context. Viewed from that perspective, nature possesses a transcendent openness to grace and, some Thomists would claim, a desiderium naturale toward fulfillment in grace. Sixteenth-century theologians, however, tended to take the natura pura to be a full reality in its own right. On the basis of Aristotle's principle concerning the proportion of ends to means, they declared this nature incapable of any supernatural desire of God. Their theological dualism was complete but remained hidden behind a traditional terminology--"natural" and "supernatural--whose meaning it subverted. In Aquinas, the term supernatural does not refer to a new order of being added to nature but to the means for attaining the one final end for which the power of nature alone does not suffice. He calls God agens supernaturalis to distinguish the order of the Creator from that of creation(in which nature and grace appear together). Nature thereby becomes the effect of a supernatural agent." -Louis Dupre, Passage to Modernity

A nature that is a full reality in its own right is fertile ground for atheism, but Reformation-era thinkers struggled to reunite nature with God via theories of grace and justification. Some, like the Jansenists, tried to resolve the tension by holding that grace abolished nature. Others reinterpreted the old saying "grace perfects nature" in a radically dualistic fashion. Still, in post-medieval theories of nature, one major theme of modernity had been established.