With the rise of the first universities, theology came more directly into contact with other forms of learning and scientific research. Although they insisted upon the organic link between theology and philosophy, Saint Albert the Great and Saint Thomas were the first to recognize the autonomy which philosophy and the sciences needed if they were to perform well in their respective fields of research. From the late Medieval period onwards, however, the legitimate distinction between the two forms of learning became more and more a fateful separation. As a result of the exaggerated rationalism of certain thinkers, positions grew more radical and there emerged eventually a philosophy which was separate from and absolutely independent of the contents of faith. Another of the many consequences of this separation was an ever deeper mistrust with regard to reason itself. In a spirit both sceptical and agnostic, some began to voice a general mistrust, which led some to focus more on faith and others to deny its rationality altogether.
In short, what for Patristic and Medieval thought was in both theory and practice a profound unity, producing knowledge capable of reaching the highest forms of speculation, was destroyed by systems which espoused the cause of rational knowledge sundered from faith and meant to take the place of faith.
The more influential of these radical positions are well known and high in profile, especially in the history of the West. It is not too much to claim that the development of a good part of modern philosophy has seen it move further and further away from Christian Revelation, to the point of setting itself quite explicitly in opposition. This process reached its apogee in the last century. Some representatives of idealism sought in various ways to transform faith and its contents, even the mystery of the Death and Resurrection of Jesus, into dialectical structures which could be grasped by reason. Opposed to this kind of thinking were various forms of atheistic humanism, expressed in philosophical terms, which regarded faith as alienating and damaging to the development of a full rationality. They did not hesitate to present themselves as new religions serving as a basis for projects which, on the political and social plane, gave rise to totalitarian systems which have been disastrous for humanity.
In the field of scientific research, a positivistic mentality took hold which not only abandoned the Christian vision of the world, but more especially rejected every appeal to a metaphysical or moral vision. It follows that certain scientists, lacking any ethical point of reference, are in danger of putting at the centre of their concerns something other than the human person and the entirety of the person’s life. Further still, some of these, sensing the opportunities of technological progress, seem to succumb not only to a market-based logic, but also to the temptation of a quasi-divine power over nature and even over the human being. — from Fides et Ratio (1998)