An overall lack of order…
Knowledge is not properly ordered today: people tend to use a specific academic discipline to address questions that fall outside the scope of that discipline. This results both from academic specialization and from the lack of dialogue between different academic departments.
If a molecular biologist, for example, spends the majority of his time studying the mechanistic workings of a particular enzyme, it is understandable that he could think about some other academic question, such as what makes an animal alive, in similar mechanistic terms. It so happens, as we have seen, that it is not possible to define life using the methods of the empirical sciences; defining life requires metaphysics. Without a robust dialogue within an academic community, such as a university aimed at seeking universal knowledge, it is difficult for a molecular biologist or almost any academic to avoid overstepping the bounds of his field.
The general principle of the need to respect the boundaries of each academic discipline is true of all sciences, as John Henry Cardinal Newman eloquently articulates in his Idea of a University. He notes that a university, with all academic departments, is necessary to avoid any one discipline transgressing the bounds of its field to the detriment of knowledge that should be rightly considered in another field. He writes: “I observe, then, that, if you drop any science out of the circle of knowledge, you cannot keep its place vacant for it; that science is forgotten; the other sciences close up, or, in other words, they exceed their proper bounds, and intrude where they have no right. For instance, I suppose, if ethics were sent into banishment, its territory would soon disappear, under a treaty of partition, as it may be called, between law, political economy, and physiology… no science whatever, however comprehensive it may be, but will fall largely into error, if it be constituted the sole exponent of all things in heaven and earth, and that, for the simple reason that it is encroaching on territory not its own, and undertaking problems which it has no instruments to solve.” Newman goes on to further note that there is a hierarchy between the different sciences, with theology being the highest followed and supported by philosophy. Since philosophy is about broader questions, it has an organizing role relative to other sciences such as the empirical sciences, history, and economics. Epistemology is the branch of philosophy that especially deals with how we know.
In today’s academic landscape the empirical sciences tend to overstep their legitimate bounds. But deficiencies in philosophy are partly to blame. Empirical science has moved into the “foreign territory” of metaphysics partly because philosophy vacated the field. This encroachment has also resulted in the banishment of the humanities into the realm of subjective human experience, denying them access to the real, objective world. As such we have lost the ability to discuss humane or ethical matters in a constructive way in the public square.
In broad terms, realist metaphysics as a science began to be pushed aside as early as Duns Scotus, then more forcefully by Francis Bacon, Rene Descartes and David Hume. Etienne Gilson gives a compelling treatment of this in his book The Unity of the Philosophical Experience. He explains how philosophy has suffered by attempts to use methods foreign to philosophy to try to address philosophical questions: Abelard’s over-application of logic, William of Ockham’s empiricism, Descartes fascination with mathematics, and Kant’s reliance on Newtonian physics. Gilson shows how the rise of skepticism, the turn toward Cartesian idealism, its breakdown, and the eventual attempt to reject metaphysics entirely all result from failing to respect the proper methods of philosophy.
Throughout the ancient world and even after the medieval synthesis broke down in skepticism, people still basically assumed unity rather than a sharp division between mind and matter, subject and object. Many fifteenth and sixteenth century thinkers were uncertain whether the world could be known accurately by reason. The emphasis on knowing reality primarily through revelation and faith led to an emphasis on mysticism. The unity between faith and reason that so characterized the classical tradition and the thought of St. Thomas Aquinas had broken down. But in the absence of another system of thought the objective world, as much as it could be known, was still the raw material upon which a weakened reason reflected.
After Rene Descartes (1596-1650) things became more complicated. Descartes attempted to escape the prevailing skepticism of his time by rebuilding metaphysics on the basis of human thought, rather than on the objective world. Though there are elements of introspective thinking earlier, in such thinkers as St. Augustine and St. Anselm, Descartes’s project to reestablish metaphysics on the foundation of thought was entirely new. He claimed to have discovered in his famous cogito ergo sum (“I think therefore I am”) a new foundation for philosophy. Upon this foundation he attempted to establish, through his version of the ontological argument, the existence of God and finally even the existence of the world. In doing so, he changed how people viewed both the world and the human person. From a Cartesian perspective, the person is a thinking subject and the world is a mechanical system. It is not clear how these two realms are related. The mind is a knowing substance; the body is a meat machine. What sense can we make of the union of such a mind with such a body? A direct result of the rise of philosophical idealism is the emergence of the mind-body problem.
The mind-body problem is entirely a modern creation, and one that is completely foreign to realism. To a young child and to a realist there is not a sharp division between an individual thinking subject and the objective world around him. The need to forge a bridge between one’s mind and the outside world does not even make sense. A realist is at home in the world and can basically trust his five senses, his capacity to form mental images, and his intellect to accurately apprehend the way the world really is. As we have seen, by simple apprehension a person abstracts from what he senses of a thing’s accidents a mental image from which he intellectually knows its substance. Since the person’s spiritual soul is also the form of his body there is nothing schizophrenic about this. The human person, present as a human body, is a composite of form and matter just as any material thing is. Just as it makes no sense to say that the unity that is water is a mere combination of hydrogen particles with oxygen particles, so it makes no sense to say that a human person is two separate things, a soul and a body, somehow mechanically combined. When the human mind is related to matter in a hylemorphic union, as form to matter, there simply cannot emerge the problem that has come to be known as the mind-body problem.
As is particularly clear from subsequent developments, Descartes’ project failed. His followers took his assertions as starting points on the path to various forms of idealism that eventually led to an even worse skepticism than before. It was worse because it was further removed from the realist philosophy capable of understanding the real world. The legacy of Descartes was a shift to the human subject as the starting point for apprehending reality, a shift that has outlasted the idealism that spawned it.
 John Henry Cardinal Newman, The Idea of a University (near the start of discourse 4).
 In his Regensburg Address, Pope Benedict XVI refers to the loss of metaphysical thinking under the broad title of the dehellenization of Western culture, which he traces back to Duns Scotus.
 Etienne Gilson in The Unity of the Philosophical Experience explains both the skepticism of the preceding century and Descartes’ attempt to reach a new mathematical-like certitude upon which to build metaphysics. This is an excellent resource for someone interested in studying this further.