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Metaphysics' own branch ontology concerns the determination simply of what exists—the establishment of categories of being—whereas metaphysics otherwise concerns the nature of and relations among the things that exist.
The metaphysical presumption or interpretation that a reality exists independently of one's mind and yet can be known is realism. The metaphysical presumption or interpretation that no mind-independent reality exists or can be known is idealism.
In the West, metaphysics is usually traced to the natural philosophers in ancient Greece, where Aristotle systematized a metaphysical description of nature equivalent to today's theoretical science. Although by the 4th century CE in Alexandria, Egypt, alchemy was starting its transformation into chemistry, the conventional view is that alchemy was steeped in mysticism and that chemistry did not quite became what we would call science until it was entering, and especially during and after, the 19th century.
In the early 17th century, Galileo introduced to physics his experimentations with earthly objects, the dawn of empirical science in Western Europe. Galilean laws of motion led to the overthrow of Aristotle's ideas, a revolution more or less completed by the wide acceptance of Cartesian physics, built upon Copernican and Galilean mechanics.
Newtonian physics rapidly replaced Cartesian physics, although Isaac Newton, like others that we now call scientists, was known as a natural philosopher. In the 1830s, Auguste Comte explicated positivism, the first modern philosophy of science, seeking science's divorce not only from religion but also from metaphysics.
In 1847, Hermann von Helmholtz's paper "On the conservation of energy", stating the first law of thermodynamics, sought to reduce physiology to physics. In 1859, Darwin posed an explanation of evolution of species that appeared both plausible and compatible with physical theory.
By the 1860s, the term science as having a meaning distinct from philosophy entered the dictionary. Today the term metaphysics usually refers to discussion of aspects of reality which are beyond physics. Particularly among those seeking to be scientific, the term metaphysics can be pejorative to varying degrees. Philosophers of science recognize, however, that science is impossible without metaphysics. At the very least, before beginning empirical investigation, one requires an ontology to establish—or presume—categories to even sort observations into.
- Hayek FA, "Scientism and the study of society", Economica, 1942 Aug;9(35):267-91