For the majority of Western intellectual history, the universe was a single place. It had a center and a periphery, and these locations had real physical significance (notice that geocentrism and heliocentrism are not really contrary theories: the theory of geocentrism involves the whole universe, whereas heliocentrism, at least as we understand it, is a theory about a vanishingly small part of the universe.) The physical events at the center were under the control of the events at the periphery, and this order of causality arose from a real division in the order of being, since the causes at the periphery were immutable and changeless whereas the events at the center were corruptible. This difference in being required a real difference in the physical structure of the things in different places, and the places themselves had a natural order among themselves. Notice the picture: the universe is a single unified place, where all the parts have degrees of being and orders of causality, and all that we can go out at night and look out and up at is an organism whose action we can trace back to a single action with a single time.
But all that’s false. So now what?
The unity in the universe is no longer a causal unity of all the parts working in concert. There might be a gravitational pull of everything on everything, but it doesn’t give rise to a gravitational system, that is, to a hierarchy of gravitational masses. The gravitational center of the universe is not the sort of center that gives rise to a hierarchy – it appears to be an accidental result of the mere sum of gravitational attractions – and similar considerations apply to all the forces of nature. Whereas Aristotle could assign a meaningful physical position and causal power to any celestial body, we are unable to see any compelling reason why any one of them should be there as opposed to in any other random place. It doesn’t even make sense for us to assign a position to the stars, as though the place we see them at is a part of any order to the whole.
The upshot of all this is that we are able to raise the question of whether all this stuff is a universe at all. If by “the universe” you mean “all the physical stuff there is” then there is certainly a universe, but it doesn’t appear to be anything beyond an entity we make by fiat. One could just as well assign a name to “all the cultures there are”, but to name such a thing doesn’t make for a single natural entity, even if we can find some common features among all of them or give some narrative of how one came from another in an historical progression. From where we stand now, it appears that “all physical stuff” is like “all governments”: neither forms a concrete unity outside of thought, even though we can find some common features among all of them (that all physical stuff arose from one big bang does not make it one single organism). Aristotle’s idea that the unity of the pure act is reflected in the universe by making the universe a single unified act is, for the moment, a failed hypothesis. The truer hypothesis appears to be the Parmenidean and Platonic idea that the universe is a more homogeneous and undifferentiated stream of becoming which we understand only according to its phenomenal character and not according to universal relation of in the things themselves. There is still involve some real relation of the universe to the unchangeable, but it is the unchangeability of thought as such, whether the thought of a human mind, or of that which transcends the whole of this order of becoming. As a consequence, metaphysics or wisdom becomes more sharply cut off from science, as everyone appears to believe it must be.