[I-ambush]

The natural sciences are derived from Aristotle via Thomas; the human soul, however, is both a part of and beyond the natural universe.

[Rockingham]

I am not so sure that the human soul is as much beyond the natural universe when fully understood as it may seem. The equations of quantum mechanics consistently yield extra dimensions, while modern cosmology finds that dark matter and dark energy are required to explain the functioning of the cosmos.

Plausibly, the soul and consciousness reside in extra dimensions and in dark matter and dark energy. It may well be that from our Creator's perspective, all of it, including our souls, is a working out of the natural universe as He made it.