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space-time is not the root level of nature
According to the theory of relativity, no system can be isolated from space and time. Even if we were able to create a 'box' which was completely free of extraneous influences, it could not exist without being placed in some spatial or temporal context.
That said, it is true that space and time are not fundamental. Atoms do not persist in any meaningful sense in my view, but rather they exist as a kind of statistical average over the behavior of smaller particles; for example: protons and neutrons.
These subatomic particles, which are smaller than atoms, do not have a definite position or momentum. Their location and velocity can only be estimated by applying probabilistic rules to the behavior of larger aggregates of those particles.
As you go to smaller scales, the uncertainty in position and velocity increases. At some point, small enough particles will be moving so as to fill the entire universe with a fog of superpositioned probabilities.
This fog of probabilities is the universe at a fundamental level. It is an entity that does not exist in space or time, but rather exists as a statistical summary of all possible realities.
This statistical entity is the true nature of reality. Space and time are abstractions from this underlying fog of possibilities, which can be thought of as a kind of 'superpositioned probability wave'.