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Thought can only be abstract. Our experience does not exist in the real world, but rather as a simulation of stimuli. Our identities, or egos, do not exist in anything other than a multimedia novel of either mind or machine.
I mean, everything that exists is "real", even a program running on a computer. It is a process caused by atoms. Everything can be reduced to math/physics.
But sure, it is important to be able to separate the different abstraction layers. Thoughts and experiences exist on a different abstraction layer than atoms, even the perspective of atoms (or quarks) is perfectly valid and correctly describes all existence.