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The very problem with metaphysics is, as you say, that it is self-proving, which means that its coherence entirely depends on the language used to portray it -- because it doesn't consist in anything else. And this is what the modern philosophers have argued -- that pure metaphysical arguments don't have any verifiable information content whatsoever, and from what I understand if you use symbolic logic instead of words you take the air out of metaphysics. Videcorspoon can elaborate on this, perhaps.
I don't think the example you've given is actually metaphysical at all. You've described two completely physical phenomena -- one is the orderliness of someone's room, and the other is the physical and biological process of his meditation. Say you demonstrate that this phenomenon is true in a huge study, thus making it an extremely scientifically sound association (as opposed to a single individual's experience). The only part about this that is available to metaphysical speculation is the explanation for this association -- but that's only because your study has not yet answered why and how (mechanistically) this meditation changes behavior. But that's certainly open to scientific inquiry as well -- for instance it might be easily proved that meditation is associated with a higher stress response to more trivial messes, and this might be measurable and quantifiable.
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