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OF COURSE, there must be DIFFERENCES between various parts, between every tiny photon or even string must be DIFFERENCE because otherwise they would be "the same thing" and our universe wouldn't exist.
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I have always thought of the universe like an engine: An engine is very complex because it has many various parts, and some of those, in turn, consist of
their own parts. On one hand, if you remove even one part of the engine, you will not truly have an engine, because it will cease to function as one. On the other hand, if you throw the engine into a super hot furnace, you will achieve the ultimate physical 'unification' of the universe because all the parts will be melded into a pile of slag, so then you'll no longer have a functioning engine.
Same thing with a TOE: we need to strike a balance between keeping all of the aspects of the universe seperate while at the same time being able to see the collection of all of the universe's parts as a single working entity.