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Sub Atomic Transmutation

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Shouldn't a lot of transmutation be at a sub atomic level? Because, depending on the composition of the thing being transmuted, and the composition of what it's being transmuted into, you'd have to change the number of protons and neutrons to do so. So wouldn't that give sub atomic level matter manipulation depending on what they transmute an object into?
 
Yes and no.

Yes in that logically one would have to be able to change the sub-atomic particles of a substance to change what kind of matter it is.

No in that most works of fiction do not give their characters this level of precision or display applications outside of transmutation.

In short, I'd say no to putting sub-atomic matter manipulation on every transmutation user's profile.
 
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