The problem of reality of atoms isboth a problem of philosophy and science. Unkniwn to many, famous physicists refused the reality of atoms in early 20th C.

But my issue here is other:is there another solution to incorporatungbthermidynamucs in the mechanical framework of description of the world that bypasses the need for the reality of atoms? Has someone done so?

If so, it means a direction science has take is largely a matter or reference to a particular solution of unification, not of truth

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