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For the record, it's not that philosopher's stones are some kinds of deus-ex machina that increase alchemic abilities to unimaginable levels because it's a philosopher's stone, it's that the raw energy contained within the stone serves as a magnifying agent of an existing transmutation.
Although the effiiciency of this process seems to vary from stone to stone (ie: the "fake/incomplete" stones used by Marcoh for healing and Cornello for his 'miracles' have a limited amount of usesbefore the stones break... when the energy is depleted). It seems that increasing the energy of the stone by increasing the amount of souls the stones are consisted of, like the case with Father, Hohenheim, and the homunculi, not only makes the stones have more uses overall, but also makes the process more efficient for each use, and in the case of hohenheim and Father, the depletion of their stones is infinitesimal, practically non-existant, except in the cases where they are used for regeneration
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