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In episode 62 of Brotherhood series, when Father's stone was nearly depleted, he started to search desperately for a new one. When he saw Edward Elric pinned down, his expression suddenly changed and he started walking towards him, as if he had found one.

If they are part human, part Philosopher's Stone, isn't it kinda ironic that what they had been looking for was inside them all along?

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There are a few different things to address here.

First off, Edward and Alphonse are fully human. This is actually addressed when Alphonse first finds out about his dad's origins. Essentially, he contains a philosopher's stone within himself, but he is still biologically human.

"My soul is fused with the philosopher's stone, but the actual core that holds me together is myself, a human being."
Click to enlarge.

Second, remember that all humans are philosopher's stones. Edward (kind of) states this in episode 41, and says that his life energy is identical to that of a philosopher's stone, and he's right. All humans are simply philosopher's stones containing exactly one soul.

"Right now, I'm nothing more than a philosopher's stone made out of one soul!"

Third, it is because of the above points that Father approached Edward. It wasn't because he'd get a lot of energy, like from a true, isolated stone (such as one of Kimblee's), but rather because Edward had one soul of energy within him. Father was desperate.

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