The simplest answer to the mystery of Phi can be summed up by something Prot said in K-Pax. He said that species on a given planet take the form that most effeciently uses the resources available. Therefore, he resembled a human on Earth so as to most effeciently take in oxygen, walk, etc. If you really think about it, there are thousands of factors that act upon all beings on earth. There is atmospheric pressure, a constant equilibrium vapor pressure, photons from the sun, nitrogen-rich atmospheric conditions, to name a few. The logical result of these constants would be evolution in favor of organisms that deal best with them. Of course, it is the human system of math that makes this commonality a number, but if numerals were not even applied here, there would still exist a natural common property amongst all beings that was the direct influence of their atmospheric constants.
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