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This delves into the question "Why is there anything at all?". If souls exist, and are created by an omnipotent being such as God, they must have been created for some reason. Why would God create a universe? Why not just be alone and perfect for all eternity? Perhaps joy and good can be found in interactions between concious beings? Perhaps God seeks companions in Heaven and life is some kind of entrance test?
I don't know, anything is possible.
As for how soul machinery works, I'm not sure. If a very small direct kinetic force was applied to various chemicals, electrons, and energy packets, it would be nearly impossible to detect from the chaos of a natural chemical process. This could be one mechanism; I'm sure there are others.
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