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So your solutions are that there is either a unconscious functioning of soul or we have three souls? I have a thread on the second solution in here: Does each human/animal/plant have many souls?. I however don’t believe on unconscious functioning.We don’t have two separate souls, but we don’t literally have two separate brains either — the brain has multiple parts/functions, some conscious and some unconscious. The soul doesn’t have parts, but it does have distinct functions (intellect and will, to name two). It doesn’t seem offensive to reason that it has other functions that don’t usually engage the intellect or the will (and therefore happen without conscious awareness or decision-making).
How does the vegetative-sensitive-rational soul setup work for humans? Presumably we either have all three (the first two being material aspects of the body, rather than immaterial like the rational soul) or else the functions of the first two in lower creatures are subsumed by the rational soul — which would be those unconscious soul functions I mention above.