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No, animals do not control everything they do with their brains. First of all, not all animals even have brains. For example, worms do not have brains, although they do have nerve ganglia. Jellyfish don't even have nerve ganglia. Secondly, there are processes that do not involve the brain, such as the secretion of various enzymes or hormones, or cellular metabolism, or the functioning of the immune system. All sorts of things happen in an animal body that the brain does not control.

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But the question is extremely interesting. If we narrow it to refer to animals that do have brains, and to animal behavior, the answer takes a different direction. The majority of people probably hold that animals do not have souls, spirits or minds in the same sense that many believe people have them. The conclusion would be then that all animal behavior is deterministic; it is the result purely of activity in the brain and nervous system, taking into account also how the brain reacts to various things like blood sugar level, the levels of various hormones and every other possible biochemical and neurochemical process that can impact the brain in any way. As soon as you begin to attribute soul, spirit or mind to animals you face the problem of concluding that non-human animals have some degree of free will, and can make decisions using faculties beyond their brains, nervous systems and bodies. Who knows-- maybe this is true. But many will not be comfortable reaching that conclusion. The related problem is that if non-human animals have behavior that is completely deterministic, what is the evidence that this is not also true for human beings?

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