Hermeticism also separates the soul from the mind, defining the mind as the actual source of your being (IE who and what you really are), while the spirit is kind of a body that you use as an interface to control your physical body. Both the spirit and the physical body would be discarded when you die.
Spiritism/Spiritualism takes this a step further by dividing humans on 4 bodies, which are the physical body, the vital essence, the soul and the mental body. The vital essense is what powers your physical body and keeps your soul tied to it, and dies along with the physical body on death. The vital essence also acts as a limiter, and generally prevents memories of your past lives from affecting your current incarnation. The difference between the soul/spirit and your mind isn't always properly described, but its has been explained that the soul is how your mind interacts with the universe, with your mind being your true self.
Gnosticism defines the soul as one of the sparks of divinity that got trapped in the physical universe by the demiurge.
The brain could be interpreted as the physical interface through which the soul interacts with the body through chemical reactions and electrical impulses.
Regardless of how its described, the concept of souls is old as hell, and may even predate religion. In fact it may have been the very thing that originated many religions (and not the other way around), but this is just speculation.
On animals: I don't know, I respect animals as living beings, but I don't believe animals are somehow magical and exempt from being evil. I'm not the kind of person that believes dogs are completely angelic beings that are only capable of love, or that some animals are inherently noble because they're pretty or such things.
I'm ok with killing insects and other things that trespass into my personal space because, well, that's a natural behavior. I mean, there are animals that will kill things for trespassing into their territory, so why wouldn't I? There are also animals that kill for fun and seem to take pleasure in torture, like dolphins.
I do believe love, empathy and compassion are virtues everyone should aim to have, but I'm omnivorous, and I'll eat meat if it is available to me, and I'll kill things if I'm in a state of need, or to protect myself or things that I want to protect.