I'm not. I am pointing that if humans have souls and a tree doesn't, that means the specific combination of molecules in a human somehow have special properties that allow us to interact with souls. That implies we could manipulate a persons interaction with a soul by manipulating said molecules.
Lets posit a hypothetical mechanism. A "soul" is actually a specific form of particles which binds to dense neural activity you see in a human brain. Over time, the neural activity in the brain causes the soul particles to create distinct patterns which contain a persons personality. Upon death, the neural activity ceases, releasing the soul but allowing the pattern of the person's mind to remain. Such a scenario explains why humans have souls and trees don't.
The problem with my scenario is that it causes problems with the real reason souls were invented: quelling fears about human mortality. If the soul is based on neural activity, that means it could altered or even removed by brain damage. Having your eternal self be mentally ill is obviously horrifying. Perhaps the biggest flaw of religion is not even the claims it makes, but rather that it doesn't consider the implications of said claims.
First off, despite religious assertions to the contrary, we don't know if trees or animals have souls or not. If we posit that the soul is some kind of coherent energy field, one we have yet to learn to detect, it would be logical to guess that it would be affected by the neuro-electrical properties of the brain. Or conversely, if the soul is in reality a energy based life-form, then its field may be affecting the brain's neuro-electrical properties. This energy field may also be a basis behind psionics, assuming one believes in them.
As to the issues you bright up, the interface between the body and soul could be as if the soul were a recording device or it could the equivalent of camera/microphone/sensors/whatever. In other words, damage to the brain results in improper input/output, but doesn't result in the soul itself becoming damaged.
The varity of potentials is vast especially when we review how much we have discovered that exists, that we were never aware of before. So then how much more is out there, affecting the universe around us, that we haven't even discovered, yet alone learn how to measure and/or manipulate.
I'd want to know how it occurred, why, how it relates to the rest of science, etc.
I would be thrilled for a second at the idea of something that huge being known.
I would be terrified a moment later know that the notion of eternal suffering or pain, or being trapped for eternity somewhere, is a reality that I cannot avoid.
Ever read Stephen King's the Jaunt?
By the OP, you wouldn't know that. For all you know there is no life after the next one, and/or the next one has a limited span like the current one does. You don't even know that you get to carry memories over from one life to the next, or maybe you do but you can't access them consciously. There is a wide range of potentials available by the way the OP is written.