But if your brain is constructed of physical matter, then are you not an automaton going through the motions?
But what does that mean?
Again, it sounds like what you're after is something like a question of free-will or perhaps subjective consciousness. How do you measure whatever this is you're talking about?
What would be the difference between a human brain and an artificially constructed brain? Perceiving your own thoughts and qualia is a function of the brain, probably a result of our evolved ability to empathize with others which allows us to empathize with ourselves. This self-awareness could be emulated in a complex artificial brain given the technology to build it, which begs the question of when emulation stops being emulation and starts being what we already are.
Yes--this is the philosophical "zombie" question. I think the problem is that whatever one thinks might be added by "the soul" is undefined, so the question is really undefined.
I agree the mind is wholly a function of the material. I see no problem with the possibility that a computer or something could be made that has enough layers of complexity that whatever that thing is--subjective consciousness, free-will or whatever it is that is lacking when an "automaton" is "just going through the motions"--could arise.
Atoms, cells--choose any unit of measurement you wish. I used "cell-based automaton" just to reference the fact that we're made of units of matter arranged to behave as a functioning system, like a robot.
And this is the part that to me sounds like a straw man.
It doesn't matter that all regular matter is based on atoms when you're talking about the brain. It also doesn't matter that all life is based on cells when you're talking about the brain. The levels of complexity that are of interest to the question you're positing start much higher. Why not say a "brain-based automaton"?
So if you're building an artificial intelligence (or "automaton"--which really isn't the same thing), for purposes of a Turing test, it doesn't matter if it's silicon or pixels or whatever. What matters is a much higher level of organization.
Here's a thought experiment for fun. Imagine Willy Wonka's teleporter was real--it took apart our atoms, shot them through a tube, and reconstructed them in another room. Would that person be alive even though they were technically "dead" as they shot through the tube as bits of matter? What is the difference between making a human being out of atoms and making a robot out of atoms? Does that mean the robot is just as alive as we are, or that we are as automatic as the robot?
Yes--you're asking the zombie question. (Except you're now getting distracted with "alive" and "dead" which really isn't what you're after at all, is it?)
So here's my response to your question: until you define what's missing without a soul (or what's present with a soul), I don't think anything is missing.
That is, I don't think the soul exists until you provide some positive proof for its existence. These thought experiments and hypothetical zombies (what you're calling automata) do not in any way at all add any evidence pointing to the existence of a soul.