For a lot of essential processes like breathing, the automatic control is in the brain stem (the primitive, or lower function, part of the brain). But consciousness arises in the cortex (the more modern, complex, higher function part of the brain. The cortex can override the brain stem when needed, and control the muscles needed for breathing by itself. Also, both the higher and lower parts of the brain can control what you are paying attention to. So, you can at times be consciously aware of your breathing, and/or control how you’re breathing. The different areas interact back and forth subconsciously. Depending on which areas “win” will determine whether you are breathing automatically or consciously.
The crazy thing is that the subconscious controls most if not all of our actions, to the point that consciousness might be an illusion. Like, different parts of your subconscious might fight about how to breathe until you start breathing deeply and slowly. But, after you start breathing like that, your subconscious tricks your conscious mind into thinking it had come up with that idea in one clean though all on its own.
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