Since you are using the code metaphor I will try to work with that. Much of your brain is not a “real time operating system”. The complexities of driving certain critical bits of hardware are given over to specialised parts of the brain, which you can think of as controller cards with their own dedicated (real time) firmware.
The controller card for breathing, heart rate and blood pressure is the medulla oblongata. This thing is almost not part of your brain, in that it sits at the top of your spinal cord.
There is a condition (Anencephaly) where infants are born missing all or some of their brain, but the body can (in some circumstances) continue to breathe due to just the presence of the medulla oblongata.
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