The triune brain theory suggests that we have three distinct parts to our brains: The reptillian brain, the limbic system and the neocortex (conscious). When we're talking about body language, we're almost exclusively talking about those things controlled by the limbic system.
Our limbic system controls the vast majority of our physical movement and positioning. It controls breathing and heartbeat, the positions of your hands and feet as you talk and all the gestures we make.
While it is possible to consciously override the limbic system, we don't have the capacity to override much of it or for very long. We can consciously control our breathing or out blink rate so long as we're thinking about it and yet the moment we're distracted, the limbic system takes over again.
The other interesting thing is that of the three parts of the brain, only one is capable of lying and that's our neocortex where the conscious mind resides. The limbic system doesn't lie.
Have you ever noticed someone verbally answer a question yes, while at the same time shaking their head no? People who haven't studied body language may notice that something feels odd but they'll have no idea why. I've seen this one in a business setting several times.
Joe Navarro is an expert is this field has has several excellent books on the subject.