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Good question!
Well, first of all there are no bones in the brain. There is a lot of bone around it (your skull) to protect it because it is so squishy.
There is a whole field in biophysics that it trying to work out how exactly your arm moves when you think about moving your arm, and whether it changes when you look at your arm or keep your eyes shut.
In short a signal comes from your motor cortex, moves down to the brain stem and then trough your spinal cord to the different arm muscles. A couple of brain centers called the basal ganglia help with precise coordination of movement.
Incidentally, those basal ganglia tend to break down in Parkinson’s disease , making patients movements uncoordinated.
A good wiki for motor control is https://en.wikipedia.org/wiki/Upper_motor_neuron
Hope that helps!
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