The main benefit in writing with pen and paper (to me), is the fact that I can write anywhere, make arrows, comments that doesn't disrupt reading the main part,

The main benefit in writing with pen and paper (to me), is the fact that I can write anywhere, make arrows, comments that doesn't disrupt reading the main part, and draw various very helpful graphics. I think I would have spend significantly more time to understand most of what I learned in CS if I only used a computer to take notes.