Instead of perfect circles, we use a shape that is taller than it is wide; instead of splitting the space in half, cross-strokes should be higher than the middle; different strokes need to be different widths in order to appear the same, etc.
There are plenty of actual scientific studies and theory behind this. See Ruder's Typography [0] and Hochuli's Detail in typography [1] for more info.
[0] http://www.amazon.com/Typographie-Manual-Design-Emil-Ruder/d...
[1] http://www.amazon.com/Detail-Typography-Jost-Hochuli/dp/0907...
I recommend Josef Muller-Brockmann's Grid Systems in Graphic Design: http://www.amazon.com/Grid-Systems-Graphic-Design-Communicat... or Emil Ruder's Typographie: http://www.amazon.com/Typographie-Manual-Design-Emil-Ruder/d....
There are many, many other good resources but those are important primary sources. So is The Elements of Typographic Style, by Robert Bringhurst: http://www.amazon.com/gp/product/0881792128/ref=pd_lpo_sbs_d....