Part of the problem is that the more research that's done into exercise, the more we see that what works for one person may not be effective for someone else. A lot depends on your metabolism and the way your body responds to the various hormones that control energy use and storage.
Try Starting Strength ( http://www.amazon.com/Starting-Strength-3rd-Mark-Rippetoe/dp... ). Most people (read: me) dick around in the gym with bicep curls and nautilus machines, which is a mistake.
I got basically no results while doing that, and my improvements have been dramatic since I started SS.
As I said above: the "black box" is enormously complex but it is not observable, so it's not useful for an ordinary person. Caloric deficit works for everyone and it can be controlled easily.