Eureqa uses (used? I haven't touched it in years) symbolic regression. Symbolic regression can certainly produce weird results, especially with low quality data, but I wouldn't rate it anywhere near classic ANNs in black-boxiness.

Also, science is unfortunately full of magic numbers - but it is pretty amazing when you feed in pendulum motion data and the resulting equation ends up being Newton's second law: http://phys.org/news/2009-12-eureqa-robot-scientist-video.ht...