Magic in the Webcomic version of Earth is an extremely varied art/science, influencing all aspects of existence.
As one purpose of the webcomic is to provide an artistic expression in which the methods of science are not shown as short-sighted or blinding, as in the vast majority of other art that treats such a topic, the physical implementation of magic has completely mundane origins. Specifically, and technically speaking, magic is a very peculiar coupling between normal, baryonic matter and the mysterious dark matter that pervades and penetrates the universe.
The "universe" containing earth is but one 3-brane in the vast 10+1-dimensional "omniverse". Gravitationally locked with our universe is another 3-brane that consists of a single field. When the branes overlap, the field of this other universe decouples the otherwise natural interaction between dark matter and baryonic matter. In other words, without the interference of this other universe, our universe would naturally contain magic.