The idea of there being an indigenous "higher-level" theory of computation is an important one. But I doubt very much it would look like physics, or have the benefits of physics that Hillis thinks are important.

Its much more likely to look like biology, eg nature's computers. Most models in physics are not inherently based on the idea of information and computation, in fact the functions that they are based on are merely primitive recursive, making them unsuitable for for descriptions of fully generally recursive computational processes.

Of course, biology is also noted for its lack of higher theory, and so when I make the above claim, the meaning is that when such a theory exists it will address both of these issues.