It would seem to me as a layman (I have a degree in CS, but my grasp of theory was always tenuous), that discussing the ability to calculate an equation that models a physical system is different than the physical system itself. The universe doesn't need to "calculate" it's systems before it executes them, they just do what they do (for lack of a better description).

That said, this feels a bit like "A New Kind of Science," where Wolfram extrapolated from computational games to saying "this is how the universe works", which was a leap that few found very compelling.