While your reference does not quite meet the standards for scientific publishing ;), your question itself addresses a very profound notion. I disagree with the appraisal of any such notion of a computational universe as being dead on arrival. Some of the best minds in physics - Wheeler, Lloyd, Wolfram, Schmidhuber and others - have been strong advocates of this paradigm.
[This is not an attempt on my part to start, or indulge in any kind of war of words, but a simple statement of my opinion. Take it or leave it.]
Let me frame the question in a slightly less controversial form than the one you put it in Xinus:
Does it make sense to address the motions and interactions of elementary particles - working within the standard Hilbert space framework of quantum mechanics - from a computational perspective?
When put this way the question appears a little less shocking. I was planning to write more here but there is a wonderfully detailed wikipedia [entry][http://en.wikipedia.org/wiki/Digital_physics] on this very issue which can answer your query in a much more complete way than I could attempt here.
ps: btw the novel in question by Jim Wills looks very intriguing and happens to be free to read online. So thanks for that !