I think the issue the author has is that what he is defining NS as is not NS. What I can gather about the author's views is that he seems to think NS needs to present a clear choice for each of its “decisions” before it is made. Since we do not know everything about everything yet it is impossible to make the predictions this author seems to be requiring. It may be possible in the future to do exactly what the author wants, but just because we can’t currently does not invalidate NS as a theory nor would it if we can't make predictions the author wants in the future because it would require us to know all possible futures of the species (know when mutations happen and how they affect a species). Additionally large amount of what we know about science is gathered in this form. We see something, we make a prediction, we see if it is right, and we then refine and retest. It is through this process that we come to know something.

Ultimately the author also seems to be searching for a unifying theory of nature; something that we can put variables into and gets some sort of predictable result out of. While there may be a unifying theory for physics there is not one for biology. Life and biology are variable by nature and NS does not try to be a unifying theory; NS intent is to be a mechanism for evoltuion.