One aspect of the article that I haven't seen much discussion of is the second part- about representing biological processes using an algebraic notation. While this might be really helpful for computational biology, it strikes me as a lousy idea for general work, because it presents an overly reductionist view of what's going on. Biomolecular pathways are almost never as simple as they seem at first, and they always interact in weird and complex ways. Presenting them as a big, gnarly, nasty diagram communicates this to readers... explaining them using nice neat equations makes the whole thing seem both simpler and better-understood than it probably really is.