Another awesome interview at Lifehacker; it's with Merlin Mann (who is, in essence, Danny O'Brien's partner in productivity).
My favorite bit of the interview:
Typically, the GUIs we all learned have used controlling metaphors that were based on physical things like desks and file cabinets and shelves. Even where these metaphors failed or misled, they were still really useful as a way of fording the no-man's-land between terrified users and seemingly complex, command line-based systems. They built an extra layer of interactivity that made learning a computer much less intimidating and abstract by translating it into work people were already familiar with.
So, flash forward 20+ years and there are a lot of us who haven't really thought in terms of those metaphors in years. In fact, the "desk" and "file cabinet" metaphors are starting to seem downright quaint; we want ways to increase our productivity and sense of response time, not a permanent set of training wheels, right?
Add to this the research into how things like extraneous navigation and modal shifting can take you out of the flow state (a pet research project that Danny's totally nicking from Mary Czerwinski). If you live forever doing real-time translation of how your computer is like a desk, you're going to always be parsing your interactions in an overly mediated way. As long as you're thinking about desks and clicking and menus and so on, you're never going to be in the desirable flow state for long.