I (Chris) got an email today from someone who had read my Nanofactory paper and asked: How can molecules be intelligent?
I assume they meant: How can molecules be active and make engineered stuff?
The answer is that molecules can be active the same way a robot or other factory equipment is active: a computer can drive them. In a modern factory, much of the machinery moves under automated control. But that does not mean intelligence is moving it.
When molecular manufacturing develops to the point that it can build machine components by joining together molecular fragments, it will be able to build computers. A nanofactory will have vast numbers of computers, all working together. Those computers will drive the robotics of the factory to make exactly what the blueprints call for. The blueprints will be fed in from outside, just as files are sent from one computer to another today.
The idea of a molecular machine making stuff might seem spooky, but it is no more weird than an industrial robot arm. There is no "special sauce" needed to make a nanofactory work. It's just a lot of mechanical engineering, and a small amount of reasonably creative chemical engineering, and a lot of fairly straightforward computer programming. We are not proposing to build life, or even intelligence--just to build new types of machines.