The first combination of two molecular machines has been claimed by Kazushi Kinbara at the University of Tokyo, Japan. The first piece is a light-driven actuator which twists a double bond one way in UV light, and the other way in visible light, causing a pliers-like pair of pieces to hinge closed and open. The ends of the pliers connect to a couple of flippers. By pulsing the light correctly, one can presumably get the flippers to kick, and make the thing swim around in a liquid.
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According to the article, research labs have produced a profusion of interesting molecular machines, but none by itself does anything complex enough to be really useful or extensible. The innovation here is supposed to be the combination of multiple machines. I'm not sure that flapping flippers is much more useful behavior than any of the individual machines would perform. It would be interesting Kinbara had found some kind of general approach by which different submachines could be built into large assemblies, but there is no evidence for that in the articles I could find. Kinbara evidently sees the value of that as a goal, and guesses that large assemblies are about five years out.