Computer circuit evolution: scientists have been "stunned" as a network of transistors systematically bred to be an oscillator turned out to be picking up radio waves. Well. Yeah. I seem to remember a while back about a programmable gate array that didn't even have a third of the gates hooked up to the circuit, but would stop running if they were removed. It turned out the system was making use of the edge conditions of the transition between high (1) and low (0) current, and the electromagnetic fields produced by the rest of the circuit. Both things we carefully ignore in our modelled, binary world.
I'm not surprised. The constraints were too simple -- evolution will produce a system that is maximally complex (because the physical universe supplies complexity for free) but the easiest to breed. Attributes such as abstraction (binary) and repeating patterns are inserted when there are more evolutionary constrains: that a circuit has to be able to share patterns, work in many environment, be easily adaptable. In our model-of-a-universe inserting these attributes is easy, it's sub-optimal design and one of our constraints is: make something that's easy given what you've already got. That's a powerful one, right there.