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The wheel and axle is an often cited example. It was a big surprise when a bacterium was discovered with a wheel-like connection to its flagellum.

True. That mechanism is there.

And yet, whoever invented the wheel and axle, I'm pretty sure they didn't do so based on the bacterium's flagellum.

So, yes, the concept existed in nature. But it wasn't the inspiration for the human invention in any way.