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Quantum Mechanics
In quantum mechanics, amplitudes are given by multiples of i, complex numbers. This looks like an application of imaginary numbers that we can't just get rid of. Schrodinger was unhappy too. He put a cat in a box, now the cat's dead. Oh, no. The reason the cat is alive and dead are pretty intimately related to these pesky complex numbers. But it doesn't look like we can change it. We just discovered them effectively. And they're there in the garden forever.