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We don't have any control over the fact that medicine and physics are complicated because they reflect nature.I don't agree that this is all that different.
In physics, some phenomenons can be either simple or complex to describe, depending on what formalism you use to describe them. And sometimes, complex formalisms can be hard to understand at first, but help producing simpler description of the phenomenons your looking at.
For example functions and derivatives are hard to understand at first, but they drastically simplify the description of classical physics.
So in programming just as in physics, you just need the right conceptual tools to describe your problem.
And while boolean logic may be hard to understand at first, it really helps specifying complex behaviors.
In that sense, I think I agree with GP: over simplifying the conceptual tools may not results in better problem descriptions.