It is a consequence of the convention F = - dU/dx. That minus sign is what caries through to make the minus sign in L = T-U.
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Well for a start that would make T=K-U so Hamiltonian systems would conserve the difference between Kinetic and Potential Energy rather than their sum, so I don't think the sign of potential energy is arbitrary.
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One of the reasons we can make a "Universe from mothing" is that the positive energy of all the mass is exactly blanced by the negative energy of the gravitational potential. This would not be true if U->-U and gravitational energy was positive.
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To recap part of my point, start with Newton's 2nd law: mx'' = ∑F there's no sign convention here, and any sign related to charge conventions is within F.
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the minus sign there has always been “magic” to me in mechanics