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Coase Theorem doesn’t say _how_ you should divide up property rights - that’s a normative statement that’s outside the scope of economics - but rather that as long as _any_ property rights are assigned, regardless of which way the assignment goes, the outcome will be economically efficient.

Also it assumes transaction costs are negligible, ie in the example in the article, the negotiations between the railway and the farmer can be done cheaply and quickly. This is somewhat like assuming a frictionless plane in physics.