Mitchell_Porter comments on A Master-Slave Model of Human Preferences - Less Wrong
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I agree this is part of the problem, but like others here I think you might be making it out to be harder than it is. We know, in principle, how to translate a utility function into a physical description of an object: by coding it as an AI and then specifying the AI along with its substrate down to the quantum level. So, again in principle, we can go backwards: take a physical description of an object, consider all possible implementations of all possible utility functions, and see if any of them matches the object.
Here's another statement of the problem: One agent's bias is another agent's heuristic. And the "two agents" might be physically the same, but just interpreted differently.