Forget what the statute says. Imprisonment for conduct determined to not have been a crime is a violation of due process. This seems obvious. What am I missing?

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I fail to see how Jones is "a tough close issue". As you spend the rest of the essay arguing, a prisoner in Jones' situation should have access to a hearing to establish their innocence and secure their freedom. Jones is factually innocent; any statute which purports to bar the courtroom door violates due process. I read Thomas's argument, which makes a statutory case that is not necessarily wrong, but which is irrelevant in the face of the result: manifest injustice.

The government may dispute Jones' knowledge of his status, but they are required to prove that beyond a reasonable doubt.

As you point out, Congress could and should address this easily, but I will also point out that the President has a role to play. This is a case for the broad use of the pardon power to expeditiously correct the invalid conviction of many, many people.

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