The central problem with the federal criminal prosecution of one-time alleged “dirty bomber” Jose Padilla, now underway in Miami, is that the trial itself will not provide any resolution to the real question that the Padilla case has always raised: Whether the U.S. government can subject U.S. citizens arrested on U.S. soil to incommunicado military detention (and, allegedly, to mental and physical abuse while in military custody).

The reason why the Padilla trial will provide no resolution of this fundamental question is simple enough: Federal district judge Marcia Cooke, who is presiding over the trial of Padilla and his two co-defendants, has made clear over a series of pre-trial rulings that Padilla’s military detention is completely irrelevant for purposes of his criminal trial, so long as the government does not introduce any evidence obtained in conjunction with that detention. All too willing to comply, the government itself has embraced this bifurcated understanding of Padilla’s confinement, going so far as to argue that the Justice Department cannot be held responsible for any unlawful actions of the Department of Defense — that the right hand simply can’t be called to account for the actions of the left.

Legally, Judge Cooke may well be correct. The government is not attempting to introduce evidence obtained from Padilla during his 1307-day stay in a South Carolina Navy brig, and so the question whether that detention (or any of the government’s actions toward Padilla during it) was unlawful would not seem to implicate any aspect of the criminal charges Padilla now faces. In effect, then, the criminal case against Padilla has proceeded upon the theory that his “incarceration” began the day he was transferred to the custody of the Department of Justice in January 2006.

But what about the previous three and a half years?