On behalf of the National Institute of Military Justice, I spent a week at the Guantanamo Bay Naval Base observing the arraignment of Abd al-Rahim al-Nashiri, who will be prosecuted before a military commission for his role in the 2000 attack on the USS Cole and other Western targets in Yemen. The participants in the hearing approached the proceedings with solemnity and professionalism.

And yet, committed individuals cannot compensate for a fundamentally flawed military commission system. Upon superficial examination, this hearing — which was held in a room with all the trappings of a standard courtroom — resembles proceedings you might observe in any federal district court. Upon closer examination, however, the deficiencies of the military commission scheme become starkly apparent.

We spent the morning, for example, hearing adversarial arguments on a number of motions that would never have been filed in a U.S. court.

One concerned the question of whether the jurors on the commission should be told that al-Nashiri will likely continue to be detained as an enemy combatant — perhaps for the rest of his life — even if he is acquitted of the charges against him. This motion turned on whether the criminal proceedings against al-Nashiri are simply theater, given the absence of any chance of a meaningful acquittal.

The defense also argued that the defendant should be entitled to seek expert assistance to prepare his defense without revealing the particulars to the prosecution. A related motion attacked the practice at the prison of having intelligence officers read attorney-client privileged communications. These last two motions raise the issue of whether any genuine attorney-client relationship, with protection for attorney work product, can be established with a client detained in a military prison.

A fourth motion, this one filed by the prosecutor, seeks a set of protective orders in the case to guard against the revelation of national security secrets or other sensitive information. This motion went largely unopposed by the defense; no doubt the defense team realizes that having such protective orders in place is the only way they will receive any discovery from the prosecution.

Even though the defendant has been in U.S. custody for almost 10 years — in a CIA “black site” until 2006 and then on Guantánamo — the defense has received no discovery at all from the prosecution, not even the defendant’s medical records. These records will be important, because Nashiri was subject to torture — including waterboarding — while in CIA custody, a fact conceded by the CIA in their own internal documents.

Given the presumption of innocence, constitutional due process protections, and long-standing protections accorded to attorney-client communications and attorney work product, none of these motions would ever have to be filed in federal court. This is not mere speculation. Ten years ago, I was on the defense team of John Walker Lindh, the “American Taliban.” Once Lindh was finally brought back to the United States, he was indicted in federal court, where he enjoyed the full panoply of constitutional protections that used to define the U.S. system of justice.

On Guantánamo, the deficiencies of the military commission became immediately apparent. As they argued the various motions filed in the al-Nashiri case, counsel and the judge instinctively reached for established federal law to address the gaps in the military commission procedures. This highlighted the question of why we were all operating in an ad hoc offshore judicial system — in what is reportedly the most expensive prison on earth — when we have a robust and well-developed system of justice right here at home.

Beth Van Schaack is an associate professor at the Santa Clara University School of Law. She wrote this for this newspaper.

Beth Van Schaack is an associate professor at Santa Clara University School of Law. She wrote this for this newspaper.