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The Obama administration has done much to clean up the legal mess in Guantánamo. But as the ongoing trial of a top al Qaeda suspects makes clear, it has not done nearly enough.

GUANTÁNAMO BAY, Cuba — I had not planned on paying a visit to Camp X-Ray on this trip to Guantánamo. The remains of the old facility, originally set up to house Haitian refugees and later used as the first detention center for prisoners captured in the "war on terror," are not much to look at: pieces of wood and razor wire, cobbled together at the bottom of a green hill. It held detainees in what were essentially small fenced-in cages, exposed to the elements. It's been closed for a long time, though it is still standing, the military escorts tell me, under a court order.

By contrast, the courthouse in nearby Camp Justice, where a handful of the remaining 168 Guantánamo detainees are now on trial, is much more imposing. A hangar-like building, designed to be portable although it is rooted firmly on the ground, it is grey and windowless, surrounded by a sea of pavement and bright orange barricades.

Had I been able to choose, I would have been in there instead of visiting what was left of Camp X-Ray. But all observers were locked out of the courthouse that Wednesday, July 18. So was the defendant in last week's hearings, Abd al Rahim al-Nashiri, who is charged with arranging the 2000 bombing of the USS Cole and other crimes. Only the judge, prosecutors and defense attorneys, some in military uniform, were allowed into the closed hearing, to start discussing how to handle classified evidence the prosecutors would eventually introduce in the case.

The closing of the hearing to review secret evidence looked dramatic. But it was only one of several questions raised in July's pretrial hearings in US v. Al-Nashiri that strike at the heart of what it means to have a fair trial.

From the outside, the hearings -- which, though closed Wednesday, were open to the media and observers on Tuesday and Thursday -- looked much like those in any other case. Lawyers argued various motions. The judge, sometimes impatient, pressed them with questions, and issued rulings. The defendant sat on the bench quietly listening. Family members of victims and observers sat and watched.

But of course, these aren't normal hearings. On the first day, a heavy military guard escorted Nashiri, a young-looking Saudi who came in dressed all in white prison garb (his lawyer later gave him a suit jacket to wear over his clothes, perhaps because of the heavy air conditioning in the room) and regularly turned around, peering intently to try to see who else was there. After being barred from participating on Wednesday, Nashiri decided not to attend the remainder of the proceedings. One prominent member of the defense team wore a kangaroo pin on his lapel, presumably to express his opinion of the court. Observers and victims' relatives were separated from the courtroom by heavy glass and heard the proceedings with a 40-second delay on closed circuit TV. This time, media and observers were also strictly separated from each other in the courthouse complex. And the setting here in Guantánamo is tightly guarded, surrounded by concertina wire, thick walls, and two layers of security checks that our Defense Department escort described as "TSA on steroids."

Nashiri's is one of only two cases being heard in the revised military commissions set up under the 2009 Military Commissions Act (the other involves the 9/11 attacks). But this is no minor test case. If convicted, Nashiri faces the death penalty -- which alone should require the highest standards of due process. And he is one of only three people the George W. Bush administration admitted to having waterboarded, a form of torture, during several years in which he was held in secret CIA detention facilities.

In motion after motion last week, the defense argued basic issues of justice and fair process: Would Nashiri be allowed to hear discussions about the evidence against him? Should the judge recuse himself because, having been called back from retirement to receive higher military pay, he had an incentive to rule in favor of the military prosecutors? Should the public be able to watch the proceedings on broadcast TV? Even resource issues, which seem dry at first glance (for example, the question of whether the defense should be allowed to hire an additional paralegal or how many pages of discovery it can have translated into Arabic) pointed to the awkward structure of the system. The Convening Authority -- a military entity aligned with the prosecution -- decides how much money the defense will get to spend in building its case. The sheer number of basic questions that needed to be resolved speaks to how new the system is, and how different from a regular civilian court proceeding.

More important, injustice is deeply embedded in the rules of the system itself. Evidence that would never be admitted in a U.S. civilian court can be used against defendants in military commissions. Some types of hearsay evidence are allowed, and coerced witness statements can be admitted as long as the judge deems them "reliable." Since much of the evidence against Nashiri is classified, his attorneys will often see only summaries of the evidence against him. Under these circumstances, it is hard to understand how defense attorneys can effectively challenge the reliability of evidence. And it is easy to imagine how someone could get convicted -- and sentenced to death -- on pretty tenuous grounds.

And then there is the elephant in the room: the issue of torture. Nashiri was tortured. The U.S. government has admitted it -- although it claimed when doing so that the waterboarding he was subjected to was not torture -- and his case is already tainted by it. Yet virtually none of the evidence of his torture will be heard in this case. The CIA has classified everything related to Nashiri's treatment and torture while he was in their custody, and the accused himself is not allowed to speak about it. This will never be discussed in an open courtroom. The public will hear about it only in passing. Coupled with volumes of secret evidence, it is hard to imagine how this trial could ever be seen to be fair. And yet a man's life hangs in the balance.

Whatever Nashiri did -- and we may never know for sure exactly what happened -- we should not compound it by further damaging the integrity and fairness of the U.S. legal system. Barack Obama's administration has made much of the improvements to the military commissions system, and has pitched them as a valid way of prosecuting terrorist suspects. Indeed, the military commissions have improved from their earlier iterations. But ultimately, the Obama administration's effort to salvage the commissions was always doomed to fail. There is simply no way to make such an untested, secretive, and unfair system legitimate, and that will only become more obvious as the cases progress.

When, more than a decade ago, the U.S. public first saw pictures of detainees in orange jumpsuits, shackled in what looked like cages at Camp X-Ray, many were shocked. Years later, I still found it disturbing to see the camp's remains. By contrast, on the surface the military commissions do not look quite as bad: They have a veneer of due process, of fairness, of equity, and many in the United States have forgotten about what is happening here. But that only makes the problem all the more pernicious. And based on last week's hearings, it looks like it's only going to get worse.

Maria McFarland Sanchez-Moreno is acting director of the U.S. Program at Human Rights Watch.

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