We now know that the reason Mr. Mukasey refused to acknowledge that waterboarding meets the legal definition of torture, or at the very least cruel, degrading and inhuman treatment, clearly had nothing to do with not being briefed about the procedure... The real reason, as mainstream news analysts now acknowledge, was that publicly admitting waterboarding is torture or cruel and inhuman would have put the president in jeopardy of criminal charges.
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The War Crimes Act of 1996 makes cruel, inhuman and degrading treatment of detainees a violation of the Geneva Conventions and a federal crime. In addition, a 1994 law, 18 USC Section 2340 (a), makes it a federal crime to engage in torture outside the US, and it also applies to those who conspire with (or aid and abet or order) torture outside the US. Both statutes apply to any US national, including the president, the vice president and other top officials, as well as subordinates, such as CIA officers or other US personnel. If the president ordered, directed or authorized waterboarding or other forms of torture or mistreatment, he may have violated these laws. They carry the death penalty in cases where the victim dies. In such cases there is no statute of limitations, so the president could be subject to prosecution for the rest of his life.
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In a February 2002 memo, then-White House counsel Alberto Gonzales warned President Bush about exposure to criminal liability under the War Crimes Act, mentioning the danger that future independent counsels or prosecutors might seek to enforce the law (they generally prosecute top government officials, including presidents). He therefore recommended opting out of the Geneva Conventions, famously calling them "obsolete." His theory was that if the Conventions didn't apply, then the War Crimes Act wouldn't apply, so no prosecutions could be brought. The president accepted Gonzales's theory and suspended the Conventions' protections for suspected al-Qaeda detainees.
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Still, holes remain in the legal barricades the Bush administration has tried to erect around itself. Even if immunity from prosecution under the War Crimes Act stands, it only applies through 2006, not for mistreatment of detainees after that. And the 1994 anti-torture law applies throughout.

As attorney general, Mr. Mukasey can try to plug these holes. He may shield President Bush and others from criminal liability; he may resist appointing an independent prosecutor to investigate White House actions. But he cannot, as the 2002 Gonzales memo recognized, tie the hands of future prosecutors. In lethal cases, our anti-torture laws have no statute of limitations. Sooner or later, those who violated US law will be held accountable to them, if not by Mukasey, then by some future AG.