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Defense Secretary Chuck Hagel had to write an official directive telling the military to ignore President Obama on sexual assault cases. When the president said in May that members of the military who commit sexual assault should be "prosecuted, stripped of their positions, court-martialed, fired, dishonorably discharged," he was also speaking as commander in chief. Military defense lawyers have argued in sexual assault cases that Obama was acting as a military commander unlawfully trying to influence military juries. The New York Times' Jennifer Steinhauer reports that Hagel wrote in an August 6 memorandum, "There are no expected or required dispositions, outcomes or sentences in any military justice case, other than what result from the individual facts and merits of a case and the application to the case of the fundamentals of due process of law."

The controversy highlights how military courts martial are very different from civilian trials. The military justice system reflects one of the most fundamental rules of the military, which is that power starts with the president and trickles down. It doesn't go the other way. That's why instead of 12 anonymous citizens, military juries are made up of military members who are higher ranking than the accused. That way a lower-ranking juror doesn't feel compelled to respect the rank of the accused and ignore the facts of the case. And as we know from the controversy over how the military handles sexual assault cases, military commanders have control over whether to prosecute the accused, and whether to uphold the sentences of the convicted.

So that is why some defense lawyers have been using Obama's remarks to keep the accused from being prosecuted. They argue his comments were "unlawful command influence" — which refers to a commander trying to influence the jury in a court martial —  and judges have agreed in several cases. The most galling might be the case of Brig. Gen. Jeffrey Sinclair, whose case demonstrates in other ways that the current military justice system is not without drawbacks. 

Sinclair is accused of forcible sodomy, adultery, and other charges, as an Army captain he had an affair with accused him of forcing her to perform oral sex on him twice. The judge said he would determine whether Obama's comments had tainted Sinclair's case during jury selection, the Times reports. Jury selection in the case has had other problems, as The Washington Posts Craig Whitlock explains. Jurors in military cases must be higher ranking than the accused — and that's hard in Sinclair's case, because the pool of officers higher ranking than Sinclair is small. Because Sinclair is so high ranking, his case is huge news, as only two other generals have been court martialed since 1952. And, since it concerns sexual assault, the case has gotten even more attention, potentially tainting the jury pool. One juror, the Post reports, "revealed that he had attended an Army-mandated training session on sexual assault prevention in which Sinclair was depicted as a case study in bad behavior."

In a June Senate hearing about possible changes to the way the military handles sexual assault cases, military leaders defending the status quo have argued that giving commanders' discretion helps them set standards and maintain discipline and respect for chain of command. A proposal from Sen. Kirsten Gillibrand would take away a commander's power to decide whether to prosecute a sexual assault case, and the power to overturn a jury's conviction. It does not address the power of presidential speeches.

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