ProPublica had a disturbing report about an attempt to censor a Johns Hopkins University computer science professor Matthew Green, an expert on cryptography, who blogged about the NSA’s efforts at breaking encryptions. The university, which is physically located very close to the NSA’s headquarters at Fort Meade, Maryland, does a lot of work for the NSA, especially in its Applied Physics Laboratory.

In his post, Green spoke about the sense of betrayal that he and other technical people feltwhen the read in the newspapers about the NSA’s actions, saying “I was totally unprepared for today’s bombshell revelations describing the NSA’s efforts to defeat encryption. Not only does the worst possible hypothetical I discussed appear to be true, but it’s true on a scale I couldn’t even imagine.”

Apparently someone from APL alerted the dean of the school of engineering who ordered Green to take down the post, although it was based entirely on material that had been published in the media. Green took down the post that was hosted by the university servers but not the same one mirrored on a commercial server. After he tweeted about the university’s action, there was a backlash against the university and the dean revered himself and issued an apology for taking the action.

The university says that no one from the NSA asked it to take action but NYU journalism professor Jay Rosen says that this episode raises some serious questions that still need to be answered.

Who was it in the Applied Physics Laboratory, with its close ties to the NSA, that raised the alarm about what a (very effective) critic of the NSA was writing … and why?

Did that person hear first from the government and then contact the Johns Hopkins officials?

Why would an academic dean cave under pressure and send the takedown request without careful review, which would have easily discovered, for example, that the classified documents to which the blog post linked were widely available in the public domain?

Why is Johns Hopkins simultaneously saying that the event was internal to the university (that the request didn’t come from the government) and that it doesn’t know how the whole thing began? The dean of the engineering school doesn’t know who contacted him about a professor’s blog post? Really? The press office doesn’t know how to get in touch with the dean? Seems unlikely. Johns Hopkins spokesman Dennis O’Shea told me this morning that university officials “were still trying to trace” the events back to their source. Clearly, there’s a lot more to the story.

The NSA seems to be really clumsy when it comes to working out in the open. That is what happens when you work in the dark and are used to not having anyone question your activities.