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If he was only taking them for personal reference (as opposed to reselling them, which it doesn't appear that he did), how is the potential 35 year jail term at all justifiable?
Wow. Especially the "stealing" makes no sense. He possibly amde copies of digital data. But that doesn't delete them AFAICS. So how can you "steal" something that is still there afterwards? Doesn't change the severity of these accusations. Should this be true it would be really worse.
This sounds really weird. I need more information about this story.
So it was a data liberation action? Still strange stuff.
Isn't there a bunch of stuff on jstor that is public domain?
+Stephen Paul Weber yep. He was catched, he admitted, he signed some whatever legal papers and now the DA is after him. Seemed to have been a data liberation action to "free" data that is kept locked in by JSTOR, partly even public domain content IIRC. Another sign of IP "terrorism"?
I'd wager most if not all of the stuff should legally be available outside of jstor but isn't because it hurts their business. If this is the case then take this to court and get jstor struck down. 
Having skimmed the indictment, it certainly does look interesting.
While I can applaud the desire to "free" data from JSTOR, his methods are clearly illegal, especially the unlawful entry to MIT's data facilities. It's not like when some of us scraped the British Royal Society via a public website.

This won't take JSTOR down. What it will do is cost Aaron a lot of money, and once again give the copyright mafia another chance to crow about how evil copyright pirates are.
The DP statement makes it sound like the data was used in an academic analysis of paper funding sources. This should be... interesting.
I smell a WiKiLeaks connection some where in all this. The Opensource concept sounds great on the surface, but not everything is open to all.

My guess: He was trying to liberate something that someone said wasn't there.

His Risk: How can I be guilty of stealing something they said they didn't have.

The Settlement; We'll drop all the criminal charges if you stay quiet. If not, you'll be in jail and we'll just keep lying about it.

The Usual setup.