A friend of mine was [...] subpoenad by a grand jury to reveal what she knew about a network of anarchists in the Portland area. They raided her house and took her and her roommates computers and phones. The fed stated that they were investigating an act of coordinated vandalism but the paperwork filed for her indictment predated the vandalism in question.
She was indicted by a grand jury and refused to testify, so they granted her immunity from prosecution which removed her fifth amendment right to not self incriminate allowing her to be charged with contempt of court. So charged they placed her in solitary confinement for weeks.
The point is that all of this happened without her ever being investigated for a crime. All that was necessary for her to be caught in such a web is a knowledge of what her social web looked like.
Encryption does not address the fact that if the NSA is gathering metadata for each call you make, if you use facebook, or if you use any sort of electronic communication then the federal government can and does use that sort of data to begin surveillance. Even if you are using encryption and they can't see the actual contents they can and will put you and your friends in a dark box alone for extended periods of time for refusing to speak to them just on the basis that you know a few people who they are interested in.
via "What we have... is... concrete proof of U.S.-based... companies participating with the NSA in wholesale surveillance on us, the rest of the world, the non-American, you and me," Mikko Hypponen, chief research officer at Finnish software security firm F-Secure. : worldnews.