The breakthrough was enormous, says the former official, and soon afterward the agency pulled the shade down tight on the project, even within the intelligence community and Congress. “Only the chairman and vice chairman and the two staff directors of each intelligence committee were told about it,” he says. The reason? “They were thinking that this computing breakthrough was going to give them the ability to crack current public encryption.”

PGP Founder's new startup, from http://www.buzzfeed.com/tommywilhelm/why-is-the-government-afraid-of-thi...

...In 1785, a resolution authorized the secretary of the Department of Foreign Affairs to open and inspect any mail that related to the safety and interests of the United States. The ensuing inspections caused prominent men, like George Washington, to complain of mail tampering. According to various historians, it also led James Madison, Thomas Jefferson and James Monroe to correspond in code. That is, they encrypted their letters to preserve the privacy of their political discussions.