He nearly says as much directly in the content of the game.

To begin with -- we're not what you'd call -- human. Over the past two hundred years -- A kind of consciousness formed layer by layer in the crucible of the White House. It's not unlike the way life started in the oceans four billion years ago. The White House was our primordial soup, a base of evolution -- We are formless. We are the very discipline and morality that Americans invoke so often. How can anyone hope to eliminate us? As long as this nation exists, so will we.

"We" being the AI that started as the personification of the mentality of The Patriots who in turn were the people running the American government throughout the 20th Century. (Keep in mind that this version of The Patriots was from before MGS3 and 4 turned them into Cipher/Zero's organization)