A computer with a rootkit is a brain in a jar, a human battery in the Matrix. You, the computer user, can ask the operating system questions about its operating environment that it will answer faithfully and truthfully, and *those answers will all be wrong*, because the *actual computer* is being controlled by the rootkit and it only tells your operating system what it wants it to know.
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20 years ago, some clever Microsoft engineers proposed a solution to this conundrum: "Trusted Computing." They proposed adding a second computer to your system, a sealed, secure chip with very little microcode, so little that it could all be audited in detail and purged of bugs.
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