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The mars rover, like most other things man has directed into outer space, receives, faithfully executes, and responds to instructions sent to it from its controllers on Earth.

Presumably (and hopefully) it takes more than thorough knowledge of specific communication protocols and sufficient broadcast power to take control of the mars rover, Hubble telescope, or any specific orbiting satellite for that matter.

What manner of security is is place to protect the information going to and from satellites, vessels, and rovers, and how has this security come along throughout history?

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Probably not applicable to newer stuff, but historically I think it was big dish and complex custom protocols rather than encryption that "protected" satellite communications. Consider the case of an older satellite that NASA allowed amateurs to try and connect to, and the obstacles they faced and overcame:

How to talk to a 36-year-old Space Probe

As the primary link is now offline, some relevant snippets:

Actually, one of the most difficult parts of this project was sifting through hundreds and hundreds of pages of specifications from NASA.

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Now that we had a system that was capable of transmitting correct commands to ISEE-3, we had a little bit of guess work to do. There were a number uncertainties about the behavior of the space craft receiver. Ambiguous specifications on items like receive lock range, phase modulation index, and mark/space tones, left us with some uncertainties to deal with. Also, a rough link budget showed that we should have about 5 dB of margin under ideal circumstances. If we had any significant pointing errors, or there were other factors we hadn’t accounted for, there was a decent chance that we were operation near the best sensitivity of the space craft receiver. This meant we could have a marginal link with frequent bit errors.

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