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What’s your favorite protocol? Defined broadly as rules of engagement for any complex behavioral domain for some mix of humans and/or machines? With link if obscure.
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The salute. It's a staple of military (and civilian) interaction but it's just beginning to prove useful in demonstrating rank and obeisance in mixed human/machine divisions
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In the examples I know of, the CO wears an insignia that is programmed in as a command function. The AI indicates by a gesture that it acknowledges that authority, i.e. a salute.
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