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Perhaps there is also the presumption that the AI components of HAL were merely riding on top of the existing system and could be removed without affecting it.
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I would agree. I remember when Televisions were valve driven and nowadays it's solid state. But if you take a closer look inside you will find a series interconnected of circuit boards. Rather than change a damaged component, it is simply the case of replacing the board containing the damaged component (a simple plug-in task). I see HAL's logic circuits as being analagous to this.