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Stronger bonds make things harder, not easier.


Yes, this exactly. I can't envision what kind of informationally-sensitive chemistry is supposed to happen at standard temperature and pressure in an aqueous environment, using "diamondoid". 

Proteins are so capable, precisely because they are free to jiggle around, assume different configurations and charge states, etc.

Without a huge amount of further clarification, I think this "nanotech doom" idea has to go. (and I'm not aware of any other instant, undetectable AI takeover scheme suggestions that don't rely on new physics)

"human" objects around that could easily be taken apart for, say, biofuel or carbon atoms

This is one aspect of the discussion that never sits right with me: the idea that what might interest a future superintelligence is our "atoms" and not our standing as the only thing that's ever created a superintelligence so far. There are lots of more efficient fuels and more readily obtainable sources of carbon atoms than all the humans scurrying (or lumbering, to take the point of your post) around the earth. 

I suppose the charitable interpretation of this is is a superintelligence will make little distinction between the human and the concrete wall they're standing next to in terms of where it might choose to scoop up some matter?