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It is important for guys like Ben to know about machine code -- that it's down there, like DNA in your cell -- but a bright kid doesn't need to actually do it, in order to be computer-literate. (Ben wants to, though. Anyone know a good kit?)
Back in the late-seventies, I learned machine code with a Heathkit course which includes a cool 6810-based microprocessor trainer which does exactly what you describe (the 6810 is a variant of the 6800, which I think is what your Commodore 64 uses). Going to www.heathkit.com, it turns out they still have that course, EB-6810 8-Bit Microprocessor Programming, and trainer. I completely agree with your general assertion that getting close to the bits is essential for later success. Besides, it's fun!