A lot of these arguments (but not all) boil down to, "This is theoretically possible, but we don't have the technology to do this right now." It seems to me that when talking about the time when an AI is developed, some combination of much higher levels of technology and much more processing power will be available, so this isn't as much of an issue.

All of these tiny machines are repeatedly described as programmable, but that doesn't make any sense. What programs are they capable of accepting or executing? What set of instructions can a collection of 50 carbon atoms accept and execute? How are these instructions being delivered?

I think he means programmable in the exact same way that DNA is programmable, that you can specify which amino acids you want and get a matching output.