Also what ever happened to Feynman's idea of building half size remote controlled arms, which we then use to build half sized of that remote controlled arms, all the way down to a very small scale? Has anyone ever tried that?
Yes, you can assemble molecules with AFM. The problem with this idea is that either (a) the molecules don't stick together at temperatures much above absolute zero, or (b) they do, in which case they might be stable at useful temperatures, in which case it's better to figure out how to get them to self-assemble or to find a catalyst/enzyme that helps them self-assemble. Because your nifty molecule just isn't that nifty if it doesn't exist in quantities of order 1 mole, and 1 mole is... a lot. You just won't believe how vastly mind-bogglingly big 10^23 is.
All of which boils down to this: This essay is great, but the meat of it really is in the first paragraph. Nanotech is a euphemism for chemistry and biochemistry. It is 100% possible -- indeed, nanotech is older than any human-invented technology by many orders of magnitude, by definition, because humans are built out of "nanotech" -- but it's all just chemistry. The real question is why the word nanotechnology is so much more fashionable in grant-writing circles than the old words.
The author thinks this is impossible because progress is slow. That's not really an argument, but I'll agree that "just you wait and see!" isn't one either.
However, biology shows us that it's not impossible to do self-replicating "machinery" so I think we'll get there one day, but it might probably be a lot more organic and a lot less mechanical than we currently envision when we say nanotech.
Later in the story he fighting with bacteria and viruses, but because of the feedback of his microscopic arm, he was injured and almost killed by these tiny creatures.
Also, self-replication is actually easier at the molecular level because all the parts are perfectly regular.
And ducks can fly with flexible wings.
And the Sun is a thermonuclear reactor.
You can find demonstrations of this type of things everywhere, that doesn't means that we can make them work with our materials, techniques and knowledge.
Nanotech seems to my like AI, always there, at just two steps... that's the type of problems that smell to vaporware from miles.
Now if only we could re-program women to make iPhones. The late-night trips to the gas station and gravel store because wife has another petroleum and sand-craving would totally be worth it.
The life if full of examples of things we know how to use but that we don't understand. Sometimes it's just impossible to control that things. Think in the stock market or economics. Chemist has been studying this type of things for centuries and you can see the result: there are chemical products everywhere you look.
What the post attack is the concept of creating nanomachines that doesn't degrade (Cosmic rays! oxidation! temperature!!) and do exactly what we want.
And about the "artificial DNA", it's something so simple... Really! the problem is in the emergent properties of DNA, proteins and environmental effects, this is where you loose control. Even nature has problems with that, life forms die, had cancer...
Drexler's egotistical to be sure. It doesn't make him wrong