Transmutation
(Photo: more reprap parts being made on a MakerBot)
One point I didn’t address in the atoms vs bits debate was transmutation. In the information domain, transmutation is fundamental, and fundamentally easy: 0 -> 1.
Transmutation in the atomic domain is… substantially less so. Some forms of transmutation are easier than others, and with varying levels of machinery atomic transmutation is possible. But it’s pretty impractical and so far we’re mostly only good at moving down in stored energy. Iron has the least energy, so transmuting it into other atoms is really hard, where super big elements like Uranium transmute on their own, and small elements like hydrogen give off energy when transmuted into bigger ones. The tradeoff is possible but requires tremendous energy and represents a significant hurdle to building an Anything Machine.
So, strictly speaking, atoms are not going to turn into bits easily, even if we get the general assembler built. But how much do we need it, and more to the point, how many of the fundamental characteristics of digital technology can we squeeze out of the atoms we have? I’d argue, quite a lot:
Say you had the General Assembler but you could only “print” in a few elements. Carbon, Hydrogen, Nitrogen, and Oxygen, let’s say. You can get these four atoms from just about anywhere. Anything organic, in fact, will have all these to spare, so our CHON assembler won’t want for components. You could hook it up to your compost pile. Or sewer line. And print any of the following: plastics, fuels, food, water, agars, glues, tape, wood, diamonds, and more.
Let’s say you had a General Assembler which could do any assembly task but could not transmute atoms. Last year’s cell phone is now next year’s cell phone. The same goes for pretty much all the gadgets. And it’s true that in recent decades there’s been a trend towards more and more exotic elements in our gadgets and daily life, but elements are a commodity, not a product, and the markets for them wouldn’t work the same way if anyone could squeeze every bit of use out of, say, a small lump of tellurium.
An early goal of alchemy was to convert other metals into gold, which was proved impossible because they are different elements. But modern chemistry certainly can turn many base things into highly precious ones, and even without transmutation, a General Assembler could spin coal into diamonds, sewage into sales binders, and hair into pasta. If technology like that isn’t fundamentally disruptive to the existing one, I don’t know what would be.

