So is the 747 made of something other than quarks? No, you're just modeling it with representational elements that do not have a one-to-one correspondence with the quarks of the 747. The map is not the territory.

It seems to me that the reductionism as advocated by Eliezer is a poor-quality model. It only works one way: you can potentially trace the 747 all the way down to its subatomic particles, but you cannot construct a particular configuration of subatomic particles that will fly, rather than bark or crawl, using just the laws of QFT. Thus it has no testable predictions (that everything we can see or touch consists of quarks, leptons and gauge bosons is not a prediction, but an observation), just like his other favorite myth, the MWI. He dislikes the term "emergence", and he is entitled to his emotions, but the sad experience is that nuclear physics is no help in psychology, not even after you say "reductionism" three times.