Given a molecular constructor able to arrange and rearrange molecular structure in some programmable way, the difficulties of self replication become more pragmatic than conceptual. He didn't foresee the merging of these two forecasts. The only self replicating systems we are familiar with are living, and we unconsciously assume that artificial self replicating systems will be similar. But the machines people make bear little resemblance to living systems. The image of a 747 going feral, swooping out of the sky to clutch an unsuspecting horse in its landing gear, seems incongruous.
Machines lack the wonderful adaptability of living systems.
A 747 requires Jet A, a refined source of energy that is delivered to it by an elaborate system that includes oil fields, pumps, tankers, refineries, fuel lines, and trucks. It can convert this artificially refined fuel into energy using engines that can run on little else. Cut off from refined fuel, airstrips, maintenance crews, spare parts, navigational systems and all the other paraphenalia that keeps it flying and a 747 is just a large piece of scrap metal. A bird, in contrast, can live on berries, seeds, worms, insects, small rodents, fish and bits of bread tossed to it by amused tourists. Its living and remarkably adaptable digestive system can convert all these and more into energy and essential raw materials for power and self repair.