A simulation cannot be operated in isolation. If it seems to be, it’s because you don’t understand the simulation well enough.
Labs like mine are now developing 3-D assemblers (rather than printers) that can build structures in the same way as the ribosome. The assemblers will be able to both add and remove parts from a discrete set. One of the assemblers we are developing works with components that are a bit bigger than amino acids, cluster of atoms about ten nanometers long (an amino acid is around one nanometer long). These can have properties that amino acids cannot, such as being good electrical conductors or magnets. The goal is to use the nanoassembler to build nanostructures, such as 3-D integrated circuits. Another assembler we are developing uses parts on the scale of microns to millimeters. We would like this machine to make the electronic circuit boards that the 3-D integrated circuits go on. Yet another assembler we are developing uses parts on the scale of centimeters, to make larger structures, such as aircraft components and even whole aircraft that will be lighter, stronger, and more capable than today’s planes — think a jumbo jet that can flap its wings.
A key difference between existing 3-D printers and these assemblers is that the assemblers will be able to create complete functional systems in a single process. They will be able to integrate fixed and moving mechanical structures, sensors and actuators, and electronics. Even more important is what the assemblers don’t create: trash. Trash is a concept that applies only to materials that don’t contain enough information to be reusable. All the matter on the forest floor is recycled again and again. Likewise, a product assembled from digital materials need not be thrown out when it becomes obsolete. It can simply be disassembled and the parts reconstructed into something new.
The most interesting thing that an assembler can assemble is itself. For now, they are being made out of the same kinds of components as are used in rapid prototyping machines. Eventually, however, the goal is for them to be able to make all their own parts.