Gavra, The point is that upon who is the burden of proof? Maybe it is upon the agnostic to prove that a complex system can self-assemble. Therefore, if he can’t, then G-d must exist.
The only alternative to G-d is self-assembly. If that is impossible, then we have conclusively proved by elimination that G-d does exist. To conjure up a process of self-assembly, it would help to have some evidence that a working device has successfully been built using that method. If one cannot point to such a device, then it is only a figment of the questioner’s imagination. He is relying on a belief in some imaginary process as a viable alternative to G-d.
If he turns around and says prove that G-d exists, since that is only a figment of your imagination, the refutation is that since you are proposing something physical in our world, it can be tested. However, we cannot test the existence of a supernatural being who exists outside of our world.
Note, let me just clarify the concept of self-assembly. Suppose you wanted to design a bookshelf that was easy for the buyer to put together. You pack the pieces which have magnets attached into a box. You instruct the user that all he needs to do is open the box, dump the pieces on the floor, and the magnets will automatically pull all the parts together into a nice sturdy bookshelf. (Note some magnetic forces will be designed to turn screws or whatever, so it will not just be held together by magnets which could pop apart. But even if you could only get the thing into the right shape and held together magnetically, that would be quite a mean feat.)
You might choose to place electrical charge instead to guide the parts, or chemical interactions among atoms. Whatever you like.
Do you think this has been successfully done in any useful device? Now, even if one did it, he is starting with parts that were initially designed a certain way. If he had only a random jumble of atoms, how much more difficult is the problem?