I identified this as an example of the error of equivocation, and pointed out that he meant two different things by "design" in the same setence. What he was really asking was, "can a system without conscious planning bring about functional complexity?".
The question becomes a lot more ordinary, and less "self-contradictory" (and thus less "loaded") when restated more precisely.
The use of "create" in the original sentence was carrying a lot of baggage as well, since it carries strong connotations of intentional purpose (as does "design" itself).