How about a storm system, or a tornado. Are the air molecules intelligent? As a simpler, if more trivial, example, the sand grains on a beach are organized. The grains are larger to smaller in size as one moves up the beach. Is the surf "intelligent"? Does it "know" to loose energy, and therefore deposit smaller grains, as it moves up the beach?
If by "intelligent" you include the attribute of personhood, I don't think so. But I am fairly certain every particle of the universe expresses itself collectively in such a way as to manifest design and intelligence.