What I'm referring to is not only synthesis (artificially generating), but design and engineering. This is substantively different than natural products, in that they are truly invented.
That being said, I think that even if you take a natural gene and modify it meaningfully - that should be patent-able. For instance, if you take an enzyme and engineer a version that doesn't degrade as readily, or has much better activity, that should be patent-able, don't you think?
EDIT: There's a good deal of prior art regarding numbers. As for patenting molecules, we allow that all the time... drugs, compounds, etc. Because they are discovered as I describe above.