I believe if it has been well established that you use some design or protocol of which is publicly known and predates the new patent request it makes for a good court argument.
However I believe it doesnt apply in this case as the protocol is implemented in a fashion that is too wide-spreadly used to be controlled (ie a biological process).
That article suggests arguing it is a natural process thus it is discovery not invention, which is valid, but I am also suggesting you can argue the pervasiveness of the object makes it unfeasible to practically control via patenting.
The same argument can be made for the aussie fellow who attempted to patent the wheel to show exploitation of the current patent laws. He didnt get it because he couldnt prove he was the inventor, as common knowledge showed it predated him. However even if he was to be successful, counter-claims in court for royalty requests along the lines of the wide-spread general use and pervasiveness of the invention would be a strong case for denying royalties. (and in chicken-egg situation, would suggest the patent itself is invalid)
Anyway things get interesting when synthetic genes become widespread via gene therapy based technologies. As you will be able to buy genes with synthetic author markers to make you fitter, stronger, so opens up the possibility of gene piracy. People will flock to TheGenePirateBay.org instead of the iGenes store..