I don't think they meant it in that way. Rather, they're looking for a trigger which led us on different evolutionary paths. I think this story was written in a sensationalist fashion. This article is very scientific and difficult to understand, but I can see they aren't making such stark claims: http://www.nature.co...ncomms2146.html
I think this is only the tip of the iceberg, as there are too many differences to be carried out by only one gene. For instance: the aids virus does not affect apes, but it does heavily affect humans. It is not only about intelligence...
Conclusions like this are really worrisome because science funding is getting scarce and things are looking ugly.
Junk genes are as junk as the ignorance of the ones who give it's name.