There's a gene that's pivotal in not only separating your right brain from your left, but also in making sure that you have two, individual eyes. That gene, and the protein it codes for, are both called Sonic Hedgehog. Here's how that happened.
As the NIH (somewhat wearily) explains in their notes on the gene, "The official name of this gene is 'sonic hedgehog.'" It is not a nickname or an epithet, if you're looking for another name to call it, the only acceptable substitutes the NIH can offer you are sonic hedgehog homolog (Drosophila), sonic hedgehog protein, or sonic hedgehog protein preproprotein. If you're really bound and determined to avoid any sonics at all costs, you can use the gene's official symbol, the almost equally evocative SHH.
So, what happened? The sonic hedgehog gene was one of a set of three genes all called hedgehog genes, due to their somewhat spiky appearance. But the Harvard lab where SHH was uncovered wasn't full of videogame fans, instead it was a six year comics fan who was responsible.
Harvard's Cliff Tabin, chair of their genetics department and the professor, whose lab was responsible for first cloning the sonic hedgehog gene, recounts that one of the lab's British post-docs, Robert Riddle, pulled the name out of a comic book that his daughter brought over from the U.K. At the time the videogame hadn't yet been released in the U.S. By the time it was, the paper detailing their process was also just being published.
As the importance of the gene began to better understood — and as Sonic the Hedgehog's videogame and then tv series really began to take off — many doctors and scientists suggested that the time had come for a change to the name. So much so that the Human Genome Organization's Nomenclature Committee put it on a top 10 list of gene names that they wanted changed (if for no other reason than to spare a doctor having to use the phrase "sonic hedgehog gene" in an explanation to a sick patient.) The name, however, stuck and continues on today.
Image: Sonic hedgehog protein structure / European Bioinformatics Institute