Sonic Hedgehog is one of three proteins in the mammalian signaling pathway family called hedgehog. This particular pathway is shaped like the animal, and that's where it got it's name.
All three proteins were discovered in 1995, and while the other two were named after actual species of hedgehogs, scientists decided to name this particular protein after the Sega character.
Sonic Hedgehog has critical roles in the development of mammalian brains. However, a potential inhibitor has been found, and dubbed Robotnikinin, a play on the name of Dr. Robotnik, Sonic's nemesis.
Some people criticize the naming as being frivolous and a little inappropriate when people have to be told that their child has a serious illness because they have a mutated sonic hedgehog. What do you think?