Carl Zimmer puts in a nice entry on the new flounder evolution paper, covering the history of the question including the debate between Darwin and Mivart about the evolution of the upward-facing flounder eye position. It's a recommended read. Here's the end:
Amphistium and Heteronectes now join the transitional fossil hall of fame, along with a fish with limbs, Tiktaalik, and the limbed cousin of whales, Indohyus. They’re also a reminder that the argument, “It can’t possibly have evolved because I can’t imagine it evolved” is not an argument at all. It may be hard to imagine Amphistium and Heteronectes, but they are real. In fact, they’ve been sitting around in museums for centuries, waiting for someone to recognize their true wonder.
I especially like the aspect of "sitting around in museums," because the truth is that there are a lot of discoveries still waiting to be made on material removed from the ground decades ago. In this case, the ability to CT-scan the fossils is a nice new addition, but in fact there are lots of things that an eye trained in modern systematics will see that someone many years ago may have missed. Of course, in science fiction novels, it's usually some horrible ancient truth waiting to be discovered, but scientists are doing the real thing all the time!
