David X. Cohen was inspired to write the episode after a trip to Manhattan's American Museum of Natural History, where he decided to turn the visit into a "business trip", and think of a possible episode connection to the museum. He initially wanted Lisa to find a "missing link" skeleton, and do an episode reminiscent of the Scopes Monkey Trial. George Meyer convinced him instead to have the focus be on an angel skeleton, while keeping an emphasis on the conflict between religion and science.
Stephen Jay Gould's original final line was "I didn't do the test. I had more important work to do", but it was cut because the writers felt it would be funnier to give him a short final line.
The only phrase that Stephen Jay Gould objected to in the script was a line that introduced him as the "world's most brilliant paleontologist".
The scene in Judge Snyder's courtroom where Lisa is put on trial for stealing the skeleton is seen as a reference to the 1920s Scopes Monkey Trial in Dayton, Tennessee, which dealt with issues of separation of church and state and the debate between creationism and evolutionism.
Both David X. Cohen and George Meyer acknowledged how silly the "angel skeleton" idea was owing to simple questions raised such as why an angel died and why bones were left behind, but they went forward with the idea anyway.