Nevertheless, some members of the organization voiced their displeasure, so the society's governing council released a statement explaining, "Contrary to typical editorial practices, the paper was published without review by any associate editor; Sternberg handled the entire review process. The council, which includes officers, elected councilors and past presidents, and the associate editors would have deemed the paper inappropriate for the pages of the Proceedings." So how did it get published? In the words of journal's managing editor at the time, Richard Sternberg, "it was my prerogative to choose the editor who would work directly on the paper, and as I was best qualified among the editors, I chose myself." And what qualified Sternberg to choose himself? Perhaps it was his position as a fellow of the International Society for Complexity, Information, and Design, which promotes intelligent design, along with being on the editorial board of the Occasional Papers of the Baraminology Study Group, a creationism journal committed to the literal interpretation of Genesis. Or perhaps it was the fact that he is a signatory of the Discovery Institute's "100 Scientists who Doubt Darwinism" statement.

Meyer's article is the first intelligent design paper ever published in a peer-reviewed journal, but it deals less with systematics (or taxonomy, Sternberg's specialty) than it does paleontology, for which many members of the society would have been better qualified than he to peer-review the paper. (In fact, at least three members were experts on the Cambrian invertebrates discussed in Meyer's paper). Meyer claims that the "Cambrian explosion" of complex hard-bodied life forms over 500 million years ago could not have come about through Darwinian gradualism. The fact that geologists call it an "explosion" leads creationists to glom onto the word as a synonym for "sudden creation." After four billion years of an empty Earth, God reached down from the heavens and willed trilobites into existence ex nihilo. In reality, according to paleontologist Donald Prothero, in his 2007 magisterial book Evolution: What the Fossils Say and Why it Matters (Columbia University Press): "The major groups of invertebrate fossils do not all appear suddenly at the base of the Cambrian but are spaced out over strata spanning 80 million years—hardly an instantaneous 'explosion'! Some groups appear tens of millions of years earlier than others. And preceding the Cambrian explosion was a long slow buildup to the first appearance of typical Cambrian shelled invertebrates." If an intelligent designer did create the Cambrian life forms, it took 80 million years of gradual evolution to do it.

Stein, however, is uninterested in paleontology, or any other science for that matter. His focus is on what happened to Sternberg, who is portrayed in the film as a martyr to the cause of free speech. "As a result of publishing the Meyer article," Stein intones in his inimitably droll voice, "Dr. Sternberg found himself the object of a massive campaign that smeared his reputation and came close to destroying his career." According to Sternberg, "after the publication of the Meyer article the climate changed from being chilly to being outright hostile. Shunned, yes, and discredited." As a result, Sternberg filed a claim against the Smithsonian National Museum of Natural History (NMNH) for being "targeted for retaliation and harassment" for his religious beliefs. "I was viewed as an intellectual terrorist," he tells Stein. In August 2005 his claim was rejected. According to Jonathan Coddington, his supervisor at the NMNH, Sternberg was not discriminated against, was never dismissed, and in fact was not even a paid employee, but just an unpaid research associate who had completed his three-year term!