Editor's note: This story is part of a series "Expelled: No Intelligence Allowed--Scientific American's Take."

In 1974 I matriculated at Pepperdine University as a born-again Christian who rejected Darwinism and evolutionary theory—not because I knew anything about it (I didn't) but because I thought that in order to believe in God and accept the Bible as true, you had to be a creationist. What I knew about evolution came primarily from creationist literature, so when I finally took a course in evolutionary theory in graduate school I realized that I had been hoodwinked. What I discovered is a massive amount of evidence from multiple sciences—geology, paleontology, biogeography, zoology, botany, comparative anatomy, molecular biology, genetics and embryology—demonstrating that evolution happened.

It was with some irony for me, then, that I saw Ben Stein's antievolution documentary film, Expelled: No Intelligence Allowed, opens with the actor, game show host and speechwriter for Richard Nixon addressing a packed audience of adoring students at Pepperdine University, apparently falling for the same trap I did.

Actually they didn't. The biology professors at Pepperdine assure me that their mostly Christian students fully accept the theory of evolution. So who were these people embracing Stein's screed against science? Extras. According to Lee Kats, associate provost for research and chair of natural science at Pepperdine, "the production company paid for the use of the facility just as all other companies do that film on our campus" but that "the company was nervous that they would not have enough people in the audience so they brought in extras. Members of the audience had to sign in and a staff member reports that no more than two to three Pepperdine students were in attendance. Mr. Stein's lecture on that topic was not an event sponsored by the university." And this is one of the least dishonest parts of the film.

At the Crossroads of Conspiracy
Ben Stein came to my office to interview me about what I was told was a film about "the intersection of science and religion" called Crossroads (yet another deception). I knew something was afoot when his first question to me was on whether or not I think someone should be fired for expressing dissenting views. I pressed Stein for specifics: Who is being fired for what, when and where? In my experience, people are usually fired for reasons having to do with budgetary constraints, incompetence or not fulfilling the terms of a contract.  Stein finally asked my opinion on people being fired for endorsing intelligent design. I replied that I know of no instance where such a firing has happened.

This seemingly innocent observation was turned into a filmic confession of ignorance when my on-camera interview abruptly ends there, because when I saw Expelled at a preview screening at the National Religious Broadcasters's convention (tellingly, the film is being targeted primarily to religious and conservative groups), I discovered that the central thesis of the film is a conspiracy theory about the systematic attempt to keep intelligent design creationism out of American classrooms and culture.

Stein's case for conspiracy centers on a journal article written by Stephen Meyer, a senior fellow at the intelligent design think tank Discovery Institute and professor at the theologically conservative Christian Palm Beach Atlantic University. Meyer's article, "The Origin of Biological Information and the Higher Taxonomic Categories," was published in the June 2004 Proceedings of the Biological Society of Washington, the voice of the Biological Society with a circulation of less than 300 people. In other words, from the get-go this was much ado about nothing.

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!

Who Speaks for Science?
The rest of the martyrdom stories in Expelled have similar, albeit less menacing explanations, detailed at www.expelledexposed.com, where physical anthropologist Eugenie Scott and her tireless crew at the National Center for Science Education have tracked down the specifics of each case. Astronomer Guillermo Gonzalez, for example, did not get tenure at Iowa State University in Ames and is portrayed in the film as sacrificed on the alter of tenure denial because of his authorship of a pro–intelligent design book entitled The Privileged Planet (Regnery Publishing, 2004). As Scott told me, "Tenure is based on the evaluation of academic performance at one's current institution for the previous seven years." Although Gonzales was apparently a productive scientist before he moved to Iowa State, Scott says that "while there, his publication record tanked, he brought in only a couple of grants—one of which was from the [John] Templeton Foundation to write The Privileged Planet—didn't have very many graduate students, and those he had never completed their degrees. Lots of people don't get tenure, for the same legitimate reasons that Gonzalez didn't get tenure."

Tenure in any department is serious business, because it means, essentially, employment for life. Tenure decisions for astronomers are based on the number and quality of scientific papers published, the prestige of the journal in which they are published, the number of grants funded (universities are ranked, in part, by the grant-productivity of their faculties), the number of graduate students who completed their program, the amount of telescope time allocated as well as the trends in each of these categories, indicating whether or not the candidate shows potential for continued productivity. In point of fact, according to Gregory Geoffroy, president of Iowa State, "Over the past 10 years, four of the 12 candidates who came up for review in the physics and astronomy department were not granted tenure." Gonzales was one of them, and for good reasons, despite Stein's claim of his "stellar academic record."

For her part, Scott is presented in the film as the cultural filter for determining what is and is not science, begging the rhetorical question: Just who does she think she is anyway? Her response to me was as poignant as it was instructive: "Who is Ben Stein to say what is science and not science? None of us speak for science. Scientists vary all over the map in their religious and philosophical views—for example, Francis Collins [the evangelical Christian and National Human Genome Research Institute director], so no one can speak for science."

From Haeckel to Hitler
Even more disturbing than these distortions is the film's other thesis that Darwinism inexorably leads to atheism, communism, fascism, and could be blamed for the Holocaust. Despite the fact that hundreds of millions of religious believers fully accept the theory of evolution, Stein claims that we are in an ideological war between a scientific natural worldview that leads to Stalin's gulag archipelago and Nazi gas chambers, and a religious supernatural worldview that leads to freedom, justice and the American way. The film's visual motifs leave no doubt in the viewer's emotional brain that Darwinism is leading America into an immoral quagmire. We're going to hell in a Darwinian handbasket. Cleverly edited interview excerpts from scientists are interspersed with various black-and-white clips for guilt by association with: bullies beating up on a 98-pound weakling, Charlton Heston's character in Planet of the Apes being blasted by a water hose, Nikita Khrushchev pounding his fist on a United Nations desk, East Germans captured trying to scale the Berlin Wall, and Nazi crematoria remains and Holocaust victims being bulldozed into mass graves. This propaganda production would make Joseph Goebbels proud.

It is true that the Nazis did occasionally adapt a warped version of social Darwinism proffered by the 19th-century German biologist Ernst Haeckel in a "survival of the fittest races" mode. But this rationale was only in the service of justifying the anti-Semitism that had been inculcated into European culture centuries before. Because Stein is Jewish, he surely knows that the pogroms against his people began ages before Darwin and that the German people were, in Harvard University political scientist Daniel Goldhagen's apt phrase (and book title), "Hitler's willing executioners."

When Stein interviewed me and asked my opinion on the impact of Darwinism on culture, he seemed astonishingly ignorant of the many other ways that Darwinism has been used and abused by political and economic ideologues of all stripes. Because Stein is a well-known economic conservative (and because I had just finished writing my book The Mind of the Market, a chapter of which compares Adam Smith's "invisible hand" with Charles Darwin's natural selection), I pointed out how the captains of industry in the late 19th and early 20th centuries justified their beliefs in laissez-faire capitalism through the social Darwinism of "survival of the fittest corporations." And, more recently, I noted that Enron's CEO, Jeffrey Skilling, said his favorite book in Harvard Business School was Richard Dawkins' The Selfish Gene (first published in 1976), a form of Darwinism that Skilling badly misinterpreted. Scientific theorists cannot be held responsible for how their ideas are employed in the service of nonscientific agendas.

Questioning Darwinism
A final leitmotif running through Expelled is inscribed in chalk by Stein in repetitive lines on a classroom blackboard: "Do not question Darwinism." Anyone who thinks that scientists do not question Darwinism has never been to an evolutionary conference. At the World Summit on Evolution held in the Galapagos Islands during June 2005, for example, I witnessed a scientific theory rich in controversy and disputation. Paleontologist William Schopf of the University of California, Los Angeles, for instance, explained that "We know the overall sequence of life's origin, that the origin of life was early, microbial and unicellular, and that an RNA world preceded today's DNA–protein world." He openly admitted, however, "We do not know the precise environments of the early earth in which these events occurred; we do not know the exact chemistry of some of the important chemical reactions that led to life; and we do not have any knowledge of life in a pre-RNA world."

Stanford University biologist Joan Roughgarden declared that Darwin's theory of sexual selection (a specific type of natural selection) is wrong in its claim that females choose mates who are more attractive and well-armed. Calling neo-Darwinians "bullies," the University of Massachusetts Amherst biologist Lynn Margulis pronounced that "neo-Darwinism is dead" and, echoing Darwin, she said, "It was like confessing a murder when I discovered I was not a neo-Darwinist." Why? Because, Margulis explained, "Random changes in DNA alone do not lead to speciation. Symbiogenesis—the appearance of new behaviors, tissues, organs, organ systems, physiologies or species as a result of symbiont interaction—is the major source of evolutionary novelty in eukaryotes: animals, plants and fungi."

Finally, Cornell University evolutionary theorist William Provine (featured in Expelled) presented 11 problems with evolutionary theory, including: "Natural selection does not shape an adaptation or cause a gene to spread over a population or really do anything at all. It is instead the result of specific causes: hereditary changes, developmental causes, ecological causes and demography. Natural selection is the result of these causes, not a cause that is by itself. It is not a mechanism."

Despite this public questioning of Darwinism (and neo-Darwinism), which I reported on in Scientific American, Schopf, Roughgarden, Margulis and Provine have not been persecuted, shunned, fired or even Expelled. Why? Because they are doing science, not religion. It is perfectly okay to question Darwinism (or any other "-ism" in science), as long as there is a way to test your challenge. Intelligent design creationists, by contrast, have no interest in doing science at all. In the words of mathematician and philosopher William Dembski of Southwestern Baptist Theological Seminary and a key witness in Stein's prosecution of evolution, from a 2000 speech at the National Religious Broadcasters convention in Anaheim, Calif.: "Intelligent design opens the whole possibility of us being created in the image of a benevolent God…. And if there's anything that I think has blocked the growth of Christ as the free reign of the spirit and people accepting the Scripture and Jesus Christ, it is the Darwinian naturalistic view."

When will people learn that Darwinian naturalism has nothing whatsoever to do with religious supernaturalism? By the very definitions of the words it is not possible for supernatural processes to be understood by a method designed strictly for analyzing natural causes. Unless God reaches into our world through natural and detectable means, he remains wholly outside the realm of science.

So, yes Mr. Stein, sometimes walls are bad (Berlin), but other times good walls make good neighbors. Let's build up that wall separating church and state, along with science and religion, and let freedom ring for all people to believe or disbelieve what they will.

Michael Shermer is Publisher of Skeptic (www.skeptic.com) and the author of Why Darwin Matters: The Case Against Intelligent Design. His new book is The Mind of the Market.