Expelled seems to me to be the right-wing analog of Fahrenheit 9/11. Stylistically, it is almost an homage to Michael Moore: From the ironic use of boomer-era musical counterpoint, to the knowingly deadpan interview style, to the extended view of a disfavored male interview subject having make-up applied, to the befuddled narrator trying to find an interview subject in the first place, it is designed to set up the image of a regular guy confronting sinister forces of immense, hidden power. At the level of ideas, the resemblance is just as obvious: An effort to take a preexisting belief about the illegitimate use of power, find some facts to fit to it, and do the rest of the work with insinuation and innuendo.
Expelled makes two key assertions. First, the scientific establishment has prevented adequate consideration of Intelligent Design (ID). Second, the scientific finding of evolution through natural selection logically entails atheism and nihilism.
There is a germ of truth to the first assertion. I’m sure that you would hard-pressed to get the editors of a reputable scientific journal to publish a paper that depends explicitly on ID. Of course, it would be just as hard to convince them to publish a paper that was premised on the phlogiston theory of combustion or that presented a perpetual motion machine.
This is because, in order to make practical progress, scientists accept paradigms (e.g., the Modern Synthesis of evolutionary biology) that have demonstrated the ability both to account for a wide range of empirical observations, and to produce useful scientific results. A paradigm helps to create a coherent discipline. The day-to-day work of scientists is to solve intellectual puzzles that fall within the relevant paradigm.
But this is just a specialized way of being close-minded, and so on its face seems like a pretty bad idea. Strangely, paradigms are useful. The reason is that to make progress you have to make some assumptions. If I started my day by demanding that I prove my own existence, I’d never get out of bed.
At this point ID advocates say Aha! You see, scientists aren’t giving ID a fair hearing, because it’s just too far outside of the box for the intellectual pygmies who comprise the biology faculties of every major research university in the world. The problem with this is that science has a proven track record of subverting existing paradigms, and replacing them, once superior alternatives are proposed. This process is imperfect and always takes time to work, but it does work. Obvious examples include the triumphs of heliocentric astronomy, the law of conservation of matter, the oxygen theory of combustion, the germ theory of disease, plate tectonics, special relativity, general relativity, and quantum mechanics.
Against this, Expelled provides the following evidence for the supposedly unique resistance of the scientific establishment to ID: Several academics claim that they have been fired or denied tenure, or had other professional setbacks, because they advocated ID. Expelled claims that the institutions responsible either didn’t respond to interview requests, or else had PR personnel repeat talking points in a robotic monotone.