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Now shift to Intelligent Design. The story is newer, and far from over. But already it’s looking like Climate Research parte deux, down to the coverage by the Chronicle of Higher Education's Richard Monastersky.

Recently, ID advocate Stephen Meyer of the Discovery Institute published a review article in a little known taxonomic journal called the Proceedings of the Biological Society of Washington (that’s D.C.). Focusing on the well-known “Cambrian Explosion,” Meyer argued that evolutionary theory could not account for the appearance of new organismal forms in a relatively short period of geological time. Instead, Meyer concluded by suggesting that “intelligent,” “rational” agents may have been responsible for the “origin of new biological information.” It was the first time the intelligent design movement has published in a peer reviewed biology journal.

Meyer had sent his article to an editor, Richard Sternberg, who sits on the editorial board of the Baraminology Study Group, which studies “creation biology” and is based at Bryan College, a fundamentalist Christian school in Tennessee named (fittingly enough) after anti-Darwin crusader William Jennings Bryan. Sternberg—who is reportedly no longer editor of the Proceedings—sent the paper out to three unnamed reviewers and claims they recommended publication.

Now comes the controversy. The pro-ID Discovery Institute has trumpeted the study, media coverage has begun, and evolution defenders predict ID advocates will use the study to try to get critiques of evolution into public schools by claiming they're based on published science.

Not surprisingly, mainstream scientists are fighting back. Several have authored a devastating critique of Meyer’s paper on the blog The Panda’s Thumb and are preparing a more thorough version, presumably for publication. The critique charges that Meyer’s article systematically ignores relevant scientific literature and contains serious “errors in facts and reasoning.” The Biological Society of Washington, meanwhile, has already issued a statement noting that the article represented a “significant departure from the nearly purely taxonomic content for which this journal has been known throughout its 124-year history” and was “inappropriate for the pages of the Proceedings.”

But once again, the damage has been done. The Discovery Institute defends Meyer’s work and will undoubtedly continue to do so. In response to the statement from the Biological Society of Washington, Discovery has accused the group of imposing a “gag rule on science” (never mind that Meyer’s article was beyond the scope and traditional subject matter of the Proceedings). Meanwhile, evolution defenders claim the article in question wasn’t even particularly original to begin with.

What conclusions can we draw from these two case studies in the publication of dubious science by peer reviewed journals?

The first is that we shouldn’t exaggerate the benefits of peer review or pretend it’s an absolute guarantor of scientific truth. On the contrary, the forms, methods, and merits of peer review vary widely both by journal and by standards of practice. Peer review is an important norm in science, and groups who make scientific claims without publishing in the peer reviewed literature should be regarded skeptically on the grounds that they're not actually engaging in the scientific process. But that doesn't mean successfully publishing a single peer reviewed article in a little known journal ensures scientific credibility.

Another conclusion is that in scientific debates with intense political and policy relevance, we shouldn’t be surprised that both camps want to claim that the evidence lies on their side. In order to do so, scientists on the fringe will inevitably seek to bolster their credibility through peer reviewed publications. Obscure journals working in controversial areas should therefore enforce rigorous quality standards, while remaining careful not to censor new ideas or limit legitimate scientific debate. They should take the stories of Climate Research and the Proceedings of the Biological Society of Washington as a serious warning. These journals have now had their reputations dragged through the mud.

Finally, politicians and policymakers need to decrease the incentives for science abuse by showing that they're unwilling to aid and abet it. So long as the James Inhofes of the world devote entire Senate hearings to single, controversial scientific papers, and announce that they shift the scientific paradigm, we will have Climate Research and Proceedings-type controversies. Instead of contested studies hot off the presses, politicians should generally restrict themselves to relying upon the conclusions of major scientific consensus documents, such as reports from the National Research Council of the National Academy of Sciences. In the long run, it would save them considerable embarrassment.

The intelligent design perspective, which is so prominent now in the evangelical church and, of course, is a flashpoint for debates about the teaching of science in schools, is basically that evolution might be OK in some ways, but it can't account for the complexity of things like the bacterial flagellum, which are considered to be irreducibly complex because they have so many working parts and they don't work with any of the parts dropping out, so you can't imagine how evolution could have produced them.

This is showing severe cracks scientifically in that the supposedly irreducibly complex structures are, increasingly, yielding up their secrets, and we can see how they have been arrived at by a stepwise mechanism that's quite comfortable from an evolutionary perspective. So intelligent design is turning out to be -- and probably could have been predicted to be -- a God-of-the-gaps theory, which inserts God into places that science hasn't quite yet explained, and then science comes along and explains them.

I think I would also say intelligent design is not only bad science; it's questionable theology. It implies that God was an underachiever and started this evolutionary process and then realized it wasn't going to quite work and had to keep stepping in all along the way to fix it. That seems like a limitation of God's omniscience.

So science figured out that one way to try to explore spiritual experience and look at the brain mechanics of religious experience is to look at people with temporal lobe epilepsy on the theory that the extreme elucidates the normal. Temporal lobe epilepsy is basically an electrical storm in the brain where all the cells fire together. Usually seizures are really horrible things. I went to a Henry Ford hospital to the epilepsy clinic and it was just -- it's a horrifying experience to watch a seizure. But in a few rare cases, people have ecstatic seizures, and they believe that they are having a religious experience. They may hear snatches of music or words, presumably from their memory bank, and they interpret it as a message from God or the music from the heavenly spheres. They may see a snatch of light and think that that's an angel.

Today a lot of neuroscientists have kind of retrofitted a lot of major religious leaders with temporal lobe epilepsy. Like Saul on the road to Damascus -- was he blinded by God and heard Jesus' voice or did he suffer, as one neurologist said, "visual and auditory hallucinations with photism and transient blindness"? Joseph Smith, the founder of Mormonism, did he see a pillar of light and two angels or did he suffer a complex partial seizure? What about Moses and the burning bush, hearing God's voice?

Now I've got to say, I have a little trouble with this kind of retrofitting, because it's hard to imagine something as debilitating as epilepsy being helpful in writing, say, the bulk of Christian doctrine, as did Paul; guiding a nation through the wilderness for 40 years, as did Moses; or founding one of the three monotheistic religions, as did Mohammed. But I do think that scientists are onto something. I think the temporal lobe may in fact be the place that mediates spiritual experience.

One of the people who convinced me of this is a guy named Jeff Schimmel. Jeff is a writer in Hollywood. He was raised Jewish, never believed in God, had no interest in spirituality. Then a few years ago, nine years ago, when he was 40 years old, he had a benign tumor in his left temporal lobe removed. The surgery was a snap, but a couple of years later, unknown to him, he began to suffer from mini-seizures. He began hearing things and having visions. He remembers twice lying in bed when he looked up at the ceiling and saw a kind of swirl of blue and gold and green all settle into a shape, a pattern. He said, then it dawned on me, it was the Virgin Mary. Then he thinks, why would the Virgin Mary appear to a Jewish guy? But a few other things began to happen to Jeff. He became fascinated with spirituality. He found himself weeping at the drop of a hat when he saw pain in other people. He became fairly obsessed with Buddhism.

But he began to wonder, could his newfound spirituality have anything to do with his brain? So the next time he visited his neurologist, he asked to see a picture of his brain scan, the most recent one. And, in fact, the temporal lobe was very different before and after the surgery. It had kind of pulled away from the skull. His temporal lobe was smaller, a different shape, it was covered with scar tissue, and those changes had begun to spark electrical firings in his brain. He essentially developed temporal lobe epilepsy. But there was no question in his mind that his faith, his newfound love for his fellow man, all of that, came from his brain.

Teacher qualifications: The No Child Left Behind Act requires that all teachers of core subjects be “highly qualified.” Definitions of “highly qualified” vary by state, but most include demonstrated competence in the teacher's teaching assignment. Our data suggest that high school teachers who completed the largest number of college-level credits in biology and life science classes and whose coursework included at least one class in evolutionary biology devote substantially more class time to evolution than teachers with fewer credit hours (Table S6). The best prepared teachers devote 60% more time to evolution than the least prepared.