The judge’s ruling was not a surprise to those of us who had spent time at the trial, which had earned the nickname Monkey Trial II, a reference to the famous 1925 court case in which Tennessee schoolteacher John Scopes was found guilty of teaching evolution. In the Harrisburg, Pa., courtroom, we could see from the first week that the trial was going badly for I.D. proponents. That the school board intended to promote their religious views was evident, as was the strong scientific consensus that the basic tenets of evolution were unimpeachable.

The much ballyhooed scientific defense of I.D. — the idea that some aspects of the natural world are best explained as designed by some unnamed intelligence rather than as the products of purely naturalistic processes — was also a dud. Then came an article in the Dec. 4 New York Times suggesting that I.D. may be losing some academic ground in the evangelical Christian colleges that were assumed to be its base.

Despite Jones’ ruling, the Discovery Institute, the Seattle-based engine of the I.D. movement, is claiming victory. “Anyone who thinks a court ruling is going to kill off interest in intelligent design is living in another world,” says John West, associate director of the Discovery Institute’s Center for Science and Culture, in a press release. “Americans don’t like to be told there is some idea that they aren’t permitted to learn about. Banning intelligent design in Dover will likely only fan interest in the theory.”

Although it seems far-fetched to spin I.D.’s loss in Dover as a triumph, I.D. remains firmly rooted in mainstream culture. After all, 2005 was a banner year for the theory. Pope Benedict XVI embraced the “intelligent project” that he said underlies nature, and President Bush endorsed teaching I.D. alongside evolution. The Kansas School Board decided to alter its definition of science to accommodate I.D., and several school boards around the country promise to follow suit.

Perhaps Tuesday’s ruling will cause people to think differently about I.D., but polls taken earlier this year suggest that most Americans consider I.D. or some form of creationism a plausible alternative to evolution. A growing majority thinks it should be taught as an alternative to Darwin’s theory in public science classrooms.

Most significantly, given that I.D. has reached a tipping point in the United States, nearly every high school biology teacher, community college instructor and college professor is being forced to deal with it in one way or another. Some dismiss it outright, but others are striving to craft intelligent ways to incorporate it into their classrooms, including the controversial approach known as “teach the controversy.” As recently as 10 years ago, few could have guessed that science teachers would be wrestling with how to weave God into their curriculums. But thanks to the publicity surrounding I.D., many teachers say they don’t have much choice.

Intelligent design did not spread through culture on its scientific merits. It got a big push from religious and political advocates. Funded by millions of dollars from some of the same religious supporters that helped put President Bush in the White House (conservatives like Philip F. Anschutz, Richard Mellon Scaife, and Howard and Roberta Ahmanson), the Discovery Institute has pushed a fringe academic movement onto virtually all the front pages and TV sets in the country. The New York Times has reported that the institute has granted $3.6 million in fellowships to 50 researchers since 1996. Those investments produced 50 books on intelligent design, innumerable articles, and two I.D. documentaries that were broadcast on public television.

Oxford biologist Richard Dawkins has said that Darwin’s theory of evolution made it possible to be an intellectually satisfied atheist. Intelligent design, it seems, has made it possible for many fundamentalists to be intellectually satisfied creationists. Wesley Elsberry, a biologist at the National Center for Science Education, says millions of evangelical Christians craved a more science-like, sophisticated yet Bible-friendly theory to explain the diversity of life on earth.

“Discovery’s early documents say that they consider the Christian community to be their base,” Elsberry says. “They mean people who are in some sort of fundamentalist faith community, which takes a literal approach to Genesis. That’s by far their biggest public base and it was ready-made for I.D.,” says Elsberry.

In fact, I.D.’s advance has been one of the great coups of modern public relations, says Barbara Forrest, philosophy professor at Southeastern Louisiana University. She points out that plenty of bad science has been launched into the orbit of public consciousness — Ronald Reagan’s space-based missile system, for one — but intelligent design is different. “I.D. is not bad science,” she says. “It is non-science.” With her Southern accent, she pronounces it “nonsense.”

Intelligence design “is not just non-science — it’s anti-science,” says Brown University biologist Kenneth Miller, who testified against I.D. at the Dover trial. It doesn’t merely defy the definition of “science,” which limits explanations to naturalistic causes, but also stops research in its tracks by attributing complex problems to supernatural causes.

Yet the I.D. movement has infiltrated the mainstream with “good slogans and sound bites,” Forrest says, adding that I.D. advocates’ “most intuitively compelling argument is their appeal to the American public and to parents to let their kids hear both sides of the debate. But it’s a bogus appeal: There’s nothing fair about trying to teach children something that isn’t true.”

West bristles at the idea that I.D.’s success is due to good P.R. “Darwinists like Forrest don’t seem to understand that by caricaturing I.D. they ultimately undercut their own efforts,” he says. “When students or scholars who have been exposed to Forrest’s straw-man version of I.D. actually read science journal articles or academic books by I.D. scholars, they suddenly discover for themselves that the evidence and arguments for I.D. are a lot more impressive and sophisticated than they’ve been led to believe. And once they start to engage the real issues raised by the scientific evidence, the spin and scare tactics pushed by Darwinian fundamentalists like Forrest don’t cut it.”

Whether I.D.’s scientific core is “impressive and sophisticated,” as West says, is debatable. Certainly Judge Jones didn’t think so. Still, biology teachers are being pressured to bring it into their classrooms. A recent study published in American Biology Teacher, for instance, shows a near doubling over the past decade of public-school teachers in Minnesota who report being pressured from students, parents or administrators to spend less time teaching evolution in their classes. The study also shows growing pressure to teach creationism as an alternative to evolution.

An increasing number of high school science teachers are happy to comply. Twenty percent of Minnesota science teachers and nearly 50 percent in Kansas have endorsed teaching some form of creationism alongside evolutionary theory.

“The real danger is not that teachers will start teaching creationism,” says geologist Warren Allmon, the director of the Museum of the Earth in Ithaca, N.Y., which features an exhibit on evolution seen by thousands of school kids every year. “It’s that they will stop, or reduce, the teaching of evolution. Many now just assign [students to voluntarily read] the chapters on evolution and don’t cover it in class, in order to avoid controversy.”

Allmon’s museum has initiated a special training program to help museum docents answer the growing number of questions about creationism and intelligent design that come from visitors. “There has been a definite increase over the past two years,” he says, “though the questions are by no means all hostile ones coming from creationists. Even visitors who understand evolution are curious about what all the commotion over I.D. is about.” The museum docents explain to visitors that the theory of evolution neither confirms nor denies the existence of God and that such questions are simply not the bailiwick of biology.

Many high school biology teachers still object to even discussing I.D. in their classrooms, saying that although there are lively controversies within evolutionary biology (arguments, for example about the relative importance of natural selection, sexual selection and physiological selection, or about the mode and tempo of evolutionary change), they are not “weaknesses” but inevitable and welcome signs of a lively science. Teaching I.D. alongside evolution would give it more scientific credibility than it deserves, they say.

“Whenever you debate, you should really have one person representing I.D. on one side and 10,000 scientists on the other,” says Brown University biologist Miller. “That would give a fair representation of the division of opinion in the scientific community.”

But refusing to discuss it gives the wrong impression, too, making it appear that scientists are afraid of it, think it is irrelevant, or are just too arrogant to bother. “There is an intellectual curiosity on the part of kids I teach,” says Mark Stefanski, a high school science teacher at Marin Academy, a private school in San Rafael, Calif. “I don’t want to teach them creationism and I won’t. But they do want to know where all of this interest in intelligent design and creationism is coming from.”

College-level academics and research scientists face a more acute Catch-22. If they debate creationists and I.D. proponents in public, they lend credibility to the notion that there is a substantial debate going on within science, says Miller, one of the few prominent biologists who publicly debates intelligent-design advocates. His many debates and published point-and-counterpoints with I.D.’ers were cited as evidence of scientific controversy in Dover. “But if we don’t engage, it can mean ceding the public square to the other side, and that can be a huge mistake as well.”

“The important thing,” Miller says, “is always to make the distinction between the very real debate that is going on over science education and the non-debate among scientists about the validity of evolution on the whole. There is not a single scientific organization of any size anywhere in the world that has endorsed the point of view that these folks want to elevate to the level of science.”

Teachers are addressing intelligent design in their classrooms in a variety of ways. Carol Dixon, a high school biology teacher in Castro Valley, a suburb east of San Francisco, tells her students that any discussion of religious subjects must be kept out of the science classroom because the First Amendment’s establishment clause, protecting the separation of church and state, requires it.

“If my students ask about intelligent design or creationism, or ask me about my own religious views, I simply tell them that it’s not an appropriate subject for science class,” she says. “If I were required to teach about creationism or intelligent design, I’d have some serious problems. I’m just not trained to teach religion. And I don’t want to.”

Melissa Kindelspire, another high school biology teacher in Castro Valley, doesn’t pull any punches when it comes to teaching evolution. “The theory of evolution via natural selection is the thing that ties everything else we are learning in my classroom together. If and when there are other [non-evolution-based] scientific theories that are accepted by scientists, I will introduce them,” she says. But in her opinion, I.D. doesn’t come close to fitting that bill.

Kindelspire says that she has heard from some students and parents who are troubled by her straightforward defense of evolution. But when parents give her brochures about creationism, she simply thanks them and puts the brochures aside. However, one recent incident did make her a little uneasy. She was told that the science department, and her name specifically, came up at a local church in a sermon about “evil influences on the parishioners’ children’s souls.”

Other teachers, such as Dawn Wendzel and Julie Olson, who teach seventh-grade science in Gull Lake Middle School, near Kalamazoo, Mich., have simply woven I.D. into their curriculum. The two teachers, both evangelical Christians, presented I.D. as an alternative to evolution and had their students write papers comparing and evaluating the two views. Complaints from parents brought their practice to a halt. But Gull Lake school administrators have decided to make I.D. the subject of an elective social study class available to high school students.

The Discovery Institute advocates “teaching the controversy” about evolution, an approach that casts doubt on the biological validity of natural selection and gives credence to I.D. The term was coined about 20 years ago by Gerald Graff, an English professor at the University of Chicago, to describe a method of exploring cultural disagreements over whether, say, Huck Finn is a racist, rather than simply teaching one side or the other of a conflict.

Graff, a self-described “secular left-liberal” says he first felt as if his “pocket had been picked when the intelligent design crowd appropriated my slogan.” But recently, in an essay in Inside Higher Ed, Graff suggests there may be a silver lining to the I.D.-evolution debate.

“I can at least imagine a classroom debate between creationism and evolution that might be just the thing to wake up the many students who now snooze through science courses,” Graff writes. “Such students might come away from such a debate with a sharper understanding of the grounds on which established science rests, something that even science majors and advanced graduate students now don’t often get from conventional science instruction.”

Some teachers, such as Susan Sperling, an anthropology and interdisciplinary studies professor at Chabot College in Hayward, Calif., have adopted a version of this process. She is trying to teach the controversy without granting undue legitimacy to I.D. as science. This semester, Sperling, a Berkeley-trained physical anthropologist, is holding a course in which her students learn about evolutionary biology by reading Charles Darwin’s “On the Origin of Species.”

In connection with the course, Sperling organized a series of three public lectures about creationism, I.D. and evolution. “I thought it would be good to have students and others in our community provided with a forum for looking at intelligent design in its larger cultural context,” Sperling says, “and to be able to see the debate from different sides.”

I decided to attend the lectures for myself. I wanted to see how the largely working-class, middle-American students at Chabot would respond to the different lecturers: Elsberry, an evolutionary biologist; Ken Malloy, a young-earth creationist and author; and Philip Johnson, a retired UC-Berkeley law professor who is considered the father of I.D.

Elsberry launched the series to a standing-room-only crowd, with a detailed review of the history of evolutionary theory from pre-Darwin days until now. It was thorough and fair and totally lacking in hype or flair. As one who has long studied evolution and natural history, I managed to follow along. But judging by the drooping heads and the dozen or so empty seats when the lights came up, I’m not sure how many of the Chabot students did.

At one point, as Elsberry was zipping through his talk about the synthesis of species, the young woman next to me muttered “Jesus” in exasperation before abandoning her frantic effort to take notes. For the rest of the talk, she just sat there, eyes half shut, letting the names, facts and figures wash over her like a foreign language.

Elsberry’s commitment to detail and lack of rhetorical flourish sent Sperling into a bit of a panic. “Dr. Elsberry is a wonderful and meticulous scientist, but I don’t think he really could see how little of what he was saying his audience even understood,” she said after his lecture. “And now, to be brutally honest, I’m worried that I may be undermining my own science teaching.” In other words, she was afraid the next speakers, the anti-evolutionists, might win the day.

I could see what an uphill climb it is for biologists trying to compete for the hearts and minds of Americans that are undereducated in the sciences, especially in evolutionary biology. Evolutionary theory isn’t Einsteinian relativity, but it is counterintuitive in many ways and a detailed explanation is needed for it to make much sense, while the essential I.D. argument has a strong intuitive appeal: Life is too complex and meaningful to be accidental.

Yet some Chabot faculty members were just happy to see students and the community showing up for a public science lecture at all. “I could never draw this kind of crowd with a straightforward lecture on astronomy,” Scott Hildreth, a lecturer in astrophysics at Chabot, told me. “This is a great forum in which to teach students about the meaning of science, where its limits are, and what it’s all about.”

A week later, Malloy, the young-earth preacher, was before the same audience explaining his literal interpretation of Genesis: Earth is about 6,000 years old, Noah’s Ark was real (it has been found in Turkey, proven authentic beyond a shadow of doubt, he says), and rescued not only two of every currently living species, but two of every species that had ever lived, including Tyrannosaurus rex. He explained that T. rex had had to be brought aboard as babies, due to space constraints. “I use the words ‘evolutionist’ and ‘atheist’ interchangeably,” he said. He dismisses carbon and other dating techniques of fossils as simply inaccurate. It was almost surreal, an evolutionist’s nightmare, seeing a fundamentalist creationist standing in a college lab teaching a biology lecture right out of the Bible.

The lab full of students sat up straight and paid attention during Malloy’s talk. For one thing, unlike Elsberry’s lecture, it allowed them to easily follow his drift, even if, as Sperling pointed out afterward, “he might as well have been a tribesman telling creation stories from the highlands of New Guinea.”

“Even though he said his claims were true, there wasn’t any mistaking them for science,” says Chabot freshman Christopher Jacob. “It was just interesting to see how different someone’s view of the world could be.”

The next lecture, by Johnson, would be more problematic for the 18-year-old Jacob, who afterward said he was thinking of studying biology to protect science from “political attacks like this.”

Johnson’s 1993 book, “Darwin on Trial,” the publication of which marks the birth of I.D., is a rhetorically powerful critique of evolutionary biology that avoids saying much about God or the Bible. In his lecture at Chabot, Johnson argued that the evidence for I.D. is strong, that evolution is full of logical and evidentiary gaps. “Science should follow the evidence wherever it leads, not draw some arbitrary line at the appearance of design,” he said. “To say, ‘Despite the evidence [for design], we won’t look there’ is very unscientific.”

Although Johnson is recovering from a stroke that impaired his speech, he had no problem holding the Chabot College audience’s attention. Even Sperling, a trained evolutionist, was compelled by some of Johnson’s arguments, saying they caused her to “think hard and long about how the boundaries of science get drawn.”

Now that the lecture series is over, Sperling says she is convinced “that the evidence, power and logic of evolution speak for themselves. As an evolutionist and teacher, I’m not in the business of compelling anyone’s opinion. There are good reasons that evolution is the organizing theory of modern biology, and my students can see that and think critically and intelligently about what they are hearing.”

Time will tell whether I.D. continues to thrive in the nation’s public schools. In the meantime, John Hoopes, an anthropologist at the University of Kansas, has designed his own intelligent approach to teaching I.D. Next fall, he will hold a class titled “Archaeological Myths and Realities.” It will cover UFOs, crop circles, ESP and intelligent design.

On Sept. 26, the first day of trial, Thompson, in an elegant dark suit, is standing on the steps of the U.S. Middle District Courthouse in Harrisburg, Pa. The trial has adjourned for the day. It is expected to continue through the first week of November.

A light rain falls as lawyers and advocates on both sides of the debate are making public comments. But nearly all of the reporters, photographers and cameramen surround Thompson. He is short and powerfully built, white-haired but bald on top, and endowed with an impressive nose and preternaturally white teeth. He has the defiant, almost menacing energy of an armed man on a moral mission.

Thompson is holding forth on his defense strategy. He says his scientific experts will show that I.D. is a valid scientific theory based on empirical observation by credentialed and respected scientists. He is arguing that no theory should be judged by its historical roots, even if they are religious, or even if they are creationist. Modern chemistry emerged from alchemy, after all, and that doesn’t make it bogus. Astronomy emerged from astrology, and we don’t hold that against it. Nor should a theory be judged by the personal ideologies of those who hold it; plenty of Darwinists are atheists, but that doesn’t disqualify evolutionary biology as an ideology, he says.

Schools that want to include the I.D. debate in their curriculum deserve the right to do so, Thompson says. Denying them that right is a form of both scientific and religious discrimination. “I.D. is seeking a place in the classroom because of its merits,” he says. “But it’s being kept out because it is harmonious with the Christian faith.”

He continues: “There are two Americas today, one that’s still very religiously based, and another that has no foundation, where everything is relative, where everything goes.” And the moral relativism that dominates the second America is an ideology enabled by Darwinism.

“All scientific theories, including Darwinism, have religious implications,” Thompson says. And the religious implication of Darwinism is atheism. Furthermore, moral relativism, atheism and the idolatry of science are symptoms of our “floundering society.” Thompson says he aims to put society back on track, and that track is there for us, laid down by God. “We do this, all of the attorneys I’m working with do this, because of our religious commitment.”

“Do you believe that we and other primates descended from common ancestors?” a British filmmaker calls out. Thompson bites his finger and says, “Do I think I evolved from an ape? No, I don’t believe my ancestor was a monkey.”

Thompson stole the lines from William Jennings Bryan.

Bryan was the lawyer, orator, statesman and progressive evangelical Christian who, 80 years ago, argued against teaching evolution in high school in the Scopes Monkey Trial in Dayton, Tenn. Although Bryan won the Scopes trial, he is remembered for taking an intellectual pummeling on the stand by Clarence Darrow — perhaps the second most famous lawyer of the day and an advocate for evolution and modernity. While the Scopes trial set off decades of anti-evolution legislation in states around the country, it is also remembered as the beginning of the end for American creationism.

Who could have guessed that the ideologies fueling the Scopes trial would evolve enough to bring us this new version four-fifths of a century (and libraries full of evolution-supporting evidence) later? Well, Thompson could have. “Questions about the role of design in creation have been asked for thousands of years,” he says. “They haven’t been put to rest at all. They’re just getting stronger.”

Kitzmiller et al. v. Dover Area School District — the trial’s official name — was hatched in October 2004 when a small south central Pennsylvania community’s school board passed a resolution mandating that ninth-grade biology teachers launch their class by reading four paragraphs to their students. The paragraphs cast doubt on the validity of evolutionary theory and say that there are competing theories (specifically I.D.) and that copies of an I.D.-friendly textbook, “Of Pandas and People,” are available in the library for anyone who wants to learn more. Several members of the school board quit in protest when the proposal passed, and in December, 11 parents sued the board, accusing it of violating the First Amendment.

The suing parents — backed by the ACLU, Americans United for the Separation of Church and State, and the huge Philadelphia law firm Pepper Hamilton LLP — are claiming that I.D. is not a scientific theory, but a religious one, namely creationism, and has no business posing as science in biology classrooms.

U.S. District Judge John E. Jones III (a George W. Bush appointee) will have to decide, following testimony by scientists, philosophers, theologians and historians of science (as well as the plaintiffs and school board members), whether telling Dover’s ninth-graders about I.D. is exposing them to an “underdog science,” as Thompson calls it, or is promoting a particular religion.

If Judge Jones decides in favor of the Dover school board, dozens of other school boards around the country are waiting in the wings to implement I.D. into their science curricula. If he decides for the defendants, Darwin’s theory of evolution alone will continue to be taught in public schools as the scientific explanation for the diversity of life. Regardless of how Judge Jones votes, both sides have said they will appeal the case all the way to the Supreme Court.

Thompson gained fame as the Michigan state prosecutor who repeatedly charged assisted-suicide advocate Jack Kevorkian with first-degree murder, and didn’t stop pursuing him until Thompson was elected out of office, in large part for hounding Kevorkian. Thompson is also known for pushing through mandatory life sentences in Michigan for drug crimes and for prosecuting more drug offenders than anyone else. And, of course, Thompson shares with Bryan the conviction that Darwinism is perhaps the world’s most dangerous idea.

But for Thompson to prevail in his quixotic battle to convince the court that I.D. has a place in a nearby high school’s ninth-grade biology class, he will need more than confidence and religious zeal. Although divine intervention might help, what he really needs are some new and compelling arguments to help I.D. sneak around the constitutional prohibition against promoting a particular religious view in the public schools. And he thinks he’s got them.

It’s a week into the trial and Thompson is cross-examining John Haught, an expert witness for the plaintiffs. Haught, a recently retired professor of theology at Georgetown University, is the author of 13 books, including “God After Darwin” and “Science and Religion in Search of Cosmic Purpose.” Haught has argued that I.D. is nothing more than a “reformulation of the old argument for the existence of God that says, ‘Where there is a design there must be a designer.’”

The famous theologian William Paley popularized this argument in the early 1800s. Upon finding a watch, he said, it would be reasonable to deduce the existence of a watchmaker. Well, explains Haught, the I.D. theorists make the same deduction from what they call the “irreducible complexity” of certain sub-cellular structures, such as the bacterial flagellum, a little motorlike propeller that moves bacteria around.

By “irreducibly complex,” the I.D.ers mean that if you remove any part of the motor, the others will no longer serve any identifiable function at all, and so the flagellum could not have been selected for by natural selection. Irreducible complexity is the core of I.D.’s criticism of evolutionary biology, and in one version or another it has always been the central creationist argument.

The biology of I.D. had been hammered by the plaintiffs’ expert scientific witness days before. Brown University biologist Kenneth Miller argued that I.D. can never be science because it resorts to supernatural explanations for natural phenomena. Miller, who described himself as a devout Catholic and a believer in God, did not claim that there are no supernatural forces in the world, only that they are not the business of science.

“Science deals with natural causes for natural phenomenon,” Miller testified. “Intelligent design is a science stopper” because “it lets scientists off the hook” precisely when things get tricky, which is also when they get interesting — that is, when a naturalistic cause isn’t obvious. But, Miller insisted, “just because you don’t see at first how something could be the product of natural selection doesn’t mean it couldn’t be. Such challenges should spur a scientist to look deeper, not tell him it’s time to retire and just attribute something to the work of an intelligent designer.”

Haught’s main job on the stand is to talk about the history and theology of I.D., which he says is a direct descendent of creation science (also called special creationism), which in turn is a descendent of the kind of primitive, young-earth creationism debated in the Scopes trial.

Young-earth creationism, Haught explains, takes Genesis literally, posits that the world is between 6,000 and 10,000 years old, and claims that animal fossils are left behind by the Great Flood. Special creationism accepts a more realistic geological age for the earth and acknowledges the influence of micro-evolution (subtle change within a species). However, special creationism still holds that God created all species separately and pretty much as they are now.

Both theories have been rejected as science by U.S. courts. In 1982, a federal court declared unconstitutional an Arkansas law requiring that evolution and young-earth creationism be taught side by side. The court said creationism was religion and couldn’t be taught as science. In 1987, in a Louisiana case, the Supreme Court declared creation science to be religion, and deemed unconstitutional a Louisiana law mandating teaching it in the public schools wherever evolution was taught. Almost immediately I.D. was born, adopting more sophisticated versions of the old creationist arguments and replacing all references to God with an unspecified intelligent designer.

As Thompson begins his cross-examination, he instinctively looks, and grins, at the jury box, where the press is sitting.

“Just because you can trace an idea back to antiquity does not in and of itself make that idea invalid, does it?” Thompson asks Haught.

“No,” Haught says.

“Because a theory belongs to an individual of a certain faith doesn’t make that theory invalid does it?” continues Thompson.

No, says Haught, pointing out that many evolutionists hold various faiths or no faith at all.

“It would be a fallacy to say that a scientific theory was invalid just because it comes from one particular tradition or another, wouldn’t it?”

“Yes.”

Thompson reads from Haught’s book “Deeper Than Darwin,” in which the theologian writes that proponents of I.D. are often highly trained and skilled scientists, that they are no more or less intelligent than their counterparts in evolutionary biology, and that they are neither stupid nor insane.

All true, acknowledges Haught.

Thompson goes to another of Haught’s books and reads a section in which the theologian criticizes Robert Pennock, a Michigan State philosopher who had testified against I.D. two days earlier. In the passage, Haught takes Pennock to task for “misleading the public by conflating ID and creationism.”

“And yet you have said today that they are the same. Are they the same or not?” asks Thompson.

“They are not exactly the same,” says Haught, his lips trembling, clearly perturbed.

Thompson reads the final sentence from an early edition of Darwin’s “On the Origin of Species”: “There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one … from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.”

So, Thompson asks, should Darwin’s “On the Origin of Species” be kept outside the science classroom because it talks about the Creator with a capital “C” breathing life into early forms?

“No,” concedes Haught.

Thompson then gets Haught to agree that several luminary evolutionary biologists draw metaphysical conclusions from their studies of evolution. “Yes, [Richard] Dawkins, [Edward O.] Wilson, and [Stephen Jay] Gould carelessly conflate their science with materialist ideology,” says Haught. (Materialism is the belief that reality is composed only of matter and nothing supernatural exists, except in imaginations.)

“Should their work be banned from science classrooms?”

“No.”

The shape of Thompson’s case is beginning to emerge and Judge Jones, suddenly sitting up attentively and tipping his head toward the lawyer, seems to be taking notice. The court, and more broadly the scientific establishment, Thompson argues, must evaluate the scientific claims of I.D. on their merits, not condemning them by association with their religious roots or boosters. And those I.D. claims, he is implying, are already engaged by evolutionary scientists in debate. And that engagement itself is proof of a scientific controversy worthy of teaching in schools.

Perhaps feeling overconfident, Thompson takes aim at the Goliath of modern evolutionary genetics. He wants to show that the correlations between different species’ genomes — humans and chimpanzees, for example, which share 98 percent of their genes — say nothing about the evolutionary relationships between organisms.

“Let’s say I have some bolts, and from them I make both a plane and a car. Yes, they have the same parts, but that doesn’t mean the car came from the plane does it?”

“Uh, no,” says Haught, pausing to consider what Thompson could be driving at.

Thompson pauses too, turns again to the jury box and smiles triumphantly. He concludes that it is therefore easy to see that it is only mere conjecture that humans and other primates share genes just because they share an evolutionary lineage.

The jury box of reporters and many courtroom spectators seem dumbfounded. How could Thompson so confidently reveal such a basic misunderstanding of the role of genomics in analyzing and confirming evolutionary relationships? There are moments in the trial when even a science-abiding secularist can be seduced by parts of Thompson’s ethical and philosophical arguments that I.D. deserves a fair hearing in the public schools. But time and again, Thompson’s insistence that I.D. is science and not religion, and therefore by law can be taught in science classes, does not appear to be making any converts in the courtroom.

Later, anthropologist Eugenie Scott, director of the National Center for Science Education, who was in the courtroom, says it was all she could do to keep from cracking up. “Thompson was not even wrong,” Scott says. “He missed the boat completely. We didn’t need genomics to demonstrate evolution. But having genomic sequences of different species nails down the big idea that the more recently that two forms shared a common ancestor, the more alike they are in anatomy, biochemistry, embryology, behavior and genetics. And it does so beautifully and quantitatively.”

When court adjourns for the day, Thompson drags his rolling suitcase filled with briefs to the aging Harrisburg Hilton, a few blocks from the courthouse. We settle down in the lobby for an interview.

“Did you see me show that there’s no scientific evidence for man coming from an ape?” he asks enthusiastically. “I shouldn’t have. But I couldn’t help myself. I just wanted to do that.”

I figure it’s best to change the subject. I tell him that in profile he looks quite a bit like Bryan. It’s a bit of a stretch, but not entirely untrue.

He laughs disarmingly, delighted. “Frederick March, the actor in the movie ‘Inherit the Wind,’ or the real William Jennings Bryan?”

The real Bryan, I say.

He hits me gently on the shoulder and laughs again, clearly pleased.

I ask Thompson why this battle matters so much to him. He pauses, putting his hands together as if in prayer. “If you are nothing but an accident of nature, then nothing you do is dependent on objective truth,” he says. “You can set your own rules. There is no life after death. There are no set moral codes. If you go to bed, and if you die its OK, you’re just another piece of matter bouncing around and you’ll change into something else. That’s why, even if 100 million scientists say we are unplanned, that we’re just purposeless beings in this universe, the general population won’t buy it. And neither will I.”

He then reiterates his notion that I.D. is an underdog science that shouldn’t be relegated to theology just because current science hasn’t caught up with it. He compares I.D. to the Big Bang Theory, which was once unpopular and thought to have been religiously motivated.

“Einstein thought the Big Bang was wrong because it didn’t fit his metaphysics,” says Thompson. “But he was the one who was wrong. Should it have been illegal to discuss the Big Bang in schools just because it was consistent with Christianity?”

As he did in court, Thompson tells me that I.D. theorists are real scientists. “They are distinguished scientists doing credible experimental work, and they have found evidence of intelligent design in the empirical data that they see,” he says. “If the evidence suggests design, well … should they ignore it?”

Early this week, Michael Behe, a biochemist from Lehigh University in Pennsylvania, and the person who put “irreducible complexity” on the map with his 1996 book “Darwin’s Black Box,” appeared on the stand for two days. He explained that natural selection could not explain the existence of DNA or the immune system. He insisted that ID is not based on any religious beliefs but “is based on observed, empirical, physical evidence from nature, and it is definitely science.” When asked if the designer was God, he said yes, but added, “I concluded that based on theological, philosophical and historical facts.”

As we talk, Thompson bristles at the notion that I.D. is and always will be excluded from science. “What is science, and what is not science, is merely a convention,” he says. “It can be challenged and changed at will by scientists themselves. And scientists are the products of their culture, too.”

Doesn’t he find it a little odd that a champion of unchanging and absolute moral values should take such a relativist stance on science? He shrugs off the question.

“Look, scientists don’t sit there and ask, ‘Am I doing science or not?’ No scientist is going to say, ‘This is empirical truth about the wrong subject so I’m not going to study it.’ No, they look at whatever the empirical data is, and draw conclusions from it.”

“So you want to change the definition of science to include the supernatural?”

“Yes,” he says, “we need a total paradigm shift in science.”

Dawkins stuck to his theme but expanded his territory in such subsequent books as “The Blind Watchmaker,” “Unweaving the Rainbow” and “Climbing Mount Improbable.” His recent work, “The Ancestor’s Tale,” traces human lineage back through time, stopping to ponder important forks in the evolutionary road.

Given his outspoken defense of Darwin, and natural selection as the force of life, Dawkins has assumed a new role: the religious right’s Public Enemy No. 1. Yet Dawkins doesn’t shy from controversy, nor does he suffer fools gladly. He recently met a minister who was on the opposite side of a British political debate. When the minister put out his hand, Dawkins kept his hands at his side and said, “You, sir, are an ignorant bigot.”

Currently, Dawkins is the Charles Simonyi Professor of the Public Understanding of Science at Oxford University, a position created for him in 1995 by Charles Simonyi, a Microsoft millionaire. Earlier this year, Dawkins signed an agreement with British television to make a documentary about the destructive role of religion in modern history, tentatively titled “The Root of All Evil.”

I met Dawkins in late March at the Atheist Alliance International annual conference in Los Angeles, where he presented the alliance’s top honor, the Richard Dawkins Prize, to magicians Penn and Teller. During our conversation in my hotel room, Dawkins was as gracious as he was punctiliously dressed in a crisp white shirt and soft blazer.

Once again, evolution is under attack. Are there any questions at all about its validity?

It’s often said that because evolution happened in the past, and we didn’t see it happen, there is no direct evidence for it. That, of course, is nonsense. It’s rather like a detective coming on the scene of a crime, obviously after the crime has been committed, and working out what must have happened by looking at the clues that remain. In the story of evolution, the clues are a billionfold.

There are clues from the distribution of DNA codes throughout the animal and plant kingdoms, of protein sequences, of morphological characters that have been analyzed in great detail. Everything fits with the idea that we have here a simple branching tree. The distribution of species on islands and continents throughout the world is exactly what you’d expect if evolution was a fact. The distribution of fossils in space and in time are exactly what you would expect if evolution were a fact. There are millions of facts all pointing in the same direction and no facts pointing in the wrong direction.

British scientist J.B.S. Haldane, when asked what would constitute evidence against evolution, famously said, “Fossil rabbits in the Precambrian.” They’ve never been found. Nothing like that has ever been found. Evolution could be disproved by such facts. But all the fossils that have been found are in the right place. Of course there are plenty of gaps in the fossil record. There’s nothing wrong with that. Why shouldn’t there be? We’re lucky to have fossils at all. But no fossils have been found in the wrong place, such as to disprove the fact of evolution. Evolution is a fact.

Still, so many people resist believing in evolution. Where does the resistance come from?

It comes, I’m sorry to say, from religion. And from bad religion. You won’t find any opposition to the idea of evolution among sophisticated, educated theologians. It comes from an exceedingly retarded, primitive version of religion, which unfortunately is at present undergoing an epidemic in the United States. Not in Europe, not in Britain, but in the United States.

My American friends tell me that you are slipping towards a theocratic Dark Age. Which is very disagreeable for the very large number of educated, intelligent and right-thinking people in America. Unfortunately, at present, it’s slightly outnumbered by the ignorant, uneducated people who voted Bush in.

But the broad direction of history is toward enlightenment, and so I think that what America is going through at the moment will prove to be a temporary reverse. I think there is great hope for the future. My advice would be, Don’t despair, these things pass.

You delve into agnosticism in “The Ancestor’s Tale.” How does it differ from atheism?

It’s said that the only rational stance is agnosticism because you can neither prove nor disprove the existence of the supernatural creator. I find that a weak position. It is true that you can’t disprove anything but you can put a probability value on it. There’s an infinite number of things that you can’t disprove: unicorns, werewolves, and teapots in orbit around Mars. But we don’t pay any heed to them unless there is some positive reason to think that they do exist.

Believing in God is like believing in a teapot orbiting Mars?

Yes. For a long time it seemed clear to just about everybody that the beauty and elegance of the world seemed to be prima facie evidence for a divine creator. But the philosopher David Hume already realized three centuries ago that this was a bad argument. It leads to an infinite regression. You can’t statistically explain improbable things like living creatures by saying that they must have been designed because you’re still left to explain the designer, who must be, if anything, an even more statistically improbable and elegant thing. Design can never be an ultimate explanation for anything. It can only be a proximate explanation. A plane or a car is explained by a designer but that’s because the designer himself, the engineer, is explained by natural selection.

Those who embrace “intelligent design” — the idea that living cells are too complex to have been created by nature alone — say evolution isn’t incompatible with the existence of God.

There is just no evidence for the existence of God. Evolution by natural selection is a process that works up from simple beginnings, and simple beginnings are easy to explain. The engineer or any other living thing is difficult to explain — but it is explicable by evolution by natural selection. So the relevance of evolutionary biology to atheism is that evolutionary biology gives us the only known mechanism whereby the illusion of design, or apparent design, could ever come into the universe anywhere.

So why do we insist on believing in God?

From a biological point of view, there are lots of different theories about why we have this extraordinary predisposition to believe in supernatural things. One suggestion is that the child mind is, for very good Darwinian reasons, susceptible to infection the same way a computer is. In order to be useful, a computer has to be programmable, to obey whatever it’s told to do. That automatically makes it vulnerable to computer viruses, which are programs that say, “Spread me, copy me, pass me on.” Once a viral program gets started, there is nothing to stop it.

Similarly, the child brain is preprogrammed by natural selection to obey and believe what parents and other adults tell it. In general, it’s a good thing that child brains should be susceptible to being taught what to do and what to believe by adults. But this necessarily carries the down side that bad ideas, useless ideas, waste of time ideas like rain dances and other religious customs, will also be passed down the generations. The child brain is very susceptible to this kind of infection. And it also spreads sideways by cross infection when a charismatic preacher goes around infecting new minds that were previously uninfected.

You’ve said that raising children in a religious tradition may even be a form of abuse.

What I think may be abuse is labeling children with religious labels like Catholic child and Muslim child. I find it very odd that in our civilization we’re quite happy to speak of a Catholic child that is 4 years old or a Muslim of child that is 4, when these children are much too young to know what they think about the cosmos, life and morality. We wouldn’t dream of speaking of a Keynesian child or a Marxist child. And yet, for some reason we make a privileged exception of religion. And, by the way, I think it would also be abuse to talk about an atheist child.

You are working on a new book tentatively called “The God Delusion.” Can you explain it?

A delusion is something that people believe in despite a total lack of evidence. Religion is scarcely distinguishable from childhood delusions like the “imaginary friend” and the bogeyman under the bed. Unfortunately, the God delusion possesses adults, and not just a minority of unfortunates in an asylum. The word “delusion” also carries negative connotations, and religion has plenty of those.

What are its negative connotations?

A delusion that encourages belief where there is no evidence is asking for trouble. Disagreements between incompatible beliefs cannot be settled by reasoned argument because reasoned argument is drummed out of those trained in religion from the cradle. Instead, disagreements are settled by other means which, in extreme cases, inevitably become violent. Scientists disagree among themselves but they never fight over their disagreements. They argue about evidence or go out and seek new evidence. Much the same is true of philosophers, historians and literary critics.

But you don’t do that if you just know your holy book is the God-written truth and the other guy knows that his incompatible scripture is too. People brought up to believe in faith and private revelation cannot be persuaded by evidence to change their minds. No wonder religious zealots throughout history have resorted to torture and execution, to crusades and jihads, to holy wars and purges and pogroms, to the Inquisition and the burning of witches.

What are the dark sides of religion today?

Terrorism in the Middle East, militant Zionism, 9/11, the Northern Ireland “troubles,” genocide, which turns out to be “credicide” in Yugoslavia, the subversion of American science education, oppression of women in Saudi Arabia, Afghanistan, and the Roman Catholic Church, which thinks you can’t be a valid priest without testicles.

Fifty years ago, philosophers like Bertrand Russell felt that the religious worldview would fade as science and reason emerged. Why hasn’t it?

That trend toward enlightenment has indeed continued in Europe and Britain. It just has not continued in the U.S., and not in the Islamic world. We’re seeing a rather unholy alliance between the burgeoning theocracy in the U.S. and its allies, the theocrats in the Islamic world. They are fighting the same battle: Christian on one side, Muslim on the other. The very large numbers of people in the United States and in Europe who don’t subscribe to that worldview are caught in the middle.

Actually, holy alliance would be a better phrase. Bush and bin Laden are really on the same side: the side of faith and violence against the side of reason and discussion. Both have implacable faith that they are right and the other is evil. Each believes that when he dies he is going to heaven. Each believes that if he could kill the other, his path to paradise in the next world would be even swifter. The delusional “next world” is welcome to both of them. This world would be a much better place without either of them.

Does religion contribute to the violence of Islamic extremists? Christian extremists?

Of course it does. From the cradle, they are brought up to revere martyrs and to believe they have a fast track to heaven. With their mother’s milk they imbibe hatred of heretics, apostates and followers of rival faiths.

I don’t wish to suggest it is doctrinal disputes that are motivating the individual soldiers who are doing the killing. What I do suggest is that in places like Northern Ireland, religion was the only available label by which people could indulge in the human weakness for us-or-them wars. When a Protestant murders a Catholic or a Catholic murders a Protestant, they’re not playing out doctrinal disagreements about transubstantiation.

What is going on is more like a vendetta. It was one of their lot’s grandfathers who killed one of our lot’s grandfathers, and so we’re getting our revenge. The “their lot” and “our lot” is only defined by religion. In other parts of the world it might be defined by color, or by language, but in so many parts of the world it isn’t, it’s defined by religion. That’s true of the conflicts among Croats and the Serbs and Bosnians — that’s all about religion as labels.

The grotesque massacres in India at the time of partition were between Hindus and Muslims. There was nothing else to distinguish them, they were racially the same. They only identified themselves as “us” and the others as “them” by the fact that some of them were Hindus and some of them were Muslims. That’s what the Kashmir dispute is all about. So, yes, I would defend the view that religion is an extremely potent label for hostility. That has always been true and it continues to be true to this day.

How would we be better off without religion?

We’d all be freed to concentrate on the only life we are ever going to have. We’d be free to exult in the privilege — the remarkable good fortune — that each one of us enjoys through having been being born. An astronomically overwhelming majority of the people who could be born never will be. You are one of the tiny minority whose number came up. Be thankful that you have a life, and forsake your vain and presumptuous desire for a second one. The world would be a better place if we all had this positive attitude to life. It would also be a better place if morality was all about doing good to others and refraining from hurting them, rather than religion’s morbid obsession with private sin and the evils of sexual enjoyment.

Are there environmental costs of a religious worldview?

There are many religious points of view where the conservation of the world is just as important as it is to scientists. But there are certain religious points of view where it is not. In those apocalyptic religions, people actually believe that because they read some dopey prophesy in the book of Revelation, the world is going to come to an end some time soon. People who believe that say, “We don’t need to bother about conserving forests or anything else because the end of the world is coming anyway.” A few decades ago one would simply have laughed at that. Today you can’t laugh. These people are in power.

Unlike other accounts of the evolution of life, “The Ancestor’s Tale” starts at the present and works back. Why did you decide to tell the story in reverse?

The most important reason is that if you tell the evolution story forwards and end up with humans, as it’s humanly normal to do so because people are interested in themselves, it makes it look as though the whole of evolution were somehow aimed at humanity, which of course it wasn’t. One could aim anywhere, like at kangaroos, butterflies or frogs. We’re all contemporary culmination points, for the moment, in evolution.

If you go backward, however, no matter where you start in this huge tree of life, you always converge at the same point, which is the origin of life. So that was the main reason for structuring the book the way I did. It gave me a natural goal to head toward — the origin of life — no matter where I started from. Then I could legitimately start with humans, which people are interested in.

People like to trace their ancestry. One of the most common types of Web sites, after ones about sex, is one’s family history. When people trace the ancestry of that name, they normally stop at a few hundred years. I wanted to go back 4,000 million years.

The idea of going back towards a particular goal called to my mind the notion of pilgrimage as a kind of literary device. So I very vaguely modeled the book on Chaucer’s “Canterbury Tales,” where the pilgrims start off as a band of human pilgrims walking backward to discover our ancestors. We are successively joined by other pilgrims — the chimpanzee pilgrims at 5 million years, then the gorilla pilgrims, then the orangutan pilgrims. Starting with humans, there are only about 39 such rendezvous points as you go back in time. It’s a rather surprising fact. Rendezvous 39 is where we meet the bacteria pilgrims.

The idea that evolution could be “random” seems to frighten people. Is it random?

This is a spectacular misunderstanding. If it was random, then of course it couldn’t possibly have given rise to the fantastically complicated and elegant forms that we see. Natural selection is the important force that drives evolution. Natural selection is about as non-random a force as you could possibly imagine. It can’t work unless there is some sort of variation upon which to work. And the source of variation is mutation. Mutation is random only in the sense that it is not directed specifically toward improvement. It is natural selection that directs evolution toward improvement. Mutation is random in that it’s not directed toward improvement.

The idea that evolution itself is a random process is a most extraordinary travesty. I wonder if it’s deliberately put about maliciously or whether these people honestly believe such a preposterous absurdity. Of course evolution isn’t random. It is driven by natural selection, which is a highly non-random force.

Is there an emotional side to the intellectual enterprise of exploring the story of life on Earth?

Yes, I strongly feel that. When you meet a scientist who calls himself or herself religious, you’ll often find that that’s what they mean. You often find that by “religious” they do not mean anything supernatural. They mean precisely the kind of emotional response to the natural world that you’ve described. Einstein had it very strongly. Unfortunately, he used the word “God” to describe it, which has led to a great deal of misunderstanding. But Einstein had that feeling, I have that feeling, you’ll find it in the writings of many scientists. It’s a kind of quasi-religious feeling. And there are those who wish to call it religious and who therefore are annoyed when a scientist calls himself an atheist. They think, “No, you believe in this transcendental feeling, you can’t be an atheist.” That’s a confusion of language.

Some scientists say that removing religion or God from their life would leave it meaningless, that it’s God that gives meaning to life.

“Unweaving the Rainbow” specifically attacks the idea that a materialist, mechanist, naturalistic worldview makes life seem meaningless. Quite the contrary, the scientific worldview is a poetic worldview, it is almost a transcendental worldview. We are amazingly privileged to be born at all and to be granted a few decades — before we die forever — in which we can understand, appreciate and enjoy the universe. And those of us fortunate enough to be living today are even more privileged than those of earlier times. We have the benefit of those earlier centuries of scientific exploration. Through no talent of our own, we have the privilege of knowing far more than past centuries. Aristotle would be blown away by what any schoolchild could tell him today. That’s the kind of privileged century in which we live. That’s what gives my life meaning. And the fact that my life is finite, and that it’s the only life I’ve got, makes me all the more eager to get up each morning and set about the business of understanding more about the world into which I am so privileged to have been born.

Humans may not be products of an intelligent designer but given genetic technologies, our descendants will be. What does this mean about the future of evolution?

It’s an interesting thought that in some remote time in the future, people may look back on the 20th and 21st centuries as a watershed in evolution — the time when evolution stopped being an undirected force and became a design force. Already, for the past few centuries, maybe even millennia, agriculturalists have in a sense designed the evolution of domestic animals like pigs and cows and chickens. That’s increasing and we’re getting more technologically clever at that by manipulating not just the selection part of evolution but also the mutation part. That will be very different; one of the great features of biological evolution up to now is that there is no foresight.

In general, evolution is a blind process. That’s why I called my book “The Blind Watchmaker.” Evolution never looks to the future. It never governs what happens now on the basis on what will happen in the future in the way that human design undoubtedly does. But now it is possible to breed a new kind of pig, or chicken, which has such and such qualities. We may even have to pass that pig through a stage where it is actually less good at whatever we want to produce — making long bacon racks or something — but we can persist because we know it’ll be worth it in the long run. That never happened in natural evolution; there was never a “let’s temporarily get worse in order to get better, let’s go down into the valley in order to get over to the other side and up onto the opposite mountain.” So yes, I think it well may be that we’re living in a time when evolution is suddenly starting to become intelligently designed.