In the beginning, there was a bang. A very big bang. Nothing exploded into something. Quarks and leptons collided violently in an intense fireball of plasma. As the plasma expanded and cooled, the collisions became less violent, and particles joined together to form protons and neutrons and electrons, then nuclei and atoms and molecules. Huge clouds of these particles coalesced into galaxies of stars and planets, still expanding, always expanding, away from the central point of the explosion.

On one particular planet, in a very ordinary galaxy, molecules somehow formed living cells. And these cells linked together to become organisms, some of which had certain genetic mutations that better enabled them to survive and replicate in the primordial atmosphere. Over the next, oh, billions of years, the fittest of these organisms evolved into plants and fish and amphibians and birds and dogs and cats and apes and humans--all thanks to the whims of chance and the laws of nature. If the pull of nuclei were slightly stronger, if the force of gravity were slightly weaker, if the speed of universal expansion were off just a hair, if the genetic mutations had been a little bit different, we wouldn't be here.

It's a fanciful story, but it's the best one that modern science has come up with so far to explain human existence. A small cadre of philosophers, scientists, and mathematicians, however, have come to the conclusion that it's a little too fanciful, that perhaps there is a better explanation for the origin and diversity of life, that perhaps that explanation involves an intelligent designer, a.k.a. God.

It's not a new argument. Eighteenth-century British natural theologian William Paley gave the intelligent-design theory its most memorable metaphor: Happening upon a watch, one would notice that its various parts work together for a purpose, that the cogs and springs and gears produce motion, and that the motion is regulated to indicate time. We would infer from the watch that it was crafted by a watchmaker. Paley argued that living organisms are more complicated than watches "in a degree which exceeds all computation," and that we, too, must therefore be the products of some grand watchmaker, an intelligence.

Since the dawn of Darwinism, Paley's watchmaker analogy has been dismissed as a quaint notion of a much simpler scientific time. Darwin's theory of natural selection explained that the design we see in nature and in ourselves is merely an illusion: What appears to be design is not, in fact, the product of a designer, but the result of a long and undirected history of evolution in which organisms became better and better adapted to their environments. Darwinism forever separated science and religion. Religion was a matter of faith; science, a matter of natural causes, observable fact, empirical evidence. Sure, you could believe in God if you wanted to, but you certainly couldn't look for him to reveal himself in the natural world.

But intelligent-design theorists are bringing religion back into the laboratory, adding bite to Paley's old watchmaker argument, attempting to show--with mathematical theories and biological examples--that a designer can be empirically detected. This has mainstream scientists hopping mad and may lead to the most intense battle between science and religion since the Catholic Church put Galileo under house arrest for suggesting that the earth was not the center of the universe.

The first major skirmish has already taken place at Baylor University, where William Dembski, a leading proponent of intelligent design, was demoted from his position as director of a center set up to study the theory. The last fight may be on your local school board.William Dembski wasn't always a religious man. The only child of a college biology professor (who, in fact, didn't question Darwin's theories) and an art dealer, he spent six days a week at an all-male Catholic preparatory school in Chicago. He went through the motions at school, but he didn't buy into Christianity. "Any sort of God who was behind it all, who we were accountable to, who really cared for us, with whom we could have any connection, that was just off my radar," Dembski says. That is, until he came upon his life's first rough spot. Dembski was always a good student, especially in math. He finished high school a year early, completing a full course of calculus in just one summer. The 17-year-old tested into some advanced mathematics courses at the University of Chicago, but he struggled in them. He was doing fair, but he wasn't used to doing fair. He couldn't handle the disappointment.

Dembski was having trouble outside of class as well. His experiences as an only child who spent most of his time in the insular world of a boys' school had not prepared him for college life. His social skills, Dembski admits, were a bit lacking. He dropped out of school and went to work in his mother's art dealership business. He built crates and typed letters, but mostly he just floundered. "It was just not a very happy time in my life," he says, "and I guess when you're not very happy, you start looking."

He read the Scriptures, trying to understand the faith. And he read creationist literature, trying to understand the world around him. He had always had a sneaking suspicion that Darwinism was an inadequate theory, and although he could not believe the doctrine of literal creationists, their criticisms of evolution fueled his active young mind. He went back to school, studying statistics at the University of Illinois and adding that knowledge to his developing disbelief in Darwinism. It seemed to him statistically improbable that natural selection could produce the diversity of life all around him. Still, he hadn't come up with an alternative theory.

Then, in 1988, he had a eureka moment. At a conference on randomness at Ohio State University, a statistician concluded the event by saying, "We know what randomness isn't. We don't know what it is." It made sense to Dembski. If God is the creator of the universe, then there should be order in the world, not randomness. Darwinists were having so much trouble defining the randomness inherent in evolutionary theory because life was essentially not random. It was designed. And randomness could be understood only in terms of that design. "That insight really has propelled me all these years," Dembski says.

Armed with Christian faith, Dembski found that he could be happy in the world of academia. In fact, he's been there ever since his religious conversion. In all, he has earned a B.A. in psychology, an M.S. in statistics, and a Ph.D. in philosophy from the University of Illinois; a Ph.D. in mathematics from the University of Chicago; and a master of divinity from Princeton Theological Seminary. He has also done postdoctoral work in mathematics at MIT, in physics at the University of Chicago, and in computer science at Princeton. But his relationship with academia would not always be pleasant. Dembski's theories were taking him further and further afield from mainstream science. His mathematics were leading him to the same place that his faith had. To his colleagues, this wasn't science; it was religion. We distinguish between intelligent and natural causes every day--every time a detective investigates a possible homicide, every time an archaeologist picks out an arrowhead from a pile of rocks, every time radio astronomers at the Search for Extra-Terrestrial Intelligence listen for patterns in the noise coming from outer space. In these cases, modern science doesn't have a problem assuming that some intelligent being is responsible for the evidence--a human, even an alien. But if you try to distinguish between intelligent and natural causes in basic biological systems, things get a little messier. If you find intelligence in biology, then who or what was the intelligent designer? It's a question science doesn't want to pose, let alone answer. But Dembski contends that if he can codify the process by which we recognize intelligence in other fields, he can justifiably apply that process to biology. If he can codify that process, he says, intelligent design is not a matter of religious belief but a matter of following the evidence wherever it leads. Such a codification is Dembski's contribution to the intelligent-design movement, and his claim to fame. It is an explanatory process that can be used for judging objects, events, and information. It begins by ruling out chance and natural law as explanations, and then infers design.

The first step in the process is what Dembski calls contingency. In other words, something that is designed must be compatible with natural law but not required by it. Something that is required by natural law leaves no room for the choices inherent in design. It is just following orders.

The second test is for complexity. Here, Dembski turns to the sci-fi movie Contact, based on a novel by Carl Sagan, for an example. In the movie, Jodie Foster and her radio astronomer friends at SETI receive a signal of 1,126 beats and pauses representing all the prime numbers from two to 101. They interpret the signal to be a sign of extraterrestrial intelligence. But if they had received a sequence of only the first three prime numbers, they would not have jumped to the same conclusion. Any random radio signal might happen to emit this sequence by pure chance. Mathematically speaking, this is a probability argument. The short sequence is simply not complex enough to be improbable as a result of chance.

But complexity by itself isn't enough. The final filter is for specification. Any particular sequence of 1,126 beats and pauses is highly unlikely. The sequence in Contact was special not just because it was complex, but because it contained an independent pattern: increasing prime numbers.

Voila. If something is contingent, complex, and specified, according to Dembski, we can infer that it is the product of intelligence. Dembski calls it the specified-complexity criterion.

The next step for intelligent-design theorists is to apply the criterion to biological systems. They start small, with bacteria and their proteins, to keep the probability computations manageable. But the idea is that if they can prove that life's subsystems are designed, then they can prove that the whole system is designed.

The bacterium's flagellum may be intelligent design's favorite subsystem. A flagellum is a whip-like outboard motor, complete with an acid-powered rotary engine, O-rings, and a drive shaft. "The scientific community has come up short with any sort of plausible, detailed explanation of how you could have gotten something like this by purely natural causes," says Dembski, "and when you start applying the sort of methods that I've developed, it clearly indicates design."

A flagellum is compatible with natural law but not required by it; after all, there are bacteria without flagella. It is specified in the sense that its pattern of parts performs a specific function. And it is complex not just in the sense of its machinelike combination of parts, but also in the improbability of its arising by chance. In fact, Michael Behe, the biochemist who most famously made the case for design in the bacterial flagellum, contends that it would be virtually impossible for the motor to come about by mutation and natural selection.

Behe calls the flagellum an irreducibly complex system. In other words, its parts are so interrelated that if one part were taken away, the entire system wouldn't work. A mousetrap, for instance, is irreducibly complex. Take away the platform, the hammer, the spring, the catch, or the holding bar, and it is impossible to construct a working mousetrap. Similarly, if you take away any one of the 50 proteins required in the bacterial flagellum, the motor ceases to work. Behe's argument is that the flagellum is too complex to arise in one single mutation and then be acted upon by natural selection, and that the undirected nature of the Darwinian mechanism could not support a gradual accumulation of the necessary proteins. Just one of these proteins offers no survival and reproductive advantage. How could nature know to preserve it for future generations? How could nature know that the bacterium was in the process of building itself a motor?

Dembski is looking to apply his specified-complexity theory on an even more microscopic scale than the bacterial flagellum: that of DNA. The precise sequence of nucleotides in DNA conveys the information necessary to build proteins. The origin of this information has become the Holy Grail of origin-of-life biology. Mainstream science is looking for an algorithm or a natural law to account for it, but Dembski says that this DNA encoding is complex, specified information if ever there was any--and thus indicative of intelligent design. Natural causes cannot originate information, Dembski argues via his complicated mathematical proof, the Law of Conservation of Information. It's a somewhat circular argument: Natural laws and algorithms cannot create complex, specified information, because they cannot create anything that is not required by natural law. Chance can generate complex, unspecified information or simple, specified information, but not information that is both complex and specified.

It is for this law that Rob Koons, an associate professor of philosophy at the University of Texas, calls Dembski the "Isaac Newton of information theory." It may be that intelligent design will revolutionize science just like Newtonian physics did. It may also be that this is just the perfect way to evangelize a generation of Americans who put their faith in science without entirely understanding it. William Dembski met Baylor University President Robert Sloan in the summer of 1996, when he was teaching Sloan's daughter at a Christian-study summer camp not far from Waco. Sloan, who is the first Baptist minister to serve as Baylor's president in more than 30 years, had read some of Dembski's work. "He liked my stuff," Dembski recalls. "He made it clear that he wanted to get me on the faculty in some way."Three years later the president offered Dembski not just a position at Baylor but a whole center dedicated to studying the relationship between science and religion and to furthering Dembski's work in intelligent design. It would be named after Michael Polanyi, a Hungarian chemist who questioned the idea that the world could be explained through natural laws alone. It was a big step for intelligent design, the first center of its kind at a major research university, a huge inroad into mainstream academia.

The Polanyi Center was established quietly in October 1999. Dembski and his like-minded colleague Bruce Gordon were hired outside the traditional academic channels of a search committee and departmental consultation. Dembski says that he did meet with some faculty, both before and after Baylor hired him. But the vast majority of them were unaware of the existence of the center until its Web site went online and scientists outside the university began sending incredulous e-mails to their colleagues at Baylor. What, they asked, was this? Had Baylor gone fundamentalist? Would they be teaching creation science instead of evolution in their biology classrooms? The Baylor scientists, already sensitive to their university's religious mission, were now the laughingstock of the scientific community, and they didn't like it.

"When you say Baylor now, people are going to go, 'Oh, yeah, they have that creationist center,'" says Charles Weaver, a professor of psychology and neuroscience at Baylor and one of the most outspoken critics of the Polanyi Center. "We fought that as a city for a long time: 'Waco. Oh, you guys are the crazy ones with Koresh.'" He worries that the Polanyi Center and Dembski's association with the intelligent-design movement will discourage promising premed students and respected faculty from coming to Baylor.

Baylor Provost Donald Schmeltekopf defends the university's actions by pointing out that there are more and more people in academia interested in questioning the naturalistic assumptions of the scientific establishment and that Dembski is one of the most visible among them. "We thought it would be an interesting thing for Baylor to get into the conversation and to be a participant," he says.

But Weaver says Baylor faculty members have been asking these questions about the relationship between science and religion for years in the school's interdisciplinary Institute for Faith and Learning. "The inference that some of us have drawn is that...we must have come up with answers that aren't those we were expected to come up with," says Weaver, who is a Presbyterian elder. "My faith background is one of asking lots of questions and living with a lot of doubts, and those may not be qualities that are valued at Baylor anymore. It may be that those of us with certainties are better adapted for the environment."

In any case, Schmeltekopf's conversation was about to turn into an argument, and a nasty one at that. In April, Dembski's Polanyi Center hosted a conference on naturalism sponsored by the Discovery Institute, a conservative think tank where Dembski is a fellow, and the Templeton Foundation, whose moneys have gone a long way to bankroll the intelligent-design movement. The conference sought to answer a very unusual question: Is there anything beyond nature? An impressive collection of scientists from all over the world attended the conference, among them Nobel Prize-winning physicist Steven Weinberg. Of course, Weinberg titled his presentation "No," a straightforward answer to the conference's central question. And other speakers announced that they were going to give their honoraria to organizations that promote the study of evolution in schools.

Baylor faculty, by and large, boycotted the conference altogether. But that wasn't all. Just days after the naturalism conference, the faculty senate voted 27-2 to dismantle Dembski's center. If there was to be a center studying the intersection of science and religion at Baylor, they held, it should be rebuilt from the ground up--with faculty input. In an editorial published in the Houston Chronicle, President Sloan charged that this uproar over faculty input was a cover for the real issue: the substance of the work being done by the center. "In my experience," he wrote, "people often object to 'the way things were done' as a rhetorical substitute for what was done." Sloan refused to dissolve the Polanyi Center, citing issues of censorship and academic integrity.

He hit the nail on the head. A lack of input might have annoyed the faculty, but it was the center's promotion of intelligent design that made them angry. Dembski claims to be doing science, a science that hopes to question the very validity of naturalism and give Darwinism a backseat to design. And that is something that Baylor's mainstream scientists cannot abide. "You can always look at something and say, 'That's something that God did,'" says Weaver. "Well, what can I do to prove you wrong?...If I can't prove your theory incorrect, it doesn't necessarily mean that it's wrong, but it means it's not science."

Weaver says that intelligent design is little more than an ego trip. How do we know a biological system has been intelligently designed? Because it's designed the way we would have designed it, in a way that we can understand it. "That's a nice little egotistical thing, isn't it?" he says. "It's designed to make us feel more comfortable. We do best when we believe ourselves to be at the pinnacle of creation. And it doesn't have much to do with theology; it has much more to do with our insecurity as a species."

Intelligent design has been completely ignored in professional literature, Weaver says. No real scientists take it seriously. "Dembski's got a whole long list of places where he's written articles and published books, and none of them are peer-reviewed. They're not done in scientifically or philosophically respectable places," Weaver says. "We judge things in the academic world not by how many books are sold at Waldenbooks," but by what a scientist's peers think of his work. Dembski's peers in mainstream science have hardly even dignified him with a response. The famous Harvard paleontologist Stephen Jay Gould, who visited Baylor in the wake of the Polanyi Center controversy, dismissed intelligent design as nothing more than modern-day creationism.

But Charles Garner, an organic chemistry professor at Baylor who says he prays with students when they come to him with problems and criticizes evolutionary theory in class, argues that it would be virtually impossible to get intelligent-design articles peer-reviewed fairly by a pro-evolution scientific establishment. "Remember," he says, "you're going to be upsetting people's worldviews with this stuff."

Sloan wouldn't shut down the center, but he had no problem holding Dembski's work up to the light of peer review, especially if it would help smooth things over with the faculty. He assembled a group of nine biologists, philosophers, science historians, and theologians--primarily from other universities--to look into the legitimacy of the center and intelligent design. Dembski was furious. The Baylor administration knew his work; he was hired because of it. Now, they were going to risk his academic reputation with a very public review by scholars he wasn't even sure were qualified to assess his work. "The peer-review committee, from my perspective, was called for purely political motives, to assuage the angry faculty," he says, "but in doing that they put me in the frying pan."

Surprisingly, Dembski emerged relatively unscathed. The review committee recommended an advisory committee to oversee Baylor's science and religion program and removed the Polanyi name from the center (even though Dembski claims he cleared the use of the name with Polanyi's son). But ultimately the outside scholars concluded that "research on the logical structure of mathematical arguments for intelligent design...have a legitimate claim to a place in the current discussions of the relations of religion and science."

Dembski was ecstatic. He issued a press release that stated in part: "Dogmatic opponents of design who demanded the Center be shut down have met their Waterloo. Baylor University is to be commended for remaining strong in the face of intolerant assaults on freedom of thought and expression."

Any progress that the review committee had made in soothing faculty concerns was undone in the space of two sentences. These were fighting words. "In academic arguments," says Weaver, "we don't seek utter destruction and defeat of our opponents. We don't talk about Waterloos."

The Baylor administration gave Dembski a chance to retract, or "contextualize," his comments, and when he refused, he was demoted. They cited a lack of "collegiality" that compromised his ability to serve as director of the center. The center that had no name now had no leader either. "We certainly didn't demote him because of positions he has taken," says Schmeltekopf. "That had nothing to do with it. We just had to move forward here."

It's true. Dembski was not demoted because of his positions. He was demoted because his positions had become a political hot potato. Initially Dembski thought that if an intelligent-design center could be successful anywhere, it would be at Baylor. Now, he thinks that if an intelligent-design center could be successful at Baylor, it could succeed anywhere. "I think what you've got at Baylor is...this whole history of the Southern Baptists with this moderate-fundamentalist controversy and split," Dembski says. "And Baylor is--I didn't fully realize this--the bastion for the moderates where anything that smacks of fundamentalism, creationism, just sends people through the roof. "Baylor may be the bastion of Baptist moderates, but some of these moderates have accused President Sloan of leaning toward the fundamentalist end of the spectrum. It is certainly difficult to see how his administration could have been blind to the fact that intelligent design comes with a political agenda that is far from moderate. The very way in which it formulates its scientific questions seeks to tear apart the Darwinian underpinnings that influence our laws, our public policies, our economic systems, our psychological theories, our schools, our sense of who we are--in short, our entire worldview. If there is a designer, do we have obligations to that designer? What are they? Do we have an intrinsic sense of morality? Have we been designed to operate best within certain constraints? "Every scientific discipline is going to have to be rethought if Darwinism and naturalism are thrown seriously into question," says Dembski. "I think the implications are huge."

If the science is sound, then perhaps we should be willing to rework our worldviews. But Baylor certainly was not willing to lead the way. "One of the things we were very clear about from the beginning," says Schmeltekopf, "was that the work of Dembski and Gordon did not have underneath it a political agenda of some kind; that is, to get into textbook wars and creationist politics and that kind of thing."

To that end, Baylor administrators pressured Dembski not to attend a May bipartisan congressional briefing by the Discovery Institute's intelligent-design program, the Center for the Renewal of Science and Culture. Dembski's colleagues presented the case for intelligent design and how it could help resolve the debate over the teaching of origins in public schools.

Dembski was surprised by Baylor's limitation of his "academic freedom." He had made no secret of his association with the Discovery Institute, which considers the "wedge strategy" one of its primary projects. The wedge strategy is a term coined by Phillip Johnson, godfather of intelligent design and author of the popular Darwin On Trial. The metaphor portrays mainstream science as a seemingly impenetrable log that can be cracked with the sharp edge of a wedge. The sharp edge of the Discovery Institute's wedge is designed to separate modern science's naturalistic bias from scientific fact. Once this crack has been made, Johnson can pound in the thicker parts of the wedge--including intelligent design, its cultural implications, and even the Bible--until eventually the log of mainstream science is split wide open. Johnson considers Dembski to be a key wedge figure.

Dembski also makes no bones about his personal position on textbooks. "My commitment is to see intelligent design flourish as a scientific research program," he says. "To do that, I need a new generation of scholars willing to consider this, because the older generation is largely hidebound. So I would like to see textbooks, certainly at the college level and even at the high-school level, which reframe introductory biology within a design paradigm." He doesn't, however, want to legislate these ideas. "I think they're powerful enough that once they get in circulation, they'll win on their own."

He might be right. Academia may not be embracing intelligent design, but the general public, it seems, is primed for it. Gallup polls over the last decade have shown that only about 10 percent of Americans believe in the scientists' definition of evolution via strictly chance mutation and natural selection. Nearly everyone else believes that God created life, either directly or by guiding the process of evolution. Last year in Kansas, the state school board voted 6-4 to no longer include evolution in statewide science tests. Intelligent design will likely prove to be a popular theory for the majority of Americans, especially because the theory can be applied to many faiths. Even though most intelligent-design researchers, like Dembski, come from a Christian background, the theory itself only detects a designer; it doesn't presume to know anything about that designer. Hence, Jews, Muslims, even agnostics, are signing on.Sitting at the dining-room table in his ranch-style home just outside of Waco, William Dembski looks more like a scientist than a minister. He's thin and stern, with a long, narrow face that mumbles through complicated mathematical theory without taking a breath. Every so often, he loses his train of thought and apologizes, saying he is quite tired. One assumes the exhaustion is a product of the ordeal at Baylor, but then a screaming toddler, recently awakened from her nap, comes running into the room to attach herself to her father's leg. Hot on the toddler's heels is Dembski's wife, her belly swollen with twins that will be born any day. It is clear that the late nights are a result of concerns much closer to the heart.Dembski spends most of his time at home with his family these days, even though he still has a five-year contract as an associate research professor at Baylor. He doesn't like going to the university's campus. He's much more comfortable here, surrounded by his stretch of land that came complete with a horse and a fishing pond. It's the perfect place to ponder life's great questions, at least when the toddler is asleep. And center or no center, there is still much work to do.

"What if science itself is coming to the place where it says we got some things wrong and, in fact, things that we ended up dismissing in religion now have to be taken seriously?" he asks. What if "that intelligence in the world that your religious faith is talking about has an ally?" What if?