Thomas Hayden, "Dances with fruit flies" (2005)

The fly, at first, looks like nothing so much as a tiny matador. Now standing still, now feinting left or darting right, he circles the petri dish arena, waving a black-tipped wing at his quarry like a red cape. But he's a lover, not a fighter, and his dance is intended to induce the fruit fly equivalent of a swoon. Scientists can no more explain why female Drosophila biarmipes flies go gaga for manly markings than they can determine what it is that attracts teenage girls to Ashton Kutcher. But the spots--unheard of in biarmipes' s cousin, the widely studied lab fly D. melanogaster --are helping to shed light on even more vexing questions of animal evolution. Among them: How can species with nearly identical DNA turn out as different as biarmipes is from melanogaster, or as humans are from chimpanzees?

We're living at a strange moment in America. Once again, evolution is becoming a controversial topic. But while school boards are revisiting the 19th-century debate over whether evolution even happens, 21st-century scientists are beginning to show exactly how the natural phenomenon works. Using the powerful tools of molecular biology and comparative genomics, they're finding specific changes in the DNA that can account for 17,000 species of butterfly or why insects have only six legs instead of a dozen. And while some 55 percent of Americans balk at the idea that humans evolved at all, analysis of the genes that build our bodies shows our clear kinship not just to the apes but all the way back to bugs, worms, and beyond. Along the way, scientists are starting to find concrete explanations for everything from our large brains to just exactly how the fruit fly--or the leopard, for that matter--got its spots.

User friendly. Sean Carroll, in whose University of Wisconsin-Madison laboratory the biarmipes flies danced, has been at the head of the new wave of evolutionary studies for two decades. An investigator with the Howard Hughes Medical Institute, Carroll sets out in his engaging new book, Endless Forms Most Beautiful (W. W. Norton), to introduce us to the field he helped found: evolutionary developmental biology, or "evo devo." Writing in a clear, straightforward style and drawing on his own love for wildlife (and classic rock) for inspiration, Carroll pulls together decades of work by hundreds of scientists. He reveals a remarkable series of insights into how evolution has shaped--and continues to shape--the wondrous assortment of creatures that share this planet with us. He emerges as the new, user-friendly public face of evolutionary science in the process.

Carroll wasn't particularly interested in bugs as a kid; growing up in Toledo, Ohio, in the 1960s, he was more of a snake guy. But laboratory science has its demands, and insects like the fruit flies--and later, butterflies--Carroll chose to study are much easier to work with than more impressive forms of wildlife. But there was a bigger problem. From Charles Darwin on, biologists suspected that the mysteries of evolution would be revealed in life's other great mystery--the development of tiny, simple fertilized egg cells into large, complex adults. "All changes in animal form come about through changes in development," Carroll says, "but we knew next to nothing about development when I started "graduate school in the late 1970s. "So I knew we would have to push the field forward first."

The rapidly improving techniques of molecular biology made that possible, and evo devo--the study of how the development process creates animal bodies and changes them over time--was born. In Endless Forms , Carroll traces the development of the field from its earliest days, starting with the first revelation in 1983 of how a small set of genes, called Hox genes, controls development in fruit flies. That seemingly arcane triumph took on much greater significance when geneticists found the same genes--doing the same jobs--throughout the animal kingdom.

That discovery pointed to the deep connections between all animals and helped scientists work out the complex details of development. But it also raised a new problem: If key developmental genes have remained largely unchanged throughout evolutionary history, how can we account for all the differences, great and small, between different species? In some cases, the answer turned out to be a process of duplication and innovation. Several key points in animal evolution are associated with an increase in the number of developmental genes. The resulting redundancy in the control system, Carroll says, allowed evolution to "experiment" with new developmental programs and body forms, allowing vertebrates to develop distinctive features like skulls and jaws, for example, without hopelessly messing up other body parts.

Color study. But those changes can explain only a subset of biological innovations. A much more pervasive mechanism for evolution of body form, Carroll says, lies in yet another level of genetic control. Every cell in the body contains all of an animal's genes, but individual cells use only a fraction of those genes at any given time. The difference between a white blood cell and a muscle cell, for example, lies in where and when specific groups of genes are "turned on" during development. That process is controlled by a complex series of genetic "switches" that regulate the timing and location of gene activity with remarkable precision.

Which is where the dancing fruit flies come in. All fruit flies have the genes needed to make wing spots, including a gene for black pigment called, confusingly enough, Yellow. That gene is turned on at low levels throughout all fruit fly wings, but only male biarmipes flies have the characteristic spot. Writing recently in Nature, Carroll's research team reported finding mutations in a genetic switch for Yellow in biarmipes flies that allow a finer level of control; one part of the switch keeps gene expression low throughout the wing, while another cranks up expression at the tips, creating the characteristic spot.

It's just one small step in the twisting path of evolution, of course. But it's not hard to see how many such changes in gene switches--accompanied by even small survival advantages such as females who prefer spotted mates--could lead over time to a new species, with little change in the genes themselves. It's a principle that is found again and again throughout the animal kingdom, Carroll says, and one that should help solve one of the greatest biological mysteries of recent years.

The Human Genome Project revealed a surprising fact: Despite our remarkable complexity and biological sophistication, human beings have just 25,000 or so genes, only twice as many as fruit flies and about the same number as other mammals and even fish. In a particularly interesting chapter on human evolution, Carroll notes that many of the differences between chimps and people--our slower development, larger brains, upright posture, and opposable thumbs, for example--represent changes in the size and shape of physical structures and the timing of development. We can't do fly-style experiments with humans, but Carroll presents a strong case that many of the key innovations that made us human lie not in our genes but in how we use them during development.

Beauty. Speaking recently in his office--a space so comfortably cluttered it almost resembles a nest--sporting shaggy hair and dressed in jeans and sneakers, Carroll seems about as content as a man can be. But the critics of evolution--he calls them deniers--are really starting to get under his skin. Like many scientists, Carroll sees no inherent contradiction between his work and a religious worldview. "I learned about Darwin and evolution from ordained teachers," says Carroll, a graduate of Catholic schools and the son of a composer of Gregorian chants. Science and religion are separate spheres, he says, and the temptation to live and let live is strong. But undermining the teaching of evolution in public schools would rob students of the chance to marvel at the beauty of the natural world, he says. "Your religious views are your own, but there is no more doubt about evolution than there is about cancer, kidney function, or volcanoes. If you reject science and deny evolution, you've picked a battle, and I'll fight it whenever and wherever I can."

Carroll hopes that the concrete steps revealed by evo devo will make evolution easier to understand for those who were confused by the abstract theories of the past and harder to refute by those who would deny its existence. (For one thing, the system of genetic controls that govern development and evolution is needlessly complex and clearly cobbled together from existing parts, Carroll notes. Surely any "intelligent designer" --an idea currently in vogue in some anti-evolutionary circles--who came up with the system would have been fired before the plans got to the blueprint stage.)

Evo devo is still a developing science, and many of its greatest advances are yet to come. The priorities, Carroll says, include understanding the basis of hard-wired behavior, like bird song and parental care, and working out the evolution of unique human attributes, such as speech and consciousness. And while further "proof" of evolution isn't a priority for scientists like Carroll, evo devo also holds the promise of not just revealing how the process works but actually re-creating some of its major steps in the lab. Ultimately, Carroll says, reaching this deeper understanding of nature--and our place in it--makes the biological realm more beautiful and inspiring, not less so. "There is mystery and wonder in the revelations of science," Carroll says, "and not being open to this is really missing a story that is fascinating and rewarding."

Born: Sept. 17, 1960 Family: Wife, Jamie; two sons and two stepsons Education: Ph.D. in immunology, Tufts Medical School, 1983 New book: Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom (W. W. Norton)