THERE HAVE BEEN three great periods of Darwinian thought -- the decades immediately following the 1859 publication of On the Origin of the Species,   when Darwin's ideas first received wide currency; the 1930s, when the work of R. A. Fisher, Sewall Wright, and their colleagues ushered in the Modern Synthesis and the beginning of mathematical work in evolution; and the sixties and seventies, when William Hamilton, G. C. Williams, Lynn Margulis, and E. O. Wilson, among others, began working out how the Modern Synthesis could convincingly explain cooperation and even altruism for everything from bacteria to humans (a field of inquiry whose avatar is Richard Dawkins, author of The Selfish Gene).

We are now entering a fourth such phase, characterized by two things: an unprecedented deepening and refining of evolutionary theory, as whole organisms -- especially humans -- have their genetic code unlocked; and the spread of Darwin's ideas outside of biology proper to influence psychology, sociology, economics, philosophy, and law. It is the purpose of "After Darwin" to cover this revolution as it unfolds.

WAS DARWIN WRONG? That question -- shorthand for a general condemnation of the theory or evolution -- was first asked in 1859 with the publication of On the Origin of Species, and is still surprisingly alive today. Much is made of the argument as it takes place at the religious edges of America, the world of the Scopes "Monkey Trial" and the Kansas Board of Education, but in reality, the objections of religious fundamentalists amount to little more than a sideshow. Anyone who asserts the literal truth of Genesis or any other creation myth is not putting the theory of evolution to the test and finding it wanting, they are simply rejecting it a priori.

The real surprise is the number of Americans of more moderate political and religious views who feel, almost 150 years after the publication of Origin, that Darwinism is still somehow a provisional theory. A New York Times poll, published on March 11 of this year, found that almost half of Americans agree with the statement: "The theory of evolution is far from being scientifically proved." This sizable a slice of the populace certainly includes people who understand that the earth revolves around the sun and is more than six thousand years old, people who would not assert the falsehood of relativity or quantum mechanics based on personal conviction, but who are ready to believe that something or someone has rendered the main force of Darwin's argument moot. These challenges to Darwinism come not just from "creation science," but from a desire to believe that some newer, more modern (and more palatable) theory has replaced Darwinism -- Roger Penrose and Ian Smith offer the hope that some aspect of quantum mechanics or mathematics provides for non-random development; J. L. Lovelock's Gaia hypothesis revives the notion of living things being in harmony with one another by pre-supposing a sentient and loving environment; and even Steven J. Gould, a self-described Darwinian who believes that the shapes life takes are if anything more random than Darwin did, is still often thought of as an anti-Darwinian rebel rather than an articulator of Darwinian theory.

Stranger still, these views are prevalent on the eve of Darwinism's greatest practical triumph, the event that will take evolutionary theory out of the realm of abstraction and weave it forever into the fabric of daily life: the sequencing of the human genome, a project that relies on Darwinian intuition to proceed. In the world of genetics, the mechanisms and history of evolution are being worked out in increasingly precise detail, with the DNA sequences of different organisms providing the what, when, where, and how to Darwin's original inquiry into why different species came into being. Biology, once reliant on counting toes and making educated guesses, has been transformed into an information-driven science, propelled by the force of Darwin's insights.

And yet the popular debate continues, all but unaffected by more than a century of scientific work, the last forty years of which include an increasingly accurate and complete gene's-eye view of the evolutionary tree. It's as if there are two Darwins: one who is the articulator of a philosophy of biological change that is taken for granted among scientists, and which is driving a biological revolution; and another Darwin, who is the proponent of merely provisional speculations, and of suspect ideas that lack the credibility of real science.

THE FIRST DARWIN, the progenitor of the current biological revolution, provided the more philosophical half of the insight needed to drive today's genetic research. The other, more practical half was provided by the monk Gregor Mendel, whose work on inheritance in peas first articulated the idea of genes. Darwin's theory of evolution and Mendel's theory of genes were first joined together in the 1930s, into what has become known as the Modern Synthesis. The fusion of Darwin's and Mendel's ideas provided nothing less than the tool-kit for modern biology. The assumption that the environment, broadly conceived, is the shaper of life and the genetic sequence is the thing that gets shaped has proven to be a tremendously adaptable and extensible idea, and is being used to guide experiments that were previously inaccessible to biological inquiry. Biological experiments no longer use Darwinism as a hypothesis -- they take it for granted. As the title of an article by biologist Theodosius Dobzhansky put it: "Nothing in biology makes sense except in the light of evolution."

Two recent biological debates -- one about one particular species, the other about the whole of the animal kingdom -- illustrate how the Modern Synthesis has permeated biological science. In the first debate, DNA sequencing is being used to inquire about the split between Neanderthals and modern humans in order to determine whether modern humans killed off Neanderthals or if the two groups simply intermarried until the Neanderthals disappeared. As evidence in this debate, DNA was recovered from the bone marrow of a Neanderthal skeleton and compared with the DNA of modern humans -- had there been interbreeding between the two primate species (human and Neanderthal), our DNA would contain similarities with that of our possible ancestors. However, our DNA showed little correlation with the Neanderthal's, strongly suggesting that extermination by Homo sapiens was the Neanderthal's lot. This kind of research would be meaningless without both a Darwinian assumption (that Neanderthals and modern humans are related species that diverged evolutionarily) and a Mendelian one (that the markers of this evolutionary divergence reside in their -- and our -- genes).

A similar inquiry into evolutionary divergence is taking place at a different scale: The rise of animal life seems to be intimately tied up with a gene called the "homeobox" gene, whose function is to arrange cells in an embryo according to a particular body plan. The homeobox gene governs how the position of heads differs from tails, and livers from lungs. More than a mere marker of animal development, the homeobox gene may well be animalness itself, the essence of the divergence of animals from all other forms of life. If the evolution of the homeobox gene is the event that gave rise to the animal kingdom, then the definition of "animal" will become simply "living thing with a homeobox gene." Gone will be observable categorizations like mobility or the nature of eating and breathing, to be replaced by a definition of "animal" that uses, even requires, an understanding of an evolutionary moment to make any sense at all.

HOW DID AMERICA end up with such a bifurcation between the professional beliefs of working biologists and the disbelief prevalent in such a large segment of the population, even comprising people who otherwise feel no particular hostility to scientific endeavor? Why, in other words, are Darwin's ideas so hard to swallow, even after all this time?

Among those who have assumed the correctness of the theory of evolution, many attempts have been made to encapsulate it in a phrase, in order to give the idea wider currency. Herbert Spencer's infelicitous "survival of the fittest," was wrongly adopted by Darwin over his own shorthand, "descent with modification" (wrongly adopted because both Spencer and Darwin misunderstood how cooperation can benefit individual organisms and, more importantly, individual genes). Richard Dawkins' recent try, "Life results from the non-random survival of randomly varying replicators" is more thorough but less memorable. No attempt better captures the radical flavor of Darwinism than the biologist D'Arcy Thompson's version: "Everything is the way it is because it got that way." This constuction -- memorable, complete, and almost tautological in its simplicity -- goes a long way towards explaining the widespread disbelief in evolution as the sole explanation of the diversity of life.

The objection to the theory of evolution and the belief, even the hope, that Darwin was wrong can be summed up in something that could be called the "Peggy Lee" objection: Is that all there is? Many of the objections to Darwinism come from people who accept the idea that new species can arise from modifications to older ones. To reject such a hypothesis would require rejecting not just Darwinism but the fossil record, as well as the whole human history of animal and plant breeding, where artificial selection has created every variety of wheat and rose and cow and dog in existence. Darwin's use of the term "natural selection" to describe his theory was intended to draw a connection between the production of new species of plants and animals by selecting for or against certain traits by breeders. The radical idea that Darwinism introduces is not just that randomly accumulated small change can create new species (and therefore explain the diversity of life on earth), but that it is the only thing that can do so, and worse, that it is all that is needed. On the Origin of Species was an attempt, for the first time, to explain the miracle of life without recourse to a miracle. In the words of the zoologist G. G. Simpson, quoted approvingly by Richard Dawkins on the first page of The Selfish Gene, "The point I want to make now is that all attempts to answer that question [What is man?] before 1859 are worthless and that we will be better off if we ignore them completely."

If Thompson (and Darwin) are right, if everything is the way it is because it got that way, then it isn't the way it is because it was created that way, or because it was straining to become that way. If everything is the way it is because it got that way, then the miracle of life is no miracle at all, just a random set of occurrences shaped by the environment of a planet with particular conditions of temperature and chemistry. Darwinism's failure to include any sort of cushioning of the idea that life proceeds because of the effect of particular environments on random variation strikes at a much larger group of people than religious zealots -- it strikes at anyone who believes that life must have a purpose. Darwinism introduces the possibility that not only is a miraculous force not needed to explain how life unfolded on earth, but that it would be difficult to shoehorn such a force, even if you wanted to. Though the "Theory of Everything" is usually thought of as a quest for physics, biology is actually the science that is closest to having one -- Darwin's theory still grates long after most scientific theories have been either accepted or replaced (or both) not because it explains so little so provisionally, but because it explains so much so well.

AND SO WE FIND ourselves in the curious position of widespread discomfort and disbelief in a scientific theory whose explanatory power and refinement grows with each passing year. We have been taught to believe that truth will out, that opposition to scientific advance is laughable, and we learn in school, over and over again, that the people who believed that the sun revolved around the earth were engaging in a pointless objection to a self-evident truth, but heliocentrism was nothing compared to evolution as a destabilizing force on whole systems of belief -- every single religion has an explanation for life, and if Darwin is right, all other attempts to explain life are wrong. This problem has been in something of a stasis from the Scopes trial until now. There have been many skirmishes in the war, but the basic outlines of the battleground have remained the same.

In the next few years, however, as improbable as it seems, we are headed for more strife over Darwinism, not less. While the biologists and biochemists and bioinformaticists have been participating in a rapidly accelerating accumulation of technique and theory based on Darwin's ideas, the populace at large still assumes that evolution is a theory that scientists think about, rather than being a tool they think with. When it becomes clear that an understanding of the human genome (and the fantastic cornucopia of medical advances it portends) requires an acceptance of the fundamentally unguided nature of genetic drift, natural selection, and evolutionary change, Darwinism will find itself faced with newly hot opposition, not from religious zealots, but from people who cannot or will not bring themselves to believe that that's all there is.

Clay Shirky is a contributing editor to FEED and Professor of Media Studies at Hunter College.