James Watson has long assumed a certain special status among American scientists. The molecular biologist was awarded the Nobel Prize in Physiology or Medicine in 1962, along with Francis Crick and Maurice Wilkins, for, as the Swedish Academy put it in its announcement for the prize, "their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material." Watson and his British colleague Crick are remembered popularly for identifying the elegant and unexpected "double helix" three-dimensional structure of deoxyribonucleic acid, commonly known as DNA. Watson's important contribution to this uncanny discovery was to define how the four nucleotide bases that make up DNA—guanine (G), cytosine (C), adenine (A) and thymine (T)—combine in pairs to form its structure. These base pairs turn out to be the key to both the structure of DNA and its various functions. In other words, Watson identified the language and the code by which we understand and talk about our genetic makeup.

I have been among those who have long held Watson in high regard for several reasons. First of all, the discovery of DNA's three-dimensional structure was counterintuitive; it was an ingenious act of deduction, using models made of cardboard and paste with an exacto knife and a straight edge. How Watson and Crick, working at the Cavendish Laboratory at the University of Cambridge, became the first scientists to identify this elusive structure is the stuff of drama, especially when we recall that Watson was just 25 years old when he and Crick published their findings in the journal Nature on April 25, 1953.

Though Watson would tell me during our recent interview that he had a rather low IQ, as proof that IQ tests aren't really that important, he enrolled at the University of Chicago when he was merely 15 and earned his B.S. in zoology there in 1947 at the age of 19 and a Ph.D. in zoology from Indiana University at age 22. He was 34 when he won the Nobel Prize. Not too shabby for a guy with a "low" IQ.

Watson's youth and a certain absent-minded professorial quirkiness made him an American hero, the symbol of American enterprise and intelligence. What's more, unlike Crick, or Einstein, say, Watson was an American born and bred: His discovery, coming at the height of the Cold War, would be hailed as attesting to American genius and the unrivaled potential of the free market system versus communism. The intrigue over allegations that Watson and Crick made unauthorized use of the seminal work on X-ray diffraction by Rosalind Franklin, a brilliant scientist who died before the Nobel Prize committee made its decision, only made Watson's story all the more titillating.

And Watson—never camera shy or publicity averse—contributed to the power of his own myth first by writing "Molecular Biology of the Gene," a 1965 textbook that, updated, remains enormously popular today, and, three years later, "The Double Helix," an account of the dramatic story of his discovery that also contained startling and scandalous revelations of petty tensions, jealousies and rivalries among scientists whom we all had assumed were motivated primarily by the pursuit of truth. Watson's book did nothing less than deconstruct the myth of the scientist as secular saint, laboring away in a laboratory for knowledge's sake at the service of mankind. (One scientist summed up Watson's view of the scientific profession as "with malice toward most and charity toward none.") But Watson's account also made his quest to determine the structure of DNA gripping and exciting, one of science's greatest and most compelling triumphs. Though he was a professor at Harvard University at the time—he taught there from 1956 to 1976—the Harvard University Press refused to publish the book because of its tell-all nature. A commercial press published it instead, it became a best-seller and Watson's celebrity only grew.

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In 1989, such was the power and force of Watson's reputation and his place in the history of science that he was named the head of the Human Genome Project at the National Institutes of Health, a position he held until 1992, when he resigned because of what he said was his opposition to NIH's intention to patent gene sequences; others suggested his ownership of stock in biotechnology companies posed a possible conflict of interest. In 1994, Watson became president of the Cold Spring Harbor Laboratory (he had been its director since 1968), a lavishly funded and idyllic center on Long Island for the advanced study of genomics and cancer that in 1998 created the Watson School of Biological Sciences. In 2004, he became Cold Spring's chancellor.

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Watson in 2007.

On Oct. 14, 2007, one of Watson's former assistants, Charlotte Hunt-Grubbe, wrote an article  about him in London's Sunday Times   that quoted him making racist comments about black people by suggesting there are inherent, unalterable biological differences in intelligence between black people and everyone else. The response was swift and impressively devastating. The father of DNA had spoken the unspeakable. Echoing racist remarks that have been used to justify the enslavement and colonization of black people since the Enlightenment (think Hume, Kant, Jefferson, Hegel), Watson's comments implied that he believed that nature had created a primal distinction in intelligence and innate mental capacity between blacks and whites, which no amount of social intervention could ever change.

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He had uttered the unutterable, the most ardent fantasy of white racists (David Duke would wax poetic on his Web site that the truth had at last been revealed, and by no less than the discoverer of the structure of DNA). His words caused a ripple effect of shock, dismay and disgust among those of us who embrace the range of biological diversity and potential within the human community. It was as if one of the smartest white men in the world had confirmed what so many racists believe already: that the gap between blacks and whites in, say, IQ test scores and SAT results has a biological basis and that environmental factors such as centuries of slavery, colonization, Jim Crow segregation and race-based discrimination—all contributing to uneven economic development—don't amount to a hill of beans. Nature has given us an extra basketball gene, as it were, in lieu of native intelligence.

Watson is no stranger to controversy. Since the heated critical reception to the publication of "The Double Helix" 40 years ago, he has seemed to delight in making, with some regularity, outrageously provocative comments, comments designed at best to disturb the status quo, to shock if not awe both his fellow scientists and the general public. His autobiography, "Avoid Boring People," published in September 2007, lambastes his fellow scientists as "dinosaurs," "deadbeats" and "has-beens." By the time the LondonSunday Times article appeared, Watson had been engaged in several controversies over genetic screening, genetic engineering, homosexuality, obesity and the purported relation between skin color and libido.

But none of those controversies could begin to prepare him for the intensity of the firestorm ignited by theSunday Times article, which quoted him as saying that "he was inherently gloomy about the prospect of Africa," since "all of our social policies are based on the fact that their intelligence is the same as ours—whereas all the testing says not really"; that "people who have to deal with black employees find that [the belief that everyone is equal] is not true"; and that "there is no firm reason to anticipate that the intellectual capacities of peoples geographically separated in their evolution should prove to have evolved identically. Our wanting to reserve equal powers of reason as some universal heritage of humanity will not be enough to make it so." Five days after the article was published, he profusely apologized in a statement to the press; on Oct. 25, he abruptly retired from his position at Cold Spring Harbor, after 40 years of service there.

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When I read about Watson's remarks, I was astonished, not to mention angered and saddened. I was also determined to ask him about these comments directly. Though The Root was still in its nascent form and we wouldn't launch until January 2008, I sent him a letter, offering him a platform in the black world through which he could explain, defend and perhaps clarify the remarks attributed to him. He accepted my invitation to give The Root his first major interview since the Hunt-Grubbe article appeared.

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Henry Louis Gates Jr.

I had read, with the admiring avidity of a high school senior hellbent on medical school, his best-selling book, "The Double Helix," back in 1968. It never occurred to me that I would one day be making documentaries for public television about the uses of DNA for ancestry tracing among African Americans. But it was not until December 2006 that I met the scientist I had so admired. I was in New York, delivering a lecture for alumni of Clare College at the University of Cambridge. I had earned my M.A. and Ph.D. in English language and literature from Clare in February 1979, and Watson was living there and working at the Cavendish Laboratory when he and Crick identified the structure of DNA. As I rose to deliver my lecture at the podium, the Master of Clare College whispered to me that James Watson was in the audience. I was astonished; I had no idea that he was still alive. Following the lecture, I was seated next to Dr. Watson at dinner. He was indeed still alive; he was a sprightly and mentally acute 78 at the time. I found him friendly, but a bit awkward in conversation; generous and thoughtful, funny, but quirky-funny. A week later, unsolicited, a signed copy of "The Double Helix" arrived at my home.

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I thought of that slightly awkward dinner conversation and his gracious gift as I arrived at his offices at Cold Spring Harbor on March 17 for our interview. We talked for well over an hour, with no holds barred.

"Well?" one of my friends asked later. "Is he a racist?"

I don't think James Watson is a racist. But I do think that he is a racialist—that is, he believes that certain observable traits or forms of behavior among groups of human beings might, indeed, have a biological basis in the code that scientists, eventually, may be able to ascertain, that the "gene" is some mythically neutral space and what it purportedly "measures" or "determines" is independent of environmental factors, variables and influences. The difference, the distinction, between being a racist and a racialist is crucial. James Watson is not the garden-variety racist as he has been caricatured by the press and bloggers, the sort epitomized by David Duke and his ilk, and he seemed genuinely chagrined, embarrassed and remorseful that Duke and other racists had claimed him as their champion, as one of their own, because of his remarks as quoted in the London Sunday Times. And, as we might expect, he apologized profusely for those remarks, contending that he had been misquoted, at worst, and his remarks taken out of context, at best. (I have not been able to determine if the writer who reported the remarks taped them or reconstructed them from notes or memory.)

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But I did leave Cold Spring Harbor convinced  that Dr. Watson believes that many forms of behavior—such as "Jewish intelligence" (his phrase) and the basketball prowess of black men in the NBA (his example)—could, possibly, be traced to genetic differences among human beings, although no such connection has been made, and will probably never be made on any firm scientific basis, it seems to me. And I have to say that it was ultimately chilling to me when he remarked, with what seemed to me to be monumental naivete, that "if they find genes for all kinds of Jewish intelligence, I don't think it's going to affect me in the slightest," especially when we couple that sort of remark with his passionate belief that "everyone should be judged as individuals. No one should be judged by a term like 'black.'"

Yet precisely because of the misuses of science and pseudoscience since the 18th century, which put into place fixed categories of  four or five "races" to justify an economic order dependent upon the exploitation of blacks (and other people of color) as cheap sources of labor, starting with slavery and continuing through Jim Crow and beyond, it has never been possible for a person of African descent to function in American society simply and purely as an "individual." And if the presidential candidacy of Barack Obama has taught him, and us, anything at all, it is that this perhaps ideal state of affairs—to function as an individual and to be judged on your individual merits—still remains a most elusive and somewhat naïve dream.

Watson's error is that he associates individual genetic differences (which, of course, do in fact exist) with ethnic variation (which is sociocultural and highly malleable). Character traits—abilities and behaviors, such as intelligence or basketball skills, that are popularly attributed to groups and are defined as "genetic"—will, in fact, continue to delimit the freedom of choice and expression of individuals who fall into those "racial" categories, regardless of our individual attainments and achievements. In the end, visions that are racialist may end up doing the same work of those that are racist.  This is a lesson Watson has lived, and it is one from which we all might learn.

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Having spent the past three decades studying racist discourse in the West (starting with my Ph.D. dissertation on the Enlightenment), I know that such conclusions—say, about an entity called "Jewish intelligence"—would deleteriously affect me as a black person because it would reinforce stereotypes about Jewish people being genetically superior to us, and that such a conclusion would reinforce stereotypes about black people being inherently less intelligent than other members of the human community. If such differences in intelligence were purported to have a genetic basis, as David Duke proclaimed on his Web site with such naked glee, all of the social intervention in the world could have only so much effect. (Head Start? Why bother, when nature is to blame.) Sooner or later, in a time of increasing economic scarcity, members of these supposedly "different" or "lesser" ethnic groups or genetic populations could very well find their life possibilities limited and perhaps even regulated. Who among us can doubt that this would be true?

Likewise, I worry even more that Dr. Watson confessed to me that "we shouldn't expect that different persons have equal intelligence, because we don't know that. And people say that these should be the same [that is, that all human beings, that all members of different "racial" groups, should have the same basic range and potential for development of intelligence genetically]. I think the answer is we don't know." And later, he remarked in passing that "we're not all the same," by which he meant genetically. Rest assured that in the very near future, some scientist somewhere will claim to have proven this through our genes, and that claim will be deeply problematic for the future development of black people in American society.

As I drove away from Cold Spring Harbor, I realized that my conversation with Dr. Watson only confirmed something I already, with great trepidation, have come to believe: That the last great battle over racism will be fought not over access to a lunch counter, or a hotel room, or to the right to vote, or even the right to occupy the White House; it will be fought in a laboratory, in a test tube, under a microscope, in our genome, on the battleground of our DNA.  It is here where we, as a society, will rank and interpret our genetic difference.