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Drawing the Map of Life is the dramatic story of the Human Genome Project from its origins, through the race to order the 3 billion subunits of DNA, to the surprises emerging as scientists seek to exploit the molecule of heredity. It’s the first account to deal in depth with the intellectual roots of the project, the motivations that drove it, and the hype that often masked genuine triumphs.

Distinguished science journalist Victor McElheny offers vivid, insightful profiles of key people, such as David Botstein, Eric Lander, Francis Collins, James Watson, Michael Hunkapiller, and Craig Venter. McElheny also shows that the Human Genome Project is a striking example of how new techniques (such as restriction enzymes and sequencing methods) often arrive first, shaping the questions scientists then ask.

Drawing on years of original interviews and reporting in the inner circles of biological science, Drawing the Map of Life is the definitive, up-to-date story of today’s greatest scientific quest. No one who wishes to understand genome mapping and how it is transforming our lives can afford to miss this book.

For Ruth

"Two opposing laws seem to me now in contest. The one, a law of blood and death, opening out each day new modes of destruction, forces nations to be always ready for the battle. The other, a law of peace, work, and health, whose only aim is to deliver man from the calamities which beset him . . . [O]f this we may be sure, that science, in obeying the law of humanity, will always labor to enlarge the frontiers of life."

Louis Pasteur,
remarks read at the dedication of
the Institut Pasteur, 14 November 1888;
quoted in Encyclopaedia Britannica,
Eleventh Edition (1911) 20, 894

PREFACE

Ten years ago, in the East Room of the White House, U.S. President Bill Clinton celebrated the completion of a "most wondrous map" of the DNA that makes up the human genome. He compared it to the map of the vast American West that Meriwether Lewis and William Clark presented to Thomas Jefferson in the White House nearly two centuries earlier. This book outlines the events leading to that ceremony and chronicles the torrent of efforts since then to fill in the genomic map and make sense of it.

This narrative of the human genome project and its consequences appears just as commercial firms are preparing to sequence the entire DNA of tens of thousands of people—only ten years after scientists managed to spell out the order of the adenines, thymines, cytosines, and guanines of just one human. The history sketched here is recent, vast, and exploding. The pages ahead summarize a continuing revolution that began in fundamental biology and now, more and more, is entering our lives to create a genomic age. It is one of the greatest positive achievements of our scientific civilization.

This book does not focus on what ought to be happening or might happen in a still-hidden future but instead concentrates on what has happened and is happening. Its fundamental question is, How did we get here?

In a limited space, only a few major topics can be explored. The story begins with the creation of the techniques and tools that enabled the genome project to begin. As attention to human genetic diseases rapidly grew, the project was organized in the late 1980s amid turmoil among biologists. Remarkably, the project did not originate from the top down, as did both the atomic-bomb and moon programs, but rather out of grassroots consultations over about three years. In the 1990s, after years of often-rocky preparation, decisions were reached about the methods to determine the sequence of human DNA. Then a highly publicized race between nonprofit and for-profit teams achieved rough drafts of the human genome in 2000.

But now, the question was: What did that sequence mean? The 3 billion subunits of human DNA were like a string of letters, with no gaps to show where the words began and ended, filling every page of a stack of telephone books. How could the sequence be interpreted to find both protein blueprints and a largely unknown array of controls? It was clear that biology had raced to the starting gate. To use the sequence to illuminate the actual sources of disease would require enormous additional effort in the years and decades beyond.

The research of the last ten years has brought a shower of scientific surprises that overturned many previous notions of what a gene or a genome is and does. Genomic knowledge is spreading into the fields of agriculture, energy, and environmental protection, all of which have the most profound implications for human health. With the appearance of new tools—growing in capacity at an amazing rate—there is a dramatic speedup in the range of problems that can be tackled.

During the race to the human sequence, the focus was on how alike individuals are. Now the focus is on differences. Researchers across the world have begun spelling out the myriad of changes in DNA that make one person more susceptible to a disease than another. To help probe more and more deeply into these predisposing mutations, thousands upon thousands of human volunteers are donating their DNA for science. Before the end of the first decade of the twenty-first century, medicine was beginning to use genomic techniques to determine which drugs would benefit particular patients.

All of these developments have taken place in the culture of doubt that pervades science. While striving to pick important problems that are amenable to experiment, scientists are enjoined to view skeptically any finding, no matter how attractive, as a possible artifact, not a real discovery. And the scientists struggle with a corollary principle: openness. The rule, never easy and not always observed, has always been, Tell all, tell it right away, and take your lumps. Famous exponents of this ruthless doctrine were two refugee founders of modern biology, Max Delbrück from Germany and Salvador Luria from Italy. Each summer in the 1940s, at Cold Spring Harbor Laboratory near Long Island Sound, they inducted small bands of researchers into a study of life at so elemental a level that the mechanics of heredity could be seen in simple terms. The organisms they worked with—and talked about so often while sitting on a lawn sloping down toward the harbor—were bacteria and the tiny viruses, called bacteriophages, that preyed on them.

Openness was at the core of the phage ethos, and it soon propagated to the genetic research systems of the future, such as yeast, the nematode C. elegans, and the fruit fly, Drosophila melanogaster. It became a dominant theme of genomics, where data are posted every day on the Internet. And even as genomics has matured and pervaded all biology, the demands of openness continue to trigger debates. One concerns continued universal access to research findings. Another concerns publishing analytical reports in such a way that any scientist can see them, even if the individual researcher or academic institutions cannot afford print or electronic subscriptions to a particular journal.

The march of genomics is taking place alongside a background of ethical and spiritual anxieties. Would the information, particularly the theories of evolution that are the core of all biology and medicine, assault people's religious faith? Would all people benefit regardless of income, in rich countries and poor, whether they suffer from infectious diseases of greatest impact on children or diseases like cancer that fall more heavily on older people? Would individuals or the medical professionals who help them comprehend information that does not constitute fate but a set of probabilities and risks? Would individuals act on information indicating they should change their lifestyles? Would the finding of susceptibility to a disease for which there is no treatment devastate individuals or families? Would the information be misused by employers and insurers—or by people wishing to design their offspring? Questions like these, which actually represent the classical challenges of all measures to protect public or individual health, constantly face humanity. Although some cite them as reasons not to perform genomic research, others have insisted vehemently that failure to learn new ways to alleviate human suffering is unacceptable. To date, this latter view has prevailed.

Some ask whether this churning world of genomics is a race between commercial and academic motives. Surely, this is a simplistic view. Commercial firms and research institutions have, in effect, cooperated by competing—just as they did in the atomic-bomb and lunar-landing programs decades ago. One side has driven the other in the heavily technological, even industrial, genomic enterprise. At many points, there was blindness on one side or the other. Of the immense quantities of sophisticated equipment and chemicals, the lion's share has come from private firms. But smart and anxious customers in academic laboratories have put the manufacturers through the wringer in tackling numerous imperfections. The major nonprofit genome centers have had to learn how to run industrial operations alongside their laboratories. And industry has had to learn how to build and finance biotechnology and genomics companies of suitable size and sustained capacity for innovation.

Competition remains equally hot in the governmental and philanthropic spheres. In the United States, the National Institutes of Health have found themselves under pressure from the Department of Energy, the National Science Foundation, and the Department of Agriculture, each of which has strong motivations to conduct genomic research. Agencies in other countries, like the huge Wellcome Trust in Britain, a private charity, have funded an important share of the total cost and stiffened the spine of other agencies at dicey moments. Volunteer associations focusing on particular illnesses, such as heart disease or cancer, have competed for many years to influence scientists, legislators, and bureaucrats to push harder for their particular concerns. Because many of the underlying biological problems, such as development from egg to adult, are general, the lobbying has helped expand health research in general. For many decades, wealthy individuals have come forward in large numbers to support biomedical research that they hope will be "transformative."

It is worth mentioning that this seemingly arcane process is not an alien implant. Genomic research grows organically from a century and a half of work on human health and nutrition. It is merely the latest phase of a biological and medical revolution that has been gathering strength continually, precipitating at least a fivefold increase in humanity's numbers. The succession of rapid achievements that seem miraculous excites the hope, the expectation—the demand—for more ways to reduce pain and hunger and to save and extend human life.

The work on genomes has grown more heavily computational and more intricately collaborative than ever before in the history of biological and medical research. It has acquired a momentum of its own, pervading biology and medicine and agriculture. As Neil Risch of the University of California, San Francisco, recalled in 2007, "It changes the way people think." We are confronting a force to be reckoned with in our lives. We have to understand the genomic enterprise to understand our times and our future.

CHAPTER ONE

Building the Toolbox

"Progress in science depends on new techniques, new discoveries and new ideas, probably in that order."

—Sydney Brenner,
The Times (London), October 29, 1986

Restriction Enzymes: Molecular Scissors

In the spring of 1968, Hamilton O. Smith of Johns Hopkins was intrigued by the possibility of removing a technical obstacle that troubled him and many of his fellow molecular biologists. Perhaps there really was a "chemical scalpel," an enzyme that could cut DNA into manageable pieces so that their sequences of subunits could be "read." Despite a string of triumphs over twenty years, including Robert Holley's painstaking decipherment of transfer RNA, biologists still lacked the tools to "see" into genes. In the late 1960s, the totality of DNA forming the genomes of humans and every other form of life were a jumble of black boxes.

Smith and hundreds of fellow molecular biologists around the world knew the outlines of genetically controlled life. They knew there is a code that spells out the makeup of the scores of thousands of proteins that do the main work of a living cell. They also knew that the code carries the vast swarm of stop-and start-signals that control which proteins exist and do their work at a given time.

Further, they knew that the code consists of an alphabet of four chemicals called bases, or nucleotides, strung along the twin sugar-phosphate backbones of the DNA double helix. Deoxyribonucleic acid (DNA) gets its name from the fact that its ribose sugar lacks one oxygen atom that is found in the related, and possibly more ancient, sister compound ribonucleic acid (RNA). The four nucleotides form links between the backbones, whose alternating sugars and phosphates repeat continually. Jutting out at right angles to the backbones, these information-bearing components are called adenine, thymine, guanine, and cytosine. These are the famous A, T, G, and C of a thousand textbooks. By means of relatively loose hydrogen bonds, the bases form complementary pairs, A always bonding with T, and G with C.

The sequences of these chemical "letters" are read in triplets, specifying another sequence: the twenty different kinds of amino acids that make up proteins. Conceptually, the chains of amino acids are parallel to the chains of DNA. The triplet ACG, for example, stands for the amino acid threonine. A mutation in the triplet CTT causes most cases of cystic fibrosis by changing just one amino acid subunit of one protein.

In the late 1960s, the explosively expanding community of molecular biologists was growing more and more impatient about obstacles to manipulating DNA so that it could be completely dissected and understood. The delay threw up a barrier to progress in research that was transforming biology into a queen of the sciences and attracting the best and the brightest. Smith, thirty-seven years old and working at the Johns Hopkins University Medical School, was at least as impatient as his colleagues. He knew very well that technical capabilities, as much as ideas, drive science. This fundamental point is at least as true in biology as in astronomy, high-energy physics, oceanography, or space exploration.

Smith was born in 1931 in New York City, where his father, an assistant professor at the University of Florida, was completing work on a doctorate in education at Columbia. Although the family shuttled back and forth from Florida, Smith's childhood memories of New York were stronger. He wrote that his parents entertained him and his elder brother, a year older, "with arithmetic problems and a small Gilbert chemistry set." After his father became a professor at the University of Illinois, Smith spent most of his boyhood in Champaign-Urbana, in what he described as "an atmosphere of intense intellectualism." Smith and his brother spent the money from their newspaper-delivery routes on equipment for their basement laboratory, where Smith laid down the habits of a craftsman, even an artist, in science. Such qualities won wide admiration. In 1999, the geneticist David Botstein said, "Ham Smith is one of the premier craftsmen of molecular biology." Smith's colleague Mark Adams said then, "A lot of us are users of the molecular biology toolkit. Ham has been, to a large extent, a creator of that toolkit." Biochemist Mark Ptashne said, "I'm not sure people realize how smart he is. He has a razor-like, laser-like intelligence."¹

As a college student at Berkeley in the early 1950s, Smith was fascinated when George Wald of Harvard, a later Nobel Prize winner, lectured on the biochemistry of the retina. After medical school at Johns Hopkins and an internship in St. Louis, where he met and married his wife, Liz, he spent two relaxed years with the U.S. Navy in San Diego. There he read of research on aberrations in human chromosomes and plunged into the study of genetics. The interest grew stronger during a medical residency in Detroit, where he first heard of the work of Max Delbrück and Salvador Luria on bacterial viruses in the 1940s and of the discovery by Francis Crick and James Watson of a structure for DNA in 1953.²

During five years at the University of Michigan, Smith made discoveries about a process known as lysogeny. He found out how a particular virus called P22 inserted its own DNA into a bacterium and dwelt there silently, instead of taking over its host and converting its machinery into a factory for more virus. It was then that he heard of Werner Arber's research in Switzerland into how bacteria defeat a viral invasion by cutting up the alien DNA (while protecting their own DNA from the same process).

Thus, Smith had been pulled into a maelstrom of new knowledge about the molecular details of genetics, which had grown rapidly since the 1940s and 1950s. A major step was establishing that DNA—long dismissed as too uncomplicated to play a commanding role in the living cell—is the "transforming principle." In 1944, Oswald Avery and colleagues at the Rockefeller Institute proved it with pneumococcus microbes, and in 1952 Alfred Hershey and Martha Chase of Cold Spring Harbor proved it with bacteria-attacking viruses. DNA was the seat of hereditary information in all cells and even most viruses. But how could DNA control heredity? The answer came from Watson and Crick's 1953 double-helix model, in which the two sugar phosphate strands wound around each other and were cross-linked by the side-group As, Ts, Gs, and Cs—A always with T, and G always with C. The two complementary strands could pull apart and be copied into "daughter" DNA for the next generation of cells.

Also in 1953, and also in Cambridge, other momentous discoveries were made. Frederick Sanger worked out the sequence of the amino acids of a relatively simple protein, insulin. Max Perutz and John Kendrew hit on a method for deciphering the three-dimensional structure of the much larger proteins, myoglobin and hemoglobin. Thus, windows were opening into how the form of proteins dictated their function. Soon after, scientists in the United States, including Arthur Kornberg, Severo Ochoa, and Marianne Grunberg-Manago, discovered specific enzymes that could copy DNA or its sister chemical RNA. The ribose sugar of RNA contains the oxygen atom missing in DNA. RNA can take several forms, such as working copies of genes, escorts of protein subunits to the place of assembly, portions of ribosome structures where proteins are stitched together, and a myriad of tiny RNAs that can interfere with stages of protein synthesis.³

How could the information in the DNA be converted into proteins? In a remarkably short time, about a decade, the main mechanisms were discovered. Crick, Sydney Brenner, Marshall Nirenberg, and others deciphered the "genetic code" in which the triplets of A, T, G, and C spelled out one of the twenty amino acids. Meanwhile, Brenner and Francois Jacob, working in Pasadena, California, and rivals in Watson's lab in Cambridge, Massachusetts, including Walter Gilbert, found the short-lived messenger RNA copy of DNA, which carries instructions from the vault (the cell's nucleus containing the DNA) out to the factory floor, where the ribosomes do their work. Forwarding this process are the transfer RNAs Crick had postulated. Transfer RNAs carry their particular amino acids to the sites of assembly on the ribosomes.⁴

In the same period, Jacob and his colleague Jacques Monod of the Pasteur Institute in Paris uncovered the first genetic brakes, which silenced the expression of the genes by preventing the copying of DNA into messengers. In 1966, Gilbert and Ptashne at Harvard isolated the predicted silencer proteins, called repressors. Others found accelerator "factors" that operated in forward gear.⁵

These feats held more than academic interest. Cancer, of growing importance in an aging population, was a genetic disease. Cancer could be inherited in families, but more often resulted from a succession of mutations in a victim's lifetime that led to an uncontrolled proliferation of particular cells. Viruses, with just a few genes, were known to cause cancer in animals. This fact indicated that only slight changes were necessary to convert cells from orderly citizens of a particular tissue into rogues that could eventually, by the process known as metastasis, enter the bloodstream, settle in distant organs, and kill the victim.

Aspiring to medical payoff for their work, molecular biologists saw the viruses as model triggers for cancer. But even a virus's few genes were, in the late 1960s, a biological black box. Robert Holley's sequence of a tiny transfer RNA was fewer than one hundred letters long. And Seymour Benzer of Purdue mapped, in ever finer detail, mutations of just one gene in a virus. But the much larger sequences of viral or cellular genes, 1,000 letters or more, were shrouded from view. A shower of Nobel Prizes had rewarded the feats of molecular biology, but the machinery of cancer remained hidden.

To open the black box and "read" the sequence of letters, molecular scissors were needed to cut the DNA into manageable pieces. One means to do this had been considered for some years. Arber in Switzerland had begun working on "restriction enzymes," which prevent an invading virus from taking over a bacterium. People began trying to isolate one of these restriction enzymes. Among them was Matthew Meselson at Harvard, who, along with Franklin Stahl, had proved in 1958 that DNA was duplicated as suggested by Watson and Crick. Meselson and Robert Yuan discovered one restriction enzyme, but it was found to cut DNA indiscriminately. ⁶

Meselson's search inspired Smith. "With great interest," he gave a seminar on Meselson's work to his colleagues at Johns Hopkins and began working on the problem himself. He and his graduate student Kent Wilcox had started studying rearrangements, or "recombination," of DNA in a microbe called Haemophilus influenzae, which caused not the flu but ear infections, meningitis, and pneumonia. They tried injecting into their new microbe radioactive DNA from the virus P22, which Smith had studied for years. P22 normally infects Salmonella; would it infect H. influenzae? To their surprise it would not. They might have expected a lot of P22 DNA after infection, but they could not "recover" any. It was May 25, 1968.

This was exciting. Had they encountered a restriction enzyme, a way for bacteria to cut up invading P22 DNA? Yes. Smith proceeded to find that their enzyme cut double-stranded DNA only. It recognized a particular six-letter sequence and cut it in the middle. They had found a powerful, "site-specific" scissors for DNA.⁷

A Hopkins colleague, Daniel Nathans (who shared a Nobel Prize in 1978 with Smith and Arber), was then on sabbatical leave in Israel. Smith wrote him about the enzyme, which was dubbed HindII and pronounced "hin D2." Some time later, in a gossipy reply, Nathans jovially wrote that he had "designs on your enzyme" for his planned mapping of genes in the cancer-causing monkey virus SV40. Nathans started using HindII and found other restriction enzymes that also cut SV40.

It was the beginning of a flood. The laboratory of Richard Roberts, a later Nobel Prize winner, at Cold Spring Harbor Laboratory (CSHL) began systematically identifying dozens of restriction enzymes. Soon companies began producing them.

By isolating the first DNA-cutting scalpel, Ham Smith's laboratory had opened up a new level of biology. But this restriction enzyme was only one of the biochemical tools that proved essential to what became the Human Genome Project. Sequencing machine pioneer Leroy Hood noted in 2004 that a battery of enzymes was needed to make the genome project possible. Most important of these, he thought, were the polymerases that built (synthesized) strings of DNA. Also essential were ligases, enzymes that knitted DNA pieces back together after the chemical scalpel had done its work, which were developed in several laboratories in the late 1960s. Reflecting on the genome project, which gave "us something to work on for the next hundred years," Hood said, agreeing with Sydney Brenner, "All of the big revolutions—they are technique driven."⁸

In the early 1970s, California scientists Herbert Boyer and Stanley Cohen made another bacterial enzyme, called Eco RI, part of their system for manipulating DNA. This involved taking pieces of DNA from one organism that had been cut by the restriction enzyme, then stitching the pieces into DNA circles called plasmids with the help of the needle-and-thread ligase enzymes. Bacteria could be induced to take in the doctored plasmids. This meant that animal genes of interest could be moved into bacteria and multiplied fantastically.⁹

This was a matter of high practical importance. A way had been found to produce industrial quantities of human insulin and human growth hormone. But more than the biotechnology industry was born. Fred Sanger in Cambridge had been working for two decades to repeat his feat with the linear sequence of insulin by deciphering the "colinear" sequence of DNA. As the restriction enzymes gradually became available in the 1970s, the production of DNA fragments that could be sequenced and read became more frequent. Sanger invented two techniques in succession and in 1977 used them to complete the first entire genome of an organism, a virus called Phi X 174. His second method became the dominant way to read DNA for the next thirty years.¹⁰

Smith did not jump into the flood of research that followed. Instead, he continued to study the bacterium that made HindII, H. influenzae. The 1978 Nobel Prize he shared with Nathans and Arber came as a shock to Smith, who doubted that he had earned it and felt Meselson had been excluded wrongly. Meselson recalled twenty years later, "Most people are pretty decent and pretty generous. But Ham is very decent and very generous." Smith struggled with the innumerable expectations and interruptions that beset a Nobel Prize winner, and his work suffered. By the late 1980s, his grant applications were being rejected, and he was thinking about closing his Hopkins laboratory.

In the early 1990s, however, a spectacular rehabilitation began. At a conference in Bilbao, Spain, Smith met the rebellious Craig Venter and plunged into a new career that included sequencing in 1995 the first free-living organism, his beloved H. influenzae.¹¹ It was the start of many years' work on stripped-down bacteria that might be tailored for such tasks as producing energy or cleaning up environments. In his sixties and seventies, working like so many biologists on a bridge between nonprofit research and commercial application, he was one of the pioneers of what became called synthetic biology.

Recombinant DNA: Fear and Promise

As the RNA and DNA technologies blossomed, a fierce and long-remembered professional and political battle broke out that threatened the very continuance of the work that had been labeled "recombinant DNA." The struggle, which rose directly out of new technical capabilities, effectively lasted about four years, from 1973 to 1977, and ended, after a succession of cliff-hangers, in the work's scientific and industrial establishment. Although the furor taught biologists lessons they have benefited from ever since and may ultimately have reinforced public confidence in the probity of scientists, it was a darker and riskier episode than some commentators recall.¹²