Ambition and Delight: A Life in Experimental Biology

Copyright © 2009 by Henry R. Bourne.

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CONTENTS

ACKNOWLEDGMENTS

PROLOGUE

CHAPTER 1

CHAPTER 2

CHAPTER 3

CHAPTER 4

CHAPTER 5

CHAPTER 6

CHAPTER 7

CHAPTER 8

CHAPTER 9

CHAPTER 10

CHAPTER 11

CHAPTER 12

CHAPTER 13

NOTES

For my children and grandchildren—Michael,

Randy, Molly, Julia, Henry, and Luke

ACKNOWLEDGMENTS

During this book’s long gestation, I received valuable help, advice, and encouragement from many people. Their advice, criticisms, and memories corrected errors and rescued me from potential disasters. These readers include my two sons, Michael Bourne and Randy Bourne, plus many friends and colleagues, including Steve Arkin, Ole Faergeman, Adrian Ferre-D’Amare, Al Gilman, Jane Hirshfield, Taroh Iiri, Matt Lerner, Dyche Mullins, John Nathan, John Newell, Miranda Robertson, Antonina Roll-Mecak, Bill Seaman, Holly Smith, and Keith Yamamoto. I followed their advice in many cases, but not all, and all the book’s faults are my own. Elaine Meng’s unique blend of esthetic and technical prowess contributed to preparation of the 3D structures of protein molecules depicted in chapter 11 and on the cover. Elizabeth Stark, a remarkable wordsmith and editor, took on the formidable task of teaching me how to craft sentences, organize paragraphs, and shape coherent chapters. She skillfully managed to criticize and encourage at the same time, improving the book immeasurably.

Finally, I want to thank Nancy Bourne, who first had to live through the life of this memoir with me, and then found herself reading the story all over again, in multiple iterations. Her memory for dates and details, along with her gift for nuance, shepherded me through thorny thickets in the writing. For her similarly generous and even more crucial help during the living of the life, I am deeply grateful.

PROLOGUE

OR

WHY READ THIS BOOK?

Why do you lab guys claim experiments are more fun than anything you can do with your clothes on? The associate dean looked puzzled, but gave me no time for an answer. Makes me wonder if you know what real fun is! he added, flashing a grin.

I laughed. With his clothes off, this distinguished, white-haired clinician was known to have had more fun than most of his colleagues—and not only in his youth.

It was also true, I reflected, that he had little knowledge of what experimental biologists do in their labs. Like many bright, sophisticated people, he couldn’t imagine anything less dreary than the apparently solitary life of a laboratory scientist.

From forty years of working in labs, I know that experimental biologists lead lives that are anything but dreary and solitary. Instead, we feel viscerally engaged for most of our working lives, driven by curiosity, hope, ambition, and delight—and sometimes, to be sure, ravaged by disappointment and despair. Intensely social, we jostle against colleagues and their ideas at every turn. We question or answer, disagree or agree, compete or collaborate—not just now and then, when the spirit moves us, but always, as if our lives depended on it, as in fact they do.

One way to tell people what our lives are really like, I thought, would be to describe the life of a real experimental biologist. The biologist whose life I know best is myself. Would telling my story be worthwhile, considering that successful books about scientists1 almost invariably depict the lives and discoveries of towering geniuses? Perhaps, on the other hand, the life of an ordinary scientist and his discoveries could offer real advantages. For one thing, stories like mine have not often been told. For another, it may be easier to understand and identify with thoughts and feelings of a non-genius, whether in triumph or in failure. (The associate dean might ask whether the average genius, fully clothed, has more fun than the ordinary scientist in the lab. My best guess is No, although I’m sure we could find a genius who disagrees.)

Beginning as an ignorant young man from the provinces, I entered science after a series of tortuous switchbacks in other directions and eventually slipped in through the back door, almost inadvertently. I took several wrong paths, and research apprenticeships with a menagerie of mentors taught me how not to do experimental biology. In my thirties, I found a marvelous mentor, and began a career as an independent scientist. Thereafter, I directed a productive research lab, taught students and postdocs and, for almost a decade, chaired an academic department in a first-rate biomedical research institution. I met with both failure and success, but over the long run, amounting to 40 years, experimental biology gave me immense satisfaction, amazing joy, and a full life, in and out of science.

My story is not representative. No one is a typical experimental biologist. Instead, scientists differ profoundly from one another, and so do their discoveries. Their personalities, virtues, faults, joys, and sorrows shape everything they accomplish, and shape their failures as well. Each brings to a question her or his unique blend of knowledge and ignorance, insight and blind spots, rigorous analysis and wandering imagination. A scientist’s life, like anyone else’s, is ineluctably contingent and unpredictable, depending on innate character, background, and chance-dependent encounters with a unique set of people and challenges.

At best an unpredictable enterprise, discovery works most efficiently by harnessing every atom of human diversity it can find. Consequently, interactions between individuals drive almost every discovery. Both the exuberant variations among scientists and their fertile conflicts and collaborations are absolutely necessary. Working together, two good minds are almost always more effective than one.2 For this reason, the isolated genius of legend has trouble keeping up, and most successful experimental biologists are intensely social creatures.

Among these interactions, the relation between young scientists and their elders plays crucial roles. By bringing two minds together, such relations often furnish the essential element for discovery. They also form the core of experimental biology’s social network, an indispensable conduit for its lore, gossip, insights, and values. I know neurobiologists, for example, who trace their heritage to scientific giants of the late 19th and early 20th centuries, like Charles Sherrington and Ramon y Cajal. My own mentors changed the course of my life in science, and my later mentoring of students and postdoctoral fellows has taught them—and me—indispensable lessons.

I’ll tell about these individuals and their interactions, focusing mainly on the process of scientific discovery. My stories describe discoveries that affected me (and others) in very different ways. The first discovery, which ultimately won the Nobel Prize, began in several competing labs, including my own. The initial findings confused many of us, but set the stage for one lab (sadly, not my own) to conceive the right strategy and do the right experiments. This discovery framed questions I would ask for three more decades.

The second discovery, which in fact comprised hundreds of individual discoveries, whirled me in a maelstrom of new ideas and opportunities for new experiments. This was a real scientific revolution, bringing scientists the very grail they always seek—new questions to explore and new experimental tools for asking them. The DNA revolution, triggered by experimenters who learned how to decipher and manipulate sequences of the genetic material, opened new avenues for exploring how cells and organisms work, and in doing so transformed the intellectual foundations and practical conduct of experiments as well as the working lives of thousands of biologists.

The first 40 years of the DNA revolution may have generated the most exciting train of discoveries and challenges experimental biology has seen or is likely to see for many decades. Although I joined the revolution rather late myself, my career in science coincided almost exactly with the rapid explosion of new molecular knowledge that transformed biology in the 20th century. My colleagues and I kept our clothes on, but we also had enormous fun, for many years.

The third kind of discovery is more circumscribed, and brings a great but very different emotional reward—the visceral, immensely satisfying click of unraveling a complex puzzle. One click story served as the spark that kindled writing this book. It begins with a rare disease, proceeds through a frustrating effort to resolve a paradox, and ends in a delicious surprise. The story will help non-scientists to feel the transcendent delight of that click, or something very like it. I want to transmit that delight for its own sake, but also because it is critical for sustaining what we call real life. Between great discoveries and scientific revolutions, scientists live for clicks like this. Minor clicks keep us going for a week or two. The click story I highlight in this book sustained me for years.

___

The twists, turns, and fun of my career are tightly bound to the biological questions I tackled in this period. Those questions formed part of the much broader effort of thousands of scientists, which aimed very high—at nothing less than understanding the molecular mechanisms that give life to the earth’s organisms. My particular questions belonged to a new field, cell signaling, focused on mechanisms cells use to detect and respond to external signals. This field hardly existed when I first entered a lab, but has now become a thriving enterprise in academia and industry. Let me try to convey a sense of what was at stake.

In the 1950s biologists knew that all organisms, even one-celled bacteria, could mount complex responses to external stimuli, like light, heat, or chemical compounds. Physiologists had established that organs and cells of multicellular organisms produce or respond to dozens of distinct chemical stimuli, or signals like insulin and other hormones or neurotransmitters like acetylcholine. (Insulin, secreted into the blood from cells in the pancreas, controls the concentration of blood sugar, and acetylcholine is released from nerves to stimulate contraction of muscles.)

As scientists identified hundreds of new intercellular signals, they began to wonder how cells detect them and convert them into responses. Most chemical signals could not penetrate into the cell directly, because they were unable to cross the fatty peripheral membrane around it. Indirect evidence suggested that these signals must associate with distinct sites on the cell’s surface. Although no one had ever seen these sites, they came to be called receptors.

How receptors initiate responses remained a mystery, partly because so little was known about chemicals inside the cell. Many of these chemicals were proteins, large molecules made up of chains of chemical building blocks. Some proteins, the enzymes, had been extracted from broken-up cells and shown to convert one chemical into another. But none of the enzymes, it seemed, served as a receptor for a chemical signal generated outside the cell.

Although many scientists feared that breaking cells would inevitably abolish responses to external stimuli, Earl Sutherland’s lab dared to try—and made a critical breakthrough, by showing how a hormone causes membranes from broken cells to produce a small chemical compound that regulates enzymes found inside the cells. This compound, cyclic AMP, represented the first-discovered biological strategy for transmitting hormonal signals across cell membranes.

I was in college when Sutherland discovered cyclic AMP. It posed appealing questions as I zigzagged through laboratories in the late 1960s, and was to play a major role in my own lab’s experiments a decade later. One of my experiments helped to set the stage for a momentous discovery by another lab, which I mentioned above. In the late 1970s, they identified, in exquisite biochemical detail, the signaling relay device cells use to convert external hormone signals into cyclic AMP signals inside the cell.

At the time no one could have imagined the cornucopia of questions and experiments that relay device would generate. It represented the first established molecular machine for transmitting external signals across membranes, and remains today the best understood of such machines. For 20 years it served as the main focus of my own research.

More broadly, this signal relay device, in combination with cyclic AMP itself and other devices soon to be discovered, created the field of cell signaling. Four fertile concepts anchored the new field to the wider enterprise of cell and molecular biology. These concepts, which I describe more fully below, include signaling pathways for transmitting information, molecular recognition of individual proteins and signals, activation of receptors or enzymes, and the pivotal roles played by the three-dimensional (3D) shapes of signaling molecules (usually proteins) in recognition and activation.

Abstractly, a signaling pathway could look something like this:

Initial stimulus 58711-BOUR-layout.pdf A 58711-BOUR-layout.pdf B 58711-BOUR-layout.pdf C 58711-BOUR-layout.pdf D 58711-BOUR-layout.pdf E 58711-BOUR-layout.pdf Response

Each letter in the pathway represents a chemical entity of some kind, which may be a protein or a small molecule like cyclic AMP. Arrows represent transfer of a signal, positive or negative, between one entity and the next.3 Signaling pathways can branch and interconnect to form huge networks, which allow combinations of signal inputs to evoke a large variety of complex output responses.

Every transfer of information in cells involves at least one molecular recognition event. A protein first recognizes a sort of tag or zip code on a second protein or a small molecule, then associates with or modifies it.

Why is molecular recognition so important for transmitting signals? The basic problem is that every cell contains about 10,000 different proteins, each present in thousands of copies. Each of these molecules needs to recognize a subset of other molecules, just as millions of New Yorkers need systems for recognizing their friends and co-workers. Instead of faces, telephone numbers, or uniforms, virtually every protein in a cell is covered with tags and tag-reading devices designed to specify which molecules will recognize each other. Each of these millions of molecules, like an air traveler inspecting luggage at a carousel, inspects the molecules it meets to identify appropriate partners and targets. Molecule A can transmit a signal to molecule B only if it recognizes it first.

How does A actually transfer a signal to B? What does the arrow really represent? Briefly, signals are transmitted in three ways. The first is direct activation: A recognizes B, associates with B, and instructs B to change its activity—in other words, A activates (or inactivates) B. Think of one partner signaling another to pirouette in a dance. Alternatively, A may recognize B and localize it to the specific site in the cell where B can accomplish some key function—like a murder in a gangster movie, signaled by Stay here, fella, and kill anybody who walks in that door! Rather than commit a murder, B is more likely to convert chemical X into chemical Y enzymatically, but can do so only if A places B in the right place to find X. In a third mode of signal transmission, A may chemically modify B, thereby attaching a new tag (or removing an old one). These metaphorical tags and tag-readers may sound fanciful, but every biotech company or pharmaceutical manufacturer uses exactly this framework to understand and create new ways for modifying signals in bacteria, plants, animals, or patients.

The last fundamental concept you will meet is the idea that the 3D shape of a molecule crucially determines its function. When I went to medical school, scientists knew the 3D shapes of less than a dozen proteins. Now they know thousands of structures, including those of receptors and signal relay proteins I studied. These shapes show us the crevices and handles signaling proteins use to recognize other molecules, as well as the molecular details of signal transmission.

The notion that these shapes transmit signals seems even more amazing when we consider how small they are. A protein is 1,000-fold smaller than a cell, which is itself pretty tiny—2,000 average cells, lined up in a row, would cover a distance of about one inch. If a cell were the size of a lecture hall big enough to seat 75 people, the average protein molecule would be the size of an electrical socket. Nonetheless, nature machines these minuscule molecules to very close tolerances. In a later chapter, for example, I tell how we traced a devastating inherited disease to a tiny change in a signaling protein, a change that altered the protein’s shape by only one part in 3,000.

Scientifically, then, the stakes were high. Outside the lab, they were even higher, and still are. As a society we are constantly pushed and pulled by discoveries made in labs, and we need to understand them well enough to make crucial social decisions about climate, energy resources, medical care, and many other problems. That means young people and adults need to know how science works and who scientists are. Citizens need to feel, in their bones, that science is a very human enterprise—not magical, not diabolical, not unknowable, not conducted in mysterious hidden rites, but instead closely enmeshed in the rough granularity of the real world around us. I hope this book will transmit the message that this human enterprise is conducted by people who are fallible, ambitious, stupid, bright, and sometimes inspired, but always human, as well. And I hope that young people will learn from it that becoming a scientist is a goal normal human beings can aspire to, and one that brings many rewards.

Finally, it’s worth noting that the decades from 1970 through the first decade of the 21st century saw profound changes in experimental biology and its practitioners. As our questions probed more deeply and our experimental tools became more powerful, the world in which we lived and worked became transformed in almost every way, from the size and organization of our research labs to training of young biologists, research funding, reward and promotion of professors, and relations between academia and industry. Today’s signaling aficionado can hardly imagine the ignorance, mistaken ideas, and technological limitations his predecessors had to deal with in the 1960s. By the same token, a researcher suddenly transplanted from a lab in 1966 into the 21st century would find opportunities, stresses, and even dangers she or he could not have imagined.

Although I did not start writing with the goal of highlighting these transformations, they frame the events and human interactions of every chapter. I touch on them explicitly in the chapter on my experience as chair of an academic department, and return to them again at the end, as possible clues to the equally profound changes future decades will bring.

___

Finally, I must confess a secret. I have found it impossible to describe my life in science without also including dollops of real science. This can be a problem, because science often baffles, bores, or mystifies smart, curious people. They are not usually baffled, I think, because the ideas are so difficult, at least not in experimental biology. (The core concepts of fields like quantum physics or string theory do baffle many ordinarily thoughtful people, me included.)

Instead, my guess is that non-scientists find science mysterious for the same reason scientists spend so much time in close-knit communities of colleagues who care about a narrow set of questions. The problem with science is that there’s just too damn much of it. Threatened with blizzards of new facts, both scientists and non-scientists hunker down like penguins, husbanding their attention and hoping the weather will clear. Confronted by the snowballing facts and terminology of an unfamiliar scientific field, even scientists know how it feels to recoil in confusion or shudder with boredom. Such experiences should help us sympathize with non-scientists.

For me, curiosity survives a fact-blizzard most successfully when I remind myself that it’s not necessary to master every scientific detail. The going will be smooth in some places, rough in others. For the latter cases, let me offer this advice: when you find yourself puzzled, do your best to relax and take it easy. It is fine to re-read a sentence, but do not trudge back through previous paragraphs or chapters. Instead, walk deliberately through murky passages, without stopping to fumble for your flashlight. Keep moving into the light. Puzzled scientists follow the same strategy, which is practical and effective. Join the club!

The strategy works because each puzzle is likely to recur in a different context, and new contexts furnish new clues. Combining these with clues recalled from the puzzle’s earlier appearances often helps. In addition, you may be bothered by an apparent contradiction between two facts or interpretations. Experimental biologists are old hands at juggling mutually incompatible ideas, sometimes for years.4 When resolution comes, it sometimes reveals that one idea was clearly correct, the other clearly wrong. More often, we find that both ideas are part correct, part wrong. The apparent contradiction vanishes when a new fact appears, or we look at the old findings from a different perspective. This experience will be familiar to anyone who has lived long enough to experience the myriad contradictions and ambiguities of ordinary human interactions.

Finally, I have tried to write for both non-specialist readers and scientists, focusing primarily on the interface between personal feelings and thoughts, on the one hand, and scientific discovery, on the other. In describing the science I often substitute metaphor and simile for technical jargon and acronyms, and relegate details to the notes at the end of the book, which also include references to scientific publications. As a result, some scientists may be disappointed by the loss of biochemical precision, but non-specialists will be spared the labor of mastering vast lexicons of mystifying technical language.

CHAPTER 1

Unconscious Decisions

GROWING UP

On a sunny afternoon in late October, I negotiate the tight curves of Route 86, a narrow road in North Carolina. Red-dirt ditches and rail fences flash past our windows, and here and there derelict tobacco barns dot green fields. I am driving Nancy from her college to our home town. We talk quietly about our families and the lazy weekend before us. We are 20 years old. The future is an opaque blur, except that we know we will marry some day.

Then, as we round a grove of trees, a beige Chevrolet crosses the lane in front of us, leaps the roadside ditch, rolls gracefully, and comes to rest in the meadow, front doors open and upside down. Everything is quiet as a silent movie, until suddenly I hear myself yelling, and find myself running, in slow motion. Why did I park so far away?

On her back in the ditch, a fat woman moans softly between snores, a pale, undulating mound of flesh. Near the Chevrolet, a man lies on the grass, arms folded comfortably in front of him. Is he asleep? Grass stains on his shirt. No blood. Hurrying from one to the other, I have no idea what to do.

Nancy runs up. We’d better call an ambulance!

We flag a passing truck, whose driver finds a nearby house with a telephone. State police arrive and calmly shoo us back to our car. They say both passengers from the beige car are alive, and ambulances take them away.

Back on the road, I am numb. Nancy and I re-live 30 minutes of helpless ignorance, in broken sentences and long pauses. But by the time we reach home I think I’ve put the whole scene behind me.

I hadn’t put the scene behind me, and still haven’t. Instead, that beige car’s spiraling trajectory marked the beginning of a new era in my life. Before the next week was out, I would tell Nancy and my parents I had made an important decision. Although no one—least of all myself—imagined that this decision might point toward a career in science, it did intertwine multiple strands of my life in the 20 preceding years. And those strands form patterns that still guide how I think, work, and communicate, in science and in my life.

___