The Tangled Tree

by David Quammen

  “Our genes are not only our genes,” he said. “Our genes are also retroviral genes.”

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  One step beyond Heidmann’s sobering message—that a sizable fraction of our human genes have come from nonhuman, nonprimate sources—lies the brave new world of CRISPR. That crisp little acronym, as you probably know, refers to something very complex: a sensationally efficient system of genome editing, famed in newspapers, bruited in magazines, heralded by the journal Science in 2015 as Breakthrough of the Year, and widely expected to bring someone a Nobel Prize. CRISPR is more than a step beyond what Heidmann said. It’s the latest big lurch toward genetically engineered futures. It’s a technique that opens the prospect of cheaply, precisely altering genomes (including human genomes) in the laboratory and (eventually) in the clinic.

  CRISPR stands for clustered regularly interspaced short palindromic repeats. A palindrome, of course, is a sequence of letters that spell the same words in either direction, front to back or vice versa. In the verbal realm, that’s wordplay, yielding gambits of strained cleverness such as “Able was I ere I saw Elba,” in the voice of Napoléon, and “A man, a plan, a canal: Panama,” referring tenuously to Ferdinand de Lesseps. A verbal palindrome says something, but what it says needn’t make much sense. For instance: “A Santa dog lived as a devil god at NASA.” My own favorite is simpler: “As I pee, sir, I see Pisa.”

  Within a DNA genome, the available alphabet for palindromic patterns is only those four coding letters, A, C, G, and T. So a palindromic repeat of DNA coding would look more like GTTCCTAATGTA-ATGTAATCCTTG. Such DNA palindromes, it turns out, can be important functional markers. They were the first evidence that led scientists to discover the CRISPR mechanism where it exists in the natural world (more on that in a moment) and, within a few years, to develop it as an extraordinary new method of genetic engineering. The full system includes other molecular elements besides the palindromes—enzymes and forms of RNA—but CRISPR has become the informal label for the whole shebang.

  CRISPR allows researchers to target any mutation, any single “wrong” letter, in the three-billion-letter human genome, and to send in biochemical tools that make a correction. It offers parents the hope that congenital defects, mutations that might kill or torment a child, can be not just detected by genetic screening but also reversed before a fetus begins to grow. Delete and replace a gene that would have brought muscular dystrophy? Wonderful. Erase a mutation that threatens cystic fibrosis? Heroic. By one count, there are more than ten thousand such heritable human disorders, each caused by a single bad gene, many or most of which could be fixable using CRISPR. Those fixes, furthermore, can be made not just to the somatic cells (the body cells) of the child but to the germline, the sacrosanct reproductive cells from which DNA passes onward to subsequent generations. How will that be done? By performing the edit very early during in vitro fertilization—one human egg in a dish, one human sperm, plus a dose of the CRISPR magic. Such germline engineering is especially powerful and controversial because it affects populations, not just individuals. A germline tweak may well become a permanent alteration within a lineage of creatures. It could change future lives, not just those in the present. It could change the evolutionary trajectory of a species—for instance, ours.

  That hasn’t happened yet. No test-tube baby, so far as we know, has been born with CRISPR modifications. Some prominent researchers in the field have called for caution, restraint, even a global moratorium on using CRISPR for human germline engineering. Others have noted that CRISPR, with its ultimate potential for inserting new bits of DNA as well as its near-term potential for fixing mutations, carries a threat of high-tech eugenics. Add a gene to your unborn child that promises higher intelligence, or athletic prowess, or first chair in cello at music camp? Ugh. And then, what, we will live in a world like Lake Wobegon, where all the children are above average? This dreamy prospect is sometimes called “voluntary” genetic modification, as distinct from therapeutic modification, driven by urgent medical need. Like other sorts of “voluntary” parental nudging of offspring up the ladder of life, such as hiring a private tutor to coach your kid for college entrance exams, it might come to seem not just tantalizing and beneficent but necessary on competitive grounds. Still, what seems necessary to the wealthy and privileged is often unthinkable for everyone else. It would exacerbate gaps between the affluent and the struggling, between the optimized and the ordinary, between well-engineered children and those haphazardly conceived the old-fashioned way. And unlike SAT tutoring, or cosmetic nose surgery, or tae kwon do lessons from the age of five, it’s a nudge whose effects, good or bad, would be passed to future generations.

  At present, germline engineering of humans is still just a looming likelihood, not a runaway trend. But among the latest news, as I write, is a report in Nature from an international team of scientists, based in Oregon and elsewhere, who used CRISPR tools on single-cell human embryos to correct a mutation.

  This particular mutation causes a heart disease called hypertrophic cardiomyopathy (HCM), which can show itself as sudden heart failure, sometimes in seemingly healthy young athletes. It kills some, and it shadows the lives of many. The work on HCM was a lab experiment, not an application of clinical medicine. It involved fifty-four human embryos, each treated with a CRISPR repair elixir, most of them successfully, some not, but none of them afterward implanted in a human womb or destined to grow into a CRISPR baby. Still, crossing that threshold is just a matter of time and, at the current pace of research, probably not much time. CRISPR is hot and democratic. It’s inexpensive and relatively easy. In fact, one company is now selling do-it-yourself CRISPR kits (for bacterial, not human, gene engineering) online at less than $200. Around the globe, well-trained researchers and perhaps also some pedestrian scientists, more ambitious than judicious, now have the tools.

  It’s not my intention here to try to detail how CRISPR works or to explore the range of its ethical implications. You’ll get plenty on that from other sources in coming years. The origins of CRISPR, not the repurposing of it by humans, are what link it to Carl Woese and the new tree of life. Those origins, seldom mentioned in press accounts of CRISPR’s whizbang applications, are fascinating in their own right and very relevant to this book.

  During the late 1980s and early 1990s, several teams of scientists discovered strange, repeating sequences in the genomes of certain microbes, including the familiar bacterium of the human gut, E. coli. The sequences were generally about thirty letters long, on each side of the midpoint, and situated like bookends around a short sequence of letters that didn’t repeat. Think of it roughly like: “Able was I ere gesundheit ere I saw Elba.” Remember that these words were all written in As, Ts, Cs, and Gs. No one knew what such odd stretches of DNA did—or whether they did anything at all. But in 2002 they were given their name and their acronym, CRISPR, and researchers continued guessing about their function. Three years later, that mystery was cracked by a Spanish scientist named Francisco Mojica.

  Mojica grew up near the Mediterranean port of Santa Pola, knew the coastline, and did his PhD work on the genome of a microbe, one of Woese’s cherished archaea, that dwelt in briny marshes of the Santa Pola area. The microbe was halophilic: salt loving. Examining its genome, he noticed an odd pattern: multiple copies of a nearly perfect palindromic repeat, with a spacer of other letters between the mirroring sides. Getting deeply curious, he spent much of the following decade looking for the same sort of pattern elsewhere. He found it—other versions, other palindromes—not just in archaea but in the published genomes of bacteria too. One case was that E. coli occurrence, reported back in 1987 by a Japanese team, who were mystified as to what it meant. By the year 2000, searching published genomes, Mojica had spotted CRISPR sequences in nineteen different microbes, a mixed list of bacteria and archaea. He suspected these similar sequences might have a common function. What particularly intrigued him were the stretches of code filling that space between the palindro
mic repeats—the gesundheit in my example, but slightly longer, a few dozen letters each—which became known as spacers. What was their meaning? What did they do? Why gesundheit in this sequence, maybe abracadabra in that one, and not damnyankees or rumplestiltskin? In 2003, during the heat of August, Mojica holed up in his air-conditioned office at the University of Alicante, just north of Santa Pola, and tried to understand it.

  He typed out spacers from one CRISPR and another, using his word processing program, and entered them into a vast database of known genomes, looking for anything similar. He found some close matches: DNA stretches within certain viruses. Equally arresting or more so, he found other matches among bacterial plasmids, those infective little particles of horizontally transferable DNA. So it seemed that CRISPR might represent a record of past infections, during which bacteria and archaea captured fragments of foreign DNA and incorporated those fragments into their own genomes. But for what purpose?

  Well, viral infection could kill the bacterium or the archaeon, and plasmid infection (horizontal transfer of DNA) could alter its genome, for better or worse. A microbe might acquire means to deter such intrusions. Maybe, Mojica speculated, these CRISPRs were some sort of immunity mechanism against reinfection by the bugs represented in the spacers. A memory of infection, as defense against future infection? There’s a word for this in our own realm. We call it vaccination.

  Mojica wrote his informed speculation into a paper, with three coauthors, and submitted it to Nature. Rejected. He tried several other leading journals in succession. Rejected. The editors didn’t see anything that seemed very new or important. Months passed. Mojica worried that he would be scooped. Finally, he sent his draft to the Journal of Molecular Evolution, the same lively outlet in which Carl Woese and four colleagues had published their first hint about the existence of a separate form of life. Mojica’s paper, suggesting that CRISPR might be involved in immune defense, appeared there in 2005.

  Meanwhile, another clue was added in 2002, when a Dutch team reported finding an odd group of four genes that occurred adjacent to CRISPR sequences in various genomes. These CRISPR-associated genes (cas genes, for short) were conspicuously absent from microbial genomes that lacked CRISPR sequences. They seemed to have some functional relationship to CRISPRs—something beyond mere happenstance proximity. At first, neither the Dutch team nor anyone else knew just what that function might be. Then, rather soon, further insights on CRISPR and cas genes emerged from several sources, and it became clear that cas genes perform the function, guided by CRISPR spacers, of attacking and dismantling invasive DNA. The Mojica hypothesis was persuasively proven: CRISPR-cas among microbes, as it has naturally evolved, is a defense mechanism against infection and infective heredity. It’s their version of an adaptive immune system. We have antibodies and white blood cells; they have CRISPR. It protects bacteria and archaea from killer viruses, and it serves as a barrier (sometimes useful, sometimes limiting) against horizontal gene transfer. It helps microbes maintain their health and their continuity of identity. HGT is still rampant among bacteria and archaea, but their CRISPR-cas genes protect them against at least some transfers.

  This is the backstory of CRISPR. The more glorious and familiar part of the narrative began later, in 2012, when other scientists established how CRISPR sequences and cas genes could be repurposed for editing mammalian genomes—those of laboratory mice, endangered species, invasive pests, and us. That enterprise is what carries CRISPR forward into the present, the future, and the wondrous and fraught possibilities of human germline engineering, among other applications. When the Nobel Prize for CRISPR is announced, the names of the winners will probably not include Francisco Mojica, nor the Dutch team, nor any of their colleagues who have worked on CRISPR purely as an evolutionary phenomenon among bacteria and archaea. More likely you will hear the names of scientists who have made CRISPR a tool for human use: Jennifer Doudna, Emmanuelle Charpentier, Feng Zhang, or possibly others. People will be gladdened and concerned, variously, about the boggling new prospects that this particular Nobel Prize will celebrate. But it seems likely that Carl Woese, if he were alive, with his strong bias against “a biology that operates from an engineering perspective,” wouldn’t cheer.

  In that cranky 2004 manifesto, “A New Biology for a New Century,” Woese wrote:

  Modern society knows that it desperately needs to learn how to live in harmony with the biosphere. Today more than ever we are in need of a science of biology that helps us to do this, shows the way. An engineering biology might still show us how to get there; it just doesn’t know where “there” is.

  The proper purpose of biology is not to change the world, he added, but to understand it. Then again, this daring new century really wasn’t his century, and he knew that.

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  Carl Woese’s death, when it happened, would leave behind vivid memories in a wide range of people, some of whom published remembrances of him, some of whom kept their stories and views private. Part of my job has been to gather samplings of those memories and put pieces together. For four years I’ve felt a bit like the newsreel reporter in Citizen Kane, assigned by his producer to track down old friends and contacts of the protagonist, the newspaper magnate Charles Foster Kane, and try to solve the mystery of his character. What drove Kane to be such a ruthless success and a needy bastard? What was the meaning of his last spoken word, “Rosebud”? Was that word, that thing—that person, if Rosebud were a person—the key to his life and his character? Or was it just a false lead? Was anything the key to the man’s life and his character, in the sense that others could find it and turn it and open him like a door? Orson Welles put the Rosebud device to good effect, and you probably remember his Kane (if you’ve seen the film, and if you haven’t, you should) as a formidable, enigmatic figure. You probably don’t remember the newsreel reporter, not by name anyway (trivia answer: Jerry Thompson), because he’s just the fellow who travels from source to source and asks the questions. Thompson’s back is always to the camera; he stands in the shadows or offscreen, and we never see his face. He’s the proxy for the audience, to whom witnesses speak. That’s how this job works.

  Ralph Wolfe told me the story, and I’ve told you, about the insult Woese suffered at a big conference in Paris, amid important biologists, long before his own burst of fame. He presented his paper, no one commented, no one asked any questions, and they all walked off to lunch. “It was almost a mortal wound,” Wolfe said. Woese resolved never again to let his work be ignored—and so he sanctioned a press release at the time of his Archaea discovery, instead of letting his journal paper speak for itself, and that approach backfired. He made the front page of the Times but got criticized by other scientists, the reality of his third domain doubted, on grounds that he had put scientific publication second to publicity.

  Was that his Rosebud moment? I don’t think so. Nor other frustrations, embarrassments, and perceived slights I’ve heard mentioned, some personal, some professional, including his lack of a Nobel Prize. I agree with Jerry Thompson’s conclusion: no word, no wound, no grudge, and no childhood deprivation can explain a person’s life. There are too many interactive pieces. Complexity theory offers better metaphors for human behavior than does this sort of mechanistic puzzle solving.

  Woese left behind no personal journal or diary. His archives in Urbana are thick with scientific papers, drafts, and professional correspondence, but very thin on personal revelation. He published only one book, The Genetic Code, early in his career, and it was neither influential on its scientific merits nor illuminating of his character. In some of his review articles and contributed chapters, he included anecdotes and a little retrospection, as in the chapter he wrote for a big edited volume on the archaea; but those human details relate to laboratory moments.

  For instance, when he recognized for the first time, from his X-ray films, that archaea represent a unique form of life: “I rushed to share my out-of-biology experience with George, a skeptical Georg
e Fox to be sure. George was always skeptical. That’s what made him a good scientist.” When the Nobel winner Salvador Luria called Ralph Wolfe, after publication of their first archaea paper, to tell Wolfe he should dissociate himself from Woese and his crackpot science: “How could this Luria fellow have the temerity to excoriate his friend and my colleague like that? What pedestal was he standing on?”

  Woese wrote no autobiography. He kept his family life very private. The closest he came to a self-portrait might be the formal, impersonal assessment of his own work and significance, written in third person, that he sent as a five-page email to Norm Pace in 1995, before his feelings toward Darwin went really sour, and probably on request at a time when Pace was nominating him for a Nobel Prize. It’s Woese on Woese, this document, making a case for himself in scientific history, as you or I might make a case for ourselves in a job application. I’ve seen it but, at present, it’s unavailable for quotation. The gist is that he saw himself as a peer of Leeuwenhoek and Darwin.

  Larry Gold, now a distinguished molecular biologist and biotech entrepreneur, also based in Colorado, knew Woese from the early days in Schenectady, when they both worked for GE, and remained close to him through the years. Woese was a thirty-two-year-old biophysicist, hired at the General Electric Research Laboratory for purposes unclear both to himself and to his bosses; Gold was a nineteen-year-old Yale student with a summer job. Gold found himself set to a grim research project that involved dosing rats with a carcinogenic chemical, then trying to prevent the cancers from happening, and while he was lost without supervision amid these sick and dying rats, Woese came to his assistance. They worked on the poor rodents together, killing many. Did Woese get interested in the experiment?

  “No, I don’t think so,” Gold told me fifty-four years later, as we sat on a bench in Urbana. “I don’t think he cared about it at all. I think what he was interested in was spending time that made him happy.” He had taken a shine to young Larry Gold. “He clearly got pleasure out of being around people who let him be exuberant.” He loved to laugh. “He had an outrageous laugh. It was almost a cackle.” They talked seriously too—or Woese talked, especially about the genetic code and the question of how it evolved, and Gold listened like a kid hearing a rabbi construe passages of Torah.