Editing Humanity: The CRISPR Revolution and the New Era of Genome Editing

CHAPTER 20 TO EXTINCTION AND BEYOND

You can’t write a book on genome editing without visiting George Church. Or so he tells me. So I make the pilgrimage to the Church lab, nestled in the complex of famous hospitals and institutes that make up Harvard Medical School, a David Ortiz home run from Fenway Park, the proud home of the Boston Red Sox. Church’s schedule is crammed with appointments: mine nestles between a check-in with a medical student and a visit from the founders of an Israeli tech company.

I scan the overflowing bookshelves that line an entire wall of Church’s office. There are copies of Church’s first book, Regenesis. There’s Hood, Luke Timmerman’s biography of the inventor of automated DNA sequencing; One in a Billion, the story of a landmark clinical case of genome sequencing; and Woolly,¹ Ben Mezrich’s book about Church’s ambitious quest to recreate the woolly mammoth, which is being made into a film. On his desk is a stack of Walter Isaacson bestseller biographies including Steve Jobs and Leonardo Da Vinci. On top of the pile is The Innovators. It occurs to me I’m looking at one. I wonder who can carry off the trademark Church beard in the Woolly movie? I’m guessing George Clooney or Jeff Bridges, but all Church will say is that it is his wife’s favorite actor.

Church is one of the most imaginative, restless, in-demand scientists alive, despite suffering from narcolepsy. He’s warned me more than once to keep panel discussions I’m moderating with him as a guest interesting or he’s liable to nod off. In 2019, Church opened a keynote lecture at a gene therapy conference by saying he hoped to make it through his lecture fully conscious. Only he wasn’t joking: the day before, he’d fallen asleep—and fallen over—while talking to guests in his office. It’s an occupational hazard he mitigates by fasting during the day and never letting his mind let up.

He launches new fields and new biotech companies with merry abandon, pairing “radical technology and radical application” to push the envelope of genetics. He’s a pioneer of systems biology and the Personal Genome Project. One of his companies has released what Church fondly calls the “zero-dollar genome,” another is developing new gene therapy vectors, yet another is trying to reverse aging. I peek into a room where some of his students are growing brain organoids, a controversial new tool to understand diseases like Alzheimer’s and schizophrenia.

If there was a tagline for Church’s sprawling operation, it might be: “Read and write DNA without limits” or “life finds a way” from Jurassic Park. The genome has become a giant experimental playground for Church. At any given time his lab is populated by dozens of wicked smart students from all corners of the globe, inspired by a legendary scientist who not only encourages but almost demands moonshots and imaginative ideas to turn science fiction into biomedical fact.

Church opens his lectures with his “conflict of interest” slide, a smorgasbord of company and university logos reflecting his incessant entrepreneurial and academic liaisons. Not every venture succeeds, but when they don’t it’s typically because Church’s ideas are too early—it takes times for everyone else to catch up. One of my favorites was a next-generation sequencing outfit in Silicon Valley called Halcyon that could read gene sequences by stretching a DNA molecule like a piece of bubble gum, allowing scientists to visualize the rungs of the double helix under an electron microscope.

He also founded Knome,^I the first company to offer personal genome sequencing years before the $1,000 genome became a reality. The first customer, a Swiss biotech executive, paid a staggering $350,000 for the privilege. Other early clients included a member of the British royal family and Black Sabbath’s Ozzy Osbourne.² One of his latest ventures, Nebula Genomics, aims to offer free genomes to customers using something he calls “sponsored sequencing.”³

He’s been a guest on the Stephen Colbert show discussing another futuristic line of research—using DNA as a computer to store reams of digital information. In 2012, Church’s team designed a bacterial genome with customized DNA sequence that encoded the full text of Regenesis. “Church has been accused of ‘playing God,’ an accusation abetted by his beard of biblical proportions,” Colbert joked in profiling Church for Time’s 100 most influential people.⁴ The comedian said Church “seems less like God and more like a cross between Darwin and Santa.”

Having spent three decades obsessing over the technology for reading DNA scripts, Church is increasingly fascinated by writing and editing DNA. He’s a leader in the synthetic biology movement and an organization called GP-Write (Genome Project-Write).^II But it’s not just human genomes that Church is interested in customizing. Church was one of the early developers of CRISPR gene editing, briefly hosting Feng Zhang and publishing one of the first demonstrations of genome editing in human cells in January 2013. Church is always looking to go cheaper, better, faster. Genome editing is no exception. Church jokes that his middle initial (M) stands for “multiplexing.”

In Oryx and Crake, Margaret Atwood introduced us to the pigoon, a hybrid creature designed for the wealthy elite to supply “an assortment of foolproof human-tissue organs in a transgenic knockout pig host—organs that would transplant smoothly and avoid rejections.”⁵ Church believes he can revolutionize organ transplantation without going quite so far by providing a safe alternative source of compatible organs from genetically edited pigs. It’s been branded “weird science,” but if successful, Church’s company eGenesis could offer hope to the 115,000 Americans on the organ transplant waiting list.

While about one hundred transplants are performed daily in the United States, twenty patients die waiting for a suitable organ donor. “The closest thing we have to death panels in this country are the decisions made about who gets transplants,” Church says. Many people are rejected from an organ transplant because they have infectious diseases or drug addiction with the argument that they wouldn’t benefit from a transplant. “But of course they’d benefit. And if you had an abundance of organs, you could do it for everyone.”⁶

Church’s cofounder and chief technology officer at eGenesis is Luhan Yang, his former grad student and postdoc. Yang grew up in Sichuan Province near Mount Emei, one of the Four Sacred Buddhist Mountains in China—what she calls “Crouching Tiger, Hidden Dragon” territory. After excelling at Peking University, Yang moved to Boston in 2008, working with Prashant Mali on the Church lab’s proof of CRISPR gene editing in human cells. Church was soon contacted by physicians at Massachusetts General Hospital (MGH) about improving the prospects of xenotransplantation patients.

eGenesis is located not surprisingly in Kendall Square, one more ambitious biotech company among scores of cool start-ups and established biotech companies. Most aspire for the commercial success of their big pharma neighbors, including Novartis, Pfizer, Amgen, and Biogen. In the company’s reception, a flat-panel TV displays a montage of staff holiday photos in Cancun, a present from the company’s investors to celebrate the birth of the latest pig litter.

I’m greeted by Wenning Qin, a veteran pharma researcher who after spending most of her career knocking out genes in mice, jumped at the chance to apply her particular set of skills to pigs. Many aspects of the miniature pig’s biology make it an ideal organ donor substitute. Pigs have a short four-month gestation and large litters. Pig heart valves and corneas are already used in operations. But two major issues must be addressed before contemplating human transplant of kidneys, livers, and other organs. First, the pig genome contains dozens of embedded viral sequences (PERV, or porcine endogenous retrovirus). While these viruses don’t apparently cause any health issues in pigs, unchecked activity in humans could be very dangerous, especially in immunosuppressed organ recipients.

In 2017, eGenesis used CRISPR to successfully remove all sixty-two PERV sequences in the DNA of a pig cell line. The record-setting multiplexing feat made the cover of Science under the tasty headline “CRISPR Pigs.”⁷ Yang’s team named the first CRISPR pig Laika, in honor of the stray Soviet dog that became the first live animal in space.⁸ Since then, Qin’s team has generated a separate line of PERV-free miniature pigs in the United States, named after Greek goddesses: Iris, Hestia, Maia, and Nike, the goddess of victory. Dozens of additional gene edits will be required before clinical trials can commence. The goal is to eliminate, or at least minimize, the risk of immune rejection of a transplanted pig organ. One target gene, for example, codes for an enzyme that produces sugar molecules on the cell surfaces of pigs and other mammals, but not humans.

The precious pig cells are kept frozen in a large liquid nitrogen tank. Any power failure would trigger multiple alarms on staff phones including Qin’s. “Would you like to see some pig cells?” she asks. Before I can answer, she lifts a plastic dish containing ninety-six wells out of an incubator and slides it under a microscope. These CRISPRed cells could one day provide a production line of life-saving organs. On a nearby farm, the first piglets with edited immune genes are already trotting around, named after characters in The Adventures of Tom Sawyer and The Last of the Mohicans.

Back in Boston, pig organs are currently being transplanted into monkeys in preclinical experiments being led by James Markmann, chief of transplant surgery at MGH. Meanwhile, in Hangzhou, China, Yang has taken on a new role as CEO of eGenesis’s sister company, Qihan Biotech. Qin tells me the name means “through learning you come to understand” and “a flower ready to blossom.”

But it’s Church’s work on another mammal that has truly captured the attention of the media (and Hollywood): the woolly mammoth, Mammuthus primigenius, the flagship project of the de-extinction revolution. Woolly’s backers include venture capitalist Peter Thiel, on a mission to defeat mortality, who donated $100,000 early on in 2015.

The story begins, and may yet resume, in Siberia—about five million square miles of permafrost. Entombed within this deep-soil layer are the remains of animals and plants, a refrigerated repository of an estimated 1,400 gigatons of carbon. If this is released as methane, as global temperatures rise, the compounding effect on the climate would be devastating. The solution proposed by father-and-son team Sergey and Nikita Zimov isn’t exactly Jurassic Park but a 4,000-acre pilot project dubbed Pleistocene Park. They plan to restore the ancient ecosystem with mammoths and other animals trampling the insulating snow to enable the arctic frost to penetrate the soil, in turn chilling and compressing the yedoma layers deeper into the ground, postponing thawing and methane release. That’s the theory, anyway.

Woolly mammoths died out about 3,000 years ago, ending 100,000 years or more of cohabitation with humans, who probably brought about their demise. Plentiful remains have been found in excellent condition suspended in the frozen tundra. Although the ancient DNA is shattered after millennia in Siberian hibernation, the carefully retrieved fragments are long enough to determine their sequence. Church believes that the woolly mammoth—or a close approximation—can be resurrected, so to speak, by introducing key woolly mammoth genes into the genome of the Asian elephant. The two species are about 0.4 percent different at the DNA level, less than the difference between humans and our closest cousin, the chimpanzee (about a 1 percent difference).

Church made his first trip to meet the Zimovs at Pleistocene Park in August 2018 with a small team including his postdoc Eriona Hysolli. During a grueling fifty-hour journey to the Arctic Circle, the group stopped off in Yakutsk in eastern Siberia. In the lobby of the Polar Star hotel, sporting a CRISPR T-shirt, Church posed for a photograph next to a full-size woolly mammoth replica.⁹ Conditions for hiking along the banks of the Kolyma River near Chersky, an arctic town 800 miles west of the Bering Strait, were not ideal. “It’s a lovely place if you don’t mind having snow flurries and being eaten alive by mosquitoes in the same day,” Church said.¹⁰ That’s on a good day. “The worst day, it’s so cold the mosquitoes cannot live, or there are enough mosquitoes it will literally kill a baby caribou.”¹¹

Donning protective overalls and gloves, Church dissected six beautiful woolly mammoth specimens with a power drill, extracting DNA from fat, marrow, and muscle. Two genes have already been brought back from extinction so to speak, including the mammoth’s hemoglobin gene. While the Zimovs wait for the “elemoths” to arrive, they use a decommissioned tank to remove trees and help other growth. Reindeer, yak, sheep, bison, and horses are already roaming the terrain. Church might need to step on the gas: in 2020, temperatures in a northeastern Siberian town above the arctic circle spiked to a record 100º F.

Beth Shapiro, a paleogeneticist at University of California Santa Cruz, and an HHMI investigator, injects a friendly note of pragmatism. She insists it is not possible to clone a mammoth, which is interesting given that she wrote a book entitled How to Clone a Mammoth.¹² Shapiro agrees we could potentially use genome editing to introduce the key base changes, if not all 1.5 million. But then, “we’d have to figure out how to get that individual into a female elephant. Then it would have to be born and raised by elephants. It’s hard to imagine that all of those things would happen and we’d end up with something more than just a slightly hairier elephant.”¹³

Moreover, Shapiro says, elephants do not fare well in captivity. Until we’ve figured out how to meet the physical, emotional, and psychological needs of edited elephants, we shouldn’t be using them for gene-editing research. She’d rather see the technology used to save endangered elephants, by giving a genetic booster shot if necessary to expand their evolutionary fitness.

Shapiro sees little point in applying heroic measures to bring back extinct species only to place these creatures in a zoo or a park named after a geological epoch. What would we do with resurrected saber-toothed tigers or mastodons? How would millions of passenger pigeons cope with our modern urban environment? But as extinction events in modern times are so often the result of human neglect or suffering, why not apply human technological ingenuity to undo our past mistakes?

A memorial to animal species that have recently gone extinct would include Toughie, the last known Rabbs fringe-limbed tree frog; Sudan, the last male white rhino who was euthanized in 2018 in Kenya; and Lonesome George, the last Pinta Island tortoise from the Galapagos Islands, who died in 2012.¹⁴ The woolly mammoth may be the fanciful face of de-extinction, but gene editing offers a ray of hope for a growing conservation movement.

In 1933, zoologist David Fleay filmed Benjamin, the last Tasmanian tiger in captivity in Hobart, Australia. The grainy black-and-white film captured the caged ferocity of this creature, with the trademark stripes across his lower back and the extraordinary elongated jaws. Three years later, the last of the thylacines was dead. Like Lonesome George and Martha, the last passenger pigeon who died at the Cincinnati Zoo in 1914, Benjamin was the last of his kind—an endling.¹⁵ It is a word, writes Ed Yong, “of soft beauty, heartbreaking solitude, and chilling finality.”¹⁶

Two years before the amphibian in his care at the Atlanta Botanical Gardens died, Mark Mandica, the executive director of the Amphibian Foundation, made a recording of Toughie the frog singing. “He was calling for a mate and there wasn’t a mate for him on the entire planet,” Mandica said. By the time a species reaches that point, it is just one small, inevitable step to extinction. On Oahu, Hawaii, a trailer provides the last refuge for dozens of species of snails, passing what could be their final days in plastic containers destined to become coffins.

Environmentalist Stewart Brand recounts the passing of Martha, the last passenger pigeon, as if she was a blood relative. Her species was the most abundant bird in the world, with flocks reportedly one mile wide and four hundred miles long, variously described as a biological storm, a feathered tempest, and distant thunder. Yet within little more than a decade, by 1914, five billion birds spanning the North American continent were reduced to zero.^III Hunters slaughtered them by the tens of thousands. The fate of the birds might have saved the endangered American bison but other species weren’t so lucky. When “Booming Ben,” the last heath hen on Martha’s Vineyard, died in 1932, it was the lead story in the local newspaper. The editorial was an obituary: “There is no survivor, there is no future, there is no life to be recreated in this form again. We are looking upon the uttermost finality which can be written.”¹⁷

We are in the middle of an existential extinction crisis—the sixth extinction.¹⁸ More than half of all mammalian species have become extinct since 1900. Conservation is a vital tool, as is genetic rescue—increasing the fitness and DNA diversity of species, from California mountain lions to Florida panthers. Genome sequencing is an important tool here for tagging and breeding endangered species—a striking example is a bid to save the endangered Tasmanian devil marsupial, which is threatened by a malignant, orally transmitted cancer. Researchers have released cancer-free devils on a small island off Tasmania in case the main population is unable to stabilize. The endangered black-footed ferret in the Great Plains is at serious risk from bacterial sylvatic (bubonic) plague. Animals bred in captivity can be vaccinated before release, but as proposed by Ryan Phelan and colleagues at the nonprofit Revive & Restore, CRISPR editing offers a means to transfer plague resistance from the domestic ferret to its black-footed cousin.¹⁹

Meanwhile, similar strategies are needed to save some other iconic American plants and wildlife. The American chestnut tree population has been ravaged by chestnut blight, a disease spread by a Japanese fungus that was first observed in the Bronx Zoo. William Powell’s team has engineered a hybrid genetically modified tree that contains a wheat gene that neutralizes the acid produced by the fungus. Powell is petitioning the US government to produce a transgenic forest species,²⁰ despite opposition from environmentalists who worry about GM trees. But splicing DNA into its nearest living relative isn’t always possible. The Stellar’s sea cow was hunted to extinction about two hundred years ago. Tempting though it might be to de-extinct this extraordinary creature, Shapiro points out that a baby Stellar’s would be larger than the most logical surrogate. Such an effort at de-extinction would end up a bit messy. She also has bad news for fans of the dodo. De-extinct dodo eggs will be just as appetizing to various animals (including humans) as the originals.

When Shapiro and colleagues decoded the first passenger pigeon genomes in 2017, using tissue samples from museum specimens, they found a bizarre pattern—high diversity at the chromosome ends but surprisingly little variation in the middle, a pattern that might have contributed to the species’ rapid demise.²¹ Her colleague Ben Novak, who has been obsessed with these birds since he was a teenager, is leading “the great comeback.” A scheme to revive the passenger pigeon begins with the bird’s closest relative, the band-tailed pigeon.

At Monash University in Australia, Novak has taken the first steps, engineering a line of pigeons expressing Cas9, priming their progeny to receive select gene edits based on their passenger pigeon cousins.²² A best-case scenario suggests that changes in around thirty genes would confer many key traits such as coloring. But editing genes is just the beginning. Novak would have to raise enough birds to coax them to flock;²³ one idea is to raise the first hybrid chicklets using surrogate homing pigeons painted to look like the Real McCoy. He’d also have to reproduce the birds’ natural habitat, perhaps the forests of the northeast United States. Novak proposes to calls his prize pigeon Patagioenas neoectopistes, or the “new wandering pigeon of America.”

“Humans have made a huge hole in nature over the last 10,000 years,” says Brand. “We have the ability now, and maybe the moral obligation, to repair some of the damage.” Revive & Restore supports projects led by Church, Shapiro, and many others. Hope for the de-extinction movement comes from the story of Celia, the last bucardo mountain goat, which roamed the mountains of Spain. Although Celia died in the wild, some of her cryopreserved ear tissue was used to produce a live animal. It was the first successful de-extinction in history, but unfortunately it died soon after birth from a lung abnormality.²⁴

On Hawaii, mosquitoes carrying avian pox and malaria have wiped out more than half of the islands’ one hundred species of native birds. Most of the rest are endangered. A species called Culex quinquefasciatus was introduced to Hawaii on ships in the early 19th century. The islands’ native birds, including the honeycreepers, had no natural resistance to the avian malaria. And with climate change, mosquitoes are able to reach “upslope” to the higher elevations that serve as a natural sanctuary for surviving species. Revive & Restore is contemplating various strategies to reduce the mosquito population, including the sterile insect technique and the introduction of a natural bacterial predator, Wolbachia. Potentially the most effective technology involves CRISPR. It is also the most dangerous.

Eradicating diseases like Lyme disease, dengue fever, and especially malaria is a grand challenge on a global scale. And it is one where CRISPR offers a radical solution. What if CRISPR could have an impact on one of the most notorious killers on the planet? Mosquitoes don’t have an important role in ecology. They don’t pollinate plants or serve as an essential food source for anything. It is unlikely they would be missed, particularly in sub-Saharan Africa. “As the apex predator throughout our odyssey, it appears that her role in our relationship is to act as a countermeasure against uncontrolled human population growth,” observes Timothy Winegard.²⁵

The solution on offer is called a gene drive; it gives researchers the power to warp the natural Mendelian pattern of inheritance, raising the prospect of halting the spread of devastating infectious diseases. A gene drive is like loaded dice, stacking the odds in favor of a particular copy or version of a gene being passed on to the next generation, rather than leaving it 50:50. Why is that interesting? For decades, biologists have tried to combat the spread of infectious disease or other pests by spraying tons of toxic chemicals or introducing a predatory species, often with dire consequences.

A gene drive offers a much more sophisticated strategy to combat deadly diseases such as malaria, which kills some 650,000 people every year. Scientists would introduce a special DNA element that would act as a sort of poison pill in the Anopheles gambiae mosquito. This selfish element can essentially clone itself by inserting a copy into the partner chromosome. The idea was first formulated B.C. (before CRISPR) in 2003 by Austin Burt at Imperial College, London. Burt suggested that a gene drive cassette introduced into 1 percent of the African mosquito population would quickly spread in a chain reaction, affecting 99 percent of insects within twenty generations.

Many observers are understandably scared that a gene drive in the wild could go awry, crossing geographic boundaries or spreading into unintended species, threatening the ecological balance of countries across the equator. Then again, trying to save the lives of more than 400,000 children who perish from malaria each year surely justifies some desperate measures.

Scientists have taken on and defeated malaria on a national scale before. In 1944, the Rockefeller Foundation and the United Nations initiated a program to eradicate malaria-carrying mosquitoes on Sardinia, which claimed 2,000 victims a year. The disease was probably introduced by North African slaves brought to the island after the conquest by the Carthaginians in 502 B.C.E. The peak assault came in the summer of 1948, likened to the Normandy landing, involving 30,000 men who sprayed more than 265 tons of DDT. The campaign eradicated three of the four zanzare—endemic species of mosquito—and wiped out malaria.²⁶

In 2009, a British biotech company, Oxitec, launched a trial using three million genetically infertile male mosquitoes in the Grand Caymans to halt the spread of dengue fever. Following similar trials in Brazil and Malaysia, Oxitec has proposed a release for the Florida Keys, but some residents worry about inadvertent consequences of the modified mosquito release.^IV

The use of a CRISPR-based gene drive allays some of these concerns as no foreign genes are inserted into the mosquito genome. With CRISPR’s ease and precision, researchers have conducted successful gene drives in small lab populations of mosquitoes. But it is one thing to perform a gene drive under the controlled conditions of a basement insectary in London or San Diego. It’s another to take this into the real world. The holdback is less technical than social.

Kevin Esvelt leads the Sculpting Evolution group at the MIT Media Lab—an institution, he says, for black sheep who don’t fit anywhere else.²⁷ Esvelt is a leading evangelist in the potential use of CRISPR-Cas9 to develop strategies, including but not limited to gene drives, to combat diseases ferried by ticks and mosquitoes. But with the power of this approach comes tremendous responsibility. Esvelt takes this very seriously: his boyish appearance with sandy hair belies his eloquent intensity.

Esvelt’s interest in evolution began with a visit to the Galapagos Islands when he was in the sixth grade. “I wanted to know, how is it that so many marvelous creatures are created? Can we learn how that is done and create equally marvelous things ourselves?” In striving to answer that question, Esvelt has formulated a few ethical objections to the way that natural evolution does things, “the apparent total indifference to animal suffering, to any kind of notion of right or wrong. Evolution is amoral. I’m not saying it is immoral, because it is a physical process. But the fact that it does not care about or optimize well-being I view as a fundamental flaw in the universe.” That was just the first minute of our interview.

Esvelt’s motto then, is “Evolution has no moral compass. We do.” At MIT, Esvelt the black sheep wants to develop technology “to continue improving human and environmental well-being” while avoiding traps that could be hazardous to our health. He quotes Charles Darwin: “Man selects for his own good, Nature for that of the being which she tends.”

Esvelt obtained his PhD at Harvard working with chemistry professor David Liu on a suitably grand idea: to fast-forward evolution in a tube to optimize the function of proteins and other biomolecules. If you don’t understand how a protein works well enough to engineer precise alterations, then generate a billion or more variants, test, pull out the ones that work the best, rinse and repeat. Directed evolution was pioneered by Frances Arnold, who won the Nobel Prize for Chemistry in 2018. But it’s a lot of work, Esvelt says, “and I’m a big fan of laziness.”

After six years, Esvelt and Liu developed a system called phage-assisted continuous evolution (PACE).^V After hundreds of cycles run over a week, they typically produced the engineered variant they’re looking for.²⁸ Esvelt next joined Church’s lab. But his early PACE experiments failed because other scientists in the lab were growing large cultures of phage, which kept infecting his cells. Esvelt turned to the CRISPR-Cas system simply as a means to fend off phage floating in the air.

In 2013, Esvelt joined Prashant Mali, Luhan Yang, and Church in publishing one of the first demonstrations of CRISPR gene editing in human cells. Next he wondered: What if you could teach the cell to do genome editing on its own so that editing could occur during each successive generation? Could there be genes that do this naturally? One possibility was a microbial homing endonuclease that cuts DNA in highly specific sequences and inserts the corresponding gene into the gap. He found Burt’s paper from 2003, in which he had tried putting I-SceI from yeast into mosquitoes, copying itself using the cell’s natural DNA repair mechanism. “Wow, this guy was a genius,” Esvelt remembers thinking. “He thought of this a decade ago!”

Indeed, Burt’s radical idea to edit mosquitoes was to harness gene drive systems that occur naturally,²⁹ probably originating hundreds of millions of years ago. (The cow genome, for instance, is littered with genetic elements from snakes that spread via a gene drive.) Eradicating a few billion A. gambiae mosquitoes would have little to no impact on the ecology of the region, while hundreds of mosquito species that do not transmit malaria would be unaffected. It took years to perfect, but in 2011, Burt and Andrea Crisanti finally reported a successful gene drive in mosquitoes in the lab.³⁰

Esvelt realized that CRISPR held advantages over endonucleases in constructing a gene drive to eradicate malaria. Prior to the development of CRISPR, nobody had contemplated being able to edit an entire wild species. “The concept was completely absent from science fiction at the time,” Esvelt told me. “Literally, no human ever conceived that we might be able to do this. All of a sudden, boom! It looks like we can.”

Teaming up with mosquito biologists, in 2014 Esvelt published the concept of a CRISPR-based gene drive.³¹ The idea went like this: encode the CRISPR system for making a mutation along with that alteration in the genome. When the mosquito mates with another insect, the offspring inherit one copy of the edited gene along with the CRISPR system that was used to generate that edit. The offspring thus inherit the machinery to cut and replace the wild-type version of the gene. This ensures that the editing is passed down, skewing the normal 50:50 mendelian ratio of inheritance.

About the same time, a group at the University of California, San Diego, led by Ethan Bier and Valentino Gantz, also developed a CRISPR-based gene drive in fruit flies. Working with Anthony James at UC Irvine, they transplanted their CRISPR system into Anopheles stephensi, responsible for a fraction of malaria cases in India.³² Meanwhile, Burt, Crisanti, Tony Nolan, and colleagues reported similar success in A. gambiae.³³

But even as gene drives showed early promise in insectaries, Esvelt worried about the ethical risks of a gene drive potentially running amok and crossing over into other species, as well as the costs of doing nothing. He wrote:

As one of those who introduced CRISPR-based gene drive to the world, I hold myself morally responsible for any and all consequences that emerge from the technology. In my eyes, if something goes wrong that I might have foreseen, that’s on me. If my actions or words inadvertently prevent gene drive from benefiting others, that’s on me. If my failure to act prevents it from saving lives, that’s on me.³⁴

The good news is that a CRISPR gene drive is relatively slow, spreading through generations, and easily detectable. “CRISPR is powerful enough that you cannot really build a gene drive that cannot be targeted with CRISPR, meaning whatever one person does, another person can override,” says Esvelt. What concerns him more is an accidental gene drive release or unauthorized use, hence the push to ensure that this research was done transparently and responsibly. “You might make a gene drive without even realizing it,” he says, which could be introduced into a wild population. A lab accident could devastate the public’s trust in science and governance, setting back gene drives the way the Gelsinger tragedy derailed gene therapy. Moreover, what sort of responsibility does the first community that approves a gene drive test have if subsequent applications go awry?³⁵

Burt leads Target Malaria, a project funded by the Bill and Melinda Gates Foundation. In a basement insectary located somewhat incongruously in South Kensington, thousands of mosquitoes are housed in cubes of white netting in precisely controlled warm and humid conditions. The male flies suck on sugar water, while the females feast on vials of warm blood. Any rogue mosquito that manages to break quarantine by escaping the double steel doors and electronic security—not to mention an electronic mosquito zapper known affectionately as the Executioner—would then face the inhospitable misery of the dank English climate. What works for malaria could similarly be applied to tackling dengue, yellow fever, Lyme disease, and the Zika epidemic.

It’s all very well scheming diagrams and building models about selfish killer genes, but do gene drives work in practice? In 2018, Burt, Crisanti, and Nolan took a giant step in that direction. In their London lair, they crashed caged populations of A. gambiae in fewer than eleven generations.³⁶ The strategy interfered with the insect’s sex chromosomes, reducing the proportion of fertile females in each successive generation until the population reached a dead end. Extrapolating from South Kensington to Burkina Faso, which has the third highest number of malaria deaths behind Nigeria and the Democratic Republic of Congo, the strategy could crash a wild mosquito population in about four years. In San Diego, Omar Akbari’s team has identified another promising target—a gene that when knocked out, prevents female Aedes aegypti mosquitoes, carriers of several viral diseases, from flying. (Males are unaffected.)

Burt says a trial would involve deploying just a few hundred gene-drive mosquitoes in each village. If the social and political concerns can be addressed, Burt reckons that this CRISPR gene drive, coupled with other public health measures such as the use of nets, could eliminate malaria across much of Africa in fifteen years. One low-tech innovation, developed by entomologist (and malaria survivor) Abdoulaye Diabaté, is the Lehmann funnel entry trap, a device that fits to windows and doors from which mosquitoes cannot escape.

As a first step, the National Biosafety Agency in Burkina Faso gave Target Malaria, working with Diabaté, approval for a limited release of a male sterile mosquito strain (not a gene drive). In July 2019, 10,000 fluorescently coated, genetically modified mosquitoes were released in the village of Bana. It was almost literally a drop in the bucket compared to the wild population, but a hugely significant step nonetheless.

But the move has encountered fierce resistance from some Burkinabes. “We refuse to be guinea pigs,” says Ali Tapsoba, an anti-GMO campaigner, who fears the irreversibility of a gene drive and his country’s lack of resources to deal with it.³⁷ Mariam Mayet, executive director of the African Centre for Biodiversity, calls Target Malaria a “neocolonial project designed and conceived in the West and telling us what’s good for us.”³⁸ It is a common charge from African activists who have campaigned vociferously against the intrusion of giant agbiotech enterprises, notably Monsanto.

“Mosquitoes don’t obey national boundaries,” says Nnimmo Bassey, a vocal Nigerian environmentalist and critic of the mosquito program in Burkina Faso. Bassey is all for eliminating malaria, but he fears the possibility of CRISPR technology being used for other purposes. “Powerful countries and corporations don’t care about people who aren’t similar to them,” he says. “If you have this power and control in the world when there’s no equity, this seemingly nice scientific invention can become extremely dangerous.” Bassey favors more mundane low-tech solutions—sanitation, social services.

Of course there are risks associated with releasing gene-edited mosquitoes. Feng Zhang believes that any efforts to unleash gene drives into the wild must include containment measures.^VI “Some days I feel it would be great to have no mosquitoes at all,” he said, but we must be wary of the ecological consequences. “You’re removing such a large fraction of the biomass. We need to be careful.”³⁹

But aren’t the dangers of not trying it even greater? “It strikes me as a fake argument to say that something is irreversible,” says Church. “There are tons of technologies that are irreversible. But genetics isn’t one of them.” If something doesn’t work properly, he says it can be fixed, as Esvelt and Church have demonstrated in yeast.⁴⁰

Church’s Harvard colleague, Amit Choudhary, grew up in India dreaming of being the next Sachin Tendulkar, the Babe Ruth of cricket, not a CRISPR scientist. His family was poor and there was no escaping the mosquitoes, but Choudhary avoided malaria thanks to a Good Knight vaporizer put out in the evening that released insect-repelling pyrethrins.

A chemist by training, Choudhary dares to compare CRISPR to some other transformational discoveries in human history such as fire or the Internet. It comes down to precision control, he says. Humankind was able to control fire. Contrast that with the chaos erupting because of a lack of precision control over the Internet.⁴¹ Gaining control of CRISPR is essential. To that end, Choudhary’s group has identified drug-like compounds that can suppress Cas9’s ability to cut DNA before it can grasp the relevant sequence.⁴²

Choudhary thinks that the vaporizers of his childhood could be repurposed to help regulate gene drives by releasing custom chemicals that would regulate the activity of gene drives. Who needs a helicopter to douse mosquitoes when there is a device that already exists in almost every Indian home?⁴³ And this could work in Africa too—anywhere dinner is cooked.

At the end of 2018, the UN Convention on Biological Diversity reached a compromise on gene drives, rejecting a moratorium but calling for the informed consent of impacted countries and local communities before contemplating any release.⁴⁴ Could a gene drive spread across borders or to other species? Yes, perhaps. But isn’t biological warfare against one of the greatest killers of humankind worth the small risk? As Esvelt puts it, “the known harm of malaria greatly outweighs every possible ecological side-effect that has been posited to date, even if all of them occurred at once.”⁴⁵

Scientists like Burt, Crisanti, and Esvelt are trying to save the lives of thousands of people each year. Crisanti rejects the criticisms that it would be immoral to attempt to use a gene drive, saying: “What about the moral issue of doing nothing?”⁴⁶

A few years ago, I was sunbathing with my family on a beach in Scituate on Boston’s south shore. As we were packing up, a woman approached me. “Hey, do you know what’s on your leg?” Sure, I replied. I was sporting a circular rash on my calf, presumably caused by a spider bite. Or so I thought. She shook her head and in a thick Boston accent said: “No. That’s a tick bite. You’ve got Lyme disease.”

“How do you know?” I responded disbelievingly.

“I’m an ER nurse, love,” she said.

A hasty trip to my GP confirmed the diagnosis, which cleared up with the appropriate antibiotic. I shouldn’t have been so skeptical: Lyme disease is particularly common in Massachusetts, where I lived. Picking deer ticks off my brindle beagle-boxer was a daily ritual after hiking in the neighborhood woods.

Tick-borne diseases might not seem to be a public health menace comparable to malaria, but Esvelt makes a convincing case. “The West Coast has earthquakes. The South has hurricanes. The middle of the country has tornadoes. The natural disaster of the Northeast is Lyme disease.”⁴⁷ Each year, some 300,000 Americans are diagnosed with Lyme disease, signaled by the telltale bullseye rash on their skin. If left untreated, the disease can be debilitating. The disease and other tick-borne diseases are particularly prevalent on the islands of Nantucket and Martha’s Vineyard off Cape Cod.

Nantucket is a popular summer retreat for New Englanders and celebrities—and a perfect ecosystem for Lyme disease. Take a large deer population that has few constraints—no wolves, not enough licensed shooting or random car collisions. Lots of deer means lots of ticks, easily evidenced if you simply drag a sheet through the brush. But the ticks’ main host is the white-footed mouse, the elusive reservoir of tick-borne disease.

Together with Joanna Buchthal, Esvelt launched the Mice Against Ticks project to engage with a local community to discuss the idea of using CRISPR responsibly to engineer environmental immunity into the mice.⁴⁸ If you could release sufficient mice edited with a gene cassette that confers resistance to Lyme disease, this could disrupt the ecological transmission cycle. By encoding antibody genes in the mouse germline that are expressed in newborn mice, Esvelt’s team could confer an inherited resistance to disease. Releasing enough genetically vaccinated mice should spread resistance to the next generation and disrupt the tick life cycle.

But first, Esvelt has to win over the residents of Nantucket. He felt a profound ethical obligation to share his research ideas with island residents, insisting that the public must have the final say. To his credit, Esvelt has spoken at public meetings on Nantucket convened by the Boards of Health, and faced vocal apprehension about the release of any genetically modified organisms. The Nantucket steering committee has some well-qualified individuals on it, including Howard Dickler, the former head of the NIAID’s infectious disease branch, and John Goldman, editor of an immunology journal. But there are skeptics, too.⁴⁹ The consensus was: interested but don’t use any foreign DNA in our engineered mice.

On the subject of misery in the world, Darwin wrote: “I cannot persuade myself that a beneficent & omnipotent God would have designedly created the Ichneumonidae with the express intention of their feeding within the living bodies of caterpillars.”⁵⁰ Beyond malaria and Lyme disease, there are many appalling diseases that could be tackled using the latest genome editing gadgetry. Taming the desert locust would be one.

In similar vein to the Ichneumonidae—wasps that paralyze caterpillars, lay their eggs, which hatch and proceed to eat the caterpillars alive from the inside out—consider the New World screwworm. One poor victim was a twelve-year-old girl who returned from a school trip to Colombia and headed straight to the hospital complaining of severe pain in her scalp. After giving the girl morphine, doctors resorted to a novel therapy as described in the medical report: “During her hospital stay, a total of 142 larvae were manually extracted, aided by the application of raw bacon which served as an attractant and petroleum jelly occlusion.” Doctors deduced that the episode resulted from a female fly laying eggs in a scalp wound.⁵¹ In another gruesome example, a British woman became infected in her ear canal after walking through a swarm of flies while on holiday in Peru. Back home, doctors found maggots had burrowed more than 1 centimeter through her ear canal. They drowned the maggots with olive oil before finally extracting the parasites.

The screwworm looks like a psychedelic housefly, with large orange eyes and a blue-green body. Its official name, Cochliomyia hominivorax, translates as “eater of man.” Pregnant “eaters of men” are adept at finding open wounds, sores, and other niches in which to lay eggs. Cattle and livestock also make unsuspecting hosts. Gratifyingly, the screwworm was eradicated across North America in the late 1960s using the sterile insect technique. By irradiating and releasing millions of sterile male flies—a factory in Florida was producing 50 million infertile flies a week—the population was halted in its tracks. During the Reagan administration, an outbreak erupted in Libya due to the import of tainted sheep from South America. The U.S. government stealthily arranged to airdrop millions of sterile flies, technically violating its own sanctions. In 2016, the menace resurfaced in the Florida Keys. After dozens of Key deer deaths, officials employed the same sterile insect technique to squash the screwworm before it could spread onto the mainland.

But this method won’t eradicate the screwworm at the source—South American sheep—because of the more rugged terrain. One option is to use the gene drive approach, if the Mercosur countries agree. Esvelt has suggested a more limited “daisy drive” approach, a self-exhausting CRISPR-based gene drive.⁵²

An even worse nightmare than accidental outbreaks or unforeseen ecological consequences of a gene drive would be the malicious use of CRISPR as a bioweapon. “Research in genome editing conducted by countries with different regulatory or ethical standards than those of Western countries probably increases the risk of the creation of potentially harmful biological agents or products,” the National Security Agency noted drily in its 2016 threat report.⁵³ CRISPR thus joined the ranks of North Korean nuclear weapons and Syrian chemical weapons.

Adding his voice to the chorus of concern is Bill Gates. “The next epidemic has a good chance of originating on the computer screen of a terrorist intent on using genetic engineering” to create a synthetic smallpox virus or a “super contagious and deadly strain of the flu”—and killing more people than nuclear weapons, Gates told a security conference.⁵⁴ His biggest worry: the nefarious use of CRISPR to engineer a new flu strain, combining potent virulence with extreme infectivity. Gates’ worry is not frivolous: CRISPR can be used easily without expensive lab equipment or specialized training. CRISPR-based kits available from outfits like the Odin, launched by biohacker Josiah Zayner, sell for less than $500 in some cases. Pathogen-specific kits are “offered up like so many choices at a grocery store,” according to a RAND Corporation report.⁵⁵

These are legitimate concerns, but have been overshadowed by recent events. As the world saw in 2020, we don’t need DNA-designing despots or basement biohackers playing with CRISPR to cause a pandemic—nature is quite capable on her own.

I. Most people pronounced the company “gnome” but Church insisted on calling it “know-me.”

II. GP-write was originally named HGP-write, but quickly dropped the H (human) prefix as it made some people uncomfortable to contemplate totally synthetic human genomes.

III. Martha is at the Smithsonian Institution in Washington, DC, although no longer on display.

IV. Oxitec has dubbed its non-biting mosquitoes Friendly™ but that hasn’t convinced all of the affected residents, or the Environmental Protection Agency.

V. In PACE, only phage that evolve with the desired gene activity can induce production of an essential protein to continue its life cycle. The phage evolve a couple of generations in an hour, generating a billion variants at a time.

VI. Neither the Broad Institute nor Caribou will grant a CRISPR license that does not include a rider that says the IP cannot be used for a gene drive.