Vishal MehtaComment

The Genesis Engine

Vishal MehtaComment

Crispr appears to be the most important bio-tech breakthrough to come along in many years. The mainstream press had largely missed its importance and then—boom—this piece from Wired and Amy Maxmen appeared. The story tackles the tough work of describing in digestible terms how Crispr allows scientists to edit DNA. That’s the immediate payoff. But it also wraps all this science up in a gripping narrative of how the discovery came to be and what it might mean for people in the future. It’s one of those rare first swing, definitive type pieces and deserves everyone’s attention.

SPINY GRASS AND SCRAGGLY PINES creep amid the arts-and-crafts buildings of the Asilomar Conference Grounds, 100 acres of dune where California's Monterey Peninsula hammerheads into the Pacific. It's a rugged landscape, designed to inspire people to contemplate their evolving place on Earth. So it was natural that 140 scientists gathered here in 1975 for an unprecedented conference.

They were worried about what people called “recombinant DNA,” the manipulation of the source code of life. It had been just 22 years since James Watson, Francis Crick, and Rosalind Franklin described what DNA was—deoxyribonucleic acid, four different structures called bases stuck to a backbone of sugar and phosphate, in sequences thousands of bases long. DNA is what genes are made of, and genes are the basis of heredity.

Preeminent genetic researchers like David Baltimore, then at MIT, went to Asilomar to grapple with the implications of being able to decrypt and reorder genes. It was a God-like power—to plug genes from one living thing into another. Used wisely, it had the potential to save millions of lives. But the scientists also knew their creations might slip out of their control. They wanted to consider what ought to be off-limits.

By 1975, other fields of science—like physics—were subject to broad restrictions. Hardly anyone was allowed to work on atomic bombs, say. But biology was different. Biologists still let the winding road of research guide their steps. On occasion, regulatory bodies had acted retrospectively—after Nuremberg, Tuskegee, and the human radiation experiments, external enforcement entities had told biologists they weren't allowed to do that bad thing again. Asilomar, though, was about establishing prospective guidelines, a remarkably open and forward-thinking move.

At the end of the meeting, Baltimore and four other molecular biologists stayed up all night writing a consensus statement. They laid out ways to isolate potentially dangerous experiments and determined that cloning or otherwise messing with dangerous pathogens should be off-limits. A few attendees fretted about the idea of modifications of the human “germ line”—changes that would be passed on from one generation to the next—but most thought that was so far off as to be unrealistic. Engineering microbes was hard enough. The rules the Asilomar scientists hoped biology would follow didn't look much further ahead than ideas and proposals already on their desks.

Earlier this year, Baltimore joined 17 other researchers for another California conference, this one at the Carneros Inn in Napa Valley. “It was a feeling of déjà vu,” Baltimore says. There he was again, gathered with some of the smartest scientists on earth to talk about the implications of genome engineering.

The stakes, however, have changed. Everyone at the Napa meeting had access to a gene-editing technique called Crispr-Cas9. The first term is an acronym for “clustered regularly interspaced short palindromic repeats,” a description of the genetic basis of the method; Cas9 is the name of a protein that makes it work. Technical details aside, Crispr-Cas9 makes it easy, cheap, and fast to move genes around—any genes, in any living thing, from bacteria to people. “These are monumental moments in the history of biomedical research,” Baltimore says. “They don't happen every day.”

Using the three-year-old technique, researchers have already reversed mutations that cause blindness, stopped cancer cells from multiplying, and made cells impervious to the virus that causes AIDS. Agronomists have rendered wheat invulnerable to killer fungi like powdery mildew, hinting at engineered staple crops that can feed a population of 9 billion on an ever-warmer planet. Bioengineers have used Crispr to alter the DNA of yeast so that it consumes plant matter and excretes ethanol, promising an end to reliance on petrochemicals. Startups devoted to Crispr have launched. International pharmaceutical and agricultural companies have spun up Crispr R&D. Two of the most powerful universities in the US are engaged in a vicious war over the basic patent. Depending on what kind of person you are, Crispr makes you see a gleaming world of the future, a Nobel medallion, or dollar signs.

The technique is revolutionary, and like all revolutions, it's perilous. Crispr goes well beyond anything the Asilomar conference discussed. It could at last allow genetics researchers to conjure everything anyone has ever worried they would—designer babies, invasive mutants, species-specific bioweapons, and a dozen other apocalyptic sci-fi tropes. It brings with it all-new rules for the practice of research in the life sciences. But no one knows what the rules are—or who will be the first to break them.

IN A WAY, humans were genetic engineers long before anyone knew what a gene was. They could give living things new traits—sweeter kernels of corn, flatter bulldog faces—through selective breeding. But it took time, and it didn't always pan out. By the 1930s refining nature got faster. Scientists bombarded seeds and insect eggs with x-rays, causing mutations to scatter through genomes like shrapnel. If one of hundreds of irradiated plants or insects grew up with the traits scientists desired, they bred it and tossed the rest. That's where red grapefruits came from, and most barley for modern beer.

Genome modification has become less of a crapshoot. In 2002, molecular biologists learned to delete or replace specific genes using enzymes called zinc-finger nucleases; the next-generation technique used enzymes named TALENs.

Yet the procedures were expensive and complicated. They only worked on organisms whose molecular innards had been thoroughly dissected—like mice or fruit flies. Genome engineers went on the hunt for something better.

Scientists have used it to render wheat invulnerable to killer fungi. Such crops could feed billions of people.

As it happened, the people who found it weren't genome engineers at all. They were basic researchers, trying to unravel the origin of life by sequencing the genomes of ancient bacteria and microbes called Archaea (as in archaic), descendants of the first life on Earth. Deep amid the bases, the As, Ts, Gs, and Cs that made up those DNA sequences, microbiologists noticed recurring segments that were the same back to front and front to back—palindromes. The researchers didn't know what these segments did, but they knew they were weird. In a branding exercise only scientists could love, they named these clusters of repeating palindromes Crispr.

Then, in 2005, a microbiologist named Rodolphe Barrangou, working at a Danish food company called Danisco, spotted some of those same palindromic repeats in Streptococcus thermophilus, the bacteria that the company uses to make yogurt and cheese. Barrangou and his colleagues discovered that the unidentified stretches of DNA between Crispr's palindromes matched sequences from viruses that had infected their S. thermophilus colonies. Like most living things, bacteria get attacked by viruses—in this case they're called bacteriophages, or phages for short. Barrangou's team went on to show that the segments served an important role in the bacteria's defense against the phages, a sort of immunological memory. If a phage infected a microbe whose Crispr carried its fingerprint, the bacteria could recognize the phage and fight back. Barrangou and his colleagues realized they could save their company some money by selecting S. thermophilus species with Crispr sequences that resisted common dairy viruses.

As more researchers sequenced more bacteria, they found Crisprs again and again—half of all bacteria had them. Most Archaea did too. And even stranger, some of Crispr's sequences didn't encode the eventual manufacture of a protein, as is typical of a gene, but instead led to RNA—single-stranded genetic material. (DNA, of course, is double-stranded.)

That pointed to a new hypothesis. Most present-day animals and plants defend themselves against viruses with structures made out of RNA. So a few researchers started to wonder if Crispr was a primordial immune system. Among the people working on that idea was Jill Banfield, a geomicrobiologist at UC Berkeley, who had found Crispr sequences in microbes she collected from acidic, 110-degree water from the defunct Iron Mountain Mine in Shasta County, California. But to figure out if she was right, she needed help.

Luckily, one of the country's best-known RNA experts, a biochemist named Jennifer Doudna, worked on the other side of campus in an office with a view of the Bay and San Francisco's skyline. It certainly wasn't what Doudna had imagined for herself as a girl growing up on the Big Island of Hawaii. She simply liked math and chemistry—an affinity that took her to Harvard and then to a postdoc at the University of Colorado. That's where she made her initial important discoveries, revealing the three-dimensional structure of complex RNA molecules that could, like enzymes, catalyze chemical reactions.

The mine bacteria piqued Doudna's curiosity, but when Doudna pried Crispr apart, she didn't see anything to suggest the bacterial immune system was related to the one plants and animals use. Still, she thought the system might be adapted for diagnostic tests.

Banfield wasn't the only person to ask Doudna for help with a Crispr project. In 2011, Doudna was at an American Society for Microbiology meeting in San Juan, Puerto Rico, when an intense, dark-haired French scientist asked her if she wouldn't mind stepping outside the conference hall for a chat. This was Emmanuelle Charpentier, a microbiologist at Ume˚a University in Sweden.

As they wandered through the alleyways of old San Juan, Charpentier explained that one of Crispr's associated proteins, named Csn1, appeared to be extraordinary. It seemed to search for specific DNA sequences in viruses and cut them apart like a microscopic multitool. Charpentier asked Doudna to help her figure out how it worked. “Somehow the way she said it, I literally—I can almost feel it now—I had this chill down my back,” Doudna says. “When she said ‘the mysterious Csn1’ I just had this feeling, there is going to be something good here.”

Back in Sweden, Charpentier kept a colony of Streptococcus pyogenesin a biohazard chamber. Few people want S. pyogenes anywhere near them. It can cause strep throat and necrotizing fasciitis—flesh-eating disease. But it was the bug Charpentier worked with, and it was in S. pyogenes that she had found that mysterious yet mighty protein, now renamed Cas9. Charpentier swabbed her colony, purified its DNA, and FedExed a sample to Doudna.

Working together, Charpentier’s and Doudna’s teams found that Crispr made two short strands of RNA and that Cas9 latched onto them. The sequence of the RNA strands corresponded to stretches of viral DNA and could home in on those segments like a genetic GPS. And when the Crispr-Cas9 complex arrives at its destination, Cas9 does something almost magical: It changes shape, grasping the DNA and slicing it with a precise molecular scalpel.

Jennifer Doudna did early work on Crispr.  PHOTO BY:BRYAN DERBALLA

Here’s what’s important: Once they’d taken that mechanism apart, Doudna’s postdoc, Martin Jinek, combined the two strands of RNA into one fragment—“guide RNA”—that Jinek could program. He could make guide RNA with whatever genetic letters he wanted; not just from viruses but from, as far as they could tell, anything. In test tubes, the combination of Jinek’s guide RNA and the Cas9 protein proved to be a programmable machine for DNA cutting. Compared to TALENs and zinc-finger nucleases, this was like trading in rusty scissors for a computer-controlled laser cutter. “I remember running into a few of my colleagues at Berkeley and saying we have this fantastic result, and I think it’s going to be really exciting for genome engineering. But I don’t think they quite got it,” Doudna says. “They kind of humored me, saying, ‘Oh, yeah, that’s nice.’”

On June 28, 2012, Doudna’s team published its results in Science. In the paper and in an earlier corresponding patent application, they suggest their technology could be a tool for genome engineering. It was elegant and cheap. A grad student could do it.

The finding got noticed. In the 10 years preceding 2012, 200 papers mentioned Crispr. By 2014 that number had more than tripled. Doudna and Charpentier were each recently awarded the $3 million 2015 Breakthrough Prize. Time magazine listed the duo among the 100 most influential people in the world. Nobody was just humoring Doudna anymore.

MOST WEDNESDAY AFTERNOONS, Feng Zhang, a molecular biologist at the Broad Institute of MIT and Harvard, scans the contents of Scienceas soon as they are posted online. In 2012, he was working with Crispr-Cas9 too. So when he saw Doudna and Charpentier's paper, did he think he'd been scooped? Not at all. “I didn't feel anything,” Zhang says. “Our goal was to do genome editing, and this paper didn't do it.” Doudna's team had cut DNA floating in a test tube, but to Zhang, if you weren't working with human cells, you were just screwing around.

That kind of seriousness is typical for Zhang. At 11, he moved from China to Des Moines, Iowa, with his parents, who are engineers—one computer, one electrical. When he was 16, he got an internship at the gene therapy research institute at Iowa Methodist hospital. By the time he graduated high school he'd won multiple science awards, including third place in the Intel Science Talent Search.

When Doudna talks about her career, she dwells on her mentors; Zhang lists his personal accomplishments, starting with those high school prizes. Doudna seems intuitive and has a hands-off management style. Zhang … pushes. We scheduled a video chat at 9:15 pm, and he warned me that we'd be talking data for a couple of hours. “Power-nap first,” he said.

If new genes that wipe out malaria also make mosquitoes go extinct, what will bats eat?

Zhang got his job at the Broad in 2011, when he was 29. Soon after starting there, he heard a speaker at a scientific advisory board meeting mention Crispr. “I was bored,” Zhang says, “so as the researcher spoke, I just Googled it.” Then he went to Miami for an epigenetics conference, but he hardly left his hotel room. Instead Zhang spent his time reading papers on Crispr and filling his notebook with sketches on ways to get Crispr and Cas9 into the human genome. “That was an extremely exciting weekend,” he says, smiling.

Just before Doudna's team published its discovery in Science, Zhang applied for a federal grant to study Crispr-Cas9 as a tool for genome editing. Doudna's publication shifted him into hyperspeed. He knew it would prompt others to test Crispr on genomes. And Zhang wanted to be first.

Even Doudna, for all of her equanimity, had rushed to report her finding, though she hadn't shown the system working in human cells. “Frankly, when you have a result that is exciting,” she says, “one does not wait to publish it.”

In January 2013, Zhang's team published a paper in Science showing how Crispr-Cas9 edits genes in human and mouse cells. In the same issue, Harvard geneticist George Church edited human cells with Crispr too. Doudna's team reported success in human cells that month as well, though Zhang is quick to assert that his approach cuts and repairs DNA better.

That detail matters because Zhang had asked the Broad Institute and MIT, where he holds a joint appointment, to file for a patent on his behalf. Doudna had filed her patent application—which was public information—seven months earlier. But the attorney filing for Zhang checked a box on the application marked “accelerate” and paid a fee, usually somewhere between $2,000 and $4,000. A series of emails followed between agents at the US Patent and Trademark Office and the Broad's patent attorneys, who argued that their claim was distinct.

A little more than a year after those human-cell papers came out, Doudna was on her way to work when she got an email telling her that Zhang, the Broad Institute, and MIT had indeed been awarded the patent on Crispr-Cas9 as a method to edit genomes. “I was quite surprised,” she says, “because we had filed our paperwork several months before he had.”

The Broad win started a firefight. The University of California amended Doudna's original claim to overlap Zhang's and sent the patent office a 114-page application for an interference proceeding—a hearing to determine who owns Crispr—this past April. In Europe, several parties are contesting Zhang's patent on the grounds that it lacks novelty. Zhang points to his grant application as proof that he independently came across the idea. He says he could have done what Doudna's team did in 2012, but he wanted to prove that Crispr worked within human cells. The USPTO may make its decision as soon as the end of the year.

  • The stakes here are high. Any company that wants to work with anything other than microbes will have to license Zhang's patent; royalties could be worth billions of dollars, and the resulting products could be worth billions more. Just by way of example: In 1983 Columbia University scientists patented a method for introducing foreign DNA into cells, called cotransformation. By the time the patents expired in 2000, they had brought in $790 million in revenue.

It's a testament to Crispr's value that despite the uncertainty over ownership, companies based on the technique keep launching. In 2011 Doudna and a student founded a company, Caribou, based on earlier Crispr patents; the University of California offered Caribou an exclusive license on the patent Doudna expected to get. Caribou uses Crispr to create industrial and research materials, potentially enzymes in laundry detergent and laboratory reagents. To focus on disease—where the long-term financial gain of Crispr-Cas9 will undoubtedly lie—Caribou spun off another biotech company called Intellia Therapeutics and sublicensed the Crispr-Cas9 rights. Pharma giant Novartis has invested in both startups. In Switzerland, Charpentier cofounded Crispr Therapeutics. And in Cambridge, Massachusetts, Zhang, George Church, and several others founded Editas Medicine, based on licenses on the patent Zhang eventually received.

Thus far the four companies have raised at least $158 million in venture capital.

ANY GENE TYPICALLY has just a 50–50 chance of getting passed on. Either the offspring gets a copy from Mom or a copy from Dad. But in 1957 biologists found exceptions to that rule, genes that literally manipulated cell division and forced themselves into a larger number of offspring than chance alone would have allowed.

A decade ago, an evolutionary geneticist named Austin Burt proposed a sneaky way to use these “selfish genes.” He suggested tethering one to a separate gene—one that you wanted to propagate through an entire population. If it worked, you'd be able to drive the gene into every individual in a given area. Your gene of interest graduates from public transit to a limousine in a motorcade, speeding through a population in flagrant disregard of heredity's traffic laws. Burt suggested using this “gene drive” to alter mosquitoes that spread malaria, which kills around a million people every year. It's a good idea. In fact, other researchers are already using other methods to modify mosquitoes to resist the Plasmodium parasite that causes malaria and to be less fertile, reducing their numbers in the wild. But engineered mosquitoes are expensive. If researchers don't keep topping up the mutants, the normals soon recapture control of the ecosystem.

Push those modifications through with a gene drive and the normal mosquitoes wouldn't stand a chance. The problem is, inserting the gene drive into the mosquitoes was impossible. Until Crispr-Cas9 came along.

Today, behind a set of four locked and sealed doors in a lab at the Harvard School of Public Health, a special set of mosquito larvae of the African species Anopheles gambiae wriggle near the surface of shallow tubs of water. These aren't normal Anopheles, though. The lab is working on using Crispr to insert malaria-resistant gene drives into their genomes. It hasn't worked yet, but if it does … well, consider this from the mosquitoes' point of view. This project isn't about reengineering one of them. It's about reengineering them all.

Kevin Esvelt, the evolutionary engineer who initiated the project, knows how serious this work is. The basic process could wipe out any species. Scientists will have to study the mosquitoes for years to make sure that the gene drives can't be passed on to other species of mosquitoes. And they want to know what happens to bats and other insect-eating predators if the drives make mosquitoes extinct. “I am responsible for opening a can of worms when it comes to gene drives,” Esvelt says, “and that is why I try to ensure that scientists are taking precautions and showing themselves to be worthy of the public's trust—maybe we're not, but I want to do my damnedest to try.”

Esvelt talked all this over with his adviser—Church, who also worked with Zhang. Together they decided to publish their gene-drive idea before it was actually successful. They wanted to lay out their precautionary measures, way beyond five nested doors. Gene drive research, they wrote, should take place in locations where the species of study isn't native, making it less likely that escapees would take root. And they also proposed a way to turn the gene drive off when an engineered individual mated with a wild counterpart—a genetic sunset clause. Esvelt filed for a patent on Crispr gene drives, partly, he says, to block companies that might not take the same precautions.

Within a year, and without seeing Esvelt's papers, biologists at UC San Diego had used Crispr to insert gene drives into fruit flies—they called them “mutagenic chain reactions.” They had done their research in a chamber behind five doors, but the other precautions weren't there.Church said the San Diego researchers had gone “a step too far”—big talk from a scientist who says he plans to use Crispr to bring back an extinct woolly mammoth by deriving genes from frozen corpses and injecting them into elephant embryos. (Church says tinkering with one woolly mammoth is way less scary than messing with whole populations of rapidly reproducing insects. “I'm afraid of everything,” he says. “I encourage people to be as creative in thinking about the unintended consequences of their work as the intended.”)

Ethan Bier, who worked on the San Diego fly study, agrees that gene drives come with risks. But he points out that Esvelt's mosquitoes don't have the genetic barrier Esvelt himself advocates. (To be fair, that would defeat the purpose of a gene drive.) And the ecological barrier, he says, is nonsense. “In Boston you have hot and humid summers, so sure, tropical mosquitoes may not be native, but they can certainly survive,” Bier says. “If a pregnant female got out, she and her progeny could reproduce in a puddle, fly to ships in the Boston Harbor, and get on a boat to Brazil.”

These problems don't end with mosquitoes. One of Crispr's strengths is that it works on every living thing. That kind of power makes Doudna feel like she opened Pandora's box. Use Crispr to treat, say, Huntington's disease—a debilitating neurological disorder—in the womb, when an embryo is just a ball of cells? Perhaps. But the same method could also possibly alter less medically relevant genes, like the ones that make skin wrinkle. “We haven't had the time, as a community, to discuss the ethics and safety,” Doudna says, “and, frankly, whether there is any real clinical benefit of this versus other ways of dealing with genetic disease.”

Researchers in China announced they had used Crispr to edit human embryos.

That's why she convened the meeting in Napa. All the same problems of recombinant DNA that the Asilomar attendees tried to grapple with are still there—more pressing now than ever. And if the scientists don't figure out how to handle them, some other regulatory body might. Few researchers, Baltimore included, want to see Congress making laws about science. “Legislation is unforgiving,” he says. “Once you pass it, it is very hard to undo.”

In other words, if biologists don't start thinking about ethics, the taxpayers who fund their research might do the thinking for them.

All of that only matters if every scientist is on board. A month after the Napa conference, researchers at Sun Yat-sen University in Guangzhou, China, announced they had used Crispr to edit human embryos. Specifically they were looking to correct mutations in the gene that causes beta thalassemia, a disorder that interferes with a person's ability to make healthy red blood cells.

The work wasn't successful—Crispr, it turns out, didn't target genes as well in embryos as it does in isolated cells. The Chinese researchers tried to skirt the ethical implications of their work by using nonviable embryos, which is to say they could never have been brought to term. But the work attracted attention. A month later, the US National Academy of Sciences announced that it would create a set of recommendations for scientists, policymakers, and regulatory agencies on when, if ever, embryonic engineering might be permissible. Another National Academy report will focus on gene drives. Though those recommendations don't carry the weight of law, federal funding in part determines what science gets done, and agencies that fund research around the world often abide by the academy's guidelines.

THE TRUTH IS, most of what scientists want to do with Crispr is not controversial. For example, researchers once had no way to figure out why spiders have the same gene that determines the pattern of veins in the wings of flies. You could sequence the spider and see that the “wing gene” was in its genome, but all you’d know was that it certainly wasn’t designing wings. Now, with less than $100, an ordinary arachnologist can snip the wing gene out of a spider embryo and see what happens when that spider matures. If it’s obvious—maybe its claws fail to form—you’ve learned that the wing gene must have served a different purpose before insects branched off, evolutionarily, from the ancestor they shared with spiders. Pick your creature, pick your gene, and you can bet someone somewhere is giving it a go.

Academic and pharmaceutical company labs have begun to develop Crispr-based research tools, such as cancerous mice—perfect for testing new chemotherapies. A team at MIT, working with Zhang, used Crispr-Cas9 to create, in just weeks, mice that inevitably get liver cancer. That kind of thing used to take more than a year. Other groups are working on ways to test drugs on cells with single-gene variations to understand why the drugs work in some cases and fail in others. Zhang’s lab used the technique to learn which genetic variations make people resistant to a melanoma drug called Vemurafenib. The genes he identified may provide research targets for drug developers.

The real money is in human therapeutics. For example, labs are working on the genetics of so-called elite controllers, people who can be HIV-positive but never develop AIDS. Using Crispr, researchers can knock out a gene called CCR5, which makes a protein that helps usher HIV into cells. You’d essentially make someone an elite controller. Or you could use Crispr to target HIV directly; that begins to look a lot like a cure.

Or—and this idea is decades away from execution—you could figure out which genes make humans susceptible to HIV overall. Make sure they don’t serve other, more vital purposes, and then “fix” them in an embryo. It’d grow into a person immune to the virus.

But straight-out editing of a human embryo sets off all sorts of alarms, both in terms of ethics and legality. It contravenes the policies of the US National Institutes of Health, and in spirit at least runs counter to the United Nations’ Universal Declaration on the Human Genome and Human Rights. (Of course, when the US government said it wouldn’t fund research on human embryonic stem cells, private entities raised millions of dollars to do it themselves.) Engineered humans are a ways off—but nobody thinks they’re science fiction anymore.

Even if scientists never try to design a baby, the worries those Asilomar attendees had four decades ago now seem even more prescient. The world has changed. “Genome editing started with just a few big labs putting in lots of effort, trying something 1,000 times for one or two successes,” says Hank Greely, a bioethicist at Stanford. “Now it’s something that someone with a BS and a couple thousand dollars’ worth of equipment can do. What was impractical is now almost everyday. That’s a big deal.”

In 1975 no one was asking whether a genetically modified vegetable should be welcome in the produce aisle. No one was able to test the genes of an unborn baby, or sequence them all. Today swarms of investors are racing to bring genetically engineered creations to market. The idea of Crispr slides almost frictionlessly into modern culture.

In an odd reversal, it’s the scientists who are showing more fear than the civilians. When I ask Church for his most nightmarish Crispr scenario, he mutters something about weapons and then stops short. He says he hopes to take the specifics of the idea, whatever it is, to his grave. But thousands of other scientists are working on Crispr. Not all of them will be as cautious. “You can’t stop science from progressing,” Jinek says. “Science is what it is.” He’s right. Science gives people power. And power is unpredictable. 

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