CAN DE-EXTINCTION SAVE SPECIES ON THE BRINK?
A Scientific Setup
IN THE SPRING of 2013, at Clare College in Cambridge, England, a group of conservation biologists found themselves on a blind date with a group of synthetic biologists. At first it seemed the date wouldn’t amount to much more than an exercise in awkwardness. It was hard to tell if the participants had anything in common with each other. After all, the conservation biologists were much older than the synthetic biologists, and a bit weary about the state of the world, while the synthetic biologists were bright-eyed and optimistic about life in that zestful way youth often are. They had a bunch of new tools to offer and were a generally hopeful bunch themselves. But even though it wasn’t exactly love at first sight, there was a palpable sense that, if the two groups would just spend some time getting to know each other, many beautiful things might be born.
A principal goal of synthetic biology is to make biology easy to engineer. By combining standardized genetic parts in novel ways within a cell, scientists can engineer organisms to produce desirable things, such as biofuels, flavors, fragrances, or drugs, as part of their biological processes. In a way, synthetic biology is a bit like writing software for cells that makes particular cellular programs run. Synthetic biologists also try to understand how biology works by building it themselves from the bottom up or stripping away components to get to the minimum set of biological bits needed to make a system tick (such as by removing all of the unnecessary genes in a microbe’s genome until it can just barely keep its functions alive). The field applies an engineer’s mindset to the biological world, creating new possibilities for life that nature does not provide on its own. And when they’re compared with conservation biologists, who’ve been fighting extinction for a long time, synthetic biologists are the new kids on the block.
When the two groups met, the idea was that if their date went well, perhaps they would see each other again. And if it went really well, maybe they could even conceive little baby endangered animal clones together.
De-extinction came up in their conversation, but so did other things they might like to do, such as reengineer corals that would be able to resist the devastating effects of climate change. Or make synthetic rhino horn in the lab, as a company called Pembient is now doing, to deter people from buying horn-based products that poachers kill rhinos for in the wild. The opportunity felt especially rich for synthetic biologists to help conservation biologists conquer invasive species, such as rats, which are responsible for loads of extinctions on islands. Scientists are good at eradicating them, but the means are often overly destructive—even dropping rat poison by helicopter, and one can well imagine that the impacts of that can be devastating when other native rodents are around. What if the synthetic biologists could create a species-specific poison for the conservationists to use—one that works only in the presence of the targeted rat’s genes?
The two groups chatted about white-nose syndrome, which has been decimating North American bats. The condition is caused by a fungus that burrows into bat noses and wings while the bats are hibernating, forcing them to wake up and spend energy they don’t have enough of. Eventually this kills them. According to Bat Conservation International, by eating insects and pollinating plants, bats contribute an estimated $23 billion to agricultural and human health worldwide every year. So there is a lot of concern about the large-scale effects of the fungus on our food systems, among other things.
Breeding fungus-resistant genes into the bat population would be an attractive idea if bats had a faster reproductive cycle. But bats produce only one pup a year, so conservationists can’t afford to wait for breeding methods to eradicate the problem. If synthetic biologists could design a genetic system that attacks the fungus without stopping the bats from eating insects and pollinating plants, much more than industry profits might be saved.
Despite the conservation biologists’ growing excitement at the meeting, they had some concerns about getting into a relationship with synthetic biologists too fast. Every time they’ve jumped into bed with a risky technology, they said, they’ve ended up getting screwed. And after all their years of working with invasive species, some were worried about synthetic organisms getting out into the wild and becoming new types of invasive threats. Still, working in conservation hadn’t been all fairytales, so some thought that hooking up with young, talented synthetic biologists might help them gain some confidence about their future career prospects. If together they could produce something of value for the world, maybe they’d feel better about what they’ve achieved.
At the same time, some of the synthetic biologists were intrigued by the older, wiser conservationists and thought they should meet again. Today, the two groups are still getting to know each other better, and determining exactly what they would like to get out of their relationship. What remains to be determined is if this is all an exciting fling, or a long-term partnership with a strong future ahead of it. Personally, I’m rooting for the latter.
Conservation’s Cold Storage
THE INACCURATE IDEA that we can bring exact versions of extinct animals back from the grave gets de-extinction into trouble—not only because it gives the public an inaccurate image of the science that grounds it, but also because it obscures other, more clearly beneficial ways that de-extinction might change the world.
For example, researchers are tinkering with many of de-extinction’s technologies to try to pull critically endangered species back from the brink of extinction. Archiving is crucial in de-extinction, and the genetic engineers who do it work with some of today’s most meticulous librarians. Once the genetic code of a long-gone species is sequenced, it gets stored in databases. Scientists can then later recall the strings of code from the databases according to their research needs. Sometimes they even file the physical strands of an animal’s DNA deep in the stacks of an archive that’s literally frozen in time. The Frozen Zoo at the San Diego Zoo Safari Park is one such place. It’s run by the park’s Institute for Conservation Research and contains frozen cells from over ten thousand individual animals and a thousand unique species.
After an endangered animal dies at the San Diego Zoo, employees immediately start to pick the body apart—a chunk of a toe here, a draw of blood there, sometimes a jab at the animal’s gonads. But there’s not an ounce of menace in this ritual; it’s just a different expression of care. By rushing to freeze biological samples of the deceased in liquid nitrogen, they’re preserving the animal’s DNA and, in some cases, whole reproductive cells. “Each cell of an individual is capable of producing the entire individual,” geneticist Oliver Ryder, director of genetics at the Frozen Zoo, explained in an Al Jazeera documentary about the Frozen Zoo. By treating the biopsies they collect right after the animal dies, Ryder and his team are able to freeze them such that they won’t be destroyed by the destructive processes that occur inside cells at low temperatures. This freezing puts the cells in a state of suspended animation, pressing pause on their biological functions without completely breaking them down. When the cells are thawed later, the biological processes inside them might then be able to be booted back up with some special assistance. This can work—as it did with Celia, the last bucardo, when she was briefly made unextinct with the help of frozen cells. The DNA inside the cells that were taken from her ear and frozen in liquid nitrogen right after she died was the most crucial ingredient for cloning her. But cells at the Frozen Zoo don’t just come from extinct species; they also come from threatened populations.
The Frozen Zoo is part of a movement that transforms zoos from outmoded menageries into participants in conservation. Many such programs exist, like the UK’s Frozen Ark, which is run by the Zoological Society of London, the University of Nottingham, and the Natural History Museum. In the U.S., the American Museum of Natural History houses eight cryogenic vats for the same purpose in an underground ark of its own. A program with even grander ambitions—Noah’s Ark, as it’s known—is based in Russia at Moscow State University. It aims to store all of life’s biodiversity, not just the DNA from creatures facing the threat of extinction, in liquid nitrogen. These programs provide the first frozen habitats for creatures whose fates may be shaped by our own technological talents. But some people say the programs are defeatist because they suggest that life can be “banked” and resurrected at a more optimal time.
Frozen DNA also creates a rich imaginary vision of what a curated wilderness could look like. In the deep freeze, scraps of species are combined in new ways that would never occur in the wild, as, for example, panda bear cells may sit next to tissue from a giant tortoise. Frozen zoos ultimately create objects that can travel into the future with multiple possibilities for what might happen to them. Freezing cells is about staving off species death, trying to keep populations alive after they have diminished in the wild—and, with the dawn of de-extinction, allow some version of the dead to rise again. The science understands life as something that is perpetually put on hold and potentially restarted, without strict pressure to do so at a specific time. In this sense, the cryopreservation of species has something to say about when—and if—a gene pool is really extinct. But it is also about locating the present in time and picturing what we might see in the future. In this way, the present is a history of the future that brings some big responsibilities with it. It asks questions about which lives are worth saving, which lives are worth recreating, and, ultimately, which lives are not worth the effort.
There are two main ways that genetic engineering is currently being used to give endangered species another chance at flourishing in the wild. The first is by increasing the diversity of DNA in a population that has become genetically depauperate, or impoverished. A phenomenon known as a population bottleneck occurs in a population when its environment changes so rapidly that only some individuals with certain genetically encoded traits are able to survive the shift. Picture a bottle full of different-sized beads. Before the bottle is poured, the beads inside are nestled among each other and the bottle is full. But when the bottle is turned upside down, the beads slam together in a gravity-driven race to escape. This jams the opening, and many beads get trapped inside. The beads that make it through the bottleneck represent the genetic diversity left in a population after an event of drastic environmental change. Such an event can cull the diversity in a population very quickly and make species vulnerable to environmental shifts that may still occur. The thinking here, then, is that by introducing genetic variation into a population after a bottleneck event has taken place, species may be better protected. Conservation biologists have been doing this for ages by mating endangered populations with other populations and subspecies that carry more variation in their gene pools. But genetic engineers, like synthetic biologists, now have more precise tools.
An example of how this may work appears in the Woolly Mammoth Revival. One of the project’s stated goals is to assist in the conservation of living elephants, many of which are endangered in the wild. By modifying the elephant genome with woolly mammoth DNA, researchers hope to create cold-tolerant elephants that have greater genetic diversity and that are able to live in habitats in which they otherwise could not. If the project is ever successful, this intervention could expand the endangered elephants’ native habitat range.
For an example that works strictly within one species, take the black-footed ferret. The last wild ferrets were wiped out in Wyoming, partly because people deemed prairie dogs—the ferrets’ main source of food—to be pests and went overboard in removing them. In 1987, some conservationists managed to collect twelve surviving ferrets, and combined them with six already in captivity to start a breeding program. Only seven of those eighteen ferrets were able to reproduce successfully. Thirty years later, with the help of the U.S. Fish and Wildlife Service, the Smithsonian, and other institutions, there are now about 8,000 black-footed ferrets that all come from those seven founders. Despite this increase and the fact that 4,100 individuals have been reintroduced into twenty sites across eight American states, Mexico, and Canada, the species has still not been properly restored. Partly this is because its wild habitat keeps diminishing. But the animals face another disadvantage independent of that fact: all of today’s living black-footed ferrets descended from those seven founders, so their diversity is constrained by a tight bottleneck. They suffer from low fecundity and have problems reproducing on their own. Scientists are now trying to revitalize their genetic profile with a high-tech diversity-boosting approach.
When the U.S. Fish and Wildlife Service caught wind of de-extinction, they approached Revive & Restore to see if their researchers had any ideas that might help them ferret out a solution to this problem. Phelan and Brand were up for the task and started a black-footed ferret recuperation program using genetic rescue techniques. They began by sequencing the genomes from two living ferrets and two ferrets that were in cold storage in San Diego’s Frozen Zoo. By comparing the ferret genomes, they were able to see that the population had experienced a serious loss of genetic diversity over time, marked by signs of inbreeding. Phelan and Brand propose that genes from more genetically diverse dead ferrets be introduced into the living population, giving it a beneficial genetic boost.
But that’s not the only engineering that Revive & Restore thinks might help. One of the biggest threats to the black-footed ferret is an infectious bacterial disease called sylvatic plague, which spreads by way of the same bacteria that cause bubonic plague in humans and is carried by fleas. Sylvatic plague also affects prairie dogs, which ferrets feast on, making it a double whammy of devastation for these guys.
Here arises the second way that the technologies used in de-extinction might help restore endangered species—by creating new individuals resistant to pathogens and parasites that threaten species in the wild. If, for example, Michael Archer and his team ever succeed in cloning the gastric-brooding frog, they could try to introduce chytrid fungus resistance into their recreated frogs’ DNA by tweaking their genes. This way, the clones might stand a chance in the face of the fungus that made their predecessors go extinct in the first place. Phelan says a light went on in her head when she realized that they could explore biotechnological approaches to conserving endangered species in tandem with their de-extinction work.
“It would be incredible if we could do this,” she says. “So many species, you know—bats with white-nose syndrome and avian malaria that is knocking out all sorts of birds in Hawaii with a non-native mosquito. There are so many challenges for endangered species that it is no longer just about habitat issues. It is also about invasive wildlife diseases.” It would be wonderful if researchers could use this technology to clone a genetically diverse member of a species that lived before a bottleneck event, or could isolate beneficial parts of its genome that might increase the variance in a genetically depleted population. It would be even better if researchers could make a species’ genes also express disease resistance or could engineer DNA insertions to create the same effect. And since those possibilities dawned on Phelan, she’s been thinking hard about how we might dial down wildlife diseases with synthetic biology techniques.
A Biotechnological Boost for the Northern White Rhino
WHEN JOURNALIST M.R. O’Connor set out to write her book Resurrection Science, there were seven northern white rhinos left on the planet, the result of rampant poaching. By the time she finished, there were only five. Three of them live at the Ol Pejeta Conservancy in Kenya, where drones, dogs, and armed rangers protect them twenty-four hours a day. For much of the time that I’ve been writing this book, there have only been four northern white rhinos left, and as I’m typing this, just yesterday, Nola, the forty-one-year-old female living at the San Diego Zoo Safari Park, was put down after she didn’t recover well from surgery. That leaves just three northern white rhinos on Earth—all of them living near the equator in the Kenyan conservancy. By the time this book is published and in front of your eyes, there could very well be fewer, though I desperately hope not.
On June 1, 2016, I found myself traveling down a bumpy gravel road in Kenya in the back seat of an old boxy car with my fiancé, Sebastian, our friend Moses, and Solomon, a ranger who works at Ol Pejeta. We cruised slowly past zebras, impalas, warthogs, and elephants that lined the driveway to the endangered animal enclosure, where the black, southern white, and northern white rhinos are kept.
At the enclosure’s entrance, Solomon hopped out to get his colleague James Mwemba, who has been working with their northern whites since 2009, when they were flown over from Dvůr Králové Zoo in the Czech Republic. A breeding program in the Czech zoo tried for years to restore the population but wasn’t very successful. Only one captured female gave birth there, and only one of her offspring managed to reproduce in the next generation. Eventually, the Czech zoo and the conservancy in Kenya decided it would be best to return the rhinos to their African homeland to see if their native environment might spur them to procreate with more success than they had in Europe.
Mwemba has been through a lot with the world’s last three northern white rhinos. Every day that he’s on the job he feeds them, rubs them, talks to them, makes sure they’re drinking well, looks out for their emotional well-being, and is their first responder if anything goes wrong. Early one morning in October 2014, while making his rounds of the endangered animal enclosure, he noticed that Suni—one of the conservancy’s two northern white rhino males at the time—seemed to be sleeping at the extreme end of the enclosure in an unnatural position. Normally at that hour the northern white rhinos are wide awake, so the fact that he wasn’t moving concerned Mwemba. As he approached Suni, he could see that his belly was fully distended—filled to the brim with gas. He didn’t need a vet to tell him that Suni was dead.
Distressed, Mwemba couldn’t quite process what he was seeing. He knew that no poachers had made it onto the site overnight, and just a day earlier Suni had been teasing him while they played together, scrubbing his hind legs on the ground like he always did. He had eaten well and spent a great deal of time in the mud, which, for a rhino, is like a day at the office for many of us—totally expected and part of the drill. The postmortem exam indicated that he had died of natural causes at just thirty-four years of age. Despite the grim circumstances, this relieved Mwemba a bit. He felt better at least knowing that Suni hadn’t died from a lack of proper care or protection. But his death raised the stakes for this species, leaving the conservancy’s other male, Sudan, as the only sperm-producing northern white rhino in the world. Sudan got his name from the country where he was captured at just two years of age. When that happened, he was taken to the Czech Republic, where he was entered into the zoo’s breeding program. Eventually, he was brought back to the continent from which he first came.
Today at Ol Pejeta a sign outside his enclosure reads, “The three Northern White Rhinos are used to being approached by people. However, all wild animals may be unpredictable,” leading me to expect that all three of them would be on the other side of the gate. But when I step inside, I can see only Sudan, way over on the opposite side of the paddock. Mwemba explains that that’s because he is now too old to live with the other two northern whites—which, in 2016, are his twenty-six-year-old daughter, Najin, and her fifteen-year-old daughter, Fatu. It is believed that Sudan’s independence minimizes the chances that he will get into an accident. They fear that if his female relatives were to playfully push him or if he were to get too excited by their presence and fall over, he might fracture something and die, the way old people can when they break a hip.
These rhinos generally live between forty and fifty years in captivity. Already, at forty-three, Sudan spends his days all alone except for sporadic company from the patrollers who surveil him 24/7 and feed him bananas, carrots, and horse cubes at 4 p.m. as part of his daily routine.
“What’s a horse cube?” I ask Mwemba, and he motions for me to accompany him into a shed with one of its doors already slung open, as if to invite me in. Inside the shed are crates upon crates of bright orange carrots, and several burlap sacks filled with brownish-green pellets, which I think look an awful lot like the Canada goose droppings that cover the Toronto Islands in the warmer months. But I understand what they are when Mwemba plunges both of his hands into a sackful. They look extremely fibrous. I pick one up and put it in my pocket, not because I expect to be able to feed it to Sudan, but because I want a souvenir of the place. I had assumed I would be spending the afternoon observing rhinos from afar, but once we leave the shed, Mwemba walks me right up to Sudan, so I can see this prehistoric-looking beauty up close. I am really excited, but also ready for Mwemba to tell me to halt at any second, before I get too near. However, this doesn’t happen. As I approach, I see that Sudan is lying in the corner of the paddock under a roof that covers more than half of his enormous cement-colored body and the rectangular pan of water beside him. His head is just poking out from shadow.
“Sudan!” Mwemba yells, and to my astonishment he responds by turning his head like an obedient dog. I’m shocked that he knows his name, and as I’m pondering this, Mwemba starts saying something that sounds like an apology. “Oh, I’m sorry, I’m sorry for that—it’s a sign of good health.” For half a moment I don’t know what he’s talking about until I realize that the sound I’m hearing is the beginning of a twelve-second-long rhino fart that sounds like a muffled machine gun, which causes me to take a step back. After it’s over, I wait for several moments more, stunned at the decibel level of his digestion, just to make sure the air’s clear before I creep in closer.
Once I’m relatively confident it’s safe, I slowly crouch down next to Sudan’s nearly three-ton body and sidle up to his side, placing my hands gently on his mud-covered neck. Most of the mud has dried and started to crack, and I’m all of a sudden reminded of what I look like when covered with a facial mud mask. I have no words to describe what it’s like to touch a creature that you know is the last male of its kind on the planet, and one of the last individuals in the world, except that it’s purely humbling. The experience of meeting, observing, and touching Sudan puts me in a reflective state of mind that stays with me for days. It certainly feels like the most important encounter I’ve ever had with a non-human animal.
When Sudan was first brought over from the Czech zoo, he was in a bigger enclosure, 780 acres, with the two females and some southern white rhinos that the zoo tried to get him to crossbreed with. Although there were matings, no successful pregnancies occurred, perhaps partly because Sudan’s sperm count is very low. Even if it were higher and he did manage to mate with the two remaining northern white females, that still wouldn’t be a perfect solution: the last living ladies are his daughter and granddaughter, which could create serious inbreeding problems. But making an inbred calf with either of them wouldn’t work out anyhow, for the females have reproductive problems of their own that make full-term pregnancy pretty much impossible. There once was hope that a northern white rhino calf would be born at Ol Pejeta before Suni died because there were records that he had mated with Najin. But after all kinds of inspections, no pregnancy was ever detected. Although at one point Najin was able to give birth, she now has a problem with her hind limbs that make her unable to support the weight of another pregnancy. And her daughter, Fatu, the youngest northern white rhino alive, is infertile as a result of a disorder that prevents embryos from implanting in her uterus. Since the last three rhinos are fragile, old, or infertile, it would seem that the species faces an evolutionary dead end.
In December 2015, a group of researchers met in Vienna to discuss what might be done about this crisis and came up with some high-tech plans for saving the northern white rhino. The first idea was to perform in vitro fertilization (IVF) by combining sperm from Sudan, or from any of the four males whose sperm is currently stored at the Frozen Zoo, with frozen oocytes (immature eggs) or with oocytes from the living females, and then implant the embryos in a surrogate mother. But since Sudan is the father and grandfather of the last remaining females, his sperm was ruled out. Frozen sperm could be used, but there are no frozen northern white rhino oocytes available. Scientists would have to get them fresh from Najin or Fatu, a process that requires anesthetic and a specialized lab, but no lab close to where they live in Kenya currently does this. Processes for IVF will need to be developed and tailored to the location, then tested on the less scarce southern white rhinos to make sure they are working efficiently before researchers try them with their much rarer relatives. Even then, without eggs from deceased northern white females available, any new rhinos made this way would be created from the eggs of only two females and the frozen sperm of four males, ensuring that they would have extremely low genetic diversity. To increase their odds of producing healthy calves, the researchers need to start somewhere else.
Another proposed solution is to save the northern whites with the same technology that the Woolly Mammoth Revival project is using to reprogram adult skin cells—fibroblasts—into induced pluripotent stem cells. Remember, these are cells that have been transformed to a highly undifferentiated state and can then be coaxed into becoming nearly any type of cell in the body.
Scientists have already created stem cells this way using cells from Fatu’s skin. The next step is to prod those stem cells into becoming specialized sperm and egg cells that can be combined—in vitro—to make northern white rhino embryos. This technique has been reported to work in mice but not yet in rhinos. If it does work, the embryos will be implanted in a surrogate mother with the hope that she can bring one to term. But given both the rarity of northern white females and their fertility issues, a surrogate from the southern white rhinos would be a better choice. Whether southern and northern white rhinos are entirely separate species or are subspecies is still disputed, but either way, several southern white females already living at the San Diego Zoo Safari Park and Ol Pejeta Conservancy might work well for the task.
But making this transfer is not without its problems, since the rhinoceros has a highly convoluted cervix that is extremely difficult to penetrate. It has been suggested that a horse could be used instead, which would make for an unbelievably surreal birth. But if researchers eventually get surrogates to birth northern white rhinos, they’ll be able to restore their population through three methods that can work simultaneously: (1) old-fashioned mating within the new generation of northern white rhinos, (2) mixing of sperm and oocytes in vitro to create embryos that get implanted in a surrogate mother, and (3) production of stem cells that can give rise to sperm and eggs that combine in vitro to make embryos to be implanted in a surrogate mother. Even using all three methods, researchers estimate that it will take at least fifty years for the northern white rhino population to be restored to non-endangered status.
This project faces many of the same ethical issues as other de-extinction endeavors. Several fertilized embryos might not take, and newborns could die before they leave the lab. No one knows how a northern white rhino calf’s microbiome or hormone interactions with its mom will be affected by being born and raised by a surrogate mother that’s not from its own exact species. For example, if the southern white rhinos’ milk is not suitable for newborn northern white rhinos, would they have to be hand-raised by humans? And if so, how would that affect not only the baby but also the southern white rhino surrogate mother that grew and birthed it?
Uncertainty about whether the northern white rhino is a separate species or a subspecies along with the more abundant southern white rhino raises another interesting ethical question. The researchers write, “Is rescuing a species or a subspecies important enough to justify subjecting members of another species or subspecies to medical interventions such as ovum pick up or embryo transfer?” In other words, is it ethically okay to subject the southern white rhino to invasive medical procedures just because the northern white rhino population is in perilous danger? And does the answer change depending on whether or not the two types of rhino are subspecies or separate species? Who gets to decide whether or not that sort of difference matters?
When I ask Mwemba what he thinks of these questions, he doesn’t seem troubled by them. “I personally believe in science, and I believe in the artificial methods to bring these species again to regeneration,” he says. “I am wholly optimistic that it is going to work, because I know there are great minds behind this.” After having met Sudan, Najin, and Fatu, I’m hoping that he’s right.
Gene Drives
SEVERAL SCIENTISTS I’VE spoken with are excited that a powerful and controversial tool known as gene drive might revolutionize the biotechnological fight against wildlife diseases. Although it has received lots of attention in recent years, the idea of gene drive is not new. Scientists have been aware for decades that it occurs naturally in the wild, but its power has been tricky to harness. What’s new is that tools like CRISPR now enable scientists to take advantage of gene drives in more precise ways to alter nearly any gene in a sexually reproducing species that will propagate it.
Here’s what’s cool about it: in sexually reproducing creatures, most genes have a 50 percent chance of being inherited in the new generation. But gene drive promotes the inheritance of a particular gene to ensure that it gets passed on, and thereby promotes that gene’s prevalence in a population—even if the gene is harmful to the organism. The gene that’s “driven” into a population could make individuals sterile, for example, and therefore could wipe out a rapidly reproducing population in just a few short generations. Or it could even make an organism resistant to a disease-carrying parasite, which would mean the organism is no longer a vector for that disease, preventing its spread to other hosts. A classic example of how one might use gene drive technology is to engineer mosquitos with CRISPR so that they no longer are susceptible to the parasite that spreads malaria to human populations, and so that they carry the genes required to propagate that protective trait in the next generation, and every other subsequent generation.
Another way of looking at it is to say that gene drive makes the genetic engineer—the scientist in the lab—obsolete after the first generation of organisms is engineered. Using the mosquito example, if a genetic engineer wanted to make sure that all generations of that mosquito species would express a gene that makes it resistant to malaria-carrying parasites, they would have to engineer the first generation of parasite-resistant mosquitos and let them out in the wild. Once the mosquitos are out in the wild, they will meet wild-type, non-engineered mosquitos, and eventually make babies with them. But those babies will only have a 50 percent chance of carrying the parasite-resistant gene that the human engineer put into the first generation of lab-made mosquitos. And those babies’ babies would then only have a 25 percent chance of inheriting the gene, and so on. The probabilities of inheritance are therefore working against what the engineer wants, and that engineer will have to do more genetic engineering by hand if he or she wants to produce more mosquitoes with the parasite-resistant gene. But with gene drive, once the genetically engineered mosquitos make it into the wild and mate with wild-type mosquitos, they will produce baby mosquitos that inherit the parasite-resistant gene nearly always. And that new generation’s babies will also carry the parasite-resistant gene, because that’s the gene that’s being “driven” into the population. In theory, this allows the genetic engineer to spend time doing other things.
Allow me to paraphrase the excellent explanation of gene drive from the fantastic radio show Radiolab: When the genetic engineer is working on editing the gene that causes some form of malaria-carrying parasite resistance into the first generation of mosquitos, they make an additional edit right next to where they made the first one in the mosquito genome. This second crucial edit encodes the genes that are needed for the CRISPR system to work in the mosquito on its own and tell it to make that particular protective genetic tweak in the next generation. So when the engineered mosquito that has both the protective anti-parasite gene and the genes needed for the CRISPR system meets an unengineered mosquito in the wild and makes babies with it, those babies end up having two sets of genes inside of it: one from mom and one from dad. However, the set of genes that came from the engineered parent mosquito have this pair of CRISPR scissors encoded into it that get expressed and that can travel over to the other set of genes from the wild-type parent. The scissors will edit that set of genes the baby got from its unengineered wildtype parent so that they end up looking identical to the ones that the baby got from its engineered parent. Now the baby mosquito has two sets of the parasite-resistant genes in its genome, which means it will express that protective trait. As Jad Abumrad, cohost of Radiolab, described it, it’s a bit like “allowing that mosquito parent to pass the scissors to the baby, and snip snip snip, and then that baby passes the scissors to the next baby, snip snip snip, and it is literally like a chain reaction.” It’s as though the successive generations, racing down the line, are passing a baton forward in a relay race.
Using gene drive, scientists at the University of California, Irvine, did this in the Anopheles stephensi mosquito, a primary vector of malaria that infects human populations. Two genetic mutations were engineered into the mosquitos, the first of which stimulates the production of antibodies right after a female mosquito has a blood meal. The antibodies then attack and destroy the malaria parasite if it is present. The second mutation ensures that the gene drive self-perpetuates in the next generation, which happened with 99.5 percent efficiency. The journal Nature describes it as “a gene that could spread through a wild population like wildfire.”
Although people are excited about gene drive’s mitigating properties for human health, the technique also holds great promise for wildlife conservation. What if scientists could use gene drive in flea populations that carry sylvatic plague so that the fleas are no longer susceptible to the bacteria that transmits the plague? That surely would help with the genetic rescue of black-footed ferrets, which easily contract sylvatic plague because they eat prairie dogs that fleas regularly infect with the disease. This works well with fast-reproducing creatures as a genetic rescue technique. However, if a gene drive were introduced into a species with a long reproductive life cycle, like humans, it would take hundreds of years before any effects were seen.
Gene drive may sound like a solid solution to wiping out vector-borne diseases and even some invasive species, but it could have serious adverse effects. For starters, once a gene is driven it into a population, its effects could be hard or even impossible to reverse. What if the gene that is programmed to be inherited with almost absolute certainty somehow spread beyond its bounds, wiping out gene pools that it wasn’t meant to?
Stewart Brand understands that the idea of gene drives may trouble those who are already critical of using biotechnology to craft aspects of the natural world. Referring to the birds of the Hawaiian archipelago that were rendered extinct by avian malaria, he tells me that bringing those birds back now might require intervention beyond the techniques used to get them back, creating an entirely new crop of ethical issues. “Well, you’re mucking around with the genes of these animals anyway,” he tells me, “and if you can bring back the Hawaiian ‘ō‘ō and we can tweak it so that it’s not susceptible to avian malaria, is that okay? Personally, I think it is okay, but I can see how lots of people would say, ‘Now you really are playing god. If it wasn’t there in the original bird, you aren’t supposed to add it.’” If it were up to him, he would “tweak the damn birds,” but he recognizes that the uncertainties about unintended effects require a great deal of research before the technique is used.
Tweaking the American Chestnut
ONE GOOD EXAMPLE of protecting an organism from infection by tweaking its genes comes not from the animal kingdom, but from the wonderful world of plants. Back when the Europeans arrived in America, the American chestnut was the most abundant tree in the east, making up one out of every four trees in the region and looming more than 100 feet above the rest of forest life. The American chestnut was a keystone species with a stable nut crop that fed a slew of forest dwellers, including passenger pigeons, blue jays, deer, bears, and raccoons. Humans, of course, liked the nuts too, which a certain Christmas song describes. We also liked to build furniture and decks with the chestnut’s rot-resistant wood, but that’s not why an estimated 4 billion trees from Maine to Mississippi became sickly in under fifty years.
An infection appeared in the 1870s, when we started importing the American chestnut’s cross-Pacific counterpart, the Asian chestnut, from Japan to North America. Hidden in the Asian chestnut was a fungus—blight—that had not done obvious damage to the tree in its native range. But it turned out that the American variety was unexpectedly devastatingly vulnerable to the chestnut blight. The blight was discovered in New York in 1904 when a scientist named Hermann Merkel noticed that a tree at the Bronx Zoo was dying from it. But by then, it was already too late to stop its spread. The blight blazed through forests of endemic trees in the northeastern U. S., leaving only dead and dying stems in its wake.
The blight is so deadly because it releases oxalic acid, which attacks the chestnut’s cambium (a cylindrical layer of tissue in the stems and roots of many plants) so that a canker forms on its trunk. Once the canker wraps around the circumference of the tree, it chokes the tree’s ability to carry water and nutrients between its roots and its branches. As a result, everything above the demarcation line dies. The stump below the canker can still send up new shoots, but it is only a matter of time until a new canker forms. Although millions of sprouts are still out in the forests and it might take several hundred, even up to one hundred thousand, years before the species completely disappears, the American chestnut is considered effectively extinct.
For the last century, scientists have been working hard to postpone the inevitable. They’ve been spraying trees with fungicides and infecting them with viruses that they hope will attack the blight. They’ve been exposing the trees to sulfur fumes and making them undergo radiation, but somehow the blight always bounces back. For the last few years, scientists at the SUNY College of Environmental Science and Forestry in Syracuse, New York, have taken a double-pronged approach to researching blight-resistant chestnut trees. At first, they tried crossing the American chestnut with the Asian chestnut in hopes of spreading fungal resistance from the latter’s genome into the former’s. Although some of the resulting hybrids ended up with blight resistance, they also carried the undesired traits of the smaller Asian orchard tree. A better solution would have been to introduce specific sequences into the American chestnut, one gene at a time.
When scientists set out to try that, no one had mapped the genome of the Asian chestnut tree, so they didn’t know which genes would be best to change. But since they wanted genes for fungal resistance, they looked at other, more thoroughly studied plants to see if any had been mapped for that trait. Fortunately, it had already been discovered that wheat fights off fungus with the help of genetic weaponry that makes enzymes that can destroy oxalic acid. So the researchers inserted genes coding for the anti-acid enzymes from wheat into American chestnut embryos. Eventually they got trees that can heal their own cankers by disarming the acid without killing the fungus itself.
On April 18, 2012, the transgenic American chestnut was brought back to the area where the blight was discovered in 1904, when SUNY researchers planted the experimental species at a test site in the New York Botanical Garden. In the future, they would like to cross their transgenic trees with trees in the wild to try to spread its acid-disabling abilities. Former mine sites where trees have been cleared and the soil is unnaturally acidic might be a good place to start. Government approval for environmental release is currently being sought from the U. S. Department of Agriculture, the Environmental Protection Agency, and the Food and Drug Administration. Once they get it, they’ll need a lot of help from the public to get the tree’s numbers back to over a billion. It’s a good thing the American Chestnut Foundation has over six thousand members—their green thumbs will be needed to plant the next generation of genetically modified chestnut trees.
Societal Acceptance of Saving Species with Biotech
OVER THE YEARS that I’ve been following this research, I’ve noticed that genetic rescue techniques for endangered species tend to receive more public approval than do straight de-extinction pursuits. Beth Shapiro’s take on the merits of the research underscore this idea. In an interview she once said, “The priority of this technology isn’t, in anybody’s mind, to bring an extinct species back to life. It’s to save species and ecosystems that are alive today from becoming extinct.” Indeed, Ryan Phelan told me to think about the beneficial domino effects of their genetic rescue work rather than to think about de-extinction alone, and she pointed me to an example that explains why.
When Revive & Restore first looked into Asian elephant biology as part of its woolly mammoth research, the researchers were surprised to learn that a strain of herpes—called elephant endotheliotropic herpesvirus, or EEHV—is a major cause of death in young calves, both in captivity and in the wild. The virus usually kills infant elephants up to the age of four within a few days to a week of onset, though there can be a long latency period between infection and the expression of the virus. Once it gets into an elephant’s bloodstream, it starts breaking blood vessels and causing its organs to bleed until the hemorrhaging turns fatal. And sadly, once signs of the virus are noticeable to humans, it is already too late for the elephant.
To diagnose EEHV, fluid that has passed through an elephant’s trunk is regularly collected and analyzed. If the elephant has herpes, the viral DNA will show up in the trunk wash, and if it is discovered early enough, it can even be treated with antiviral drugs. But treatment is not a cure, and there is no such thing yet for this virus. That’s partly because no one has ever been able to synthesize its DNA in a lab to study how the virus makes elephants vulnerable to it. Some researchers are trying to do this now, however. In April 2015, Revive & Restore hosted a conference that gathered fifty-two specialists to brainstorm genetic rescue techniques that could target wildlife diseases and invasive species. Paul Ling, a leading researcher studying the virus at Baylor College of Medicine, was there and met George Church. Their shared interest in proboscideans came up in conversation, and before long, they had assembled a team to try to synthesize EEHV in Church’s lab.
Researchers make viruses in labs all the time—for example, the polio virus was synthesized in 2002, and the 1918 flu virus was synthesized in 2005. Doing so with EEHV might allow researchers to develop a system in the Asian elephant genome that makes elephants resistant to EEHV altogether. Phelan’s eyes widened when she told me this. “Can you imagine how profound that would be if we could have more examples like that? Where we know there is a disease susceptibility and the solution for it could be as simple as altering a few genes?”
Ling’s group had already sequenced the virus from pieces of DNA they found in trunk washes from infected elephants and gave its genomic sequence to Church so that his team could attempt to synthesize it in the lab. When that’s done, they hope to transfer the virus into bacterial cultures that can grow many copies of it and then insert those viral copies into Asian elephant cells to test what they do to elephant tissues. This will allow them to discover preventive vaccines and treatments for EEHV infection by searching for the proteins that the virus uses to infect its host and then creating synthetic systems that attack those proteins. In humans, for example, a certain group of proteins is produced before the herpes virus forms, while other proteins are produced later. If the same is true for elephants, then a clever strategy may involve halting the development of early-stage proteins by disabling the genes that code for them before any proteins are made. Those genes could be disabled by using CRISPR to cut the essential genes of the EEHV virus that code for those proteins, without cutting DNA sequences in the elephant genome. That way, the viral genes cannot be expressed and the viral particles are not formed. Bobby Dhadwar, who works on this project as well as on the Woolly Mammoth Revival at Harvard Medical School, says, “If we are able to come up with a treatment, that would help people realize that this is not just about doing crazy things with the mammoth. It is about doing elephant conservation as well.”
I wonder if there will be any public backlash against saving species with things like gene editing and stem cells as these technologies become increasingly applied. What will happen when the three remaining northern white rhinos die? Will people feel the same about using biotechnology to recreate the rhinos after they’re all dead as they felt about using biotechnology to prevent their extinction up until the moment before the last ones expired? In other words, is it somehow more reasonable to be opposed to the idea of de-extinction of the northern white rhino after Sudan, Najin, and Fatu die than to oppose the northern white rhino’s restoration now while those three are still with us, even though the same types of advanced biotechnologies are used in both scenarios? What are the material, ethical, and environmental distinctions here between de-extinction and genetic rescue of an endangered species, other than the existence of a few remaining individuals hanging on for dear life?
Would waiting one day after the last individual bites the dust be too soon for the establishment of a de-extinction project to be considered acceptable? How about a year? A decade? A century?
The more I think about this, the more questions I have. Such as: Would it be more or less ethical to put resources now toward resurrecting a species of rhino that’s already gone, like the West African black rhinoceros, instead of toward trying to help the northern whites? And even more puzzling: Is the moment when the last individual of a species dies even the real extinction event, or is it impossible to attach the completion of an extinction to a single point in time? What is society’s threshold for human intervention along the extinction continuum? Can it even be said that there is one threshold, or might society have many, depending on the specific candidate species being considered? We seem to widely recognize that endangered species have a right to be here. But when Phelan asks me, “If they have a right to be here today, why don’t they have a right to be here tomorrow?”—meaning the day after the last member of a species has died—I’m left scratching my head.