The Quest to Resurrect Extinct Species

A father-son duo of biologists has set the stage for so-called de-extinction. But should we be doing this at all?

By Virginia Gewin|Thursday, January 22, 2015
RELATED TAGS: GENETICS, ANIMALS, BIOTECHNOLOGY
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Marcos Chin
Hendrik Poinar had no idea the bizarre turn his day was about to take.

Perched on a leather sofa in a downtown Toronto office, his host, a wealthy businessman, uncorked a $7,000 bottle of wine and outlined the multimillion-dollar offer: leave behind his research position at McMaster University’s Ancient DNA Centre in Ontario and work full time to bring the extinct woolly mammoth back to life.

The businessman went on to describe a grand vision — a “Pleistocene Park” housed on 150 acres north of Toronto, where visitors would pay to see the herbivorous beasts. Throughout the three-hour lunch, he peppered Poinar with questions about the risks and feasibility of such an endeavor, trying to feel out how much skin Poinar was willing to put in the game.

Poinar was stunned. On this spring day in 2006, he was flying high on the heels of his recent study published in the journal Science. He and his colleagues had reconstructed the partial genome of a woolly mammoth found frozen in Siberia, and he was convinced that researchers like himself would soon be able to take bits of degraded tissue samples, extract ancient DNA and use them to piece together whole genomes of extinct animals. Poinar was thrilled that he was finally on the verge of uncovering genomic clues to past extinctions. But an ice age wildlife park wasn’t quite what he had in mind.

Hendrik Poinar and his father, George Poinar Jr., an insect pathologist with a penchant for amber, have spent their careers exploring portals to the prehistoric past — tracing species’ appearances, movements, adaptations and extinctions.

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George (left) and Hendrik Poinar, whose work helped make de-extinction possible, sit in George’s home laboratory in Corvallis, Ore., where George studies specimens from his collection of amber-encased insects.
Leah Nash

George, 78, is one of a vanishing breed of natural historians who have built whole careers out of careful observation. By focusing on creatures trapped in amber, he revealed the workings of bygone ecosystems. He has discovered the world’s oldest-known bee and mushroom, the earliest evidence of flowering plant sex and, most recently, a fossilized ancestor of the bacterium that causes Lyme disease. But it was a cell nucleus in an amber-embedded fly that helped launch the study of ancient DNA, which quickly sparked notions of reviving extinct species and inspired Michael Crichton’s novel-turned-movie, Jurassic Park.

Throughout his career, George, now a professor emeritus at Oregon State University, has kept his focus on creatures in amber. Hendrik, for his part, spent years plying through caves sampling preserved poop, probing permafrost and helping exhume mass graves, all to uncover well-preserved pockets of DNA that could shed light on how ancient creatures lived, died and evolved. In addition to sequencing the woolly mammoth genome, Hendrik has reconstructed the diets of extinct giant sloths, debunked a hypothesis about the origin of human immunodeficiency virus (HIV) and sequenced the genome of the bacterium that caused Black Death.

Together the Poinars have helped set the stage for what promises to be a dramatic advance: resurrecting extinct species. George led early clandestine explorations of the notion before essential technology was invented. Later, Hendrik created blueprints of extinct life. With these blueprints in hand, scientists have begun exploring how to re-create an extinct species by manipulating the genome of its closest living relative. For example, a team could soon create something strongly resembling a passenger pigeon by altering a band-tailed pigeon’s genes to craft the extinct bird’s long tail, red eyes and peach-colored breast.

Today, Hendrik, 45, has almost completed the woolly mammoth genome. Harvard geneticist George Church is altering elephant genes to make them more mammoth-like, which could one day help produce elephant-mammoth hybrids. Australian researchers have begun sequencing the Tasmanian tiger’s genome and hope to resurrect the extinct marsupial.

The prospects of de-extinction have inspired conservationists who want to use it to restore ecosystems and absolve the sins of past human-caused extinctions. The idea has proven so inspiring that affluent environmentalist and futurist Stewart Brand, the former publisher of the Whole Earth Catalog, launched a nonprofit group called Revive & Restore solely to advance the science of de-extinction and rally support for it.

Although it won’t happen immediately, the technology and momentum suggest that some version of extinct animals will most likely roam the planet again. “Who wouldn’t want to see a woolly mammoth?” Hendrik says. George hopes he’s alive to see one revived — but he and Hendrik worry about what will happen when we do.

Back in Toronto, Hendrik met with his would-be benefactor a few more times before declining the offer. “I think he was surprised that I wasn’t willing to take exorbitant sums of money to do this really cool stuff,” Hendrik says.

It is, undeniably, cool. But as the technological pieces fall into place, it’s startling to realize how close we may be to bringing back new versions of extinct species — and how ill-prepared we are.
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The passenger pigeon could be resurrected by splicing its genes into the genome of its cousin, the band-tailed pigeon.
Robert L. Kothenbeutel/Shutterstock; Inset: Tim Hough
Old Amber, New Finds

The quest to resurrect ancient species began, as many scientific quests do, with a happenstance finding. In 1980, George Poinar and his future wife, Roberta Hess, an electron microscopist, cracked open a piece of 40-million-year-old Baltic amber containing a remarkably well-preserved female fly. Roberta spent days, using tiny pliers and a glass knife, slicing ultrathin layers of the fly’s internal organs and preparing them to view through an electron microscope.

George, then 44, was trying to determine whether bacterial spores could survive in amber for millions of years, part of his larger efforts to trace the ancient origins of modern disease. When George was a boy, his mother gave him a book graced by a picture of a weevil trapped in amber, and that single image sparked a lifelong fascination with insects and other ancient creatures trapped in the fossilized tree resin.

As a professor of entomology at the University of California, Berkeley, George studied insects and their parasites, traveling to amber hot spots like the Dominican Republic, Canada, Mexico and northern Europe to collect and describe just about anything trapped in resin, from feathers to frogs. But the samples he saw never contained intact organelles — specialized cell structures with dedicated jobs. When Roberta peered through the microscope at samples from the fly, she was amazed to find mitochondria, ribosomes, muscle bands — and the nucleus, which houses the cell’s genome. George returned from the university library one day to find a note Roberta left on his door: “SUCCESS!”

The findings, which garnered headlines when they were published in Science in 1982, raised a provocative question. Since the nucleus houses the cell’s genetic material, could scientists resurrect ancient DNA? If so, that DNA would serve as a biological time machine that effectively allows scientists to revisit Earth’s past and watch as proteins and species evolve.

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George Poinar examines slides of insects and arachnids in his home lab. He works to understand ancient creatures and the diseases they carried.
Leah Nash
On the surface, the notion seemed plausible, since intact tissues from woolly mammoths, which roamed northern grasslands and tundra until about 11,000 years ago, had been discovered recently in Siberian permafrost. But to most scientists, the idea seemed far-fetched.

Molecular tools were already reshaping biology, emphasizing the role of genetics, but the methods available were primitive. To characterize an ancient DNA fragment, scientists first had to clone it. That meant extracting it from tissue, treating it with enzymes to sew the ancient DNA into a small loop of bacterial DNA, then propagating that DNA in bacteria. Then they had to determine its sequence of nucleotide “letters,” which was equally laborious. Even if DNA could be extracted from amber-preserved tissues, it, too, would likely be in fragments, which made isolating an ancient gene a daunting prospect.

George and Roberta’s finding sparked the interest of a rag-tag group of scientists who banded together with George to form the Extinct DNA Study Group. They aimed to extract ancient DNA from organisms trapped in amber to sequence extinct genes, recover dormant life forms and study protein evolution.

The group corresponded for more than a year and finally met in March 1983 in Bozeman, Mont., where they contemplated what one member called a “far-out” idea. Somewhere, they mused, a mosquito that fed on a dinosaur might be trapped in amber, and white blood cells from the dinosaur might be preserved in the mosquito’s stomach. If so, they might be able to transplant a white blood cell nucleus into an egg from a frog or other animal that has been enucleated, or stripped of its own nucleus. Then, by using standard tissue culture methods, they might be able to grow dinosaur tissue in the lab.

The notion of replicating extinct life forms was crazy enough that the group agreed to keep their work secret and not talk to the media. “We thought they would make fun of it or wouldn’t take it seriously or would shut us down,” George recalls. They also contemplated ethical dilemmas that still trouble scientists today. Was it OK to bring back an extinct species, or something like it, simply out of scientific curiosity? What if it is not adapted to the current environment, or if it suffers? What if it unleashes a dormant pathogen and spreads disease?

At the time, George had begun collaborating with molecular biologist Allan Wilson, a colleague at Berkeley who had just cloned gene fragments from the 140-year-old pelt of a quagga, an extinct brown-and-white-striped zebra relative. The work proved for the first time that DNA from nonliving tissue could be reproduced, and Berkeley quickly became a hotbed of ancient DNA research. The scientists detected some evidence of fossil insect DNA in amber samples, but they couldn’t rule out contamination by microbial or human DNA. Grants to fund additional work were denied, Wilson was diagnosed with cancer (he died in 1991), and the project was shelved.

With such dim prospects in the near term, George lost hope — that is, until six years later, when Hendrik entered the field.

Gold Rush for Ancient Genes

As a boy, Hendrik sometimes followed his dad into the field to collect insects, but he was far more content in George’s lab. There he played with desiccated, ghostlike roundworms, which he could disintegrate with a touch or bring back to life with a few drops of water. He became fascinated with their state of suspended animation, poised between life and death.

Like his dad, Hendrik loved to ponder events that shaped the natural world. But he admits to being frustrated by the limited explanations George could offer based on observations alone. “I needed something more concrete,” he says. “I wanted to understand the molecular mechanisms that allow organisms to sit in an animated state.”
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Hendrik Poinar holds a giant tooth from a massive mammoth.
Leah Nash
To do that, Hendrik had to examine the genes of long-dormant or dead organisms. Few scientists thought that ancient DNA could last thousands of years, in part because DNA breaks down into smaller fragments when exposed to microbial activity, sunlight, heat and humidity. But as an undergraduate molecular biology researcher at California Polytechnic State University (Cal Poly) in San Luis Obispo in the late 1980s, Hendrik was determined to test the notion anyway. Since amber preserved ancient animal and plant tissue so well, it seemed as good a place as any to look for preserved DNA that could tell the tale of vanished creatures.

Hendrik began working in the lab of Cal Poly microbiologist Raúl Cano, and Hendrik teamed up with his father, who eagerly gave him samples of 40-million-year-old amber from the Dominican Republic containing stingless bees. To extract DNA cleanly from such samples without contaminating it, Hendrik developed a new method. He quick-froze the amber in liquid nitrogen, which is cheap, harmless to cells and extremely cold. Warming the amber then fractured it, exposing the internal tissue for DNA extraction. Hendrik recovered several short gene fragments, which represented just one-ten-thousandth of 1 percent of the bee’s total genetic information.With George as a co-author, it was Hendrik’s first scientific paper, published in Medical Science Research in 1992.

The next year, the Poinars and Cano built on that work, reporting what they described as DNA sequences from a 120-million-year-old amber-encased weevil. They published the work in the journal Nature, timed to coincide with the premiere of the blockbuster movie Jurassic Park.

Next-Gen Sequencing and Ancient DNA

To characterize the genes and genomes of long-gone organisms, scientists first extract whatever DNA remains from scarce bits of preserved tissue. They then chemically label the DNA — typically tiny, degraded fragments contaminated with microbial DNA from the environment and human DNA from being handled — to form a library consisting of thousands of DNA fragments. They use one of several proprietary methods to determine the sequence of nucleotide “letters” (A, C, G and T) that encode genetic information. A computer program uses telltale genetic signatures to distinguish fragments of ancient DNA from contaminating DNA. It then connects simulated DNA fragments with overlapping sequences to reconstruct longer stretches of ancient DNA and, eventually, sections of the genome.

Today, Hendrik Poinar and other ancient DNA researchers can sequence more DNA in one week than a well-equipped research team relying on 1990s-era technologies could have done in 20 years. And since the cost of genome sequencing has plummeted to one-thousandth of its initial cost, it’s clear that the Neanderthal, a 700,000-year-old horse and the woolly mammoth will simply be the first of many ancient genomes to be sequenced. — VG

Just a couple of years earlier, George learned that he and Roberta were thanked in the acknowledgments of Crichton’s 1982 novel, and he realized then that a tall, lanky fellow who visited his lab years earlier was Crichton. George’s Baltic fly nucleus convinced Crichton that dinosaur DNA could plausibly be extracted from an amber-entombed mosquito. When the Poinars’ Nature paper was published, several reporters asked Hendrik and George the same question: Could extinct animals ever be brought back to life? Interviewed by Katie Couric on the Today show on the night of the movie’s premiere, Hendrik assured her that dinosaurs would never roam Earth again.

The next dozen years saw researchers rush into the field to hunt for ancient DNA. Many were enticed by the tantalizing prospect of finding prehistoric genetic material that could shed light on extinct species and evolution itself. These scientists used polymerase chain reaction (PCR), a powerful, new method at the time, that makes millions of copies of degraded ancient DNA fragments. They scrambled to outdo one another by publishing DNA sequences that were ever more ancient, with one fantastically claiming to have sequenced 80-million-year-old DNA from dinosaur bones. But it soon became clear that PCR was yielding plenty of fool’s gold — DNA from humans or modern-day microbes that had contaminated samples. In fact, the so-called dinosaur DNA turned out to from a human Y chromosome.

By the late 1990s, Hendrik had completed a doctorate in molecular biology with Svante Pääbo, a Swedish paleobiologist who trained with Wilson at Berkeley. Pääbo and Hendrik recognized that some of their early samples could have been contaminated. To prevent such errors, over time the two established several protocols to combat contamination, using bleach, ultraviolet lights and positive-pressure clean rooms. They also emphasized the need to replicate findings in a second laboratory, and they policed research in the field. “My dad taught me how to think outside the box, but Svante shaped me to be meticulous,” Hendrik says.

In 2000, Hendrik co-authored a powerful letter in Science that outlined the rigor required, titled, “Ancient DNA: Do it right or not at all.” The ancient DNA gold rush waned in the early 2000s, and Hendrik became convinced that if some technological breakthrough didn’t happen soon, the field would soon die.

Cheating Extinction

As researchers struggled to reconstruct ancient genomes, the world’s first de-extinction had already, surreptitiously, taken place. In 2003, Spanish scientists had used the same cloning method that helped create Dolly the sheep to resurrect the Pyrenean ibex, a wild goat endemic to the French mountain range. They injected intact nuclei from the last living ibex into more than 400 enucleated eggs of the domestic goat. They then implanted those eggs into surrogate mothers — either Spanish ibexes or ibex-goat hybrids. Six of the seven animals that became pregnant miscarried, and the other gave birth via Caesarean section to a kid that died after just 10 minutes. More recently, an Australian team used the same strategy to resurrect the gastric-brooding frog, a fantastical creature that swallowed its eggs and coughed up babies. They managed to transfer the extinct frog’s nuclei into the egg cells of a barred frog, but so far, the embryos have yet to fully develop.

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Alison Mackey, Discover; Asian Elephant: Jan Havlicek/Shutterstock; Mammoths: Ozja/Shutterstock
Such methods may help resurrect recently departed species, but it will be all but impossible to find tissues with intact nuclei for long-gone species. To resurrect these species, scientists plan to use the extinct organism’s genetic code as a blueprint. That became feasible in 2005 when the first commercial next-generation (next-gen) DNA sequencing machines became available. “This is what we had been waiting for,” says Hendrik. Today, next-gen sequencing allows scientists to sequence an entire human genome in hours for less than $1,000, far faster and cheaper than ever before. And the same technology enables researchers to uncover the genetic blueprint of an extinct animal.

To turn that blueprint into a living organism, scientists will also need a surrogate mother. A modern relative is the best bet. Beth Shapiro, an ancient DNA researcher at the University of California, Santa Cruz, is using the band-tailed pigeon genome as a guide to piece together a draft passenger pigeon genome. Ben Novak, a biologist funded by Revive & Restore, the nonprofit group Brand established, will use that blueprint to try to revive the extinct bird. So far, Shapiro and Novak have amassed 88 passenger pigeon samples from museum collections, but it will be a long, hard slog to determine which genes distinguish a passenger pigeon from a rock pigeon, and what the genes do, Shapiro says.

It’s the woolly mammoth that’s probably the furthest along toward de-extinction. Hendrik plans to publish the most complete woolly mammoth genome yet, and George Church’s team at Harvard is already introducing specific DNA variants — genes for hair, tusks, subcutaneous fat and cold resistance in blood — into cultured cells from Asian elephants, with the goal of preparing the rebuilt mammoths for life on the tundra. But even making an elephant whose genes are 9 percent mammoth might take 20 years, and we may never re-create an exact duplicate of the extinct species, Church says.

Because it’s so hard to replace all the genes that make a woolly mammoth — or a passenger pigeon or dodo or Steller’s sea cow — a unique species, the re-created animals won’t be exactly what went extinct. Some will be clones, like the baby Pyrenean ibex. Some could be genetically engineered hybrids. Others will likely be wholly synthesized — new beasts altogether.

Taking Secrets to the Stage

In March 2013, 30 years after the only Extinct DNA Study Group meeting, Hendrik strolled onstage before a standing-room-only crowd at the TEDx conference on de-extinction in Washington, D.C. With an image of an amber-ensconced insect from Jurassic Park on a giant screen behind him, Hendrik described how he and his father used to imagine long-gone insects waking up and crawling out of the resin. He described how the woolly mammoth disappeared, like 99 percent of all animals ever to walk the Earth, then he walked the audience through the steps needed to resurrect one. But he ended on a cautionary note: “I have to admit that part of the child in me would love to see these creatures walk across the permafrost, but part of the adult in me wonders whether we should.”

In the past, scientists played their cards close to the vest as they developed, then commercialized, powerful new technologies. Often, they were sure that what was best for the science was best for society. And time after time, their secrecy and paternalism fed fears that sparked a public backlash — over technologies as diverse as test-tube babies, cloned animals like Dolly the sheep and genetically modified organisms. “The reason we’re in this situation with [the backlash against] genetically modified organisms is because we didn’t talk about it clearly enough, early enough,” Church says.

The TEDx conference, which was organized by Stewart Brand and his wife, genomics entrepreneur Ryan Phelan, represented a historic break from that tradition — a high-profile bid to convince the public that de-extinction was feasible and worth doing. Proponents like Church contended that the herbivorous woolly mammoths could help preserve essential carbon-storing grasslands in the Arctic north, while Brand made the case that resurrecting species would atone for human-caused extinctions.

Hendrik and Ross MacPhee, curator at the American Museum of Natural History, pushed successfully to include philosophers, historians and ethicists at the conference to weigh the promise and the perils of de-extinction. The fact that humans will effectively be creating organisms that could never have existed before is a terrifying prospect, says MacPhee. “It’s Brave New World-ish.”

It’s been nearly two years since that conference, and no extinct animals have yet been resurrected. This buys us all time to discuss, publicly and openly, the impacts of such life-altering endeavors, Hendrik says. There’s time to consider whether bringing back ancient animals might cause them to suffer, release dormant diseases or harm today’s already struggling species and ecosystems.

On a summer afternoon, an unfinished Yahtzee game is evidence of the family vacation underway at George’s home on the Oregon coast. George and Hendrik take part in a favorite pastime — friendly debate. Should we resurrect extinct organisms? “Sure, if we can,” George says. Hendrik bristles, suggesting it’s just this attitude that is the problem. “It’s this idea that science marches ahead and does things just because we can,” he says.
The generation gap between father and son lays bare a subtle, but momentous, shift taking place in modern science. George and his contemporaries feared that taking their concerns public could have jeopardized their ability to move the science forward.

Hendrik and his cohorts, on the other hand, worry that a lack of transparency could foster a destructive mistrust of science that jeopardizes us all.

As Hendrik and George have shown, the discovery of ancient DNA created a de facto time machine, and new genetic technology is speeding its development. And, at least in fiction, the only thing certain about a time machine is that it will tamper with the present.

[This article originally appeared in print as "Jurassic Ark."]

The Quest to Resurrect Ancient Species

Key points along the path to de-extinction 

1980: George Poinar and Roberta Hess discover intact nuclei in 40-million-year-old fly in amber.

1983: Polymerase chain reaction (PCR) technique is developed to copy DNA fragments. Extinct DNA Study Group holds its first (and only) meeting.

1984: Allan Wilson and Russ Higuchi clone gene fragments from 140-year-old quagga pelt, proving DNA in nonliving tissue can be reproduced.

1987: First commercial PCR machine lets biologists fish out genes from miniscule tissue samples.

1990: Michael Crichton's Jurassic Park is published.

1992: Hendrik and George Poinar report new freeze-fracture method to extract ancient DNA from amber.

1993: The Poinars and Raúl Cano use PCR to obtain DNA from 120-million-year-old amber-trapped weevil. Jurassic Park, the film, is released.

1994: Svante Pääbo and Hendrik Poinar start developing rigorous new methods to counter dubious claims of DNA from plants and dinosaurs millions of years old, including the Poinars’ weevil claim.

1996: Dolly the sheep provides proof that animals can be cloned by somatic cell nuclear transfer.

2000: Hendrik Poinar co-authors “gold criteria” to ensure reliable sequencing of degraded ancient DNA.

2003: First de-extinction: Pyrenean ibex. Results not reported until 2009.

2005: First commercial next-generation (next-gen) sequencing system is released.

2006: Hendrik Poinar uses next-gen sequencing to partially sequence woolly mammoth genome.

2010: Svante Pääbo publishes draft sequence of Neanderthal genome.

2011: Australian team creates embryo of extinct gastric-brooding frog.

2012: The nonprofit Revive & Restore is founded to enhance biodiversity by reviving endangered and extinct species.

2013: Ethics discussion is part of pioneering TEDx de-extinction conference.

2014: George Church uses genome-editing techniques to begin altering Asian elephant genome to resemble woolly mammoth's.

2015: Hendrik Poinar plans to publish the most complete woolly mammoth genome yet.

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