Can We Bring Back the Passenger Pigeon?

Ever since Richard Leakey and Roger Lewin published The Sixth Extinction in 1995, we have known that humanity is extirpating species at a rate unmatched since the demise of the dinosaurs 65 million years ago. Hunting, deforestation, the introduction of nonnative organisms and diseases, and now climate change have increased the rate of species loss to the point that scientists fear for the functioning of entire ecosystems, and even the stability of the earth’s self-regulatory mechanisms. Until recently it seemed that once a species went extinct, there was little we could do. Extinction truly was forever. But recent developments in genetics have given researchers some hope that extinct species might be brought back to life.

Extinction, of course, involves more than a loss of genes. The cellular environment in which the nuclear genes operate is also lost when a species goes extinct, as are learned behaviors, which can be vital for survival. Undaunted by the formidable complexity of the task, small groups of researchers are working on various aspects of the science increasingly known as de-extinction, and many remarkable advances have been made. In March 2013, for example, a group of Australian scientists funded through a philanthropic donation, and collaborating on what they called “The Lazarus Project,” announced that they had brought a long-extinct species back to life.¹

Australia’s southern gastric brooding frog was a very distinctive amphibian that had a unique method of reproduction: the female swallowed her eggs shortly after they were laid, somehow transforming her stomach from an organ of digestion into a brood chamber. Months later, fully formed froglets would leap from their mother’s mouth. Medical researchers hoped that the species’ ability to transform its stomach might hold the key to curing various digestive ailments. But just eleven years after it was discovered, and before medical researchers could study it, the southern gastric brooding frog became extinct.

Between 1982 and 2013 no living individuals existed. But then, for three days early in 2013, the species was again counted among the living. The body of a gastric brooding frog had been kept in a deep freeze at an Australian university. Cell nuclei were taken from the frozen corpse and placed in eggs from one of its living relatives, the great barred frog, from which the original nuclei had been removed. The eggs transformed into embryos, and grew for three days before dying. The leader of the project team, the paleontologist Mike Archer, proclaimed that “we are watching Lazarus arise from the dead, step by exciting step.”²

This is not a new approach. Researchers first successfully transferred a nucleus into a denucleated frog’s egg in 1952, and it’s been known since that if the nucleus and egg come from the same species, a viable tadpole can result. But if the nucleus and egg belong to different species, the nucleus divides for a few days before the embryo dies, most likely because of a mismatch between the nuclear genes and the cellular environment (including the mitochondria, the “powerhouse” of the cell). The Lazarus Project has made no further announcements, but it illustrates the point that even if we possess the DNA of an extinct species, there is no guarantee that an extinct organism can be resurrected.

M.R. O’Connor’s Resurrection Science gives an up-to-date account of de-extinction science. But it also examines many associated issues, including the human impacts on the process of evolution itself. Its format is one beloved of journalist-authors, progressing through a series of case studies, each of which sheds light on a particular dilemma or issue the author wishes to highlight. While entertaining, the format all too often fails to develop into “one long argument,” as Darwin famously described his Origin of Species, and which is so useful when one is trying to elucidate a complex idea. But the method has another pitfall. Traveling to remote locations to conduct interviews and see research firsthand is expensive and time-consuming, and the author must make a guess in advance about which case studies will best illustrate his or her point. What happens if they don’t serve the purpose intended, or better illustrate some other point? The result can be an uneven, or even disjointed, book.

Resurrection Science begins with a story of habitat destruction. The one-inch-long Kihansi spray toad was found only in the spray zone of a Tanzanian waterfall slated for hydropower development. Tanzania’s need for electricity is dire: only 2 percent of its rural population have access to power, and compared even with other African nations its per capita use of electricity is small. Today, solar and wind power would be Tanzania’s first choice, but in the 1990s, hydropower was the best option. There really was no question of stalling the 180-megawatt, World Bank–funded project in order to save the toad. Nonetheless, great—and extremely expensive—efforts were made to ensure that the creature survived.

The Kihansi spray toad’s total habitat consisted of around five acres of perpetually mist-soaked “quaking bog,” virtually all of which started to dry out as water was diverted into the power plant’s turbines. So an irrigation system was installed to keep the bog saturated. This required six full-time staff to maintain. But changes in land use upriver, and possibly the arrival of the chytrid fungus—a disease fatal to many amphibian species, and the likely cause of extinction of the southern gastric brooding frog—drove the Kihansi spray toad to extinction in the wild by 2004. Fortunately, five hundred toads had earlier been taken into captivity by a consortium of US zoos. Despite early setbacks, some of the captive animals bred, and from 2010 onward, individuals have been periodically returned to the wild, where some manage to survive.

Many of the remaining wild areas of our planet will doubtless be “developed” as the global population swells to 10 billion and the poor demand higher standards of living. The fate of the Kihansi spray toad is a great illustration of how biodiversity is likely to suffer as these developments proceed, and how expensive it will be to keep affected species on what is effectively life support. But O’Connor perceives far deeper issues at play. Perhaps, she writes, the reintroduced adult toads do not survive well at the falls because their behavior and genetics have been altered by over fifty generations in captivity. But at least the toads have a habitat to return to, unlike fifty-two of the 110 species currently held in captive breeding programs in zoos worldwide. With their very ecosystems are extinct, what is to be done with them?

The dilemma posed when humans try to preserve endangered animal populations is drawn out further in a chapter on the Florida panther. Long thought to be extinct, in the early 1970s an isolated population of a few dozen was discovered in southern Florida. They were severely inbred, with kinked tails, odd-shaped hair-whorls, and with 80 percent of males having just one functioning testicle. These genetic problems made it clear that simple in-situ protection would not be enough: both genes and habitat were too limited to ensure long-term survival.

But all was not lost. Until the nineteenth century, panthers ranged across a vast area from Texas to Florida. In 1995, in an attempt to improve the gene pool, eight Texan females were released in Florida’s Big Cypress swamps. The genetics of the Floridian population were thereby improved, but even this brought only a temporary reprieve. The panthers needed more habitat if they were to enjoy a secure future. And indeed a viable habitat exists in northern Florida and Georgia. But rivers, highways, and the dense developments of central Florida prevent the panthers from expanding into it. The obvious thing to do is to translocate some panthers, but thus far no authority has proved willing to negotiate the strained politics required.

When humans do translocate organisms, O’Connor says, we can unwittingly become agents of extraordinary evolutionary change. The two-inch-long White Sands pupfish inhabits four waterways in the New Mexico desert. Pupfish are resilient creatures. The desert pupfish, for example, can survive in water as hot as 113˚F, while the White Sands pupfish thrives in waters ranging from highly saline to fresh. Each population is different, and instantly recognizable by details of its body shape and fins. The four populations were thought to have been long isolated, and thus worthy of individual conservation programs. But historical and genetic research revealed a different story. In the 1970s Ralph Charles, who worked for the Bureau of Reclamation, and an unknown farmer had released pupfish into two waterways where they had not previously existed. Over just thirty years the translocated fish had changed their body shape and salinity tolerance to a degree that astonished the scientists.

Varying salinity proved to be the decisive factor. Saline water is more difficult for fish to swim through than fresh water, so among fish translocated from fresh water to saline, natural selection strongly favors the gracefully streamlined. Courtesy of a human translocation, the rate of evolution of the White Sands pupfish, as defined by its changing body shape, is now one of the fastest ever recorded for any vertebrate. Indeed, it “expanded what biologists thought possible when it came to rates of evolution.”

The North Atlantic right whale offers another example of historical and genetic studies turning conventional wisdom on its head. Long thought to have been driven to the brink of extinction as a result of whaling, careful recovery programs were crafted for it. But analysis of whale bones preserved in the San Juan galleon, a whaling vessel which was lost off the coast of Labrador in 1565, revealed a different story. Of the twenty-one flipper bones found in the wreck, only one was from a right whale. And it was genetically identical to individuals living today. Subsequent research has confirmed that the species had always been rare and genetically uniform. The “recovery programs” for the species were thus attempts at manufacturing a situation for the animals that had never existed.

Looking at human impacts worldwide, the case of the North Atlantic right whale is clearly the exception that proves the rule. Indeed, human influences on the earth are now so profound that a case is being built for proclaiming a new geological period, the Anthropocene—in recognition of the ubiquitous human impact on our planet. In September 2015 the Royal Geographical Society devoted its entire annual meeting to a discussion of the subject, and next year, at a meeting in South Africa, a formal proposal for recognition of the Anthropocene will be moved. The early chapters of Resurrection Science could well serve as evidence in the case for the affirmative.

Crows, ravens, and rooks are among the most intelligent of birds. The New Caledonian crow, for example, has been observed manufacturing three distinct types of tools out of pandanus leaves and other materials. But intelligence has not saved some crow species from extinction. The New Zealand crow became extinct around nine hundred years ago, soon after the Maori arrived. And the Hawaiian crow became extinct in the wild in 2002, when the last two individuals disappeared from their native forests in the Kona district of the big island. But a few individuals had been taken into captivity in 1985, and their living descendants, along with frozen tissues that may one day be able to be used to increase genetic diversity, are all that remain beyond bones and dry skins.

The emotional lives and behaviors of creatures as intelligent as crows are far more complex and liable to be disrupted by captivity than are those of toads or fish. Crows live in learned cultures, and have been observed “mourning, calling to, and revisiting their dead.” The captive breeding program for the Hawaiian crow involved the removal and artificial incubation of every egg laid: until 2013, no captive Hawaiian crow had been raised by its family. An attempt in the 1990s to release captive birds into the wild revealed that they no longer knew how to avoid predators, or even find food. Perhaps a creature as smart as a crow can relearn such things. But if it did, would it be the same, in ecological and cultural terms, O’Connor asks, as its wild ancestors?

From rapid evolution in captivity to genetic and cultural loss, the preservation of endangered species is a fraught business. But recent advances in technology will soon add a whole new dimension of complexity. In 2006 the Japanese scientist Shinya Yamanaka announced that he had discovered a method of transforming any mature living cell into a stem cell that is capable of giving rise to any kind of cell in a body, including eggs and sperm.

Soon after this breakthrough, researchers applied Yamanaka’s technique to cells from the world’s most endangered rhino—the northern white. Genetic studies show that it split from the southern white rhino about a million years ago, and is as genetically distant from white rhinos as from black. Just a few decades ago, the northern white existed in the thousands, but the chaos of civil wars has most likely driven it to extinction in the wild. The stem cell researchers obtained some skin tissue from a captive individual, and soon had petrie dishes brimming with rafts of northern white rhino stem cells. The San Diego Zoo holds frozen tissue samples from twelve northern white rhinos—four times as many as are known to be alive, so the possibility exists to develop genetically diverse eggs and sperm, which might be used to found a sustainable population. But research on the project has stopped: “There’s no clear economic incentive to making northern white rhinos in the laboratory,” O’Connor tells us. Meanwhile, efforts to breed hybrids of northern rhinos and the more abundant southern white rhino, in order to preserve at least some northern white rhino genes in living individuals, have failed.

While the fate of the northern white rhino hangs in the balance, de-extinction science as a whole is booming. A loose network of researchers (of whom I am one), encouraged and coordinated by Stewart Brand of Whole Earth Catalog fame, help guide the movement. Currently, the most prominent de-extinction project under consideration concerns the passenger pigeon. A young North Dakotan researcher, Ben Novak, has been preparing and extracting DNA from the 1,500 museum specimens of passenger pigeons known to exist. Novak has no Ph.D. and no publications. But he is obsessive about passenger pigeons. “If you love pigeons, it is your life,” he says. And his obsession is paying off. Nearly every one of the museum samples he examined yielded higher-quality DNA than expected, the most complete sequence coming from a specimen held in the Royal Ontario Museum.

But how might this DNA be used to recreate a passenger pigeon? It turns out that the passenger was a very different kind of bird. Its nearest living relative is the band-tailed pigeon of the American West. But the two species have been isolated ever since the Sierra and Cascade Mountains began to form and split an ancestral pigeon population into eastern and western types 22 million years ago. About 3 percent of the DNA of the passenger pigeon is different from that of the band-tailed pigeon. If one were to start with band-tailed DNA and transform it into passenger pigeon DNA, thousands of changes would need to be made.

Until a recent, astonishing scientific breakthrough was announced, there was no way that that could be achieved. However, it has been found that CRISPR-Cas9 is a sequence of DNA that acts as a type of immune system in prokaryotes, which include bacteria and other primitive organisms. In 2012, Jennifer Doudna of the University of California, Berkeley, and her colleagues used CRISPR-Cas9 as a kind of genetic scissors, to precisely cut out and replace human genes. It has since been used in a wide variety of species, from yeast to fish and monkeys.

Novak plans to use the unprecedented power of CRISPR technology to edit band-tailed pigeon DNA in primordial germ cells, so that they are transformed into passenger pigeon DNA. The germ cells thus created could form an embryo—the first passenger pigeon to live since Martha, the last of her kind, died in the Cincinnati zoo in 1914. Other new technologies may also be used to help revive the species. In 2012 a company announced that it had found a new way to propagate endangered birds. The testicles of a more common species are colonized by germ cells from a rarer type, allowing the common bird to father the rare species.

Assuming that a living passenger pigeon embryo can be “resurrected” (or perhaps, some would prefer to say, created) using such technologies, many hurdles remain. Will the passenger pigeon nuclear genes be able to work with the mitochondria and other cellular structures? And even if a few birds survive to adulthood, could they ever survive in the wild? Researchers worry that thousands—and maybe millions—of passenger pigeons would be needed. After all, the gigantic flocks observed by the American colonists famously darkened the sky for days and nested in colonies of millions.

Intriguingly, archaeological research indicates that the passenger pigeon’s story might not be that simple. The bones of passenger pigeons are rare in pre-Columbian archaeological deposits, suggesting that the birds were scarce until colonial times. Ecologists now think that the vast flocks may have emerged only after a declining Indian population left enough acorns and other seeds and nuts for the pigeon population to build up. Because passenger pigeons are so distantly related to other species, and because pigeon reproduction and genetics are not well understood, attempts at resurrecting it are likely to be difficult.

Still there is a species whose biology and reproduction are known in extraordinary detail, and which has extinct relatives whose DNA are also well understood. Neanderthals were human-like beings who differed from us in their larger brains, greater physical strength, simpler material culture, and possibly the lack of language. They diverged from the human lineage a little over 500,000 years ago, and they were driven to extinction around 30,000 years ago, most likely by the humans who colonized Europe. The recovery of the first complete Neanderthal genome was announced in 2013. The de-extinction of a Neanderthal looks to be, from a technical point of view, relatively easy compared with the de-extinction of the passenger pigeon. Yet the very prospect of such an attempt brings into sharp focus all of the moral, ethical, social, and environmental dilemmas inherent in the new technology—and indeed in de-extinction science itself.

Resurrection Science demonstrates unequivocally that the Anthropocene has already dawned, and that we are ill-equipped to deal with its consequences. There is no doubt that we humans have now crossed a technological Rubicon, and at some time in the future extinct species will once again be breathing and interacting with other living things, in zoos if not in nature. Typically, the technology has arrived in advance of the wisdom to use it judiciously. Debate will doubtless rage over whether the first resurrected species are indeed the same as their extinct forebears, and whether they function in the ecosystem in the same way. The wisdom of creating them will be doubted, even as we go on destroying ever more species through reckless “development.” But there will be no going back to that pre-Anthropocene age in which our species could dodge responsibility and decision-making on behalf of the planet.