Instead of the Noah you know, the one who built the ark, sheltered all those animals, sailed for 40 days and 40 nights and got to see God’s rainbow, instead of him, I want you to meet a new one. An updated version.
This Noah shows up in a tough little essay written by Amy Leach, of Bozeman, Montana, who knows her science, knows there’s a flood coming—a flood of humans, seven billion and counting, already swamping the Earth, crowding the land, emptying the sea, and her more modern Noah—informed, practical, not inclined to miracles—has a different plan. He announces,
The old Noah, you may remember, squeezed eight humans (wife, kids, their spouses) and at least two of every critter, big and small, onto his crowded ship. But the new Noah, being more practical, feels he can winnow a little. “Everybody” is a lot of animals, more than you know. Back in the day, Amy Leach writes,
And, honestly, (I’m thinking to myself), if the world lost a scorpion or two, would anyone notice? Or want them back? And blotchy toads, biting little flies—some animals are hard to keep going on a tight, crowded ship. On the last voyage, dormitory assignments were beyond difficult.
And all those supplies? Amy Leach writes how the first Noah would have had …
This doesn’t mean we don’t care, new Noah says to the animals. We definitely, absolutely want to bring a bunch of you with us. But, we’ve got to be practical.
Even if our ark has grown to the size of a planet, carrying everybody through is not going to be logistically possible, which is why, he says,
And anyway, that first Noah? He lived in a different age, a time they call the Holocene, before humans began to dominate and crowd out the other species. Back then, there weren’t as many people. And there were more kinds of animals, closer by, hiding in the woods, clucking in the yard, so the world was more various then, more intimate, more riotous, and thinking about it (a little wistfully, if only for a moment), the new Noah quietly recalls that on that first ark …
And now, animals, it’s time for many of you to step away. You’ve had your unruly eons. They were wild, unplanned, noisy, great fun. Natural selection ran the world. Crazy things happened. Those were good times, Amy’s essay concludes …
Amy Leach is a writer living in Bozeman. Her collection of very short pieces—about jellyfish, beaver, salmon, plants that go topsy turvy and stand on their heads—are collected in a wonderful little book called “Things That Are.” In this column I do to Amy what the new Noah is doing to our planet: I edited her down, sliced, diced, slimmed (lovingly, I hope), trying to give you a taste for her fierce, crazy prose. But like the planet, she’s wilder in the original, so I hope you go there and sample the unedited version.
In 1986, after almost five years of construction, the Diama Dam was finally completed along the mouth of the Senegal River. The dam stopped saltwater from intruding upstream, thus creating a stable reservoir of freshwater for farmers and for Senegal’s capital city of Dakar.
But it also had unintended consequences. By restraining the saltwater, the dam favoured the growth of freshwater algae and plants, which in turn fed large numbers of snails. The snails are hosts for parasitic flatworms that cause schistosomiasis—a horrible water-borne disease that damages the kidneys, bladder, intestines, and liver. As the snail population boomed, they triggered a huge outbreak of schistosomiasis, which spread with unprecedented speed and still persists today. In some places, more than 90 percent of villagers are infected. In damming the river, Senegal also damned the people along it.
But help is at hand. A team of scientists led by Susanne Sokolow from Stanford University has been working on a way of stopping the outbreak by bringing the snails—and their parasites—under control. Their plan? Add prawns.
The lower Senegal River used to be home to a hand-sized, long-clawed prawn called Macrobrachium vollenhovenii, that would devour the parasite-carrying snails. Every year, the female prawns would walk downstream to the estuary to lay their eggs; later, the larvae would swim back upstream. The Diama Dam cut off both routes and exterminated the prawns. By reintroducing them, Sokolow hopes to control the rampant snails and bring schistosomiasis to heel.
“It’s not a new idea,” she says. In 1999, a team of scientists successfully used crayfish to reduce both snail populations and schistosomiasis infections in a couple of Kenyan villages. Unfortunately, they used an American crayfish that had been introduced to Africa several decades before, and was considered an invasive species. “There was a strong backlash from the environmental community, so nothing ever came of it,” says Sokolow.
Buoyed by that success, the team staged a pilot experiment in June 2011. At a village called Lampsar, they netted off a part of the river that villagers frequent, and stocked it with prawns. At a nearby village, slightly upstream but otherwise as similar to Lampsar as possible, they did nothing.
Before the prawns arrived, the Lampsar villagers were five times more likely to carry schistosomiasis parasites than their upstream peers. After they added the prawns, Sokolow’s team treated anyone who was infected with drugs. Eighteen months later, they checked for re-infections. This time, they found the opposite ratio: the upstream village had four times as much schistosomiasis as Lampsar, whose waters contained half as many snails and a fifth as many parasite-shedding ones. The village, which had been written about since World War II as a hotspot for schistosomiasis, had become almost free of disease.
In other words: the prawns had worked.
Sokolow would be the first to admit that with just two villages, it is impossible to draw any broader conclusions about how effective the prawns might be. “We know that it was just a demonstration,” she says. The promising results are consistent with ecological theory, the lab experiments, and the Kenyan trial, but “we need to do a wide-scale replicated study and really nail the proof of concept.”
Sokolow’s colleague Giulio de Leo created a mathematical model to predict what would happen. He found that at a certain density—0.3 prawns per square metre—the prawns will completely eliminate schistosomiasis by eating any newly infected snails before they can release their own parasites. This will take at least 20 years, but not if infected villagers are also treated with the drug praziquantel. Then, schistosomiasis ought to decline and disappear within just five years.
De Leo says that this combined approach has many advantages over praziquantel alone, effective though the latter is. “After praziquantel administration, villagers in rural areas of Senegal have no other option than go back to river and step into schistosome-contaminated waters for their daily chores, thus getting re-infected over and over again,” says de Leo. In other words, the villagers might briefly shake off the disease, but the river will never let them forget it.
By contrast, the prawns should prevent infections in the first place, by decimating the snails that harbour and transmit the parasites. Others have tried to do this by attacking the snails with toxic “molluscicides”. Like praziquantel, that was just a temporary measure, and one heavy in collateral damage: the chemicals killed off many fish and crustaceans, too. “Re-introduction of native prawns may offer an ecologically friendly and much more lasting solution to snail control,” says de Leo. “We believe that, when coupled with praziquantel administration, it may be the game changer in the fight against schistosomiasis.”
“We have too long been enamored of the idea that pills alone could solve the problem,” says Eric Loker from the University of New Mexico, who led the Kenyan study in 1999. “I commend the authors for putting a needed spotlight back on what happens in the water. The snails are abundant, often resilient, and impart stability to the transmission cycle. We don’t have a bed-net like option for snail control like we do for the mosquitoes that transmit malaria.”
But “a dose of reality is also in order,” he says. The snails often live in “complex, heavily vegetated, small bodies of water”, many of which were created by the construction of the Diama dam. Whether the prawns can even reach their pre-dam levels, let alone penetrate these new habitats, is unclear.
Meanwhile, the dam still prevents the prawns from travelling to and from their breeding grounds. If the team wants a new population to establish itself in the river, they’ll have to create some kind of bypass around the dam—a “prawn passage”—that will allow the animals to traverse their old migration routes.
Even that might not be enough. De Leo’s model shows that to eradicate schistosomiasis entirely, the team will need densities of prawns 2.5 times higher than what they actually managed in their small pilot study. That’s not unachievable, but it might be higher than what artificial prawn corridors can maintain. So, in areas where schistosomiasis is especially common, the team might have to regularly supplement the waters with prawns raised in aquaculture.
This isn’t a problem, though. It might even be a good thing, because the prawns have two important benefits beyond their hunger for snails: they are tasty, and valuable. They can sell for three to five times the price of local fish. The Upstream Alliance team believes villagers should be able to rear them in small aquaculture facilities to get both food and money. This idea is especially feasible because it’s the small, fast-growing prawns that kill the most snails, leaving villagers to harvest the larger and more valuable individuals with impunity. (It’s also okay to eat prawns that have dined on infected snails because their digestive systems kill the parasites.)
These economic benefits are crucial. Schistosomiasis affects more than 260 million people around the world, including some 114 million children. These huge numbers make it unfeasibly expensive to treat people with even a really cheap drug. But if countermeasures can actually return money to a community, they stand an even greater chance of succeeding. It’s a rare win-win-win scenario, where conserving a displaced animal can benefit human health and alleviate poverty. “We’re now working with geographers, ecologists, economists, and government ministries to find out how we can optimise a sustainable, long-term strategy,” says Sokolow.
Reference: Sokolow, Huttinger, Jouanard, Hsieh, Lafferty, Kuris, Riveau, Senghor, Thiam, N’Diaye, Faye & de Leo. 2015. Reduced transmission of human schistosomiasis after restoration of a native river prawn that preys on the snail intermediate host. PNAS http://dx.doi.org/10.1073/pnas.1502651112
“Will there ever be a real Jurassic Park?” I’ve heard this question more times than I can count. The answer is always “No“. Aside from the problem of getting a viable clone to develop inside a bird egg – one that scientists haven’t cracked yet – DNA’s postmortem decay happens too fast to give us any hope of saying “Bingo! Dino DNA!” someday. But just because it won’t work for Tyrannosaurus doesn’t mean that it’s impossible for other forms of life. In How to Clone a Mammoth, ancient DNA expert Beth Shapiro offers a thrilling tour of the science that might – might – recreate lost worlds from the not-too-distant past.
The book’s title is a bit of a bait-and-switch. On the very first page, Shapiro explains that for long-extinct organisms such as “the passenger pigeon, the dodo, the mammoth – cloning is not a viable option.” If at all, these organisms are going to come back to us piecemeal as revived genetic material expressed in hybrid creatures that may, or may not, look like the lost species. And this cuts to the core of what de-extinction is really all about.
From a purist’s perspective, extinction really is forever. It’s impossible to recreate lost species exactly as they were, down to every last gene and quirk of behavior. But with a broader definition of de-extinction – creating organisms that can fill vacant ecological roles – an elephant with a touch of mammoth trundling around the Arctic steppe would count as what Shapiro dubs an unextinct species. This is the goal of de-extinction efforts – not to recreate extinct species down to the finest detail, but to generate organisms that rehabilitate ecosystems. Not so much resurrection as carefully-crafted reinvention focused on ecosystem-scale repair.
As a researcher who is shaping this field, Shapiro is the perfect guide to the ongoing discussion about de-extinction. While many news items and conference presentations have focused on the technology required to recreate extinct life, Shapiro carefully considers every step along the journey to de-extinction, from choosing a species to revive to making sure they don’t become extinct all over again. As Shapiro says herself, she’s a realist rather than a cynic, and her finely-honed prose cuts through the hype that has clouded the debate around whether or not we should be striving to recreate lost species when so many living species are hanging on by the barest thread.
In fact, Shapiro uses the tension between those advocating for the return of extinct species and critics who argue that the effort would be better spent saving today’s imperiled organisms to propose a third option that has barely been discussed. Whether or not proxy mammoths, dodos, or sabercats come back, exploring such possibilities may give conservationists new tools to manage and assist threatened species and ecosystems. We’re already carrying out conservation triage on the weak and wounded, so why not use every tool at our disposal to sustain – and perhaps even improve – what we’re already managing by hand? Or, as Shapiro writes near the end of the book, “De-extinction is a process that allows us to actively create a future that is really better than today, not just one that is less bad than what we anticipate.”
Will genetically-modified pseudo-mammoths or passenger-ish pigeons be the first symbols of a new age in conservation? That’s still unclear. But even if we never see shaggy elephants or the shade cast by immense pigeon flocks, de-extinction research already underway has the potential to both tell us about the past and provide us with new tools to decide the future shape of nature. Whether you’re all for de-extinction or against it, Shapiro’s sharp, witty, and impeccably-argued book is essential for informing those who will decide what life will become.
In 1959, off the southern coast of France, a tuna boat hauled up a largetooth sawfish. The catch wasn’t particularly large. The razor-snouted fish only stretched about four feet long; still a baby by the standards of its species. But it was one of the last to be seen in those waters. Within a decade, the largetooth sawfish entirely disappeared from the Mediterranean Sea.
Such accidental catches and sightings in the Mediterranean have often been regarded as signs of largetooth and smalltooth sawfish migrating into the sea from the coast of Africa. When sawfish experts gathered in London in May 2012 under the auspices of the IUCN, they concluded that the Mediterranean gets too cold in winter to have hosted resident populations of the warm-water fish. Therefore all the historic accounts must have referred to “vagrant” animals, and sawfish blades in museums were brought to coastal museums by trade routes that have been in place for centuries. But after trawling through bibliographic records and museum displays, Hopkins Marine Station biologist Francesco Ferretti and colleagues have suggested a different interpretation. The Mediterranean is missing its native sawfishes.
Ferretti and coauthors cast a wide net. They searched everything from records on pre-dynastic Egypt through modern ocean biodiversity databases to find any sign of sawfishes in the Mediterranean. Being that the science of ichthyology didn’t get going until the 16th century, it’s not surprising that the earlier part of their timerange came up empty. But between the 18th and 20th century – when naturalists often kept track of who was landing what at the local docks – the researchers turned up 48 original accounts of sawfish in the Mediterranean, 24 of which could be verified in the literature or in museums. These verified records were split between largetooth and smalltooth sawfish, and the size of many of these fish hint that they were not migrants from the African coast.
Largetooth and smalltooth sawfish grow slowly. Largetooth sawfish, in particular, take between eight and ten years to reach maturity, at which time they’re about 10 feet long and start reproducing. But in their youth, sawfish typically stick very close to the place they’re born. Smalltooth sawfish, for example, have a home range of less than a half a mile. Ferretti and coauthors counted 15 sawfishes in their sample that fell within the juvenile category.
If those juvenile sawfishes were swimming from the nearest population centers to the Mediterranean, they must have journeyed more than 2,000 miles – over ten times the distance an adult sawfish has ever been observed to travel. Unless the historic populations of large and smalltooth sawfish undertook truly exceptional journeys, Ferretti and colleagues argue, it’s more likely that they had a resident population in the Mediterranean.
While lacking in as much detail as modern biologists wish for, the 18th and 19th century naturalist accounts of sawfishes also throw some support to the idea that sawfish had a home in the Mediterranean. Some accounts list them as relatively rare, and others as common, but there doesn’t seem to be any hint that it was strange to see sawfishes along Europe’s southern coastlines. It was only in the 20th century – when sawfish populations plummeted and totally disappeared – that sawfishes were regarded as especially rare and the idea of migration started to take hold.
Not all marine biologists are convinced by the historic evidence. In a paper published around the same time as the paper by Ferretti and coauthors, Nicholas Dulvy and colleagues argue that the Mediterranean gets too cold for sawfishes and that the past occurrences really do represent piscine vagrants. More than that, Dulvy and colleagues write, “Whether or not sawfishes were previously extant in the Mediterranean Sea has little bearing on current conservation priorities as any activities benefitting West African sawfishes can only restore migration and improve the likelihood of vagrancy to the Mediterranean Sea once again.”
Ferretti and colleagues disagree on both counts. Regarding temperature, the researchers suggest, past Mediterranean sawfish populations may have been better-adapted to cooler waters than others. If not that, then young sawfishes could have taken refuge in deeper water that maintains warmer, more constant temperatures than those at the surface during winter. There may not be a way to know for sure – the Mediterranean sawfishes are all gone – but temperature alone can’t be used to rule out the previous presence of resident populations.
And this question does have relevance for the future of the largetooth and smalltooth sawfish. If sawfishes previously had a home in the Mediterranean, perhaps they could live there again. Ferretti and colleagues even have a spot in mind – a national park in southern France near where the last recorded sawfishes were seen. What hopes sawfishes might have for survival in such a place are murky, but if restoration attempts are to be considered at all, the Mediterranean may be a place where these awkwardly charismatic fish may find a refuge.
How long the longtooth and smalltooth sawfish will survive is unknown, and their fate largely rests on the decisions we make. And in making those decisions we must be aware of our own history. The only good records of Mediterranean sawfishes we have come from a timespan when these vulnerable fish had already been coping with centuries of human disturbance to their nearshore haunts. Our species only started keeping track of what was “natural” when the sawfishes were already in decline. Marine biologists know this as “shifting baselines“, and it’s the same reason why many don’t feel the absence of ground sloths and mastodons in North America’s forests. The megamammals were already gone by the time naturalists started paying attention to the woods, and we don’t consider how empty the landscape is. We just don’t know what we’re missing.
If you go for a walk through the rocky hills of Finland’s Aland archipelago, you might come across a medium-size snake with gunmetal grey scales and darker diamonds running down its back. It looks a little bit like an adder, but it can’t be because its head is thin and tapered…
Wait, did that snake just change its head?
You can’t be sure, but now its head is definitely flat and triangular—the defining shape of adders and other vipers. That means it’s venomous. There are people living nearby, with kids and pets. You decide to kill the snake with a rock. That was a poor decision, especially since the dead snake wasn’t an adder. It was a smooth snake—completely harmless, rather endangered, and now very slightly more endangered.
The smooth snake is found throughout Europe but its populations are small and thinly scattered. It could be easily wiped out, so the European Union has listed it as a specially protected species. In Finland, it’s classified as “vulnerable”, and may be bumped up by one degree of concern to “endangered”.
For much of its existence, the smooth snake protected itself by mimicking the far more dangerous adder, and its charade (especially its shape-shifting head) is good enough to fool even trained biologists. But this disguise is now the snake’s undoing. The fear of venomous snakes might compel birds to flee, but it sometimes compels humans to kill the potential threat.
This is doubly problematic for the smooth snake because its brand of mimicry (known as Batesian mimicry) only works if the noxious creature it mimics is plentiful. If an island contains a lot of adders, birds soon learn that attacking a long thing with a triangular head and a diamond back is a very bad idea. That’s good for the smooth snake, whose predators avoid it too. But if an island contains no adders, birds could attack the smooth snakes with impunity. Why wouldn’t they? They’re never come to associate those markings with possible death. Batesian mimics should always be in the minority if their copycat acts are to work.
Johanna Mappes from the University of Jyvaskyla in Finland showed this in 1997, by creating an artificial example of mimicry. She injected mealworm larvae with a foul-tasting liquid, and stuck small sugarballs (the ones used to decorate cakes) onto their heads—these were the models. She stuck the same balls onto other mealworms without the nasty liquid—these were the mimics. She then presented both groups to great tits in varying ratios. Mappes found that if the number of mimics equalled or exceeded that of the models, the benefits of their disguises disappeared.
This is bad news for the smooth snake. On Aland archipelago, they already outnumber adders. If Mappes is right, their defence should already be worthless. “For the successful conservation of smooth snakes in Aland, it seems crucial to also protect adders,” writes Mappes, along with colleague Janne Valkonen. “Our results provide foresight to prevent a potential disaster in a situation where a mimic becomes endangered due to the decreased frequency of its model species.”
This might apply to other species too. Many harmless snakes mimic venomous ones, and many snake populations are crashing all over the world. The smooth snake example suggests that protecting an endangered mimic is when an endangered species mimics a dangerous one, we might need to protect both to save the former—a one-for-the-price-of-two deal.
Reference: Valkonen & Mappes 2014. Resembling a Viper: Implications of Mimicry for Conservation of the Endangered Smooth Snake. Conservation Biology http://dx.doi.org/10.1111/cobi.12368
Since the 1990s, the world has witnessed the rise of one of the most terrifying diseases to afflict any animal group: a doomsday fungus that is ripping through the world’s frogs and amphibians. Known as Batrachochtyrium dendrobatidis, or Bd for short, it causes a disease that has wiped out dozens of species and endangered hundreds more. It’s a global problem and earlier this year, it was finally found in Madagascar—the last Bd-free amphibian stronghold. “That’s it. The worst news imaginable,” wrote one herpetologist.
Bd news is almost always bad news. But this week, Taegan McMahon from the University of South Florida has a more positive to tell—or, at least, what passes for positive when you’re dealing with Bd. Her team showed that frogs become more and more resistant to the fungus if they are repeatedly infected and cured. They even became more resistant after the team exposed them to dead fungus.
These results offer a small sliver of hope. Perhaps conservationists might be able to vaccinate frogs against Bd using dead versions of the fungus, just as humans protect ourselves from polio or rabies. They could inoculate captive individuals before releasing them, prepared and protected, into the big, bad, Bd-filled world.
“This is the beginning to a long line of work—the first information that we need to figure out whether it’s really practical in the field,” says McMahon. “We need to test this on a larger scale, but we’re super-optimistic with it.”
Other frog specialists are more skeptical. Lee Skerratt from James Cook University in Australia praised the team’s experiments but said, “The fungus still appears to be highly virulent after four previous exposures, which fits with our current understanding. It still kills the majority of frogs after a short period of time. In comparison, inoculations with many other pathogens provide almost complete protection against future exposure.”
Karen Lips from the University of Maryland also doubts that the results will make much practical difference. “It’s already a Bd world. Essentially all amphibian species have already been exposed at some point. Many have been shown to self-clear infections, some get reinfected, some die, some don’t.” The point is that they’ve already had a chance to become resistant, only some have taken it, and we still don’t understand why.
However, she adds, “Any evidence that some amphibians are surviving with disease is good news. [And] anything that zoos and NGOs can do to promote or allow evolution of captive assurance populations would be good.”
McMahon’s team repeatedly exposed Cuban tree frogs to Bd and then raised their temperatures to clear their infections. With each passing exposure, the team found that the frogs became more and more resistant to the fungus. By the third exposure, they carried 75 percent less of it on their skins. They also mounted stronger immune responses and made more white blood cells in response to the threat. That was a surprise—Bd can suppress amphibian immune systems but it seems that, over time, the frogs can compensate.
Spraying live fungus onto frogs, especially endangered species or those only exist in captivity, would be a non-starter. So the team exposed the frogs to dead fungus to see if they could trigger the same resistance. It did, and to almost the same extent as the live fungus. “I was hopeful but not as confident that the dead fungus would work,” says McMahon. “It did, and that’s extremely exciting.”
But Lips warns that strong immune responses aren’t necessarily cause for celebration. In her own research, she found that harlequin frogs that naturally recover from a bout with Bd will die just as fast as naive frogs if re-infected, even though they mount vigorous immune responses.
In McMahon’s experiment, only 20 percent of the animals that had acquired “resistance” to the fungus were still alive after five months. They fared better than the completely naive animals, all of whom were killed, but a survival rate of 20 percent is probably not good enough to sustain a wild population. And what happens after five months? Does their shred of immunity disappear, or do the frogs lose it over time?
There are other unknowns. Bd has wildly varying effects on different frogs—harlequin frogs almost always die, but cane toads (predictably, sadly) are almost impossible to kill. It’s not clear if other frogs would react to the fungus in the same way that the Cuban tree frogs did.
Most importantly, what would happen in the wild? Lips adds that when she pits amphibians against Bd in her lab, context is everything. The same fungal strains will kill infected salamanders at 13 degrees Celsius but spare their lives at 17 degrees. “In terms of relevance for wild populations, what will happen when winter comes and temperatures drop?” she asks. Field tests are everything.
McMahon agrees. She now wants to expose frogs in mesocosms—enclosures that sit in natural settings, but that can still be carefully manipulated. That will tell her not only whether the frogs can resist the fungus outside of a lab, but also whether spraying dead fungus has any unintended consequences. After all, she previously showed that Bd can release an unknown toxin that can kill crayfish at a distance. “We want to make sure that if we’re spraying the fungus, there aren’t effects we don’t expect,” she says.
Reference: McMahon, Sears, Venesky, Bessler, Brown, Deutsch, Halstead, Lentz, Tenouri, Young, Vicitello, Ortega, Fites, Reiner, Rollins-Smith, Raffel & Rohr. 2014. Amphibians acquire resistance to live and dead
The black robin is an endearing ball of beaked fluff, found only in the Chatham Islands off the eastern coast of New Zealand. By 1980, there were just five of them left.
They lived in a rocky outcrop about the size of a few city blocks. The precipitous cliffs kept them safe from the cats, stoats and rats that sailors had brought to the islands. But the high winds were too much for these small birds, and most of the survivors had died. With a single breeding pair left—Old Blue and Old Yellow—their future looked bleak.
Don Merton and a team of conservationists mounted a heroic effort to save them. They relocated the tiny population to larger islands and managed their reproduction over many years, transferring their eggs to foster parents for incubation. By 1989, there were 80 robins. By 1998, there were over 200. Once the world’s most endangered bird, the black robin became a flagship example of conservation success.
But it’s also an example of good intentions leading to unintended consequences.
In those early years, when the team was still carefully managing the birds, they noticed that many females laid their eggs on the rims of their nests, rather than the centre. Precarious positions aside, these “rim eggs” were never incubated and never hatched. With the species’ fate hanging in the balance, every egg was precious. The team repositioned the ones on the rims.
Without this move, it’s unclear if the species would have made its dramatic recovery. But it also saddled the robins with a difficult legacy.
Melanie Massaro from Charles Sturt University in Australia has now shown that rim-laying had a strong genetic basis. Under normal circumstances, natural selection would have quickly weeded out the alleles (versions of a gene) behind the behaviour, because any female who carried them would lay doomed eggs. By saving those eggs, the conservationists inadvertently gave the rim-layers a pass, turning their maladaptive behaviour into a neutral one. They allowed for “survival for the not-so-fit”.
Sure enough, the alleles for rim-laying spread through the growing robin population. The speed of this spread became clear when Massaro checked old records of the robins’ behaviour. Old Blue, the last fertile female as of 1980, laid eggs in the normal way. By 1984, there were five females and one laid a single rim egg. By 1989, there were 35 females, of whom 18 (more than half) were rim-layers.
You can see the spread for yourself in the family tree below, which shows the relationships between every breeding robin during the 1980s. Blue circles represent females that lay eggs in the right place; the rim-layers are in red. This is the sort of diagram you can make when a species only has a few dozen survivors, and you know all of them.
It’s possible that the robins increasingly laid eggs on rims as a response to their environment, but the pattern in the family tree suggested otherwise. It looked like rim-laying had a strong genetic basis. In fact, it was most probably caused by a dominant allele—a version of a gene that produces rim-laying even when a bird inherits just one copy from either of its parents.
If the team had continued to replace the rim eggs, you could imagine a future when the robins were entirely dependent on humans for their survival. They’d effectively be living in a wild zoo. Consider the domesticated silkworm—the moth that provides us with silk. Five thousand years of coddled breeding at the hands of humans have left these insects unable to fly or feed themselves as adults.
Thankfully, “the black robin just narrowly escaped such a fate,” Massaro wrote.
The team stopped repositioning the eggs in 1990, once robin numbers had bounced back to more promising levels. Natural selection started doing its thing and the proportion of rim-laying females has fallen from 50 percent to around 10 percent. The allele is still around though, hiding from natural selection in the bodies of males, and waiting to pass to another generation.
The goal of conservation isn’t just to save a species temporarily, but to create a wild population that can sustain itself without our help. The black robin shows just how difficult this goal can be. The team saved the bird, but their practices threatened to leave it incapable of breeding on its own. That would have been no use: conservation programmes are laborious and expensive, and can’t go on forever.
As the team write, “Conservation planning has to overcome this fundamental dilemma of rapidly increasing the size of severely endangered populations to avoid immediate extinction but without simultaneously increasing the frequency of detrimental alleles that are already present in the population.”
PS: As per usual, the acknowledgements of the paper detailed what each of the authors did, by their initials. It says who performed the experiments, analysed the data, contributed materials and tools, and wrote the paper. And rather delightfully, it ends with: “Led the team that saved the black robin from extinction: DM.” Well done, Don Merton. Well done.
A few years ago, Stephen Trumble contacted the Santa Barbara Museum of Natural History and asked if they had some earwax from a blue whale.
In 2007, a large ship travelling off the coast of California collided with a male blue whale, ending its life at the tender age of 12. It was one of three similar strikes that year. The animal’s 21 metre carcass washed up on the beach, and scientists from the local museum examined and dissected it with machetes and excavators. They collected several tissues and organs, including a 25-centimetre tube of earwax.
Earplugs are common to blues and other large whales like fins and humpbacks. They are similar to the ones in your ears, although obviously much bigger. Each is an oily build-up of wax and fats that accumulates through the whale’s life. “It looks like a long candlestick that’s been beat up a bit,” says Sascha Usenko, Trumble’s colleague at Baylor University. “It’s not appealing-looking.”
A whale produces a lighter-coloured wax during the time of year when it’s feeding, and a dark-coloured version when it migrates. If you cut through the earplug, you can see these varieties as alternating light and dark bands. They’re like tree rings. And just like tree rings, you can use them to estimate a whale’s age. That’s why scientists often collect and store the wax from dead whales.
But Trumble and Usenko have shown that the wax can reveal much more. It also preserves a chemical biography of a whale’s life, from its birth to its untimely ship-inflicted death. It records some of the hormones that surged through its body and the pollutants that it absorbed.
The duo previously measured environmental contaminants in whale blubber, but they realised that the same chemicals also ought to build up in earwax, which is made of similar fatty substances. “It was really an ‘A-ha!’ moment,” says Usenko. To find fresh whale wax, they contacted Michelle Berman-Kowalewskic from the Santa Barbara Museum of Natural History, who handed over the earplug from the dead blue whale they had dissected in 2007.
The plug showed that the whale’s testosterone levels rose during its first three years of life, fell until it was nine, and then shot up by around 200 times. That’s almost certainly the point when it became sexually mature. When other scientists have tried to work out this age using body length, ovaries or blubber, they’ve come up with estimates ranging from 5 to 15 years. “We didn’t really know,” says Udenko. “Now, we’ve nailed that down with tight resolution for one animal, and it’ll be really exciting to do a bunch more.”
Meanwhile, the whale’s levels of cortisol—a stress-related hormone— rose steadily over the course of its life and peaked a year after its testosterone spike. This might reflect the need to compete for mates, or to interact with other mature whales. “I think about what I was like at that age,” says Udenko. “A raging bull, trying to figure out my place in the social order… I was pretty stressed out.”
In the earplug, the team also found traces of several contaminants. There were 16 pesticides, flame retardants and other pollutants that tend to persist in the environment for a long time, such as the long-banned insecticide DDT. These were most concentrated during the first six months of the whale’s life, suggesting that they were inherited from its mother, either through the womb or from her milk.
There was also a fair amount of mercury, which gradually accumulated over the whale’s life and peaked twice, once when it was five years old and again when it was ten. Human industries like gold-mining can release large amounts of mercury into the oceans. Perhaps this whale was caught in a few such surges during its travels past California.
The chemical contents of the whale’s blubber matched those within its wax, which assured Trumble and Usenko that their readings were accurate. But blubber has no rings, so it can only give you an overall picture of the whales’ life. Earwax can tell you what happened every six months. Blubber gives the sum of the whale’s chemical bill; the earplug shows the individual lines.
“I was surprised at how well [the technique] worked, not only for persistent chemicals but for hormones that typically rapidly degrade,” says Usenko. “It allows us to ask more complex questions that are difficult to get at, like: What are the impacts of contaminants or stress on these animals?”
To get the same sorts of readings, Usenko says that he would need to follow a blue whale around for years, and take tissue sample from it every six months. “You couldn’t do it,” he says. “People have tried, but it’s difficult and you have to be committed for 30 years. Here, we can go to a lab and reconstruct the same effort in a month.”
But the earplugs have several limitations, says John Wise, a toxicologist at the University of Southern Maine who specialised on marine mammals. They only capture certain pollutants that accumulate in fat, they don’t tell us how those pollutants affect the animal’s health, and they can only be extracted from a dead whale. “Nevertheless, it’s a new and useful part of our whale conservation toolbox as we seek to better understand ocean pollution,” he says.
And, of course, the team have only looked at one earplug from one whale. Usenko acknowledges this, and says the study is meant to be a proof-of-principle. “We want to encourage museums to keep and collect these samples,” he says.
Existing earplugs should already provide a trove of data. The Smithsonian Institute alone has hundreds of plugs in its collection, many of which have been traced back to specific whales. They’re not in pristine condition, but they could be useful. Charles Potter, who manages the institute’s marine mammal collection and is a co-author on the paper, is now thinking about how to preserve these waxy treasures.
PS: In case anyone was wondering, it doesn’t seem that the earplugs prevent the whales from hearing. In fact, some scientists have suggested that the plugs might actually help to channel sound towards the eardrum.
And finally, this is a good chance to reprise my blue whale facts:
Blue whales are so big that each one can grow as large as a fully grown blue whale. That’s huge!
If you take all the blue whales in the world and put them on a giant weighing scale, you are on drugs.
A blue whale’s main artery is so big that a human could swim through it, but it’s generally not advised.
A blue whale’s heart is the size of a Volkswagen beetle, but its steering is rubbish.
If you take a blue whale’s intestines and lay them in a line, the whale will die. Also, what’s wrong with you, you sick bastard?
In southern India, near the Bandipur Reserve, a hungry Asian elephant walks towards a farm in search of food. This region has one of the densest populations of Asian elephants in the world. During the dry season, when food is sparse in the forest, they find the surrounding farmlands irresistible. Conflict between farmers and crop-raiding elephants is a huge problem here. It costs some people a third of their income and, every year, it claims the lives of 400 humans and 100 elephants.
But this particular elephant doesn’t get close enough to farmland to cause a problem. Tripping an infrared beam that’s laid across the path, it triggers a nearby speaker. A low growl emerges, deep and loud. It’s the sound of a tiger, and the elephant knows it. Silently, it retreats.
The recorded growls were set up by Vivek Thuppil and Richard Coss from the University of California, Davis, who have been testing them as ways of diverting elephants from Indian farms. “We’d heard anecdotal reports that elephants are scared of tigers, and that farmers had used playbacks of growls to deter elephants from their fields,” says Thuppil.
They began by recording the growls of a leopard and a tiger at the Bannerghatta Zoological Park. In their paper, they write:
“To engender growling, both cats were agitated similarly when the keeper entered their cages and banged a stick repeatedly. We did not repeat this procedure with other individuals owing to the potential danger involved.”
You don’t say.
The two cats sound very different. Even when equalised, the tiger’s growl is deeper and feels louder, while the leopard is raspier and guttural. “Every human we’ve spoken to says the leopard growl sounds scarier,” says Thuppil.
The elephants clearly think otherwise. When Thuppil and Coss played tiger growls from their hidden speakers, elephants immediately backed away, slowly and quietly.
If they played leopard growls, they trumpeted and grunted, investigated the surrounding area, searched for sounds and smells, and kicked the dirt. Only then did they walk away.
Their reactions are prudent. Tigers are the greater threat, since they’ll occasionally kill elephant calves. Farmers find the body of a half-eaten calf at least once or twice a year, and scientists have found elephant remains in tiger droppings. But leopards are smaller and less powerful and there are no reports anywhere of them killing elephants.
However, the elephants might not be weighing any risks. Thuppil says that tigers will actually growl to deter an approaching elephant, while leopards would just retreat. Their agitated behaviour upon hearing the leopard growl might just be a reaction to something new. Still, they can clearly distinguish between the two types of sounds.
It’s not the most surprising result, given other studies about elephant behaviour. African elephants, especially the older matriarchs, can distinguish the sound of male lions, which pose the greatest threat to their herds. They can also smell the difference between clothes worn by Massai hunters who kill elephants, and Kamba cattle-herders who do not. Clearly, these are intelligent animals that can react in sophisticated ways to different degrees of danger. Still, no one had shown that they can tell the difference between the sounds of two big cats.
The growl playbacks worked to a point, but they weren’t a sustainable solution. “If you have elephants that come back repeatedly, they tend to habituate,” says Thuppil. “They learn that there’s no real threat.” He and Goss are now trying to adapt the playbacks to stop the elephants from getting accustomed to them. “One idea is to have a dynamic playback system, so the location of the sound keeps changing depending on where the elephant is. That would simulate a moving predator rather than a stationary one.”
Some people try to deter crop-raiding elephants by digging deep elephant-proof trenches, but rain can often transform these into gentle-sloping dips. Electric fences are commonly used, but elephants can destroy these with their tusks or by pushing trees onto the fences. Some farmers sit in tree platforms and harass the elephants with drums, shouts, torches, flashlights, or fireworks, but the agitated animals can sometimes run amok.
The imperfect nature of these solutions has prompted conservationists to search for alternatives. In Africa, Lucy King from the charity Save the Elephants has been using beehive fences to deter the giants. African elephants might stand up to lions, but bees can sting them in their eyes, behind their ears and inside their trunks. If they hear buzzing, they will flee. As a bonus, the fences also provide local people with a source of income: Elephant-Friendly Honey. You can find out more about King’s project here.
Thuppil & Coss. 2012. Using Threatening Sounds as a Conservation Tool: Evolutionary Bases for Managing Human–Elephant Conflict in India. Journal of International Wildlife Law and Policy http://dx.doi.org/10.1080/13880292.2012.678794
The Cold War may be over but its fallout still remains. Thanks to nuclear explosions from these fearful decades, scientists can now work out if elephant tusks were illegally traded, or glean historical droughts from hippo teeth.
In the 1950s and 1960s, America and Russia repeatedly tested their new nuclear arsenals. The fallout from the explosions spread far and wide, blanketing the world in radioactive isotopes, such as carbon-14. This heavy form of carbon is normally a bit-player in the atmosphere, but levels rose so sharply during the Cold War that they created a noticeable spike—the bomb curve.
Some of the carbon-14 was converted into carbon dioxide and taken in by plants. Animals ate the plants and incorporated the carbon-14 into their hair, bones, teeth, and more. In other words, every animal that was around since the Cold War carries traces of its legacy within its body. This radiation is too weak to be harmful but strong enough to act as a timestamp. By measuring the carbon-14 in an animal’s remains and calibrating them against the bomb curve, we can work out when it lived and died.
Scientists have used bomb-curve dating to work out how often the human body makes new tissues, like neurons or heart muscle. Now, Kevin Uno from the University of Utah thinks the same technique can be used to foil poachers and study our wildlife.
Uno’s team analysed 29 samples of hair, horn, teeth, tusks and stems from different animals and plants, whose ages were all known. They used, for example, a discarded oryx horn collected in the field in 1972. They also used tusks from two elephants—Amina, an old female who died in Kenya in 2006, and Misha, who died in Salt Lake City’s Hogle Zoo in 2008.
By measuring the carbon-14 in these samples, and matching them against the bomb curve, Uno managed to estimate their age to within a year or so. Look at graph below, which plots the estimated ages against the actual ones—it’s a nigh-perfect match. The one exception is a blue monkey supposedly collected in the Congo in 1962. That can’t possibly be true. The carbon-14 in its hair is so low that the monkey must have died many years before it found its way into a museum and was tagged.
The technique should work for any date after 1955, when carbon-14 in the atmosphere really started to climb, and around 2030, when levels will fall back to pre-nuke levels. “I am still very amazed at how well it works,” says Uno. “We validated the method using a wide variety of tissues spanning the entire bomb-curve.” The success of the method means that researchers don’t have to be fussy. You can analyse virtually any bit of an elephant’s tusk and get the same age.
Uno think that bomb-curve dating has huge potential in conservation. Consider elephants. There are only around 400,000 African elephants and 50,000 Asian one left in the wild. Poaching is the main threat to their survival, and tens of thousands are killed every year to fuel the illegal trade in ivory. More than 46 tons of the stuff was seized in 2011, with even more expected in 2012. (Read National Geographic’s incredible investigation for more.)
This shouldn’t be happening. The Convention of International Trade of Endangered Species (CITES) banned the trade of ivory form Asian elephants in 1976, and from African elephants in 1989. But loopholes exist. For example, ivory can still be legally traded if it was imported into the US before the ban, allowing sellers to exchange freshly poached ivory by claiming that it’s old. Uno’s technique can help to test these claims by accurately dating a seized piece of ivory. “To my knowledge, it’s the first method that tells us when an elephant died,” he says.
His work complements that of Sam Wasser at the University of Washington. He uses DNA to work out where pieces of ivory came from, and identify Africa’s major poaching hotspots. “It would greatly help to know how recent ivory originated from an area as this helps us determine how recent a hotspot has been active,” he says. And if a seized shipment of ivory includes specimens of varying age, it might mean that people are smuggling ivory from government stockpiles back into the market. “We see great potential in combining our “when” and “where” methods to help address the poaching crisis,” says Uno.
“Ivory aging tools would be most useful for policing large ivory markets such as those in Chinatown in San Francisco, LA and Honolulu,” says Wasser. These sites are selling massive volumes of allegedly legal ivory. “We could randomly test these samples and close these shops down if they are breaking the law.”
The bomb-curve technique has other applications too. By measuring carbon-14 at different parts of hippo teeth and elephant tusks, Uno could work out how fast these tissues grew. And that could unlock a huge treasure trove of information about these animals, and their extinct relatives.
As a graduate student, Uno studied the chemical composition of fossil teeth. The levels of carbon revealed information about their owners’ diet, while the levels of oxygen show how much water there was in their environment. Uno could use these measurements to reconstruct how an animal’s menu and surroundings changed over time.
But over how much time? You can’t tell unless you know how quickly the teeth grow. All you have is a graph without an x-axis—a trend that floats freely in time. With the bomb-curve measurements, that all changes. By combining measurements of carbon-14 and other isotopes, Uno used teeth from two hippos, which died 11 years apart, to construct an 18-year timeline of environmental change in Kenya’s Tsavo National Park. He could even discern the presence of a severe drought in 1995, which forced the hippos to change their diet for years.
“Field observations of animals is expensive and time-consuming,” he says. “Hippos are active mostly at night, making observation impossible, and the habitat of forest elephants makes them hard to see any time of day. So these stable isotope records an efficient, cost effective alternative to that type of monitoring. Isotopes don’t lie.”
Reference: Uno, Quade, Fisher, Wittemyer, Douglas-Hamilton, Andanjeh, Omondi, Litoroh & Cerling. 2013. Bomb-curve radiocarbon measurement of recent biologic tissues and applications to wildlife forensics and stable isotope (paleo)ecology. PNAS http://dx.doi.org/10.1073/pnas.1302226110
It’s been an eventful 75 years for the Hula painted frog. Having clung to existence while its closest relatives embraced the cuddle of extinction, it was then discovered by scientists, lost for decades, declared extinct and turned into a symbol of a conservation crisis, before literally hopping back into the limelight. It’s the Frog That Lived, Then Died, Then Lived Again.
The Hula painted frog was discovered in March 1940, when Heinrich Mendelssohn and Heinz Steinitz spotted two beautiful individuals in the wetlands of Israel’s Hula Lake. They had distinctive dark bellies with white spots, and streaks of olive, black and rust on their backs. A third adult was found in 1955, and that was the last anyone saw of it for decades. Many searched; none succeeded. In the meantime, the wetlands of the Hula Valley had been drained to make way for encroaching farmlands.
With its habitat degraded and its presence undetected, things didn’t look good for the frog. In 1996, after four decades of failed searches, it became the first amphibian to be classified as extinct by the International Union for Conservation of Nature (IUCN). That, unfortunately, was an omen of things to come. We now know that frogs and other amphibians are among the most threatened of all animal groups. Around a third of them are classified as “threatened” and up to 165 species might already have gone extinct. Their habitats are disappearing. Pollution is killing them. A deadly fungus is wiping them out.
The picture is certainly bleak, but that might partly be because many amphibians live in inaccessible places and are hard to find. They were seen once, maybe twice, and then never again. Have they actually died out, or are there small populations clinging onto life? If it’s the latter, we could double our efforts to protect the survivors, or enrol them in breeding programmes. But first, we’d have to find them.
To that end, Conservation International launched the “Search for Lost Frogs” in 2010—a huge search for 100 species that hadn’t been seen for at least a decade. They only found four of their wishlist, such as the Rio Pascado stubfoot toad, re-discovered after a 15-year absence. These were small consolations for a project that otherwise failed. The world still needed hopeful stories.
Enter—or perhaps, re-enter—the Hula painted frog. Since the last individual was seen, the lake where the frogs lived had been turned into Israel’s first nature reserve. Protected against the devastating drainage project, it became a haven for migrating birds, rare plants, and fish. Yoram Malka, a range for the Israel Nature and Parks Authority, was convinced that the painted frog was still there. He had no evidence, just a gut feeling.
In 2010, Malka relayed his suspicions to Sarig Gafny, a river ecologist from the Ruppin Academic Center in Israel, who was studying invertebrates at the lake. “I told him: Until you get me a frog with a black belly and white spots, you don’t have it,” says Gafny. “He said: Give me a year and I’ll get you a specimen.”
Exactly one year later, in October 2011, Gafny returned to his office in the late afternoon to find 20 missed calls on his phone. It was Malka. Earlier that day, on a routine patrol, a Hula painted frog has just leapt out in front of him. “He told me: Sarig, we found it.” Gafny jumped into his car and drove to the reserve, armed with a copy of the original 1943 paper describing the frog. He checked off every physical feature against Malka’s specimen. It was indeed the right animal, in the not-extinct flesh.
The frog’s reappearance is doubly important because it turns out to be the last survivor of an otherwise extinct genus called Latonia. Back in the 1940s, Mendelssohn and Steinitz classified it as Discoglossus nigriventer, making it one of several Discoglossus painted frogs. “It was a reasonable classification because they didn’t have DNA sequencers or CT scanners as we have now,” says Gafny. But when his team analysed the DNA from their newly-found specimens, they found that the frog isn’t part of the Discoglossus group, and had split away from them around 32 million years ago.
So what was it? Rebecca Biton from the Hebrew University of Jerusalem had the answer. She had been studying the bones of fossil frogs found in Israel, and showed that many “Discoglossus” skeletons actually belonged to Latonia. She eventually worked with Gafny and placed the four dead Hula painted frogs in a CT scanner. Sure enough, their bones had the distinguishing marks of Latonia, corroborating the story that the DNA had crafted.
There are no other living Latonia species. The rest died out during the Pleistocene period, with the last one living to around 15,000 years ago. If the Hula painted frog—now Latonia nigriventer—had actually gone extinct in the 1950s, its entire genus would have disappeared too.
Gafny’s team have now found a total of 14 individuals. (Their new paper says 11 but they’ve found three more since, and one just in the last week!) One had been killed by a farmer (by accident) and three had been killed by kingfishers (probably not by accident). The rest were alive. And when news of the rediscovery broke in 2011, Gafny got an email from a tourist who had snapped a photo of a Hula painted frog two years earlier! “Our finding got so much media exposure that it reminded him of something, and he went back to his camera,” says Gafny.
“Rediscoveries like this are important in fostering interest in conservation and a generating sense of optimism,” says Robin Moore, who works for the IUCN and has visited the Hula Nature Reserve with Gafny. “We need flagships for conservation to generate a sense of optimism and this story is about as good as it gets. The frog became a symbol of extinction in Israel. It is even included in school curricula, and my taxi driver to Tel Aviv airport knew its story!”
But if the frog was there the whole time, why could no one find it? Because, Gafny thinks, they weren’t looking hard enough. That’s not a slight; the frogs have only been found around a single pond and they live among dense vegetation. “You have to crawl into this very dense canopy of blackberries, which aren’t very polite to you,” says Gafny. “Then you have to dig into the decaying vegetation. They usually sit covered by leaf litter.”
The more hopeful answer is that the frogs’ population is increasing. Gafny says that the water in the lake has become cleaner and more plentiful since the nature reserve was set up. He hopes that by continuing to protect this delicate ecosystem, he can give the frogs a fighting chance. He’s especially hopeful because the deadly chytrid fungus that is killing frogs all over the world has never been found in the region. “I’m looking for it just in case, but we have no record of it,” says Gafny.
“Habitat loss remains the biggest threat to the survival of amphibians around the world, and it’s important to be reminded that strategies to address it can work,” says Moore, “We need these positive stories amid the doom and gloom.”
Reference: Biton, Geffen, Vences, Cohen, Bailon, Rabinovich, Malka, Oron, Boistel, Brumfeld & Gafny. 2013. The rediscovered Hula painted frog is a living fossil. Nature Communications http://dx.doi.org/10.1038/ncomms2959
Drylands—areas that get little rain—cover around 40 percent of the Earth’s surface. They are already fragile places and a combination of drought, climate change, overgrazing, and unsustainable farming can finish off any plants precariously clinging to life there. Without roots to hold the soil together, wind and water erode the top layers, leaving only the infertile lower ones. In this way, more and more land transforms into barren desert with each passing year.
There are many possible ways of countering or preventing desertification but the Imperial team wanted to try something new. They added a set of genes to the gut microbe Escherichia coli that allow it to detect malate—a chemical released by plant roots. When placed in soil, the bacteria swim towards roots and gets taken up by the plant. Once inside, they use another second set of added genes to produce auxin, a hormone that stimulates the growth of roots. Longer roots mean more stable soil, which means less desertification.
Individually, the bacteria, genes and hormones are all found in nature. But it was the combination of these components that yielded a synthetic organism unlike anything seen before—a plant-tracking, root-making, soil-stabilising gut bug.
This project is just one example of synthetic biology, a growing field that brings engineering principles to the world of cells, genes and living things. It’s telling that the team described their creations in the lingo of engineers. They took genetic “parts” from a standardised registry, packaged them into different “modules” and shoved them into a bacterial “chassis”. Other scientists should be able to assemble the same parts in new combinations to do different jobs, just like Lego bricks.
It’s grander in scope than most genetic modification, which involves modestly changing a few genes. By contrast, synthetic biologists work with large networks of genes to produce yeast that can brew antimalarial drugs instead of beer or cells that self-destruct if they turn cancerous. In his new book Creation, Adam Rutherford compares the field to the hip-hop scene of the 1970s, where DJs would start to create new music by mixing existing beats, riffs and lyrics. “Synthetic biology is remixing,” he wrote. “The ethos of this emergent scene is one of unprecedented and unbridled creativity.”
Take the root-making bacteria. It was the second-place winner of the 2011 iGEM (International Genetically Engineered Machine)—a vibrant talent competition where teams of undergrads design and build new genetic machines to solve a problem, using an inventory of standard “parts”. They have 10 weeks—it’s basically a summer project. While many college students spend similar projects on achingly dull menial tasks, the iGEM competitors tinker with biology before they even enter a PhD programme.
Two households, both alike in dignity
Chris Schoene, now at Oxford University, was part of the Imperial iGEM team and described their work at a conference at Cambridge, UK, entitled “How will synthetic biology and conservation shape the future of nature?” The meeting aimed to bridge these fields, which rarely talk but definitely should. Many of the mooted applications for synthetic biology have the potential to affect the planet for good or ill, from yeast engineered to make fuels, to plants modified to use resources more efficiently, to sensors that detect and break down pollutants.
But while both camps are often looking at the same problems, their outlooks are so different that tensions inevitably emerge. As conference organiser Kent Redford from the Wildlife Conservation Society said, “Conservationists get more pessimistic when they drink, but synthetic biologists only get more optimistic.”
Synthetic biologists combine the brash hopefulness of people in a hot, growing field with the can-do attitudes of engineers. Like the iGEM competitors, they look for solutions and work backwards. But conservationists are facing huge and depressing challenges, and they’ve been burned by the unintended consequences of well-meaning solutions. Many hear “synthetic biology” and their minds race to creatures like cane toads and mongooses that were introduced to islands to deal with pests and ended up killing local wildlife instead. Or, as someone inevitably mentioned, Jurassic Park.
“It’s not like engineering a machine. If you make a really bad car, it won’t make itself,” said Steve Palumbi , an ecologist from Stanford University. If you make a mistake with a living thing, “you may be stuck with your ‘solution’ forever.”
Many of these concerns are longstanding ones, imported from debates over genetically modified organisms. Synthetic biology stands out if only for the complexity of its manipulations. Also, cheapening technology and the field’s free-spirited ethos mean that amateur “biohackers” now have the tools to run experiments in their garages or kitchens. As one delegate said, “There could be thousands of people making millions of invasive species.”
Adding known genes to well-studied microbes like E.coli, as the Imperial iGEM team did, is unlikely to have such dire consequences. But even then Paul Falkowski from Rutgers University noted that we have sequenced scores of microbial genomes, but still don’t know what 40 percent of the identified genes are doing. “We are monkeying with stuff we don’t really understand,” he says. “We say we’re going to invent a bug that will make a fuel and solve problems? It’s naive.”
Jim Haseloff, a synthetic biologist from the University of Cambridge who works on plants, understands the risks of introducing species into new environments (“I’m Australian!”). But he noted that possible harms are a given for any new technology. Focusing upon that ignores the fact that conservationists already face a dire uphill battle and need new solutions. “We’re living in an environment where we’re progressively eroding the natural environment—that’s the default,” he said. “Can we divert or deflect that harm?”
Peter Kareiva, chief scientist at the Nature Conservancy, adds that ecologists have learned from the lessons of the past. “Mongooses and Jurassic Park are old stories. Ecologists know not to release predators,” he says. By contrast, most modern invasive species are escapees from the pet and aquarium trade. Those are existing challenges that worry Kareiva more than any synthetic organisms might.
Still, risks exist, and Palumbi would be reassured if the synthetic biology community devoted as much creativity and cleverness into avoiding unintended consequences as it does into cool engineering fixes. “We want a culture where containment is as well-researched as creation,” he said.
Doing it right
Amid all the hype and hubris, the doom and gloom, Schoene’s root-making bacteria stood out as a tangible, grounded nexus for discussion. For starters, their goal seemed sensible. Jon Hoekstra from the World Wildlife Fund noted that the world has around 2 billion hectares of degraded land—an area the size of South America. Rehabilitating that land, either to create spaces where life can thrive or to grow crops that then don’t have to encroach on pristine spaces, is a goal that synthetic biology could realistically help with.
They were also wary of risks from the start and consulted extensively with biotech companies like Syngenta and environmental organisations like Greenpeace. Again and again, the same concern came up: Genes from the synthetic bugs might move into naturally occurring ones. Microbes, after all, can swap genes with tremendous ease, especially by exchanging mobile rings of DNA called plasmids.
So Schoene and his crew created a containment system called GeneGuard. They loaded their microbes with plasmids containing a toxin gene that kill the bacteria by making them literally split their sides. The only thing saving them is an antitoxin gene in the bacteria’s main genome. If the engineered bug passes its plasmid into a wild one, the recipient would make the toxin but not the anti-toxin, and self-destruct.
The team took steps to mitigate other risks. They chose to modify a gut bacterium rather than a more obvious soil-dweller like Bacillus subtilis because they didn’t want the engineered microbe to outcompete others in its environment. They consulted with ecologists who confirmed that the extra auxin wouldn’t cause problems if it leached into the soil, because it breaks down quickly outside a plant. They talked to the Berkeley Reafforestation Trust about how they might eventually piggyback off existing reforestation initiatives. And through panel discussions, they discussed whether the engineered bacteria could ever harm human health or hurt their plant partners.
“It’s a really nice example of not just solving a problem, but talking to people and finding out the issues that they’re concerned about,” said Keith Crandall, a geneticist from Brigham Young University. “That’s really the key— putting in safeguards that will satisfy the community.” The iGEM judges felt similarly, and specifically commended the team for being inclusive.
Plasters, panaceas and open doors
But the root-making bacteria also became a symbol for a different debate: Should synthetic biology play a role in conservation at all? Does it merely provide “sticking-plaster solutions” that seductively tackle some aspects of conservation problems, while distracting from more important issues. Desertification, for example, is largely caused by overgrazing. What will root-making bacteria do about that?
“The starting point of taking a tool and asking how it will solve a set of problems is putting the cart before the horse,” said Jim Thomas from The ETC group, a watchdog organisation looking at ecological aspects of new technologies. “Farmers already have other techniques to deal with desertification. The danger is that these inventive technological fixes might develop a halo as a way of dealing with the problem.”
“It would be hubristic to claim that the project was a panacea, but I didn’t hear anyone claim that,” countered Luke Alphey from the University of Oxford, who is developing genetically-modified mosquitoes to control dengue fever. “It would be equally hubristic to claim that these problems are so complex that no new technology could contribute to a solution.”
“It’s nowhere near perfect, and we haven’t been able to test it in a normal field, let alone in arid environments,” said Schoene. “It was a 10-week project.” Indeed, by the end of the competition, the team had tested the bacteria’s root-finding and auxin-making modules, but had not completed the GeneGuard. And since then, they have disbanded and started their own graduate programmes. The root-making bacteria are languishing in development limbo. Their legacy isn’t so much as a barricade for deserts, but as a symbol of tensions between a young hopeful discipline and an older weary one.
But they also show that tentative bridges are starting to form between the two communities. In 10 short weeks, the Imperial team focused on a relevant problem, carried out an incredible amount of engineering, took due heed of potential risks, and engaged with people from all sides. Perhaps, as one delegate suggested, if conservation biologists could take part in the next iGEM alongside synthetic biologists, they could infuse the competition and the discipline with their own values and priorities.
“You’re pushing against a huge open door, and I invite you to walk through,” said Paul Freemont, co-director of a synthetic biology centre at Imperial College London, to the assembled crowd. And with a smile: “And do please cheer up just a little bit.”
Last month I attended a TEDx symposium on the controversial prospect of “de-extinction.” All day long, I heard researchers of various stripes give their expert opinions on whether we can – and should – reinvent extinct species to add a new dimension to conservation. But there is another way to de-extinctify a species. Researchers Heiko Stuckas, Richard Gemel, and Uwe Fritz have just removed a turtle from the ever-growing list of extinct species by demonstrating that the reptile never existed in the first place.
Sometime between 1901 and 1906, the Natural History Museum in Vienna, Austria acquired a trio of turtle specimens from the Zoological Museum Hamburg. According to the labels, the reptiles had been collected by the German naturalist August Brauer a decade before, when Brauer sampled critters from the island of Mahé – part of the Seychelles island chain, situated nearly halfway between India and Madagascar. Strangely, though, the turtles closely resembled a species found hundreds of miles away on mainland Africa.
When the Viennese zoologist Friedrich Siebenrock had a look at the preserved reptiles in 1906, he was struck by how closely Brauer’s turtles resembled a turtle now known as Pelusios castaneus – a turtle found over a wide swath of western Africa. If the distance between the mainland and island turtles were not so great, Siebenrock commented in his description of the Mahé turtles, he’d be tempted to call them the same species. But there was no way the little turtles could have crawled all the way across Africa, nor somehow dispersed from habitat to habitat around the edge of the continent. The distance deemed that the two had to be different species.
Not everyone agreed with Siebenrock’s conclusion. For years afterward, different researchers often lumped Brauer’s turtles into the west African species or another island species on the basis of anatomy. That is, until 1983 when herpetologist R. Bour proposed that Brauer’s old specimens truly did represent a distinct species. Bour called the turtles Pelusios seychellensis, and it seemed that Brauer had collected some of the last ones. Several searches after 1983 tried, and failed, to find the turtles. In the span of a century, it seemed, Pelusios seychellensis had gone extinct – perhaps the only time on record that humans totally exterminated a species of freshwater turtle.
But Siebenrock’s hunch about the connection between the island and mainland turtles was more right than he knew. When Stuckas, Gemel, and Fritz sampled mitochondrial DNA from the museum specimen that bears the name Pelusios seychellensis and compared those genetic clues to those of other turtles, they found that the museum specimens fell within the range of variation for west African Pelusios castaneus individuals. The unique island species never actually existed. Somehow, researchers had misidentified Brauer’s specimens. But how could west African turtles have found their way to Mahé? According to Stuckas and colleagues, they didn’t.
There’s no evidence that Brauer’s turtles hauled themselves clear across Africa. Nor is there any indication that humans brought them there at some point in the past. All this confusion might simply be the result of poor labeling and miscommunication.
Brauer took the trip during which he was supposed to have collected the turtles between May 1895 to January 1896. But he didn’t immediately give his finds to a museum. Specimens from his private collection didn’t get transferred to the Zoological Museum Hamburg until five years after the Seychelles trip, and those turtles soon went on to Vienna’s Natural History Museum. Somewhere in all that shuffling, the west African turtles might have been lumped in with the Seychelles reptiles or otherwise confused. Whatever happened, though, a prominent clue indicates that the turtles were not collected from the wild. One, and possibly two, of the turtles have a perforation through their shells identical to the sort that turtle purveyors have traditionally used to tie turtles together until they are sold for food. Wherever Brauer got the turtles from, he seems to have purchased them.
This isn’t the first time bad bookkeeping has led zoologists to erroneously erect new species. Stuckas and coauthors point out two other instances – a mislabeled American snapping turtle was confused for what was thought to be a new species from New Guinea’s Fly River, and a supposed new tortoise found in Vietnam turned out to be “an escaped pet tortoise from Madagascar.” This is why well-kept locality data and responsible curation practices are essential. We need to know when, where, and how a specimen was collected to understand what we’re studying. (Paleontologists also know this well.) And that context is not only essential for exploring the diversity of life, but also conservation. In our efforts to assist imperiled species, we need to know whether or not we’re looking at something unique and critically endangered, a wayward member of a more common species, or whatever other alternative may be the case. Understanding even such a basic facet of ecology as the identity of a species requires a great deal of attention and care.
When life sticks you on an isolated island surrounded by shark-infested waters, make utterly badass weapons out of shark teeth.
This is what the people of the Pacific Gilbert Islands have been doing for centuries. Sharks are a central part of their lives. Many social customs and taboos revolve around the finer points of shark-hunting. Young boys go through initiation rites where they kneel on a beach, looking towards a rising sun and slice their hairlines open with shark teeth, letting the blood run into their eyes until sunset. And with no metal around, they used shark teeth to adorn their weapons.
A shark is a fast, electric-sensing torpedo, whose business end holds two conveyor belts of regenerating steak knives. To further weaponise its weapons is practically the definition of being badass. Here’s how to do it: You drill a tiny hole in each tooth, and bind them in long rows to a piece of wood, using braided coconut fibres and human hair. Depending on the shape of the wood, you can make a sword. Or a dagger. Or a trident. Or a four-metre-long lance. And then, presumably, you hit people really hard with them.
No one knows when the Gilbertese first fashioned these arms, but they were already doing so by the time the first Western sailors arrived on the islands in the late 18th century. Many of them ended up in museums and Chicago’s Field Museum of Natural History has a particularly rich collection. It includes 124 specimens, including swords, tridents and a lance that Joshua Drew from Columbia University describes as “2.5 interns tall”.
Drew saw this collection was more than just an amazing armoury. It was also a time capsule. Since every item was carefully tagged with date and place of collection, and since different shark species have distinctively shaped teeth, Drew could use the weapons to identify the sharks that swam round the Gilbert Islands in centuries past.
The teeth came from 8 different species. Tiger sharks feature heavily—their thick, cleaver-like teeth, which can punch through turtle shells, make for good cutting edges. Most of the weapons featured teeth from just one shark species, but several have a rare blue shark tooth in the penultimate position—possibly the signature of an artisan.
But the biggest surprise was that some of the teeth belonged to two species—the dusky and spottail sharks—which no longer exist near the Gilberts!
Back then, they were common enough that their teeth were among the most popular choices for weaponsmiths. Today, no one has seen them within several thousand kilometres of the islands. Even before scientists knew that they were there… they weren’t any more.
(Drew has also found teeth from a third missing species—the bignose shark—on a weapon held at the American Museum of Natural History.)
Could these teeth have been imported from neighbouring people? No, says Drew. The Gilbertese had a strong culture of shark-fishing and if they were already heavily catching sharks, why would they trade for teeth? Besides, there is no historical, linguistic or archaeological evidence that these people communicated with those who live in the areas where those missing sharks are now found.
Could it be that the three species still live near the Gilberts but that no one has seen them? Again, it’s unlikely. All three are quite common in the areas where they actually live, so it’s doubtful that biologists have simply missed them.
It’s not clear why the sharks disappeared. Humans may well have been responsible—people were hacking off shark fins in the Gilbert Islands as far back as 1910 and by the 1950s, around 3,000 kilograms of fins were being shipped from the islands ever year. For sharks, many of which grow and reproduce slowly, it doesn’t take long for finning operations to drive a population locally extinct.
Whatever the reason, the teeth are signs of what Drew describes as “shadow diversity”—fleeting ghosts of the vivid splendour that once existed in the same waters. “Today’s Gilbertese live in a fundamentally duller environment than their forefathers,” he says.
That’s an important reminder for conservationists. Both coral reefs and shark populations are under severe threat and scientists are working on ways of restoring them. But what state are we going to restore them to? “Nested within this story is a cautionary tale of… how what we see today is not necessary indicative of the past,” Drew writes. We must not succumb to a “cultural amnesia, where people forget how vibrant reefs really were. “
Note: I originally covered this research for Nature News when it was presented at the 2012 Ecological Society of America Annual Meeting in August, 2012. Here is the original piece.
Every species becomes extinct eventually. Some leave descendants that continue the evolutionary proliferation of life that kicked off on this planet over 3.5 billion years ago, but no parent species is immortal. Life on Earth is in continual flux, with new lineages emerging as others die back.
But what if we could resurrect lost species? And even if we developed the technology to do so, are such efforts wise during a time when the same attention and energy could be applied to preventing extant species from slipping away? This Friday, researchers are going to converge at the TEDX DeExtinction symposium, partnered with National Geographic, to discuss the possibilities and pitfalls of reviving species that have been lost over the past 12,000 years.
The woolly mammoth – the shaggy Ice Age icon that persisted until a scant 3,700 years ago – is probably the most charismatic “deextinction” candidate. For decades now, scientists have been considering how the lost proboscidean might be brought back through cloning, and we’re continually told that the necessary advances to accomplish the task are just around the corner. (Although, much like a Windows software release, the debut of woolly mammoth 2.0 has long been delayed. I’m not optimistic about estimates that we’re only four or five years away from squeeing over the photos of the first cloned baby mammoth.) But the woolly mammoth may be more of a symbolic conversation-starter that has obscured other Lazarus-wannabes, including the Tasmanian tiger, passenger pigeon, Steller’s sea cow, and the Xerces blue butterfly.
These candidate species, the “Revive & Restore” project says, were selected according to three sets of criteria. These requirements run the gamut from the squishy and snuggly – “Is the species missed?” – to matters of technological knowhow and whether the species is “rewildable.” What seems missing, or at least glossed over, are the ecological and ethical implications of reviving these lost species, and the focus on charismatic species has skewed attention towards animals that may not actually be good selections for resurrection.