Issue 15.4: August/September 2012

Moorea's Ark

Story by Michael Shapiro

Photos by David Liittschwager





With 3:46 left to play, the Giants are down by three after clawing their way back from an eight-point deficit in the third quarter. From his own twelve-yard line, Eli Manning completes a miraculous thirty-eight-yard pass to Mario Manningham. For the first time in the game, the Giants have a real shot at beating the Patriots. The scientists and the deep divers, most of them Giants fans and several Hinanos into the game, leap from their seats to shout variations of “Allllriiight!” and “Yeeeeahhh!” in the otherwise empty bar at the Hilton Moorea Lagoon Resort. Probably every American on the small French Polynesian island of Moorea is sitting in this room; the Europeans and Tahitians have better things to do than waste an idyllic afternoon yelling at a screen. But apart from a Super Bowl, there’s probably nothing that could have pulled these guys away from the work they’re doing here. Casual observers might take them for a bunch of yahoos getting amped over a football game—which maybe they are—but they’re also explorers on a voyage of discovery, the modern equivalents of Charles Darwin and Captain Cook and James T. Kirk.


I’ve just arrived for the last seven days of that voyage: the Moorea Biocode Project, perhaps the most ambitious survey of its kind ever attempted. Its four-year mission: to seek out new life by cataloging every non-microbial thing living on and around the island of Moorea—every species of plant, animal and fungus that can be seen with the naked eye. To do it, teams of scientists from around the world have taken turns converging on the tiny Richard B. Gump South Pacific Research Station on the edge of Cook’s Bay. Each team specializes in one of seven domains: terrestrial vertebrates, terrestrial invertebrates, marine vertebrates, marine invertebrates, plants, fungi and marine algae. They’ve helicoptered to remote peaks and dived to the deep reefs; they’ve delved into caves and poked around people’s yards. By combining traditional collecting techniques with new genetic sequencing tools, Biocode aims to take a snapshot of an entire tropical ecosystem, something that’s never been tried—partly because no one thought it could be done.


“Maybe it can’t be done,” shrugs Smithsonian Institute biologist Chris Meyer while giving me an overview of the project during halftime. Meyer’s both Biocode’s overall project director and a member of the marine invertebrate team. “It’s a tremendously ambitious project, a huge challenge, unprecedented,” he says. “We vacillate between saying, ‘OK, we’ve got a handle on it’ and, ‘Oh crap, it’s overwhelming.’ But you don’t run from that; you take it head-on. Yeah, it’s ambitious, but you’ve gotta start somewhere.”


Moorea makes for an ideal somewhere because it’s isolated, it’s small, it’s diverse but not too diverse and there are two biological research stations already on the island. It had already been well surveyed before the Biocode scientists showed up, with about five thousand known species. (It’s also beautiful, which takes the edge off the drudgery of lab work.) And now, after forty-eight intense months and nearly fifty thousand samples collected, the pace isn’t slackening; it’s going to come down to the last play of the game. Work will continue until the last ferry leaves for Papeete next Sunday. Hundreds of species new to science have already been discovered, and odds are that even in these final hours, more will be found.


Over the next week I’ll be embedded with the marine invertebrate team led by Gustav Paulay, whom Meyer calls “the best marine invertebrate zoologist in the world right now.” Paulay’s team arguably has the biggest to-do list: Marine invertebrates account for some 60 percent of Moorea’s total biodiversity. Working alongside the marine inverts team are the deep divers— four crazy guys from Hawai‘i who use mixed gases and rebreathers to dive three hundred-plus feet down, where they’re finding on average twelve new species per hour.


Unlike journalists embedded with military units, who mainly watch the action and try not to die, I’ll be working on the front lines—diving, collecting, analyzing samples, going for Nutella and beer runs. Not many laypeople get to watch the world’s experts in their fields conducting top-flight science, much less join in. But all that starts tomorrow; for now it’s football, where the game’s come down to the last play. Tom Brady’s desperate Hail Mary pass is batted down. Giants win, the television  goes dark and the serene, glittering waters of Moorea beckon.






Biologist Chris Meyer
removes an ARMS--an
autonomous reef monitoring
structure--from the reef.
Meyer works to remove a piece of rebar drilled into the coral while a quartet of seven-foot lemon sharks cruise like phantoms at the edge of visibility. Two days ago those sharks chased the scientists off this site; today the sharks are placid, but nobody wants to spend more time down here than they have to. We’re out beyond Moorea’s fringing reef recovering three autonomous reef monitoring structures, or ARMS, which were placed about forty feet deep thirteen months earlier. “Autonomous reef monitoring structure” is a fancy name for a simple device: a stack of ten one-squarefoot PVC plates spaced about an inch apart. No moving parts, no complicated electronics and each one fits inside a milk crate. Bolt it to the sea floor, leave it for a while, then come back to see what sort of critters are growing on or hiding in it.


After more than a year of waiting, Meyer’s eager to get the ARMS back to the lab, where they’ll be pulled apart. The “big” stuff will be gingerly brushed into a tray to be sorted by hand. The rest—coral, tunicates, sponges, copepods and whatever else is stuck to the plates—will be scraped into an ordinary kitchen blender.


It’s a big moment in the lab when a member of Meyer’s team, a young French biologist named Matthieu Leray, finally hits the purée button. The resulting tawny, foul-smelling slurry contains the DNA of every living thing scraped from one of the ARMS. The ability to read that DNA en masse constitutes a quantum leap in this kind of science, a technique that makes something as unthinkably grandiose as Biocode not just thinkable but possible. If you analyzed a sample of something as complex as a coral reef by eye alone, you’d miss a lot—extremely tiny things, things that look almost identical, things hiding deep in crevices, things living inside of other things. But if you took that sample, blended it up and “barcoded” it, i.e., sequenced the DNA in the sample, you’d get everything. Suddenly the tree of life would have thousands of leaves you didn’t see before. Until recently it was prohibitively laborious and expensive to barcode large quantities of DNA. Now, thanks to advances in both technology and techniques —some of them pioneered by Biocode scientists —you can blend up a reef smoothie and sequence away till the cows come home.


Biocode represents the first attempt to apply barcoding to the study of ecology. “We’re not looking for a genome,” says Meyer, referring to the term for a single organism’s DNA, “but an ecome,” a new coinage for the total genetic signature of an ecosystem. That quixotic dream is what inspired Neil Davies, the executive director of the Gump Research Station, to float the idea to Craig Venter’s research team. Venter is famous for his work on the Human Genome Project, the first attempt to sequence human DNA completely. In 2004 Venter’s yacht was in Moorea as part of a global effort to document the biodiversity of ocean microbes, and Davies had come aboard. Davies was regarding the rainforest carpeting the improbable spires rising behind Cook’s Bay when the idea struck: “You know, we could sequence the island of Moorea,” Davies said, to the general amusement of everyone who heard him. “No,” he insisted. “We should sequence an island. Wouldn’t that be cool?”


The Gordon and Betty Moore Foundation, which funds conservation efforts and scientific research throughout the world, thought it would be cool—cool enough to grant $5.3 million to the attempt. Eight years later, in a lab reeking of formalin and brine, Leray hefts the crowning achievement of that four-year scavenger hunt like a pitcher of margaritas. “Salut!” he toasts.






cowrie (Cypraea poraria)

Two things that are simultaneously tedious and exciting: The first is counting a large sum of your own money. The second is science. I’m in the lab sorting through a tray full of live invertebrates—the aforementioned “big” stuff that came off the ARMS recovered yesterday. Big is all relative, though. “How does it feel to hold a thousand species in your hands?” Leray had asked as he passed the tray to me. I realized then that I was one of only a few human beings to have held that many species at once. No pressure, though.


Now I’m three hours into picking through the sample, and a thousand, it turns out, might have been lowball. Just when I think I’ve trapped the last minuscule snail between my tweezers, I find something else. What looks like a grain of sand starts crawling, or a transparent shrimp the size of a dust mote becomes visible. My job is to sort the creatures into plastic cups according to their morphology—that is, what they look like. A cup for squat lobsters, a cup for scallops, a cup for cone snails. I do my best, but I’ve undoubtedly lumped disparate species together. Even so, there are already two hundred cups on the table and counting. It’s like staring at a fractal image—the more you look, the more you see; increase the magnification, and a new level of complexity opens up.


Finding physical specimens is a necessary complement to the DNA barcoding. Genetic information doesn’t tell you much, says Meyer, only what something roughly is (crab, snail, urchin) and that it’s there. Nothing else. “You don’t know if it’s a juvenile or adult, what it’s eating, what’s eating it.” Meyer, when trying to explain Biocode to the uninitiated, often resorts to car metaphors. “We know the license plates but we don’t see the cars. With barcoding we’ve found thousands of new plates.” To fill in the gaps, he says, “we need to find the cars.”


Easier said than done. Gathering animals requires sampling—collecting buckets of sand and coral rubble, dragging nets, diving to the deep reefs, placing ARMS in shark-infested waters. Meyer calls these as-yet-unseen cars “dark taxa,” akin to cosmic “dark matter”: We know almost nothing about dark taxa except that they exist. Yet just as this mysterious dark matter comprises most of the physical stuff of the universe, there are more unknown than there are known species. Our understanding of biodiversity, then, is not merely incomplete; it’s adolescent.


“These guys?” says Meyer, picking up one of the cups containing fifty or so hermit crabs not much larger than a period on the page you’re now reading. “Most of these are new.”


New? All these little buggers I’m pulling out?”


“We’re up to seventeen new hermit crabs in the project. They’re the most common things in our devices, yet only one is described. Unregistered cars!” he shrugs. “Lots of unregistered cars out there.”







Everyone’s exhausted. New trays of creatures and buckets of coral rubble keep flowing in. The scientists are wilting over their scopes, but they’re buoyed by slow and steady elation: Every hour or so someone says something along the lines of, “Huh, that’s new.”


“Ain’t science a blast?” I ask Gustav Paulay, who looks pretty much like you’d expect a guy who’s been glued to a microscope for the past three days to look. A dozen Petri dishes full of wriggling things the diving team vacuumed off the reef earlier that morning await his inspection.


“Of course it is!” he says, impervious to my sarcasm. “Why do you think we’re doing it? I love this stuff. Every day we’re finding twenty to thirty new things. It’s like a treasure hunt.”


“Anything really cool?”


“They’re all really cool!” he replies, half joking and maybe half offended.


“Anything really, really cool?”


“We got a facetotectan, a crustacean known only from its larvae. We don’t know what the adults are. They’re almost certainly parasitic, but we don’t know who the hosts are.” Before him on the table are other oddities: an “echinoderm vampire”— a snail that sucks the blood of urchins and starfish—as well as a new sea fan from the deep reef and what’s probably a new polychaete worm with helical markings down its back.


For Meyer, though, nothing beats the Cypraea bernardi, a cowrie the deep divers brought back. It’s not new but it is incredibly rare. “I’ve been studying cowries for twenty years, and I’ve never seen one alive,” he says. “It’s so rare that we know of one that showed up in 1983 on Tahiti after a cyclone. It’s a big find. Gigantic.”


Then there are the really strange things, like the worm that has Paulay flummoxed. “It looks like a whale except it’s only 100 microns long. It has this big fluke at the end of its body. I’m looking at it, and I’m like, ‘What the hell is this thing?’”


“There’s lots of other cool stuff we find, rare sea urchins and things,” says Meyer. “And it’s not all in weird, remote habitats. Some of it’s right in front of you. You’ve just got to look.” He gestures toward François Michonneau, a PhD student who’s photographing under a microscope every creature that comes through the lab. He’s trying to focus down on a pudgy, sausage-like thing that’s the discovery du jour: a new species of sea cucumber collected a few feet off one of Moorea’s most popular beaches.


“We weren’t expecting that,” says Michonneau, who happens to specialize in sea cucumbers.


“Jeez,” I reply. “You’ve only got three days left, and you’re pulling new species off a public beach?”


“I know,” he shrugs. “Scary.”






peppermint angelfish (Centropyge boylei)

“When I identify you in my story on Biocode,” I say, “is it safe to call you the foremost copepod expert in the United States?”


“Sure,” laughs Jeffrey Cordell, “but there aren’t many of us. It’s a small club. The kids today just aren’t that interested in copepods.”


Copepods are tiny crustaceans—less than a millimeter long—but they’re one of the most important organisms in the ocean because a lot of things eat them. They live wherever there’s water, Cordell says, “in the deepest trenches, inside of other invertebrates, near thermal vents where the water’s so hot you can’t touch it. Studying them is like going to another planet, because they’re so small nobody sees them. But put a microscope to some water and suddenly you’ve got this alien world looking back, all these bizarre colors and forms. They’re super-cool animals.”


Copepods constitute a large enough number of unregistered cars that Paulay brought in the big guns. A research scientist at the University of Washington, Cordell has come for the last two weeks of the project to deal with copepods. He’s spent fourteen-hour days in the lab. The result? Over two hundred new species and counting.


“It’s exciting,” he says. “Pretty much everything I’m looking at is newly discovered. I didn’t come expecting anything in particular, but two hundred new species? That’s a lot. The stuff I’m collecting is going to be a gold mine for someone in a museum somewhere.”






flame angelfish (Centropyge loricula)

Most people who know what Richard Pyle does think he’s nuts. Pyle, a zoologist at Bishop Museum in Honolulu, leads the deep diving team; its members have been spending six to eight hours a day underwater and hitting depths over three hundred feet. The other members of the team are John Earle, a retired Hawaiian Airlines pilot; Dave Pence, a mixed gas instructor at the University of Hawai‘i; and newcomer Rob Whitton, who just a couple of days ago spent a night in a hyperbaric chamber in Papeete as a precaution after coming up from a dive with shoulder pain—a possible symptom of the bends. Everyone on the team except Earle has been bent—some badly. Pyle himself was nearly paralyzed from the bends when he was 19. Now he routinely hunts fish in the so-called “twilight zone” of the reefs, where the light begins to fail and very little is known about the inhabitants. Some might call that crazy, but Pyle prefers to be called brave because, he points out, he’s risking his life in the spirit of exploration. The deep diving team’s come back with both rare and new invertebrates, like Meyer’s coveted cowrie. But since Wednesday they’ve had their eye on a vertebrate prize: Centropyge boylei, the peppermint angelfish.


“It’s the most spectacular of angelfishes,” says Pyle. “So-bright-red-you-can-barely- look-at-it bright red. And the brightest white stripes you can imagine against them. Fantastic.”


“Looks like it should be hanging from a Christmas tree,” adds Earle. “It’s not been found in the Society Islands before. It’s known only from Rarotonga in the Cook Islands.”


It was in fact Pyle who first described that fish in Rarotonga in 1992. Until the deep divers spotted one at 350 feet on Wednesday, it was thought to be endemic to the Cook Islands, occurring nowhere else in the world. Today Pyle is out to catch one and dramatically expand the peppermint angelfish’s range. At 4 p.m. he does it. He had to drop down to 375 feet to succeed, but he’s returned with the boylei—along with a new species of damselfish—in a plastic container. It’s every bit as vibrant as advertised, and so far as anyone knows it is the only peppermint angelfish in captivity. Were it to be sold to a private aquarist, it would fetch as much as $20,000.


“Almost everything we see down on the deep reefs is new,” says Earle. “The reef is an ancient environment analogous to a tropical rainforest, but the percentage of unknown species is even higher than it is in the Amazon. That’s what’s exciting about it.”


But that excitement comes with risks. After the dive, Pyle comes up feeling “weird.” He’d pushed the limits a bit to get the boylei, so now he’s back in the water, breathing pure oxygen and submerging himself for as long as he can to stave off decompression sickness. “Diving at these depths …,” says Earle, watching Pyle from the dock, “it’s a dodgy thing.”


“New species or not,” I tell Pyle once he’s recovered, “I still think you’re crazy.”






squat lobster (Galathea)

“A toast,” says Meyer as he stands with a raised Hinano at the project’s wrap-up dinner. “The money’s run out, and we’ve therefore sequenced every species on the island. Congratulations, everyone! Mission accomplished.”


This sets off a round of laughter. Biocode hasn’t come anywhere close to bagging everything. “A complete failure!” says Paulay, again half joking. “We have to start over.” Meyer does some quick math: He figures Biocode will have logged around fifteen thousand species, triple the number they started with. They’ve more than doubled the numbers of known marine invertebrates, with about half the collected samples yet to be coded. And there have been happy surprises: “The numbers of species coming off the ARMS,” says Meyer, “has to be the biggest.” He’d expected around five hundred per ARMS; they each averaged fifteen hundred.


Still, Meyer estimates that the project has nailed down perhaps 50 to 75 percent of what’s out there. Paulay is similarly cautious—he figures there could be ten thousand species of marine invertebrates alone waiting to be discovered. The scientists, by their own admission, acknowledge that a fully comprehensive survey was an unlikely prospect to start with. So why do it?


“We’re marrying old-style expeditionary science with modern tools to capture Moorea’s genetic heritage and use it as a benchmark for diversity,” Meyer says. “And we’ve built this huge reference library that we can now use to answer questions we couldn’t have answered before about how ecosystems work. That’s the big innovation. But this is only the beginning. In science you stand on the shoulders of those who came before you. We’ve tried to build some tall shoulders here.”






hermit crab (Pylopaguropsis lemaitrei)

The day’s been a blur of packing, including bagging the three thousand or so specimens collected into oversize Pelican cases. Those will head to the Smithsonian where they’ll be kept for posterity. Except for the peppermint angelfish; it’s bound for the Waikiki Aquarium where, if it survives the journey, it will stay for as long as it lives.


Sitting on the ferry’s sundeck, I watch the jagged profile of Moorea recede into a pastel haze. I picture the island not as it appears, with its forests and mountains, but as a web of information—of genetic codes rippling over its surface like the rain of green glyphs in The Matrix. Everything expressed as data, every bit in communication, somehow, with every other bit. And the gaps—huge voids of information— where the dark taxa live.


“Do you think it’s ironic,” I ask Meyer, who’s lost in reflection beside me, “that in the midst of the seventh mass extinction event the Earth has experienced, you’re finding such an incredible abundance of new species?”


He laughs with what I can describe only as grim optimism.


“When the future regards us,” he says, “one of the questions they’re going to ask is, ‘How could they have let biodiversity go? They had the tools; it was right in front of them.’ We can say there were some people at least shining a light and saying, ‘Look, there’s this amazing amount of diversity.’ If we don’t lock it down now, if we lose genomes, if we lose the blueprints, they’re gone forever. There are tons of new species out there. Let’s take the time and find them. Let’s see if we can.”