Deep Discoveries

With Atlantis and Alvin, a scientist explores underwater frontiers, encountering marine life never before seen, sampled, or studied.

It is 7:53 a.m., and Peter Etnoyer '88, M.E.M '01 is just moments away from his first dive in the deep-sea submersible Alvin. The sun--long up but only partially piercing the thin morning fog--promises another brilliant day on the Gulf of Alaska. With only a light breeze and little swell, it is a peaceful morning. Sleepy scientists mill around the deck of the R/V Atlantis, talking in small groups over muted clanks as the Alvin team adds steel weight stacks to the base of the sub.

Near the starboard railing, Etnoyer is doing his Elvis impersonation, popping onto his toes and flashing a bright-eyed, dimpled smile. His dance routine is meant to show off the strength of the shiny white, steel-toed, Wrangler tennis shoes that gleam below his rolled-up, gray jeans. Steel-toed shoes are the only kind of footwear allowed on the fantail (rear work deck) of the Atlantis during Alvin operations. By the afternoon, Etnoyer's shoes would be scribbled over in brightly colored permanent marker, part of his initiation as a first-time diver that also involved buckets of icy water and assorted food products.

"Here we go, down to zee bot-tem. We are in search of zee beeg bamboo coh-ral," Etnoyer says in his best Pep? Le Pew imitation, brandishing a piece of bamboo coral skeleton that he is carrying for luck.

The ship's horn sounds--the cue for the divers to enter the Alvin. Etnoyer follows the pilot up the narrow metal staircase on the side of the massive hydraulic A-frame that will hoist the Alvin off the deck of the Atlantis. On the platform at the top of the stairs, Etnoyer removes his dancing shoes (socks only in the Alvin). He turns just before entering the sub, flashes his Hollywood smile at the collection of scientists and crew on the deck below, and intones in his best Arnold Schwarzenegger voice, "We'll be back!"

Etnoyer is one of four main scientists--principal investigators (P.I.'s)--awarded grants by the National Oceanic and Atmospheric Administration's Office of Ocean Exploration that enabled them to participate in a twenty-five-day research expedition aboard the research vessel Atlantis last summer. (Created in 2001, the Office of Ocean Exploration is the hub of NOAA's activities to explore and map the farthest reaches of the world's oceans.)

The Atlantis, the 274-foot floating home of the DSV Alvin (deep submergence vehicle)--best known for its role in the exploration of Titanic--is one of the premier vessels operated by the Woods Hole Oceanographic Institution. Etnoyer and the other scientists aboard the Atlantis are using the Alvin to study five unexplored seamounts--underwater volcanoes that are part of the Kodiak-Bowie Chain. This seamount chain stretches across a 400-mile section of the Northeast Pacific, from the Aleutian Trench off Kodiak Island to an area just west of the Queen Charlotte Islands. Some of the scientists on this mission are studying the origin and age of the seamounts while others, like Etnoyer, are concentrating on the deep-sea corals and other marine life that are found on the seamounts. I am aboard as the expedition's Web coordinator, documenting the mission through daily science logs, photographs, and video posted on the Web.

The largest seamounts in the Gulf of Alaska rise over 3,000 meters--almost two miles--above the sea floor and act as islands for marine life in an otherwise barren deep-sea desert. Despite freezing temperatures, a total lack of light, and low levels of dissolved oxygen in the water around them, many seamounts support veritable forests of deep-sea corals and sponges. Each of the coral colonies--the individual trees in the coral forests--are in turn home to an entire community of invertebrates, such as shrimp, sea stars, polychaete worms, and crabs. Today, diving to 450 meters on Dickins Seamount, Etnoyer hopes to find an abundance of bamboo corals.

In the lab later that afternoon, after he has recovered from his icy initiation and changed out of his sopping clothes, and after the scientists' excitement over the day's samples has subsided, Etnoyer and his assistant Aur?lie Shapiro M.E.M. '01 struggle to move a bamboo coral that is more than two-feet wide and dripping clear mucous. In her life as a landlubber, Shapiro works for NOAA in the Special Projects Office of the National Ocean Service, where she specializes in satellite mapping of shallow-water coral reefs and other marine habitats.

"Okay, grab your toothbrushes and start scrubbing!" Etnoyer is much more excited about the task at hand than Shapiro and Shinobu Okano, a NOAA student intern who is working with Shapiro as Etnoyer's second assistant. These two will have the pleasure of scrubbing the fleshy tissue and mucous (nicknamed ectoplasm after the goo in Ghostbusters, which had been screened in the Atlantis' movie lounge the night before) from the bamboo coral's calcareous skeleton.

When I join Shapiro and Okano outside on the deck twenty minutes later to document their work, both have abandoned their meager tools and are up to their elbows in brown coral goo. I watch from a safe distance as their efforts reveal the beautiful ivory skeletal structure of the coral. Bony calcareous segments, each a few inches long, are connected by dark, gorgonin disks--similar in composition to deer hooves--to create what appear to be the branches of an eerie skeleton tree. This specimen, Isadella n.sp, is the most ubiquitous genera of bamboo coral at shallow depths in the Gulf of Alaska.

Deep-sea bamboo corals are from the subclass Octocorallia, a collection of soft corals, sea fans, and other similar colonial animals that are distinguished by the eight feather-like (pinnate), nonretractile tentacles that surround the mouth of each polyp. Each individual coral colony (tree) comprises thousands of individual coral polyps; these polyps form the fleshy, living sheath that covers the bony coral skeleton.

Elongated polyps up to several inches long form a hula skirt around the base (trunk) of each bamboo coral colony. Underwater video from Alvin shows these "sweeper tentacles" billowing in the currents. Etnoyer says he suspects that these polyps may be packed with harpoon-like stinging cells called nematocysts, similar to those found in jelly fish.

Once Shapiro and Okano have cleaned the Isadella skeleton, it will be dried, photographed, and scrutinized in the lab. After the cruise, this and other prime specimens from the expedition will be shipped to the Smithsonian Institution, where Etnoyer has been studying deep-sea corals for the last two years.

At breakfast time, the Atlantis' mess is an intersection of smells: freshly baked muffins and eggs from the kitchen, sweat and grease from the engineers just coming off their shifts, the clean smell of Irish Spring from those who have started their day with the bars of soap that are standard issue in each cabin of the ship.

From my over-the-pancake vantage on one of our first mornings out of Seattle, Etnoyer and Shapiro strike me as poster children for a new school of applied marine science. Bright, creative, and keeping the rest of us at the table in stitches, this dynamic duo turns the old stereotype of nerdy, introverted scientists on its head. Etnoyer is a master of comical accents and facial expressions and has a charisma that he can turn on like a light. Fueled by fresh fruit, pancakes, and the excitement of a new adventure, he is in rare form this morning.

"Dohh... I just keep thinking of more things that I forgot. Tick, tick, tick," says Etnoyer, extending a finger for each forgotten item.

"Like what?" Shapiro asks, with a mouthful of eggs. She's already in the habit of late nights at the computer and last-minute breakfast appearances. This morning, she displays a prominent set of bed lines on her left cheek.

"Shampoo, for one. I guess it's Irrrish Sprrring for me," Etnoyer trills. His hair looks like he might have washed it with Irish Spring this morning, or not at all. The blond ponytail that I remember from our time together in graduate school is long gone; in its place is a mussy, almost spiky bed head. But it fits--with his black, polyester, Adidas warm-up pants, and his square, brown GQ glasses, it's easy to imagine Etnoyer as comfortable at some trendy caf? near his home in L.A. as he is on this ship. (He lost his glasses two days later over the starboard side of the ship. His comment: "Oh well, now I have eyes at the bottom of the sea.")

Coral close-up; Etnoyer examines coral samples in the cold room.

 Coral close-up: Etnoyer examines coral samples in the cold room. Photo:Jeffrey Pollack


The name "cold room" is misleading--it is absolutely freezing in here! The small metal room looks like a meat locker. It is empty, save for a large, white laboratory table and a few buckets of seawater, and there's a strange salty-sweet smell that I can't quite place. Etnoyer doesn't seem to notice the cold, even though he is wearing far fewer layers than I am. Before him on the table are a dissecting microscope and a half-dozen petri dishes with coral clippings of various shapes and colors. He cycles through the samples, placing one on the lighted platform under the scope just long enough to glance through the eyepieces and mutter something that is inaudible over the noisy refrigerator fan.

"Jeffrey Polyp," he sings out suddenly in a Yiddish accent, stepping back from the scope. "I can't get these things in focus." He is using a digital camera to photograph the magnified coral polyps and sclerites. Sclerites are spindly, crystal-like calcareous bones that are found inside the coral polyps and in the fleshy tissue (coenenchyme) between polyps. Sclerites of different shapes are given names like rods, clubs, needles, and thorn-stars, and while each species of deep-sea coral has a dozen or more different shapes of sclerites, all of the species within a given genus exhibit similar sclerites. Sclerite morphology--categorizing sclerite shape and size--is one of the key modes of description used to identify different coral species.

Traditional taxonomic classification of deep-sea corals is based on a combination of branching morphology (the branching pattern of the tree-like coral colony), polyp retractability, and sclerite morphology. Traditional taxonomy is now augmented by genetic analysis, but contemporary genetic advances have yet to eclipse the traditional methods.

"Back in the day, all of the scientists on a cruise like this would have amazing illustrators," Etnoyer tells me. "Art--sketching--was part of old biology curricula. Some of the best old-timers at the Smithsonian are the guys whose drawings our coral taxonomy is based on. That's why these pictures are so important." He readjusts the mini-halogen under the backlit petri dish.

"All those guys ever saw was dead, dried-up coral."

Scientific illustration may be a dying art, but there are new digital photography and videography techniques that, judging from Etnoyer's almost imperceptible adjustments of the microscope-mounted camera, require their own artistry. Many of the photographs that he has taken on this cruise are the first-ever photo documentation of live polyps for certain deep-sea coral species.

"For every coral sample that we send to the Smithsonian, we want to be able to send video taken from the Alvin's on-board cameras of that species alive, in situ," he says. "The museum exhibits of the future will be multi-media."

That's where Etnoyer's background--an unusual blend of arts and science--comes in. He majored in English as a Duke undergraduate. At the same time, he was one of the first participants in a certificate program in film and video. This early exposure was the beginning of a decade-long stint in the film industry. After five years doing camera work on feature films in California, he moved back to the Northeast, where he spent another five years directing commercials and music videos in Philadelphia and New York. As his success in the film industry grew, so did the disposable income that allowed him to go scuba diving. And the more Etnoyer went diving, the more his boyhood fascination with marine science was revived.

Etnoyer says he knew he wanted to integrate two very different disciplines, marine biology and physical oceanography, even before he enrolled in the Coastal Environmental Management program at the Nicholas School. "I started working on my master's project, studying larval dispersal in the Philippines and ocean circulation patterns in the Caribbean, the day I walked through the door."

During his first year at Duke, he worked with the U.S. Navy on its Layered Ocean Model, three-dimensional computer simulations of oceanic circulation. This was the first in a serendipitous string of experiences that would help him carve out a professional niche developing methods to visualize the ocean and the distribution of marine life within it. Etnoyer recently created a consulting firm, Aquanautix, in part to meet the demand for oceanic visualization products.

Etnoyer's adviser in the Nicholas School, Larry Crowder, helped steer him into a position with the Marine Conservation Biology Institute (MCBI). At MCBI, Etnoyer went to work on the "Baja to Bering" project, a product of the NAFTA Commission for Environmental Cooperation. Etnoyer and partners compiled vast amounts of marine-science data--including records of the distribution of deep-sea corals--to identify biodiversity hotspots that could be part of a chain of marine protected areas (think oceanic national parks) in the northeast Pacific Ocean.

In the summer of 2002, fellow Nicholas School alumnus Jeremy Potter M.E.M. '03, who had heard about his work with deep-sea corals, called Etnoyer from the Office of Ocean Exploration to offer him a berth on a research expedition to study seamounts and deep-sea corals. It was this first Gulf of Alaska expedition that allowed Etnoyer to capitalize on his Duke background in spatial analysis and his familiarity with video editing to create fly-throughs--animated, three-dimensional maps that take the viewer on a virtual roller-coaster ride through the terrain of the seamounts being studied.

After participating in the 2002 Gulf of Alaska expedition, Etnoyer received a series of subsequent grants from the Office of Ocean Exploration, including one to develop protocols for deep-sea coral collection and one that landed him a spot as a P.I. on this 2004 Gulf of Alaska exploration.

In planning for this mission, Etnoyer wanted someone with the skills to help him make fly-throughs and other visualization products accessible to the household viewers who would be tracking the expedition on the Web--part of his commitment to taking science out of the lab and using it to enrich the everyday lives of nonscientists. He had Shapiro in mind from the beginning.

Etnoyer leans on the lab table to Shapiro's right and squints at the computer screen in front of her. "That satellite data isn't bad, huh?"

Shapiro bobs her head to the drumbeat thumping from her computer speakers. "Dude, no one should be dissin' satellite data. When I use Landsat imagery like this to map coral reefs, it's accurate within fifty meters. When we overlay that satellite imagery with nautical charts from the northwest Hawaiian Islands, the satellite imagery gives us better shallow-water detail than the nautical charts."

Etnoyer seems impressed. I learn later that Landsat 7 is a U.S. satellite used to capture images of Earth's land and coastal regions.

Aurlie Shapiro exudes style, from the silver stud in her left nostril to her hand-knit, mustard-color winter hat. She is almost always wearing one of her funky home-made necklaces, which sell faster than she can make them in boutiques around Washington, and on her website, (a word play on the feeding apparatus--called the oral groove--of a single-celled organism called a paramecium). Whenever her shipboard tasks necessitate a work vest and hardhat, she always color-coordinates--even when she's working in the middle of the night.

Shapiro could have opted for a career in music (she's a classically trained cellist who now plays in a hip-hop band), but instead she went to the Nicholas School, where she and Etnoyer were classmates, to study landscape ecology--the study of the distribution patterns of ecosystems and communities and the processes that affect those patterns over time.

On this cruise, in addition to dominating at the Ping-Pong table (she attributes her prowess to a summer spent at a table-tennis camp near her grandmother's house in southern France), Shapiro's main focus is a high-resolution, sonar-based mapping technology called Multibeam. Sonar systems measure the time it takes for signals emitted from a transducer in the hull of the ship to reflect off features on the sea floor and bounce back to the ship. Traditional sonar devices generate a narrow line of soundings; Multibeam provides a swath of coverage by sending out multiple sonar beams in a fan-shaped pattern that is oriented perpendicular to the ship's track. With this technology, scientists aboard the Atlantis can map an entire seamount in less than a day of surveying.

Prep work:Pollack shoots Shapiro with sea star.

 Prep work: Pollack shoots Shapiro with sea star. Photo: George Schmahl


After making the post-dive exit from Alvin for the fourth and final time during the cruise, Etnoyer skirts the splash zone around his dive-partner's initiation rites and joins the other scientists who are waiting for the 35,000-pound sub to crawl along the twenty yards of metal tracks back to its hangar. Once the Alvin team has secured the sub, the scientists swarm the collection boxes on the front of the sub to retrieve the samples. Cameras flash, latex hands are everywhere; within minutes, the scientists and their assistants have looted all of the artifacts from the deep and have raced back to their workstations.

"Caught red-handed!" Etnoyer says, reaching into one of the white Plexiglas bioboxes, all of which are covered with dings and scratches that hint of a history of tight navigation on the seafloor and rough recoveries on the sea surface. He pulls out a puffy, butterscotch-colored, five-armed sea star and flips it over to reveal rows of squirming suction cups--tube feet--that are still clinging to two skinny stalks of bright white bamboo coral. I lean in for a closer look and notice that there are a few shards of pinkish tissue still clinging to the coral skeleton.

In the lab later that evening, I loom over Shapiro's shoulder as she positions the sea star on its back in a shallow plastic petri dish. The last inch of each of its five arms dangles over the side of the dish and doubles back, allowing its tube feet to attach loosely to the tabletop. I'm reminded of an old-time Western in which a dusty, oversized cowboy squeezes into a metal wash tub, his booted feet hanging over one end.

Shapiro uses a syringe to squirt fresh water into the sea star's oral disc, the round, toothed mouth in the middle of its underside. She is flushing the contents of its stomach into the dish. Etnoyer hopes that examination of the sample under the dissecting scope will reveal sclerites that match those isolated from what little coral tissue could be recovered from the sea star's suspected snack. "When we were here in 2002," Etnoyer tells me later, "we saw dead bamboo corals, and now we can confirm at least one reason why: predation by sea stars like the one we grabbed today."

I leave Shapiro to her work and move to an adjacent table to join two other scientists peering over the lip of the clear plastic cylinder at what looks to be an overgrown tadpole. The fish's appearance--a translucent body, dark, almost black, eyes and a big, cartoon mouth--seems to mock its own significance.

Etnoyer walks over and jostles for position around the fish. "Talk about a needle in a haystack! We got pictures of one of these guys on a bamboo coral on Warwick Seamount when we were here in 2002, but this is the first-ever collection of a Liparid from this region." Not surprisingly, the collection of the Liparid has created a buzz among those scientists trying to compare the animal communities on different seamounts.

"Finding two of those guys on the same species of coral in the same depth of water on two different seamounts really frames the issues of continuity between seamount communities," Etnoyer explains. Defining the creatures that make up seamount communities is the first step toward defining impacts to those communities from destructive activities, which is a priority for agencies like NOAA's Office of Habitat Conservation.

Liparids, commonly known as snail fish, are demersal, which means they hang out on or near the sea floor--a life strategy that is confirmed by their flat bellies. Over the ages, snail fish have evolved a modified pectoral fin that functions as a sucker to keep them anchored to whatever substrate they are resting or feeding upon. It works pretty well, too.

"You shoulda seen it. This thing was hanging on like you wouldn't believe. I didn't think our vacuum was going to be enough!" Etnoyer pantomimes the action of the sub's slurp gun, leaning back with feigned effort as he struggles to hold an imaginary slurp gun with two hands. The slurp gun is one of several collection apparatuses on the Alvin, including two, multi-jointed titanium arms that the pilot manipulates, like a puppeteer, from inside the sub.

After a few minutes, the scientists return to their tasks around the lab, and I follow Etnoyer back to his bamboo samples.

Seven hours spent sharing a six-foot by six-foot sphere with two other men has done nothing to dampen Etnoyer's enthusiasm about the day's dive, or about this mission as a whole.

"Did I tell you about the bioluminescence?

"We turned off the lights in the sub and shook one of the Isadella samples, and it glowed. Spooky green light running up and down the axis. It was unbelievable." It turns out the deep-sea light show he's describing was the first documentation of bioluminescence in this genus of bamboo coral.

His excitement grows. "Last expedition, we saw what we thought were isolated colonies of bamboo corals, but, based on the evenly spaced colonies we saw today, we're starting to think that those colonies actually make up big monotypic fields of coral--some bigger than a kilometer and a half!" The light field around the sub is only about thirty feet; if the corals are twenty-five feet apart or more, looking at a field of coral through the sub's four-inch portholes would be a lot like trying to explore a forest in the dark, one tree at a time, using only a flashlight.

"And take a look at this." He's in overdrive now. "It's a biomaterials dream come true! This calcareous holdfast isn't going anywhere." He rubs his finger across a flat white disc about the size of a silver dollar, where the bony, white aragonite of the bamboo coral seems to have melted down onto a rock.

"Completely dried out and still hanging tough." Etnoyer beams like a proud father.

"I'm going to send this to Germany. I know a guy at the Max Bergman Center of Biomaterials at the Technical University of Dresden who is gonna freak out! We're going to learn how to recreate this in the lab."

Aside from his all-around fascination with marine science, Etnoyer's passion springs from the realization that time is of the essence when it comes to studying deep-sea corals. In several regions of the world, destructive fishing practices level seamount coral habitats before scientists ever have a chance to study them, flattening--sometimes in a matter of months--entire coral communities that may take hundreds of years to recover. Etnoyer knows that no single scientist can do it all, and he takes every opportunity to build collaborations with other researchers. As we talk, he subdivides each bamboo coral specimen into a half-dozen samples that are destined for different labs around the globe.

The post-cruise party at the Portway Bar in Astoria, Oregon, was a rowdy affair. The P.I.'s were footing the tab, and the karaoke machine--normally reserved for Thursday and Friday nights--was humming. Etnoyer and I were next to each other at the bar, yelling over a Hank Williams Jr. sing-along. I had long since confessed my karaoke-phobia to Etnoyer when the DJ called Aur?lie, Jeff, and Peter to the front for an all-Duke performance. I clutched the bar and shook my head, making it clear that this night would not be the start of a burgeoning karaoke career. Etnoyer just flashed me his million-dollar smile, turned, and grooved his way toward the front of the crowd.

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