At 3 p.m. on this dim, socked-in afternoon, the Nathaniel B. Palmer reached its rendezvous point—63.7658 degrees south, 56.8273 degrees west—an unremarkable patch of water littered with scraps of sea ice. Ten months earlier a treasure had been dropped into the sea at this spot and anchored to the muddy bottom, 2,112 feet below, by a lead weight. On this day Craig Smith, a marine ecologist from the University of Hawaii at Manoa, was returning on the Palmer to reclaim his treasure. His prospects looked grim.

Smith keyed a four-digit code into his console, and a sonar transponder draped off the edge of the ship pinged a message to the box of treasure nearly half a mile below. If all went well, the ping would awaken the high-tech box, prompting it to disengage a metal hook holding it to the seafloor. The dishwasher-size object would levitate from the mud, lifted by slabs of buoyant foam. Sonar bleeps would track its rise over a period of 20 minutes, until it bobbed to the surface and was retrieved. But 40 minutes after sending his signal, Smith still hadn't caught sight of his device.

Disappointment set in, and people speculated about the box's fate. Its metal hook had corroded. Its sonar receiver had died. Its floats had imploded under the ocean's 950-pound-per-square-inch pressure. “It could be hooked on a rock,” said Smith as he peered into his sonar console. Crew members who had gathered in anticipation drifted away. The ship ran maneuvers to triangulate and hopefully locate the box, wherever it might lie. If all else failed, scientists on board might search for the box with an unmanned submarine on the way home six weeks from now. No one thought to tell Ernest Stelly, third mate of the Palmer. He had continued his search from the top of the ice-lookout tower, eight levels of stairs and ladders above the main deck—the highest point on the ship.

Stelly, a six-foot, native of Beaumont, Texas, with a southern drawl, scanned the ocean through binoculars; his eyes came to rest on a red flag, barely perceptible, bobbing in the water 500 yards away.

Minutes later the object was snagged with a grapple hook and winched from the water. Puddles of black water drained from it as it sat on the rear deck. A sewer stench billowed into the air. The rotting whale bones strapped to the container, coated in mats of bacteria, glistened in blacks, browns, and whites.

These 14 assorted whale bones are Smith's sunken treasure. He had sterilized the bones before anchoring them to the bottom of the ocean last March. By studying the animals and bacteria that had grown on the bones during their time on the seafloor, he hopes to learn more about the largely untapped biodiversity of Antarctica's waters.

The sperm whale vertebra that Smith and David Honig (a graduate student from Duke University) lower into an aquarium is mottled with patches of black—a sign that the bacteria devouring its oils have resorted to anaerobic metabolism, churning out chemicals called sulfides (the same substances that give sewers and farts their bad smell). A large whale skeleton can live on for 70 years in this smoldering state of decay, all the while providing food to hungry mouths.

The floor of the deep sea is like a desert, with only small amounts of food filtering down from the life-filled waters above. When a whale carcass sinks, it becomes a nutritional oasis in the abysmal desert where it rests. That feast can become a hot spot of biodiversity.

Smith motions to the whale vertebra in the aquarium. It looks barren. “There are probably a hundred animals of many different kinds living on this bone,” he says.

Most of the worms and tiny crustaceans that live on it are no larger than a few 16ths of an inch and have withdrawn into burrows in the bone. Many of these animals would not exist if not for whale falls like this. Take the tiny bone-eating worms called osedax, which are slowly eroding this bone. A whale skeleton at its height of glory might give roof and comfort to 100,000 osedax. Collectively, those worms may pump out five million eggs a day. Those microscopic eggs and larvae drift freely in the sea. Most will starve or be eaten. A lucky one in a thousand may come to rest on another whale skeleton, where it will eat, mature, and continue the species.

Smith will work late into the night to pick each and every animal off the bones, so that they can be viewed under microscopes, DNA fingerprinted, and studied in a menagerie of other ways. By the time he retires to bed, he'll have been up for 24 hours. He'll sleep seven hours, then work another 24 straight to finish the job. On this research vessel in the Antarctic summer, the sun shines nearly 24 hours. The days are long. So is the work. —Douglas Fox

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