When English explorers first ventured into the Gulf of Maine in the early seventeenth century, they found marine resources the likes of which they'd never seen. There were banks of codfish the size and weight of a grown man, rivers choked with shoe-sized oysters, and fifteen-pound lobsters lurking in the rockweed. Fishing off Cape Cod in 1602, Captain Bartholomew Gosnold's men reported being so "pestered" by codfish "that we were forced to throw numbers of them overboard again."

New England, as we know it, began in pursuit of the Gulf's bounty.By the time the Mayflower arrived in Plymouth, year-round fishing stations on the Maine coast had been thriving for at least a decade. When the pilgrims were starving in the spring of 1622, they traveled to Damariscove Island, off Boothbay, and begged food from the fishermen there. Cod was so vital to the economy of colonial Massachusetts that the Commonwealth officials displayed its image on coins, tax stamps, and the walls of both Boston city hall and the legislative assembly. By the nineteenth century, fishing was central to the economy, culture, and character of hundreds of Maine fishing towns and villages.

But as boats and fishing technology improved over the twentieth century, most of the Gulf's commercial fish populations were reduced to a shadow of their former selves, and some of the most important stocks simply collapsed. Between 1965 and 1999, New England's haddock catch fell by 95 percent, halibut by 92 percent, and cod by 40 percent, prompting managers to close many fishing grounds and impose ever-tightening limits on what, when, how, and for how long fishermen can do their work. The pain of those restrictions - combined with soaring waterfront real estate prices - is dismantling the economic foundations of Maine's fishing communities and with them much of the cultural legacy of the coast.

The destruction of these and other fisheries around the world has presented society with one of the greatest marine policy challenges in history: figuring out how to manage our activities on the ocean so that we don't do severe damage to biodiversity, critical habitats, and the overall function of the ecosystem. The approach is called "ecosystem-based management" and nobody knows how to do it yet. Even in the Gulf of Maine, a relatively well-studied body of water, scientists don't know what is there, what lives where, and how events in one part of the Gulf affect life somewhere else.

But for the past two years, dozens of scientists across New England and the Canadian Maritimes have been engaged in a new and unprecedented effort to gain enough knowledge about the Gulf to enable ecosystem-based management by 2010. The Gulf of Maine Census of Marine Life, supported by the Alfred P. Sloan Foundation, is one of seventeen marine censuses now under way worldwide, but the only one to focus on ecosystem-based management, meaning it is serving as a pilot project for the entire world.

"We need to know the big picture of how it happens," says Gerhard Pohle of the Huntsman Marine Science Centre in St. Andrews, New Brunswick, who is helping the census compile a comprehensive list of all the species found in the Gulf of Maine, including the Bay of Fundy, Georges Bank, and some deepwater seamounts out toward the edge of the continental shelf. "If we take one rivet out of the airplane, will it crash? If so, which rivet? Those are the sorts of questions we're struggling with."

It's also requiring an understanding of the past. Scientists have had only the haziest notion of what the Gulf of Maine was like before the advent of steam-powered trawlers, hydraulic winches, fish-finding sonar, onboard fish processing plants, and other twentieth-century industrial fishing technologies. That's starting to change, however, and the first glimpses of that world hint at an ecosystem of staggering diversity.

As part of the census, University of New Hampshire historian W. Jeffrey Bolster has been building a picture of Maine's inshore cod stocks, a fishery whose existence had been all but forgotten. In the 1860s, fishermen on these vessels were paid piecemeal, based on the number of fish they caught, so skippers kept detailed logbooks of how many fish each man caught, plus how much the overall catch weighed when they sold it to merchants. Hundreds of these logbooks have survived, allowing Bolster's team to reconstruct both the scale of the cod catch and the average size of the fish.

The results have stunned fisheries scientists. In 1861 alone the inshore fishermen of a single customs district encompassing Mount Desert Island and the Gouldsboro peninsula caught more fish than were caught in the entire Gulf of Maine between 1996 and 1999 by all the United States and Canadian fishing fleets put together. The ecosystem was so vibrant that a bunch of guys in small wooden sailboats, fishing with baited hooks within a few miles of shore, could outperform today's modern trawler fleets. Today, Bolster says, there are virtually no cod in the area.

"What our numbers indicate is that there was an ecosystem that was structured very differently from the one we have today, one in which there were colossal quantities of cod," says Bolster. "Ask yourself, 'what were they eating?' When you think about the copepods and krill, all the way up to the alewives and mackerel that had to be present in the inshore area to feed them, it's flabbergasting."

Bolster's team plans to extend the study to sturgeon, salmon, and alewives, but he says the big picture is already clear: humans have done far more damage to the Gulf than previously understood. "The world we have today was made by fisheries management," he says. "In terms of engineering desired outcomes, it's been a disaster story."

I'm following Tom Trott across the exposed seafloor at the foot of West Quoddy Head in Lubec, the easternmost point in the United States. The fog is so thick that the West Quoddy lighthouse has been reduced to a shadowy silhouette on the cliff above, its horn plaintively wailing every thirty seconds to ward ships off the ledges we're scampering over. A powerful wind is driving bands of fog in from the Bay of Fundy, covering every surface in a blanket of water droplets.

We clamber over boulders and ridges carpeted in a painter's palette of seaweeds until we reach the water's edge, several hundred yards from the high-tide mark. For intertidal scientists like Trott, who teaches at Boston's Suffolk University, the Passamaquoddy Bay region is akin to what the Amazon is to botanists. Its cold waters and powerful, twenty-two-foot tides have made it one of the most diverse and productive intertidal systems on the Atlantic seaboard, and one in which dozens of creatures usually found well below the low-tide mark can often be observed by simply taking a walk among the tide pools.

The first thing I notice are the periwinkles, which are two or three times bigger than they should be, a local phenomenon noted by nineteenth-century naturalists, and one that has made Down East Maine the center of the state's "wrinkle" fishery. Trott is turning over rocks to see what is living underneath. Amid the familiar green crabs, limpets, and barnacles, he points out little shiny yellow and red patches on the stone, which turn out to be a tiny sponge and an exceedingly flat flatworm, one filtering the seawater for specks of food, the other scouring algae off the stone. There's a full-grown starfish species no bigger than a dime and, flopping in the water, an eel-shaped fish called a rock gunnel displeased with our presence.

Soon, on the underside of the rockweed, we begin seeing little clusters of bright yellow rings clinging to the underside of the rockweed, each a few millimeters across and resembling a fluorescent Cheerio. It's the egg packet of one of two species of Arctic gastropods that, elsewhere in the world, are only found subtidally. "We're getting close," Trott says as another cloud of fog sweeps over us.

Then we find it, nestled to a rock among the holdfasts of Irish moss, the object of our quest: Margarites halcinius or pink topshell, an unassuming animal looking much like a periwinkle with a thin pink shell, but only a centimeter or two across. "This is the species I'm most concerned about," he says. "Twenty-five or thirty years ago, scientists found these everywhere. You still find them out here, but they've disappeared inside the bay."

Early the next morning Trott rows out to one of his study sites inside Cobscook Bay, a multi-chambered extension of the sea reaching ten miles into the eastern end of Maine between Eastport and Lubec. The bay's mirrored surface reflects upside-down images of the spruce-covered shores and the only sounds are the creaks of the dory's oarlocks. As the sun climbs higher in the sky, the veil of mist begins to lift, revealing the Birch Islands and their seaweed-covered underpinnings, exposed by the tide.

Trott starts at the very top of a ledge, where seagulls have created a boneyard of urchins, moonshells, and crab parts, then works his way down to the low-tide mark. He finds green crabs and periwinkles, translucent anemones and sea cucumbers with groping appendages, banks of mussels and armies of sea urchins. When we stand still, we can hear the tinkling, scraping, and popping sounds of green crabs and other creatures living beneath the rockweed. The topshells, however, are nowhere to be found.

Thirty years ago, scientists designated the Birch Islands and other study sites in the bay as critical invertebrate habitat under Maine's Critical Areas Program, largely because of the incredible abundance of the pink topshell and a related species, the striated topshell. As part of the census, Trott revisited these sites in recent years and, to his surprise, discovered that the topshells were practically nonexistent. He also found extensive mussel beds in places where they had not existed before, often covered in layers of sticky mud.

"The very character of these eco-systems has changed," he says. "It's as if you remade the soup, giving it a totally different flavor." He's pretty sure he knows why.

"Here," he says, pulling up a small scallop from six inches of water. The scallop is rapidly clicking its shell open and shut like a wind-up toy in a vain attempt to swim out of his hand. When it finally pauses, rows of eyes can be seen along its fleshy lips, a reminder that the scallop is much more sophisticated than a clam or mussel, a creature that swims through the water and peers out at the world with dozens of image-focusing eyes. "They drag for these right here."

It's hard to believe, standing in a few inches of water in this narrow arm of the bay, but at high tide, scallop draggers can fish right where we're standing, pulling a dredge through the mud and gravel to snare the tasty shellfish. Draggers and bottom trawlers have been shown to cause all sorts of collateral damage by tearing up seafloor habitat and killing lots of innocent bystanders, from juvenile fish to the invertebrates they eat. And Trott believes the sediments they stir up are changing life in the intertidal zone, pushing out species whose larvae settle on clean, rocky surfaces and replacing them with those that don't mind mud.

"Mussels don't care as much about sediment on the bottom, and they seem to be far more abundant in Cobscook," says Trott, who is from a fishing family and worked on his father's bottom trawler in his youth. "It's hard to say what this means for people, but it could be that we'll have a system that produces mussels instead of scallops." It's also a system that doesn't seem to be to the liking of topshells and a variety of other invertebrates that lived here in great numbers just a few decades ago.

Trott knows this raises all sorts of important questions. At what point did the system change? Was it more productive in the past, and could it change back if the stresses were removed? Is there something people can or should be doing about it? And why should we care?

It's these kinds of questions that scientists are confronting throughout the Gulf of Maine, a massive ecosystem whose living resources helped found and shape the culture, economy, and people of Maine and New England. For the past two years, a network of marine scientists have been working to try to fill in critical gaps in our understanding of the inner workings of this system, which includes Canada's Bay of Fundy and Georges Bank, whose shoal waters separate the Gulf from the open Atlantic. The hope is that this knowledge will help people hasten the recovery of a badly damaged ecosystem.

The tide having changed, Tom Trott clambers back into the dory and begins rowing back to the Edmunds shore, where Suffolk University has its field station. The channels between the islands are rapidly filling up, and in a few hours the seaweed-covered rocks we were walking on will be under twenty feet of water. Scientific investigation will have to wait until the next low tide, and there's a lot yet to be done. "To really understand a change, you have to track it over time," he says, as a bald eagle passes overhead searching for fish. "If you aren't doing that you can't tell what's normal from what isn't."

A few miles offshore Portland, the R/V Galatea is powering through a twenty mile-an-hour headwind and attendant whitecaps, her bow pointed toward a submerged mountain hiding beneath the horizon and 150 feet of seawater.

It's not a dangerous situation for the thirty-seven-foot research vessel, but it makes for an uncomfortable ride. The course is such that the boat has taken on a nauseating roll, forcing those prone to seasickness to stick close to the leeward rail. Spray covers the wheelhouse windows and flies along the starboard side in sheets thick enough to refract the early morning sunlight, a short-lived rainbow for every wave splattered against the hull. Looking astern, the twin goalposts of Cape Elizabeth's Two Lights hang on the horizon, eight miles away, the last bit of land to vanish behind Galatea's wake.

Scientific instruments are strapped to the deck or bolted to the rail, a variety of specialized sensors and sampling devices to taste, probe, and survey the currents, attributes, and occupants in the surrounding seawater. With them the six scientists on board have been piecing together what makes life tick on the offshore banks of the Gulf of Maine, where whales, dolphins, seabirds, and tuna suddenly gather for massive summer banquets and then vanish again a few days or weeks later. For two summers now, the census' chief scientist, Lewis Incze, of the University of Southern Maine, has been commuting to one of these banks, forty miles out to sea, to try to understand why.

"I think these offshore banks will turn out to have a very important role in maintaining biodiversity in the Gulf of Maine as a whole," Incze says, as an offshore bird called a gannet soars by the boat. "If we want to maintain that diversity, we need to know what goes on in the banks so we can figure out other things: how many banks do we need, and do we need to manage some or all of them in a particular way?"

Two and a half hours from Portland, skipper Mackie Green throttles down the diesel engine. An electronic chart plotter indicates that Platts Bank, a submerged two-peaked mountain of sand and gravel, is rising up beneath the Galatea. Green, a fisherman from Campobello Island, New Brunswick, leads whale rescue teams in his spare time and has a knack for spotting and tracking the big mammals, who like to frequent the banks. "We're here," he says.

At first, the ocean surface looks exactly the same as everywhere else we've been: dark blue sea, angry whitecaps, a handful of birds. But as the boat proceeds onto the bank, the air and sea are suddenly swarming with seagulls, terns, and storm-petrels. Seconds later, Green thrusts his finger out over the bow, where the backs of two whales can be seen arching toward the depths.

"Gentlemen," Incze says, smiling, his arms outstretched theatrically, "I give you Platts Bank."

When the bank is active, as it is now, it's not uncommon for the boat to be surrounded by whales, dolphins, or roiling swarms of herring sweeping through clouds of krill so thick that they turn the sea's surface red. Today the weather is too rough to see the krill and herring, but one or another of the sonar devices now hanging over the side has the ability to see them under the water. Another instrument can plot under-water currents in incredible detail, and it's this information that is helping Incze's team understand why marine life will suddenly congregate here and then, days or weeks later, leave with equal abruptness.

A little-known fact: in addition to the waves on the surface, there are also waves traveling under the sea, where the sun-warmed surface layer meets the cold water underneath. Incze has found that Platts Bank seems to be active when weather and tides cause these waves to run into the bank, throwing pulses of turbulence toward the surface. This oceanographic quirk sets off a chain of events that turns the surface of Platts Bank into a banquet table. The disturbances frighten little creatures like copepods and krill, causing them to flee toward the surface and crowd together there, making an ideal target for schools of herring and hungry humpback and fin whales, who rush to the area. Seabirds and dolphins join in to eat the herring, which stick around until the subsurface currents change, ending the disturbance and causing the copepods and krill to disperse.

"The whales seem to sense when these events are happening from a great distance, and may be able to sense the internal waves or hear the activity of the krill on the surface," says Incze. "They want to be right there, because the krill need to be concentrated for the whales to feed on them."

A discovery like this represents a piece in the larger ecological puzzle. Figuring out how the pieces fit together - and what it means for ecosystem-based management - is a daunting organizational exercise, one that requires being able to integrate huge quantities of disparate data.

At the Huntsman Marine Science Centre in St. Andrews, New Brunswick, Lou Van Guelpen and Gerhard Pohle have been piecing together a basic, but essential, set of data: a list of all the species found in the Gulf of Maine. The preliminary list, assembled from a century's worth of scientific books and papers, came to more than 3,300 species, 50 percent more than previously assumed. That figure is likely to grow, Van Guelpen says, because there are still large gaps to be filled in the data, particularly for the poorly studied deep basins of the Gulf and for certain categories of organisms like sponges and marine worms, which few people study. The list also needs careful editing: genetic analysis has shown that some very different looking animals are, in fact, the same species, or in other cases, individuals that look exactly the same turn out to be separate species.

It is no accident that the species list is being assembled at Huntsman, which houses a taxonomic center where many mysterious marine creatures are sent for identification. Van Guelpen shows me their library: a warehouse of mobile, floor-to-ceiling shelves, each packed with specimen jars. There are fish eggs and whole herring, sponges and blue mussels, and, in large metal boxes, adult cod and halibut, and even a five-foot long squid. New samples arrive by truck at the loading dock, where technicians sort and preserve them.

Making the species list accessible is almost as hard as compiling it. "A lot of museums haven't even gone to computer cataloging yet, and if they have, they're not readily compatible with one another," says Pohle, who is working to standardize these data sets so that they can be merged with one another and accessed as one integrated online reference tool.

It's not just species lists that need to be made accessible if ecosystem-based management is to get off the ground. The census is also creating a Dynamic Atlas of the Gulf of Maine, a sophisticated online Geographic Information System for the ocean itself. When completed, users will be able to build customized maps that integrate and overlay a vast array of data: commercial fish surveys conducted by United States and Canadian fisheries management agencies, sea surface temperature records, and phytoplankton concentrations collected by the buoys and satellites of the Gulf of Maine Ocean Observing System (GoMoos), high-resolution maps of the seafloor created by specialists at the universities of New Hampshire and New Brunswick, the movements of tagged humpback whales, or the year-to-year densities of lobster larvae found by scientists at the University of Southern Maine (USM) and Rockland's Island Institute.

It's a tool essential to helping scientists make sense of larger scale puzzles. "When we're finished, if somebody wants to understand, say, the northern shrimp, they can call on the Department of Marine Resources' database on shrimp landings, merge it with GoMoos measurements of temperature and salinity, and compare it from year to year," says USM's Evan Richert, the census' director. "It lets scientists do things with data that were never possible before." And that, Richert hopes, will help us all use the oceans more sustainably in the future.