Puget Sound Journalism and Local Issues : Ross Anderson : RossInk

   In the spring of 1792, Captain George Vancouver and some 145 sea-weary crew members in two ships sailed around Cape Flattery and into the Strait of Juan de Fuca, searching for the “expansive Mediterranean ocean” rumored to exist in this largely uncharted corner of the Pacific.
   As they entered Puget Sound and surveyed the landscape, the stern and often crotchety Englishman sang its praises. “The surface of the sea was perfectly smooth,” he wrote in his journal. :”And the country before us exhibited everything that bounteous nature could be expected to draw into one point of view.”
   There was little time for poetry, however. Over the next six weeks, Vancouver and company sailed and rowed through much of this int4ricate inland sea, meticulously charting its length and breadth and depth, assigning names to its islands, channels and bays, and ultimately compiling the first map of Puget Sound. It was a remarkable achievement. Published in 1799, Vancouver’s charts of the Northwest coast quickly circulated throughout Europe, luring more sthips to this newly discovered land.
   Two centuries later, Puget Sound is home to 4 million people in a dozen cities from Bellingham to Olympia and Bremerton. Its waters are spanned by bridges, cables and super ferries.. Yet the map Vancouver started inking remains very much a work in progress. Much of the thousand miles of shoreline he sketched from his vessel, Discovery, has been reshaped or obliterated by everything from timbered bulkheads to world-class seaports. And only recently have scientists devised ways to peer beneath the surface, adding a third, all-important dimension to this map.
    Earlier this month, the University of Washington research ship Thompson set out on much the same voyage – from Admiralty Inlet, down Hood Canal and back out into the southern fjords, then north into the San Juans. For five days, some 20 oceanographers and students worked around the clock, probing the sound, carefully drawing water samples from its depths and rushing them into the on-board laboratory.
    It was, said oceanographer Mark Warner, the first time in 40 years that scientists have attempted a comprehensive assessment of Puget Sound in a single voyage. Their objective: To gather data on currents, water quality, temperatures and productivity at some 30 specific stations – data demanded by a powerful new UW computer program called the Puget Sound Regional Synthesis Model, or PRISM.
   UW researcher Jeff Richey, who heads the PRISM project, and his colleagues are today’s Vancouver’s, pushing the boundaries of scientific knowledge and compiling it into a dynamic, “virtual Puget Sound” available to researchers, teachers, planners and policy-makers.
   The oceanographers are not the only ones retracing Vancouver’s 200-year-old course. Today, The Seattle Times begins its own exploration of Puget Sound. We are a crew of two or three – this reporter and UW historian of science Keith Benson, joined from time to time by photographer Tom Reese – aboard Benson’s 32-foot sailboat, “Velella.”
   Over the month to come, we will retrace the voyage of the Discovery, and of the Thompson. Our mission is to re-explore a place that is both familiar and foreign. What Vancouver saw freshly, we will see through the eyes of scientists gradually learning some of Puget Sound’s secrets. Unlike our predecessor, we will not have to wait seven years to share our findings. With a laptop computer linked to a cellular phone, we will be able to bring readers with us, reporting what we learn as we learn it.
   First, a few basics: Puget Sound is an inland sea or estuary, of about 2,000 square miles, containing about 1 trillion cubic meters of water, give or take a few billion. It is an extremely complex body of water, due to factors such as its extreme depth (an average of 600 feet), its intricate shoreline, its fierce tides and currents, and its maze of fjord-like channels. It is both one ecosystem and a collection of ecosystems that may or may not be linked. The water itself is complicates – layers of salt water imported from the North Pacific and huge volumes of fresh water delivered by rivers such as the Nisqually, Skagit and Dosewallips.
    For these and other reasons, Puget Sound is also one of the world’s most productive inland seas. Its cloudy waters are an indication not of sickness, but of dense concentrations of marine life ranging from microscopic plants to orca whales.
    Yet, the Sound is also a troubled sea. Once-healthy populations of salmon, herring, rockfish and other species have dwindled. Something out there is not working right. Fifteen years ago, the region launched a concerted effort to preserve Puget Sound. Billions of dollars have been spent building sewage-treatment plants and addressing polluted bays. New laws have made it more difficult to build on the waterfront. Commercial and sports fishing have been cut back dramatically.
   There has been some payoff. Earlier this year, the state Puget Sound Water Quality Action Team reported that water quality has improved in most places. Previously closed shellfish beds have been reopened. But nobody believes the sound is fixed. The federal government recently warned that it intends to formally list Puget Sound Chinook salmon runs as endangered, potentially invoking restrictions on cities, businesses and homeowners from the shores of the Sound to the crest of the Cascades.
    And most people seem amazingly willing to swallow their medicine. Surveyed last month by pollster Stuart Elway, 74 percent of Puget Sound voters contacted said they were aware of the salmon problem. Four out of five agreed that salmon are an indicator of environmental health and that government should do what is necessary to save them – whatever ithe costs.
   So what now? Polls suggest that people blame some combination of pollution, sprawl, over-fishing, poor management, logging, dams, agriculture and El Nino. The rogue’s gallery of culprits may suggest confusion, but it also reflects reality. If science can provide any answers, we certainly are in the right place. Puget Sound is home to thousands of marine biologists and oceanographers working for dozens of institutions. Yet most scientists are deeply reluctant to assign blame or to prescribe solutions for the state of our waters. There are too many uncertainties. For all our efforts to understand, the sound remains an enormous black box. On one hand, its waters are transparent; yet they are also dark, apaque and seemingly impenetrable. Ten feet beneath the surface, light begins to dim; at 100 feet, it is virtually gone.
   Still, confronted by declining salmon runs, taxpayers long for simple diagnoses and simple solutions. Ban gill nets. Shoot sea lions. Tear down dams. End logging. Trouble is, instant analysis doesn’t work out there. The one thing we know about marine biology is that it is profoundly different from the biology in our back yard. Take reproduction: Most fish produce thousands, even millions of eggs and larvae during their lives. Those offspring are immediately left to fend for themselves, drifting in a fluid environment where most are eaten by larger fish – possibly Mom or Dad. Nature’s strategy is a massive smorgasbord that allows only one in a thousand to reach maturity and perpetuate the lineage.
   Scientists believe that a minute change in the environment – water temperature, currents or an upwelling of microscopic plankton thousands of miles away – can profoundly affect which creatures survive and which don’t Unraveling that web is a daunting challenge. Consider, for example, the perspectives of just two of the oceanographers who worked aboard the Thompson this month. Jan Newton, who works for the state Department of Ecology, studies diatoms –microscopic, single-celled plants that drift beneath the surface of the sea. To her, water samples crqwn from the depths of the Sound are pure gold, a micro-world that supports all other life in the sea. The rate at which diatoms provides critical clues to the health of the sound, she says.
   UW oceanographer Mitsuhiro Kawase sees the same ecosystem very differently. His view is global. As a computer modeler at Princeton, he studied oceans for 15 years without ever going to sea. At the UW, his focus has narrowed to Puget Sound as a marine system composed of tides and currents, deep water and shallow water, layers of salt water and fresh, seasonal fluctuations and more. Kawase studies the sound as displayed on a computer monitor. The same spaceshiplike gadget that collects Jan Newton’s water samples carries an array of instruments that measure water temperature, salinity and oxygen content at different depths and transmit that data directly into the computer.
   “The data provides an opportunity to test the model,” he says. “So far, it has done a pretty god job of predictions circulation, layering fresh water and salt water. But it is not perfect. We haven’t been able to factor for wind.” He steps across the room and calls up PRISM, clicking his mouse to take a simulated flight over a simulated sea, clicking again for an animated display of undulating arrows that show tide cycles in Admiralty Inlet or Tacoma Narrows. “It’s working pretty well so far,” he says. “Our main limitation is memory.”
   To most Sound dwellers, Puget Sound conjures up images of leaping salmon and killer whales. But these are only the marquee players in a vast cast that also includes untold trillions of microscopic plankton, millions of herring and unknown numbers of 10-foot, bottom-dwelling sharks we rarely, if ever, see. As the Elway poll shows, the collective will already exists to preserve our regional sea. But effective strategies must be based on the best science, the broadest data available. We need wisdom, but first we need more memory.
   This is our modest mission – to add a little more data to the collective memory. Before leaving the dock in Seattle, we equipped the good ship Velella with an odd cargo -- journals from Vancouver’s voyage, cardboard boxes jammed with inter view3 notes and biological studies of Puget Sound We have a laptop computer linked via cellphone to The Times newsroom. We have lightweight kayaks on deck, a hand-held GPS device and, for diving, a drysuit, mask and snorkel.
     Over the next few weeks, we will sail to Discovery Bay, where Vancouver began his exploration, then down the Kitsap Peninsula and to the soughern inlets, back north along the urbanized shores of Taoma and Seattle and finally into the San Juans. Along the way we will visit with scientists and others who endeavor to peer beneath the surface. We will visit the notorious toxic hot spots and a couple of environmental success stories, and try to explore some puzzling questions: What in the world are diatoms and why should we care? Why are salmon and other fin fish declining while oysters and crab and other shellfish seem to be doing very well, thank you? Why are harbor seal populations growing while their food supply dwindles? Are expensive sewage-treatment plants worth the expense?
    We have an itinerary, but no agenda. We sail with no intention of making rand discoveries or scientific breakthroughs. We have no interest in pointing fingers, nor in preaching ecological virtue. Instead our job is to take a fresh look at this grand inland sea through the eyes of both Vancouver, who explored these waters when they were supposedly undisturbed, and through the eyes of today’s scientists, Vancouver’s intellectual descendants, who are still trying to finish his map.

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     The world keeps passing this place by, riding the daily ebbs and floods, bound for somewhere else.  In the spring of 1792, Capt. George Vancouver stopped for just a couple of hours. He and a handpicked crew had packed a week's worth of supplies, left their ships anchored in Discovery Bay and set out in a boat no bigger than ours, determined to explore the foggy "inlet" that turned out to be Puget Sound. At Point Wilson, the northeast tip of Port Townsend, they beached the boat and stepped ashore, waiting for the "heavy vapour" to lift.
   "The shores here are sandy and pebbly," wrote Archibald Menzies, the Scottish botanist who traveled with Vancouver. "The point we came to was low and flat with some marshy ground behind it, and a pond of water surrounded with willows and tall bulrushes. Behind this a green bank stretched to the southward a little distance from the shore, which was marked with the beaten paths of deer and other animals. I ascended this bank and strolled over an extensive lawn, where solitude, rich pasture and rural prospects prevailed."
   Judging from their journals, the visitors were taken not just by the natural beauty of Puget Sound, but by its potential for exploitation. Menzies remarked on a land "where the plough might enter at once without the least obstruction and where the soil . . . appeared capable of yielding in this temperate climate luxuriant crops of European grains or of rearing herds of cattle . . ."
    Meanwhile, the crew set a small seine net, trying to catch some fish, but "without the least success." So they got back into their boat and rowed on south into the sound.
    Two centuries later, this windblown peninsula, with its green lawns and evergreens atop weathered bluffs, closely resembles what Menzies described. We stand on the same pebbly beach, gazing across Admiralty Inlet, Puget Sound's grand entryway, watching the world go by. Inbound is the Princess Marguerite with its load of tourists, and an ominous Trident submarine; outbound is a trio of purse seiners steaming toward the Alaska salmon grounds, and a massive grain freighter - all setting course to or from the Puget Sound seaports that Port Townsend once aspired to be but never became.
    But people here don't seem to care about this. They may raise a few cows, but Port Townsend's passion is the sea. Scores of businesses build or repair fishing boats, kayaks, traditional wood-hulled boats, sails or a thousand other things that link a terrestrial species to the inland sea that virtually surrounds them. At low tide on a Sunday afternoon, there must be 20 kids scattered across the tideflats, peering into pools and shouting for mom to come look. Others walk their dogs, sail along the waterfront or sit in folding chairs next to motor homes, drinking in the seascape.
    Down at the boat harbor, we berth the Velella near the Brendan D. II, the weathered, 48-foot vessel from which Jim Norris conducts his ongoing investigation of Puget Sound. "I wish I could tell you what's going on out there," he says wistfully, nodding toward the broad, shallow bay that is Port Townsend's front yard. "We know more than we did 10 years ago, but that's not saying much."
   Norris is not your usual scientist. He launched his career 25 years ago on the deck of a gill-net boat, chasing the elusive salmon. Ten years later, he returned to the University of Washington and fished his way to a Ph.D. in marine biology. Since then, he has refitted his boat to serve double duty as a floating platform to study Puget Sound's fisheries as well as to harvest them. Working with middle-school students and volunteers at the Port Townsend Marine Science Center, Norris helps the state monitor water quality, eelgrass growth, weather and wildlife in Port Townsend's bay. Last week, he conducted his annual "trawl survey," dragging a small trawlnet through the bay, one section at a time, then carefully documenting what it brought to the surface.
   After nearly a decade of surveys, "there doesn't seem to be any consistent pattern," he says. "Some species show a downward trend, but others are going up." He runs his finger down a computer printout listing yearly counts of Pacific tomcod, snake prickleback, walleye pollock, Pacific herring, sculpin and many more.
   Last month, he says, some Oregon biologists came to Port Townsend looking for signs of pollock, a cod-like fish whose numbers appear to have dwindled in Northwest waters. They found fewer than 50 - not good. Last week, trawling in the same bay, Norris caught 150 pollock - the second highest recorded by his surveys. The same nets brought up more young cod than all previous years combined, he says.
   "As a fisherman, nothing surprises me," he says. "We'll have great luck at a certain place year after year, so you go back the next year expecting it to happen again. And you come up empty."
Norris wonders if he isn't seeing evidence of what is called the decadal oscillation, an emerging theory that fish populations vary dramatically in long-term cycles that may be linked to ocean temperatures. A growing number of adherents believe that, for some 20 years, Mother Nature has favored fish in Alaskan waters over the Pacific Northwest, and that the oscillation, if it exists, is beginning to oscillate back in favor of Puget Sound.
   So goes the theory. Alas, the same scientists warn that the most predictable law of the sea is its unpredictability, the cycles and variables they still don't understand. Like the ocean at large, Puget Sound is simply not the homogenous monoculture many people think it is, Norris says. Its habitat and wildlife vary dramatically from year to year, place to place.
   Even Port Townsend's bay, only about five miles long, appears to be comprised of two ecosystems, he says. The northeast half is dominated by rock sole, Pacific sand dab, spotted rockfish; the southwest by pricklebacks, tomcod and herring. The apparent boundary is a riptide that runs north to south from the marina to Indian Island. East of that rip, Norris says, water temperatures drop by two degrees, a significant difference in the marine environment. Why the difference? Probably because the water in the southwest is relatively stable, while the northeast is in constant turmoil, agitated by the powerful currents of Admiralty Inlet.
   Sorting out Puget Sound's complex ecosystem will take many years, Norris says. Scientists need long-term data in order to recognize and begin to study its biological cycles. "We need a 100-year database," he says. "And in this bay, we only have 10 years."
   But if it is daunting, it need not be costly. Norris and the local marine-science center operate on a shoestring budget, using mostly volunteer assistants. Water-quality data is gathered by eighth-grade students from local schools. Norris' crew last week was comprised of schoolteachers taking a summer course. Still more volunteers conducted wildlife tours along the seashore.
   Port Townsend is not the only place where citizens have become invested in the health of Puget Sound. Communities from Skagit County to Hood Canal and South Puget Sound have demonstrated that there is a payoff in making marine science accessible to nonscientists.
   "You don't need a Ph.D. to read the meters, only to interpret them," he says. "I believe we're producing research-quality data at a fraction of the normal cost."
    Encouraged by those words of encouragement, we cast off our lines and point our sloop southward toward the foggy vapours of Puget Sound.

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    "The region . . . seemed nearly destitute of human beings. . . . The brute creation also had deserted the shores. The tracks of deer were no longer to be seen, nor was there an aquatic bird in the whole extent of the canal. Animated nature seemed nearly exhausted, and her awful silence was only now and then interrupted by the croaking of a raven or the scream of an eagle. Even these solitary sounds were so seldom heard that the rustling of the breeze . . . gave rise to ridiculous suspicions in our seamen of hearing rattlesnakes and other hideous monsters. . . ." Capt. George Vancouver, 1792 

     In the evening shadow of a forested ridge, we steer the sloop Velella into a bay near the Hood Canal floating bridge and drop our anchor, which instantly disappears into a green, unenticing soup. We can hear the rumble and groan of the nearby highway and the shouts of a group of teenagers at a rowdy beach party, complete with firecrackers. It will not be a quiet evening on Hood Canal.
   Safely anchored, I settle back with a glass of wine while Keith Benson, skipper and science consultant, talks about the disappearing anchor. Even a century ago, he says, scientists understood that water quality and water clarity are linked. To measure clarity, then and now, they lower a white disk about a size of a long-play phonograph record into the water and note the depth at which it becomes invisible. That link between clarity and quality is complicated, however, Benson warns.

    With this in mind I revisit my trusty copy of George Vancouver's journal. In the first week of May 1792, Vancouver and a small company rowed their launch south into Hood Canal, stopping when the tide turned against them, then resuming exploration. It was to be his first experience with the Northwest's glacial fjords, some of which lead somewhere, most of which don't.  In his journal, he noted the change in landscape - steep, forested walls plunging into the bottomless channel - and the eerie silence of the place.
   The whistle of the wind in the trees frightened the crew, he wrote, conjuring fears of "rattlesnakes" and "hideous monsters." In an odd and accidental way, the superstitious sailors were right. For, unknown to the captain and company, they were floating above a veritable explosion of life forms completely foreign to them, and to most of us today.
    Puget Sound's springtime boom begins with untold trillions of microscopic plants and animals collectively called plankton, the primordial soup that is the basis for all life in the oceans. The explosion begins innocently enough with diatoms - microscopic, single-celled plants shaped like aspirin tablets, but so tiny that a million would fit inside a single pill. During the winter, they drift in a state similar to hibernation, deep in the sea.
    In April or May increased sunlight and warmer water trigger photosynthesis and the silent explosion begins. Fed by nutrients from decaying plants and animals, the diatoms begin to reproduce. Each divides into two identical offspring, which promptly divide again. If this binary fission occurs daily, which is not uncommon, it will take only a month for one diatom to become one billion. Scientists call this a plankton bloom, and it will be the first of many. The water in channels like Hood Canal, relatively clear during the winter, suddenly turns murky and green and may remain so all summer. The murkiness is an indicator of life. The ecosystem is shifting into a higher gear.
   Nobody has ever seen a diatom without the aid of a microscope. Yet their massive blooms can be seen from airplanes and, in at least one case, from the space shuttle. Other phytoplankton - the plantlike organisms that can create oxygen - have similarly dramatic effects, such as the "red tides" and shellfish poisoning that proved fatal to one of Vancouver's crew. Plankton also provide the marvelous bioluminescence that adds sparkle to a moonless night.
    Within a few weeks, the initial bloom sets off more biological explosions as all those diatoms become food for larger organisms - especially shrimplike copepods. Copepods are among the zooplankton, tiny animals rather than plants. Viewed through a microscope, copepods, with segmented shells and a dinosaur-like head complete with flailing antenna, resemble the hideous monsters so feared by Vancouver's crew.
    As one of the oldest forms of life on Earth, plankton exist in all the world's oceans. But Puget Sound is particularly friendly. In his 1983 book, "The Fertile Fjord: Plankton in Puget Sound," University of Washington oceanographer Richard Strickland wrote: "Puget Sound is to plankton what Florida is to oranges, what Iowa is to corn, and what the Cascades are to Douglas fir." Never mind Boeing 747s and Windows 98. From a biological point of view, at least, plankton is our primary product. 
    When the UW research ship Thompson cruised around Puget Sound, one of its missions was to test for plankton at each of 39 stations, including places in Hood Canal. To do this, oceanographers lowered a gazebo-shaped frame holding remote-controlled bottles that close at various depths, capturing water samples to return to the ship.
   "We're less interested in how much than in where they are - depth and location," explained Jan Newton, a Department of Ecology oceanographer who also teaches at the UW. "We know, for example, that the bloom occurs earlier in Hood Canal and the South Sound, later in the main basin." By early summer, she says, the diatoms will burn themselves out and be replaced by dinoflagellates, smaller plants that use whiplike flagella to propel themselves.
   She and others are interested in plankton for a variety of reasons. Phytoplankton produce about half the world's oxygen. They are key players in delivering the sun's energy to virtually every other creature in the sea.
    But for Puget Sound, their abundance can become a serious problem. When plankton do well, they tend to overdo it. Eventually the zooplankton prevail, consuming all the available oxygen and ultimately self-destructing. That's where people enter the equation. Phytoplankton mostly subsist on nitrogen and phosphorous, referred to by scientists as nutrients, familiar to the rest of us as, among other things, municipal sewage, farm fertilizers and the leftovers of any number of human enterprises.
   "Too much agricultural runoff or undertreated sewage, and we essentially tip the natural system out of balance," Newton says.
    Scientists call this eutrophication, or over-enrichment. That is what went wrong 35 years ago in Lake Washington. Sewage, rich in phosphorous and nitrogen, didn't poison the lake; it fertilized it, breeding a phenomenal growth of algae, another form of plankton. The algae consumed too much oxygen in the water, making the lake unhealthy for salmon and other fish.
    In the 1980s, concerns about potential over-enrichment prompted Puget Sound cities to spend hundreds of millions of dollars on upgraded sewage treatment. It is also what kept Newton and her colleagues busy in Hood Canal last month. Their method was to take water samples, plankton and all, add small amounts of nutrients to some of the samples, then leave them in a plexiglass tank on the deck of the Thompson. The rate of photosynthesis in the samples would provide a clue as to whether an area faced potential trouble.
    There are signs or indications of declining amounts of oxygen in the water in Hood Canal, the kind of dead-end fjord that is a prime candidate for over-enrichment. If the amount of oxygen available in Lower Hood Canal declines dramatically, Newton says, it suggests an overabundance of plankton. That could be a monster of a different order than Vancouver's shipmates feared.
Would too much plankton implicate some human activity ashore? "As scientists, we don't like to say anything until we have proof positive," Newton says.
   By the wee small hours, the teenagers across the bay are partied out and Hood Canal falls silent. I lie in my bunk, listening to water lapping rhythmically against the wooden hull of the Velella.
   For me, as with most people, Puget Sound has always conjured images of silvery salmon in sparkling water. But inevitably it's more complicated than that. The regional totem is ultimately dependent on invisible organisms in a soupy green sea.
    It's time to move on and learn more about the curious link between the two.

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   "The serenity of the climate, the innumerable pleasing landscapes, and the abundant fertility that unassisted nature puts forth, require only to be enriched by the industry of man with villages, cottages and other buildings, to render it the most lovely country that can be imagined. . . ." Capt. George Vancouver, 1792

    On a gray July morning, we steer the sloop Velella south along the east shore of Bainbridge Island, past beach cottages and million-dollar mansions huddled nearly wall-to-wall along the narrow ledge between island and sea. Across Puget Sound, the glass towers of downtown Seattle glisten like an artist's overstated rendition of a futuristic city.

   We wonder if this is what Capt. George Vancouver had in mind when he suggested all Puget Sound needed was "the industry of man."
   Two hundred years ago, Vancouver followed a similar course before dropping anchor at the southeast corner of Bainbridge Island. Here the Discovery stayed for 12 days while the ship's company set out in small boats to explore the south Sound.
   We cruise past Vancouver's anchorage and across to Manchester, mooring the Velella offshore from a nondescript compound of frame buildings and floating pens on the shallow bay. These are the Manchester labs of the federal Northwest Fisheries Science Center, where some of Puget Sound's smartest scientists are busily trying to apply the industry of man to problems created in large part by the industry of man.
   Over the next several hours, we peer into perhaps a dozen prosaic, 20-foot diameter tanks, each containing marine creatures - copper rockfish, sablefish, halibut and more. But the stars of this show are in two tanks marked "Redfish Lake sockeye." These are the prized progeny of the last 16 sockeye that struggled up the Columbia and Snake rivers to an Idaho lake whose salmon run teeters on the brink of extinction.
   "They're about ready to spawn," explains biologist Tom Flagg, peering over the edge of the tank.

     He speaks much as a proud father would at the graduation of his first-born son.
    How these Idaho sockeye came to rural Kitsap County is a story about innovation and technology in the marine environment. It may also be a glimpse into the future of Puget Sound chinook salmon, the runs considered to be most at risk of extinction. Puget Sound salmon always have been highly cyclical. A century of harvest data looks like a statistical roller coaster of good years plummeting to bad and back again. To offset the low years, the government long ago began trying to hatch and grow salmon artificially, removing eggs from female fish, hatching them under controlled conditions, then releasing them into the Sound or Pacific Ocean so fishermen could catch them. In the past four decades, salmon hatcheries have grown like crazy from Puget Sound to Japan, releasing 5.5 billion juvenile salmon a year to the Pacific, including nearly 1 billion to the waters around Washington.
    But while hatcheries pump out juvenile fish, natural-salmon populations have plummeted. Several Columbia River runs already are formally listed as endangered, and Puget Sound runs are likely to be next. Confronted by this growing crisis, scientists such as Flagg started working on another strategy. They began breeding Pacific salmon in captivity. Eventually, they applied what they had learned to Atlantic salmon, which were dwindling even faster in New England.
Atlantic salmon proved to be easier to "domesticate," and the project worked. The result is a salmon-farming industry that now reaches from Norway and Scotland to Chile and is as close as Bainbridge Island. Just across the channel from Manchester, Global Aquaculture plans to harvest and sell 6 million pounds of Atlantic salmon this year.
    Now, as Puget Sound runs dwindle, the scientists at Manchester are trying to invent strategies for preserving fish at their doorstep. The concept is simple. In their natural environment, a spawning salmon will produce thousands of eggs, Flagg says. The vast majority of those eggs will die or be eaten by other fish. If just one-tenth of 1 percent of them survive to spawn again, the run will be considered successful.
    In the controlled environment at Manchester and other labs, they can achieve success rates of 50 percent to 70 percent. "Even if we only have a few spawners, we can take thousands of eggs and amplify them to thousands of adults," Flagg says.
    And if it works with salmon, why not copper rockfish or sablefish?
     So today we have two alternatives to Mother Nature: hatcheries that produce juvenile fish and release them into the ocean to be caught later by fishermen; and floating farms that hatch and raise salmon much like chickens. On the surface, at least, both strategies appear to have been hugely successful. About 65 government and tribal-owned hatcheries produce salmon in Puget Sound. There are far fewer salmon farms in local waters, but dozens along the British Columbia coast.
    These days, however, each of those technologies is increasingly suspected of contributing to the demise of Puget Sound's wild salmon. Critics say hatchery fish mingling with wild salmon weaken the gene pool or spread disease among wild stocks. They compete for food, and the younger wild fish frequently are the losers. One Oregon study suggests that in some cases larger hatchery fish feed on wild juveniles. Flagg recently co-authored an academic paper that asks whether releasing 5.5 billion hatchery fish every year is taxing the ecosystem not just of Puget Sound but of the North Pacific. While there is no conclusive evidence, the risks should be enough to cause governments to rethink how many fish they are adding to the environment, he and his colleagues say.
   Bern Shanks, the former state fisheries director, came under fire in part because he listened to biologists who argued that hundreds of millions of dollars worth of hatcheries may have done salmon runs more harm than good. Under his leadership, the state adopted a controversial policy requiring that sports and commercial fishing be regulated in a way that prevents depletion of wild runs. Putting that policy into effect may require cutting back or even closing hatcheries whose fish compete with wild runs.
    Salmon farms, on the other hand, are attacked for introducing pollution, including fish feces, to the environment. And the escape of 300,000 Atlantic salmon from the Global Aquaculture farm at South Bainbridge last year raised fears of East Coast salmon interbreeding with Puget Sound stocks.
    There is no evidence, however, to support those fears, says Dayton Lee Alverson, a Seattle consultant and respected authority on marine sciences. It might be accomplished in laboratory conditions, but the chances of it occurring in the wild are slim, he says.
    These fears are not new to the biologists at Manchester, and Flagg thinks some of them are legitimate. Fish raised in hatcheries or pens are not the equal of those raised in their natural environment, he says. To offset the problems of captivity, Flagg and his colleagues find themselves in the odd position of teaching salmon to behave like salmon. Before releasing mature fish they expose them to the scents of potential predators or even to the predators themselves. They even constructed an artificial raceway that emulates a natural stream with real gravel, logs and other obstacles likely to be encountered in nature.
    And there's good reason they're keeping rockfish and other less familiar in nearby tanks: They're learning how to breed these species in captivity just in case they, too, become threatened.
    Back on the sloop we sit with Alverson, who years ago served as teacher and mentor to many of the scientists now trying to rescue Puget Sound's wildlife. The wild-salmon debate is interesting, he says. In a complex ecosystem like Puget Sound, nature is bound to be affected by the genetics of hatcheries and salmon farms. Scientists call this genetic drift, the tendency for organisms to undergo genetic change when isolated from their natural environment.
   "But out here, the issues of genetics are subordinate to habitat," he says, nodding across the Sound toward the Seattle skyline. "Puget Sound's population has doubled in a generation, and it will have doubled again in the next generation. I don't see how we can sustain that growth without substantially changing the ecosystem."
   The scientists here are trying to anticipate those changes, much as Vancouver surveyed this seascape, conjured images of cities and towns, and made a map for those who would follow to apply the industry of man. 
  

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   `In the southwest corner of the cove was a small village among the trees. Beyond the termination, the country had the appearance of a level forest . . . We pulled in towards the village and observed a canoe paddling from it . . . They lay about twenty yards from us, continually pointing eastward, expressive of a wish that our departure would be more agreeable than our visit.' - Peter Puget, Vancouver's lieutenant, at Burley Lagoon in May 1792

   A few miles north, they stopped at Raft Island, whose "only inhabitants were an astonishing quantity of crows," Puget wrote. Today, as suburbs creep around the South Sound, the birds are supplanted by homes occupying virtually every square foot of waterfront.
   Further north, at Burley Lagoon, the Englishmen encountered a larger village - and a less-hospitable reception. Three Natives in a dugout canoe approached them, clearly gesturing their preference that "our departure would be more agreeable than our visit." Under strict orders to avoid conflicts, Puget sailed on to explore the opposite shore.
    Today we anchor the Velella offshore, probably within a few feet of that encounter. We take the dingy through the narrow cut under a low highway bridge and into Burley Lagoon, a 2-mile-long inlet nearly enclosed by a spit across the entrance. We tie up at a ramshackle dock alongside Western Oyster Co., which occupies a point of land behind a supermarket and strip mall in Purdy.
    Our arrival appears agreeable to Jerry Yamashita, the pioneer oysterman who runs Western Oyster. The wiry 75-year-old shuffles down the dock to meet us wearing a cotton work shirt, worn boots, snow-white hair tucked beneath a weathered baseball cap, and a warm grin. Excuse the mess, he says, shaking his head. He has long since moved his processing to Thurston County. All that's left here are a half-million oysters.
    He shepherds us onto a small, outboard-powered barge, which ferries us across the lagoon to a complex of wooden floats - horizontal rectangles constructed of heavy beams, spanned by narrow planks some 12 inches apart. This is Yamashita's farm. On the beach he appeared frail and tottering, but out here he steps sure-footedly from one plank to the next.
    He stoops, pulls a 3-foot-long cluster of oysters and seaweed from the water and plucks a 4-inch shell from the mass. A shucking knife appears magically in his other hand and the shell pops open like a spring-loaded pocket watch. Smiling, he hands over the prize.
    One sloshed oyster, and I know the flavor of Paradise. 

   Never mind chinook salmon. From Samish Bay up north to Eld Inlet near Olympia, Puget Sound is oyster country. While the salmon flounder, local oysters flourish, catering to a fast-growing, nationwide market for oysters on the half shell.
   In the wild, oysters begin life as drifting larvae that attach themselves to hard surfaces, preferably fellow oysters, in shallow water. Then they get on with the serious business of pumping water - some 40 gallons a day for mature oysters - in and out of their shells, filtering out the plankton along the way.
   Puget Sound being a natural plankton factory, it stands to reason it would favor plankton-gobbling oysters.
   Oysters are not only ravenous bivalves, they're also prolific. For the first year they are males, fertilizing the eggs of female oysters, explains Keith Benson, the Velella's skipper and my scientific mentor. Then they conveniently switch sexes. Eventually, each mature oyster will produce some 50 million eggs, most of which will be eaten by other creatures - a classic example of the scattergun strategy that feeds the world's oceans.
   "When things get tough, they switch back to males," Benson adds. "It takes far more energy to produce eggs than sperm."
   Puget Sound's native oyster is the Olympia. Vancouver, whose crew sampled the Olympias at Discovery Bay in 1792, found them mushy. ("Probably spawning," Yamashita speculates.)
   Half a century later, the miners of the California Gold Rush made no such complaint. They paid $20 a plate for Olympias shipped from Washington, spinning off a sort of "gray rush" in Puget Sound. By the Depression, the Olympias had been depleted.
   So along came Yamashita - not Jerry but his father, Masahide Yamashita, a first-generation Japanese immigrant. The elder Yamashita leased some tidelands on Samish Bay, near Bellingham, imported Pacific oyster seed from Yokohama, and the rest is history.
    "By the time it arrived, most of the seed was shot," recalls Jerry Yamashita as he pops another Pacific. "But they planted it anyway and, much to their surprise, it grew. And grew. And grew. "It was quite amazing. It had to be the water temperature, or the nutrients, or something."
   The larger, faster-growing Pacific oysters, now known under grower names such as Shoalwaters or Wescott Bays, soon dominated the Puget Sound market.
    Still, the Yamashitas encountered daunting obstacles. They challenged the Japanese seafood conglomerates for a piece of the Japanese market, and lost. Then came Pearl Harbor; the Yamashita company was "liquidated," and the family sent to an internment camp.
    After the war, they started over in South Puget Sound, eventually purchasing part of Burley Lagoon. "It's quite rich and there were no pulp mills," he says. "In Samish Bay, the Bellingham pulp mill was a big problem."
   The industry took off with new growing techniques - particularly the suspended culture that Yamashita employs. Discarded shells are suspended on strings a few inches apart, seeded with larvae, then hung from rafts in warm, shallow water - a sort of oyster condominium that allows hundreds of shellfish per square foot. With this technique, Pacifics reach maturity in 15 to 18 months, he says.
    To achieve this, though, shellfish need clean water. In the mid-1980s, scores of shellfish operations, including Yamashita's, were closed down. State health officials cited pollution, apparently from shoreside sewers or septic tanks. Yamashita moved his oysters elsewhere, which, he says, "took all the profit." That lasted 12 long years.
    Now they're back. Thanks to tougher pollution laws and sewage treatment, water quality has improved. Throughout the Sound, shellfish beds that had been closed for years are being re-opened. In 1995, Puget Sound growers produced 431,000 gallons of Pacific oysters (or 1.3 million dozen) worth $6.4 million - their best year since 1984. This year, Yamashita hopes to produce 20,000 gallons, most of which will be sold in California.
   Other shellfish - clams, geoducks, crab, shrimp - also appear to be prospering while salmon and other fin fish dwindle.
    Benson suggests several reasons nature might favor oysters and friends. Shellfish don't rely as  heavily on freshwater habitat, nor on conditions in the open ocean, he says. And they don't appear to be affected by the infamous El Nino weather; if anything, they may benefit from warmer water.
Still, Yamashita's problems are far from over. Health authorities warn that Burley Lagoon still has borderline pollution problems. Yamashita suspects some combination of Canada geese droppings and leaky septics beneath the houses that ring the lagoon. And Yamashita knows some neighbors consider his farm to be unsightly. They would like to see him take his oysters and go away.
   Back on shore, Benson and I walk up to the supermarket to restock our galley. The minimall is a rude interruption to our voyage. The store is busy; out on the highway afternoon commuters are backed up a half-mile toward Tacoma. Waiting in line, we overhear one woman ask her friend how she plans to celebrate the Fourth of July.
    "Maybe we'll burn down the oyster company," the other laughs.
    Benson shakes his head. "Jerry's oysters are their best friends," he says. Purdy's suburban sprawl, complete with leaky septic tanks, lawn fertilizers, animal feces and oily runoff from the supermarket parking lot, inevitably pollutes the lagoon. At 40 gallons a day, each of Yamashita's oysters is working round-the-clock, filtering the waters of Burley Lagoon, removing the plankton and anything else floating out there, Benson says. What Vancouver called "the industry of man" created the oyster farm, and now, once again, threatens to destroy it. Yamashita's farm is not the polluter; it's the pollutee.
    "You look down into those floats, and the water is perfectly clear," Benson says. "You couldn't ask for a cleaner organism than an oyster."
    We make it back to the Velella and pull anchor, suddenly imbued with a nagging suspicion that our departure would be more agreeable than a visit.

   Pushed by a stiff south wind, we cruise the jagged shores of South Puget Sound, bound for Burley Lagoon. This maze of channels, inlets and islands would be confounding, except for Peter Puget's 200-year-old sailing directions lying beside us in the cockpit of the sloop Velella.
   In May 1792, Puget and company were on a weeklong voyage in a small, open boat, charting these intricate waterways, tracing each inlet to its conclusion. At Wollochet Bay, south of Gig Harbor, they visited with a group of Natives "drying clams, fish, etc., which they readily parted with for buttons and trinkets."

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   "Having passed round the point, we found the inlet to terminate here in an extensive, circular, compact bay whose waters washed the base of Mount Rainier . . . The forest trees, and the several shades of verdure that covered the hills gradually decreased in point of beauty until they became invisible . . . the whole producing a most grand, picturesque effect." - George Vancouver at Commencement Bay, May 16, 1792

   To Vancouver and his crew of Englishmen, the sheer scale of Mount Rainier was beyond comprehension. The captain figured the base of the mountain was just beyond the "circular, compact bay" on which he floated. Archibald Menzies, the expedition's scientist, guessed it to be "10 to 12 leagues off" - about 30 miles.

    In reality, it is 45 miles. Whatever the distance, they were captivated by what Menzies called the "most beautiful and majestic mountain of great elevation, whose line of ascent appeared equally smooth and gradual on every side, with a round obtuse summit covered with perpetual snow."
   Two centuries later, we sail on an ebb tide from South Puget Sound through the Tacoma Narrows and around Point Defiance. To the southeast, the mountain is enveloped in meteorological concrete. Still, we drift for a while just off the point, comparing our view with Vancouver's engraving of Commencement Bay lapping at the base of Mount Rainier. No question: The scene was sketched from within a few feet of Point Defiance.
    Today, however, the focus of the picture is not The Mountain. It is The Mill. For decades, the huge pulp mill at the mouth of the Puyallup River loomed over Commencement Bay like a grim, medieval castle, its towering smokestacks serving as symbols of a sick Puget Sound. The mill belched smoke and steam that produced the legendary "Aroma of Tacoma," and spewed a witch's brew of pollutants into the bay, helping put Commencement Bay at the top of the federal government's list of toxic-waste hot spots.
   Today, as we tour the site, Commencement Bay is in the midst of a comeback. The arsenic plant across the bay has disappeared. Tacoma has renovated much of its waterfront. And this once-notorious mill, which produces 1,200 tons a day of pulp used mostly for packaging, is now deemed one of the heroes.
    "It's a real success story," says Allison Hiltner, Superfund manager for the Environmental Protection Agency. "In fact, it is one of the first sites in the country to be partially deleted from the Superfund list."
   How this occurred may hold some lessons for shaping the future of Puget Sound, says Dave McEntee, environmental manager at Simpson Tacoma Kraft. McEntee is a friendly, clean-cut biologist who looks like he should be teaching high-school biology and coaching the tennis team. 

   He cheerfully walks us through the sprawling 55-acre plant, which is not a pretty sight.
But that was never the point. Puget Sound's pulp mills are classic examples of what Capt. Vancouver foresaw as the "industry of man" that would tame this soggy Pacific Northwest wilderness. Waterfront sites made it easy to acquire the softwood logs, then to ship the product to markets. Early in this century, Puget Sound's shore was home to hundreds of pulp, paper and sawmills. Tacoma's mill was the largest, and one of the oldest.
    But the mills were also prime targets of the popular uprising against water pollution in the 1970s and 1980s. Reducing logs to pulp and paper generates huge volumes of effluent - woody waste mixed with water and various chemicals. While that waste is mostly organic, feeding the microscopic plankton that live in sea water, it also tends to over-fertilize and throw the ecosystem out of balance. Worse still, when Seattle-based Simpson Timber bought the aging mill in 1985, it learned that the mill's effluent also included dangerous quantities of copper and phenols not usually found in pulp waste. "Big problems," says McEntee.
   So Simpson met with its neighbors and critics, and went to work. The company attacked its air emissions by upgrading its gas-collection system throughout the mill, reducing emissions by more than 90 percent, McEntee says. Meanwhile, it agreed to cut production, if necessary, to achieve agreed-upon standards. Water pollution was curtailed by recycling the lignin, the natural "glue" in the raw wood; the stuff is now isolated and burned to generate 75 percent of the mill's power needs. And the mill's waste outfall, which had dumped millions of gallons of pollutants onto the beach, was extended 600 feet out into deep water, where it is not considered a problem.
   Still, those things did nothing to address 80 years of putrid residue already lying on the bottom off the bay just offshore from the plant. After studying the alternatives, Simpson and environmental officials agreed on a novel strategy. They would not dredge and remove those poisoned sediments, for fear of disturbing the toxins and creating new problems. Instead they would cap them, dumping clean, new sediments on top of the old. Using clean mud from the nearby Puyallup River, they created a new bottom spanning 17 acres of the bay, the cap ranging from 6 to 40 feet deep. Of the 17 acres, seven are new "intertidal habitat" - mud flats, complete with rocks and contours that are dry at low tide and submerged at high tide, thereby recreating a "a nursery area," McEntee says, for juvenile salmon and other marine life.
   That was in 1988. Ten years later, the company celebrated it success. . McEntee walked us down to the seawall to show off the results. Near low tide, it resembled what Vancouver might have seen two centuries ago. The imported rocks are encrusted with barnacles, the mud flats strewn with shiny orange bull kelp. A harbor seal patrols deeper water and a great blue heron struts across the flats, scouring the shallows for fish.
   "We added contours and tide pools and texture," says McEntee. "The idea was basically, `Build it and they will come.' And they came! Our sampling shows a natural bottom-dwelling community that looks healthy. There are adult salmon feeding in the shallows. We find dungeness crab, shrimp, copepods . . ."
   Simpson's success has been noted elsewhere. Several toxic sites in Seattle's Elliott Bay have been capped in recent years. Similar projects are under way as far away as New York City's harbor.
     "Capping is pretty low-tech," says Hiltner of the EPA. "But Commencement Bay tells us that, in the right environment, it works. Marine organisms are happy to recolonize in new sediments."
   The cleanup of Commencement Bay is far from finished, she adds. Work at nearby sites such as the Thea Foss Waterway and the Hylebos Waterway has barely begun. And most private companies are reluctant, or unable, to spend the $250 million Simpson says it has spent on new technology, cleanup and restoration.
    McEntee points out that restoring the 17 acres of habitat was the cheapest item on the list - about $5 million. The other expenses made the operation more efficient as well as cleaner.
Most of Puget Sound's mills failed because they were inefficient, he says. "It had little or nothing to do with the environmental costs. The successful companies today are the ones that take a long-term view. And a lot of companies outside the Northwest haven't learned that."
    As we resume Vancouver's route up Colvos Passage, I wonder what makes the difference on Commencement Bay. Is it a simple question of environmental virtue, of good guys and bad guys? Of long and short-term perspectives? Is it as simple as seeing the mountain on a cloudy day, or calculating its distance on a clear one? Maybe we'll find some clues in Elliott Bay, Seattle's front door and our next port of call.

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"The men remained in their canoes, bartering their bows and arrows, garments and a very few indifferent sea-otter skins. . . . These they exchanged in a very fair and honest manner for copper, hawk's bells and buttons. . . . Their merchandise would have been infinitely more valuable to us had it been comprised of edibles such as venison, wild fowl or fish, as our sportsmen and fishermen had little success in these pursuits." - Capt. George Vancouver, May 21, 1792, near West Seattle

   Vancouver never found his way into Seattle's bay. Must have been the traffic. Instead, they anchored off the southern tip of Bainbridge Island, where the crew went to work. Some set off on small-boat explorations or felled trees to be fashioned into new spars for His Majesty's Ship Discovery. Still others engaged in friendly commerce with the natives, trading buttons and beads for bows and arrows and, if they were lucky, food.
    Two centuries later, we sail the sloop Velella into an Elliott Bay ruled by a higher level of commerce - hundreds of human enterprises, large and small, ranging from world-class shipyards and cement plants to marinas and seafood restaurants. The effects on Puget Sound - docks, bulkheads, huge landfills, sewers, pollution and more - could hardly be more profound. Elliott Bay bears little resemblance to what Vancouver viewed from afar.
    B.J. Cummings' job is to check that dramatic rate of change. As an environmental organizer who works for Seattle's nonprofit Puget Soundkeepers Alliance, she leads a team of volunteer kayakers, scuba divers, lawyers and other self-styled pollution vigilantes, tracking down polluters and blowing the whistle on them.
   Cummings steps aboard the Velella carrying the tools of her trade - a plastic crate full of files and documents and a pair of binoculars. We have invited her aboard to guide us through the ecological inferno of Elliott Bay and the lower Duwamish River. For the next three hours, we cruise the industrial waterfront, Cummings pointing to the shipyards and cement plants and sewer outfalls that the Soundkeepers have caught dumping illegally.
    "There are 24 Superfund sites here," she says as we enter the lower Duwamish River. "The Port of Seattle promises to clean them up, but we'll be watching that very closely." 
   Yet. in 1998, the alliance reported that half the Puget Sound companies that hold government permits to discharge pollutants exceeded their legal limits, that a third of those violators are repeat offenders and that fewer than 10 percent were fined for their violations.
    In Seattle the risk is not just biological. A recent King County study shows that thousands of people fish in Elliott Bay for Dungeness crab and other bottom-dwelling seafood. Like other shellfish, crab tend to accumulate toxic chemicals in their tissues - a health risk to people. People will not put up with this, Cummings says. When companies resist, the alliance has been known to file lawsuits. More frequently, they rely on the threat of publicity and environmental outrage to enforce the laws. "Our greatest ally is public opinion," she says. "Public opinion will take us where we want to go."
   Lincoln Loehr is a trained oceanographer who monitors Puget Sound from a very different perspective - high in the Columbia Tower, where he works as an environmental analyst for a local law firm. The Soundkeeper concept works by drawing attention to polluters, he says. But public opinion is a poor substitute for good science. In principle at least, nobody would argue with that. In practice, however, science sometimes collides head-on with popular wisdom, he says. And when that happens, science usually loses.
   The best example, Loehr says, is Seattle's brand new, $500-million sewage-treatment plant at West Point, the northern tip of Elliott Bay. In the early 1980s, the federal government required most U.S. cities to upgrade their sewage plants from primary treatment, which mostly dilutes and removes solids, to far more costly secondary treatment, which removes most of the organic material. Seattle, however, asked for and was given an exemption, or "waiver," from that requirement. Scientists and engineers at Metro, the regional sewer agency, cited evidence that sewage was quickly diluted and flushed away by Puget Sound's powerful tides. Secondary treatment, they said, would be a waste of tax dollars.
   Instead, Loehr and others argued that the region should focus its efforts and money on controlling sewer overflows. Like most cities, Seattle's rainwater drains in its sewer system. During heavy rains, the sewers tend to overload, dumping huge amounts of raw sewage into overflow pipes that spill into local waters - especially Puget Sound. Even one such overflow probably pollutes the sound more than a consistent stream of primary-treated sewage, Loehr argues. So he and many other marine scientists suggested that, for the same amount of money,     Puget Sound would derive far greater benefits by redesigning its sewer system.
   Seattle and other Puget Sound cities debated the issue in the early 1980s, and public opinion shifted in favor of secondary treatment - despite the costs. In the end, the issue was swayed largely by politics 3,000 miles away in New Jersey and Washington, D.C. In 1984, congressmen from New Jersey wanted the federal government to force New York City to install secondary sewage treatment. To make their pressure appear even-handed, they needed another region to help force the issue. Seattle fit the bill, and the law was amended to take away Seattle's waiver, along with New York's.
   The next problem was the Magnolia neighborhood, which supported secondary treatment - but not at its front door at West Point. Neighbors relented only when local government sweetened the pot with promises of a beachfront park.
    "Ultimately, science was irrelevant to the decision," Loehr says. "So what do we get for $500 million? A state-of-the-art treatment plant that was not necessary and a $100 million beach for the people in Magnolia."
   This, he adds, is the price of public outrage.
    Fourteen years later, few complain about the treatment plant, the beach or even the price tag. But is secondary treatment making a difference to the ecology of Puget Sound?
   Probably not, says Alan Mearns, a fisheries biologist at the National Oceanic and Atmospheric Administration in Seattle. The main ingredients in sewage are nitrates and phosphates that actually fertilize the sea, feeding the microscopic plankton that are, in turn, fed upon by fish. Mearns wonders aloud if the new plant actually diminishes the food supply for salmon and other wildlife.
    But there is no hard evidence one way or the other. The science of Puget Sound is laced with uncertainty. For every Mearns who argues that West Point was a waste of money, there is another who will argue that it was a wise, long-term investment. Among these is Keith Benson, skipper and scientific adviser to our Puget Sound voyage. In Asia, Benson says, rice farmers dump their sewage into the rice paddies to fertilize the fields and feed the carp. "That works fine in a rural village, but in Seattle?" He shudders.
    "Maybe we overshoot the mark on some environmental projects, but I'd rather err on the side of caution."
     Cummings guides us into the shallows of Kellogg Island, the last remnant of the original, twisting Duwamish River. Once scheduled for development of yet another seaport terminal, the tiny island has instead been preserved in something resembling its natural state. Great blue herons nest in the trees and stalk proudly along its muddy banks, all in the shadow of giant container ships and loading equipment.

    "So much of Puget Sound is so beautiful, it's hard to convince people that we have real problems out there," says Cummings. "That's frustrating, but it's also encouraging. I don't think I'd want to do this job in a place where there was no hope."
   With this thought, we sail north, tracing Capt. Vancouver's incomplete map, fueled by a gentle summer wind and prospects of finding a smarter balance between science and popular wisdom.

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"The sandy beaches abounded with fine clams . . . gulls, shags and other oceanic birds. . . . Accordingly we were visited from one of the islands by a small party of natives . . . with little pieces of porpoise and seal flesh in their hands which they offered in the most open and friendly manner. And though these presents were not accepted, their generosity and good intentions were rewarded by some little presents." - Archibald Menzies, botanist with the Vancouver expedition, 1792

    After a long day crossing the strait, we slip through Cattle Pass on the slack tide and tuck around the lower end of the island into Griffin Bay, where our course is tracked by the sad, black, liquid eyes of some 40 harbor seals hauled out on the rocky outcrop. We drop anchor a few hundred feet offshore from a serene wildlife refuge and watch the hook descend into the bay. Here plankton blooms are sparse and the water clearer, reminding us that the islands are less of Puget Sound than they are of the North Pacific Ocean.
    Immediately we are surrounded by perhaps a dozen of those mottled-gray streamlined heads, circling us like earless Labrador retrievers. We are not threatened, just watched with considerable skepticism.
   During his six weeks in Puget Sound in 1792, George Vancouver carefully recorded his observations of land and sea, weather and wildlife. And he did not record seeing seals. Even Archibald Menzies, a naturalist whose journal focuses on wildlife, mentions seals only twice. Approached by natives offering "pieces of porpoise or seal flesh," the sailors shuddered and politely declined. Maybe seals were too humanlike or simply too bloody cute; whatever the reason, there would be no seal meat in the English diet.
   Our visitors remind us of sailing into Discovery Bay two weeks ago and discovering an ecological whodunit: What has become of a once-prolific run of herring? None of the usual suspects appears guilty. Fishermen have not fished those herring for years. Habitat and water quality appear healthy. And most of their natural predators, including salmon, are declining as well, except for one predator: harbor seals. So suspicion naturally falls on the closest predators, the seals at neighboring Protection Island.
    The Pacific harbor seal is a major player in coastal ecosystems from Baja California to the Gulf of Alaska. Pups are born in the summer and weaned in about four weeks. From then on, they're on their own, growing eventually to about 150 pounds, consuming about 10 percent of their body weight a day - up to 15 pounds of fish. Females may live 30 years, males up to 20.
   If Puget Sound is in crisis, somebody forgot to tell the seals, who appear to be thriving. In 1978 wildlife authorities estimated there were 10,000 seals in Washington waters. By 1994 the population was at 35,000 and growing 7 percent a year, which means there are about 40,000 today. Of these, more than half are in Puget Sound, where there are more than 200 known "haulouts," the rocks or beaches frequented by seals.
    Sea lions, their close cousins who breed in California and winter here, also are increasing; in-season, the population has grown from 100 to 1,000 in 20 years. During our voyage, we have seen no sea lions; they're summering down south. But seals appear everywhere: massed on the beach at Gertrude Island in the south Sound, their weight sinking a pier on Hood Canal, patrolling the shores of Bainbridge Island, Vashon Island and Commencement Bay, or lounging in the afternoon sun at their federal refuge just outside Discovery Bay.
   There's the first clue. Two thousand to 3,000 seals now live around Discovery Bay, says Steve Jeffries, a state wildlife official. It's precisely where schools of herring gather early in the year to spawn in Discovery Bay. I scribble the arithmetic. Starting with the mid-estimate of 2,500 seals, I multiply by 10 pounds of fish per day, multiply again by 360 days . . . and gulp. That's 9 million pounds of fish a year, all in one small area. Coastwide, from Puget Sound to California, federal biologists estimate that harbor seals consume 70,174 tons of fish a year, about half of that in Washington.
    "They're upper-level predators and highly opportunistic," says Jeffries. And nobody preys on seals. The region's orca whales eat primarily salmon and herring, not seals. For at least a century, the only predator was us. Fishermen viewed seals as competitors for salmon and other fish, and shot them. It was not only legal but encouraged by wildlife authorities. That all changed with the 1972 Marine Mammal Protection Act, which prohibited any shooting or culling of seal, sea lions and their relatives.
    Since then, populations have mushroomed, and tempers have flared. Witness the Ballard Locks, where sea lions have feasted on endangered salmon and steelhead while fishermen watch and seethe. Now, with more salmon headed for the endangered-species list, fishermen ask: Why spend millions of dollars restoring salmon runs that will be simply be gobbled up by seals?
   One answer might be this: Seals and fish have co-existed for eons, so let nature take its course. But if seals were thriving 200 years ago, why didn't Vancouver and Menzies report their presence? Because they probably were not thriving, Jeffries says. Indians hunted them, as evidenced by the natives' sales pitch to Vancouver's crew.

   "To the natives, seals were food!" Jeffries says. "They may also have been competition. I suspect the Muckleshoots or Nisquallys would not have tolerated seals swimming up into their salmon streams, taking fish along the way. They would have been easy to kill."

   If so, the seal population may have been controlled, which would explain the sparse reports from Vancouver. Absent human predators, there may be more seals in Washington waters today than in many hundreds of years.
   "They have increased because we protect them," Jeffries says. "If this goes on, we could be headed for a crash, and if everything crashes I don't know how we'll restore the system."
   Any mere mention of the alternative - killing the critters - appears to be strictly taboo. State officials shudder at the thought.
   So much for the prosecution. Here's the case for the defense: Yes, seals will eat salmon and herring. But, as Jeffries points out, seals will eat just about anything that swims. Dozens of isolated seal studies, usually of scat, show widely varying diets. For example, a 1994 study at Gertrude Island, one of the largest seal haulouts in Puget Sound, showed traces of salmon and herring but much larger amounts of whiting, perch, flatfish and squid. Similar results have emerged from studies in Hood Canal, Everett and the Strait of Juan de Fuca.
   In one study, state officials reasoned that most Puget Sound salmon come from hatcheries, which tag their fish with tiny wire tags that can be detected with a handheld device. When officials sampled seal scat at Gertrude Island, they found little evidence of salmon tags. And a herring run at the south end of Vashon Island actually is increasing, despite its proximity to hundreds of seals.
   The case against harbor seals is mostly circumstantial, says Joe Scordino, a federal biologist. Seals appear to prefer whatever is easiest to catch. And that usually means something slower than salmon or herring. "The predator-prey relationship is never as simple as you'd like it to be," Scordino says. "We get little pieces of evidence here and there, but you're still in the gray zone."
Meanwhile, a study last year by the National Marine Fisheries Service cautioned that culling seal herds could lead to unintended consequences. For example, seals also prey on cod, whiting and other fish that eat herring and juvenile salmon. That study concluded that growing seal and sea-lion populations brought "new problems and conflicts," but could not establish how they are affecting the ecosystem.
    So the jury is out. Scientists say they need more research to understand how seals and fish are linked. And even if scientists could find seals guilty, one wonders if 4 million Puget Sound residents could stomach the idea of shooting a creature so high on the cuteness scale.
   Here in Griffin Bay, we are a jury of just two. And after a long evening of deliberation, we are hopelessly deadlocked.

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"Mr. Broughton informed me that the part of the coast he had been directed to explore consisted of an archipelago of islands lying before an extensive arm of the sea stretching in a variety of branches." - Capt. George Vancouver, 1792

     George Vancouver never ventured into these islands. Instead he dispatched the ship Chatham and its crew, commanded by William Broughton, who spent a week exploring and charting the twisting channels, tidal currents and jagged shorelines. No record of Broughton's foray survives, but his verbal report convinced Vancouver that these intricate waters were too risky for His Majesty's ships, and that future explorations would be pursued in small boats. This despite the risk that "such a service in open boats would necessarily be extremely laborious and expose those so employed to numberless dangers and unpleasant situations."
    Among those dangers would be hidden rocks, sea monsters and people peddling timeshare condominiums. So forewarned, we sail the sloop Velella into the heart of the islands, around Shaw Island and into Wasp Channel, where a gentle breeze nudges us between Shaw and Orcas islands.
    A mile west of the Orcas ferry landing we drift past tiny Bell Island, seemingly uninhabited but posted with signs - two hands cradling a spiny, speckled rockfish and labeled: "No Take." Bell Island and seven similar, small niches of island shoreline are the last refuge for copper rockfish and other bottom fish whose rapidly diminishing numbers have alarmed biologists.
   In a region enamored of slick, silvery salmon, bottom fish get precious little respect. Biologists have identified more than 80 species, including halibut, skates, ratfish, cod, pollock, several species of sole, and an array of homely, spine-covered creatures generically known as rockfish.
    Hunkered down on the sea floor, rockfish do their best to blend in, rarely if ever visiting the surface. Divers can swim within a foot or two, but rockfish tend to stay put, stone-still, camouflaged with mottled colors and webbed spines, their oversized eyes declaring: "Don't mind me. Just another wad of seaweed and rock. So just move on and find yourself a silver salmon."
   Rockfish have dignity. Left alone, copper rockfish may patrol the same watery neighborhood for 60 years, and some species may live up to a century. Cod and pollock are known to migrate substantial distances, but rockfish are homebodies, inhabiting the same rocky habitat for a lifetime.
   In Puget Sound, bottomfish are the territory of Wayne Palsson and Robert Pakunski, odd men out in a state fisheries department obsessed with salmon. These unsightly creatures never have been thoroughly understood, Palsson says. State research dollars go mostly to salmon programs, federal dollars to the big-money fisheries in Alaska and the Bering Sea. Now all those years of neglect appear to be catching up with us.
    We chatted at the stern of the small, fiberglass boat in which they have spent two weeks working side-by-side with Canadian biologists, conducting bottom fish surveys in the boundary waters. To do this, they had to invent their own tools. Bottom fish, it seems, present a scientific challenge: The fish are way down there, and the researchers are not.

     "We used to scuba dive, but you can only do two dives per day," Pakunski explains. "That would take a lifetime."

   So the biologists fabricated a frame of iron rebar, attached an underwater video camera on a motorized swivel, hooked it to a remote control, and lowered the contraption to the sea bottom. It looked like something from a Star Wars junkyard, but it worked. In the past few years, they have lowered their gadget more than 2,000 times into the nooks and crannies of Puget Sound, the straits and the islands.

    Each "drop" lasts six minutes, during which the camera makes a full revolution, recording on videotape any life within a radius of four meters. More recently, they have added a device that projects laser beams, providing an accurate measure of the size of the subject creature. The researchers note the numbers, species and size of fish on the tape, then extrapolate that data, coming up with what they believe to be reliable estimates of who lives where at the bottom.
    The results are discouraging. Rockfish appear to be in steep decline, they say - both in numbers and size. "There are too many areas of ideal habitat where nobody's home," says Pakunski. "It's depressing."

   Predation is the problem, they say, and the evidence points to people. With salmon runs in decline, sports fishermen have turned increasingly to bottomfish, figuring a spiny rockfish is better than going home empty-handed. That pressure is beginning to depress stocks of fish, the biologists conclude after studying video of areas where fishing is allowed and "no-fishing" areas such as Bell Island.
    The best example is the underwater park in Edmonds, north of Seattle. The park is frequented by scuba divers and is within a stone's throw of downtown Edmonds and its busy ferry dock. Yet there are twice as many lingcod and 10 times more copper rockfish than at at similar sites up and down the shoreline. The Edmonds fish also are larger and older. Why? Because there is no fishing allowed, Palsson says.
   Research at Bell Island and other no-take areas points to the same conclusion. Where there is no fishing, there are more and larger fish. "Fishermen ask why we're taking it out on them," Palsson says. "And it's true there are lots of stresses on those fish - seals, sea lions, shoreline development, changing beach patterns. . . . But fishing is one stress we have some control over."
   In Washington, the mere mention of "no-fishing" can get a state biologist into hot water. Scientists are supposed to be politically objective, interested only in scientific facts, not public policy.
   "But our jobs are changing," Palsson says, "from fishery biologists to conservation biologists. It's a subtle and important change from the old days, when we heard the governor telling us: We want to be the sports-fishing capital of the world."
   Instead, Palsson and Pakunski advocate designation of more, and perhaps larger marine reserves, where fishing is either prohibited or strongly discouraged. It will take years, but rockfish should begin to recover. "San Juan County voluntarily designated eight bottom-fish recovery areas, and we already can see the difference," Palsson says. "But that's still less than 1 percent of the critical habitat in the Puget Sound area."
   In the San Juans, no-fishing areas have become a cause celebre. And there is no more enthusiastic supporter than Dennis Willows, longtime director of the University of Washington marine laboratories at Friday Harbor. "I'm not particularly green, and I'm not a fisherman," Willows says. "But the scientific data is so obvious, it's stunning."
   He pulls a tattered file and exhibits a set of graphs, not from Palsson and company, but fishing statistics provided by the state. The graphs show plunging catch rates for rockfish and several other species. Puget Sound and the San Juans are ecosystems that demand systemwide responses, he says. The systems are remarkably resilient, able to withstand overfishing and other environmental abuse - "until some unknown threshold is reached."
   "It may still look fine, but in the background there is water quality insult, reproduction insult, . . . and I worry that we are getting dangerously close to that threshold."
   Selected fishing closures eventually will provide scientists with critical data, a broader extension of what Palsson has collected with his odd home videos. This, says Willows, is not environmental advocacy; it is a logical extension of good science.
   In 1792, Capt. Vancouver and company repeatedly set their nets in Puget Sound - usually with little or no success. They must have wondered where the fish had gone. And so it goes for 200 years. The fish don't change, but the fishermen get smarter, better-equipped with electronic fish-finders, high-test lines, trolling motors. These days, one can actually buy an off-the-shelf underwater video camera that sounds more sophisticated than the one invented by Pallson and Pakunski.
   You look at this stuff, and you wonder how any fish are left out there. But there are. Those grainy home videos are evidence that rockfish, while scarce, are also survivors. There are plenty of rocky shoals and kelp forests ready to be repopulated with some homely bottomfish.
   All they ask is an even break.

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"Accompanied by Mr. Broughton and some of the officers, I went on shore about one o'clock, pursuing the usual formalities which are generally observed on such occasions, and under the discharge of a royal salute from the vessels, took possession accordingly of the coast." - George Vancouver, June 4, 1792.

    On the last day of our voyage, I launch my kayak from the stern of the Velella, anchored in tranquil Strawberry Bay, where Vancouver anchored in 1792. The kayak carves a liquid V on a mirrorlike surface as I paddle out to Strawberry Island, a forested gem about 200 yards long at the focal point of the bay.
   Here seagulls perch on the tidal rocks, each with its beak tucked neatly into one wing. Pigeon guillemots - sleek, black seabirds with remarkable red feet - inhabit the granite cliffs. A lone fisherman in his small aluminum boat drifts just off the kelp, his fish line glinting in the morning sun as he leans back with a cup of coffee and grins at me as if to say, "It doesn't get any better than this."
   I beach my boat and climb to the top of the island, stopping to admire the wind-weathered madronas and Douglas firs, some of which appear old enough to have been admired by Vancouver. The view from the top encompasses 100 square miles of inland waters and 50 miles of coastline. The sole signs of humanity are the Anacortes ferry steaming across the southern horizon and my fisherman friend working the kelp. This does not look like a sick ecosystem. It looks like Paradise.
   Yet, paradoxically, scientists seem to agree that, for all their splendors, these waters are troubled. Most of Puget Sound's fish populations - salmon, herring, rockfish - are in serious decline. Federal endangered-species listings are imminent, with as-yet-unknown impacts on people's lives. To scientists, natural beauty and ecological trouble are not contradictions. Puget Sound, like all oceans, mirrors daylight while shrouding the biological complexity beneath the surface.
   Over the past three weeks, we have sailed more than 400 miles of this inland sea, retracing the 1792 route of George Vancouver from Discovery Bay to the South Sound, from Bainbridge to Strawberry Bay. Our days turned on tide and wind as we relearned how to live with, not resist, the rhythmic ebb and flow of nature. We dreaded our return to the city.
    From an aesthetic standpoint, at least, we came home encouraged. We saw virtually no litter, not a single plastic six-pack yoke or hamburger wrapper, and none of those surface "rainbows" that indicate oil on the water. Even in notorious corners such as Elliott Bay and Eagle Harbor, the sound looks remarkably clean. Everywhere we sailed, we encountered bald eagles, great blue herons and harbor seals.
    While prices for waterfront property inflate, much of the shoreline resembles what Vancouver described two centuries ago. There are miles of seemingly pristine shore in areas such as the western bluffs of Whidbey Island and the eastern shore of Hood Canal. State officials consider two-thirds of Puget Sound's shoreline to still be "natural."
    Admitted, these observations are not scientific and we are not scientists. I am a journalist; my old friend and skipper Keith Benson is a historian of science. In lieu of scientific expertise, we brought to this voyage our keen, personal interest in preserving this inland sea. Along the way, we conferred with biologists and oceanographers, fishermen and environmentalists. We glimpsed the endangered Redfish Lake sockeye at the Manchester labs near Port Orchard and sampled oysters plucked straight from the waters of Burley Lagoon in the South Sound.
   Here is the essence of what we learned: Puget Sound is far more complex than we give it credit for. It is both an ecosystem and a web of ecosystems that invite oversimplification and defy understanding. For all its ecological woes, Puget Sound also shows many signs of health. State officials, who test these waters on a regular schedule, report that water quality is generally improved. Horribly polluted sediments in Elliott Bay and Commencement Bay have been cleaned up or capped. Sewage treatment has been upgraded, and outfalls have been moved so discharges are more effectively diluted.
   Less obvious are the neighborhood responses. In Port Townsend, eighth-graders collect data from monitoring stations on the bay. In Seattle and other urban ports, scores of volunteers with the Puget Soundkeeper Alliance track down polluters, then work with them to find nonpolluting alternatives. In the San Juans, citizens have created mini-reserves for depleted rockfish.
   Although most fin fish have declined, shellfish show steady improvement. Commercial and recreational oyster beds that had been closed for years have been reopened, and oyster growers had their best year since 1984. Mussels, which naturally accumulate pollutants, now accumulate far fewer of them. Last spring, hundreds of people turned out on Hood Canal to harvest healthy populations of shrimp and crab.
   Some fin fish - halibut, for example - show improvement. And although herring runs are generally down, they're on the upswing in certain spots such as Vashon Island's Quartermaster Harbor.
Scientists are much better at identifying these trends than they are at explaining them. There is reason to believe rockfish have been overharvested, but herring have not been heavily fished for several years. Biologists disagree on whether salmon have been overfished, but both sides seem to agree that the biggest problems are environmental - not in Puget Sound, but in the rivers and the ocean.
The ocean is the wild card. There is growing evidence of what scientists call a "Pacific decadal oscillation," meaning long-term temperature cycles in the North Pacific that appear to have favored fish in Alaskan waters at the expense of Washington's for the past 20 years. But researchers can't say if or when that oscillation will swing back in favor of Puget Sound.
   All this uncertainty breeds two schools of thought. One says: Err on the side of caution. Crack down on all forms of pollution - industrial outfalls, undertreated sewage, overloaded septic tanks and oily bilges. Prohibit or curtail construction along the shoreline. Ban fishing. Spare no expense, because we cannot afford to lose Puget Sound.
   The other says: Be sensible. Our biggest problems can be traced to ocean temperatures beyond our control. Meanwhile, Puget Sound is far healthier and more resilient than we think. It has survived more than a century of human development and, if we proceed with common sense, it will survive for centuries to come.
    There is ample science to support either point of view. Most scientists do their best to stay out of the fray.

   I think back to a conversation two weeks ago on the Seattle waterfront with biologists from the Muckleshoot Indian tribe, who face a dilemma of science and politics. After years of unrelenting pollution, Elliott Bay and the Duwamish River are being cleaned up, they said. As part of that effort, the Muckleshoots closed their own salmon fishery for four years to help rebuild depleted Duwamish runs. This summer, those closures are expected to pay off with the return of up to 100,000 salmon above the level needed for sustainable spawning. This may include several thousand surplus chinook - the same species deemed endangered. Tribal fishermen want to net those fish in Elliott Bay, but county officials fear that an Indian fishery would lead to conflicts with non-Indians who can't fish.

   Science says: Go fishing. Politics says: Stay on the beach.
   Similar debates have occurred over the need for costly sewage-treatment plants or the fish-gobbling sea lions at the Ballard Locks. Science gives us information on which to base decisions, but it does not make those decisions.
   In Strawberry Bay I climb back into my kayak and paddle around tiny Strawberry Island. An incoming tide is now streaming past, and I paddle onto a bed of kelp to hold my position while I jot some thoughts. Back aboard the Velella are two cardboard boxes of interview notes, books and charts I have accumulated - a makeshift log of my voyage, literal and intellectual, through Puget Sound. There is much to see and learn and think about.
    I watch six of those sleek guillemots work the tide. Starting at the southern end, they ride the current, dipping their heads into the water and occasionally diving for prey. At the north end, they take to the air and race back to repeat the process, wing tips leaving a trail of tiny splashes on the surface.
    Now I watch the happy fisherman work the opposite side of the channel, drifting with the tide at the foot of a granite cliff, revving his outboard to run back against the current, then repeating his course. His strategy mimics the guillemots, though not as effectively.
   Back on the Velella, Benson returns from his own foray to Cypress Island and displays a delicate pink blossom - "Hooker's onion," he says. Archibald Menzies, the botanist aboard Vancouver's ship, identified the same plant here in 1792.
   Twenty years ago, Cypress Island came very close to being bulldozed. It was privately owned and slated for massive clear-cutting, 1,000 homes and condominiums, a 100-slip marina and 18-hole golf course - all approved by the state. It was rescued by a few far-sighted citizens, by the nonprofit Nature Conservancy, and finally purchased by the state. Today the island is preserved in its natural state, a permanent memorial to the power of citizen action.
   Given declining fish runs, this is no time for complacency, but neither is it a time for despair. We have done well over the past 15 years - cleaning up sewage and toxic sediments, preserving wildlife habitat, instilling an environmental ethic. Polls show a broad public consensus that favors doing the right thing for Puget Sound.
    But what might that be? People crave direct causes and effects, heroes and villains. Some would close down fishing altogether. Others demand tougher laws against pollution. Others want more public ownership of critical wildlife habitat. Science provides no road map. On the contrary, with each new breakthrough, the oceans become more complex and the solutions less obvious. 

     Our best bet is a deeper and broader understanding of a marine web composed not just of leaping salmon and noble orcas but of microscopic diatoms, prosaic herring and homely rockfish.
   This is the lesson learned by those eighth-graders in Port Townsend, or the rockfish defenders in the San Juans. For all those costly sewage plants, individual action still matters. A better understanding of this intricate inland sea should lead to wiser decisions and enrich future voyages of discovery.

Puget Sound: A changing profile
-- Area: 2,000 square miles.
-- Shoreline: 2,300 miles.
-- Mean depth: 600 feet.
-- Volume: About 1 trillion cubic meters.
-- Temperature range: 45 to 60 degrees F.
-- Adjacent human population: 3.8 million .
-- Government jurisdictions: 8 counties, 5 major cities.
-- Recreational vessels: 16,000 power boats, 21,500 sailboats, 43,500 canoes and kayaks.
-- Ship traffic: 3,000 cargo and passenger ships per year; 560 tankers, 4,000 oil and chemical barges.
   Shoreline: Of Puget Sound's 2,300 miles of shoreline, about one-third has been modified by development ranging from timber bulkheads to world-class seaports. Two-thirds, or 1,541 miles, remain essentially natural.
   Water quality: Generally improved from a decade ago, probably because of better sewage treatment and enforcement of pollution laws.
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