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The Show "Deep Crisis" premiered January 28, 2002,

				Out West - Conquering the Columbia, Part 1 Biologists find ways to increase young salmons' chances of getting around dams and to the sea.
		Select text to jump ahead in the clip: When Lewis and Clark explored the West 200 years ago, they saw sights like this. On the Columbia River, the salmon were jumping very thick, wrote John Ordway, the expedition's senior sergeant. So, what are all these slots in here? ALDA: Today the Columbia is just one part of a settled and industrialized Pacific Northwest. It's not impossible to see a wild salmon jumping a waterfall, just a lot harder. Dams are the most visible of many reasons for the decline of the Northwest's salmon. Here on the Washington-Oregon border, the Army Corps of Engineers' McNary Dam, opened in 1953, reaches for a mile across the river. It's one of hundreds of large dams distributed throughout the enormous Columbia-Snake River system, which stretches across four states and up into Canada. Several of those dams completely blocked fish from going upstream, knocking out more than a third of the system's salmon habitat. The dams made life for the remaining salmon much harder. When young fish head out to the ocean, for example, they have to contend with this. McNary's electric generating turbines can kill young fish, but about 15 years ago the way the dam was run began to change. Is it that the environmental protection laws have required you to run the plant in the way that's best for the fish? MAN: Oh, yes. So it's not just running the plant; you have to worry about the fish as part of your job now? Guaranteed. I mean, when I first hired on the Corps, the most important thing in this facility was the safety of the employees, navigation law and power. Since I've been here, safety is number one, fish is number two. ALDA: You can see the result in the control room. The 14 turbines could together produce 980 megawatts, but today they're running at less than 860. This is a salmon smolt, a one-year-old fish that's ready to move downriver to the ocean. It's about to experience McNary's turbines firsthand and then report back. First there's a mild anesthetic, so a radio transmitter and flotation balloons can be attached. This is one of millions of smolts raised in hatcheries each year. At the last instant, a foam mixture is added to the balloons, and then... Now he goes down through the turbine? Yes, he's going right through the turbine. ALDA: Down it goes, 70 feet deep, through the spinning turbine blades, then out below the powerhouse. By now the flotation balloons will have inflated, so the fish will be somewhere downstream on the surface. Meanwhile the researchers are sending down a somewhat less lively instrument package. In the river below the dam, the recovery crew is on the lookout. Within minutes they pick up the radio signals from the fish and the instrument package. Three o'clock. ALDA: Surprisingly enough, the smolt made it through unharmed. In fact, around 90% survive if the turbines are run at flow rates which reduce forces on the fish, as they are today. Those forces can be measured with the instrument package, while turbine speeds are adjusted. Now, all the Army Corps's Columbia turbines are run to minimize fish losses. On a typical Columbia dam, half the structure is the powerhouse; the rest is spillway. As with the turbines, spillways are also now operated with fish in mind. ALDA: That's a great sound. It sounds like Niagara Falls. It kind of is like that, for a spillway. Today we're spilling about 100 kcfs. That's a spectacular sight. ( water roaring ) The ability to do a spill like this on the dam-- was that intended originally as a kind of a pressure valve when there were flood conditions? Correct. It wasn't with the fish in mind at all? No way. Now you open the spill for the fish as well as for the flood. And it's an interesting story, because originally when you had a spring runoff like this that's forced spill, it used to cause a lot of harm for fish because the water used to plunge straight down, supersaturate the water... uh, nitrogen... they'd get like the bends and it'd cause a lot of mortality. So all the dams have been retrofit with what they call "flip lips" that actually slides the water kind of out instead of plunging it down. ALDA: With flip lips, and if the flow rates are just right, approaching 100% of young salmon can make it through a spillway. So it doesn't sound too hard for a young fish to get past McNary Dam. But that's a small part of the challenges facing the Pacific Northwest's salmon. Let's take a look at the Columbia system from a salmon's point of view. In we come from the Pacific Ocean, through the estuary. We've been using our internal compass to get here, but now as we head upstream, we're beginning to pick up the distinctive smell that we remember from the water where we hatched four or five years ago. We're determined to spawn in the exact same river, lake or stream, and we're prepared to travel 500 miles inland-- a thousand or so river miles-- to get here. Now we've arrived in central Idaho or eastern Oregon. Once there were hundreds of different groups of us salmon in the Columbia system, distinct stocks that each used the system in its own unique way. We find the stream, find the right kind of gravel, find a mate, and make a nest for the eggs. Next spring the fry hatch, then hang out and grow for a year before hitching a ride as smolts on the following spring runoff. Down the river we go, out to sea for a couple of years to eat and grow. Today, more than half the Columbia's original stocks are extinct. For thousands of years, Native Americans were the only people who exploited the Columbia's salmon, but that couldn't make a dent in the ten to 15 million fish that returned each year. Then, as the numbers of settlers grew in the 19th century, salmon came under increasing pressure. Large-scale net fisheries were established in the Columbia estuary. Canneries were set up. By the 1930s, returning fish numbers were down by half. At the same time another bonanza was under way in the forests through which many salmon rivers and streams flowed. MAN: Timber! FILM NARRATOR: Chute them off the hillside, snake them down the creek, raft them down the river out to the Pacific, to Africa and Australia and Ireland. Feeder logs for the plywood mills of Japan, ties for the Trans-Siberian Railway, timbers for North China mines. ALDA: Logging was devastating for the salmon. It turned clear, cool streams into muddy, warm pools that no longer support spawning. Some attempts are made to protect streams today, but it's still a serious problem. And then on top of the fishing pressure and the logging...

				Out West - Conquering the Columbia, Part 2 Biologists find ways to increase young salmons' chances of getting around dams and to the sea.
		Select text to jump ahead in the clip: FILM NARRATOR: At Bonneville, Oregon, man takes up the struggle against the frontier. Cascade Rapids-- since pioneer days the graveyard of ill-fated ships-- in 1933 make way for Bonneville dam. America's conquest of the Columbia has begun. Just as the Nile is the lifeblood of the historic land it drains, so this river of the West is the key to the future of the Oregon country. An unshackled giant becomes a seaway to an empire, the promise of power for every corner of the Northwest. Power to make a million and a quarter acres bloom again. Power to push the city to the farthest county line, to bring better crops and better living to the farmers of the region. Power for the home, good light for Billy's eyes, electric cooking for Mother, the comfort of electric heat and electric cold. Leisure to replace the burdens of an outworn era. Power to make the American dream come true. ALDA: As far back as the 1870s, it was thought that we could have the American dream and salmon, too, by building these. It's a hatchery where young salmon are raised for a year until they're ready to go to sea as smolts. There are about a hundred hatcheries in the Columbia system, producing about 200 million smolts a year. All hatchery smolts are marked by clipping a fin that's not used for swimming-- an evolutionary leftover. This mark persists with the adult fish, so it's been possible to track how well hatchery fish do compared to their wild companions. Only about ten percent of the smolts in the Columbia system are wild-- spawned, hatched and raised naturally without human intervention. But up to 30% of the adults that make it back from the ocean were wild smolts. Wild fish do much better in the ocean and the river. Biologists think they're more aggressive, know how to avoid predators-- just smarter and tougher. Dams have made the river more difficult for all smolts, wild and hatchery. For example, there's not enough flow in the reservoirs behind the dams to carry young fish downstream, so they have to use precious energy to swim. Since the 1970s a lot of effort and hundreds of millions of dollars have been put into helping smolts down the river. The most important dams have been fitted with elaborate screen systems to catch the smolts and divert them around the turbines and spillways. This is just one part of one of the 42 fish screens at McNary Dam. The system works by directing the young fish up and away from the turbine intakes and into a separate channel inside the dam. The channel leads to a special fish-processing facility. At the heart of the system are stainless-steel screens that create a cushion of water to guide the fish. This is sophisticated and expensive engineering. McNary's screens alone cost $17 million. ALDA: The water is hitting that screen. COLEMAN: Correct. And it's backing up a little bit. Yes, and the fish are actually tumbling kind of back with their tail to the stream. Why are the fish going backwards? They're not really swimming to the ocean. They're just flowing with the current, heading to the sea. Oh, is that how they ordinarily go down? Yeah, there's a big spring runoff. Just Mother Nature takes care of them and flushes them. You know, you could have told... You could have asked me a million times; I would never have said, uh, "They go backwards to the ocean." I mean, that's... Okay, well... What's happening here? We're closing down shop. They've got work to do. You're okay. If you don't move, you're okay. You're okay if you don't move. It's not an unusual amount of water... ALDA: Dave Coleman took me down inside the dam to see the channel where the separated fish end up. We're entering the juvenile collection channel, designed to pass 2,000... ALDA: We're here at the height of spring runoff, when they're collecting 350,000 smolts a day. The screens are not perfect. They catch 75% of some species but only 30% of others. ALDA: Don't they get shaken up a lot? That's really going very fast, isn't it? That's engineered by the greatest fish design engineers in the world, and that's perfectly acceptable. ALDA: The quarter-mile-long channel is just the beginning of a peculiar journey for the young fish. I saw my chance to check if they really were going backwards. You can start seeing some of the fish right here. There's one. There's one. There's one. Oh, yeah, now I can see them. ALDA: Dave was right. They do go backwards. ALDA: You know what it is? When you go some place in the car, you can't find your way back because the scenery looks different in the other direction. They go backwards so they see what it looks like coming the other way, so they know where to go. ALDA: Actually they head into the flow because that gives them maximum control. The diverted fish emerge from the dam in this pipe, which loops down into the fish facility. A sample is anesthetized so they can be identified and counted. The Columbia has five salmon species and two closely related steelhead. Hatchery and wild fish are counted. ( clicking ) And now the smolts' journey is about to get more peculiar. For 15 years, about half the smolts in the Columbia system have been given a ride downstream courtesy of the Army Corps of Engineers. They're loaded into specially built barges-- a quarter of a million fish at a time-- and driven downriver in luxury, safe from turbines, spillways, predatory fish and hungry birds. It takes a couple of days for smolts to get down below the Bonneville Dam, the last on the river. Almost all survive the barge trip, and a higher proportion of barged fish return as adults compared to those that came down the river on their own. But the return rate for both groups is very low, only a percent or two-- much less, it's believed, than made it back historically. There's a net system used to count smolts as they leave the river. One theory is that both groups are in poor shape as they go out to sea-- the barged fish because they have to cope with saltwater before they're ready, and the others because their river journey has been so stressful. Many smolts heading out to sea-- still backwards-- have electronic tags that the net system detects. They're called PIT tags-- microchips containing unique ID numbers. Once implanted, the tags stay with the fish for life. In the last decade, more than five million have been used on the Columbia, and they've revolutionized research. PIT tags have told us about the effects of barging. These fish are part of the continuing barging study. They've told us about the effects of turbines and spillways. They're a sophisticated tool to match the technology that, to the dismay of environmentalists, is now an integral part of the life of Columbia River salmon. These are fish that have been collected up on the face of the dam and through a series of pipes. ALDA: I'm at the McNary Fish Facility with Mike Schiewe, the biologist who runs much of the research on the effects of technology on fish. This is the, uh, juvenile fish separator, and this is where the different size juveniles are sorted. ALDA: The facility is a maze of pipes and channels equipped to detect PIT tags and automatically divert a fish that's part of a study, for example. If it were to detect a fish, now, there's... the, uh... what would happen is... ( detection door hisses ) And then the fish just drops down below. It's like an amusement park. Oh, it is, yeah. It's amazing. Let me do that again. ( door hisses ) So, what, the fish goes through here? Yes. And the tag is read by the computer, and that gate opens that fast. So by the time the fish gets there, the gate's open. That's correct. ( gate hisses ) It's an amazing system. It's what the computer age has brought to fisheries. ALDA: The computer age arrived on the Columbia just in time to help study a crisis. In the '60s and '70s, four new dams were built on the Snake River. Now Snake River fish had twice as many dams to pass to reach the ocean. Four salmon stocks began to collapse. They and eight more stocks elsewhere in the system were declared endangered. For West Coast salmon today, the count is 26 endangered stocks-- half of those that are left. The response at the eight Snake and Columbia dams was the measures we've seen-- fish screens, spilling water and adjusting the turbines. Even so, about ten percent of smolts are lost at each dam. Bypassing with barges helps make up some of the losses. ALDA: Does the fact that ten percent die lead you to think that maybe the dams are stressing the fish and that's why a lot of that ten percent may be perishing? Well, I don't think there's a question that the fish would survive at a higher rate without the dams. Um, we've made major improvements, I think, in the system and how it operates in the last 20 years. Survival now for the yearling fish, uh, is... is roughly 50% to 60% through the whole system-- the eight dams coming down from the Snake River to the, uh... below the Bonneville Dam at the Pacific Ocean. Uh, this compares with what the survival was about 20 to 30 years ago when there were only four dams in place. But we hit a real low point in the, uh, '70s, uh, when more dams were coming on-line when the operations were not as... as, uh... as safe for fish. Uh, so we're making progress in that regard. ALDA: We're heading back to where we picked up the smolt that came through the turbine. It's a measure of how unnatural things are that there's a program to reduce the number of predators that hunt salmon smolts. Smolts make easy prey in the reservoirs where there's no shelter and also as they emerge disoriented from the turbines and the spillways. MAN: Be careful not to touch the water when the generator's on. Okay. It might, uh, give you a little buzz. Don't touch the water while the generator's on. Liable to get electrocuted. ALDA: The electric shock stuns all the fish around the boat for a few seconds. These are American shad. They're a game fish introduced from the East Coast. ALDA: We're going to pick out the three important smolt predators. Those are all large-scale suckers. That's what we're looking for. Got a keeper. This is a walleye. ALDA: Now, that's a predator? That is a predator. ALDA: Back at the dock, the unfortunate walleye showed us where about 12 million smolts a year end up-- six percent of the smolts in the system. FRIESEN: That is a fish that just popped out of the stomach. ALDA: Then Tom Friesen did a surprising thing. Back in the water. Now, if he's a predator, why do you release him? He's going to be able to get more salmon, right? Walleye are pretty highly regarded game fish. So if we just removed all we could, there would be people upset that they couldn't fish for walleye anymore. And smallmouth bass are the same way. ALDA: So our smallmouth bass was also released. But not so the third fish. There's a million or more of them. They're not game fish, and fishermen are paid to catch them. That's probably a northern pike minnow. ALDA: It's hard to know how much effect this all has on how many adult salmon eventually make it back from the ocean, and that's the case with virtually everything we're doing on the river. This is the fish ladder at McNary, and right now it's full of returning adults. Last year was pretty good, too, with a million returns. That's good news, but it's confusing. They got down to only a quarter of a million returns in the 1990s, just when all the efforts to help juvenile fish survive the downstream trip should have been paying off. So there are still big unknowns out at sea. ALDA: Wow, these are big guys, aren't they? Oh, they're beautiful fish. These are, uh, summer chinook. They've been, uh, down through the system as juveniles and been out to sea for two, three, four years and now they're coming back. Do you count every single fish that comes through? Every fish that comes through the, uh... the ladder is... comes by this window. So this is where they come in? Yes, it is. What, you narrow it down so that you only get one at a time? Exactly. Now, that's a shad. Big chinook. Another chinook. That ladder looked like a pretty long, uh, structure. Is... Does that put them through more work than they would ordinarily have to go through to get up the river if there weren't a dam they had to climb up? Well, before the dams, they, uh, definitely climbed falls, uh, and so they went through those kinds of structures. Uh, sometimes they have a little trouble finding the entrance to the fish ladder, but once... once they do, uh, they move through it fairly quickly. Uh, fish ladders are one of the real success stories of, uh, salmon migration. ALDA: As the observers do the count, they distinguish between wild and hatchery fish. ( clicks ) Here's a wild chinook with its rear fin intact. And here's a hatchery fish with the fin missing. Overall about two-thirds of adults are from hatcheries. Hatchery fish saved the salmon fishing industry in the Northwest, but one concern is that hatchery and wild fish may interbreed. The remaining wild stocks could begin to lose their unique adaptations. Some wild stocks are now down to a few thousand returning adults. With some, only half of one percent of the smolts that went to sea make it back. So there may be a million salmon in the Columbia, but some may still be headed for extinction. It's vital, says Mike Schiewe, to preserve the variety of salmon stocks that we still have left. It's not just saving some salmon. It's trying to save as many kinds of salmon as you can. Otherwise you're just leaving them open to the elements and they could get wiped out at any... anytime. We couldn't predict when, huh? SCHIEWE: No, that's exactly right. You're buying insurance against, uh, variations that are bound to occur. Populations of fish rise and fall over the years, uh, and this, uh... this diversity of different life-forms utilizing the habitats and the food resources in different ways allow the salmon to persist at the levels that they do. So saving the diversity of salmon is every bit as important as just talking about numbers.

				Down East - The Extinction Vortex Biologists work to save the dwindling wild salmon stocks in Maine and eastern Canada.
		Select text to jump ahead in the clip: ALDA: We're heading up the Narraguagus River in Down East Maine. For the biologists we're with, this rugged and beautiful country is in the grips of a catastrophe. This river, along with seven others nearby, is losing its last few wild Atlantic salmon, and they don't know why. It's spring runoff, and the traps in the river have been set to sample the two-year-old salmon smolts heading downstream to the Atlantic Ocean. Every year the numbers go down-- just 2,000 this year, one-tenth of the numbers in the past. MAN: One American eel. ALDA: The traps catch everything. The smolts they're looking for are wild, descended from wild parents that know only this river. One salmon smolt. Okay, we've got two smolts. ALDA: As in the Pacific Northwest, hatchery fish that are not adapted to a particular place are not counted as wild. Dorsal score? Zero. ALDA: The last wild Atlantic salmon in the U.S. are confined to eight Maine rivers, and all eight stocks are officially endangered. The numbers are incredibly low. In 2001, less than 150 wild adult fish returned to all eight rivers combined. The numbers of smolts heading out are correspondingly low-- for example, in the nearby Pleasant River. MAN: Our crew here is... I think they're really feeling the numbers going down. It's not just looking at them on paper. Having been here last year, handled 60, 70 smolts a day, this year we haven't even broke 20 smolts a day. ALDA: Things got this way in the Northeast for the same reasons the Columbia salmon declined. Atlantic salmon were once abundant everywhere north of the Hudson River. But change came with colonization. There was large-scale fishing. Thousands of dams were built to power mills and factories. The Connecticut River, a major salmon habitat, was completely blocked. Logging, agriculture and water pollution all took their toll. Throughout the Atlantic salmon's range, from Canada to Russia, the same processes were under way. It's now extinct in half the 50 or so major river systems it once inhabited. Healthy populations remain in parts of just four countries. The big concern is that numbers have continued to plummet, even after heavy fishing in the salmon's ocean feeding grounds off Greenland was stopped 15 years ago. In Maine, research is going on to try to understand the causes. They're going to implant an acoustic transmitter in a smolt and then follow it down the river and out into the Gulf of Maine. At the start of the research, they tested the effects of the implant and, surprisingly enough, neither the fish's behavior nor its health seem to be affected. The body cavity starts healing almost immediately postsurgery. Within a very short period of time everything will be back to normal and the fish will be on their way into the river and then out to sea. ALDA: Once the smolt has recovered from the anesthetic, it's released. ( transmitter beeping ) Okay, we got a good signal on him. ( transmitter continues beeping ) ALDA: They follow the fish for a few hours to make sure it's healthy and the system's working. BELAND: The signal's really strong. The fish is quite close to us, probably within 40 or 50 feet, right up against the riverbank. ALDA: Right now we know surprisingly little about the life of an Atlantic salmon smolt. BELAND: What we're hoping is by understanding where mortality may or may not be occurring... Is there a single smoking gun? Are there a number of factors each of which contributes a little bit? And in total, we're really sort of writing a missing chapter in the life history book. ALDA: An array of 20 remote receivers is set out in the river and the ocean just offshore. They'll record the signal if the fish passes. So far they've tracked 400 smolts, and only half have made it out to sea. That's as bad as the smolts that have to get through eight Columbia River dams, and it's a surprise. But there is a pattern emerging. BELAND: It's a little suspicious that we're having more mortality than expected, and it seems to be occurring disproportionately in or about the area where they first hit saltwater. ALDA: Research in Norway suggests that young salmon from acidified rivers have trouble regulating salt. So New England's notorious acid rain may be, if not the smoking gun, at least one of them. In the 1980s, the Pleasant River had a couple of dozen adult returns a year. It's just a few now-- in some years, none. It's called an extinction vortex-- not enough breeding adults to stay ahead of the losses. As a last desperate measure, biologists are trapping and removing smolts to be raised in captivity. This is the strategy being tried with the California condor, for example. Got a smolt! ALDA: The young fish has the special adaptations that suit it to just this river. As in the Columbia, the only way to keep wild fish in the river is to preserve each unique stock. KOCIK: There are differences between this river and the Narraguagus River right down the road, differences in rearing habitat that we think, over time, have led to local adaptations. So it's important to put fish back into the river their parents came from. ALDA: Young fish from six of the eight Maine rivers have now been removed for captive breeding. Genetic tests have confirmed that each river's fish are distinct. They're kept separately, and they're only bred within their own group. This is exactly what salmon hatcheries in both the Northeast and Northwest have not done, which is one reason hatchery fish have low survival rates. Their genetic adaptations have been mixed up so they don't know how to use particular places. A puff of air helps this Machias River female release her eggs. She was brought here as a six-inch-long smolt three years ago, so now she's ready to breed. Her mate has the same impeccable credentials. The eggs hatch in spring, as they would in the river, and in about a month they're one-inch-long fry. These are what will go back into the wild to the specific river their parents came from. We're on the Machias River for spring fry stocking. This river also gets very low or zero adult returns. MAN: Run her all the way through, Dan. ALDA: River-specific breeding and fry stocking have been in operation in six Maine rivers since the mid-1990s, with over a million fry a year distributed. Why don't we swing close to these little rocks over here and I'll put out a few? ALDA: It's no exaggeration to say that whether or not wild Atlantic salmon have a future in the United States depends on the river-specific program. If it doesn't work, there's very little chance that the species can recover on its own. The fry hang out in the river for two years, until they're ready to go to sea as smolts. Then they catch a ride on the spring runoff, like the Pacific salmon, and head out to Greenland to feed and grow. Two years later, the survivors should be back in the same river to mate, and the cycle begins again. We're back on the Machias River in the fall of 2000, five years since the river-specific program geared up on this river. It's the first year we could see a boost in the number of returning adults. WOMAN: Do you know how many there were here last year or the year before? MAN: The year before, I counted ten or 11 in here. ALDA: We're looking for salmon nests, or redds, in the gravel. There's no redds-- it's kind of surprising. This is a really nice spot here-- you have the ideal or the classic- type spawning gravel here. There's... here's one here. There's a redd? Mm-hmm. ALDA: The patch of disturbed gravel is easy to spot. Each female typically builds two redds during the fall spawning season, so it's not hard to estimate adult numbers by counting redds. The disturbance in the gravel is where the female flapped her