Concerns Aired Over Draft BiOp; New Round Of Litigation Promised
 Fall Chinook Study Challenges Old Assumptions
 Ninth Circuit Upholds Corps' Operations On Lower Snake
 Biologists Take Aim At Feds' Proposed Hatchery Policy
 Tribal Fishery May Not Reach Fall Chinook Goals
 CONCERNS AIRED OVER DRAFT BIOP; NEW ROUND OF LITIGATION PROMISED
The federal government told BiOp remand judge James Redden that its new biological opinion for hydro operations is solidly on track after the judge called a Sept. 28 meeting in Portland to air both his and others' concerns over the direction of the new document. But it also seems likely that the government's new way of analyzing dam operations has put the coming BiOp solidly on track for more litigation in Redden's court.
The judge admitted the meeting was an unusual step. "But we're not attacking the BiOp," he said. "I am concerned about whether or not there is a train wreck in our future." He said if his concerns are realized, a "legally infirm revised BiOp will be filed and if it is filed and if it is legally infirm, it necessarily will be vacated."
He said it doesn't mean dams will be breached anywhere, "but there will be serious legal consequences for the government if they have no biological opinion in effect."
Redden said he questioned whether the government could change the environmental baseline for the new BiOp "in midstream," in order to obtain a "no-jeopardy" conclusion for dam operations. The new analysis in the draft BiOp has separated effects of dam operations from the dams' existence.
"We're going down the track, and I don't know, maybe the government is absolutely right, they can do everything they say they do." But Redden said if the new BiOp is nullified, it would be exposed to legal consequences that he didn't think had ever happened before.
Redden said though they may change, the government's own figures indicate that the wild runs are on an "extinction pathway."
Justice Department attorney Fred Disheroon defended the new analysis, saying that the ESA requires NOAA Fisheries to "come up with the current depiction of what actions are being evaluated," federal actions which fund or carry out particular proposals that are likely to affect endangered species under section 7.A.2 of the ESA that calls for consultation.
In the new action, Disheroon said federal agencies took the "Reasonable, Prudent Alternative" from the old BiOp with some changes. The previous RPA spelled out 199 different actions to help proposed hydro operations in the 2000 BiOp overcome the NOAA's judgment that they jeopardized ESA-listed stocks in the Columbia Basin.
Those changes, according to Disheroon, were included to keep from relying on non-federal fish recovery actions that Redden had used as a basis to nix the old BiOp. The judge had ruled in May 2003 that those kinds of actions weren't reasonably certain to occur.
Though Disheroon said the modifications required a significant revision of the jeopardy analysis, he emphasized that many, "if not most," of the actions in the original RPA will be included in the proposed action, "so the agencies have come to the same conclusion, avoidance of a jeopardy conclusion."
Disheroon said the new BiOp will also reflect changes in "circumstances" between that time and updated scientific information. From a legal perspective, he said NOAA Fisheries doesn't think there has been a change in the environmental baseline, but "circumstances" have now allowed NOAA to separate effects of the dams' existence and their operations.
Disheroon said proposed operations will include specific actions that will be carried out by federal action agencies themselves and not rely on third parties, which the judge had ruled were not reasonably certain to occur in the earlier BiOp.
Disheroon said the feds feel the new Biop will be legally defensible and a much better opinion, and specific to the actions of the hydro system. "We don't believe we were headed for a train wreck.," he told Redden. "If we were, I don't believe, your Honor we'd be here today telling you this."
Earthjustice attorney Todd True, representing the National Wildlife Federation and other groups who successfully sued to bring the old BiOp down, agreed with defendant-intervenor Idaho that the federal agency has broad discretion during the remand to come up with a lawful plan, but it's really not "altogether" apparent that the feds have avoided the earlier problems in the previous BiOp
"The elephant in the room here is that this is just not a situation where the former RPA has been modified and become a new proposed action," said True. "The agency has also fundamentally changed the way it evaluates jeopardy..." And it was on that point that some of the most "serious questions" arise, he added.
True said plaintiffs think this new draft biological opinion is based on a new set of legal errors in interpreting and applying the ESA regulations, and "it will ultimately come back to the court to say what the law is, and if the government doesn't get it right ... we will be facing quite a situation, because we have a second time that the government has offered up a plan that does not comply with the law."
Oregon's representative David Leith questioned the agency's "gap analysis," the new framework used by the feds to measure effects on fish from the proposed hydro operations compared to a theoretical "reference" operation that maximizes survival. Leith characterized the issue as "whether species will go extinct quicker or if they will go extinct at the same speed they were going to go extinct anyway."
But written comments offered by the Columbia-Snake Irrigators' Association took a potshot at the "reference" operations in the draft BiOp, which they called an inappropriate baseline because it didn't include sufficient flood control or irrigation "to fall within the discretionary authority of the federal agencies. They also questioned the federal draft because it required dam operators to offset future federal decisions that might boost harvest rates of listed species.
But by the end of the meeting, there was little doubt that the new BiOp will be challenged by the same groups that took the previous one to court in 2001 and questions were raised about scheduling briefs for the next round of litigation.
"Clearly, we are headed for litigation," said attorney David Cummings, representing the Nez Perce Tribe. He said plaintiffs will probably want judicial review of the new BiOp before next spring's salmon migration.
Judge Redden said he was naive enough to think the remand would get to the endgame, but "now we start all over again." He didn't see how it would take less than another year to finish briefing in the litigation expected over the next BiOp.
An Odd Request
Several weeks ago, Judge Redden released his order, expressing "concerns" whether the remand process had "divulged significantly" from the intent and terms of his May 2003 order and if the draft BiOp released Sept. 9 is "consistent with the law in this case."
Noting that the draft BiOp differs both in its analytical approach and conclusions, the judge asked defendants if they have used the remand period to create a new biological opinion rather than modifying the old one to address his specific concerns over where some fish mitigation actions were reasonably certain to occur.
The new draft has an admitted change of focus. NOAA Fisheries ' regional administrator Bob Lohn said as much at a Sept. 9 press conference when the details of the new draft were released. Lohn said newer survival data on fish passage had allowed his agency to change the environmental baseline by separating effects of the federal dams' operations from their existence.
Lohn said the new analysis, which also reflected the improved numbers of salmon and steelhead in ESA-listed runs throughout the Columbia Basin, has led the agency to conclude that the operation of the hydro system does not jeopardize the listed stocks.
But Judge Redden wanted to know what evidence supported changing the baseline and what gave the agency the legal authority to do so. And even with the change, "why would all the detrimental impacts on the fish from all sources not require a jeopardy conclusion?"
The change in the baseline was an issue that had already been raised at an earlier status review hearing in Redden's court by Earthjustice attorney Todd True, who had characterized the new BiOp's focus on operations as moving the goalposts in the middle of the game. The feds announced the new framework for analysis after several collaborative sessions with state and tribal co-managers ordered by the judge as part of the remand process.
On Sept. 9, Lohn said that Judge Redden's opinion clearly directed his agency to focus on the [dam] effects "we're being asked to consult on."
Lohn said the BiOp was only a part of the overall salmon recovery picture, with the Northwest Power and Conservation Council's subbasin planning effort an important foundation of the effort. Lohn said his agency remained committed to an approach that was expected to cost $6 billion over the next 10 years and included improvements in hatchery operations, harvests, and habitat.
Several attorneys involved in the remand were surprised by the order, noting that the baseline change was no secret, since NOAA Fisheries had opted for the new direction in the BiOp analysis months ago. Another party familiar with the remand considered the judge's questioning an attempt to embarrass the Bush Administration before the election. -Bill Rudolph
 FALL CHINOOK STUDY CHALLENGES OLD ASSUMPTIONS
A freshly minted academic paper that examines Snake River fall chinook populations may prove to have profound effects on future hydro operations. Though it hasn't yet been officially printed, the document has been cited in the draft BiOp and other places, and has created quite a stir because it challenges the validity of current analyses used by NOAA Fisheries analysts in the draft BiOp.
The paper, titled "Two Alternative Juvenile Life History Types For Fall Chinook Salmon," has been accepted for publication in the peer-reviewed journal, Transactions of the American Fisheries Society. It reports on an analysis that suggests a good portion of the fall population in the Snake River Basin do not migrate to the ocean a few months after emergence from gravel, as most biologists have thought, but spend the winter in reservoirs to migrate by early the following spring. Scale analysis of returning adults has shown about 41 percent of wild fish and 51 percent of hatchery fish had been reservoir-type juveniles.
The later migrating fish are much larger, which gives them a huge survival advantage over sub-yearlings, according to the paper's lead author, USFWS scientist Billy Connor. Connor is based in Ahsaka, Idaho, and has studied the fall stock all 17 years of his professional life. He told NW Fishletter that nobody is sure which reservoirs these fish like to hang out in during the winter, but there is some evidence from radio-tagging juveniles caught by hook-and-line that some do move past Lower Granite Dam to other reservoirs downstream after the dam bypass systems have been shut down.
The paper suggests that about half of the juvenile fish from the lower Clearwater River, an area characterized by the researchers as "one of the coolest, least productive contemporary spawning areas," exhibited such a reservoir-type life history.
But, on average, only 2 percent of the wild fish from the upper reach of the Snake, which is the warmest, most productive spawning area for the fall chinook stock, showed the "reservoir-type" life history.
The scientists said, based on their analyses, "There is no typical juvenile life history for the Snake fall chinook," but both types are important to recovery and without summer flow augmentation, mortality of these later migrating fish would be higher. They believe that the fish which stay behind are a "successful response" to the great changes in historical habitat that have been improved by summer flow augmentation.
The authors also say that the decision to de-water the six dam bypass systems at Snake and Columbia River dams during the winter is not supported by the existence of the reservoir dwelling type of fall chinook. Moving past dams in the winter means these fish suffer higher mortality because they must pass through turbines. The authors also suggested that some water now used for summer flow augmentation should be saved for release in September.
As reported in the draft BiOp, up to 80 percent of the original spawning and rearing habitat of Snake River fall chinook was blocked by the Hells Canyon Complex, three large dams constructed by Idaho Power. The first large dam, Brownlee, was completed in 1959, and the last, Hells Canyon, was finished in 1967.
Since then, an effort to establish fall chinook in the much colder Clearwater River has been underway using hatchery-raised fish released in the river. Redd counts have increased from about 30 in 1994 to over 500 in 2002. In the mainstem Snake, redd counts have improved dramatically as well, with the help of a kindly ocean and hatchery supplementation, going from 67 in 1994 to 1,113 in 2002.
These findings could have important consequences for future fish research. As noted in the paper, transportation studies all have a basic assumption that the fish being barged are all leaving the reservoir at the same time, in the first year. But Connor and his fellow authors say ongoing studies likely violate that assumption and that scale patterns should be examined to identify the life history of returning adults from the transportation study.
The lower Clearwater-- where more fall chinook are flaunting a new lifestyle.
(Photo courtesy COE)
However, ongoing research has already run into some snags. NOAA Fisheries failed to gain the endorsement of regional fish managers to collect scale samples this fall at Lower Granite Dam. In a Sept. 24 letter, the managers said it would be better to delay the work until next year, to better define objectives and proposed research and "will allow additional time for the development of scientific objectives," which they said would benefit the research by "reducing controversy and conflict in the application of the research results to significant hydrosystem decisions, as well as potential impacts on other fishery management activities such as run reconstruction data collection by the state and tribal co-managers."
Conner said he is already sampling scales from transported fall chinook and that should help begin to clear up some of the current unknowns. But he noted that current estimates of juvenile in-river survival may be too low if a good portion of the run doesn't even leave until late in the fall or the following spring. At this point, scientists may be over-estimating the relative survival of barged fish, Conner said.
Current operations call for barging over 90 percent of the fall run, and the draft BiOp calls for maintaining that strategy because no clear direction for future policy has come from present research. However, analysis of Snake fall chinook survival in the draft has estimated that proposed operations would kill about 13 percent more fish than hypothetical hydro operations maximized for fish benefits.
But NOAA Fisheries' own scientists are expressing caution about that analysis. In a late August memo released when the draft BiOp went public, federal scientist John Williams said "we have no idea what effect reference actions might have on the yearling-migrant portion of the population. Changes in summer river conditions under the reference action might benefit subyearling migrants, but have no effect on yearling migrants, the life-history stage that has produced approximately half of the adult returns. On the other hand, changes to flow and spill under the reference action might encourage some fish to migrate as subyearlings, and in terms of their chances of ultimate survival to adulthood, this would lead to a lower adult return rate than if they had migrated as yearlings the following spring. Thus, considering all segments of the population, the reference actions might actually decrease overall stock performance rather than increase it. We just don't know - we have no data that could provide a basis for meaningful modeling of this important aspect of the complex life cycle of Snake River fall Chinook salmon."
Williams told NW Fishletter that Connor's latest paper will be also be cited in his group's final full-length report of dam effects on fish survival that will be released soon. -B. R.
 NINTH CIRCUIT UPHOLDS CORPS' OPERATIONS ON LOWER SNAKE
A three-judge panel from the Ninth Circuit Court has voted 2-1 to deny an appeal by the National Wildlife Federation and other environmental and fishing groups who challenged operations of the four federal dams on the lower Snake River, part of a nationwide campaign that still calls for breaching them to save fish runs listed under the ESA. The groups claimed the Corps of Engineers violated state and federal statutes by operating the dams and often exceeded temperature and dissolved gas limits set by the Clean Water Act.
The original suit was brought in 1999 in Oregon District Court and amended in 2001 after the Corps modified its earlier records of decision on operations to acknowledge that the construction and existence of the dams may have contributed to a shift in the temperature regime of the lower Snake. The agency promised it would take more steps in line with the NMFS 2000 BiOp to improve compliance with state standard.
The panel's majority said it was not persuaded by an EPA model that found the dam operations did raise temperatures above the standard. They noted the model results were based on a comparison of operations with the dams in place and with them removed, not on comparisons of different operations with the dams in place.
The Corp's own model concluded the dams' existence caused temperature increases after they were constructed, when a general temperature shift took place in that part of the river, with water staying cooler longer in the spring, but once warm, staying warmer longer.
The panel's majority opinion, written by Ronald Gould, disagreed with the plaintiffs, who contended the Corps' 2001 record of decision was arbitrary and capricious because it distinguished between the dams' existence and their operations. They could not agree with the plaintiffs' contention from the EPA study that the operations caused the higher temperatures. "To the contrary," they wrote, "The EPA supports the Corps's contention that it is the existence of the dams that is causing temperature exceedences."
The panel cited a recent ruling by the US Supreme Court in Norton v. S. Utah Wilderness Alliance that protects agencies from undue judicial interference, noting that their job wasn't to second-guess the Corps' decisions, but to determine whether its actions "were arbitrary and capricious, an abuse of discretion, or contrary to law."
But the panel said the district court ruling was partly erroneous to conclude that because the agency had adopted the recommendations in the 2000 BiOp to satisfy ESA obligations, the Corps had also complied with the CWA.
Dissenting judge Margaret McKeown said the decision inverted a fundamental principle of review under the Administrative Procedures Act because "it allows an agency decision to stand simply because it perceives an absence of conclusive supporting evidence, even when no supporting evidence exists." She said the court record was lacking any evidence that the Corps' operations of the dams was not one of the causes for exceeding temperature standards.
"Even talking about removal of the dams is a lightning rod we need not strike," McKeown wrote in her dissent, noting that compliance with the CWA and the "continued presence of the dams are not mutually exclusive options." She said the Corps' failure to tackle the CWA issue required remand.
Earthjustice attorney Kristen Boyles said plaintiffs hadn't decided whether to pursue an appeal. Two options were possible, she said, either call for a re-hearing by the three-judge panel or ask for an en banc hearing by a full panel of 11 judges from the Ninth Circuit. -B. R.
 BIOLOGISTS TAKE AIM AT FEDS' PROPOSED HATCHERY POLICY
A group of mostly-retired Northwest biologists with years of experience dealing with artificial propagation have called NOAA Fisheries' proposed hatchery policy "seriously flawed," and said it should be "immediately terminated." The new policy is being developed to satisfy a 2001 court decision that said hatchery fish in the same environmentally significant unit as wild fish must have the same protection under the Endangered Species Act.
In Aug. 24 comments sent to the federal agency, the group of 11 scientists said the new proposals still won't make any substantive changes in the way hatchery and wild fish are considered for listing under the ESA.
"The overarching problem," they say, "is that the ESA is being administered as a fish management policy, not a statute to protect endangered species."
The group, which includes Ernie Brannon from the University of Idaho, James Lannin, emeritus professor from Oregon State University, and Gary Wedemeyer (emeritus) from the National Fisheries Research Center in Seattle, says that federal policymakers tend to ignore the second part of the law that calls for a program for the conservation of endangered and threatened species.
They also criticized the 2001 conclusions of the Independent Scientific Review Board--the science panel used by NOAA Fisheries and the Northwest Power and Conservation Council--that were used as a primary reference for the proposed policy. The retired biologists said the ISRB report didn't accurately reflect the evidence, that the board members "incorrectly attribute poor performance of hatchery fish to artificial propagation when the factor responsible was fisheries management."
The group of retired scientists has previously weighed in on hatchery issues, circulating their own white paper a few years ago that bucked official thinking on many hatchery issues. Now they say artificial propagation has taken the blame for management errors, distorting the view of ESA administrators that don't have enough experience to know the difference between the two.
"When poorly adapted fish are introduced in a stream, it is not the fault of the fish," they said, pointing to supplementation efforts that have proved successful.
But by allowing the harvest of hatchery fish in the same ESU as wild fish, the scientists say it's apparent that the feds still view them as "extraneous" to listed populations.
NOAA Fisheries released the proposed federal policy last June after years of interim policymaking and confusion led to several lawsuits that brought the issue to a head. Now federal agencies are scrambling to complete a joint policy with the Department of Interior on hatchery practices and their ESA obligations.
NOAA Fisheries has extended the public comment period on the new hatchery and listing policies until Oct. 20, and has hosted meetings throughout the region, scheduling a Seattle get-together on Oct. 5 and one for Portland on Oct. 13.
The proposed policy has recently taken criticism from other university scientists as well. A peer panel convened by NOAA Fisheries earlier this year went public in Science magazine in April, saying the new hatchery policy was too lax.
The six ecologists on the peer review panel said hatcheries generally reduced fitness and inhibit future adaptation of natural populations, and that the legal definition of an ESU must be unambiguous. "Hatchery fish should not be included as part of an ESU," they said. The scientists said they went public after the federal agency resisted their findings and said their conclusions went beyond the science into policy.
Idaho professor Brannon said the panel's comments in Science was "an opinion piece, not science."-B. R.
 TRIBAL FISHERY MAY NOT REACH FALL CHINOOK GOALS
More than half a million fall chinook have been counted over Bonneville Dam since August and a thousand or two more are still passing the concrete every day, but tribal fishers on the Columbia River have only caught a bit more than half of their allocation of upriver brights. With harvests limited by impacts to wild ESA-listed Snake River fall chinook and upriver steelhead stocks, the fishery ended early last year when the steelhead quota was reached with about half the URB allocation still on the table. Low prices for fish in 2003 also reduced the number of harvesters.
Prices are up considerably this year. It was reported that wholesalers were paying $1.00/lb for upriver brights, three times what they were paying last year, but the tribal harvest effort is still down considerably from a few years ago.
By the end of September, some harvest managers thought the tribes would reach their quota of ESA-listed steelhead (about 2,000) before they filled their quota of upriver brights, but a last-minute bump in expected steelhead returns has kept them fishing into October.
Tribal harvesters had caught about 124,000 fall chinook by Oct. 1, which includes an estimated 48,000 upriver brights, only about 14 percent of their 23-percent share of that run. The latest figures show that their 972-fish impact on wild B-run steelies headed for Idaho is now about 9 percent of the latest estimate of that run size (about 11,900 to the river mouth), up more than 3,000 fish from the managers' estimate three weeks ago.
Because they reached their steelhead quota fairly early last year, the tribal fishery ended before they reached their allotment of upriver brights, in spite of attempts over the past few years to encourage tribal netters to use larger-mesh nets that had less lethal impact on the listed steelhead. In 2000, BPA bought $300,000 worth of special nets for the fishery to encourage steelhead passage through the Zone 6 tribal fishery that begins behind Bonneville Dam.
The chinook quota may not be reached simply because there are less nets fishing than a few years ago. In 2001, about one-third of the 600 tribal nets counted in the river were the larger-mesh variety, but no one keeps track of them these days, said WDFW harvest manager Cindy LeFleur.
This year, about half of the tribal harvesting effort, 115 set nets, were being fished in John Day Pool to stay away from the low-value tule chinook who call Bonneville Pool home. More than 170,000 tules along with 376,000 mid- and upriver brights had been tallied at Bonneville Dam by Sept. 29. Spring Creek hatchery found itself with a 70,000-tule surplus after picking 7,000 for broodstock purposes.
WDFW personnel reported that wholesale buyers were only paying $.10/lb for tules this year, the same price they offered for steelhead and coho. But prices for upriver bright chinook were much better, about $1.00/lb, reflecting higher demand coast-wide for wild chinook this year. Some tribal fishers received twice that when they sold directly to the public, "over-the-bank" style.
Wild fish advocates should be happy though, if the tribes' share come up short again this year, it's likely to translate into a few more ESA-listed Snake fall chinook making it past the last of several fisheries before hitting their home river. Starting in Southeast Alaska, fishermen target the fall stocks and catch about half of them before they have passed all the trollers, netters and sporties. Last year, it was estimated that nearly 4,000 wild falls made it back to Idaho, about one-third of the nearly 12,000 hatchery plus wild fish counted at Lower Granite Dam for the season.
With more than a hundred falls still passing Lower Granite every day, the 13,000-fish count has already surpassed last year's tally and should bode well for this year's wild run, not to mention the large numbers of fish piling into the Hanford Reach, where numbers over McNary Dam exceed 153,000, more than three times the upriver fall chinook escapement goal set by harvest managers. Another 36,000 or so chinook have even passed the Reach and were counted over Priest Rapids Dam, where many will spawn in the tailrace of Wanapum Dam.
The fall chinook run has been so good overall that harvest managers decided to let sporties retain chinook in the Lower Columbia after Sept. 30 and gave commercial non-Indian gillnetters more fishing time in October.
A strong run of hatchery steelhead has also paved the way for Washington fish managers to open the mid-Columbia to fishing for the fin-clipped finnies, with a 2-fish per day bag limit. The rule holds for the Columbia above Rocky Reach Dam and in the Methow and Okanogan rivers. -B. R.
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