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Part three of a three-part series by Daniel Zwerdling and Margot Williams.

The long, clunky-looking fishing boat pulls up to Day Boat Seafood's dock near Fort Pierce, Fla., after 10 days out in the Atlantic. The crew lowers a thick rope into the hold, and begins hoisting 300-pound swordfish off their bed of ice and onto a slippery metal scale.

As the staff weighs them, a computer printer churns out packing slips signifying these fish are superior to more than 90 percent of the seafood caught around the world — at least, that's what an international nonprofit organization would tell you. Every swordfish that Day Boat catches can carry a special label when it shows up at the supermarket that says "certified sustainable seafood."

The seal of approval comes from the Marine Stewardship Council, which has pledged to promote fisheries that protect the oceans, not plunder them. The MSC says its system has certified more than $3 billion worth of seafood, representing at least 8 percent of the world's annual seafood catch.

Many environmentalists say the MSC system is flawed because it has expanded too fast. They say the growing demand for sustainable-labeled seafood is pressuring the program to certify fisheries that don't deserve it.

But just about everybody NPR talked to about Day Boat, including environmentalists and food industry executives alike, said that Day Boat's story reflects the good that the MSC system can do.

The way Day Boat's owners tell their story, they decided to go through the complicated process of getting certified mostly because of their major client, Whole Foods. Co-owners Howie Bubis and Scott Taylor began supplying the upscale chain soon after they founded their seafood company in 2006.

They say business was good. But executives at Whole Foods announced that they were going to buy as much seafood as possible with the MSC label. "We decided we wanted to keep them for a customer," says Bubis, "and in order for us to do that, we had to move into sustainable-type fishing." He and his partner hoped that MSC approval would give them a competitive edge — and Whole Foods might pay them more than fishing companies that didn't have it.

Getting Certified

Day Boat applied for MSC certification in 2010. In retrospect, they say they didn't quite realize what they were getting into. The MSC does not certify fisheries itself; instead, a fishery that wants the label hires any one of roughly a dozen commercial auditing companies, which can cost up to $150,000 or more, to decide whether the fishery's practices comply with the MSC standards.

Day Boat hired MRAG Americas, a firm that has consulted with a who's who of governments and international organizations from the U.S. to New Zealand. Bob Trumble, a vice president at MRAG, says his first step was to assemble a team of four ocean specialists that included him. The MSC requires the auditors to score each fishery on a checklist of more than 30 items, designed to measure whether the fishery meets the MSC's three main principles.

The principles are designed to ensure:

-- that fishing companies do not overfish (that they do not deplete the population of seafood that they are aiming to catch)

-- that fishing companies protect other kinds of life in the environment

-- and that each fishery is run by good managers who keep track of the latest research and adjust their methods, when necessary, to minimize their impact.

Trumble says that when MRAG's team evaluates a company, "we don't do the research ourselves." In Day Boat's case, they gathered all the studies they could find on swordfish off the Florida coast, by government and academic researchers. How fast do the swordfish reproduce? How have their numbers changed over the years? Of course, Trumble says, researchers can't count every fish in the ocean — they can only take a snapshot and then use mathematical models to extrapolate.

MRAG's auditors also pored through Day Boat's fishing records to see how its practices compared with the rest of the industry. Day Boat's owners say they assigned a staff member to work almost full time for two years, just to supply MRAG with information.

And Day Boat's owners say there was something more they had to do. The MSC rules say, in effect, that when companies are applying to be certified, they have to listen and respond to anybody who objects — including other fishing companies and environmentalists.

Learning To Compromise

Talking to environmentalists? Scott Taylor wasn't too crazy about that part. "The environmentalists would prefer no fishing whatsoever," Taylor says. "That would be their first goal, that we would go away."

"That's not true," laughs Shannon Arnold, who was then co-director of the Canada-based Ecology Action Centre. "I eat fish and I enjoy it."

But Ecology Action and several other environmental groups tried to block Day Boat's application. They cited evidence that swordfish boats in Florida accidentally kill endangered turtles.

Taylor insisted that Day Boat's crews didn't kill turtles, but he agreed to negotiate with the environmental groups over the issue — a big step for a man who sometimes talks about environmentalists with a scornful tone. And he ended up promising to make changes.

Taylor promised, among other things, that his boats would use a different kind of hook that scientists say kills fewer turtles. He pledged that within five years of being certified, Day Boat would put observers or video cameras on all of their boats, so researchers can study exactly what the company's crews catch on every fishing trip. Environmentalists have been pushing fishing companies for years to adopt that policy, usually in vain.

"We could either take the tact that we were not going to let them derail us from the way that we were going to operate," Taylor says, "or that we were going to reach across the aisle in a way that was uncommon and really unheard of."

Praise For Day Boat

In December 2011, MRAG announced that Day Boat could receive the MSC certification. And now, some of the same environmentalists who tried to block the certification praise Day Boat's owners.

"It is pretty rare to get someone from such a big industry" to compromise," says Arnold, of the Ecology Action Centre. "And I think it's a breath of fresh air."

Arnold says despite her praise, she still doesn't believe the MSC should call Day Boat's fishing methods "sustainable." So far, she says, Day Boat's owners have only promised to change their methods. "Day Boat should get certified only if and when they actually make those changes," Arnold says.

Still, she applauds the way Day Boat's owners worked with their critics. "It wasn't easy," says Arnold. "I think there was a year of some pretty contentious stuff that went on, and then they both decided, 'Let's try and work through this.' And what came out at the other end has been much better for the animals on the water, that's for sure."

Day Boat's owners say the process cost more than $200,000 — at least half for the audit company and the rest for related expenses. "It's occupied three years of our life," says Bubis. But he and his partner say the MSC label has been good for business: They have been selling their swordfish for 10 percent more than competitors who don't have it.

A 'Misleading' Label

Environmentalists say if you just heard Day Boat's story, you might conclude that the MSC is a great system. But they argue that it's deeply flawed. They say for every fishery like Day Boat, they can point to another certified fishery with major problems. So the sustainable label "is misleading," says Gerry Leape, who helps run oceans programs at the Pew Environment Group.

"The consumer looks at the fish, and says, 'Oh, it has the label on it, it must be sustainable,' " Leape says. But "in some fisheries that the MSC has certified, that's not necessarily the case."

Leape says swordfish are a perfect example. The fillets labeled "certified sustainable" at the local supermarket might come from Day Boat in Florida, which environmentalists applaud. Or they might come from long-line boats in Canada, more than 2,000 miles away. The MSC has labeled those Canadian swordfish sustainable, even though many environmental groups denounce the fishery because evidence suggests its boats accidentally catch tens of thousands of sharks every year.

MSC's chief executive, Rupert Howes, staunchly defends their program. "The MSC standard is rigorous, it's science-based, and assessment is based on the evidence," he says. "The beauty of the MSC program is every year, that fishery has to have an annual surveillance audit," Howes says. "Those numbers are checked again. If new stock assessment data suggests the population can't withstand that pressure, new conditions can be invoked, or indeed certificates can be withdrawn."

But many scientists and environmentalists charge that in some fisheries, there is not enough data to conclude that they're sustainable.

Consider the buttery white fillets popularly known as Chilean sea bass. That's the usual supermarket and restaurant term for a deep-water species called toothfish, some of which are caught in the Ross Sea near Antarctica. When the MSC gave its seal of approval in 2010 to several companies that catch those fish, dozens of scientists protested.

"They do not know the most elementary things about the life cycle of this Antarctic toothfish," says Jim Barnes, director of the Antarctic and Southern Ocean Coalition, which represents dozens of environmental groups around the world. "Nobody has ever seen toothfish eggs," Barnes says. "Nobody has ever seen little baby toothfish, for that matter. And in the face of that gap, the MSC is cheerfully ready to say, 'Oh, what this fishery is doing is perfectly sustainable.' "

Critics say MSC's apparent inconsistencies stem partly from the way MSC executives have structured the system: Each fishery that wants the label has to pay a commercial auditing firm to decide whether it is sustainable, just as Day Boat hired MRAG. Sources who have worked with several audit firms, including Intertek Moody Marine, Scientific Certification Systems and Food Certification International, told NPR that the industry is fiercely competitive. There are only around a dozen auditing companies vying to get contracts to certify fisheries around the globe.

"To me, that's a direct conflict of interest," says Barnes. "What incentive does the certifying [company] have to say no?" Barnes asks. "It has no interest in doing that," he says, because then the company might scare away business from other fisheries that want the MSC's sustainable label.

Since the MSC was set up in 1997, the audit firms have certified about 200 fisheries as sustainable and rejected fewer than 10 fisheries that applied. There are now 189 certified fisheries globally.

Controversial Toothfish

Take a closer look at the controversy swirling around the Ross Sea toothfish. After the Antarctic and Southern Ocean Coalition protested, the MSC hired a respected international lawyer, Michael Lodge, to serve as a kind of referee. The MSC provides "adjudicators," as it calls them, whenever groups formally object. The process can cost tens of thousands of dollars. There have been 21 objection filings since the MSC was created.

Lodge's report sharply criticized the audit company that certified toothfish, Intertek Moody Marine, for some of the ways it handled the case. The "conclusion reached by [Moody's] assessment team is not supported by the evidence," Lodge wrote in one section. Part of Moody's evaluation, Lodge wrote, "can be described as arbitrary or unreasonable in the sense that no reasonable certification body" could have reached the conclusion Moody did "on the evidence before it."

"There are instances in the toothfish case when [Moody] had not been sufficiently rigorous, sufficiently careful," Lodge later told NPR. "You can call that sloppy. Certainly in those instances they were not doing their job properly," he says. "[Moody] failed to do what they were required to do as a certification body."

Moody's general manager, Paul Knapman, rejects the notion that his company's work has ever been "sloppy." Moody has certified more fisheries than any other company, according to the MSC's website. Moody gave the seal of approval to the controversial Canadian swordfish industry. "We have scientists on our team who look at the information that's been gathered," Knapman says. "It's all evidence-based. And if they say that the fishery meets the standard, then we are able to determine the fishery should be certified."

Knapman notes that despite Lodge's criticism, the MSC gave Ross Sea toothfish the sustainable label. But under the MSC rules, adjudicators like Lodge have limited options. They are not allowed to reverse a certifying company's decision even if they conclude, as Lodge did, that the company didn't properly review all the evidence. The adjudicators can rule only that the company must re-evaluate the evidence and reconsider its original decision. That is what Lodge ordered Moody to do. Moody's auditors reached the same conclusion as they did the first time and labeled the fishery sustainable.

The MSC's Howes is nonplussed when he hears about controversies swirling around some of the fisheries. "Yes, there are controversial fisheries; there are bound to be," he says. "We have nearly 300 fisheries from pretty much every ocean in the world either assessed or under assessment. I'm confident in the MSC program and its assessment process. No system is perfect."

Environmental groups and others have filed 21 official objections since the MSC was created. So does that low number suggest that environmentalists endorse most MSC-labeled fisheries? Many environmentalists we talked to say no.

Barnes, Leape and others say that they have not filed many objections mainly because they do not have enough staff, money or time. Directors of Canada's Ecology Action Centre, for example, say that fighting the decision to certify Canadian swordfish diverted them from working on other priorities, and soaked up "literally thousands of volunteer hours" of research.

"The outcome is almost the same as if we'd done nothing," says Susanna Fuller, co-director of marine programs at the Ecology Action Centre. So she and her colleagues have decided not to file any more objections with the MSC. Of course, the objections are not a burden only for environmental groups. They cost time and money for fishing companies and their audit firms, too.

Conflicts Of Interest Among Certifiers?

A few years ago, leaders of the Pew Environment Group became so concerned about potential problems in the MSC system that they hired an outside lawyer to investigate. Attorney Stacey Marz's confidential report for Pew, which NPR obtained, warned "there will always be suspicions about the independence of certifiers when they are paid by those they are assessing."

The attorney recommended that the MSC or other groups set up a central fund, which fisheries would pay when they apply to be certified. Then the fund's overseers would decide which auditing firm should evaluate which fishery — preventing fishing company executives from handpicking and paying the firm that decides their fate.

Knapman, Moody's general manager, dismisses concerns about potential conflicts of interest. He says Moody, which has certified more fisheries than any other audit company, hires different teams of independent experts to evaluate each fishery. "They are by and large academics who have their own reputations, are established in their field. Those individuals certainly are not thinking long term about repeat work. The focus is on the fishery. Ultimately it's their reputation which is at stake."

Howes, MSC's chief executive, says the system of allowing companies to choose and pay the auditing firms that evaluate them is "the way that our global market-based corporations operate." He notes that many corporations, in industries from banking to manufacturing, routinely choose and pay independent auditing firms to evaluate the way they do business.

The MSC has extensive "checks and balances to assure that the accreditor does do a thorough job," Howes says. "If an audit firm got a reputation for doing a bad job in its certifications," he adds, "I suspect they would lose an awful lot of business, very, very quickly."

Howes sees the growing criticism of the MSC as evidence that the system is working well. "This was a fantastic idea. We've learnt by doing."

He later continues: "Part of the success of the program is, we're a broad church," he says. "We're very involved with all of our stakeholders, and many of them are very critical of some of the assessments. Most of the people who criticize the program, I think, are completely committed to an organization like the MSC existing. They see us as part of the solution. But it is their role to keep testing us, to keep pushing us, whether it's on the industry side or the NGO side, to get better at what we're doing."

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