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NEWPORT, R.I. – Even before mechanics found deeply pitted bearings near crankshafts in its generators, problems that could have led to catastrophic engine failure, the Henry B. Bigelow was running more than a month behind.

Now, the government research vessel is embarking on its annual spring voyage later than ever before, a delay that could have serious consequences for scientists’ ability to assess the health of some of the 52 fish stocks they survey, from the waters off North Carolina to the eastern reaches of the Gulf of Maine.

Fish migrate and change their feeding patterns as waters warm, which might make it difficult for National Oceanic and Atmospheric Administration scientists to compare this spring’s survey of fish populations with previous counts.

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The prospect of skewed data could complicate efforts for policy makers to set proper quotas, potentially leading either to overfishing or unnecessarily strict catch limits.

“I worry that this will create statistical noise and more uncertainty,” said Gary Shepherd, a fishery biologist at NOAA’s Northeast Fisheries Science Center in Woods Hole, where he and other scientists recommend quotas based on what the Bigelow catches, along with other data.

For species such as Atlantic cod, whose ranks have plunged some 97 percent below what scientists consider healthy, any statistical blip in the surveys could have significant implications. Depending on the results, fishermen might call for catch limits to be relaxed, while environmental advocates could lobby to ban fishing in certain areas.

“We do everything in our power to make sure that we do the same thing over space and time, so that the changes in abundance that we observe are comparable from year to year,” said Teri Frady, a spokeswoman for the science center. “Doing the surveys at the same time every year is part of that effort at standardization.”

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David Iaciofano, 51, field service technician for Milton Caterpillar, worked to replace the bearings of the generator’s engine on the NOAA vessel.
David Iaciofano, 51, field service technician for Milton Caterpillar, worked to replace the bearings of the generator’s engine on the NOAA vessel.Lisa Hornak for the Boston Globe

The Bigelow typically leaves Newport in March for the spring survey, but this year was delayed by routine maintenance for more than a month. When it finally left its shipyard in Brooklyn, N.Y., last month, it had to return to port to ride out a nor’easter. Then the mechanics discovered the problem in its generators, and the ship didn’t depart until last Friday.

The delay has already raised concerns among fishermen, many of whom have long questioned NOAA’s methodology and findings.

A $54 million ship that went into service in 2006, the Bigelow uses massive nets to trawl for different species at 377 predetermined areas along the East Coast. Over two months at sea, the crew collects samples from fish to determine a range of characteristics, from age and sex to what they eat and whether they’re spawning.

That information, as well as the number of fish they catch, helps guide the stock assessments, which also use data from commercial and recreational fishermen. But fishermen have long argued that the data are inaccurate.

“There is a wide gap between what fishermen are seeing on the water and what the assessments are reporting,” said Jackie Odell, executive director of the Northeast Seafood Coalition, an advocacy group for commercial fishermen in Gloucester. “We question the validity of the data in general.”

She worries that the late start — the agency has usually completed its survey by this point — might mean that important data won’t be available for stock assessments slated for the coming months, including struggling species such as Georges Bank cod and witch flounder.

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If the data aren’t available, scientists will have to rely on previous surveys.

“Our greatest concern is that they’re using outdated data and the assessments aren’t based on the current reality,” Odell said.

As the waters warm, some of the fish, such as herring, migrate out of the survey area and into the region’s rivers. Other species, such as squid, which are short-lived, might not survive in representative numbers through June, when the Bigelow is now scheduled to finish its survey.

“If the survey had started at its normal time, it would have found squid on the continental shelf,” said Robert Vanasse, executive director of Saving Seafood, a Washington-based group that represents the fishing industry. “But now it won’t because the survey doesn’t sample Nantucket Sound.”

For many environmental advocates, the chief concern is that fishermen will use the delay as ammunition to dispute the validity of findings that hurt their earning potential.

“Some fishermen — who will remain nameless — will use the delay to reject any assessment that doesn’t tell them what they want to hear,” said Peter Shelley, senior counsel for the Conservation Law Foundation.

Recommendations based on the surveys are sent to regional fishing councils, which are composed of fishermen, scientists, and public officials. The councils set quotas, which NOAA officials then approve or reject.

Gib Brogan, a fisheries policy analyst for the Washington-based advocacy group Oceana, said the delayed survey isn’t the first to experience glitches.

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“Field science has hiccups sometimes,” he said. “The blizzard wipes things out, you lose your gear, or your boat needs to get fixed. But then you adapt.”

Others suggested the delay could have benefits.

The Gulf of Maine has been warming rapidly in recent years — faster than just about any other saltwater body in the world, scientists say — and the later survey might provide deeper insight to the effects of that change.

This year, above-average water temperatures have already accelerated the migratory cues that fish receive by as much as three weeks, said Andrew Pershing, chief scientific officer at the Gulf of Maine Research Institute.

That “will magnify the effect” of the survey’s delay, he said, but also open new areas of study.

“It provides an opportunity to learn more about the annual cycles and how they are affected by temperature,” he said.

In Newport, where the big white ship idled at its naval mooring, grease-covered contractors recently crouched in the belly of the Bigelow, using torque wrenches and working long shifts to repair its generators.

As the departure date continued to slip, the crew was growing anxious.

“We’re working as hard and as fast as we can,” said John Hohmann, the ship’s chief engineer.

“We’re working as hard and as fast as we can,” said John Hohmann, the ship’s chief engineer.
“We’re working as hard and as fast as we can,” said John Hohmann, the ship’s chief engineer.Lisa Hornak for the Boston Globe/Globe Freelance

David Abel can be reached at dabel@globe.com. Follow him on Twitter @davabel.