BOSTON » In the world of environmental regulation, where the hope is to write rules that both industry and science can live with, few areas are as contentious as fishing. Especially on the East Coast, fishermen attack scientists as mired in bottomless ignorance about how fish are actually caught. Scientists sometimes describe fishermen as racing to catch the last fish, regardless of the harm to vanishing species.

But new efforts to protect marine creatures have gained surprising support from researchers, regulators, engineers and fishermen.

The issue is bycatch — fish, whales, turtles, sea birds and even corals killed or injured by fishermen in search of other species. The best-known example is dolphin caught in tuna nets, but the problem is far more extensive than that.

“It’s part of the collateral damage fishing causes,” said Tim Werner, who directs the marine conservation engineering program at the New England Aquarium. “You deploy a net and catch a turtle, put out a pot for a lobster and entangle a whale, put out a trawl and pull up coral.”

The problem affects marine species around the world, many of them endangered. Though much attention is paid to overfishing, “often our greatest impact is not on the species we target to catch but the species we did not intend to catch,” Werner said.

“The seafood on your plate,” he added, “is not the only animal that gave its life to feed you.”

The new efforts focus on modifications to fishing gear. They include relatively simple steps, like changes in hook design, and more complex ones: making fishing lines more visible to whales, changing noise levels on fishing boats and impregnating metal gear with substances meant to repel “bycatch species” like sharks.

Engineered bycatch reduction goes back to the 1990s in the Gulf of Maine, where harbor porpoises were turning up in fishermen’s nets. On the theory that porpoises are sensitive to noise, engineers and biologists developed beer-can-size devices that emitted pinging noises underwater. Within weeks of attaching the pingers to their nets, fishermen saw porpoise bycatch drop 90 percent.

“It is a little more expensive for the fishermen, but most fishermen are willing to put up with the expense,” said Scott Kraus, vice president for research at the New England Aquarium, headquarters for the Consortium for Wildlife Bycatch Reduction, one of several cooperative efforts.

He added that researchers were now working to design noisemakers that could be installed on boats to keep bycatch species away. And they are testing whether the sound of hauling in fish is like a dinner bell, attracting these species to nets.

This year the National Oceanic and Atmospheric Administration, which regulates fishing in federal waters, began requiring fishermen in the Gulf of Mexico to use another innovation: hooks that are robust enough to catch “target” species like yellowfin tuna or swordfish but bend and release when grabbed by heavier species like bluefin tuna.

Chris Rilling, a fishery biologist at NOAA, said experiments by researchers and fishermen showed that these “weak hooks” reduced bycatch of bluefin tuna in the gulf by 56 percent — a considerable success, he said, because bluefin tuna are severely overfished and the Gulf of Mexico is a major spawning ground.

Elsewhere, he said, the agency is moving to require the use of the circle hook, so called because “it largely comes around and wraps back on itself,” unlike conventional J-shaped hooks. When they were adopted in Hawaii, he said, sea turtle bycatch fell more than 80 percent, so “we have really been pushing for circle hooks all over the world.”

Rilling said the government had a host of other proposals to reduce sea turtle bycatch, including requiring boats fishing for albacore tuna to keep hooks at least 328 feet below the surface — where, he said, they will be “out of the way of the turtles.”

“This comes back to the fishermen telling us when, where and how they set their gear where they don’t have much bycatch and trying to get those lessons learned and get them more widely adopted,” said Rilling, who fished for salmon, herring and halibut in Prince William Sound, Alaska, in the 1980s and ’90s. “They know how they interact with their gear.”

Another gear modification was invented by two Rhode Island fishermen, Phil Ruhle and his son Phil Jr., with the help of gear researchers at the University of Rhode Island. The Ruhles fished for haddock, which NOAA describes as a relatively healthy fish stock, and wanted to avoid catching cod, a depleted species.

They modified the mesh size of their nets and redesigned them to capitalize on their observation that frightened haddock tend to swim up, while species like cod dive for deeper water. Phil Ruhle Sr. died at sea in 2008, but the “Ruhle trawl” is now in wide use.

As many as 80 percent of North Atlantic right whales, an endangered species, carry scars from entanglements with fishing gear. At the New England Aquarium here, researchers are working with engineers and fishermen on experimental lines colored or illuminated to make them easier for whales to spot.

While the whales “appear to be colorblind,” Werner said, they seem to be able to make out the reddish color of the tiny crayfish and other copepods that are the major part of their diet.

In the Bering Sea, pollock fisheries are closely monitoring accidental catches of salmon; Rilling of NOAA says the companies relay information to their fleets “almost instantaneously” so fishermen can avoid areas where salmon are turning up in pollock nets. A similar effort is under way in Massachusetts, he said, where scallop fishermen track inadvertent catches of yellowtail flounder.

But Werner said that for some species in need of protection, “we don’t really have anything off the shelf ready to go.”

That is the case with sharks, for instance, though there are some promising leads. Researchers have noticed that sharks avoid encounters with certain rare metals, used in computers and other devices. “Maybe you can attach these elements to fishing gear,” Werner said. “The jury is still out on that.”

Researchers are also investigating whether an electric signal might lure sharks away from baited hooks. Werner said fishermen would help test this approach off the southeast coast of the United States.

Some people remain skeptical that such collaborations will lead to lasting gains. David Cousens, who heads the Maine Lobstermen’s Association, says that while his members have worked hard to accommodate the demands of conservationists, the changes tend to be expensive and cumbersome, and he is waiting for data to show that they are beneficial.

“The thing is driven so hard by the conservation community,” he said. “They have money and lawyers, and when they are not happy about something they sue. We are at the mercy of lawyers and judges who know nothing about fishing.”

And some problems persist despite cooperation.

Those porpoise-saving pingers, for example, may be doing too good a job, experts say — driving the creatures away from otherwise useful habitat. Kraus, of the New England Aquarium, says it turned out that raising the frequency of the pings reduced the area of ocean affected, a discovery that led regulators in Europe to alter pinger requirements.

But the U.S. regulations state explicitly what the ping frequency must be, and it cannot be changed unless too many porpoises start being caught again — something he called unlikely, given the pingers’ efficiency.

He was asked if that was an example of stupid regulation. “Choicer words have been used,” he replied.

Still, researchers and regulators are praising the new atmosphere.

Until recently, Werner said, fishing regulation in the United States was too often a matter of environmental litigation in which “the fishermen are cast as the villains, and get ever more restrictive regulation on where they fish, how they fish.

“That’s not the approach we take,” he went on. “We are trying to be proactive, to recognize that fishermen are not the villains in this play, but really a critical part of the solution.”

© 2011 The New York Times Company