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University of Washington scientist launches effort to digitize all fish

July 27, 2016 — SEATTLE — University of Washington biology professor Adam Summers no longer has to coax hospital staff to use their CT scanners so he can visualize the inner structures of stingray and other fish.

Last fall, he installed a small computed tomography, or CT, scanner at the UW’s Friday Harbor Laboratories on San Juan Island in Washington state and launched an ambitious project to scan and digitize all of more than 25,000 species in the world.

The idea is to have one clearinghouse of CT scan data freely available to researchers anywhere to analyze the morphology, or structure, of particular species.

So far, he and others have digitized images of more than 500 species, from poachers to sculpins, from museum collections around the globe. He plans to add thousands more and has invited other scientists to use the CT scanner, or add their own scans to the open-access database.

“We have folks coming from all over the world to use this machine,” said Summers, who advised Pixar on how fish move for its hit animated films “Finding Nemo” and “Finding Dory” and is dubbed “fabulous fish guy” on the credits for “Nemo.”

He raised $340,000 to buy the CT scanner in November. Like those used in hospitals, the CT scanner takes X-ray images from various angles and combines them to create three-dimensional images of the fish.

With each CT scan he posted to the Open Science Framework, a sharing website, people would ask him, “What are you going to scan next?” He would respond: “I want to scan them all. I want to scan all fish.”

Read the full story from the Associated Press at the New Bedford Standard-Times

Maine fishermen testing a ‘game-changer’ for protected cod

July 25, 2016 — GEORGETOWN, Maine — Like many Maine fishermen, Bryan Kelley faces a dilemma as he looks to diversify beyond the lobster that account for the bulk of his catch.

To target pollock, which are relatively common in the Gulf of Maine, he has to fish in the same areas frequented by cod, a type of groundfish protected through strict federal catch limits.

“We literally have to stay away from the codfish,” Kelley said while standing on his 40-foot boat moored in the Five Islands harbor of Georgetown. “I could fill this with codfish if I wanted to, but that wouldn’t help anybody in this sector and that is not why we are out here.”

To help him catch the groundfish he wants and avoid the species he doesn’t, Kelley has begun experimenting with a contraption akin to a conventional fishing reel on steroids and with an electronic brain. The “automatic jigging machines” loaned to Kelley and a handful of other fishermen by The Nature Conservancy allow them to more accurately target the water column where pollock hang out and stay off the bottom where cod lurk. The machines’ simple hooks and lures also ostensibly reduce inadvertent “by-catch” of cod while avoiding other downsides of trawlnets and gill nets more commonly used by fishermen.

“That’s part of the draw of it: It’s the quickest and easiest I have ever rigged anything up in my life,” Kelley said.

Geoff Smith, marine program director at the Maine chapter of the The Nature Conservancy, said preliminary reviews of the machines have been largely positive.

“This project is really about helping fishermen target those healthy stocks (of fish) while avoiding the codfish to allow them to rebuild,” said Smith, whose organization owns several groundfish permits in the Gulf of Maine. “We really feel that these jigging machines, if fished properly, can be selective and have minimal impact on the seafloor. … And if they work for fishermen, we think they could be a real game-changer.”

Read the full story at the Portland Press Herald

Researchers register success in breeding Pacific blue tangs aka ‘Finding Dory’ fish

July 25, 2016 — You can call it ‘Finding Dory’ effect, as a rise has been witnessed in the sales of Pacific blue tang since the movie has been released. Blue tangs can only be captured in the wild. As per experts, the methods used for the same are environmentally harmful.

For past many years, researchers have been tried to replicate the species; mating, hatching and growing behavior. Researchers from the University of Florida have achieved success in the same and have been able to breed Pacific blue tangs.

The research was carried out by the university researchers along with Rising Tide Conservation and the SeaWorld-Busch Gardens Conservation Fund. The species is considered to be the most difficult fish. In fact, only 12.5 to 15% of aquarium creatures can be bred in captivity. It has now become vital to increase the percentage.

As mentioned above, only method to get them is from the wild. Blue tangs are not going to become extinct, as they reproduce in large number and live in reefs across the world. But reefs are what giving concerns to scientists.

Read the full story at NorcalNews

Life on the Line: OSU scientists track effects of a changing ocean on tiny sea life

July 22, 2016 — NEWPORT, Ore. — In a cold mist under gray skies, the Pacific Ocean heaved against the boat as two scientists from Oregon State University pulled a net full of life from the deep.

It was a July day, but it felt like a day in December.

In the net life swarmed, much of it too small to be seen with the unaided eye. The net held the keys to help scientists unlock how creatures of the sea are affected by changing ocean conditions and those effects on the aquatic food chain. And more specifically, the effects to salmon, a fish of much importance to humans.

For 20 years scientists have made bi-monthly trips on what is called the Newport Hydrographic Line, which takes them to the same seven sampling stations along a 25-mile path perpendicular to the coast. The stations are physical points on a map. There are no buoys or other structures that mark their locations. The scientists find them using GPS.

They launch their research vessel, the R/V Elakha, from a dock in Yaquina Bay that sits along a jagged bulge of land on which OSU’s Hatfield Marine Science Center resides. The trips have amassed an extraordinary amount of data about the sea and the life within it. The data is routinely posted on the National Oceanic and Atmospheric Administration’s Northwest Fisheries Science Center website and is used primarily to help forecast salmon runs. But the data has also told the story of changing ocean conditions and its impact on the food chain.

“We can also look at the changes in the bioenergetics of the food chain across the whole 20-year time series,” says OSU research assistant Jennifer Fisher. “It doesn’t just relate to salmon; it relates to sardines and (other) fish. It gives us an idea of ocean acidification, toxic algae – lots of things.”

Fisher has been going on these trips to sea for five years aboard the 54-foot research vessel owned and operated by OSU.

On this day, Fisher, OSU lab technician Tom Murphy and deckhand Dave Weaver use two different cone-shaped nets to capture organisms that live in the sea and that form the basis of the oceanic food chain.

Fisher’s primary interest in the day’s catch is in a tiny crustacean called a copepod. These creatures feed on the sea’s phytoplankton. Copepods are animals with large antennae and are only a millimeter or two in length. Under a microscope their bodies are an elongated oval protected by an exoskeleton. But they are nearly transparent. And inside their bodies scientists have discovered a lipid sac, or stored fat.

Read the full story at KVAL

UMass invention could cut fish monitoring costs

July 21, 2016 — Researchers at the University of Massachusetts Dartmouth have been awarded a patent for technology they say could reduce the costs of fishing vessel monitoring, a cost fisherman say threatens their livelihood, the school announced this week.

Dr. Brian Rothschild, the retired founding head of the UMass-Dartmouth School of Marine Science and Technology, and graduate student Glenn Chamberlain said their on-board 3D camera system would reduce costs, ensure accuracy and expand the scope of what information could be collected.

“Broad-based and accurate counting of the fish being caught is critical to our collective efforts to sustain critical fish stocks and thus the commercial fishing industry,” Rothschild said in a statement. “We believe we have found a way to count the fish being caught in a relatively low-cost manner that will increase confidence among the federal regulators and the fishing industry.”

The camera system, which would cost about $500 to install on a vessel, utilizes stereo photogrammetry, a system used by meteorologists to collect information about tornadoes, to capture images of fish either on the deck or passing through a net, according to the university. Those images could then be analyzed to produce “a permanent record of each sampling tow or catch in the fishery and to determine the species and size composition of each tow,” the university said.

Last year, Hampton, New Hampshire, fisherman Dave Goethel and a fishing sector filed a lawsuit challenging the legality of a mandate requiring them to carry at-sea monitors on their vessels and pay the cost of hosting those federal enforcement contractors. The government shifted the cost of paying for monitors from itself to fishermen earlier this year.

Read the full story at the Gloucester Daily Times

SMAST wins patent on 3D counting, measuring fish on deck of a boat

July 20, 2016 — NEW BEDFORD — A newly patented 3-D photograph system developed at the UMass Dartmouth School for Marine Science and Technology soon may greatly add to scientists’ knowledge about ocean fish populations, the school announced Tuesday.

The device, the work of now-retired dean Dr. Brian Rothschild and graduate student Glenn Chamberlain, includes two digital cameras and a reference frame.

Using a common technique called stereo photogrammetry, the device essentially uses 3-D images to map the surface of the fish. The reference frame will permit the monitoring not only of the number of fish, but their size. The fish can be on the deck, or in a net, and the data obtained can be stored permanently, Rothschild said.

“The concept is very simple,” Rothschild said, and the parts are easily obtainable commercially; the two cameras cost about $500, he said.

Read the full story at the New Bedford Standard-Times

Closing parts of the ocean to fishing not enough to protect marine ecosystems

July 18, 2016 — A University of Washington fisheries professor argues that saving biodiversity in the world’s oceans requires more than banning fishing with marine protected areas, or oceanic wilderness areas. In a three-page editorial published in the journal Nature, he argues that this increasingly popular conservation strategy is not as effective as properly managing recreational and commercial fisheries. “There’s this idea that the only way you can protect the ocean is by permanently closing parts of the ocean to fishing, with no-take areas,” said Ray Hilborn, a professor in the UW’s School of Aquatic and Fishery Sciences. “You protect biodiversity better by regulating fisheries over the country’s entire economic zone.”

Marine protected areas have grown in popularity since the early 2000s. Recent examples include an area twice the size of Texas in the central Pacific established in 2014 by President Barack Obama, and a proposal to close 25 percent of the Seychelles’ exclusive economic zone, an island nation off Africa’s east coast.

Several environmental organizations have set a longer-term goal of making 30 percent of the world’s oceans into no-take marine protected areas by the year 2030. But Hilborn believes this is not the best way to protect global marine ecosystems.

“If the problem is overfishing or bycatch, then fisheries management is much more effective than establishing MPAs because you regulate the catch over the entire economic zone,” Hilborn said. “I don’t see how anyone can defend MPAs as a better method than fisheries management, except in places where you just can’t do management.”

In countries with functioning fisheries management systems, Hilborn believes, conservationists and the fishing industry should work together on large-scale protection of marine biodiversity and sensitive marine habitats.

Read the full story at Science Daily

Counting cod: New trawl survey aims to determine status of iconic fish

July 18, 2016 — SCITUATE, Mass. — The coastline had melted into a gray slurry, its shapes barely visible through intermittent rain and mist, when the Miss Emily made her first of two scheduled tows last week about seven miles off this South Shore port.

Despite the weather, the waters remained sedate as the 55-foot gillnetter, skippered by owner Capt. Kevin Norton, steamed at about three knots for 30 minutes, its net set at 36 fathoms, or about 216 feet.

Its target? What else? The iconic, oft-debated and oft-elusive cod.

“It will be interesting to see what we come up with today,” Norton said as he feathered the Miss Emily through the harbor and out into open waters. “Usually, at this time of year, there’s nothing really here because the water has begun to warm and the fish already have moved further out.”

On this day, as he has all summer, Norton was not fishing so much for himself as he was for the people of the commonwealth, by way of the state’s Division of Marine Fisheries.

While most of what came on deck from his nets would be his to sell, the primary mission of the trip was to assist the state agency with its ongoing industry-based trawl survey, which aims to help determine the true status of the Gulf of Maine cod stock.

“This whole survey is designed with cod in mind,” said Micah Dean, a research scientist at DMF. “There’s never been a fishing-industry trawl survey in June or July, so this should give us a new perspective.”

Read the full story at the Gloucester Daily Times

Exclusive: Q&A with Ray Hilborn regarding conflict of interest accusations

July 16, 2016 — In response to accusations of conflicts of interest made against him by Greenpeace, renowned global fisheries expert Ray Hilborn compiled documents defending his work from leading academic journals in which he published his research, as well as from an official at the University of Washington who helped lead an official review of his work at the university (The documents can be found at the bottom of this story). Hilborn also answered questions posed by SeafoodSource regarding Greenpeace’s claims via email.

SeafoodSource: Do you feel like you’ve adequately disclosed your funding sources and any potential conflicts of interest in your publications and public statements?

Hilborn: As UW, PNAS and Science concluded, I complied with the regulations required by the University and journals. I will now be much more explicit in the future since this has been raised and Science has changed its policies since 2009.

SeafoodSource: Can you explain how industry co-funding of research contributes to better fisheries management?

Hilborn: It would take pages to document all the ways that I know of that industry co-funding has contributed to management. I chaired a National Research Council report on this subject – National Research Council. 2003, Cooperative research in the National Marine Fisheries Service. National Research Council Press, Washington D.C.

Read the full story at SeafoodSource.com

Ray Hilborn fights back against Greenpeace accusations

July 15, 2016 — Global fisheries expert and University of Washington Professor Ray Hilborn is fighting back against accusations made in May by the environmental activist group Greenpeace alleging he did not appropriately disclose funding he received from the seafood industry.

In an email to SeafoodSource, Hilborn denied any conflict of interest in his work and attached copies of emails sent from representatives of the academic journals Proceedings of the National Academy of Sciences (PNAS) and Science backing the integrity of his contributions to both publications. Hilborn also attached a copy of an email from Mary Lidstrom, the vice provost for research at the University of Washington, showing that a university review of Hilborn’s actions did not reveal any violations of the university’s policies or procedures governing conflicts of interest or outside consulting.

“As UW, PNAS and Science concluded, I complied with the regulations required by the University and journals,” Hilborn told SeafoodSource. (See the full interview here).

In her email, which was sent to PNAS Deputy Executive Editor Daniel Salsbury, Lidstrom said the university reviewed Hilborn’s funding types and sources, publication history and disclosures, as well as approvals for outside consulting and checked them against UW policies.

“We have not identified any actions or lack thereof, engaged in by Dr. Hilborn which violate University policies or procedures governing conflicts of interest or outside consulting,” Lidstrom wrote.

Read the full story at Seafood Source