The Hubbs-SeaWorld Research Institute is trying to build a massive fish farm off the San Diego coast, the most ambitious aquaculture project of its kind in the United States .
The ocean farm could ultimately raise about 11 million pounds of fish a year in cages about five miles off the coast.
But a much smaller Hubbs undertaking to breed fish has drawn the attention of environmentalists and state regulators, and not always in a good way. Over the past two decades, Hubbs has received $28 million from the state Department of Fish and Wildlife to run an experimental program to help restock the ocean with white seabass.
Fish spawned as part of that effort have horns, deformed hearts or are blind.
The state is now auditing the whole program. It’s unclear if it’s had any significant effect on the white seabass population, which was in decline  because of pollution, overfishing and habitat destruction.
In internal documents, one of the state’s top fish scientists said  Hubbs basks in the positive attention while burying important facts about its operations “under a mountain of bullshit.”
An untold number of Hubbs fish are deformed and thought unlikely to survive long in the wild.
Hubbs has also killed hundreds of thousands of white seabass through negligence  and mishaps or because its fish were deemed too genetically alike, misshapen or diseased.
Most of the government records that form the basis of this story were first obtained by San Diego Coastkeeper, an environmental organization that requested documents about the white seabass program from the state.
Coastkeeper is seeking to block construction of the new offshore farm. If Hubbs is having trouble running one fish-farming operation, it shouldn’t be trusted with another, the group argues.
The white seabass program is a manmade attempt to solve a manmade problem. If human interference with the ocean is hurting fish, can’t humans just breed more fish to replenish the ocean?
The idea came from Larry Stirling, a former San Diego assemblyman.
As a young lawmaker in the early-1980s, Stirling found himself in the middle of a fight between commercial fishers and recreational fishers over the size of fishing net holes.
Stirling realized the two fishing factions were fighting so hard because fish were in short supply.
“I came up with the idea, Well, why don’t we just hatch them more fish?” he said.
Stirling looked for someone who could make more fish. He came across Don Kent, who was at Hubbs just out of graduate school.
Stirling asked Kent if restocking would work.
“He gave me the right answer,” Stirling recalled. “He said, ‘I don’t know, but we sure ought to try.’”
Stirling’s idea became law in 1982.
Kent is now president of Hubbs. The state Department of Fish and Wildlife hired Hubbs to run the fish-making program.
Hubbs is a nonprofit started in 1963 by Milton Shedd, one of the founders of SeaWorld. Hubbs receives about 10 percent of its budget from SeaWorld and several SeaWorld executives sit on Hubbs’ board of trustees . SeaWorld is uninvolved in the day-to-day operations of the white seabass breeding program.
In 1990, the state made a fateful decision: It would focus on restocking the ocean with white seabass. Nobody had ever tried to rear white seabass like this before.
“This is not a lake that we’re dumping trout into and six months later everybody comes and catches a trout,” Kent said in an interview. “What we’re trying to do is build the corpus of the wild population back up to a more sustainable level so it can be self-sustaining, so that we can learn from the mistakes that got the fishery down to the level it’s been at for the longest time.”
The white seabass project really got under way when Hubbs opened its hatchery in Carlsbad in the mid-1990s.
Hubbs’ hatchery is a low-slung industrial building along the Agua Hedionda Lagoon, between the I-5 and the ocean.
Fish there have died in nearly every way imaginable.
Breeding white seabass turned out to be harder than expected.
Hubbs touts the fact that it’s released more than 2 million white seabass. But that’s far short of the hatchery’s capacity, and short of the 4 million fish it’s had permission to release.
Here’s what else isn’t touted:
• Some of those 2 million fish were hatchery-reared fish who were eaten by predators within days  of their release – a free lunch for sea lions and birds, at the government’s expense.
• The number of fish released from the hatchery does not begin to reveal the countless fish Hubbs has killed inside the hatchery.
Among people who pay attention to fish, hatchery-reared fish are known to be susceptible to diseases and deformities. Hubbs’ are no exception. Indeed, Hubbs is dealing with a fish species that was poorly understood and has proved difficult to deal with.
Hubbs fish begin their lives as eggs spawned by captive adult white seabass. Hubbs will get hundreds of millions of eggs a year.
From eggs, the fish grow into larvae, which are wisps of tissue with little beating hearts, as one former employee put it in an interview. They look like pepper flakes.
Juvenile fish spend several months at the hatchery before typically spending several more months in cages along the coast, where they grow larger.
When they are released into the wild, Hubbs’ white seabass are usually less than a foot long.
Misfortune has struck Hubbs’ fish at every stage of life.
From summer 2011 to summer 2012, about as many juvenile Hubbs fish died or were euthanized as were released into the wild: According to state records, Hubbs lost over 168,000  because of fungal infections, bacterial infections, deformities, a leak from the nearby desalination plant, cannibalism and because fish were left exposed to bird and sea lion attacks. During roughly the same period, 145,000 fish  ended up in the wild, according to Hubbs.
Here are other ways Hubbs’ fish have died, according to government records:
• Panicked adult fish have slammed themselves to death  against tank walls.
• Manmade conditions inside the hatchery have repeatedly damaged the eyes of juvenile fish. Continued exposure to these conditions cause bubbles to form behind the eye and in the cornea eventually leading to the loss of the eye. Hubbs then kills fish found to be suffering from this condition.
When Hubbs euthanizes fish, it may kill whole groups of them by filling their tanks with carbon dioxide.
Other times, Hubbs workers will sort fish one by one and kill diseased or deformed fish by dropping them into a bucket filled with MS-222, a chemical that in high concentrations makes fish go belly up.
It’s hard to compare Hubbs to other hatcheries, because other hatchery programs have different goals, release fish at different ages and use different species. Some level of deformity, disease and death is to be expected at any hatchery. One reason the state is now auditing Hubbs’ program is to see whether the problems with the white seabass program are normal or if the state would be better off breeding a different fish.
“I don’t know what is normal, to be honest with you,” said Tom Barnes, a Fish and Wildlife official who helps oversee Hubbs’ work.
Hubbs officials say that when they can compare themselves to other hatcheries, their numbers fare well.
“Where you can make the apples-to-apples or oranges-to-oranges comparisons, we are recognized as a leader,” said Pamela Yochem, a Hubbs veterinarian who is also the nonprofit’s vice president.
Hubbs has an internal process to euthanize deformed fish before they leave the hatchery.
But deformed fish keep showing up outside of the hatchery.
Months before Hubbs releases fish into the ocean, it transfers most of its young fish from the hatchery to a series of cages up and down the Southern California coast.
A few months’ stay in these ocean cages is supposed to give fish a better chance of survival once they are released. In the ocean cages, fish can adjust to Pacific waters and grow a bit larger before they’re exposed to the vast ocean and the other animals in it that will eat little white seabass.
A state fish pathologist, Mark Okihiro, has found severely deformed fish in these cages, readied for release. His job is to make sure the fish going into the ocean don’t have a disease that could be passed on to other fish.
But Okihiro has also found so many deformed fish that he concluded Hubbs is “conducting a large-scale experiment by releasing thousands of deformed fish into the wild.” Some of the fish have deformities – including the blindness commonly caused by the conditions of their captivity – that seem to make their chance of survival in the wild low.
A sample last summer of 50 fish  from Hubbs cages near the hatchery in the Agua Hedionda Lagoon showed every single fish had a deformity. The average fish from the sample had four deformities apiece.
“The fish’s ability to see, smell, hear, capture prey, digest food, adjust buoyancy, and sense changes in water pressure are all damaged by the myriad of deformities in hatchery fish,” Okihiro wrote in one email to other Fish and Wildlife officials. “The differences between life and death in the marine environment are so small that handicapped and deformed hatchery fish have almost no chance of surviving into adulthood.”
Hubbs’ deformed fish are all around us:
Of 50 fish sampled  from a cage at the Southwestern Yacht Club in Point Loma last summer, 22 fish had eye problems. In another sample from the same location, all but one of 20 fish had a condition known as “BAD heart ,” which means the fishes’ hearts were the wrong size, the wrong color, the wrong texture or were leaking blood.
Hubbs points out the Yacht Club cage and other coastal cages are run by volunteers, not Hubbs staff. That means some deformities may not be Hubbs’ fault if something happened to the fish after they left the hatchery.
But similar deformities have been identified by the state pathologist at the hatchery itself and in cages of Hubbs fish up and down the Southern California coast – outside the yacht club in Point Loma, in cages near Grape Street in downtown San Diego, in Dana Point, Newport Beach, even at schools that receive fish from Hubbs as part of its “Seabass in the Classroom” program.
Fish and Wildlife officials refused to let Okihiro speak for this story, even though he has been studying Hubbs’ fish for 15 years. Voice of San Diego reviewed scores of his emails and pathology reports.
Sometimes, his conclusions sparked conflict with Hubbs, as did his blunt assessments of Hubbs’ work.
Hubbs researchers published a paper in a peer-reviewed science journal in 2010  that concluded the fish it releases are more likely to survive than fish released from other hatcheries. The same paper found the hatchery’s fish do not survive as well as wild fish.
In an interview with senior Hubbs officials, they suggested it’s not clear what should be considered a deformity in its fish: Sometimes deformities are in the eye of the beholder. They said fish look different. How often wild white seabass have such deformities is also not known.
Water-quality issues and poor nutrition at the hatchery are suspected to cause some of the deformities. Hubbs has worked for years to get the right combination of food to young white seabass, a species that had not been farmed before. The Carlsbad hatchery is also not beside the most pristine water in the region. State officials point out that the site receives pollution runoff from a nearby strawberry field, golf course and flower farm.
While blindness and a weak heart seem likely to effect a fish’s chances in the wild, some deformities are more cosmetic. One common deformity is known as “horn head.” These fish have bumps of varying heights atop their heads. Such horns have not been seen in wild white seabass and their cause is unknown.
Hubbs tries to kill all the fish with horns before they are released from the hatchery because they’re “unsightly.” But, Okihiro, the state’s pathologist, has found fish with horns outside of the hatchery, in cages waiting to be released into the ocean.
When Hubbs releases deformed fish, officials at Hubbs said it’s because the state hasn’t stopped them from doing so.
“Anything that is in the wild is the department’s call,” said Yochem, the Hubbs official.
Indeed, the Department of Fish and Wildlife does not prevent the release of deformed Hubbs fish, as long as the deformities can’t be passed from fish to fish.
“It’s not really our business, the department’s business – it’s Hubbs’,” said Bill Cox, the head of fish production at the Department of Fish and Wildlife.
Like Hubbs, Cox said fish deformities fall along a spectrum. He said chances are that some deformities affect a fish’s survival, but that has not been studied.
Any hatchery’s fish may tend to display more deformities than wild fish, Cox said. That’s because a deformed fish in the hatchery is protected from predators. If hatchery fish are hungry but bad at hunting, the hatchery feeds them. If hatchery fish are sick with an ailment that would kill them in the wild, the hatchery may try to treat their ailment. That all increases the chances of seeing a deformed fish in a hatchery that would not have made it long enough to be seen in the wild.
Several years ago, the state was even working with Hubbs to sell “surplus” white seabass to Mexico, including hatchery fish with slight deformities.
That effort would have raised new money for the white seabass program, which has faced funding challenges that may contribute to some of its problems. The market for Hubbs’ surplus fish never materialized in Mexico.
Barnes, the Fish and Wildlife official, said the whole white seabass program, which spans four decades, should be considered a grand experiment.
Hubbs has found less than 2,000  of its white seabass in the wild. More hatchery white seabass have been sucked up and killed by coastal power plants than found at local fish markets.
The survey numbers certainly don’t identify every hatchery fish caught, but the numbers are so low that Fish and Wildlife officials interviewed for this story were unable to call the program a success.
The state has hired California Sea Grant to audit  the whole white seabass program. Cox, the state fish production manager, said the study will consider whether the breeding program is a “legitimate thing to be engaged in and paying for.” That study is expected to be finished next year.
Theresa Talley, an extension specialist at the Scripps Institution of Oceanography who is helping put together the study, said she doubts the white seabass program will be declared a success or a failure, because things are not that black or white.
The department continues to pay Hubbs more than $1 million a year to run the hatchery effort, known as the Ocean Resources Enhancement and Hatchery Program. The agency’s website calls it “a model for stocking programs worldwide .”