01-22-15 Pt Reyes Light: Seal Expert Says Federal Agency Ignored His Findings, by Samantha Kimmey

 “A scientist told a national magazine that a federal agency changed his analysis of photographs of Drakes Estero to justify a claim of environmental harm against Drakes Bay Oyster Company, which ceased operations last month….

In a Newsweek story published online last Sunday, Mr. Stewart said, “It’s clear that what I provided to them and what they produced were different conclusions and different values.” He added, “In science, you shouldn’t do that.” 

Seal expert says agency ignored his findings
By Samantha Kimmey
A scientist told a national magazine that a federal agency changed his analysis of photographs of Drakes Estero to justify a claim of environmental harm against Drakes Bay Oyster Company, which ceased operations last month. 
Brent Stewart, who has been a senior research scientist at Hubbs-SeaWorld Research Institute for decades, analyzed a selection of time-lapse photographs taken by a Point Reyes National Seashore camera for a 2012 United States Geological Survey report on harbor seals, a report later cited in the environmental impact statement on the oyster farm. 
He found no correlation with oyster boats, but the report said otherwise. 
In a Newsweek story published online last Sunday, Mr. Stewart said, “It’s clear that what I provided to them and what they produced were different conclusions and different values.” He added, “In science, you shouldn’t do that.” 
In response to a query from the Light, Mr. Stewart emailed that he was traveling and could not answer questions by press time. Allegations that oyster boats disturbed harbor seals—federally protected under the 1972 Marine Mammal Protection Act—were for years made by the National Park Service and environmentalists championing the Drakes Bay’s removal. Others vociferously refuted those claims. After the park service was found to be in possession of hundreds of thousands of time-stamped photographs and then criticized for not taking advantage of them to assess the potential impacts of the farm, the park service asked the geological survey to undertake a report. 
The final version of the environmental impact statement on the farm, published in late 2012, cited that report, saying its analysis “attributed” two disturbance events to farm boats.
Mr. Stewart’s public allegations come two months after the geological survey dismissed a 2013 scientific misconduct complaint over the representation of Dr. Stewart’s study. The complaint was the seventh filed by Corey Goodman, a scientist and Marshall resident who became an outspoken critic of science produced and used by the park to oust the oyster company. 
A U.S.G.S. spokeswoman, Anne-Berry Wade, said the lead author of the agency’s seal report, William Lellis, could not speak to the press because of ongoing litigation over the complaint. 
An earlier allegation of scientific misconduct over the suppression the photographs was investigated by Gavin Frost, a solicitor for the Department of the
In his 2011 report, Mr. Frost described what he called “administrative misconduct.” Seashore scientists didn’t meet the bar of scientific misconduct, he wrote, because they did not fabricate or misrepresent data with the intent to deceive; however, they might have violated the park service’s scientific research policy and they “blurred the line between exploration and advocacy through research,” he said. Seashore scientists also erroneously believed that, because the camera project followed no stringent protocols, the photos were not actually research or data, Mr. Frost wrote. 
Because the park service didn’t undertake a thorough assessment of the images, the report said “potentially powerful evidence remains unknown.” 
Seal controversy
Drakes Bay Oyster Company was first accused of threatening harbor seal populations in 2007. Assertions that the farm had spurred an 80 percent decrease in seals in one area was removed from a park service report and later publicly retracted by the report’s author, but continued controversy over the impact of the farm’s two small boats led the National Academy of Sciences to examine the existing body of research on the impacts and the Marine Mammal Commission to consider the impacts to seals specifically. 
The academy’s 2009 report said that there was a “lack of strong scientific evidence that shellfish farming has major adverse ecological effects on Drakes Estero.” But it also said that independently verifiable data, “such as time and date stamped photographs,” could help determine whether boat activity affected the seals. 
The committee was not aware that such photographs existed.
In 2010, Mr. Goodman discovered—in a footnote of a park service document meant to rebut Mr. Goodman’s claims about other disturbance events—that that the park service had a cache of hundreds of thousands of photographs taken between 2007 and 2010 from wildlife cameras placed on the bluffs overlooking Drakes Estero. 
Park scientists denied that the camera’s existence was intentionally withheld, but they did not mention it during the Marine Mammal Commission meetings in early 2010 when a panel member noted how useful one might be. Sarah Allen, the scientist in charge of the camera project, denied hearing the suggestion, according to Mr. Frost.
The commission’s report said that the photos, in combination with a separate video made by a park volunteer, provided “convincing evidence” of one instance of oyster boat disturbance, on May 15, 2008, but that all the photos should be examined more closely. Park data that was used to establish a correlative relationship between seal populations and oyster harvests was “scant and stretched to its limit,” the report said.
A draft of the environmental impact statement on the oyster farm, released in 2011, was criticized for not taking advantage of the photos. 
In response to that critique and the commission’s suggestion, the National Park Service enlisted the geological survey to assess the pictures. 
Mr. Lellis, the deputy associate director of the survey’s ecosystems research department, said in a 2012 email to a colleague that the report was critically
“The NPS needs this analysis done by the end of March to brief Secretary Salazar who needs to make a decision on the Wilderness Status for the park…This is a high profile project. Very high profile, so we need to put our best people on it,” Mr. Lellis wrote to a colleague. 
Citing the volume of photos, their mediocre quality and the difficulty of evaluating individual photos for meaningful data, the geological survey created 191 time-lapse videos from over 3,000
The U.S.G.S. hired Mr. Stewart to assess a selection of these videos in which it thought there might be human-caused disturbances; Mr. Stewart was told to classify each video based on whether he found a disturbance and whether he could identify causation or just correlation.
The geological survey’s final report said that photos taken on two separate days—May 15 and June 11, 2008—showed flushing events correlated with boats. “[B]oat traffic at nearby sandbars… could be directly connected, or at least associated with a flushing level of disturbance,” it asserted. (Of the 10 total disturbances the report documented, it said two came from kayakers, two from birds and four from unknown sources.)
But in data and a two-page report Mr. Stewart submitted, boats were not responsible for disturbing the seals. In the video sequences he analyzed, he said he found seven disturbance events—meaning that he could see seals flushing—potentially related to human presence. In one, he writes that the seals seem to clearly flush because of a nearby kayak. But he couldn’t link the presence of oyster skiffs to the three other events when boats were present in the frames. (For the other three videos, he could find no apparent human cause.)
The U.S.G.S. later asked Mr. Stewart to take another look at videos from two days: May 15 and June 11, the dates of the two incidents cited in the final U.S.G.S. report.
Mr. Stewart again said there was no correlation between seal movements and the appearance of a boat. He wrote that on May 15, a boat appeared in the frame at 1:55 p.m. and left nine minutes later. A small number seals then flushed into the water and some others moved toward the water, but he wrote there was no obvious stimulus. The June 11 photographs showed a “minor startle” of seals about 10 minutes after a boat leaves the area, but he didn’t believe they had been flushed.Mr. Stewart told Newsweek that he asked the geological survey if he could fix the report after it was published. He was told that it was too late, a response Mr. Stewart described as “shocking.”
This November, well over a year after Mr. Goodman filed his last complaint, the U.S.G.S. closed the case, finding no misconduct. On a website detailing closed scientific complaint cases, the agency asserted that its report “made no claim” correlating disturbances of harbor seals with boat activity from the oyster farm. The rebuttal also cites sections of the final report that discuss the difficulty and limitations of analyzing the photographs. 
But the report itself said “two [flushing events] were associated with boat activity”—a finding the park service turned into “Two flushing disturbance events were attributed to boat traffic at nearby sand bars” in the oyster farm’s 2012 impact statement. 
The park service ultimately concluded that continued operations would lead to long-term moderate adverse impacts to harbor seals. The environmental impact statement also cites other reports in the section on harbor seals—including the one by park service scientists correlating oyster harvest with harbor seal populations, and the Marine Mammal Commission report, both heavily criticized.
When then-Secretary of the Interior Ken Salazar decided to close the farm, he acknowledged that the park, advocates of wilderness and farm supporters had vigorously debated the science around the farm. He said he based his decision on law and policy, not environmental impacts. Yet although they were “not material to the legal and policy factors that provide the central basis for my decision, they have informed me with respect to the complexities, subtleties and uncertainties of this matter and have been helpful to me in making my decision.”
Melanie Gunn, the outreach coordinator for the seashore, echoed that sentiment this week. “There may always be debate about the science of Drakes Estero, which I am sure you have heard from all sides, but ultimately, the Secretary of the Interior made his decision based on law and policy, a decision that has been upheld in federal court. This has been a challenging issue for the park [and] community. We are pleased to have reached a joint settlement agreement with Drakes Bay Oyster Company that allows all parties to move forward,” she wrote to the Light.
The oyster farm closed its cannery last summer, and December saw that last harvest. Within days the buildings were torn down, and the park service is working to remove remaining shellfish because the state health department is no longer testing them. 
But Mr. Goodman says what happened between Mr. Stewart’s report and the farm’s impact statement still matters. “As scientists, we believe that when the government publishes a report…it should be accurate and should have integrity,” he said.
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