THE BLOG
08/30/2015 07:07 pm ET Updated Aug 30, 2016

The Oyster War: Part 3 -- Scientific Misconduct

Over the past month, I posted on this blog a pair of short reviews of the new book The Oyster War by Summer Brennan, focusing on whether she told the true story in defending the government's misrepresentations of science to support the ideological decision to remove the 80-year old oyster farm from Drakes Estero.

Several people have written posts in defense of Brennan. Adam Turner disputed my conclusion that the National Park Service falsified the findings of its own independent harbor seal expert, Dr. Brent Stewart. Brennan herself has now posted a lengthy blog accusing me of "libel," and again defending the Park Service's use of science. I respond to Turner and Brennan here. This response, in turn, further shows that officials in the Department of the Interior committed scientific misconduct, and that Interior still needs to implement a meaningful scientific integrity policy.

In my review, I reported that the Park Service falsified the findings of its own harbor seal expert, Dr. Brent Stewart, by transforming his finding that there was "no evidence" that the oyster farm disturbed harbor seals into the false conclusion, in the final Environmental Impact Statement (EIS), that the farm was causing serious harm to harbor seals.

Turner defended the Park Service by asserting that Stewart did not work alone in analyzing the Park Service photos, but rather was part of a team. That is misleading. Stewart was contracted by Interior and was the sole author on a May 2012 Report, concluding that there was "no evidence" of disturbance by the oyster farm. When I began to point out the contradiction between his report and the final EIS, the government went back to Stewart in December 2012 and asked him -- and him alone -- to re-analyze certain photographs, and he came back in writing with the same conclusion of no evidence of disturbance.

Turner asserted that the government had multiple marine mammal behavior experts analyze the photos. That is just wrong. On December 3, 2012, I wrote to USGS Dr. Lellis, the senior author of the USGS Report, and asked him why they turned to an outside scientist, and whether Stewart was their major harbor seal behavior expert. The next day, Lellis replied in writing: "Two people screened each video and recorded incidences of human activity, seal haulout, and potential flushing. This was done at the USGS. Photographs of potential flushing events and human activities were sent to Brent Stewart for analysis. As you noted, Brent was the harbor seal behaviorist on this project." In other words, the videos that showed "potential" disturbances by the oyster farm were sent to Dr. Stewart who alone analyzed them for whether they showed actual disturbances by the oyster farm. On December 5, 2012, Dr. Lellis confirmed that Dr. Stewart's May 2012 spreadsheet "is Appendix 1 of the [USGS] report." Stewart's spreadsheet showed that there was no evidence of disturbances caused by the oyster farm. In Appendix 1, however, USGS changed Stewart's spreadsheet - without telling him - and deleted the four words "no evidence of disturbance" from one entry.

Turner then asserted that Stewart analyzed a random 10% of the photos. Wrong again. USGS considered such an approach, but in the end dropped it, and instead made the NPS photographs into movies of every incident in which there was a "potential" flushing and sent those photos to Stewart for analysis.

Turner finally claimed that Stewart did not play a major role in the project, and that Stewart did not investigate seal disturbances. Wrong yet again. From a Freedom of Information Act request, I obtained Interior emails confirming the importance of Stewart's analysis. For example, on February 7, 2012, Dr. Lellis called his analysis a "...very high priority animal behavior project ..." and wrote "the NPS needs this analysis done by the end of March to brief Secretary Salazar who needs to make a decision on Wilderness Status for the park." "This is a high profile project. Very high profile ..." On April 20, 2012, USGS scientist Laurie Allen wrote to Dr. Stewart: "NPS is chomping at the bit (they've got deadlines for deciding on the permit)" On May 1, she wrote back to Dr. Stewart: "NPS will be breathing down my neck this week, when do you think you'll be able to transmit something?" A month later, she wrote to another USGS colleague: "NPS knows about these developments and we are keeping the department informed." That hardly sounds like either Dr. Stewart or the project was of little importance to Interior Secretary Salazar's decision.

Interestingly, what has not yet been put into the public record is the written interview that Dr. Alan Thornhill, one of Interior's Scientific Integrity Officers, conducted with Dr. Stewart in February 2014 in response to my May 2013 scientific misconduct complaint concerning the misrepresentation of Stewart's Report. Dr. Stewart's responses confirm what I have written.

Thornhill asked Stewart to respond to the following statement: "Regarding Dr. Stewart's role on the publication writing team: Dr. Stewart's report was part of the input to the final USGS report. Dr. Stewart was part of the team ..." Stewart responded: "I was not part of a team, either during the analysis or during the writing of the USGS report. I was very simply contracted by the USGS to do an independent assessment of a selection of time-lapse photographic records that USGS provided to me at the time of the contract award." In other words, Dr. Stewart worked alone, was the harbor seal behavior expert, and was the one who did the behavioral analysis of the photographs. His conclusion that there was "no evidence" that the oyster farm disturbs the harbor seals was falsified by the USGS and National Park Service.

As for Brennan: given that scientific misconduct, or lack thereof, is a central theme of both Brennan's book and my critique of it, I was surprised to read her lengthy response to my two reviews on tumblr entitled On Matters of Fact and Opinion. In her 2500 word response, laced with accusations of libel and continued settling of personal scores, she devoted only 31 words to this central issue. She wrote: "The scientists of Point Reyes National Seashore were never found guilty of scientific misconduct. It's a long and complicated but fascinating story, which I explore in detail in The Oyster War."

It is indeed a long and complicated story, but Brennan continues to get it wrong. Scientific misconduct is the intentional misrepresentation of facts. Did the Park Service intentionally misrepresent its own facts? Brennan says no. You be the judge.

Example 1: the 2008 Report from Interior's Inspector General. Interior's Inspector General, in a July 21, 2008 report, found that Dr. Sarah Allen (the Park's top scientist at Point Reyes National Seashore) "had misrepresented research" and wrote: "While Allen denied any intentional misrepresentation ..., our investigation revealed that Allen was privy to information contrary to her characterization ... and she did nothing to correct the information before its release to the public."

Why didn't the Inspector General find her guilty of scientific misconduct? Because at the time, neither Interior nor the National Park Service had a formal scientific integrity policy. The IG wrote: "Our investigation determined that NPS did not have a "Scientific Code of Conduct" in place ..."

In April 2010, Interior's IG released another report entitled Interior Lacks a Scientific Integrity Policy. In describing why scientific integrity is so important to Interior's mission, and how it was violated concerning the oyster farm, the IG wrote that the senior scientist "misrepresented research ..., failed to provide information sought after from a Freedom of Information Act request, and misinformed individuals in a public forum regarding sea life data, which put into question NPS' scientific integrity."

Example 2: the 2009 National Academy of Sciences Report. The National Academy of Sciences (NAS) released its report on Park Service science at Drakes Estero on May 5, 2009. Emails reveal that in January 2009, many panel members believed the Park was guilty of misconduct, and were struggling with what to say in their report. Panel chair Dr. Pete Petersen wrote to fellow panel members and Ocean Studies Board Director Dr. Susan Roberts on January 9, 2009: "I personally have no doubt that there was intent, based upon the directional bias of the putative impacts of the oyster farm reported by NPS. However, I would agree that it may not serve our charge or the good of the process to be so judgmental." Two months later, William Colglazier (the Academy's Executive Officer) formally announced: "This study was never intended to be an inquiry of potential scientific misconduct, and will make no such determination."

While side-stepping the issue of misconduct, the NAS Report found: "The National Park Service ... in some instances selectively presented, over-interpreted, or misrepresented the available scientific information ..." on oyster farm impacts on Drakes Estero. They went on to conclude: "... there is a lack of strong scientific evidence that shellfish farming has major adverse ecological effects on Drakes Estero."

The Academy acknowledged the controversy concerning the Park Service claims that oyster operations disturbed harbor seals, and concluded that resolving the controversy "... would require a data collection system that could be independently verified, such as time and date stamped photographs."

But what the Academy didn't know is that the Park Service had put in place a secret system to take time and date stamped photographs more than two years earlier. The Park Service had already analyzed those photographs, and found no evidence that oyster operations were disturbing seals. The Park Service kept this camera program, and its conclusions, secret from the Academy, even though the Academy had asked for all of the Park's data and analysis.

Example 3: the 2011 Frost Report from Interior's Solicitor's Office. In the summer of 2010, I discovered the Park's secret camera program. In November 2010, I filed a misconduct complaint with Interior Secretary Salazar. The Secretary asked his own lawyers in the Solicitor's Office to handle the review. That review was conducted by Field Solicitor Gavin Frost. Concerning the Frost Report, Brennan writes in her book: "While Frost was clearly unimpressed with the rigor of the science in question, he did not issue a guilty verdict." Once again, Brennan misses the story.

Shortly before submitting his report, on January 24, 2011, Field Solicitor Frost and I talked by phone. Frost told me that he had found "multiple NPS employees guilty of scientific misconduct." Frost told me that the "EIS process for the oyster company was tainted with the same bad science." Two days later, on January 26, Frost telephoned Kevin Lunny (owner of the oyster farm), and told him that his report was nearly finished and would be submitted within days. Moreover, Frost told Lunny that he had "found scientific misconduct." Both of Frost's conversations were publicly disclosed in the local newspaper in April 2011 (the same one Brennan later worked for), and although he has been asked on multiple occasions, Frost has never denied those statements.

Interior initially refused to release the Frost Report. But then, after intense pressure, several months later, on March 22, 2011, Interior released a redacted, revised public version. This redacted version concluded that the NPS scientists showed "bias," "advocacy," a "troubling mind-set," "mishandled" data, and a "willingness to allow subjective beliefs ... to guide scientific conclusions." These "mistakes," the report concluded, "stem from the refusal ... to modify [the Park's scientists'] intuitive, but statistically and scientifically unproven, belief that DBOC mariculture activities ..." disturb harbor seals in Drakes Estero. The Report went on to conclude: "this misconduct arose from incomplete and biased evaluation and from blurring the line between exploration and advocacy through research." Note the word "misconduct" within the body of the report.

The Frost Report concluded that five NPS employees "violated [the] NPS Code of Scientific and Scholarly Conduct" (a code put in place after the 2008 OIG report). Those five NPS employees included Superintendent Neubacher and four NPS scientists (including Dr. Allen, the Park scientist called out for different misrepresentations in the 2008 IG Report).

While the public version of the Frost Report found that five NPS officials and scientists had violated the NPS Code of Scientific and Scholarly Conduct, the Report defined this violation not as "scientific misconduct" but rather as "administrative misconduct." The Frost Report provided no federal document for a definition of "administrative misconduct" and Frost himself subsequently admitted (in a phone call with me) that Interior invented the term.

When the Frost Report was released in March 2011, Interior put out a press release that stated: "Interior Report Finds Mistakes Made, but No Scientific Misconduct at Point Reyes National Seashore." While that is the narrative that Interior wants us to believe, and that Brennan co-opts in her book, it is not the true story.

Example 4: the 2012 Stewart Report, USGS Report, and NPS Environmental Impact Statement. For nearly a decade, the most important scientific charge against the oyster farm was that its operations were disturbing harbor seals. That charge is repeated as fact in Brennan's book, even though the government's expert came to the opposite conclusion. Indeed, Brennan failed to cite (or interview) the government's expert, Dr. Stewart, who analyzed the government's cache of hundreds of thousands of secret photographs of oyster boats and seals, and concluded that there was "no evidence" that the oyster farm disturbed seals.

In Brennan's blog in response to my book review, she fails to comment on why she neither cited nor interviewed Dr. Stewart. Is it possible she didn't know? My misconduct complaint about the misrepresentation of Stewart's Report was widely featured throughout 2013 and 2014 in the local newspaper, filings in federal court, and in the national press, including, for example, Emily Yehle's story in Greenwire on May 14, 2013 entitled Rushed USGS report on oyster farm misrepresented biologist's findings. Most important, Dr. Stewart finally spoke to the press for an article entitled The Oyster Shell Game in Newsweek on January 18, 2015 (over six months before Brennan's book was published). Brennan communicated frequently with the investigative journalist who wrote the Newsweek story, Michael Ames. But Stewart's name can't be found in her book.

As Ames reported: "On May 3, 2012, Stewart filed his reports, determining there were no disturbances attributable to the oyster farm's boats. But when the USGS published its final report that November, Stewart discovered that his findings had been altered and that the study reached conclusions his research directly contradicted. 'It's clear that what I provided to them and what they produced were different conclusions and different values,' says Stewart. 'In science, you shouldn't do that.'

"For example, the USGS had deleted his words "no evidence of disturbance" for one date, and in its analysis stated that two disturbances "were associated with boat activity"--despite Stewart's study that showed otherwise. Strangely, USGS went back to Stewart months later and asked him to double-check his work on two dates in particular. He did as requested and reiterated his findings, but even this did not alter the final report's inaccuracies. In its Final Environmental Impact Statement, the Park Service took this alteration one step further by implying causation between the boats and the seals, something Stewart had explicitly ruled out. Eventually, this Impact Statement would be used by Department of Justice lawyers in their arguments against Lunny before the 9th U.S. Circuit Court of Appeals.

"Stewart told his contacts at the USGS that their report had errors and asked if he could correct them. "The response I got was, 'No, it's done. It can't be changed.' That was a bit shocking.""

In May 2013, I filed a scientific misconduct complaint against both NPS and USGS in which I reiterated how the agencies had twisted Stewart's findings. Over 18-months later, Interior finally responded to my complaint. As Ames wrote: "This past November, the USGS dismissed Goodman's 160-page complaint with a one-page letter. The agency's Scientific Integrity Office did not address the specifics of Goodman's report in either their letter or in a brief overview published on the DOI website. In the latter, the USGS stated that "no evidence was provided by the complainant, nor found during the inquiry of any significant departure from accepted practices...nor was there any evidence of intent to deceive or misrepresent work." When pressed for explanation of their decision, the USGS did not respond."

Yet none of this is mentioned either in Brennan's book or in her 2500-word response.

Charge of Libel. Finally, I must respond to Brennan's claim that I have somehow libeled her by pointing out some of the hundreds of factual errors and omissions in her supposedly "True Story." If there was any substance to her accusation, she would do something about it legally rather than repeat it over and over again on social media, but she hasn't.

Brennan plays loose with the facts in her response. She claims she interviewed, or at least tried to interview me, for her book. Here are the facts. On September 7, 2014, she wrote me by email: "I wanted to reiterate my request to you for an interview. Can we set up a preliminary over the phone?" A few minutes later, I answered: "Shall we talk on Wednesday or Thursday?" She responded: "Sounds good Corey - let's plan to talk Wednesday." She never called or contacted me that Wednesday, and never did again for either a phone or in person interview.

In her blog, she writes: "For the Point Reyes Light article "Ragen Rebukes Scientist," I interviewed Corey over the phone three times at length ..." That too is false. There was only one interview. As I wrote in my review: "During that bizarre phone conversation, she couldn't find her notes, didn't have any questions to ask, and suggested we reschedule for the following morning."

Since Brennan is refuting my statement, and accusing me of libel, I elaborate here on what really went on, as documented in contemporaneous notes and emails. Brennan called me at 5:35 pm on Monday night July 23, 2012. From the outset, Brennan told me that she was deeply upset because a friend had just told her something personally very disturbing. In our 20-minute conversation, Brennan repeatedly acknowledged that she was emotionally upset and distracted. She apologized for being so spaced out. We agreed to conduct the interview the next morning.

Less than 30 minutes later, I wrote her editor that I had just had an "incoherent talk" with Brennan, that "She said ... that someone just really upset her personally, so she was in a really bad shape." The next morning, as I reported previously, Brennan ducked my phone calls three times.

She did finally call me to fact check something trivial at 6:10 pm on Wednesday night July 25 as her story was going to press. When I asked her why she had not interviewed me for a story that was about me, she justified her behavior by saying that the story (entitled Ragen Rebukes Scientist) wasn't about me, although I am the scientist cited in the title. For the record, Brennan's story was retracted two weeks later, with the editor writing: "Regrettably we failed to dig deep enough, and as a result we missed puzzling statements in the letter that, among other things, reverse Dr. Ragen's official position on the impacts of mariculture on harbor seals in Drakes Estero. In other words, we missed the story."

Brennan continues to miss the true story by failing to check the facts, failing to interview the key players, and letting science take a back seat to ideology.