6. CSG's Scientific Misconduct Complaint Sent to Jewell 5.13.13

8/10/2019 6. CSG's Scientific Misconduct Complaint Sent to Jewell 5.13.13

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May 13, 2013

From: Dr. Corey S. Goodman

To: Sally Jewell, Secretary, Department of the Interior

Re: Request that Interior investigate allegations of scientific misconduct involving the

National Park Service (NPS) and U.S. Geological Survey (USGS)

Dear Secretary Jewell,

As the new Secretary of the Department of the Interior, you assumed leadership of aDepartment in trouble due to unchecked scientific misconduct at NPS that has nowpermeated another of your agencies, the USGS. Over the past six years, NPS engaged inscientific misconduct concerning the oyster farm at Drakes Estero. Most recently, NPSwas aided by another agency – USGS – as a partner to that misconduct.

The case for scientific misconduct presented here concerns new information obtainedsince last November 2012, and some of it obtained only in the past week in the form of

USGS emails concerning this issue, and a previously undisclosed supplemental report.I request that you conduct an unbiased and independent investigation of scientificmisconduct at NPS and USGS. Whether Interior can conduct such an unbiased andindependent investigation – given the inherent conflicts-of-interest – and whetherInterior is capable of a finding against itself, will be a test of your leadership.

The four allegations of misconduct (see Appendix 1), involving two DOI agencies, are:

1. USGS , in its USGS Report on their analysis of the NPS photographs concerningthe oyster farm at Drakes Estero, misrepresented the record from the StewartReport (by Hubbs-SeaWorld Research Institute harbor seal behavior expert Dr.Brent Stewart), falsely claimed a correlation of oyster farm activity and disturbance

of harbor seals based upon Dr. Stewart finding of no evidence of disturbance , and inso doing violated the DOI Scientific Integrity Policy.

2. NPS , in its Final EIS (FEIS) concerning the oyster farm at Drakes Estero,misrepresented the USGS Report, falsely claimed causation of oyster farm activityand disturbance of seals based upon the USGS Report finding of a correlation (inturn based upon Dr. Stewart’s finding of no evidence of disturbance), leading to anoverall finding in the NPS FEIS of a moderate adverse impact , and in so doingviolated the DOI Scientific Integrity Policy.

3. USGS and NPS , in their claims that the USGS analysis of the NPS photographswas very high profile and very high priority , and needed to inform Secretary Salazar forhis decision on the oyster farm permit, apparently briefed Assistant SecretariesCastle and Jacobson with false claims of evidence of oyster farm disturbances ofseals in Drakes Estero, and in so doing violated the DOI Scientific Integrity Policy.

4. USGS , after its Report was released, requested a subsequent re-review of key

data by Dr. Stewart in his Supplemental Report that confirmed his earlier finding ofno evidence of disturbance , a report that should have led USGS to retract its USGSReport, inform NPS of the major mistakes in their FEIS, and inform the Secretaryof mistakes in what was presented to inform his high profile decision, but insteadwas covered up, and in so doing violated the DOI Scientific Integrity Policy.



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1. White House OSTP Instructed Me to File This Complaint with Interior

Like me, you are a scientist by training. As a mechanical engineer, you rely on data andfacts. In your statement to the Senate Energy and Natural Resources Committee onMarch 7, 2013, you spoke of the importance of the Department of the Interior using “thebest science available” to make the best decisions, using the “vast scientific” resources atInterior.

As a fellow scientist, I applauded your statements, much as an elected member of theNational Academy of Sciences (NAS), I applauded President Obama when, on April 27,2009, in his address to the NAS, he said:

“we are restoring science to its rightful place”

“the days of science taking a back seat to ideology are over”

I applauded again when the President addressed the NAS on April 29, 2013 and said:

“one of the things that I've tried to do … is to make sure that we are promotingthe integrity of our scientific process”

“I will keep working to make sure that our scientific research does not fall victim

to political maneuvers or agendas that in some ways would impact on theintegrity of the scientific process”

In contrast to the President’s stated policies, as applied to Drakes Estero, science hastaken a back seat to ideology, and science has fallen victim to political maneuvers. Those“vast” resources you cited at NPS and USGS have been squandered and tarnished byNPS before you took over leadership of Interior.

Some of these allegations (#1 and #2) were submitted in March 2013 to Dr. JohnHoldren, the President’s science advisor, OSTP Director, and architect of the President’sScientific Integrity Policy. I had five reasons for taking this complaint to the WhiteHouse.

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First, there has been a repeated pattern of unabated scientific misconduct at NPS,with a six-year history of false claims of harm to harbor seals (see Appendix 3.1).• Second, Interior has been biased in protecting its own rather than upholding its

Scientific Integrity Policy (see Appendix 3).• Third, Interior’s Scientific Integrity Officers are biased, conflicted, and

unresponsive concerning NPS and USGS scientific misconduct (see Appendix 2).• Fourth, the Interior Inspector General inexplicably dismissed allegations of

misconduct against NPS based on far-fetched and tortuous reasons, reinforcingthat they are incapable of an honest investigation of NPS (see Appendix 4).

• Fifth, NPS Director Jarvis boldly declared in response to a Data Quality Actcomplaint about incorrect science in the NPS DEIS that science at his agency is

beyond accountability (the Jarvis Doctrine, see Appendix 3.2).As a result of these biases and conflicts, on March 4, 2013, I wrote to OSTP Director Dr. John Holdren and asked him to oversee a blue-ribbon panel to investigate scientificmisconduct at NPS and USGS.

On March 15, OSTP General Counsel Rachael Leonard told me that OSTP takes thesecharges seriously. She said OSTP understands concerns about the conflicts-of-interestand lack of independence at Interior, and about the Jarvis Doctrine stating that NPSscience is beyond accountability. Nevertheless, she said she was compelled to instructme to file my complaint with the Department of the Interior. I suggested that this was



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circular reasoning that would lead to more of the same – bias, a lack of independence,and a resulting whitewash.

In the past week, new, previously undisclosed documents were obtained, documents notavailable when I originally filed allegations #1 and #2 with OSTP. These newdocuments reinforce this complaint by providing evidence that (i) two AssistantSecretaries apparently were briefed with this false science to inform the Secretary’s high

profile decision, and (ii) USGS staff covered-up a subsequent Supplemental Report thatconfirmed the false science. These revelations lead to allegations #3 and #4 (seeAppendix 1).

I must admit that I am a bit apprehensive, given the history (see Appendices 2-4) aboutsubmitting this scientific misconduct complaint to Interior (see Appendix 1). I am baffled as to how you can proceed, but given your background as a scientist, yourleadership, and your statements to the Senate Committee, I am confident you will find away. Please be forewarned that in the system you inherited, you will find conflicts-of-interest, particularly in your various Scientific Integrity Officers (see Appendix 2).

2. Overview of Allegations of Scientific Misconduct

On November 20, 2012, a new generation of misconduct emerged when NPS released theFinal Environmental Impact Statement (FEIS) for the oyster farm permit at Drakes Estero(see Appendix 1). This is not the first episode of scientific misconduct concerning NPS,and in particular false claims of evidence that the oyster farm disturbs the harbor seals inDrakes Estero, but it now involves another agency within Interior in addition to NPS,namely, USGS.

After six years, secret cameras, and millions of dollars of taxpayer money, there is noevidence that the oyster farm is disturbing or has disturbed the harbor seals in DrakesEstero. The oyster boats stay over 700 yards from the seals, with a sandbar betweenthem. Dr. Brent Stewart (Hubbs-SeaWorld Research Institute harbor seal behavior

expert) found no evidence for disturbance , the USGS Report misquoted him and claimed hefound two correlations , and then the NPS FEIS further misrepresented the USGS Reportand claimed causation , and with it, a finding of a moderate adverse impact. The serialmisrepresentations, and subsequent cover-up of this misdeed, were done knowingly.

On November 20, 2012, NPS released the NPS FEIS for the Drakes Bay Oyster Company(DBOC) Special Use Permit. The FEIS concluded that continuation of the oyster farmwould result in a long-term “moderate adverse impact” on harbor seals due to the “ potential for disturbances” and “continued disturbances” caused by DBOC oyster boats.

This single determination had a significant impact on other findings in the FEIS, and onSecretary Salazar, other top leaders at Interior, elected officials, the public, and media.After six years of false public claims and manipulated reports, NPS claimed that an

independent analysis by USGS of NPS photographs supported this finding.USGS and NPS staff discussed how this analysis was of “very high priority” and wasnecessary to inform the Secretary for his decision on the oyster farm permit. TwoAssistant Secretaries apparently were briefed. The NPS FEIS finding of a “moderateadverse impact” was presented by Department of Justice lawyers to the Ninth CircuitCourt of Appeals as the reason why the public good is in favor of removing the oysterfarm.

This analysis was considered “very high profile ,” and USGS and NPS knew it was wrong



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and misrepresented Dr. Stewart’s findings. Moreover, USGS received a SupplementalReport from Dr. Stewart further showing that the USGS Report and NPS FEIS werewrong, and they did not disclose the Supplement Report, retract the USGS Report, notifyNPS that their FEIS was incorrect, or apparently notify the Secretary, his lawyers, andthe court that his decision had been misinformed by false science. That was a cover up.

The facts, based upon the “ preponderance of evidence” reveal that the claim of scientific

evidence of oyster farm disturbances was based upon misrepresentations made“intentionally, knowingly, or recklessly,” the standard for determining misconductaccording to the Federal Policy on Research Misconduct.

The NPS FEIS claimed evidence that the oyster farm occasionally disturbed harbor seals.This finding was inconsistent with the physical landscape: the oyster boats typically stayover 700 yards away from the harbor seals, with an intervening sandbar blocking theirview and buffering their sound, while the NOAA and NPS recommendations andprotocols call for a 100 yard buffer (facts not disclosed in the FEIS).

NOAA, the agency charged with overseeing the Marine Mammal Protection Act of 1972,recently concluded the harbor seal population in and around Drakes Estero is at or nearits carrying capacity. During the Draft EIS (DEIS) comment process, NOAA, the federal

agency responsible for administration of the Marine Mammal Protection Act, reported toNPS, in their comments on the DEIS, that their agency had not received reports of harborseal disturbances by the oyster farm in Drakes Estero.

What data supported the NPS finding in the FEIS of oyster farm disturbances of seals?

The NPS cited a 2012 USGS Report that analyzed, at NPS request, a large subset (165,000photos from the 2008 harbor seal pupping season) of the over 300,000 time- and date-stamped NPS photographs of the oyster boats and harbor seals (from secret camerasoperational for three and one-half years from 2007 to 2010). The FEIS quoted the USGSReport as concluding that on two occasions in 2008, oyster boats caused seals to flushinto the water.

There are, however, two major problems with this claim: NPS misquoted the USGSReport, and USGS misquoted the original expert’s findings (Dr. Brent Stewart, Hubbs-SeaWorld Research Institute). In so doing, both agencies misrepresented the primaryscientific analysis and altered the scientist’s conclusion.

The USGS Report did not conclude what the NPS claimed. Rather, USGS found an“association” (a weak correlation) and not causation of oyster boats and harbor sealsgetting flushed into the water (a major disturbance) on these two occasions. The USGShad no harbor seal behavior expert, and so relied on an analysis of NPS photos, ascontracted by NPS, conducted by Dr. Brent Stewart, a harbor seal behavior expert atHubbs-SeaWorld Research Institute in San Diego (the 2012 Stewart Report). The USGSReport quoted the Stewart Report as finding two “associations” of oyster boats and

harbor seals getting flushed into the water (on May 15 and June 11, 2008).The Stewart Report did not conclude what the USGS claimed. Rather, Dr. Stewart found“no evidence of disturbance” of harbor seals by the oyster farm on both of these dates. Areview of his spreadsheet, submitted to both NPS and USGS, confirms his clarity forthese two dates. The USGS Report misrepresented the Stewart Report, claiming acorrelation where Dr. Stewart found none, and then the NPS FEIS misrepresented theUSGS Report, claiming causation where the USGS claimed a weak correlation.

In this way, a finding of “no evidence of disturbance” was transformed into a finding ofcausation (“attribution”) that led to a finding in the FEIS of “moderate adverse impact.”



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Was this a clerical error in copying Dr. Stewart’s spreadsheet from one report toanother? Unlikely. Consider: (i) the evidence for serial misrepresentations ofdisturbances in the Stewart, USGS, and NPS FEIS Reports; (ii) the history of repeatedNPS false claims of harbor seal disturbances by the oyster farm since 2007; (iii) thatthis is the only evidence for such disturbances over the past six years; (iv) that this wasa high priority project that apparently led to briefings of two Assistant Secretaries ofInterior to inform the Secretary’s decision; and (v) the cover-up of the subsequent

Supplemental Report by Dr. Stewart (requested by USGS) confirming his initialfinding of no seal disturbances by the oyster farm (on May 15 and June 11, 2008).

It is alleged that the “ preponderance of evidence” (as defined by the DOI and WhiteHouse Scientific Integrity Policies) leads to the conclusion that these serialmisrepresentations and cover-up by USGS and NPS were committed “intentionally,knowingly, or recklessly.” False science was used to inform the Secretary for a highprofile policy decision. The Secretary, public, and federal court were deceived.

3. Interior Scientific Integrity Officers and Interior Inspector General AreConflicted Concerning Allegations of Misconduct at NPS and USGS

Nine reasons lead me to conclude that Interior’s Scientific Integrity Officers and theInterior Inspector General are conflicted concerning allegations of misconduct at DOI.

1) Inspector General offices (OIGs) are in general unable or unwilling to properlyinvestigate allegations of scientific misconduct, and have no scientists on staff.

2) The Department of the Interior (DOI) OIG provides investigatory oversight forNPS and USGS, but the DOI OIG abdicated its independent investigatoryoversight, and went further to engage in a cover-up of NPS misconduct.

3) In its most recent report, the DOI OIG went to great lengths to dismissallegations of scientific misconduct concerning soundscape analysis in the NPS

DEIS, altering and ignoring some allegations, creating straw-man arguments,cherry-picking law and policy, and accepting explanations and testimony despiteevidence to the contrary – evidence in the form of documents and emails.

4)

The Public Employees for Environmental Responsibility wrote the DOI OIGpulled its punches and compromised its independence to please superiors.

5) The House Committee on Natural Resources wrote that it is deeply concernedthat DOI OIG actions are inconsistent with the role of independent watchdog.

6) If allegations involve high-level officials, the Scientific Integrity Officersthroughout Interior are no less conflicted that the DOI OIG, lacking theindependence or willingness to investigate allegations of scientific misconduct.

7)

The Scientific Integrity Officer for NPS is conflicted by his reporting line (i.e.,reporting to NPS Director) and by his prior involvement in this issue.

8) The Scientific Integrity Officer for USGS is conflicted and has been unresponsiveto repeated requests to describe the nature of her investigation, if any. The USGSSIO was repeatedly notified of allegations #1 and #2 presented here, butremained silent and did not even acknowledge receipt of the allegations.

9) The Scientific Integrity Officer for DOI and USGS Acting Director is conflicted bythe allegations concerning USGS and the lack of responsiveness by the USGSSIO. How can the DOI SIO also be the Director of USGS and investigate USGS?



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4. Request That DOI Establish a Blue-Ribbon Panel of Eminent Scientiststo Investigate These Allegations

This issue has outgrown Drakes Estero. It is no longer a local issue. It involves NPSand USGS. The DOI OIG and three DOI Scientific Integrity Officers have shown theirinability to properly investigate misconduct within Interior.

The NPS false science in the FEIS has been used by Department of Justice lawyers in theNinth Circuit Court of Appeals to assert that the public good favors removing theoyster farm. The false science in the FEIS has been used in regulatory hearingsinvolving oyster farms in other parts of the U.S., and growers in other countries are becoming increasingly concerned. Many people inside and outside government arewatching and waiting.

Allowing the scientific misconduct to stand is already having – and will continue tohave – a corrosive impact on scientists throughout Interior. It sends a message not toreport the facts and data objectively as you find them, but rather to report data assomeone else in a powerful position wants them to be reported. It is not healthy forscience at Interior, and it undermines what the President hoped to accomplish.

At this juncture, the only way to make sure that science does not take a back seat toideology is for you, as the new Interior Secretary, to direct a truly independentinvestigation of the science in this matter at NPS and USGS. It is incumbent upon youto bypass the biases and conflicts that have dominated previous investigations underthe leadership of your predecessor, and to find a path forward that is unbiased.

In the January 23, 2013 Huffington Post, Dr. Peter Gleick, President, Pacific Institute(environmental NGO), elected member, NAS, and MacArthur Fellow, wrote:

“… the National Park Service, the Department of the Interior (DoI), and somelocal environmental supporters (with whom I often have strong common cause)manipulated, misreported and misrepresented science in their desire to supportexpanded wilderness. In an effort to produce a rationale to close the farm, false

arguments were made that the farm damaged or disturbed local seagrasses, waterquality, marine mammals and ecosystem diversity. These arguments have, oneafter another, been shown to be based on bad science and contradicted by evidencehidden or suppressed or ignored by federal agencies. The efforts of local scientists,especially Dr. Corey Goodman, professor emeritus from both Stanford andBerkeley and a member of the U.S. National Academy of Sciences, were central torevealing the extent of scientific misconduct. Reviews by independent scientistsand now confirmed by investigations at the Department of Interior and the U.S.National Academy of Sciences show that arguments of environmental harm fromthe oyster farm were misleading and wrong.”

“… scientific integrity, logic, reason, and the scientific method are core to the

strength of our nation. We may disagree among ourselves about matters ofopinion and policy, but we (and our elected representatives) must not misuse,hide or misrepresent science and fact in service of our preferences and ideology.”

The scientific method is core to the strength of our nation. It is also core to thePresident’s Scientific Integrity Policy. The Jarvis Doctrine (see Appendix 3.2) overturnsand undermines what you stand for as a scientist and a leader. It is time for Interior torestore science to its rightful place and not allow science to take a back seat to ideology.



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In summary, this issue requires your immediate attention and action. I request that:

(1)

We meet so I can present the allegations and propose a proper investigation.

(2) The DOI establish a blue-ribbon panel of eminent scientists to conduct thisinvestigation, bypassing its conflicted SIOs and conflicted outside contractors.

(3) The panel investigate these allegations in a transparent fashion, allowing both

sides to respond to statements made by the other in an open fashion.I look forward to discussing these issues with you as soon as possible.

Sincerely yours,

Corey S. Goodman, Ph.D.

[email protected] 663-9495; 650 922-1431 (mobile)

Appendices

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Appendix 2: Why the DOI OIG and SIOs Cannot Resolve These Allegations of ScientificMisconduct

Appendix 3: Overview of the History of NPS Scientific Misconduct

Appendix 4: Analysis of DOI OIG Investigative Report on DBOC EIS: The DOI OIG DidNot Conduct a Proper and Independent Investigation of NPS Misconduct

Appendix 5: Dr. Corey Goodman, Brief Resume and History of Involvement



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Appendix 1:

Overview of Allegations of Scientific Misconduct

Table of Contents

1. Summary of Allegations of Scientific Misconduct ............................................................. 2-4

2. Documents and Communications Supporting These Allegations .................................. 4-5

3. Allegations #1 & #2: USGS & NPS Misrepresented the Stewart Report ...................... 5-15

4. Allegation #3: USGS & NPS Used False Science to Brief the Secretary ...................... 15-18

5. Allegation #4: Dr. Stewart Re-Reviewed Key Data, Confirmed Initial Findings of No

Evidence of Disturbance, & USGS Covered Up His Report ............................................. 18-21



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1. Summary of Allegations of Scientific Misconduct The four allegations of misconduct, involving two DOI agencies, are:

1. USGS , in its USGS Report on their analysis of the NPS photographs concerningthe oyster farm at Drakes Estero, misrepresented the record from the StewartReport (by Hubbs-SeaWorld Research Institute harbor seal behavior expert Dr.Brent Stewart), falsely claimed a correlation of oyster farm activity and disturbanceof harbor seals based upon Dr. Stewart finding of no evidence of disturbance , and inso doing violated the DOI Scientific Integrity Policy.

2. NPS , in its Final EIS (FEIS) concerning the oyster farm at Drakes Estero,misrepresented the USGS Report, falsely claimed causation of oyster farm activityand disturbance of seals based upon the USGS Report finding of a correlation (inturn based upon Dr. Stewart’s finding of no evidence of disturbance), leading to anoverall finding in the NPS FEIS of a moderate adverse impact , and in so doingviolated the DOI Scientific Integrity Policy.

3.

USGS and NPS , in their claims that the USGS analysis of the NPS photographswas very high profile and very high priority , and needed to inform Secretary Salazar for

his decision on the oyster farm permit, apparently briefed Assistant SecretariesCastle and Jacobson with false claims of evidence of oyster farm disturbances ofseals in Drakes Estero, and in so doing violated the DOI Scientific Integrity Policy.

4. USGS , after its Report was released, requested a subsequent re-review of keydata by Dr. Stewart in his Supplemental Report that confirmed his earlier finding ofno evidence of disturbance , a report that should have led USGS to retract its USGSReport, inform NPS of the major mistakes in their FEIS, and inform the Secretaryof mistakes in what was presented to inform his high profile decision, but insteadwas covered up, and in so doing violated the DOI Scientific Integrity Policy.

On November 20, 2012, NPS released the NPS Final Environmental Impact Statement(FEIS) for the Drakes Bay Oyster Company (DBOC) Special Use Permit. The FEIS

concluded that continuation of the oyster farm would result in a long-term “moderateadverse impact” on harbor seals due to the “ potential for disturbances” and “continueddisturbances” caused by DBOC oyster boats.

A “moderate” adverse impact is defined as “impacts on harbor seals would result in readilyapparent effects on the population, natural processes, or habitat in the project area.” It is thesecond most serious category of adverse impacts.

This single determination of a “moderate adverse impact” on the harbor seals at DrakesEstero had a significant impact on other findings in the FEIS, and on Secretary Salazar,other top leaders at Interior, elected officials, the public, and media. After six years offalse public claims, manipulated reports, and secret cameras – and millions of taxpayerdollars – NPS claimed that an independent analysis by USGS of NPS photographssupported this finding.

The facts, based upon the “ preponderance of evidence” reveal that both claims of scientificevidence were based upon misrepresentations made “intentionally, knowingly, orrecklessly,” the standard for determining misconduct according to the Federal Policy onResearch Misconduct.

The NPS FEIS claimed evidence that the oyster farm occasionally disturbed harbor seals.This finding was inconsistent with the physical landscape: the oyster boats typically stayover 700 yards away from the harbor seals, with an intervening sandbar blocking their



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view and buffering their sound, while the NOAA and NPS recommendations andprotocols call for a 100 yard buffer (facts not disclosed in the FEIS).

NOAA, the agency charged with overseeing the Marine Mammal Protection Act of 1972,recently concluded the harbor seal population in and around Drakes Estero is at or nearits carrying capacity. During the Draft EIS (DEIS) comment process, NOAA, the federalagency responsible for administration of the Marine Mammal Protection Act, reported to

NPS, in their comments on the DEIS, that their agency had not received reports of harborseal disturbances by the oyster farm in Drakes Estero.

What data supported the NPS finding in the FEIS of oyster farm disturbances of seals?

The NPS cited a 2012 USGS Report that analyzed, at NPS request, a large subset (165,000photos from the 2008 harbor seal pupping season) of the over 300,000 time- and date-stamped NPS photographs of the oyster boats and harbor seals (from secret camerasoperational for three and one-half years from 2007 to 2010). The FEIS quoted the USGSReport as concluding that on two occasions in 2008, oyster boats caused seals to flushinto the water.

There are, however, two major problems with this claim: NPS misquoted the USGSReport, and USGS misquoted the original expert’s findings (Dr. Brent Stewart, Hubbs-SeaWorld Research Institute). In so doing, both agencies misrepresented the primaryscientific analysis and altered the scientist’s conclusion.

The USGS Report did not conclude what the NPS claimed. Rather, USGS found an“association” (a weak correlation) and not causation of oyster boats and harbor sealsgetting flushed into the water (a major disturbance) on these two occasions. The USGShad no harbor seal behavior expert, and so relied on an analysis of NPS photos, ascontracted by NPS, conducted by Dr. Brent Stewart, a harbor seal behavior expert atHubbs-SeaWorld Research Institute in San Diego (the 2012 Stewart Report). The USGSReport quoted the Stewart Report as finding two “associations” of oyster boats andharbor seals getting flushed into the water (on May 15 and June 11, 2008).

The Stewart Report did not conclude what the USGS claimed. Rather, Dr. Stewart found“no evidence of disturbance” of harbor seals by the oyster farm on both of these dates. Areview of his spreadsheet, submitted to both NPS and USGS, confirms his clarity forthese two dates. The USGS Report misrepresented the Stewart Report, claiming acorrelation where Dr. Stewart found none, and then the NPS FEIS misrepresented theUSGS Report, claiming causation where the USGS claimed a weak correlation.

In this way, a finding of “no evidence of disturbance” was transformed into a finding ofcausation (“attribution”) that led to a finding in the FEIS of “moderate adverse impact.”

Was this a clerical error in copying Dr. Stewart’s spreadsheet from one report toanother? Unlikely. Consider:

(i) The evidence for serial misrepresentations of disturbances in the Stewart, USGS,and NPS FEIS Reports – the USGS misrepresented the Stewart Report, and thenthe NPS misrepresented the USGS Report (allegations #1 and #2);

(ii) The history of repeated NPS false claims of harbor seal disturbances by the oysterfarm since 2007;

(iii) That this is the only evidence for such disturbances over the past six years;

(iv)

That this was a high priority project that apparently led to briefings of twoAssistant Secretaries of Interior to inform the Secretary’s decision (allegation#3); and



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(v) The cover-up of the subsequent Supplemental Report by Dr. Stewart (requested by USGS) confirming his initial finding of no seal disturbances by the oysterfarm (on May 15 and June 11, 2008) (allegation #4).

It is alleged that the “ preponderance of evidence” (as defined by the DOI and WhiteHouse Scientific Integrity Policies) leads to the conclusion that these serialmisrepresentations and cover-up by USGS and NPS were committed “intentionally,

knowingly, or recklessly.” False science was used to inform the Secretary for a highprofile policy decision. The Secretary, public, and federal court were deceived.

2. Documents and Communications Supporting These Allegations My analysis leading to these four allegations was based upon:

i. Dr. Stewart’s May 12, 2012 report and spreadsheet analysis (together the StewartReport) submitted to NPS (submitted to USGS on May 3). These documents wereobtained from Dr. Stewart at Hubbs-SeaWorld Research Institute. The November26, 2012 USGS Report with Appendix 1 based on Dr. Stewart’s Report (togetherthe USGS Report).

ii.

The November 20, 2012 NPS FEIS, which relied on the USGS Report and StewartReport.

iii.

USGS emails obtained in response to a FOIA request (“2013.5.7 Batch #1.pdf”)submitted to USGS on December 14, 2012 by Cause of Action, a Washington D.C.non-profit. These documents were obtained on May 8.

iv.

Emails between USGS Dr. William Lellis (Deputy Associate Director, Ecosystems,and senior author of USGS Report) from December 3 to 13, 2012 (see below).

v. Contemporaneous notes from a phone conversation between USGS Dr. Lellis andme on December 7, 2012 (see below).

vi.

A Supplement Report filed by Dr. Brent Stewart with Dr. Carrie Blakeslee onDecember 10, 2012 (“BSS Suppl review.pdf”) in response to a USGS request onDecember 5 that Dr. Stewart re-review the photographs for May 15 and June 11,2008. This document was obtained from Dr. Stewart on May 9 after I requestedthe documents he provided to Dr. Stephanie Owens, NOAA Sea Grant KnaussFellow working for Congressman Jared Huffman, on April 30, 2013 in response toher request for documents on April 29, 2013.

I thank Dr. Brent Stewart, Hubbs-SeaWorld Research Institute, and Cause of Action forsupplying me with these documents.

It is important to note that several requests made to USGS Dr. Lellis in December (both by email and telephone) for copies of Dr. Stewart’s May 2012 Report were not answered.

Moreover, Dr. Lellis never told me that while we were having our discussions fromDecember 3 to 13, 2012, that he and Dr. Blakeslee requested a re-review of the May 15and June 11, 2008 data by Dr. Stewart on December 5, and that Dr. Stewart respondedwith his Supplemental Report on December 10. I did not know the existence of theSupplemental Report until after it was provided to Congressman Huffman’s office onApril 30 (as requested by staffer Dr. Owen) and subsequently provided to me on May 9,2013.



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To my knowledge, the existence of this Supplemental Report (enclosed here as asupporting document and discussed below) has not been publicly disclosed prior to thefiling this scientific misconduct complaint on May 13, 2013.

It is important to note that the May 2013 USGS response to the FOIA request did notinclude the USGS email requesting Dr. Stewart’s re-review on December 5, Dr. Stewart’sDecember 10 Supplemental Report, or his transmittal email back to USGS, even though

the two emails and Report should have been included in the response. USGS did notindicate that anything had been withheld in their response to the FOIA request. Thisraises serious questions as to whether the Report and emails were withheld (in violationof FOIA), or alternatively, whether the USGS staff used private email addresses (ratherthan their official USGS email addresses) to contact Dr. Stewart and seek his re-review ofthe May 15 and June 11, 2008 photographs. Either alternative is troubling given the highprofile of this issue, and the importance of Dr. Stewart’s Report.

Early in this investigation, Interior should determine why these materials were notprovided in response to the FOIA request, and whether private email addresses wereused for these communications. If so, then Interior should investigate what othercommunications within USGS, between USGS and NPS, and between USGS and othersused private email addresses so as to avoid disclosure under FOIA.

3. Allegations #1 & #2: USGS & NPS Misrepresented the Stewart Report

1.

USGS , in its USGS Report on their analysis of the NPS photographs concerningthe oyster farm at Drakes Estero, misrepresented the record from the StewartReport (by Hubbs-SeaWorld Research Institute harbor seal behavior expert Dr.Brent Stewart), falsely claimed a correlation of oyster farm activity and disturbanceof harbor seals based upon Dr. Stewart finding of no evidence of disturbance , and inso doing violated the DOI Scientific Integrity Policy.

2. NPS , in its Final EIS (FEIS) concerning the oyster farm at Drakes Estero,

misrepresented the USGS Report, falsely claimed causation of oyster farm activityand disturbance of seals based upon the USGS Report finding of a correlation (inturn based upon Dr. Stewart’s finding of no evidence of disturbance), leading to anoverall finding in the NPS FEIS of a moderate adverse impact , and in so doingviolated the DOI Scientific Integrity Policy.

These two allegations of scientific misconduct are interconnected, and arise from ananalysis of the scientific basis for the claim made in the NPS Final Environmental ImpactStatement (FEIS) for the Drakes Bay Oyster Company (DBOC) Special Use Permit,released by the National Park Service (NPS) on November 20, 2012, that continuation ofthe oyster farm would result in a long-term “moderate adverse impact” on harbor seals dueto the “ potential for disturbances” and “continued disturbances” caused by DBOC oyster

boats (FEIS, pg. 377).In particular, these allegations are based on the scientific analysis submitted to NPS andthe U.S. Geological Survey (USGS) by Hubbs-Sea World Research Institute (HSWRI)harbor seal behavior expert Dr. Brent Stewart, who was contracted by NPS to perform athird-party review of NPS photographs of harbor seal behavior in Drakes Estero (FEIS,pg. 371), to provide that analysis of the NPS photos to both NPS and USGS.

My findings are summarized in the following five conclusions:



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1) The May 2012 Stewart Report (contracted by NPS, and submitted to NPS andUSGS) concluded that there was no evidence that DBOC oyster boats causeddisturbances of harbor seals in the NPS photographs reviewed (165,000photographs taken during the 2008 harbor seal pupping season) (Stewart Report,spreadsheet). The key words were “no evidence of disturbance.”

2)

The November 2012 USGS Report based on the Stewart Report did not have

scientific evidence to conclude that two flushing disturbances of harbor seals were“associated with [DBOC] boat activity” (USGS Report, pg. 3) because the StewartReport found no such association and no evidence for DBOC disturbances(Stewart Report, spreadsheet).

3) The FEIS lacked the scientific evidence to conclude that two flushing disturbancesof harbor seals were “attributed” (another word for causation) to DBOC boats because the FEIS relied on both the USGS Report and the Stewart Report, neitherof which found a cause-and-effect relationship between flushing disturbances andDBOC’s oyster boats (FEIS pg. 376). In fact, the Stewart Report found no evidencefor DBOC disturbances.

4) Dr. Stewart’s finding of no harbor seal disturbances by DBOC oyster boats was

transformed by two sequential misrepresentations — the first by USGS and thesecond by NPS — from a finding of no evidence of DBOC boat disturbances ofharbor seals to the cause-and-effect conclusion made in the FEIS.

5)

In summary, the FEIS lacked the scientific evidence to conclude that continuationof the oyster farm would result in a long-term “moderate adverse impact” on harborseals due to the “ potential for disturbances” and “continued disturbances” caused byDBOC oyster boats (FEIS, pg. 377).

NPS Conclusions Regarding DBOC Seal Disturbances in the FEIS

In response to criticism that the Draft EIS (DEIS) failed to analyze over 300,000 NPS

photographs of harbor seal haul-out areas in Drakes Estero, the NPS turned to the USGSto provide a third-party review of those photographs.

“… NPS initiated a third-party review of the photographs with the USGS, inconsultation with a harbor seal specialist with the Hubbs-Sea World ResearchInstitute. The USGS assessment (Lellis et al. 2012) focused on the 2008 harborseal pupping season, when more than 165,000 photos were collected from twosites overlooking Drakes Estero between March 14, 2008 and June 23, 2008.” (FEIS, pg. 371)

The NPS conclusion in the FEIS of a “moderate adverse impact” to harbor seals by DBOCoperations appears to be based in large part upon the NPS’s interpretation of the USGSassessment of NPS photographs, entitled “Assessment of Photographs from Wildlife Monitoring Cameras in Drakes Estero, Point Reyes National Seashore, California ,” by WilliamA. Lellis, Carrie J. Blakeslee, Laurie K. Allen, Bruce F. Molnia, Susan D. Price, Sky Bristol,and Brent Stewart, United States Geologic Survey (Open-File Report 2012-1249) (USGSReport) (FEIS, pgs. 376-377).

The USGS Report in turn was based in large part upon a NPS commissioned third-partyevaluation of the NPS photographs by Dr. Brent Stewart, Ph.D., J.D., Senior ResearchScientist at the Hubbs-SeaWorld Research Institute (HSWRI), entitled “Evaluation ofTime-Lapse Photographic Series of Harbor Seals Hauled Out In Drakes Estero,



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California, For Detecting and Assessing Disturbance Events,” Technical Report 2012-378,submitted to the NPS, on May 12, 2012 (Stewart Report) (Technical Report 2012-378). Inits discussion of the USGS Report in the FEIS, NPS wrote:

“Further, after examining individual disturbance records, MMC (2011b)concluded that, “from time to time, shellfish operation activities have disturbedthe seals. However, the data used in the analysis are not sufficient to support firm

conclusions regarding the rate and significance of such disturbance” (MMC2011b). Additionally the USGS assessment (Lellis et al. 2012) of the more than250,000 digital photographs taken from remotely deployed cameras overlookingharbor seal haul-out areas in Drakes Estero attributed a specific stimulus to 6 ofthe 10 observed flushing disturbance events. Two flushing disturbance eventswere attributed to [DBOC] boat traffic at nearby sand bars, two were attributedto a kayak using the lateral channel (note kayak was in Drakes Estero in violationof seasonal closure), and two appeared to be related to seabirds landing among theseals.

Alternative B [DBOC 10-year renewal] would result in long-term moderateadverse impacts on harbor seals for another 10 years due to the seal displacementeffects of human activities in Drakes Estero associated with DBOC’s operation,and the potential for disturbances known to disrupt harbor seal behavior.” (FEIS,pgs. 376-377).

It is noteworthy that NPS found that the USGS Report “attributed” two seal “ flushingdisturbance events . . . to [DBOC] boat traffic at nearby sand bars . . . .” (FEIS, pg. 376). In thissense, “attributed” appears to refer to a cause-and-effect relationship (i.e., causation).

The NPS reference to “ MMC 2011b” in the quote above is a reference to the MarineMammal Commission’s November 22, 2011 report, entitled “ Mariculture and Harbor Sealsin Drakes Estero, California” (MMC Report). After reviewing NPS records prepared byvolunteers and the NPS photographs at issue here, the MMC Report concluded that,“ from time to time, shellfish operation activities have disturbed the seals” (MMC Report, pg.

ii). The MMC Report described a potential DBOC oyster boat disturbance on May 15,2008, based upon analysis of the NPS photographs, and advised that “[a] fullerexamination of the photographs is necessary to form a conclusion with a reasonable level ofconfidence.” (Id. , pgs. 26-27).

Thus, according to NPS, the USGS Report validated the MMC finding of a DBOCdisturbance on May 15, 2008. According to the NPS FEIS, there were now twoindependent verifications – one by MMC and the other by USGS – of a DBOC oyster boat disturbance to harbor seals on May 15, 2008.

Based upon the combined assessments of the MMC and the USGS reports, the NPSconcluded that continuation of the oyster farm would result in a long-term “moderateadverse impact” on harbor seals due to the “ potential for disturbances” and “continued

disturbances.” (FEIS, pg 377).

“Association”: USGS Report Claimed a Weak Correlation of DBOC Boats with TwoHarbor Seal Flushing Events

All of the authors of the USGS Report are USGS employees except for Dr. Brent Stewart,Ph.D., J.D., Senior Research Specialist, a harbor seal behavioral expert from the Hubbs-SeaWorld Research Institute, who was hired under contract with NPS to analyze theUSGS-prepared videos composed of the series of photographs of potential harbor seal



8

disturbance events from the 2008 NPS photographs.

The USGS Report summarized its methodology and findings in this way:

“Photographic sequences of each event, plus the 10 photographs before the start ofeach event and the 10 photographs after the end of each event (3,140 photographstotal) were analyzed for incidence and cause of seal disturbance. Ten of the 75events were classified as containing behaviors indicative of disturbance in the

form of flushing (table 1, figs. 2-11, appendix 1). Two flushing events wereassociated with the presence of a kayak, two were associated with birds landing inthe area, two were associated with boat activity, and four occurred when noobvious stimuli were visible within the field of view of the camera.” (USGSReport, pg. 3).

Thus, the USGS Report associated two flushing disturbance events with DBOC boats.The USGS also reported that over 40 reviewed instances of DBOC boat visits to theadjacent sand bar did not cause a disturbance of the harbor seals (Id. , pg. 5).

Later in the report, the USGS Report concluded that a “ flushing level of [harbor seal]disturbance” on May 15, 2008, and June 11, 2008, “could be directly connected, or at leastassociated with … [DBOC] boat traffic at nearby sandbars …” (USGS Report, pg. 5).

This statement in the USGS report is misleading. The USGS wrote that the stimuli(kayaks, birds, and DBOC boats) “could be directly connected, or at least associated with a flushing level of disturbance in the OB seals …” (Id.). When the entire USGS Report iscarefully reviewed, it becomes clear that the USGS Report concluded that severaldisturbance events can be directly connected to kayaks and birds, but that the twodisturbance events are only “associated” — i.e., weakly correlated with, but not caused by— DBOC oyster boats.

This statement in the text of the USGS Report is contradicted by analysis of Appendix 1in the USGS Report which summarized Dr. Stewart’s research analysis (i.e., hisspreadsheet) used to reach the conclusions in the main report. In fact, Appendix 1

contradicts the USGS Report’s conclusion on June 11, 2008 that an oyster boat was atleast associated with a disturbance. That is so because Appendix 1 observed in the“Connection Between Stimulus and Seal Flushing” column, “ Minor flushing before boat arrival,cause unknown ,” and described the event in detail in the “Comments” as follows: “Boatvisits area; people walking; very poor camera focus; rafting birds scattered; brief movement ofseals toward water's edge several minutes before boat arrives but none seen to enter water; noobvious disturbance to seals” (USGS Report, pg. 24; Appendix 1, June 11, 2008,emphasis added).

With respect to May 15, 2008, Appendix 1 does not document any evidence of a harborseal disturbance caused by DBOC oyster boats. Appendix 1 provides no conclusion inthe “Connection Between Stimulus and Seal Flushing” column, and described the event as

follows: “Boat visits area; people walking; very poor camera focus; some seals flush into water just after boat leaves the area” (USGS Report, pg. 23, Appendix 1, May 15, 2008).

Accordingly, Appendix 1 of the USGS Report does not support the report’s finding of an“association” between DBOC oyster boats and harbor seal flushing events on May 15,2008, or June 11, 2008.



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“ No Evidence of Disturbance”: Hubbs-SeaWorld Report Found No Evidence of HarborSeal Disturbance by DBOC Oyster Boats

As described in the FEIS, the USGS worked “… in consultation with a harbor seal specialistwith the Hubbs-SeaWorld Research Institute” (FEIS, pg. 371). That expert was Dr. Stewart,the Hubbs-SeaWorld Research Institute harbor seal behavior specialist. Dr. Stewart is anamed author on the USGS Report.

Between December 3 and 13, 2012, I exchanged a series of emails with Dr. William Lellis,Deputy Associate Director, Ecosystems, USGS, and senior author of the USGS Report,regarding the report (enclosed here). I had a 90-minute phone call with Dr. Lellis onDecember 7, 2012 (notes enclosed here). In those communications Dr. Lellis confirmedthree key points regarding Dr. Stewart’s role in the preparation of the USGS Report:

1) Dr. Stewart was the harbor seal behavior expert on the USGS review of NPSphotographs (none of the other USGS scientists had this expertise – they relied onDr. Stewart);

2) Dr. Stewart’s work provided the analysis on a spreadsheet to determine if therewas an association (according to USGS, a weak correlation), and if so, whetherthere was a cause-and-effect relationship between a harbor seal flushingdisturbance and a specific stimulus, and

3) Dr. Lellis confirmed that Dr. Stewart’s work was presented in specific columns inAppendix 1 in the USGS Report. He told me that Appendix 1 represented Dr.Stewart’s analysis. When I wrote on December 5 and asked him for a copy of Dr.Stewart’s Report, he replied: “Yes, essentially that is Appendix 1 of the report.”

I acquired Dr. Stewart’s May 12, 2012 report and spreadsheet with his supportinganalysis (together the Stewart Report), as submitted to NPS and USGS, by requesting itdirectly from the Hubbs-SeaWorld Research Institute.

Dr. Stewart wrote in his report that he evaluated time-lapse NPS photographic recordsprovided to him by USGS “to determine if there were disturbances to harbor seals and if there

were correlative potential human related stimuli recorded in the photographs” (Stewart Report,pg. 1).

Dr. Stewart’s written report is brief — only two pages. The supporting analysis for theconclusions in his report is found in the accompanying Excel spreadsheet, which wasreproduced by USGS as several columns in Appendix 1 of the USGS Report.

After reviewing the time-lapse photographs, Dr. Stewart focused on three disturbanceevents where the potential stimulus of an oyster skiff (DBOC oyster boat) was present.After analyzing each of the three events, Dr. Stewart concluded that none of the eventswere determined to have been caused by or attributed to the presence of an oyster skiff:

“Four of those disturbance events corresponded with potential stimuli nearby,

once when a kayak was present and three times when a skiff was present. Thedisturbance event associated with the kayak appears to have been directly causedby the close presence of the kayak and the seals’ detection of it. One disturbancereaction of seals correlative with the presence of a skiff beached on mud flatsseveral hundred meters away can not [sic] be causally linked to human presenceas no humans were in the field of view of the camera when the seals’ movementsoccurred. Another movement of seals toward the water (but where none enteredthe water) occurred several minutes before a skiff was observed in the area andcould not be determined [to] have been caused by [a] skiff’s presence in the area.



10

The third disturbance event occurred when a skiff and people associated [with] itwere within the field of view of the camera and several hundreds meters away from the seals; that event was difficult to attribute directly to human presencebecause the seals appeared to respond to birds that had evidently flushed from anarea near the camera site rather than near the persons working near the skiff.There was no identifiable stimulus source for each of the other three disturbanceevents.” (Stewart Report, pg. 2).

More detailed information is provided in Dr. Stewart’s Excel spreadsheet entitled,“Drakes Estero Harbor Seals HSWRI.xlsx”, which provides the detailed analysis hesummarized in his report. Dr. Stewart’s notes for May 15, 2008, and June 11, 2008, thetwo dates the USGS Report found a flushing disturbance was “associated” with DBOC’soyster skiffs, contradict the USGS Report’s findings. Dr. Stewart found no evidence forDBOC disturbances. [Note: the version of Dr. Stewart’s spreadsheet provided on April30, 2013 to Dr. Owen in Congressman Huffman’s office is entitled: “Drakes Estero HarborSeals HSWRI Revised.xlsx.” I do not know what if anything has been revised, but theentries for May 15 and June 11, 2008 remain the same, including the spelling mistakes.]

May 15, 2008. The most important insight from Dr. Stewart’s spreadsheet is that thisdate is NOT one of his seven disturbance events evaluated in the body of his report(although June 11, 2008 is one of the seven).

In the section “Stimuli and disturbances” of Dr. Stewart’s spreadsheet, he wrote thefollowing about the May 15, 2008 photographs:

“very poor camera focus; skiff visits; no evidendence [sic] of disturbance toseals” (Stewart Report, spreadsheet, May 15, 2008)

Dr. Stewart’s conclusion was clear. The NPS photographs from May 15, 2008,contained no evidence of disturbance to seals. Dr. Stewart acknowledged thepresence of the DBOC “skiff ,” but wrote “no” in the column titled “evidence of

disturbance to seals.”For most dates, the USGS Report’s Appendix 1 accurately represented theanalysis presented in Dr. Stewart’s Excel spreadsheet. I confirmed bycomparison that the Appendix accurately reflects Dr. Stewart’s Excel spreadsheetfor over 40 individual dates. On May 15, 2008, however, there is a strikingdivergence in Appendix 1 from Dr. Stewart’s spreadsheet. The USGS ReportAppendix 1 entry for May 15, 2008, was re-written, and excluded Dr. Stewart’sconclusion, “no evidendence [sic] of disturbance to seals.” Thus, the USGS Reportappears to have misrepresented Dr. Stewart’s findings for May 15, 2008.

June 11, 2008. Dr. Stewart found “no obvious disturbance” in the photographs for June 11, 2008. On his spreadsheet, he wrote:

“very poor camera focus; rafting birds scattered; skiff visits; brief movement ofseals towards waters edge several minutes before skiff arrives but none seem toenter water; no obvious disturbance” (Stewart Report, spreadsheet, June 11,2008)

In his spreadsheet, Dr. Stewart acknowledged the presence of the DBOC “skiff,”and wrote “ yes, minor before skiff arrival” in the column noting “evidence ofdisturbance to seals.” He concluded that there was no evidence that the DBOC



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oyster boat caused the disturbance, and thus, did not attribute it to the DBOCoyster boat, but rather wrote, “no obvious disturbance.”

Summary

The NPS FEIS finding that two harbor seal flushing disturbances were “attributed” to

DBOC oyster boats by the USGS Report is a misrepresentation of the findings in thatreport because the USGS Report only noted an “association” — a weak correlation — not“attribution ,” or a cause-and-effect relationship.

Further, the USGS Report’s finding that two harbor seal flushing disturbances were“associated” with DBOC oyster boats is a misrepresentation of the findings reached bythe team’s harbor seal behavior expert, Dr. Stewart. This is so because Dr. Stewartconcluded that there was no evidence of disturbance by DBOC’s oyster boats on the twodays — May 15, 2008, and June 11, 2008 — identified in the USGS Report.

In fact, there does not appear to be evidence to support the NPS’s assertion in the FEISthat DBOC oyster boats have caused disturbances to harbor seals and, therefore,evidence to conclude that future disturbances will occur.

The NPS conclusion in the FEIS was based upon two sequential misrepresentations — aFEIS misrepresentation of the USGS Report, and a USGS Report misrepresentation of itsprimary source, Dr. Stewart’s analysis.

Furthermore, Dr. Stewart’s finding that there was no evidence of seal disturbance onMay 15, 2008 provides the further expert analysis called for in the 2011 MMC Report toeliminate the episode from consideration.

Accordingly, the NPS FEIS’s conclusion of a “moderate adverse impact” to harbor seals byDBOC is a misrepresentation because the two disturbance events it relied upon do notappear to have been related to DBOC’s oyster boats.

In summary, based on the analysis performed by Dr. Stewart, there is no evidence that

DBOC oyster boats caused a flushing disturbance of harbor seals in Drakes Estero in theNPS photographs analyzed by the USGS and Dr. Stewart.

Were the two misrepresentations committed “intentionally, knowingly, or recklessly”?

The USGS Report misrepresented the Stewart Report, and the NPS FEIS misrepresentedthe USGS Report. The Stewart Report was contracted by NPS, and Dr. Stewartsubmitted his report simultaneously to both NPS and USGS on May 12, 2012. The NPSEIS team had access to the Stewart Report. From Dr. Stewart’s finding of “no evidence ofdisturbance ,” two serial misrepresentations transformed that finding into one ofattribution of two disturbances caused by DBOC oyster boats, which led to a finding of

“moderate adverse impact.”

NPS scientific misconduct. Were these two serial misrepresentations committed“intentionally, knowingly, or recklessly”? The misrepresentations were reckless on behalfof NPS, and apparently knowingly and intentionally as well. For six years, NPS hasclaimed – at every opportunity and in multiple forums, testimony, and reports – thatoyster boats disturb harbor seals. All of the previous NPS claims of evidence have fallen by the wayside. The MMC Report suggested one potential DBOC disturbance on May



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15, 2008, based upon analysis of the NPS photographs, and advised that “[a] fullerexamination of the photographs is necessary to form a conclusion with a reasonable level ofconfidence.” (Id. , pgs. 26-27).

Thus, according to NPS, the USGS Report validated the MMC finding of a DBOCdisturbance on May 15, 2008. According to the NPS FEIS, there were now twoindependent verifications – one by MMC and the other by USGS – of a DBOC oyster

boat disturbance to harbor seals on May 15, 2008.Based upon the combined assessments of the MMC and the USGS reports, the NPSconcluded that continuation of the oyster farm would result in a long-term “moderateadverse impact” on harbor seals due to the “ potential for disturbances” and “continueddisturbances.” (FEIS, pg 377).

Thus, Dr. Stewart’s finding – as reflected in the USGS Report and as submitted directlyto NPS – was critical to permit NPS to make this finding in the FEIS. Given the six-yearcontroversy concerning this exact topic, it would have been crucial for those preparingthe EIS to examine the Stewart Report to see if Dr. Stewart actually reported a finding ofa DBOC disturbance on May 15, 2008 (he did not). Moreover, even if the authors of theFEIS only examined the USGS Report (which would be negligent, given the submission

of the Stewart Report to NPS), then nevertheless, they misrepresented the (incorrect)finding of “association” (a weak correlation) in the USGS Report, and called it“attribution” (causation) in the FEIS.

When considered within the six-year history of false claims by NPS of DBOCdisturbances of harbor seals, and the use of the USGS Report and Stewart Report to drivethe FEIS finding of a “moderate adverse impact ,” the preponderance of evidence leads tothe conclusion that this represents scientific misconduct by unknown NPS employees(allegation #6 here).

USGS scientific misconduct. USGS does not have a six-year history with this issue.

Why did USGS Dr. Lellis, senior author of the USGS Report, and Dr. Carrie Blakeslee,the person who evidently did most of the writing of the USGS Report (see USGS emails),change this entry (May 15, 2008) in the appendix of the USGS Report to not accuratelyrepresent the Stewart Report? What happened between May 3, 2012, when the StewartReport was submitted to USGS, and November 2012, when both the NPS FEIS and USGSReport were publicly released?

How did Dr. Lellis make these two mistakes to misrepresent the Stewart Report, therebyproviding NPS with the finding of disturbances they were seeking? Dr. Lellis providedNPS with their so-called independent verification of DBOC disturbances, in the form oftwo “associations,” evidence that Dr. Stewart did not find.

Was this an innocent clerical mistake? Much time was spent on the part of USGS

scientists generating the videos, analyzing the videos, identifying all of the potentialflushing events, sending them to Dr. Stewart, reviewing Dr. Stewart’s findings, andultimately writing the USGS Report. Given that this was a major finding of the report,did anyone double-checked the Stewart Report for accuracy? The USGS Report hadhigh-level visibility; USGS Director Dr. Marcia McNutt reviewed the report.

This misrepresentation by USGS appears to have been committed “intentionally,knowingly, or recklessly.” OSTP needs to investigate who in NPS discussed the StewartReport and USGS Report with Dr. Lellis. Was Dr. Lellis pressured in any way tomisrepresent the Stewart Report? Were changes made during the review of the draft



13

USGS Report? Were NPS or DOI employees involved in that review process? Why didDr. Lellis make these misrepresentations?

On December 16, 2012, I spoke by telephone with Dr. Marcia McNutt, Director, USGS,about the misrepresentations of the Stewart Report in the USGS Report, and thesequential misrepresentations of the USGS Report in the NPS FEIS. She asked me tosend her the Stewart Report, and said that she would ask Dr. Linda Gundersen, USGS

Scientific Integrity Officer, to investigate the issue. I told Dr. McNutt that I hadadditional information based upon several email exchanges, and seven pages of notesfrom a lengthy telephone discussion, with USGS Dr. Lellis, the senior author on theUSGS Report. I offer those same emails and notes to the OSTP panel that investigatesthis matter.

On December 17, I sent the Stewart Report and my analysis to Dr. McNutt, and wrote:

It appears that the USGS report misrepresented Dr. Stewart’s analysis inAppendix 1, and then incorrectly concluded that there was an association of theDBOC boat with the harbor seal disturbance on May 15, 2008. Finally, the NPSFEIS misrepresented the USGS report and claimed that the USGS had attributedthe May 15, 2008 disturbance to the DBOC boat. Two layers of successive

misrepresentations led to the opposite conclusion by NPS as compared to harborseal expert Dr. Brent Stewart.

I appreciate your willingness to investigate this issue. As you can imagine, this isa very important matter for the DBOC-NPS issue. But I also think this is a veryimportant matter for USGS, which has long been the most trusted scientific bodyin the U.S. government.

Dr. McNutt did not respond. On December 23, 2012, I wrote again:

I wanted to get back to you about the materials that I sent you last Monday. Ihave extensive notes from my conversation with Dr. Lellis, and my many emailsback and forth with him. When will the USGS Scientific Integrity Officer be

contacting me and arranging for an interview? Would you please send me a copy your directive or memo to the USGS SIO specifying the nature of your request.Thank you for recognizing the significance of the apparent contradictionsbetween Dr. Stewart's report, the USGS report, and the NPS FEIS. …

Thanks very much. I look forward to receiving your directive, and speaking with your Scientific Integrity Officer about my conversations and emails.

Neither Dr. McNutt nor Dr. Gundersen responded. I never heard back from either oneof them. On January 17, 2013, I wrote to USGS SIO Dr. Gundersen:

“I write to ask for an update of your investigation of the USGS Reportmisrepresentation of the Stewart Report. Are you in fact conducting aninvestigation? When will you be interviewing me?

First you need to determine if the USGS Report in fact misrepresented theStewart Report, and if so, if that misrepresentation was done intentionally,knowingly, or recklessly. Please focus on one particular date: May 15, 2008.

Second, if you find that the USGS Report misrepresented the Stewart Report, thenI ask you to retract or correct the USGS Report, and to publicly notify the NPS(and public) that they need to revise their Final EIS on Drakes Estero in that theUSGS Report was incorrect, and the NPS further misrepresented your report.

It should not surprise you that once a federal scientific document is released into



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the public domain, unless corrected or retracted, it can and will be used indecision-making processes throughout the nation, and around the world. In thiscase, I have already been notified that the NPS FEIS has been raised in casesinvolving mariculture in two other states, and in two other countries.

After examining the videos of the NPS photographs prepared by USGS, Dr. BrentStewart wrote in his report that he found no evidence for disturbances by the

oyster farm. Your USGS Report incorrectly listed that as a finding of twoassociations (a correlation), and the NPS FEIS further incorrectly listed that as a finding of two attributions (cause and effect), thus allowing them to conclude amoderate adverse impact of the oyster farm on the harbor seals. I ask you to pleasecorrect the public documents and public record.

Please get it touch with me to schedule an interview. I look forward to talkingwith you.”

Dr. Gundersen did not reply. I wrote back to her on January 23, 2013:

I have not heard back from you since my email of January 17. It is now over onemonth since I alerted Dr. McNutt to this issue that the authors of the USGSReport misrepresented the Stewart Report, and she agreed to investigate whetherthis misrepresentation was done intentionally or knowingly, or was an honesterror.

When I spoke with USGS Director Dr. McNutt on December 16, she indicatedthat there were two alternatives: either Dr. Stewart changed his conclusions after filing his May 2012 Stewart Report with NPS and USGS, in which case thereshould be a written record of that change, or alternatively someonemisrepresented his report in the USGS Report. Have you determined whichalternative is correct?

To date, Dr. Gundersen has not responded to my emails, has not confirmed if she isconducting an investigation or not, has not interviewed me, has not sought additional

information from me, and if she has conducted an investigation, has not informed me ofthe outcome. Based on the available information, such behavior is not consistent withwhat OSTP intended for the White House Scientific Integrity Policy.

Towards the end of March 2013, I became aware that Interior had appointed Dr. SuzetteKimball as Acting Director, USGS (and DOI Scientific Integrity Officer), and that she hadappointed Dr. Alan D. Thornhill at USGS Scientific Integrity Officer. On March 31, 2013,I wrote to Dr. Thornhill, coped Dr. Kimball, and included the string of emails to previousUSGS Director Dr. McNutt and USGS SIO Dr. Gundersen:

Dear Dr. Alan D. Thornhill,

I write to you as USGS Scientific Integrity Officer. As you will see by the stringof emails, correspondence, and documents below, on Sunday December 16, 2012,I alerted then-USGS Director Dr. Marcia McNutt in a phone conversation to a possible case of scientific misconduct at USGS. She told me she would notify herScientific Integrity Officer at the time, Dr. Linda Gundersen, on MondayDecember 17. Dr. McNutt found the allegations very troubling. Since that time,I wrote to Dr. McNutt on December 17 and December 23, and heard no reply. Isubsequently wrote to Dr. Gunderson on January 17 and January 23, and heardno reply.

I do not know when the SIO position changed from Dr. Gundersen to you, and if



15

you are aware of the allegations. Would you please respond to me and let mewhether USGS has or has not conducted an investigation (and if so, its outcome),or whether USGS is or is not currently conducting an investigation (and if so,when you are planning on interviewing me). The complete silence from USGSwhen confronted with serious allegations of misconduct is troubling, and appearsinconsistent with the President's Scientific Integrity Policy.

I request a phone call with you this next week to bring you up-to-speed on thisissue, and to discuss whatever action USGS is taking. I look forward to talkingwith you.

Sincerely,


As of the submission of this complaint on May 13, 2013, Dr. Thornhill never respondedto my email.

In summary, the Stewart Report was submitted to NPS and USGS. Stewart found noevidence of disturbance of harbor seals by DBOC boats. The USGS Report incorrectlyquoted the Stewart Report as finding a correlation. The NPS FEIS incorrectly quoted the

USGS Report and Stewart Report as finding causation. Both agencies had the StewartReport as of May 12, 2012. These serial misrepresentations meet the “knowingly” test.Given the six-year history of false NPS claims concerning DBOC disturbances of harborseals, making these claims without double-checking the Stewart Report meets the“recklessly” test. The Stewart Report was in their hands for six months prior to therelease of both the FEIS and the USGS Report. Was it intentional? OSTP needs toinvestigate. The record is replete with NPS preoccupation with false claims of DBOCdisturbances of harbor seals. These misrepresentations need to be viewed in the contextof the six-year history of NPS false claims concerning so-called oyster farm disturbancesof harbor seals.

4. Allegation #3: USGS & NPS Used False Science to Brief the Secretary

3.

USGS and NPS , in their claims that the USGS analysis of the NPS photographswas very high profile and very high priority , and needed to inform Secretary Salazar forhis decision on the oyster farm permit, apparently briefed Assistant SecretariesCastle and Jacobson with false claims of evidence of oyster farm disturbances ofseals in Drakes Estero, and in so doing violated the DOI Scientific Integrity Policy.

When NPS released the Draft EIS in September 2011, they dismissed the 300,000 NPSphotographs from the secret cameras, and detailed NPS logs, in a single sentence:

“Because the collection of these photos was not based on documented protocolsand procedures, the body of photographs does not meet the Department’sstandards for a scientific product. As a result, the photographs have not beenrelied upon in this EIS.”

The DEIS did include, however, other data without documented protocols, such as aerialphotos, maps, and other data, not to mention use of data in a paper (Becker et al 2011)from 1982 and 1983 notebooks from Dr. Sarah Allen prior to when she worked for NPSand prior to current protocols for data collection. Nevertheless, the NPS dismissed the300,000 photos and the detailed NPS logs that showed no DBOC disturbances of harbor



16

seals over a three and one half year period.

The NPS received complaints that they failed to include the analysis of the photographsin the DEIS. As a result, instead of relying on the detailed NPS logs, NPS asked USGS toanalyze the photos for seal disturbances. We don’t know when they asked. The firstrecord (see emails below) is February 7, 2012.

The NPS FEIS (released November 20, 2012) found that the oyster farm had a “moderate

adverse impact” on the harbor seals at Drakes Estero. This single determination had asignificant impact on other findings in the FEIS, and on elected officials, the public, andmedia. After six years of false public claims, manipulated reports, and secret cameras –and millions of taxpayer dollars – NPS used the USGS Report to claim a moderateimpact.

The NPS cited a 2012 USGS Report that analyzed, at NPS request, over half of the300,000 time- and date-stamped NPS photographs of the oyster boats and harbor seals(from secret cameras operational for three and one-half years from 2007 to 2010). TheUSGS Report analyzed around 165,000 photos from the 2008 harbor seal puppingseason. The FEIS quoted the USGS Report as concluding that on two occasions in 2008,oyster boats caused seals to flush into the water. This was a key finding for the FEIS.

There are, however, two major problems with this claim: NPS misquoted the USGSReport, and USGS misquoted the original harbor seal behavior expert’s findings (Dr.Brent Stewart of Hubbs SeaWorld Research Institute). In so doing, both agenciesmisrepresented the primary scientific analysis.

The USGS Report was authored by William Lellis, Carrie Blakeslee, Laurie Allen, BruceMolnia, Susan Price, Sky Bristol, and Brent Stewart (all from USGS except Dr. Stewartwho is from Hubbs-SeaWorld Research Institute). Dr. Lellis was the senior author.

On December 14, 2012, Cause of Action, a Washington D.C. non-profit focused ongovernment accountability, submitted a FOIA request to USGS. USGS provided a 91-page response on May 8, 2013. Below is a timeline of quotations from emails produced

by USGS in response to FOIA.What this timeline shows is that the USGS analysis of the NPS photos relied on outsideharbor seal behavior expert Dr. Brent Stewart from Hubbs-SeaWorld Research Institute.Moreover, it was not just a small, technical part of the NPS FEIS. Rather, it was a “veryhigh profile” project that had “very high priority” because it was needed for NPS “tobrief Secretary Salazar who needs to make a decision on Wilderness Status for thepark.”

A key author of the USGS Report wrote that “the analysis must be done quicklybecause NPS needs to give their final report to Ken Salazar by March 30th.” The USGSanalysis involved officials at the very highest level of the Department of the Interior.

While the public was told that the USGS analysis was done independently, the emailsreveal that NPS was intimately involved and “chomping at the bit,” “breathing downmy neck,” and needed it done because “they’ve got deadlines for deciding on thepermit.” NPS was constantly in the loop as USGS staff wrote of “keeping thedepartment informed.” The analysis of the photos was kept “on the fast track” becauseit was needed to inform the Secretary for his decision.

In the end, who was briefed? Nearly five months prior to when both the NPS FEIS andUSGS Report was released to the public, the following three people apparently were briefed about the USGS findings: USGS Director Dr. Marcia McNutt, Assistant Secretary



17

Anne Castle (who oversees USGS and reports to the Secretary), and Assistant SecretaryRachel Jacobson (who oversees NPS and reports to the Secretary).

The USGS analysis of the NPS photos, based upon Dr. Brent Stewart’s analysis, wasapparently presented to two Assistant Secretaries (Castle and Jacobson) in early July tohelp inform the Secretary’s decision. These emails suggest that the Secretary’s decisionwas indeed informed by the science. We imagine that the two Assistant Secretaries

were presented the same misrepresentations found in the USGS Report.We know that when Dr. Brent Stewart filed his report on May 3, 2012 with USGS, hefound “no evidence of disturbance” of harbor seals by DBOC. We also know that when theUSGS Report was released to the public nearly seven months later in November, itclaimed Dr. Stewart found two examples of correlations of disturbances with DBOC boats, and when the NPS FEIS was released to the public in the same month, it claimedthe USGS Report found two examples of causation of disturbances by DBOC boats.

What was presented to Director McNutt, Assistant Secretary Castle, and AssistantSecretary Jacobson in late June and early July? If they were presented with a finding thatincluded anything other than “no evidence of disturbance ,” then they were presented withfalse science to help the Secretary make his decision concerning the DBOC permit.

Brief timeline of key statements in USGS emails [bold emphasis added]:

(1)

February 7, 2012: Dr. William (Bill) Lellis, Deputy Associate Director, Ecosystems,USGS, writes to Carrie Blakeslee (USGS):

a. “… very high priority animal behavior project starting immediately?” b. “The NPS needs an evaluation of whether or not the photos can be used to

determine disturbance events of seals.”c. “The NPS needs this analysis done by the end of March to brief

Secretary Salazar who needs to make a decision on Wilderness Status forthe park.”

d.

“This is a high profile project. Very high profile …”(2)

March 5, 2012: Carrie Blakeslee to Sally Holl (USGS): “The analysis must bedone quickly because NPS needs to give their final report to Ken Salazar by March30th.”

(3) April 20, 2012: Laurie Allen to Brent Stewart (Hubbs-SeaWorld Research Inst.):“NPS is chomping at the bit (They’ve got deadlines for deciding on the permit,)…”

(4)

May 1, 2012: Laurie Allen to Brent Stewart: “NPS will be breathing down myneck this week, when do you think you’ll be able to transmit something?”

(5) May 15, 2012: Laurie Allen to Carrie Blakeslee: “We need to keep this on the fasttrack, …”

(6) June 18, 2012: Laurie Allen to Carrie Blakeslee: “NPS knows about these

developments and we are keeping the department informed.” (7) June 25, 2012: Bill Lellis to Carrie Blakeslee: “We have two briefings on Points

Reyes: Tuesday, June 26, 3:00-4:00 pm. USGS Director, Marcia McNutt. Monday, July 2, 11:00-12:00 am. Assistant Secretary of Interior for Water & Science, AnneCastle.”

(8)

June 26, 2012: Hannah Hamilton (USGS Liaison to Water and Science) to Bill Lellisand Anne Kinsinger: “The briefing date and time needed to be changed to: Tuesday July 3rd from 12noon – 1PM, same location, room 6641. We needed to accommodateRachel Jacobson’s schedule.” [Jacobson was Acting Assistant Secretary of Interior for



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Fish and Wildlife and Parks](9) December 3, 2012: Bill Lellis to Carrie Blakeslee: “With Salazar’s decision to not

extend the lease, I wonder if they are closing the books on this”

For a detailed timeline of quotations from the USGS emails, see enclose “timeline andquotations from USGS FOIA response.05_13_13.pdf”

Summary

The USGS and NPS, in their claims that the USGS analysis of the NPS photographs wasvery high profile and very high priority , and needed to inform Secretary Salazar for hisdecision on the oyster farm permit, apparently briefed Assistant Secretaries Castle and Jacobson with false claims of evidence of oyster farm disturbances of seals in DrakesEstero. I conclude the following:

(i) The USGS analysis of the NPS photographs was a very high priority project,

(ii)

Dr. Brent Stewart played the key role in determining whether disturbances took

place and found “no evidence for disturbance” by the oyster farm,(iii) The USGS misrepresented Dr. Stewart’s findings concerning May 15 and June 11,

2008,

(iv) This false science was apparently presented to two Assistant Secretaries (Castleand Jacobson) to inform the Secretary’s decision concerning the oyster farmpermit,

(v) If they presented what is in the USGS Report, then Interior employees committedscientific misconduct,

(vi) If they presented what is in the USGS Report, then the Secretary’s decision wasinformed by false science, and

(vii)

The Department of Justice lawyers have misinformed the Federal Court withincorrect claims of adverse impacts in the NPS FEIS based upon false science.

5. Allegation #4: Dr. Stewart Re-Reviewed Key Data, Confirmed InitialFindings of No Evidence of Disturbance, & USGS Covered Up His Report

4.

USGS , after their Report was released, requested a subsequent re-review of keydata by Dr. Stewart in his Supplemental Report that confirmed his earlier finding ofno evidence of disturbance , a report that should have led USGS to retract its USGSReport, inform NPS of the major mistakes in their FEIS, and inform the Secretary

of mistakes in what was presented to inform his high profile decision, but insteadwas covered up, and in so doing violated the DOI Scientific Integrity Policy.

Dr. Lellis and I exchanged emails from December 3 to 13, 2012, and talked by telephonefor 90 minutes on December 7. Although I repeatedly asked him about Dr. Stewart’sReport, and asked him for a copy of Dr. Stewart’s Report (which he never provided tome), Dr. Lellis never mentioned during that extended email and telephone exchange thaton December 5, either he or his colleague Dr. Blakeslee went back to Dr. Stewart andasked him to re-review the May 15 and June 11, 2008 NPS photographs, and that Dr.



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Stewart provided a new Supplemental Report (“BSS Suppl review.pdf”) to either Dr.Lellis or Dr. Blakeslee on December 10, a report that confirmed (in greater detail) whathe had filed in his original report in May 2012, namely that there was no evidence fordisturbance of the harbor seals by the oyster farm in the NPS photographs.

On December 3, 2012, I emailed USGS Dr. William Lellis (senior author of the USGSReport), and asked him some questions about methodology, and specifically about the

so-called May 15, 2008 disturbance event (see enclosure “USGS Dr. Lellis & Dr.Goodman conversation and emails.pdf”). I also asked in Dr. Brent Stewart was theharbor seal behavior expert on the project.

On December 4, Dr. Lellis responded that “Brent [Dr. Brent Stewart] was the harbor sealbehaviorist on this project.”

On December 5, I responded to Dr. Lellis and asked him for a copy of Dr. Stewart’sreport. Later that same day, Dr. Lellis responded, failed to provide Dr. Stewart’s report,and instead wrote: “Yes, essentially that is Appendix 1 of the report” (i.e., Dr. Stewart’sReport is Appendix 1 of the USGS Report). Over the next day, we arranged to speak bytelephone on December 7, 2012, at noon PT (3 pm ET).

According to Dr. Stewart, on December 5, he was contacted by telephone and email bythe USGS scientists, asking him to re-review the videos of the photographs from May 15and June 11, 2008. He submitted his report (“BSS Suppl review.pdf”) to Carrie Blakesleeon December 10. Neither his Supplemental Report, nor any of the request or submittalemails, were contained in the USGS response to the FOIA request provided in May 2013,suggesting that these exchanges may have taken place using private email addresses.

On December 7, 2012, Dr. Lellis and I spoke by telephone for over 90 minutes. Mydetailed notes of that conversation are provided as an enclosure (“USGS Dr. Lellis & Dr.Goodman conversation and emails.pdf”). Dr. Lellis described in detail the history andmethodology for the USGS analysis. He never mentioned just how high profile was hisproject, and how he briefed two Assistant Secretaries of their findings. He claimed thathe was glad that he had no familiarity with the Drakes Estero controversy and the

previous reports. Whether this is correct or not for Dr. Lellis, we certainly know fromthe USGS emails provided in response to FOIA that Dr. Blakeslee read the previousreports and was very familiar with the issues.

I pointed out to Dr. Lellis the following contradiction. In the text of the USGS Report, heconcluded a harbor seal disturbance took place on June 11, 2008 and that the presence ofthe oyster boat correlated with this disturbance. Yet in Appendix 1, which he told merepresented Dr. Stewart’s report, it said “no obvious disturbance” took place. After aperiod of silence, Dr. Lellis answered:

“There is a contradiction right there.”

“That would be a contradiction.”

“That is an obvious contradiction.”

“That didn’t get caught in the review.”

“Only incident of seals flushing towards the water” 3 minutes prior to the boatarriving. “No cause and effect.”

I next asked him about the May 15, 2008 photographs. I asked him whether Dr. Stewartdid or did not find any evidence for an oyster farm disturbance in those photos. Dr.Lellis interrupted me, and said something that contradicted what he had said for theprevious hour. He said Dr. Stewart’s report was not the final word, that there was some



20

back and forth. This was quite different from what he told me at the beginning of theconversation. This change in his answer was triggered by my asking him about May 15,2008. I asked him for a copy of Brent’s spreadsheet. He told me it was nearly identicalto Appendix 1 in the USGS Report. I asked again. He did not offer to send it to me.

Unbeknown to me, Dr. Stewart sent his Supplemental Report to Dr. Blakeslee andpossibly Dr. Lellis on December 10. In it, he once again confirmed (in great detail) his

finding of no evidence of disturbance on May 15 and June 11, 2008.Concerning the May 15, 2008 NPS photographs, Dr. Stewart wrote:

“The small movement of seals obvious in this sequence appeared to me to be mostsimilar to responses of small number of neighboring seals to sudden movements ofrecently hauled out seals (especially juveniles) that are settling at haulout butenergetic and active. I did not consider this to be a flush in response to some otherkind of stimulus, and no other stimulus was apparent to account for it.”

Concerning the June 11, 2008 NPS photographs, Dr. Stewart wrote:

“The minor startle of seals unexplained, but I don’t consider this to be a flush butrather likely a startle of most seals owing to a sudden movement or startle of one

or two seals with or without external stimulus.”Dr. Stewart presented a minute-by-minute analysis of each sequence of photographs.Both both he concluded that “I did not consider this to be a flush” and “I don’t consider this tobe a flush.” In other words, no disturbance took place. Dr. Stewart’s more detailedanalysis in his Supplemental Report confirmed what he wrote in his original report inMay 2012, namely, that the May 15 and June 11, 2008 photographs provided no evidenceof harbor seal disturbances by the oyster boats.

On December 11, 2012, I emailed Dr. Lellis and once again requested a copy of Dr.Stewart’s Report, and I also asked him what he was going to do about the contradiction between the way in which his USGS Report calls June 11, 2008 a correlated disturbanceand the description in Appendix 1 of “no obvious disturbance.”

Dr. Lellis did not answer. On December 13, I emailed him again and asked him again fora copy of Dr. Stewart’s Report, and his thoughts about the analysis of the June 11, 2008photographs.

Dr. Lellis responded on December 13. He did not send me a copy of Dr. Stewart’sReport. He also did not disclose Dr. Stewart’s new Supplemental Report on the May 15and June 11, 2008 photographs. Rather, Dr. Lellis wrote:

I'm really locked down right now between a Research Grade Evaluation Paneland budgetary preparations and contingency planning for multiple federalappropriations scenarios. I'll try to get back to you when I have a little time to focus. I need to put some thoughts down on paper about our conversation last

week which really caught me off guard. We have come at this question from avery different angle than the one you were asking me about and it took me sometime to understand that. In fact, I'm still not sure I understand it. We werelooking at the forest. The approach you were discussing was looking at the trees.In fact, not just the trees, but a specific tree and perhaps even just the bark of thattree. I'm not sure if we completely missed the question we were being asked toaddress, or if somehow the conversation took a completely different direction afterwe became involved, but there really is a big disconnect in what we attempted toaddress in the report and what you were attempting to extract.



21

Let's talk after I've had time to gather my thoughts and revisit the report.

Dr. Lellis never responded again. He never sent me Dr. Stewart’s report orspreadsheet. He never commented on June 11, 2008. He never commented onMay 15, 2008. He never told me about Dr. Stewart’s Supplemental Report onDecember 10, 2012. Three days later, on Sunday December 16, I spoke at lengthwith then-USGS Director Dr. Marcia McNutt about this issue.

Summary

The USGS scientists (either Dr. Lellis, Dr. Blakeslee, or both), after their Report wasreleased, requested a subsequent re-review of key data by Dr. Stewart in his SupplementalReport that confirmed his earlier finding of no evidence of disturbance , a report that shouldhave led USGS to retract its USGS Report, inform NPS of the major mistake in their FEIS,and inform the Secretary of mistakes in what was presented to inform his high profiledecision. It appears as if none of this occurred. The USGS covered-up Dr. Stewart’sSupplemental Report. This was scientific misconduct.

I conclude the following:

(i)

Beginning on December 3, 2012, I contacted Dr. Lellis and asked questions aboutthe USGS Report finding of disturbances on May 15 and June 11, 2008, noted thecontradiction between the text of the USGS Report and Appendix 1 concerningthe June 11 analysis, asked what Dr. Stewart found, and asked for a copy of Dr.Stewart’s Report.

(ii) Even though I asked for a copy repeatedly, Dr. Lellis never provided me with acopy of Dr. Stewart’s Report.

(iii) In our telephone conversation of December 7, Dr. Lellis agreed that there was acontradiction in the June 11 finding in the text of his USGS Report and thefinding of “no obvious disturbance” in Appendix 1.

(iv)

On December 5, 2012, either Dr. Lellis or Dr. Blakeslee requested that Dr. Stewartre-review the May 15 and June 11 data. Dr. Stewart submitted his SupplementalReport on December 10, 2012. Neither those emails nor the report wereprovided in the USGS response to a FOIA request, suggesting the possibilitythat this communication might have taken place by private email addresses.

(v) I only obtained a copy of Dr. Stewart’s Supplemental Report because a staffer forCongressman Jared Huffman, Dr. Owens, requested all of Dr. Stewart’sdocuments and he provided the Supplemental Report to the Congressman.

(vi) Dr. Stewart re-reviewed the May 15 and June 11 data at the request of USGS. HisSupplemental confirmed his earlier finding of no evidence of disturbance.

(vii)

USGS suppressed Dr. Stewart’s Supplemental Report and finding of nodisturbances, thus covering up their earlier misrepresentation of Dr. Stewart’sinitial analysis. This is further confirmation of serial scientific misconductinvolving the USGS misrepresentation of Dr. Stewart’s analysis, and the NPSFEIS misrepresentation of the USGS Report.



1

Appendix 2:

Why the DOI OIG and SIOs Cannot Resolve These Allegations ofScientific Misconduct

Table of Contents

1. The DOI OIG Abdicated Its Oversight ............................................................................... 1-9a. DOI OIG: example #1 .................................................................................................................. 1-3

b. DOI OIG: example #2 ..................... ...................... ....................... ....................... ...................... ... 3-4c. DOI OIG: example #3 .................................................................................................................. 4-8d. DOI OIG: Internal Survey Reported They Pull Their Punches ............................................ 8-9e. DOI OIG: House Committee on Natural Resources Investigative Report Confirms ThatThey Pull Their Punches ..................................................................................................................... 9

2. The NPS Scientific Integrity Officer is Conflicted ........................................................... 9-10

3. The DOI Scientific Integrity Officer is Conflicted ......................................................... 10-11

4. The USGS Has a Scientific Integrity Officer, But They Have Been Unresponsive ... 11-14



2

1. The DOI OIG abdicated its oversight.

The Department of the Interior (DOI) OIG handles investigatory oversight of NPS andUSGS. I wrote to Secretary Salazar on April 27, 2009 (and again on May 10 and May 16,2009), and warned him that his presumptive nominee for NPS Director, Jon Jarvis, had“a pattern of flagrantly ignoring … the OSTP Federal Policy on Scientific Misconduct. Histrack record is not consistent with the standard of integrity and transparency set by President

Obama…”My May 16, 2009 letter to the Secretary, copied to Dr. Holdren (Director, OSTP),described a 21-point case for scientific misconduct against Mr. Jarvis. Mr. Jarvis repliedto the Secretary on May 17, responding to only seven of the 21 points, leaving 14 pointscompletely unanswered. As I wrote to Dr. Holdren on May 19, 2009, of the limitedresponses Jarvis provided, some were straw man arguments (i.e., the answers wereirrelevant to the charges), a few were misleading, and at least one contradicted formaltestimony he gave to the DOI OIG for its July 2008 report.

The allegations of scientific misconduct against Jon Jarvis were never properlyinvestigated, and Mr. Jarvis began his service as NPS Director in September 2009. Thecase for scientific misconduct presented here, now stretching across six years and three

federal agencies, is the result of Secretary Salazar not heeding those allegations, and boththe Interior Solicitor’s Office, and the OIG that Congress intended to be Interior’swatchdog, allowing the problem at NPS to continue and to spread to other agencies.

a. DOI OIG: example #1.

At the time of the Jarvis confirmation hearing on July 28, 2009, the DOI OIG wrote amisleading memo to the Secretary of the Interior and the Senate Committee on Energyand Natural Resources suggesting that they had investigated all of the allegations ofmisconduct, when the record showed they had not. Committee Chair Senator Bingaman(D-NM) opened the nomination hearing and stated: "The Department of Interior's Office of

Inspector General has completed an inquiry into that allegation and has reported that it has foundno evidence to support the allegation." He apparently did not know that the OIG did notinvestigate 95% of the allegations and thus misled the Senate.

The DOI OIG investigated only one of the 21-points of scientific misconduct in the May16, 2009 complaint filed with Secretary Salazar. As described above, Mr. Jarvis did notanswer most of those 21 points when given the opportunity. However, Mr. Jarvis didprovide an answer to a single issue – his involvement (or asserted lack thereof) with thedifferent versions of the NPS Drakes Estero Report. Mr. Jarvis answered that one chargewith plausible deniability. Even though he was placed in charge on all science mattersconcerning Drakes Estero, he claimed that he did not ‘write’ the July 2007 version of thediscredited NPS Report. It was that single issue (and only that issue of the 21) that the

DOI OIG investigated and dismissed.Why didn’t the DOI OIG investigate the other unanswered points? Why did the DOIOIG ignore Jarvis’ answer to one point (in his May 17 letter to the Secretary) in which hecontradicted his previous interview under oath to the DOI OIG? The OIG failed toinform the Senate that they had not investigated the substantive allegations against Jarvis, and instead informed the Senate Committee that they found no evidence tying Jarvis to the NPS Drakes Estero Report authored by his direct report, SuperintendentDon Neubacher.

On August 24, 2009, I discussed the DOI OIG finding with Assistant Inspector General



3

John Dupuy by telephone. He acknowledged quite candidly that regarding my entirecomplaint, the OIG only investigated one narrow procedural issue, and that the OIGnever examined the detailed list of scientific misconduct allegations.

When asked about the bulk of the misconduct claims against Mr. Jarvis, Mr. Dupuyreaffirmed that the OIG doesn’t have scientists and doesn’t investigate scientificmisconduct – i.e., the DOI OIG never looked at the issues of scientific misconduct, the

foundation of my complaint.When asked who, therefore, investigates scientific misconduct in the federalgovernment, Mr. Dupuy answered that it was not NPS, not DOI, not the DOI OIG, notNAS, and not MMC. Mr. Dupuy was unable to identify who would adjudicateallegations of scientific misconduct, especially concerning a high ranking official (in thiscase, a NPS Regional Director who was about to be confirmed as NPS Director).

Nearly three years later, on May 30, 2012, the DOI Office of the Secretary repeated to twoSenators this misrepresentation of the DOI OIG’s actions in July 2009 concerning theallegations against Director Jarvis. Rachel Jacobson, Acting Assistant Secretary for Fishand Wildlife and Parks, in responding on behalf of the Secretary to a February 13, 2012letter from Senators David Vitter and James Inhofe, wrote on May 30, 2012:

“The Department has taken very seriously the allegation of scientific misconductand concerns about scientific quality included in the three letters you reference –April 27 and May 10, 2009 letters to Secretary Salazar and the May 16, 2009letter to Dr. Holdren as well as in several other related submissions to theDepartment by Dr. Goodman. … the Senate was fully aware of the allegationsmade by Dr. Goodman against Director Jarvis during his pendency of hisnomination and those allegations were addressed formally in the records of hisconfirmation hearing.”

Ms. Jacobson failed to answer Senator Vitter’s and Senator Inhofe’s questions in theirFebruary 13, 2012 letter as to whether the Senator Committee had all three of my lettersfrom April and May 2009, and whether the Senate Committee was aware that Mr. Jarvis

had responded to only 7 of the 21 points in my May 16, 2009 letter. Instead, Ms. Jacobson restated that the DOI OIG had dismissed the allegations, when their precisewording was “allegation.” Ms. Jacobson failed to tell the two Senators that of the 21points outlined in the May 16, 2009 letters to both the Secretary and you, then-RegionalDirector Jarvis answered only 7 of the 21 (most with irrelevant or misleading answers),and the DOI OIG investigated only one point – one of the few that Jarvis had previouslyanswered.

The Senate was misinformed on July 28, 2009, and Senators Vitter and Inhofe weremisinformed on May 30, 2012. The DOI OIG never considered 20 of the 21 allegationsagainst Jon Jarvis, including none of the 14 he did not answer on May 17. Ms. Jacobsonwrote to the two Senators that “the Department is committed to scientific integrity … as well

as to transparency with Congress.” It is difficult to reconcile that statement with what wenton in July 2009, what the Senate Committee was told, what the two Senators asked in2012, and what the Assistant Secretary answered.

b. DOI OIG: example #2.

In a second example, on October 22, 2010, the DOI OIG was informed of allegations that



4

NPS failed to publicly disclose their secret camera program, 300,000 photos, and detailedlogs (which, as with the 2007 secret document, also contradicted NPS public statements).On November 9, 2010, the DOI OIG wrote that they asked NPS to investigate theallegations, and that they would subsequently “evaluate their response to determine whetheror not appropriate action was taken or further involvement by our office appears warranted.”NPS, in consultation with the Secretary’s office, directed the DOI Solicitor’s Office toconduct the investigation. Field Solicitor Gavin Frost, an attorney in the Billings, MT

Solicitor’s office, was directed to conduct the investigation.While the OIG did not investigate the allegations against Mr. Jarvis in 2009, his directreports were investigated two years later at the direction of the OIG, but not by the OIG.According to Gavin Frost, his report was finalized in late January or early February 2011,and released in a public, redacted version on March 22, 2011.

On March 22, 2011, DOI Field Solicitor Gavin Frost found that five NPS employees,including Superintendent Neubacher and West Regional Chief Scientist Dr. Graber (bothof whom reported to Jarvis), and three other Point Reyes scientists (Dr. Allen, Dr. Becker,and Mr. Press, all of whom reported to Neubacher), violated the NPS Code of Scientificand Scholarly Conduct.

Many aspects of the Frost Report were inadequate. For example, in 2008, the NationalAcademy of Sciences (NAS) requested all NPS harbor seal data concerning the oysterfarm and Drakes Estero. On May 5, 2009, the NAS released its report, which stated thatthe analysis of time- and date-stamped photographs could help resolve the controversy.

On that date, Neubacher and his NPS scientists (reporting to Jarvis) had two years of justsuch secret photographic data, and yet failed to disclose them to the NAS. Mr. Frostfound no misconduct in this failure to disclose these key data, data that contradicted thepublic claims NPS made to the NAS.

Although the DOI OIG told me on October 7, 2011 (when I met with them in their officein Washington, D.C.) they agreed and found the Frost Report inadequate, two yearslater, in spite of repeated requests for further involvement (letters from me to John

Dupuy, Assistant Inspector General for Investigations, DOI OIG, on September 14, 2011and March 19, 2012), no additional action has been taken by the OIG, and according tothe OIG FOIA officer, the November 2010 file remains open and unresolved as of January 2013.

c. DOI OIG: example #3.

In a third example, a misconduct complaint was filed with the DOI OIG on April 24,2012 concerning misrepresentations in the soundscape section of the DraftEnvironmental Impact Statement (DEIS) for the oyster farm at Drakes Estero.

For a more detailed analysis of the latest DOI OIG Report, see Appendix 4.The DEIS, for example, misrepresented noise data as coming from a 4-stroke, 360 cc, 20horsepower (HP) oyster skiffs on Drakes Estero in 2011, when in fact the data came froma loud, fast Kawasaki Jet Ski (2-stroke, 750 cc, 70 HP) recorded for the New Jersey StatePolice in 1995. The DEIS also misrepresent noise data from the plastic oyster tumblerwith the ! HP, 12-volt, electric motor, when in fact the data came from a 400 HP cementmixer truck recorded elsewhere.

The DOI OIG said they would finish and publicly release the results of theirinvestigation and report by early fall 2012, before NPS released the Final EIS (FEIS) and



5

prior to the Secretary’s decision.

After the NPS FEIS was released on November 20, 2012, and in response to inquiries asto the outcome of their investigation, the DOI OIG said the report was completed, beingheld internally, wouldn’t be released any time soon, and would not be made publicunless requested by FOIA.

On December 21, 2012, Senator David Vitter wrote to DOI Acting Inspector General

Mary Kendall. The Senator quoted from his colleague, Senator Dianne Feinstein, whowrote to Secretary Salazar on March 29, 2012 that:

“The Park Service’s latest falsification of science at Point Reyes National Seashoreis the straw that breaks the camel’s back.”

Concerning my still-outstanding April 24, 2012 complaint, based upon the samefalsification of science cited in Senator Feinstein’s letter, Senator Vitter wrote:

“It is frustrating that the Office of the IG seems incapable of acting independentlyor able to provide clear determinations on violations of the Data Quality Act, aswell as other White House and internal agency standards for scientific integrity.In this Drakes Estero situation alone, it is clear that NPS employees in multiple

instances eschewed meeting standards of scientific integrity. Additionally, I havesome very significant concerns that your office may have gone out of its way to protect Interior employees for which you were supposed to be independentlyinvestigating.”

“This suggests that the DOI OIG has no intention of making this investigation public in a timely fashion, and certainly not in the time promised by theinvestigators.”

“… can the investigation truly be considered independent?”

On January 16, 2013, Deputy Inspector General Mary Kendall responded to SenatorVitter. Two points from that response are pertinent here.

First, she wrote concerning the length of time required for a proper DOI OIGinvestigation:

“The process can be extremely lengthy, but it ensures that OIG reports are well-written, understandable, and factually accurate. Therefore, while theinvestigation itself may be completed, the report may be far from complete.”

She stressed the importance of accuracy in the lengthy review process for an IG report.This is interesting given the serious errors of fact in the final IG report released onFebruary 7, 2013 (see appendices 3 and 4).

For example, the IG report erred in misrepresenting the most important conclusion fromthe DEIS – the finding of two major adverse impacts (of which soundscape was one).

IG report page 6, ¶ 2:

“The September 2011 draft identified two areas that were assessed as havingmajor impacts on the Seashore using thresholds ranging from negligible, minor,moderate, to major; the two areas assessed as major were soundscape andsocioeconomic.” [bold emphasis added]

As shown in Table ES-4 in the executive summary of the DEIS, the two areas assessed ashaving major adverse impacts were soundscape and wilderness, not socioeconomic.



6

There was another potential assessment category that the IG did not mention: beneficial.The socioeconomic resource topic was the one area in which the alternatives in whichDBOC remained for the next decade was considered a “beneficial impact.”

Had the IG properly fact-checked their report, they could have avoided this major error.How did the IG misquote the two major adverse impacts in the DEIS?

A second example of the lack of fact checking involves a claim on page 10 of the IG

report concerning how VHB found and used the Jet Ski measurement in the NoiseUnlimited 1995 report to misrepresent the DBOC oyster skiff. . The IG report stated:

“VHB’s acoustics representative and director of Air Quality and Noise Servicesspoke with us regarding the sound-level data used in the DEIS. He informed usthat he possessed more than 40 years of sound and acoustics experience and thathe was the project technical advisor for the DEIS and reviewed its soundscapesections for accuracy. He stated that during his research for this project, he personally located the NU 1995 report on the Internet and subsequentlyselected the watercraft measurements from the NU report to represent Companyboats, which was based on information collected by VHB staff members duringCompany site tours.” [Bold emphasis added]

In my May 2012 interview, I told the IG that the Noise Unlimited 1995 report was notavailable on the Internet. Given the claim by the VHB acoustics representative about theInternet being the source of the Noise Unlimited report, it would seem that the IG wouldhave at least done its own confirmatory web search and published the web link for thereport. However, there is no such information provided in the IG report. I searchedagain, and conclude that there is no website accessible to a public search that containsthe Noise Unlimited report. In fact, I first found the report by asking an assistant to seekthe report from Noise Unlimited (which was out of business) and then from the New Jersey State Police (who no longer had the report). Given those dead ends, we noticed acitation to the report (but not the report itself) on the Internet, and as a result, theassistant finally obtained a copy from the Personal Watercraft Association.

In summary, what is troubling about these errors is that they indicate that the IG did notcarefully read the DEIS, and did not carefully fact-check their own IG report. Moreover,it indicates that during the several intervening months in which NPS and DOI hadcopies of the draft IG report, they also did not properly review the IG report foraccuracy, because all of them missed these errors. This contradicts the letter fromDeputy Inspector General Kendall to Senator Vitter in which she claimed that the longdelay in issuing the IG report was to ensure accuracy, and to make sure the IG report iswell written. I encourage you to read the IG report and judge for yourself whether it isclear and well written or not.

Second, concerning scientific misconduct, Deputy Inspector General Kendall wrote:

“For allegations of scientific misconduct, the OIG has an agreement in place tocoordinate with the DOI or bureau Scientific Integrity Officer. Because the OIGdoes not have scientific expertise, the scientific aspect of alleged scientificmisconduct is addressed by the Scientific Integrity Officer, not the OIG.”

This statement concerning the collaboration of the Scientific Integrity Officers (SIOs) andthe OIG to Senator Vitter stands in marked contrast to what actually occurred inresponse to my April 24, 2012 complaint filed with the DOI OIG. In my complaint, Ialleged (and provided details) that the NPS and DOI SIO’s had conflicts of interest. Isubmitted eleven questions to be asked of Drs. Machlis and Morgenweck to determine



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whether or not they were conflicted, and whether they should participate in theinvestigation. In the final IG report on February 7, 2013, the DOI neither providedanswers to those questions, nor indicated whether the SIO’s participated in theinvestigation. This is in contrast to Kendall’s letter to Vitter suggesting that the SIO’s didplay a major role. The IG report is silent on this issue of participation and authorship.

OIG Special Agents Vince Haecker and Cordell DeLaPena came to my office and

interviewed me for over seven hours on November 16, 2012.Within less than one week, Mr. Haecker telephoned me and asked if I would be willingto allow the DOI Scientific Integrity Officer (SIO) Dr. Ralph Morgenweck and NPS SIODr. Gary Machlis to collaborate with the OIG concerning investigating the allegations ofNPS scientific misconduct. I answered “yes” so long as they would show the OIG andme their independence (i.e., that they were behaving as SIO’s independent of the NPSDirector and DOI Secretary to whom they reported) by their willingness to spend timeinterviewing me and discussing the scientific data and allegations.

On May 23, 2012, Mr. Haecker wrote to me:

I just wanted to follow up on our very brief conversation to make sure we were onthe same page regarding DOI's Science Integrity Officers and to ensure I passalong the right message. You mentioned you were open to meeting with Dr's. Machlis and/or Morgenweck to discuss the science aspects of your complaint andhow their willingness to meet and discuss the issues with, could prove to youtheir ability to operate independently. Again, all I can do is act as the messenger,but I wanted to ensure that I pass along the right message to Dr's Machlis & Morgenweck and how this potential meeting could better show you theirapproachability and engagement on the issues you raised with the DEIS.

Less than one hour later, I responded:

“I am very open to meeting with Drs. Machlis and Morgenweck to (i) openlydiscuss and acknowledge (and hopefully be able to put aside) the conflict issues,

and (ii) discuss the science (hopefully this takes up most of our time). Perhapsone of you from the OIG would attend as well (I certainly would not want you to feel excluded). I would be delighted [if] all of us were able to leave the meeting feeling that Drs. Machlis and Morgenweck could indeed operate independently.This could be a tremendous step forward.”

Having heard nothing in response from Mr. Haecker or Drs. Morgenweck or Machlis, on June 1, 2012, I wrote again to Mr. Haecker:

I have neither heard from you, nor from Drs. Machlis or Morgenweck, since Imade this proposal to you. In fact, I have heard nothing from NPS concerning thescientific misconduct allegations. I also have not heard from NPS about therequested data. This silence from NPS/DOI is an all too familiar pattern. Can

we discuss today?Within a few hours, Mr. Haecker wrote back and suggested we have a phone call thatday. In our phone call, he was vague and avoided directly telling me why neither theDOI SIO nor the NPS SIO was willing to meet with me to discuss the scientific data andallegations.

Although Mr. Haecker and I communicated by email and phone many times over thesummer 2012, and he continued to ask me for various documents, he never again brought up the issue of either the DOI SIO or the NPS SIO interviewing me. I brought





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whether the IG "conducts its work in a manner that is independent (free from improperinfluence) from the Department [of Interior] ," nearly one in seven said no, more than aquarter would not say either way, and fewer than 60% said yes. Several staffcommented:

"I think there is widespread distrust and low morale in the organization rightnow. There are at least perceptions the acting IG and COS [Chief of Staff] did not

do the right thing, ie [sic], improperly quashed investigations, and have not been forthright with Congress";

"Wake up and quit trying to ‘get approval' from DOI … we have a job to do"; and

"Be careful with how much reports get softened to avoid 'slamming' theDepartment in the interest of maintaining a good relationship."

In response to this survey, Jeff Ruch stated:

"… this watchdog is not just on a very tight leash, it is on a choke chain."

"Under the current system, IGs revel in petty scandals and flee profoundcorruption."

The case for scientific misconduct at NPS (having now spread to MMC and USGS aswell) is one of profound corruption, with involvement at the highest levels, and thusunlikely, in the words of PEER Executive Director Jeff Ruch, to get an appropriateinvestigation by the DOI OIG. In this case, the DOI OIG has shown its inability over andover again to conduct truly independent investigations.

e. DOI OIG: House Committee on Natural Resources investigative reportconfirms that they pull their punches.

On February 21, 2013, Congress released a report documenting those criticisms alluded

to by PEER. The U.S. House of Representatives Committee on Natural Resources, Officeof Oversight and Investigations, released an investigative report entitled “HoldingInterior Watchdog Accountable.” The House Committee found that the DOI OIG pulledits punches and accommodated DOI leadership rather than investigate serious chargesof misconduct. The details described in the 75-page report are troubling and a reveal alack of independence of the DOI OIG, IG reports getting softened, and findingswhitewashed, so as not to find misconduct.

As cited in the House report, DOI special agent Richard Larrabee commented in writingthat he was “deeply concerned” that the Secretary’s Office receives “ great deference ,”suggesting it uses its influence to persuade OIG employees to stand in line with theDepartment’s politics.

If the DOI OIG cannot function as an independent watchdog, then it is even less likelythat the internal Scientific Integrity Officers can function in an independent fashion, asdescribed below.

2. The NPS Scientific Integrity Officer is Conflicted.

As I wrote to DOI Inspector General Kendall on April 24, 2012, Dr. Machlis, NPSScientific Integrity Officer is conflicted. First, Dr. Machlis, NPS Scientific IntegrityOfficer and Science Advisor, reports to NPS Director Jarvis, the person at the center of



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this dispute for six years and for whom unresolved charges of scientific misconduct pre-date his appointment as Director. Second, Dr. Machlis demonstrated his conflicts by hisactions and words.

The Department of Transportation VOLPE 2011 Report (cited in the FEIS) is a publicdocument. The data used to generate that published report should be publicly available.I requested the VOLPE data from the lead author and she referred me to the NPS

soundscape scientists at Fort Collins. For nearly a week in early April 2012, the NPSscientists were cooperative and collegial, responding to my emails, supplying me withsome of the requested data, and providing guidance on clarification of methods.

Beginning on April 13, 2012, they abruptly stopped responding to my emails andstopped supplying the requested data. On April 16, I wrote to Dr. Machlis and askedhim to help facilitate my data request. He did not respond. I asked him again on April18. On April 19, Dr. Machlis wrote:

“I have received your emails and review each carefully as it comes in. We are following DOI policies on allegations of scientific misconduct.”

According to Dr. Machlis, he initiated a scientific misconduct review. However, thereexists no such scientific misconduct review by Dr. Machlis in the available record. If Dr.Machlis did initiate a review, then the resulting report disappeared. I was neitherinterviewed nor asked to clarify a single substantive issue. Dr. Machlis failed to respondto my data request and gave no assurance that I would receive the requested data.

Finally, on Friday April 20, I was contacted by the NPS branch chief in Fort Collins, notthe scientists, and directed to file a FOIA request to obtain the data. One week earlier,the NPS scientists were collegial and sharing data. The next week they went silent, andtheir supervisor told me I must file a FOIA request to obtain the relevant data, data Irequested 18 days earlier. All of this hindered and restricted my scientific analysis andviolated the DOI Code of Scientific and Scholarly Conduct.

Dr. Machlis, by all indications, appeared to be a participant in the decision to prevent me

from obtaining relevant data from a published study (VOLPE 2011 Report) and hinderedmy scientific analysis. The DOI Code of Scientific and Scholarly Conduct states:

“I will not intentionally hinder the scientific and scholarly activities of others …”

“I will fully disclose methodologies used, all relevant data...”

Dr. Machlis became a participant of an investigation, rather than the investigator.Clearly, Dr. Machlis should not oversee– or have any management involvement – aninvestigation of NPS scientific misconduct.

3. The DOI Scientific Integrity Officer is Conflicted.

Dr. Morgenweck, Interior’s Scientific Integrity Officer (from 2011 to the first half of2012), also had a conflict of interest. Dr. Morgenweck commissioned the ATKINS peer-review of the NPS DEIS “in recognition of high interest in the science.” Dr. Morgenweckthen released the ATKINS peer-review of the DEIS on March 19, 2012. In the DOI Officeof the Secretary news release, he was quoted as follows:

“The peer-review accomplished exactly what we were seeking – that is, specificrecommendations on how to improve the final environmental impact statement tomake it a better science product,” stated Dr. Ralph Morgenweck, Interior’sScientific Integrity Officer.



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We now know that the ATKINS Report was tainted by the NPS decision to include falserepresentations of soundscape data in the DEIS. The peer-reviewer of the soundscapeanalysis, Dr. Christopher Clark of Cornell University, was, by his own words, “deceived.”Upon seeing the origin of the data he reviewed, and the real data collected at DrakesEstero by ENVIRON, Dr. Clark changed his major conclusion in a conversation with me.Thus, the peer review was corrupted by NPS misrepresentations.

By including Dr. Morgenweck in commissioning the tainted peer-review of the DEIS,and quoting him as giving praise to the report in the Interior press release accompanyingthe public release of the ATKINS peer review, Interior included their SIO as part of theEIS process, rather than as someone who could independently evaluate allegations ofscientific misconduct.

From the outset of the DOI OIG investigation into the allegations of misconduct againstNPS in May 2012, I was told that both Dr. Machlis and Dr. Morgenweck were going tocome out to California to interview me at length to discuss the data and allegations ofmisconduct. As described above (DOI OIG: example 3#), the DOI SIO and NPS SIO,even though represented by the DOI OIG and invited by me in May 2012 to participatein the investigation of NPS scientific misconduct, neither one of them ever talked to me,let alone interviewed me. Neither asked a single question or sought any substantiveinformation about my allegations of scientific misconduct.

In summary, neither NPS nor DOI are capable of investigating their own organizationswhen it comes to allegations of scientific misconduct involving high-level officials,including the NPS Director. There are simply too many layers of conflicts.

4. USGS Has a Scientific Integrity Officer, But She Has BeenUnresponsive.

The USGS has a Scientific Integrity Officer: Dr. Linda Gundersen. On December 16,2012, I spoke by telephone with Dr. Marcia McNutt, Director, USGS, about the

misrepresentations of the Stewart Report in the USGS Report, and the sequentialmisrepresentations of the USGS Report in the NPS FEIS. She was familiar with the 2012USGS Report concerning the NPS photographs at Drakes Estero.

I described to Dr. McNutt the Stewart Report, and Dr. Stewart’s finding of “no evidence ofdisturbance” by the oyster farm for the exact dates and times in which the USGS Reportclaimed that Dr. Stewart found an association, or weak correlation, and the NPS FEISsubsequently claimed cause-and-effect. Dr. McNutt was disturbed by the revelations.She asked me to send her the Stewart Report, and said that she would ask Dr. LindaGundersen, USGS Scientific Integrity Officer, to investigate the issue.

On December 17, I sent the Stewart Report and my analysis to Dr. McNutt, and wrote:

It appears that the USGS report misrepresented Dr. Stewart’s analysis inAppendix 1, and then incorrectly concluded that there was an association of theDBOC boat with the harbor seal disturbance on May 15, 2008. Finally, the NPSFEIS misrepresented the USGS report and claimed that the USGS had attributedthe May 15, 2008 disturbance to the DBOC boat. Two layers of successivemisrepresentations led to the opposite conclusion by NPS as compared to harborseal expert Dr. Brent Stewart.

I appreciate your willingness to investigate this issue. As you can imagine, this isa very important matter for the DBOC-NPS issue. But I also think this is a very



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important matter for USGS, which has long been the most trusted scientific bodyin the U.S. government.

Dr. McNutt did not respond. On December 23, 2012, I wrote again:

I wanted to get back to you about the materials that I sent you last Monday. Ihave extensive notes from my conversation with Dr. Lellis, and my many emailsback and forth with him. When will the USGS Scientific Integrity Officer be

contacting me and arranging for an interview? Would you please send me a copy your directive or memo to the USGS SIO specifying the nature of your request.Thank you for recognizing the significance of the apparent contradictionsbetween Dr. Stewart's report, the USGS report, and the NPS FEIS. …

Thanks very much. I look forward to receiving your directive, and speaking with your Scientific Integrity Officer about my conversations and emails.

Neither Dr. McNutt nor Dr. Gundersen responded. I never heard back from either oneof them. It is now one month since I first notified USGS that the USGS Reportmisrepresented the Stewart Report, and I have not been contacted by the ScientificIntegrity Officer, and have not been interviewed about my lengthy conversation andemail exchanges with the senior author of the USGS Report.

The USGS has yet to acknowledge my complaint and have not indicated that aninvestigation was initiated I have not been contacted. I have not been interviewed.

Given the lack of communication and transparency concerning the potentialinvestigation of the USGS Report by the USGS Scientific Integrity Officer, and theconnection with the NPS FEIS, this further disqualifies anyone at DOI from managingthis investigation of the misrepresentation and falsification in the USGS Report, and thesequential misrepresentation and falsification in the NPS FEIS. Both misrepresentationsconcern the original finding of “no evidence of disturbance” by Dr. Stewart in the HubbsSeaWorld Stewart Report. Dr. Stewart’s May 12, 2012 Report was contracted by NPS,and sent to both NPS and USGS, and thus this investigation involves NPS and USGS,

and how Dr. Stewart’s scientific analysis became misrepresented by both agencies.On January 17, 2013, I wrote to Dr. Gundersen:

“I write to ask for an update of your investigation of the USGS Reportmisrepresentation of the Stewart Report. Are you in fact conducting aninvestigation? When will you be interviewing me?

First you need to determine if the USGS Report in fact misrepresented theStewart Report, and if so, if that misrepresentation was done intentionally,knowingly, or recklessly. Please focus on one particular date: May 15, 2008.

Second, if you find that the USGS Report misrepresented the Stewart Report,then I ask you to retract or correct the USGS Report, and to publicly notify the

NPS (and public) that they need to revise their Final EIS on Drakes Estero in thatthe USGS Report was incorrect, and the NPS further misrepresented yourreport.

It should not surprise you that once a federal scientific document is released intothe public domain, unless corrected or retracted, it can and will be used indecision-making processes throughout the nation, and around the world. In thiscase, I have already been notified that the NPS FEIS has been raised in casesinvolving mariculture in two other states, and in two other countries.

After examining the videos of the NPS photographs prepared by USGS, Dr. Brent



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Stewart wrote in his report that he found no evidence for disturbances by theoyster farm. Your USGS Report incorrectly listed that as a finding of twoassociations (a correlation), and the NPS FEIS further incorrectly listed that as a finding of two attributions (cause and effect), thus allowing them to conclude amoderate adverse impact of the oyster farm on the harbor seals. I ask you to pleasecorrect the public documents and public record.”

Dr. Gundersen did not reply. I wrote back on January 23, 2013:I have not heard back from you since my email of January 17. It is now over onemonth since I alerted Dr. McNutt to this issue that the authors of the USGSReport misrepresented the Stewart Report, and she agreed to investigate whetherthis misrepresentation was done intentionally or knowingly, or was an honesterror.

I am puzzled by your silence over the past month. When do you plan oninterviewing me?

When I spoke with USGS Director Dr. McNutt on December 16, she indicatedthat there were two alternatives: either Dr. Stewart changed his conclusions after filing his May 2012 Stewart Report with NPS and USGS, in which case thereshould be a written record of that change, or alternatively someonemisrepresented his report in the USGS Report. Have you determined whichalternative is correct?

To date, Dr. Gundersen has not responded to my emails, has not confirmed if she is or isnot conducting an investigation, has not interviewed me, has not sought additionalinformation from me, and if she has conducted an investigation, has not informed me ofthe outcome. Surely, such behavior is not consistent with what OSTP intended for theWhite House Scientific Integrity Policy.

Towards the end of March 2013, I became aware that Interior had appointed Dr. SuzetteKimball as Acting Director, USGS (and DOI Scientific Integrity Officer), and that she had

appointed Dr. Alan D. Thornhill at USGS Scientific Integrity Officer. On March 31, 2013,I wrote to Dr. Thornhill, coped Dr. Kimball, and included the string of emails to previousUSGS Director Dr. McNutt and USGS SIO Dr. Gundersen:

Dear Dr. Alan D. Thornhill,

I write to you as USGS Scientific Integrity Officer. As you will see by the stringof emails, correspondence, and documents below, on Sunday December 16, 2012,I alerted then-USGS Director Dr. Marcia McNutt in a phone conversation to a possible case of scientific misconduct at USGS. She told me she would notify herScientific Integrity Officer at the time, Dr. Linda Gundersen, on MondayDecember 17. Dr. McNutt found the allegations very troubling. Since that time,I wrote to Dr. McNutt on December 17 and December 23, and heard no reply. I

subsequently wrote to Dr. Gunderson on January 17 and January 23, and heardno reply.

I do not know when the SIO position changed from Dr. Gundersen to you, and if you are aware of the allegations. Would you please respond to me and let mewhether USGS has or has not conducted an investigation (and if so, its outcome),or whether USGS is or is not currently conducting an investigation (and if so,when you are planning on interviewing me). The complete silence from USGSwhen confronted with serious allegations of misconduct is troubling, and appearsinconsistent with the President's Scientific Integrity Policy.



I request a phone call with you this next week to bring you up-to-speed on thisissue, and to discuss whatever action USGS is taking. I look forward to talkingwith you.

Sincerely,


As of the submission of this complaint on May 13, 2013, Dr. Thornhill never respondedto my email.