CSG's Scientific Misconduct Complaint Sent To Jewell 5.13.13

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 a
Department in trouble due to unchecked scientific misconduct at NPS that has now
permeated another of your agencies, the USGS. Over the past six years, NPS engaged in
scientific misconduct concerning the oyster farm at Drakes Estero. Most recently, NPS
was aided by another agency USGS as a partner to that misconduct.
The case for scientific misconduct presented here concerns new information obtained
since 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 scientific
misconduct at NPS and USGS. Whether Interior can conduct such an unbiased and
independent investigation given the inherent conflicts-of-interest and whether
Interior 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 concerning
the oyster farm at Drakes Estero, misrepresented the record from the Stewart
Report (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 in
so 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 activity
and disturbance of seals based upon the USGS Report finding of a correlation (in
turn based upon Dr. Stewarts finding of no evidence of disturbance), leading to an
overall finding in the NPS FEIS of a moderate adverse impact, and in so doing
violated the DOI Scientific Integrity Policy.
3. USGS and NPS, in their claims that the USGS analysis of the NPS photographs
was very high profile and very high priority, and needed to inform Secretary Salazar for
his decision on the oyster farm permit, apparently briefed Assistant Secretaries
Castle and Jacobson with false claims of evidence of oyster farm disturbances of
seals 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 of
no evidence of disturbance, a report that should have led USGS to retract its USGS
Report, 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 instead
was covered up, and in so doing violated the DOI Scientific Integrity Policy.
1
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 and
facts. In your statement to the Senate Energy and Natural Resources Committee on
March 7, 2013, you spoke of the importance of the Department of the Interior using the
best science available to make the best decisions, using the vast scientific resources at
Interior.
As a fellow scientist, I applauded your statements, much as an elected member of the
National 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 promoting
the 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 the
integrity of the scientific process
In contrast to the Presidents stated policies, as applied to Drakes Estero, science has
taken 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 by
NPS before you took over leadership of Interior.
Some of these allegations (#1 and #2) were submitted in March 2013 to Dr. John
Holdren, the Presidents science advisor, OSTP Director, and architect of the Presidents
Scientific Integrity Policy. I had five reasons for taking this complaint to the White
House.
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, Interiors 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, reinforcing
that they are incapable of an honest investigation of NPS (see Appendix 4).
Fifth, NPS Director Jarvis boldly declared in response to a Data Quality Act
complaint 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 scientific
misconduct at NPS and USGS.
On March 15, OSTP General Counsel Rachael Leonard told me that OSTP takes these
charges seriously. She said OSTP understands concerns about the conflicts-of-interest
and lack of independence at Interior, and about the Jarvis Doctrine stating that NPS
science is beyond accountability. Nevertheless, she said she was compelled to instruct
me to file my complaint with the Department of the Interior. I suggested that this was
2
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 not
available when I originally filed allegations #1 and #2 with OSTP. These new
documents reinforce this complaint by providing evidence that (i) two Assistant
Secretaries apparently were briefed with this false science to inform the Secretarys high
profile decision, and (ii) USGS staff covered-up a subsequent Supplemental Report that
confirmed the false science. These revelations lead to allegations #3 and #4 (see
Appendix 1).
I must admit that I am a bit apprehensive, given the history (see Appendices 2-4) about
submitting 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, your
leadership, and your statements to the Senate Committee, I am confident you will find a
way. Please be forewarned that in the system you inherited, you will find conflicts-ofinterest, 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 the
Final 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 in
Drakes 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 no
evidence that the oyster farm is disturbing or has disturbed the harbor seals in Drakes
Estero. The oyster boats stay over 700 yards from the seals, with a sandbar between
them. Dr. Brent Stewart (Hubbs-SeaWorld Research Institute harbor seal behavior
expert) found no evidence for disturbance, the USGS Report misquoted him and claimed he
found two correlations, and then the NPS FEIS further misrepresented the USGS Report
and claimed causation, and with it, a finding of a moderate adverse impact. The serial
misrepresentations, 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 farm
would 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 on
Secretary 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 was
necessary to inform the Secretary for his decision on the oyster farm permit. Two
Assistant Secretaries apparently were briefed. The NPS FEIS finding of a moderate
adverse impact was presented by Department of Justice lawyers to the Ninth Circuit
Court of Appeals as the reason why the public good is in favor of removing the oyster
farm.
This analysis was considered very high profile, and USGS and NPS knew it was wrong
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and misrepresented Dr. Stewarts findings. Moreover, USGS received a Supplemental

Report from Dr. Stewart further showing that the USGS Report and NPS FEIS were
wrong, and they did not disclose the Supplement Report, retract the USGS Report, notify
NPS that their FEIS was incorrect, or apparently notify the Secretary, his lawyers, and
the 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 misconduct
according 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 stay
over 700 yards away from the harbor seals, with an intervening sandbar blocking their
view and buffering their sound, while the NOAA and NPS recommendations and
protocols 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 near
its carrying capacity. During the Draft EIS (DEIS) comment process, NOAA, the federal
agency 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 harbor
seal 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 (165,000
photos from the 2008 harbor seal pupping season) of the over 300,000 time- and datestamped NPS photographs of the oyster boats and harbor seals (from secret cameras
operational for three and one-half years from 2007 to 2010). The FEIS quoted the USGS
Report as concluding that on two occasions in 2008, oyster boats caused seals to flush
into the water.
There are, however, two major problems with this claim: NPS misquoted the USGS
Report, and USGS misquoted the original experts findings (Dr. Brent Stewart, HubbsSeaWorld Research Institute). In so doing, both agencies misrepresented the primary
scientific analysis and altered the scientists 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 seals
getting flushed into the water (a major disturbance) on these two occasions. The USGS
had no harbor seal behavior expert, and so relied on an analysis of NPS photos, as
contracted by NPS, conducted by Dr. Brent Stewart, a harbor seal behavior expert at
Hubbs-SeaWorld Research Institute in San Diego (the 2012 Stewart Report). The USGS
Report 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. A
review of his spreadsheet, submitted to both NPS and USGS, confirms his clarity for
these two dates. The USGS Report misrepresented the Stewart Report, claiming a
correlation where Dr. Stewart found none, and then the NPS FEIS misrepresented the
USGS 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 of
causation (attribution) that led to a finding in the FEIS of moderate adverse impact.
4
Was this a clerical error in copying Dr. Stewarts spreadsheet from one report to
another? Unlikely. Consider: (i) the evidence for serial misrepresentations of
disturbances in the Stewart, USGS, and NPS FEIS Reports; (ii) the history of repeated
NPS false claims of harbor seal disturbances by the oyster farm 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 two Assistant Secretaries of
Interior to inform the Secretarys decision; and (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 oyster farm (on May 15 and June 11, 2008).
It is alleged that the preponderance of evidence (as defined by the DOI and White
House Scientific Integrity Policies) leads to the conclusion that these serial
misrepresentations and cover-up by USGS and NPS were committed intentionally,
knowingly, or recklessly. False science was used to inform the Secretary for a high
profile policy decision. The Secretary, public, and federal court were deceived.
3. Interior Scientific Integrity Officers and Interior Inspector General Are

Conflicted Concerning Allegations of Misconduct at NPS and USGS
Nine reasons lead me to conclude that Interiors Scientific Integrity Officers and the
Interior Inspector General are conflicted concerning allegations of misconduct at DOI.
1) Inspector General offices (OIGs) are in general unable or unwilling to properly
investigate allegations of scientific misconduct, and have no scientists on staff.
2) The Department of the Interior (DOI) OIG provides investigatory oversight for
NPS and USGS, but the DOI OIG abdicated its independent investigatory
oversight, 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 dismiss
allegations 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 despite
evidence to the contrary evidence in the form of documents and emails.
4) The Public Employees for Environmental Responsibility wrote the DOI OIG
pulled its punches and compromised its independence to please superiors.
5) The House Committee on Natural Resources wrote that it is deeply concerned
that DOI OIG actions are inconsistent with the role of independent watchdog.
6) If allegations involve high-level officials, the Scientific Integrity Officers
throughout Interior are no less conflicted that the DOI OIG, lacking the
independence 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 unresponsive
to repeated requests to describe the nature of her investigation, if any. The USGS
SIO was repeatedly notified of allegations #1 and #2 presented here, but
remained silent and did not even acknowledge receipt of the allegations.
9) The Scientific Integrity Officer for DOI and USGS Acting Director is conflicted by
the allegations concerning USGS and the lack of responsiveness by the USGS
SIO. How can the DOI SIO also be the Director of USGS and investigate USGS?
5
4. Request That DOI Establish a Blue-Ribbon Panel of Eminent Scientists

to Investigate These Allegations
This issue has outgrown Drakes Estero. It is no longer a local issue. It involves NPS
and USGS. The DOI OIG and three DOI Scientific Integrity Officers have shown their
inability to properly investigate misconduct within Interior.
The NPS false science in the FEIS has been used by Department of Justice lawyers in the
Ninth Circuit Court of Appeals to assert that the public good favors removing the
oyster farm. The false science in the FEIS has been used in regulatory hearings
involving oyster farms in other parts of the U.S., and growers in other countries are
becoming increasingly concerned. Many people inside and outside government are
watching and waiting.
Allowing the scientific misconduct to stand is already having and will continue to
have a corrosive impact on scientists throughout Interior. It sends a message not to
report the facts and data objectively as you find them, but rather to report data as
someone else in a powerful position wants them to be reported. It is not healthy for
science 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 to
ideology is for you, as the new Interior Secretary, to direct a truly independent
investigation of the science in this matter at NPS and USGS. It is incumbent upon you
to bypass the biases and conflicts that have dominated previous investigations under
the 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 some
local environmental supporters (with whom I often have strong common cause)
manipulated, misreported and misrepresented science in their desire to support
expanded wilderness. In an effort to produce a rationale to close the farm, false
arguments were made that the farm damaged or disturbed local seagrasses, water
quality, marine mammals and ecosystem diversity. These arguments have, one
after another, been shown to be based on bad science and contradicted by evidence
hidden or suppressed or ignored by federal agencies. The efforts of local scientists,
especially Dr. Corey Goodman, professor emeritus from both Stanford and
Berkeley and a member of the U.S. National Academy of Sciences, were central to
revealing the extent of scientific misconduct. Reviews by independent scientists
and now confirmed by investigations at the Department of Interior and the U.S.
National Academy of Sciences show that arguments of environmental harm from
the 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 of
opinion 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 the
Presidents Scientific Integrity Policy. The Jarvis Doctrine (see Appendix 3.2) overturns
and undermines what you stand for as a scientist and a leader. It is time for Interior to
restore science to its rightful place and not allow science to take a back seat to ideology.
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 this
investigation, 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.

corey.goodman@me.com
415 663-9495; 650 922-1431 (mobile)
Appendices
Appendix 1: Overview of Allegations of Scientific Misconduct
Supporting documents:

Stewart Report, May 2012 (HSWRI Tech Rept and HSWRI excel spreadsheet)
USGS Report, November 2012
NPS Final Environmental Impact Statement, November 2012
USGS Dr. Lellis & Dr. Goodman conversation and emails.pdf
USGS response to FOIA: 2013.5.7 Batch #1.pdf
Timeline and quotes from USGS FOIA response.05_13_13.pdf

Dr. Brent Stewarts Supplemental Report: BSS Suppl review.pdf
Appendix 2: Why the DOI OIG and SIOs Cannot Resolve These Allegations of Scientific
Misconduct
Appendix 3: Overview of the History of NPS Scientific Misconduct
Appendix 4: Analysis of DOI OIG Investigative Report on DBOC EIS: The DOI OIG Did
Not Conduct a Proper and Independent Investigation of NPS Misconduct
Appendix 5: Dr. Corey Goodman, Brief Resume and History of Involvement
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
1. Summary of Allegations of Scientific Misconduct

The four allegations of misconduct, involving two DOI agencies, are:
4.
USGS, after its Report was released, requested a subsequent re-review of key
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 moderate
adverse impact on harbor seals due to the potential for disturbances and continued
disturbances caused by DBOC oyster boats.
A moderate adverse impact is defined as impacts on harbor seals would result in readily
apparent effects on the population, natural processes, or habitat in the project area. It is the
second most serious category of adverse impacts.
This single determination of a moderate adverse impact on the harbor seals at Drakes
Estero 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 of
false public claims, manipulated reports, and secret cameras and millions of taxpayer
dollars NPS claimed that an independent analysis by USGS of NPS photographs
supported this finding.
The facts, based upon the preponderance of evidence reveal that both claims of scientific
evidence were based upon misrepresentations made intentionally, knowingly, or
recklessly, the standard for determining misconduct according 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 stay
over 700 yards away from the harbor seals, with an intervening sandbar blocking their
2
view and buffering their sound, while the NOAA and NPS recommendations and
protocols 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 near
its carrying capacity. During the Draft EIS (DEIS) comment process, NOAA, the federal
agency 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 harbor
seal 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 (165,000
photos from the 2008 harbor seal pupping season) of the over 300,000 time- and datestamped NPS photographs of the oyster boats and harbor seals (from secret cameras
operational for three and one-half years from 2007 to 2010). The FEIS quoted the USGS
Report as concluding that on two occasions in 2008, oyster boats caused seals to flush
into the water.
Report, and USGS misquoted the original experts findings (Dr. Brent Stewart, HubbsSeaWorld Research Institute). In so doing, both agencies misrepresented the primary
scientific analysis and altered the scientists 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 seals
getting flushed into the water (a major disturbance) on these two occasions. The USGS
had no harbor seal behavior expert, and so relied on an analysis of NPS photos, as
contracted by NPS, conducted by Dr. Brent Stewart, a harbor seal behavior expert at
Hubbs-SeaWorld Research Institute in San Diego (the 2012 Stewart Report). The USGS
Report 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. A
review of his spreadsheet, submitted to both NPS and USGS, confirms his clarity for
these two dates. The USGS Report misrepresented the Stewart Report, claiming a
correlation where Dr. Stewart found none, and then the NPS FEIS misrepresented the
USGS 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 of
causation (attribution) that led to a finding in the FEIS of moderate adverse impact.
Was this a clerical error in copying Dr. Stewarts spreadsheet from one report to
another? 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 then
the NPS misrepresented the USGS Report (allegations #1 and #2);
(ii)
The history of repeated NPS false claims of harbor seal disturbances by the oyster
farm 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 two
Assistant Secretaries of Interior to inform the Secretarys decision (allegation
#3); and
3
(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 oyster
farm (on May 15 and June 11, 2008) (allegation #4).
It is alleged that the preponderance of evidence (as defined by the DOI and White
House Scientific Integrity Policies) leads to the conclusion that these serial
misrepresentations and cover-up by USGS and NPS were committed intentionally,
knowingly, or recklessly. False science was used to inform the Secretary for a high
profile 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. Stewarts May 12, 2012 report and spreadsheet analysis (together the Stewart
Report) submitted to NPS (submitted to USGS on May 3). These documents were
obtained from Dr. Stewart at Hubbs-SeaWorld Research Institute. The November
26, 2012 USGS Report with Appendix 1 based on Dr. Stewarts Report (together
the USGS Report).
ii.
The November 20, 2012 NPS FEIS, which relied on the USGS Report and Stewart
Report.
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 and
me on December 7, 2012 (see below).
vi.
A Supplement Report filed by Dr. Brent Stewart with Dr. Carrie Blakeslee on
December 10, 2012 (BSS Suppl review.pdf) in response to a USGS request on
December 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 requested
the documents he provided to Dr. Stephanie Owens, NOAA Sea Grant Knauss
Fellow working for Congressman Jared Huffman, on April 30, 2013 in response to
her request for documents on April 29, 2013.
I thank Dr. Brent Stewart, Hubbs-SeaWorld Research Institute, and Cause of Action for
supplying 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. Stewarts May 2012 Report were not answered.
Moreover, Dr. Lellis never told me that while we were having our discussions from
December 3 to 13, 2012, that he and Dr. Blakeslee requested a re-review of the May 15
and June 11, 2008 data by Dr. Stewart on December 5, and that Dr. Stewart responded
with his Supplemental Report on December 10. I did not know the existence of the
Supplemental Report until after it was provided to Congressman Huffmans office on
April 30 (as requested by staffer Dr. Owen) and subsequently provided to me on May 9,
2013.
To my knowledge, the existence of this Supplemental Report (enclosed here as a

supporting document and discussed below) has not been publicly disclosed prior to the
filing this scientific misconduct complaint on May 13, 2013.
It is important to note that the May 2013 USGS response to the FOIA request did not
include the USGS email requesting Dr. Stewarts re-review on December 5, Dr. Stewarts
December 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 not
indicate that anything had been withheld in their response to the FOIA request. This
raises serious questions as to whether the Report and emails were withheld (in violation
of FOIA), or alternatively, whether the USGS staff used private email addresses (rather
than their official USGS email addresses) to contact Dr. Stewart and seek his re-review of
the May 15 and June 11, 2008 photographs. Either alternative is troubling given the high
profile of this issue, and the importance of Dr. Stewarts Report.
Early in this investigation, Interior should determine why these materials were not
provided in response to the FOIA request, and whether private email addresses were
used for these communications. If so, then Interior should investigate what other
communications within USGS, between USGS and NPS, and between USGS and others
used private email addresses so as to avoid disclosure under FOIA.
3. Allegations #1 & #2: USGS & NPS Misrepresented the Stewart Report
These two allegations of scientific misconduct are interconnected, and arise from an
analysis of the scientific basis for the claim made in the NPS Final Environmental Impact
Statement (FEIS) for the Drakes Bay Oyster Company (DBOC) Special Use Permit,
released by the National Park Service (NPS) on November 20, 2012, that continuation of
the oyster farm would 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 (FEIS, pg. 377).
In particular, these allegations are based on the scientific analysis submitted to NPS and
the 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 a
third-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 and
USGS) concluded that there was no evidence that DBOC oyster boats caused
disturbances of harbor seals in the NPS photographs reviewed (165,000
photographs 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 Stewart
Report 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 disturbances
of harbor seals were attributed (another word for causation) to DBOC boats
because the FEIS relied on both the USGS Report and the Stewart Report, neither
of which found a cause-and-effect relationship between flushing disturbances and
DBOCs oyster boats (FEIS pg. 376). In fact, the Stewart Report found no evidence
for DBOC disturbances.
4) Dr. Stewarts finding of no harbor seal disturbances by DBOC oyster boats was
transformed by two sequential misrepresentations the first by USGS and the
second by NPS from a finding of no evidence of DBOC boat disturbances of
harbor seals to the cause-and-effect conclusion made in the FEIS.
5) In summary, the FEIS lacked the scientific evidence to conclude that continuation
of the oyster farm would 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 (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 USGS
to provide a third-party review of those photographs.
NPS initiated a third-party review of the photographs with the USGS, in
consultation with a harbor seal specialist with the Hubbs-Sea World Research
Institute. The USGS assessment (Lellis et al. 2012) focused on the 2008 harbor
seal pupping season, when more than 165,000 photos were collected from two
sites 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 DBOC
operations appears to be based in large part upon the NPSs interpretation of the USGS
assessment of NPS photographs, entitled Assessment of Photographs from Wildlife
Monitoring Cameras in Drakes Estero, Point Reyes National Seashore, California, by William
A. 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) (USGS
Report) (FEIS, pgs. 376-377).
The USGS Report in turn was based in large part upon a NPS commissioned third-party
evaluation of the NPS photographs by Dr. Brent Stewart, Ph.D., J.D., Senior Research
Scientist at the Hubbs-SeaWorld Research Institute (HSWRI), entitled Evaluation of
Time-Lapse Photographic Series of Harbor Seals Hauled Out In Drakes Estero,
6
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). In
its 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 disturbed
the seals. However, the data used in the analysis are not sufficient to support firm
conclusions regarding the rate and significance of such disturbance (MMC
2011b). Additionally the USGS assessment (Lellis et al. 2012) of the more than
250,000 digital photographs taken from remotely deployed cameras overlooking
harbor seal haul-out areas in Drakes Estero attributed a specific stimulus to 6 of
the 10 observed flushing disturbance events. Two flushing disturbance events
were attributed to [DBOC] boat traffic at nearby sand bars, two were attributed
to a kayak using the lateral channel (note kayak was in Drakes Estero in violation
of seasonal closure), and two appeared to be related to seabirds landing among the
seals.
Alternative B [DBOC 10-year renewal] would result in long-term moderate
adverse impacts on harbor seals for another 10 years due to the seal displacement
effects of human activities in Drakes Estero associated with DBOCs 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 flushing
disturbance events . . . to [DBOC] boat traffic at nearby sand bars . . . . (FEIS, pg. 376). In this
sense, 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 Marine
Mammal Commissions November 22, 2011 report, entitled Mariculture and Harbor Seals
in Drakes Estero, California (MMC Report). After reviewing NPS records prepared by
volunteers 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] fuller
examination of the photographs is necessary to form a conclusion with a reasonable level of
confidence. (Id., pgs. 26-27).
Thus, according to NPS, the USGS Report validated the MMC finding of a DBOC
disturbance on May 15, 2008. According to the NPS FEIS, there were now two
independent 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 NPS
disturbances. (FEIS, pg 377).
Association: USGS Report Claimed a Weak Correlation of DBOC Boats with Two
Harbor 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 HubbsSeaWorld Research Institute, who was hired under contract with NPS to analyze the
USGS-prepared videos composed of the series of photographs of potential harbor seal
7
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 of
each event and the 10 photographs after the end of each event (3,140 photographs
total) were analyzed for incidence and cause of seal disturbance. Ten of the 75
events were classified as containing behaviors indicative of disturbance in the
form of flushing (table 1, figs. 2-11, appendix 1). Two flushing events were
associated with the presence of a kayak, two were associated with birds landing in
the area, two were associated with boat activity, and four occurred when no
obvious stimuli were visible within the field of view of the camera. (USGS
Report, 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 the
adjacent 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 least
associated 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 is
carefully reviewed, it becomes clear that the USGS Report concluded that several
disturbance events can be directly connected to kayaks and birds, but that the two
disturbance 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 1
in the USGS Report which summarized Dr. Stewarts research analysis (i.e., his
spreadsheet) used to reach the conclusions in the main report. In fact, Appendix 1
contradicts the USGS Reports conclusion on June 11, 2008 that an oyster boat was at
least 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: Boat
visits area; people walking; very poor camera focus; rafting birds scattered; brief movement of
seals toward water's edge several minutes before boat arrives but none seen to enter water; no
obvious 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 harbor
seal disturbance caused by DBOC oyster boats. Appendix 1 provides no conclusion in
the 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 reports finding of an
association between DBOC oyster boats and harbor seal flushing events on May 15,
2008, or June 11, 2008.
No Evidence of Disturbance: Hubbs-SeaWorld Report Found No Evidence of Harbor

Seal Disturbance by DBOC Oyster Boats
As described in the FEIS, the USGS worked in consultation with a harbor seal specialist
with 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 a
named 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 on
December 7, 2012 (notes enclosed here). In those communications Dr. Lellis confirmed
three key points regarding Dr. Stewarts role in the preparation of the USGS Report:
1) Dr. Stewart was the harbor seal behavior expert on the USGS review of NPS
photographs (none of the other USGS scientists had this expertise they relied on
Dr. Stewart);
2) Dr. Stewarts work provided the analysis on a spreadsheet to determine if there
was an association (according to USGS, a weak correlation), and if so, whether
there was a cause-and-effect relationship between a harbor seal flushing
disturbance and a specific stimulus, and
3) Dr. Lellis confirmed that Dr. Stewarts work was presented in specific columns in
Appendix 1 in the USGS Report. He told me that Appendix 1 represented Dr.
Stewarts analysis. When I wrote on December 5 and asked him for a copy of Dr.
Stewarts Report, he replied: Yes, essentially that is Appendix 1 of the report.
I acquired Dr. Stewarts May 12, 2012 report and spreadsheet with his supporting
analysis (together the Stewart Report), as submitted to NPS and USGS, by requesting it
directly from the Hubbs-SeaWorld Research Institute.
Dr. Stewart wrote in his report that he evaluated time-lapse NPS photographic records
provided 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. Stewarts written report is brief only two pages. The supporting analysis for the
conclusions in his report is found in the accompanying Excel spreadsheet, which was
reproduced by USGS as several columns in Appendix 1 of the USGS Report.
After reviewing the time-lapse photographs, Dr. Stewart focused on three disturbance
events 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 events
were 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. The
disturbance event associated with the kayak appears to have been directly caused
by the close presence of the kayak and the seals detection of it. One disturbance
reaction of seals correlative with the presence of a skiff beached on mud flats
several hundred meters away can not [sic] be causally linked to human presence
as no humans were in the field of view of the camera when the seals movements
occurred. Another movement of seals toward the water (but where none entered
the water) occurred several minutes before a skiff was observed in the area and
could not be determined [to] have been caused by [a] skiffs presence in the area.
9
The third disturbance event occurred when a skiff and people associated [with] it
were 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 presence
because the seals appeared to respond to birds that had evidently flushed from an
area 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 disturbance
events. (Stewart Report, pg. 2).
More detailed information is provided in Dr. Stewarts Excel spreadsheet entitled,
Drakes Estero Harbor Seals HSWRI.xlsx, which provides the detailed analysis he
summarized in his report. Dr. Stewarts notes for May 15, 2008, and June 11, 2008, the
two dates the USGS Report found a flushing disturbance was associated with DBOCs
oyster skiffs, contradict the USGS Reports findings. Dr. Stewart found no evidence for
DBOC disturbances. [Note: the version of Dr. Stewarts spreadsheet provided on April
30, 2013 to Dr. Owen in Congressman Huffmans office is entitled: Drakes Estero Harbor
Seals HSWRI Revised.xlsx. I do not know what if anything has been revised, but the
entries for May 15 and June 11, 2008 remain the same, including the spelling mistakes.]
May 15, 2008. The most important insight from Dr. Stewarts spreadsheet is that this
date 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. Stewarts spreadsheet, he wrote the
following about the May 15, 2008 photographs:
very poor camera focus; skiff visits; no evidendence [sic] of disturbance to
seals (Stewart Report, spreadsheet, May 15, 2008)
Dr. Stewarts conclusion was clear. The NPS photographs from May 15, 2008,
contained no evidence of disturbance to seals. Dr. Stewart acknowledged the
presence of the DBOC skiff, but wrote no in the column titled evidence of
disturbance to seals.
For most dates, the USGS Reports Appendix 1 accurately represented the
analysis presented in Dr. Stewarts Excel spreadsheet. I confirmed by
comparison that the Appendix accurately reflects Dr. Stewarts Excel spreadsheet
for over 40 individual dates. On May 15, 2008, however, there is a striking
divergence in Appendix 1 from Dr. Stewarts spreadsheet. The USGS Report
Appendix 1 entry for May 15, 2008, was re-written, and excluded Dr. Stewarts
conclusion, no evidendence [sic] of disturbance to seals. Thus, the USGS Report
appears to have misrepresented Dr. Stewarts 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 of
seals towards waters edge several minutes before skiff arrives but none seem to
enter 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 of
disturbance to seals. He concluded that there was no evidence that the DBOC
10
oyster boat caused the disturbance, and thus, did not attribute it to the DBOC
oyster 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 that
report because the USGS Report only noted an association a weak correlation not
attribution, or a cause-and-effect relationship.
Further, the USGS Reports finding that two harbor seal flushing disturbances were
associated with DBOC oyster boats is a misrepresentation of the findings reached by
the teams harbor seal behavior expert, Dr. Stewart. This is so because Dr. Stewart
concluded that there was no evidence of disturbance by DBOCs oyster boats on the two
days May 15, 2008, and June 11, 2008 identified in the USGS Report.
In fact, there does not appear to be evidence to support the NPSs assertion in the FEIS
that 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 a
FEIS misrepresentation of the USGS Report, and a USGS Report misrepresentation of its
primary source, Dr. Stewarts analysis.
Furthermore, Dr. Stewarts finding that there was no evidence of seal disturbance on
May 15, 2008 provides the further expert analysis called for in the 2011 MMC Report to
eliminate the episode from consideration.
Accordingly, the NPS FEISs conclusion of a moderate adverse impact to harbor seals by
DBOC is a misrepresentation because the two disturbance events it relied upon do not
appear to have been related to DBOCs 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 the
NPS 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 misrepresented
the USGS Report. The Stewart Report was contracted by NPS, and Dr. Stewart
submitted his report simultaneously to both NPS and USGS on May 12, 2012. The NPS
EIS team had access to the Stewart Report. From Dr. Stewarts finding of no evidence of
disturbance, two serial misrepresentations transformed that finding into one of
attribution 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 behalf
of NPS, and apparently knowingly and intentionally as well. For six years, NPS has
claimed at every opportunity and in multiple forums, testimony, and reports that
oyster 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
11
15, 2008, based upon analysis of the NPS photographs, and advised that [a] fuller
examination of the photographs is necessary to form a conclusion with a reasonable level of
confidence. (Id., pgs. 26-27).
Thus, according to NPS, the USGS Report validated the MMC finding of a DBOC
disturbance on May 15, 2008. According to the NPS FEIS, there were now two
independent 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 NPS
disturbances. (FEIS, pg 377).
Thus, Dr. Stewarts finding as reflected in the USGS Report and as submitted directly
to NPS was critical to permit NPS to make this finding in the FEIS. Given the six-year
controversy concerning this exact topic, it would have been crucial for those preparing
the EIS to examine the Stewart Report to see if Dr. Stewart actually reported a finding of
a DBOC disturbance on May 15, 2008 (he did not). Moreover, even if the authors of the
FEIS 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 DBOC
disturbances of harbor seals, and the use of the USGS Report and Stewart Report to drive
the FEIS finding of a moderate adverse impact, the preponderance of evidence leads to
the 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 accurately
represent the Stewart Report? What happened between May 3, 2012, when the Stewart
Report was submitted to USGS, and November 2012, when both the NPS FEIS and USGS
Report were publicly released?
How did Dr. Lellis make these two mistakes to misrepresent the Stewart Report, thereby
providing NPS with the finding of disturbances they were seeking? Dr. Lellis provided
NPS with their so-called independent verification of DBOC disturbances, in the form of
two 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 potential
flushing events, sending them to Dr. Stewart, reviewing Dr. Stewarts findings, and
ultimately 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 had
high-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 Stewart
Report and USGS Report with Dr. Lellis. Was Dr. Lellis pressured in any way to
misrepresent the Stewart Report? Were changes made during the review of the draft
12
USGS Report? Were NPS or DOI employees involved in that review process? Why did
Dr. 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 the
sequential misrepresentations of the USGS Report in the NPS FEIS. She asked me to
send 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 had
additional information based upon several email exchanges, and seven pages of notes
from a lengthy telephone discussion, with USGS Dr. Lellis, the senior author on the
USGS Report. I offer those same emails and notes to the OSTP panel that investigates
this 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. Stewarts analysis in
Appendix 1, and then incorrectly concluded that there was an association of the
DBOC boat with the harbor seal disturbance on May 15, 2008. Finally, the NPS
FEIS misrepresented the USGS report and claimed that the USGS had attributed
the May 15, 2008 disturbance to the DBOC boat. Two layers of successive
misrepresentations led to the opposite conclusion by NPS as compared to harbor
seal expert Dr. Brent Stewart.
I appreciate your willingness to investigate this issue. As you can imagine, this is
a very important matter for the DBOC-NPS issue. But I also think this is a very
important matter for USGS, which has long been the most trusted scientific body
in 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. I
have extensive notes from my conversation with Dr. Lellis, and my many emails
back 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 contradictions
between 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 one
of 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 Report
misrepresentation of the Stewart Report. Are you in fact conducting an
investigation? When will you be interviewing me?
First you need to determine if the USGS Report in fact misrepresented the
Stewart 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 that the
USGS Report was incorrect, and the NPS further misrepresented your report.
It should not surprise you that once a federal scientific document is released into
13
the public domain, unless corrected or retracted, it can and will be used in
decision-making processes throughout the nation, and around the world. In this
case, I have already been notified that the NPS FEIS has been raised in cases
involving mariculture in two other states, and in two other countries.
After examining the videos of the NPS photographs prepared by USGS, Dr. Brent
Stewart 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 two
associations (a correlation), and the NPS FEIS further incorrectly listed that as a
finding of two attributions (cause and effect), thus allowing them to conclude a
moderate adverse impact of the oyster farm on the harbor seals. I ask you to please
correct the public documents and public record.
Please get it touch with me to schedule an interview. I look forward to talking
with 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 one
month since I alerted Dr. McNutt to this issue that the authors of the USGS
Report misrepresented the Stewart Report, and she agreed to investigate whether
this misrepresentation was done intentionally or knowingly, or was an honest
error.
When I spoke with USGS Director Dr. McNutt on December 16, she indicated
that there were two alternatives: either Dr. Stewart changed his conclusions after
filing his May 2012 Stewart Report with NPS and USGS, in which case there
should be a written record of that change, or alternatively someone
misrepresented his report in the USGS Report. Have you determined which
alternative is correct?
To date, Dr. Gundersen has not responded to my emails, has not confirmed if she is
conducting 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 of
the outcome. Based on the available information, such behavior is not consistent with
what OSTP intended for the White House Scientific Integrity Policy.
Towards the end of March 2013, I became aware that Interior had appointed Dr. Suzette
Kimball 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 previous
USGS 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 string
of 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 her
Scientific Integrity Officer at the time, Dr. Linda Gundersen, on Monday
December 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 heard
no reply.
I do not know when the SIO position changed from Dr. Gundersen to you, and if
14
you are aware of the allegations. Would you please respond to me and let me
whether 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 USGS
when confronted with serious allegations of misconduct is troubling, and appears
inconsistent with the President's Scientific Integrity Policy.
I request a phone call with you this next week to bring you up-to-speed on this
issue, and to discuss whatever action USGS is taking. I look forward to talking
with you.
Sincerely,
As of the submission of this complaint on May 13, 2013, Dr. Thornhill never responded
to my email.
In summary, the Stewart Report was submitted to NPS and USGS. Stewart found no
evidence of disturbance of harbor seals by DBOC boats. The USGS Report incorrectly
quoted 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 Stewart
Report 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 harbor
seals, 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 the
release of both the FEIS and the USGS Report. Was it intentional? OSTP needs to
investigate. The record is replete with NPS preoccupation with false claims of DBOC
disturbances of harbor seals. These misrepresentations need to be viewed in the context
of the six-year history of NPS false claims concerning so-called oyster farm disturbances
of harbor seals.
4. Allegation #3: USGS & NPS Used False Science to Brief the Secretary
When NPS released the Draft EIS in September 2011, they dismissed the 300,000 NPS
photographs from the secret cameras, and detailed NPS logs, in a single sentence:
Because the collection of these photos was not based on documented protocols
and procedures, the body of photographs does not meet the Departments
standards for a scientific product. As a result, the photographs have not been
relied upon in this EIS.
The DEIS did include, however, other data without documented protocols, such as aerial
photos, 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 NPS
and prior to current protocols for data collection. Nevertheless, the NPS dismissed the
300,000 photos and the detailed NPS logs that showed no DBOC disturbances of harbor
15
seals over a three and one half year period.

The NPS received complaints that they failed to include the analysis of the photographs
in the DEIS. As a result, instead of relying on the detailed NPS logs, NPS asked USGS to
analyze the photos for seal disturbances. We dont know when they asked. The first
record (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 a
significant impact on other findings in the FEIS, and on elected officials, the public, and
media. 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 moderate
impact.
The NPS cited a 2012 USGS Report that analyzed, at NPS request, over half of the
300,000 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). The
USGS Report analyzed around 165,000 photos from the 2008 harbor seal pupping
season. 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.
Report, and USGS misquoted the original harbor seal behavior experts findings (Dr.
Brent Stewart of Hubbs SeaWorld Research Institute). In so doing, both agencies
misrepresented the primary scientific analysis.
The USGS Report was authored by William Lellis, Carrie Blakeslee, Laurie Allen, Bruce
Molnia, Susan Price, Sky Bristol, and Brent Stewart (all from USGS except Dr. Stewart
who 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 on
government accountability, submitted a FOIA request to USGS. USGS provided a 91page 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 outside
harbor 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 very
high profile project that had very high priority because it was needed for NPS to
brief Secretary Salazar who needs to make a decision on Wilderness Status for the
park.
A key author of the USGS Report wrote that the analysis must be done quickly
because NPS needs to give their final report to Ken Salazar by March 30th. The USGS
analysis 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 emails
reveal that NPS was intimately involved and chomping at the bit, breathing down
my neck, and needed it done because theyve got deadlines for deciding on the
permit. NPS was constantly in the loop as USGS staff wrote of keeping the
department informed. The analysis of the photos was kept on the fast track because
it 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 and
USGS Report was released to the public, the following three people apparently were
briefed about the USGS findings: USGS Director Dr. Marcia McNutt, Assistant Secretary
16
Anne Castle (who oversees USGS and reports to the Secretary), and Assistant Secretary
Rachel Jacobson (who oversees NPS and reports to the Secretary).
The USGS analysis of the NPS photos, based upon Dr. Brent Stewarts analysis, was
apparently presented to two Assistant Secretaries (Castle and Jacobson) in early July to
help inform the Secretarys decision. These emails suggest that the Secretarys decision
was 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, he
found no evidence of disturbance of harbor seals by DBOC. We also know that when the
USGS Report was released to the public nearly seven months later in November, it
claimed 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 claimed
the USGS Report found two examples of causation of disturbances by DBOC boats.
What was presented to Director McNutt, Assistant Secretary Castle, and Assistant
Secretary Jacobson in late June and early July? If they were presented with a finding that
included anything other than no evidence of disturbance, then they were presented with
false science to help the Secretary make his decision concerning the DBOC permit.
Brief timeline of key statements in USGS emails [bold emphasis added]:
(1)
(2)
(3)
(4)
(5)
(6)
(7)
(8)
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 for
the park.
d. This is a high profile project. Very high profile
March 5, 2012: Carrie Blakeslee to Sally Holl (USGS): The analysis must be
done quickly because NPS needs to give their final report to Ken Salazar by March
30th.
April 20, 2012: Laurie Allen to Brent Stewart (Hubbs-SeaWorld Research Inst.):
NPS is chomping at the bit (Theyve got deadlines for deciding on the permit,)
May 1, 2012: Laurie Allen to Brent Stewart: NPS will be breathing down my
neck this week, when do you think youll be able to transmit something?
May 15, 2012: Laurie Allen to Carrie Blakeslee: We need to keep this on the fast
track,
June 18, 2012: Laurie Allen to Carrie Blakeslee: NPS knows about these
developments and we are keeping the department informed.
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, Anne
Castle.
June 26, 2012: Hannah Hamilton (USGS Liaison to Water and Science) to Bill Lellis
and 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 accommodate
Rachel Jacobsons schedule. [Jacobson was Acting Assistant Secretary of Interior for
17
(9)
Fish and Wildlife and Parks]

December 3, 2012: Bill Lellis to Carrie Blakeslee: With Salazars 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 and
quotations from USGS FOIA response.05_13_13.pdf
Summary
The USGS and NPS, in their claims that the USGS analysis of the NPS photographs was
very high profile and very high priority, and needed to inform Secretary Salazar for his
decision on the oyster farm permit, apparently briefed Assistant Secretaries Castle and
Jacobson with false claims of evidence of oyster farm disturbances of seals in Drakes
Estero. 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. Stewarts findings concerning May 15 and June 11,
2008,
(iv) This false science was apparently presented to two Assistant Secretaries (Castle
and Jacobson) to inform the Secretarys decision concerning the oyster farm
permit,
(v)
If they presented what is in the USGS Report, then Interior employees committed
scientific misconduct,
(vi) If they presented what is in the USGS Report, then the Secretarys decision was
informed by false science, and
(vii) The Department of Justice lawyers have misinformed the Federal Court with
incorrect claims of adverse impacts in the NPS FEIS based upon false science.
5. Allegation #4: Dr. Stewart Re-Reviewed Key Data, Confirmed Initial

Findings of No Evidence of Disturbance, & USGS Covered Up His Report
4. USGS, after their Report was released, requested a subsequent re-review of key
Dr. Lellis and I exchanged emails from December 3 to 13, 2012, and talked by telephone
for 90 minutes on December 7. Although I repeatedly asked him about Dr. Stewarts
Report, and asked him for a copy of Dr. Stewarts Report (which he never provided to
me), Dr. Lellis never mentioned during that extended email and telephone exchange that
on December 5, either he or his colleague Dr. Blakeslee went back to Dr. Stewart and
asked him to re-review the May 15 and June 11, 2008 NPS photographs, and that Dr.
18
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) what
he had filed in his original report in May 2012, namely that there was no evidence for
disturbance 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 USGS
Report), 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 the
harbor seal behavior expert on the project.
On December 4, Dr. Lellis responded that Brent [Dr. Brent Stewart] was the harbor seal
behaviorist on this project.
On December 5, I responded to Dr. Lellis and asked him for a copy of Dr. Stewarts
report. Later that same day, Dr. Lellis responded, failed to provide Dr. Stewarts report,
and instead wrote: Yes, essentially that is Appendix 1 of the report (i.e., Dr. Stewarts
Report is Appendix 1 of the USGS Report). Over the next day, we arranged to speak by
telephone on December 7, 2012, at noon PT (3 pm ET).
According to Dr. Stewart, on December 5, he was contacted by telephone and email by
the USGS scientists, asking him to re-review the videos of the photographs from May 15
and June 11, 2008. He submitted his report (BSS Suppl review.pdf) to Carrie Blakeslee
on December 10. Neither his Supplemental Report, nor any of the request or submittal
emails, 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. My
detailed 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 and
methodology for the USGS analysis. He never mentioned just how high profile was his
project, and how he briefed two Assistant Secretaries of their findings. He claimed that
he 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 from
the USGS emails provided in response to FOIA that Dr. Blakeslee read the previous
reports and was very familiar with the issues.
I pointed out to Dr. Lellis the following contradiction. In the text of the USGS Report, he
concluded a harbor seal disturbance took place on June 11, 2008 and that the presence of
the oyster boat correlated with this disturbance. Yet in Appendix 1, which he told me
represented Dr. Stewarts report, it said no obvious disturbance took place. After a
period of silence, Dr. Lellis answered:
There is a contradiction right there.
That would be a contradiction.
That is an obvious contradiction.
That didnt get caught in the review.
Only incident of seals flushing towards the water 3 minutes prior to the boat
arriving. No cause and effect.
I next asked him about the May 15, 2008 photographs. I asked him whether Dr. Stewart
did 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 the
previous hour. He said Dr. Stewarts report was not the final word, that there was some
19
back and forth. This was quite different from what he told me at the beginning of the
conversation. This change in his answer was triggered by my asking him about May 15,
2008. I asked him for a copy of Brents spreadsheet. He told me it was nearly identical
to 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 and
possibly 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 most
similar to responses of small number of neighboring seals to sudden movements of
recently hauled out seals (especially juveniles) that are settling at haulout but
energetic and active. I did not consider this to be a flush in response to some other
kind 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 dont consider this to be a flush but
rather 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 dont consider this to
be a flush. In other words, no disturbance took place. Dr. Stewarts more detailed
analysis in his Supplemental Report confirmed what he wrote in his original report in
May 2012, namely, that the May 15 and June 11, 2008 photographs provided no evidence
of harbor seal disturbances by the oyster boats.
On December 11, 2012, I emailed Dr. Lellis and once again requested a copy of Dr.
Stewarts 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 disturbance
and 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 for
a copy of Dr. Stewarts Report, and his thoughts about the analysis of the June 11, 2008
photographs.
Dr. Lellis responded on December 13. He did not send me a copy of Dr. Stewarts
Report. He also did not disclose Dr. Stewarts new Supplemental Report on the May 15
and June 11, 2008 photographs. Rather, Dr. Lellis wrote:
I'm really locked down right now between a Research Grade Evaluation Panel
and budgetary preparations and contingency planning for multiple federal
appropriations 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 a
very different angle than the one you were asking me about and it took me some
time to understand that. In fact, I'm still not sure I understand it. We were
looking 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 that
tree. I'm not sure if we completely missed the question we were being asked to
address, or if somehow the conversation took a completely different direction after
we became involved, but there really is a big disconnect in what we attempted to
address in the report and what you were attempting to extract.
20
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. Stewarts report or
spreadsheet. He never commented on June 11, 2008. He never commented on
May 15, 2008. He never told me about Dr. Stewarts Supplemental Report on
December 10, 2012. Three days later, on Sunday December 16, I spoke at length
with then-USGS Director Dr. Marcia McNutt about this issue.
Summary
The USGS scientists (either Dr. Lellis, Dr. Blakeslee, or both), after their Report was
released, requested a subsequent re-review of key data by Dr. Stewart in his Supplemental
Report that confirmed his earlier finding of no evidence of disturbance, a report that should
have 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 profile
decision. It appears as if none of this occurred. The USGS covered-up Dr. Stewarts
Supplemental Report. This was scientific misconduct.
I conclude the following:
(i)
Beginning on December 3, 2012, I contacted Dr. Lellis and asked questions about
the USGS Report finding of disturbances on May 15 and June 11, 2008, noted the
contradiction between the text of the USGS Report and Appendix 1 concerning
the June 11 analysis, asked what Dr. Stewart found, and asked for a copy of Dr.
Stewarts Report.
(ii)
Even though I asked for a copy repeatedly, Dr. Lellis never provided me with a
copy of Dr. Stewarts Report.
(iii) In our telephone conversation of December 7, Dr. Lellis agreed that there was a
contradiction in the June 11 finding in the text of his USGS Report and the
finding of no obvious disturbance in Appendix 1.
(iv) On December 5, 2012, either Dr. Lellis or Dr. Blakeslee requested that Dr. Stewart
re-review the May 15 and June 11 data. Dr. Stewart submitted his Supplemental
Report on December 10, 2012. Neither those emails nor the report were
provided in the USGS response to a FOIA request, suggesting the possibility
that this communication might have taken place by private email addresses.
(v)
I only obtained a copy of Dr. Stewarts Supplemental Report because a staffer for
Congressman Jared Huffman, Dr. Owens, requested all of Dr. Stewarts
documents 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. His
Supplemental confirmed his earlier finding of no evidence of disturbance.
(vii) USGS suppressed Dr. Stewarts Supplemental Report and finding of no
disturbances, thus covering up their earlier misrepresentation of Dr. Stewarts
initial analysis. This is further confirmation of serial scientific misconduct
involving the USGS misrepresentation of Dr. Stewarts analysis, and the NPS
FEIS misrepresentation of the USGS Report.
21
Appendix 2:
Why the DOI OIG and SIOs Cannot Resolve These Allegations of
Scientific Misconduct
Table of Contents
1. The DOI OIG Abdicated Its Oversight ............................................................................... 1-9
a. DOI OIG: example #1 .................................................................................................................. 1-3
b. DOI OIG: example #2 .................................................................................................................. 3-4
c. DOI OIG: example #3 .................................................................................................................. 4-8
d. DOI OIG: Internal Survey Reported They Pull Their Punches ............................................ 8-9
e. DOI OIG: House Committee on Natural Resources Investigative Report Confirms That
They 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
1. The DOI OIG abdicated its oversight.

The Department of the Interior (DOI) OIG handles investigatory oversight of NPS and
USGS. 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. His
track 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 replied
to the Secretary on May 17, responding to only seven of the 21 points, leaving 14 points
completely unanswered. As I wrote to Dr. Holdren on May 19, 2009, of the limited
responses Jarvis provided, some were straw man arguments (i.e., the answers were
irrelevant to the charges), a few were misleading, and at least one contradicted formal
testimony he gave to the DOI OIG for its July 2008 report.
The allegations of scientific misconduct against Jon Jarvis were never properly
investigated, and Mr. Jarvis began his service as NPS Director in September 2009. The
case 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 both
the Interior Solicitors Office, and the OIG that Congress intended to be Interiors
watchdog, 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 a
misleading memo to the Secretary of the Interior and the Senate Committee on Energy
and Natural Resources suggesting that they had investigated all of the allegations of
misconduct, 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 found
no evidence to support the allegation." He apparently did not know that the OIG did not
investigate 95% of the allegations and thus misled the Senate.
The DOI OIG investigated only one of the 21-points of scientific misconduct in the May
16, 2009 complaint filed with Secretary Salazar. As described above, Mr. Jarvis did not
answer most of those 21 points when given the opportunity. However, Mr. Jarvis did
provide an answer to a single issue his involvement (or asserted lack thereof) with the
different versions of the NPS Drakes Estero Report. Mr. Jarvis answered that one charge
with plausible deniability. Even though he was placed in charge on all science matters
concerning Drakes Estero, he claimed that he did not write the July 2007 version of the
discredited NPS Report. It was that single issue (and only that issue of the 21) that the
DOI OIG investigated and dismissed.
Why didnt the DOI OIG investigate the other unanswered points? Why did the DOI
OIG ignore Jarvis answer to one point (in his May 17 letter to the Secretary) in which he
contradicted his previous interview under oath to the DOI OIG? The OIG failed to
inform 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, Superintendent
Don Neubacher.
On August 24, 2009, I discussed the DOI OIG finding with Assistant Inspector General
2
John Dupuy by telephone. He acknowledged quite candidly that regarding my entire

complaint, the OIG only investigated one narrow procedural issue, and that the OIG
never examined the detailed list of scientific misconduct allegations.
When asked about the bulk of the misconduct claims against Mr. Jarvis, Mr. Dupuy
reaffirmed that the OIG doesnt have scientists and doesnt investigate scientific
misconduct 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 federal
government, Mr. Dupuy answered that it was not NPS, not DOI, not the DOI OIG, not
NAS, and not MMC. Mr. Dupuy was unable to identify who would adjudicate
allegations of scientific misconduct, especially concerning a high ranking official (in this
case, 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 two
Senators this misrepresentation of the DOI OIGs actions in July 2009 concerning the
allegations against Director Jarvis. Rachel Jacobson, Acting Assistant Secretary for Fish
and Wildlife and Parks, in responding on behalf of the Secretary to a February 13, 2012
letter from Senators David Vitter and James Inhofe, wrote on May 30, 2012:
The Department has taken very seriously the allegation of scientific misconduct
and 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, 2009
letter to Dr. Holdren as well as in several other related submissions to the
Department by Dr. Goodman. the Senate was fully aware of the allegations
made by Dr. Goodman against Director Jarvis during his pendency of his
nomination and those allegations were addressed formally in the records of his
confirmation hearing.
Ms. Jacobson failed to answer Senator Vitters and Senator Inhofes questions in their
February 13, 2012 letter as to whether the Senator Committee had all three of my letters
from 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 precise
wording was allegation. Ms. Jacobson failed to tell the two Senators that of the 21
points outlined in the May 16, 2009 letters to both the Secretary and you, then-Regional
Director 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 previously
answered.
The Senate was misinformed on July 28, 2009, and Senators Vitter and Inhofe were
misinformed on May 30, 2012. The DOI OIG never considered 20 of the 21 allegations
against Jon Jarvis, including none of the 14 he did not answer on May 17. Ms. Jacobson
wrote 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 went
on in July 2009, what the Senate Committee was told, what the two Senators asked in
2012, 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
3
NPS failed to publicly disclose their secret camera program, 300,000 photos, and detailed
logs (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 the
allegations, and that they would subsequently evaluate their response to determine whether
or not appropriate action was taken or further involvement by our office appears warranted.
NPS, in consultation with the Secretarys office, directed the DOI Solicitors Office to
conduct the investigation. Field Solicitor Gavin Frost, an attorney in the Billings, MT
Solicitors office, was directed to conduct the investigation.
While the OIG did not investigate the allegations against Mr. Jarvis in 2009, his direct
reports 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 (both
of 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 Scientific
and Scholarly Conduct.
Many aspects of the Frost Report were inadequate. For example, in 2008, the National
Academy of Sciences (NAS) requested all NPS harbor seal data concerning the oyster
farm and Drakes Estero. On May 5, 2009, the NAS released its report, which stated that
the 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 just
such secret photographic data, and yet failed to disclose them to the NAS. Mr. Frost
found no misconduct in this failure to disclose these key data, data that contradicted the
public claims NPS made to the NAS.
Although the DOI OIG told me on October 7, 2011 (when I met with them in their office
in Washington, D.C.) they agreed and found the Frost Report inadequate, two years
later, in spite of repeated requests for further involvement (letters from me to John
Dupuy, Assistant Inspector General for Investigations, DOI OIG, on September 14, 2011
and March 19, 2012), no additional action has been taken by the OIG, and according to
the 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 Draft
Environmental 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, 20
horsepower (HP) oyster skiffs on Drakes Estero in 2011, when in fact the data came from
a loud, fast Kawasaki Jet Ski (2-stroke, 750 cc, 70 HP) recorded for the New Jersey State
Police in 1995. The DEIS also misrepresent noise data from the plastic oyster tumbler
with the HP, 12-volt, electric motor, when in fact the data came from a 400 HP cement
mixer truck recorded elsewhere.
The DOI OIG said they would finish and publicly release the results of their
investigation and report by early fall 2012, before NPS released the Final EIS (FEIS) and
4
prior to the Secretarys decision.

After the NPS FEIS was released on November 20, 2012, and in response to inquiries as
to the outcome of their investigation, the DOI OIG said the report was completed, being
held internally, wouldnt be released any time soon, and would not be made public
unless 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, who
wrote to Secretary Salazar on March 29, 2012 that:
The Park Services latest falsification of science at Point Reyes National Seashore
is the straw that breaks the camels back.
Concerning my still-outstanding April 24, 2012 complaint, based upon the same
falsification of science cited in Senator Feinsteins letter, Senator Vitter wrote:
It is frustrating that the Office of the IG seems incapable of acting independently
or able to provide clear determinations on violations of the Data Quality Act, as
well 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 have
some very significant concerns that your office may have gone out of its way to
protect Interior employees for which you were supposed to be independently
investigating.
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 the
investigators.
can the investigation truly be considered independent?
On January 16, 2013, Deputy Inspector General Mary Kendall responded to Senator
Vitter. Two points from that response are pertinent here.
First, she wrote concerning the length of time required for a proper DOI OIG
investigation:
The process can be extremely lengthy, but it ensures that OIG reports are wellwritten, understandable, and factually accurate. Therefore, while the
investigation 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 on
February 7, 2013 (see appendices 3 and 4).
For example, the IG report erred in misrepresenting the most important conclusion from
the 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 having
major impacts on the Seashore using thresholds ranging from negligible, minor,
moderate, to major; the two areas assessed as major were soundscape and
socioeconomic. [bold emphasis added]
As shown in Table ES-4 in the executive summary of the DEIS, the two areas assessed as
having major adverse impacts were soundscape and wilderness, not socioeconomic.
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 which
DBOC 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 Noise
Unlimited 1995 report to misrepresent the DBOC oyster skiff. . The IG report stated:
VHBs acoustics representative and director of Air Quality and Noise Services
spoke with us regarding the sound-level data used in the DEIS. He informed us
that he possessed more than 40 years of sound and acoustics experience and that
he was the project technical advisor for the DEIS and reviewed its soundscape
sections for accuracy. He stated that during his research for this project, he
personally located the NU 1995 report on the Internet and subsequently
selected the watercraft measurements from the NU report to represent Company
boats, which was based on information collected by VHB staff members during
Company site tours. [Bold emphasis added]
In my May 2012 interview, I told the IG that the Noise Unlimited 1995 report was not
available on the Internet. Given the claim by the VHB acoustics representative about the
Internet being the source of the Noise Unlimited report, it would seem that the IG would
have at least done its own confirmatory web search and published the web link for the
report. However, there is no such information provided in the IG report. I searched
again, and conclude that there is no website accessible to a public search that contains
the Noise Unlimited report. In fact, I first found the report by asking an assistant to seek
the 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 a
citation to the report (but not the report itself) on the Internet, and as a result, the
assistant 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 not
carefully 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 had
copies of the draft IG report, they also did not properly review the IG report for
accuracy, because all of them missed these errors. This contradicts the letter from
Deputy Inspector General Kendall to Senator Vitter in which she claimed that the long
delay in issuing the IG report was to ensure accuracy, and to make sure the IG report is
well written. I encourage you to read the IG report and judge for yourself whether it is
clear 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 to
coordinate with the DOI or bureau Scientific Integrity Officer. Because the OIG
does not have scientific expertise, the scientific aspect of alleged scientific
misconduct is addressed by the Scientific Integrity Officer, not the OIG.
This statement concerning the collaboration of the Scientific Integrity Officers (SIOs) and
the OIG to Senator Vitter stands in marked contrast to what actually occurred in
response to my April 24, 2012 complaint filed with the DOI OIG. In my complaint, I
alleged (and provided details) that the NPS and DOI SIOs had conflicts of interest. I
submitted eleven questions to be asked of Drs. Machlis and Morgenweck to determine
6
whether or not they were conflicted, and whether they should participate in the
investigation. In the final IG report on February 7, 2013, the DOI neither provided
answers to those questions, nor indicated whether the SIOs participated in the
investigation. This is in contrast to Kendalls letter to Vitter suggesting that the SIOs did
play 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 willing
to allow the DOI Scientific Integrity Officer (SIO) Dr. Ralph Morgenweck and NPS SIO
Dr. Gary Machlis to collaborate with the OIG concerning investigating the allegations of
NPS scientific misconduct. I answered yes so long as they would show the OIG and
me their independence (i.e., that they were behaving as SIOs independent of the NPS
Director and DOI Secretary to whom they reported) by their willingness to spend time
interviewing 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 on
the same page regarding DOI's Science Integrity Officers and to ensure I pass
along 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 and
how their willingness to meet and discuss the issues with, could prove to you
their 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 their
approachability 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) openly
discuss 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). Perhaps
one 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 I
made this proposal to you. In fact, I have heard nothing from NPS concerning the
scientific misconduct allegations. I also have not heard from NPS about the
requested 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 that
day. In our phone call, he was vague and avoided directly telling me why neither the
DOI SIO nor the NPS SIO was willing to meet with me to discuss the scientific data and
allegations.
Although Mr. Haecker and I communicated by email and phone many times over the
summer 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
7
up the issue a month or so later in one of our phone calls, and he deflected the question
and blamed the lack of follow-up on him and not them.
Not only are these communications in contrast to what Ms. Kendall wrote to Senator
Vitter, but they also show the refusal of the DOI SIO or the NPS SIO to meet with me in
an investigation of scientific misconduct that involves this issue so intimately tied to
NPS Director Jarvis. Ill return to this issue below of the inability of the various SIOs to
investigate these allegations, in spite of Interior Scientific Integrity Policy.
The DOI OIG responded to my misconduct complaint on February 7, 2013. The IG
dismissed all allegations of misconduct concerning the soundscape data (see appendix
3). The IG inexplicably accepted the NPS use of a Kawasaki 2-stroke, 750 cc, 70
horsepower (HP) Jet Ski to misrepresent the 4-stroke (quieter), 360 cc (smaller), 20 HP
(less powerful), oyster skiff; and a 400 HP cement mixing truck to misrepresent the
plastic oyster tumbler with a HP, 12-volt (much quieter, smaller, less powerful) electric
motor.
The IG went to great lengths to dismiss the allegations, altering and ignoring some
allegations, creating straw-man arguments, cherry-picking law and policy, and accepting
explanations and testimony despite evidence to the contrary evidence in the form of
documents and emails. In so doing, the DOI OIG confirmed what the House Committee
on Natural Resources (Office of Oversight and Investigation, in its 75-page report:
Holding Interior Watchdog Accountable) recently concluded about the OIG, namely,
that it lacks independence and is too accommodating to Interiors top leadership (see
below).
In summary, given that the MMC has no OIG, and NPS and USGS have an OIG that
appears to have abdicated its timely and responsive investigatory oversight for such
matters, the only path forward for upholding the White House Scientific Integrity
Policy is to bring this matter to the White House Office of Science and Technology
Policy.
d. DOI OIG: internal survey reported they pull their punches.

On September 19, 2012, DOI OIG Deputy Inspector General Mary Kendall circulated the
DOI OIG 2012 employee survey to OIG staff. On October 9, 2012, Jeff Ruch, Executive
Director, Public Employees for Environmental Responsibility (PEER), released a
statement entitled:
Rising Doubts on Independence of Interior Inspector General
Staff Survey Shows Only 60% Believe IG Operates "Free from Improper Influence"
PEER wrote:
A sizeable and growing segment of the investigators and supervisors within the
Interior's Department's Office of Inspector General (IG) believes the office is
pulling punches to avoid embarrassing the administration, according to new staff
survey results posted today by Public Employees for Environmental
Responsibility (PEER). These concerns echo criticisms by Congress and PEER
that under acting Inspector General Mary Kendall the Interior IG has
compromised its "independence and honesty" to please political superiors, in the
words of one agent.
The 2012 survey was completed by 82% of DOI IG staff. In response to the question of
8
whether the IG "conducts its work in a manner that is independent (free from improper
influence) from the Department [of Interior]," nearly one in seven said no, more than a
quarter would not say either way, and fewer than 60% said yes. Several staff
commented:
"I think there is widespread distrust and low morale in the organization right
now. 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' the
Department 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 profound
corruption."
The case for scientific misconduct at NPS (having now spread to MMC and USGS as
well) is one of profound corruption, with involvement at the highest levels, and thus
unlikely, in the words of PEER Executive Director Jeff Ruch, to get an appropriate
investigation by the DOI OIG. In this case, the DOI OIG has shown its inability over and
over again to conduct truly independent investigations.
e. DOI OIG: House Committee on Natural Resources investigative report

confirms 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, Office
of Oversight and Investigations, released an investigative report entitled Holding
Interior Watchdog Accountable. The House Committee found that the DOI OIG pulled
its punches and accommodated DOI leadership rather than investigate serious charges
of misconduct. The details described in the 75-page report are troubling and a reveal a
lack of independence of the DOI OIG, IG reports getting softened, and findings
whitewashed, so as not to find misconduct.
As cited in the House report, DOI special agent Richard Larrabee commented in writing
that he was deeply concerned that the Secretarys Office receives great deference,
suggesting it uses its influence to persuade OIG employees to stand in line with the
Departments politics.
If the DOI OIG cannot function as an independent watchdog, then it is even less likely
that the internal Scientific Integrity Officers can function in an independent fashion, as
described below.
2. The NPS Scientific Integrity Officer is Conflicted.

As I wrote to DOI Inspector General Kendall on April 24, 2012, Dr. Machlis, NPS
Scientific Integrity Officer is conflicted. First, Dr. Machlis, NPS Scientific Integrity
Officer and Science Advisor, reports to NPS Director Jarvis, the person at the center of
9
this dispute for six years and for whom unresolved charges of scientific misconduct predate his appointment as Director. Second, Dr. Machlis demonstrated his conflicts by his
actions and words.
The Department of Transportation VOLPE 2011 Report (cited in the FEIS) is a public
document. 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 NPS
scientists were cooperative and collegial, responding to my emails, supplying me with
some of the requested data, and providing guidance on clarification of methods.
Beginning on April 13, 2012, they abruptly stopped responding to my emails and
stopped supplying the requested data. On April 16, I wrote to Dr. Machlis and asked
him to help facilitate my data request. He did not respond. I asked him again on April
18. 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, there
exists 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 neither
interviewed nor asked to clarify a single substantive issue. Dr. Machlis failed to respond
to 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, not
the 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, and
their supervisor told me I must file a FOIA request to obtain the relevant data, data I
requested 18 days earlier. All of this hindered and restricted my scientific analysis and
violated 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 hindered
my 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 an
investigation of NPS scientific misconduct.
3. The DOI Scientific Integrity Officer is Conflicted.

Dr. Morgenweck, Interiors Scientific Integrity Officer (from 2011 to the first half of
2012), also had a conflict of interest. Dr. Morgenweck commissioned the ATKINS peerreview of the NPS DEIS in recognition of high interest in the science. Dr. Morgenweck
then released the ATKINS peer-review of the DEIS on March 19, 2012. In the DOI Office
of the Secretary news release, he was quoted as follows:
The peer-review accomplished exactly what we were seeking that is, specific
recommendations on how to improve the final environmental impact statement to
make it a better science product, stated Dr. Ralph Morgenweck, Interiors
Scientific Integrity Officer.
10
We now know that the ATKINS Report was tainted by the NPS decision to include false
representations of soundscape data in the DEIS. The peer-reviewer of the soundscape
analysis, 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 Drakes
Estero 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 accompanying
the public release of the ATKINS peer review, Interior included their SIO as part of the
EIS process, rather than as someone who could independently evaluate allegations of
scientific misconduct.
From the outset of the DOI OIG investigation into the allegations of misconduct against
NPS in May 2012, I was told that both Dr. Machlis and Dr. Morgenweck were going to
come out to California to interview me at length to discuss the data and allegations of
misconduct. 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 participate
in 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 substantive
information about my allegations of scientific misconduct.
In summary, neither NPS nor DOI are capable of investigating their own organizations
when 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 Been

Unresponsive.
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 sequential
misrepresentations of the USGS Report in the NPS FEIS. She was familiar with the 2012
USGS Report concerning the NPS photographs at Drakes Estero.
I described to Dr. McNutt the Stewart Report, and Dr. Stewarts finding of no evidence of
disturbance by the oyster farm for the exact dates and times in which the USGS Report
claimed that Dr. Stewart found an association, or weak correlation, and the NPS FEIS
subsequently 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. Linda
Gundersen, 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. Stewarts analysis in
Appendix 1, and then incorrectly concluded that there was an association of the
DBOC boat with the harbor seal disturbance on May 15, 2008. Finally, the NPS
FEIS misrepresented the USGS report and claimed that the USGS had attributed
the May 15, 2008 disturbance to the DBOC boat. Two layers of successive
misrepresentations led to the opposite conclusion by NPS as compared to harbor
seal expert Dr. Brent Stewart.
I appreciate your willingness to investigate this issue. As you can imagine, this is
a very important matter for the DBOC-NPS issue. But I also think this is a very
11
important matter for USGS, which has long been the most trusted scientific body
in 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. I
have extensive notes from my conversation with Dr. Lellis, and my many emails
back 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 contradictions
between 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 one
of them. It is now one month since I first notified USGS that the USGS Report
misrepresented the Stewart Report, and I have not been contacted by the Scientific
Integrity Officer, and have not been interviewed about my lengthy conversation and
email exchanges with the senior author of the USGS Report.
The USGS has yet to acknowledge my complaint and have not indicated that an
investigation was initiated I have not been contacted. I have not been interviewed.
Given the lack of communication and transparency concerning the potential
investigation of the USGS Report by the USGS Scientific Integrity Officer, and the
connection with the NPS FEIS, this further disqualifies anyone at DOI from managing
this investigation of the misrepresentation and falsification in the USGS Report, and the
sequential misrepresentation and falsification in the NPS FEIS. Both misrepresentations
concern the original finding of no evidence of disturbance by Dr. Stewart in the Hubbs
SeaWorld Stewart Report. Dr. Stewarts 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. Stewarts 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 Report
misrepresentation of the Stewart Report. Are you in fact conducting an
investigation? When will you be interviewing me?
First you need to determine if the USGS Report in fact misrepresented the
Stewart 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 that
the USGS Report was incorrect, and the NPS further misrepresented your
report.
It should not surprise you that once a federal scientific document is released into
the public domain, unless corrected or retracted, it can and will be used in
decision-making processes throughout the nation, and around the world. In this
case, I have already been notified that the NPS FEIS has been raised in cases
involving mariculture in two other states, and in two other countries.
After examining the videos of the NPS photographs prepared by USGS, Dr. Brent
12
Stewart 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 two
associations (a correlation), and the NPS FEIS further incorrectly listed that as a
finding of two attributions (cause and effect), thus allowing them to conclude a
moderate adverse impact of the oyster farm on the harbor seals. I ask you to please
correct 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 one
month since I alerted Dr. McNutt to this issue that the authors of the USGS
Report misrepresented the Stewart Report, and she agreed to investigate whether
this misrepresentation was done intentionally or knowingly, or was an honest
error.
I am puzzled by your silence over the past month. When do you plan on
interviewing me?
When I spoke with USGS Director Dr. McNutt on December 16, she indicated
that there were two alternatives: either Dr. Stewart changed his conclusions after
filing his May 2012 Stewart Report with NPS and USGS, in which case there
should be a written record of that change, or alternatively someone
misrepresented his report in the USGS Report. Have you determined which
alternative is correct?
To date, Dr. Gundersen has not responded to my emails, has not confirmed if she is or is
not conducting an investigation, has not interviewed me, has not sought additional
information from me, and if she has conducted an investigation, has not informed me of
the outcome. Surely, such behavior is not consistent with what OSTP intended for the
White House Scientific Integrity Policy.
Towards the end of March 2013, I became aware that Interior had appointed Dr. Suzette
Kimball 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 previous
USGS 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 string
of 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 her
Scientific Integrity Officer at the time, Dr. Linda Gundersen, on Monday
December 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 heard
no 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 me
whether 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 USGS
when confronted with serious allegations of misconduct is troubling, and appears
inconsistent with the President's Scientific Integrity Policy.
13
I request a phone call with you this next week to bring you up-to-speed on this
issue, and to discuss whatever action USGS is taking. I look forward to talking
with you.
Sincerely,
As of the submission of this complaint on May 13, 2013, Dr. Thornhill never responded
to my email.
14

CSG's Scientific Misconduct Complaint Sent To Jewell 5.13.13

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CSG's Scientific Misconduct Complaint Sent To Jewell 5.13.13

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May 13, 2013

From: Dr. Corey S. Goodman

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

2. Overview of Allegations of Scientific Misconduct

and misrepresented Dr. Stewarts findings. Moreover, USGS received a Supplemental

3. Interior Scientific Integrity Officers and Interior Inspector General Are

4. Request That DOI Establish a Blue-Ribbon Panel of Eminent Scientists

Corey S. Goodman, Ph.D.

1. Summary of Allegations of Scientific Misconduct

The evidence for serial misrepresentations of disturbances in the Stewart, USGS,

The cover-up of the subsequent Supplemental Report by Dr. Stewart (requested

2. Documents and Communications Supporting These Allegations

USGS emails obtained in response to a FOIA request (2013.5.7 Batch #1.pdf)

To my knowledge, the existence of this Supplemental Report (enclosed here as a

disturbance events from the 2008 NPS photographs.

No Evidence of Disturbance: Hubbs-SeaWorld Report Found No Evidence of Harbor

seals over a three and one half year period.

Fish and Wildlife and Parks]

5. Allegation #4: Dr. Stewart Re-Reviewed Key Data, Confirmed Initial

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

1. The DOI OIG abdicated its oversight.

a. DOI OIG: example #1.

John Dupuy by telephone. He acknowledged quite candidly that regarding my entire

b. DOI OIG: example #2.

c. DOI OIG: example #3.

prior to the Secretarys decision.

d. DOI OIG: internal survey reported they pull their punches.

e. DOI OIG: House Committee on Natural Resources investigative report

2. The NPS Scientific Integrity Officer is Conflicted.

3. The DOI Scientific Integrity Officer is Conflicted.

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

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