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Dennis Lynch is the lead federal scientist overseeing the science and engineering process for the Secretary of the Interior on Klamath River dam removal. Dr Paul R. Houser was the top scientist in the Bureau of Reclamation and hired as a science integrity officer. When he confronted Department of Interior on lack of integrity in the Klamath Dam Removal agenda and presentation of science, he was fired. Rather than discussing the issues with Houser, Lynch decided to devalue Houser in the media. First is Houser's response, followed by Lynch's opinion piece which ran in Redding Searchlight, Siskiyou Daily News and Capital Press.

Dr. Paul R. Houser

Klamath Science-Informed Decision Making Process Needs Improvement

In April 2011, I was hired as the Bureau of Reclamation‘s science adviser and scientific integrity officer.  After I questioned the accuracy of science reporting and summary documents related to the Klamath River Dam Removal Secretarial Decision in September 2011, I faced systematic reprisal and my job was terminated on February 24, 2012.   On that day, I filed a scientific integrity allegation in accordance with the Department of the Interior’s Scientific Integrity Policy, and a whistle-blower protection claim with the Department of the Interior Inspector General’s Office and the Office of Special Council.

I did a great deal of soul-searching and consultation before filing the allegation.  Making the allegation has significant implications for my career and family, and I wanted to make sure I was not pursuing it for selfish or political reasons.  I decided to file the allegation for three reasons: (1) my obligation to scientific integrity as a scientist, (2) for the benefit of my replacement, so that they can uphold the public trust by providing honest scientific advisement without fear of losing their job, and (3) so that the Secretarial Decision is well informed.  I attest that I have no fiduciary ties or conflicts associated with the Klamath River Secretarial decision process. I do not have any financial relationships with Klamath River associated industry, employment, consultancies, stock ownership, honoraria, expert testimony, either directly or through immediate family. I am not an author of any reports or the recipient of any research support associated with the Klamath River. I do have personal impact (loss of job), but have nothing to directly gain from the potential result of the allegation.  Since my allegation went public through a third party, my philosophy has been to accept all interview and speaking requests, and I have been adamant about not accepting payment for them.  I am also not for or against dam removal, but rather I am an advocate for the best science-informed decision that meets the multi-objectives of obeying the law, protecting the environment and advancing society.

In early May 2012 I was invited to speak publically about my allegation and to address the Siskiyou County Board of Supervisors.  The emphasis of these talks was the details of my scientific integrity allegation.  In virtually every venue, I was confronted with a very wide range of questions, many of which I declined to answer because I did not have topical knowledge.  However, if I had an opinion or information, I offered it with that caveat.

Starting on 11 June 2012, Mr. Dennis Lynch (USGS) offered some perspective on my answers in a number of OpEd articles, for example: “Klamath science process is solid”. I note that Mr. Lynch did not refute the points of my scientific integrity allegation, but rather focused on unrelated information or opinions I conveyed during the question and answer sessions. As an aside, it is very discouraging to be personally attacked on these details after mustering the courage to take a stand for scientific integrity and for the public-trust.  In taking the mandatory No-Fear Act training last year, I could never have imagined that in short order a senior government official would be actively and publicly attacking me in the press.   On 11 June I invited Mr. Lynch to discuss my concerns and rebuttal below.

The remainder of this discourse is in response to some of the concerns Mr. Lynch raises in his article:

1)      Mr. Lynch states that the KHSA calls for the Secretary of the Interior to make a science based decision on dam removal, and that is why Dennis’s team is developing new scientific information.  In fact, it is well documented that the Secretary has already decided to remove the dams, so Dennis’s team is therefore developing science that must support dam removal.  This assertion is obvious from the tone of Dennis’s opinion post, as well as a recent editorial from BOR Commissioner Connor and press release from Secretary Salazar that strongly supports the Klamath agreements and is making efforts to make them a reality.  Also note that new government-sanctioned science information is not the only valid source of scientific information, and for systems as complex as the Klamath, the available scientific information is often contradictory and uncertain.  Science does not always result in black and white answers, and disagreements are common in the scientific community.

 2)      Mr. Lynch states that “our team summarized these findings in an Overview Report that received a second layer peer review from six independent experts.”  Dennis fails to mention the peer review comment 3-5: “The Summary and Findings section does not sufficiently express the uncertainties in the responses to restoration options” which is generally consistent with my concerns over the September 21, 2011 “Summary of Key Conclusions” expressed in my September 2011 disclosure.  Note that the summaries included in the draft EIS/EIR are more detailed than the Summary of Key Conclusions, but still have bias.  Also note Comment 4-2: “Make the process of evaluating the scientific information clearer (e.g., in Section 3)…”  For example, the expert panels conclude that most issues could be answered only qualitatively rather than quantitatively, as would be hoped for from scientific information. It is summarized succinctly by the final Coho/Steelhead expert panel report: “… a decision to proceed with the [dam removal] projects should be understood as a decision to pursue a hypothesis of increased fish production, for which there is evidentiary support for qualitative responses, but whose quantitative outcome is largely unknown” (p. 71).  These concerns can be addressed by writing a new summary that accurately portrays the uncertainties and risks associated with removing the dams, and the additional actions that will be needed to meet the environmental and societal goals; but no such summary has been written.

 3)      Mr. Lynch states that the Klamath science process is open and transparent, and it does appear that in many aspects there has been great progress toward these goals.  However, according to Patrick Higgins (Two Rivers Tribune, 27 July 2011), “DOI lawyer John Bezdek’s claim that all KHSA/KBRA processes are open is simply incorrect. All committees and processes are open only to those who have signed the agreements. Critical documents like the Drought Plan are crafted behind closed doors by Parties and then the non-Party Tribes and the public can comment, but there is no assurance that appropriate changes will be made. Thus, the KBRA sets up a class system on the Klamath River for decision making that would perpetuate social injustice for 50 years.”  Note that Patrick Higgins is a Fisheries Biologist who consults and represents the Resighini Rancheria Tribe.  Despite the progress, more efforts are needed to make the Klamath science process open and transparent, and to involve all of the stakeholders on an equal basis.

4)      Mr. Lynch disagrees with my comment that a more in-depth engineering analysis is needed to assure that Iron Gate Dam is removed safely.  My comment was based on an EIS/EIR comment submitted by Stephen Koshy, who has a long history in engineering and public works.   The “extensive engineering studies” that Dennis cites are not readily attainable.  A 2009 engineering report appears to be extremely preliminary, only devoting a page of hand-waiving dam removal process ideas for Iron Gate Dam.   The draft EIS/EIR has even less engineering analysis devoted to this issue, and no government response to Mr. Koshy’s concern is posted.    These concerns are also straightforward to address, by providing a public response to Mr. Koshy’s concerns and by attaching the relevant engineering analyses.

5)      Mr. Lynch disagrees with my comment that the sediment coming out of the dams would be the equivalent volume of one to three feet of silt covering the 150 foot wide river channel from Iron Gate Dam to the ocean.  Part of the uncertainty in these numbers is that the Department of the Interior’s own analyses have discrepancies.  The initial Fish and Wildlife Service sediment study projected 20.4 million cubic yards with 84% washing down river.  The draft EIS/EIRreports 13.1 cubic yards with 41% to 65% washing down river.  The initial sediment study volume would be equivalent to covering 190 miles of a 150’ wide river with 3.1 feet of sediment.  The second analysis would be between 1.0 and 1.5 feet.  Much of the sediment would be washed through the system, but because the sediment would be transported during high flows, much would also likely remain on river banks and depressions.  In fact, the draft EIS/EIR states: “Once eroded from the reservoir, the fine sediment would continue to be suspended in the river water downstream to the ocean. Large quantities of sediment would remain in place after dam removal, primarily on areas above the active channel”. “Short-term (2–yr) aggradation of sediment from the dams could be substantial below Iron Gate Dam downstream to Willow Creek, with up to 5 feet of deposition within 0.5 miles downstream of the dam, to 1.5 feet of deposition near Willow Creek. The amount of deposition within these reaches is expected to bury any salmonid redds and associated eggs to such a depth that alevin emergence would likely be adversely affected.”  These reports suggest that downstream impacts of sediment are a significant concern, so alternate options such as dredging may also need to be more seriously considered.

6)      Mr. Lynch disagrees with my concerns that the released sediments may be harmful to fish, and may have a significant impact for 1-2 years.  The draft EIS/EIRhas a number of relevant quotes:

While sediment release during dam removal could cause short-term (1 to 2 years) impacts on fisheries downstream of the Hydroelectric Reach, salmon and other aquatic resources would be expected to return to existing 2010 levels within 5 years.

Sediment release during dam removal will have significant and deleterious effects on the aquatic environment from Iron Gate Dam to the Pacific Ocean during the period of dam removal.

“…some short-term effects are anticipated and, for water quality, would be heavily influenced by the release of fine sediment deposits currently stored behind the dams to the downstream river reaches, the estuary, and the marine near shore environment. This is because mobilization of reservoir sediment deposits would be most intense during the first year or two following dam removal, when the majority of sediments would be eroded by river flows (Greimann et al. 2011, Stillwater Sciences 2008).”


Water quality and reservoir sedimentation in the Klamath basin are very complex issues.  While a 2011 DOI report did show that the reservoir sediments have toxic elements below most government guidelines, the upper basin is well known to have water and sediment quality issues, and these sediments are being deposited in the reservoirs.  The relevant story is told in the draft EIS/EIR:

The relatively low relief, volcanic terrain of the upper Klamath Basin (see Section 3.11, Geology, Soils, and Geologic Hazards) supports large, shallow natural lakes (Upper Klamath Lake, Agency Lake, Tule Lake, Lower Klamath Lake) and wetlands, with soils that are naturally high in phosphorus. Human activities in the upper basin, including wetland draining, agriculture, ranching, logging, and water diversions have altered seasonal stream flows and water temperatures, increased concentrations of nutrients (nitrogen and phosphorus) and suspended sediment in watercourses, and degraded other water quality parameters such as pH and dissolved oxygen concentrations.”

Dams slow the transport of water downstream, intercept and retain sediment, organic matter, nutrients, and other constituents that would otherwise be transported downstream …” 

“The characteristically slow-moving waters in reservoirs result in trapping of deposition of fine sediments and organic particulate matter. Contaminants found in the bottom sediments of reservoirs are typically transported from the watershed in association with particulate matter. Trace metals are mostly attached to (inorganic) clays and silts. Organic contaminants, such as pesticides and dioxin, are attached (adsorbed) to organic matter.”

Existing interception and retention of mineral (inorganic) sediments [and nutrients] by the dams is potentially beneficial.”

Dioxin, a known carcinogen, was also measured in the Shannon & Wilson (2006) study. Long-term exposure to dioxin in humans is linked to impairment of the immune system, the developing nervous system, the endocrine system and reproductive functions. In the 2004–2005 reservoir samples, measured levels were 2.48–4.83 pg/g (picograms per gram or parts per trillion [ppt] expressed as Toxic Equivalent Concentrations) and did not exceed applicable screening levels for human health and ecological receptors (Shannon & Wilson, Inc. 2006, Dillon 2008, USEPA 2010b) or estimated background dioxin concentrations (2–5 ppt) for non-source-impacted sediments throughout the U.S. and specifically in the western U.S. (USEPA 2010b). The measured levels did exceed Oregon human health and bioaccumulation thresholds; however, Oregon’s human health thresholds include risk-based values for subsistence fishers as well as the general consuming public and are quite a bit lower (0.0011–1.1 pg/g dry weight (DW) Toxicity equivalency quotient [TEQ]) than many other screening levels (ODEQ 2007) (see Appendix C for more detail).”

Combined with the sediment contaminant data (see above), inorganic and organic contaminants are present in reservoir sediments at levels that have the potential to cause minor or limited adverse effects (i.e., toxicity or bioaccumulation) to freshwater aquatic species (Figure 3.2-2).”

In summary, existing fish tissue, bioassay, and sediment chemistry data indicate that continued retention of sediments behind the KHP dams under the No Action/No Project Alternative may result in concentrations of inorganic and organic contaminants at levels that adversely affect beneficial uses or are toxic to humans in the Hydroelectric Reach.” (This quote seems inconsistent with the assertion that the sediments are non-toxic.)

Under the Proposed Action, the short-term (<2 years following dam removal) increases in SSCs in the lower Klamath River and the Klamath Estuary would be a significant impact.”

I also point to a 2006 PacifiCorp study Causes and Effects of Nutrient Conditions in the Upper Klamath River”, that indicates the 4 reservoirs act as net sinks for nitrogen, phosphorous and organic matter.  The report concludes that the absence of the project reservoirs would exacerbate water quality impairment by increasing biogeochemical oxygen demand, reducing dissolved oxygen and further promoting growth of benthic algae.  Note that the water quality issues above the 4 PacifiCorp dams may be amongst the most significant risks to successful restoration of the river; these water quality issues should be mitigated prior to dam removal to assure success.  Further, based on a simple mass balance concept, the retention of contaminants in the reservoirs indicates that the sediments must contain contaminants.  The available studies on sediment contamination seems to be contradictory, which warrants additional efforts to fully understand and mitigate the risks.

7)      Finally, Mr. Lynch objects to my statement that nonnative coho salmon were introduced in the Klamath starting in 1895.  In fact, The California Department of Fish and Game’s 2002 report “Historical Occurrence of Coho Salmon in the Upper Klamath, Shasta, and Scott Rivers” confirms my statement and further indicates that “historically, the practice of importing non-native fish was common, especially in systems where native fish had been extirpated or were in low abundance. Following completion of Iron Gate Hatchery in 1966, adult coho salmon returns were less than 500 fish. After the completion of Trinity River Hatchery in 1963, adult coho salmon returns at this facility rarely exceeded 1,000 fish prior to 1971. In an effort to increase returns to Iron Gate Hatchery, coho salmon from the Cascade River in Oregon were stocked in 1966, 1967 and 1969 (CDFG 1994). The first significant transfer of coho salmon to Trinity River Hatchery occurred in 1964 when Eel River coho salmon stock were brought in. This was followed by plantings of coho salmon originating from the Cascade River, Oregon in 1966, 1967 and 1969. Noyo River stock was also planted in 1969 and Alsea River stock was planted in the Trinity in 1970 (CDFG 1994). It appears the intent of these out-of-basin transfers was to augment already existing, albeit dwindling, natural coho salmon populations. Current California Fish and Game Commission policy now essentially prohibits all out-of-basin fish transfers.”

The report indicates that information on the historical occurrence of coho salmon in the upper Klamath River is sparse and uncertain, and that “it cannot be determined with absolute certainty that the 1895 stocking did not result in a portion of the runs observed 15 years later in the Klamath River.”  However, based on the population dynamics after 1895, the report concludes that “the Department believes that coho salmon are native to the upper Klamath River system.”

The draft EIS/EIR states that “the vast majority of coho salmon that spawn in the Klamath Basin are believed to be of hatchery origin, although the percentage varies among years (Ackerman et al. 2006).

Based on the century-long history of nonnative salmon transfers and hatchery origin fish, it would seem to be next to impossible to identify a truly native wild Klamath coho. Regardless of this past, the Klamath coho salmon is listed as threatened but not endangered, and it is the law to make reasonable and scientifically justified efforts to preserve them.


I applaud Mr. Lynch’s commitment to accuracy in these studies, and hope that he takes advantage of my invitation to discuss these scientific concerns.  Although Mr. Lynch did not mention scientific integrity in his post, his work is bound by the Department of the Interior’s Scientific Integrity Policy and Scientific Code of Conduct. This policy sets the bar very high for objectivity, conflict of interest, welcoming constructive criticism, adherence to laws protecting natural and cultural resources, communicating honestly and thoroughly, considering all viable alternatives in an unbiased fashion, and advancing science and scholarship for the purpose of serving the public with sound decision making on the part of all government agencies.  During my recent interactions with many talented Klamath basin scientists, engineers and decision makers, I have heard about several innovative and economical solutions to meet the multi-objective law, environment and society goals that are not being actively considered by the draft EIS/EIR because they fall outside the politics of the Klamath agreements (Table 2-2) – it is in the public trust, and a duty of scientific integrity to actively consider these alternatives.

In summary, decision makers often use science to support predetermined decisions rather than using science to help inform decisions. Decision makers, scientists and peer-reviewers may have conflicts of interest, and biased media reports can skew public understanding. The 2011 expert panels concluded that removing the dams without addressing the water quality issues, reducing disease, enabling free migration to the upper basin, preventing hatchery salmon from not overwhelm spawning grounds, reducing predation to sufficiently low levels, accounting for climate change, addressing reductions in fall flows, and mitigating long-term sediment impacts, there is a low probability that coho salmon will thrive in the Klamath river. The outcomes of dam removal on this scale and in this unique environment have significant risks and uncertainties. A positive outcome is not guaranteed and a tragic outcome is possible. All I am trying to accomplish is to make sure that decision makers are aware of these risks and uncertainties, and account for them in their decision-making process. By only reporting the positive aspects of dam removal without the uncertainties and additional needed mitigation, the meaning of the science is perturbed, which may lead to poor decisions.

Dr. Paul R. Houser is a Hydrologist with over 25 years of experience.  Dr. Houser in an internationally recognized expert in local to global land surface-atmospheric remote sensing, in-situ observation and numerical simulation, development and application of hydrologic data assimilation methods, scientific integrity and policy, and global water and energy cycling.   More information can be found at http://www.prhouser.com.



Filed in: Klamath

Dr. Paul R. Houser

About the Author (Author Profile)

Dr. Houser in an internationally recognized expert in local to global land surface-atmospheric remote sensing, in-situ observation and numerical simulation, development and application of hydrologic data assimilation methods, scientific integrity and policy, and global water and energy cycling. He received his B.S. and Ph.D. degrees in Hydrology and Water Resources from the University of Arizona in 1992 and 1996 respectively. Dr. Houser's previous experience includes internships at the U.S. Geological Survey and at Los Alamos National Laboratory. Dr. Houser joined the NASA-GSFC Hydrological Sciences Branch and the Data Assimilation Office (DAO/GMAO) in 1997, served as manager of NASA’s Land Surface Hydrology Program, and served as branch head of the Hydrological Science Branch. In 2005, he joined the George Mason University Climate Dynamics Program and the Geography and Geoinformation Sciences Department as Professor of Global Hydrology, and formed CREW (the Center for Research for Environment and Water). Dr. Houser has also teamed with groundwater development and exploration companies (EarthWater Global and Geovesi) and has served as Science Advisor to the U.S. Bureau of Reclamation. Dr. Houser has led numerous scientific contributions, including the development of Land Data Assimilation Systems (LDAS), the Hydrospheric States Mission (Hydros/SMAP), the Land Information System (LIS), the NASA Energy and Water cycle Study (NEWS), and the Water Cycle Solutions Network (WaterNet).



Dennis Lynch: Klamath science process is solid

The Klamath Hydroelectric Settlement Agreement calls on the secretary of the interior to make a decision on whether to remove four Klamath River dams based on a foundation of scientific findings. That is why more than 100 experts on my team, including biologists, engineers, economists, hydrologists, and others, have been developing and sharing new scientific information for the past two years.

In developing this information, my team used the universal principles of the scientific method to produce 50 new reports: literature review, hypothesis (assumption) testing, data collection and analysis, and publication of peer-reviewed, publicly available reports which are available at KlamathRestoration.gov. Our team summarized these findings in an Overview Report that received a second layer of peer review from six independent experts. We also obtained independent expert critiques of some existing reports, convened four independent science panels to provide points-of-view separate from those of federal scientists, and obtained valuable input during 25 public meetings since 2010.

At these public meetings, people brought forward new information, topics for investigation, and their scientific assumptions. This was an open, transparent, and useful public process, and our reports are better because of it. During our scientific analyses, we investigated many assumptions, including those raised by the public. Some assumptions proved to be supported by facts, while other assumptions proved to be inaccurate or incorrect.

Dr. Paul Houser, in a series of speaking engagements last month in the Klamath Basin, discussed many scientific assumptions that our analyses have shown to be inaccurate or incorrect. Although space won't allow a response to each of these inaccurate assumptions, responding to a handful of the more important ones is warranted.

Dr. Houser suggested that the federal engineers didn't adequately study whether Iron Gate Dam would fail during removal. The engineering analysis of Iron Gate Dam removal was rigorous, the detailed plan fully describes the process to safely remove this large earth-fill dam with a clay core, and this plan underwent multiple layers of peer review.

Dr. Houser stated that "the devastation of the lower Klamath from all that sediment coming out is between one and three feet of the river channel, 150 feet wide, being covered with silt all the way down to the ocean." This is incorrect. Sediment-transport modeling shows that dam removal would release 5.4 million to 8.6 million cubic yards of reservoir sediment. About 85 percent of this sediment is silt and clay that would be readily transported to the ocean by winter flows during reservoir drawdown. Very little of this sediment would remain in the river channel.

Dr. Houser stated that the "reservoir sediments are quite toxic" and are "high in phosphorus and probably quite a few other chemicals that have been banned for years." Findings from our study, and an independent study in 2006, are contrary to these conclusions. An analysis of over 500 chemicals in 77 sediment cores did not show high concentrations of toxic chemicals. Chemical concentrations are below "Critical Guidelines" for sediment disposal and thus these reservoir sediments could be safely released downstream if dams were removed.

Dr. Houser stated that sediment release "will devastate fisheries for at least a year or two." Our analysis shows that a winter release of sediment in a single year, even under a "worst-case" condition (dry year), would result in less than 10 percent basin-wide mortality of coho and chinook salmon, and 20 to 30 percent basin-wide mortality of steelhead. Proposed mitigation measures would decrease this short-term mortality. In the long term, dam removal would benefit all three fish populations.

Dr. Houser stated "one of the things I do know is salmon were introduced in the Klamath in about 1895, intentionally, by people" suggesting that coho or chinook salmon are nonnative. Dr. Houser may have been referring to a plant of coho salmon in 1895 in the Trinity River Basin that was overseen by the U.S. Commission on Fish and Fisheries. This was an effort to replenish over-harvested native Klamath coho runs with stocks from nearby streams; it was not an introduction of a nonnative species.

Dr. Houser has never spoken with me regarding these scientific concerns, or any other scientific concerns regarding the accuracy of our studies. As senior scientist on this project, I am committed to bringing accurate, objective, fact-based scientific findings forward for the secretary's decision. If my team has erred in an analysis, missed a valuable information source, or failed to investigate an important assumption or concern, my science team stands ready, as always, to evaluate new ideas and information sources, and to correct any errors. This decision is too important to leave any stone unturned.

Dennis Lynch has been a hydrologist with the U.S. Geological Survey for 32 years, including studies in the Klamath Basin for 17 years. He is the lead federal scientist overseeing the science and engineering process for the secretary of the interior on Klamath River dam removal.


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