Independent Scientific Review Panel

for the Northwest Power & Conservation Council 

851 SW 6th Avenue, Suite 1100 

Portland, Oregon 97204 

www.nwcouncil.org/fw/ISRP

Review of FY 2007-09 

Innovative Proposals 

for the Columbia River Basin 

Fish and Wildlife Program

ISRP 2007-9 

June 26, 2007 
ISRP Members 

J. Richard Alldredge, Ph.D., Professor of Statistics at Washington State University.

Peter A. Bisson, Ph.D., Senior Scientist at the Olympia (Washington) Forestry Sciences 

Laboratory of the U.S. Forest Service (former ISAB member). 

John Epifanio, Ph.D., Director and Associate Professional Scientist for the Center for 

Aquatic Ecology at the Illinois Natural History Survey, an expert in conservation genetics 

and molecular ecology. 

Linda Hardesty, Ph.D., Associate Professor of range management at Washington State 

University, an expert in the biological diversity of eastern Washington. 

Charles Henny, Ph.D., Senior Research Scientist at the U.S. Geological Survey in 

Corvallis, Oregon, an expert in wildlife and environmental toxicology. 

Colin Levings, Ph.D., Scientist Emeritus and Sessional Researcher, Department of 

Fisheries and Oceans. Canada (also an ISAB member). 

William Liss, Ph.D., Professor Emeritus of Fisheries at Oregon State University (former 

ISAB member).

Eric J. Loudenslager, Ph.D., Hatchery Manager and Adjunct Professor of Fisheries 

Biology, Humboldt State University, California, an expert in genetics and fish culture. 

(ISRP Chair, former ISAB member)

Katherine Myers, Ph.D., Principal Investigator of the High Seas Salmon Research 

Program at the School of Aquatic and Fishery Sciences, University of Washington.

Thomas P. Poe, M.S., Consulting Fisheries Scientist, an expert in behavioral ecology of 

fishes, formerly with the U.S. Geological Survey (also an ISAB member). 

Bruce Ward, Fisheries Scientist, Ministry Of Environment, Aquatic Ecosystem Science 

Section, University of British Columbia, Vancouver, B.C., Canada. 

Staff 

Erik Merrill, ISRP and ISAB Coordinator, Northwest Power and Conservation Council. 

Acknowledgement 

Special thanks to Eric Schrepel, Council staff, for designing the ISRP’s online innovative 

review site, which allowed for an efficient review process and could be used as a model 

for other proposal review processes. 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

ISRP Review of FY 2007-09 Innovative Proposals

Contents 

Table of Proposals with Page Index................................................................ ii

Five Ranked, Innovative, On-the-Ground, and Highly Justified Proposals.................... ii 

Four Ranked, Innovative, On-the-Ground, and Adequately Justified Proposals............ ii 

Five Ranked, Innovative, Research-oriented, and Highly Justified Proposals ..............iii 

Forty-Five Unranked Proposals .....................................................................................iii 

Background..................................................................................................... 1

Review Process and Overall Results .............................................................. 1

Programmatic Comments ............................................................................... 3

ISRP Comments on Each Proposal................................................................. 5

Five Ranked, Innovative, On-the-Ground, and Highly Justified Proposals.................... 5 

Four Ranked, Innovative, On-the-Ground, and Adequately Justified Proposals.......... 10 

Five Ranked, Innovative, Research-oriented, and Highly Justified Proposals ............. 15 

Forty-Five Unranked Proposals .................................................................................... 19 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

Table of Proposals with Page Index 

Of the 59 proposals submitted, the ISRP finds that nine proposals substantially meet the 

innovative solicitation criteria: employ innovative techniques, are on-the-ground, 

describe scientifically sound techniques, and offer potential benefits to fish and wildlife. 

Five of these are highly justified, and four are adequately justified. In addition, the ISRP 

identifies five proposals that are innovative and highly justified, but are research oriented 

and thus are not on-the-ground. These 14 ranked proposals are presented first by rank 

order then project number. The remaining 45 unranked proposals are presented next. For 

a variety of reasons, these proposals did not meet the standards for funding under the 

innovative solicitation. 

Five Ranked, Innovative, On-the-Ground, and Highly Justified Proposals 

Proposal# Title Funding

Request 

Page Priority

200752100 Improving Fish Habitat Using Innovative

Strategies to Remediate Contaminated 

Sediments in the Columbia River Basin 

$185,112 5 A1

200752400 Integrated Non-Lethal Electric Barrier and 

Sonar System to Deter Marine Mammal 

Predation on Fish in the Columbia River 

System: A Demonstration Project 

$1,440,483 6 A1 

200751300 Eelgrass enhancement and restoration in the 

Columbia River Estuary through innovative 

site selection and planting techniques 

$252,794 7 A2

200751600 Enhancing Summer Instream Flow and 

Reducing Temperature in Agricultural

Watersheds

$224,766 7 A2 

200755700 What was old is new again: evaluate 

traditional gears for selective harvest 

$444,971 9 A2

 Total Request Top Five Ranked 

Proposals 

$2,548,126 

Four Ranked, Innovative, On-the-Ground, and Adequately Justified 

Proposals 

200753500 Physical and Biological Field Testing of a Flow 

Velocity Enhancement System (FVES)

$318,310 10 B1 

200752600 Lake oxygenation pilot study: Improving

Redband Trout habitat quality in Twin Lakes, 

WA 

$271,634 11 B2

200751800 Evaluation of artificial upwelling to enhance 

lower Columbia River Gorge chum salmon 

spawning 

$173,590 12 B3 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200754200 Shad for Nutrient Enhancement -- 

Demonstration of Fishery Supply, Disease 

Evaluation, Product Type and Potential Use 

$163,400 14 B4

 Total Request Ranked Proposals - B List $926,934 

Five Ranked, Innovative, Research-oriented, and Highly Justified Proposals 

Proposal# Title Funding

Request 

Page Priority 

200753800 Predicting the future effects of climateinduced stream warming on spring Chinook 

salmon and their predators in the John Day 

River Basin 

$214,959 15 R1 

200755400 Using advanced technologies to help reduce 

the impacts of global warming on 

anadromous and resident fish populations in 

the Columbia Basin 

$294,302 16 R2

200750800 Designing Pre- and Post-Fire Restoration 

Strategies For Recovery of Salmonid

Habitats in a Period of Climate Change and 

Increased Forest Fire Disturbance 

$88,300 17 R3 

200750200 Application of Innovative Acoustic Telemetry 

Technology to Underpin Statistically-Valid

Survival Estimates for Chinook Salmon in the 

Nearshore Ocean Off the Mouth of the 

Columbia River 

$532,680 18 R4

200751100 DNA typing to identify native inland

Oncorhynchus mykiss 

$217,364 18 R5 

 Total Request Ranked Researchoriented Proposals $1,347,605 

Forty-Five Unranked Proposals 

Proposal# Title Funding

Request 

Page Priority

200750000 A New Aging Technique For Lake Trout and

Northern Pikeminnow Using Allometric 

Relationships Between Fish Size and Otolith 

Mass 

$115,240 19 Unranked

200750100 Adapting tree-ring techniques to 

reconstruct stream environmental histories 

from the growth increments of long-lived 

freshwater mussels 

$73,502 20 Unranked

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

Proposal# Title Funding

Request 

Page Priority

200750300 Assessment of Functional Biological

Differences Between Natural and HatcheryRaised Redfish Lake Sockeye Salmon

$199,751 21 Unranked

200750400 Automated Scale Image Analysis (ASIA) $198,250 22 Unranked

200750500 Catching Predator fish with commercial

traps 

$400,000 23 Unranked

200750600 Chiwawa River Adult Spring Chinook Otolith 

Study 

$47,913 23 Unranked

200750700 Crumble-Crete Habitat Revegetation and

Stability Blocks - Development of 

degradable bank protection/reveg block to 

provide temporary stability during recovery

of natural bank-stabilizing vegetation. 

$27,738 24 Unranked

200750900 Develop structure for implementing and 

maintaining a Master Sample of rivers and 

streams in the Columbia Basin, and 

develop statistical tools for analyzing 

Master Sample applications.

$386,806 25 Unranked

200751000 Development of a Low-cost Dual-Frequency

Acoustic Tracking Capability for Ocean & 

Freshwater Components of the POST

Tracking Array 

$330,199 26 Unranked

200751200 Documentation of food-web linkages in the 

mainstem Columbia River: towards 

understanding the role of invasive species 

and establishing a baseline trophic state 

$337,374 27 Unranked

200751400 Effectiveness monitoring of in-stream 

habitat restoration using tools from 

population ecology 

$193,624 27 Unranked

200751500 Elemental analysis of fin spines: A potential 

tool for assessing movement of white 

sturgeon (Acipenser transmontanus) within 

the Lower and Mid-Columbia River basin 

$42,122 29 Unranked

200751700 Estimating abundance of white sturgeon by

using visual strip-transects; an alternative 

to mark-recapture population estimates 

$590,925 29 Unranked

200751900 Feasibility of using a computerized video 

system to estimate lamprey passage at 

Bonneville Dam 

$93,532 30 Unranked

200752000 Genetic Predisposition of Smoltification in

Rainbow Trout and Steelhead 

$89,978 31 Unranked

200752200 Innovative Fish Sample Gear for Reducing

Stress and Mortality in the Catch and 

Increasing Efficiency in Monitoring the 

Effectiveness of Dike Removal Projects 

$7,838 32 Unranked

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

Proposal# Title Funding

Request 

Page Priority

200752300 Innovative methods to quantify transport of 

hydrophilic and legacy pesticides to the 

riparian zones within the Yakima Basin 

$216,909 33 Unranked

200752500 Integrating Ecological Flows into River 

Management on the Willamette River 

$64,150 34 Unranked

200752700 Lake Roosevelt Littoral Habitat 

Enhancement Project 

$574,112 35 Unranked

200752800 Little McCormick Creek: Investigating 

Placer Mine Impacts to Streamflow 

Connectivity and Developing New 

Restoration Techniques

$96,800 36 Unranked

200752900 Loss of salmon and steelhead productivity

due to barriers in the Lower Columbia River

ESU 

$158,326 37 Unranked

200753000 MADS Weir Demonstration Project in Walla 

Walla Subbasin (MADS - Modular Arch Drop 

Structure) 

$118,750 38 Unranked

200753100 Microbial Assessment of Thermal Impacts

of Dworshak Reservoir Releases 

$165,473 38 Unranked

200753200 Molalla-Pudding Sub basin Assessment; 

utilizing the new EPA Watershed 

Assessment of the River Stability and 

Sediment Supply(WARSSS)procedural 

methods to increase anadromous fish

survivability 

$271,222 39 Unranked

200753300 Monitoring fine sediment delivery to fish 

habitat in the Entiat River subbasin 

$295,000 40 Unranked

200753400 Performance comparison of a stationary PIT 

tag antenna array in Lookingglass Creek, 

Oregon 

$47,829 40 Unranked

200753600 Piloting StreamBankTM Web Tool and

permitting efficiencies to achieve Middle

Fork John Day River Channel Reactivation 

and Floodplain Restoration. 

$354,941 41 Unranked

200753700 Population specific in-season forecasts of

Columbia River Chinook salmon 

(Oncorhynchus tshawytscha) returns for 

allowing selective in-river fisheries 

$99,762 42 Unranked

200753900 Promote Kokanee Repopulation in Lake 

Pend Oreille using Autonomous Underwater 

Vehicles (AUVs) for Location and 

Verification of Lake Trout Spawning Areas. 

$400,177 44 Unranked

200754000 Quantitative Assessment Sampling for 

Pacific Lamprey in Cedar Creek (Lewis

River Subbasin), Washington 

$140,000 44 Unranked

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

Proposal# Title Funding

Request 

Page Priority

200754100 Reecer Creek Floodplain Restoration Project

to support ecosystem function using buildin-the dry and 3 yrs revegetation to 

encourage channel dynamics, habitat 

formation and natural sediment 

management 

$428,307 45 Unranked

200754300 Simmons Dike Removal feasibility study $43,000 46 Unranked

200754400 Spawning Channel for Chum Salmon at

Beaver Creek Hatchery

$398,000 46 Unranked

200754500 Stock specific run timing and upstream

migration mortality of adult Chinook 

salmon and steelhead through genetic 

stock identification and PIT tagging at

Bonneville Dam 

$123,150 48 Unranked

200754600 Test of protocols and validation of 

estimates derived with traditional and new 

methods for steelhead adults, smolts, and 

parr using an instream PIT-tag 

interrogation system 

$236,785 49 Unranked

200754700 The Natural Tag - TNT $229,288 50 Unranked

200754800 The use of cDNA microarrays to develop

biomarkers of environmental stress in 

salmonids and other fishes 

$572,352 51 Unranked

200754900 Toppenish Creek Well Modification Project $351,423 51 Unranked

200755000 Toxics as a limiting factor for salmon 

recovery throughout the Columbia River 

Basin: understanding the enhanced toxicity 

of pesticide mixtures 

$199,244 52 Unranked

200755100 Use of a novel technique to compare of 

Pre-and Post-migratory energy storage and 

use in upriver coho salmon: How much 

change can occur with intense selective 

pressure. 

$49,245 53 Unranked

200755200 Use of LA-ICPMS and fin ray 

microchemistry to examine historic and

present movement patterns in Upper

Columbia River white sturgeon 

$75,525 54 Unranked

200755300 Using acoustic telemetry to evaluate the 

behavior, habitat use, and survival of 

tagged juvenile salmonids in the John Day

Reservoir 

$977,335 55 Unranked

200755500 Using otolith microchemistry and

microstructure to assess the causes and 

consequences of alternative life history 

strategies for Snake River fall Chinook

$573,252 55 Unranked

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

Proposal# Title Funding

Request 

Page Priority

200755600 Water Stargrass Demonstration and 

Management in the lower Yakima River for 

Spawning Habitat, Water Quality and 

Beneficial Uses (WiSDoM)

$372,450 56 Unranked

200755800 Willamette Mitigation $277,644 57 Unranked

Total Request Unranked Proposals $11,045,243

Total Request All Proposals $15,867,908 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

ISRP Review of FY 2007-09 Innovative Proposals 

Background 

This FY 2007-09 innovative proposal solicitation continues the effort of the Northwest 

Power and Conservation Council (Council) to encourage creative solutions for improving 

the benefits to fish and wildlife in the Columbia River Basin from projects implemented 

through their Fish and Wildlife Program. This is the third innovative solicitation with 

other specific innovative solicitations undertaken for FYs 2001 and 2002. The ISRP’s 

1997-2005 Retrospective Report details the creation and outcomes of the past innovative 

solicitations.1

 

The FY 2007-09 innovative proposal solicitation specified the following requirements 

that a proposal: 

• offers a method or technology designed to directly benefit fish and wildlife, that 

(1) has not previously been used in Columbia River Basin fish and wildlife 

projects or (2) if used before in other projects, has not been used in the proposed 

application 

• is an innovative on-the-ground “demonstration” or “pilot” project with a focus on 

testing or demonstrating new methods or technologies 

• if successful will contribute to direct improvements in the survival or productivity 

of Columbia River fish or wildlife species. (Investigations of basic biological and 

physical phenomenon are not targeted with this solicitation.) 

• is consistent with the Council’s Program

• address key management questions or limiting factors identified in the Program’s 

subbasin plans or mainstem amendments 

• be feasible to complete within 18 months, including one year to implement the 

work and six months to complete reports and other deliverables as appropriate 

• meet the ISRP’s review criteria in Section 4(h)(10)(D) of the Northwest Power 

Act. 

For more information on the solicitation see: www.nwcouncil.org/fw/budget/innovate. 

Review Process and Overall Results 

Fifty-nine proposals were submitted for the FY 2007-09 innovative proposal solicitation, 

requesting about $16 million. The Bonneville Power Administration agreed to make 

available up to a total of $2 million to fund innovative projects during these fiscal years. 

The ISRP’s review process for innovative proposals is anonymous. There is no ISRP 

interaction with project sponsors, project presentations, site visits, or response loops. 

Also unlike the annual basinwide and rolling province reviews, proposals are ranked by 

the ISRP based on the innovation offered, technical merit, and potential benefits. This 

 

1 www.nwcouncil.org/library/isrp/isrp2005-14.htm; pages 10-11 and Appendix, pages 118-120. 

1 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

ranking is possible because the set of proposals is small enough for the ISRP to discuss 

and compare all the proposals in a consistent and equitable manner. 

Each of the 59 proposals was evaluated by a subset of ISRP members who provided 

individual comments and a categorical rank for group discussion at the ISRP’s project 

evaluation meeting. Reviewers evaluated each proposal for its technical sufficiency and 

potential to contribute benefits to fish and wildlife. Each reviewer also evaluated whether 

a proposal met the definition of “innovative” and “on-the-ground” described in the 

solicitation for proposals. At the meeting, the ISRP discussed each proposal and reached 

consensus recommendations and rankings. 

The ISRP found that nine proposals substantially met the solicitation criteria: were 

innovative, were on-the-ground, described scientifically sound techniques, and offered 

potential benefits to fish and wildlife. Of the nine, five proposals (two ranked A1 and 

three ranked A2), stood out as proposals that are high priority meriting immediate 

funding. The proposals ranked from B1 through B4 offered potentially valuable 

contributions to the Fish and Wildlife Program but did not stand out for their innovation 

nor demonstrate as strong a potential to provide significant benefits as those ranked A1 or 

A2. An additional five proposals employed innovative methods, but were not on-theground demonstration or pilot projects. These projects have the potential to make 

important contributions to the Fish and Wildlife Program by providing analytical 

methods that could be used to improve decision making and adaptive management. 

These five projects are ranked R1 through R5 (R for research), and would be fully 

justified for inclusion in the Fish and Wildlife Program. Comments on these fourteen 

ranked proposals are presented below by rank order and project number. 

The ISRP did not rank the other 45 proposals submitted. For a variety of reasons, these 

proposals did not meet the standards for funding under the innovative solicitation. A few 

of these proposals were not innovative but offered approaches that could benefit the Fish 

and Wildlife Program (e.g., 200755000 Toxics as a limiting factor for salmon recovery 

throughout the Columbia River Basin: understanding the enhanced toxicity of pesticide 

mixtures). Several others were innovative, but the ISRP had questions about 

experimental designs or the likelihood and timeframe to demonstrate benefits to fish and 

wildlife (e.g., 200750300 Assessment of Functional Biological Differences Between 

Natural and Hatchery-Raised Redfish Lake Sockeye Salmon, 200754800 The use of 

cDNA microarrays to develop biomarkers of environmental stress in salmonids and other 

fishes). A few proposals were to collect basic biological information on focal species 

(e.g. 200754500 Stock specific run timing and upstream migration mortality of adult 

Chinook salmon and steelhead through genetic stock identification and PIT tagging at 

Bonneville Dam). A number of these proposals were reviewed in the FY 2007-09 

general solicitation and received favorable ISRP recommendation, but were not funded. 

These proposals continue to be suitable for consideration in the general solicitation, but 

did not meet all of the parameters of this innovative solicitation. Comments on these 45 

proposals are presented following the 14 ranked proposals. 

2 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

In conclusion, the ISRP believes that high quality proposals were received in this 

solicitation. There is a demonstrated need for these projects which underscores the value 

of this funding category; in fact, the ISRP believes that the amount of funding available 

for subsequent innovative solicitations should be increased. 

Programmatic Comments 

 

During the review of these proposals, the ISRP identified several themes for 

consideration by project sponsors and the Council. 

Solicitation Timing and Limits: The timing of the solicitation announcement and 

proposal due date was brief. Potential contributors to innovation in the Fish and Wildlife 

Program, such as out-of-basin scientists and engineers, might not have had knowledge of 

the solicitation. For the next round, broad distribution beyond the standard Fish and 

Wildlife Program community is encouraged. Regular (annual or biannual) solicitations in 

this category, on a regular annual calendar, would facilitate the research community’s 

preparation and anticipation of the funding opportunity. If individuals with innovative 

ideas are aware that there will be annual (or biannual) solicitations for projects that are of

pilot or demonstration scale, they are more likely to commit time and energy to the initial 

stages of development. They would have reason to believe there was a vehicle to bring 

the innovation to the next stage of development – a pilot or demonstration scale exercise. 

The timeframe for the projects, 12 month implementation and 6 month reporting, may 

have created difficulties for some projects because of the brief open solicitation period. 

The work could reasonably be completed within this framework but not given the brief 

period to prepare the proposal. There are also potential innovative methods that could 

require more than 12 months to complete the primary tasks. This applies to a lot of

habitat restoration projects where the time frame to measure benefits is much longer. This 

time frame may need to be reconsidered in future innovative solicitations. The important 

element is that the proposal should be for a pilot or demonstration of an innovative 

method or strategy. It would be unfortunate if an outstanding idea was not considered 

because a pilot scale exercise required 24 months to compete. 

Research and Needed Projects: Even though the solicitation requested proposals for onthe-ground “demonstration” or “pilot” projects, about half the submitted proposals were 

to conduct research or assessments. This indicates that there is capacity in the basin for 

research to address important uncertainties. Many of these research proposals would 

have met standard ISRP review criteria. 

Elemental Analysis: A number of proposals offered to analyze chemical elements in fins 

or otoliths and use these to identify where fish had lived during a portion of their life. 

Most of these proposals intended to collect information on basic biological parameters for 

these fish species, so they did not fit the solicitation criteria. Nonetheless, it appeared to 

the ISRP that validation of the chemical signatures was needed to apply these methods, 

and this had not yet been completed. This approach requires differences in water 

chemistry between the different watersheds of interest. This background information 

3 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

needs to be systematically collected. As found elsewhere, testing is required to determine 

if annual variation within a watershed exceeds that among watersheds. Collaboration 

between various investigators interested in applying this method to white sturgeon and 

salmon could also be improved to avoid duplication of effort. 

Hatcheries: Although a significant portion of the Fish and Wildlife Program involves 

hatchery production of fish, few proposals were submitted aimed at improving artificial 

production. Research proposals were submitted that would add information about basic 

biological attributes of hatchery fish, but none that were evaluating alternative culture 

methods. It is not clear to the ISRP whether funding through the general FY 2007-09 

solicitation provided the necessary resources to the fish culture community or whether the 

format of this innovative solicitation was not sufficiently attractive. 

In summary: The ISRP continues to believe the recommendation from the 

Retrospective Report 1997 – 2005 (ISRP 2005-14) is worthy of consideration: 

The ISRP recommends that an annual budget for the innovative proposal 

solicitation be committed to (especially if advertised in a solicitation) and perhaps 

increased, and that a separate budget be set aside for targeted Requests for 

Proposals (RFPs). While the Innovative Funding Category has been allocated at 

just over 1% of the Fish and Wildlife Program’s annual budget, results from 

several innovative projects have had important benefits to the region. The 

retrospective review by ESSA Technologies (Marmorek et al. 2004; Innovative 

Project 34008) of past habitat improvement actions and their effect on salmon 

survival and abundance led directly to many recommendations on data needs, and 

coordination among projects that are currently being addressed by the developing 

Research, Monitoring, and Evaluation plan. 

4 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

ISRP Comments on Each Proposal

Five Ranked, Innovative, On-the-Ground, and Highly Justified Proposals 

200752100 - Improving Fish Habitat Using Innovative Strategies to Remediate 

Contaminated Sediments in the Columbia River Basin 

Sponsor: Washington State University 

FY08-09 budget: $185,112 

Short description: Contaminated sediments represent a critical environmental problem 

that impairs aquatic ecosystems. The purpose of this proposal is to demonstrate an 

innovative cleanup strategy designed to treat toxic sediments to improve fish habitat. 

(View full proposal online)

Recommendation: Ranked A1, Innovative, On-The-Ground, Highly Justified 

This well-described proposal investigates an innovative in-situ method of remediating 

chemically contaminated sediments. The proposed approach has been used successfully 

for “enhanced aerobic bioremediation” in other situations (soil and groundwater) 

especially for PAHs, but not in sediment. Basically, the reactive solid/chemical oxidant 

will be a block containing CaO(OH)2 as an active ingredient that slowly releases oxygen 

in the presence of water to enhance biodegradation of contaminants. Treatment and 

control plots are in the Coeur d’Alene subbasin along the St. Joe River that contains 

creosote-contaminated sediments, resulting in high PAH concentrations. These PAHs 

will be used as a model contaminant that will be monitored at the plots over time. 

Additional evaluations include sediment collected from 20 different locations (prime 

habitat for endangered or threatened fish, and areas with known high PBDE and PCB 

concentrations) in the Columbia River Basin. These samples will be brought into the 

laboratory to determine toxics present and to evaluate the effectiveness on each 

contaminant class when exposed to the “reactive solid” including possible adverse effects 

on fish. If successful this approach could be a viable alternative to the draconian 

approach of dredging or capping. The proposal did an excellent job of describing the 

problem and the need to find an alternative method of cleaning up contaminated sediment 

in streams and rivers. The proposal, with a combination of field and laboratory 

techniques, addresses an under-investigated issue with a new technology and a solid 

scientific approach. The area of restoration of contaminated sites is certainly underrepresented in regional restoration activities. This technology has the potential of 

benefiting both focal and non-focal species and could have application throughout the 

basin. 

5 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200752400 - Integrated Non-Lethal Electric Barrier and Sonar System to Deter 

Marine Mammal Predation on Fish in the Columbia River System: A 

Demonstration Project 

Sponsor: Smith-Root, Inc 

FY08-09 budget: $1,440,483 

Short description: This proposal would develop and evaluate a passive, integrated 

electric barrier and sonar array that selectively inhibits upstream marine mammal 

movements and predation on fish, without injuring pinnipeds or affecting anadromous

fish migrations. 

(View full proposal online)

Recommendation: Ranked A1, Innovative, On-The-Ground, Highly Justified 

This proposal would assess the potential to deter movement of marine mammals into fish 

ladders and therefore alleviate predation on Columbia Basin fish species. This will be

accomplished using an electric barrier to deter entry to the ladders coupled with a sonar 

array that detects the presence of marine mammals and activates the electric barrier. It is 

intended to function without injuring pinnipeds or affecting anadromous fish migrations. 

This project meets the criteria for this solicitation - it is innovative, on-the-ground, and a 

demonstration project that can be completed within 18 months. There is a highly visible 

problem of marine mammal predation on salmon and sturgeon at fish ladders in the lower 

Columbia River. Efforts to deter marine mammal predation on salmon at fish ladders, 

using methods that do not harm the mammals, have been unsuccessful. The integrated 

non-lethal electric barrier combined with sonar to detect the presence of pinnipeds has the 

potential of significant benefits for adult salmon, white sturgeon, and steelhead to be 

realized fairly quickly if it works. The proposal is well written, and the project well 

designed. 

Preliminary testing has been performed with captive animals and in rivers in British 

Columbia, Canada. Data from these preliminary trials appear favorable, and the larger 

scale demonstration project proposed is the appropriate next step in evaluating this 

technology. 

Possible effects on Pacific lamprey passage/immigration behavior should be included in 

the experiment, since lamprey are known to be sensitive to electric fields (e.g. electric 

barriers have been used in the Great Lakes tributaries to prevent sea lamprey from

establishing new spawning grounds). The final pilot should include a specific protocol for 

examining if there are responses by lamprey to the barrier. Human safety testing and 

consideration is also needed. 

The budget proposed is expensive, and the Council may wish to explore ways to conduct 

the test at lower cost. 

6 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200751300 - Eelgrass enhancement and restoration in the Columbia River 

Estuary through innovative site selection and planting techniques 

Sponsor: Pacific Northwest National Laboratory 

FY08-09 budget: $252,794 

Short description: Strong flows in the Columbia River likely limit the success of 

eelgrass seed dispersal and new plant establishment. We propose using innovative site 

selection techniques to identify 5-10 areas suitable for eelgrass enhancement, plant, and 

monitor success. 

(View full proposal online)

Recommendation: Ranked A2, Innovative, On-The-Ground, Highly Justified 

This well-written proposal documents the need for eelgrass beds in the lower Columbia 

River estuary, and hypothesizes the reason why no natural range expansion of eelgrass is 

occurring (shortage of seeds, and cannot expand upstream in Columbia River). The 

proposal uses innovative and detailed site selection techniques (GIS spatial assessment of 

previously identified environmental controlling factors and stressors) to identify 5-10 

areas suitable for eelgrass enhancement by planting. Eelgrass enhancement has been used 

elsewhere, but not in the lower Columbia River estuary. The project is clearly linked to 

subbasin plans and other ongoing efforts to improve habitat conditions in the Columbia 

River estuary. The experimental eelgrass plantings will be monitored not only for 

survival but also for use by focal and non-focal species. The project is aimed at salmonids 

but will also most likely benefit crabs and other invertebrates. Even black brant, which 

historically wintered in areas with eelgrass beds along the Pacific Coast of the United 

States, may benefit from this project. Most black brant now winter in Mexico. Personnel 

are well qualified and facilities and equipment are available for the project. The authors 

definitely understand the estuary and know the ongoing research of others. The eelgrass 

plantings will need further monitoring after completion of this project before a final 

evaluation of success can be made. 

200751600 - Enhancing Summer Instream Flow and Reducing Temperature in

Agricultural Watersheds 

Sponsor: Washington State University 

FY08-09 budget: $224,766 

Recommendation: Ranked A2, Innovative, On-The-Ground, Highly Justified 

This project proposes to explore groundwater recharge via direct seeding (no-till). The 

approach is not new but the research into effectiveness and use of no-till as a method to 

increase summer flows has not been adequately demonstrated. This pilot project and 

simulation model development exercise should provide the test and useful insight on notill effectiveness on infiltration changes and ground water recharge towards augmentation 

of summer flows – an M&E requirement that ISRP has called for over several years. 

The proposal provides a thorough background to the problem and the need to reduce 

surface water and soil runoff from tilled agricultural fields. The problem is well7 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

documented. Many streams in arid areas of the Columbia Basin suffer from low instream

flow and high stream temperatures which are critical limiting factors for native fishes. 

The sponsors propose to test a method (no till, direct seeding of agricultural crops) that 

could lead to increased infiltration and storage of water in the soil that will be released

during the summer and lead to increased flow. This project tests a method of farming—

no till-- that, if widely implemented, could significantly improve habitat conditions for 

native fishes. Apparently no till is a limited but accepted practice in eastern Washington

and this project could demonstrate to farmers that the no-till practice benefits fish as well 

as themselves, possibly making the practice more broadly acceptable within the 

agricultural community. 

The potential benefits from this project are great. It remains questionable, and perhaps 

outside the realm of this work, if potential increased discharge would be provided for fish 

or simply allow an increase in agricultural consumption of stream water. If improved 

water infiltration takes place as project sponsors anticipate, a wide variety of species will 

benefit. The project could benefit focal species by demonstrating that an agricultural 

practice (no till) can lead to improved stream flows and temperature. The project could 

benefit non-focal species that depend on high stream flows and lower water temperatures 

The proposed work complements many activities in the basin that address low flow and 

high temperature problems. 

The experimental design is well explained in general. Details on different management

practices are sketchy, and perhaps limited in application, and there may be issues of 

replication and sample size, as well as randomization, that could weaken the analyses. It 

was not clear if the sampling sites would include a range of soil conditions and parent

geological materials (to the extent this is possible in the Pataha). Nonetheless, a 

competent and proven team of researchers from WSU are involved, in collaboration with 

the conservation district (Pomeroy/Pataha watershed). Facilities, equipment and 

personnel seem very well qualified to do the work. The sponsors seem to be using stateof-the-art methods and will evaluate and modify existing models of subsurface flow 

processes. They are very experienced with the proposed procedures and techniques. 

There may also be an issue of scale; i.e., the amount of no-till area that might be required 

to stimulate a measurable response. Because the first year of the project will be devoted 

primarily to model testing, only 6 months will be available to evaluate infiltration field

trials; however, this should be sufficient to answer the initial questions. 

Useful, publishable, scientific results are potential with this work that is relevant over 

large areas within the Columbia River Basin. The objectives are clear and

accomplishable, and it appears that the work can be completed in the allotted time. An 

information transfer plan was included that listed reports, publications, and workshops. 

Details about data archiving were not given. Information will be disseminated through

workshops, technical publications, and conference presentations. The workshops will 

include farmers and land managers. 

A similar proposal was reviewed positively by ISRP in 2002 but not funded by BPA. 

8 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

This is one of the better proposals, and could provide strong evidence that an alternative 

agricultural practice (direct seeding) will benefit fish and wildlife. It is on the border of

innovative and on-the-ground, but meets the on-the-ground criteria because it involves a 

restoration technique and its evaluation, with test sites. The sponsors appear to be ready 

to implement immediately. 

200755700 - What was old is new again: evaluate traditional gears for selective 

harvest 

Sponsor: Washington Department of Fish and Wildlife 

FY08-09 budget: $444,971 

Short description: Three traditional fishing gears will be evaluated for the selective 

harvest of fall Chinook and coho salmon: beach seine; pound net; and fishwheel. We will 

coordinate this work with an advisory group so that socio-economic aspects are 

addressed. 

(View full proposal online)

Recommendation: Ranked A2, Innovative, On-The-Ground, Highly Justified 

Although the techniques of beach seining, stationary net traps (pound nets), and 

fishwheels have been used before in the Columbia River Basin, their potential to capture 

live fish with less harm than tangle nets or gill nets does provide innovative possibilities. 

This proposal will test, in detail, several types of traditional gear for capture and release. 

Sooner or later these selective fishing techniques will be tried again, and the quality of 

the proposal suggests that this team of scientists and fishers is well qualified to conduct 

such a trial. Post-release survival and reproductive success of fall Chinook salmon are 

included in the monitoring plan. The technical and scientific background is well 

presented with regard to the traditional gears themselves. 

The only weakness here was a lack of detail on how using the gears would be accepted

by commercial, tribal, and recreational fishers. Similar gear trials have been done in the 

Fraser River and elsewhere in British Columbia, and the lesson learned was that the 

fishing community should be involved. Project sponsors should research and review the 

Canadian selective fishery initiative. Is there strong local resistance to these types of 

harvest gears in the Lower Columbia? Measuring acceptance of the traditional gears by

stakeholders was not given much attention and would benefit from the addition of a 

natural resource sociologist to the team. The issue of seals and sea lion 

predation/mortality could also be problematic, especially with the pound nets. Bycatch of 

non-target species should also be considered. 

The costs of the project appear high to the ISRP; the Council should explore whether the 

project could be funded at a lower level without significant loss of information. 

Nevertheless, this proposal was well written and persuasive. 

9 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

Four Ranked, Innovative, On-the-Ground, and Adequately Justified 

Proposals 

200753500 - Physical and Biological Field Testing of a Flow Velocity 

Enhancement System (FVES) 

Sponsor: Natural Solutions 

FY08-09 budget: $318,310 

Short description: Natural Solution’s patented FVES provides migration cues using 

mechanically generated turbulent-flow fields. Field testing will evaluate effectiveness of 

induced flow for enhancing & guiding smolt migration, important for developing 

efficient bypasses. 

(View full proposal online)

Recommendation: Ranked B1, Innovative, On-The-Ground, and Adequately Justified 

This proposal was reviewed by the ISRP in several earlier solicitations (see below). 

In concurrence with earlier recommendations, the ISRP finds the proposed project 

deserves support. 

This proposal describes an on-the-ground field test of a flow velocity enhancement 

system (FVES) to provide mechanically produced turbulent flow fields to guide juvenile 

salmonids to safe collection and bypass facilities at hydroelectric dams. The 

demonstration site is in the Cowlitz River and takes advantage of an ongoing radio 

telemetry study to determine the effectiveness of the FVES system to alter migrational 

routes and improve fish collection during on/off days of FVES operation. Support and 

collaboration will be provided by WDFW, USGS, Tacoma Power, and Dr. Charles 

Coutant, and will be necessary to ensure a successful demonstration project. If successful 

at the demonstration stage, turbulent flow systems could next be situated and tested in the 

forebays of mainstem Columbia and Snake River dams for improving passage efficiency 

and reducing delay in passage (potentially reducing predation-related mortality). 

In the previous ISRP reviews, there was some concern for potential injury and mortality 

of juvenile and larval fish that may be entrained in the system. Since those reviews, the 

proposal sponsor conducted some tests of injury or mortality to juvenile fish entrained in 

the eductors. The sponsor stated that test results (Jones 2003) indicated that mortality of 

the test group did not exceed the control group. However, the proposal did not adequately 

provide test data results, only the in-house 2003 reference. The proposal needs to include 

provisions for testing of potential injury or mortality of juvenile salmonids entrained into 

or exposed to high velocities produced near the nozzle. 

Independent Scientific Review Panel Final FY 2007-09 Review (August 31, 2006) 

Recommendation: Fundable 

Comments: The problem regarding migrational passage problems of juvenile 

salmonids at hydroelectric projects is extensively described, and the rationale for 

potential passage benefits of an effective system is well defined. The “low flow” 

fish passage problem is identified in several subbasin plans. The proposal makes 

good use of studies in the basin that have described behavior of juvenile 

10 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

salmonids in response to flow, and identifies a device that might produce flows 

for guiding them to appropriate passage routes. 

There is nothing quite comparable being funded through the Fish and Wildlife 

Program. The proposal includes reference to an existing research project, the 

Cowlitz Falls Fish Collection Facility (presumably funded by Tacoma Power 

Public Utility District (PUD)), which includes radio tagged juvenile salmonids 

used to evaluate the effectiveness of a trap above Cowlitz Falls Dam. Fish that 

escape the trap will be available for use in evaluation of the device’s (eductor) 

effects on migrating fish. The trap is operated by WDFW. The operators will 

provide data on timing of fish migrations and other elements. The phased, 

systematic development of the eductor technology is good. 

They propose to set up the turbulence-generating eductors, characterize the flows, 

observe fish-flow interactions with a Didson camera, and enumerate the guidance 

of fish into a trap. It is not clear how they will express the flows and the 

turbulence intensity, or what aspect of the generated flows will be related to fish 

behavior. For example, if they see a fish response, will they know what precise 

aspect of the flow field caused it? Unless they are able to focus on particular 

parameters (e.g., velocity difference between the spot where fish reacted and that 

in reservoir, or turbulence intensity or size), they will not know what to 

manipulate experimentally in Phase II. There is a need to get away from trial-anderror that characterizes many of these studies. 

The proposal was responsive to earlier concerns (ISRP comment in 2003) that 

shear-related mortality might be a factor in this experimental system. This 

research has potential of facilitating or improving effectiveness of juvenile fish 

passage facilities in the basin such as the removable spillway weir (RSW). 

200752600 - Lake oxygenation pilot study: Improving Redband Trout habitat 

quality in Twin Lakes, WA 

Sponsor: Washington State University 

FY08-09 budget: $271,634 

Short description: This innovative project will evaluate the efficacy of lake oxygenation 

to improve summertime habitat for native redband trout in Twin Lakes, WA by 

enhancing dissolved oxygen levels in bottom waters. 

(View full proposal online)

Recommendation: Ranked B2, Innovative, On-The-Ground, and Adequately Justified 

The project describes an "on-the-ground" application of oxygen supplementation for the 

Twin Lakes, Washington. The application is intended to improve summer deep water 

dissolved oxygen conditions to benefit redband trout as a resident, inland focal species. 

Lake oxygenation is not a routine method to improve water quality in small 

impoundments as opposed to simple aeration (although previous applications were 

discussed) where anoxia limits deep water habitats. Ultimately, small impoundments 

11 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

have the potential to serve as refugia for native inland trout stocks used in reintroduction 

efforts or as broodstock for hatchery production. 

This project is designed with a treatment and reference lake, so evaluation will be built 

into the project. From an engineering standpoint, there is no description or design 

specifications about what is necessary (or likely) to achieve summer oxygenation in the 

treatment lake or how it will be determined as successful. As such there is too little detail 

in the monitoring design specifications to determine whether sufficient oxygen can be 

added to the bottom strata to actually reduce anoxia. The methyl mercury portion of the 

study was a unique component that adds value to the proposal. However, as a minor 

recommendation, the methyl mercury portion needs to be related to benefits to fish and 

wildlife species as well as the human risk perspective. Moreover the paired lake 

(treatment/control) is a generally good approach, but it is unclear whether the two lakes 

are sufficiently similar prior to treatment to avoid misinterpretation about after treatment 

effects (i.e., post-treatment response is due to oxygen supplementation). It is unclear 

whether baseline measurements (pre-treatment) will occur as well; thus, we would 

recommend a pre-treatment survey be included. Lastly, the sponsors describe measuring 

for a biological response following a single treatment year. While this funding is for a 

short period, is there an expectation/prediction that a longer-term treatment is needed to 

uncover an effect or is a one-time treatment sufficient? 

200751800 - Evaluation of artificial upwelling to enhance lower Columbia River 

Gorge chum salmon spawning 

Sponsor: Pacific Northwest National Laboratory 

FY08-09 budget: $173,590 

Short description: Evaluate efficacy of using artificial hyporheic upwelling to enhance 

chum salmon spawning habitat. 

(View full proposal online)

Recommendation: Ranked B3, Innovative, On-The-Ground, and Adequately Justified 

This is a well-prepared proposal to develop artificial upwelling zones in chum spawning 

areas. It meets the innovative criteria, but success is uncertain in this research and 

development work. Nonetheless, broader application may be possible for this technique 

that has been used for lake shore spawners, but not in streams. The proposal seeks to 

increase available chum salmon spawning habitat by employing a method to artificially 

upwell warmer water to attract spawning fish. The problem was well defined and 

adequately justified. 

The primary response measure will be the number and location of chum redds relative to 

the artificially-created upwelling areas. It would be helpful to add survival to emergence 

to the variables monitored, if other confounding factors could be controlled (e.g., density, 

substrate). The testing and outcome will depend upon the magnitude of the chum run and 

egg-to-fry survival. The proposal lacked sufficient detail about the inclusion of estimates 

of egg and alevin survival in redds located in the vicinity of the upwelling sites that were 

created, and that constitutes the main test of the advantage of the proposed approach. 

12 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

There is a need to monitor survival of fry to emergence as a more thorough testing of the 

proposed methodology. The sponsors acknowledged that they will not attempt to 

determine if an observed increase in spawner density results from attraction to the area by 

upwelling water or simply from increased abundance of adults. Furthermore, it is not 

clear from the proposal that they will have enough water to create adequate upwelling. 

Although it is not clear from the proposal if this technology represents a long-term

solution to chum salmon spawning in the lower river, it would serve as a demonstration 

that hyporheic upwelling is critical to redd selection in this species, if results were not 

confounded by density. A high density of chum spawners may force spawners into 

marginal habitat. Furthermore, superimposition of redds limits chum spawning success, 

and thus this study’s results. 

This is a technique that perhaps does not address the limiting factor for chum in the 

Columbia River. Given that 90% of their life history is salt water, variability in 

abundance from year to year might indicate that the problem is not in fresh water. The 

work is interesting and could provide a useful approach to expanding chum salmon 

spawning areas and conceivably lead to an increase in chum abundance if not limited 

elsewhere. The amount of water that can be obtained from the hyporheic zone may be 

insufficient to induce spawning. 

The proposed work is related to several other chum salmon projects funded by BPA. The 

results could be useful to a BPA project to restore chum to Duncan Creek. However, it 

does not involve the restoration of natural riverine/riparian and hyporheic interactions but 

rather creates artificial upwelling zones using perforated pipe. This will limit the spatial 

extent of the enhanced spawning area since it will not be feasible to install pipes over 

many potential chum spawning areas of the mainstem river. The technique may not be as 

effective as the development of off-channel spawning habitat but may have an application 

in off-channel spawning habitat if it improves on survival to fry emergence. 

Methods are appropriate, follow logically from the objectives, and were well-documented 

in the scientific literature. The methods described should allow the sponsors to 

accomplish the stated objective in the allotted time frame. Methods for data analysis were 

adequately described. The pilot study will be conducted at only one location. 

Consequently, one uncertainty is whether a sufficient quantity of hyporheic water can be 

delivered to the potential spawning site to induce spawning. If the quantity of hyporheic 

water is small, few or no chum may be induced to spawn. 

The facilities, equipment and personnel are well qualified to carry out this work. Plans for 

information storage and reporting were clearly described. The sponsors state that results 

would be shared with other researchers involved in increasing chum productivity. (e.g., 

project 200105300 Reintroduction to Duncan Creek). The sponsors have a strong history 

of producing peer-reviewed publications and undoubtedly will publish the results of this 

work if it is successful. 

13 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

This project could attract other late-spawning species such as late-run coho, which might 

interfere with chum reproduction. In general, however, the project will not negatively 

impact (and may benefit) non-focal species. The project has the potential to benefit chum

salmon by increasing their spawning area possibly leading to increased production of 

juveniles and overall abundance. 

This is an interesting study, but it remains unclear if an increase in chum recruitment 

would result. This might have application for other species. The proposed upwelling 

system may develop maintenance problems that could limit some applications. 

200754200 - Shad for Nutrient Enhancement -- Demonstration of Fishery Supply, 

Disease Evaluation, Product Type and Potential Use 

Sponsor: Washington Department of Fish and Wildlife 

FY08-09 budget: $163,400 

Short description: A pilot project to evaluate the efficacy of using the abundant 

Columbia River Shad run as a resource for stream nutrient enhancement throughout the 

Basin. Potential would be evaluated by four criteria: availability, disease risk, fish 

product, and demand. 

(View full proposal online)

Recommendation: Ranked B4, Innovative, On-The-Ground, and Adequately Justified 

This project would explore an obvious use of unwanted shad carcasses as a nutrient 

enrichment tool for streams, but any effort of this nature deserves a thorough and well 

documented monitoring and evaluation program. Success is subject to acquiring shad 

(capture that needs to be non-incidental on salmon and trout capture) and a company to 

produce analogs. The possibility of using shad or pasteurized shad carcass analogs is 

intriguing, and in general this proposal describes an innovative project. However, no 

proposed location or experimental design is given, so it was difficult to classify it as onthe-ground. Capture of shad to use in development of carcass analogs is not without 

problems, including shad capture and salmon interception, as well as potential conflict 

with a developing fishery. 

This screening work is to provide pathology evaluations, and product quality testing. The 

work is not in itself innovative, the shad use is purported as the innovation, and is 

required according to the investigators because salmon carcasses demand will exceed 

supply from hatchery fish -- the latter remains to be seen. Other fishes have been 

considered elsewhere (e.g., pollock). 

The investigators have a very good background in this field, with current work on salmon 

carcasses, carcass analogs from salmon, and inorganic nutrient experiments in progress. 

The shad work is an interesting addition to those efforts. The technical and scientific 

background section is well presented. The proposal presents a brief but adequate 

description of its relationship to other projects. It would have been helpful to have 

summarized the findings of other carcass and carcass analog trials in more detail. 

14 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

The design, methods, and location of the study needed additional detail for a proper 

scientific evaluation. For example, at what scale would shad carcasses or carcass analogs 

be introduced (reach versus whole stream)? What would be the spatial and temporal 

variation in shad placement and density? How will control sites be established and 

monitored? Most importantly, where will the work be done and what assurances will 

there be that other enhancement projects will not confound the results? The project is 

investigative and developmental towards a potential tool for nutrient enrichment (shad 

carcass analogs) but some logistical issues remain (e.g., supplier). The facilities, 

equipment and personnel are well qualified to conduct this work. 

Deliberately introducing the carcasses of a non-native species to streams deserves very 

careful monitoring, both of focal and non-focal species. The timing and form of nutrient 

additions will be very important. Unanticipated effects on non-focal species could take 

place and will require careful scrutiny. Impacts are unknown for the most part at this 

point; a component of the investigation is to determine potential impacts (e.g., disease). 

There were few details on where they are going to get the shad, where they're going to 

place the shad, or what their experimental design is. More details would be needed before 

this could be funded. Nonetheless, the lead scientist has a good track record on other 

related efforts. 

Five Ranked, Innovative, Research-oriented, and Highly Justified Proposals 

200753800 - Predicting the future effects of climate-induced stream warming on 

spring Chinook salmon and their predators in the John Day River Basin 

Sponsor: University of Washington 

FY08-09 budget: $214,959 

Short description: We propose an innovative modeling approach that integrates climatechange projections, riparian land-use scenarios, and stream temperature modeling, to 

predict potential impacts on Chinook salmon, smallmouth bass and northern pikeminnow. 

(View full proposal online)

Recommendation: Ranked R1, Innovative, Research-oriented, Highly Justified 

This proposal describes a research project to develop models for use as a planning tool to 

incorporate climate change effects into habitat protection and restoration management

and to predict future climate change impacts to spring Chinook salmon, the focal species 

in the John Day River subbasin. On that basis, the project could make essential and clear 

assistance to subbasin planners and managers. The tasks are not "on-the-ground", but the 

timelines provided indicate that the model development and analyses would be 

accomplished within the 18-month schedule requirement. 

An excellent overview of the problem is provided in the technical background section, 

along with a thorough discussion of key references. The logical need for applied research 

on the effects of climate on fish populations is explained. The project proponents will use 

15 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

a series of models that cleverly link climate change, thermal niches, enhanced invasive

species, and focal species survival. 

This project will provide benefits to fish and wildlife through development of a modeling 

tool which will help to predict species distributional responses, patterns of species cooccurrence (establishing the potential for predatory or competitive interactions), and 

potential future impacts by smallmouth bass and northern pikeminnow on Chinook 

salmon in a changing climate. In addition, the model will also be used to identify critical 

areas for riparian habitat restoration, protection, and conservation easements to mediate 

stream warming in a changing climate. This objective is clearly one of the first steps 

needed for future protection and conservation of John Day spring Chinook salmon. 

It is also certain that changes in stream temperatures will have a dramatic effect on the 

coexistence of native and nonnative cold-water fish species in the John Day River, 

including bull trout, westslope cutthroat, rainbow trout and steelhead and nonnative 

brook trout. Model predictions should also be possible for these species. 

In summary, the ISRP finds this proposal to be an innovative research proposal 

addressing a high priority in the Fish and Wildlife Program, climate change effects on 

spring Chinook salmon in the John Day River, and although it does not precisely fit the 

on-the-ground requirement, it is an excellent proposal deserving support. If it is not 

selected for Innovative Proposal funding, the ISRP believes that it deserves support for 

inclusion in the Fish and Wildlife Program under some other funding mechanism.

200755400 - Using advanced technologies to help reduce the impacts of global 

warming on anadromous and resident fish populations in the Columbia Basin 

Sponsor: US Forest Service - Rocky Mt Research Station 

FY08-09 budget: $294,302 

Short description: This proposal examines effects of global warming on critical habitats 

for salmonid fishes, develops and applies innovative management tools to lessen the 

effects of climate change, and provides training to facilitate tool adoption. 

(View full proposal online)

Recommendation: Ranked R2, Innovative, Research-oriented, Highly Justified 

This exemplary proposal addresses a high priority issue in the Pacific Northwest and for 

the Fish and Wildlife Program -- climate change effects on salmonids. It exceeds/meets 

almost all ISRP ranking criteria and is a comprehensive modeling project which could 

yield some new and innovative management tools to deal with climate change and 

headwater Columbia River Basin salmonids. However, the ISRP concludes the project 

does not meet the on-the-ground criteria because implementation of results would be 

longer term and difficult to achieve in the time frame of the innovative criteria 

There is clearly a need for improving the processes available to managers for prioritizing 

where and when to implement mitigative actions in response to climate change and 

warming. The proposal does a good job of explaining the problem and previous work is 

16 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

well referenced. However it is very complex and results could not be used to direct 

improvements in survival or productivity in the 18 month time frame. 

Discussions with stakeholders and managers have to be held and models calibrated, run, 

and verified. The proposal could therefore be improved by careful review and revision of 

objectives and possible reduction in scope. If this research project were funded, or even a 

part of it, the results would provide a foundation for future work. Resolving mitigation 

for climate change is going to be a long term process and any well-done incremental 

steps are important. 

200750800 - Designing Pre- and Post-Fire Restoration Strategies for Recovery 

of Salmonid Habitats in a Period of Climate Change and Increased Forest Fire 

Disturbance 

Sponsor: Earth Systems Institute 

FY08-09 budget: $88,300 

Short description: We propose to apply new watershed analysis tools to identify critical 

pre-fire and post-fire restoration and management strategies for enhancing recovery of 

Chinook, steelhead, and bull trout habitats in a period of increasing natural disturbance. 

(View full proposal online)

Recommendation: Ranked R3, Innovative, Research-oriented, Highly Justified 

This innovative proposal ranks with the other climate-change proposals as a highly 

justified, priority modeling, assessment tool, for aiding watershed rehabilitation and 

evaluation. This is developmental research that deserves support and is proposed by an 

expert team (lead by a renowned geomorphologist at Earth Systems partnered with an 

established leader in fish habitat and biology with USFS) that will develop watershed 

analysis tools (NetMap) along with a digitized watershed database to be made available 

to other scientists, stakeholders (many groups) and via workshops. Fire disturbance and 

the associated rehabilitation options will gain increasing priority with the warmer 

environment predicted for the Columbia Basin, and elsewhere. The assessment and 

modeling approach is a good test of the application of pre- and post-fire restoration 

strategy using modern tools and techniques. Validation over a longer time frame than 

accommodated in this solicitation may be appropriate, and should prove very useful. 

The first analysis is proposed for the Methow basin but the potential for broader 

application seems high; a value-added component is that the digital watershed database, 

in conjunction with new analysis software, could provide the basis for development of a 

regional monitoring and evaluation framework. The latter requires further description 

and development, but shows promise. The proponents should be encouraged to develop 

this tool to the implementation stage, and provide for field-testing and on-the-ground 

application. This type of developmental research within the Columbia Basin needs an 

avenue of support that may not fit this particular solicitation well (i.e., not on-the-ground 

for the most part, lacking evaluation of effectiveness, and difficult to complete in the 

limited time frame), but is nonetheless needed. 

17 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200750200 - Application of Innovative Acoustic Telemetry Technology to 

Underpin Statistically-Valid Survival Estimates for Chinook Salmon in the 

Nearshore Ocean Off the Mouth of the Columbia River 

Sponsor: Pacific Northwest National Laboratory 

FY08-09 budget: $532,680 

Short description: The purpose of this project is to establish innovative methods that can 

enhance and expand into the nearshore ocean estimates of juvenile salmonid survival and 

migration patterns, especially for subyearling Chinook salmon. 

(View full proposal online)

Recommendation: Ranked R4, Innovative, Research-oriented, Highly Justified 

This important research project is a study to use available acoustic tagging technology to 

improve estimates of survival and distribution of Chinook in the Lower Columbia River 

Estuary, specifically very near the river mouth and in the plume. An incremental 

approach to monitor tagged individuals is proposed with receiver arrays set up in about a 

20 kilometer range around the river mouth. This appears to be a useful approach to 

improve data in this poorly known area. The grid proposed for monitoring is more 

comprehensive than previous studies in these reaches, but in general the project is not 

innovative. The proposal is well written. Methods and work elements are extensively 

detailed and justified, citing pertinent references. If the results were linked to survival 

estimates in other reaches of the Columbia River they could help direct improvements in 

the survival or productivity of Chinook. As a stand-alone project however they are not, 

and therefore the project is not on the ground. The proposal would also be improved by a 

better explanation of the relationship between U.S. Army Corps of Engineers 

contributions and the current Fish and Wildlife Program request. 

200751100 - DNA typing to identify native inland Oncorhynchus mykiss 

Sponsor: Washington State University 

FY08-09 budget: $217,364 

Short description: New DNA-based tests which distinguish the inland and coastal forms 

of rainbow trout will be developed. These tests should be widely useful for genetic 

characterization of Columbia Basin rainbow trout populations. 

(View full proposal online)

Recommendation: Ranked R5, Innovative, Research-oriented, Highly Justified 

This is an innovative research project to develop new (updated) Single Nucleotide 

Polymorphism markers (SNPs) from AFLPs to identify hybrids between hatchery 

rainbow trout and native redband trout. It does not meet the criteria of an on-the-ground 

pilot or demonstration project. However, this research proposal could produce benefits to 

fish and wildlife in a shorter time frame than some of the other research proposals. 

Identifying hybrids between hatchery rainbow trout and native redband trout has been 

challenging because these species are so closely related. Genetic markers that have

proved useful for identifying hybrids between rainbow and cutthroat trout are not 

informative for these related species. Any methodological advance would be helpful. 

18 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

The existing methods for discriminating between these species and their hybrids have 

hindered native inland trout conservation and restoration. 

The personnel have a demonstrated track record of accomplishment. There is no doubt 

they could fulfill the goal of developing additional markers within the time frame. 

Sponsors have a record of widely disseminating data and results through all appropriate 

venues (peer-reviewed journals as well as directly with managers). 

The benefits to fish and wildlife (fish) would be through better decision making. The 

magnitude of the problem (hybridization) and the likelihood of remediation (removal of 

hybrids - with reintroduction) is hard to judge from the proposal. 

Forty-Five Unranked Proposals 

200750000 - A New Aging Technique for Lake Trout and Northern Pikeminnow 

Using Allometric Relationships between Fish Size and Otolith Mass 

Sponsor: University of Montana 

FY08-09 budget: $115,240 

Short description: We propose to develop and test multiple regression age models for 

northern pikeminnow and lake trout using allometric relations between fish size and 

otolith mass. 

(View full proposal online)

Recommendation: Unranked 

The proposed project is essentially a methodological research project rather than an “onthe-ground” project. Moreover, the sponsors did not truly connect how the information 

(and methodology) is a highly critical uncertainty and would directly improve focal 

species populations rather than a basic improvement in understanding population 

dynamics of lake trout and pike minnows. 

As for the proposed project, establishing a direct relationship between otolith mass and 

body size may provide the basis for useful shortcut to aging (presuming there is also a 

relationship between age and otolith size, which preliminary data appear to suggest). The 

project sponsor contend that the methods to be ground-truthed will provide a substantial 

time and cost savings; however, no support is provided for this as to the magnitude of the 

savings over more commonly applied otolith aging methods (counting annuli). 

The proposal could be strengthened by the sponsor providing a more substantial 

justification of the specific "need" for alternate aging methods, as well as a direct linking 

of how age data will be used by resource co-managers. 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200750100 - Adapting tree-ring techniques to reconstruct stream environmental 

histories from the growth increments of long-lived freshwater mussels 

Sponsor: Oregon State University 

FY08-09 budget: $73,502 

Short description: We apply tree-ring techniques to i) develop chronologies from the 

growth increments of freshwater mussels, and ii) use mussel and tree-ring chronologies to 

reconstruct aquatic environmental variability prior to the beginning of instrumental 

records. 

(View full proposal online)

Recommendation: Unranked 

The proposal aims to reconstruct continuous annual temperature regimes from river 

systems with freshwater mussel populations, based on variation in annual growth rings. It 

will be helpful in reconstructing thermal conditions for the last century; however, it will 

probably not be able to reconstruct pre-development thermal regimes because of the lifespans of the region's mussel species. The project is innovative in the sense that this 

technique has not been used with freshwater mussels in the Columbia River Basin before, 

although it has been used with marine bivalves in other locations. It has the potential to 

show trends over the last century but is of limited use in forecasting changes over the 

next century. 

The technical background is clearly explained, although the relevance of the project to 

specific fish and wildlife management issues in the Columbia Basin could have been 

more thoroughly developed. In particular, the background could have explored the types 

of thermal changes, and their causes, that might be reflected in mussel growth patterns. 

Additionally, beyond the need to fill in the gaps in temperature and flow records in 

various subbasins, the proposal does not indicate why this research is strongly needed at 

this time. For example, the authors could have mentioned how these data could be used to 

choose locations for habitat improvement projects. The methods and analyses are well 

described, and the scientists have clearly had considerable experience with performing 

these types of studies. It would have been helpful to have included an objective explicitly 

describing how the results of this study would be incorporated into environmental 

planning in the context of future habitat restoration. This would have demonstrated the 

link between what happened in the past and how the information from the study can be 

used to improve management actions in the face of additional climate change. 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200750300 - Assessment of Functional Biological Differences between Natural 

and Hatchery-Raised Redfish Lake Sockeye Salmon 

Sponsor: University of Idaho - Aquaculture Research Institute 

FY08-09 budget: $199,751 

Short description: The project will use microarray analysis and quantitative PCR to 

quantify differences in gene expression between natural and hatchery-raised Redfish 

Lake sockeye salmon. Functional genetic differences will then be correlated with 

reproductive success. 

(View full proposal online)

Recommendation: Unranked 

The proposal is for the innovative use DNA microarrays to evaluate which genes are 

being expressed in natural and hatchery sockeye salmon from Redfish Lake. It is not an 

on-the-ground pilot or demonstration project. 

Microarrays are very recently developed technology useful in a variety of applications to 

assess differences in gene expression. They have not been used in the Columbia River 

Basin Fish and Wildlife Program. In the near term this work would lay an important 

foundation for beginning DNA microarray technology development with salmon. It is 

unlikely to provide benefits to fish or wildlife in the near term. 

No explanation is provided why Redfish Lake sockeye salmon were chosen as the 

experimental subject. Why not steelhead? Why not spring-Chinook? The experimental 

design was not adequately summarized. The sponsors suggest that they were going to 

follow both hatchery and natural fish through the entire life-cycle, including returning 

anadromous adults. No natural anadromous adult sockeye salmon have returned to 

Redfish Lake in years. Consequently it was not clear what the various sources of fish 

would be. 

It is not clear how any differences detected in expressed genes would be interpreted. The 

summary states that the investigation would include survival through adult stages, but 

that would take more years than the innovative project covers. Further, because so little is 

known about the functional differences in gene expression between individuals and 

populations, it is not likely that differences observed between natural and hatchery fish 

will be easily interpreted. Certainly it would be difficult to extrapolate any observed 

differences to rearing conditions that could be manipulated or to relate these differences 

to survival differences. 

A general framework with two objectives, an experimental design, and identification of 

the statistical methods used to analyze and interpret the data are provided. Because the 

methods used are atypical in this type of application, a much clearer explanation would 

be required for the ISRP to conclude that the experimental design being used could lead 

to interpretable data, under any assumptions of differences between natural and hatchery 

fish. Specifically, the sponsors propose to identify differences in gene expression 

between natural and hatchery fish, and then relate (correlate) this difference with survival 

21 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

differences. They are also looking at developmental differences in gene expression. 

What is not clear to the ISRP is how you would know what the gene expression would 

have been at an earlier life-stage in the various fish that survive. It certainly will not be 

known what the gene expression would have been in the fish that do not survive. 

No estimate is provided of the benefits to fish and wildlife, that is, how they will take the 

differences they detect and turn that into altered fish culture practices and how that in 

turn will yield improved survival in the hatchery fish. No timeline is given for moving 

this technology from the laboratory/experimental phase to yield improved fish survival. 

200750400 - Automated Scale Image Analysis (ASIA) 

Sponsor: Biopar, LLC 

FY08-09 budget: $198,250 

Short description: A system for quickly and automatically extracting data from fish 

scales (scale cards) to automatically age fish and perform stock identification. 

(View full proposal online)

Recommendation: Unranked 

This project involves proof-of-concept demonstrations of Automated Scale Image 

Analysis (ASIA). The project is innovative in that it applies a technology developed 

using National Science Foundation funding to Columbia River salmon populations. 

However, the ISRP concludes that agencies and the sponsors on their own initiative could 

undertake this proof-of-concept work, as the technology has already been developed. If 

agencies like this technology they will adopt it regardless of whether or not this project is 

funded. If they do not like the technology, they will not adopt it. The technical and 

scientific background in the proposal is insufficient, i.e., one short paragraph that refers 

to information in an attachment. No problem is identified. No scientific and technical 

justification for the project is provided. The project’s goals (increase speed and improve 

the accuracy of ageing fish scales or, in some cases, stock identification) are not directly 

linked to the goals and objectives of Columbia River subbasin plans and regional 

programs. According to the sponsors, there is already some ongoing work with Nez Perce 

Tribe and the Oregon Department of Fish and Wildlife to demonstrate feasibility of this 

technology. The online form identifies BPA project 198805301 for aging and stock 

identification work (if this proposal is funded). The project objectives are stated as tasks, 

e.g., “collect and scan enough scale cards” and “demonstrate the automated throughput” 

rather than as desired outcomes. 

There is no explanation in the proposal’s methods section of how the automated scanning 

of scale acetates can be used to perform the "stock identification" function or task. The 

explanation of the statistical confidence in the aging of the fish from automated reading 

of the scales is not very clear. The inclusion of a lawyer as a co-principal investigator on 

this project is not adequately justified. The sponsors’ CVs do not include any reports or 

publications of their previous work. Information transfer involves reports, public 

databases, and public presentations, but would be improved by scientific peer-reviewed 

publication of results. There are potential benefits to the Fish and Wildlife Program if the 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

technology improves efficiency and cost effectiveness of scale ageing. Reducing the 

current time frame needed to age fish scales, however, would not necessarily lead to 

estimation of vital parameters and increases in abundance or productivity of Columbia

River salmon. 

200750500 - Catching Predator fish with commercial traps 

Sponsor: Gulf Vessel Management Inc. 

FY08-09 budget: $400,000 

Short description: Place baited commercial traps (pots) in pools with high predator

volumes. Traps keep fish alive thus only targeted fish will be eliminated

(View full proposal online)

Recommendation: Unranked 

The proposal was incomplete. The proposal narrative is a brief three paragraphs that does 

not provide sufficient information to conclude that the methods and tasks are innovative 

and that there would be benefits to fish and wildlife (fish in this case). The proposal does 

not appear to include innovative methods or technologies. 

200750600 - Chiwawa River Adult Spring Chinook Otolith Study 

Sponsor: Wild Fish Conservancy (formerly Washington Trout) 

FY08-09 budget: $47,913 

Short description: Analyze microchemistry of otoliths from post-spawn adult species to 

determine location of pre-smolt overwintering habitats 

(View full proposal online)

Recommendation: Unranked 

This proposal is essentially a methodological research project that approaches questions 

using methods widely used in the Columbia and other watersheds (e.g., east coast shad 

and Great Lakes steelhead) or circumstances, thus does not merit innovative standing. 

The project, in and of itself, will not improve populations but could provide data to assist 

managers in understanding the biology of the Chiwawa Chinook and make betterinformed decisions. 

However, the proposed work as presented does not meet scientific criteria largely 

because of an inadequacy in establishing chemical “signatures” for the reference streams. 

The approach, design, methods, and breadth for collecting water and establishing the 

scale of resolution to evaluating life-history differences is critical, especially here to 

assign the overwinter localities in assayed fish. There is also uncertainty about the actual 

sample sizes to be used (N>2 up to n=50) and whether this would be sufficient to answer 

the basic question (uncertainty). 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200750700 - Crumble-Crete Habitat Revegetation and Stability Blocks - 

Development of degradable bank protection/reveg block to provide temporary 

stability during recovery of natural bank-stabilizing vegetation. 

Sponsor: WDFW and CRITFC 

FY08-09 budget: $27,738 

Short description: Hollow blocks will be formed (trials of straw, gravel and cement) and 

installed in a ditch bank, filled with soil and planted with riparian vegetation. Block 

strength, transport, durability and rate of root development in the fill soil will be 

monitored. 

(View full proposal online)

Recommendation: Unranked 

This technique has been used elsewhere (e.g., coconut and concrete mats) yet is new to 

the Columbia Basin, and is potentially promising. The physical testing of the technology 

as proposed is not adequate, and lacks valid comparison to other techniques. Pilot tests on 

the crumble-crete might be included or combined with another larger restoration project 

and monitoring effort, in comparison to other restoration methods. The proposal doesn't

go far enough to develop the comparative evaluation in physical or biological terms. 

Even as proposed, it may be difficult to complete in the time frame of this solicitation.

An explanation of the manner in which the crumble-crete blocks are degradable was 

required, including discussion of the tests to determine their durability, duration, and 

benefits. 

Although the concept is interesting, few details about location, implementation methods, 

or post-implementation monitoring were provided. There appeared to be no biological 

monitoring, other than possibly monitoring the survival of tree cuttings planted among 

the crumble-crete blocks. The sponsors do not describe how long the tests for vegetative 

growth and block degradation will last. There was very little discussion of the effects of 

the project on either focal or non-focal species. Although the project could benefit focal 

and non-focal species by improving riparian habitat conditions, the sponsors did not 

discuss the potential benefit. 

In sum, the proposed project could benefit riparian restoration actions, but it probably is 

not of highest priority in most rehabilitation plans. Discussion that would have improved 

understanding the potential application include describing the sites where crumble-crete 

application is appropriate for streambank stabilization compared to sites where willow 

bundles or natural channel meandering would eventually result in quality fish habitat, and 

discussion of the selection of sites where crumble-crete application is appropriate. 

Perhaps there are particular river channel configurations that are better suited than others 

for this treatment, or perhaps it has limited application. Potential negative effects of 

crumble-crete on habitat were not considered, if any. However, the sponsors did clearly 

point out some of the problems with "non-deformable engineered bank stabilization, such 

as riprap and rock barbs." 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200750900 - Develop structure for implementing and maintaining a Master 

Sample of rivers and streams in the Columbia Basin, and develop statistical tools 

for analyzing Master Sample applications. 

Sponsor: Oregon State University 

FY08-09 budget: $386,806 

Short description: The project will create and administer a Master Sample from which 

sub-samples can be drawn to meet specific needs of particular monitoring programs, 

create compatible web-accessible analysis statistical tools, and advise on Master Sample 

applications.

(View full proposal online)

Recommendation: Unranked 

The ISRP and ISAB have expressed concern over the adequacy and potential redundancy 

in the collection of data on fish populations and habitats. Having a Master Sample is 

probably a good idea, but adopting it will require buy-in from the agencies that collect the 

data. That buy-in may be more difficult to achieve than the Master Sample. It is not clear 

that the results of this project will be used by other organizations. Creation of a Master 

Sample and training in its use does not necessarily mean that fish and wildlife will 

benefit. Evidence of support from potential users in the region should be provided. 

The problem of overlap in monitoring responsibility, site selection, and indicator 

variables is briefly presented. A weakness in the technical and scientific background 

section is that it does not address the "gate keeper" that is required to implement any 

Master Sample. Additional justification concerning the innovative nature of the project 

and benefits expected is necessary. An improvement in the proposal would be 

identification of the limits BPA and Council wish to have on monitoring within the Fish 

and Wildlife Program and how this Master Sample could be used to achieve those goals. 

The work is related to EPA funded work in the region. The sponsors state that the project 

would complement PNAMP and CSMEP efforts by creating the Master Sample 

framework thus allowing implementation of particular designs. Additionally the project 

would make statistical tools and guidance available to organizations on Master Sample 

applications. Perhaps this proposal should be incorporated into CSMEP, not generated as 

a stand-alone effort. 

The objectives are clearly stated in the proposal. The work elements are appropriate for 

the objectives. The facilities and personnel are appropriate. The personnel have a history 

of achievement in this area. No provisions for monitoring and evaluation of the products 

and services offered to others are mentioned. A plan to evaluate adoption of the Master 

Sample would improve the proposal. 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200751000 - Development of a Low-cost Dual-Frequency Acoustic Tracking 

Capability for Ocean & Freshwater Components of the POST Tracking Array 

Sponsor: Kintama Research 

FY08-09 budget: $330,199 

Short description: We propose to develop a small and long-lived acoustic tag 

compatible with the POST array. This should allow seamless measurement of movements 

and survival of ocean-type chinook >90 mm FL, and permit direct assessment of the role 

of the ocean on survival.

(View full proposal online)

Recommendation: Unranked 

This project is an extension of existing POST Tracking Array study and proposes 

methods to incorporate a smaller tag that uses a higher frequency into POST. The ISRP 

concludes that the development of such a tag would be an important technological break 

through. Such a tag would enable data acquisition on river, estuary, and ocean 

distribution and survival of wild chinook (ocean type) (> 95 mm) as well as "pre smolts" 

of other species. However, this project is similar in design to a previously-funded 

innovative project. As such, the surgical and field trials with a new version of the 

acoustic tag, array optimization, and deployment of a test array do not seem sufficiently 

different from previous and ongoing BPA-funded projects to be considered innovative. In 

addition, there is no compelling evidence that this project will contribute to direct 

improvements in the survival or productivity or Columbia River fish -- the main POST 

project does not directly improve survival or productivity of salmon. Consequently, the 

proposal does not fit the definition of “on-the-ground” used in the solicitation. 

The assumed minimum size range of smolts that could be tagged with the new V6 is 90-

95 mm. The proposal would be improved if information was presented on how this 

compares to the minimum size of ocean-type Chinook salmon smolts in the Columbia

River. Collaboration efforts are not given. The background section of the proposal could 

be improved as it contains very few citations to papers in the peer-reviewed scientific 

literature or technical literature. The ISRP also suggests that the proposal could be 

improved by provision of more information on collaborative efforts with other 

researchers working on acoustic tagging in the Columbia River Basin. 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200751200 - Documentation of food-web linkages in the mainstem Columbia 

River: towards understanding the role of invasive species and establishing a 

baseline trophic state 

Sponsor: US Geological Survey - Cook 

FY08-09 budget: $337,374 

Short description: We propose to use stable isotopes to document food web linkages in 

the Bonneville Reservoir. We propose to determine isotopic signatures of representative 

trophic levels and use multi-source mixing models to quantify food web sources and 

pathways 

(View full proposal online)

Recommendation: Unranked 

Stable isotope analysis (SIA) is not a new method but has not yet been applied in the 

Columbia River (except for a thesis project in the estuary and a study of bear ecology); 

thus the project marginally meets the innovation criteria. The effects of invasive species 

on fish and wildlife in the Columbia River Basin deserve attention. However, using SIA 

to trace food web relationships involving invasive species is complex, and the ISRP 

concludes that the proponents have underestimated the difficulty of the task. At this stage 

of our understanding of Columbia River ecosystems, results of SIA analyses will not 

contribute to direct improvements in survival or productivity of Columbia River 

salmonids. Therefore the project is not on the ground. The methods are well described 

and sound but do not measure properties that fish and wildlife managers can use directly. 

This proposal is definitely research oriented and would take far longer than 18 months to 

achieve results. It deals with a research need that should be a high priority in the 

mainstem Columbia and Snake reservoirs, but the proposal is not fully developed. 

200751400 - Effectiveness monitoring of in-stream habitat restoration using tools 

from population ecology 

Sponsor: US Forest Service - Pacific Northwest Research Station 

FY08-09 budget: $193,624 

Short description: Habitat availability and diversity have been identified as limiting 

factors for rearing juvenile salmonids. We propose research to aid monitoring and 

evaluation (M&E) efforts used to scientifically validate the effectiveness of habitat 

restoration. 

(View full proposal online)

Recommendation: Unranked 

This is a project to evaluate habitat restoration strategies in the Entiat subbasin, with extra 

effort applied to measure density dependence within treatment and reference reaches. The 

proposed project could improve knowledge about processes relating habitat restoration 

and fish response. As such it is collecting basic life-history data on fish, not actually 

attempting an innovative restoration approach. Furthermore, plans to evaluate how 

knowledge gained in the project would apply to larger scale restoration activities are 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

lacking. That is, will results obtained from this investigation necessarily apply to other 

situations or be localized in time and space? 

The proposed project seems to be determining if mechanistic processes relating 

macroinvertebrate abundance, foraging rates, and density dependence, coupled with 

bioenergetics models, can be used to predict carrying capacity at larger scales. A series of 

experiments are proposed to allow hypothesis testing. The project would compare growth 

and survival of fish in treated versus untreated stream reaches. 

The general problem of establishing the capacity of a stream for salmon and steelhead is 

identified and appreciated by the sponsors. In-stream structural modifications have had 

variable success so the sponsors identify the need for new protocols for the effectiveness 

monitoring of restoration actions. The solution to this problem, for generating both 

realistic program objectives for abundance and productivity for salmon within a 

watershed, and for choosing among restoration sites and actions should be explained 

more clearly. 

The sponsors note that key difficulties include assessing the biotic response of fish and 

macroinvertebrate populations. Although experiments conducted using artificial 

placements of structure on a small scale are proposed to enable replication and 

manageable microhabitat units, it is not clear that the work proposed will produce a 

solution to the dilemma. 

The objectives and experimental design are reasonably clear. Provisions are made for 

analysis of experiments to identify processes that relate some habitat restoration activities 

to fish response. What is absent is linkage to the planning that would be necessary to gain 

any benefit from the project. It is also unclear how the small scale results will be 

validated with respect to large scale (subbasin) effects and differences in predictions 

resolved. 

Monitoring and evaluation of this project would involve determining whether the density 

dependent functions established in the BACI experiments of habitat restoration had been 

incorporated into the planning of restoration actions for the Entiat and other subbasins. 

No plan for monitoring is evident. 

Benefits for focal species are difficult to assess. The project is not intended to improve 

habitat conditions for focal species. Instead, the project is designed to improve the M&E 

of habitat restoration. This could lead to benefits to focal species, but the magnitude of 

the benefits is not easily estimated. 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200751500 - Elemental analysis of fin spines: A potential tool for assessing 

movement of white sturgeon (Acipenser transmontanus) within the Lower and 

Mid-Columbia River basin 

Sponsor: Oregon Department of Fish & Wildlife 

FY08-09 budget: $42,122 

Short description: This project will investigate the utility of fin rays as biochemical 

markers in white sturgeon, and the potential use of fin ray microchemistry to describe 

movement of white sturgeon within the lower and mid-Columbia River basin 

(View full proposal online)

Recommendation: Unranked 

The proponents have done a thorough job of describing the pros and cons of the 

elemental analysis as a tool in fish ecology. Elemental analysis has been applied 

previously for studies of white sturgeon in the Columbia River Basin, so this project does 

not meet the innovative criteria. Improvements in our ability to identify migration 

patterns using the method will not contribute to direct improvements in the survival or 

productivity of white sturgeon in Columbia River Basin. If this research project is 

funded, results would provide baseline data on elements in white sturgeon fin rays which 

could lead to formulation of specific hypotheses about movements of the species. There 

would be a valued-added component if it is conducted in collaboration with another 

project proposed for upriver white sturgeon, as the proponents suggest. If the method was 

used as a technique in a broad scale, comprehensive program to identify limiting factors 

for white sturgeon, it would have merit. A fundamental problem with this project is that 

the methods to determine the spatial and temporal variation in elemental signatures in the 

Columbia River Basin are not well explained. For example the rationale for choosing 

certain sites for water collection needs to be explained. There is an ambitious program of 

field sampling of water, sediments, and white sturgeon described. It is unlikely all the 

work could be done, analyzed, and reported in 18 months. 

200751700 - Estimating abundance of white sturgeon by using visual striptransects; an alternative to mark-recapture population estimates 

Sponsor: US Geological Survey - Cook 

FY08-09 budget: $590,925 

Short description: We will determine if acoustic imaging technologies and visual striptransect abundance estimation techniques can be used to estimate numbers of white 

sturgeon present in river reaches. This would add value to ongoing sturgeon stock 

assessment activities. 

(View full proposal online)

Recommendation: Unranked 

This proposal meets the criteria for innovation because it involves the use of underwater 

visualization of white sturgeon (side scan sonar, digital camera) to assess their 

abundance. These methods have not been used for sturgeon in the Columbia River Basin 

before and in only a few rivers elsewhere. The team has the required expertise for 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

underwater imaging as well experience with white sturgeon population dynamics. 

Capture/recapture methods involve repeated handling of animals and are subject to biased 

estimates, so there is merit in looking for alternate methods. However, the ISRP 

concludes that the proposal is not “on the ground” and that the proposal would be 

improved by a detailed description about how application of the image data would 

improve white sturgeon management. Specifically more information about how improved 

population estimates would result is required. Plans to evaluate and validate population 

estimates compared to capture/recapture methods are unclear. How will discrepancies

among methods be resolved if both methods are subject to uncertainties and biases? In 

addition, 18 months seems too short to test and implement the side scan method. A 

number of mark-recapture experiments would have to be conducted to fully compare the 

two data sets. 

200751900 - Feasibility of using a computerized video system to estimate 

lamprey passage at Bonneville Dam 

Sponsor: Columbia River Inter-Tribal Fish Commission 

FY08-09 budget: $93,532 

Recommendation: Unranked 

This proposal describes an innovative research project to address a problem in making 

accurate counts of adult Pacific lamprey passing mainstem Columbia and Snake river 

dams. Currently, counts of lamprey passing mainstem dams are made during daylight 

hours, but it is known that the peak passage periods of lamprey are at night. This project 

will develop software to make an efficient analysis of video tapes or DVDs to accurately 

count lampreys passing at night. The method is not entirely new but has not been used in 

such an application for lamprey. 

The project does not appear to be on-the-ground. It improves population estimates of 

lamprey but does not directly improve their abundance or productivity. The proposal 

does not specify how improving lamprey counts at night with this system will benefit 

lamprey, but it is assumed that improved counts will help to evaluate passage success and 

set recovery goals for lamprey. It appears that the proposed project will take more than 

18 months to complete but could potentially be done in less than 2 years. If a proposed 

schedule was included we could better determine this. 

If the system is successfully developed, it could also have benefits for automated 

counting of other fish species. 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200752000 - Genetic Predisposition of Smoltification in Rainbow Trout and 

Steelhead 

Sponsor: Columbia River Inter-Tribal Fish Commission 

FY08-09 budget: $89,978 

Short description: This proposal seeks to identify quantitative genetic characteristics 

that predispose individual O. mykiss to smoltification. We will investigate the potential 

of resident rainbow trout to contribute to the recovery of ESA listed steelhead 

populations. 

(View full proposal online)

Recommendation: Unranked 

The proposal is for a research project aimed at addressing a critical uncertainty regarding 

the control of smoltification. The application of microarray genotyping is a relatively

new technique that offers great promise in understanding functional gene expression and 

important physical traits. However the basic approach outlined in the proposal begs the 

question as to how the information will be used within a management context – i.e., there 

is no obvious “on-the-ground” activity that follows this work. 

There are also several questions about the experimental design of the proposed work. For 

example, there are a number of design issues about what specifically the gene chips can 

find. The genetic foundation (either additive or major gene) for smoltification is 

uncertain and needs to be identified prior to a search for candidate genes. The 

operational steps establishing heritability for anadromy is not presented in the proposal. 

This should be demonstrated with more traditional quantitative genetic methods. Then, a 

persuasive explanation of how the chip technology can be applied to management options 

is needed. 

Other mapping techniques using QTL approaches may get at the answer as well. 

Moreover, the apparent experimental design aside from the laboratory work is rather 

complex especially in terms of creating lines – it may not be completed within the time

frame for the project. Many of the comments from the review of this project during the 

FY 2007-09 proposal reviews remain in force. The concerns were expressed in that 

review and not addressed here. 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200752200 - Innovative Fish Sample Gear for Reducing Stress and Mortality in 

the Catch and Increasing Efficiency in Monitoring the Effectiveness of Dike 

Removal Projects 

Sponsor: Columbia River Estuary Study Taskforce 

FY08-09 budget: $7,838 

Short description: To improve monitoring of newly evolving estuarine habitat behind 

breached dikes, CREST is proposing the construction of innovative fish sampling gear 

that will decrease salmonid stress / mortality and provide better safety and efficiency for 

field staff. 

(View full proposal online)

Recommendation: Unranked 

This project is small in scope (build four new fish traps), inexpensive, and potentially 

important if the proposed sampling gear can lower salmonid stress and mortality. The 

innovation is an apparently relatively minor change in trap design. According to the 

proponents, the design is not new but to their knowledge has not been used in the lower 

Columbia River estuary. The problem is relatively well defined, but the scientific and

technical background did not provide any information to demonstrate that salmonids are 

actually stressed or experiencing mortality caused by the current traps. For example, 

there are no references to stress or mortality from capture in fishing gear of any type 

(including fyke nets). Because the proposed trap design is not new and has been used in 

areas outside the Columbia River estuary, some examples w/citations to literature on its 

successful use in other areas would have improved the proposal. Restored tidal creek 

evaluation is being conducted elsewhere in Columbia River Basin (e.g., Crimms Island), 

but because of hydrological differences (e.g., salinity) the work proposed is probably 

only relevant to the estuary itself. There are no collaborative efforts identified other than 

those internal to the Grays River group. 

The design of the project is not well developed or scientifically based. No details are 

given on exactly where and when the work would be done. The trap modification is 

described in some detail, but the explanation would be improved by inclusion of a photo 

or sketch of the trap design and the geomorphological setting where it would be used. 

The gear might have to be modified again as the tidal channels evolve into different 

configurations. Therefore, results will only be applicable to a specific stage of 

geomorphological development. Has the proposed new trap design already been tested 

relative to a present trap? The proposal would be improved by more attention to the 

quantitative assessment of the two key variables (mortality and stress) that would be used 

to compare the effectiveness of new and old trap types. Some increment of improvement 

in survival (SARs) of fish captured in the evaluation of restored tidal creeks might be 

expected, but measurement of this improvement relative to other factors could be 

difficult. The ISRP recommends that the sponsors seek the advice of an 

investigator/colleague with statistical and sampling expertise. Given the low cost it is 

surprising that the proponents cannot fund the work to build the fish traps internally or 

via partner agencies. Perhaps, this proposal could be revised and submitted for a future 

request for scientific research proposals. 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200752300 - Innovative methods to quantify transport of hydrophilic and legacy

pesticides to the riparian zones within the Yakima Basin 

Sponsor: U.S. Geological Survey- Washington Water Science Center 

FY08-09 budget: $216,909 

Short description: The transport of hydrophilic pesticides to the riparian zone will be

examined using electrical resistivity methods and of legacy pesticides in surface waters of 

the Yakima Basin will be examined by collection by time-integrated sediment sampler 

(View full proposal online)

Recommendation: Unranked 

Although developing innovative sampling techniques is commendable, this proposal did 

not sufficiently explain the potential benefits of improved sampling to fish, wildlife, or 

riparian vegetation. The proposal was to investigate a new sampling technique, in which 

a successful outcome will be to estimate the amount of "legacy" and hydrophilic 

pesticides adsorbed on suspended sediment in the Yakima River and deposited in riparian 

zones. The title suggests that the project will estimate the fluvial delivery of pesticides to 

riparian zones; however, the methods section does not describe how pesticide deposition 

in riparian areas will be measured. 

The proposal describes the need for a time-integrated sediment sampler but does not go 

into much detail about why the sampler is needed in the context of native fish recovery in 

this subbasin. It points out that pesticide contamination of fish tissues in the Yakima

subbasin poses health risks for human consumption, but it does not discuss how 

pesticides can affect riparian vegetation and fish populations. Although it describes other 

federal and state water quality monitoring programs, it is very weakly linked to the 

Yakima Subbasin Plan and other habitat and water quality improvement projects in the 

lower basin. The sampler is adequately described, but there is no discussion of how 

sediment and pesticide delivery to riparian areas would be estimated using this technique. 

Although there could be benefits to focal and non-focal species, the thrust seems to be 

measuring pesticide levels that can be correlated with contaminated fish tissues to gauge 

the risk to humans from consumption. Risks of pesticides to riparian vegetation are not 

described. The proposal’s focus seems to be on instream depositional processes, as 

opposed to incorporation of pesticides into riparian vegetation as suggested by the title. 

33 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200752500 - Integrating Ecological Flows into River Management on the 

Willamette River 

Sponsor: Nature Conservancy 

FY08-09 budget: $64,150 

Short description: The project will identify ecological flow requirements for the 

Willamette River and its tributaries and design and test alternative flow releases from

Corps and EWEB dams to achieve more natural flow regimes for the benefit of fish and 

wildlife. 

(View full proposal online)

Recommendation: Unranked 

The sponsors propose to develop and implement a flow management plan for the 

Willamette River that more closely approximates the natural flow regime. The project 

could benefit focal species by, for example, providing high flow to facilitate migration, 

reconnecting the river with the floodplain, improving rearing habitat, and establishing a 

more natural temperature regime. Unfortunately the proposed work does not fit the 

criteria for innovative. For the most part it simply applies existing methods to a problem

that has been at least partially addressed by other projects. The proposal would be 

appropriate in a subbasin-specific project solicitation. 

The stated objectives reasonably define the approach needed to accomplish the major 

purpose of the project which is to alter Willamette flow regimes. For the most part the 

methods seem adequate. Several elements of the proposal deserved greater explanation. 

One work element is to "Develop and implement a field monitoring program to assess the 

ecological and biological benefits of changes in flow." The sponsors needed to explain in 

more detail how they propose to go about developing an M&E program for a large and 

complex basin such as the McKenzie. 

The sponsors will involve stakeholders in a one day workshop and will keep them

informed and will provide updates to interested parties. This process is likely to be 

contentious and the sponsors should at least acknowledge how difficult it will be to gain 

consensus from stakeholders. 

The sponsors propose to implement the altered regime by changing the operation of the 

Willamette River dams. The sponsors make this task seem easy to accomplish but in 

reality it will likely be very difficult. The difficulties of implementing flow regime

changes should have been discussed more thoroughly. 

34 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200752700 - Lake Roosevelt Littoral Habitat Enhancement Project 

Sponsor: Colville Confederated Tribes 

FY08-09 budget: $574,112 

Short description: Spring drawdown of LR desiccates eggs of native resident littoral 

species and increases predation on the young of year reducing numbers of available prey 

species within the Lake and hence increasing predation on focal species of kokanee and 

rainbow trout. 

(View full proposal online)

Recommendation: Unranked 

The proposal generally meets the ISRP scientific review criteria for projects included in 

the Council Fish and Wildlife Program. However, the proposal elements only meet the 

innovative criteria "in part." The sponsor proposes analyzing and modeling data on 

nearshore habitats to quantify fish loss due to draw down of Lake Roosevelt at Grand 

Coulee Dam. This does not meet the innovative criteria in the solicitation. There are also 

elements to use floating substrates to substitute for littoral habitat. This element is "onthe-ground," but insufficient information is provided to conclude that it is innovative in 

the Columbia River Basin. More information is needed on use of substrates elsewhere, 

and what types of substrates are in current use. 

The background section of the proposal is too long, including too much extraneous 

material. More information is needed on examples of the use of substrates to replace 

littoral habitat and on the types of structures that may be used. Only in the proposal 

Abstract is there a statement that a habitat enhancement approach (i.e. artificial 

substrates) will be tested, and there is a lack of description of the artificial substrates (the 

key focus of the proposal) to be employed. 

Only several short and general statements are made regarding the monitoring and 

evaluation of the habitat enhancements. The schedule and frequency of monitoring are 

missing. No milestones are set for successful use of artificial habitats. 

The potential benefits of the project are not well quantified and there was no discussion 

of potential adverse effects. But, perhaps the substrates could be a habitat attracting 

introduced fishes or invertebrates and could actually degrade the existing environmental 

conditions. This should be considered. 

35 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200752800 - Little McCormick Creek: Investigating Placer Mine Impacts to 

Streamflow Connectivity and Developing New Restoration Techniques 

Sponsor: Trout Unlimited 

FY08-09 budget: $96,800 

Short description: TU plans to restore surface flow and fish habitat in one mile of Little 

McCormick Creek. By studying bedrock geology, groundwater flows, and placer 

disturbance, TU will develop assessment and restoration techniques that are transferable 

in the region 

(View full proposal online)

Recommendation: Unranked 

The problem is adequately explained and the proposal justification is generally well 

written, although a little weak on references. The sponsors wish to evaluate three 

alternative surface water retention technologies - impermeable barrier, geotextile fabric, 

and compacted inorganic fines - to restore surface flows in a stream that has been 

severely altered by recent placer mining. The sponsors have worked on many projects of 

this type in the past and have outlined the technical issues important to a successful 

completion of the project 

This project is not truly innovative, in the sense that groundwater retention sills have 

been used by project sponsors in another Idaho stream (Eustache Creek); however, the 

other project was only partially successful. Although the sponsors propose to test three 

surface water retention technologies, the bulk of the proposed work is simply stream

rehabilitation and is not innovative. 

The objectives are very broad, and measurable outcomes are not given. The methods in 

Phase I of the work are not very detailed. This project mostly seems to be an application 

of standard stream restoration techniques. Phase II and III of the project is a major stream

restoration activity including, among other things, channel reconstruction and placement 

of large wood. In short, the work includes much more than the stated objective of the 

proposal. 

One significant unknown is whether retention sills are a suitable approach to restoring 

surface flows at this particular site. Because the geological survey has not yet been 

completed, the depth of bedrock has not been established, and it is not certain that sills 

are appropriate. If not, the experiment designed to evaluate the three water retention 

technologies - impermeable barrier, geotextile fabric, and compacted fines - will be 

impossible at this location. 

36 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200752900 - Loss of salmon and steelhead productivity due to barriers in the 

Lower Columbia River ESU 

Sponsor: Washington Department of Fish and Wildlife 

FY08-09 budget: $158,326 

Short description: Washington Department of Fish and Wildlife proposes an innovative 

approach to develop a predictive model for steelhead, Chinook, coho, and chum salmon 

to determine productivity loss due barriers using representative sampling, GIS, and 

culvert inventory. 

(View full proposal online)

Recommendation: Unranked 

The proposal is marginally innovative. This project proposes to develop a model to 

prioritize barriers that impede movement of fish upstream. The prioritization will be 

based upon the lineal distance of habitat that will be opened by barrier removal. Lineal 

distance is taken to be indicative of the potential of the barrier removal to increase fish 

abundance and productivity. This approach could be important as barrier removal 

projects rarely attempt to assess the importance of the area above the barrier for salmon 

and the gain in production that can be accrued. 

The objectives are clear and consistent with the Fish and Wildlife Program. The final 

product will be a model predicting lineal miles of stream above barriers that are suitable 

for salmon. The results will be used to prioritize barrier removal projects. The methods 

are clearly explained and involve sampling fish to assess the extent of their upstream

distribution in several watersheds and using this information, combined with physical 

data on the stream and watershed, to develop a predictive model. 

The sponsors should consider the quality of the habitat as well as the lineal extent in their 

prioritization. No field validation of the model will apparently occur and follow-up work 

to determine if the projects are successful in improving salmon production was not 

discussed. As such, the proposal did not meet the criteria of being an "on-the-ground" 

demonstration or pilot project. 

37 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200753000 - MADS Weir Demonstration Project in Walla Walla Subbasin (MADS 

- Modular Arch Drop Structure) 

Sponsor: Steward and Associates (in conjunction with the Walla Walla County Soil and 

Water Conservation District) 

FY08-09 budget: $118,750 

Short description: This project will demonstrate the effectiveness of a low cost method 

for addressing fish passage problems caused by perched culverts, incised channels, and 

water diversion structures, including push up dams. 

(View full proposal online)

Recommendation: Unranked 

The proposal is incomplete. Only an abstract and a resume of the Principal Investigator is 

provided. On the basis of this information the ISRP is unable to establish that the MADS 

is innovative using the definition provided with the solicitation instructions. The proposal 

is to use pre-fabricated fiber-reinforced concrete modular structures to replace failed 

culverts. No sites are identified; no cooperators that are interested in using the structures 

are identified. 

The ISRP believes that if modular concrete culverts are cost effective replacements for 

failed culverts, agencies responsible for the engineering and construction of replacements 

will adopt them without the necessity of a pilot under to auspices of the Fish and Wildlife 

Program. 

200753100 - Microbial Assessment of Thermal Impacts of Dworshak Reservoir 

Releases 

Sponsor: Washington State University 

FY08-09 budget: $165,473 

Short description: The primary purpose of this project is to develop a methodology to 

evaluate the impacts of cold water releases from Dworshak Reservoir using innovative 

microbial assessment techniques. 

(View full proposal online)

Recommendation: Unranked 

The proposal describes a research study to examine the linkages between water 

temperature, microbial communities, and juvenile steelhead growth. These linkages are 

not well described, and the proposal does not offer a scientifically defensible approach. 

Getting data on temperature profiles in reservoirs is needed, but the relationship to 

microbial populations is questionable. The technical background on this key part of the 

project needs improvement. Basic citations on key variables such as steelhead growth 

rates in the Clearwater River also need to be provided. No real documentation is given of 

hypothesized problems. Benefits are uncertain. 

38 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200753200 - Molalla-Pudding Sub basin Assessment; utilizing the new EPA 

Watershed Assessment of the River Stability and Sediment Supply (WARSSS) 

procedural methods to increase anadromous fish survivability 

Sponsor: Molalla River Watch 

FY08-09 budget: $271,222 

Short description: The Molalla supports habitat for rearing, migrating anadromous 

species and resident cutthroat. The impairments within the Molalla River watershed are 

documented. However, the analysis to identify where to implement on the ground 

restoration is not developed 

(View full proposal online)

Recommendation: Unranked 

The thrust of this proposal is to apply an EPA model - Watershed Assessment of River 

Stability and Sediment Supply (WARSSS) - to the lower Mollala River/Pudding River 

watershed for the purposes of identifying major sediment contribution areas, which can 

then be targeted for remediation. According to the proposal, the model has not yet been 

applied elsewhere in the Columbia Basin. The project is not an on-the-ground effort, in 

the sense that it does not actually involve reducing sediment inputs, but instead offers a 

new technique for identifying problem areas. It is confined to the lower watershed and

does not include the headwaters. The proposed work could have broad application across 

the Columbia Basin for planning and prioritization purposes. The sponsors state that this 

effort will be the first application of WARSSS in the west. A true test of the methodology 

in the west should involve application to river basins that vary in climate, geology, and 

land use patterns. A more detailed summary of the method and the specific products was 

needed. 

The proposal points out shortcomings in the Lower Mollala and Milk Creek Watershed 

Assessment with regard to pinpointing sediment sources, although it does not provide 

details about the WARSSS model specifically. It only generally describes the relevance 

of the project to key fish species, and it does not mention specifically what species or life 

stages stand to benefit from sediment abatement in the basin. The proposal could have 

provided an explanation of why the model will represent an improvement over other 

techniques of identifying sediment sources in low gradient rivers. Additionally, the 

proposal does not suggest how the model could be linked to biologically measurable 

performance indicators that can be used to gauge the benefits of sediment control in this 

watershed. Successful accomplishment of the WARSSS methodology could produce a 

river rehabilitation plan and provide prioritized sites for habitat restoration in the Molalla 

basin. Although testing a new model that can identify chronic sediment source areas is 

desirable, this proposal did not really fit the overall goals of the innovative project 

solicitation (both innovative and on-the-ground). It would be worthwhile to apply 

WARSSS during the next round of watershed assessments. 

39 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200753300 - Monitoring fine sediment delivery to fish habitat in the Entiat River 

subbasin 

Sponsor: PNW Research Station -- Wenatchee 

FY08-09 budget: $295,000 

Short description: Test and demonstrate an improved method of monitoring fine 

sediment delivery to the habitat of sensitive salmonids. 

(View full proposal online)

Recommendation: Unranked 

This project proposes to develop and test protocols for sampling fine sediment in streams 

and its impact on salmon habitat. The proposal is well written and scientifically sound. 

The sponsors convincingly argue that current methods of monitoring sediment in streams 

are less than adequate. The objectives are clear and quantifiable. The work appears to be 

able to be accomplished within the allotted time frame. Benefits will not accrue directly, 

but this project could add to knowledge base that will eventually generate benefits that 

could be long-term.

The timeline of this funding probably is not sufficient to generate much data once the 

equipment is in place. The funding from the innovative solicitation really would be only 

for a start-up with most of what would be contributed in terms of data collection and 

analysis having to follow in subsequent years. Procedures are well chosen and described, 

but the project will not be mature at the end of funding period. 

The work could be improved if the proposed new method for assessing sediment rates 

were rigorously compared to results from standard techniques. While fine sedimentation 

is clearly a problem in parts of the Columbia Basin, it is not clear that development of a

new method for measuring it is of the highest priority at this time. The proposal is 

innovative in the sense that a new assessment technique will be developed. 

200753400 - Performance comparison of a stationary PIT tag antenna array in 

Lookingglass Creek, Oregon 

Sponsor: Confederated Tribes of the Umatilla Indian Reservation 

FY08-09 budget: $47,829 

Short description: This project will compare estimates of migration timing, survival, 

and abundance for juvenile spring Chinook salmon outmigrants from Lookingglass 

Creek, Oregon. Comparison will be made between a screw trap and passive, stationary 

PIT tag array. 

(View full proposal online)

Recommendation: Unranked 

The sponsors propose to compare estimates of salmonid outmigrant abundance, survival 

and migration timing to Lower Granite Dam between rotary screw trapping and a remote 

PIT tag detection system. The sponsors clearly point out problems with using screw traps 

to monitor smolts and the need for an alternative counting technology such as a PIT tag 

40 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

array is clearly explained. Of course, monitoring the movement of PIT-tagged fish, as 

opposed to collecting fish from a trap, will mean the loss of ability to measure growth 

and perform other actions that require direct handling. If the performance of the rotary 

traps and stationary arrays is similar, the PIT tag system could replace some screw traps 

in the Columbia River Basin resulting in substantial monetary savings. The distinguishing 

features of this proposal are that it attempts to monitor PIT-tagged fish movements in a 

larger stream than those in which fixed antenna technology has been used before, and it 

performs essentially a side-by-side comparison of a rotary smolt trap and a full stream

PIT-tag antenna array. The objectives and methods are very well described, and the 

details presented are indicative of a project where little would be left to chance. 

It is essential to recognize that this project does not attempt to determine which of the two 

techniques yields the best survival estimates but rather to see if the estimates generated

by the two are similar. The whole point of this proposal is to determine which of the two 

census methods is the most cost-effective, not the most accurate. A central shortcoming 

of this one-year project is the uncertainty of stream conditions, particularly extreme 

conditions like chronic flooding, that could seriously impair the operation of the rotary 

trap or diminish its efficiency so much that comparison with the PIT tag array would not 

be very meaningful. An adequate test of the proposed methodology would likely require 

several years of work to take into account the effects of variable stream conditions.

200753600 - Piloting StreamBankTM Web Tool and permitting efficiencies to 

achieve Middle Fork John Day River Channel Reactivation and Floodplain 

Restoration. 

Sponsor: Oregon Trout 

FY08-09 budget: $354,941 

Short description: Oregon Trout seeks to bring web-based innovation and increased 

efficiency to stream restoration work in connection with a large-scale restoration project 

on private land in the John Day River Basin. 

(View full proposal online)

Recommendation: Unranked 

The proposal is to develop a web tool (StreamBank) to permit efficient organization of 

restoration work in streams, but further justification on the need is required. This webbased software component is purported to accelerate watershed rehabilitation, but it is an 

organizational tool for the most part. In addition, the project may be unable to test the 

software development adequately within this basin (one site only proposed, no controls) 

or within this time frame. Also included in the proposal is a stream restoration project in 

an area of the John Day River. This involves several hundred hours of restoration effort 

and most of the budget, and will exceed the time frame of this solicitation. This 

component appears more suitable for the standard annual/provincial projects solicitation. 

A good description of the software is needed, with an explanation of the attendant goals 

and functions, and discussion of how each component would be tested and the results 

integrated with the subbasin plan. Most of the components that this tool is purported to 

41 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

assist with seem already available and in operation in this subbasin. Consequently the 

immediate utility of the tool is questionable. The software may be new, and helpful, but 

the field project is not, and the need to link testing of the software and its efficiencies to 

the field project requires further work. Furthermore, the time frame for the field project 

is probably over-optimistic and there would be no time in this solicitation cycle for 

effectiveness monitoring. Evaluation of efficiencies gained through use of StreamBank 

would be difficult to assess since no reference area or independent evaluation team is 

included. The monitoring and evaluation proposed is largely verbal, through interviews 

and comment, thus lacking scientific rigor. Testing the software efficiency, particularly 

of this nature, is difficult, and beyond the scope of the intent of this solicitation. 

 

200753700 - Population specific in-season forecasts of Columbia River Chinook 

salmon (Oncorhynchus tshawytscha) returns for allowing selective in-river 

fisheries 

Sponsor: Columbia River Inter-Tribal Fish Commission 

FY08-09 budget: $99,762 

Short description: We will make accurate in-season forecasts of Columbia River 

Chinook salmon population-specific returns to increase the resolution of in-river harvest 

selection between weak wild and healthy wild or hatchery populations. 

(View full proposal online)

Recommendation: Unranked 

This proposed work’s purpose is to generate in-season, real-time, escapement estimates 

to judge run strength and guide more effective harvest of strong versus weak stocks of 

salmon in the Columbia River. The project would also result in quantification of 

uncertainty in forecasts. The proposed technology is Genetic Stock Identification (GSI) 

combined with PIT tagging. 

PIT tagging technology is not new, nor is assigning salmon to stocks of origin using 

multilocus genotyping. What is new is forecasting run size and timing on a real-time 

basis, in season. Genetic technologies were used in the Columbia River Basin in the early 

to mid-1980s to estimate the catch of depleted Snake River spring-Chinook on a real-time 

basis. The idea was to open or close the fishery on a weekly basis, based on the catch of 

Snake River spring-Chinook. When the season quota of this stock was reached the fishery 

was closed until the stock had passed a particular fishing zone. 

The proposed project relates to the overall goal of increasing harvest by increasing the 

resolution of a harvest selection. Collaboration with several other agencies is noted, 

mainly to use data already being collected. The project would intersect and inform many 

other restoration, mitigation, and fishery projects in the basin. The project will 

necessarily rely on the efforts of cooperative groups (to collect and deliver tissue samples 

and provide PIT tag data) for the in-season forecast modeling. The proposal would be 

enhanced with a description of whether these groups would participate and if the 

relationships to other projects that were essential to completing this innovative effort 

were clearer. 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

One major problem was inadequately addressed in the proposal. Even with GSI aided 

estimates of the composition (%) of a mixed-stock selective fisheries (whether 

commercial, recreational, or subsistence) one must rely on the ability of the fishers to

discriminate healthy versus weak stocks at the time of capture if the weak stocks are to be 

avoided. Also, once strong stocks are targeted and removed, the composition (%) of the 

mixed stocks change as they move up river. Similarly, as spawning rivers are passed and 

stocks peel-off to spawn, composition (%) of the mixed stocks change. GSI models have 

yet to accommodate these factors. The large omission in the proposal is a discussion of 

how one will execute a fishery if the fish are mixed together. The proposal would be 

improved with inclusion of a discussion of how to harvest mixed fish populations. 

Furthermore, targets for precision of the data should be provided. 

The methods are explained in general, but there is little description of the particulars of 

the GSI approach (number of loci used, differences among reference populations defined 

as the 13 stocks, robustness of data sets to assumptions, expected sample sizes passing 

through Bonneville, etc.). A missing element is a discussion of the improvement 

necessary, or the precision required, in the run size and time forecast that is required to 

make the process useful in yearly harvest management. The methods do not appear to be 

directed toward assessing whether this precision can be attained. It is more of an effort to 

obtain estimates, including a probability distribution of potential estimates. 

The assembled team has the expertise and facilities to accomplish and carry out the work 

elements. Although with sample sizes unknown, the current facilities could quickly 

become over-run with samples (unless a regular system of sub-sampling will be

employed). 

The principal uncertainty is whether any scheme exists to harvest fish in a mixture 

containing both weak and strong stocks. This is a classic dilemma in salmon management 

and more information on the stocks will not help. It will just make it clearer why fishing 

will not be permitted when there are abundant fish around. 

43 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200753900 - Promote Kokanee Repopulation in Lake Pend Oreille using 

Autonomous Underwater Vehicles (AUVs) for Location and Verification of Lake 

Trout Spawning Areas.

Sponsor: University of Idaho - Microelectronics Research & Communications Institute 

(MRCI) 

FY08-09 budget: $400,177 

Short description: The proposed work will apply underwater robotics technology to 

allow researchers to visually survey large areas of the floor of Lake Pend Oreille to locate 

and verify Lake Trout spawning areas. 

(View full proposal online)

Recommendation: Unranked 

This is a well written proposal that can potentially answer a question (Where do lake 

trout spawn in Lake Pend Oreille?) that would otherwise be difficult and dangerous to 

answer. The technical background is presented effectively, and the project’s justification 

is reasonably clear. Causes of the Lake Pend Oreille kokanee declines are not fully 

known, so controlling lake trout spawning may or may not be the “silver bullet” that will 

facilitate kokanee recovery. The presumed issue is that lake trout are limiting kokanee 

populations by predation, and the autonomous underwater vehicles (AUVs) will help 

identify lake trout spawning grounds so that adults can be netted before they can 

reproduce successfully. The proposal would have benefited from a more thorough 

discussion of possible applications of the technology in the Columbia River Basin other 

than to identify deep water spawning areas in this particular lake. Nevertheless, this 

proposal does apply a novel technological approach to the problem of identifying major 

deep water spawning sites, and it may offer applications to other areas of the Columbia

River Basin where diving is hazardous. The ISRP wondered if the AUVs have been 

tested in rivers. Some explanation of possible wider applications of the technology for 

fisheries research would have made the proposal more relevant to a broader set of issues, 

and therefore more appealing. 

200754000 - Quantitative Assessment Sampling for Pacific Lamprey in Cedar 

Creek (Lewis River Subbasin), Washington 

Sponsor: US Fish & Wildlife Service 

FY08-09 budget: $140,000 

Short description: A Quantitative Assessment Sampling Program will be developed to 

estimate the production of Pacific lamprey macropthalmia from Cedar Creek in the Lewis 

River subbasin. It can be used to quantitatively assess lamprey populations in the 

Columbia River basin. 

(View full proposal online)

Recommendation: Unranked 

The project has the potential to provide significant benefits by developing an approach 

for sampling lamprey larvae that could provide more accurate and rigorous estimates of 

juvenile abundance. Their approach is based on a well-tested protocol developed in the 

44 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

Great lakes for sea lamprey. The new approach could have broad applicability across the 

Columbia Basin, and it could become part of standard monitoring and evaluation 

protocols for lamprey. 

Each objective appears to be both measurable and accomplishable within the 18 month 

time frame. The methods for objective 1 appear adequate, but the methods for objective 2 

needed to be described much more thoroughly. Specifically, the sponsors needed to detail 

how the results from objective 1 and 2 would be used to develop the model for predicting 

macropthamia abundance. 

The sponsors propose to develop a stock assessment tool for lamprey that could be 

broadly applicable throughout the basin. While this work is exceedingly important and in 

the past has been supported by the ISRP, the proposal only marginally meets the 

innovative criteria because, although it involves field sampling, it really is not an on-theground demonstration or pilot project. The purpose of the work is to synthesize a 

Quantitative Assessment Sampling Program, not to test it. The data collected by field 

sampling would be used in development of the Assessment Program. 

200754100 - Reecer Creek Floodplain Restoration Project to support ecosystem

function using build-in-the dry and 3 yrs revegetation to encourage channel 

dynamics, habitat formation and natural sediment management 

Sponsor: South Central Washington Resource Conservation and Development 

FY08-09 budget: $428,307 

Short description: Restore 69ac of historic floodplain on City of Ellensburg land to 

increase channel length, complexity and habitat area, add high flow channels and 

backwater swales to support water quality, dissipate flood energy, increase rearing and 

spawning habitat. 

(View full proposal online)

Recommendation: Unranked 

Off-channel and in-channel habitat rehabilitation in this manner and as proposed has 

occurred elsewhere, thus few if any innovative approaches are evident. More certainty is 

needed in the proposal to establish that truly innovative techniques would be used, and 

that the habitat and fish population benefits of the project would be monitored. This 

proposal strongly emphasizes a bioengineered approach to floodplain reconnection. For 

the most part the floodplain reconnection and channel contouring techniques are in wide 

use elsewhere. The sponsors state that dirt bags and crumble-crete blocks "will be

considered." But apart from these tools (which are the subject of a separate innovative 

proposal), there is little in the project description to qualify as a truly innovative 

approach. 

While the effort to reconnect a 3/4 mile section of lower Reecer Creek with its floodplain 

is commendable, and should perhaps be contained within the subbasin plan, there is not 

enough detail in the proposal for a sufficient understanding of the biological benefits of 

this project. A brief list of focal species is given, but it was not clear how many of these 

45 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

species, or what life stages, would benefit from the project in some way. The proposal 

describes other floodplain reconnection and side channel enhancement projects within the 

Yakima subbasin but does not provide a clear description of how the findings from this 

project would be used to aid those projects or floodplain restoration work in the future. 

The brief description of a monitoring program contained too many uncertainties (e.g., 

"Redd surveys may also be conducted") to provide confidence that the project will be 

properly monitored for biological benefits. No details about fish surveys or vegetation 

survival studies were given, nor were personnel and facilities adequately described. 

Reconnecting lower Reecer Creek with its historical floodplain will probably benefit both 

focal and non-focal species, but this project plan was not sufficiently detailed to ensure

that the benefits will be documented. 

200754300 - Simmons Dike Removal feasibility study 

Sponsor: Umatilla Basin Watershed Council 

FY08-09 budget: $43,000 

Short description: Funding sought for feasibility study to remove a 1000'levee on the 

Umatilla River. Designs will be drafted to reshape and restore stream/floodplain 

connectivity, and restore wetland function. 

(View full proposal online)

Recommendation: Unranked 

This proposal was incomplete and not scientifically reviewable. 

200754400 - Spawning Channel for Chum Salmon at Beaver Creek Hatchery 

Sponsor: Washington Department of Fish and Wildlife 

FY08-09 budget: $398,000 

Short description: WDFW proposes and innovative proposal that modifies the return 

water from the Beaver Creek Hatchery facility on the Elochoman River into a chum

salmon spawning channel. 

(View full proposal online)

Recommendation: Unranked 

This project is a test of the utility of developing and operating spawning channels for 

chum salmon using water that is discharged from a hatchery. The approach, if successful, 

might be applied at other Lower Columbia River hatcheries (the number of potential sites 

was not specified). However, the sponsors needed to explain how water quality issues 

would be addressed. 

The principal innovative aspect of this proposal, if any, is that it will use return water 

from the Beaver Creek hatchery for the spawning channel. Otherwise, spawning channels 

for chum salmon have been used before by diverting stream water or in groundwater 

channels. The objective is clear and measurable and likely can be attained in the allotted 

time for the project. As part of the objective, however, the sponsors set an escapement 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

goal of 200 fish returning to the spawning channel. This part of the objective will not be 

attainable in the given time frame. 

The methods for collection and analysis of biological data are not adequately described, 

and the benefits of this project are not justified. A 500 foot channel will not likely 

provide much benefit relative to the overall magnitude of the chum run. The water quality 

will likely be an issue, resulting in excessive periphyton growth and the need to clean the 

channel regularly, as experienced at other spawning channels for chum and sockeye 

salmon. The methods for constructing the spawning channel are straight-forward. The 

sponsors needed to indicate when the channels would be constructed. 

The argument that a spawning channel for chum salmon at the Beaver Creek Hatchery 

discharge stream would be beneficial should have been made more quantitatively. 

Although the project sponsors estimate that the channel could support 200 or more adults, 

it was not clear whether these fish could have spawned elsewhere, and with greater 

success, in the lower Elochoman, or if a limiting factor analysis had indicated lack of 

suitable spawning sites as a population bottleneck in this system. The issue of potential 

redd fouling by periphyton resulting from the nutrient-rich hatchery return water was not 

addressed. Although this proposal gives a detailed summary of the current status of 

Columbia River chum salmon, it does not provide a sufficiently thorough explanation of 

why adding a 500' x 15' spawning channel will result in an average increase in the chum 

run size of 200 or more adults, and whether this is a significant addition. The problem is 

clear according to the proponent: chum salmon are at low abundance in the Lower 

Columbia in part because of the lack of suitable spawning areas. If chum are to recover, 

additional spawning areas must be provided. Since the Beaver Creek hatchery is located 

about 10 miles above the confluence of the Elochoman and Columbia Rivers, it would 

have been helpful to have cited more quantitative evidence that suitable sites for chum 

spawning are scarce in the lower Elochoman and that normal floodplain restoration 

methods will not result in sufficiently increased spawning areas. Variation in chum

abundance is not explained by the availability and historical variation in spawning 

habitat. 

It was not clear from the proposal how the upwelling features that attract chum salmon 

would be incorporated into the spawning channel design. Additionally, the work elements 

did not specify if access to the spawning channel would be restricted to chum (as opposed 

to, say, late-run coho) or if a water quality and sediment monitoring program would be in 

place to prevent fouling of redds by periphyton resulting from the nutrient-rich hatchery 

return water.

The proposal describes other projects to increase chum salmon spawning in the lower 

Columbia. It would have been helpful to include estimates of the numbers of chum adults 

that were produced by the Duncan Creek spawning channel. The proposed work is related 

to the Elochoman subbasin plan and the Lower Columbia Salmon and Steelhead 

Recovery Plan. 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

Data management and reporting will be through quarterly PISCES reports, annual reports 

to BPA, and presentations to local interest groups. The sponsors will disseminate 

information through reports and presentations to the public. 

200754500 - Stock specific run timing and upstream migration mortality of adult 

Chinook salmon and steelhead through genetic stock identification and PIT 

tagging at Bonneville Dam 

Sponsor: Columbia River Inter-Tribal Fish Commission 

FY08-09 budget: $123,150 

Short description: This project seeks to use Genetic Stock Identification (GSI)and 

Passive Integrated Transponder (PIT) tags to better assess Chinook salmon and steelhead 

adult migratory timing and survival through the Columbia River hydrosystem.

(View full proposal online)

Recommendation: Unranked 

The proposal is neither innovative nor an on-the-ground pilot or demonstration project. 

This proposal is to use PIT tag and genetic analysis of microsatellite loci in combination, 

to assign upstream migrating adult salmon and steelhead to the stock of origin and then 

use the PIT tag to evaluate fall back at dams, travel time upstream, and pre-spawning 

mortality of adult fish. Neither the PIT tagging or the genetic analysis is innovative. 

They are routinely employed in Columbia River Basin salmon management. They may 

not have been used in this combined fashion to evaluate upstream migrating adults. 

The proposal is little changed from one submitted in the FY 2007-09 solicitation, 

200701400. The ISRP recommended a Fundable (qualified) for that proposal. The current 

proposal does not address the PIT tag sampling adequacy raised by the ISRP in the earlier 

review. 

The ISRP recognizes the value of improved information on straying, fall back, adult 

travel time, and pre-spawning mortality. These investigations would qualify for 

consideration within the usual solicitation process. Using the definition of innovative 

established for this solicitation, the project does not appear to fulfill the necessary 

criteria. 

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200754600 - Test of protocols and validation of estimates derived with traditional 

and new methods for steelhead adults, smolts, and parr using an instream PITtag interrogation system 

Sponsor: US Geological Survey - Cook 

FY08-09 budget: $236,785 

Short description: The goal of this project is to compare adult, smolt, and parr steelhead 

migrant estimates from conventional trapping and mark-recapture methods to estimates 

from an instream PIT-tag interrogation system. 

(View full proposal online)

Recommendation: Unranked 

The ISRP highly supports this work. A fish counting technique of this sort needs to be 

implemented by the time Hemlock dam is removed (provisionally scheduled for summer 

2008). Although this is not strictly an innovative proposal, there is a strong need to 

monitor population recovery in Trout Creek, which is part of the Wind River Intensively 

Monitored Watershed project and is a major summer steelhead spawning and rearing 

stream. This is a well-prepared proposal, but it is site specific and does not yet have wide 

application to the Columbia River Basin. The project is justified, but probably not under 

the innovative solicitation. However, there is one somewhat novel aspect of the proposed 

work. It is apparently the first time this particular type of in-stream PIT-tag interrogation 

technology will be used on upstream migrating adults to replace an adult fish counting 

facility at a fish ladder. 

The proposal does not go into sufficient detail regarding the construction of the PTIS 

system itself (three two-antenna arrays arranged longitudinally in the channel) or present 

a strong reason why it will be located at river mile three of Trout Creek, i.e., above the 

existing reservoir. It is assumed that this location will prevent it being overwhelmed with 

sediment when the dam is removed, but the reasons could have been made clearer. The 

linkage between this PTIS system and other projects is acknowledged; however, lessons 

learned from implementing the technology elsewhere are not given. More details about 

construction and maintenance of the PTIS would have helped, and the number of PIT 

tags needed for the study could have been provided, based on the adult escapement into 

Trout Creek and the estimated smolt production from screw-trap sampling in recent 

years. Although the ISRP does not find a particularly good fit between the proposal and 

the overall objectives of the innovative solicitation, we reiterate that this is a worthwhile 

project that deserves to be funded. 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200754700 - The Natural Tag - TNT 

Sponsor: Biopar, LLC 

FY08-09 budget: $229,288 

Short description: An automated, non-invasive, individual identification technology, 

applicable to both commonly tagged species (such as fish) and difficult-to-tag species, 

such as amphibians, insects, crustaceans, and other indicator species. 

(View full proposal online)

Recommendation: Unranked 

The proposed biometric technology is described by the sponsors as new, while at the 

same time described as "developed in 1985." Apparently, the innovation is that the 

technology has not been used in the Columbia River Basin. However, a demonstration 

project is already underway (pictures of fish to be transferred from an ODFW hatchery to 

NOAA Manchester) for the ongoing Captive Brood Stock program for Catherine Creek, 

Lostine, and Grande Ronde Rivers. The technical background is vague with no citations 

to published scientific or technical literature. Given that the technology was developed in 

1985, the lack of citations to publications is troubling. A National Science Foundation 

grant is cited by number, but background information on the results of this grant is 

insufficient. 

The proposal addresses a general need to accurately identify individual organisms with 

non-invasive technology but does not present a convincing case as to how the work will 

further the goals of the 2000 Fish and Wildlife Program, subbasin plans, or other plans. 

No specific problem is identified. The sponsors would like to collaborate with numerous 

agencies in the Columbia River Basin and have established relationships with groups 

ranging from high school biology classes to government hatcheries. Details of imaging 

technology and data analysis and evaluation methods are insufficient to judge the 

scientific or technological merit of the six proposed demonstration projects. The 

technology might be useful as a method for scientific research proposals that address a 

specific issue, where there is a need to identify individual organisms without invasive 

procedures. 

The sponsors do not present a convincing case that their proposed demonstration projects, 

objectives, methods, and products will provide any direct improvements in the survival or

productivity of Columbia River fish or wildlife species. Although the sponsors claim

successful application of their technology to fish (especially grayling), there are no peerreviewed citations in their CVs. It is not clear why a lawyer is included as a coinvestigator on this project. If the results of the demonstration projects were published in 

a peer-reviewed journal, the findings would have some long-term benefits to numerous 

focal species. They might be especially relevant to rare and endangered species where 

there are actually only a few hundred living animals. 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

200754800 - The use of cDNA microarrays to develop biomarkers of 

environmental stress in salmonids and other fishes 

Sponsor: US Geological Survey - Cook 

FY08-09 budget: $572,352 

Short description: This project will use cDNA microarrays to identify molecular 

biomarkers of environmental stress, such as exposure to high temperatures or toxicants, 

in fish. Our goal is to develop a tool for use in ecophysiological monitoring, research, and 

management. 

(View full proposal online)

Recommendation: Unranked 

The proposed project is essentially a methodological research project rather than an onthe-ground and innovative application to directly improve focal species populations. The 

proposal describes an ambitious effort to find expressed functional genetic markers for 

various stresses experienced widely by Columbia Basin focal species (thermal, 

contaminant, anoxia, physical, and so on). The microarray approach is relatively novel 

and offers great promise in such gene discovery efforts. That said, it is not clear what 

problem this effort will eventually solve. Ultimately, the outcome of the research effort 

will be increased basic information on stress response in salmon and lamprey, and 

additional tools for screening fish to detect a stressed state. There are likely to be benefits 

to fish from improved understanding of stressors and improved screening protocols. 

These benefits are unlikely to be realized as an immediate follow-up to the project. 

A unique component of this study is the sponsor's intent to design and produce a DNA 

microarray for pacific lamprey, and then use it to evaluate gene expression in lamprey in 

response to environmental stress. The sponsoring principal investigators appear to have 

the expertise to carry out this work. However, producing a DNA microarray for lamprey, 

and screening for stressors in a little more than a year seems intractable, and the sponsors 

do not provide a schedule to complete the work. 

200754900 - Toppenish Creek Well Modification Project 

Sponsor: Yakama Nation 

FY08-09 budget: $351,423 

Short description: Modify wells by installing deeper grout seals to prevent the drainage 

of shallow groundwater to deeper aquifers and to restore shallow groundwater which 

formerly supported springs, streamflow and riparian habitat. Wells should not 

interconnect aquifers. 

(View full proposal online)

Recommendation: Unranked 

Although the objectives of the project seem worthwhile, this proposal was reviewed by 

the ISRP in an earlier iteration (FY 2007-09 solicitation) and the techniques involved do 

not seem to be sufficiently innovative to satisfy the goals of the current solicitation. The 

proposal provides some background for the problem and does give an example from

Arizona where well grouting has helped restore surface flows, but the identification of the 

51 
ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

most significant wells potentially contributing to shallow aquifer water loss is vague, and 

it is not clear if all the well owners have agreed to the modifications if the project is 

funded. 

A greater problem is that insufficient information is presented to demonstrate that leakage 

around the well casings is actually the cause of subsurface flows in Toppenish Creek. 

Rather than attempting to re-grout each well in the area, it would seem prudent to first 

estimate how much shallow ground water is actually being lost around wells and which 

of the wells are the major culprits. It may be that eliminating the leakage at a few key 

wells may substantially correct the problem. Until some basic information on the extent 

and nature of this problem has been collected, applying the proposed corrective measures 

in a blanket fashion may be premature. The monitoring component of the project is not 

explained in very much detail. The proposal gives reasons why surface runoff would be a 

poor indicator of project success, but groundwater monitoring details are generally 

lacking. 

200755000 - Toxics as a limiting factor for salmon recovery throughout the 

Columbia River Basin: understanding the enhanced toxicity of pesticide mixtures 

Sponsor: Northwest Fisheries Science Center 

FY08-09 budget: $199,244 

Short description: Evaluate the extent that exposure to environmental levels of pesticide 

mixtures impacts neurological function as well as swimming and feeding behavior of 

juvenile salmon. 

(View full proposal online)

Recommendation: Unranked 

This is an important proposal but does not fit this solicitation because it is research and 

not on-the-ground. The proposal would be more appropriate for a standard project 

solicitation or an RFP on this subject area. This project must be conducted under 

laboratory conditions (not in the Columbia River basin) because it is the only approach 

that can be used to understand the subtle, but perhaps serious consequences of salmon 

exposure to mixtures of current use pesticides that inhibit cholinesterase activity. The 

objectives appear reasonable and straight-forward and address the important issue of the 

impacts of chemical interactions. The problem that toxic substances may pose to salmon 

is a potentially serious issue that needs to be addressed. The proposal calls for an 

evaluation of realistic pesticide mixtures that have been reported in water from the 

Columbia River (USGS NAWQA Program data). The sponsors clearly document the 

presence of modern pesticides, sometimes at high concentrations, as a major source of 

uncertainly with respect to habitat quality for salmon that may represent a major limiting 

factor. While studies of pesticide interactions have been conducted, the sponsors state 

that no studies of interaction have been conducted at concentrations that commonly occur 

in the rivers of the Columbia Basin. Anti-cholinesterase pesticides began being used in 

Columbia Basin agriculture lands in the 1950s but have become more important as less 

toxic but more persistent organochlorine (DDT, heptachlor, dieldrin, etc.) pesticides were 

banned. Some of these pesticides alone have been shown in laboratory studies to reduce 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

growth and survival of salmon at low concentrations, and the question of mixtures (which 

are often present in the waters) pose additional complications which are quite well 

addressed in this proposal. The personnel and facilities are exceptional, and the sponsors 

have an excellent record of publication and likely will publish the results in peer 

reviewed scientific journals. The project could also benefit non-focal species that may be 

sensitive to toxic substances. 

200755100 - Use of a novel technique to compare of Pre-and Post-migratory 

energy storage and use in upriver coho salmon: How much change can occur 

with intense selective pressure. 

Sponsor: Yakama Nation 

FY08-09 budget: $49,245 

Short description: We intent to compare changes in energy allocation between the 

developing Wenatchee River coho population to data collected from the previous 

generation and the founding population. 

(View full proposal online)

Recommendation: Unranked 

This is a scientific research proposal to use a commercially-marketed, non-invasive probe 

(fat meter) to measure lipid reserves of lower Columbia River coho salmon naturalized to 

the Wenatchee River, lower Columbia River coho released in the Wenatchee (but of 

recent hatchery introduction, i.e., "reprogrammed"), and coho salmon returning to 

Bonneville hatchery. From this experiment the sponsors wish to make inferences about 

natural selection for improved energy reserves in individuals that have successfully 

naturalized in the Wenatchee River. 

While this proposal addresses an interesting scientific research question, it does not 

appear to be a pilot study or demonstration which if successful will contribute to direct 

improvements in the survival or productivity of Columbia River Basin coho salmon. It 

will only establish a potential explanatory mechanism for the current observations on 

limited success of coho salmon reintroduction. The sponsors link their proposed project 

to work throughout the basin at a very general level. The proposal would benefit from a 

concise description of how the data/results from the proposed project would be used in 

the other projects (at least potentially). 

Methods would be improved by a short discussion on potential problems and limits of the 

fat meter for studies of live fish. Is holding the fish out of water for two minutes a 

problem? Which body parts of the fish will be measured by the fat meter? What variation 

in lipid measurements is expected? The sponsors do not indicate whether they have any 

experience using the fat meter. It is uncertain how intensive the effort must be to 

recapture fish at multiple points with staff available and with a single (?) fat meter. This 

effort and mobility of equipment deserves some additional description. The sponsors’ 

plans for information transfer would be improved if results were to be published in a 

peer-reviewed scientific or technical journal. Potential lethal effects on coho salmon from

use of anesthetics and holding fish out of water are not discussed. A positive aspect of 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

this project is that it could potentially lead to selection of an appropriate stock or locally 

adapted donor stock for reintroduction programs in the Wenatchee Subbasin. The 

proposed methods could potentially provide a useful tool for monitoring the success of

other reintroduction programs, as well as the general patterns of energy store usage by

migrating salmon. Perhaps, this proposal could be revised and resubmitted under a future 

solicitation for scientific research proposals. 

200755200 - Use of LA-ICPMS and fin ray microchemistry to examine historic 

and present movement patterns in Upper Columbia River white sturgeon 

Sponsor: Ministry of Environment 

FY08-09 budget: $75,525 

Short description: We will determine whether LA-ICPMS techniques are able to discern 

movement patterns in Columbia River mainstem areas with high tributary inflows, and 

potential changes in movement patterns associated with completion of the Keenleyside 

Dam (1969). 

(View full proposal online)

Recommendation: Unranked 

The proponents thoroughly describe the pros and cons of the elemental analysis as a tool 

in fish ecology and have related the methods to other techniques such as genetics. 

Elemental analysis has been applied previously for studies of white sturgeon in the 

Columbia River Basin, so this project does not meet the innovative criterion. 

Improvements in our ability to identify migration patterns using the method will not 

contribute to direct improvements in the survival or productivity of white sturgeon in 

Columbia River Basin. Therefore the project is not on-the-ground. 

If this research project was funded, results would provide baseline data on elements in 

white sturgeon fin rays which could lead to formulation of specific hypotheses about 

movements of the species. There would be a valued added component if it was conducted 

in collaboration with another project proposed for downriver white sturgeon, as suggested 

by the proponents. If the method were used as a technique in a broad scale, 

comprehensive program to identify limiting factors for white sturgeon, it would have 

merit. 

A fundamental problem with this project is that the methods to determine the spatial and 

temporal variation in elemental signatures in the Columbia River Basin are not well 

explained. For example, the rationale for choosing certain sites for water collection needs 

to be explained. There is an ambitious program of field sampling of water, sediments, and 

white sturgeon described. It is unlikely that all the work could be done, analyzed, and 

reported in 18 months. Details of the proposed Bayesian analysis are insufficient. No 

information on facilities, equipment, and personnel involved in water chemistry analysis 

is provided. 

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200755300 - Using acoustic telemetry to evaluate the behavior, habitat use, and 

survival of tagged juvenile salmonids in the John Day Reservoir 

Sponsor: US Geological Survey - Cook 

FY08-09 budget: $977,335 

Short description: Large numbers of tagged juvenile salmonids are being released as 

part of behavior and survival research at mainstem dams. We propose to assess the 

feasibility of extending the use of these fish to better assess reservoir habitat use, 

behavior, and survival 

(View full proposal online)

Recommendation: Unranked 

This proposal describes a pilot research study which will be linked to a major action in 

the hydrosystem, (drawdown of John Day Reservoir to MOP) which is a very uncertain 

action and will need major regional approvals before it is implemented. The project will 

use an existing tool (acoustic telemetry) to accomplish its objectives and is somewhat 

innovative in that acoustic telemetry has not been used in this way before. 

The proposal is somewhat incomplete. The problems that this proposal is attempting to 

address (migratory delays and mortality in specific habitats) are not even specifically 

documented and are assumed. The objectives are not clearly stated and are described as a 

plan to develop a plan for evaluating an uncertain future hydrosystem action. Monitoring 

and evaluation are not specifically identified, but this entire study is basically a 

monitoring and evaluation study. 

This proposal would address a high priority need in the future, if John Day drawdown 

becomes a likely hydrosystem action. 

200755500 - Using otolith microchemistry and microstructure to assess the 

causes and consequences of alternative life history strategies for Snake River fall 

Chinook 

Sponsor: Northwest Fisheries Science Center 

FY08-09 budget: $573,252 

Recommendation: Unranked 

This is a scientific research proposal that addresses basic biological phenomenon, i.e., 

alternative life history strategies of Snake River fall Chinook salmon and the effects of 

environmental conditions on their growth and relative productivity. The proposed 

technology (otolith microchemistry analysis) has been used in other Columbia River 

Basin projects. The sponsors do not address the assumptions and potential problems in 

the use of otolith microchemistry to reconstruct fish life history, e.g., see Elsdon and 

Gillandes (2003; Reviews in Fish Biology and Fisheries 13(3):217-235. Relations of the 

proposed project to seven ongoing projects are described, although information provided 

is insufficient to adequately assess the level of collaboration. The objectives are stated as 

tasks, e.g., "Collect otolith and water samples" and "Analyze microstructure of otoliths" 

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ISRP 2007-9 INNOVATIVE PROPOSAL REVIEW

rather than as desired outcomes. The project involves more than one year of field work, 

and it is likely that the project would not be completed in the proposed time frame. 

Information transfer would be improved by publication of important scientific results in a 

peer-reviewed journal. The sponsors do not present a convincing case for direct benefits 

to survival or productivity of Snake River fall Chinook salmon. This was one of a number 

of proposals to use otolith microchemistry techniques to reconstruct Columbia Basin fish 

life-histories. The ISRP encourages collaboration among Columbia River Basin otolith 

microchemistry researchers to establish water chemistry baseline data, which are a 

necessary precursor to successful completion of these projects. While this proposal is not 

innovative, it does address an important uncertainty in the Columbia River Basin. 

Perhaps, this proposal could be revised and resubmitted under a future solicitation for 

research proposals. 

200755600 - Water Stargrass Demonstration and Management in the lower 

Yakima River for Spawning Habitat, Water Quality and Beneficial Uses 

(WiSDoM) 

Sponsor: Benton Conservation District 

FY08-09 budget: $372,450 

Short description: Water stargrass (Heteranthera dubia) threatens lower Yakima River 

salmon spawning habitat, water quality and beneficial uses. H. dubia will be harvested to 

restore these functions. H. dubia will be evaluated as a livestock feed to mitigate disposal 

cost. 

(View full proposal online)

Recommendation: Unranked 

This proposal describes an approach to solve a serious problem (stargrass proliferation) in 

the Yakima River, but the proposal is not quite well enough developed. The most 

innovative portion is using stargrass as a livestock feed to partially defray the harvest 

cost. It would seem that some preliminary work could be conducted regarding the 

nutrient value of the stargrass. We encourage the project sponsors to resubmit this 

proposal when a suitable riverine harvesting method is identified and a monitoring 

program is developed that can track removal effectiveness and post-harvest stargrass 

regrowth. Also, the actual cause of the stargrass irruption in recent years is not clear and 

deserves attention so that the root cause can be understood and addressed long term. 

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200755800 - Willamette Mitigation

Sponsor: The Nature Conservancy 

FY08-09 budget: $277,644 

Recommendation: Unranked 

This project proposes to evaluate projected conservation returns from alternative wildlife 

mitigation investment strategies in the Willamette subbasin, i.e., evaluate “return on 

investment.” Three investment approaches would be used in the comparison: (1) 

acquisition of fee interests and mitigation easements, (2) “working” land easements 

(restricting only development rights and following best practices), and (3) incentives and 

technical assistance with no long-term use restrictions. The concept sounds interesting 

and potentially could be extremely useful in capturing conservation opportunities that 

might otherwise soon be lost. The decision analysis tool is not in general innovative, 

although this particular application could be considered innovative in the Columbia River 

basin. This is not on-the-ground. This is an assessment exercise. 

However, apparently little upfront work has been completed to determine the types or 

amounts of data available for evaluation, or sites obtained under different investment 

strategies (with associated biological data) that could be used in this analysis. The 

methods are not well enough developed to justify the project. There is insufficient detail 

about the rule sets that will be developed by a panel of wildlife biologists. These rule sets 

should be developed prior to submittal of the proposal. Also, perhaps focal species could 

be chosen for each of the six focal habitats. More information on the points above needs 

to be presented. Although the concepts are presented, and sound intriguing, details on the 

project are lacking. 

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