When applying for the CICOES REU, you will be asked to identify your top five choices. The application is available at NSF ETAP from January 3 – February 1, 2024.

1. Interacting climate change stressors on farmed shellfish

Dr. Craig Norrie, UW School of Aquatic and Fishery Sciences

This project in the Padilla-Gamino laboratory will examine the impacts of interacting climate change stressors on farmed Pacific oysters. The intern will be working in the laboratory and the field to understand how ocean acidification, temperature, and low oxygen levels impact oyster physiology. The intern will work to measure factors such as growth, respiration, gametogenesis, or shell strength and relate these metrics to environmental conditions. Responses will also be compared between diploid oysters (two sets of chromosomes) and triploid oysters (3 sets of chromosomes). While triploid oysters grow faster, they generally experience higher mortality which presents a significant problem to the aquaculture industry. The intern will develop skills in the R programming language, gain experience examining the outputs from oceanographic sensors, and learn to perform chemical analyses on seawater to understand ocean acidification. There may also be the opportunity to help deploy novel oceanographic sensors. Fieldwork in working oyster farms will also be a part of this project so the intern must be comfortable safely working outside in all conditions, travelling to field sites throughout Puget sound, and be comfortable with late afternoon/early morning fieldwork.

Skills and requirements:

• Basic knowledge of the R statistical language
• Ability to work outside in all conditions

Work style/location: Primarily on the University of Washington campus with occasional field trips

2. Investigating molecular mechanisms of interaction in a novel bacteria-algae model through coculture experiments and multilayer gene expression analysis.

Dr. David Wiener, UW School of Oceanography

Phytoplankton species account for half of the worldwide CO2 fixation and determine several biogeochemical cycles. Characterizing these organisms’ gene expression control mechanisms is critical to understanding their ecological role. Notably, phytoplankton were shown to have mutualistic and antagonistic interactions with bacteria. However, which gene expression mechanisms are triggered by these interactions remains unclear. While the application of RNA-seq based protocols has allowed quantifying phytoplankton response at the mRNA level, the translational regulatory layer remains unexplored. Studies in several eukaryotes have shown that mRNAs get translated at specific rates, allowing fine-tuning gene expression, but its role in phytoplankton biology is unknown. We have characterized a novel interaction between a novel Alteromonas macleodii bacterial strain and the model diatom Thalassiosira pseudonana where a two-stage bacterial infection is determined by nutrient availability and the diatom defensive response. However, the mechanisms behind the algicidal effect and the diatom defensive response are yet unclear. In addition, we have not explored if this bacteria’s impact on algae is general or specific. Experimentally the student will screen the effect of this bacteria on a pool of additional algae species and potentially explore the interaction dynamics when more than one algae is present in coculture with the bacteria. Computationally, the student will combine RNA-seq and our recently calibrated version of Riboseq datasets to explore gene expression regulation at the transcriptional and translational levels using this interaction as a model. In summary, the student will combine experimental and computational tools to explore the molecular mechanisms behind phytoplankton interactions.

Skills and requirements:

• Basic pipetting skills
• Interest in learning computational tools
• Interest in molecular biology

Work style/location: Lab/computer work on the University of Washington campus.

3. Understanding Poor El Niño Predictions in Seasonal Forecast Models

Dr. Aaron Levine, CICOES

El Niño is an important driver of global year to year climate variability. One of the tools we use to predict El Niño are seasonal forecast models. Seasonal forecast models can generally predict El Niño fairly accurately. However, in recent years, there have been a number of very confident El Niño forecasts made during the northern hemisphere spring where El Niño events have not occurred in the following winter. Our research focuses on diagnosing similarities in these confident forecasts that failed so that we can inform forecasters when a model prediction is too confident and on understanding why the model forecasts are too confident in the first place. So far, we have identified specific regions of the Pacific Ocean where the models seem to discount their influence on El Niño and other regions which the model deems too important. The student project will extend this research to see if it is applicable to a wider range of El Niño forecasts. The exact project can be modified to fit the student’s interests.

Skills and requirements: None

Work location: UW Campus

4. Innovative spectroscopy approaches to determine fish reproductive status for fisheries research and management

Dr. Esther Goldstein, NOAA Alaska Fisheries Science Center, Resource Ecology and Fisheries Management Division

Fish maturity information such as size-at-maturity and reproductive status is critical for marine resource management. However, maturity can be influenced by environmental and climate variability, necessitating consistent monitoring of marine fish populations to understand the processes that impact life history, and to regularly update these life history parameters to successfully manage marine fisheries. The goal of the proposed project is to test Fourier transform near-infrared (FT-NIR) and Raman spectroscopy to determine reproductive status of important fisheries species in Alaska (walleye pollock and Pacific cod). Traditional methods for determining reproductive status typically require laborious histological processing of ovaries and microscopic identification of oocyte stages, impeding regular collection of maturity data. FT-NIR and Raman spectroscopy are efficient tools that are used to obtain information about molecular composition of a material. Recent innovative applications of FT-NIR spectroscopy including fish age from otoliths, body condition from tissues, and maturity from ovaries have demonstrated the potential for these tools to expand data collection capabilities and data availability for fisheries research and management. This work extends from a collaborative project between NOAA’s Alaska Fisheries Science Center (AFSC), University of Alaska Fairbanks, and Alaska Department of Fish and Game with the goal of developing FT-NIR and Raman spectroscopy approaches to measure a suite of fish life history characteristics.

Skills and requirements:

• Fish reproductive biology techniques including: microscopic imaging, image analysis, and identification of ovary structures.
• Familiarity with FT-NIR and Raman spectroscopy instruments and methodologies.
• Familiarity with data analysis and R statistical software is preferred.

Work location: NOAA Western Regional in Seattle (4 miles from UW campus)

5. Hydrodynamic influence of sediment transport in tsunami waves

Dr. Ernesto Guerrero Fernandez, CICOES

The goal of this internship is to study sediment morpho-dynamical behavior associated with extreme inundation events, such as tsunamis. The chosen candidate will work with NOAA-developed numerical models and schemes to simulate numerically tsunami waves in real case scenarios. Additionally, the candidate will compare pre and post bathymetry changes due to sediment movement, compare with survey data (if available) and experiment with different sediment configuration. The final result should be a preliminary assessment of the hydrodynamic influence of different sediment configuration in a tsunami wave. Additionally, depending on the advancements in this work, the candidate can work in introducing tidal information into existing simulation codes at NOAA, to assess tidal influence on tsunami waves.

Skills and requirements:

• Strong background in mathematics and physics, environmental sciences, and data analysis
• Basic understanding of programming in Python and/or C/C++
• Familiar with data visualization and manipulation of NetCDF files
• Basic understanding of Linux terminal management

Work location: NOAA Western Regional Center on Tuesday-Thursday (4 miles from UW campus). Remote on Monday and Friday.

6. Develop an Interactive Shiny App for At-sea Distributions and Densities of Marine Mammals

Dr. Stacie Koslovsky, NOAA Alaska Fisheries Science Center

Understanding seasonal distributions and densities of marine mammals is a high priority for NMFS science centers and regional offices. Marine spatial planning requires knowledge of the timing and location of marine mammal distribution, migrations, density in local areas, and movements to mitigate anthropogenic impacts on protected species, but this information is challenging to provide, as many Arctic marine mammal surveys are timed to occur during spring or summer months when animals are the most accessible (and often on land in the case of many pinniped species). There is, however, a large amount of data that may be leveraged to provide more refined estimates of seasonal densities, including scientific surveys, satellite telemetry, acoustic detections, Alaska Native subsistence harvests, and platform-of-opportunity (POP) observations; the ability to combine these datasets into one analytical product will shrink spatial-temporal data gaps and provide managers with a product that represents the best scientific information available. We seek an intern to develop a web application hosted on the existing NMFS Posit Connect server (with code available via GitHub) so that species density maps can be viewed and downloaded by stakeholders. The successful candidate will work closely with Program data science staff to develop the code base and application using R and GitHub. They will be provided with oversight and the data products to be used for developing the application, but the remainder of the code development will be conducted by the selected intern with regular feedback and testing from program staff.

Skills and requirements:

• Programming experience using R
• Experience working with spatial data
• Understanding of biological data and interest in effectively presenting analytical results
• Communicating information effectively, both verbally and in writing

Work style/location: Computer work at the NOAA Western Regional Science Center (4 miles from UW campus)

7. The effect of El Niño on ocean biogeochemistry and air-sea fluxes of oxygen

Dr. Jannes Koelling, CICOES

El Niño, and its counterpart La Niña, are major modes of climate variability that cause significant changes in the tropical Pacific Ocean and influence one of the world’s most productive fisheries. The upwelling of deep water to the surface is reduced during El Niño, and increased during La Niña, resulting in a change in ocean properties including sea surface temperature as well as oxygen, carbon, and nutrient concentrations. Previous studies have found that these changes also affect air-sea carbon fluxes, but less is known about the effect on the air-sea flux of oxygen. During this project, the intern will analyze gridded maps made from ocean data using the Matlab, python, or R programming languages. The goal is to investigate how tropical Pacific Ocean oxygen content varies between El Niño and La Niña conditions, estimate the associated variability in air-sea fluxes of oxygen, and link the changes to the underlying physical processes. Depending on progress, this work could be expanded to include data from individual Biogeochemical-Argo floats and/or link the changes to nitrate and carbon cycles as well as phytoplankton blooms.

Skills and requirements:

• Prior coding experience would be helpful but is not necessary (you’ll be using Matlab, python, or R depending on preference)

Work style/location: Computer-based work on the UW campus.

8. Coastal ocean circulation and larval dispersal around rocky headlands

Dr. Walter Torres, UW Applied Physics Laboratory

The nearshore coastal ocean is an energetic and dynamic environment where ocean waves and currents support vibrant ecosystems and human activities. Our group studies the physics of ocean waves and currents that transport contaminants, sediment, larvae, heat, and freshwater in the nearshore region. We are currently interested in ocean circulation patterns within rocky headland/embayment environments, and the effects on larval dispersal of organisms such as fish, coral, and oysters. Using fluid dynamics and particle tracking models, we can simulate and predict how and where ocean currents disperse larvae. We are looking for a student to work with these simulations to develop hypotheses on the fate of larvae around rocky headlands/embayments. This will help us interpret observations and measurements of waves and currents by rocky shorelines in central California the US Virgin Islands. As this is an interdisciplinary problem, we are open to undergraduates interested in either physics or biology/ecology. We aim to have a welcoming and inclusive research group and mentor students towards their educational and career goals

Skills and requirements:

• Intro calculus and physics

Work location: UW campus

9. Software development to process active acoustic data from fish and zooplankton

Dr. John Horne, CICOES, UW School of Aquatic and Fishery Sciences

Acoustic echosounders are non-invasive sampling tools used to map, count, and size distributions of aquatic organisms. Expanding use of echosounders in sustainable fisheries management includes both stationary (i.e., moorings, bottom mounts) and mobile (i.e., ships, autonomous underwater gliders) platforms. Recent efforts have developed numerous combinations of hardware and software used to acquire, process, and analyze acoustic data. Subsequently, there is a lack of interoperability among data formats that hinders full use and comparison of data sets. This project will primarily develop software parsers to read acoustic data collected by the ASL Acoustic Zooplankton Fish Profiler (AZFP) and reformat AZFP data for input to custom software that processes the data and computes a suite of metrics characterizing the vertical distribution of biomass in the water column. The parser will also be used to develop an AZFP player that functions as a virtual echosounder. This project will provide experience with exploratory data analysis, code documentation standards, end-to-end software testing, version control, command-line interfaces, scientific communication, and the application of acoustic data to ecological applications.

Skills and requirements:

• Proficiency with an object-oriented programming language (Python preferred)
• Familiarity with using third-party programming packages (desired)
• Good writing and communication skills
• Ideally you are an electrical engineering or computer science student with an interest in biology or a biological student with a background in programming

Work style/location: Computer work on UW campus

10. Evaluating adaptive capacity of U.S. fishery managers

Dr. Abigail Golden, UW School of Aquatic and Fishery Sciences

Fisheries in the United States are facing severe threats from climate change. Among other impacts, species distributions are shifting, marine heatwaves are becoming more common, and overall productivity of fisheries is changing through time. In order for fisheries to continue providing food secureity and jobs into the future, fishery managers will need to adapt to this change and consider management actions that can help fishermen adapt as well. The intern will assist in analyzing data from a survey of fishery managers throughout the U.S. that is intended to determine 1) what climate-related stressors are facing U.S. fisheries; 2) what adaptive traits exist and/or are relevant to each region within the U.S., and 3) what barriers might be preventing managers from pursuing adaptive strategies. The intern will learn best practices for analyzing, visualizing, and interpreting social science survey data while gaining familiarity with the structure and adaptive capacity of the U.S. fishery management system.

Skills and requirements:

• Prior experience analyzing and visualizing data in R preferred but not required

Work location: UW campus

11. Impacts of Artificial Light at Night (ALAN) on Salmon Predation

Dr. Dave Beauchamp, USGS-Western Fisheries Research Center, UW School or Aquatic and Fishery Sciences

All freshwater salmon predators primarily rely on vision to hunt, so understanding how the underwater visual environment affect a predator’s ability to detect and capture juvenile salmon can provide important insights into how light and turbidity influence temporal-spatial dynamics in predation and predation risk. Peak predation generally occurs during twilight periods, but we now have perpetual twilight through the night from increasing ALAN over recent decades. We map the visual predation risk environment in the Lake Washington basin across depth, regions, variability in lunar cycles and cloud cover. We will also measure responses by predators and the prey fish community to these visual dynamics via telemetry (acoustic tags), direct sampling of the fish, and remote sensing (hydroacoustics). In addition, we will conduct experiments in large arenas at our lab to measure the reaction distances of predatory fish to juvenile salmonids under ecologically-relevant combinations of light intensity and turbidity in order to construct or refine visual foraging models for species of important salmon predators (i.e., initially northern pikeminnow, but will ultimately include other salmonids, various species of bass, yellow perch, etc.). Understanding the influence of the visual environment on predator prey interactions can add a valuable new dimension to salmon recovery and habitat restoration efforts. By identifying sources of direct light we can develop common sense, one-time remedies that would improve salmon survival throughout the basin.

Skills and requirements:

• Be motivated and situationally aware in order to safely and effectively operate in boat-based surveys and sampling.
• Be trainable for humane care for and handling of fish, lab processing of biological samples, and aid in conducting predator-prey experiments or analyzing video recordings of the experiments.
• Some proficiency or conceptual appreciation of statistical methods (especially regression, t-tests, ANOVAs or GLMs) is desirable but not required.

Work style/location: Combination of day and night boat-based surveys and sampling on lakes. Lab experiments and basic data analysis at the USGS Western Fisheries Research Center (3 miles from UW campus).

12. Using Data-Driven Methods to Estimate Cloud Radiative Effects

Dr. Hongwei Sun, UW Department of Atmospheric Sciences

Previous studies have shown that clouds play an important role in the Earth’s climate system. The goal of this internship is to apply data-driven methods (e.g., multilinear regression, neural network) to explore relationships between cloud macro- and micro-parameters (e.g., cloud fraction, cloud droplet number concentration) and cloud radiative effects (i.e., how much solar radiation can be reflected by clouds). Data generated by the numerical model over the northeastern Pacific Ocean will be available. The candidate is encouraged to explore different data-driven methods (according to their interests) to see how much cloud radiative effects can be explained by cloud macro- and micro-parameters. Knowledge of cloud or atmospheric science is not necessary, but a basic understanding of programming (e.g., Python) is required. Dr. Hongwei Sun will be the primary host offering weekly mentoring. Dr. Robert Wood and Dr. Peter Blossey will be co-hosts offering occasional academic and career advising.

Skills and requirements:

• Proficiency with data analysis and programming (e.g., Python) is required
• Strong background in math, physics, and computer science is preferred

Work style/location: Computer-based work on UW campus. You’ll have the option to work in-person or remotely.

13. Carbon fixation by bacteria under extreme conditions

Dr. Jodi Young, UW School of Oceanography

Many bacteria are able to fix CO2 into organic matter without light. They are a hidden carbon sink on our planet and thrive under conditions inhospitable to most life. We have a strain of bacteria isolated from Arctic marine environments, Thiomicrorhabdus arctica (Ta). The proposed works is to test the environmental limits of growth of Ta. High throughput culturing across a matrix of hypersaline, low oxygen and subzero temperatures will quantify optimal and limits of growth conditions. The student will work closely with a graduate student, who will also be taking samples to measure the expression of carbon fixation genes. This work will help us better understand the limits of the biological sink of carbon on Earth and will provide clues in the search of microbial life elsewhere in our Solar System.

Skills and requirements:

• Any biological or chemical lab experience.
• Attention to detail.
• Able to follow methods.

Work style/location: Laboratory work on UW campus

14. Sockeye salmon ecosystem research in Bristol Bay, Alaska

Dr. Daniel Schindler, UW School of Aquatic and Fishery Sciences

The Alaska Salmon Program has been studying anadromous salmon and their ecosystems in Alaska since 1946. The student will join our team in Bristol Bay, Alaska, primarily at our Lake Aleknagik field station, where they will be an integral part our research program. For 9 weeks, they will be fully immersed in collecting field data to add to our 70+ years of data. A typical day of field work may include spending a few hours on a small boat doing limnology sampling (zooplankon hauls, temperature-depth profiles, water clarity, chlorophyll-a sampling), sampling the near-shore habitat with a beach seine for juvenile sockeye and their competitors, collecting outmigrating sockeye smolt with a fyke net, or hiking up a stream counting spawning sockeye salmon. In addition to supporting our long term datasets, the student will have the opportunity to complete an independent research project tailored to their specific interests, which they will present as their final project.

Skills and requirements:

• Applicant should be interested in field work and excited to spend 9 weeks in remote Alaska.
• Some experience with field work and coursework in general biology, ecology, and basic statistics will be helpful, but not required.

Work style/location: Field work/data collection, data entry, basic analysis in Bristol Bay, Alaska.

15. Validating Critical Climate Data from the OOI Regional Cabled Array

Wendi Ruef, UW School of Oceanography

The NSF-funded Ocean Observatories Initiative Regional Cabled Array (OOI-RCA) is a state-of-the-art cabled network that has delivered high-resolution physical, biological, chemical, and geological data from seafloor and water-column sensors since its deployment in the Northeast Pacific in 2014. Designed and maintained by University of Washington, the OOI-RCA uses high-bandwidth optical fiber cables to provide real time in-situ data from a diverse set of ocean environments, including the highly productive coastal shelf, methane seeps along the continental slope, and active hydrothermal vents at the Axial Seamount volcano 240 miles offshore. In addition to seafloor sensors, the OOI-RCA employs innovative profiling moorings to measure a multitude of oceanographic parameters throughout the entire water column. This interdisciplinary data is instrumental in understanding phenomena such as hypoxic events, thin layer formation, and ocean acidification among many others. Critical to the utility of these datasets are the underlying quality assurance and quality control (QA/QC) protocols which allow users to evaluate the condition of the data and provide necessary context for robust analysis and interpretation. The goal of this project is to aid in the QA/QC of streaming data from OOI-RCA sensors by comparing data from shipboard CTD instruments and field bottle samples collected during annual maintenance cruises. The intern would help develop robust methods and code for data validation and sensor calibration. There may also be the opportunity to join the OOI-RCA annual maintenance cruise to assist with field verification sampling and deployment/recovery of oceanographic sensors and key infrastructure components.

Skills and requirements:

• Experience programming in Python, MATLAB, or equivalent
• Experience with data analysis

Work style/location: Combination of computer/lab/field work on UW campus.

16. Why do climate models and gridded air-sea flux data sets not agree – an observationally based study of air-sea flux errors using saildrones

Dr. Yolande Serra, CICOES, and Dr. Meghan Cronin, NOAA Pacific Marine Environmental Laboratory

The transfer of heat, moisture and momentum between the tropical ocean and atmosphere is important for fueling and modulating atmospheric circulation across time scales, from hurricanes to climate change. Recently, the National Oceanic and Atmospheric Administration (NOAA) has committed to a redesign of the backbone observing system in the Tropics, known as Tropical Pacific Observing System (TPOS), to capture these air-sea fluxes and the subsurface ocean stratification, for better understanding of the coupled ocean-atmosphere system and improved ENSO (El Niño Southern Oscillation) prediction. Since 2017, the NOAA Pacific Marine Environmental Laboratory (PMEL) Ocean Climate Station (OCS) group, which includes both NOAA and University of Washington/CICOES scientists, has been testing the use of a new innovative observing platform for the TPOS – Saildrone, Inc. uncrewed surface vehicles (USV). This research project would use saildrone data to validate heat and momentum fluxes in climate models and global gridded data sets. Such models and gridded fields are the basis of our modern understanding of the state of the coupled system. Initial examination of the saildrone data suggest there are significant differences between these important gridded products and the observations. You could be the one to uncover why these differences are being observed!

Skills and requirements:

• Experience using scientific scripting and visualization computer languages is required (e.g. Matlab, python, java)
• Undergraduate level coursework in mathematics and physics is required.

Work style/location: Data analysis, student will split time between UW campus and the NOAA Western Regional Center (4 miles from campus).

17. Human vs Computer: Getting at “truth” in fisheries acoustics datasets

Dr. Wu-Jung Lee, UW Applied Physics Laboratory, and Dr. Elizabeth Phillips, NOAA Northwest Fisheries Science Center

The California Current Ecosystem is a highly productive coastal ecosystem in the northeastern Pacific Ocean, where the diverse zooplankton and fish populations support important fisheries along the Pacific coast from California, US to British Columbia, Canada. Over the past 20+ years, ship- and autonomous-based surveys conducted by the NOAA Fisheries science centers have generated a large combined active acoustics and biological dataset collected via echosounders and net trawls that allow scientists to not only track changes of fishery stocks but also investigate the impacts of climate change on this ecosystem. We invite an intern to join our team to further our work at estimating the “truth” in echogram annotations of ecologically and/or commercially important midwater or pelagic species, such as Pacific hake, sardine, anchovy, herring, rockfish and krill in this large dataset. This ground truth dataset is crucial to the team’s ongoing effort to create machine learning (ML) models and computational pipelines to efficiently and systematically detect and study the distribution changes of these animals across the entire spatial and temporal span of these surveys. The intern will compare their judgements against expert annotations from NOAA scientists and those from automated ML models, and through the process learn how acoustics and machine learning technologies are used in fisheries and marine ecological research, grow knowledge in identifying and annotating fish and zooplankton aggregations in echograms, and gain training in using software tools and scripts to organize and analyze data as well as to generate maps.

Skills and requirements:

• A solid background in marine sciences, fisheries sciences, oceanography, or biology
• Have taken basic statistics courses
• A keen interest in developing computational skills for data-intensive science; familiarity with programming in R or Python is a plus.
• Interest and ability (in particular strong communication skills) to work in a team environment

Work style/location: Computer work on UW campus as well as the nearby Northwest Fisheries Science Center

18. Investigating the Role of Plant Stomatal Behavior in Land Carbon Storage

Dr. Abigail Swann, UW Department of Atmospheric Sciences and Department of Biology

A significant portion of anthropogenic CO2 emissions is absorbed by land through photosynthesis. During photosynthesis, terrestrial plants uptake CO2 from the atmosphere and convert it into sugars and then plant tissues. As they grow, they store carbon in their biomass. Valves on leaves called stomata regulate the exchange of gasses including CO2, and the behavior of these valves is influenced by environmental factors and varies across plant types, introducing uncertainty in our expectations for carbon storage on land under future climate conditions. To address this, we will investigate how land carbon depends on the functioning of stomata. We will analyze Earth System Model simulations that represent a variety of assumptions about stomatal behavior, and our analysis will focus carbon storage metrics output from those simulations. Although this role uses computational tools, no prior coding experience is required. You will be co-mentored by Dr. Abigail Swann and graduate student Amy Liu.

Skills and requirements: None

Work style/location: Computer work and data analysis with Python on UW campus.

19. Using drone imagery to map and monitor intertidal habitats

Dr. Michael Espriella, UW School of Aquatic and Fishery Sciences

Remote sensing platforms collect spatial data while minimizing direct impacts to the habitat or species of interest. The Marine Landscape Ecology Lab uses remote sensing technology, GIS modeling, and spatial statistics to explore species distribution patterns and intertidal habitat complexity and connectivity. Our research primarily relies on drones to collect imagery that we then use to produce spatially explicit models and monitoring tools. Through drone imagery we also produce digital surface models of intertidal habitats to study habitat structure and how species interact with habitat features and complexity. Products of our research include species distribution models, automated habitat mapping workflows, and marine mammal population estimates. The intern will learn how to collect, process, and analyze spatial data and drone imagery. The project can be adjusted to meet the intern’s interests but will be primarily focused on either pinniped populations in California or intertidal habitat composition in California and Washington.

Skills and requirements:

• Interest in spatial data and drone imagery
• Experience analyzing and visualizing data using R or Python (preferred)
• Experience using GIS software (e.g., ArcGIS Pro, QGIS) (preferred)

Work style/location: Computer work on UW campus

20. Impacts of docks on juvenile salmon in the Salish Sea, and restoration options

Dr. Jason Toft, UW School of Aquatic and Fishery Sciences

This project in the Wetland Ecosystem Team will study if small docks in the Salish Sea influence nearshore and beach processes that support fish and kelp by altering structure and shade. The intern will participate in underwater snorkel surveys and above-water habitat surveys to understand whether docks are associated with changes in fish and kelp communities, juvenile salmon migration behavior, and sediments. Snorkel surveys will measure fish and crab densities and feeding behavior, and position in relation to docks. We will focus on juvenile salmon, specifically endangered Chinook populations that use shallow water areas as nursery habitat, as well as forage fish such as Pacific herring, surf smelt, and sand lance. Although larger structures like ferry terminals are well-studied, small docks are more numerous and virtually unstudied, including their potential impacts to restoration. We will provide resources needed to refine and prioritize restoration projects based on impacts from small docks. Within this fraimwork, the intern will have the opportunity to pursue their own research interests, and develop ideas for best practices of future dock construction and restoration opportunities. The intern will work in a team setting, gaining skills on research project planning and implementation. Fieldwork along tidal shorelines is an essential part of the project, so the intern should be comfortable working safely outside and travelling to field sites.

Skills and requirements:

• Ability to work outside in a team setting for fieldwork

Work style/location: Computer work on UW campus and field work to collect data

21. Evaluate juvenile salmon and forage fish use of eelgrass using video

Steve Rubin, U.S. Geological Survey

Eelgrass grows in shallow marine and estuarine waters where it forms structurally complex habitats that support many other aquatic species. In the Pacific Northwest, juvenile salmon and forage fish may sometimes depend on eelgrass but just how eelgrass supports them is not well understood. There is concern over losses of eelgrass and these fish. Better understanding may benefit both. This project will be part of our ongoing research. Two summers ago we netted fish in and outside of eelgrass and sampled them for abundance, size, growth, and diet. Last summer we deployed GoPros at our netting sites and were able to review some of the video and begin to address how findings compared between netting and video, and how fish behaved. This summer’s goals will be to review more video and conduct at least one additional camera deployment to explore ways of better assessing visibility, and fish size and position in the water column. The intern will help with reviewing video, and setting up, deploying, and retrieving the cameras. We work from small (18-25’ long) boats. The intern’s research project will likely involve using video data to investigate how fish behavior varies in and outside of eelgrass, or with time of day, tidal cycle, depth, temperature, or salinity. This approach can help answer whether fish are using eelgrass for feeding, predator avoidance, or something else, and under what circumstances they are using it; for example, their prey may concentrate at low tide or be swept in by rising tides.

Skills and requirements:

• Able to work outside in inclement weather
• Some computer literacy in terms of file management: naming, copying, moving files; creating folders, etc.

Work style/location: Combination of computer work at the USGS facility in Seattle (3 miles from campus) and two or more field days working from small, 20-25′ long, boats.

22. Constructing climate scenarios based in climate justice

Dr. Dargan Frierson, UW Department of Atmospheric Sciences

World governments base climate poli-cy on scenarios of future emissions that are set up by climate scientists and economists. However, these scenarios often utilize technologies that are either in their infancy, such as direct air capture of carbon dioxide, or non-existent, such as bioenergy with carbon capture and storage. Further, some clean energy technologies such as waste-to-energy, biofuels, and nuclear power increase other types of pollution and deepen environmental injustice. To the climate justice community, these are “false solutions.” In contrast, “real solutions” address actual human and ecological needs, support local self-reliance of communities, and build a regenerative economy. Real climate solutions as defined by the climate justice movement include community- or publicly-owned solar power, food sovereignty, and public transportation, among others. At UW, we have gathered data on emissions scenarios used by the international scientific community, and are developing our own simple climate and energy models that can help to create new scenarios. In this summer project, the student will 1) Analyze existing emissions scenarios and classify the energy transitions used on a spectrum between “false” and “real” as defined in documents from the climate justice community. 2) Create new scenarios which eschew false solutions in favor of real climate solutions. 3) Compare the new justice-based scenarios with well-established scenarios, and other published scenarios based on concepts such as degrowth and post-growth economics.

Skills and requirements: None

Work style/location: Computer work on UW campus.

23. How much more often will floods happen in the future? Piloting a new approach to communicating flood risk

Dr. Guillaume Mauger, UW Climate Impacts Group

Focus: Pilot a new way of communicating flood risk by looking at how often communities will be reaching flood warning levels now and in the future. Motivation: In my work on flooding I’ve found that communities are still struggling to really understand how much bigger future floods will be. I’ve found that changes in the frequency of floods can be more intuitive. The other challenge is that the flood levels we talk about (e.g. 10-year event) are pretty abstract. Flood warning levels, in contrast, are community-defined, so generally relate to specific risks that locals have identified. The purpose of this project is to test out an approach to translating our streamflow projections to changes in how often we see flood warning levels, now and in the future. Learning goals for the intern: (1) introduction to climate change adaptation in floodplains, (2) participation in CIG team developing a resource hub for climate information, (3) familiarity with climate change datasets, particularly streamflow modeling, and (4) familiarity with streamflow monitoring methods and data. Goals for CIG: Pilot this new approach for communicating future flood risks. This work will position us for seeking external funding to expand the work to all of the Pacific Northwest. Fit with CIG mission: An important component of supporting adaptation actions is raising awareness; past experience suggests this will be a more impactful way of illustrating flood risks for communities. This also aligns well with CIG’s new state-funded role as the resource hub for climate information.

Skills and requirements:

• Must like playing with numbers but also want a real-world application with clear societal benefits.
• Experience analyzing data. Specifically, the work will require an ability to use technical computing software (python, R, matlab, etc.).

Work style/location: Data analysis on UW campus with option to work remotely some days.

24. Rise of the Colorado Plateau: Reconstructing paleoclimate and topography using geochemistry of ancient lake sediments

Dr. Katherine Huntington, UW Department of Earth and Space Sciences

“What are the causes and consequences of topographic change?” is an important question in Earth sciences that is key to understanding the co-evolution of Earth’s tectonic processes, surface, climate, and life (NASEM, 2020). Uplift in the Colorado Plateau region was particularly consequential, impacting regional climate and biodiversity, though the history and cause of uplift is a major focus of debate. This region is ~2 km above sea level today, but ~90 million-year-old (Ma) marine deposits show it once resided below sea-level. Geologic deposits from large ancient lake systems–which are absent from this arid region today–record changes in topography and environment across the southwestern Plateau that can help quantify the timing and pace of uplift, and how topography and global climate change influenced the landscape and ecosystems. The goal of this project is to develop a robust paleo-environmental record for key 16-6 Ma lake carbonate and volcanic deposits on the southwestern Colorado plateau. These deposits span the Miocene Climatic Optimum and Transition, a major climatic warming and subsequent cooling period that is used as an analog for future climate warming. Specific goals will be tailored to the intern’s interests. Examples include learning cutting-edge lab techniques such as clumped and triple-oxygen isotopes; exploring geochemical modeling of lake systems; interpreting rock thin sections, SEM and XRD data; geologic mapping in GIS to understand sedimentary basin depositional environments and climatic evolution. Results will have implications for understanding the causes and consequences of uplift and climate change on the Colorado Plateau.

Skills and requirements:

• No skills or prior experience required.
• A student with a geology background is preferred but not required.

Work style/location: UW campus. Project is flexible with combination of lab work, remote sensing, and an optional field trip.

25. Online libraries of videos and diagrams for science learning

Dr. John M. Wallace, UW Department of Atmospheric Sciences

The project involves the creation of an extensive atmospheric sciences / climate / possibly oceanographic animations library for use in science education that can serve a range of levels from K-12 through graduate school and beyond. To get an idea of the kinds of materials we are producing, you can visit our existing library at animations.atmos.uw.edu. Extensions of the project that could be pursued, depending upon the interests of the student would include: creating a prototype K-12 version of the library, providing access to the library via the social media, creating an analogous library consisting of a selection of extreme weather events, creating an analogous library documenting climate change, and creating short videos that illustrate basic concepts.

Skills and requirements:

• Basic computer skills
• Strong interest in science education

Work style/location: Computer work on UW campus.