Oregon State University Archives - Page 2 of 4 - Geospatial Ecology of Marine Megafauna Laboratory

Data Wrangling to Assess Data Availability: A Data Detective at Work

By Alexa Kownacki, Ph.D. Student, OSU Department of Fisheries and Wildlife, Geospatial Ecology of Marine Megafauna Lab

Data wrangling, in my own loose definition, is the necessary combination of both data selection and data collection. Wrangling your data requires accessing then assessing your data. Data collection is just what it sounds like: gathering all data points necessary for your project. Data selection is the process of cleaning and trimming data for final analyses; it is a whole new bag of worms that requires decision-making and critical thinking. During this process of data wrangling, I discovered there are two major avenues to obtain data: 1) you collect it, which frequently requires an exorbitant amount of time in the field, in the lab, and/or behind a computer, or 2) other people have already collected it, and through collaboration you put it to a good use (often a different use then its initial intent). The latter approach may result in the collection of so much data that you must decide which data should be included to answer your hypotheses. This process of data wrangling is the hurdle I am facing at this moment. I feel like I am a data detective.

Data wrangling illustrated by members of the R-programming community. (Image source: R-bloggers.com)

My project focuses on assessing the health conditions of the two ecotypes of bottlenose dolphins between the waters off of Ensenada, Baja California, Mexico to San Francisco, California, USA between 1981-2015. During the government shutdown, much of my data was inaccessible, seeing as it was in possession of my collaborators at federal agencies. However, now that the shutdown is over, my data is flowing in, and my questions are piling up. I can now begin to look at where these animals have been sighted over the past decades, which ecotypes have higher contaminant levels in their blubber, which animals have higher stress levels and if these are related to geospatial location, where animals are more susceptible to human disturbance, if sex plays a role in stress or contaminant load levels, which environmental variables influence stress levels and contaminant levels, and more!

Alexa, alongside collaborators, photographing transiting bottlenose dolphins along the coastline near Santa Barbara, CA in 2015 as part of the data collection process. (Image source: Nick Kellar).

Over the last two weeks, I was emailed three separate Excel spreadsheets representing three datasets, that contain partially overlapping data. If Microsoft Access is foreign to you, I would compare this dilemma to a very confusing exam question of “matching the word with the definition”, except with the words being in different languages from the definitions. If you have used Microsoft Access databases, you probably know the system of querying and matching data in different databases. Well, imagine trying to do this with Excel spreadsheets because the databases are not linked. Now you can see why I need to take a data management course and start using platforms other than Excel to manage my data.

A visual interpretation of trying to combine datasets being like matching the English definition to the Spanish translation. (Image source: Enchanted Learning)

In the first dataset, there are 6,136 sightings of Common bottlenose dolphins (Tursiops truncatus) documented in my study area. Some years have no sightings, some years have fewer than 100 sightings, and other years have over 500 sightings. In another dataset, there are 398 bottlenose dolphin biopsy samples collected between the years of 1992-2016 in a genetics database that can provide the sex of the animal. The final dataset contains records of 774 bottlenose dolphin biopsy samples collected between 1993-2018 that could be tested for hormone and/or contaminant levels. Some of these samples have identification numbers that can be matched to the other dataset. Within these cross-reference matches there are conflicting data in terms of amount of tissue remaining for analyses. Sorting these conflicts out will involve more digging from my end and additional communication with collaborators: data wrangling at its best. Circling back to what I mentioned in the beginning of this post, this data was collected by other people over decades and the collection methods were not standardized for my project. I benefit from years of data collection by other scientists and I am grateful for all of their hard work. However, now my hard work begins.

The cutest part of data wrangling: finding adorable images of bottlenose dolphins, photographed during a coastal survey. (Image source: Alexa Kownacki).

There is also a large amount of data that I downloaded from federally-maintained websites. For example, dolphin sighting data from research cruises are available for public access from the OBIS (Ocean Biogeographic Information System) Sea Map website. It boasts 5,927,551 records from 1,096 data sets containing information on 711 species with the help of 410 collaborators. This website is incredible as it allows you to search through different data criteria and then download the data in a variety of formats and contains an interactive map of the data. You can explore this at your leisure, but I want to point out the sheer amount of data. In my case, the OBIS Sea Map website is only one major platform that contains many sources of data that has already been collected, not specifically for me or my project, but will be utilized. As a follow-up to using data collected by other scientists, it is critical to give credit where credit is due. One of the benefits of using this website, is there is information about how to properly credit the collaborators when downloading data. See below for an example:

Example citation for a dataset (Dataset ID: 1201):

Lockhart, G.G., DiGiovanni Jr., R.A., DePerte, A.M. 2014. Virginia and Maryland Sea Turtle Research and Conservation Initiative Aerial Survey Sightings, May 2011 through July 2013. Downloaded from OBIS-SEAMAP (http://seamap.env.duke.edu/dataset/1201) on xxxx-xx-xx.

Citation for OBIS-SEAMAP:

Halpin, P.N., A.J. Read, E. Fujioka, B.D. Best, B. Donnelly, L.J. Hazen, C. Kot, K. Urian, E. LaBrecque, A. Dimatteo, J. Cleary, C. Good, L.B. Crowder, and K.D. Hyrenbach. 2009. OBIS-SEAMAP: The world data center for marine mammal, sea bird, and sea turtle distributions. Oceanography 22(2):104-115

Another federally-maintained data source that boasts more data than I can quantify is the well-known ERDDAP website. After a few Google searches, I finally discovered that the acronym stands for Environmental Research Division’s Data Access Program. Essentially, this the holy grail of environmental data for marine scientists. I have downloaded so much data from this website that Excel cannot open the csv files. Here is yet another reason why young scientists, like myself, need to transition out of using Excel and into data management systems that are developed to handle large-scale datasets. Everything from daily sea surface temperatures collected on every, one-degree of latitude and longitude line from 1981-2015 over my entire study site to Ekman transport levels taken every six hours on every longitudinal degree line over my study area. I will add some environmental variables in species distribution models to see which account for the largest amount of variability in my data. The next step in data selection begins with statistics. It is important to find if there are highly correlated environmental factors prior to modeling data. Learn more about fitting cetacean data to models here.

The ERDAPP website combined all of the average Sea Surface Temperatures collected daily from 1981-2018 over my study site into a graphical display of monthly composites. (Image Source: ERDDAP)

As you can imagine, this amount of data from many sources and collaborators is equal parts daunting and exhilarating. Before I even begin the process of determining the spatial and temporal spread of dolphin sightings data, I have to identify which data points have sex identified from either hormone levels or genetics, which data points have contaminants levels already quantified, which samples still have tissue available for additional testing, and so on. Once I have cleaned up the datasets, I will import the data into the R programming package. Then I can visualize my data in plots, charts, and graphs; this will help me identify outliers and potential challenges with my data, and, hopefully, start to see answers to my focal questions. Only then, can I dive into the deep and exciting waters of species distribution modeling and more advanced statistical analyses. This is data wrangling and I am the data detective.

What people may think a ‘data detective’ looks like, when, in reality, it is a person sitting at a computer. (Image source: Elder Research)

Like the well-known phrase, “With great power comes great responsibility”, I believe that with great data, comes great responsibility, because data is power. It is up to me as the scientist to decide which data is most powerful at answering my questions.

Data is information. Information is knowledge. Knowledge is power. (Image source: thedatachick.com)

Understanding sea otter effects through complexity

By Dominique Kone, Masters Student in Marine Resource Management

Species reintroductions are a management strategy to augment the reestablishment or recovery of a locally-extinct or extirpated species into once native habitat. The potential for reestablishment success often depends on the species’ ecological characteristics, habitat requirements, and relationship and effects to other species in the environment[1]. While the science behind species reintroductions is continuously evolving and improving, reintroductions are still inherently risky and uncertain in nature. Therefore, every effort should be made to fully assess ecological factors before a reintroduction takes place. As Oregon considers a potential sea otter reintroduction, understanding these ecological factors is an important piece of my own graduate research.

Sea otters are oftentimes referred to as keystone species because they can have wide-reaching effects on the community structure and function of nearshore marine environments. Furthermore, relative to other marine mammals or top predators, several papers have documented these effects – partially due to the ease in observing their foraging and social behaviors, which typically take place close to shore. In many of these studies, a classic paradigm repeatedly appears: when sea otters are present, prey densities (e.g., sea urchins) are significantly reduced, while macroalgae (e.g., kelp, seagrass) densities are high.

While this paradigm is widely-accepted amongst researchers, a few key studies have also demonstrated that the effects of sea otters may be more variable than we once thought. The paradigm does not necessarily hold true everywhere sea otters exist, or at least not to the same degree. For example, after observing benthic communities along islands with varying sea otter densities in the Aleutian archipelago, Alaska, researchers found that islands with abundant otter populations consistently supported low sea urchin densities and high, yet variable, kelp densities. In contrast, islands without otters consistently had low kelp densities and high, yet variable, urchin densities[2]. This study demonstrates that while the classic paradigm generally held true, the degree to which the ecosystem belonged to one of two dominant states (sea otters, low urchins, and high kelp or no sea otters, high urchins, and low kelp) was less obvious.

This example demonstrates the danger in applying this one-size-fits-all paradigm to sea otter effects. Hence, we want to achieve a better understanding of potential sea otter effects so that managers may anticipate how Oregon’s nearshore environments may be affected if sea otters were to be reintroduced. Yet, how can we accurately anticipate these effects given these potential variations and deviations from the paradigm? Interestingly, if we look to other fields outside ecology, we find a possible solution and tool for tackling these uncertainties: a systematic review of available literature.

Two ecosystem states as predicted by the classic paradigm (left: kelp-dominated; right: urchin-dominated). Source: SeaOtters.com.

For decades, medical researchers have been conducting systematic reviews to assess the efficacy of treatments and drugs by combining several studies to find common findings[3]. These findings can then be used to determine any potential variation between studies (i.e. instances where the results may conflict or differ from one another) and even test the influence and importance of key factors that may be driving that variation[4]. While systematic reviews are quite popular within the medical research field, they have not been applied regularly in ecology, but recognition of their application to ecological questions is growing[5]. In our case of achieving a better understanding of the drivers of ecological impacts of sea otter, a systematic literature review is an ideal tool to assess variable effects. This review will be the focus of my second thesis chapter.

In conducting my review, there will be three distinct phases: (1) review design and study collection, (2) meta-analysis, and (3) factor testing. In the first phase (review design and study collection), I will search the existing literature to collect studies that explicitly compare the availability of key ecosystem components (i.e. prey species, non-prey species, and macroalgae species) when sea otters are absent and present in the environment. By only including studies that make this comparison, I will define effects as the proportional change in each species’ or organism group’s availability (e.g. abundance, biomass, density, etc.) with and without sea otters. In determining these effects, it’s important to recognize that sea otters alter ecosystems via both direct and indirect pathways. Direct effects can be thought of as any change to prey availability via sea otter predation directly, while indirect effects can be thought of an any alteration to the broader ecosystem (i.e. non-prey species, macroalgae, habitat features) as an indirect result from sea otter predation on prey species. I will record both types of effects.

General schematic of a meta-analysis in a systematic review. A meta-analysis is the process of taking multiple datasets (i.e. Data 1, Data 2 etc.) from literature sources, calculating summary statistics or effects (i.e. Summary 1, Summary 2, etc.) for each dataset, running statistical procedures (e.g. SMA = sequential meta-analysis) to relate summary effects and investigate between study variation, and identifying important features driving variation. Source: MediCeption.

In phase two, I will use meta-analytical procedures (i.e. statistical analyses specific to systematic reviews) to calculate one standardized metric to represent sea otter effects. These effects will be calculated and averaged across all collected studies. As previously discussed, there may be key factors – such as sea otter density – that influence these effects. Therefore, in phase three (factor testing), effects will also be calculated separately for each a priori factor to test their influence on the effects. Such factors may include habitat type (i.e. hard or soft sediment), prey species (i.e. sea urchins, crabs, clams, etc.), otter density, depth, or time after otter recolonization.

In statistical terms, the goal of testing factors is to see if the variation between studies is impacted by calculating sea otter effects separately for each factor versus across all studies. In other words, if we find high variation in effects between studies, there may be important factors driving that variation. Therefore, in systematic reviews, we recalculate effects separately for each factor to try to explain that variation. If, however, after testing these factors, variation remains high, there may be other factors that we didn’t test that could be driving that remaining variation. Yet, without a priori knowledge on what those factors could be, such variation should be reported as a major source of uncertainty.

Predicting or anticipating the effects of reintroduced species is no easy feat. In instances where the ecological role of a species is well known – and there is adequate data – researchers can develop and use ecosystem models to predict with some certainty what these effects may be. Yet, in other cases where the species’ role is less studied, has less data, or is more variable, researchers must look to other tools – such as systematic reviews – to gain a better understanding of these potential effects. In this case, a systematic review on sea otter effects may prove particularly useful in helping managers understand what types of ecological effects of sea otters in Oregon are most likely, what the important factors are, and, after such review, what we still don’t know about these effects.

References:

[1] Seddon, P. J., Armstrong, D. P., and R. F. Maloney. 2007. Developing the science of reintroduction biology. Conservation Biology. 21(2): 303-312.

[2] Estes, J. A., Tinker, M. T., and J. L. Bodkin. 2009. Using ecological function to develop recovery criteria for depleted species: sea otters and kelp forests in the Aleutian Archipelago. Conservation Biology. 24(3): 852-860.

[3] Sutton, A. J., and J. P. T. Higgins. 2008. Recent developments in meta-analysis. Statistics in Medicine. 27: 625-650.

[4] Arnqvist, G., and D. Wooster. 1995. Meta-analysis: synthesizing research findings in ecology and evolution. TREE. 10(6): 236-240.

[5] Vetter, D., Rucker, G., and I. Storch. 2013. Meta-analysis: a need for well-defined usage in ecology and conservation biology. Ecosphere. 4(6): 1-13.

Plastics truly are ubiquitous in the marine environment

By Lisa Hildebrand, MSc student, OSU Department of Fisheries and Wildlife, Geospatial Ecology of Marine Megafauna Lab

As I enter my second term at OSU as a Master’s student, the ideas and structure of my thesis are slowly coming together. As of right now, my plan is to have two data chapters: The first chapter will assess the quality of zooplankton prey gray whales have access to along the Oregon coast, by looking at energetic value and microplastic content. I will contemplate about how my results potentially affect gray whale health. The second chapter will investigate fine-scale foraging and space use of gray whales in the Port Orford area to determine whether individual specialisation exists.

Fig 1. What it feels like when you start a literature review. Source: Harvard Blogs.

When I first started digging into the scientific literature to prepare for writing my thesis proposal (which is still underway but I’m getting close to the end of a first draft…), one sentence that I seemed to stumble across more often than not was “Marine plastics are ubiquitous” or “Plastics have become ubiquitous in the marine environment” or some other, very similar, iteration of that statement (e.g. Machovsky-Capuska et al. 2019; Eriksen et al. 2014; Fendall & Sewell 2009).

Many of the papers I first read were review papers on microplastics that mostly discussed general concepts like dispersal mechanisms, trophic transfer, or how microplastics become degraded. While I often think of review papers as treasure chests, since they neatly and succinctly summarise an often complicated and busy area of research into just a few pages, sometimes the fine-scale detail can go missing. Therefore, when reading these review papers, I wasn’t learning the in depth details about specific studies where microplastics had been detected in a group of individuals, population or species. So I felt the statement “Plastics are ubiquitous” was just a good (and pretty dramatic) opening line for a paper. However, once I delved into the studies on single species, I was overwhelmed by the amount of results that GoogleScholar spit out at me. If you type “microplastics marine” into the search bar, you’ll get about 7,650 results. This amount might not sound like a lot, especially if you compare it to say “gray whale”, which generates 96,600 results. Yet, the microplastic extraction method typically used was only developed in 2004 (Thompson et al. 2004). Hence, in a span of just 15 years, over 7,000 studies have detected microplastics in over 660 marine organisms (Secretariat of the Convention on Biological Diversity 2012) – a fact I find extremely troubling.

Fig 2. Graphic explaining how plastics don’t go away. Source: Biotecnika.

Microplastics are most commonly viewed as particles <5 mm in size (though there is some contention on this size classification, e.g. Claessens et al. 2013). Microplastics arise from several sources, including fragmentation of larger plastics by UV photo-degradation, wave action and physical abrasion, loss of pre-production pellets (nurdles) and polystyrene beads from shipping vessels, waste water discharge containing microbeads used in cosmetics and microfibers released during the washing of textiles and run-off from land (Nelms et al. 2018). Their small size makes these persistent particles bioavailable to ingestion by a variety of marine taxa, ranging from small prey organisms such as zooplankton, to large megafauna such as whales.

Zooplankton are at the base of marine food webs and are therefore consumed in large quantities by a large number of consumers. The propensity of zooplankton to feed in surface waters makes them highly susceptible to encountering and ingesting microplastics as this is where these synthetic particles are highly abundant (Botterell et al. 2018). Microplastics have been detected in zooplankton from the Northeast Pacific Ocean (Desforges et al. 2015), northern South China Sea (Sun et al. 2017), and Portuguese coast (Frias et al. 2014). Additionally, there is documented overlap between microplastic and zooplankton occurrence at many more locations (e.g. North Western Mediterranean Sea, Collignon et al. 2012; Baltic Sea, Gorokhova 2015; Arctic Ocean, Lusher et al. 2015a). As microplastics research is still in its relative infancy, the extent to which microplastics are ingested by zooplankton and the consequences of this behaviour are uncertain. Nevertheless, exposure to microplastics could lead to entanglement of particles within feeding appendages and/or block internal organs, which may result in reduced feeding, poor overall health, injury and death (Desforges et al. 2015). Though a lab study has found that microplastics are expelled by zooplankton after ingestion, the gut-retention times varied between species, and there is the potential risk of exposure to toxins that leech off of particles while in the body (Cole et al. 2013; the below video is from the afore-mentioned study showing how plankton eat plastics, which are illuminated in fluorescent green).

The large knowledge gap regarding the health implications indicates a strong need for more laboratory studies that investigate the long-term effects of persistent exposure to microplastics on lower trophic organisms, as well as continued short-term experiments that examine whether different zooplankton species are affected differently, since morphologies and life-histories vary widely.

Let’s take a step back and re-focus our lens onto a marine taxa that is much, much bigger in size than a zooplankton: cetaceans. Plastic debris has been documented in the stomachs of stranded individuals of several cetacean species (See Baulch & Perry 2014 for a review), however findings of microplastics in cetaceans are less common. Since cetaceans consume large amounts of prey a day, up to several tons daily for some baleen whales, the likelihood that they are ingesting microplastics through their prey is relatively high (Nelms et al. 2018). Therefore the low number of reported cases is again likely due to the relative novelty of microplastic detection methods. Despite the paucity of studies, microplastics have been found in a True’s beaked whale (Mesoplodon mirus, Lusher et al. 2015b), a humpback whale (Megaptera novaeangliae, Besseling et al. 2015) and an Indo-Pacific humpback dolphin (Sousa chinensis, Zhu et al. 2018), showing that microplastic ingestion by cetaceans does occur. Whether these individuals actively (i.e. active feeding) or passively (i.e. uptake through prey consumption) consumed the microplastics, or inhaled them at the water-air interface, is unknown. As with zooplankton, the short- and long-term impacts of ingesting microplastics by marine mammals is also unknown, though impacts on survival, feeding and uptake of toxins are all possibilities.

Fig 3. Example of a light trap sample collected off the Newport coast. Source: L. Torres.

The data collection and analysis I am doing for my thesis will hopefully fill small pockets in these large knowledge gaps. I hope to be able to quantify the extent of microplastic pollution among zooplankton species in nearshore Oregon waters. By comparing samples from several years, months and locations, I will determine whether microplastic loads vary spatially and temporally. Since their abundance and presence have been described as being patchy due to the influence of oceanographic and weather conditions (GESAMP 2016), it would seem reasonable to assume that there will be variation. But, results are a ways away as we have not even started our microplastic extraction techniques, which involves digesting samples in potassium hydroxide solution, incubating them at 50ºC for 48-72 hours, sorting through the dissolved material to identify potential plastics and sending them away for analysis. We first have to work our way through jars upon jars of unopened zooplankton light trap samplesthat need to be sorted by species. I am thankfully joined by undergraduate Robyn Norman who has already assisted this project immensely over the last two years with her zooplankton sorting prowess. So in case anyone wants to come looking for us over the next few weeks, you’ll find both Robyn and me sitting in front of a laminar flow hood in the lab of ecotoxicologist Dr. Susanne Brander, with whom we are collaborating on the microplastics portion of my thesis.

References

Baulch, S., & Perry, C., Evaluating the impacts of marine debris on cetaceans. Marine Pollution Bulletin, 2014. 80(1-2): 210-221.

Besseling, E., et al., Microplastic in a macro filter feeder: humpback whale Megaptera novaeangliae. Marine Pollution Bulletin, 2015. 95: 248-252.

Botterell, Z.L.R., et al., Bioavailability and effects of microplastics on marine zooplankton: a review. Environmental Pollution, 2018. 245: 98-110.

Claessens, M., et al., New techniques for the detection of microplastics in sediments and field collected organisms. Marine Pollution Bulletin, 2013. 70(1-2): 227-233.

Cole, M., et al., Microplastic ingestion by zooplankton. Environmental Science & Technology, 2013. 47(12): 6646-6655.

Collignon, A., et al., Neustonic microplastic and zooplankton in the North Western Mediterranean Sea. Marine Pollution Bulletin, 2012. 64(4): 861-864.

Desforges, JP.W., et al., Ingestion of microplastics by zooplankton in the Northeast Pacific Ocean. Archives of Environmental Contamination and Toxicology, 2015. 69(3): 320-330.

Eriksen, M., et al., Plastic pollution in the world’s oceans: more than 5 trillion plastic pieces weighing over 250,000 tons afloat at sea. PLoS ONE, 2014. doi.org/10.1371/journal.pone.0111913.

Fendall, L.S., & Sewell, M.A., Contributing to marine pollution by washing your face: microplastics in facial cleansers. Marine Pollution Bulletin, 2009. 58(8): 1225-1228.

Frias, J.P.G.L., et al., Evidence of microplastics in samples of zooplankton from Portuguese coastal waters. Marine Environmental Research, 2014. 95: 89-95.

GESAMP, Sources, fates and effects of microplastics in the marine environment: part 2 of a global assessment. Second United Nations Environment Assembly, 2016. http://www.gesamp.org/site/assets/files/1720/rs93e.pdf

Gorokhova, E., Screening for microplastic particles in plankton samples: how to integrate marine litter assessment into existing monitoring programs? Marine Pollution Bulletin, 2015. 99(1-2): 271-275.

Lusher, A.L., et al., Microplastics in Arctic polar waters: the first reported values of particles in surface and sub-surface samples. Scientific Reports, 2015a. 5: 14947.

Lusher, A.L., et al., Microplastic and macroplastic ingestion by a deep diving, oceanic cetacean: the True’s beaked whales Mesoplodon mirus. Environmental Pollution, 2015b. 199: 185-191.

Machovsky-Capuska, G.E., et al., A nutritional perspective on plastic ingestion in wildlife. Science of the Total Environment, 2019. 656: 789-796.

Nelms, S.E., et al., Investigating microplastic trophic transfer in marine top predators. Environmental Pollution, 2018. 238: 999-1007.

Secretariat of the Convention on Biological Diversity and the Scientific and Technical Advisory Panel – GEF (2012), Impacts of marine debris on biodiversity: current status and potential solutions. Montreal, Technical Series. 67: 1-61.

Sun, X., et al., Ingestion of microplastics by natural zooplankton groups in the northern South China Sea. Marine Pollution Bulletin, 2017. 115(1-2): 217-224.

Thompson, R.C., et al., Lost at sea: where is all the plastic? Science, 2004. 304(5672): 838.

Zhu, J., et al., Cetaceans and microplastics: First report of microplastic ingestion by a coastal delphinid, Sousa chinensis. Science of the Total Environment, 2018. 659: 649-654.

Science (or the lack thereof) in the Midst of a Government Shutdown

By Alexa Kownacki, Ph.D. Student, OSU Department of Fisheries and Wildlife, Geospatial Ecology of Marine Megafauna Lab

In what is the longest government shutdown in the history of the United States, many people are impacted. Speaking from a scientist’s point of view, I acknowledge the scientific community is one of many groups that is being majorly obstructed. Here at the GEMM Laboratory, all of us are feeling the frustrations of the federal government grinding to a halt in different ways. Although our research spans great distances—from Dawn’s work on New Zealand blue whales that utilizes environmental data managed by our federal government, to new projects that cannot get federal permit approvals to state data collection, to many of Leigh’s projects on the Oregon coast of the USA that are funded and collaborate with federal agencies—we all recognize that our science is affected by the shutdown. My research on common bottlenose dolphins is no exception; my academic funding is through the US Department of Defense, my collaborators are NOAA employees who contribute NOAA data; I use publicly-available data for additional variables that are government-maintained; and I am part of a federally-funded public university. Ironically, my previous blog post about the intersection of science and politics seems to have become even more relevant in the past few weeks.

Many graduate students like me are feeling the crunch as federal agencies close their doors and operations. Most people have seen the headlines that allude to such funding-related issues. However, it’s important to understand what the funding in question is actually doing. Whether we see it or not, the daily operations of the United States Federal government helps science progress on a multitude of levels.

Federal research in the United States is critical. Most governmental branches support research with the most well-known agencies for doing so being the National Science Foundation (NSF), the US Department of Agriculture (USDA), the National Oceanic and Atmospheric Administration (NOAA), and the National Aeronautics and Space Administration. There are 137 executive agencies in the USA (cei.org). On a finer scale, NSF alone receives approximately 40,000 scientific proposals each year (nsf.gov).

If I play a word association game and I am given the word “science”, my response would be “data”. Data—even absence data—informs science. The largest aggregate of metadata with open resources lives in the centralized website, data.gov, which is maintained by the federal government and is no longer accessible and directs you to this message:Here are a few more examples of science that has stopped in its track from lesser-known research entities operated by the federal government:

Currently, the National Weather Service (NWS) is unable to maintain or improve its advanced weather models. Therefore, in addition to those of us who include weather or climate aspects into our research, forecasters are having less and less information on which to base their weather predictions. Prior to the shutdown, scientists were changing the data format of the Global Forecast System (GFS)—the most advanced mathematical, computer-based weather modeling prediction system in the USA. Unfortunately, the GFS currently does not recognize much of the input data it is receiving. A model is only as good as its input data (as I am sure Dawn can tell you), and currently that means the GFS is very limited. Many NWS models are upgraded January-June to prepare for storm season later in the year. Therefore, there are long-term ramifications for the lack of weather research advancement in terms of global health and safety. (https://www.washingtonpost.com/weather/2019/01/07/national-weather-service-is-open-your-forecast-is-worse-because-shutdown/?noredirect=on&utm_term=.5d4c4c3c1f59)

An example of one output from the GFS model. (Source: weather.gov)

The Food and Drug Administration (FDA)—a federal agency of the Department of Health and Human Services—that is responsible for food safety, has reduced inspections. Because domestic meat and poultry are at the highest risk of contamination, their inspections continue, but by staff who are going without pay, according to the agency’s commissioner, Dr. Scott Gottlieb. Produce, dry foods, and other lower-risk consumables are being minimally-inspected, if at all. Active research projects investigating food-borne illness that receive federal funding are at a standstill. Is your stomach doing flips yet? (https://www.nytimes.com/2019/01/09/health/shutdown-fda-food-inspections.html?rref=collection%2Ftimestopic%2FFood%20and%20Drug%20Administration&action=click&contentCollection=timestopics&region=stream&module=stream_unit&version=latest&contentPlacement=2&pgtype=collection)

An FDA field inspector examines imported gingko nuts–a process that is likely not happening during the shutdown. (Source: FDA.gov)

The National Parks Service (NPS) recently made headlines with the post-shutdown acts of vandalism in the iconic Joshua Tree National Park. What you might not know is that the shutdown has also stopped a 40-year study that monitors how streams are recovering from acid rain. Scientists are barred from entering the park and conducting sampling efforts in remote streams of Shenandoah National Park, Virginia. (http://www.sciencemag.org/news/2019/01/us-government-shutdown-starts-take-bite-out-science)

A map of the sampling sites that have been monitored since the 1980s for the Shenandoah Watershed Study and Virginia Trout Stream Sensitivity Study that cannot be accessed because of the shutdown. (Source: swas.evsc.virginia.edu)

NASA’s Stratospheric Observatory for Infrared Astronomy (SOFIA), better known as the “flying telescope” has halted operations, which will require over a week to bring back online upon funding restoration. SOFIA usually soars into the stratosphere as a tool to study the solar system and collect data that ground-based telescopes cannot. (http://theconversation.com/science-gets-shut-down-right-along-with-the-federal-government-109690)

NASA’s Stratospheric Observatory for Infrared Astronomy (SOFIA) flies over the snowy Sierra Nevada mountains while the telescope gathers information. (Source: NASA/ Jim Ross).

It is important to remember that science happens outside of laboratories and field sites; it happens at meetings and conferences where collaborations with other great minds brainstorm and discover the best solutions to challenging questions. The shutdown has stopped most federal travel. The annual American Meteorological Society Meeting and American Astronomical Society meeting were two of the scientific conferences in the USA that attract federal employees and took place during the shutdown. Conferences like these are crucial opportunities with lasting impacts on science. Think of all the impressive science that could have sparked at those meetings. Instead, many sessions were cancelled, and most major agencies had zero representation (https://spacenews.com/ams-2019-overview/). Topics like lidar data applications—which are used in geospatial research, such as what the GEMM Laboratory uses in some its projects, could not be discussed. The cascade effects of the shutdown prove that science is interconnected and without advancement, everyone’s research suffers.

It should be noted, that early-career scientists are thought to be the most negatively impacted by this shutdown because of financial instability and job security—as well as casting a dark cloud on their futures in science: largely unknown if they can support themselves, their families, and their research. (https://eos.org/articles/federal-government-shutdown-stings-scientists-and-science). Graduate students, young professors, and new professionals are all in feeling the pressure. Our lives are based on our research. When the funds that cover our basic research requirements and human needs do not come through as promised, we naturally become stressed.

An adult and a juvenile common bottlenose dolphin, forage along the San Diego coastline in November 2018. (Source: Alexa Kownacki)

So, yes, funding—or the lack thereof—is hurting many of us. Federally-funded individuals are selling possessions to pay for rent, research projects are at a standstill, and people are at greater health and safety risks. But, also, science, with the hope for bettering the world and answering questions and using higher thinking, is going backwards. Every day without progress puts us two days behind. At first glance, you may not think that my research on bottlenose dolphins is imperative to you or that the implications of the shutdown on this project are important. But, consider this: my study aims to quantify contaminants in common bottlenose dolphins that either live in nearshore or offshore waters. Furthermore, I study the short-term and long-term impacts of contaminants and other health markers on dolphin hormone levels. The nearshore common bottlenose dolphin stocks inhabit the highly-populated coastlines that many of us utilize for fishing and recreation. Dolphins are mammals, that respond to stress and environmental hazards, in similar ways to humans. So, those blubber hormone levels and contamination results, might be more connected to your health and livelihood than at first glance. The fact that I cannot download data from ERDDAP, reach my collaborators, or even access my data (that starts in the early 1980s), does impact you. Nearly everyone’s research is connected to each other’s at some level, and that, in turn has lasting impacts on all people—scientists or not. As the shutdown persists, I continue to question how to work through these research hurdles. If anything, it has been a learning experience that I hope will end soon for many reasons—one being: for science.

Inter- and Transdisciplinary Sea Otter Research

By Dominique Kone, Masters Student, Marine Resource Management

As the human population continues to grow, so does our impact on marine environments. In many cases, these problems – such as microplastics, vessel noise, or depleted fisheries – are far too grand for any one person to tackle on their own and it takes a team effort to find adequate solutions. Experts within a single field (e.g. ecology, economics, genetics) have been collaborating to tackle these issues for decades, but there is an increasing interest and recognition of the importance in working with others outside one’s own discipline.

It’s not surprising that most collaborative efforts are between experts from the same field. It’s easier to converse with those with similar vocabulary, we often enjoy learning from our peers, and our thought-processes and problem-solving skills are typically very similar. However, as issues become more complex and stretch across disciplines, the need for interdisciplinary collaboration becomes more and more imperative. As a graduate student studying marine resource management, I’ve learned the great value in conducting interdisciplinary work. Yet, I still have much to learn if I want to continue to help find solutions to the many complex marine issues. Therefore, over the next year, I’ve committed to joining a interdisciplinary team of graduate students, as part of an NSF-funded fellowship program at Oregon State University (OSU), to further investigate a potential sea otter reintroduction to Oregon. Here, I provide a brief overview of the program and my team’s goals for the coming year.

The fellowship program emphasizes both interdisciplinary and transdisciplinary approaches, so before I explain the program, it’s important to first understand these terms. In short, interdisciplinarity typically relates to experts from different fields analyzing, synthesizing, and coordinating their work as a whole (Choi & Pak 2006). Another way to think about this, in more practical terms, is if two or more experts share information and learn from one another; each expert can then individually apply that information or lessons-learned to their own line of work. In contrast, transdisciplinary work is slightly more collaborative, where experts work more hand-in-hand to develop a product or solution that transcends their disciplines’ traditional boundaries. The experts essentially create a product that would not have been possible working in isolation. In practice, the product(s) that stems from inter- and transdisciplinary work – if they truly are inter- or transdisciplinary by definition – is potentially very different.

With an increasing interest in interdisciplinary work, the National Science Foundation (NSF) developed the National Research Traineeship (NRT) program to encourage select universities to develop and implement innovative and transformative models for training graduate students in STEM disciplines. After soliciting proposals, the NSF awarded OSU one of these NRT projects to support OSU’s Risk and Uncertainty Quantification in Marine Science NRT Program. OSU’s NRT program was born out of the recognition that much of the complexity of marine issues is largely due to the uncertainty of natural and human systems. Therefore, the primary purpose of this program is to train the next generation of natural resource scientists and managers to be better equipped to study and manage complex marine systems, especially under extreme uncertainty and potential risk.

This NRT program trains graduate students in three core concept areas: coupled natural human systems, big data, and risk and uncertainty analyses and communications. To learn these core concepts, students fulfil a minor that includes coursework in statistical inference, uncertainty quantification, risk analyses, earth system science, and social systems. In addition to the minor, students also conduct collaborative research in small (3-5 students) cross-disciplinary teams to address specific issues in marine resource management. Within each team, students come from different disciplines and fields, and must learn to work together to produce a transdisciplinary research product. Throughout the year, each team will develop a set of research questions to address their issue at hand, conduct research which links all their fields, and produce a transdisciplinary report summarizing the process they undertook and the end product. Most students who are accepted into the NRT program are awarded one-year fellowships, funded by the NSF.

At the start of this academic year, I was awarded one of these NRT fellowships to address the many issues and implications of a potential sea otter reintroduction to Oregon. Over the next year, I will be working with two other OSU graduate students with backgrounds in genetics and social sciences. Our task is to not only investigate the ecological implications – which I am currently doing for my own thesis – but we are to expand this investigation to also address many of the genetic, political, and social factors, as well. While each of us is capable of addressing one of these factors individually, the real test will be in finding linkages between each of our disciplines to make this project truly transdisciplinary.

Structure and vision of OSU’s NRT program. Source: Oregon State University.

Since our project started, we have worked to better understand each another’s expertise, interests, and the general need for a transdisciplinary project of this sort. After acquiring this base understanding, we spent a considerable amount of time developing research questions and potential methods for addressing our issue. Throughout this process, it’s already become apparent that each of us is starting to learn important teamwork and collaboration skills, including effective communication and explanation of complicated concepts, active listening, critical thinking, and constructive feedback. While these skills are imperative for our research over the next year, they are also life-long skills that we’ll continue to use in our careers beyond graduate school.

As I’ve stated previously, learning to be an effective collaborator is extremely important to me. Getting the opportunity to work interdisciplinarily is what attracted me to my thesis, the marine resource management program, and the NRT program. By choosing to take my graduate education down this path, I’ve been fortunate to obtain important skills in collaboration, as well as work on a project that allows me to tackle real-world issues and creatively develop scientifically-based solutions. I have high hopes for this NRT project, and I’m excited to continue to conduct meaningful and targeted research over the next year with my new team.

2018-19 OSU NRT Cohort. Source: Oregon State University.

References:

Choi, B. C., and A. W. Pak. Multidisciplinarity, interdisciplinarity and transdisciplinarity in health research, service, education and policy: 1. Definitions, objectives, and evidence of effectiveness. Clinical and Investigative Medicine. 29(6): 351-64.

Who Am I? Exploring the theory of individualisation among marine mammals

By Lisa Hildebrand, MSc student, OSU Department of Fisheries and Wildlife, Geospatial Ecology of Marine Megafauna Lab

“Just be yourself!” is a phrase that everyone has probably heard at least once in their lives. The idea of being an individual who is distinctly different from other individuals is a concept that is focal to the society we live in today. While historically it may have been frowned upon to be the “black sheep in the crowd”, nowadays that seems to be the goal.

This quest for uniqueness has resulted in different styles of fashion, speech, profession, interest in art, music, literature, automobile types – the list is endless. The American Psychological Association defines personality as the “individual differences in characteristic patterns of thinking, feeling and behaving”¹. So, all of the choices we make on a daily basis shape our behaviour, and our behaviour in turn shapes our personality.

Since personality is something that is so engrained within human society, it isn’t surprising that ecologists have explored this concept among non-humans. Decades of research have resulted in an abundance of literature detailing personality in many different taxa and species, ranging from chimpanzees to mice to ants². Naturally, the definition of personality for animals differs from that for humans since the assessment of animal thoughts and feelings is still somewhat of a locked box to us. Nevertheless, the behavioural aspect of the two definitions remains consistent whereby animal personality is broadly defined as “consistent variation in behavioural traits between individuals”³.

Although I am an early career marine mammal ecologist finding my footing in this rapidly expanding field, I have a keen interest in teasing apart possible cases of individual specialisation within marine mammal populations. So, before getting straight into the nitty gritty of individual specialisation, it is important for me to take a small step back and consider the concept of specialisation as applied to small subgroups or populations of marine mammals.

Specialisations are mostly related to foraging or feeding behaviour whereby a subgroup of individuals will develop a novel method to locate and capture prey. These behaviours have been reported for several marine mammal species, and are strongly coupled to intra and inter-specific competition with other predators for prey and habitat characteristics. Furthermore, it is posited that factors such as resource benefits (e.g. energy content of prey), prey escape rates, and handling times can be minimised if specialisation for a particular prey type or habitat occurs⁴.

In Florida Bay, Torres & Read⁵documented two distinct foraging strategies employed by two bottlenose dolphin ecotypes. One dolphin ecotype was found to forage using deep diving with erratic surfacings, whereas the second ecotype chose to forage through mud ring feeding and were mostly seen in shallow habitats. The latter ecotype is in fact so adapted to shallow depths that dolphins were typically observed foraging in waters <2 m deep. In this example, the foraging tactics of the two ecotypes are strongly driven by habitat conditions, specifically depth. The video below is aerial footage of bottlenose dolphins performing mud ring feeding.

Such group specialisations have been identified not only in several other bottlenose dolphin populations around the world^6,7, but also in other cetacean species, including killer whales (distinct differences in target prey between transients and residents⁸), Guiana dolphins (mud-plume feeding⁹), humpback dolphins (strand feeding¹⁰), and several others. Noticeable here is that these records concern Odontocete species, which is not surprising since these toothed whales are vastly different to baleen whales in that they often live in structured groups with bonds between individuals sometimes lasting for decades¹¹. Long-term relationships are conducive to developing specialised group hunting strategies as individuals will spend considerable time with one another and the success of obtaining prey depends on the cooperation and coordination of the group.

For baleen whales and other marine mammals, such as pinnipeds, where life history and social organisation is more geared toward a solitary life, examples of group specialisations are relatively rare (with the exception of the well-documented bubble-net feeding exhibited by humpback whales¹²). While group specialisation may not be as prevalent in Mysticetes, the same problems of inter and intra-specific competition persists among these more solitary species too, which would suggest that individuals should develop their own unique foraging tactics and preferences. Evidence for individualisation is hard to obtain since it requires repeated observations of the same individuals over time with good knowledge of the prey type being consumed and/or the habitat being used to forage in.

Nevertheless, examples do exist. Perhaps the most well-documented case of individualisation within a population for marine mammals is of the sea otter. Estes et al. (2003) describe 10 female sea otters in Monterey Bay that had high inter-individual variation in diet, which they investigated over a scale of 8 years¹³. Most females specialised on 1-4 types of prey, with marked differences between the diets chosen by each female, despite habitat overlap. This individualisation of diet was not attributable to variation in prey availability; hence, authors concluded that this extreme specialisation occurred to reduce intra-population competition for prey.

Ecologists have historically (and probably still to this day) disagreed on whether individualisation actually matters in the grand scheme of things. There are generally three schools of thought on the matter: (1) individual specialisation is rare and/or weakly influences population dynamics and so is not very important; (2) while individual specialisation does occur and may in fact be commonplace, it does not affect ecological processes at the large population scale; and (3) individual specialisation is widespread and can significantly impact population dynamics and/or ecosystem function.

As you might have guessed by this point, I find myself in the third school of thought. There are many arguments supporting this theory, and what I believe to be very good arguments against statements 1 and 2. While I have only provided one specific named example for individual specialisation in a marine mammal, there are several documented cases of such occurrences among other marine taxa (e.g., pinnipeds¹⁴, sharks¹⁵, fish¹⁶) and a much larger number of studies for terrestrial species⁴. Thus, the claim that it is rare or weak, seems implausible to me.

Statement 2 is a little more complicated to tackle as it involves understanding how actions on a relatively small scale affect a whole population or even an ecosystem. For instance, consider two female sea otters living in a small coastal area where one sea otter prefers to eat turban snails and the other exclusively feeds on abalone. The sudden decline in abundance of either of these prey could lead to serious health and reproductive issues for those females. Should the low prey abundance persist, then poor health and reproduction of several females in a population that specialise on that prey item can rapidly lead to genetic loss and an overall population decline. Particularly if an individual’s or species’ home range is rather restricted or small. In the case of the sea otter, which are often touted as a keystone species due to its presence preventing sea urchin barren formation that is known to wreak havoc on kelp forests, knock-on effects of such a population decline could result in poor overall ecosystem health.

It may be easy to assume that one individual dolphin, otter, seal or whale cannot possibly make a difference to a whole population or ecosystem. This assumption strikes me as a little odd since humans are always told to ‘be the change they wish to see in the world’ and that ‘every person can make a difference’. Why then should these sentiments not be applicable to non-humans? While a gray whale may not hold a sign at a protest or run for president (actions commonly considered to cause change in the human world), perhaps the choice that a gray whale makes every day to only consume one species of zooplankton, can influence other gray whales in the area, predators from other taxa, habitat structure, other prey availability, and/or cause trophic cascades.

Through my research, I aim to elucidate whether the gray whales display some level of foraging individualisation while feeding in Port Orford, Oregon. I will use data from four years to compare tracks of individual whales with zooplankton samples collected in the area to correlate each individual’s movement patterns with prey availability. I will assess the quality of prey through bomb calorimetry and microplastic analysis of the zooplankton samples to determine energetic content and pollutant levels, respectively. This prey assessment will describe the potential effects of prey specialization on whales, which is fundamental to assessing overall population health. Individualisation can strongly affect fitness of individuals, either positively or negatively depending on several factors, which will undoubtedly have an impact at the population level.

(The videos below are examples of two different tactics we see the gray whales display while foraging along the Oregon coast in the summer months. The first video shows a whale foraging among kelp with some very acrobatic moves, while the second is of a whale employing the ‘sharking’ method where the whale is feeding benthically in such shallow depths that both the pectoral fin and the fluke stick out of the water, making the whale look like a ‘shark’.)

References

American Psychological Association, Personality. Retrieved from: https://www.apa.org/topics/personality/.
Carere C., & Locurto, C., Interaction between animal personality and animal cognition. Current Zoology, 2015. 57(4): 491-498.
Gosling, S.D., From mice to men: what can we learn about personality from animal research?Psychological Bulletin, 2001. 127(1): 45-86.
Bolnick, D.I., et al., The ecology of individuals: incidence and implications of individual specialisation. The American Naturalist, 2003. 161(1): 1-28.
Torres, L.G., & Read, A. J., Where to catch a fish? The influence of foraging tactics on the ecology of bottlenose dolphins (Tursiops truncatus) in Florida Bay, Florida. Marine Mammal Science, 2009. 25(4): 797-815.
Gisburne, T.J., & Connor, R.C., Group size and feeding success in strand-feeding bottlenose dolphins (Tursiops truncatus) in Bull Creek, South Carolina. Marine Mammal Science, 2015. 31(3): 1252-1257.
Gazda, S.K., et al., A division of labour with role specialization in group-hunting bottlenose dolphins (Tursiops truncatus) off Cedar Keys, Florida.Proceedings of the Royal Society: Biological Sciences, 2005. 272(1559): 135-140.
Ford, J.K.B., et al., Dietary specialization in two sympatric populations of killer whales (Orcinus orca) in coastal British Columbia and adjacent waters. Canadian Journal of Zoology, 1998. 76(8): 1456-1471.
Rossi-Santos, M.R., & Wedekin, L.L., Evidence of bottom contact behaviour by estuarine dolphins (Sotalia guianensis) on the Eastern Coast of Brazil.Aquatic Mammals, 2006. 32(2): 140-144.
Peddemors, V.M., & Thompson, G., Beaching behaviour during shallow water feeding by humpback dolphins (Sousa plumbea). Aquatic Mammals, 1994. 20(2): 65-67.
Tyack, P., Population biology, social behavior and communication in whales and dolphins. Trends in Ecology & Evolution, 1986. 1(6): 144-150.
Wiley, D., et al., Underwater components of humpback whale bubble-net feeding behaviour.Behaviour, 2011. 148(5/6): 575-602.
Estes, J.A., et al., Individual variation in prey selection by sea otters: patterns, causes and implications. Journal of Animal Ecology, 2003. 72(1): 144-155.
Cherel, Y., et al., Stable isotopes document seasonal changes in trophic niches and winter foraging individual specialization in diving predators from the Southern Ocean. Journal of Animal Ecology, 2007. 76(4): 826-836.
Matich, P., et al., Contrasting patterns of individual specialization and trophic coupling in two marine apex predators. Journal of Animal Ecology, 2010. 80(1): 294-305.
Svanbäck, R., & Persson, L., Individual diet specialization, niche width and population dynamics: implications for trophic polymorphisms. Journal of Animal Ecology, 2004. 73(5): 973-982.

Why Feeling Stupid is Great: How stupidity fuels scientific progress and discovery

By Alexa Kownacki, Ph.D. Student, OSU Department of Fisheries and Wildlife, Geospatial Ecology of Marine Megafauna Lab

It all started with a paper. On Halloween, I sat at my desk, searching for papers that could answer my questions about bottlenose dolphin metabolism and realized I had forgotten to check my email earlier. In my inbox, there was a new message with an attachment from Dr. Leigh Torres to the GEMM Lab members, saying this was a “must-read” article. The suggested paper was Martin A. Schwartz’s 2008 essay, “The importance of stupidity in scientific research”, published in the Journal of Cell Science, highlighted universal themes across science. In a single, powerful page, Schwartz captured my feelings—and those of many scientists: the feeling of being stupid.

For the next few minutes, I stood at the printer and absorbed the article, while commenting out loud, “YES!”, “So true!”, and “This person can see into my soul”. Meanwhile, colleagues entered my office to see me, dressed in my Halloween costume—as “Amazon’s Alexa”, talking aloud to myself. Coincidently, I was feeling pretty stupid at that moment after just returning from a weekly meeting, where everyone asked me questions that I clearly did not have the answers to (all because of my costume). This paper seemed too relevant; the timing was uncanny. In the past few weeks, I have been writing my PhD research proposal —a requirement for our department— and my goodness, have I felt stupid. The proposal outlines my dissertation objectives, puts my work into context, and provides background research on common bottlenose dolphin health. There is so much to know that I don’t know!

Alexa dressed as “Amazon Alexa” on Halloween at her office in San Diego, CA.

When I read Schwartz’s 2008 paper, there were a few takeaway messages that stood out:

People take different paths. One path is not necessarily right nor wrong. Simply, different. I compared that to how I split my time between OSU and San Diego, CA. Spending half of the year away from my lab and my department is incredibly challenging; I constantly feel behind and I miss the support that physically being with other students provides. However, I recognize the opportunities I have in San Diego where I work directly with collaborators who teach and challenge me in new ways that bring new skills and perspective.
(Image source: St. Albert’s Place)
Feeling stupid is not bad. It can be a good feeling—or at least we should treat it as being a positive thing. It shows we have more to learn. It means that we have not reached our maximum potential for learning (who ever does?). While writing my proposal I realized just how little I know about ecotoxicology, chemistry, and statistics. I re-read papers that are critical to understanding my own research, like “Nontargeted biomonitoring of halogenated organic compounds in two ecotypes of bottlenose dolphins (Tursiops truncatus) from the Southern California bight” (2014) by Shaul et al. and “Bottlenose dolphins as indicators of persistent organic pollutants in the western north Atlantic ocean and northern gulf of Mexico” (2011) by Kucklick et al. These articles took me down what I thought were wormholes that ended up being important rivers of information. Because I recognized my knowledge gap, I can now articulate the purpose and methods of analysis for specific compounds that I will conduct using blubber samples of common bottlenose dolphins
Image source: memegenerator.net
Drawing upon experts—albeit intimidating—is beneficial for scientific consulting as well as for our mental health; no one person knows everything. That statement can bring us together because when people work together, everyone benefits. I am also reminded that we are our own harshest critics; sometimes our colleagues are the best champions of our own successes. It is also why historical articles are foundational. In the hunt for the newest technology and the latest and greatest in research, it is important to acknowledge the basis for discoveries. My data begins in 1981, when the first of many researchers began surveying the California coastline for common bottlenose dolphins. Geographic information systems (GIS) were different back then. The data requires conversions and investigative work. I had to learn how the data were collected and how to interpret that information. Therefore, it should be no surprise that I cite literature from the 1970s, such as “Results of attempts to tag Atlantic Bottlenose dolphins, (Tursiops truncatus)” by Irvine and Wells. Although published in 1972, the questions the authors tried to answer are very similar to what I am looking at now: how are site fidelity and home ranges impacted by natural and anthropogenic processes. While Irvine and Wells used large bolt tags to identify individuals, my project utilizes much less invasive techniques (photo-identification and blubber biopsies) to track animals, their health, and their exposures to contaminants.
(Image source: imgflip.com)
Struggling is part of the solution. Science is about discovery and without the feeling of stupidity, discovery would not be possible. Feeling stupid is the first step in the discovery process: the spark that fuels wanting to explore the unknown. Feeling stupid can lead to the feeling of accomplishment when we find answers to those very questions that made us feel stupid. Part of being a student and a scientist is identifying those weaknesses and not letting them stop me. Pausing, reflecting, course correcting, and researching are all productive in the end, but stopping is not. Coursework is the easy part of a PhD. The hard part is constantly diving deeper into the great unknown that is research. The great unknown is simultaneously alluring and frightening. Still, it must be faced head on. Schwartz describes “productive stupidity [as] being ignorant by choice.” I picture this as essentially blindly walking into the future with confidence. Although a bit of an oxymoron, it resonates the importance of perseverance and conviction in the midst of uncertainty.
(Image source: Redbubble)

Now I think back to my childhood when stupid was one of the forbidden “s-words” and I question whether society had it all wrong. Maybe we should teach children to acknowledge ignorance and pursue the unknown. Stupid is a feeling, not a character flaw. Stupidity is important in science and in life. Fascination and emotional desires to discover new things are healthy. Next time you feel stupid, try running with it, because more often than not, you will learn something.

Image may contain: 1 person, sitting, table, child and outdoor — Alexa teaching about marine mammals to students ages 2-6 and learning from educators about new ways to engage young students. San Diego, CA in 2016. (Photo source: Lori Lowder)

Oregon Sea Otter Status of Knowledge Symposium

By Dominique Kone, Masters Student in Marine Resource Management

Over the past year, the GEMM Lab has been investigating the ecological factors associated with a potential sea otter reintroduction to Oregon. A potential reintroduction is not only of great interest to our lab, but also to several other researchers, managers, tribes, and organizations in the state. With growing interest, this idea is really starting to gain momentum. However, the best path forward to making this idea a reality is somewhat unknown, and will no doubt take a lot of time and effort from multiple groups.

In an effort to catalyze this process, the Elakha Alliance – led by Bob Bailey – organized the Oregon Sea Otter Status of Knowledge Symposium earlier this month in Newport, OR. The purpose of this symposium was to share information, research, and lessons learned about sea otters in other regions. Speakers – primarily scientists, managers, and graduate students – flew in from all over the U.S. and the Canadian west coast to share their expertise and discuss various factors that must be considered before any reintroduction efforts begin. Here, I review some of the key takeaways from those discussions.

To start the meeting, Dr. Anne Salomon – an associate professor from Simon Fraser University – and Kii’iljuus Barbara Wilson – a Haida Elder – gave an overview of the role of sea otters in nearshore ecosystems and their significance to First Nations in British Columbia. Hearing these perspectives not only demonstrated the various ecological effects – both direct and indirect – of sea otters, but it also illustrated their cultural connection to indigenous people and the role tribes can play (and currently do play in British Columbia) in co-managing sea otters. In Oregon, we need to be aware of all the possible effects sea otters may have on our ecosystems and acknowledge the opportunity we have to restore these cultural connections to Oregon’s indigenous people, such as the Confederated Tribes of Siletz Indians.

Source: The Elakha Alliance and the Confederated Tribes of Siletz Indians.

The symposium also involved several talks on the recovery of sea otter populations in other regions, as well as current limitations to their population growth. Dr. Lilian Carswell and Dr. Deanna Lynch – sea otter and marine conservation coordinators with the U.S. Fish & Wildlife Service – and Dr. Jim Bodkin – a sea otter ecologist – provided these perspectives. Interestingly, not all stocks are recovering at the same rate and each population faces slightly different threats. In California, otter recovery is slowed by lack of available food and mortality due to investigative shark bites, which prevents range expansion. In other regions, such as Washington, the population appears to be growing rapidly and lack of prey and shark bite-related mortality appear to be less important. However, this population does suffer from parasitic-related mortality. The major takeaway from these recovery talks is that threats can be localized and site-specific. In considering a reintroduction to Oregon, it may be prudent to investigate if any of these threats and population growth limitations exist along our coastline as they could decrease the potential for sea otters to reestablish.

Source: The Seattle Aquarium and U.S. Fish & Wildlife Service.

Dr. Shawn Larson – a geneticist and ecologist from the Seattle Aquarium – gave a great overview of the genetic research that has been conducted for historical (pre-fur trade) Oregon sea otter populations. She explained that historical Oregon populations were genetically-similar to both southern and northern populations, but there appeared to be a “genetic gradient” where sea otters near the northern Oregon coast were more similar to northern populations – ranging to Alaska – and otters from the southern Oregon coast were more similar to southern populations – ranging to California. Given this historic genetic gradient, reintroducing a mixture of sea otters – subsets from contemporary northern and southern stocks – should be considered in a future Oregon reintroduction effort. Source-mixing could increase genetic diversity and may more-closely resemble genetic diversity levels found in the original Oregon population.

At the end of the meeting, an expert panel – including Dr. Larson, Dr. Bodkins, Dr. Lynch, and Dr. Carswell – provided their recommendations on ways to better inform this process. To keep this brief, I’ll discuss the top three recommendations I found most intriguing and important.

Gain a better understanding of sea otter social behavior. Sea otters have strong social bonds, and previous reintroductions have failed because relocated individuals returned to their capture sites to rejoin their source populations. While this site fidelity behavior is relatively understood, we know less about the driving mechanisms – such as age or sex – of those behaviors. Having a sound understanding of these behaviors and their mechanisms could help to identify those which may hinder reestablishment following a reintroduction.
When anticipating the impacts of sea otters on ecosystems, investigate the benefits too. When we think of impacts, we typically think of costs. However, there are documented benefits of sea otters, such as increasing species diversity (Estes & Duggins 1995, Lee et al. 2016). Identifying these benefits – as well as to people – would more completely demonstrate their importance.
Investigate the human social factors and culture in Oregon relative to sea otters, such as perceptions of marine predators. Having a clear understanding of people’s attitudes toward marine predators – particularly marine mammals – could help managers better anticipate and mitigate potential conflicts and foster co-existence between otters and people.

While much of the symposium was focused on learning from experts in other regions, I would be remiss if I didn’t recognize the great talks given by a few researchers in Oregon – including Sara Hamilton (OSU doctoral student), Dr. Roberta Hall (OSU emeritus professor), Hannah Wellman (University of Oregon doctoral student), and myself. Individually, we spoke about the work that has already been done and is currently being done on this issue – including understanding bull kelp ecology, studying sea otter archaeological artifacts, and a synthesis of the first Oregon translocation attempt. Collectively, our talks provided some important context for everyone else in the room and demonstrated that we are working to make this process as informed as possible for managers. Oregon has yet to determine if they will move forward with a sea otter reintroduction and what that path forward will look like. However, given this early interest – as demonstrated by the symposium – we, as researchers, have a great opportunity to help guide this process and provide informative science.

References:

Estes, J. A. and D. O. Duggins. 1995. Sea otters and kelp forests in Alaska: generality and variation in a community ecological paradigm. Ecological Monographs. 65: 75-100.

Lee, L. C., Watson, J. C., Trebilco, R., and A. K. Salomon. 2016. Indirect effects and prey behavior mediate interactions between an endangered prey and recovering predator. Ecosphere. 7(12).

The Beauty of Scientific Conferences

By Lisa Hildebrand, MSc student, OSU Department of Fisheries and Wildlife, Geospatial Ecology of Marine Megafauna Lab

Science is truly meaningful because it is shared amongst colleagues and propagated to the wider public. There are many mediums through which information dissemination can occur. A common and most rigorous form is the peer-review scientific publication of papers. The paper approval process is vigorous, can last a long time – sometimes on the scale of several years – and is therefore an excellent way of vetting science that is occurring all over the world in many different disciplines. New studies build upon the results and downfalls of others, and therefore the process of research and communication of knowledge is continuous.

However, scientific journals and the publications within them can be quite exclusive; they are often only accessible to certain members of the scientific community or of an educational institution. For a budding scientist who is not affiliated with an institution, it can be very hard to get your hands on current research. Having said that, this issue is slowly becoming inconsequential since open access and free journals, such as PeerJ, are becoming more prevalent.

How some students feel after reading scientific publications. Source: Know Your Meme.

Something that is perhaps more restrictive is the amount of topic-specific jargon used in publications. While a certain degree of jargon is to be expected, it can sometimes overwhelm a reader to the point where the main findings of the research become lost. This typically tends to be the case for those just at the beginning of their scientific journeys, however I have also known professors to comment on confusing sections of publications due to the heavy use of specific jargon.

Conferences on the other hand offer an opportunity to disseminate meaningful science in a more open and (sometimes) more laid-back setting (this may not always be true depending on the field of science and the calibre of the conference). Researchers of a particular field congregate for a few days to learn about current research efforts, ponder potential collaborations, peruse posters of new studies, and argue over which soccer team is going to win the next World Cup. That is the beauty of conferences – it is very possible to get to know each other on a personal level. These face-to-face opportunities are especially beneficial to students as this relaxed atmosphere lends itself to asking questions and engaging with scientists that are leaders in their fields.

Logo for the Marine Technology Summit. Source: MTS.

Just over a week ago, the GEMM Lab had the opportunity to do all of the above-mentioned things. PI Dr Leigh Torres and I participated in the Marine Technology Summit (MTS) in Newport, OR, a “mini-conference” at which shiny, new technologies for use in marine applications were introduced by leading, and many local, tech companies. While Leigh and I are not technologists, we are ecologists that have greatly benefitted from recent, rapid advances in technology. Both of our gray whale (Eschrichtius robustus) research projects use different technologies to unveil hitherto unknown ecological aspects of these marine mammals.

Leigh presented her research that involves flying drones over gray whales that grace the Oregon coastal waters in the spring and summer. Through these flights, many previously undocumented gray whale behaviours have been captured and quantified¹, such as headstands, nursing and jaw snapping (check out the video below). Furthermore, still images from the videos have been used to perform photogrammetry to assess health and body condition of the whales². These drone flights have added a wealth of valuable data to the life histories of individual whales that previously were assessed mainly through photo-identification and genetics. This still fairly new approach to assess health by using drones can be relatively cost-effective, which has always been one of Leigh’s key aims throughout her research so that methods are accessible to many scientists. These productive drones used by the GEMM Lab are commercially available (yup, just like the ones you see on the shelves at your local Best Buy!).

The use of cost-effective technologies is a common theme in the GEMM Lab and is also central to my research. The estimation of zooplankton density is vital to my project to determine whether gray whales in Port Orford select areas of high prey density over areas with less dense prey. However, the traditional technology used to quantify prey densities in the water column are often bulky or expensive. Instead, we developed a relatively cheap method of measuring relative zooplankton density using a GoPro camera that we reel down through the water column from a downrigger attached to our research kayak. While we are unable to exactly quantify the mass of zooplankton in the water column, we have been successful in assessing changes in relative prey density by scoring screenshots of the footage.

Screenshot of a GoPro video from this summer’s field season in Port Orford, OR revealing a thick layer of zooplankton. Source: GEMM Lab.

While our drones and GoPro technology is not without error, technology rarely is. In truth, we lost our GoPro for several days after it became stuck in a rock crevice and Leigh’s team regrettably lost a drone to the depths of the ocean this summer. This technology reality was part of the reason I presented at the MTS as I wanted to involve technologists to find solutions to some of the problems I have experienced. Needless to say, I got a lot of excellent input from many different people, for which I am very grateful. In addition to developing new opportunities to collaborate, I was very content to sit in the audience and hear about the ground-breaking new marine technologies that are in development. Below are short descriptions of two new technologies I learned about that are revolutionising the marine world.

ASV Unmanned Marine Systems develop autonomous surface vehicles that are powered by renewable energies (solar panels and wind turbines). These vessels are particularly useful for oceanographic monitoring as they are more capable than weather buoys and much more cost effective than manned weather ships or research vessels. Additionally, they can be used for a lot of different marine science applications including active acoustic fisheries monitoring, water quality monitoring, and cetacean tracking. Some models even have integrated drones that are launched and retrieved autonomously.

The Ocean Cleanup is a company that develops technologies to clean garbage out of our oceans. There is presently a large mission underway by The Ocean Cleanup to combat the Great Pacific Garbage Patch (GPGP). The GPGP is essentially a large island in the middle of the North Pacific Ocean comprised of diverse plastic particles – wrappers, polystyrene, fishing line, plastic bags, the list is endless³. A recent study estimates the amount of plastic in the GPGP to be at least 79 thousand tonnes of ocean plastic⁴. Unfortunately, the GPGP is not the only one of its kind. The Ocean Cleanup hopes to reduce this massive plastic accumulation with the development of a system made up of a 600-m long floater that sits on the ocean’s surface with a 3-m deep skirt attached below it. The skirt will collect debris while the float will prevent plastic from flowing over it, as well as keep the whole system afloat. The system arrived at the GPGP last Wednesday and the team of over 80 engineers, researchers, scientists and computational modellers have successfully installed the system. The team posts frequent updates on their Twitter and I would highly recommend you follow this possibly revolutionary technology.

While attending the MTS, it felt like there are no bounds for the types of marine technology that will be developed in the future. I am excited to see what ecologists working with technicians can develop to keep applying technology to address challenging questions and conservation issues.

References

Torres, L., et al., Drone up! Quantifying whale behaviour from a new perspective improves observational capacity.Frontiers in Marine Science, 2018. 5, DOI:10.3389/fmars.2018.00319.
Burnett, J.D., et al., Estimating morphometric attributes on baleen whales using small UAS photogrammetry: A case study with blue and gray whales, 2018.Marine Mammal Science. DOI:10.1111/mms.12527.
Kaiser, J., The dirt on the ocean garbage patches. Science, 2018. 328(5985): p. 1506.
Lebreton, L., et al., Evidence that the Great Pacific Garbage Patch is rapidly accumulating plastic. Scientific Reports, 2018. 8(4666).

Over the Ocean and Under the Bridges: STEM Cruise on the R/V Oceanus

By Alexa Kownacki, Ph.D. Student, OSU Department of Fisheries and Wildlife, Geospatial Ecology of Marine Megafauna Lab

From September 22^nd through 30^th, the GEMM Lab participated in a STEM research cruise aboard the R/V Oceanus, Oregon State University’s (OSU) largest research vessel, which served as a fully-functioning, floating, research laboratory and field station. The STEM cruise focused on integrating science, technology, engineering and mathematics (STEM) into hands-on teaching experiences alongside professionals in the marine sciences. The official science crew consisted of high school teachers and students, community college students, and Oregon State University graduate students and professors. As with a usual research cruise, there was ample set-up, data collection, data entry, experimentation, successes, and failures. And because everyone in the science party actively participated in the research process, everyone also experienced these successes, failures, and moments of inspiration.

The science party enjoying the sunset from the aft deck with the Astoria-Megler bridge in the background. (Image source: Alexa Kownacki)

Dr. Leigh Torres, Dr. Rachael Orben, and I were all primarily stationed on flybridge—one deck above the bridge—fully exposed to the elements, at the highest possible location on the ship for best viewing. We scanned the seas in hopes of spotting a blow, a splash, or any sign of a marine mammal or seabird. Beside us, students and teachers donned binoculars and positioned themselves around the mast, with Leigh and I taking a 90-degree swath from the mast—either to starboard or to port. For those who had not been part of marine mammal observations previously, it was a crash course into the peaks and troughs—of both the waves and of the sightings. We emphasized the importance of absence data: knowledge of what is not “there” is equally as important as what is. Fortunately, Leigh chose a course that proved to have surprisingly excellent environmental conditions and amazing sightings. Therefore, we collected a large amount of presence data: data collected when marine mammals or seabirds are present.

High school student, Chris Quashnick Holloway, records a seabird sighting for observer, Dr. Rachael Orben. (Image source: Alexa Kownacki).

When someone sighted a whale that surfaced regularly, we assessed the conditions: the sea state, the animal’s behavior, the wind conditions, etc. If we deemed them as “good to fly”, our licensed drone pilot and Orange Coast Community College student, Jason, prepared his Phantom 4 drone. While he and Leigh set up drone operations, I and the other science team members maintained a visual on the whale and stayed in constant communication with the bridge via radio. When the drone was ready, and the bridge gave the “all clear”, Jason launched his drone from the aft deck. Then, someone tossed an unassuming, meter-long, wood plank overboard—keeping it attached to the ship with a line. This wood board serves as a calibration tool; the drone flies over it at varying heights as determined by its built-in altimeter. Later, we analyze how many pixels one meter occupied at different heights and can thereby determine the body length of the whale from still images by converting pixel length to a metric unit.

High school student, Alishia Keller, uses binoculars to observe a whale, while PhD student, Alexa Kownacki, radios updates on the whale’s location to the bridge and the aft deck. (Image source: Tracy Crews)

Finally, when the drone is calibrated, I radio the most recent location of our animal. For example, “Blow at 9 o’clock, 250 meters away”. Then, the bridge and I constantly adjust the ship’s speed and location. If the whale “flukes” (dives and exposes the ventral side of its tail), and later resurfaced 500 meters away at our 10 o’clock, I might radio to the bridge to, “turn 60 degrees to port and increase speed to 5 knots”. (See the Hidden Math Lesson below). Jason then positions the drone over the whale, adjusting the camera angle as necessary, and recording high-quality video footage for later analysis. The aerial viewpoint provides major advantages. Whales usually expose about 10 percent of their body above the water’s surface. However, with an aerial vantage point, we can see more of the whale and its surroundings. From here, we can observe behaviors that are otherwise obscured (Torres et al. 2018), and record footage that to help quantify body condition (i.e. lengths and girths). Prior to the batteries running low, Jason returns the drone back to the aft deck, the vessel comes to an idle, and Leigh catches the drone. Throughout these operations, those of us on the flybridge photograph flukes for identification and document any behaviors we observe. Later, we match the whale we sighted to the whale that the drone flew over, and then to prior sightings of this same individual—adding information like body condition or the presence of a calf. I like to think of it as whale detective work. Moreover, it is a team effort; everyone has a critical role in the mission. When it’s all said and done, this noninvasive approach provides life history context to the health and behaviors of the animal.

Drone pilot, Jason Miranda, flying his drone using his handheld ground station on the aft deck. (Photo source: Tracy Crews)

Hidden Math Lesson: The location of 10 o’clock and 60 degrees to port refer to the exact same direction. The bow of the ship is our 12 o’clock with the stern at our 6 o’clock; you always orient yourself in this manner when giving directions. The same goes for a compass measurement in degrees when relating the direction to the boat: the bow is 360/0. An angle measure between two consecutive numbers on a clock is: 360 degrees divided by 12-“hour” markers = 30 degrees. Therefore, 10 o’clock was 0 degrees – (2 “hours”)= 0 degrees- (2*30 degrees)= -60 degrees. A negative degree less than 180 refers to the port side (left).

Our trip was chalked full of science and graced with cooperative weather conditions. There were more highlights than I could list in a single sitting. We towed zooplankton nets under the night sky while eating ice cream bars; we sang together at sunset and watched the atmospheric phenomena: the green flash; we witnessed a humpback lunge-feeding beside the ship’s bow; and we saw a sperm whale traveling across calm seas.

Sperm whale surfacing before a long dive.

On this cruise, our lab focused on the marine mammal observations—which proved excellent during the cruise. In only four days of surveying, we had 43 marine mammal sightings containing 362 individuals representing 9 species (See figure 1). As you can see from figure 2, we traveled over shallow, coastal and deep waters, in both Washington and Oregon before inland to Portland, OR. Because we ventured to areas with different bathymetric and oceanographic conditions, we increased our likelihood of seeing a higher diversity of species than we would if we stayed in a single depth or area.

Humpback whale lunge feeding off the bow.

	Number of sightings	Total number of individuals
Humpback whale	22	40
Pacific white-sided dolphin	3	249
Northern right whale dolphin	1	9
Killer whale	1	3
Dall’s porpoise	5	49
Sperm whale	1	1
Gray whale	1	1
Harbor seal	1	1
California sea lion	8	9
Total	43	362

Figure 1. Summary table of all species sightings during cruise while the science team observed from the flybridge.

Pacific white-sided dolphins swimming towards the vessel.

Figure 2. Map with inset displaying study area and sightings observed by species during the cruise, made in ArcMap. (Image source: Alexa Kownacki).

Even after two days of STEM outreach events in Portland, we were excited to incorporate more science. For the transit from Portland, OR to Newport, OR, the entire science team consisted two people: me and Jason. But even with poor weather conditions, we still used science to answer questions and help us along our journey—only with different goals than on our main leg. With the help of the marine technician, we set up a camera on the bow of the ship, facing aft to watch the vessel maneuver through the famous Portland bridges.

Video 1. Time-lapse footage of the R/V Oceanus maneuvering the Portland Bridges from a GoPro. Compiled by Alexa Kownacki, assisted by Jason Miranda and Kristin Beem.

Prior to the crossing the Columbia River bar and re-entering the Pacific Ocean, the R/V Oceanus maneuvered up the picturesque Columbia River. We used our geospatial skills to locate our fellow science team member and high school student, Chris, who was located on land. We tracked each other using GPS technology in our cell phones, until the ship got close enough to use natural landmarks as reference points, and finally we could use our binoculars to see Chris shining a light from shore. As the ship powered forward and passed under the famous Astoria-Megler bridge that connects Oregon to Washington, Chris drove over it; he directed us “100 degrees to port”. And, thanks to clear directions, bright visual aids, and spatiotemporal analysis, we managed to find our team member waving from shore. This is only one of many examples that show how in a few days at sea, students utilized new skills, such as marine mammal observational techniques, and honed them for additional applications.

On the bow, Alexa and Jason use binoculars to find Chris–over 4 miles–on the Washington side of the Columbia River. (Image source: Kristin Beem)

Great science is the result of teamwork, passion, and ingenuity. Working alongside students, teachers, and other, more-experienced scientists, provided everyone with opportunities to learn from each other. We created great science because we asked questions, we passed on our knowledge to the next person, and we did so with enthusiasm.

High school students, Jason and Chris, alongside Dr. Leigh Torres, all try to get a glimpse at the zooplankton under Dr. Kim Bernard’s microscope. (Image source: Tracy Crews).

Check out other blog posts written by the science team about the trip here.

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