Looking Back: Three Years After Grad School

By Courtney Hann (NOAA Fisheries, West Coast Sustainable Fisheries Division)

Thinking back, as Leigh’s first M.Sc. student for the GEMM Lab, I wonder what poignant insight could have prepared me for my future endeavors. And having faced years of perseverance and dedication in the face of professional unknowns, perhaps the answer is none at all; fore maybe it was the many unknown challenges met that led me to where I am today.

I graduated in December of 2015, with my Masters in Marine Resource Management, and stamped completion of my research with the GEMM Lab. While my research focused on marine mammals, my broader love for the Earth’s oceans and lands guided my determination to help keep our planet’s precious ecosystem resources wild and free. So when I landed a position in terrestrial ecology after graduating, I chose to embrace the challenging decision of jumping away from theoretical research and moving back towards applied research. Consequently, I fell in love with botany, moth identification, birding, and explored the unknowns of a whole new world of conservation biology in Scotland with the Royal Society for the Protection of Birds. Not only was this work incredibly fun, interesting, and spontaneous, it offered me an opportunity to take my knowledge of developing research projects and apply it to nature reserve management. Every survey I completed and dataset I analyzed provided information required to determine the next land management steps for maximizing the conservation of rare and diverse species. From the GEMM Lab, I brought skills on: how to work through what, at times, seemed like an impassible barrier, complete tasks efficiently under a tight deadline, juggle multiple activities and obligations, and still make time to ponder the importance of seeing the bigger picture, while having fun learning new things.

Above: Botanizing and birding in Scotland with the best botanist I have ever known and my boss, Jeff Waddell, with the Royal Society for the Protection of Birds.

For me, the long game of seeing the bigger picture has always been key. And at the end of the day, I remained steadfast in answering the questioned I posed myself: Why do all of this work if not to make a truly positive impact? With that in mind, and with an expiring visa, I moved back to the West Coast of the U.S. and landed a contracting position with NOAA Fisheries. Where I met my second female mentor, Heidi Taylor, who inspired me beyond words and introduced me to the amazing world of fisheries management. All the while, I kept working my second part-time job with the West Coast Regional Planning Body (now called the West Coast Ocean Alliance, WCOA). Working two jobs allowed me to not only accelerate my learning capacity through more opportunities, but also allowed me to extend the reach of growing a positive impact.  For example, I learned about coordinating region-wide ocean management, facilitation of diverse groups, and working with tribes, states, and federal agencies while working for the WCOA. While there were moments that I struggled with overworking and fatigue, my training in graduate school to persevere really kicked in. Driven by the desire to attain a permanent position that complimented my talents and determination to provide sustained help for our Earth’s ecosystems, I worked for what sometimes felt endlessly to reach my goal. Getting there was tough, but well worth it!

One of the most challenging aspects for me was finishing my last publication for the GEMM Lab. I was no longer motivated by the research, since my career path had taken a different turn, and I was already burnt out form working overtime every week. Therefore, if it was not for Leigh’s encouraging words, the promise I made to her to complete the publication, and my other co-author’s invitation to submit a paper for a particular journal, then I likely would have thrown in the towel. I had to re-do the analysis several times, had the paper rejected once, and then ended up re-writing and re-structuring the entire paper for the final publication. In total, it took me two and half years and 100s of hours to complete this paper after graduating. Of course, there was no funding, so I felt a bit like an ongoing graduate student until the paper was finally accepted and the work complete. But the final acceptance of the paper was so sweet, and after years of uncertain challenges, a heavy weight had finally been lifted. So perhaps, if there is one piece of advice I would say to young graduate students, it is to get your work published before you graduate! I had one paper and one book chapter published before I graduated, and that made my life much easier. While I am proud for finishing the final third publication, I would have much preferred to have just taken one extra semester and finished that publication while in school. But regardless, it was completed. And in a catharsis moment, maybe the challenge of completing it taught me the determination I needed to persevere through difficult situations.

Above: Elephant seal expressing my joy of finishing that last publication! Wooohoooooo!

With that publication out of the way, I was able to focus more time on my career. While I no longer use R on a daily basis and do not miss the hours of searching for that one pesky bug, I do analyze, critique, and use scientific literature everyday. Moreover, the critical thinking, creative, and collaborative skills I honed in the GEMM Lab, have been and will be useful for the rest of my life. Those hours of working through complicated statistical analyses and results in Leigh’s office pay off everyday. Reading outside of work, volunteering and working second jobs, all of this I learned from graduate school. Carrying this motivation, hard work, determination, and perseverance on past graduate school was undeniably what led me to where I am today. I have landed my dream job, working for NOAA Fisheries Sustainable Fisheries Division on salmon management and policy, in my dream location, the Pacific Northwest.  My work now ties directly into ongoing management and policy that shapes our oceans, conservation efforts, and fisheries management. I am grateful for all the people who have supported me along the way, with this blog post focusing on the GEMM Lab and Leigh Torres as my advisor. I hope to be a mentor and guide for others along their path, as so many have helped me along mine. Good luck to any grad student reading this now! But more than luck, carry passion and determination forward because that is what will propel you onward on your own path. Thank you GEMM Lab, it is now time for me to enjoy my new job.

Above: Enjoying in my new home in the Pacific Northwest.




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.

Big Data: Big possibilities with bigger challenges

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

Did you know that Excel has a maximum number of rows? I do. During Winter Term for my GIS project, I was using Excel to merge oceanographic data, from a publicly-available data source website, and Excel continuously quit. Naturally, I assumed I had caused some sort of computer error. [As an aside, I’ve concluded that most problems related to technology are human error-based.] Therefore, I tried reformatting the data, restarting my computer, the program, etc. Nothing. Then, thanks to the magic of Google, I discovered that Excel allows no more than 1,048,576 rows by 16,384 columns. ONLY 1.05 million rows?! The oceanography data was more than 3 million rows—and that’s with me eliminating data points. This is what happens when we’re dealing with big data.

According to Merriam-Webster dictionary, big data is an accumulation of data that is too large and complex for processing by traditional database management tools (www.merriam-webster.com). However, there are journal articles, like this one from Forbes, that discuss the ongoing debate of how to define “big data”. According to the article, there are 12 major definitions; so, I’ll let you decide what you qualify as “big data”. Either way, I think that when Excel reaches its maximum row capacity, I’m working with big data.

Collecting oceanography data aboard the R/V Shimada. Photo source: Alexa K.

Here’s the thing: the oceanography data that I referred to was just a snippet of my data. Technically, it’s not even MY data; it’s data I accessed from NOAA’s ERDDAP website that had been consistently observed for the time frame of my dolphin data points. You may recall my blog about maps and geospatial analysis that highlights some of the reasons these variables, such as temperature and salinity, are important. However, what I didn’t previously mention was that I spent weeks working on editing this NOAA data. My project on common bottlenose dolphins overlays environmental variables to better understand dolphin population health off of California. These variables should have similar spatiotemporal attributes as the dolphin data I’m working with, which has a time series beginning in the 1980s. Without taking out a calculator, I still know that equates to a lot of data. Great data: data that will let me answer interesting, pertinent questions. But, big data nonetheless.

This is a screenshot of what the oceanography data looked like when I downloaded it to Excel. This format repeats for nearly 3 million rows.

Excel Screen Shot. Image source: Alexa K.

I showed this Excel spreadsheet to my GIS professor, and his response was something akin to “holy smokes”, with a few more expletives and a look of horror. It was not the sheer number of rows that shocked him; it was the data format. Nowadays, nearly everyone works with big data. It’s par for the course. However, the way data are formatted is the major split between what I’ll call “easy” data and “hard” data. The oceanography data could have been “easy” data. It could have had many variables listed in columns. Instead, this data  alternated between rows with variable headings and columns with variable headings, for millions of cells. And, as described earlier, this is only one example of big data and its challenges.

Data does not always come in a form with text and numbers; sometimes it appears as media such as photographs, videos, and audio files. Big data just got a whole lot bigger. While working as a scientist at NOAA’s Southwest Fisheries Science Center, one project brought in over 80 terabytes of raw data per year. The project centered on the eastern north pacific gray whale population, and, more specifically, its migration. Scientists have observed the gray whale migration annually since 1994 from Piedras Blancas Light Station for the Northbound migration, and 2 out of every 5 years from Granite Canyon Field Station (GCFS) for the Southbound migration. One of my roles was to ground-truth software that would help transition from humans as observers to computer as observers. One avenue we assessed was to compare how well a computer “counted” whales compared to people. For this question, three infrared cameras at the GCFS recorded during the same time span that human observers were counting the migratory whales. Next, scientists, such as myself, would transfer those video files, upwards of 80 TB, from the hard drives to Synology boxes and to a different facility–miles away. Synology boxes store arrays of hard drives and that can be accessed remotely. To review, three locations with 80 TB of the same raw data. Once the data is saved in triplet, then I could run a computer program, to detect whale. In summary, three months of recorded infrared video files requires upwards of 240 TB before processing. This is big data.

Scientists on an observation shift at Granite Canyon Field Station in Northern California. Photo source: Alexa K.
Alexa and another NOAA scientist watching for gray whales at Piedras Blancas Light Station. Photo source: Alexa K.

In the GEMM Laboratory, we have so many sources of data that I did not bother trying to count. I’m entering my second year of the Ph.D. program and I already have a hard drive of data that I’ve backed up three different locations. It’s no longer a matter of “if” you work with big data, it’s “how”. How will you format the data? How will you store the data? How will you maintain back-ups of the data? How will you share this data with collaborators/funders/the public?

The wonderful aspect to big data is in the name: big and data. The scientific community can answer more, in-depth, challenging questions because of access to data and more of it. Data is often the limiting factor in what researchers can do because increased sample size allows more questions to be asked and greater confidence in results. That, and funding of course. It’s the reason why when you see GEMM Lab members in the field, we’re not only using drones to capture aerial images of whales, we’re taking fecal, biopsy, and phytoplankton samples. We’re recording the location, temperature, water conditions, wind conditions, cloud cover, date/time, water depth, and so much more. Because all of this data will help us and help other scientists answer critical questions. Thus, to my fellow scientists, I feel your pain and I applaud you, because I too know that the challenges that come with big data are worth it. And, to the non-scientists out there, hopefully this gives you some insight as to why we scientists ask for external hard drives as gifts.

Leila launching the drone to collect aerial images of gray whales to measure body condition. Photo source: Alexa K.
Using the theodolite to collect tracking data on the Pacific Coast Feeding Group in Port Orford, OR. Photo source: Alexa K.




“This is what I would do if I weren’t afraid” – New Zealand blue whale field season 2016

By Dr. Leigh Torres, Assistant Professor, Oregon State University, Geospatial Ecology of Marine Megafauna Lab

Two years ago I documented a blue whale foraging ground in an area of New Zealand called the South Taranaki Bight (STB) – the country’s most industrially active marine area with intense oil and gas exploration and extraction since the 1970’s, elevated vessel traffic, and potential seabed mining (Figure 1). Over just five days of survey effort we observed 50 blue whales and documented foraging behavior. But we still know next to nothing about where and when blue whales are in the STB, how many whales use this area, how important this area is as a feeding area, or to what population the whales belong. Without answers to these questions effective management of human activities in the region to protect the whales and their habitat is unfeasible.

I am now heading back to New Zealand to collect the data needed to answer these questions that will enable successful management. That’s my goal.

Figure 1. Illustration of a space-use conflict between industry activity and blue whales in the South Taranaki Bight, which lies between the north and south islands of New Zealand. Blue whale sightings and strandings recorded between 1970 and 2012.
Figure 1. Illustration of a space-use conflict between industry activity and blue whales in the South Taranaki Bight, which lies between the north and south islands of New Zealand. Blue whale sightings and strandings recorded between 1970 and 2012.

Such research costs money. In collaboration with the Bioacoustic Research Program at Cornell University (birds.cornell.edu/brp), we are deploying five hydrophones to listen for blue whales across the region for 2 years. We will conduct vessel surveys for 1 month in each year to find whales and collect data on their habitat, behavior, and individual occurrence patterns. As far as field research projects go, this work is not very expensive, but we still need to pay for vessel time, equipment, and personnel time to collect and analyze the data. This is an ugly truth of scientific research – it costs money and there is not a lot out there.

For two years I’ve had my fund raising hat on (Not my favorite hat. I much prefer my research hat). I believe that industry groups active in the STB should take an active role in supporting the necessary research. They exploit the natural resources in the region and should therefore take responsibility for ensuring the ecosystem’s sustainability and health. Right? They did not agree.

I emphasized to these groups that by supporting the project they would demonstrate their environmental responsibility and ultimately be engaged in discussions of management options based on project findings. Despite hundreds of emails, phone calls and discussions, all the oil and gas companies, the seabed mining group, and the maritime traffic organization declined to fund the project, claiming lack of funds or lack of relevance to their interests. Meanwhile, other groups who prioritize conservation management are supporting the project. I am grateful to The Aotearoa Foundation, The National Geographic Society Waitt Foundation, The New Zealand Department of Conservation, Greenpeace New Zealand, OceanCare, Kiwis Against Seabed Mining, and an anonymous donor.

Lately I have been reading Sheryl Sandberg’s poignant book, Lean In, which I feel is a call to women to take responsibility for our equality and leadership. Those familiar with this book will recognize the opening of my blog title from her valid push for women to take more risks and push ourselves beyond our comfort zones. In many ways I feel I am doing this now. It would be much easier for me to withdraw from this project, say I tried, and let things carry on until someone else takes the challenge. Funding is short, last minute contract issues abound, equipment logistics are running late, I fear political pushback, and I have a sore throat. But it’s time for this project to happen. It’s time to recognize biodiversity’s innate right to healthy habitat. It’s time for industry groups to acknowledge their potential impacts on blue whales through elevated ocean noise, vessel strikes, and habitat degradation and displacement. It’s time for management to have the tools to act.

Figure 2. A blue whale surfaces in front of an oil rig in the South Taranaki Bight, New Zealand. Photo by Deanna Elvines.
Figure 2. A blue whale surfaces in front of an oil rig in the South Taranaki Bight, New Zealand. Photo by Deanna Elvines.

I remain hopeful that industry groups will engage in this research effort. Through diplomacy, transparency and robust science I want to bring together industry, NGOs, and management groups to develop effective conservation strategies to protect blue whales and their habitat in the STB. Collaboratively we can balance industry activity and biodiversity protection.

Since reading Lean In, I’ve been wondering if the conservation movement suffers because of women’s reluctance to challenge, take risks, and ‘sit at the table’ as Sandberg says. The conservation field is heavily dominated by women. For progress to happen we must be willing to force issues, be perceived as aggressive, and not be nice all the time. Just like men are expected to be.

Over the next four weeks colleagues and I will conduct research in the STB on blue whales. Stay tuned to this blog for updates.