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.

Feed from the scientific network: the digital library of a millennial student

Solène Derville, Entropie Lab, Institute of Research for Development, Nouméa, New Caledonia (Ph.D. student under the co-supervision of Dr. Leigh Torres)

If you are a follower of our blog, you may have noticed that bioinformatics and statistics hold a very important role in the everyday life of the GEMM Lab. As good-old field observations remain essential to the study of animal behaviour and ecosystems, the ecology field has greatly benefited from advances in information technologies. In fact, data analysis is now a discipline in itself, as innovative solutions must continuously be developed to cope with the challenges of ever increasing dataset size and complexity.

communications-jpg-800x600_q96Artist’s impression of a complex network. ©iStock.com/Vertigo3d

So how does a poor biology student find her/his way in this digital and mathematical world? Most ecology departments will provide classes to learn the basics of statistical modelling and data analysis, but there is only so much you can learn through formal education. In practice, we ultimately always run into a problem, an exception that we have never heard of, and we have to figure it out on our own. As my initial training was in fundamental biology, self-teaching of other disciplines (statistics and bioinformatics) has taken a lot of my time as a Master’s student and now as a PhD student. This has made me feel lonely and a bit lost at times when I run into challenges that always seemed too big for me. But in the end, there is nothing more rewarding then solving problems by yourself after long hours of mind-scrambling.

Oh, sorry, did I say by myself? Nothing could be more wrong and more true at the same time! Because the place where I find all the answers to my questions, is in fact born from the contribution of thousands of scientists, which, despite not actually knowing each other, all work together to develop innovative solutions to modern world scientific challenges. The internet scientific network has been my best colleague over these past years and here I would like to share my enthusiasm for some of its best features that have helped me in my research.

If you look at my Firefox toolbar you will find two types of websites: let’s call them the “practical” and the “reflectional”.

The practical websites:

These are the websites I consult if I have a specific and practical question. Many forums exist where people exchange their experiences solving a great variety of problems. But sometimes conversations get lost in never-ending exchanges of opinions, some of which are not always scientifically well-founded. On the contrary, the StackExchange platform launched in 2009 has a strict policy on how questions should be asked (as precise and focused as possible) and should be answered (in an objective, opinion-free way). This makes it a very powerful tool to find quick and practical solutions to your everyday problems. This platform includes 136 different websites, each dedicated to a different topic. In my field, I mostly use: CrossValidated for statistical issues (e.g., Why does including latitude and longitude in a GAM account for spatial autocorrelation?) and StackOverflow for programming (e.g., plotting pie graphs on map in ggplot).

The latter will usually provide you with codes in the programming language of your choice (R, python, java, sql, etc.). Interestingly, even with more queries regarding Python to StackOverflow in 2015, R was the fastest-growing language between 2013 and 2015 on this same platform. If you haven’t decided on the language you want to “speak” yet, check out this fun infographic. But always remember that these tools keep evolving

4a9d355949d9cb77f8128dd517395405Academia can also be useful for questions regarding publications. For instance: How to reference multiple authors of a chapter from a book [APA]? Why might a journal editor reject a submission, but suggest submission to a sister journal? Or, how to best kill a manuscript as a peer reviewer?

And finally, if you’ve always wondered, “Why don’t we remove door handles and let doors open both ways (inwards, outwards)?, you’ll be pleased to know that other out-of-the-box-thinking people are sharing their opinion on the web…

Coming back to serious matters, it is important to recognize that you need the right key-word to access this gold-mine of website knowledge and sharing. The accuracy of your search answer will only be proportional to the quality of your question. In R for instance, if you keep googling “table” instead of “dataframe”, “list” instead of “vector”, or “size” instead of “dimensions”, you will likely get quickly drowned in the google-limbo. One way to be more efficient at your search strategy is to make sure you know your basics. Most of the programming languages used in ecology (e.g., R, Python, Matlab) share a similar vocabulary and structure, but before you start to run all sorts of crazy statistical analysis it is important to know what types of objects you are working with and how you want to format them. In R, I have found Hadley Wickham’s book, Advanced R, particularly useful to understand what happens back-stage.

Another good reference in the spatial ecology field is ZevRoss “Technical Tidbits From Spatial Analysis & Data Science. This website is a particularly up-to-date blog for data processing and visualization in R.

More generally, I regularly check R-bloggers or simply the Comprehensive R Archive Network. A note on the latter: I know it doesn’t look pretty and the reference manuals for R packages are rather intimidating but it is still the number one reference to check when encountering a problem with a given function. Some authors make a special effort to write more user-friendly tutorials to their packages. Check for those by looking at the CRAN page of a given package, in the “downloads” section, “vignettes” subsection (e.g., for the adehabitatLT package vignette).

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 The reflectional websites:

The web is also an amazing media to reflect on our scientific practices, learn about current ecological theories, and acquire general knowledge across disciplines. In the scientific network, many blogs and forums exist where scientists can converse and debate ideas without the pressure of publication requirements. As a student trying to find my way in the great world of statistical modelling, I find these discussions and blogposts most useful to put my methodological choices in perspective and progressively build myself an opinion (still rather vague I’ll admit). Some of my most recent findings are: Dynamic Ecology Multa novit vulpes and From the bottom of the heap, the musings of a geographer. I am sure each of you has your own “rock star of the web”, so please share your favorite sites with us in the comments below.

Science not longer needs to wait for publication to be shared between peers and with the general public. The web offers us a new space to communicate, not only on that small part of our work that led to positive results, but also our negative results, frustrations and failures, which can at times be as informative and useful to the scientific community than our successes. So, wherever you stand, tell us about your ideas, and tell us about the challenges you have encountered, where you failed and where you succeeded. Because, this is what ecology is all about. Sharing knowledge across borders and cultures to understand the planet we live on and together take better care of it.