Research in the time of COVID

Research in the time of COVID

 

A Semi-Personal Reflection of Life in the Lab during COVID

It has been one year since the first deaths in the United States from the coronavirus disease 2019, also known as COVID. The full effect of the outbreak didn’t hit our department until one month later, in March of 2020. For many us of researchers, the changes were sudden but uncertain. As a first year PhD student I had just started learning my way around the lab. It felt like a large step back to find myself stuck at home in a studio apartment (only slightly larger than the lab) with just my dog and my laptop. Fortunately, my advisor was empathetic and helped me prioritize my mental health in those first few weeks, so we could later successfully develop a new timeline for my dissertation.

Those first few weeks in quarantine were like stabilizing a rocking boat. My pre-COVID days used to include rushing to feed and walk my dog before morning meetings, rushing to classes, recitations, office hours, and various extracurricular meetings and campus events and talks. I would meet my coworkers for coffee in the conference room or offices semi-casually and pick up bits of advice here and a bit of reassurance there. Then I would rush home to walk my dog before heading out to grab drinks at networking events or watch a Philadelphia game at one of the many stadiums. My days were unremarkable in the sense that everyone was just as busy as I was.

I remember the first time that I stood in a library classroom preparing to teach my first recitation in January of 2020. I had fallen in love with teaching while directing a garden club in Senegal, but I wasn’t as confident teaching in English as I had been in Pular. I didn’t have the language-barrier excuse to fall back on since English is my native language. But teaching was everything I remembered it to be: fun, engaging, challenging, and exhausting. I was shaking and sweating after the first day, but just as much from excitement as from nerves. I vaguely remember telling students to stay safe over spring break, and I looked forward to seeing them in a few weeks. Unfortunately, I wasn’t able to meet with them again. Everything moved online to asynchronous recordings after the university sent everyone, including me, home.

My first post-COVID days were unremarkable in the sense that everyone was just as unproductive as I was. In between teaching my dog new tricks and organizing my Tupperware cabinet, I read some papers and responded to some emails. My coworkers and I drank wine and put on face masks over zoom. We met (virtually) every week for coffee, which helped immensely even if we just stared at each other and made awkward small talk.

Eventually, cleaning my apartment and doing yoga multiple times a day to distract myself from the unfolding economic collapse stopped working, so I jumped on the opportunity to sign up for re-entry into lab spaces in June. This brought up a wave of grief that many of us have had to process simultaneously. I am fortunate to have only lost three months of lab time, and not my source of income or health insurance, but the impact of the lost time is undeniable. My summer plans included traveling to a soil institute for a two-week professional development program and mentoring a female undergraduate in our lab. It is tempting to reflect upon those changed plans with anemoia or bitterness, but the more peaceful perspective is to imagine each life that was saved when these plans changed. Airline attendants, hotel sanitation staff, elder soil scientists, the list is infinite. A shift in my dissertation timeline is a small price to pay for the lives of fellow Americans.

This perspective shift closed the book on the first chapter of lab work during COVID and brought in a second chapter. With the guidance of my advisor (and his tireless dedication to realist-optimism), I began re-imagining the path I would take for my doctorate. I began developing a professional skill most people find through personal crisis – significantly adjusting your methods to achieve your goals. I could see how easy it would be to fall into a “professional depression”, especially as I was navigating a personal depression. Often, projects at the doctoral level are the culmination of years of a science community clarifying a vision and a researcher building their career to explore that vision. Throwing a huge, global pandemic sized wrench into that process could be debilitating if not destructive.

But one of the things COVID has taught us is that our professional trajectory can be just as vulnerable as our personal journey. I spent the entire summer running a time-intensive procedure. Every week, alone in the big lab, I bleached around 16 soil samples, eventually building a set of around 300 bleached soil samples. When the fall semester began, I was able to focus on less time-intensive procedures such as surface area analyses of the bleached samples and carbon/nitrogen analyses while I navigating the new structure of zoom classes. I became grateful for the time I spent solely reading and organizing papers in March and April as my qualifying exam approached.

Now, in the early spring semester of 2021, there is a new world. I get excited to log into my zoom recitation so I can try out new ways to engage with students and get them to connect with the material. My excitement and motivations for teaching are the same, but my methods are different. Next week, a new female undergraduate will be joining our research team and I feel confident we can collaborate under COVID-safe protocols. My dissertation proposal may be a bit more preliminary data and literature review heavy instead of grand paragraphs about what methods I learned and potential collaborators I met at Colorado, Rutgers, or Berkley, but my hypotheses and research questions will still be scientifically valid and meaningful (inshallah). Every dissertation journey in the Plante lab may be different but the flexibility, innovation, and support in the lab allows each one to be successful.

PhD fellowship opportunities available

The Terrestrial Biogeochemistry Laboratory in the Department of Earth and Environmental Science of the University of Pennsylvania invites applicants for competitive Ph.D. fellowships in one of two research areas: Soil carbon biogeochemistry: Projects seek to quantify and characterize the recalcitrant pools of pyrogenic and geogenic carbon in soils. We’ll examine chemical transformations and dissolution as mechanisms controlling their fate in the critical zone. Urban biogeochemistry: New and evolving research projects to study the biogeochemical functioning of urban ecosystems with emphasis on cycling and storage of carbon and nutrients. Positions are ideal for candidates who have completed an MSc in soil science, geosciences, environmental chemistry, ecosystem science or related fields, but outstanding BSc graduates in such programs will be considered. For further information, please contact Dr. Alain Plante by email (aplante@sas.upenn.edu) or consult the department website (www.sas.upenn.edu/earth). Applications can be submitted directly online (https://www.applyweb.com/upenng/) before December 15.

Madison and the SSA

Madison and the SSA

In our our ongoing video series, “What are you doing today?“, undergraduate research assistant Madison Bell-Rosof explains why measure the specific surface area of soil samples.

 

Hannah picking biochar

Hannah picking biochar

In our our ongoing video series, “What are you doing today?“, undergraduate research assistant Hannah Sanders explains why she’s using dental tools to pick biochar chunks clean of soil.

 

Hi Penn!

Hi Penn!

Hi all!lab-selfie

I am extremely excited to be the latest addition to Prof. Plante’s lab (and thrilled about the new Netzsch autosampler); we have been planning this collaboration since first meeting at AGU (American Geophysical Union Fall Meeting) in 2013. At that time, I was a Ph.D. candidate Tulane University with Prof. Brad Rosenheim. My research focused on using thermal analyses and coupled radiocarbon and isotopic analyses to characterize organic matter stability in coastal soils and sedimentary deposits. After completing my Ph.D. the following year, I began a postdoctoral research position at the University of California – Merced with Prof. Marilyn Fogel. My research grew to focus on using hydrogen and carbon isotopes to trace inputs and subsequent storage of organic matter in forest soils, characterize dynamics of physical and chemical stabilization, as well as address the potential of soil organic matter in recording climate (precipitation) signals. Now, finally, as a postdoc at the University of Pennsylvania through a fellowship from the Office of the Vice Provost for Research, I am excited to continue researching mechanisms controlling organic matter stability and storage in soils, specifically, mineral interactions, effects of biochar/black carbon addition, and microbial impacts as well as improving our understanding of thermal analyses as they relate to particulate organic matter cycling.

~Liz Williams

 

Increased thermal analysis capacity

Increased thermal analysis capacity

A new grant (#1541588) from the Instrumentation and Facilities program in the NSF Division of Earth Sciences (NSF-EAR/IF) has allowed us to acquire new thermal analysis instrumentation for increased capacity of characterization of organic matter in soils and sediments. In addition to our existing Netzsch STA409 instrument coupled to an LI-840A CO2 and H2O infrared gas analyzer, we now have a Netzsch STA499 F3 Jupiter with a robotic automatic sample changer. The new instrument is also coupled to its own LI-840A for CO2 and H2O evolved gas analysis.

double_the_STA_fun

Our new STA449 instrument (right) has an automatic sample changer, and substantially increases our sample throughput compared to our older STA409 instrument (left).

Thermal analysis techniques are increasingly used as part of a suite of methods to characterize organic matter stability and quality in soils, sediments, composts, biochars, and other environmental samples. Our previous equipment was a single-sample, manual-loading operation that could handle 3-4 samples per working day. That kind of sample throughput was unable to meet the geoscience research community’s demand for rapid and data-rich characterization of organic matter in soils and sediments. The new autosampler-equipped thermal analyzer will allow samples to be analyzed unsupervised around the clock, thus allowing its application in large, multidisciplinary projects such the cross-CZO characterization of controls on soil organic matter dynamics. Other research projects that will greatly benefit from the new instrumentation include correlation of thermal analysis results with conventional, analytical methods of characterizing SOM composition, simultaneous quantification of organic, inorganic and pyrogenic C in soils and sediments, and thermal fractionation as a preparatory step for radiocarbon analysis. At present, the feasibility of these large-scale, “big-data” styled research projects is severely limited by low sample throughput. The new instrument is part of an open multi-user facility that will be available for collaborators locally and worldwide. The relative ease and speed of analysis enables its use by undergraduate students, directly supporting undergraduate research and teaching tool in the Earth, environmental, and materials sciences. We are currently working on updating our data processing pipeline to allow users and collaborators to access raw data and process them using open and reproducible methods that can be accessed online.