Ecotoxicology (“Worm Lab”)

Dr. Sharon Pochron, Sustainability Studies Program, Stony Brook University

EHI 350: Design and Implement a Research Project in Ecotoxicology


EHI 351: Conduct and Communicate a Research Project in Ecotoxicology

We begin the first semester by articulating the environmental toxins that currently concern the students. For the last three years, most students have been focused on Roundup, since it’s just been reclassified as a probable carcinogen and since it’s found in virtually all of our food. Over the summer of 2016, a soccer-playing student came to me with a concern about artificial fields, so we studied that. Students then perform an extensive review of published literature regarding their toxin using Web of Science, Google Scholar and/or PubMed. After reading the literature, we walk through what we know and don’t know about the risks associated with the toxin, and we devise a way to test the risk using earthworms and soil microbes. At this point, we discuss sample size issues, costs, and how to interpret various outcomes. If the students want to use techniques that I don’t personally have in my toolkit, we discuss ways to get access to them. This has led to teaming with chemistry professors, ecotox labs, and Brookhaven National Laboratories. After they get the project underway, the Fall students draft high-quality Introduction and Methods sections for their research. The Spring students complete the research and writing.

By its nature, ecotoxicology pulls in policy and culture. For instance, it was the WHO that reclassified Roundup’s main ingredient as a probable toxin, and it is school districts across Long Island, the US and Europe who are pulling out grass fields and replacing them with fields made of recycled tires. In the Spring semester, we discuss effective ways and venues for communicating our findings, thereby engaging local citizens in science in general and our research in particular.

Instructor’s Goals:
My goal is to get students excited about science. I want them to be able to say exactly what scares them about a particular chemical or environmental exposure. I want them to be able to access the scientific literature and determine whether or not being nervous about a substance is warranted. If it is, I want them to feel empowered that THEY can determine if the substance is actually dangerous. I want them to be able to devise an experiment that answers their question, and I want to help them set up that experiment. During the data-collection phase, they should be learning the strengths and weaknesses of the scientific method. It is easy to screw things up in the lab, and they need to care enough to minimize errors, not because of a grade repercussion but because they might not be able to answer their question. By the end of the second semester, the students should intellectually own their research question. They should have a deep understanding of what they know and what other scientists know. At that point, we focus on communicating their findings to others. I want them to come up with groups of people who might be interested in their research. They should be able to target that audience, explaining their research and why it’s important to not just the students but the community as a whole.

Student Learning Objectives

From EHI 350, Design and Implement a Research Project in Ecotoxicology:

  1. Understand the methods scientists use to explore natural phenomena including observation, hypothesis development, measurement and data collection, experimentation, and evaluation of evidence.
  2. Assess scientific information and understand the application of scientific data, concepts, and models in the natural sciences.
  3. Make informed decisions on contemporary issues involving scientific information.
  4. Locate and organize information from a variety of appropriate sources.
  5. Analyze the accuracy of information and the credibility of the sources.
  6. Determine the relevance of the information.
  7. Use the information ethically and responsibility to produce novel hypotheses.
  8. Design a research project that functions to test their hypotheses.
  9. Set up their novel research design.
  10. Collect data from their research.
  11. Write a high-quality Introduction and Methods section in APA journal style.

From EHI 351, Conduct and Communicate a Research Project in Ecotoxicology:

  1. Understand the methods scientists use to explore natural phenomena including observation, hypothesis development, measurement and data collection, experimentation, and evaluation of evidence.
  2. Assess scientific information and understand the application of scientific data, concepts, and models in the natural sciences.
  3. Make informed decisions on contemporary issues involving scientific information.
  4. Interpret and draw inferences from statistical models.
  5. Employ statistics to solve problems.
  6. Check statistical results for reasonableness.
  7. Recognize the limits of statistical methods.
  8. Research a student-selected topic in ecotoxicology, develop an oral and written argument, and organize supporting details.
  9. Deliver an oral presentation for the intended audience using a research-focused poster.
  10. Determine if the research is suitable for publication in a peer-reviewed scientific journal.


Linking Science and Social Issues

Civic or Social Issue Science Concept
Acid rain, originating from old coal burning plants in Indiana, falls heavily in the Northeast. How does acid rain affect living organisms that contribute to soil health (e.g. earthworms)?
  • How to make “acid rain.”
  • How acidic should the acid rain be?
  • How to determine if acid rain affects earthworms?
  • How big should our sample size be?
  • How does soil chemistry interact with acid?
  • How does earthworm biology interact with acid?
  • How to use Web of Science to formulate hypotheses.
In an urban setting, people often use fertilizer and Roundup, sometimes alone and sometimes together. How does fertilizer affect earthworms? How does Roundup affect earthworms? How do the two chemicals interact to affect the earthworms?

Overview: Students as citizens need to be able to articulate issues that concern them. This class focuses on environmental toxins, but the framework works for many issues. My goal in making then conduct a literature review is to help them internalize the fact that scientists probably have studied some aspect of the thing that worries them. My goal in making them read the literature is help them believe that they actually CAN know something approximating the truth. Then, in setting up the project, they should feel empowered to know that they can actually DO something about the toxin that concerns them. They can devise a project that helps them see the danger and communicate that risk to others. Once they have data, we work together to analyze and interpret it. Sometimes the project yields great data, and other times, something has gone wrong. What does it mean not just for this project, but for other scientists who’ve conducted similar project? What does it mean to know something? In the communication phase, I help students find ways to convey their knowledge to two audiences: scientists and the public. How are the ways of communicating similar, and how are they different?

The Course

Syllabus for EHI 350, Design and Implement a Research Project in Ecotoxicology
Syllabus for EHI 351, Conduct and Communicate a Research Project in Ecotoxicology

Evaluating Learning

I grade fully on participation. We have no exams or quizzes. The students have to set up the project (which includes putting exact amount of soil, weighed and pre-stressed earthworms, and earthworm food into experimental containers), they have to maintain the project (which usually includes watering the experimental and stock worms, including my personal projects), and they have to collect the data (which usually includes extracting worms, weighing them, and subjecting them to stress until they die). These requirements usually mean that they have to invest their time outside of the classroom on their projects, and no student has ever complained. I usually give them the day off after a day of data collection, and they still come to the lab, mostly because they’re dying to know the results. Occasionally I have students who are more interested in say worm husbandry than writing, and I try to shift her or his responsibilities to maximize their happiness. The students have to work in groups of two or three to write a Methods section. They have to take their version to the Writing Center. I read all of them out loud and critique them. They have to take my oral comments and work together on creating one version. We repeat this for the Introduction, which is based on their literature review. I have a checklist in Blackboard for contribution to all of these activities, and I keep track of their participation that way. The Writing Center sends me a list of who came to them for help, so I keep track of student writing that way.

Background and Context

Course History

I came to Stony Brook University’s Sustainability Studies Program with a strong background in primatology, having studied baboons in Tanzania for my doctorate and lemurs in Madagascar for my post doc. I had more than 20 publications in my field, including an awesome one, written by Patricia Wright’s entire team, in PNAS.

When SBU offered me a full-time position, the director at the time, Martin Schoonen, had an expectation that we’d get our students involved in real-world problems and hands-on activities. For me, that meant getting students involved in STEM research. The students love this idea. They really want to DO things, and they know the difference between canned labs and actual research. While primatology has a million unanswered questions that students would love to try to study, all the primates live far away. Who can afford to send students to Tanzania or Madagascar? Or even the Bronx Zoo. Plus, I wanted to give ALL of my students a chance to conduct meaningful research. I might find funding to send one or two students overseas, but that left a lot of unfilled need back home.

Anyone can help an A student to the reach her or his full potential. But I have a lot of empathy for the B student. I had this idea that if you engage B students in the actual process of science, they put in the work to become scientists. They fight their apathy for organic chemistry and calculus. After all, that’s how it’d worked for me. Also, some students who like science have strong affinities to become things like journalists, economists, politicians, or city planners. Teaching them the value of science struck me as just as important as teaching science to pre-med and pre-graduate school students. So when Martin challenged me to get students involved in research, I asked myself, what’s the cheapest, most accessible research I could get Sustainability Studies students involved in? I needed something cheap–dirt cheap. Thus, the Sustainability Studies Earthworm Ecotoxicology Lab was born.

I started the Worm Lab with seven students, all volunteers who received no academic credits or pay. We sat around a conference table and asked what sort of questions we’d like to ask using worms. The students decided that they wanted to study the effects of acid rain on earthworms. Acid rain plagues the Northeast, and students had been learning about it in more traditional classes. They wanted to use lab time to see its effects in action. We brought a chemistry professor into the mix because we needed to put the acid into our artificial acid rain. We brought a geologist into the mix because we didn’t know the distribution of calcium in soils throughout the Northeast. We found that the calcium in our soil protected the earthworms for the acid rain, even under very acidic conditions. The students presented their research at Stony Brook University’s huge science fair and at two local high schools.

The next semester I had more than 20 students who wanted to work in the lab. Seeing how popular this was becoming, our undergraduate advisor, Ginny Clancy, suggested that I turn it into a class. It was an easy fit because students had to research their topic using Web of Science (as a primatologist, I knew nothing about soil ecology), they had to set up a project, run it, collect data, analyze it, and communicate it. For two years, I ran the worm lab as a topics course. (SBU saves topics designations for experimental classes.) After I had the kinks worked out, I wrote two syllabi for worm lab classes (EHI 350 and EHI 351) and had them approved by the committee. They’ve been officially in the bulletin for three semesters.

Students decide on research projects, although we generally build on previous projects. All projects have human angle: how dangerous is (fill in the blank with an environmental toxin) to soil and the creatures that live in soil? Over the course of two semesters, we conduct at least one research project, sometimes two or more, we write the paper (Fall students write the Introduction and Materials and Methods; Spring students write the Results and Discussion), and the Spring students present their research at SBU’s science fair. I also encourage students to present their research at the local high schools, generally by reaching out to the science clubs. I close the class at 20 students, but I usually have about 30 per semester.

Institutional Context

Students who major in Ecosystems and Human Impact (EHI) must take four courses in what we call “Group 1.” By taking EHI 350 and/or EHI 351, students fulfill their Group 1 requirements. Students who major in Sustainability Studies (SUS) can also fulfill requirements by taking these courses.

Resulting Projects, Research, Recognition

One of the expected outcomes of EHI 351 is an actual poster that gets presented at SBU’s science fair. Since 2012, students working on the worm lab have produced 10-15 posters. We’ve submitted papers to peer-reviewed journals and have two in review as of Oct. 2016. Read abstracts of some of the posters here:

Download (PDF, 17.23MB)

Many worm students become URECA Researchers of the Month:


Two students have won the Chancellor’s Award in part because of their research in the worm lab:

Ecosystems and Human Impact Alumni Spotlight: Kerri Mahoney


  • Student Shamin Sahebzada graduated with honors using his research in the worm lab for his honors project.
  • I’ve had two high school students conduct their research using the worm lab. Both competed in the Intel/Regeneron.

Using the worm lab, I’m working with other faculty to co-opt the worm immune system to grown quantum dots, which will be potentially usable for medical imaging. I’m conducting that research with colleagues from Brookhaven National Laboratories and SBU’s Ecology and Evolution Department. Working with other SoMAS faculty, I’m developing a plan to quantify the gut microbes of worms that consume conventional diets versus those that eat organic diets. I’m also working with other SoMAS faculty to begin quantifying the amount of glyphosate (the active ingredient in Roundup) in soil under different conditions; I hope to get one or two students involved in that.