Organismal Form and Function Lab

Christopher Oufiero, Towson University

Location: Maryland

Abstract

Invertebrates use movement of their bodies and structures in diverse ways to interact with their environment. This includes general locomotion (e.g., walking, jumping, flying) to specific forms of locomotion (e.g., gliding on water), using limbs to acquire food (e.g., raptorial forelegs in the praying mantis) and using structures to communicate (e.g., cricket calls). These movements have been the focus of bioinspiration studies to understand how these small organisms, with compact nervous systems, are able to achieve their movements. Given the diversity of invertebrates and the lack of information on the variation in their movements, the goals of this course are to understand the variation in invertebrate movement and explore the factors that may affect that variation. In this course, students have the opportunity to develop and test their own research hypotheses associated with variation in the movement of invertebrates. Using high-speed cameras, students are instructed on filming techniques to quantify animal movement, the use of the R programming language to obtain basic kinematics of movement and analyze their data, and the process of science from hypothesis formation to presentation of results. Research questions change each iteration based upon the hypotheses students develop, but the same instructional material and skillsets (e.g., quantifying animal movement) are consistently used. Results from each student group are presented during a departmental wide poster symposium and can be written up for publication, where applicable.

Student Goals

  1. Gain experience in organismal biology with a focus on form, function, and performance relationships
  2. Obtain a set of hard (e.g., data collection and analysis) and soft (e.g., time management and group work) skills
  3. Experience the scientific process from start to finish, including developing and testing their own hypotheses, presenting results, and obtain ownership of their research

Research Goals

  1. Understand the variation in invertebrate movement
  2. Determine factors that may affect invertebrate movement, such as morphological and ecological differences

Context

The Organismal Form and Function CURE is a one-semester (16-week) class offered in the Fall to take advantage of the abundant invertebrate fauna at the beginning of the term. The course is designed to accommodate up to 20 students working in groups of 4. The enrollment can be increased if students use their own recording devices (e.g., high-speed cameras on their phones). This course is intended to be at the introductory level to encourage students to gain research experience early. Therefore, it is assumed students only have an introductory biology understanding of the material. Students do not need to know about the diversity of the organisms in the area, as learning the natural history of their chosen subjects is part of the course. Students are instructed during the first, scaffolding, half of the course on basic content focused on the ecology and evolution of animal performance, basic biomechanics likely to be encountered, and muscle physiology. Additionally, during this time students learn the techniques needed to collect their data and practice using the equipment. This includes learning the principles of high-speed videography, tracking structures on the animals to quantify movement, and basic kinematic analysis in R to obtain displacement, velocity and acceleration. R script is provided that students can modify based on their research questions. During the second half of the course, time is dedicated to student-driven inquiry, where the class collects, analyzes and presents data.

Target Audience: Introductory, Major, Upper Division
CURE Duration:A full term

CURE Design

The research theme of the Organismal Form and Function CURE is quantifying the variation in animal movement, using locally collected invertebrates as a model. Each team of students develops their own research project under this broad theme. Therefore, each iteration of the course is unique in the specific projects, while using the same skills and techniques. Students are instructed in how to use high-speed videos to quantify animal movement from the start of the course. The class collects locally to determine what is available to the students and inspire the students to develop questions regarding animal movement. Given the abundance of invertebrates, but lack of information on variation in their movement, the course provides students the flexibility to design their own hypotheses. Students are assessed on the process, not the hypothesis or questions being asked to ensure that even a failed project can still be successful, as this is part of the scientific process. The first half of the class uses individual assignments to assess students on their knowledge of the content covered and techniques used to collect data. The second half switches to assessing the groups, including peer evaluation to ensure all students are participating.

The stakeholders outside of the classroom include the general and local scientific audience. This course provides the opportunities for students to make discoveries and potentially publish their work. It is modeled after field based research courses, where students are immersed for a few weeks to conduct research. The students' work is shared publicly through the courses Twitter account and website. Furthermore, students present their research at the end of the semester to the Department's Fall Poster session. Lastly, if projects are suitable, they can be written up for publication to share with the broader scientific audience.

Core Competencies: Analyzing and interpreting data, Asking questions (for science) and defining problems (for engineering), Planning and carrying out investigations, Using mathematics and computational thinking
Nature of Research: Basic Research, Field Research

Tasks that Align Student and Research Goals

Research Goals →
Student Goals ↓
Research Goal 1: Understand the variation in invertebrate movement
Research Goal 2: Determine factors that may affect invertebrate movement, such as morphological and ecological differences


Student Goal 1: Gain experience in organismal biology with a focus on form, function, and performance relationships

- Collect specimens locally
- Use high-speed videos of animal movement
- Use modern tracking programs to digitize structures for analysis
- Obtain basic kinematics of the structures to quantify movement
- Use statics (histograms, ANOVA, correlations) to determine variation in movement

- Develop research question with one categorical predictor
- Learn how to measure body size and why it is important
- Use dissecting scopes when needed to measure specific structures
- Use statistics to quantify significance in the predictors of animal movement



Student Goal 2: Obtain a set of hard (e.g., data collection and analysis) and soft (e.g., time management and group work) skills

- Use high-speed cameras
- Use tracking programs
- Use R programming language
- Create a schedule to film organisms while in class
- Curate dataset to be submitted at the end of the semester
- Work in groups of 3 to 4
- Complete weekly progress reports
- Keep on track with assignments

Same as in column 1
- Use of ImageJ to measure specimens
- Use of dissecting scope and calipers to measure specimens
- Understand statistics to determine if an independent trait has a significant effect



Student Goal 3: Experience the scientific process from start to finish, including developing and testing their own hypotheses, presenting results, and obtain ownership of their research

- Develop a hypothesis based on observation
- Refine hypothesis
- Choose from final list of class approved hypotheses
- Develop experimental design to test hypothesis
- Collect the necessary data to test hypothesis
- Use appropriate statistics to assess hypothesis
- Effectively present results in oral and written presentations

Same as column 1
- Establish an independent factor to examine
- Determine the experimental design to test the effects of the independent factor


Instructional Materials

A list of equipment can be found here: https://wp.towson.edu/off-lab/course-equipment/
Note: other types of cameras, such as camera phones, capable of recording at 120-240 frames per second can be used in place of high-end cameras. The movies obtained from them can be analyzed in the Tracker program. Other tracking programs also can be used, some of which implement machine learning.

Course Syllabus (Microsoft Word 2007 (.docx) 33kB Jul20 21)
Using an iPhone to record in slow motion (MP4 Video 167.6MB Jul20 21)
Using Tracker to analyze high-speed video (Quicktime Video 1361.6MB Jul20 21)

Assessment

More assessment material, including additional assignments and rubrics can be found on the course website: http://wp.towson.edu/off-lab/events/

Scientist Spotlight Assignment (Microsoft Word 2007 (.docx) 14kB Jul20 21)
Progress Report Assignment (Microsoft Word 2007 (.docx) 14kB Jul20 21)
Video, tracking, digitizing assignment (Acrobat (PDF) 106kB Jul20 21)

Instructional Staffing

In addition to the instructor, the course also employs 1 graduate student teaching assistant and 1 undergraduate learning assistant (ULA) who has taken the course or participated in similar research.

Author Experience

Christopher Oufiero, Towson University

The motivation for this CURE was to provide organismal based research experiences to a larger diversity of students during a full semester. I was motivated by my experiences attending research based classes at field stations, my diverse research program, and the lack of CUREs that incorporated organismal research, biomechanics, evolution and ecology. I wanted to provide students in-class opportunities to formulate a hypothesis, design experiments, collect data, analyze, and present their results within one semester.


Read full Instructor Story »

Advice for Implementation

- Allow for flexibility in the course schedule and syllabus. Be open with the students about it as research, especially on live animals, does not always go as planned.
- Sacrifice content for research time. The whole course could be on biomechanics or the diversity of arthropods, but allow the students room to explore the specific topics related to their research questions.
- Have contingency days, that is days that are built in "free time" to allow room to troubleshoot collecting, filming, working in R, and/or analyses. If the contingency days aren't used, they can be used as extra time in class for students to work on projects. 
- Keep the focus on the process not the outcome. As failure is common in science, make it clear that a failed project does not result in a failure in the class. Emphasize this is part of science and what we can learn from the failures. If students have no data to write up, they could write a proposal on what they would do next time.
- Keep the students motivated. For example, even if they get negative or non-significant results, emphasize it is still a result if we are testing a hypothesis.
- If students are developing their own questions, keep it a theme from the beginning, but also provide some examples. Allow students to determine if the project is feasible. Provide time for students to "speed-date" projects after the initial hypothesis assignment.

Iteration

 

This CURE is designed to allow freedom in research projects under the general goal of assessing variation in movement of an invertebrate. The study organisms, types of movement, and specific questions are up to the students, with input from other students and the instructor. Therefore, the students are directly involved in the troubleshooting and problem-solving associated with their research. In particular, most of the students work with the instructor, TA or ULA when initially setting up for filming to ensure the movement of interest can be capture and the organisms can be motivated. This is usually one of the biggest hurdles in the class. Having experience filming animals performing a task helps to understand what does and does not work, but is not necessary. Furthermore, students are directly involved in the troubleshooting of tracking and analyzing the tracked data as there are often issues with using R and translating the basic kinematic code to more specific examples.

As this research is only tangentially related to the instructors research, the students have the opportunity to "fail" without it affecting their grade or the instructors research program. All assignments are focused on the process and not the end scientific result. If organisms do not cooperate we try to identify this early on so projects can be switched. We discuss sample sizes and experimental design to ensure students are testing a hypothesis. Even if there are negative results, if it is testing a hypothesis it is part of the process, which is the focus of the assessment.

The only opportunity for repeating aspects of the research in class is to assess the repeatability of the movement being examined. This is discussed during lecture portions of the course, offering as a potential research question as the repeatability of many of the performances encountered has not been investigated.

There is time built in to the course to allow flexibility in case research projects do not go as planned. After the scaffolding portion during the first half of the semester, the remainder of the course is mostly open lab time for students to collect and analyze data. The goal is to provide in class time to conduct research. During this time, projects can be adjusted, more specimens can be collected, and troubleshooting occurs. This is where sacrificing content for research time is important. Even if it seems as though there is nothing planned, that flexibility is needed in case problems arise and to provide time for students to work through their research.

 

Using CURE Data

 

In this CURE, each individual project is its own entity and is therefore not aggregated to answer one big research question. However, if a project is successful students have the opportunity to continue in independent research credits to continue the project, further analyze it, or write it up for publication.

Research progress is assed by the instructor through weekly progress reports. The quality of the data is ensured through uploads of videos and tracked points to a shared drive and final submission of all data at the end of the semester. As each project is its own contained entity, any publications that may result will include all students associated with the particular project, the instructor and graduate student and ULA where appropriate.

Results of projects are shared locally at the Fall Poster Symposium within the Department of Biological Sciences. Portions of the results are also shared publicly via the courses website (see below) and twitter account.

 

Resources

 

More resources can be found on the course website:
http://wp.towson.edu/off-lab/

Additional information can be found in the following publication on this CURE:
Oufiero, C. E. (2019). The Organismal Form and Function lab-course: a
new CURE for a lack of authentic research experiences in organismal biology. Integrative Organismal Biology, 1, 1–14. https://doi.org/10.1093/iob/obz021

Related CUREs:
Price, S. A., Larouche, O., Friedman, S. T., Corn, K. A., Wainwright, P. C., & Martinez, C. M. (2020). A CURE for a major challenge in phenomics: a practical guide to implementing a quantitative specimen-based undergraduate research experience. Integrative Organismal Biology, 2(1), obaa004.

Full, R. J., Dudley, R., Koehl, M. A. R., Libby, T., & Schwab, C. (2015). Interdisciplinary laboratory course facilitating knowledge integration, mutualistic teaming, and original discovery. Integrative and comparative biology, 55(5), 912-925.

Reference material used during the scaffolding session, including a selection of papers read (which may change across iterations):
Irschick, D. J., & Higham, T. E. (2016). Animal athletes: an ecological and evolutionary approach. Oxford University Press.

Biewener, A., & Patek, S. (2018). Animal locomotion. Oxford University Press.
Winchell, K. M., Maayan, I., Fredette, J. R., & Revell, L. J. (2018). Linking locomotor performance to morphological shifts in urban lizards. Proceedings of the Royal Society B, 285(1880), 20180229.

Mendoza, E., Azizi, E., & Moen, D. S. (2020). What explains vast differences in jumping power within a clade? Diversity, ecology and evolution of anuran jumping power. Functional Ecology, 34(5), 1053-1063.

Combes, S. A., Salcedo, M. K., Pandit, M. M., & Iwasaki, J. M. (2013). Capture success and efficiency of dragonflies pursuing different types of prey. Integrative and comparative biology, 53(5), 787-798.