Backward Design

The relationship between protein structure and function is a foundational concept in undergraduate biochemistry. We find this theme is best presented with assignments that encourage exploration and analysis. Here, we share a series of four assignments that use open-source, online molecular visualization and bioinformatics tools to examine the interaction between the SARS-CoV-2 spike protein and the ACE2 receptor. The interaction between these two proteins initiates SARS-CoV-2 infection of human host cells and is the cause of COVID-19. In assignment I, students identify sequences with homology to the SARS-CoV-2 spike protein and use them to build a primary sequence alignment. Students make connections to a linked primary research article as an example of how scientists use molecular and phylogenetic analysis to explore the origins of a novel virus. Assignments II through IV teach students to use an online molecular visualization tool for analysis of secondary, tertiary, and quaternary structure. Emphasis is placed on identification of noncovalent interactions that stabilize the SARS-CoV-2 spike protein and mediate its interaction with ACE2. We assigned this project to upper-level undergraduate biochemistry students at a public university and liberal arts college. Students in our courses completed the project as individual homework assignments. However, we can easily envision implementation of this project during multiple in-class sessions or in a biochemistry laboratory using in-person or remote learning. We share this project as a resource for instructors who aim to teach protein structure and function using inquiry-based molecular visualization activities.

Primary image: Exploration of SARS-CoV-2 spike protein: student generated data from assignments I - IV. Includes examples of figures submitted by students, including a sequence alignment and representations of 3D protein structure generated using UCSF Chimera. The primary image includes student generated data and a cartoon from Pixabay, an online repository of copyright free art. 

Students use their number sense to make observations and come up with reasonable guesses or explanations for the patterns shown.

Understanding the scientific method provides students with a necessary foundation for careers in science-related fields. Moreover, students can apply scientific inquiry skills in many aspects of their daily lives and decision making. Thus, the ability to apply the scientific method represents an essential skill that students should learn during undergraduate science education. We designed an interrupted case study in which students learn about and apply the scientific method to investigate and recapitulate the findings of a published research article. This research article addresses the question of how parents recognize their own young in a system where birds of the same species lay eggs in each other's nests. The researchers approach the question through three experiments in which the bird's own offspring and unrelated offspring hatch in different orders. This experiment specifically tests for the effect of hatching order on the bird's ability to recognize its own offspring. In the case study, students form hypotheses based on behavioral observations made while watching a video clip, together with background information provided by the instructor. With additional information about the experimental design, students make graphical predictions for the three related experiments, compare their predictions to the results, and draw conclusions based on evidence. This lesson is designed for introductory undergraduate students, and we provide suggestions on how to adjust the lesson for more advanced students. This case study helps students differentiate between hypotheses and predictions, introduces them to constructing and interpreting graphs, and provides a clear example of the scientific method in action.

Actively engaging students during a lecture class can come through many formats.  The 4-Minute Summary is a versatile pedagogy that can be readily applied to any class format (e.g., traditional, flipped), any class size, and any content.  Students benefit by engaging with peers while at the same time recapping and recalling content in their own words.     

The 4-Minute Summary allows students to

1. engage with peers,
2. engage with content,
3. recap/recall content in their own words,
4. practice speaking the content and
5. provide a venue for questions to be answered. 

Luckily, students also enjoy using 4-Minute Summaries as a way to check their understanding while interacting with their peers.    

Collecting data from experimental observations is an important component of the scientific process; likewise, the analysis of the data is essential to understanding the observed trends and patterns from any experiment. Allowing students to practice data collection and analysis is valuable to their scientific literacy and capacity. In this paper, we present a fly trap experiment that gives students the opportunity to discover which combinations of baits and trap types yield the best fly traps. Baits and traps can be made from easily available household goods, allowing this experiment to be set up with minimal preparation and at low cost. Students, individually or in small groups, set up their specific trap and bait combinations and the instructor collects them and places them in an area with flies. After a period of time, the instructor returns the traps to students who count the numbers of trapped flies. With these data, students summarize the results and evaluate the success of different combinations of trap type and baits. The experiment requires one session to construct and set-up the traps and a second session to count the flies and analyze and interpret the data. The experiment is designed for undergraduate students and can be modified to fit students’ past experience with experimental design and statistical analysis.  

Accompanying article about online adaptation of this lesson: Online Adaptation to "Gotcha! Which fly trap is the best? An introduction to experimental data collection and analysis"

Ensuring students' science literacy is essential for preparation for study in science disciplines and is of critical importance given contemporary challenges in determining the legitimacy and accuracy of science in popular media. This lesson describes the effectiveness of an undergraduate biology course designed to improve students' scientific literacy through meaningful engagement with science news sources. Students were surveyed at the beginning and end of the course to determine their preferred science news sources. Though 45% of students reported not accessing any science news sources in their daily lives at the beginning of the term, 100% of students reported accessing science news at the end of the term. Backward design and Scientific Teaching ensured that assignments meaningfully related to course learning goals, and formative assessment allowed the instructor to track student metacognition regarding science news throughout the term. These findings highlight the value of incorporating science news into undergraduate science courses with meaningful effects for science engagement and literacy beyond the classroom.

Workshop about models for introducing social justice issues into classes developed in a Faculty Mentoring Network. Presented at the 2021 BIOME Institute.

Professional development workshop slides to help curate conversations in teaching statistics with a critical inquiry lens.

As instructors, we continually look for new ways to create equitable learning environments and support learning for all students in our courses. Recently, we have explored ways that we can increase structure to better support students. We have identified four evidence-based elements that we include in our course design and implementation: 1) structured assessments and feedback; 2) structured out-of-class learning; 3) structured class time using inclusive practices; and 4) structured assignments using transparent design. In this essay, we identify some relevant literature to address each of these levels of structure and describe our experiences with implementation at each level to support equitable classroom environments.

This webinar will explore how faculty can teach with a growth mindset and identify some potential areas of fixed mindset that might prove to be obstacles for many students.

Basic data handling and data analysis skills are introduced to visualize and analyze ‘big data.’ Environmental justice is introduced to give students an understanding of tools and strategies to explore while developing advocacy and communication skills.

In this lesson, students plot data and interpret graphs of the metabolic responses of fish to hypoxic conditions. Then, students view and reflect on an interview with fish ecophysiologist Benjamin Negrete, Jr., who collected the data that they graph.

The integration of virtual technology is becoming a common trend in anatomy education at the undergraduate and graduate levels. The incorporation of virtual 3D anatomical models into the classroom is beneficial to students, especially if they do not have access to cadavers. This lesson is a hybrid kinesiology laboratory module that includes virtual anatomical and traditional physiological laboratory components. The module contains procedures that are easy for undergraduate students to follow while also containing advanced content to promote higher order thinking. This lesson provides a brief description of the learning context, time and pace, lesson plan, and teacher and student evaluations. During the learning activities, students will use a virtual dissection Anatomage Table and conduct modified Wingate tests and accumulated oxygen deficit experiments. This module will be useful for anatomy and physiology instructors who want to blend virtual and traditional learning modalities, embrace active learning, and make advanced concepts more accessible to students.

Primary image: A photograph of the Anatomage Table in its vertical orientation, revealing three different layers of the virtual male donor model in virtual dissection. 

Vision and Change in Undergraduate Biology Education (American Association for the Advancement of Science, 2011) stresses the importance of fostering an understanding of the relationship between science and society. We describe a library-based activity that enables students in an undergraduate microbiology class to explore this relationship over the course of centuries, with the library functioning as a laboratory. Students are guided by a worksheet as they explore historical materials such as books, newspapers, letters, government publications, articles, scientific treatises, and artifacts. Working in pairs, students answer questions about the content and reflect on how the ideas in the documents relate to the scientific understanding at the time. Exploring authentic materials in a library setting provides a powerful learning experience. This activity was also successful using digitized documents during the COVID-19 pandemic, when remote teaching was required. Student responses to a post-activity questionnaire indicated that the activity sparked a keen interest in the history of science as well as introspection about the relationship between science and society. This approach can be generalized for different biology courses and education levels.

Primary image:  Students examining historical books and microscopes. Students working in pairs to complete worksheet questions during one of two visits to the University of Colorado Boulder’s Special Collections.

The biology classroom is not separate from the greater context of society; social issues can and should be presented in connection with the content. Here we present an example of antiracist teaching using the molecular/cellular biology of cancer in an introductory biology course as a topic through which to address historic racial disparities. Through this lesson, students analyzed biological science through the lens of social justice, specifically looking at disparities of cancer incidence with ties to health outcomes and environmental racism. The synchronous activity begins with personal tie-ins to the broader subject of cancer and then dives into the molecular regulation involved in creating cancerous phenotypes. Cancer biology is explored using an active-learning style based in process-oriented guided inquiry learning (POGIL) tactics. Multiple levels of assessments pushed students to grapple with data about racial health disparities and make explicit connections between these data and molecular mechanisms of cancer formation. This paper provides activity worksheets, an activity timeline, an example of assessment items, and teacher preparation for other instructors who want to emulate this lesson either directly or as an example of adjusting other science topics towards this lens. For those teaching in different topics, we offer advice and examples to help instructors to include social justice lenses into their science teaching.

Primary image: Malignant History. Artwork by Heidi-Marie Wiggins and Jeannette Takashima.

Three resources for faculty interested in an introduction to Universal Design for Learning (UDL).

This framework, developed by ISKME in partnership with SERC, provides a practical reference for curators and authors of STEM OER, with 23 accessibility criteria, or elements, to reference as they curate, design and adapt materials to be accessible.

This resources provides a framework for students to write a Microbiology Resource Announcement, collaboratively.

Radical innovations in DNA sequencing technology over the past decade have created an increased need for computational bioinformatics analyses in the 21^st century STEM workforce. Recent evidence however demonstrates that there are significant barriers to teaching these skills at the undergraduate level including lack of faculty training, lack of student interest in bioinformatics, lack of vetted teaching materials, and overly full curricula. To this end, the James Madison University, Center for Genome & Metagenome Studies (JMU CGEMS) and other PUI collaborators are devoted to developing and disseminating engaging bioinformatics teaching materials specifically designed for streamlined integration into general undergraduate biology curriculum. Here, we have developed and integrated a fun introductory level lesson to command line next generation sequencing (NGS) analysis into a large enrollment core biology course. This one-off activity takes a crucial but mundane aspect of NGS quality control (QC) analysis and incorporates the use of Emoji data outputs using the software FASTQE to pique student interest. This amusing command line analysis is subsequently paired with a more rigorous research-grade software package called FASTP in which students complete sequence QC and filtering using a few simple commands. Collectively, this short lesson provides novice-level faculty and students an engaging entry point to learning basic genomics command line programming skills as a gateway to more complex and elaborated applications of computational bioinformatics analyses.

Primary image: Undergraduate students learn the basics of command line NGS quality analysis using the FASTQE and FASTP programs.

Introduction into computational approaches in phylogeny and protein modeling based on coronavirus SARS-CoV-2 (caused COVID-19 pandemic). Two self-guided tutorials for standard lab classes of 2.5 hours. Level: undergraduate students majoring in biology.