Do you see what I see?

Regional workshops to assess biomolecular visual literacy

Published December 01 2017

Bioscience textbooks contain an enormous number of figures representing structures, pathways, mechanisms and interactions. Educators tacitly assume that these representations illuminate student understanding of complex ideas, but we may not make explicit the learning goals and objectives upon which assessment of visual literacy is based.

Work has begun to develop explicit standards and assessments for visual literacy for metabolic pathway maps (1). With the help of a National Science Foundation Improving Undergraduate STEM Education grant, the open BioMolViz group ( has been developing competencies and assessment questions that target 12 overarching themes and associated learning goals and objectives based on a biomolecular visualization framework (2).

Courtesy of Chris Schaller, College of St. Benedict/St. John’s University

Without understanding structure, can students understand the biosciences and stay in the field? Textbooks show 2-D images of complicated 3-D structures. Textbook websites and others such as Protopedia offer animations and interactive molecular models. Some faculty have students manipulate structures using visualization software like Pymol and Chimera, create Jsmol tutorials and even print 3-D models.

Workshop schedule

Jan. 20: Georgia Institute
of Technology, Atlanta
Feb. 24: Washington University, St. Louis
March 10: Morgan State University, Baltimore
April 20: University of San Diego

Yet all this activity prompts these questions: Are students gaining insight into the fundamentals of structure-function relationships, or are they just algorithmically and passively observing colorful displays without acquiring the literacy we faculty assume? Do they know the learning goals of the faculty, who may not have made these goals explicit? Can we expect students to hold visual imagery, symbolic representations and existing conceptual understandings simultaneously as they build new ones?

Biochemistry educators have deemed biomolecular visualization a threshold concept (3), implying that students struggle with it. Ask anyone who has graded exams about the difficulty of such a cognitive synthesis.

Misconceptions abound. Protein alpha helices are not filled with water. Molecules are not static. Most polar uncharged amino acid side chains are not on the surface of a protein. A mutation does not change the structure of double-stranded DNA. Nucleic acids do form secondary and tertiary structures.

The BioMolViz group

Diane Dean,
University of Saint Joseph
Daniel Dries,
Juniata College
Margaret Franzen,
Milwaukee School of Engineering
Henry Jakubowski,
St. Benedict/St. John’s University
Wally Novak,
Wabash College
Kristen Procko,
University of Saint Joseph
Alberto Roca,
Cassidy Terrell,
University of Minnesota Rochester

The BioMolViz group, along with Paul Craig of the Rochester Institute of Technology and Laura Listenberger of St. Olaf College, has developed the present incarnation of the biomolecular visualization framework (2). But as an African proverb states, “If you want to go fast, go alone. If you want to go far, go together.” To that end, and with the help of the NSF, we will hold four regional Saturday workshops to bring together faculty and postdocs to address biomolecular visualization literacy. Specifically, we will develop and vet competencies (the final skills and knowledge expected after a course of study) and some assessment questions targeting specific learning goals for four overarching themes: alternative renderings, molecular interactions, monomer recognition and topology/connectivity. Grant funds will help cover registration, food, transportation and accommodations for those traveling longer distances.

We hope to build a community of educators who understand the need for and gains from clear competencies and assessment tools to promote biomolecular visualization literacy. Look for targeted advertisements in ASBMB Today and in Biochemistry and Molecular Biology Education. We invite you to join us in this metacognitive adventure. For more information and an application form, please email the group.

1. dos Santos, V.J., & Galembeck, E. Biochem. Mol. Biol. Educ. 43, 162-167 (2015).
2. Dries, D.R., et al. Biochem. Mol. Biol. Educ. 45, 69-75 (2016).
3. Loertscher, J., et al. CBE Life Sciences Education 13 (3), 516-528 (2014).

Henry Jakubowski Henry Jakubowski is a professor of chemistry at the College of St. Benedict/St. John’s University, Minnesota.

Margaret Franzen Margaret Franzen is program director at the Milwaukee School of Engineering Center for BioMolecular Modeling.

Daniel Dries Daniel Dries is an assistant professor of chemistry at Juniata College, Pennsylvania.