Lighten the Load: Scaffolding Visual Literacy in Biochemistry and Molecular Biology

Modeling in molecular genetics allows students to make connections between biological scales

Students often see college courses as the presentation of disconnected facts, especially in the life sciences. Student-created Structure Mechanism/Relationship Function (SMRF) models were analyzed to understand students' abilities to make connections between genotype, phenotype, and evolution. Students were divided into two sections; one section received instructions that included a specific gene as an example related to larger issues like human disease or the environment. The other section was only given generic examples, like gene X and phenotype Y. Coding of exam models and a comprehensive (extensive) model reveled students were able to make links and work within and between biological scales of organization. Modeling provided a way to show and allow students to practice and demonstrate the ability to build step-by-step causal relationships that link ideas together. We also observed a small differing with students receiving the specific prompt performing better than students receiving generic prompt at the point in the semester where linking across many biological scales was required to be successful.

Reading Primary Scientific Literature: Approaches for Teaching Students in the Undergraduate STEM Classroom

Teaching undergraduate students to read primary scientific literature (PSL) is cited as an important goal for many science, technology, engineering, and math (STEM) classes, given a range of cognitive and affective benefits for students who read PSL. Consequently, there are a number of approaches and curricular interventions published in the STEM education literature on how to teach students to read PSL. These approaches vary widely in their instructional methods, target student demographic, required class time, and level of assessment demonstrating the method's efficacy. In this Essay, we conduct a systematic search to compile these approaches in an easily accessible manner for instructors, using a framework to sort the identified approaches by target level, time required, assessment population, and more. We also provide a brief review of the literature surrounding the reading of PSL in undergraduate STEM classrooms and conclude with some general recommendations for both instructors and education researchers on future areas of investigation.

Visual Literacy of Molecular Biology Revealed through a Card-Sorting Task

Visual literacy, which is the ability to effectively identify, interpret, evaluate, use, and create images and visual media, is an important aspect of science literacy. As molecular processes are not directly observable, researchers and educators rely on visual representations (e.g., drawings) to communicate ideas in biology. How learners interpret and organize those numerous diagrams is related to their underlying knowledge about biology and their skills in visual literacy. Furthermore, it is not always obvious how and why learners interpret diagrams in the way they do (especially if their interpretations are unexpected), as it is not possible to "see" inside the minds of learners and directly observe the inner workings of their brains. Hence, tools that allow for the investigation of visual literacy are needed. Here, we present a novel card-sorting task based on visual literacy skills to investigate how learners interpret and think about DNA-based concepts. We quantified differences in performance between groups of varying expertise and in pre- and postcourse settings using percentages of expected card pairings and edit distance to a perfect sort. Overall, we found that biology experts organized the visual representations based on deep conceptual features, while biology learners (novices) more often organized based on surface features, such as color and style. We also found that students performed better on the task after a course in which molecular biology concepts were taught, suggesting the activity is a useful and valid tool for measuring knowledge. We have provided the cards to the community for use as a classroom activity, as an assessment instrument, and/or as a useful research tool to probe student ideas about molecular biology.

Putting the Pieces Together: Student Thinking about Transformations of Energy and Matter

Research on student thinking facilitates the design of instructional materials that build on student ideas. The pieces framework views student knowledge as consisting of independent pieces that students assemble in fluctuating ways based on the context at hand. This perspective affords important insights about the reasons students think the way they do. We used the pieces framework to investigate student thinking about the concept transformations of energy and matter with a specific focus on metabolism. We conducted think-aloud interviews with undergraduate introductory biology and biochemistry students as they solved a metabolism problem set. Through knowledge analysis, we identified two categories of knowledge elements cued during metabolism problem solving: 1) those about the visual representation of negative feedback inhibition; and 2) those pertaining to student focus on different metabolic compounds in a pathway. Through resource graph analysis, we found that participants tend to use knowledge elements independently and in a fluctuating way. Participants generally showed low representational competence. We recommend further research using the pieces perspective, including research on improving representational competence. We suggest that metabolism instructors teach metabolism as a concept, not a collection of example pathways, and explicitly instruct students about the meaning of visual representations associated with metabolism.

The DNA Landscape: Development and Application of a New Framework for Visual Communication about DNA

Learning molecular biology involves using visual representations to communicate ideas about largely unobservable biological processes and molecules. Genes and gene expression cannot be directly visualized, but students are expected to learn and understand these and related concepts. Theoretically, textbook illustrations should help learners master such concepts, but how are genes and other DNA-linked concepts illustrated for learners? We examined all DNA-related images found in 12 undergraduate biology textbooks to better understand what biology students encounter when learning concepts related to DNA. Our analysis revealed a wide array of DNA images that were used to design a new visual framework, the DNA Landscape, which we applied to more than 2000 images from common introductory and advanced biology textbooks. All DNA illustrations could be placed on the landscape framework, but certain positions were more common than others. We mapped figures about "gene expression" and "meiosis" onto the landscape framework to explore how these challenging topics are illustrated for learners, aligning these outcomes with the research literature to showcase how the overuse of certain representations may hinder, instead of help, learning. The DNA Landscape is a tool to promote research on visual literacy and to guide new learning activities for molecular biology.

Strategies for the Production of Molecular Animations

Molecular animations play an increasing role in scientific visualisation and science communication. They engage viewers through non-fictional, documentary type storytelling and aim at advancing the audience. Every scene of a molecular animation is to be designed to secure clarity. To achieve this, knowledge on design principles from various design fields is essential. The relevant principles help to draw attention, guide the eye, establish relationships, convey dynamics and/or trigger a reaction. The tools of general graphic design are used to compose a signature frame, those of cinematic storytelling and user interface design to choreograph the relative movement of characters and cameras. Clarity in a scientific visualisation is reached by simplification and abstraction where the choice of the adequate representation is of great importance. A large set of illustration styles is available to chose the appropriate detail level but they are constrained by the availability of experimental data. For a high-quality molecular animation, data from different sources can be integrated, even filling the structural gaps to show a complete picture of the native biological situation. For maintaining scientific authenticity it is good practice to mark use of artistic licence which ensures transparency and accountability. The design of motion requires knowledge from molecule kinetics and kinematics. With biological macromolecules, four types of motion are most relevant: thermal motion, small and large conformational changes and Brownian motion. The principles of dynamic realism should be respected as well as the circumstances given in the crowded cellular environment. Ultimately, consistent complexity is proposed as overarching principle for the production of molecular animations and should be achieved between communication objective and abstraction/simplification, audience expertise and scientific complexity, experiment and representation, characters and environment as well as structure and motion representation.

Implementing Fabrication as a Pedagogical Tool in Vertebrate Anatomy Courses: Motivation, Inclusion, and Lessons

Increasing course structure by incorporating active learning and multimodal pedagogical strategies benefits all learners. Students of vertebrate anatomy can especially benefit from practicing fabrication, or "making", incorporating skills such as 3D digital modeling, 3D printing, and using familiar low-tech materials to construct informed replicas of animal anatomy. Student perceptions of active learning projects are shaped by motivation theories such as the expectancy-value theory and self-directed learning, both of which are briefly reviewed here. This paper offers inspiration and resources to instructors for establishing a makerspace in an anatomy lab and leveraging community partners to stimulate students to construct their own versions of nature's designs. Learning science in informal environments and specifically in makerspaces has been shown to promote equity and increase motivation to study science. Examples here emphasize accessibility for diverse learners, including strategies for instructors to ensure ease of student access to 3D technology. Scaffolding formative assessments builds student confidence and expertise, further closing opportunity gaps. Two specific cases are detailed where fabrication and the use of 3D digital models are used to augment student learning of vertebrate anatomy at a small liberal arts college. In a semester-long research project in an introductory biomechanics course, students investigate, write about, and build models of animal anatomy of their choice. They use simple materials, crafting supplies, household tools, and/or 3D printing to demonstrate structures of interest, enhancing understanding of the physical principles of animal form and function. Given increased availability of CT data online, students can download, analyze, and 3D print skeletal models of both common and endangered animals. Comparative anatomy students reported that they had increased motivation to study intricate skeletal anatomy simply by manipulating bones in a 3D software assignment. Students in both classes reported enjoying the use of fabrication in learning vertebrate anatomy and this may establish a pattern of lifelong learning.

Design and Implementation of a Tool to Assess Students' Understanding of Metabolic Pathways Dynamics and Regulation

Metabolic systems form the very foundation of life and as such are broadly taught in the molecular life sciences. Here, we describe the biochemistry educator community-based development and use of an assessment instrument designed to evaluate students' ideas about metabolic pathway dynamics and regulation in undergraduate biochemistry courses. Analysis of student responses showed that most students were able to interpret visual representations in an unfamiliar metabolic pathway and that many could make basic predictions about how the system would be expected to respond to changes. However, fewer students generated nuanced responses that accounted for both microscopic changes at the protein level and macroscopic changes in pathway product outputs. These findings identify some of the challenges of meaningfully assessing students' understanding of metabolic pathways and could inform how instructors think about teaching and assessing metabolism in undergraduate biochemistry and beyond. The results also suggest future avenues for biochemistry education research.

Data-rich textbook figures promote core competencies: Comparison of two textbooks

Many molecular biology and biochemistry instructors have altered their classroom behavior in favor of evidence-based, active learning instructional strategies. Overwhelming evidence confirms that lecture-only classrooms are detrimental to student learning outcomes, but we know less about the impact textbooks have on students outside the classroom. Two influential projects, the AP Biology redesign and Vision and Change, called for extensive restructuring of course content and hoped that textbooks would be restructured accordingly. This study evaluated all figures and tables from two introductory biology textbooks to quantify how well they implement recommendations from Vision and Change and AP Biology redesign. We documented significant differences among figures and tables when looking for experimental data, questions for students to answer, and quantitative interpretation. Using think-aloud interviews, we interrogated whether students engage differently with figures from the two textbooks. When figures provided take-home messages, students relied on written text rather than analyzing the graphical information for their understanding. Students frequently employed words from summaries within the figures to construct "inflated explanations" that mimicked comprehension.

Kinesthetic and visual scaffolding for understanding oxygen delivery and reading hemoglobin oxygen curves

I describe a kinesthetic activity about oxygen handling by hemoglobin with two specific goals: 1) to help students gain a better understanding of how hemoglobin properties affect oxygen delivery and 2) to improve the ability of the students to actually read the hemoglobin oxygen-binding curve. The activity makes understanding oxygen delivery more intuitive, provides a kinesthetic analog to delivery of oxygen, and provides data to plot for the hemoglobin-oxygen curve.

Game-based activities targeting visual literacy skills to increase understanding of biomolecule structure and function concepts in undergraduate biochemistry

Introductory biochemistry courses are often challenging for students because they require the integration of chemistry, biology, physics, math, and physiology knowledge and frameworks to understand and apply a large body of knowledge. This can be complicated by students' persistent misconceptions of fundamental concepts and lack of fluency with the extensive visual and symbolic literacy used in biochemistry. Card sorting tasks and game-based activities have been used to reveal insights into how students are assimilating, organizing, and structuring disciplinary knowledge, and how they are progressing along a continuum from disciplinary novice to expert. In this study, game-based activities and card sorting tasks were used to promote and evaluate students' understanding of fundamental structure-function relationships in biochemistry. Our results suggest that while many markers of expertise increased for both the control and intervention groups over the course of the semester, students involved in the intervention activities tended to move further towards expert-like sorting. This indicates that intentional visual literacy game-based activities have the ability to build underdeveloped skills in undergraduate students.

Scaffolding Activities Increase Performance and Lower Frustration with Genotype-to-Evolution Models in Molecular Genetics

Conceptual modeling was introduced in molecular genetics so students could integrate topics and apply molecular reasoning and mechanisms to phenotype, inheritance, and population dynamics. Structure Mechanism Relationship Function (SMRF) models were introduced. SMRF models focus on the function of a specified system using structures/nouns in boxes and processes/relationships/verbs on arrows. This SMRF model formatting enables discussion, feedback, and assessment.  Scaffolding activities were introduced to provide students with support for modeling and were intended to decrease or prevent students’ frustration, intimidation, and discouragement during the learning process.  Comparing a semester without scaffolding activities to semesters with scaffolding results indicate the following benefits: 1) better performance on modeling on first exam, 2) less student resistance towards modeling, and 3) better use of class time.  This article has the training activity for SMRF modeling, scaffolding activities, a grading rubric, and selection of adaptable question prompts to make conceptual modeling more accessible to instructors.

The Biochemical Literacy Framework: Inviting pedagogical innovation in higher education

When developing meaningful curricula, institutions must engage with the desired disciplinary attributes of their graduates. Successfully employed in several areas, including psychology and chemistry, disciplinary literacies provide structure for the development of core competencies-pursuing progressive education. To this end, we have sought to develop a comprehensive blueprint of a graduate biochemist, providing detailed insight into the development of skills in the context of disciplinary knowledge. The Biochemical Literacy Framework (BCLF) aspires to encourage innovative course design in both the biochemical field and beyond through stimulating discussion among individuals developing undergraduate biochemistry degree courses based on pedagogical best practice. Here, we examine the concept of biochemical literacy aiming to start answering the question: What must individuals do and know to approach and transform ideas in the context of the biochemical sciences? The BCLF began with the guidance published by relevant learned societies - including the Royal Society of Biology, the Biochemical Society, the American Society for Biochemistry and Molecular Biology and the Quality Assurance Agency, before considering relevant pedagogical literature. We propose that biochemical literacy is comprised of seven key skills: critical thinking, self-management, communication, information literacy, visual literacy, practical skills and content knowledge. Together, these form a dynamic, highly interconnected and interrelated meta-literacy supporting the use of evidence-based, robust learning techniques. The BCLF is intended to form the foundation for discussion between colleagues, in addition to forming the groundwork for both pragmatic and exploratory future studies into facilitating and further defining biochemical literacy.

Diagram comprehension ability of college students in an introductory biology course

College biology courses commonly use diagrams to convey information. These visual representations are embedded in course materials with the expectation that students can comprehend and learn from them. Educational research, however, suggests that many students have difficulty understanding diagrams and the conventions (e.g., labels, arrows) they contain. The present study evaluates biology students' ability to comprehend scientific diagrams and the diagram characteristics that affect this comprehension. Participants were students in a physiology course who completed a multiple-choice test of diagram comprehension ability (DCA) (Cromley JG, Perez TC, Fitzhugh SL, Newcombe NS, Wills TW, Tanaka JC. J Exp Educ 81: 511-537, 2013). We coded the conventions used in each test diagram and used these codes to capture the diagram characteristics of conventions and complexity. Descriptive analyses examine students' ability to understand scientific diagrams and which diagram characteristics cause the most difficulty. We also compared groups with low and high DCA scores to evaluate how students at different levels of comprehension ability are affected by diagram characteristics. Results show relatively poor DCA; the average total test score was only 69.5%. The conventions used in a diagram also affected diagram comprehension, and results show students had the most difficulty comprehending diagrams using a letter or numbering system, where arbitrary letters/numbers were used to signify objects and diagrams using cut-outs that showed cross sections and magnified interior views. Additionally, students' comprehension was higher on diagrams with higher complexity (i.e., more types of conventions used), potentially indicating students are able to take advantage of the supports that different conventions provide. Implications for instruction are identified.

Using expert data to inform the use of research methods and representations to enhance biochemistry instruction and textbook design

Biochemistry textbooks often provide a disconnected, highly mathematical, and decontextualized treatment of thermodynamic and kinetic principles, which renders topics like protein folding difficult to teach. This is concerning given that graduates entering careers, like the pharmaceutical industry, must be able to apply such knowledge and related research methods to solve biochemistry research problems. Thus, it is essential that instructors have strategies to incorporate research methods and representations to help students understand the source of such scientific knowledge. Therefore, the goal of our work is to examine expert practice and use the findings to identify instructional strategies to incorporate more cutting-edge research and authentic ways of knowing into science classrooms and textbooks. Toward this goal, we examined how four scientists explain protein folding and dynamics research, focusing on the interaction of spoken language and representations, including gesture. Our analysis indicates that experts employ multiple representations and research methods to communicate how evidence can be used to understand phenomena. In contrast, textbooks explain what is known but seldom use representations to explain how it is known. Based on our findings, we suggest implications for instruction, including the design of textbooks, as well as potential instructional strategies to incorporate discussion of experimental methods and interpretation of representations during classroom activities. © 2019 International Union of Biochemistry and Molecular Biology, 47(5):513-531, 2019.

Characterizing Students' Ideas about the Effects of a Mutation in a Noncoding Region of DNA

Understanding student ideas in large-enrollment biology courses can be challenging, because easy-to-administer multiple-choice questions frequently do not fully capture the diversity of student ideas. As part of the Automated Analysis of Constructed Responses (AACR) project, we designed a question prompting students to describe the possible effects of a mutation in a noncoding region of DNA. We characterized answers from 1127 students enrolled in eight different large-enrollment introductory biology courses at three different institutions over five semesters and generated an analytic scoring system containing three categories of correct ideas and five categories of incorrect ideas. We iteratively developed a computer model for scoring student answers and tested the model before and after implementing an instructional activity designed to help a new set of students explore this concept. After completing a targeted activity and re-answering the question, students showed improvement from preassessment, with 64% of students in incorrect and 67% of students in partially incorrect (mixed) categories shifting to correct ideas only. This question, computer-scoring model, and instructional activity can now be reliably used by other instructors to better understand and characterize student ideas on the effects of mutations outside a gene-coding region.

Medical Biochemistry Without Rote Memorization: Multi-Institution Implementation and Student Perceptions of a Nationally Standardized Metabolic Map for Learning and Assessment

Despite the growing number of patients worldwide with metabolism-related chronic diseases, medical biochemistry education is commonly perceived as focusing on recall of facts irrelevant for patient care. The authors suggest that this focus on rote memorization of pathways creates excessive cognitive load that may interfere with learners' development of an integrated understanding of metabolic regulation and dysregulation. This cognitive load can be minimized by providing appropriate references during learning and assessment. Biochemistry educators collaborated to develop a medically relevant pathways of human metabolism map (MetMap) that is now being used at many medical schools as a nationally standardized resource during learning and assessments. To assess impact, students from three medical schools were surveyed about its benefits and disadvantages. Responses were obtained from 481 students (84%) and were examined using thematic analysis. Five main themes emerged as perceived benefits of using the MetMap: (1) aids visual and mental organization, (2) promotes deep learning and applied understanding, (3) decreases emphasis on memorization, (4) reduces anxiety on exams, and (5) aids recall. Perceived disadvantages were (1) fear of underpreparation for licensing exams, (2) overwhelming nature of the map, and (3) reduced motivation for and time spent studying. Results affirm that students' perceive use of the MetMap promotes focus on broader metabolic concepts and deep versus surface learning, supporting a shift in cognitive load toward desired goals. Although the long-term impact on learning needs to be further studied, the use of the MetMap represents a step toward open-reference exams that reflect "real-world" practice.

A Method for the Symbolic Representation of Neurons

The field of neuroanatomy has progressed considerably in recent decades, thanks to the emergence of novel methods which provide new insights into the organization of the nervous system. These new methods have produced a wealth of data that needs to be analyzed, shifting the bottleneck from the acquisition to the analysis of data. In other disciplines, such as in many engineering areas, scientists and engineers are dealing with increasingly complex systems, using hierarchical decompositions, graphical models and simplified schematic diagrams for analysis and design processes. This approach makes it possible for users to simultaneously combine global system views and very detailed representations of specific areas of interest, by selecting appropriate representations for each of these views. In this way, users can concentrate on specific details while also maintaining a general system overview - a capability that is essential for understanding structure and function whenever complexity is an issue. Following this approach, this paper focuses on a graphical tool designed to help neuroanatomists to better understand and detect morphological characteristics of neuronal cells. The method presented here, based on a symbolic representation that can be tailored to enhance a particular range of features of a neuron or neuron set, has proven to be useful for highlighting particular geometries that may be hidden due to the complexity of the analysis tasks and the richness of neuronal morphologies. A software tool has been developed to generate graphical representations of neurons from 3D computer-aided reconstruction files.

From Atoms to Cells: Using Mesoscale Landscapes to Construct Visual Narratives

Modeling and visualization of the cellular mesoscale, bridging the nanometer scale of molecules to the micrometer scale of cells, is being studied by an integrative approach. Data from structural biology, proteomics, and microscopy are combined to simulate the molecular structure of living cells. These cellular landscapes are used as research tools for hypothesis generation and testing, and to present visual narratives of the cellular context of molecular biology for dissemination, education, and outreach.

Physical models can provide superior learning opportunities beyond the benefits of active engagements

The essence of molecular biology education lies in understanding of gene expression, with subtopics including the central dogma processes, such as transcription and translation. While these concepts are core to the discipline, they are also notoriously difficult for students to learn, probably because they cannot be directly observed. While nearly all active learning strategies have been shown to improve learning compared with passive lectures, little has been done to compare different types of active learning. We hypothesized that physical models of central dogma processes would be especially helpful for learning, because they provide a resource that students can see, touch, and manipulate while trying to build their knowledge. For students enrolled in an entirely active-learning-based Cell & Molecular Biology course, we examined whether model-based activities were more effective than non-model based activities. To test their understanding at the beginning and end of the semester, we employed the multiple-select Central Dogma Concept Inventory (CDCI). Each student acted as their own control, as all students engaged in all lessons yet some questions related to model-based activities and some related to clicker questions, group problem-solving, and other non-model-based activities. While all students demonstrated learning gains on both types of question, they showed much higher learning gains on model-based questions. Examining their selected answers in detail showed that while higher performing students were prompted to refine their already-good mental models to be even better, lower performing students were able to construct new knowledge that was much more consistent with an expert's understanding. © 2018 The Authors. Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology., 46(5):435-444, 2018.

Student difficulties during structure-function problem solving

Protein structure-function is a key concept in biochemistry. We used the perspective of domain-specific problem-solving to investigate students' solutions to a well-defined protein structure-function problem. We conducted think-aloud interviews with 13 undergraduate students and performed qualitative content analysis to examine the differences in the domain-general and domain-specific knowledge among correct and incorrect solutions. Our work revealed that students used domain-general and domain-specific knowledge in their problem solving. We also identified difficulties for students with the amino acid backbone, amino acid categorization, and causal mechanisms of noncovalent interactions. Using the identified difficulties, we make recommendations for the design of instructional materials targeted to improve protein structure-function problem solving in the biochemistry classroom. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):453-463, 2018.

Molecular Illustration in Research and Education: Past, Present, and Future

Two-dimensional illustration is used extensively to study and disseminate the results of structural molecular biology. Molecular graphics methods have been and continue to be developed to address the growing needs of the structural biology community, and there are currently many effective, turn-key methods for displaying and exploring molecular structure. Building on decades of experience in design, best-practice resources are available to guide creation of illustrations that are effective for research and education communities.

Visual Literacy in Bloom: Using Bloom's Taxonomy to Support Visual Learning Skills

Vision and Change identifies science communication as one of the core competencies in undergraduate biology. Visual representations are an integral part of science communication, allowing ideas to be shared among and between scientists and the public. As such, development of scientific visual literacy should be a desired outcome of undergraduate instruction. We developed the Visualization Blooming Tool (VBT), an adaptation of Bloom's taxonomy specifically focused on visual representations, to aid instructors in designing instruction and assessments to target scientific visual literacy in undergraduate instruction. In this article, we identify the need for the VBT, describe its development, and provide concrete examples of its application to a curriculum redesign effort in undergraduate biochemistry.

Arrows in Biology: Lack of Clarity and Consistency Points to Confusion for Learners

In this article, we begin to unpack the phenomenon of representational competence by exploring how arrow symbols are used in introductory biology textbook figures. Out of 1214 figures in an introductory biology textbook, 632 (52%) of them contained arrows that were used to represent many different concepts or processes. Analysis of these figures revealed little correlation between arrow style and meaning. A more focused study of 86 figures containing 230 arrows from a second textbook showed the same pattern of inconsistency. Interviews with undergraduates confirmed that arrows in selected textbook figures were confusing and did not readily convey the information intended by the authors. We also present findings from an online survey in which subjects were asked to infer meaning of different styles of arrows in the absence of context. Few arrow styles had intrinsic meaning to participants, and illustrators did not always use those arrows for the meanings expected by students. Thus, certain styles of arrows triggered confusion and/or incorrect conceptual ideas. We argue that 1) illustrators need to be more clear and consistent when using arrow symbols, 2) instructors need to be cognizant of the level of clarity of representations used during instruction, and 3) instructors should help students learn how to interpret representations containing arrows.