Development of the Central Dogma Concept Inventory (CDCI) Assessment Tool

A genomics learning framework for undergraduates

Genomics is an increasingly important part of biology research. However, educating undergraduates in genomics is not yet a standard part of life sciences curricula. We believe this is, in part, due to a lack of standard concepts for the teaching of genomics. To address this deficit, the members of the Genomics Education Alliance created a set of genomics concepts that was then further refined by input from a community of undergraduate educators who engage in genomics instruction. The final genomics concepts list was compared to existing learning frameworks, including the Vision and Change initiative (V&C), as well as ones for genetics, biochemistry and molecular biology, and bioinformatics. Our results demonstrate that the new genomics framework fills a niche not addressed by previous inventories. This new framework should be useful to educators seeking to design stand-alone courses in genomics as well as those seeking to incorporate genomics into existing coursework. Future work will involve designing curriculum and assessments to go along with this genomics learning framework.

Design principles for molecular animation

Molecular visualization is a powerful way to represent the complex structure of molecules and their higher order assemblies, as well as the dynamics of their interactions. Although conventions for depicting static molecular structures and complexes are now well established and guide the viewer's attention to specific aspects of structure and function, little attention and design classification has been devoted to how molecular motion is depicted. As we continue to probe and discover how molecules move - including their internal flexibility, conformational changes and dynamic associations with binding partners and environments - we are faced with difficult design challenges that are relevant to molecular visualizations both for the scientific community and students of cell and molecular biology. To facilitate these design decisions, we have identified twelve molecular animation design principles that are important to consider when creating molecular animations. Many of these principles pertain to misconceptions that students have primarily regarding the agency of molecules, while others are derived from visual treatments frequently observed in molecular animations that may promote misconceptions. For each principle, we have created a pair of molecular animations that exemplify the principle by depicting the same content in the presence and absence of that design approach. Although not intended to be prescriptive, we hope this set of design principles can be used by the scientific, education, and scientific visualization communities to facilitate and improve the pedagogical effectiveness of molecular animation.

Changing colors and understanding: the use of mutant chromogenic protein and informational suppressor strains of Escherichia coli to explore the central dogma of molecular biology

The central dogma of molecular biology is a key concept for undergraduate students in the life sciences as it describes the flow of information in living systems from gene-to-gene product. However, despite often being covered in many introductory life science courses, students may still have misconceptions surrounding the central dogma even as they move on to advanced courses. Active learning strategies such as laboratory activities can be useful in addressing such misconceptions. In the laboratory exercise presented here, senior undergraduate students explore the intricacies of nonsense suppressor mutations to challenge their understanding of the central dogma. The students introduce a plasmid carrying a nonfunctional chromogenic protein gene due to a nonsense mutation in a codon encoding the chromophore to various nonsense suppressor strains of Escherichia coli. Students then observe distinct chromogenic phenotypes, depending on the suppressor strain. Students showed a moderate increase in understanding of the central dogma. While the central dogma remains a challenging concept, active learning strategies like the one presented here can help reduce conceptual errors.

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.

Teaching meiosis with the DNA triangle framework: A classroom activity that changes how students think about chromosomes

Many biology students struggle to learn about the process of meiosis and have particular difficulty understanding the molecular basis of crossing over and the importance of homologous pairing for proper segregation. To help students overcome these challenges, we designed an activity that uses a newly developed Chromosome Connections Kit® from 3-D Molecular Designs to allow learners to explore meiosis at the molecular level. We took a backwards design approach in constructing an effective classroom activity. We developed evidence-based learning objectives and designed a crossing over activity that targets students' misconceptions and key concepts about meiosis. Assessment questions were designed based on the learning objectives and common student misconceptions. The activity consists of three parts: an interactive introductory video, a model-based activity, and reflection questions. The activity was first beta-tested with a small number of students and revised based on feedback. The revised activity was deployed in a mid-level Cell and Molecular Biology course. Analysis of pre-/post-assessment data from students who completed the activity (n = 83) showed strong learning gains on concepts related to ploidy, homology, segregation, and the mechanism and purpose of crossing over. Additionally, students who participated in the activity outperformed nonparticipants on a Genetics assessment about meiosis the following semester.

Punnett Squares or Protein Production? The Expert-Novice Divide for Conceptions of Genes and Gene Expression

Concepts of molecular biology and genetics are difficult for many biology undergraduate students to master yet are crucial for deep understanding of how life works. By asking students to draw their ideas, we attempted to uncover the mental models about genes and gene expression held by biology students (n = 23) and experts (n = 18) using semistructured interviews. A large divide was identified between novice and expert conceptions. While experts typically drew box-and-line representations and thought about genes as regions of DNA that were used to encode products, students typically drew whole chromosomes rather than focusing on gene structure and conflated gene expression with simple phenotypic outcomes. Experts universally described gene expression as a set of molecular processes involving transcription and translation, whereas students often associated gene expression with Punnett squares and phenotypic outcomes. Follow-up survey data containing a ranking question confirmed students' alignment of their mental models with the images uncovered during interviews (n = 156 undergraduate biology students) and indicated that Advanced students demonstrate a shift toward expert-like thinking. An analysis of 14 commonly used biology textbooks did not show any relationship between Punnett squares and discussions of gene expression, so it is doubtful students' ideas originate directly from textbook reading assignments. Our findings add to the literature about mechanistic reasoning abilities of learners and provide new insights into how biology students think about genes and gene expression.

Another look at the core concepts of physiology: revisions and resources

In 2011, we published a description of 15 core concepts of physiology, and in 2017 we described how core concepts could be used to teach physiology. On the basis of publications and conference presentations, it is clear that the core concepts, conceptual frameworks, and the homeostasis concept inventory have been used by faculty in many ways to improve and assess student learning and align instruction and programs. A growing number of colleagues focus their teaching on physiology core concepts, and some core concepts have been used as explicit themes or organizing principles in physiology or anatomy and physiology textbooks. The core concepts published in 2011 were derived from inputs from a diverse group of physiology instructors and articulated what this group of instructors expressed a decade ago. On the basis of current feedback from the physiology teaching community as a consequence of the use of core concepts in teaching and learning, we have revisited these concepts and made revisions to address issues that have emerged. In this article, we offer revised definitions and explanations of the core concepts, propose an additional core concept ("physical properties of matter" which combines two previous concepts), and describe three broad categories for the revised core concepts. Finally, we catalog published resources for each of the core concepts that provide instructors tools to focus facilitation of student learning on goals (learning outcomes), activities and assessments to enable students to develop and apply their understanding of the core concepts of physiology.

An Online Interactive Video Vignette that Helps Students Learn Key Concepts of Fermentation and Respiration

Topics related to energy transformation and metabolism are important parts of an undergraduate biology curriculum, but these are also topics that students traditionally struggle with. To address this, we have created a short online Interactive Video Vignette (IVV) called To Ferment or Not to Ferment: That is the Question. This IVV is designed to help students learn important ideas related to cellular respiration and metabolism. Students in various courses across four institutions were assigned the IVV as an out-of-class preinstruction homework assignment. To test the effectiveness of this IVV on student learning, we collected and analyzed data from questions embedded in the IVV, open response reflection questions, and pre- and postassessments from IVV watchers and nonwatchers. Our analysis revealed that students who completed the IVV activity interacted productively with this online tool and made significant learning gains on important topics related to cellular respiration and metabolism. This IVV is freely available via https://www.rit.edu/cos/interactive/MINT for instructors to adopt for class use.

The Genetic Code Kit: An Open-Source Cell-Free Platform for Biochemical and Biotechnology Education

Teaching the processes of transcription and translation is challenging due to the intangibility of these concepts and a lack of instructional, laboratory-based, active learning modules. Harnessing the genetic code in vitro with cell-free protein synthesis (CFPS) provides an open platform that allows for the direct manipulation of reaction conditions and biological machinery to enable inquiry-based learning. Here, we report our efforts to transform the research-based CFPS biotechnology into a hands-on module called the “Genetic Code Kit” for implementation into teaching laboratories. The Genetic Code Kit includes all reagents necessary for CFPS, as well as a laboratory manual, student worksheet, and augmented reality activity. This module allows students to actively explore transcription and translation while gaining exposure to an emerging research technology. In our testing of this module, undergraduate students who used the Genetic Code Kit in a teaching laboratory showed significant score increases on transcription and translation questions in a post-lab questionnaire compared with students who did not participate in the activity. Students also demonstrated an increase in self-reported confidence in laboratory methods and comfort with CFPS, indicating that this module helps prepare students for careers in laboratory research. Importantly, the Genetic Code Kit can accommodate a variety of learning objectives beyond transcription and translation and enables hypothesis-driven science. This opens the possibility of developing Course-Based Undergraduate Research Experiences (CUREs) based on the Genetic Code Kit, as well as supporting next-generation science standards in 8–12th grade science courses.

Molecular Concepts Adaptive Assessment (MCAA) Characterizes Undergraduate Misconceptions about Molecular Emergence

This paper discusses the results of two experiments assessing undergraduate students' beliefs about the random nature of molecular environments. Experiment 1 involved the implementation of a pilot adaptive assessment ( n = 773) and focus group discussions with undergraduate students enrolled in first- through third-year biology courses; experiment 2 involved the distribution of the redesigned adaptive assessment to the same population of students in three consecutive years ( n = 1170). The overarching goal of the study was to provide a detailed characterization of learners' perceptions and beliefs regarding molecular agency, environments, and diffusion and whether or not those beliefs change over time. Our results indicated that advanced learners hold as many misconceptions as novice learners and that confidence in their misconceptions increases as they advance through their undergraduate education. In particular, students' understanding of random/Brownian motion is complex and highly contextual, suggesting that the way in which we teach biology does not adequately remediate students' preconceived notions of molecular agency and may actually reinforce them.

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.

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.

A focus on polarity: Investigating the role of orientation cues in mediating student performance on mRNA synthesis tasks in an introductory cell and molecular biology course

The central dogma has served as a foundational model for information flow, exchange, and storage in the biological sciences for several decades. Despite its continued importance, however, recent research suggests that novices in the domain possess several misconceptions regarding the aforementioned processes, including those pertaining specifically to the formation of messenger ribonucleic acid (mRNA) transcripts. In the present study, we sought to expand upon these observations through exploration of the influence of orientation cues on students' aptitude at synthesizing mRNAs from provided deoxyribonucleic acid (DNA) template strands. Data indicated that participants (n = 45) were proficient at solving tasks of this nature when the DNA template strand and the mRNA molecule were represented in an antiparallel orientation. In contrast, participants' performance decreased significantly on items in which the mRNA was depicted in a parallel orientation relative to the DNA template strand. Furthermore, participants' Grade Point Average, self-reported confidence in understanding the transcriptional process, and spatial ability were found to mediate their performance on the mRNA synthesis tasks. Collectively, these data reaffirm the need for future research and pedagogical interventions designed to enhance students' comprehension of the central dogma in a manner that makes transparent its relevance to real-world scientific phenomena. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):501-508, 2017.

Development, Validation, and Application of the Microbiology Concept Inventory

If we are to teach effectively, tools are needed to measure student learning. A widely used method for quickly measuring student understanding of core concepts in a discipline is the concept inventory (CI). Using the American Society for Microbiology Curriculum Guidelines (ASMCG) for microbiology, faculty from 11 academic institutions created and validated a new microbiology concept inventory (MCI). The MCI was developed in three phases. In phase one, learning outcomes and fundamental statements from the ASMCG were used to create T/F questions coupled with open responses. In phase two, the 743 responses to MCI 1.0 were examined to find the most common misconceptions, which were used to create distractors for multiple-choice questions. MCI 2.0 was then administered to 1,043 students. The responses of these students were used to create MCI 3.0, a 23-question CI that measures students' understanding of all 27 fundamental statements. MCI 3.0 was found to be reliable, with a Cronbach's alpha score of 0.705 and Ferguson's delta of 0.97. Test item analysis demonstrated good validity and discriminatory power as judged by item difficulty, item discrimination, and point-biserial correlation coefficient. Comparison of pre- and posttest scores showed that microbiology students at 10 institutions showed an increase in understanding of concepts after instruction, except for questions probing metabolism (average normalized learning gain was 0.15). The MCI will enable quantitative analysis of student learning gains in understanding microbiology, help to identify misconceptions, and point toward areas where efforts should be made to develop teaching approaches to overcome them.

Teaching Genetics: Past, Present, and Future

Genetics teaching at the undergraduate level has changed in many ways over the past century. Compared to those of 100 years ago, contemporary genetics courses are broader in content and are taught increasingly differently, using instructional techniques based on educational research and constructed around the principles of active learning and backward design. Future courses can benefit from wider adoption of these approaches, more emphasis on the practice of genetics as a science, and new methods of assessing student learning.

Diagnostic of students' misconceptions using the Biological Concepts Instrument (BCI): A method for conducting an educational needs assessment

Concept inventories, constructed based on an analysis of students’ thinking and their explanations of scientific situations, serve as diagnostics for identifying misconceptions and logical inconsistencies and provide data that can help direct curricular reforms. In the current project, we distributed the Biological Concepts Instrument (BCI) to 17-18-year-old students attending the highest track of the Swiss school system (Gymnasium). Students’ performances on many questions related to evolution, genetics, molecular properties and functions were diverse. Important common misunderstandings were identified in the areas of evolutionary processes, molecular properties and an appreciation of stochastic processes in biological systems. Our observations provide further evidence that the BCI is efficient in identifying specific areas where targeted instruction is required. Based on these observations we have initiated changes at several levels to reconsider how biological systems are presented to university biology studies with the goal of improving student’s foundational understanding.

Investigating Novice and Expert Conceptions of Genetically Modified Organisms

The aspiration of biology education is to give students tools to apply knowledge learned in the classroom to everyday life. Genetic modification is a real-world biological concept that relies on an in-depth understanding of the molecular behavior of DNA and proteins. This study investigated undergraduate biology students' conceptions of genetically modified organisms (GMOs) when probed with real-world, molecular and cellular, and essentialist cues, and how those conceptions compared across biology expertise. We developed a novel written assessment tool and administered it to 120 non-biology majors, 154 entering biology majors, 120 advanced biology majors (ABM), and nine biology faculty. Results indicated that undergraduate biology majors rarely included molecular and cellular rationales in their initial explanations of GMOs. Despite ABM demonstrating that they have much of the biology knowledge necessary to understand genetic modification, they did not appear to apply this knowledge to explaining GMOs. Further, this study showed that all undergraduate student populations exhibited evidence of essentialist thinking while explaining GMOs, regardless of their level of biology training. Finally, our results suggest an association between scientifically accurate ideas and the application of molecular and cellular rationales, as well as an association between misconceptions and essentialist rationales.

The DNA Triangle and Its Application to Learning Meiosis

Although instruction on meiosis is repeated many times during the undergraduate curriculum, many students show poor comprehension even as upper-level biology majors. We propose that the difficulty lies in the complexity of understanding DNA, which we explain through a new model, the DNA triangle The DNA triangle integrates three distinct scales at which one can think about DNA: chromosomal, molecular, and informational Through analysis of interview and survey data from biology faculty and students through the lens of the DNA triangle, we illustrate important differences in how novices and experts are able to explain the concepts of ploidy, homology, and mechanism of homologous pairing Similarly, analysis of passages from 16 different biology textbooks shows a large divide between introductory and advanced material, with introductory books omitting explanations of meiosis-linked concepts at the molecular level of DNA. Finally, backed by textbook findings and feedback from biology experts, we show that the DNA triangle can be applied to teaching and learning meiosis. By applying the DNA triangle to topics on meiosis we present a new framework for educators and researchers that ties concepts of ploidy, homology, and mechanism of homologous pairing to knowledge about DNA on the chromosomal, molecular, and informational levels.

Integrating Concepts in Biology Textbook Increases Learning: Assessment Triangulation Using Concept Inventory, Card Sorting, and MCAT Instruments, Followed by Longitudinal Tracking

The purpose of this study was to examine the educational impact of an intervention, the inquiry-focused textbook Integrating Concepts in Biology (ICB), when used in a yearlong introductory biology course sequence. Student learning was evaluated using three published instruments: 1) The Biology Concept Inventory probed depth of student mastery of fundamental concepts in organismal and cellular topics when confronting misconceptions as distractors. ICB students had higher gains in all six topic categories (+43% vs. peers overall, p < 0.01). 2) The Biology Card Sorting Task assessed whether students organized biological ideas more superficially, as novices do, or based on deeper concepts, like experts. The frequency with which ICB students connected deep-concept pairs, or triplets, was similar to peers; but deep understanding of structure/function was much higher (for pairs: 77% vs. 25%, p < 0.01). 3) A content-focused Medical College Admission Test (MCAT) posttest compared ICB student content knowledge with that of peers from 15 prior years. Historically, MCAT performance for each semester ranged from 53% to 64%; the ICB cohort scored 62%, in the top quintile. Longitudinal tracking in five upper-level science courses the following year found ICB students outperformed peers in physiology (85% vs. 80%, p < 0.01).

Development and Validation of the Homeostasis Concept Inventory

We present the Homeostasis Concept Inventory (HCI), a 20-item multiple-choice instrument that assesses how well undergraduates understand this critical physiological concept. We used an iterative process to develop a set of questions based on elements in the Homeostasis Concept Framework. This process involved faculty experts and undergraduate students from associate's colleges, primarily undergraduate institutions, regional and research-intensive universities, and professional schools. Statistical results provided strong evidence for the validity and reliability of the HCI. We found that graduate students performed better than undergraduates, biology majors performed better than nonmajors, and students performed better after receiving instruction about homeostasis. We used differential item analysis to assess whether students from different genders, races/ethnicities, and English language status performed differently on individual items of the HCI. We found no evidence of differential item functioning, suggesting that the items do not incorporate cultural or gender biases that would impact students' performance on the test. Instructors can use the HCI to guide their teaching and student learning of homeostasis, a core concept of physiology.

How Question Types Reveal Student Thinking: An Experimental Comparison of Multiple-True-False and Free-Response Formats

Assessments represent an important component of undergraduate courses because they affect how students interact with course content and gauge student achievement of course objectives. To make decisions on assessment design, instructors must understand the affordances and limitations of available question formats. Here, we use a crossover experimental design to identify differences in how multiple-true-false (MTF) and free-response (FR) exam questions reveal student thinking regarding specific conceptions. We report that correct response rates correlate across the two formats but that a higher percentage of students provide correct responses for MTF questions. We find that MTF questions reveal a high prevalence of students with mixed (correct and incorrect) conceptions, while FR questions reveal a high prevalence of students with partial (correct and unclear) conceptions. These results suggest that MTF question prompts can direct students to address specific conceptions but obscure nuances in student thinking and may overestimate the frequency of particular conceptions. Conversely, FR questions provide a more authentic portrait of student thinking but may face limitations in their ability to diagnose specific, particularly incorrect, conceptions. We further discuss an intrinsic tension between question structure and diagnostic capacity and how instructors might use multiple formats or hybrid formats to overcome these obstacles.

Using the Biology Card Sorting Task to Measure Changes in Conceptual Expertise during Postsecondary Biology Education

While there have been concerted efforts to reform undergraduate biology toward teaching students to organize their conceptual knowledge like experts, there are few tools that attempt to measure this. We previously developed the Biology Card Sorting Task (BCST), designed to probe how individuals organize their conceptual biological knowledge. Previous results showed the BCST could differentiate between different populations, namely non-biology majors (NBM) and biology faculty (BF). In this study, we administered the BCST to three additional populations, using a cross-sectional design: entering biology majors (EBM), advanced biology majors (ABM), and biology graduate students (BGS). Intriguingly, ABM did not initially sort like experts any more frequently than EBM. However, once the deep-feature framework was revealed, ABM were able to sort like experts more readily than did EBM. These results are consistent with the conclusion that biology education enables advanced biology students to use an expert-like conceptual framework. However, these results are also consistent with a process of "selection," wherein students who persist in the major may have already had an expert-like conceptual framework to begin with. These results demonstrate the utility of the BCST in measuring differences between groups of students over the course of their undergraduate education.