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

Promoting student interest in plant biology through an inquiry-based module exploring plant circadian rhythm, gene expression, and defense against insects

We present a weeklong curricular module for high school biology students that promotes knowledge of phytohormones, the circadian clock, and the Central Dogma. The module, which relies on easily accessible items and requires minimal space, integrates a hands-on experiment that guides students through replicating research examining circadian entrainment in postharvest cabbage from groceries. This work found that plants have cyclical, circadian expression of genes that produce phytohormones, and that such cyclical expression influences herbivory by caterpillars. Such cyclical patterns were found in plants both in situ and in postharvest cabbage. This work thus provides an ideal platform to shape student conceptions of circadian rhythms, gene expression, and plant herbivory by having students use light timers to entrain postharvest cabbage to alternating light and dark cycles and then measuring herbivory in these plants. The results should replicate previous work and demonstrate less herbivory when both plant and caterpillar are entrained to the same light and dark cycles since the expression of phytohormones involved in plant defense will be greatest when caterpillars are active. The module then concludes with a discussion of gene regulation and how this influences phytohormones. This module was field tested at four public schools, reaching over 600 students, and we present data demonstrating that the module led to learning gains and likely increases in interest in plant biology and self-efficacy.

Missed connections: Exploring features of undergraduate biology students' knowledge networks relating gene regulation, cell-cell communication, and phenotypic expression

Explaining biological phenomena requires understanding how different processes function and describing interactions between components at various levels of organization over time and space in biological systems. This is a desired competency yet is a complicated and often challenging task for undergraduate biology students. Therefore, we need a better understanding of their integrated knowledge regarding important biological concepts. Informed by the theory of knowledge integration and mechanistic reasoning, in this qualitative case study, we elicited and characterized knowledge networks of nine undergraduate biology students. We investigated students' conceptions of and the various ways they connect three fundamental subsystems in biology: 1) gene regulation, 2) cell-cell communication, and 3) phenotypic expression. We found that only half of the conceptual questions regarding the three subsystems were answered correctly by the majority of students. Knowledge networks tended to be linear and unidirectional, with little variation in the types of relationships displayed. Students did not spontaneously express mechanistic connections, mainly described undefined, cellular, and macromolecular levels of organization, and mainly discussed unspecified and intracellular localizations. These results emphasize the need to support students' understanding of fundamental concepts, and promoting knowledge integration in the classroom could assist students' ability to understand biological systems.

Here Is the Biology, Now What is the Mechanism? Investigating Biology Undergraduates' Mechanistic Reasoning within the Context of Biofilm Development

Understanding molecular processes and coordinating the various activities across levels of organization in biological systems is a complicated task, yet many curricular guidelines indicate that undergraduate students should master it. Employing mechanistic reasoning can facilitate describing and investigating biological phenomena. Biofilms are an important system in microbiology and biology education. However, few empirical studies have been conducted on student learning of biofilms or how students utilize mechanistic reasoning related to systems thinking to explain biofilm formation. Using mechanistic reasoning and the theory of knowledge integration as conceptual and analytical frameworks, we examined the features of 9 undergraduate biology students' mechanistic models of a specific transition point in biofilm development. From these data, we constructed a model of knowledge integration in the context of biofilms, which categorizes students' knowledge based on features of their descriptions (e.g., entities, correct connections, and the nature of connections). We found that 4 of 9 students produced a fragmented model, 4 of 9 students produced a transitional model, and 1 student produced a connected model. Overall, students often did not discuss cell-cell communication mechanics in their mechanistic models and rarely included the role of gene regulation. Most connections were considered nonnormative and lacked important entities, leading to an abundance of unspecified causal connections. We recommend increasing instructional support of mechanistic reasoning within systems (e.g., identifying entities across levels of organization and their relevant activities) and creating opportunities for students to grapple with their understanding of various biological concepts and to explore how processes interact and connect in a complex system.

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.

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.

CCR5 and Biological Complexity: The Need for Data Integration and Educational Materials to Address Genetic/Biological Reductionism at the Interface of Ethical, Legal, and Social Implications

In the age of genomics, public understanding of complex scientific knowledge is critical. To combat reductionistic views, it is necessary to generate and organize educational material and data that keep pace with advances in genomics. The view that CCR5 is solely the receptor for HIV gave rise to demand to remove the gene in patients to create host HIV resistance, underestimating the broader roles and complex genetic inheritance of CCR5. A program aimed at providing research projects to undergraduates, known as CODE, has been expanded to build educational material for genes such as CCR5 in a rapid approach, exposing students and trainees to large bioinformatics databases and previous experiments for broader data to challenge commitment to biological reductionism. Our students organize expression databases, query environmental responses, assess genetic factors, generate protein models/dynamics, and profile evolutionary insights into a protein such as CCR5. The knowledgebase generated in the initiative opens the door for public educational information and tools (molecular videos, 3D printed models, and handouts), classroom materials, and strategy for future genetic ideas that can be distributed in formal, semiformal, and informal educational environments. This work highlights that many factors are missing from the reductionist view of CCR5, including the role of missense variants or expression of CCR5 with neurological phenotypes and the role of CCR5 and the delta32 variant in complex critical care patients with sepsis. When connected to genomic stories in the news, these tools offer critically needed Ethical, Legal, and Social Implication (ELSI) education to combat biological reductionism.