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As an instructional tool, models can transform the student experience from the static to the dynamic, the flat to the 3D, and the siloed to the integrated. Few practical resources exist to help instructors transition toward model-based classroom practices. The "Modeling in the Classroom" evidence-based teaching guide provides instructors with a tool kit for incorporating models and modeling into their classrooms (https://lse.ascb.org/evidence-based-teaching-guides/modeling-in-the-classroom). The guide discusses the underpinnings of modeling as a core scientific practice, one that can enable student development of systems thinking skills and understanding of biological concepts. The guide describes a variety of model types, including phylogenetic trees, simulations, animations, diagrams, conceptual models, concept maps, and tactile models supported by summaries of and links to articles and resources. In this paper, we will introduce key findings describing why and how to use models in the classroom. We also describe open research questions needed to address classroom implementation, instructional design, and development of students' knowledge and skills. It is our hope that the guide will provide a suitable combination of research-based findings and practical suggestions that instructors will be supported and encouraged to thoughtfully incorporate modeling to support learning goals.

Phylogenetic trees have become increasingly important across the life sciences, and as a result, learning to interpret and reason from these diagrams is now an essential component of biology education. Unfortunately, students often struggle to understand phylogenetic trees. Style (i.e., diagonal or bracket) is one factor that has been observed to impact how students interpret phylogenetic trees, and one goal of this research was to investigate these style effects across an introductory biology course. In addition, we investigated the impact of instruction that integrated diagonal and bracket phylogenetic trees equally. Before instruction, students were significantly more accurate with the bracket style for a variety of interpretation and construction tasks. After instruction, however, students were significantly more accurate only for construction tasks and interpretations involving taxa relatedness when using the bracket style. Thus, instruction that used both styles equally mitigated some, but not all, style effects. These results inform the development of research-based instruction that best supports student understanding of phylogenetic trees.

The availability of reliable evidence for teaching practices after professional development is limited across science, technology, engineering, and mathematics disciplines, making the identification of professional development "best practices" and effective models for change difficult. We aimed to determine the extent to which postdoctoral fellows (i.e., future biology faculty) believed in and implemented evidence-based pedagogies after completion of a 2-yr professional development program, Faculty Institutes for Reforming Science Teaching (FIRST IV). Postdocs (PDs) attended a 2-yr training program during which they completed self-report assessments of their beliefs about teaching and gains in pedagogical knowledge and experience, and they provided copies of class assessments and video recordings of their teaching. The PDs reported greater use of learner-centered compared with teacher-centered strategies. These data were consistent with the results of expert reviews of teaching videos. The majority of PDs (86%) received video ratings that documented active engagement of students and implementation of learner-centered classrooms. Despite practice of higher-level cognition in class sessions, the items used by the PDs on their assessments of learning focused on lower-level cognitive skills. We attributed the high success of the FIRST IV program to our focus on inexperienced teachers, an iterative process of teaching practice and reflection, and development of and teaching a full course.

Mutation is the key molecular mechanism generating phenotypic variation, which is the basis for evolution. In an introductory biology course, we used a model-based pedagogy that enabled students to integrate their understanding of genetics and evolution within multiple case studies. We used student-generated conceptual models to assess understanding of the origin of variation. By midterm, only a small percentage of students articulated complete and accurate representations of the origin of variation in their models. Targeted feedback was offered through activities requiring students to critically evaluate peers' models. At semester's end, a substantial proportion of students significantly improved their representation of how variation arises (though one-third still did not include mutation in their models). Students' written explanations of the origin of variation were mostly consistent with their models, although less effective than models in conveying mechanistic reasoning. This study contributes evidence that articulating the genetic origin of variation is particularly challenging for learners and may require multiple cycles of instruction, assessment, and feedback. To support meaningful learning of the origin of variation, we advocate instruction that explicitly integrates multiple scales of biological organization, assessment that promotes and reveals mechanistic and causal reasoning, and practice with explanatory models with formative feedback.

Research in contemporary biology has become increasingly complex and organized around understanding biological processes in the context of systems. To better reflect the ways of thinking required for learning about systems, we developed and implemented a pedagogical approach using box-and-arrow models (similar to concept maps) as a foundational tool for instruction and assessment in an Introductory Biology course on genetics, evolution, and ecology. Over the course of one semester, students iteratively constructed, evaluated, and revised "Gene-to-Evolution" (GtE) models intended to promote understanding about the connections linking molecular-level processes with population-level outcomes. In practice, a successful GtE model contextualizes information provided in a case study and explains how genetic-level variation originates at the molecular level, is differentially expressed among individuals, and is acted upon by the environment to produce evolutionary change within a population. Our analyses revealed that students' ability to construct biologically accurate models increased throughout the semester. Model complexity peaked near mid-term then subsequently declined. This suggests that, with time, students were building more parsimonious models, shedding irrelevant information, and improving in their ability to apply accurate and appropriate biological language to explain relationships among concepts. Importantly, we observed the greatest relative gains in model correctness among students who entered the course with lower mean GPA. In an analysis comparing performance among achievement tritiles, lower-performing students effectively closed the achievement gap with the highest performing students by the end of the semester. Our findings support the effectiveness of model-based pedagogies for science teaching and learning, and offer a perspective on pedagogical application of modeling strategies to foster systems thinking and knowledge structuring in college-level biology. (Contains 4 tables and 6 figures.)

Biology majors often take introductory biology, chemistry, and physics courses during their first two years of college. The various and sometimes conflicting discourse about and explanations of matter and energy in these courses may contribute to confusion and alternative conceptions (those that differ from scientific consensus) in biology learners. An important area of biology education research--students' alternative conceptions--has produced a lengthy list of alternative conceptions related to students' understanding of matter and energy flow through biological systems through processes such as photosynthesis and cellular respiration. By synthesizing the research literature and conducting interviews of science faculty members, we have identified similarities and differences in matter and energy discourse and teaching in these different science disciplines. This study can help biology instructors recognize and appreciate the ways in which instructors present concepts related to energy and matter in their courses and alter their discourse and teaching practices to promote learning and minimize confusion among their students.