MACH: A model for explaining molecular and cellular mechanisms

Biologists use mechanistic explanations to understand behaviors of the immense complexity of molecular and cellular systems. In undergraduate biology courses, students are expected to explain molecular and cellular mechanisms, but teaching this skill presents many challenges due to the highly abstract, intangible nature of the cellular world, the influence of everyday language, and the tendency of students to overestimate how much they can explain. Therefore, across three studies this dissertation addresses these obstacles to teach undergraduate biology students to explain molecular and cellular mechanisms. ^ The first step was to model how biology experts explain molecular and cellular mechanisms, and to test the validity of this model by examining how experts from different biology sub-disciplines explain a mechanism they study. A literature review was performed to develop an initial model and then to determine the model\u27s validity, it was tested against explanations made during interviews by life scientists who work on molecular and cellular mechanisms. The interview data were subjected to thematic analysis and four themes were found. Explanations of molecular and cellular mechanisms include: Methods (M) used in research to inform ideas about the mechanism, Analogies (A) such as representations, models, stories, and diagrams to illustrate the explanation, Contexts (C) to emphasize the social importance and biological setting of the mechanism, and How (H) the mechanism works to address the organization of biological entities and their activities. Biologists who are experts in their sub-disciplines integrated all four components to explain cellular and molecular mechanisms. These themes formed the components of the MACH model, which extends previous models of molecular explanations and identifies components to include when teaching students how to explain biological mechanisms. ^ Then a teaching intervention using the MACH model was implemented in an introductory undergraduate biology course to find out: How does using the MACH model change the explanations written by life science students? Why do students think learning about the MACH model is useful, if at all? Student explanations collected before and after an intervention were subjected to content and statistical analysis. Student interviews were conducted and subjected to inductive analysis. Before the intervention, about 30% of responses included all MACH components; after the teaching intervention, the frequency rose to 90%. It was found that students used the model to monitor their understanding, to communicate completely and concisely, and to reveal gaps in their explanations. Results indicated a successful implementation of the model in the classroom, as well as, some unexpected problems. For instance, many students, unlike experts, struggled to integrate the MACH components in their explanations, and instead treated each component as a separate section. ^ Written for biology instructors, the third study presents knowledge and resources for using the MACH model in a classroom setting, and in doing so, furthers an understanding of how to make the components of explanation comprehensible to students. We discover pedagogical content knowledge (PCK) for teaching with the MACH model by asking: How does one help instructors and students understand and include the components biologists use to explain molecular and cellular mechanisms? Along with PCK, we present teaching resources including a tetrahedral model, a teaching activity, and a rubric for evaluating how well students use the MACH components when explaining molecular and cellular mechanisms. ^ As for the result of the three studies, a new framework for researching, teaching, and communicating molecular and cellular mechanisms has been developed. Future research will test the model against a large pool of explanations by scientists who study a variety of topics such as evolution or chemistry. Additionally, future studies will replicate the intervention presented, vary factors in more carefully controlled quasi-experimental studies, or study the development of explanatory skills without any intervention in naturalistic settings. Teachers may also develop new applications for teaching with the model across additional institutes, biological topics, student populations, and educational settings. The MACH model will further the scholarship of both research and teaching

A Tetrahedral Version of the MACH Model for Explaining Biological Mechanisms

This document is intended for both instructors and students. Modified from the original MACH model this version, once cut and folded, creates a tetrahedral model that can conveniently be used as a teaching and learning tool to inform and guide students on how to write expert quality explanations of biological mechanisms. Each vertex of the tetrahedron represents a component of the model namely, Methods, Analogy, Context, and How. For a coherent and complete explanation about molecular mechanisms, it is important to integrate information pertaining to all four components of the model. The tetrahedral MACH model has been tested in both undergraduate biology and biochemistry courses and is recommended for use by both practitioners and students in the life sciences. Details of its use as a classroom activity can be found in the Purdue International Biology Education Research Group (PIBERG) ePubs collection. This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License

Exploring the MACH Model’s Potential as a Metacognitive Tool to Help Undergraduate Students Monitor Their Explanations of Biological Mechanisms

When undergraduate biology students learn to explain biological mechanisms, they face many challenges and may overestimate their understanding of living systems. Previously, we developed the MACH model of four components used by expert biologists to explain mechanisms: Methods, Analogies, Context, and How. This study explores the implementation of the model in an undergraduate biology classroom as an educational tool to address some of the known challenges. To find out how well students’ written explanations represent components of the MACH model before and after they were taught about it and why students think the MACH model was useful, we conducted an exploratory multiple case study with four interview participants. We characterize how two students explained biological mechanisms before and after a teaching intervention that used the MACH components. Inductive analysis of written explanations and interviews showed that MACH acted as an effective metacognitive tool for all four students by helping them to monitor their understanding, communicate explanations, and identify explanatory gaps. Further research, though, is needed to more fully substantiate the general usefulness of MACH for promoting students’ metacognition about their understanding of biological mechanisms

An Activity Aimed at Improving Student Explanations of Biological Mechanisms

This document is intended for use by instructors and their students. The activity contains steps to introduce students to the MACH model involving analyzing and discussing explanations about biological mechanisms. Initially, students read modified articles about biological mechanisms during class, although instructors may prefer to assign readings outside of class before the activity. During the activity, students are required to analyze the readings for evidence of research methods, analogies, context, and mechanisms. In so doing, students learn how to integrate the information pertaining to each of the MACH model components into a coherent explanation about their biological mechanism. After performing the above activities individually, students discuss findings in pairs, and then share their ideas with the class. After discussion, the instructor presents the MACH model. In our experience once the above activity has been successfully completed, students show strong evidence of competence in the writing of explanations about mechanisms. Details of the tetrahedral MACH model, and its related class activities, are freely available in the Purdue International Biology Education Research Group (PIBERG) ePubs collection. Together with the description of the activity, we have included advice on suggested topics, citations of suggested readings, and examples of typical student analyses of such readings. This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License

A Model of How Different Biology Experts Explain Molecular and Cellular Mechanisms

Constructing explanations is an essential skill for all science learners. The goal of this project was to model the key components of expert explanation of molecular and cellular mechanisms. As such, we asked: What is an appropriate model of the components of explanation used by biology experts to explain molecular and cellular mechanisms? Do explanations made by experts from different biology subdisciplines at a university support the validity of this model? Guided by the modeling framework of R. S. Justi and J. K. Gilbert, the validity of an initial model was tested by asking seven biologists to explain a molecular mechanism of their choice. Data were collected from interviews, artifacts, and drawings, and then subjected to thematic analysis. We found that biologists explained the specific activities and organization of entities of the mechanism. In addition, they contextualized explanations according to their biological and social significance; integrated explanations with methods, instruments, and measurements; and used analogies and narrated stories. The derived methods, analogies, context, and how themes informed the development of our final MACH model of mechanistic explanations. Future research will test the potential of the MACH model as a guiding framework for instruction to enhance the quality of student explanations

The Expression of irx7 in the Inner Nuclear Layer of Zebrafish Retina Is Essential for a Proper Retinal Development and Lamination.

Irx7, a member in the zebrafish iroquois transcription factor (TF) family, has been shown to control brain patterning. During retinal development, irx7\u27s expression was found to appear exclusively in the inner nuclear layer (INL) as soon as the prospective INL cells withdraw from the cell cycle and during retinal lamination. In Irx7-deficient retinas, the formation of a proper retinal lamination was disrupted and the differentiation of INL cell types, including amacrine, horizontal, bipolar and Muller cells, was compromised. Despite irx7\u27s exclusive expression in the INL, photoreceptors differentiation was also compromised in Irx7-deficient retinas. Compared with other retinal cell types, ganglion cells differentiated relatively well in these retinas, except for their dendritic projections into the inner plexiform layer (IPL). In fact, the neuronal projections of amacrine and bipolar cells into the IPL were also diminished. These indicate that the retinal lamination issue in the Irx7-deficient retinas is likely caused by the attenuation of the neurite outgrowth. Since the expression of known TFs that can specify specific retinal cell type was also altered in Irx7-deficient retinas, thus the irx7 gene network is possibly a novel regulatory circuit for retinal development and lamination

The EvoDevoCI: A Concept Inventory for Gauging Students’ Understanding of Evolutionary Developmental Biology

The American Association for the Advancement of Science 2011 report Vision and Change in Undergraduate Biology Education encourages the teaching of developmental biology as an important part of teaching evolution. Recently, however, we found that biology majors often lack the developmental knowledge needed to understand evolutionary developmental biology, or “evo-devo.” To assist in efforts to improve evo-devo instruction among undergraduate biology majors, we designed a concept inventory (CI) for evolutionary developmental biology, the EvoDevoCI. The CI measures student understanding of six core evo-devo concepts using four scenarios and 11 multiple-choice items, all inspired by authentic scientific examples. Distracters were designed to represent the common conceptual difficulties students have with each evo-devo concept. The tool was validated by experts and administered at four institutions to 1191 students during preliminary (n = 652) and final (n = 539) field trials. We used student responses to evaluate the readability, difficulty, discriminability, validity, and reliability of the EvoDevoCI, which included items ranging in difficulty from 0.22–0.55 and in discriminability from 0.19–0.38. Such measures suggest the EvoDevoCI is an effective tool for assessing student understanding of evo-devo concepts and the prevalence of associated common conceptual difficulties among both novice and advanced undergraduate biology majors

The EvoDevoCI: A Concept Inventory for Gauging Students’ Understanding of Evolutionary Developmental Biology

The American Association for the Advancement of Science 2011 report Vision and Change in Undergraduate Biology Education encourages the teaching of developmental biology as an important part of teaching evolution. Recently, however, we found that biology majors often lack the developmental knowledge needed to understand evolutionary developmental biology, or “evo-devo.” To assist in efforts to improve evo-devo instruction among undergraduate biology majors, we designed a concept inventory (CI) for evolutionary developmental biology, the EvoDevoCI. The CI measures student understanding of six core evo-devo concepts using four scenarios and 11 multiple-choice items, all inspired by authentic scientific examples. Distracters were designed to represent the common conceptual difficulties students have with each evo-devo concept. The tool was validated by experts and administered at four institutions to 1191 students during preliminary (n = 652) and final (n = 539) field trials. We used student responses to evaluate the readability, difficulty, discriminability, validity, and reliability of the EvoDevoCI, which included items ranging in difficulty from 0.22–0.55 and in discriminability from 0.19–0.38. Such measures suggest the EvoDevoCI is an effective tool for assessing student understanding of evo-devo concepts and the prevalence of associated common conceptual difficulties among both novice and advanced undergraduate biology majors

Getting to Evo-Devo: Concepts and Challenges for Students Learning Evolutionary Developmental Biology

To examine how well biology majors have achieved the necessary foundation in evolution, numerous studies have examined how students learn natural selection. However, no studies to date have examined how students learn developmental aspects of evolution (evo-devo). Although evo-devo plays an increasing role in undergraduate biology curricula, we find that instruction often addresses development cursorily, with most of the treatment embedded within instruction on evolution. Based on results of surveys and interviews with students, we suggest that teaching core concepts (CCs) within a framework that integrates supporting concepts (SCs) from both evolutionary and developmental biology can improve evo-devo instruction. We articulate CCs, SCs, and foundational concepts (FCs) that provide an integrative framework to help students master evo-devo concepts and to help educators address specific conceptual difficulties their students have with evo-devo. We then identify the difficulties that undergraduates have with these concepts. Most of these difficulties are of two types: those that are ubiquitous among students in all areas of biology and those that stem from an inadequate understanding of FCs from developmental, cell, and molecular biology

Getting to Evo-Devo: Concepts and Challenges for Students Learning Evolutionary Developmental Biology

To examine how well biology majors have achieved the necessary foundation in evolution, numerous studies have examined how students learn natural selection. However, no studies to date have examined how students learn developmental aspects of evolution (evo-devo). Although evo-devo plays an increasing role in undergraduate biology curricula, we find that instruction often addresses development cursorily, with most of the treatment embedded within instruction on evolution. Based on results of surveys and interviews with students, we suggest that teaching core concepts (CCs) within a framework that integrates supporting concepts (SCs) from both evolutionary and developmental biology can improve evo-devo instruction. We articulate CCs, SCs, and foundational concepts (FCs) that provide an integrative framework to help students master evo-devo concepts and to help educators address specific conceptual difficulties their students have with evo-devo. We then identify the difficulties that undergraduates have with these concepts. Most of these difficulties are of two types: those that are ubiquitous among students in all areas of biology and those that stem from an inadequate understanding of FCs from developmental, cell, and molecular biology