Caleb Trujillo

A model of how different biology experts explain molecular and cellular mechanisms.

This study used a literature review and interviews with practicing biologists to develop the MACH model, a Venn diagram of the components research scientists include when explaining molecular and cellular mechanisms. Seven biologists from different subdisciplines included research Methods, Analogy, Context, and How the mechanism works to explain the systems they investigate.

The EvoDevoCI: a concept inventory for gauging students' understanding of evolutionary developmental biology.

The authors present the development and validation of the EvoDevoCI, a concept inventory for evolutionary developmental biology. This CI measures student understanding of six core evolutionary developmental biology (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.

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

In this study we used surveys of evo-devo experts to identify the core concepts of evo-devo and outline an underlying conceptual framework. We also use interviews and surveys of conceptual difficulties with these concepts.

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, irx7s 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 irx7s 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.

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

This multiple case study explores a teaching intervention in an introductory undergraduate biology classroom that aimed to guide students to explain biological mechanisms using the MACH model, a previously developed model of the components used by interviewed biologists to explain mechanisms.

An instructional design process based on expert knowledge for teaching students how mechanisms are explained.

In biology and physiology courses, students face many difficulties when learning to explain mechanisms, a topic that is demanding due to the immense complexity and abstract nature of molecular and cellular mechanisms. To overcome these difficulties, we asked the following question: how does an instructor transform their understanding of biological mechanisms and other difficult-to-learn topics so that students can comprehend them? To address this question, we first reviewed a model of the components used by biologists to explain molecular and cellular mechanisms: the MACH model, with the components of methods (M), analogies (A), context (C), and how (H). Next, instructional materials were developed and the teaching activities were piloted with a physical MACH model. Students who used the MACH model to guide their explanations of mechanisms exhibited both improvements and some new difficulties. Third, a series of design-based research cycles was applied to bring the activities with an improved physical MACH model into biology and biochemistry courses. Finally, a useful rubric was developed to address prevalent student difficulties. Here, we present, for physiology and biology instructors, the knowledge and resources for explaining molecular and cellular mechanisms in undergraduate courses with an instructional design process aimed at realizing pedagogical content knowledge for teaching. Our four-stage process could be adapted to advance instruction with a range of models in the life sciences.