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The purpose of this paper is to share the iterative process we used to design a task that elicits causal mechanistic reasoning and how the subsequent student responses can be analyzed. Our goal in this task is to strike a balance between eliciting as much student knowledge as possible without providing so much structure that the answer becomes obvious. The task development was approached using (1) a resources perspective of learning, (2) principles of scaffolding, and (3) evidence-centered design, for which we specified evidence that would be considered a fully causal mechanistic explanation. That is, an explanation which pays explicit attention to the properties, interactions, and behaviors of entities that are involved at a scalar level below the phenomenon under consideration. Since our eventual goal is to characterize how students use knowledge across disciplinary boundaries, the phenomenon of protein--ligand binding was chosen as the context for this task, because it requires students to apply ideas learned in chemistry courses to a biological phenomenon. After three rounds of iterative refinement, a final task was developed. To characterize students' responses to this task, we developed a coding scheme which can be used to code explanations based on the presence or absence of three key ideas relevant to this phenomenon. In this paper, we share the detailed processes and approaches used in task development, which we hope will provide insight into instructors and researchers as they, too, develop such tasks to explore student reasoning.

Introduction: Open educational resources (OERs) provide instructors access to no-cost lesson materials they can incorporate into their courses. OER lessons can promote the use of innovative and evidence-based educational practices in biology education. Prior research suggests that teaching strategies are often implemented in different ways which can impact student learning. However, few studies have explored how OER lessons are modified to fit their local context. Methods: We used the teacher-curriculum framework to understand how and why instructors modify these materials. Additionally, we explored how these materials supported instructors in enacting national priorities from Vision and Change. We surveyed 139 instructors who implemented lessons published in CourseSource , a peer-reviewed journal specifically designed to share OERs. Results: We found that the majority of instructors who used the lesson materials (e.g., slides, worksheets, assessments, protocols) did so without making substantial modifications, in contrast with prior research. Furthermore, we found that these materials were particularly helpful in incorporating student-centered teaching practices, like group work or discussions, sometimes for the first time. Discussion: These insights into what instructors value in lesson materials can inform OER publishing guidelines so that these materials best meet instructional needs. [ABSTRACT FROM AUTHOR]

Computer-assisted analysis of students' written responses to questions is becoming a possibility due to developments in technology. This could make such constructed response questions more feasible for use in large classrooms where multiple choice assessments are often considered a more practical option. In this study, we use a previously developed prompt and coding scheme to characterize students' explanations of the origins of London dispersion forces in order to develop machine learning resources that can carry out such an analysis for large numbers of students. We found that by using large numbers of human coded student responses (N = 1,730) we could subsequently automatically characterize students' responses at a high level of accuracy compared to human coders. Furthermore, these resources were developed using responses from several different groups of students across multiple institutions to ensure both that our resources can work well with students from different backgrounds and that these computer resources can detect the different ways in which students explain this phenomenon. Such resources may help instructors to administer more complex open-ended assessment tasks to larger numbers of students and analyze the responses capturing language corresponding to causal mechanistic reasoning. Instructors could then use this information to better support their students' learning.

London dispersion forces (LDFs) are the most fundamental of the noncovalent interactions in that they are interactions that act between all molecular species and require only that students can use the "electron cloud" model of atomic structure. In this longitudinal study we investigate how students respond to prompts, designed to elicit causal mechanistic reasoning about the origins of LDFs, using a modified coding scheme from a previous study. We find that including explicit scaffolding improves students' representations of the mechanism compared to student responses to an unscaffolded prompt. When, on a later administration of a similar prompt, the scaffolding is removed, the sophistication of the students' representations decreases, but does not decline to the level of students who had never been exposed to a scaffolded prompt. We also explore the connection between student drawing and writing and find that there is a significant association between the reasoning level of the drawing and the written explanation. Finally, we show that there appears to be no significant difference between performance on ungraded (formative) and graded (summative) items that are administered in the second semester when LDFs are not explicitly covered. That is, students respond to ungraded homework activities similarly to examinations at time points where LDFs are not explicitly discussed in the course.

Characterizing how students construct causal mechanistic explanations for chemical phenomena can provide us with important insights into the ways that students develop understanding of chemistry concepts. Here, we present two qualitative studies of undergraduate general chemistry students' reasoning about the causes of London dispersion forces in nonpolar species such as helium atoms. In the first study, we used semi-structured interviews to examine students' verbal explanations for how and why electrical interactions arise between helium atoms. In the second, we used an online short-answer version of the interview task to examine the prevalence of the drawing and explanation types we observed in student interviews. We present a characterization of students' explanations and drawings in terms of increasing sophistication and demonstrate how it may be used as a model for assessing students' ability to engage in scientific practices such as explanation.

ABSTRACT We used molecular dynamics (MD) simulations for structure refinement of Critical Assessment of Techniques for Protein Structure Prediction 10 (CASP10) targets. Refinement was achieved by selecting structures from the MD-based ensembles followed by structural averaging. The overall performance of this method in CASP10 is described, and specific aspects are analyzed in detail to provide insight into key components. In particular, the use of different restraint types, sampling from multiple short simulations versus a single long simulation, the success of a quality assessment criterion, the application of scoring versus averaging, and the impact of a final refinement step are discussed in detail. Proteins 2014; 82(Suppl 2):196-207. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

In undergraduate life sciences education, open educational resources (OERs) increase accessibility and retention for students, reduce costs, and save instructors time and effort. Despite increasing awareness and utilization of these resources, OERs are not centrally located, and many undergraduate instructors describe challenges in locating relevant materials for use in their classes. To address this challenge, we have designed a resource collection (referred to as Open Resources for Biology Education, ORBE) with 89 unique resources that are primarily relevant to undergraduate life sciences education. To identify the resources in ORBE, we asked undergraduate life sciences instructors to list what OERs they use in their teaching and curated their responses. Here, we summarize the contents of the ORBE and describe how educators can use this resource as a tool to identify suitable materials to use in their classroom context. By highlighting the breadth of unique resources openly available for undergraduate biology education, we intend for the ORBE to increase instructors' awareness and use of OERs., Competing Interests: The authors declare no conflict of interest.