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Expert Explanations of Protein-Folding and Dynamics Research: Implications for Biochemistry Instruction

posted on 15.05.2019 by Kathleen Jeffery
Recent calls in education have emphasized the critical need for curricula in the sciences to support student development of the general and disciplinary-specific practices that are relevant to modern scientific research and careers, as well as foundational scientific knowledge that reflects recent advances. In this regard, the life sciences, including biochemistry, have been under pressure to develop curricula that reflect current research knowledge and practices, and that develop student competence in areas such as experimentation and visualization. In contrast to these calls, biochemistry textbooks, and instruction based on them, seldom discuss how disciplinary knowledge is combined with experimental work or other disciplinary resources to investigate and communicate about biochemical phenomena. This is of great concern given that graduates entering life science careers must be able to reason with relevant disciplinary knowledge, utilize experimental research methods, and navigate data representations in order to solve research problems. It is therefore crucial for biochemistry instruction to expose students to the ways in which expert scientists navigate and reason with disciplinary resources in cutting-edge scientific research on topics such as protein folding and dynamics, the focus of this project. Thus, this dissertation aims to fill a gap in our understanding of how expert research scientists explain protein-folding and dynamics research, and how that research knowledge can be used to inform the development of instructional materials in this crucially important area of biochemistry. To address this goal, we explore three overarching research questions: How can we model experts’ explanations of their research related to protein folding and dynamics? (RQ1); How do experts use representations to explain their protein-folding and dynamics research? (RQ2); and How can we use expert research to inform the design and implementation of instructional materials aimed at developing biochemistry students’ understanding of protein-folding and dynamics? (RQ3). To address these research questions, we first collected and analyzed interview data from four experts to explore the nature of their research explanations. This data was used to develop a model (i.e. the MAtCH model) of how experts integrate theoretical knowledge with their research context, methods, and analogies when explaining how phenomena operate (RQ1). In doing so, we also established how the experts use and combine explanatory models depending on the phenomena discussed and their explanatory aims, as well as how they explain thermodynamic and kinetic concepts relevant to protein folding in ways that align with their experimental research methods. We then examined selected representations from the expert interviews to explore how experts use language and representations to create meaning when explaining their research (RQ2). In comparing these to representations from biochemistry textbooks, analysis of the data indicated that textbooks generally explain ‘what is known’ but seldom explain ‘how it is known,’ whereas the experts use a combination of language, multiple representations, and gestures to explain how experimental research methods can provide evidence for phenomena. From this analysis, suggestions were made regarding the design of instructional materials to support discussion of experimental research methods and student interpretation of representations in classroom activities. In the final study, these suggestions were used in combination with additional analysis of expert research to inform the development anticipated learning outcomes (ALOs) and the design of instructional materials aimed at developing biochemistry students’ understanding of protein folding and dynamics (RQ3). The materials focus on the use of hydrogen-deuterium exchange mass spectrometry (HDX-MS) to study changes in protein structure due to denaturation and interactions with other molecules. The instructional materials were piloted in an undergraduate biochemistry course for the health sciences, and the nature of students’ understandings were explored. Our findings suggest that research practice – including research context, experimental methods, and representations – influences reasoning and explanation, providing additional evidence of the importance of developing discursive literacy in science students. To that end, a major implication of this work is that student knowledge of experimentation and representation may be a critical component of developing functional scientific understanding. Each of the studies contained in this dissertation therefore suggests ways in which practitioners may use our findings to modify instruction and instructional materials so that they are more aligned with expert practices. In order to teach students how scientific research underpins factual knowledge in biochemistry, future research should continue to explore experts’ use of disciplinary resources and ways of thinking in order to inform teaching and learning strategies and materials that can support the development of students’ disciplinary literacy.


Degree Type

Doctor of Philosophy



Campus location

West Lafayette

Advisor/Supervisor/Committee Chair

Trevor Anderson

Additional Committee Member 2

Chittaranjan Das

Additional Committee Member 3

Minjung Ryu

Additional Committee Member 4

David Eichinger