Opening Up Biochemistry

James Madison University Faculty

17 Opening Up Biochemistry

Christopher E. Berndsen, Chemistry and Biochemistry

Project Title and Abstract:

Opening up Biochemistry

Publicly available resources in chemistry and biology such as the Protein Data Bank and UniProt have been repositories for many of the landmark findings of the late 20th and early 21st centuries. When combined with the movement toward open science and open data, scientific knowledge is no longer restricted to a few elite institutions. However, few outside of academia know how to use these resources, if they even know of their existence at all. The project aims to increase student awareness of open access biological and chemical resources and to provide students with an open, hands-on opportunity to use these tools to carry out scientific investigations. Through these activities, students will gain skills in the scientific method and working under the principles of open science/data. The results will be that the students increase their proficiency in working with data and become better communicators. All of these objectives will benefit students in their careers. The long-term goal is to develop a framework of lessons and activities that could be used in any discipline at any level to engage students with hand-ons, open access research projects.

Rationale:

Google is a common starting place of student questions. While amusing and frustrating to faculty, physicians, etc., it highlights the problem: Where should students/the public find trustworthy information about a topic? In chemistry and biology, there are many well-curated, open access databases which are unused or unknown to the public and even students in those disciplines. In science and more specifically chemistry and biology, hands-on experiences most often occur in laboratory courses. However, what laboratory course teaches about information, databases, and repositories? These resources are typically covered in graduate level courses or during the scholarship period of graduate/post-doctoral training. This approach creates a barrier between freely available information and the students/public who could benefit from this knowledge. Beyond the basic repositories, there are other open access resources and open science tools which aim to engage the community with science. However, faculty knowledge and perceptions of these tools and resources varies greatly (for examples of faculty surveys see: (Creaser et al., 2010; Gaines, 2015; Lawrence-Kuether, n.d.; Peekhaus & Proferes, 2015). Thus, those who could contribute to these databases through their own scholarship may be uninformed of the existence, uses, and benefits to their careers, their students, and their community. Therefore, there is an opportunity to inform students (and faculty) about these resources which can lead to a better informed and engaged society.

In the course of this project, students will use publicly available scientific repositories as a starting point to carry out novel biochemical investigations that illustrate the principles of biochemistry. By providing an immediate and practical application of the scientific content and incorporating the content into a series of authentic applications, the hope is that students will internalize the knowledge and practices with increased enthusiasm. Through the proposed activities, students will not only become aware of the publicly available resources in the scientific community but engage with these resources over the course of group and individual projects leading to novel research products. Student products will be refined and collected in the Open Science Framework (OSF) and Protocols.io to train students in the practice of good data management and open science. These latter products may develop into professional portfolios for the students, which may aid in the students’ movement towards a career. Students leaving the course will have developed a framework to use when answering scientific questions as well as a knowledge-base of where to find reliable information sources in science.

Instructional design and implementation plan:

Course-based undergraduate research experiences (CUREs) projects and Project Oriented Guided-Inquiry-based Learning (POGIL) are widely used in chemistry and biology laboratory courses including those at JMU (JMU examples not involving the PI: (Amenta & Mosbo, 1994; Hyman et al., 2019; MacDonald, 2008; Temple, Cresawn, & Monroe, 2010). This project is an application of those instructional approaches that incorporates student directed projects and the novel scientific questions into a Biochemistry course. The primary distinctions from these previous efforts are the environment being a non-laboratory course and the scale with 50 to 100+ students in a single section.

I currently teach the Biochemistry course as a “lecture-free” zone, preferring to engage with students and student groups to solve problems in Biochemistry. In the first part of the proposed approach, I will incorporate 5 group projects that teach students to use scientific repositories such as PubChem, UniProt, NCBI, and ExPASy to solve biochemical problems and illustrate biochemical concepts and principles (Gasteiger et al., 2005; Kim et al., 2016; UniProt Consortium & The UniProt Consortium, 2018). These projects will last approximately 1 week (two class meetings) and require the students to collaboratively construct an OSF wiki to report their results (Sullivan, DeHaven, & Mellor, 2019). Additionally, all the data from the project will have to be made available on OSF and adhere to the principles of good data management and open science. Student groups will receive feedback from the instructor and from their peers, as I have found peer critiques to be a useful classroom tool that works in both directions. In the second part of the proposed approach, students will then be asked to individually answer a research question and demonstrate their knowledge of biochemistry, scientific resources, and open science. The project will be structured so that it uses the skills the students developed in the group activities and pushes them to explore in an environment where a negative result is an acceptable outcome as long as the methods and data support this through transparent reporting and methods. Students methods will be shared in a course-specific group on Protocols.io to foster collaboration and show students the diversity of approaches that are possible to answer the same question. Finally, students will be given the option to make their Protocols.io methods or OSF projects public to help them develop their professional portfolios.

Incorporation of open access/science tools into these pedagogical approaches is not a radical departure from the norms but adding a framework to ensure that the scientific investigations are reproducible, reliable, and shared appropriately. Effective open science principles structure the course materials by providing checklist dictating file formats, data reporting expectations, organization of projects, and communication of methods and results. To assess the project, prior to and following participating in the project, students will be asked to reflect on their knowledge of and confidence using open access resources and open science tools. The survey will be adapted from existing surveys from OA Academy, ITHAKA S+R, and Gold, et al. to focus on how undergraduates in the course think about open science and where they find information (Blankstein & Wolff-Eisenberg, 2019; Gold et al., 2019; “Open Access Academy survey,” n.d.). Throughout the process, students will participate in collaborative critiquing activities with the instructor and peers to spark conversation, reflection, and learning.

Given that all of the targeted resources in this project are maintained external to JMU, the primary support will be from the JMU Libraries to help design or adapt materials for referencing sources and to teach open science practices. On the assessment side, it would be useful to have assistance to make sure the survey is focused properly. Long-term, I would to develop a virtual poster conference for students in my course and others on campus like to share results. Aid in amplifying this event and using social media effectively would be helpful as well.

Project Transferability:

There are open access resources in most scientific and non-scientific fields that could be substituted into the chemistry and biology resources used in this project. Open science principles are largely consistent across disciplines with some modifications for work with human subjects or other identifiable information. Therefore, this project should be straight-forward to transfer to other scientific fields and non-physical/life science disciplines. The use of the Open Science Framework and Protocols.io for management of student work should be transferable as these platforms are largely discipline agnostic instead focusing more on reproducibility and transparency.

Additionally, there is a significant opportunity for collaboration between faculty on and off-campus in this project. Colleagues who have a research project or question that is amenable to the approaches in this classroom project could work with the class and me to work on their scholarship. This may provide an alternative approach to ease faculty into this style of teaching by engaging faculty in a way that is linked to where most faculty have their training, their scholarship.

Innovative and creative teaching outcomes:

The innovative aspects of this project are the scale of the instructional setting as CUREs are typically implemented in a 20 student lab course rather than a 50+ student lecture course. The immediate outcomes from this project fall into two areas. The first is that students will become more aware of resources that may help in their lives/careers to stay informed of scientific information and reproducible science. The second outcome are more approaches and tools to provide active and engaging scientific instruction that helps students make connections to applications of the content. The first outcome will be assessed by the pre- and post-participation assessments of knowledge of the resources/tools and student confidence in using them. The second outcome is directly tied to transferability and will require collaboration across campus/other institutions to implement parts/all of the tools developed by this project.

Outgrowths from the success of outcome one are increased student marketability by having participated in a research project but also having developed a portfolio of work. Also, the data generated from the in-class projects contributes to the scholarship of the instructor which may generate preliminary results for seeking project funding or publication of the results. This outgrowth could be assessed by looking at whether data contribute to successful grant applications, poster/oral presentations at conferences, and journal publications which are also tied to sustainability.

Result dissemination plan:

The Open Science Framework will host all of the materials including lesson design, instructor guides, and results of assessment (after aggregation and scrubbing of any identifiable information). Moreover, this repository can be a collaborative space for future examples of using open science in the classroom.

Information about the materials and the OSF space will be disseminated via presentations at meetings such as the ASBMB Transforming Education in the Molecular Life Sciences meeting which is held every two years or at the annual ASBMB meeting which has an active and engaged education community. Publication of the project would be pre-printed in BioRxiv, a well-established and popular pre-print hosting site which allows contributions from educators, then published in the open access science education journal Course Source.

A long-term level of dissemination will be to establish a virtual poster conference modeled after the Royal Society of Chemistry’s annual Twitter poster conference (Gempf, n.d.). In 2019, the RSC conference had over 500 participants reaching an audience of 2 million and no one had to leave their couch or try to get a poster tube through airport security. Through this activity, students or student groups could share aspects of their work in the course project and this event could potentially extend to other courses and disciplines across campus. This aspect of the dissemination would encourage open sharing of science and highlight one of the hallmarks of the JMU experience, engaging undergraduates in scholarly projects.

Impact of COVID-19 on the project

During the Spring semester of 2020, the COVID-19 pandemic closed JMU to face-to-face instruction, disrupting some of the activities of this project. However, it also turned out to be an opportunity for students to see the gains and risks of open science as much of the research on the COVID-19 virus is freely available through various pre-print servers, journals making articles open access, and databases increasing annotation and aggregation of coronavirus and related research. In the initial weeks of online learning, students explored the data related to the virus and reported what was known as of early-April 2020. While definitively not the situation the instructor or students wanted, it was an experience that aligned well with the project goals.

As the Spring semester closed and the Summer instructional session began, many of the proposed project components such as using Protocols.io and open access resources turned out to be helpful for remote learning. The PI along with the course TAs developed several guided activities using Protocols.io to have students use open access scientific resources so that students could succeed even when far away. These protocols are in the process of revision to be made public as of May 2020.

References

Amenta, D. S., & Mosbo, J. A. (1994). Attracting the New Generation of Chemistry Majors to Synthetic Chemistry without Using Pheromones: A Research-Based, Group Approach to Multistep Syntheses at the College Sophomore Level. Journal of Chemical Education, 71 (8), 661.

Blankstein, M., & Wolff-Eisenberg, C. (2019). Ithaka S+R US Faculty Survey 2018. Retrieved from ITHAKA S+R website: https://sr.ithaka.org/wp-content/uploads/2019/03/SR-Report-US-Faculty-Survey-2018-04122019.pdf

Creaser, C., Fry, J., Greenwood, H., Oppenheim, C., Probets, S., Spezi, V., & White, S. (2010). Authors’ Awareness and Attitudes Toward Open Access Repositories. New Review of Academic Librarianship, 16 (sup1), 145–161.

Gaines, A. M. (2015). From Concerned to Cautiously Optimistic: Assessing Faculty Perceptions and Knowledge of Open Access in a Campus-Wide Study. Journal of Librarianship and Scholarly Communication, 3 (1), 1212.

Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S. ’everine, Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein Identification and Analysis Tools on the ExPASy Server. In J. M. Walker (Ed.), The Proteomics Protocols Handbook (pp. 571–607). Totowa, NJ: Humana Press.

Gempf, K. L. (n.d.). 2019 #RSCPoster Twitter Conference. Retrieved September 6, 2019, from http://blogs.rsc.org/rscpublishing/2018/12/10/rsc-twitter-poster-conference-2019/?_ga=2.178396772.1735926899.1567781199-1284531956.1565102232&doing_wp_cron=1567781230.3592429161071777343750

Gold, E. R., Ali-Khan, S. E., Allen, L., Ballell, L., Barral-Netto, M., Carr, D., … Thelwall, M. (2019). An open toolkit for tracking open science partnership implementation and impact. Gates Open Research, 3 , 1442.

Hyman, O., Doyle, E., Harsh, J., Mott, J., Pesce, A., Rasoul, B., … Enke, R. (2019). CURE-all: Large Scale Implementation of Authentic DNA Barcoding Research into First-Year Biology Curriculum. CSH Protocols, 6 . https://doi.org/10.24918/cs.2019.10

Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., … Bryant, S. H. (2016). PubChem Substance and Compound databases. Nucleic Acids Research, 44 (D1), D1202–D1213.

Lawrence-Kuether, M. A. (n.d.). Virginia Tech Through the Lens of Social Exchange. Retrieved from https://pdfs.semanticscholar.org/4285/31d5eb45d05ac5e90e00105c13d2eba98a01.pdf

MacDonald, G. (2008). Teaching Protein Purification and Characterization Techniques. A Student-Initiated, Project-Oriented Biochemistry Laboratory Course. Journal of Chemical Education, 85 (9), 1250.