Inquiry Driven Exploration of online cloning tools for an Undergrad Molecular Biology course

Molecular Biology is a field that encompasses both theory and technique intimately linked to one another. Fundamental principles in molecular biology inform and support an understanding of the techniques used to explore the field. New discoveries in molecular biology routinely lead to the development of new techniques, often focused on the cloning and manipulation of genes. At the same time, molecular cloning requires a firm grasp of the fundamental principles of molecular biology. Students in molecular biology are fortunate to have access to many freely available online tools that can aid in the development of cloning strategies, and experimentation with these tools can reinforce basic principles. The undergraduate molecular biology class (BIOL 390) that I direct does not include a laboratory component, but an understanding of experimental design and the techniques associated with the field is vital to understanding and integrating the theoretical course material. Each semester, students work in teams to design a molecular cloning strategy to transfer a cDNA into an expression vector to generate a fusion protein. They are provided written primers, links to a short list of cDNAs and expression vectors, and access to a variety web resources, but there are no lectures specifically focused on cloning techniques. Instead, students must draw on their developing knowledge of fundamental principles placed in the context of genetic cloning and manipulation. This year as part of the cohort study, I developed an in-class exercise where students were led through an inquiry-driven exploration of various free online cloning tools.

There were three main project goals:

  1. Integrate basic science concepts with practical applications
  2. Develop self-confidence and competency in the use of online cloning tools
  3. Think critically about the uses of online cloning tools and the sources of online data

The project took on a typical “flipped classroom” format, including pre-exercise preparation, in-class activity, and follow-up in the form the ITEL cohort questionnaire.

  1. Preparation: Students examined links to online tools and were asked to identify similar tools. They also had access to a written cloning primer that I developed specifically for this course.
  2. Activity: Students worked in teams to complete three exercises using the online tools provided to them and the ones they had identified on their own (exercise sheet attached)
  3. Wrap-up: teams reported back on what they found at the end of the class session
  4. Reflection: Students were asked to complete the Cohort questionnaire along with project specific questions. They also provided narrative feedback about their experience.

Importantly, this exercise did not replace the team cloning project. Instead it was intended to complement that project by providing the students with a framework to explore the cloning tools that they need to complete that project.

The success of the project in terms of impact on learning was assessed in three ways: observation during the exercise, response to the ITEL cohort questionnaire, and performance on the written cloning project. The in-class exercise itself ran smoothly; there were no connectivity issues. The exercise filled the allotted class time, although groups worked at different rates. This indicates that it does not need to be significantly altered in terms of length for future years. Students in the class were actively engaged throughout the exercise. While each was working on his or her own lap top, they actively interacted with the members of their groups giving one another pointers and solving problems together. There were several opportunities for students to integrate their basic science knowledge with the practical task, as evidenced by questions asked during the exercise. Some students even asked about things they had heard about in other science courses or laboratory experiences, indicating that they were using this exercise to integrate knowledge across several domains. This was a fortunate and unanticipated outcome. Some questions asked by students revealed that they had a level of discomfort with the inquiry-based nature of the exercise. For example, one student wanted to know whether I would be providing the “correct” answers at the end of the exercise, even though these questions where meant to drive exploration rather than lead to objective truth. This question reflects a concern that some students express every year regarding the cloning project itself. Namely, how do they know that they have found the correct strategy. I explain that the correct strategy is one that achieves the project goal of developing a vector for an in-frame fusion protein; there are hundreds of correct strategies. I also noticed that some teams wished to use the class-time to directly tackle their cloning project. While this was not the original purpose of the exercise, which instead was meant to educate them in the use of the cloning tools, explicit integration of the cloning project into the exercise is a good idea for future iterations. To accomplish this I plan to assign the cloning primer prior to the exercise and ask that teams select their cDNA and vector before they begin.

Feedback on the exercise was collected through study-specific questions in the ITEL cohort questionnaire. The majority of the class (13/16 students) completed all or part of the survey. Most agreed or strongly agreed that the exercise was a good use of class time and (Lickert 4.33/5.0) and that it helped them with their cloning projects (Likert 4.58/5.0). They also felt that they benefitted from working in teams (Likert 4.58/5.0), and did not believe that the exercise would be better deployed outside of the classroom setting (Likert 2.42). Most students (8/12) did not report encountering significant problems with the technology during the exercise, however the remainder apparently did encounter issues. I plan to monitor technology problems more closely in future years as no students reported these issues to me during the exercise itself. In terms of meeting the project goals, students reported that the exercise did help them integrate basic science knowledge with practical applications (Likert 4.25/5.0) and enhanced their understanding of online cloning tools (Likert 4.17/5.0).

Students also provided narrative feedback in the form of comments and suggestions as to how the exercise could be improved. It is not at all surprising that the most common suggestion for improvement was to provide a demonstration or lecture before the exercise. In fact all students who made suggestions for improvement (8/16) gave some form of this answer. I plan to make the goals of the exercise more explicit in the future. However, demonstrating the tools or providing explicit instructions in their use would actually defeat the purpose of the exercise. For example, one team discovered and deployed a new online tool that I did not know existed; there are hundreds of these tools and more are coming online every year. If I had given explicit instructions on what to use and how, these students would not have had an opportunity to find their own path and make this discovery. Many students at this stage of learning still view science as a field of memorization and emulation as opposed to exploration and discovery. Thus this exercise and the cloning project as a whole take them outside of their comfort zones. However, they are given assistance once they meet a roadblock that they find insurmountable, and all teams successfully complete their projects every year.

Comments in response to the effectiveness of the exercise reflect the mixture of attitudes and learning styles. For example, some students clearly grasped the discovery-oriented nature and benefitted from it: “The activity was effective in getting me to think about the process cloning. Previously cloning was a nebulous concept to me, and now I know exactly what needs to be done to accomplish the process (since I went through it myself),” and “I started the exercise with absolutely no knowledge on how to clone genes; I finished the exercise with a good semi-practical sense of how to do so.” Others struggled after completion “I thought it was informative, but despite the extensive instructions I was still somewhat confused.” While still others were unable to grasp the purpose of inquiry-based learning “The main limitation of the activity was our initial lack of knowledge about the subject. It took a lot of trouble shooting and self-learning to begin to get on the right track. Overall I think the project was low-yield in terms of time put in, and knowledge taken away.” The irony is that this student actually went through the process exactly as intended. They started out with “little knowledge” (this is a student, so that’s not surprising); they went through a process of discovery (“trouble-shooting and self-learning”), and they succeeded! However, overall they did not feel that they benefitted. As a medical school instructor, the last part of the comment is one I am quite familiar with. “High yield” is very common parlance among medical and pre-medical students and usually refers to the rapid acquisition of knowledge purely for the purpose of test performance. More information regarding the benefits of this type of learning in terms of deep understanding and long-term retention may help students warm to the struggle associated with it.

One way in which I plan to modify the project in the future arose from suggestions of other cohort members as opposed to student feedback. Students compare and contrast online cloning tools as part of the exercise. In the future I will ask them to submit their responses in a more formal format and collect them as part of a class portfolio to be enhanced every year as more students take the course. This portfolio can serve as a resource for researchers on campus or elsewhere. The generation of the tangible artifact may help students focus and better grasp the value of their inquiry.