I believe that direct faculty mentorship combined with independent scientific research experiences for undergraduates can significantly enhance their learning outcomes, especially in STEM. Through active mentorship and by providing semi-structured, classroom-based, independent research opportunities, I provide students a foundation in biological concepts, develop and guide scientific research, and support diverse independent research experiences. These types of educational opportunities promote hands-on experiences and engage students through different learning approaches, which are critical both in and out of the classroom. I recognize that both students and educators must work together to establish clear learning expectations and determine specific ways to achieve these goals. As an instructor, I promote a learning environment that encourages students to be curious and ask questions, which enhances their educational experiences at multiple levels. By fostering a collaborative learning environment, students are quick to set their own goals, are motivated to accomplish them, and find the experience transformative.

Providing students early training and direct mentorship through independent research experiences is known to be an effective approach to increasing student retention in science, technology, engineering and math (STEM) disciplines. These research experiences further enhance diversity and promote an inclusive training environment when these approaches are integrated into class curriculum, which broadens the recruitment and retention of diverse students in STEM. Over the last three years, we have offered a new curriculum based research experience through the School of Life Science in the College of Natural Sciences at UHM to provide students science education through discovery-based research experiences in the classroom. SEA–PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is designed to increase participation and retention of students in STEM fields. Through this program, we provide students with a series of structured but self-guided independent research experiences, where research activities are scaffolded across the entire 16-week semester and designed to support a diverse and comprehensive scientific research experience.

Viruses are abundant in the environment and many do not cause diseases in humans, yet there is still much to learn about them. Through this two-semester program, students have the opportunity to survey the unknown microscopic diversity and directly contribute to the knowledge of microbes around the world. Students will collect soil samples and use cutting edge molecular and microbiology techniques to find new viruses from Hawaiʻi. After genetically sequencing these viral isolates, students spend the second semester annotating the complete genome of their new viruses and conduct independent bioinformatic research projects based on their virus genomes.

Using the SEA-PHAGES genome annotations as an entryway, we have specifically expanded our SEA-PHAGES II Bioinformatics course to provide students with a structured but self-guided independent research experience. Based on the SEA-PHAGES framework, the first third of our course is structured to introduce students to working with genomic data through bioinformatic analyses and genome annotation. This process culminates in students proposing and conducting their own independent research projects based on their knowledge base and particular research interests.

1. Training, data exploration, and literature review. – Specifically, building off of their newly developed bioinformatic skills, students explore primary literature to expand their basic understanding and begin to identify gaps in the scientific knowledge surrounding phage genomes.
2. Questions, hypotheses, and experimental approach. – After the annotation phase of the course, students individually identify broad areas of interest based on these literature explorations and discussions. Based on shared interests, students are then placed into research groups of three to four students to collaborate on developing a research question, testable hypotheses, and an appropriate experimental approach. A strength of this approach is that students are allowed to follow their scientific interests, which promotes student investment in the project, self-motivation in completing the work, and shared interests promotes a collaborative atmosphere. First and foremost, students get to pursue a diversity of research topics, ranging from phylogeography, molecular evolution, protein structure and function, links between gene evolution and viral ecology, to name a few.
3. Synthesis and communication. – To promote science communication, students are tasked with presenting their scientific research in both oral and multiple written formats. Research paper components are scaffolded throughout the semester, with students working on each major section individually and getting both instructor feedback and peer-reviews before completing a final draft. Finally, students communicate their research at the end of semester in the form of oral-poster presentations during the UH-SEAsymposia and submit a completed scientific paper summarizing their research projects.

The larger SEA-PHAGES initiative led by the Howard Hughes Medical Institute allows faculty and universities from around the nation to increase undergraduate interest and retention in the biological sciences through research-based curricula early in their academic careers. By incorporating our pedagogical approach of a structured but self-guided independent research experience, we have further enhanced the beneficial outcomes of the SEA-PHAGES program on students, as reflected by consistently higher scores across all PITS (Persistence in the Sciences) assessment metrics, particularly for project ownership and self-identifying as a scientist. Our integrated and systematic approach allows students to work closely with faculty and experience immediate immersion in authentic, valuable yet accessible research while pursuing their education in STEM disciplines.

Final assessments provide evidence of the effectiveness of this pedagogical approach and impact on student learning. All students completed the research projects, presented their final presentations in class, and submitted a scientific paper summarizing their scientific results. In the end, all but one student received acceptable scores on the combined final assessment. Based on instructor evaluations as well as peer evaluations, all 16 students’ work showed understanding of the scientific method, applied the scientific method to diverse research topics, and effective communication of results and significance. Feedback from student evaluations highlights that we “created a positive classroom” where students were “excited about what we were learning about”. Throughout the process, we were “approachable” and there to “address any questions”. Many students found that the diverse “feedback was always helpful”. In the end, one student mentioned they “feel more confident in (their) scientific abilities, and feel more prepared for major core science classes that I will take later in my college career”. In the end most students learn a “lot about bacteriophages, and research in general, which will be helpful for future science classes and even careers as well”. Collectively, these results suggest that the pedagogical approach of a structured but self-guided independent research experience in the classroom is an extremely engaging and highly impactful experience for students.