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Incorporating research into science courses

by Cynthia Brame

There is long-standing and widespread support for educational initiatives that introduce undergraduates to scientific research (see, for example, Kurukstis and Elgren, 2007; Healey 2013; Alberts 2009). Authentic research experiences have been shown to lead to student-reported gains in general skills (e.g., oral visual, and written communication)as well as more specific research-associated skills (e.g., research design, hypothesis formation, data analysis) (Seymour et al., 2004; Lopatto, 2006; Laursen et al., 2010).  Increasingly, educational initiatives focus on providing authentic research experiences in credit-bearing courses. Incorporating research experiences into credit-bearing courses not only has the potential to extend the benefits of participating in research to a larger group (PCAST, 2012; Shaffer et al., 2010), but may also help faculty members integrate their responsibilities as researchers and educators. This effect can be valuable both for faculty members at primarily undergraduate institutions, where teaching responsibilities may threaten to overwhelm time for research, and faculty members at research-intensive universities, where research responsibilities may threaten to overwhelm time devoted to teaching.

There are several ways to introduce students to scientific research in credit bearing courses, ranging from investigations of the literature to incorporation of course-based research experiences.

Can you get research benefits without doing lab or field work?

One of the major benefits of introducing students to scientific research is to develop students’ understanding of the nature and development of scientific knowledge (Lopatto, 2003; National Research Council, 2003). Several groups have demonstrated that careful analysis of common forms of science communication (e.g., the research talk and primary research articles) can provide this benefit, thereby providing a low-barrier, low-resource gateway for students into research.

“Deconstructing” scientific research: Using the research talk to help students understand the research process and how knowledge is constructed. HHMI Professor Utpal Banerjee and colleagues sought a low-cost, low-space-requiring mechanism to introduce first- and second-year undergraduates to the process of scientific discovery (Clark et al., 2009). The solution they developed:
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Each student completes two modules during the course.

Banerjee and colleagues used the Classroom Undergraduate Research (CURE) survey to determine whether this approach achieved the goals of undergraduate research (Lopatto, 2007). They found that students completing this course exhibited self-reported learning greater than students completing summer research experiences in several categories, notably

  • Understanding the research process
  • Understanding supporting evidence
  • Understanding how new knowledge is constructed.

Thus the model Banerjee and colleagues propose may provide a readily adaptable tool for helping students gain an understanding of the process of research.

 

Following the path: Using the CREATE model to analyze scientific literature and understand the process of discovery (Gottesman and Hoskins, 2013; Hoskins et al., 2007). Sally Hoskins and colleagues developed the CREATE model of analyzing the scientific literature to give undergraduates an understanding of how scientific knowledge is generated and how research projects progress over time. CREATE focuses on a sequence of articles that reports a single line of research from one laboratory. Students receive each article in sections (Introduction, Results and Methods, and Discussion), and are asked to work through the data as if they had generated it themselves. The steps they follow:

 

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Students analyze the papers in the series sequentially, discussing each paper before moving on to the next, related paper. This allows the students to see if the experiments they proposed are those selected by the authors, both helping them understand the role of creativity in scientific progress and creating a “lab meeting” atmosphere in the class.

 

Hoskins and colleagues have implemented this approach in both upper-level and introductory classes. Its use in an upper-level course led to gains in students’ content integration, critical thinking ability, and self-assessed learning gains (Hoskins et al., 2007). It was adapted for use in a course for first-year students by use of popular press articles based on journal articles and by use of more single papers and parts of papers.  The CREATE approach was maintained, however, and these exercises served as a “warm up” to two sequential research papers. Students in the first-year course showed a significant increase in critical thinking ability, experimental design ability, and self-rated abilities such as decoding literature, thinking like a scientist, and understanding research in context (Gottesman and Hoskins, 2013). Thus the CREATE approach to analyzing primary literature may also provide a readily adaptable tool for helping students gain an understanding of the process of research.

What are different ways to implement research experiences for undergraduates in your courses?

The Course-based Undergraduate Research Experiences Network (CUREnet) defines undergraduate research in a credit-bearing course as an experience that integrates five essential elements (Auchincloss et al., in press):

  1. Engagement in multiple scientific practices, such as asking questions, building and evaluating models, proposing hypotheses, designing studies, and gathering and analyzing data.
  2. Discovery, meaning that students are “addressing novel scientific questions aimed at generating and testing new hypotheses. In addition, when their work is considered collectively, students’ findings offer some new insight into how the natural world works.”
  3. Work that fits into a larger scientific effort relevant beyond the scope of the course.
  4. Collaboration, both among students and between students and instructors
  5. Iteration, to increase the reliability or scope of findings.

Auchincloss and colleagues draw a contrast between CUREs and three other laboratory learning environments: the traditional laboratory course; the inquiry laboratory course; and a research internship (in press). They note that inquiry-based labs focus on the student learning process but not discovery of new knowledge that contributes to greater understanding of the natural world, while an essential element of CUREs is such discovery. They also note that while CUREs can have much in common with research internships, the element of collaboration with peers is highly emphasized in CUREs in a way that is typically absent in research internships.

How have other instructors adapted their research for use in a course? What are some of the key elements in this approach?

CUREs can focus on questions that are either instructor-defined or student-defined. There are many instructor-defined CUREs reported in the literature (see, for example, Healey, 2013; Wei and Woodin, 2011; CUR, 2007) and many more that have not been reported. Here, we summarize three large national projects that support CUREs at a variety of institutions and two CUREs developed from individual faculty research questions, noting the common features that appear to be important for implementation and some of the steps necessary for this approach.

The Genome Education Partnership (GEP)

Spearheaded by HHMI Professor Sarah Elgin, this project is a collaboration between multiple colleges and universities and the Department of Biology and Genome Center of Washington University (Shaffer et al., 2010).  Undergraduate researchers improve the sequence of and annotate various Drosophila genomes to allow analysis of the differences between heterochromatin and euchromatin. Single students or small groups of students can work on sequence improvement, designing primers to target areas of interest, specifying the type of sequencing to be done, and analyzing the sequence data. Alternatively, they can work on an annotation project, identifying putative start and stop sites and intron and exon boundaries to produce a gene model. Projects have been adapted for stand-alone courses as well as modules within existing lab courses as well as for courses at both small and large institutions. The program provides support for faculty through online resources (gep.wustl.edu) and a week-long workshop that introduces them to the project. Pre- and post-course quizzes suggested an increase in content knowledge, while a post-course survey adapted from the SURE and CURE surveys suggested professional and learning gains similar to students in summer research programs (Lopatto et al, 2008; Shaffer et al., 2010; Trosset et al., 2010).

 

Science Education Alliance Phage Hunters Integrating Research and Education (SEA PHIRE)

This project, led by HHMI Professor Graham Hatfull, centers around a two-semester course in which students isolate and characterize bacteriophage (that is, viruses that infect bacteria) from local soils, extract and purify DNA for sequencing by the US Department of Energy Joint Genome Institute, and annotate the genome (Hattfull et al, 2006). The course has been offered at more than 60 institutions, and has been adapted for introductory and non-majors courses as well as for high school courses. SEA provides significant resources, including instrumentation, materials, and training for faculty members implementing the course, which may improve students’ academic performance and attitudes toward science and may increase the likelihood of student persistence in science (Harrison et al., 2011;).

To increase the opportunity for students to learn about experimental design, the project is being adapted to allow students to characterize the function of genes in the phages they discover (Phanning the Phlames: Expansion of the Phage Hunters Integrating Research and Education (PHIRE) Program; Hatfull, 2010).

 

Center for Authentic Science Practice in Education (CASPiE)

CASPiE is a collaboration among chemistry departments at Purdue University and several other universities and colleges (Weaver et al., 2006). The model it uses to engage students in course-associated research is a hybrid between the “join a big effort” approach described for GEP and SEA PHIRE and the individual instructor-designed CUREs described below. Specifically, research scientists design modules, based on their own research, that can be adopted by first- and second-year chemistry lab courses. Using peer-led team learning approaches, students in the courses design experiments and generate results that can be used by the module author in his or her research program. The module author may have no involvement with the courses that have adopted his or her module, but contributes to educational efforts by developing the module—and reaps the reward of the students’ efforts. Course instructors may develop their own modules and share them for use at other institutions as well.

Like GEP and SEA PHIRE, there is a central support structure, with CASPiE faculty and staff providing guidance on module development, helping with module testing, and providing a remote instrument resource.

The research modules that have been developed are appropriate for General Chemistry and Organic Chemistry courses, and range from questions about the effects of food processing on phytochemical antioxidants, to design of a potential anti-viral drug candidate, to characterization of semiconducting films’ use for solar energy conversion.

Russell and Weaver demonstrated that students participating in research as part of this program showed greater understanding of essential elements of scientific research concepts (e.g., controls, repeatability, and the importance of unanticipated results) than did students in inquiry-based or traditional labs (2011).

 

ALLURE: Investigating catalytic versatility and substrate promiscuity in cytochrome p450s.

This project, developed by Susan Rowland, Elizabeth Gillam, and colleagues, grows out of the Gillam lab’s efforts to create libraries of cytochrome p450 mosaics for potential use as biocatalysts (Rowland et al., 2012).  In the ALLURE program, undergraduates who self-selected into a research-focused lab section conducted a preliminary metabolic characterization for a few mutant enzymes. The students were responsible for designing, implementing, and troubleshooting their own experiments, which were reported in a journal-style manuscript. This project was used in a high-enrollment, sophomore level class that enrolls both science majors and non-majors.

 

Investigating conserved features of CK1 protein kinases

In this project, developed by Cynthia Brame and Lucy Robinson, undergraduates use bioinformatics tools to identify amino acids that are conserved in CK1 protein kinases but not in other protein kinase subfamilies. After visualizing the location of the conserved amino acids using protein imaging tools, students form hypotheses about their function. Working in groups, students design mutations to test their hypotheses and then generate and test the mutant alleles in vivo and in silico using molecular dynamics software (Chiang et al., 2013; Brame et al., 2008), with several student groups working collaboratively to study complementary mutations that test a common hypothesis.  Students present their results in a manuscript and as a poster at a student research forum. The project is most appropriate for an upper-level majors course, but could readily be adapted for use with other proteins. Students completing the course showed significant gains in content knowledge, ability to communicate research results in written format, and self-assessed understanding of some research processes.

There appear to be key elements that are consistent among these and other CUREs:

  • Well-defined problems: The project focuses on a well-defined problem, where individual student projects have well-defined goals. Small student projects generate real knowledge and often contribute to a larger project, such as understanding of mycobacteriophage diversity in the SEA PHIRE project.
  • Important but not “hot”: Although the research completed in these CUREs generates new knowledge that is of interest beyond the scope of the class, all investigate a research question that tolerates the slower pace of undergraduate research.
  • Bite-sized projects: The student projects are designed such that they can largely be completed in time allotted for the class, with minimal out-of-class lab work required.
  • “Common tools, different problems” (Shaffer et al, 2010): In the CUREs described here, students use the same techniques to work on different projects. This allows for greater peer teaching and lower resource use, including the resource of faculty time.
  • Amenable to iteration. Because developing a CURE requires a significant amount of time and energy and because multiple (perhaps dozens or more) students will be working on the project each year, it’s important that the project have interesting subquestions that don’t require a complete project redesign.
  • Low resource requirements. In general, the projects described here have relatively low resource demands, using cheap model systems and relatively inexpensive reagents. In the case of the large national projects, important resources are provided by a central source and funded by a national funding agency.
  • Student collaboration. Although designated by CUREnet as an essential element of all CUREs, it’s worth noting that all of the CUREs outlined here explicitly include student collaboration.
  • Faculty guidance. All of the CUREs described here carefully guide students through the projects, providing regular meetings with set milestones to keep relatively large groups of students on track.
  • Collaboration across institutions. Although it’s not an essential element, many faculty who have developed CUREs find it advantageous to collaborate across institutions. Faculty at research-intensive institutions may have resources that can help projects move over unanticipated roadblocks, while faculty at PUIs may be able to carry the project forward in different contexts. In addition, these cross-institutional collaborations can provide opportunities for undergraduates to do research in a different context, or graduate students or post-docs to teach in a different context  than at their home institution.

CUREs that derive from large national projects and from individual investigator projects offer similar potential benefits for students, but they offer somewhat different benefits for the instructor. Instructors who develop CUREs based on large national projects such as SEA PHIRE or GEP receive significant support, including training, centralized resources, and a community of like-minded teacher-scholars. Instructors who develop CUREs based on their own research forgo these benefits (although joining groups like CUREnet or CUR can provide such a community), but have the satisfaction of driving their own research question forward. In addition, opportunities for funding and publication may be greater for independently developed CUREs.

How have other instructors introduced student-driven research projects into their courses? What are some of the key elements in this approach?

CUREs can also focus on questions that are student-defined. As for the instructor-defined CUREs, there are many that have been reported in the literature (see, for example, Healey, 2013; CUR, 2007) and many more that have not been reported. Here, we summarize two such projects and note some common features that appear to be important.

Suggesting questions and assembling diverse teams to promote research in Animal Behavior and Ecology

In Practicing Science, Weld and Heard describe a project that they have adapted for both Animal Behavior and Ecology courses, both of which enroll a diverse student population (first year to graduate students, majors and nonmajors) (2001). At the beginning of the project, the instructor presents three or four tractable behavioral or ecological questions and hypotheses and leads a discussion of background information, logistical considerations, and goals and expectations. Students sign up for one of the questions, are assembled into teams of four or five, and then design experiments to test their predictions. They then carry out their plan. Attendance at scheduled lab meetings is not required, except for a progress-report meeting one-third of the way through the semester. Students report their work in the form of a scientific paper, putting their research question in the context of past work. Importantly, the investigations “are of current topics of research and results are unknown in advance.”

 

Using a theme to promote collaboration around individual geology projects in a required, non-capstone course

In the Council of Undergraduate Research’s Developing and sustaining a research-supportive curriculum: A compendium of successful practices, Reinin and colleagues describe their systematic efforts to incorporate controlled research experiences into the Geology curriculum to complement their capstone research projects (2006).  One of the major curricular adjustments they made to reach this goal was the design of a Research Methods course with a shifting focus. Each year, the course is designed around a central theme or location, which allows students to develop individual projects but also promotes group collaboration. For example, in 2002, the central theme was field-based research at San Onofre State Beach, CA, a theme that led to one subgroup of students collaborating to collect data relevant to rock deformation—but then individually collecting additional data to complete individual projects.  The course includes written and oral presentations, with iteratively revised journal-style manuscript. Pre- and post-course surveys indicated that the course provided benefits similar to that students experienced in summer research internships. In addition, informal assessment indicated that the faculty perceived an increase in the quality of senior theses. Finally, they observed an increase in the number of students who were active in research, both in and out of class, noting an increase from 17% to 30% of students presenting a conference abstract and an increase from 8% to 28% participating in research prior to senior year.

 

These examples share some of the same features observed in CUREs focused on instructor-defined questions. Common characteristics:

  • Discovery.  The projects focus on questions with an unknown and interesting outcome. The instructor helps ensure this element by establishing a theme or themes for the course and by discussing relevant background information, but does not define the question as tightly as in the instructor-defined CUREs above. Notably, most instructor-defined CUREs that have been reported are in genomics or other fields that present significant barriers to entry for novices, while many student-defined CUREs that have been reported are in fields where methods and language are more accessible to novice researchers.
  • Bite-sized projects. The student projects are designed such that they can largely be completed in time allotted for the class, although that time may be distributed differently than in a traditional course arrangement.
  • Low resource requirements. In general, the projects have relatively low resource demands, using relatively inexpensive methods.
  • Student collaboration. Although designated by CUREnet as an essential element of all CUREs, it’s worth noting that all of the CUREs outlined here explicitly include student collaboration. Even when students complete individual research projects, collaboration is built into the course design.
  • Faculty guidance. Faculty guidance is particularly important during the experimental design phase, after which they tend to serve as a resource as students work through and troubleshoot their projects.

Student-defined CUREs offer many of the same potential benefits as instructor-defined CUREs but have the additional benefit of allowing greater student autonomy and ownership. This increased freedom, however, carries a potential downside: the instructor has to build in mechanisms to ensure that students are sufficiently familiar with relevant background information to ask novel questions, and that students are sufficiently invested in the project to ask non-trivial questions.

What existing tools can I use for assessment?

There are several existing tools that can be used to assess undergraduate research experiences, including the following:

  • CURE Survey (Lopatto and Tobias, 2010), which incorporates three elements: an instructor report of the extent to which the CURE resembles scientific research; student report of learning gains; student report of attitudes toward science.
  • Colorado Learning Attitudes about Science Survey (CLASS)
  • Undergraduate Research Student Self-Assessment (URSSA) (Hunter et al., 2009)
  • Scientific identity scale (Chemers et al., 2011; Estrada et al., 2011)
  • The Project Ownership Survey (Auchincloss et al., in press)
  • Views of the nature of science questionnaire (Lederman et al, 2002)

Dolan and colleagues emphasize the importance using tools for which validity and reliability information are available, and propose steps that need to be taken for more effective CURE assessment (Auchincloss et al., in press). Toward this goal, they propose two models that may help guide CURE development and assessment.

What are additional resources?

  • CUR (Council for Undergraduate Research)
  • CUREnet (Course-based Undergraduate Research Experiences Network)
  • CASPiE (Center for Authentic Science Practice in Education)
  • Resources provided by Mick Healey
  • How-To Guide to help you step through establishing a CURE in your course

 

References

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