Building KU's Teaching and Learning Community

Thinking About the Process of Scientific Inquiry—Jen Roberts (2005)

Students in the fieldOverview

A geology professor focuses her geomicrobiology course on scientific inquiry to introduce students to a rigorous means of using the scientific method.


My motivation for developing this course stemmed from my experiences preparing seniors and first year graduate students for graduate study. I observed that students often lack skills in applying the scientific method, as well as overall experience analyzing real data sets. Unlike many subdisciplines in geology, my research program in geomicrobiology relies heavily on experimental research. This field is relatively new, with few textbooks, and is moreover interdisciplinary, drawing from biology, geology, chemistry, and engineering. Therefore, I decided to focus my geomicrobiology course on scientific inquiry in order to introduce students to a rigorous means of utilizing the scientific method.

I based the course on a novel experiment in a specific area of geomicrobiology and taught the course in parallel with a colleague at Allegheny College. Co-teaching in this way allowed us to stress the importance of scientific collaboration on a number of levels. Each class ran separate, but related, experiments, which required interdependence and cooperation among class members and resulted in active learning and teaching by students. We also introduced students to the culture of scientific peer review by having them present and defend their experimental results to their colleagues at the other institution. Overall, the exercise was intended to promote scientific curiosity and rigor, while giving students a sense of ownership in the data they produced.


Students actively participated in the course by conducting scientific research. As such, students were asked to do the following activities:

  1. Develop a proposal for experimental design based on a given research question and hypothesis.
  2. Design and conduct laboratory batch reactor experiments as a class.
  3. Gain specific skills necessary to collect data from the designed experiment.
  4. Compile and interpret data.
  5. Give a presentation and defend design and data interpretations.
  6. Evaluate original design in light of data collected and propose and defend an improved approach.
  7. Make temporal predictions of the outcome of course experiment if it were allowed to run for a longer period of time.

Lectures and laboratories were used to introduce basic knowledge and skills needed to perform the above activities. Additionally, in-class exercises and discussion using real data and primary literature were used to engage students in specific aspects of scientific discovery, such as hypothesis testing and complex experimental systems.

Student Work

Students showed impressive progress in intellectual development, particularly with regard to hypothesis testing, as assessed through proposal writing. All students took responsibility for data collection and most were capable of making astute interpretations by the end of the course. However, students' absolute grasp of newly introduced topical knowledge varied and, in most cases, this information was not completely mastered. Students also rated their own learning in the course and all students reported improvement in all aspects of the course.


Overall, this approach was highly effective in engaging students in original research and acquainting them with a more rigorous use of the scientific method. This course could be easily tailored to other disciplines because its basic premise, the scientific method, is universal to all fields of science and, in some cases, engineering. A unique component of this class was the heavy emphasis on group work combined with the fact that it was co-taught at two different universities. While group work was a valuable part of the process and realistic to the professional and academic environments, in the future I will need to maintain a manageable group size to achieve maximum student involvement and ensure active learning. Also, I will need to dedicate more time to laboratory skills so that students have ample time to acquire lab skills and assign grading credit that reflects the time and effort students put forth.

My personal interactions with students beyond the course suggest a greater retention of basic skills, such as proposal writing, and even more encouraging, a scientific curiosity and creativity that the students are applying to their personal research projects. After completing the course, students exhibit a greater level of confidence in performing research, and this contributes positively to their ability to embark on independent research, particularly at the graduate level.

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students working in the fieldBackground

Course context
Geomicrobiology is a relatively new subdiscipline in geosciences; it draws on concepts from traditional subdisciplines such as sedimentology, hydrogeology, and paleontology and melds these with microbiology and molecular biology. No standard textbooks exist for this course topic, and the field methods and lab components inherent to geomicrobiology make a lecture-only format inadequate for exposing students to the discipline. This, together with my observation that beginning graduate students often lack training in scientific inquiry, motivated me to design a course that would help students develop discipline-specific knowledge, involve them in original research experiments, and practice critical thinking and communication skills.

I addressed these issues by emphasizing research and experimental design in a new three-credit course: Applied Methods in Geomicrobiology, GEOL 591 (pdf). I taught this course concurrently and collaboratively with a colleague at Allegheny College, Dr. Rachel O'Brien. While this course is a junior/senior level course for Allegheny students, it is a senior/first-year graduate course at KU. Undergraduate students are upper-level geology majors; graduate students typically pursue advanced degrees in the natural sciences.

Learning goals
My overarching goal for the course was to get students to think about the process of scientific inquiry in the context of systems-based science—viewing the earth system as having components that are fundamentally linked rather than taking a reductionist approach typical of most experimental design in geoscience. Thus, I wanted students to design, conduct, and report experiments, not simply perform tasks that we presented to them. In doing so, I wanted students to demonstrate mastery in three areas:

  1. Proposal writing as it applies to critical thinking and evaluation of scientific questions and hypotheses.
  2. Fundamentals of experimental design in a systems-based experiment.
  3. A deep understanding of the physical, chemical, and microbiologic processes that occur and interact in shallow, low-temperature geologic systems.

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students working in the fieldImplementation

The approach: I used a six-week research project as the context for teaching geomicrobiology subject material and the process of scientific inquiry. Specifically, my collaborating instructor and I asked students at each institution to design and conduct laboratory batch reactor experiments as a class, collect data, compile and interpret data, interpret results, present and defend design choices, and propose improvements, then make predictions for the experiment if it were to run for a longer period of time.

Early in the term, my class took a field trip to a petroleum-contaminated aquifer near Bemidji, MN. (For pictures of the field trip, please click on the thumb nails at the bottom of the page.) This site has been studied extensively by the USGS and other scientists as an example of natural attenuation of hydrocarbons by in situ subsurface microorganisms, and it has produced new insight into our understanding of microbe-mineral-water interactions. The field trip allowed us to collect necessary materials such as sediment and groundwater that we later used in our experiments. Furthermore, the field experience helped students conceptually connect their experimental laboratory work to the field site. It also provided exposure to field sampling of sediment and groundwater and preservation techniques necessary for successful sampling of labile solutions and microorganisms. Due to lack of resources, the Allegheny students couldn’t attend; however, the Allegheny instructor attended and videotaped the field trip. To maintain consistency in experimental design between classes at each school, KU students constructed experimental samples in vessels for both institutions, then shipped them to Allegheny for analyses.

We also dedicated several class meetings to data discussions during which students in each class critically examined a particular dataset (i.e. one component of the system, such as pH, biomass, etc.). Different students were asked to prepare pertinent figures and tables for each data discussion. They were also encouraged to refer to course materials as a basis for interpreting data. Students needed to provide justifications for their interpretations and generate alternative hypotheses or null hypotheses. Although it felt forced at first, this interaction led students to make better interpretations as the semester went on. Students developed a critical eye for potential errors and became accustomed to trouble-shooting a technique to understand inherent discrepancies in data. These class meetings were essential for addressing some of the practicalities of scientific inquiry, such as imperfect data, and instrument and analyst error.

Assessment: To assess learning progress, we used three scaffolded assignments, a mid-term proposal, a group presentation, and a final report.

Assignments:  To help familiarize students with the subject and develop a context for their research, I created short writing assignments to augment lectures. These assignments each had a similar format: several questions that increased in difficulty (within a single assignment) from basic definitions to conceptual synthesis, and ultimately asking students to design an experiment to address the topic. See writing assignment #1 and rubric.

Mid-term proposal: In the third week of class Dr. O'Brien and I assigned the first major assignment to prepare students for the design and construction of the course experiment. After introducing the fundamentals of geomicrobiology and experimental design, we presented each class with a set research question: How do increases in silicate-bound Ni concentration impact microbially-mediated silicate weathering by a native microbial consortia?

Allegheny students were asked to consider aerobic consortia, while KU students considered anaerobic consortia. This division was based on the premise that each metabolic guild has different requirements for Ni, which, in turn, might impact weathering. We also gave the students some sense of our expected results. We then asked them to design an experiment to answer the posed question. For guidance, we gave them a defined number of issues that they had to address; we also built a grading rubric directly from these guidelines. (See experimental design exercise.)

Once the proposals were complete, we presented each class with a final experimental design and detailed instructions on how we would be constructing the experiment. We then had a discussion about the pros and cons of our decisions and alternate choices we might have made.

Group presentation: We assessed the ability of students to interpret and synthesize their data using group presentations. We based their grade on a rubric we distributed earlier in the semester. Students from the two schools interacted via digital slide presentations delivered during a teleconference session. Grading was based on presentation and interpretation of data, as well as questions posed and answered. (See grading criteria for final project.)

Final report: Originally Dr. O'Brien and I had envisioned a final report in which students came up with a completely new research question and design. However, because group proposals and presentations exposed some gaps in knowledge, we decided that students would benefit from continuing their evaluation of the course experiment. We therefore designed a final assignment based on the previous ones. It focused students' energy in a direction in which they had already invested and had confidence. We asked them to evaluate the original experimental design in light of the results collected and propose a new and improved design. We also asked them to predict the outcome of the current experiment were it to be continued. (See writing assignment guidelines.)

Lepland, A., van Zuilen, M.A., Arrhenius, G., Whitehouse, M.J., and C.M. Fedo, 2005. Questioning the evidence for the Earth’s earliest life—Akilia revisited. Geology, 33 (1), pp. 77-79.

Mojzsis, S.J., Arrhenius, G., McKeegan, K.D., Harrison, T.M., Nutman, A.P and C.R.L. Friend, 1996. Evidence for life on Earth before 3,800 million years ago. Nature, 348, p. 55-59.

Schopf, J.W., 1978. The Evolution of the Earliest Cells (chapter 1), in Life at the Edge: Readings from Scientific American. Gould, J.L. and C.G. Gould (eds.) NY: Freeman Press, 1989.

Field trip pictures
Please click on the thumbnails below for full-sized pictures of the class field trip.

Statue of Paul Bunyan's "Babe"
Students working with equipment
measuring tools
Student holding a pipe
students unhauling equipment from a truck
students working in the field
laboratory equipment
a group of students
students working with equipment
students measuring water samples
students cutting a piece of pipe
students measuring water samples
students going over some data
students working in the field
a collection of soil samples
jars of soil samples

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Students working in the fieldStudent Work

Approaching the course as an experiential research experience necessarily decreased the overall breadth of coverage in the subject area. However, we saw impressive gains in students’ intellectual development and ability to think critically about the scientific process. Such gains were reflected in their writing assignments (see examples from assignment 3 below). Moreover, I observed that during data discussions students became increasingly eager to participate and seemed invested in data quality.

Proposal: As expected, no one student completed all aspects of the proposal satisfactorily, but all of them grasped a majority of the concepts. We critically evaluated these assignments and gave students lots of feedback to use in their data interpretation and final reports, but gave the assignment less weight towards the final grade than originally planned. Please see the examples below for examples of student work and our feedback.

Group Presentation: Both groups performed well in terms of presentation quality; however, the Allegheny group (pdf) was more successful in their interpretation and synthesis due, in part, to a clear-cut data set. KU students (pdf) found their data to be more complex, and while their interpretations were defendable, there was more synthesis needed.

Final Report: Students showed exceptional improvement from their initial proposal and by the end of the course, demonstrated true understanding of experimental design (as judged by the first component of the assignment). However, only a few students demonstrated a clear understanding of the complex processes which dictated biogeochemical change in their experiments, and only these students were able to make reasonable and supported predictions about the sequence of events that would occur in the ongoing experiment.

Students were also asked to complete a self-evaluation (pdf). Significantly, all students reported improvement (rated as “some” and “significant”) in all queried topics. Graduate students reported less significant improvement in individual topics than did undergraduates. Most students had little knowledge of geomicrobiology prior to the course; they felt that the hands-on approach was valuable and that they gained significant knowledge in the field.

For more information, please see this graph of the course's grade distribution.

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students working in the fieldReflections

Class dynamics and flow
The KU group was larger, and this made group work difficult to manage. Feedback from students suggested that there was some resentment about group grading. In the future I will need to break the class into smaller groups in order to make this a rewarding experience for students and to better evaluate their learning. By taking academic level into account when assigning groups, I may decrease the discrepancy in experience that appeared to cause unbalanced workloads between graduate and undergraduate students. However, for some assignments, I will continue to assign a single grade to group work in order to familiarize students with common workplace practices.

Both KU and AC undergraduate students felt the pace of the course was too fast, and a majority of KU and AC students felt that the workload was too heavy for at least part of the semester. Specifically, students felt that too much credit was given to the writing assignments (which were universally reviled) and not enough to data collection. These were viewed as time and thought intensive endeavors that were not rewarded in kind. In the future I will need to redistribute credit given for writing assignments and data collection. To further address this issue, I will likely add a lab/discussion period to the course and perhaps increase the credit load. This will give the students dedicated time to collect data and additional time to work on writing assignments in weeks when data collection is lighter. Adding a credit and a lab would also give me a chance to interact with students to a greater extent in the laboratory environment.

Lasting effects
Both instructors have found that the interaction between students and instructors has continued beyond the completion of the course and to a greater extent than in other courses we’ve taught. This interaction has focused primarily on students who pursue independent research projects (not supervised by the instructor). At KU both graduate students and one undergraduate have continued to collaborate with the instructor on their independent research. One graduate student proposed a new line of experimental inquiry to explain trends in field data. The undergraduate student took the skills learned in the course and applied it to her senior research, which has resulted in a publishable manuscript. Impressively, both students took ownership of their studies and implemented their knowledge into ongoing research.

Overall, I found that my graduate students who were enrolled in the course transitioned into proposal writing and laboratory work with less angst relative to previous years when I taught the same material in a lecture-style format. Before, I taught a course that covered the topical material, then met with students separately to go over field and lab techniques, and some time later met to discuss proposal writing. The geomicrobiology course synthesized different aspects of research and seemed to decrease the steepness of the learning curve for students embarking on independent research. Students from the course also took less time to initiate and engage in active research.

Almost all aspects of my approach to teaching this class were new, including co-teaching. Though I have collaborated with other researchers on proposals and manuscripts, I had not encountered a clash in personal work styles until this class. For example, to ensure continuity between lectures given separately at each campus, I proposed we exchange PowerPoint lectures (the cost and trouble for videoconferencing or pre-recording were prohibitive at that point). Thus, we divided the course topics and each designed half of the lectures. However, the Allegheny instructor hadn’t previously taught with PowerPoint. This, along with different expectations for the degree (and timing) of preparation for class, created frustration for both instructors. Moreover, although the PowerPoint slides were the same for each class, we did not have an ordained leader to make decisions on pace and delivery style, resulting in a lack of consistency between classes. In addition, students did not have direct access to both instructors and therefore could not capitalize on their individual expertise. Conflicts in our teaching approaches were likely exacerbated by the geographic distance between the two institutions.

In hindsight, however, I learned a lot from my collaborator’s approach. In particular, I learned to take more cues from the class and modify my teaching approach to facilitate understanding, regardless of the schedule. In addition, I valued our teamwork in identifying the overall goals of the class and designing the major learning components. These were collaborations that were successful and met the needs of both classes, despite our different teaching styles. We hope that the experience will translate into a manuscript, and we believe that the basic skeleton of the course would translate well to a number of different scientific fields.

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