Thinking About the Process of Scientific Inquiry
Summary: A geology professor focuses her geomicrobiology course on scientific inquiry
to introduce students to a rigorous means of using the scientific method.
Background
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.
Implementation
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 Performance
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.
Reflections
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 cotaught 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.
Background
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 threecredit course: Applied Methods in Geomicrobiology, GEOL 591. 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.
Implementation
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. 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.
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.
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.
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.
Student Performance
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. 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.
Group presentation: Both groups performed well in terms of presentation quality;
however, the Allegheny group was more successful in their interpretation and synthesis
due, in part, to a clear–cut data set. KU students 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. 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.
Reflections:
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.
Co-teaching
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.