We conducted a three-hour bioinformatics workshop with the student teachers, whose various backgrounds included biology, chemistry, agriculture, earth science, and mathematics. The workshop constituted an introduction to Biology Workbench for all, and an introduction to bioinformatics for all but the biology majors. We divided the workshop into three sections, beginning with a context-setting discussion activity, followed by a pencil and paper exercise to introduce sequence data analysis and interpretation, and concluding with an investigation using Biology Workbench. After each section, the whole class discussed the learning and teaching that had occurred.
The context-setting activity consisted of several scenarios that connect with the field of bioinformatics, including issues surrounding the human genome project, genetic screening, forensics, and agriculture. It is designed to stimulate discussion and thought about the scientific, as well as the medical, ethical, economic, and political aspects of bioinformatics. During the discussions, students drew on their background knowledge as they engaged in discussion with each other and with us. It provided us the opportunity to learn what the students knew (and what they didn't know). In a short amount of time, the multiple connections with "real-world" topics provoked and stimulated considerable enthusiasm and interest.
The pencil and paper exercise had two parts. The first introduced students to raw amino acid sequence data, representing a wide range of primate and non-primate mammals. Students were presented with an sequence of unknown origin (collected as forensic evidence from an importer) and asked to determine if the sample was from a primate (illegal to import) or from a non-primate mammal (probably legal to import). Students confronted a small pre-selected set of short segments of sequence data from these animals, and they were to try to make sense of the data. The segments were printed out horizontally on slips of paper, and the students performed a sequence comparison, using scissors, tape and magic markers. During this exercise, students were encouraged to ask questions, and they asked interesting and relevant questions, some basic ones, such as, "What do the letters mean?" and others more complex and interpretive such as, "Why does this one area change so much and other areas stay pretty much the same for each string?"
In the second and third parts of this exercise, students were provided with outputs from the Biology WorkBench (a multiple sequence alignment and an unrooted tree) generated using the segments they just analyzed. Students worked to draw inferences about the animals' relatedness from these analyses which involved understanding something about how the data was processed, how to interpret the representations of the results, and how to draw conclusions from these representations.
These activities taught the student teachers the rudiments of sequence alignment and analysis, and how to interpret representations of data generated by bioinformatics tools. It gave them direct experience with the functions performed much more rapidly and on a much larger scale by computers in bioinformatics, but it also gave them, importantly, experience with the kinds of biological questions that can be addressed with molecular data.
In the third and final section of the workshop, we gave a brief introduction to the Biology WorkBench, and provided students with a set of data collected to look at the relationship between three sub-species of chimpanzees and their distribution across different locations. The students were asked to design an investigation that assessed the genetic basis for the differences between the three sub-species of chimpanzees.
After each section of the workshop, we discussed their answers to the following questions:
During the week after the workshop, the students wrote written responses to these questions:
The seminar's discussions and responses to these questions were thoughtful and varied, and demonstrated the following themes:
*The reason given for both #4 and #5 was that students would lack the necessary background to be successful with the activities.
As the workshop leaders, we noted a dissonance created by the student teachers' participation and the in-class responses of the non-biology teachers on one hand, and the in-class and after-class responses of the biology teachers on the other hand. All the student teachers said that real learning had taken place and they were able to articulate the components of that learning, and the non-biology teachers felt that some form of these exercises would be appropriate for and useful in their classrooms. Despite these testimonials from their classmates, the biology teachers were less sanguine about using these activities with their own students. Although the data are striking, our interpretation of the dissonance is still in the formative stages; more data collection and analysis are under way.