Mining Databases and Solving Problems: 
Modeling Biology Learning on Biology Research


at the


University of Wisconsin-Madison


prepared for


The Institute on Learning Technology


part of the


 


Spring 2001

This quicklook also is available from the
Learning Through Technology web site,
http://www.wcer.wisc.edu/nise/ilt/


Mining Databases and Solving Problems: 
Modeling Biology Learning on Biology Research


Sam Donovan
Visiting Assistant Professor, Biology Department
Assistant Director, BioQUEST Curriculum Consortium
Beloit College
Beloit, Wisconsin


Why use technology?
I want my students to get experience in what biologists actually do. To do that, IÕve worked at 
taking the tools that biologists use in the real world and finding ways to bring them into the 
classroom. It seems unrealistic to expect students to develop any appreciation for what science 
is if we only present them what is already known and have them do labs that are designed to 
confirm expected outcomes. At some point in each of my courses I want students to pursue a 
problem that they have had some role in shaping, using methods that reflect realistic scientific 
inquiry.

Computers play a variety of roles in biological research (e.g., data acquisition and analysis, 
modeling and simulation) and I try to take advantage of those different functions when I am 
providing investigative opportunities for students. I am concerned about finding a balance 
between wet lab experiences and computer based experiences. You canÕt rely exclusively on 
either approachÑthey complement one another in very important ways. The challenge for me 
involves trying to find a balance between different types of research, trying to find ways to 
integrate them so that the simulations the students are running complement what theyÕre doing 
in a wet lab, and making sure that both complement lecture and discussion.

Beloit College is a small liberal arts college in Southern Wisconsin that emphasizes innovative 
teaching and student-faculty collaboration. The academic culture here at Beloit is such that 
students expect to do research projects in all their science courses, and technology is highly 
integrated across the curriculum. Besides being a supportive environment for trying new things 
in the classroom, Beloit is also the home (since 1986) of the BioQUEST Curriculum Consortium, 
an international group of educators and institutions dedicated to the reform of undergraduate 
biology education (http://bioquest.org). BioQUEST materials emphasize giving students the 
opportunity to learn science by identifying and solving problems using the same methods and 
tools that research scientists use. The teaching philosophy has been described as the 3Ps: 
Problem Posing, Problem Solving, and Peer Persuasion (see http://bioquest.org/peas.html for 
more information).


The courses
IÕve taught a variety of courses here at Beloit including Human Biology; Biological Issues: 
Understanding Evolutionary Explanations; Genetics; and Evolution. All of these courses have 
labs associated with them; they serve 20-30 students; and IÕve used learning technology in all of 
them. 


The strategy
It has been my experience that most students come to a science course expecting to be told 
what the facts are in that discipline. While there is certainly a great deal of accumulated 
knowledge in any field of scientific inquiry, I resist taking on a role as the dispenser of what is 
known, because it tends to reinforce several problematic misconceptions about the nature of 
science. Instead, I try to put students into situations where they need to make sense of data and 
apply theoretical models to explain phenomena. This helps them understand that doing science 
is actually a very dynamic, creative, and social process. 

I suppose that another way to characterize the approach I take to teaching is to think of the 
factual information as the starting point for understanding the discipline, not the end product. 
Thinking about a course this way, one would learn about something like the central dogma (the 
flow of information from DNA to RNA to protein) as a means of addressing some interesting 
biological problems, such as how we can understand the genetic inheritance patterns for certain 
diseases. If you can make this shift away from an emphasis on rehearsed facts and toward 
using what we know to solve problems, it really opens up opportunities for students to apply 
what they know and see the relevance of the material beyond the scope of the course.

The difficult part, of course, is finding ways to create these "open-ended" learning environments 
for students. It is also tricky to get students used to defining their own problems and pursuing 
them without strict protocols to follow. I rely heavily on learning technologies (e.g., simulations, 
modeling tools, and electronic data sets) to provide rich problem spaces for students. I think the 
best way to help students learn how to work on problems is to give them lots of practice. In the 
Genetics course, for example, students prepared weekly poster presentations of their findings 
from computer-generated problems they had been assigned. As they worked each week to 
convince their peers that they had viable solutions to the problems, they became much more 
comfortable with their own ability to collect and analyze data in support of a particular 
hypothesis. Over the course of the semester students learned to take information from the 
textbook (such as a description of epistasis - the interaction of several genes to produce a 
phenotype) and apply it, as a researcher would, to develop tests that check to see if the 
inheritance of a character is following that model.


The learning technology
The Genetics Construction Kit (http://bioquest.org/BQLibrary/library/gck.html) is a simulation 
that provides students with populations of fruit flies they can cross in order to discover the 
patterns of inheritance for various characters. What I like about this program is that I have a 
great deal of flexibility in defining the genetics of the populations students will work with. 
However, because GCK is a "problem generator," each group of students can work on a unique 
problem though they all share the same underlying genetics. This means that there is no pre-
determined right answer and we all are forced to look at the evidence they collect to support 
their hypotheses. 


BIRDD: The Galapagos Finch Database (http://bioquest.org/BQLibrary/firstreview/birdd.html) is 
a big collection of raw research data on the Galapagos Islands and the finches that live there. 
The strength of this resource is that it brings together so many types of data (maps, habitats, 
weather, morphology, distribution, songs, molecular sequences, etc.) that students can do the 
kinds of integrative analyses that evolutionary biology demands. I have had success using 
BIRDD data as the basis for original research projects in both majors and non-majors courses. 
There was a real sense of scientific community established when we were all working on 
different aspects of the same system.

The Biology Student WorkBench (http://bioquest.org/bioinformatics/ and 
http://glycine.ncsa.uiuc.edu/educwb/): is a set of resources for the analysis of molecular 
sequence and structure data. The Biology Workbench was designed as a research tool, but we 
have a National Science Foundation funded project to bring these powerful bioinformatics 
resources to an education audience. The use of bioinformatics tools to organize and analyze 
massive amounts of publicly available biological data is revolutionizing research in many 
disciplines. The Biology WorkBench (http://workbench.sdsc.edu/) provides students (and 
researchers) with web-based access to an integrated suite of bioinformatics resources. Within a 
common interface, students are able to do things like search databases, align sequences, 
predict restriction sites, build phylogenetic trees, and view 3-dimensional protein structures. 
Because the Biology WorkBench is Web-based, it can be accessed from a PC or a Macintosh 
and you can save your work within the Workbench, without having to download anything.  

In my genetics course, students worked in groups to investigate a family of related proteins 
(such as the globins or the potassium channels) that have similar functions. In addition to doing 
the background research on the natural history of the gene family, they were able to compare 
different proteins to identify conserved functional domains and hypothesize about different 
mechanisms that may have lead to the changes in sequence and function of the different family 
members. In the evolution course we examined the phylogenetic relationships between the 
primates by analyzing a variety of gene sequences. In addition to considering how different 
genetic markers (such as restriction sites and microsatellites) can be used to build phylogenies, 
we were able to compare trees built from genes that have experienced very different selection 
pressures over evolutionary time. Each of these investigations required that students spend 
some time learning how to use the Biology WorkBench tools. However, because these are real 
research tools, understanding how to use them was a valuable part of what students took away 
from the experience. 


The results
There are always a few students who have a negative initial reaction to the use of technology in 
my courses. I've found that by using the same tools several times for different assignments, 
students are able to work past their barriers to the technology and see the computers as ways 
to work on interesting biological problems. In general, I think we tend to overestimate the impact 
of the first exposure to a tool on students' learning. On the other hand, I think we underestimate 
the impact that can be achieved by more in-depth use of a real research tool. As students gain 
familiarity with the details of how to use a piece of software, they can begin to use it more 
effectively. We often get trapped jumping from one tool to another in our teaching and never 
letting students feel a sense of control over the technology they are using. There are aspects of 
biology that can only be done with the aid of computers, so we will need to continue to work on 
ways to help students effectively use these tools.

If you have any questions about BioQUEST, GCK, BIRDD, or the Biology Student Workbench, 
please contact me at: donovans@beloit.edu


LINKS
BioQUEST:
http://www.bioquest.org/
BioQUEST Library:
http://www.bioquest.org/BQLibrary/index2.html
3P's:
http://www.bioquest.org/peas.html
Genetics Construction Kit (GCK):
http://www.bioquest.org/BQLibrary/library/gck.html
BIRDD: 
http://www.bioquest.org/BQLibrary/firstreview/birdd.html
Biology Workbench:
http://workbench.sdsc.edu/
Biology Workbench Investigative Portal:
http://glycine.ncsa.uiuc.edu/educwb/
Biology Workbench-Bioinformatics:
http://www.bioquest.org/bioinformatics/
BioQUEST ordering information:
http://www.apnet.com/bioquest/order.htm