Democratizing Bioinformatics Research

in a High School Biology Classroom

Bertram C. Bruce, Umesh Thakkar, Eric G. Jakobsson, Jo Williamson, Paul R.

Lock

U. of Illinois at Urbana-Champaign

How can education reflect new ways of doing science?

Bioinformatics

• Just as astronomy was transformed through the invention of the optical telescope, and later, the radio telescope, biology is becoming a new science, one which links studies of biochemistry, genetics, cellular processes, anatomy, physiology, and evolution through the structure and properties of macromolecules (Gibas & Jambeck, 2001)

• A major tool in this transformation is Biology Workbench (Subramaniam, 1998)

Biology Workbench

• Sequence alignment• Visualization• Digital library• New knowledge: potassium channels; compare

sequences from various cells, tissues, & organisms; insights into the structural correlates of ionic selectivity, permeability regulation, toxin sensitivity

• Available since June 1996• 11,000 registered users; 150,000 computing

sessions a month

Single Site Mutation in Hemoglobin

Mutated Residue in the Structure of Hemoglobin

Alignment of Sequences from Horse,

Chicken, Cow, Vulture, Dogfish, Tuna, Mole

Phylogenetic Tree from the Alignment

Open-World Learning

• open data and problems

• open computational environment

• open community

Mr. Lock’s information Ecology

• University connections• Projects in which “students have to … [find]

things that really aren’t covered in the book.” • Students have access to technologies that

professional scientists use everyday in their work.

• Collaborative learning• Articulation of learning

Inquiry-Based Learning

learning tools that are "open-ended, inquiry-based, group/teamwork-oriented, and relevant to professional career requirements”

National Science Foundation (1998). Information Technology: Its impact on undergraduate education in science, mathematics, engineering, and technology. Arlington, VA: National Science Foundation.

Inquiry Page

Inquiry Unit

• Ask: How are different organisms related? How can we show their evolutionary history?

• Investigate: Identify the evolutionary history of a group of organisms through protein sequence analysis.

• Create: Show how similar organisms are related using phylogenic trees (cladistic diagrams) .

• Discuss: Present findings in a poster session.• Reflect: Examine the learning process.

Rooted/Unrooted Trees

Presentation

Cetacean Relatedness

Chain of Use

1) The teacher educator needs to understand and value the technology

2) Education students need to be able to use and learn from the technology

3) The education student/teacher needs to take it from the college classroom to the school

4) High school biology students need to be able to use and learn from the technology

Conclusion

• challenge of integrating into educational system

• students part of a larger community of inquiry• eliding distinctions between

– practice/research– student/teacher– learner/researcher– learning/research