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Bioinformatics in the Biology Classroom

Kathleen M. Gabric

articlehighlights

Bioinformatics — any use of computers to handle biological information — offers students the opportunity to:

  • experience inquiry-based learning
  • apply real-life data to problem-solving
  • understand how bioscience concepts are connected
  • discover ethical issues of real-world science

May 2003

The students chatted excitedly at the start of class; but it wasn’t about the recent basketball win or the latest real-TV episode. It was about the next gene they had just “discovered.” Can it be genetically engineered for the advancement of humankind?

Great teaching materials are often free from reliable sources.
gabric.jpg

Screenshots of the excel workbook ABO Blood Group Frequencies to compare methods for calculating allele frequencies of ABO blood groups. Authors: 
John R. Jungck and Jennifer A Spangenberg, Beloit College. Publisher/Photo: BioQUEST Curriculum Consortium.

This isn’t some teacher’s fantasy biology class. I frequently hear students discussing their recent discoveries as I eavesdrop on classroom conversations during lab time. Since the implementation of sophisticated bioinformatic databases such as Biology Workbench and the Online Mendelian Inheritance in Man, I have witnessed an improvement in the level of biological questions and discussions in my classroom. If your school has computers and an Internet connection, this could happen in your classroom, too. The new student interface at Biology Student Workbench makes maneuvering through sequence databases very intuitive. All you need is a curious mind and you can bring your students into the real world of science exploration, taking them from textbook to cyberscience. On top of all this, these resources are provided free of charge by very reliable sources: the National Center for Supercomputing Applications and the National Institutes of Health.

Bioinformatics will play a key role for science students pursuing higher education.

“Roughly, bioinformatics describes any use of computers to handle biological information.”12 In addition to its immediate value in the high school classroom, many students will likely benefit from an introduction to bioinformatics if they intend to pursue higher studies in bioscience disciplines such as:

  • computational molecular biology, where computers are used to characterize the molecular components of living things
  • comparative genomics, that looks for the differences and similarities in the genes of species
  • structural genomics, i.e., identifying and predicting protein structures
  • medical informatics, the management of biomedical data
  • pharmacogenomics, that aims to identify drug targets by applying genomic approaches and technologies
  • … and many more

Inquiry-based technique

Using bioinformatics can foster inquiry learning of content that has often been taught in a dry manner.

“The explosion of data produced by the Human Genome Project has called forth the creation of a new discipline — bioinformatics, whose focus is on the acquisition, storage, analysis, modeling, and distribution of the many types of information embedded in DNA and protein sequence data.”9 The hope of this article is to encourage teachers, high school through college, to integrate bioinformatic tools in their classroom as a means of providing inquiry-based teaching techniques in subject areas that have been more “chew and chuck” in the past. By this, I refer to giving students the facts and then having the facts regurgitated without meaningful learning having occurred.

“The fundamental nature of science is imbedded in inquiry-based learning. Inquiry can be a very effective mechanism for better understanding the essence of science, its technical and reasoning processes, and the attitudes that accompany these processes.”8 Inquiry learning directly translates from the classroom to society as students search for answers to problems they have encountered in their home, school, or community. Using bioinformatic tools, students generate real data and more importantly apply these applications to independent problem solving. During this process they are actively engaged in the process of learning, and active learning strategies promote more effective learning.3

The U.S. National Science Education Standards (NSES) have provided guidelines to improve the learning environment. “The standards have, in turn, yielded a widely endorsed set of specific goals, such as the following:

The NSES endorses standards for inquiry-based learning.
  • Students should learn science and mathematics as active processes focused on a limited number of concepts.
  • Curricula should stress understanding, reasoning, and problem solving rather than memorization of facts, terminology, and algorithms.
  • Teachers should engage students in meaningful activities that regularly and effectively employ calculators, computers, and other tools in the course of instruction.”2

Bioinformatics will help teachers and students achieve these goals by providing opportunities to use new technologies during science activities.

Bioinformatics as a unifying tool

Bioinformatics can provide the thread that ties your class together.

Bioinformatics can provide the thread that connects many topics: protein structure, protein function, nucleic acids, genetics, genetic disease, evolution, cell biology, botany, and zoology. Most students view these topics as individual chapters in a book, unrelated to one another despite teachers’ attempts to unify the material. Students study biochemistry, get their test grade, and then forget the material. Use of bioinformatics ties this information together while teaching analysis and interpretation skills in an active, productive learning environment. Biology Student Workbench is a wonderful tool for students to experience the Central Dogma of biology:

  • DNA and replication
  • RNA and transcription
  • proteins and translation

and then to apply it to

  • genetic disease
  • evolution
  • human physiology

As a result, students are better able to construct meaning from the content and show a greatly increased ability to make connections between units of study.

Real world science

Integration of bioinformatics into the high school curriculum will improve biology teaching.

Integration of bioinformatics into the high school classroom will further advance biology education. “Technology makes learning more interactive, enjoyable, and customizable, and this improves students’ attitudes toward the subject and their interest in learning.”10 In addition, it can be argued that the introduction of this technology will prove to be an increasingly important aspect of science education. The National Science Education Standards states: “The relationship between science and technology is so close that any presentation of science without developing an understanding of technology would portray an inaccurate picture of science.”6 Bioinformatics promotes the application of basic scientific research to the teaching of biology. These tools have been used in the classroom to

  • demonstrate the importance of the primary structure in proteins,
  • visualize the mechanism of translation from nucleic acid to protein,
  • and teach about DNA sequencing, the Human Genome Project, and other topics that have previously left little room for student exploration.

Bioinformatics supports the biotechnological techniques that are applied in the classroom. Certain techniques such as DNA fingerprinting and PCR are being used more and more frequently in high school classrooms, and can be facilitated by bioinformatics. For example, if a class performs electrophoresis of the proteins in fish muscle, they can then go a step further and explore whether the actin found in both salmon and trout is identical or if there have been any evolutionary changes.

Many current social and ethical controversies, such as

Learning of biotech issues and ethics can be augmented by bioinformatics.
  • genetic engineering
  • biological warfare
  • stem cell research

as well as unsolved biological mysteries, such as

  • the history of human evolution
  • phylogenetic trees
  • origins of species

are raised by the students as they manipulate this data, thus leading to further explorations. Utilizing technology students can capitalize on these related explorations and thus exercise learner-control while increasing their motivation and making connections to the real world. “Technology also allows for data-driven assessments tied to content standards that, when implemented systemically, enhance the achievement of students as measured in a variety of ways, including, but not exclusively limited to, standardized achievement tests.”10

Bioinformatics in the classroom exposes students to real-world science.

The goal of integrating bioinformatics in the classroom is to expose students to real-world science and the use of bioinformatics in solving real-world problems. Tutorials are available online to help students and teachers learn how to navigate the student interface of Biology Student Workbench and gather data that can be applied to original questions. Lessons have been developed that are appropriate for the high school level. These lessons center on topics such as

  • DNA sequencing
  • the role of amino acids in protein functioning
  • the molecular basis of genetic diseases
  • the use of protein sequences in determining evolutionary relationships

A recent observer of a class involved in such a lesson commented on how amazing it was to see that all the students were busy, engaged, and involved while the teacher operated from the sidelines. Some students exhibited concentration that was narrowly focused as they manipulated their data while others discussed their findings enthusiastically with their neighbor. In all cases, the discussions were centered on bioinformatics.

Conclusion

Conclusion: Bioinformatics can help reform biology teaching and improve learning.

All science instructors, from kindergarten teachers to college professors, are aware of the national call for reform in science education.1,5,6,7 Further investigation is needed into what constitutes best practice. The nature of this research needs to emerge from the extensive data that qualitative research affords. This data emerges from the classroom. It does not appear in the form of tests or worksheets, but in the body of work the students produce, the quality of projects, and the “Aha!” moments that the teacher witnesses.11 A test at the end of term cannot capture those points in time.

Leamnson in the article “Learning as Biological Brain Change” discussed the difficulty of teaching: “The really difficult part of teaching is not organizing and presenting the content but rather in doing something that inspires students to focus on that content … to have some level of emotional involvement with it.”4 Bioinformatics turns students and teachers into researchers in their own classroom and inquirers into the teaching and learning process. Experience those “Aha!” moments in your classroom by giving bioinformatics a try.

Kathleen Gabric teaches biology at Hinsdale Central High School in Illinois. For the last 2 years, under a National Science Foundation GK12 grant through the University of Illinois, a molecular biology Ph.D. student helps Gabric in her classroom several times a month. Together, they have developed curriculum utilizing the vast resources offered by bioinformatics. Gabric received her B.A. in Zoology from DePauw University in Indiana and an M.S. in Biology from Illinois State University in 1985. She has made pedagogical presentations at numerous conventions, including the American Assoc. for the Advancement of Science (2003) and has been recognized as an outstanding teacher in Illinois by several awards. She is in her 18th year of teaching.
http://www.hinsdale86.org/staff/kgabric/gabric.html

Bioinformatics in the Biology Classroom

Biology Student Workbench Interface

An educational-oriented interface to the Biology Workbench developed for people who have little experience with bioinformatics and associated tools.
http://bighorn.animal.uiuc.edu/cgi-bin/sib.py

National Center for Supercomputing Applications

The NCSA is “a leader in defining the future’s high-performance computing infrastructure for scientists and for society” and “works with government agencies, communities, and schools to discover how high-performance computing and communication can benefit them.”
http://www.ncsa.uiuc.edu/

Online Mendelian Inheritance in Man

  • » OMIM: This database was developed for the World Wide Web by the National Center for Biotechnology Information (NCBI) and provides a catalog of human genes and genetic disorders. The database contains textual information, pictures, and reference information.
    http://www.ncbi.nlm.nih.gov/omim/
  • » Entrez Gene is a searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer
    http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene

Guide to Selected Bioinformatics Internet Resources

This 2002 guide offers information, guidelines, and an extensive list of links, organized by topic. Educators with limited knowledge of bioinformatics can try one of the online tutorials suggested.
http://www.istl.org/02-winter/internet.html

Bioinformatics resources/tutorials

“This site provides short and concise introductions to basic concepts in molecular and cell biology and bioinformatics. The main emphasis is placed on making it as easy as possible for the user to understand which tools and databases are available from the EBI (European Bioinformatics Institute) and from sites belonging to its collaborators.”
http://www.ebi.ac.uk/2can/home.html

Molecular visualization

Free software for 3D molecular visualization that is provided in a downloadable format.

Inquiry Page

“A dynamic virtual community where inquiry-based education can be discussed, resources and experiences shared, and innovative approaches explored.”
http://www.inquiry.uiuc.edu/

Bioinformatics projects

A web page by Kathleen Gabric, author of the above article, on which several bioinformatics projects for her honors biology class are posted.
http://www.inquiry.uiuc.edu/bin/update_unit.cgi?command=select&xmlfile=u11901.xml

National Institutes of Health

This U.S. government site provides information on health issues and scientific resources.
http://www.nih.gov/

Read a book

Bionformatics for Dummies, by Jean-Michel Claverie (one of the founders of modern bioinformatics) and Cedric Notredame, is aimed at people who are beginners and offers the basics, practical advice, and help with web resources and tools (John Wiley and Sons, 2003).

Bioinformatics.org

An international non-profit organization “which promotes freedom and openness in the field of bioinformatics … by providing free and open resources for research, development and education.”
http://bioinformatics.org/

nwabrlogosmall.png

Teaching Resources from the Northwest Association for Biomedical Research (NWABR)

The Northwest Association for Biomedical Research (NWABR) strengthens public trust in research through education and dialogue. Its diverse membership spans academic, industry, non-profit research institutes, health care, and voluntary health organizations. Through membership and extensive education programs, it fosters a shared commitment to the ethical conduct of research and ensures the vitality of the life sciences community.

Introductory Bioinformatics: Genetic Testing
The curriculum unit explores how bioinformatics is applied to genetic testing. Students are also introduced to principles-based bioethics in order to support their thoughtful consideration of the many social and ethical implications of genetic testing. Throughout the unit, students are presented with a number of career options in which the tools of bioinformatics are used.
http://www.nwabr.org/curriculum/introductory-bioinformatics-genetic-testing
Advanced Bioinformatics: Genetic Research
This curriculum unit explores how bioinformatics is used to perform genetic research. Students examine DNA sequences from different animal species, investigate the relationship between protein structure and function, and explore evolutionary relationships among eukaryotic organisms. Throughout the unit, students are presented with a number of career options in which the tools of bioinformatics are developed or used.
http://www.nwabr.org/curriculum/advanced-bioinformatics-genetic-research
NWABR Research Study on Bioethics Education
Fostering Critical Thinking, Reasoning, and Argumentation Skills through Bioethics Education –results show that when students learn strategies for ethical reasoning, they grow significantly in their ability to develop strong arguments for their positions.
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0036791

  1. American Association for the Advancement of Science (1990). Science for all Americans: Project 2061. New York: Oxford University Press.
  2. Division of Research, Evaluation and Communication, Directorate for Education and Human Resources. The Learning Curve: What We Are Discovering about U.S. Science and Mathematics Education. Edited by Larry E. Suter. Washington, DC: National Science Foundation, 1996 (NSF 96-53). http://www.nsf.gov/pubs/1996/nsf9653/nsf9653.htm (accessed May 10, 2003)
  3. Jones, B., Valdez, G., Nowakowski, J., & Rasmussen, C. (1994). Designing Learning and Technology for Education Reform. Oak Brook, IL: North Central Regional Educational Laboratory.
  4. Leamnson, R. (2000, November/December). “Learning as biological brain change.” Change, pp 34-40.
  5. National Commission on Excellence in Education. (1983). A Nation at Risk: A Report to the Nation and the Secretary of Education, US Department of Education. Washington, DC: Government Printing Office.
  6. National Research Council. (1996a). National Science Education Standards. Washington, DC: National Academy Press.
  7. National Research Council. (1996b). From Analysis to Action: Undergraduate Education in Science, Mathematics, Engineering, and Technology. Washington, DC: National Academy Press.
  8. Northwest Regional Educational Laboratory. (December, 1999). Science Inquiry for the Classroom. Portland, Oregon. http://www.nwrel.org/msec/images/science/pdf/litreview.pdf (accessed May 10, 2003)
  9. Rowen, L., Mahairas, G. & Hood, L. (1997). “Sequencing the human genome.” Science, 278, 605-607.
  10. Valdez, G., McNabb, M., Foertsch, M., Anderson, M., Hawkes, M., and Raack, L. (2000). Computer-Based Technology and Learning: Evolving Uses and Expectations. Oak Brook, IL: North Central Regional Educational Laboratory.
  11. Wiggins, G. & McTighe, J. (1998). Understanding by Design. Alexandria, VA: Association for Supervision and Curriculum Development.
  12. “What is Bioinformatics?” from Bioinformatics.org http://bioinformatics.org/faq/#whatIsBioinformatics (accessed May 10, 2003)

author glossary

Bioinformatics: the application of computer technology to gather, store, analyze and integrate biological and genetic information

Biotechnology: biological science when applied especially in genetic engineering and recombinant DNA technology

DNA sequencing: determining the order of nucleotides (adenine, thymine, guanine, and cytosine) in a section of DNA

Electrophoresis: the movement of molecules (such as proteins and nucleic acids) through a gel due to electrical poles established by electrodes in contact with the medium. The process separates molecules into bands according to size

Evolution: a theory that the great array of species has their origin in other preexisting types and that the distinguishable differences are due to modifications in successive generations

Genetics: a branch of biology that deals with the heredity and variation of organisms

Human Genome: the entire collection of genes within human cells

Human Genome Project: a massive effort funded by the U.S. government to map each of the human chromosomes

Inquiry Learning: a hands on approach to learning that involves asking questions, making discoveries, and rigorously testing those discoveries in the search for new understanding

Nucleic acids: DNA or RNA

Polymerase chain reaction (PCR): a common method of creating copies of specific fragments of DNA

Replication: making an identical copy of DNA before cell division

Transcription: making a RNA copy from a strand of DNA

Translation: making a protein from the message encoded in the RNA by DNA

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