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Genome Island

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© 2008 Mary Anne Clark

EDUCAUSE Review, vol. 43, no. 5 (September/October 2008)

Genome Island

Mary Anne Clark

Mary Anne Clark ("Max Chatnoir" in Second Life) is Professor of Biology at Texas Wesleyan University. Comments on this article can be sent to the author at mclark@txwes.edu and/or can be posted to the web via the link at the bottom of this page.

Genome Island (http://slurl.com/secondlife/Genome/118/145/53) was created to explore the potential for creating an interactive laboratory environment in the 3D virtual world of Second Life. College and university science courses that include a laboratory typically, because of the constraints of class scheduling, separate the lecture and laboratory components into different time blocks, and one of the challenges of college/university science becomes the meaningful integration of the two experiences. Virtual worlds offer the opportunity to eliminate the lecture/lab boundary by immersing students in an environment to be investigated. At Genome Island, that environment is populated with cats and chromosomes, flowers and fruit flies, mice and mixollamas (mythical creatures that started to be hippos but mutated somewhere along the way), each of which responds to a touch by acting out some principle of genetics.

The objects are organized into several clusters (http://faculty.txwes.edu/mclark/Genome/Genome_Map.htm). In the southeast quadrant are the abbey and gardens, whose peas and flowers represent basic Mendelian inheritance patterns. The northeast quadrant is composed of several terraces, housing animal models that illustrate more complex inheritance patterns, along with a garden of prokaryotic genomes. In the northwest quadrant are the tower, which houses molecular and human genetics, and a boardwalk with representative eukaryotic genomes. The southwest quadrant is home to the gene pool, representing population genetics, and a student atelier, where students or collaborators can create their own genetic models.

Genome Island was built for college and university undergraduates studying biology; most of the material is suitable for entry-level students. For most biology majors, a visit to the island might occupy just a few weeks of an introductory biology course. However, a full-immersion course for students at my university, Texas Wesleyan, is scheduled for Fall 2008. The island is open to the public, and anybody is welcome to drop in. Currently, Genome Island gets about 225 unique visitors a month. For each of the sixteen different activity areas monitored, the mean number of visitors is about 100, so an average visitor might encounter about half of the available activities. The mean time spent on the island per visitor is about two hours. Although I have no means of distinguishing casual visitors from other people's students on assignment, I would estimate that 10 to 20 percent of the island's visitors are students.

There are hundreds of interactive objects on Genome Island. Among these are about forty sets of experimental objects that generate analyzable data. Others are primarily informational, although the information they provide can be used for comparative purposes. The following three examples illustrate the range of activities now available on the island.

Information is provided about the features of eighteen prokaryotic and fifteen eukaryotic genomes. The human genome is represented by the Gallery of Human Chromosomes (http://faculty.txwes.edu/mclark/Educause/Chromosomes.ppt), which shows the size, DNA content, and banding patterns for all twenty-four human chromosomes. For each of the chromosomes, the location, structure, and function of one or more resident genes are described. Many of the genes selected have been associated with human genetic disorders. Near the gallery is another exhibit comparing the organization of the human genome with that of other mammals: chimpanzee, macaque, and mouse. Although these two exhibit areas are informational rather than experimental, they provide a striking illustration of how genomic organization contributes to species differences.

Experiments produce datasets of two different types. In some experiments, the numbers of objects of different types must be counted, and relative numbers are important for analysis. For example, in a reconstruction of one of Mendel's classic experiments (http://faculty.txwes.edu/mclark/Educause/Monohybrid.ppt), green peas are crossed with yellow peas, and the progeny of the hybrids can be followed for several generations. The results of this and similar experiments led to the formulation of the basic laws of inheritance. When Mendel crossed pure-breeding green and yellow peas, the hybrid progeny (F1) all resembled the yellow parent. Allowing these hybrids to self-fertilize produced the next generation (F2), in which the green color reappeared in about one-fourth of the progeny. The next generation of progeny (F3) showed that while the green F2 peas always produced only green offspring, there were two classes of yellow peas: some that produced only yellow offspring and some that produced about one-fourth green offspring. Because keeping track of the numbers is important in these experiments, the traits expressed by each pea appear in the Second Life chat record. Data from the chat record can then be copied and pasted into spreadsheets (provided) or other documents for analysis. The results of breeding experiments that would otherwise take many months to perform can be collected in less than an hour.

In other experiments, the student must observe the effect of different variables. In the Bacterial Transformation Experiment (http://faculty.txwes.edu/mclark/Educause/Griffith.ppt), there are four different cultures of a bacterial species that causes pneumonia. Clicking on each culture describes its contents, and a syringe to inject a mouse appears. Clicking on the mouse then shows the results of the injection. Type S cultures have genes that allow the bacteria to establish a lethal infection. Type R cultures lack these genes, and the mice can survive the infection. Killing the S cells renders them harmless. But what happens when the combination of living R cells and dead S cells, each harmless alone, is injected? The results of this experiment, first performed by Griffith in 1928, indicated that genetic information had some kind of chemical basis, eventually leading to the identification of DNA as the informational molecule. It is a dramatic experiment, but cannot be done live in most undergraduate laboratories.

Second Life has a number of features that facilitate the creation of virtual laboratories by anybody willing to experiment and to risk the temporary embarrassment of attaching a large box to one's head. Simple building blocks can quickly be modified and combined to create objects. Scripts enable objects to pop out an informational note, speak to nearby visitors, change color or shape, appear and disappear, open a web page, send a message, play sounds, or any combination of actions. Linden Lab encourages educational use of Second Life by offering discounted island purchase and maintenance fees and by assigning intellectual rights for objects to their creators. Although Second Life is still somewhat beset by growing pains associated with its technological demands, misunderstandings of its environment, and the learning curve required of new users, I believe that it has great potential for the creation of dynamic communities in which students can learn and come to love science.

 

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