Computer simulation links genetics, biochemistry, molecular biology and evolution
When Brian White was a child, his kindergarten teacher wrote in his student record that he would only talk to the other children if the topic was science. Throughout his childhood, White’s fascination with science led him to take batteries apart, blow things up, and to build radios and computer components.
Now an associate professor in the biology department at the University of Massachusetts, Boston, White is the winner of the Science Prize for Inquiry-Based Instruction (IBI). He won the award for his creation of Aipotu, a computer-simulated world in which students apply the tools of genetics, biochemistry, molecular biology and evolution to develop an understanding of the formation of color in a flower.
“What I’m trying to do is give people the tools to play around,” says White, who explains that Aipotu is “utopia” backward. “What I’ve always liked about science is what you could do with what you learned.”
Science’s IBI Prize was developed to showcase outstanding materials, usable in a wide range of schools and settings, for teaching introductory science courses at the college level. The materials must be designed to encourage students’ natural curiosity about how the world works, rather than to deliver facts and principles about what scientists have already discovered. Organized as one free-standing “module,” the materials should offer real understanding of the nature of science, as well as providing an experience in generating and evaluating scientific evidence. Each month, Science publishes an essay by a recipient of the award, which explains the winning project. The essay about Aipotu will be published on July 27.
“We’re trying to advance science education,” says Bruce Alberts, editor-in-chief of Science. “This competition provides much-needed recognition to innovators in the field whose efforts promise significant benefits for students and for science literacy in general. The publication in Science of an article on each laboratory module will help guide educators around the globe to valuable free resources that might otherwise be missed.”
After many hours of experiments in his parents’ basement, White went on to MIT for his undergraduate work. Many of his classes were lectures, but by his junior year, he was able to take a class that had him in the lab all afternoon every day.
“I cooked up many harebrained experiments,” White says. “In the lab, you learn problem-solving. Most of the time, what you attempt doesn’t work, so you have to figure out why.”
Throughout his education, White had some wonderful teaching experiences, he says, including at a science camp in Woods Hole, Massachusetts, where one of his students built a pinball machine that kept score. White said demonstrating the machine to the student’s parents was an amazing moment, one of many that White had early on that drew him into education.
While working as a lab tech at Stanford, White saw an intriguing example of how a computer could be used to teach. Professor John Jungck had developed a genetics simulation that, instead of just showing an animation of a process, had students direct the process and witness how it worked. “You used it as a tool to figure out the answer. You had to use your wits all along the way,” White says. “Once I saw that, I said, ‘That is how to use computers to teach.’”
Luckily, although White’s field is biology, he was able to work on his own computer simulation, having learned to program very early on. “I used to say that I was a recovering nerd, but I’m not really making strong efforts to recover,” he says, laughing.
One of White’s colleagues, computer scientist Ethan Bolker, helped White with the thorny issue of how to approximate the complex and three-dimensional process of folding proteins. When Bolder suggested a way to represent protein-folding in two dimensions, White was skeptical. He realized, however, that the simplification was necessary if students were going to have a chance at getting the big picture of a biological phenomenon—connecting genetics, biochemistry, molecular biology, and evolution—within a single course. Like on Star Trek, where travel at the speed of light is a given if the show is going to be at all interesting—”otherwise, you can’t get from planet to planet in a lifetime,” White says—some liberties had to be taken with regard to the biological processes Aipotu presents.
Showing the connections between genetics, biochemistry, molecular biology and evolution is White’s primary objective, and he says using Aipotu, versus a real-life lab setting, enables it. The mechanisms represented in the Aipotu world—phenotype determination, color formation, protein folding and engineering a pure-breeding organism, for example—would take years to experience in an actual lab. With Aipotu, students not only get to experience the processes and their interaction, but they find answers on their own about how the processes work.
“Aipotu software will never tell students the answer, but rather it acts as a tool that students learn to utilize in order to discover the answer,” says Melissa McCartney, Science editorial fellow. “Perhaps most importantly, students are given freedom to explore their misconceptions of biology, especially with regard to evolutionary concepts.” Such common misconceptions include the ideas that selection causes beneficial mutations, mutations are always deleterious and mutations cannot create new features.
It’s not only White’s students who can take advantage of Aipotu. Downloadable for free, it is available to anyone who would like to use it.
“What I learned from science was if you find a something good, you give it away and let someone else use it,” White says, adding that teachers in general don’t ever seem to have extra money for their classrooms, and their use of the software is simply easier for them if there are no license restrictions.
Still, White says, it has been hard to get the word out about Aipotu, and he hopes that his winning the IBI and having an essay published in Science will alert the science community about the software’s existence.
“I think the Science article will be huge,” White says, “because it’s read by just the right kind of people.”
To visit Aipotu, go to aipotu.umb.edu.
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