Volume 4, Issue 27 April 2007
Teaching Biology In the Twenty-First Century
Yeast geneticist Jasper Rine has been named a Howard Hughes Medical Institute Professor and the director of UC Berkeley's Center for Computational Biology.
Since Aristotle's first attempts to classify the animals, biology has been a primarily descriptive pursuit. Even well into the twentieth century, much painstaking work was required to produce precious little biological data. But as researchers have learned to manipulate the genome with ever greater facility, that equation has undergone a fundamental shift.
UC Berkeley Professor of Genetics, Genomics and Developmental Biology and QB3 faculty affiliate Jasper Rine has had a front row seat to this revolution during his thirty-year career as a professional scientist. And he sees the trickle of data biologists once wrested from their experiments exploding into a flood.
While the Human Genome Project required some 13 years and $2.7 billion taxpayer dollars, Rine predicts that within ten years, the average American will be able to have his or her personal genome sequenced for less than $1,000.
Interpreting what those genes do, however, is proving problematic. At present, scientists understand less than one percent of the variations in people's genome sequences. "If we don't do something soon, we'll be at a time when parents will have the sequence of their child, will see that their child is different than 'normal' and we won't be able to interpret 99 percent of the differences between this child and the reference 'normal' human genome sequence. We'll have the key to the kingdom of understanding our individual biology, but not know where the lock is," Rine says.
Berkeley's behemoth introductory biology course enrolls 1,200 undergraduates per year.
Rine and UC Berkeley are acting to channel the information overflow in new and more efficient ways. This fall, Rine was named director of the university's Center for Computational Biology for a three-year term. By bringing together experts in genetics, computer science, mathematics, and other fields, the center will arm a new generation of scientists with the tools to analyze genomes and model complex biological processes. Research so far has included computer programs that help predict protein function by applying principles of evolution to the study of genomes, studies of genome organization and control, and the historical events that led to the evolution of humans from their last common ancestor with other primates.
These innovations have the potential to transform the curiosity of a personalized genome sequence into lifesaving information. Any two people differ in about 6 million letters of the 3 billion letter human genome sequence. Some of these differences are of no importance to us, whereas others play a critical role in our health and well-being. For example, 30 percent of people in the United States carry a gene variant that elevates the amount of a chemical called homocysteine in their blood. High homocysteine levels are associated with a higher risk of cardiovascular problems such as stroke and heart attacks. Those who know they have the defect can compensate by eating more of the vitamin folate – a simple change that could fundamentally improve their health and longevity.
Ironically, the very advances that have opened these new vistas into the life sciences have left a key component of Berkeley's undergraduate biology program lagging behind. More than 1,200 undergraduates per year take the Introductory Biology course, also known as Bio1A. This instructional behemoth includes a laboratory component that runs more like an aircraft carrier with great momentum but one that has difficulty changing course.
"We have lab sections every morning, afternoon, and evening, Tuesday through Friday. Monday, we need all day to set up the labs. The staff have done an amazing job just keeping this course on track. However, over the last few decades, the field has moved more quickly than the labs have been able to adapt," says Rine.
This state of affairs won't last for long. Last April, Rine was awarded $1 million by the Howard Hughes Medical Institute expressly to revamp Bio1A's labs.
Jasper Rine will use a million-dollar grant to inject elements of modern genetics, statistics, and the spark of original experimentation into the venerable Bio1A lab classes.
Most labs conducted on such an industrial scale teach useful laboratory skills, but traditionally ask students to obtain answers to experiments whose results are already known. Rine wants to introduce the element of novel scientific investigation, including having students sequence a segment of their own mitochondrial DNA.
"These genes have an evolutionary clock that ticks faster than the clock in nuclear DNA. Because there will be more differences in each person's mitochondrial genome, it will make it easy to track population evolution," Rine says. The late UC Berkeley biochemist Allan Wilson used the same approach to calculate that the last common maternal ancestor of all humans lived in East Africa about 200,000 years ago. "I want to build on that history and let students see how their sequence fits into the tree of humanity," Rine says.
Other potential experiments include having students analyze algae strains with novel mutations in their photosynthetic machinery, and isolating viruses from bacteria found in the poop of zoo animals. The idea is to inspire students to conduct their own research and potentially join the labs of campus scientists.
Rine's plans to renovate all twelve lab modules over four years. He'll be developing and testing three new modules at a time over the summers with the assistance of undergraduates, staff, and HHMI teaching fellows such as geneticist and postdoctoral student Jacob Mayfield. "A million dollars sounds like a lot of money, but over four years, with supplies and the price of equipment—like the two $30,000 spectrophotometers we'll need—it goes quickly." But to produce the biologists of the twenty-first century, it's money well spent.