Professor Compares Teaching New Science to "Photographing Fog"
December 10, 2001
It was a cutting-edge, challenging fall semester for the fourteen students in Malcolm Campbell's genomics class at Davidson College. Their textbook, which Campbell wrote from scratch as the first-ever in this new field of biological investigation, was presented in loose-leaf form because it hadn't been printed yet. Many of the web sites referred to in the book were evolving so rapidly that students regularly encountered broken links or different data sets than they expected.
Senior Ben Havard noted that the discipline itself is so new that the title of the course can't be found in dictionaries yet! He said, "When I type 'genomics' on my computer, the spell-checker always underlines it in red as a misspelling. That's really annoying!"
Campbell, an associate professor of biology and national leader in promoting the study of genomics in undergraduate education, anticipated some bumpy air in launching his inaugural course. But he said it's inevitable when trying to help students master a discipline that's evolving every day they come to class.
During the fifteen weeks of Davidson's genomics course this fall, the Web site "Genomics Today" posted scores of tantalizing headlines from world media sources shouting out the revolutionary possibilities of the new science. As scientists learn to manipulate the genetic material that dictates the attributes of life, the form and quality of that life could be dramatically altered. The scope and speed of the genomics revolution are indicated by the fact that all the following headlines appeared on the Web site in the same week: "Gene Points to Mental Retardation Therapy," "Twin Gene Idea Could Wipe Out Malaria Mosquito," "Created Bacteria Selectively Target Advanced Tumors," and "Gene Study Hunt Finds New Clue to Premature Heart Attacks."
Those were all overshadowed by the hoopla surrounding the recent announcement of a cloned human embryo. That led to calls for prohibitive legislation, and wild speculation about "custom-made children."
"We're living in a world of 'genomania,'" said Campbell. "The media is in a feeding frenzy over the new discoveries being made daily."
Campbell prepared to teach a genomics course to Davidson students by spending his sabbatical during academic year 2000-2001 working in a genomics lab in Seattle. He had no model syllabus to follow, since no one else had ever taught genomics to undergraduates before. There was no textbook either, so he wrote Genomics, Proteomics & Bioinformatics with a colleague in the mathematics department, Assistant Professor Laurie Heyer. He knew that the rapidly-developing field would quickly outdate any attempt to include current news in the book, so he crafted it as a case-study approach. His first students used a pre-publication copy of the book, which is being published next August as the first-ever joint venture of Cold Spring Harbor Laboratory Press and Benjamin Cummings Publishers.
Despite the lack of a road map to guide his teaching, Campbell has from the beginning been convinced that genomics is an ideal, and important, field for liberal arts study. He described it is a "systems" approach to biology, a comprehensive science that considers the entire "web" of interaction inside a cell. It requires a knowledge of biology, physics, and mathematics to understand how genes, proteins, carbohydrates, lipids, and other cellular ingredients interact. That understanding will allow scientists to manipulate them to create everything from improved medications to replacement human organs. Campbell said, "Genes, and the proteins they create, interact in tremendously complex ways that we know very little about. Genomics seeks the 'Holy Grail' of understanding the interactions inside the 'cell web.'"
The development of the science carries both promises and perils that will require intelligent and enlightened consideration.
He emphasized that the genomics course is not aimed solely at future scientists. "Whatever you're going to be doing, genomics will affect your life," he noted. "I'm trying to develop a course that will prepare students to understand the issues, to create an educated public that can deal intelligently with genomics whether they encounter it in science, economics, politics, or business."
In addition to teaching the course at Davidson, Campbell founded the Genome Consortium for Active Teaching (GCAT) 18 months ago to bringing genomics research methods to undergraduate colleges. The consortium is comprised of about thirty-five faculty members from around the country who are using DNA microarrays (or DNA chips) with their undergraduate students to produce original genomic data.
The National Science Foundation recently made a $58,000 grant to GCAT so the organization could purchase its own DNA chip reader, which Campbell maintains at Davidson. This centralized facility for GCAT members is permitting GCAT members to conduct genomic research on yeast, a flowering plant, E. coli, and human DNA chips that are being provided for free by academic labs around the country. GCAT also has access to powerful bioinformatics software needed to analyze results of the microarray.
Campbell worked to make sure his Davidson students understood the basic biological science involved, knew where to find the resources and literature they would need, and had a chance to ponder and discuss some of its ethical consequences.
They completed several Web-based assignments during the semester designed to help them understand genomics from both a popular and scientific point of view. For their first assignment, they selected a gene reported by the popular press as "responsible for ___" (fill in the blank with hair color, cancer, obesity, etc.), and compared what the popular press reported with what scientists reported in their scientific papers.
Three other web assignments were designed to model real scientific process. Students had to select a gene and find out all they could about it, explain a protein that's encoded by the gene, and make predictions about the protein's function in cellular life.
All the assignments involved investigation of public databases posted by scientists researching genetic material, and put the students in the front line of the real world of scientific investigation. Campbell recalled, "I e-mailed one developer to let him know we were having trouble getting a protein analysis to work on his database. He replied that they knew about the glitch and had been planning to let it go, but since we had discovered it they would fix it. So our undergrads were pushing researchers and developers. That's unheard of!"
Senior student Elizabeth Sellars said the assignments helped her understand the process of investigating things unknown. "We just had to go for it and think for ourselves. You can't be afraid what you don't know, you just have to get out there and chip away at it. Even if our hypotheses turned out to be wrong, we at least eliminated those possibilities as answers."
They learned in their semester of study that the "pie in the sky" isn't going to be as easy to slice and serve as the popular press leads readers to believe. "Genomes are not as simple as many people think," he said. "You can't control height, personality, body weight, cancer, or sexual preference by manipulating a single gene. It's much more complex than that."
The door to genomics opened just a few years ago with the invention of high-throughput sequencing methods that made it possible to sequence a lot of DNA quickly and cheaply. The other critical component was computer software and hardware that permitted researchers to collect, analyze and piece together long sequences of DNA. That new ability to spell out read an organism's genetic code as a long sequences of the letters "G,C,A, and T," reveals a tremendous amount of information about life.
But Campbell points out that it's only the beginning point for genomics. Genes create a wide array of proteins, which do the actual work in cells, and scientists can't yet catalogue proteins with the same ease as genes.
La Powell, a junior biology major, said the course was both a beginning and ending. "It's like an ending course in that it pulls everything I've learned in previous courses together. But it's like a beginning because here at the end of the course the questions are completely open-ended. We find that there are very few answers, and only have the tools needed to begin doing what we want with it."
Another student noted, "Genomics is like molecular biology gone post-modern. You learn that you have to study genes and their proteins in context, because context has such an effect on their behavior."
By the end of the course, Campbell's pre-publication textbook included a lot of red ink to indicate typos, freshly developed ideas, and notations of new web sites to include. "It's like trying to take a picture of fog," he admitted. "I don't think you can ever publish the perfect book because the field changes so rapidly. But it's too important not to start somewhere."
In his last class session of the semester, he called his students the first wave of genomics "disciples," and charged them with helping the public understand its implications. "Once people know you have some understanding of this, they're going to ask you all sorts of questions," he said. "My daughter asked me the other day how skin knows to stop growing when you skin your knee and it begins healing. That's just one example."
Some of the students who took genomics this fall will enroll in another ground-breaking course this spring. Campbell's mathematics colleague, Laurie Heyer, is offering a course in "Computational Genomics" that will explore how math is used to extract meaning from the raw data gathered in microarray analysis. It's likely they'll encounter the same challenges grappling with that new aspect of the science that they did in Campbell's class.
But student Ben Havard concluded that it's well worth the effort. "We're beginning to understand the big picture, and that's phenomenal. It's something no other undergraduates are getting right now."
Davidson is a highly selective independent liberal arts college for 1,600 students. Since its establishment in 1837, the college has graduated 23 Rhodes Scholars and is consistently ranked in the top ten liberal arts colleges in the country by U.S. News and World Report magazine. Davidson is currently engaged in "Let Learning Be Cherished," a $250 million campaign in support of student financial assistance, academic resources, and community life.