Isaac H. Clothier Jr. Professor of Biology
(on leave F'20-S'21)
1983 Ph.D., Biochemistry, University of Illinois, Urbana-Champaign
1983-85 Postdoctoral Fellow, Immunology (Cancer Biology), Stanford University
1985-89 Assistant Professor of Biology, Mills College
1989-92 Visiting Assistant Professor of Biology, Swarthmore College
1992-96 Assistant Professor of Biology, Swarthmore College
1996-2004 Associate Professor of Biology, Swarthmore College
2003-05 Chair, Department of Biology
2004-2016 Professor of Biology
2013-2016 Chair, Department of Biology
2016-present Isaac H. Clothier, Jr. Professor of Biology, Swarthmore College
2017-present Director, Swarthmore Summer Scholars Program, Swarthmore College
As the only faculty member in this department who studies and teaches about prokaryotes, I take every opportunity to increase awareness about the contributions of bacteria and archaea to the history of the earth and their impact on humans.
Cool facts about bacteria:
- many bacteria are easy to culture, have short generation times (20-30 minutes)
- we can modify genes in bacteria and see what effects they have fairly quickly
Bacteria are marvelously diverse, occupying many unique niches:
- some thrive in hot water pipes
- some survive under many feet of Antarctic ice
- some only live in the guts of large deep sea-dwelling red tube worms
They make many different kinds of products:
- flavors in cheeses (almost all of the smelly ones!)
- yogurt, soy sauce, sauerkraut, and many other foods
- enzymes that we use in out laundry detergent
- enzyme used in PCR for diagnostics and forensics
They can extract energy from:
- the sun
- hot sulfurous gas from deep thermal ocean vents
- methane bogs
To humans they are important:
- to basic research about life on earth
- for biotechnological applications
- only some cause nasty diseases
- others make products with antibacterial activity, used to limit disease
- many degrade wastes that are toxic to other life forms
- those that live naturally in and on our bodies protect us from harmful organisms
I have said elsewhere that it is a great time to be a microbiologist. It is certainly a privilege to spend my time at Swarthmore engaging students in classroom and laboratory activities that explore the world of bacteria.
Biology 001: Cellular and Molecular Biology
This is a team-taught fall semester course targeted at both majors and non-majors, in which each of 4 faculty members gives 8-9 lectures. Weekly laboratory sections are led by faculty - I teach the same 20-25 students in the weekly laboratory for the entire fall semester. I am assisted in the lab by a Laboratory Instructor and a senior biology major.
Writing assignments, quizzes and a final exam are the ways in which performance is assessed. Knowledge of general principles and important concepts is demonstrated by application and analysis, rather than be memorization.
Biology 16 and 17:
These are courses that I teach in alternation in the spring semester. Students may take one or the other, but not both courses. The primary reason for this restriction is that the laboratory portions of the 2 courses are identical. Standard microbiological techniques are introduced in the laboratory, which is open 24 hours. Students are expected to follow up on experiments outside of the formal laboratory period. It is the lecture content of the two that differs. Evaluation of student performance includes essay exams, short writing assignments, laboratory write-ups, oral presentations and a laboratory practical.
Biology 16 is Microbiology
This course, with its weekly laboratory, focuses on general areas of microbiology including: bacterial structure and function; metabolism and physiology,;bacterial genetics and regulation of gene expression; growth and control of growth; evolution of life on earth; ecology and nutrient cycling; symbiosis and unique niches (extremophiles); viruses; systematics and taxonomy; antibiotics and resistance; industrial and food microbiology; and a brief introduction to immunity and immunochemistry.
Biology 17 is Microbial Pathogenesis and the Immune Response. This is a course that I designed so that I could teach about co-evolutionary mechanisms. Some of the topics overlap with Biology 16 (and the weekly lab is identical), but many lectures emphasize the interactions of hosts and pathogens: bacterial structure and function; metabolism and physiology; bacterial genetics and regulation of gene expression; viruses; antibiotics and resistance; symbiosis and pathogenicity; innate immunity; T cells and the MHC; B cells and the antibody response; virulence mechanisms; vaccines; molecular diagnostics and immunochemistry.
Biology 116 is Microbial Processes and Biotechnology
Over the years, this honors seminar, in which students read and present the primary literature, has evolved from a course in advanced bacterial genetics to one on advanced bacterial physiology and metabolism. In fact, we still learn a great deal of bacterial genetics, but do so now in the context of metabolic complexity. Students become familiar with many biochemical pathways of intermediary metabolism and learn why these are interesting areas of investigation in the fields of pathogenesis, microbial ecology and evolution, pharmacology, enzymology and basic bacterial physiology. Students also conduct independent research projects in small groups. Additionally, each student writes an extensive research proposal on a biological problem that affects a third world country and outlines a biotechnological solution. Students gain experience with oral presentations, building a logical set of arguments, based on principles and precedence, writing short and long papers, use and proper citation of literature and participating in the peer-review process. Students who complete Biology 16 or 17 with a minimum grade of B are encouraged to enroll.
Since 1995, many honors students have stood for oral and written exams, given by external examiners, in Biology 116 (which used to have a different number: Biology 55). External examiners come from microbiology programs at major colleges and universities. They write a 3-hour, closed book exam based on the papers that students have read and presented in Biology 116. Some examiners also are asked to evaluate honors theses. Previous honors examiners in microbiology (seminar or thesis) have included: Yves Brun, Indiana University; Heidi Kaplan, University of Texas Medical School; Roberto Kolter, Harvard University; Stanley Maloy, University of Illinois, Urbana-Champaign; Mitchell Singer, University of California, Davis; Clay Fuqua, Indiana University; Joanne Willey, Hostra University; Nancy Love, Virginia Tech; Patrick Piggot, Temple University; Tony Lobo, Ursinus College.
Other Swarthmore courses that I have taught (but not on a regular basis)
Biology 5/Philosophy15: Biotechnology and Society: The Case of Agriculture
Team-taught in 1999 and 2000 with Professor of Philosophy Hugh Lacey (who has since retired)
This course was cross-listed in both departments, but did not satisfy major requirements in either. It was weekly a 3-hour discussion with no lab. It was billed as an introduction to biotechnology, as it pertained to the development of genetically modified organisms (GMOs) and to their uses in agriculture, and to related issues in the ethics and philosophy of science. Topics included: methods and possibilities of genetic engineering; ethical questions raised by research and development of GMOs for use in agriculture, and associated legal issues; risks that may be occasioned for consumer rights, human health, the environment and the maintenance of biodiversity; long-term conduct of agricultural practices for the sake of feeding the whole world: the growth of agribusiness and the struggle for alternative forms of agriculture to survive; patents/intellectual property rights and their effects on the conduct of science; third world perspectives. Students were evaluated on presentations, participation in discussions and collaborative projects, and written work. Enrollment was open to anyone with introductory biology (or AP credit) and one introductory philosophy course.
Unfortunately, I have not had a partner to co-teach this course since 2002.
Biology 93: Directed Reading in Virology
This course is only available if 2 or more students, who have already completed Biology 16 or 17 with a minimum grade of B, are willing to meet with each other for 3 hours per week and with the instructor for an hour a week. Reading material include virology texts as well as classical papers on bacteriophage lambda and the primary research literature. Two extensive research papers on 2 different virus systems are required. Each professor in Biology has the option of offering Directed Reading courses in his/her area. They are listed as separate sections of Biology 93.
Life Long Studies 122: Why We Get Sick, or Not
This course is an adult education course that is offered as a part of the LLS program at Swarthmore. Students in the course are local Swarthmore residents, alumni and friends of the College. The course meets for 8 weeks, 2 hours per week, in the evenings. Readings are based on a text by Williams and Nesse: Why We Get Sick, literature published by the American Society for Microbiology for the public, as well as articles from current magazines and newspapers. Students participate in discussions and have a brief presentation during one week. It was offered in the spring of 2006 for the first time and may be offered again in 2008.