Bioinformatics Activities

Advisory Board
The Advisory Board for our project is composed of pioneers and practicing scientists in the field of Bioinformatics as well as historians and sociologists of science who have written on the history of contemporary genetics and biomedical science. The Advisory Board provides valuable assistance in identifying key areas to include in our study as well as liaison to the community of scientists who have contributed to the fields of computational molecular biology and bioinformatics. Biographical sketches of the Advisory Board members appear below:

Douglas Brutlag received his B.S. in chemistry from the California Institute of Technology and his Ph.D. in biochemistry from Stanford University in 1972, where he has remained as professor. He is the co-founder of IntelliGenetics, Inc. and IntelliCorp, and is currently the Chief Scientific Officer of DoubleTwist, Inc. Brutlag has been the Director of the Bioinformatics Resource at Stanford and he was cofounder of the International Society for Computational Biology. Brutlag states that his primary research objective is to understand the flow of genetic information from the genome to the phenotype of an organism. This includes understanding the sequence-structure dependencies and the structure-function dependencies of macromolecules. These goals represent the bioinformatic and functional-genomic approach to predicting structure and function from sequence. Specifically, we develop computer representations that can discover structural and functional properties of DNA, RNA and protein from sequences and from first principles. We spend much of our time learning the first principles of molecular and structural biology from known examples. We are also interested in predicting the interactions between ligands and proteins and between two interacting proteins. Given the structure, function and interactions of the proteins in a cell, we will eventually be able to simulate the metabolism of the organism. We attack these critical problems using a variety of different representations of sequences, structures and functions. Multiple representations of sequences include simple consensus sequence patterns, parametric representations, probabilistic techniques, graph theoretic approaches as well as computer simulations. Much of our work consists of developing a new representation of a structure or a function of a macromolecule, applying the methods of machine learning to this representation, and then evaluating the accuracy of the method. We have developed novel representations of sequence correlations that have predicted amino acid side chain interactions that stabilize protein strands and helices. We have developed novel algorithms for aligning sequences that give insight into the secondary structure of proteins. We have developed novel methods for discovering both sequence and structural motifs in proteins that help establish semantics of protein structure and function.

Joshua Lederberg was born in Montclair, New Jersey on May 23, 1925, the son of a rabbi. Lederberg's interest in a scientific career began quite early. His family moved to New York City when Lederberg was a child, and Lederberg was able to attend Stuyvesant High School, which concentrated in the sciences. In New York Lederberg was also able to take advantage of facilities such as the American Institute, which made laboratory space and equipment available to talented high school science students. Upon graduating from high school at 16, Lederberg took advantage of a local scholarship to attend Columbia University. After his experiments with Edward L. Tatum that demonstrated sexual recombination in bacteria, Lederberg decided to leave medical school to pursue a Ph.D., which he received from Yale in 1948. He then joined the Genetics Department at the University of Wisconsin, which at the time was part of the University's School of Agriculture. He eventually helped form and served as chair of the Department of Medical Genetics.

Lederberg received the Nobel Prize in 1958. Shortly afterward he joined the new Department of Genetics at Stanford University's School of Medicine, where he remained until 1978, when he left Stanford to become President of Rockefeller University.

Computer science and molecular biology caught Lederberg's scientific imagination during the mid-1960s at Stanford. In collaboration with computer scientists Edward A. Feigenbaum and Bruce Buchanan and chemist Carl Djerassi, Lederberg developed DENDRAL (DENDRitic ALgorithm), one of the first "expert" or "knowledge-based" systems. DENDRAL was designed to further two goals. The first was to aid scientists by determining the molecular structure of a chemical compound of known composition. The second was to investigate the combination of acquired knowledge and experience and inductive reasoning that a human would use to solve similar problems. Lederberg was involved in other early computer science, artificial intelligence, and cooperative communications projects, like SUMEX-AIM (Stanford University Medical EXperimental-Artificial Intelligence in Medicine). In a very early realization of the Internet, remote users could connect to a mainframe at Stanford to collaborate on problems that applied the methods and theories of artificial intelligence-the use of computers in complex decision making-to questions of medical science and medical diagnosis.

He became a professor emeritus in 1990, and he continues to research, lecture, and serve on a number of advisory panels.

Stephen Hilgartner is Associate Professor in the Department of Science and Technology Studies at Cornell University. He has his Ph.D. in sociology from Columbia University. His research interests span the fields of biology, ethics, and values; social studies of biology, biotechnology, and medicine; science as property; ethnography of science; risk. Hilgartner has written extensively on genomic research, including: "The Dominant View of Popularization," Social Studies of Science (1990); co-author with S. Brandt-Rauf of "Controlling Data and Resources: Toward Empirical Studies of Access Practices," Knowledge (1994); author of "The Sokal Affair in Context," Science, Technology & Human Values (1997); and "Data Access Policy in Genome Research," in A. Thackray (ed.) Private Science (1998).His recent book, Experts on Stage: Science Advice as Public Drama (Stanford, 2000) explores the processes through which scientific expertise is established as a tool for decision making. He is currently completing a book on the Human Genome Project.

Evelyn Fox Keller received her B.A. from Brandeis University in Physics in 1957, and her Ph.D. Ph.D. in theoretical physics from Harvard Universityin 1963. worked for a number of years at the interface of physics and biology. Her research focuses on the history and philosophy of modern biology and on gender and science. Keller taught at Northeastern University, S.U.N.Y. at Purchase, and New York University, before moving to the University of California, Berkeley, where she was Professor in the Departments of Rhetoric, History, and Women’s Studies (1988-1992). Since 1992 she has been Professor of History and Philosophy of Science in the Program in Science, Technology and Society at MIT. Her current research is on the history and philosophy of developmental biology. Evelyn Fox Keller has been the recipient of numerous awards, including the MacArthur Fellowship. She is the author of several books, including: A Feeling for the Organism: The Life and Work of Barbara McClintock; Reflections on Gender and Science; Secrets of Life, Secrets of Death: Essays on Language, Gender and Science; Refiguring Life: Metaphors of Twentieth Century Biology and, most recently The Century of the Gene.

Daniel J. Kevles is the J. O. and Juliette Koepfli Professor of the Humanities at the California Institute of Technology.  After obtaining his Ph.D from Princeton, Daniel Kevles joined Caltech in 1964 where he has studied and written on the interplay of science and society past and present, the history of science in America, the history of modern physics, the history of modern biology, the history of environmentalism, as well as scientific fraud and misconduct.  Kevles's historical articles and essays have appeared in dozens of diverse publications ranging from The New Yorker and Los Angeles Times Magazine to Physics Today, Biotechnology, Isis, and The Journal of American History. His books include: The Physicists: The History of a Scientific Community in Modern America (Alfred A. Knopf, 1978); In the Name of Eugenics: Genetics and the Uses of Human Heredity (Alfred A. Knopf, 1985); The Code of Codes: Scientific and Social Issues in the Human Genome Project, edited with Leroy Hood (Cambridge: Harvard University Press, 1992); and, most recently, The Baltimore Case (W. W. Norton, 1998), a Los Angeles Times bestseller and winner of the History of Science Society's 1999 Watson Davis and Helen Miles Davis Book Prize. Kevles also is the founder and current faculty chair of the Science, Ethics, and Public Policy Program for undergraduate and graduate students at Caltech.

Hans-Jörg Rheinberger was born in Grabs, Switzerland. He took undergraduate degrees in philosophy and biochemisry at the University of Tübingen and the Free University of Berlin. After obtaining his Ph.D. in molecular genetics at the Free University of Berlin, Rheinberger was a research scientist at the Max-Planck-Institute for Molecular Genetics in Berlin beginning in 1982. From 1985-1990 he was a group leader at the Max-Planck-Institute working on protein synthesis.

Rheinberger has had a dual career as a historian of science. He has held positions in the history of science at the University of Innsbruck, University of Lübeck, University of Salzburg, and University of Göttingen. Since 1997 Rheinberger has been the co-founding director of the Max-Planck-Institute for the History of Science in Berlin.

The author or co-author of numerous scientific articles Rheiberger has published widely in the history of science. His book, Toward a History of Epistemic Things: Synthesizing Proteins in the Test Tube (Stanford,1997) explores the primacy of the material arrangements of the laboratory in the dynamics of modern molecular biology.