Biomedical Informatics

Volume 569 of the series Methods in Molecular Biology™ pp 55-87


System Biology of Gene Regulation

  • Michael BaitalukAffiliated withSan Diego Supercomputer Center, University of California – San Diego

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A famous joke story that exhibits the traditionally awkward alliance between theory and experiment and showing the differences between experimental biologists and theoretical modelers is when a University sends a biologist, a mathematician, a physicist, and a computer scientist to a walking trip in an attempt to stimulate interdisciplinary research. During a break, they watch a cow in a field nearby and the leader of the group asks, “I wonder how one could decide on the size of a cow?” Since a cow is a biological object, the biologist responded first: “I have seen many cows in this area and know it is a big cow.” The mathematician argued, “The true volume is determined by integrating the mathematical function that describes the outer surface of the cow’s body.” The physicist suggested: “Let’s assume the cow is a sphere.…” Finally the computer scientist became nervous and said that he didn’t bring his computer because there is no Internet connection up there on the hill.

In this humorous but explanatory story suggestions proposed by theorists can be taken to reflect the view of many experimental biologists that computer scientists and theorists are too far removed from biological reality and therefore their theories and approaches are not of much immediate usefulness. Conversely, the statement of the biologist mirrors the view of many traditional theoretical and computational scientists that biological experiments are for the most part simply descriptive, lack rigor, and that much of the resulting biological data are of questionable functional relevance.

One of the goals of current biology as a multidisciplinary science is to bring people from different scientific areas together on the same “hill” and teach them to speak the same “language.” In fact, of course, when presenting their data, most experimentalist biologists do provide an interpretation and explanation for the results, and many theorists/computer scientists aim to answer (or at least to fully describe) questions of biological relevance. Thus systems biology could be treated as such a socioscientific phenomenon and a new approach to both experiments and theory that is defined by the strategy of pursuing integration of complex data about the interactions in biological systems from diverse experimental sources using interdisciplinary tools and personnel.

Key words

System biology Gene expression Gene regulation Network topology Graph analysis Pathways