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A Glossary for Systems Biology Contents Index - Glossary - Motivation Introduction Introduction Submit - Comment A History of Systems Biology Historically, biologists have tried to understand organisms by investigating progressively smaller details of those organisms to gain an understanding of the larger concepts. Recently, there is a trend to look for properties that emerge when groups of such elementary components interact. This is a relatively new trend in biology, but there have been attempts at such an approach in the past which originated in other fields of science. Scientists from other disciplines - such as physicists or (later) systems theorists - have been interested in applying their science to biology for quite some time [62]. From Cybernetics... As early as 1948, NORBERT WIENER, the founding father of cybernetics, explicitly considered technical as well as biological systems as objects for the same scientific approach [61]. Later, notably in the 1960s, systems theory and biology enjoyed ``considerable interest among eminent scientists, mathematicians and engineers'' [62]. Also about that time, suggestions of an application of ideas from physics to biology led to controversy and discussion of the limitations of 'classical' systems biology. Starting around the same time, other attempts were made, some still under the name of cybernetics, that kept the idea alive through the following decades. Prominent are Biochemical Systems Theory (BST), developed in the late 1960s, and a related approach, Metabolic Control Theory (MCT), proposed in the mid 1970s [55]. BST [59] and MCT [23] are two ways to create simplified mathematical models of biological systems. Such models represent systems at and around a steady state. Although they were conceived as modeling approaches, both BST and MCT have resulted in quite a number of tools and methods for analyzing systems modeled in the respective way. All these attempts at systems level understanding of biological systems suffered from inadequate data to base their theories and models on [27,31]. This, again, had its reasons in limitations of measurement technology at that time. ... and (Cell) Biology ... Cell biology has a long history. It goes back to at least 1838, when SCHLEIDEN and SCHWANN proposed cell theory, postulating that all organisms are built from cells. Further milestones in the following decades were the first time DNA was isolated (1869), the chromosome theory of heredity (1883), a number of analytical techniques like fluorescent labeled antibodies (1941), the discovery of DNA's double-helix structure (1953), transgenic (1981), knockout (1987) and cloned mice (1998) and the draft of the human genome sequence (2000) [4]. In recent years, new attempts have made use of breakthroughs in measurement techniques in the wake of the human genome projects [9]. They can be subsumed in the two groups of bottom-up and top-down approaches. The former tries to compile independent experimental data into a conclusive representation of a gene regulatory network, the latter uses high-throughput data from DNA micro-array and other new measurement technologies [31]. An overview of these recent developments can be found in KITANO (2001) [31], a further one together with an extrapolation into the future in HOOD (2001) [24]. One aim of systems biology is to overcome the deficiencies of current models and to create fully $\rightarrow dynamical$ $\rightarrow models$. Recent developments in measurement precision, gene decoding, understanding of gene regulation and a number of other fields have brought this into reach [32]. A lot of further breakthroughs will be necessary, though, to finally reach this goal [34]. ... to Systems Biology There are two approaches to how deficiencies of current models could be remedied. One group of researchers wants to tackle them by integrating data from different levels and sources [25]. The other wants to shift the focus from the elementary components of biological processes to systems of such components [34]. Both approaches bring together scientists from a lot of different disciplines, such as biology, systems theory, computer science, physics, chemistry, and interdisciplinary areas of applied science like measurement instruments development.   Contents   Index Glossary Submit Comment

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