Systems Biology: Properties of Reconstructed Networks (Palsson, 2006)

Systems Biology: Properties of Reconstructed Networks (Palsson, 2006)

Genome sequences are now available that enable us to determine the biological components that make up a cell or an organism. The new discipline of systems biology examines how these components interact and form networks, and how the networks generate whole cell functions corresponding to observable phenotypes. This textbook describes how to model networks, determine their properties, and relate these to phenotypic functions. Some knowledge of linear algebra and biochemistry is required, since the book reflects the irreversible trend of increasing mathematical content in biology education.

JLJ - The systems perspective seems to hit mainstream science in the form of systems biology. Perhaps the systems view can now advance in other areas, such as game theory.

p.1 Suddenly, systems biology is everywhere.

p.2 The advent of high-throughput experimental technologies is forcing biologists to view cells as systems, rather than focusing their attention on individual cellular components. Not only are high-throughput technologies forcing the systems point of view, but they also enable us to study cells as systems.

p.2 It is thus likely that over the coming years and decades biological sciences will be increasingly focused on the systems properties of cellular and tissue functions. These are the properties that arise from the whole and represent biological properties. These properties are sometimes referred to as "emergent" properties since they emerge from the whole and are not properties of the individual parts.

p.4 Evolution may be viewed as the "tuning" or "honing" of circuits to improve performance and chances of survival.

p.5 The ability to generate detailed lists of biological components, determine their interactions, and generate genome-wide data sets has led to the emergence of systems biology.

p.18 Some of the key features of biological networks that distinguish them from other networks need to be accounted for in the analysis of their systemic properties. The first basic feature of biological networks is that they evolve; they change with time. They are time variant... The second feature that has to be taken into account is the fact that they have a sense of purpose. The fundamental purpose is survival. However, in complicated organisms that fundamentally comprise many networks, some will have goals that are subtasks to the overall goal of survival... linking many biological components together forms a network.

p.23 Evolution is a "tinkerer" that combines the elements at hand together in new and unpredictable ways.

p.188 Biology, by necessity, employs a one-step look-ahead procedure, that is probabilistically based through the generation of alternatives. Then selection follows. The engineer, by contrast, can employ a multistep look-ahead strategy. The goal for engineering design is typically well defined as opposed to the survival objectives of cells, and different survival strategies may succeed.

p.193 The process of evolution is fundamental to the biological sciences.

p.201 Network properties and functional states are often referred to as emergent properties since they do not depend on the functions of any particular component, but "emerge" from the interactions of the components functioning together.

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