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Plant Physiology 132:403

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EDITORIAL

Plant Systems Biology

This Arabidopsis special issue devoted to Plant Systems Biology goes to press on the heels of the 50th anniversary of the discovery of the structure of DNA. With the more recent advent of genome scale data, we have gone from studying one gene—one protein at a time—to the whole genome. In the new era of Systems Biology, our challenge will be to incorporate information on all genes and proteins in a cell into a composite model of interacting components. Despite the power of its promise, Systems Biology is still in its infancy. Our intention in publishing this first-of-its-kind issue devoted to Plant Systems Biology was to help nucleate this new effort within the plant community. Buying into this effort will require a sea change in our way of thinking.

The reductionist way of thinking (one gene, one mutant at a time) has played a fundamental role in biology, especially in the field of genetics. Mendel's laws were discovered because he applied the reductionist approach to his crossing experiments. Mendel selected pairs of inbred lines with a single contrasting character and in doing so created a one-dimensional genetic difference (variate). Many people before Mendel had tried similar crossing experiments but failed because they worked with multivariate lines. Thus, Mendel's success was a result of using a reductionist approach. By analogy, this reductionist approach has accounted for the success of modern day plant studies encompassing plant molecular biology and molecular genetic studies in Arabidopsis.

Despite its advantages, the reductionist approach also has its limitations: (a) It only works for systems that involve minimal interactions, (b) the laws discovered using the reductionist approach usually apply locally or in a narrow domain, (c) it takes a long time to discover the laws governing the whole system, and (d) it is expensive in the sense that one needs to do many independent one-dimensional experiments to collect the same amount of information as a single multidimensional experiment.

Contrary to the reductionist approach, the field of systems biology utilizes a multidimensional approach. The challenge of systems-based approaches lies in extracting information from the multivariate experiments and in building models that incorporate all of the data. This is why systems biology was not popular before the advent of genomic and computer technology. With the advent of high-power computers and computational-based statistical methods, it is now possible to extract the maximum amount of information from experiments involving genome-scale data. In systems biology, math and computer tools are required not just to analyze the genomic data generated but, importantly, to design the experimental spaces needed for model building. Testing such models in vivo with mutants, makes the circle complete. Systems biology approaches will enable us to model the cellular activity of a set of genes/proteins as a functional network. This should then enable researchers to devise predictive models that may eventually permit intervention for practical purposes. Thus, by combining new tools in genomic biology and math/computer sciences, systems biology will make it possible to unravel the real world of biology.

This Arabidopsis special issue highlights examples of new and emerging research in the area of Plant Systems Biology. The issue begins with the Editor's Choice report article. This report covers a Workshop, sponsored by the Department of Energy Biosciences Program of DOE held January 19, 2003, in Riverside, CA. The report is written in a manner that will stimulate and inform both scientists and nonscientists. The report is followed by a series called "Perspectives" on Systems Biology, and then by a review of a recent meeting on Plant Systems Biology at the University of California (Riverside). These overviews are followed by a special section of research papers related to systems biology; Systems Biology/Genomics/Biofinformatics, and Breakthrough Technologies. This special section of research papers is then followed by general Arabidopsis research papers organized according to the usual research areas.

We hope that this special issue of Plant Systems Biology will stimulate further research in this exciting new area of Biology. We would also like to thank the various contributors to this issue for helping to make the nascent field of Plant Systems Biology a growing reality.

Natasha V. Raikhel, Editor-in-Chief of Plant Physiology and Gloria M. Coruzzi, Associate Editor of Plant Physiology

FOOTNOTES

www.plantphysiol.org/cgi/doi/10.1104/pp.023929.




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G. Sriram, D. B. Fulton, V. V. Iyer, J. M. Peterson, R. Zhou, M. E. Westgate, M. H. Spalding, and J. V. Shanks
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[Abstract] [Full Text] [PDF]

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