Collector's Issue: Inauguration of Plant Systems Biology
Highlights from the Arabidopsis Special Issue devoted to
Plant Systems Biology/Genomics (June 2003)

In June 2003, Plant Physiology® published an Arabidopsis Special issue devoted to Plant Systems Biology. Systems biology is a new branch of biology that attempts to discover and understand biological properties that emerge from the interactions of many system elements. Because we believe we are witnessing an important moment in the future of plant biology, we decided to publish a short Collector's Issue commemorating the inauguration of Plant Systems Biology. This short issue highlights perspectives and overviews of plant systems biology, and shows a few examples of research in this new field. We hope that this issue will serve to educate the research community about the enormous potential of plant systems biology, and to stimulate young researchers -at the bench and at the computer- to join forces in this new effort.

The Arabidopsis Special issue went 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 prior to 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 it's advantages, the reductionist approach also has its limitations: (a) it only works for systems which 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 prior to 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 Collector's 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 in January 19, 2003 in Riverside, California. The report is written in a manner that will stimulate and inform both scientists and non-scientists. 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 UC Riverside. These overviews are followed by three research articles on plant systems biology.

We hope that this short Collectors issue devoted to 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 collection, for helping to make the nascent field of Plant Systems Biology a growing reality.

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

View the articles within the book:

Achieving the in Silico Plant. Systems Biology and the Future of Plant Biological Research
Peter V. Minorsky prepared this summary report with assistance from participants of the DOE workshop on Plant Systems Biology

Towards a Modeling Infrastructure for Studying Plant Cells
Thomas Girke, Mihri Ozkan, David Carter and Natasha V. Raikhel

Plant Systems Biology: Lessons from a Fruitful Collaboration
Dennis E. Shasha

Attacking Complex Problems with the Power of Systems Biology
Fumiaki Katagiri

Predictive Metabolic Engineering: A Goal for Systems Biology
Lee J. Sweetlove, Robert L. Last, and Alisdair R. Fernie

A Systems Approach to the COP9 Signalosome
Daniel A. Chamovitz and Avital Yahalom

Frontiers of Plant Cell Biology: Signals and Pathways, System-Based Approaches 22nd Symposium in Plant Biology (University of California-Riverside)
Peter V. Minorsky

Building Integrated Models of Plant Growth and Development
Jennifer L. Nemhauser, Julin N. Maloof, and Joanne Chory

Light- and Carbon-Signaling Pathways. Modeling Circuits of Interactions
Karen E. Thum, Dennis E. Shasha, Laurence V. Lejay, and Gloria M. Coruzzi

AraCyc: A Biochemical Pathway Database for Arabidopsis
Lukas A. Mueller, Peifen Zhang, and Seung Y. Rhee