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What is the biggest hurdle facing systems biology, and how can it be overcome?

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A.The biggest hurdle is the expense for performing well-designed experiments that will enable the investigator to apply mathematical modeling approaches to the resulting data. Both gene expression microarray and proteomics experiments still are expensive, especially if you add on 3-4 replicates for each data point and do the reiterative sampling of time or dose (8-10 different data points) that is required for systems biology.

Part of this hurdle can be overcome by designing the most cost-effective and minimal, intelligent, and logical experiment that one can. The other part is considering the most effective technology platform for the goal of the experiment.

Mary Jane Cunningham
Associate Director
Life Sciences & Health HARC (Houston Advanced Research Center)

 

A.We are trained to think reductionistically, to take a problem and parse out smaller and smaller focused questions. We look at one thing at a time — a molecule, its phosphorylation site, at a specific junction between cells such as synapse, at a specific brain region’s activation under a very specific paradigm.

Systems biology is needed to get an idea of the big picture, to fit the pieces together. This means learning from scientists working in game theory, stock market analysis, artificial intelligence, sophisticated computer models, and complexity theory. It also means learning more from each other.

Margit Burmeister
Associate Professor
Psychiatry and Human Genetics Mental Health Research Institute
University of Michigan

 

A.We are essentially falling into a groove where it is considered almost impolite to raise the issue of gaps among gatherings of systems biologists. None more than systems biologists are aware of the gaps in the data. All are constrained to deal with these inadequacies by building coping strategies into their models, ultimately chipping away at their usefulness.

Patrick Leahy, Manager
Gene Expression Array Core Facility Comprehensive Cancer Center,
Case Western Reserve University and University Hospitals of Cleveland

 

A.1) A lack of consensus on what it is and what it means2) A lack of knowledge about systems biology3) Negative attitudes, closed-mindedness, or ignorance about how powerful and useful systems biology can be.

Bioinformatics is a fundamental part of systems biology, but many scientists know little to nothing about the kind of information that can be gleaned by computational analysis, a thorough review of existing data, and an integrative approach to answering fundamental questions in biology and molecular biology.

Jeff Lerner
Adjunct Professor
Department of Natural Sciences
Assumption College

 

A.One of the biggest hurdles is that [systems biology] will be considered a fad. To avoid this, we should recognize [Ludwig] von Bertalanffy’s development of the field in the 1930s. His thinking has had a profound influence on systems engineering and management, but has been harder to implement in experimental biology. By reconsidering that the roots of systems biology start with him, we can better recognize that we are not in the midst of a fad, but now have the analytical tools to ground his abstract vision in reality.

William Opel
Executive Director
Huntington Medical Research Institutes

A.A big hurdle for researchers in systems biology is to integrate our research efforts as well as biological systems naturally do. Darwin’s hypothesis is that such evolution might take some generations of scientists, working under conditions of selection. The successful designs of our integrative attempts will probably end up looking very much like some biological systems.

David C. Sands
Professor of Plant Pathology
Department of Plant Sciences and Plant Pathology
Montana State University

 

A.The biggest hurdle facing systems biology is technology development. Scientists appreciate the value of integrative biology, but most do not have the tools to implement this new approach. There is a need to have new bioinformatics tools that are user-friendly that would allow for non-computing types to take advantage of legacy databases. The second challenge is to get the researchers out of the R01 silos and consider, and get credit for, working in fully integrated, multidisciplinary teams.

Jose M. Velazquez, Program Director, Genetics & Proteomics
Division of Metabolism and Health Effects
National Institute on Alcohol Abuse and Alcoholism, NIH

 

A.The biggest hurdle will be standardization and sharing of data in an efficient and understandable format. This will include adoption and integration of standards like Health Level 7’s Reference Information Model for clinical information management, Object Management Group’s MicroArray Gene Expression Object Model, SNOMED Clinical Terms, etc.

The solution is the implementation of these standards in new products as they come to the market, and the insistence by scientists that products include these standards.

Thomas P. Caruso
Director, Research Initiatives
Virginia-Maryland Regional College of Veterinary Medicine

 

A.The biggest problem with systems biology has got to be defining what it actually is. For us that’s using lots of raw data, coffee, and computers to create biologically relevant information.

David A. Bailey
Group Leader, Bioinformatics
Genpath Pharmaceuticals

 

A.What is the biggest hurdle facing systems biology? Misunderstand[ing of] systems biology and doubt about [the] success of systems biology; lack of funding.

How can it be overcome? Tap funding sources; publish more positive papers on systems biology; encourage different approaches to systems biology.

Momiao Xiong
Human Genetics Center
University of Texas Health Science Center at Houston

 

A.The biggest hurdle is the ignorance or arrogance of the people who “invented” the field: good researchers are always interdisciplinary and will bring all technology and approaches to bear on the system they wish to solve. Thus, the name and field are absolutely unnecessary!

Juergen Reichardt
Institute for Genetic Medicine
USC Keck School of Medicine

 

A.For performing a systems biology project, from the experimental design to data collection and analysis, we need people [who] understand not only biology but also bioinformatics, computer science, statistics, math, physics, and so on.

Therefore, a good interdisciplinary education is a good solution. Five or 10 years later, systems biology will be so common like molecular biology today. At that time, new generations of biologists cannot know only biology.

Edwin Wang
Bioinformaticist
Biotechnology Research Institute
National Research Council Canada

 

A.The biggest hurdle we have to overcome is the inertia of the previous success of reductive science. The genomics data have already proven that the ‘bang for the buck’ in discovery science and systems biology can vastly outpace that of traditional reductive approaches.

Funding agencies (NSF, NIH, and many of the philanthropics) have gotten it, but the reviewers lag. This is probably not totally the reviewers’ fault, since funding agencies in the US for so long have demanded tightly defined, reductive research. There is a resistance to moving toward integrative research, which is too easily labeled as a fishing expedition.

Gregory A. Buck
Director, Center for the Study of Biological Complexity
Professor, Microbiology and Immunology
Virginia Commonwealth University

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