This is from a Perspective piece in the Oct. 2 issue of Science:
The relative value of discovery aimed at hypothesis generation versus hypothesis testing has been debated. High-profile journals publish systems biology studies, including the human genome sequence, but most papers focus on hypothesis-driven investigations.
The human genome sequence is systems biology? Really? I can't blame the author here: most "systems biology" conferences I've attended have been indistinguishable from genomics conferences. For some, systems biology is just a sexier term for genomics. If we're measuring the entire 'system' at once, with the latest genomic technique, such as ChIP-seq of various histone forms, that's systems biology, right?
Unfortunately, this kind of thing has made the term systems biology radioactive in certain segments of the biomedical community. Systems biology has become the latest buzz-word, instead of an emerging discipline focused on new questions that were difficult to study 20 years ago.
Sequencing a genome is not, and should not be systems biology. Instead of Genomics 2.0 (which is basically, in my view, cartography: better and better high-throughput or computational techniques that map genome-wide phenomena of protein-protein and protein-DNA interactions, gene expression profiles, chromatin states, etc. - important, but still genomics), systems biology should be a natural evolution of genetics and biochemistry. Systems biology should be a hypothesis-driven field that studies the dynamical principles that account for the behavior of biological regulatory systems like gene circuits.
Systems biology should build on the questions about regulatory systems that were being asked by biochemists back in the 1970's and 1980's - before people had some of the amazing computational and experimental tools we have now.
This conflation of genomics with systems biology has had negative consequences for those of us who are interested in hypothesis-driven, principles-based questions about regulatory systems. If we attend conferences (or read papers) labeled systems biology, we're unlikely to find the kind of research we're looking for, which is instead found at meetings like "Computational Cell Biology."
Even worse, in a typical genetics or biochemistry NIH study section, if your stuff gets labeled systems biology, you're toast, as I was told directly by one of the program officers at the NIH. Old-school biochemists, molecular biologists, and cell biologists, who should be interested in fruitful models regulatory systems, associate you with 'hypothesis-free' genomics/computational biology, and quickly write you off.
For these people, the term systems biology has been tainted beyond rehabilitation, so perhaps we need a new term to capture the kind of work that's being done by people like John Tyson, James Ferrell, Michael Elowitz, Michael Savageau, Eric Siggia, and many, many others who are using both experimental and mathematical tools to understand the principles underlying the behavior of biological regulatory systems. Something like "Biological Dynamics" could capture what is distinct about this unamed field, distinguish this work from genomics, and help people recognize that there are some exciting questions that should be addressed, now that we have some very good maps of the interactions that are happening inside of the cell.
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