Writing in last week's Nature, Nobel laureate Paul Nurse came down on the side of systems biology but was careful to distance the concept from the 'big biology' tag that the field's critics are attaching to it.
For Nurse, "biology stands at an interesting juncture". Previous advances, he argued were based mostly on molecular biology: "applying the ideas that the gene is the fundamental unit of biological information and that chemistry provides effective mechanistic explanations of biological processes". But he warned:
"...comprehensive understanding of many higher-level biological phenomena remains elusive. Even at the level of the cell, phenomena such as general cellular homeostasis and the maintenance of cell integrity, the generation of spatial and temporal order, inter- and intracellular signalling, cell 'memory' and reproduction are not fully understood."
Although systems biology is meant to encompass everything from the environment down to molecular reactions, Nurse pointed to a level of abstraction that seems tractable but which can capture the complexity that systems biologists believe is needed to accurately represent what is going on.
"The study of cells is likely to be particularly effective for this programme because the cell is the simplest entity that shows complex biological phenomena...Given the conservation of many processes, model eukaryotic systems [such as bacteria, yeasts and developing eggs] have the added advantage of being relevant to human cells. The aim should be to analyse cells more effectively with the intention of then applying those approaches to more difficult organismal problems and to human disease."
This probably won't have many biologists screaming "heretic!". But, Nurse moves on to the subject of databases – this is one of those subjects that has more traditionally minded investigators rolling their eyes:
"The next steps will be to use the databases...to determine the probability that specific components of the chemical tool-kit are associated with a particular logic module. Finally, the modules will be linked together into a complete circuit, allowing outputs to be predicted so that the functioning of the circuit can be translated into a narrative of information flow to describe how the cellular phenomenon works."
However, Nurse steps away from the idea that there is one big encompassing database for this, which may please those who worry about data-mining coming to modern biology:
"What is required that is not already generally in place to pursue this programme effectively? Perhaps the most pressing need is to develop the appropriate theoretical approaches to analyse the management of information flow and to investigate the logic systems that are responsible for that flow."I see this best being developed not as a 'big science' project but by individual scientists working alone and together in small interactive workshop groups meeting on a regular basis. The groups will need to be multidisciplinary, including information theorists, mathematicians, physicists, chemists and computer scientists working closely with experimental biologists who have good biological intuition and who can communicate with members of the other disciplines. Different workshop groups could interact with each other through digital conversations to share ideas."
At a small scale, this is already happening. Meetings of systems biologists often involve a phase of what you might call "database discovery" in which people find out about sources of data that might help out with their next experiment, and then discover some incompatibility in the protocol that throws a spanner in the works.
A bigger problem might be that education and the relentless pursuit of specialism:
"The training of advanced undergraduate and graduate biologists also needs to shift in its emphasis. The separation of molecular and cell biologists from those that study organism biology, ecology and evolution has weakened biomedical research, and the emphasis on learning large numbers of facts in molecular- and cell-biology courses and during medical training has reduced the necessary exposure to the ideas central to biology.Time needs to be made during education to expose biomedical scientists to other scientific disciplines to ensure good communication between biologists and other disciplines so that theory is always well embedded in biological facts and experiments."
