The central approach of biology during the 20^th century was reductionism, or working to understand life by analyzing the thousands of molecular machines that make up a living being one at a time and in isolation. This approach has resulted in very detailed knowledge of many individual components of life. However, our understanding of how these components interact with each other to define the cellular, organismal, and population-level behaviors of living beings remains far less sophisticated.

The new approaches and techniques required to understand these higher levels of organization, broadly termed as “systems biology” makes up a major part of what the Pakrasi lab practices. Systems biology should provide enabling technologies to examine complex biological processes, which in turn result in predictive understanding of how an organism behaves and responds to environmental changes. For example, we have identified broad groups of genes that are activated in response to environmental stresses in Synechocystis 6803 (see Singh et al 2010, BMC Sys Bio), or whose expression oscillates during a diurnal cycle in Cyanothece 51142 (see Stockel et al 2011, PLoS ONE):

To implement a systems approach, biochemists and molecular biologists, chemical engineers, mathematicians and model builders, and others work side by side in our lab. Many of the techniques that have been developed to understand the workings of computer networks or the chemistry of an oil refinery can be applied to understanding how a cell regulates its internal biochemistry to adapt and thrive in an ever-changing environment, or how microbes capable of churning out products valuable to humans might be designed and built. In this way, systems biology serves as one of the major enabling technologies for building new types of organisms via synthetic biology.