Introduction to Systems Biology

The field of systems biology has emerged as a result of two revolutions. The first is decades of progress in molecular biology and biochemistry which have identified many of the molecules and chemical reactions needed for life. The second is the 'omics revolution which has enabled these measurements to be conducted at high throughput. Systems biology seeks to convert such observations into a holistic understanding of biological systems. The motivating question for this course is, how does life emerge from a collection of dead molecules? We explore how simple conceptual ideas can explain the seemingly complicated nature of biological systems. We explore how similar design principles appear across various biological systems and scales. For example, the negative feedback motif is present at the cellular scale (in gene regulatory networks), at the organismal scale (in glucose homeostasis), and at the ecological scale (through predator-prey dynamics). We also consider the general nature of input-output responses, the role of energy expenditure, robustness and ultra-sensitivity, bet hedging, and whether biological systems operate optimally. Simple mathematical models are used to explore these topics. We discuss what a model can and cannot do and common pitfalls in modeling. This course is not too mathematically technical; one of its themes is that relatively simple math can go a long way.