The meaning of mechanism in gene circuits

7 July 2017

James Sharpe
Centre for Genomic Regulation
Barcelona, Spain


We use the term "mechanism" every day, but what does it really mean? In the most general sense, we may see it as "how something works". In the context of systems biology, it may be the combination of two things: both the "causal relationships" between components of the system (for example the regulatory interactions between molecules or genes in a circuit), and the resulting dynamics, which together explain the behavior of the system.

However, understanding the necessary causal relationships in a circuit is not trivial. A given function may be achieved by two different circuit topologies. How do we determine if these 2 circuits function in fundamentally different ways, or instead are just "versions" of the same thing? In other words how do we determine mechanism? How do we compare and contrast mechanisms in a rigorous way?

In this talk I will propose a particular answer to these questions. I will introduce a graphical method we developed in 2010 called a Complexity Atlas [1], which is related to the concept of neutral networks [2], and which provides a useful first step, and then develop the ideas further using phase portrait analysis, from dynamical systems theory


  1. J Cotterell, J Sharpe, "An atlas of gene regulatory networks reveals multiple three-gene mechanisms for interpreting morphogen gradients", Mol Syst Biol 6:425 2010. PubMed
  2. P Schuster, W Fontana, P F Stadler, I L Hofacker, "From sequences to shapes and back: a case study in RNA secondary structures", Proc Biol Sci 255:279-84 1994. PubMed

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