SimSoup is a project for the investigation of non-genetic mechanisms of evolution, especially evolution of chemical networks in the context of the Origin of Life. I am using an artificial chemistry approach, and SimSoup is also the name of the simulation program that I have developed to investigate the dynamic behaviour of chemical networks and the molecular structures that determine the properties of these networks.

Early Evolution - Smart Molecules or Networks?

Since the discovery of the structure of DNA there has been a focus on the role of template replicating molecules in biology. The insights and achievements that have followed are real and very substantial. There is however a growing sense that life cannot be explained solely in terms of complex molecules with highly specialised properties. In his wonderful little book 'The Music of Life', Denis Noble notes that the popular misconception that the DNA code 'causes' life has been called 'DNA-mania' by André Pichot.

I refer to template replicating molecules, and the complex enzymes that are required for accurate replication, as 'smart' molecules. The SimSoup project seeks to investigate the role of non-genetic (ie non-template or 'metabolism first') mechanisms in the Origin of Life. In particular, SimSoup is about understanding the dynamic properties of chemical networks, and the role these could have played in the first evolving systems. The aim is not to show that a chemical network can produce a 'smart' molecule that can carry inherited information and evolve; it is to show that a chemical network containing molecules much simpler than DNA has sufficient information carrying properties to enable evolution to begin.

SimSoup does not make any assumption about whether the prebiotic world was heterotrophic or autotrophic. The network oriented evolutionary process envisaged is applicable to either case, although my own preference is for small molecule theories, such as that of Günter Wächtershäuser. The name 'SimSoup' does not imply an organic soup - see the quote from Günter Wächtershäuser in the Quotes section.

The SimSoup Artificial Chemistry Simulator

The SimSoup model enables a Chemistry to be defined in terms of Molecule Types and the possible Interactions between them. A simulation run involves setting up a number of Molecules of various Molecule Types in a Reactor, and then allowing Interactions to take place over a period of time. Interactions taking place in the Reactor are shown on a graphical display.

Although the motivation for development of the program is to enable investigation of 'metabolism first' theories of the Origin of Life, the basic design of SimSoup supports modelling of any network in which interactions can take place between nodes.

Model Features - Current Release

The main features of SimSoup are: SimSoup in open source code, released under the GNU Public License (GPL) Version 3.