SimSoup

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.

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 only 'dumb' molecules 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

SimSoup version 0.3 includes the following features:-

• A Chemistry including Molecule Types and Interaction Types
• A Reactor in which Interactions take place between Molecules
• Graphical views of the Chemistry and Reactor. Interactions taking place in the Reactor are displayed in real time
• Display of Simulation Statistics in real time. Statistics can be displayed in two formats:-
  • Data Series Plots: These show the real-time behaviour of a range of variables that are monitored as the simulation runs. The Data Series to be displayed are selectable from a list
  • Manhattan Plot: This shows the amount of variability in the composition of the material in the Reactor.
• Simulation Control facilities, including the ability to use Predefined Scenarios to control the operation of the simulation, and a facility enabling 'Action Requests' to be setup to customise Predefined Scenarios or create user defined scenarios.
• A (partly hidden) System Monitor screen - mainly for diagnostic purposes

The SimSoup design includes three Interaction Types as shown in the following table. A, B and C are molecutes that are either consumed or produced by the Interaction.

Interaction Type	Interaction Scheme
Transformation	A --> B
Construction	A + B --> C
Fission	A --> B + C

The three Interaction Types can occur in various sequences to produce more complex Compound Interactions. Some of these are shown in the following table. A, B, C and D are molecules that are either consumed or produced by the Compound Interaction. Several of the Compound Interactions are catalytic, and in such cases X represents the catalyst. Some of the Compound Interactions involve Intermediate Procucts that are unstable and short lived, and which give rise to further products through Fission. Intermediate Products are labeled U and V.

Compound Interaction	Component Interaction Types	Overall Scheme
Recombination	A + B --> U (Construction) U --> C + D (Fission)	A + B --> C + D
Catalytic Construction	A + X --> Y (Construction) Y + B --> U (Construction) U --> C + X (Fission)	A + X + B --> C + X
Catalytic Fission	A + X --> U (Construction) U --> X + V (Fission) V --> B + C (Fission)	A + X --> X + B + C
Catalytic Recombination	A + X --> Y(Construction) Y + B --> U (Construction) U --> X + V (Fission) V --> C + D (Fission)	A + X + B --> X + C + D
Catalytic Transformation	A + X --> U (Construction) U --> B + X (Fission)	A + X --> B + X

Model Features - Development Version

The current development version of SimSoup includes support for thermodynamics, and cycle detection using 'Trackers'. See the News section for more on this.

SimSoup Design and Construction

SimSoup has an object oriented design.The main benefit of this is that it allows concepts such as 'Molecule' and 'Interaction Type' to be represented as self contained units in the program. This makes understanding the code easier, and therefore improves maintainability of the code. I use techniques such as inheritance and polymorphism sparingly, but they are used in the case of the Interaction Types listed above. See the Design section for more on this.

SimSoup Licensing (Summary)

SimSoup Versions 0.2 and 0.3 for Linux are free software. It is released under the terms of the GNU General Public License Version 2.

SimSoup Version 0.1 - Prototype for Linux is free software. It is distributed under the terms of the GNU General Public License Version 2.

SimSoup Version 0.1 - Prototype for Windows is provided at no cost, but is for Personal use only.

For details see the licence files incuded in the downloads.