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:
- A Chemistry: Including Molecule
Types and Interaction Types
- A Reactor: In which interactions take place
between Molecules of the various types
- Graphical Views of the Chemistry and Reactor: This
includes display of the Molecules / Molecule Types present
and their structures
- Graphical Display of Simulation Statistics: Statistics showing
the behaviour of the simulation over time can be displayed in two
formats:
- Time Series Plots: These show the real-time behaviour
of a range of variables, including numbers of Molecules
of each type. The Data Series to be displayed are
selectable from various lists
- Manhattan Plot: This shows the variability in the
composition of the material in the Reactor over time
- Scenario Display: A display of the current scenario and status
information on its progress
- Action Requests: These are requests for events to take
place at particular times. For example, an Action Request
can be setup to cause a Molecule of a particular type to be
added to the Reactor at a particular time
- Input Processor: This enables a simulation scenario to be
defined in a file and loaded to SimSoup. Any errors in the file are
detected and reported to the user.
SimSoup in open source code, released under the GNU Public License
(GPL) Version 3.