Urdar - A digital ecology

This page contains an applet which illustrates the dynamics of the artificial life system Urdar. Below the applet, you can find a tutorial and a description of the system. In order to run the applet you need to have Java Runtime Environment installed. The source code of the full model and documentation can be downloaded here.

Philosophy

**Cross-feeding - ** The dynamics of cross-feeding can in
general terms be described by the figure below.

- The agents in the model digest binary strings by applying CA-rules, transforming r to r'. To each such metabolic step we can associate a difference in energy dE (visualised with dot- ted lines). The reproduction of each agent depends on how much it can decrease the energy of the binary string and oc- curs with probability P(dE) (represented by the arrows on the left hand side). The binary strings exist in a common pool which they enter (and leave) at a rate gamma, as shown by the arrows on the right hand side.
- This framework is very general and in Urdar we have made the following choices:
- (i) The agents
**a**are chosen to be nearest-neighbour one-dimensional elementary cellular automata (CA), one of the simplest notions of digital algorithms. - (ii) The metabolites
**r**are taken to be binary strings - (iii) The energy function
**E**is taken to be an approximation of the Shannon entropy, which gives an estimate of the amount of disorder a binary string contains, associating a low entropy (low level of disorder) with a high "energy" state of the string, i.e. we set E = 1 - s.

** Implementation -** The dynamics, depicted schematically in
the above figure, in the model during one update can be described in
the following way:

** Dynamics -** The growth rate of a species (i.e. CA-rule)
depends on how good it is at increasing the disorder of the
food-strings in the resource pool. This in turn depends on the
composition of the resources which is determined by the totality of
species present in the system. Thus we see that the fitness of a
species is not easily defined and is contingent on the ecosystem as a
whole. This gives rise a large degree of species co-existence as can be
seen in the applet.

Tutorial

Two parameters of the system can be controlled by the user: the flow rate of food strings into the system and the mutation rate.