Xholon - Life

What is it

This is a model of various biological systems, from individual cells, to organisms, to an entire ecosystem. It's purpose is to explore how Xholon can be used to model a large system, in this case a set of nested biological systems.

The model includes a Sun to provide light and energy, and an ecology in which various organisms can interact. The ecology includes a lettuce plant and a human being. The lettuce photosynthesizes the light, and sometimes reflects it to the eye of the human. The lettuce also absorbs water, carbon dioxide, and nutrients from its environment (a lake, an atmosphere, and some soil). The human can see the lettuce, and through a nervous system can move its mouth to eat some of the lettuce. The digestive system then converts nutrients in the lettuce into a more usable form. The circulatory system circulates blood, that transports nutrients between different parts of the body.

There's a lot happening in this simulation, so you'll need to take some time to explore it.

How to use it

Run it:

  1. Run the Java application through the Xholon GUI (org.primordion.xholon.app.Xhn.java), and select File --> Open --> cellontro --> Life --> Life_xhn.xml.
  2. Expand the Controller node in the tree.
  3. Press the Start node.
  4. You should initially see a list of the parameters used in the model, displayed in the console window. Each time step, various objects in the simulation will display information about themselves, for example:

sun_2 is shining.
lettuce_21707 is absorbing nutrients from soil_21721.

lettuce_21707 is reflecting received light to coneOuterSegment_261.
sun_2 is shining.
At timestep 1, gPase:gPase_177 is slicing glycogen_59 into glucose_1_Phosphate_58 49.0,1.0 .
lettuce_21707 is absorbing nutrients from soil_21721.

...

axonSegment_6849 is sending an action potential to terminalButtons_6855.
coneOuterSegment_261 is sending a PSP to neuronCellBody_14.
axonHillock_6847 is sending an action potential to axonSegment_6849.
lettuce_21707 is photosynthesizing received light.
neuronCellBody_6801 is sending a PSP to axonHillock_6847.
neuronCellBody_6801 is sending a PSP to axonHillock_6847.
sun_2 is shining.
lettuce_21707 is absorbing nutrients from soil_21721.

...

axonSegment_6849 is sending an action potential to terminalButtons_6855.
axonSegment_6943 is sending an action potential to terminalButtons_6949.
axonSegment_7045 is sending an action potential to terminalButtons_7051.
coneOuterSegment_261 is sending a PSP to neuronCellBody_14.
axonHillock_6746 is sending an action potential to axonSegment_6748.
axonHillock_6847 is sending an action potential to axonSegment_6849.
axonHillock_6941 is sending an action potential to axonSegment_6943.
axonHillock_7143 is sending an action potential to axonSegment_7145.
lettuce_21707 is reflecting received light to coneOuterSegment_261.
neuronCellBody_6700 is sending a PSP to axonHillock_6746.
neuronCellBody_6801 is sending a PSP to axonHillock_6847.
neuronCellBody_6801 is sending a PSP to axonHillock_6847.
neuronCellBody_6895 is sending a PSP to axonHillock_6941.
neuronCellBody_6895 is sending a PSP to axonHillock_6941.
neuronCellBody_6997 is sending a PSP to axonHillock_7043.
neuronCellBody_7097 is sending a PSP to axonHillock_7143.
sun_2 is shining.
mucosalCell_21661 bilayer is transporting glucose to bloodPlasma_5228.
lettuce_21707 is absorbing nutrients from soil_21721.

Extending the model

The model could be extended by adding additional detail to any of the subsystems already in it. The challenge with this model is to keep adding detail, while still allowing everything that's already there to continue working. This is the goal of Xholon itself.

Xholon and Ealontro features

A version of the model, Life_StaticFactory_xhn.xml, uses a static factory rather than the usual dynamic factory, to create xholon instances at runtime.

Credits and references

This model is partly described in a journal paper.

Webb, K., & White, T. (2005). Cell Modeling with Reusable Agent-based Formalisms. JAI 2005.

An older version of this model is described in the appendices to Ken Webb's university honors project.

Webb, K. (2003). Autopoiesis - A comparison of two computational models. Ottawa, Canada: Carleton University, BA Honours Project.