Supporting and supplemental information for the paper
"Evolution and Morphogenesis of Differentiated Multicellular Organisms:
Autonomously Generated Diffusion Gradients for Positional Information"
On this web page you can find additional results we could not fit into the paper. Especially videos and an interactive Java applet will hopefully allow you to get a better idea of this work - but please read the paper as well, there is some serious research behind the colorful self-organizing flags!
Executables and source code now available!

Evolutionary target: 60 by 40 pixel French flag
(this work is not endorsed and the authors are not paid by the French government)

What is in the paper?
Abstract    Development is the powerful process involving a genome in the transformation from one egg cell to a multicellular organism with many cell types. The dividing cells manage to organize and assign themselves special, differentiated roles in a reliable manner, creating a spatio-temporal pattern and division of labor. This despite the fact that little positional information may be available to them initially to guide this patterning.
Inspired by a model of developmental biologist L. Wolpert, we simulate this situation in an evolutionary setting where individuals have to grow into "French flag" patterns. The cells in our model exist in a 2-layer Potts Model physical environment. Controlled by continuous genetic regulatory networks, identical for all cells of one individual, the cells can individually differ in parameters including target volume, shape, orientation, and diffusion. Intercellular communication is possible via secretion and sensing of diffusing morphogens.
Evolved individuals growing from a single cell can develop the French flag pattern by setting up and maintaining asymmetric morphogen gradients - a behavior predicted by several theoretical models.
Full paper available from MIT Press open access and locally here.

Videos and interactive Java applet
Please choose by selecting from the drop-down menu< CLICK FOR APPLET
In the applet you can replay development (choose between cell color or concentration of a morphogen).
By clicking a cell you can inspect and plot its parameters over time (drop-down in the lower right corner of the applet).

Distorted flags
For comparison same individual after 200 time steps:
Left with Morphogen, right without Morphogen (secretion disabled)

Result of morphogenesis (same gene network again) when starting angle (orientation) in the initial cell and grid is rotated by 90 degrees - a bit distorted but still one can recognize the rotated flag

Executables and C++ source code

All this software is distributed under the GNU General Public License (GNU GPL). So you are welcome to use the code free of charge as long as you make the resulting applications available under GNU GPL again and you cite the original work. There is no warranty of any kind.

Cadherin plugin parameters
Values used for the "ContactMultiCad" plugin that comes with CompuCell3D. See there for details. The only addition in our software was that every cell's GRN could individually control expression levels of the three cadherins.
  <Plugin Name="ContactMultiCad">
   <Energy Type1="Medium" Type2="Medium">1</Energy>
   <Energy Type1="Blue" Type2="Blue">-1</Energy>
   <Energy Type1="White"    Type2="White">-1</Energy>
   <Energy Type1="Red"    Type2="Red">-1</Energy>

   <Energy Type1="Red" Type2="Medium">0</Energy>
   <Energy Type1="White"    Type2="Medium">0</Energy>
   <Energy Type1="Blue"    Type2="Medium">0</Energy>
   <Energy Type1="White"    Type2="Red">0</Energy>
   <Energy Type1="White"    Type2="Blue">0</Energy>
   <Energy Type1="Blue"    Type2="Red">0</Energy>

      <Specificity Cadherin1="Cad1" Cadherin2="Cad1">-20</Specificity>
      <Specificity Cadherin1="Cad2" Cadherin2="Cad2">20</Specificity>
      <Specificity Cadherin1="Cad1" Cadherin2="Cad2">0</Specificity>
      <Specificity Cadherin1="Cad3" Cadherin2="Cad3">-5</Specificity>
      <Specificity Cadherin1="Cad1" Cadherin2="Cad3">5</Specificity>
      <Specificity Cadherin1="Cad2" Cadherin2="Cad3">5</Specificity>


Reference / Bibtex
Knabe, J. F., Nehaniv, C. L. and Schilstra, M. J. Evolution and Morphogenesis of Differentiated Multicellular Organisms: Autonomously Generated Diffusion Gradients for Positional Information. In Artificial Life XI: Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems, pages 321-328, MIT Press, 2008.

    author = {Johannes F. Knabe and Chrystopher L. Nehaniv and Maria J. Schilstra},
    title = {Evolution and Morphogenesis of Differentiated Multicellular Organisms:
        Autonomously Generated Diffusion Gradients for Positional Information},
    booktitle = {Artificial Life XI: Proceedings of the Eleventh International  
       Conference on the Simulation and Synthesis of Living Systems},
    editor = {S. Bullock and J. Noble and R. Watson and M. A. Bedau},
    year = {2008},
    pages = {321--328},
    publisher = {MIT Press},
    ee = {},
    url = {}

2008-04-18; University of Hertfordshire, Hatfield AL10 9AB, UK; Version 1.2 - added Java applet
2008-03-14; University of Hertfordshire, Hatfield AL10 9AB, UK; Version 1.1 - added distorted flags
2008-03-06; University of Hertfordshire, Hatfield AL10 9AB, UK; Version 1.0
You might want to visit Johannes Knabe's homepage and other publications as well.