By Sanjeev Kumar; Peter Bentley
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Extra info for On growth, form and computers
Cellular encoding takes the form of a grammar-tree, used to encode a developmental process. The language upon which the grammar is defined uses instructions that correspond to local graph transformations controlHng cell division (the genotype). Each cell retains a copy of the entire grammar-tree, but has a pointer pointing to different sub-trees of the main tree. Development begins with a single cell, which is subjected to cell division by duplication, according to the instructions in the genome.
Genes consist of two objects: a cis-regulatory region and a coding region. Cis-regulatory regions consist of transcription factor target sites that bind TFs, triggering transcription of the adjacent coding region. Each number denotes a protein. The gene then integrates these TFs and either switches the gene 'on' or 'off.
This is the reason for the success of Fleischer's, Sims's and Hornby's research - their environments were rich with dynamics such as surface tension, gravity, friction, inertia, moments and energy dissipation. It is also the reason for the success of many of the models of development presented in this book. If you can get the laws of physics right in your model, then your modules (be they genes or cells) will be given intrinsic properties such as adhesion, diffusion, friction and mass. Evolution (or you) can then design developmental processes that exploit these intrinsic properties of modules and their environment.
On growth, form and computers by Sanjeev Kumar; Peter Bentley