Fig. 1.

Generative model. a An organism with N = 3 genes and two cell types. Circles represent all possible cell types. The organism is composed of cell types represented by white circles and does not contain the gray cell types. Binary strings written inside the circles represent the presence (1) or absence (0) of determinants in those cell types. b–e The rules for the development of the organism in a. b Cell division matrix CD. In the model, daughter cell types cannot contain determinants not present in the mother cell type; therefore, in the figure, such positions in CD are represented by empty boxes. For all j such that CD(i,j)=1, cell type i produces cell type j upon cell division. c Signaling matrix SG. Determinants 1 and 3, which are labeled in blue, act as signaling molecules. d Signaling adjacency matrix A. A(i,j)=1 implies that cell type j receives all signals produced by cell type i. The rows for cell types [000] and [010] are grayed out, since these cells produce no signaling molecules. e Gene regulation matrix GR. GR(i,j)=1 implies that cell type j is a stable cell type, and cell type i maps to cell type j. f Schematic of “organismal development” in the model. All cell types synchronously undergo cell division according to CD; the daughter cells exchange signals according to SG and A, and cells respond to signals through gene regulation according to GR. The process repeats until it reaches a steady state. Here, we show how the homeostatic organism in a is obtained using the developmental rules matrices in b–e. g Lineage graph of the homeostatic organism in a