The differentiation code

In code biology we seek a presumably arbitrary, and thus symbolic relationship between two or more entities, such as the relationship of the DNA triplet code to amino acids. Here we review the differentiation code from the code biology point of view. We observe that lineage trees of mosaic organisms can be subsumed as special cases of differentiation trees of regulating embryos. The latter can be empirically discovered as a bifurcating tree of contraction and expansion differentiation waves that recursively divide the embryo into its cell types. A binary digit, 0 or 1, assigned to each wave results in a binary number corresponding to each cell type, and may be called the differentiation code for that cell type. The differentiation tree has a correspondence in the genome, in terms of the genome's logical structure. For a given cell type, the path to it from the zygote is marked epigenetically on the genome. Thus the differentiation code symbolically maps an epigenetically marked subset of the logical structure of the genome to the phenotype of a particular cell type. The waves involved and signal transduction from the cell state splitter to the genome are intermediaries in this relationship, and may also be arbitrary choices, and thus part of the code. In full, differentiation code ⇔ history along the differentiation tree of the differentiation wave types leading to a given cell type ⇔ contraction or expansion of the cell's cell state splitter ⇔ activation of one of two signal transduction pathways from the cell state splitter to the nucleus ⇔ activation of one of two readied gene cascades (the "nuclear state splitter") ⇔ epigenetic marking of the selected portion of the logical path. Each wave is in effect a cybernetic control system that results in differentiation of a set of cells and initiation of two new waves (cybernetic systems) as its goals. The differentiation code forms a basis for open evolution and its appearance was one of the major evolutionary transitions.