Dynamic DNA Processing: A Microcode Model of Cell Differentiation

The question of how a single fertilized cell in eukaryotic organisms is able to differentiate into so many specialized cell types, each differing significantly in form and function, requires the existence of an asymmetry at each stage, and an individual  developmental program for each cell lineage. Models depending on an asymmetric distribution of specific compounds to each daughter cell during cell division have a number of conceptual difficulties, which we discuss. In our work, we propose, instead, that 3-D DNA computation is ideally suited to direct the process of differentiation. By modeling each cell in eukaryotic organisms as a processor having a unique set of allowed states, represented by a specific DNA sequence, we demonstrate a method by which gene expression can be regulated. As the theory is developed, we suggest reasons for the complementary, quaternary (4-base) coding scheme used in most eukaryotes. A role for transposable elements is suggested, as is a role for the abundance of noncoding DNA, along with a method by which single nucleotide polymorphisms (SNPs) may alter gene expression. The effect of various errors is considered, and may explain the aneuploidy (abnormal chromosomal numbers and structures) frequently observed in certain cancers. Finally, a mechanism for inter-processor communication is proposed to explain cell-cell recognition processes, which leads to an elucidation of a possible pathway by which nonmutagenic carcinogenic agents may act. This presupposes that cells may not only read from, but also write to their DNA, and we suggest that this may plausibly occur in living cells.