Rapid, massive genomic restructuring is not only possible, it is an everyday occurrence, even in somatic cells. This is feasible because the natural genetic engineering toolkit – the total set of tools that every cell has to restructure its genome – is enormous.
When a mammal cell divides, 30,000–50,000 DNA decisions must be made. Selecting the genes for cell replication involves many choices. Genic expression in multicellular organisms must account for cell identity, different conditions of growth, and DNA damage. Flexibility cannot be accommodated by simply following DNA scripts.
Natural genetic engineering is needed for cells to restructure their genome to ensure survival and reproduction. To allow appropriate decision-making, epigenetic mechanisms may control replication origins, affecting chromosomal dynamics and gene expression.
Chloroplasts and mitochondria are not identical in all eukaryotes. Major genomic restructuring was repeatedly undertaken to adaptive advantage.
Plants tend to carry considerably more genes in their mitochondria than animals, though their coding capacity is not known to be greater.
The genome is an expansive library for living. A variety of means evolved to edit genic scripts and regulate gene expression.
DNA-binding proteins format DNA for many interactions, not just replication. These proteins and their relations operate cooperatively, and often in a combinatorial manner. Proteins make informed decisions: behaving differently depending upon communications with various molecules, including other proteins. That cells actively repair DNA damage demonstrates that the genetic code is not a script blindly followed, and that cells understand how DNA works.