|Evolution of DNA -
Let's take a closer look at a few specific types of cell structures, and examine how Foxy may have been involved with them.
Much of the basic metabolism of life takes place in the mitochondria, a Eukaryotic organelle that contains its own DNA.
There is strong evidence that mitochondria were originally rikettsia-like bacteria which were absorbed by early Eukaryotic cells. The relationship was probably symbiotic at first, but eventually the mitochondria lost many of its metabolic functions, which were replaced by genes in the eukaryote itself.
Eukaryote mitochondria contain much more structure than bacteria, which may be the result of Foxy scripts. Arranging metabolic enzymes into precise structures could increase efficiency and create compounds that might not be possible to synthesize otherwise, so the mitochondria certainly seem like an excellent place for Foxy scripts to be used.
Mitochondrial DNA is circular like bacterial DNA, but in most species it contains more introns than the typical bacterial cell. However many mitochondrial proteins are transcribed from genes in the nucleus of the parent cell, so any repetitive scripts could just as easily be located there.
Some early Eukaryotes also assimilated another small organism-- a blue-green algae, which is pretty much just a bacteria that is capable of photosynthesis.
As with the mitochondria, chloroplasts have their own DNA, although some of the structure within the chloroplast is coded in the main cell DNA instead.
Eukaryote chloroplasts have a much more sophisticated level of organization within the chloroplast, then their blue-green algae precursors, and it's very likely to be the result of Foxy scripts.
We've already talked a little about the rough endoplasmic reticulum, where the cell's protein synthesis takes place (it's rough because of all the ribosomes on its surface).
There is also a smooth version of the same tissue, and it's the location for most chemosynthesis in eukaryotic cells. Along with the Golgi apparatus, this organelle is basically a whole scad of membrane surface filled with enzymes.
Advanced chemosynthesis is the perfect place for Foxy to have a role. By choosing from a 'library' of possible enzymes and placing them in specific positions, simple script changes could lead to different synthetic pathways that would produce entirely different compounds.
That kind of specifying would be particularly useful in the plant kingdom, where the creation of a new chemical compound might have a huge effect on survival value, by eliminating a pest, poisoning a competitor or attracting a pollinator.
All biochemical reactions are based on only a small number of basic chemical changes: oxidations, reductions, dehydrations, hydrations and so on. It's quite reasonable to suppose that a scripted sequence of basic enzymes positioned properly along a tubule could create an exotic new compound without need for any new enzymes at all.
Of course, even if new enzymes evolved in a cell, Foxy positioning would still be useful to position any coenzymes or assisting enzymes into optimum position near the new enzyme.