Evolution of DNA -
One interesting feature in the fossil record is the Cambrian explosion, as recorded in the Burgess shales and other locations. The earth suddenly was filled with many new phyla, in an flurry of differentiation that was never seen since.
Moxy had probably already been around for a while before that explosion-- most likely there were many earlier explosions of important physiological innovations that were in smaller, soft-bodied life forms not preserved well in the fossil record. However, once a Moxy started to manage scripts for hard body parts, it would have created an explosion in any random script that led to a useful multi-cellular organism-- whether a gastropod, an echinoderm, a crustacean, or some other entirely different phylum. Such a well-timed Moxy script might have caused the creation of dozens of new phyla almost instantly.
Each script would have evolved into the most efficient versions of that basic structure. After that, regular Darwinian selection and evolution would have led to the perpetuation of any phyla with excellent structures. Of course, any phyla that were not good enough to survive day to day competition, and the occasional massive meteor impact, would have eventually become extinct.
Phylum, Class, Genus, Species
The presence of Foxy and Hoxy probably changes the appropriate way to look at phylogenetic trees, since much of the difference between different organisms would be coded in the script portions of the genetic code, and not so much in the protein-coding portions.
Of course, tracing mutations and genetic drift in protein-coding genes is still a useful way to track the genetic relatedness of different organisms, but the actual differences might be primarily in the higher-level scripts.
It seems likely that complex organisms would be controlled by many layers of scripting.
The very most basic scripts are probably very conserved, since changes there would cause huge structural changes that would usually be lethal. Changes in upper level scripts would tend to produce new organisms in an entirely different phylum, and the evolutionary trend seems to be that all the good scripts are already in use.
Changes in successively lower-level scripts would tend to produce new orders, classes or genera. Changes in still lower-level scripts would produce new species. And changes in the very lowest level scripts would create the minor quirks and glitches that mark each individual within a species.
For example, the very smallest mutations in scripts might simply produce a hair out of place, an extra bump in an antenna, or a behavioral oddity.
Insects are the dominant form of life today, and the reason for that may simply be that they are extraordinarily well adapted to scripting changes.
For example the external multiple mouth parts in arthropods in general would lend themselves very well to control via scripts. Random changes in mandible or maxilla might occasionally result in a physical structure that would allow a new style of food gathering, grooming or other behavior.
The wings, hairs and other exoskeletal features of insects (and arthropods in general) are also highly 'programmable' into new shapes and patterns.
And of course insect brains are just good enough to be reasonably evolvable by script changes, giving the potential for effective new behavior patterns. Just good enough to say extract a bit of blood from their way smarter but still vulnerable mammalian neighbors (swat).
In the plant kingdom, scripting would also have many potential uses for accelerated evolution.
Precise positioning of enzymes in the mitochondria would allow plants to create specific biochemicals to assist in their never-ending struggle to poison their parasites and competitors, attract pollinators and seed dispersers, and grow more effectively than their neighbors.
It may be no accident that plant mitochondria contain a large quantity of repetitive DNA (while animal mitochondrial DNA contains no introns or repetitive segments). Plants are stuck in one place and don't have much defense other than thorns and toxic chemicals-- so the synthesis of some new compound frequently would have survival value to them. Animals, on the other hand, have plenty of defense options that don't require exotic chemicals, so their mitochondria can be much simpler.
Scripting would also help plants to quickly change gross physical details such as the overall size and shape of leaves and stems, in response to short term pressures caused by parasites, climate change or adjustments in the plant's best evolutionary niche.
In the Gymnosperms, flowering structures appear to be under scripted control, so they have been able to develop a wide variety of methods for pollination and seed dispersal relatively quickly.
Particularly good examples for plant structures controlled by scripts would be rapidly evolving structures such as orchid flower shapes, egg-mimicing structures in Passiflora, fruiting bodies in grasses and phytochemicals in toxic species such as the Labiatae, Solaniferae and Leguminosae.
If script theory is correct, then nearly all plant breeding to date has been based on selection of new scripts that code for larger seeds, fewer toxic phytochemicals and bigger, tastier plant structures in general.
We multi-cellular creatures do some interesting things. We scratch ourselves to remove ectoparasites, and when predators attach, we fun away/fight back/play dead/squirm around, depending on circumstances and species. All of us have some sort of clever behavior that gets us food, and we have clever ways to mate and reproduce.
In order for behavior to evolve, it needs to have a solid linkage between genotype (the DNA tha produces a brain structure) and the phenotype (the brain structure that produces the behavior). So there really needs to be a 'gene' devoted specifically to each behavioral trait, so it can pass along to the offspring.
There aren't enough protein-coding genes to code for all the myriad behaviors present in even a simple brained organism. Anyways, it's hard to imagine how changing a protein could ever manage to reliably arrange neurons in the correct pattern to produce it.
In order to make evolution work for behavior, there must be an extremly detailed arrangement of scripts controlling neuron placement in the rains of arthropods, vertebrates and other 'brainy' orders. Most likely it is a 'programming language' that is far more detailed than anything used by human programmers.
It would be interesting to explore scripting changes in say the Golden Retriever, where a rather profound behavioral change was added within a few generations, back when Chesapeake goose hunters needed an easier way to fetch game from swamps. A well-designed script system might explain how an innate desire to fetch tennis balls might have been 'programmed' into their brain structure so quickly.
Obviously any scripts controlling behavior would be extremely complex and not so easy to crack. Without much notion on how neurons manage behavior, it would be even tougher to know how a script itself would affect neuron placement in a way that would result in a specific behavior pattern.
Any theories on how Moxy might work to control neurons and their connections would necessarily be extremely speculative, but here are some possible ways it could work:
1. A short Moxy script might guide the growth of a neuron's axon fiber by some sort of up-down and left-right coding, so it could reach a distant tissue.
2. Moxy could give key neurons a 'cell ID' sequence, and have them emit an unique RNA sequence or amino acid sequence into surrounding tissues. The axons of other neurons could then link to specific cells by ID, by growing towards the higher density region of those ID compounds.
3. Moxy could create subsidiary cells positioned so they would guide the growth of axon fibers in the correct direction-- and then kill those cells when their role was completed (or turn them into glial cells to help electrically insulate the axons).
Cracking the scripting codes for brain development would be an enormous task, with profound consequences.
Cipher vs Code
You might say that scripting truly brings the code into the 'genetic code'.
Technically speaking, DNA's protein transcription process is really a cipher, not a code. It's like a simple substitution of letters, not unlike the 'secret codes' that many kids develop-- perhaps by shifting each letter by pof mfuufs jo uif bmribcfu. Ciphers are relatively easy to crack. Codes are harder.
Complex organisms such as ourselves probably have many, many layers of subroutines, spelling out the developmentof each cell type, tissue and organ. Our 600 to 700 megabytes of DNA script data will not be a snap to decode.
Computer programmers sometimes need to 'reverse engineer' a function, which they can do by 'disassembling' a program into its machine instructions, and then using various tools to translate them into more human-based languages. It can be more of an art than a science.
Tracking down the useage of each of our scripts will be a similar challenge, and some of the tricks of computer programming and systems design may also come in handy for this new task.
Most likely the best approach will be to work with the 'gene ID' addresses, since that is the link between a script and the regular protein-coding gene that uses it. Perhaps some homeobox gene in a sponge or hydra would be a good place to start.
When parsing unknown computer data, another useful technique is to look at the raw 'texture' of the data.
In our DNA, sections of extremely repetitive base pairs are probably coding for very simple data-- the size or position of a structure, or the time that some process should run. In some cases, extremely repetitive DNA may also have some structural or 'spacing' function, unrelated to scripts.
More random-looking sequences may be protein coding, a 'gene ID' that links one gene to another, or a 'script ID' that links a gene to its data.
The sequences that are mostly repetitive, but slightly irregular, are probably the most interesting bits of DNA. Most likely, they are the scripts that do some sort of interesting, structural positioning-- whether it is a few molecules in a cell, a few cells in a tissue, or a few tissues in an organ.