In simple self-replicating machines (exclusive of developmental automata), the structure of the description (machine genome) is very simple. For the von Neumann model, the description is organised in a row major/column minor (or the reverse) order, and is clearly a blueprint. Biological genomes are seen as being strictly not of a blueprint nature but, it is clearly the case that whatever the architecture of the biological genome, it must be manipulable by the cell; the genome is, after all, totally inert.
So, the question pertains to all characters of biological genome architecture, and their delineation. Also, this question has strong potential for elucidating semiotic features of genome architecture.
The kind assistance of other researchers will certainly find value in the theory of developmental automata.
Hi William, you are right, the biological genome is certainly not a blueprint. For me, it helped a lot to see the genome and the cell as a tangled network. Both levels are interdependent and none fully determines the other. A good discussion of tangled networks is provided in "Goedel, Escher, Bach" by Douglas Hofstadter (https://www.amazon.de/Godel-Escher-Bach-Eternal-Golden/dp/0465026567).
GEB got me started back in the early 1980s. See my paper Apple Worms, on the RG profile. My work has derived a self-replicating machine that displays ontogeny; it has a zygote, that grows incrementally to become the adult, and only the adult can self-replicate, and it does so through the construction of zygotes.
You might also like to consider that the non-blueprint yields surprising levels of similarity, one generation to another; sometimes, the similarities are uncanny. I suggest that there is a bit of blueprint still in that recipe.
One last point, the genome generally is irrelevant, for detailed understanding of component molecules, and many other things, allows for the artificial construction of a genome that yields stasis of the cell. Mathematically, there are an infinite number of genomes that are suitable to stasis of any host cell. What matters is the interpreter. All meaning in any self-replicating system resides in the machine component, not the description component.
It is the interpreter that is important.
I can not help you because I do not work in this research orientation
Sorry
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