An important source of evidence for the strong constraints & invariants that must prevail during embryogenesis is supplied by the tetragametic chimerism phenomenon. This is the development of Chimeras from embryos formed by the fusing of two [fraternal twins] fertilized eggs. The resulting embryos have two complete and distinct genomes & originate from four gametes (tetragametic): two sperms and two eggs. Please refer to a clear description of chimerism.
Several cases of chimerism are described in:The Stranger Within What is important, from the embryogenesis point of view, is that these cases show that cell differentiation processes can execute harmoniously & result in viable individuals even though driven by two distinct genomes. The definitive proof that we see two distinct cell differentiation processes is supplied by the case of individuals with two distinct sets of sex organs, one male & the other female. Such cases arise from the fusion of male (XY) & female (XX) zygotes. We see, in fact, that a viable individual can arise that has portions of a female body as well as portions of a male body. This clearly shows that cell duplication & differentiation, in these regions, is under the control of two distinct genomes.
What is very significant, from a computational point of view, is that such development can occur without disrupting the over all harmony & balance of the resulting individual. For this to occur it is necessary that the individual cell duplication & differentiation processes be either strongly compatible, to begin with, or that the processes are self regulating, in the sense that the final body part sizes and relative positioning are not just the result of explicit coding in the genome, but the result of dynamic self regulating feedback mechanisms. In any event the study of chimerism, in human and other vertebrates, in our opinion, will prove out to be a rich source of evidence about the specific nature of the cell duplication & differentiation sub-processes of the embryogenesis process.
Sexual reproduction is an additional constraint on such processes. Namely, the DNA from the two gametes MUST not lead to architecturally incompatible cell duplication & differentiation processes. This must be true regardless of the selection of mates. This and the chimerism based arguments require that the genome not explicitly specify size of organs & body parts or their relative positioning. In other words, the genome, most likely, does not explicitly defines the organism architecture. The genome must explicitly specify: all the GeNets, their pertinent cell differentiation precedence relations and all body proteins.