On Causality in Biology

I was interested in what other leaders of the third way of evolution are doing, so I read one very interesting interview with Denis Noble, made by Suzan Mazur, link to which I found on thethirdwayofevolution.com:
 Replace the Modern Synthesis (Neo-Darwinism): An Interview With Denis Noble
What first struck my attention was the mentioned work of Yong-Hua Sun and his colleagues:
>>What Yong Hua Sun et al. did was take the nucleus of one species of fish and insert it into the denucleated but fertilized egg cell of a different species. What they got as an adult — it’s very rare that you get an adult from such a cross-species clone — but what they got as an adult is intermediate between the two, whereas, of course, in a gene-centric view you should — and assuming the genes are defined as DNA — you should get the animal from which the nucleus was taken. That doesn’t happen in Yong Hua Sun’s experiment.<<
There were several intriguing (to me at least) questions related to that experiment:
1. How and where in cytoplasm is written the information that contributed to development of NT embryo, ie that resulted in a hybrid clone? At that moment when I was reading that, I wasn't even aware of the existence of mitochondrial DNA, so that possible answer didn't occur to me at that point, and at this moment, I'm still not sure this is the right answer. I am inclined to think it is, due to a logic that the same type of molecules serves the same function, ie DNA is memory, and proteins are processors. And I'm not sure because I studied these answers: What are the differences between mitochondrial and nuclear DNA
2. How does the cell know it's an egg (ovocyte), fertilized or not, if it's denucleated? Well, regarding that, I knew from the start it was a question of gene expression in a differentiated cell, because if it was, for example, a sperm instead, it would have (among other things) a flagellum developed, etc.
3. How does the egg cell know it's fertilized, if it's denucleated, where is it written? Although nuclear DNA synthesis is not the only impact of a sperm entry, as described here Oocyte activation, this was still the most intriguing part for me.
So I read the relevant paper that describes the experiment of Chinese scientists, Cytoplasmic Impact on Cross-Genus Cloned Fish Derived from Transgenic Common Carp (Cyprinus carpio) Nuclei and Goldfish (Carassius auratus) Enucleated Eggs , I guess that's the one Noble is talking about, and realized that in the interview, their work was not quite precisely described. Namely, in "Preparation of Recipient Enucleated Eggs" chapter, it specifically says that the goldfish eggs were unfertilized:
>>The unfertilized eggs were placed into a trypsin solution of 0.25% ...<<
Which means that the other effects of sperm entry are not relevant, or at least not crucial for embryogenesis, that is effects on cytoplasm, the crucial factor is nuclear DNA synthesis. And that was actually done during a preparation of donor nuclei:
>>Fertilized eggs from transgenic F3 red common carp were cultured in Holtfreter solution (0.35% NaCl, 0.01% CaCl₂, 0.005% KCl [w/v], 50 IU/ml streptomycin, and 100 IU/ml ampicillin) up to the blastula stage. The blastoderms were cut from the yolk with a fine glass needle and placed into Holtfreter dissociation solution (Ca²⁺-free Holtfreter solution with 0.15 mM EDTA). After 2 min, cells of the blastoderms were dissociated and would be used as donors for nuclear transplantation.<<
So, the donor nuclei were actually taken from embryonic cells that have adequate degree of potency, and that was sufficient for recipient enucleated unfertilized eggs to adapt and reprogram nuclei to direct the embryogenesis and ontogenesis. As much as it all looks impressive and fascinating for someone who faces such science for the first time, such as I do, I must say that it also works in a general fashion: "Let's screw things up maximally for both goldfish and red common carp cells, and see what can survive out of it". And some small percentage really does, and one can count the vertebral number of the cloned fish, and see that it's inherited from goldfish, and not from red common carp (due to interspecies difference and intraspecies relative stability of that parameter). Other than that, most of the traits are inherited from red common carp. Plus, one of conclusions in the presented study was that the mitochondrial DNAs from the nuclear donor cells (probably introduced due to an imperfection of the nuclear transplantation technique) were eliminated during the development of the cloned fish, just mimicking the destiny of the sperm-derived mtDNA in the sexual hybrid fish. That maybe answers somewhat my question number 1. And maybe not, because, there is a part of that study that I don't understand even more than the others, and it is somewhat explained here:
https://en.wikipedia.org/wiki/Somitogenesis
https://en.wikipedia.org/wiki/Clock_and_wavefront_model
So, the better answer to the question number 1 may be this excerpt from the study:
>>Our data suggest that the somite number or segmentation clock of fish is determined in early embryogenesis under the regulation of egg cytoplasmic components during the formation of presomitic mesoderm. During the somite stages, somitogenesis-related genes are expressed cyclically, resulting in the formation of somites. Meanwhile, as a result of hierarchical activation of cascades of nuclear genes, cell fates and most of the developmental characteristics of fish are controlled by the temporal and spatial expression of nuclear genes. Therefore, the cross-genus cloned fish showed to be almost the same as donor common carp in exterior appearance.<<

But the core issue is: what is actually driving the whole proces, DNA or proteins, nucleus or cytoplasm (obviously, one cannot identify DNA with nucleus and proteins with cytoplasm, so this rethorical question shouldn't be read that way), what is active and what is passive? It seems a bit like a chicken and egg question, but let's recall that the cytoplasm was from unfertilized unipotent egg cell, before totipotent nucleus was inserted into it. Let's ask the same question in a little bit different way:

 

This is a picture of Von Neumann's architecture, who seems like an omnipresent and unavoidable guy in all discussions about mathematical description of life. What unit is in that architecture active, and what is passive, memory or CPU? Considering the fact that memory unit contains the program, ie instructions for CPU, one might think it's memory, but, it really is a passive store for both data and programs, that actually CPU actively processes and executes, and can change. This is actually a solid, although not full analogy, but it gives a perspective why is replicator<-->vehicle actually very limited paradigm. Namely, every cell differentiation acts upon DNA code, silencing (or as Bert Hubert says in DNA seen through the eyes of a coder "conditionally compiling") certain its parts, although, the full copy is still retained by that process. And again, the instruction for that process is of course, contained in DNA, where else. For example, during the embryonic stage, here it says that it is controlled by a single gene called G9a: Mechanism That Triggers Differentiation Of Embryo Cells Discovered, during the adult stage, stem cells may be caused to differentiate by different signals/genes. But still, the effect of proteins on DNA is a matter of every day routine, so why wouldn't it be possible for them to also act in a way that doesn't retain the full copy of DNA code intact, performing the natural genetic engineering that way?