Synthetic biology uses the prokaryotic bacteria to run industrial processes, because the prokaryotic cell has no choice. It is permanently set on "run"! Thus like a washing machine when it is loaded with its wash and powered up it runs through its cycle. And the cycle is key, this is an endless iterative process.
The Eukaryotic cells have one distinction, the nucleus. This provides a control interface, a nucleus wall between the processing of the cell and the processing of the DNA. This interface screens what gets into the "Internal" processing and what gets out to the external process. This kind of control is the same as that of a transistor valve. This provifes for a level of contro; that a prokaryotic cell does not have.
What controls this eukaryotic cell? Epigenetic conditions!
We can programme a prokaryotic cell by using a programming "language" the cell responds to :DNA strands with the correct 3'and 5' sites. These strands are introduced into the cells DNA. This DNA is not in the double helix form, because this form only occurs just prior to mitosis or meiosis. The image of the whole strand of DNA being copied is false. The whole strand is gathered into genetic bundles, discrete, called chromosomes. The Chromosomes are collections of genes combined together. How these genes are combined is pretty standard, but not always stable! Sometimes genes apparently jump about. This is not the case. The standard combination and folding of the DNA into chromosome from the diffuse state is o complex that it is a miracle that it happens reliably most of the time. By reliable i mean stably.
The question is what makes this combination so stable? How do the packagers remember which part goes back together with which? The information is in the 3' and 5' sites read by the gluesomes, the reverse of the splicesomes.
So introducing a strand of DNA with the correct coding means the prokaryotic cell will process it as if part of its own DNA. However if it is not quite correct, the gluesomes will not add them to theDNA helix and copy them into the [ackaged chromosomes. It will not process beyond an initial start!
Eukaryotic cells will resist this happening easily/ Only when the nucleus is penetrated will it be possible, and the splicesomes in the nucleus make it less certain that the proper encoding will take place for the intended procuct. The only difference therefore is the gene variability that the nucleus would produce in a eukaryotic cell. Eukaryotic cells provide this variability that makes the cell adaptive at a colonic level to any environmental changes.
The virus reprogrammes the eukaryotic cell, but bacteriophages sre the form that reprogrammes the prokaryotic cell. The use of synthetic biology on the back of virus reprogramming is hailed as a new level of human control. This is delusional. The biomass of bacteriophages means we will never be in control, we will always be subject to the greater environmental dominance. The future therefore for this type of "technology" is unpredictable and will require constant vigilance.
Now what if we can replace not just a strand, but the whole chromosomal load in the eukaryotic or prokaryotic cell? This then provides the rest of the cell machinery with a different relationship to its DNA.
The central dogma has been that the DNA controls the cell. This dogma has been replaced by the reality that the cell is in an epigenetic relationship with the environment, and this relationship drives an evolutionary process in eukaryotic cells. If we take the whole genome, that is the chromosomalload of a cell and replace it by one we have designed, we have no way of knowing its environmental viability. However if we take the whole genome and only take out a specific sequence that codes for a specific protein, then the environmental viability , presumably would be hatdly altered. This is so badly mistaken that i cannot begin to describe how!
The variation in a niche is driven by small changes in the environment. These select those genetic variations that fit the niche. The vertical reproductive strategy means that this cell soon develops dominance in that niche, This provides competitive pressure that drives niche changes for other cells. These cells evolve to compete, and the change in the environment gets into a reaction chain that changes everything unpredictably.
Now that is a simplified scenario. It assumes so much about the cell environment and cell reproduction. We know that cell reproduction is due to vertical and horizontal processes! The web of cells has evolved to exist in a much freer and more volatile environment of so called Viral loads. These viruses include Bacteriophages, the role of which are fundamental to the creation of bacterial cells as well as to their destruction! This means the fundamental of the eukaryotic cell, the prokaryotic cell, exists in a much greater unknown viral environment.
The viruses that exist in the environment which specifically target eukaryotic cells are not fully known. Thus, wefind ourselves in the role of a virus, infecting and altering the cell biology of our environment in ways we do not fully compehend.
What this all means is that we should not be arrogant or vaunted! We should realise the insignificant place we have in the whole scheme of things. The dangers and benefits are finally beyond our control. All we can do is try to make the short term consequences are not disatrous, and remain eternally vigilant and humble before the epigenetic forces that we are contributing to.