[SPOILERS] SOMA and The Matrix similarities

[Omnitool]

I think they can modify it, but my default their bodies are modeled from what I presume some kind of DNA, so in the same way that an exact "image" of their brain would resume to function the same way the real one would, I suppose the bodies would evolve the same, although they could easily modify themselves to be immortal.

I think they are stuck in the simulation, they can edit aspects of the simulation, but have no control over the physical probe, and would be unable to foresee any impending doom (probe running out of power, or crashing into something or any other physical damage), but presumably an event unlikely enough to not worry about it.

As I wrote here https://www.frictionalgames.com/forum/thread-31212.html , I believe they are in a form similar to some sort of human DNA, and could even reproduce.

There is also the possibility that people inside the Ark get older and die just like normal people, and they can actually have children.
Think about it like in real life:
- In real life, our physical appearance information is stored in our DNA. A child's physical appearance is the result of combined DNA from both parents, and the child's counciousness is a result of the social envirnoment, education and life experience (the child also imitates the parent's personality on an involuntary, subcouncious level).
- In the ARK, people's counciousness also contains their projected physical appearance, and all this is stored in code, as digital information. When a child is born in the Ark, both his/her appearance and personality traits are a perfect result of a 50/50 combination of the parent's traits, the child's gender is random (also a 50/50 chance). Given that all people in the Ark are the world's most brilliant minds (scientists, scholars) this is not a bad thing at all!

This would generate an interesting ethical dillema: Is a "lifeform" born from two scans inside the Ark considered a separate being, equal with its parent scans, or just an AI made from mixing features from the two parent scans with a 50/50 ratio? When it is born as a baby does it have the intelligence of an adult (given that it also takes personality traits and memories from its parent scans)?
My opinion is that it should be considered a human being equal with the others, and it is very possible that it will have a superior intelligence from a very young age, but it will also grow a personality of his/her own, built on top the "inherited" one.

Also, they have quite a lot of control over the Ark, both physically and regarding the simulation running inside it.

The Ark is governed by a simple AI system of its own, that manages the simulated envirnoment, weather, physics and all other factors. However, the original team that developed the Ark could have total control over the system. They could expand the envirnoment as much as the storage space permits and even control the trajectory of the space probe containing the Ark, and probably even fix and maintain it in some manner!
Proof in this direction is found within the game:
- During a conversation between Simon and Catherine, he asks her what will be the first thing she will do after they launch the Ark. She replies something like: "I will deploy the solar panels, stabilise the trajectory, etc" this proves that she has total control over the space probe containing the Ark.
- During the game Simon finds numerous diagrams detailing how the Ark is built, and its specs. They show that it is equipped with a remotely controllable robotic arm. It could be used for maintanance and repairs while the Ark is floating through space, controlled from within the ark via a simulated computer terminal or even a Pilot Seat.