If you want to use internal nanomachines then you'll need to make sure they have a significant biological component to overcome the immune response (or effectively make the immune system assume they're naturally meant to be there).

Also, I wouldn't have the AI tightly controlling the genetic pool to reduce diversity. This simply increases the likelihood of disease spreading and affecting the majority of the population and potentially across multiple colonies. Whilst the AI can regulate the nanomachines and enhance the attributes needed for space survival, I don't think scientists would find limiting genetic diversity to be a particularly good idea in the mid to long-term.

Basically What i said and still a good point. I think a lot of "fun" could be had with an indepth upgrade system as they work out the kinks in the nanomachine system. Also I don't know if he was talking about genetic diversity too much, just cultural diversity. I agree with your point completely tho Diversity is important 

Interesting!  =D 

My story compared yours is like this 

Colonies are self governed and self contained (like nations today), they have organizations such as "UC" (United Colonies) that debates political arguments and what not. 

The story stars whne Humans are already settled for thousands of years in ever expandable colonies keep in mind colonies don't always mean space stations they include privately/government owned planets (yeah rich folks can own a planet for their own) 

Lawless or outlaw people are normally evicted by the colonies and become "Drifters" , Elyzium is home for the homeless, that was established years after the colonies existed as a revolt against the strict laws of the colonies, in this "Boundless" colony there exists organizations such as Scientists Beyond Boundaries (think more radical Scientists without borders) , Mercenaries Beyond Boundaries (Elyzian Fields is one of them) ...ect, the colony's political stance is "Technocracy"

What is your story's religions ?

Naturally, yes diversity is important. But in this case it is really not, because these colonies are seperated by upwards of thousands of years. If diversity was allowed to occur then when these colonies meet up again they will likely be different species entirely. In fact, diversity is important in the natural world because of a constantly changing environment. The environmnet inside these colonies will not only be stable but identical with every other colony.

In this case, I don't think diversity would be beneficial and possibly even harmful.

Well each Colony is self contained and identical.

The most ideal way to describe each colony would be an Autonomous Cybercracy, secrelty moderated by an impartial AI. For example, the planned main character is a peace keeper who hunts down those who disconnect from the network as these are also the ones responsible for wreaking the most havoc and cuasing strain on the ship. The reason she does this, is because All peacekeeprs in the organization do this, and the peacekeepers before them did it as well. Religions did occur earlier as humans had freshly migrated to Earth but it faded out as the generations went on. It might make a resurgence if the colonies are reunited.

Well, speciation would take longer than thousands of years. Maybe hundreds of thousands of years, but even then, if the environment of each colony is tightly controlled and identical, the selection pressures will also be the same effectively reducing the chances of speciation. The need for diversity in such a setting is more as a plan B in case a virus mutates within the environment and infects and kills the majority of the population due to a lack of diversity. Or if something from the external environment contaminates the colony.

The more I read the more I am reminded of the Borg from star trek. Now don't get me wrong I'm not saying it's exactly the same, Clearly it's not but star trek had some great ideas for them and some of those ideas are here in one way or another. Which is why i think you have a great idea on your hands and I am definitely intrigued by it. I would suggest testing out the concept in table top like a game like D&D just to see how other gamers adapt to it.

Good point, I hadn't considered that. Although, I don't know if specicition would even take thousands of years in some cases unregulated, because Allopatric speciation, speciation by geographic isolation, has occured in within a couple of generations, mainly this: http://en.wikipedia.org/wiki/Allopatric_speciation#Genesis_of_reproductive_barriers.

And increased radiation could easily lead to a lot more mutations.

But even if Diversity should be preseved, its hard to explain how diversity can be both encouraged while simultaneously maintaining the sturucter of genetic code, when the nanomachines prevent the very thing, mutations, that the process of diversifying consists of.

I also assumed that the nanomachines would also act as a buffered immune system eliminating any kind of pathogens, if the environment wasn't completely sterile in the first place.

My story focuses on different characters from different points of view there is no "bad" people as I want to make them all get reasons of what they do, in fact all the characters do questionable acts such as Marianne who is a rich and tries to build a monopoly on a certain industry, she does it through legal and illegal acts, I don't really like writing about characters that are "perfect" sometimes they are pretty prentious too lol , I find a lot of books the main character is that handsome guy/hot girl that only says the things that are cool as hell and never does mistakes and when they do mistakes they always try to redeem them to "live happily ever after", I find having multiple layers of good and bad is how I like the characters, one of the guys in that chapter I posted steal organs and sell them to doctors, a scavenger.