Regarding nanotech, at that point, are we still even human?
Yes and no. As soon as we tweak our genes we stop being humans as in
Homo Sapien. That species is well defined and though we get all sentimental about it there's really no reason to care if we stop being
homo sapien. Everything that matters - heritage, culture, morals, science, philosophy, history, ect all stays exactly the same.
But we would still be "human" because all members of a subclade can be referred to by the name of any basal clade. We are in fact monkeys. And all monkeys are fish. So you are a fish. Congrats!
I meant the difference between a medicine only approach
The distinction here is fuzzy. What's the difference between a nanite and an enzyme? Once computer models are sufficiently advanced, there's no reason that new enzymes cannot be made biologically (that is, synthesizing gene sequences and splicing them into organisms), and those enzymes open the gates to the use of materials that generally aren't found in living things, which further opens the flood gates to newer enzymes that can do even more... eventually you get molecules that barely resemble their organic roots and... is that an enzyme, organelle, cell or a nanite?
But, if we rewrote our genes "medically" and changed all the cellular receptors, the respective ph's, salt concentrations, etc of our bodies, few if any organisms could adapt to a sudden 1 generation change like that. Remember Malaria has had issues with wrong cell shapes for millenia (Sickle Cell). As you indirectly mentioned, HIV is particularly susceptible to changes in the CD4 receptor site.
Not that I think that's really feasible in absolute terms.
Not
today. Our models are weak and the computers necessary to compute better models are too expensive. But you seem to be thinking that because a rocket program was out of the budget of ancient Egypt, humans can never reach there. Better tech is getting cheaper. Fast. And the science is advancing at an extreme rate (wrong CPU or I'd link you to an amazing ted talk about just that).
You'd want a cell that does the same things normal human cells do, but you want to build them out of entirely different components that won't be susceptible to any pathogen. It's a pretty tall order, even if you're not concerned with how you'll actually transform the cell.
You wouldn't need to do that. You could, as I said earlier, but even if you didn't want to, you could still change all the receptor sites a little bit, change the ph in a few places (with buffers and other things in places you want to keep the same) and most organisms are suddenly incapable of doing anything in the host.
With dog breeding, I'm not following you. Limitations? Dogs have been bred with traditional artificial selection, yes, but the point is the results. You have tons of different breeds created to satisfy whims and nearly all of them suffer from congental genetic disorders.
The disorders are a direct result of using 3,000 year old technology. 3,000 years is a long time. We have better methods now.
To clarify, I'm talking about mass implementation of genetic engineering and what will happen in that implementation, not about the technical side.
It all depends. You're imagining a free society with an open market, and that that open market is what drives genetic innovation. That's not the only feasible model. A hive mind (the topic of the OP) or a totalitarian state could easily make everyone's genetics uniform and here would be no drive from a hypothetical market.
Assuming we
are dealing with an advanced market society, different objectives does not automatically mean genetic error. The genetic errors we see in dogs are because breeders could not pinpoint desired genes. If a breeder wanted a short dog he'd take [SHORT+CANCER+SHORT_LIFE+UGLY] and breed it repeatedly with [SHORT+RENAL_FAILURE+CRIPPLED+PRETTY] until he was reasonably certain he'd eliminated all the alleles for tall - regardless of all that other junk that has now gotten thoroughly mixed in. He'd then take the new short breed and perhaps breed that repeatedly with PRETTY until he had a batch of [SHORT+PRETTY+etc] with who knows what else. Eventually he'd have a mix of sufficient "good" traits and not enough "bad" traits to make the breed useless and that's what we have today. It's 3,000 year old technology. It has no relation to modern genetic engineering at all.
Modern genetic engineering would take genes from possibly thousands of species and combine them into a base species to create [SHORT+HEALTHY+FRIENDLY+PRETTY] in one shot - or at least try to. We don't have a complete understanding of all the relevant systems nor have we successfully modeled an entire organism to any sufficient granularity
today so unforeseen consequences can arise
with today's limitations... but give us 200+ years of rapidly advancing computers and that's hardly a problem. Heck - with more computing power and time to run groundwork, we might start being able to model
new enzymes and other biological nanites. It's more likely to occur in the next few decades than centuries, in fact.