So during the Eddie Winter quest, you find a holotape that instructs the real Nick Valentine to turn himself over to CIT for some "therapeutic" brain experiments.
The real Nick had no idea what the true nature of the procedure was. I've been wondering ever since what happened to him once his brain was scanned and the copy put inside the synth Nick.
Was he murdered and disposed of after the procedure? Did he die during the procedure? Was his entire consciousness actually put inside Nick, so the synth Nick is actually the REAL Nick?
I've seen a theory thrown out that the Institute was trying to find some way to live forever. Once they had succeeded in taking over the surface with synths, they would control everything from underground -- for all time. And this could have been the reason behind the experiment on Kellogg that allowed him to live so long.
Father says in his terminal that the other scientists are jealous of Kellogg's immortality. I think it was their plan all along to live forever. In experimenting on Nick, they could have been attempting to find someway to preserve human consciousness in a synth host. But once it worked, they realized Nick was too good. He could never be someone like Kellogg: a minion who would do the evilest things for a few trifling bottlecaps. Nick had too good of a heart and could not be manipulated, so he was tossed out in the garbage. Their first attempt at a perfect, almost-human-but-not-quite synth specimen was out the window.
They tried again with Kellogg. And while Kellogg did live over a hundred years, he could not be controlled. As I said in my University Point theory, I think there was even a point where Kellogg tried to sabotage the Institute.
Then the Institute created coursers. Cold. Emotionless. Perfectly obedient.
But the problem of their mortality was still there. They could give a mercenary eternal life but could not cure the common cold. So the experiments on the bioengineered synths began. We actually see a scientist in the Institute (the one who says "we can't cure the common cold") doing experiments on a synth subject.
It seems they are trying to figure out how to combat disease, perhaps at Father's insistence because of his cancer, but also for the sake of honing the perfect synth host for their later use. If the scientists in the Institute were one day able to do what Curie did (and the real Nick did, to some extent) in possessing a synth host, then they would live forever.
And depending on whether or not the Sole Survivor destroys them, perhaps the Institute will one day figure it out.