Some have posited that aliens could be time travelers from Earth, from a future when they have manipulated their DNA for numerous reasons -- some of which may be to exist in space or on other worlds or by preference for certain traits.
In that way, a return to our time when we have relatively clean DNA is like a gold mine for them. If the miniseries aliens are Earth humanoid in origin, then they should still have similarities.
Otherwise, it's very unlikely they would be able to copulate in the normal way as we do and produce a fetus. Quite a lot of help would be necessary in the lab. I have explained this upthread. No one has come forth to explain how else it would happen. John's idea of our differences may only mean that it is indeed possible in a lab, rather than not.
I don't have any problem with the aliens being scientists come here to learn. It fits in fine; they are doing that. To the next point, the aliens are telepathic with us and with each other. That capability creates a radically different set of circumstances for interaction between beings.
When everything is felt universally by everyone, cruelty and compassion wouldn't exist as we know it. They are functions of solitary individuals for one another. No member of a telepathic species would have to be told not to be cruel or to be compassionate. The ramifications of everyone's actions towards others are immediately felt.
But those emotions not existing as we know it is not the same as not existing at all. In order for aliens to appreciate our kindness, they must recognize it, which they do. Those feelings still exist, though they have become moot because of telepathy.
If what the aliens wanted was to recapture emotions like compassion and cruelty, they would probably have to give up telepathy. And if that were what they were trying to do with a breeding program, then they would put some amount of human DNA into an alien host and have their prototype.
But that was not what they wanted -- nor what John meant. Sally's kindness was a signal that perhaps they could have a relationship with humans. Or perhaps they could settle here. Their breeding program didn't put human DNA into an alien -- it put alien DNA into a human.
So what they have is a human hybrid, looking like a human, who is sympathetic to the aliens. You don't have aliens who are recapturing compassion and cruelty. Their breeding program is to create human hybrids who aren't afraid of them -- indeed who support and accept them.
The aliens' ultimate goal was never revealed in the production, but the results of their breeding program indicate they could create a covert, advance guard as a prelude to settlement. Personally, I would not want to be an ordinary human on a world with many of those around.
As to John's wording: "greatest" is the superlative form of "great," with the comparative form being "greater." So at least three stages exist to arrive at "greatest" -- and potentially a nearly infinite number. That quote from John doesn't indicate when their breeding program began. It doesn't indicate what the focus of it is.
I shudder to think why he called it their greatest experiment; it could mean the end of humanity.
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