Here is what I am pondering about the Engineers in Prometheus.
Please note: if your answer to any of the below is "movie magic", fair enough, point made. But what I am really interested in is any cool explanations and speculations for how it might actually work as a story, sci fi or not.
Question 1 (has many parts). Did the Engineers pop along to earth 3.5 billion years ago to start all of life on earth.. or 85 million years ago to start just the primates.. or between 400,000 and 250,000 years ago to start homo sapiens?
How close was the the DNA match between humans and engineers?
How quickly does DNA in general change with evolution? I am wondering this because if the story is asking us to believe we are an exact DNA match with the Engineers, then there is a big puzzle regarding how we turned from crumbling Engineer who drank the black juice to a new race a) within a short enough time that our DNA stayed the same and b) how we managed to "inject" ourselves into the fossil records?
I can imagine that they popped along to earth at any of the times listed above and that their tech is somehow so super smart that it could have even have triggered homo sapiens at any time in the chain - maybe it was like some sleeping function in the DNA that waited for the right conditions before working its magic?
Question 2. Why did they trigger the cave paintings to be made? (And was it indeed an invitation or something else?)
Question 3. Of course, the third question is the same question asked in the movie: why did they change their minds and decide to destroy us with alien black goo?
My pet theory for 2 and 3 is that they were truly interested in creating life and leaving a sign to see if we could grow up enough to follow it. But then over the proceeding thousands of years, their society changed and became more aggressive, more warlike. Perhaps they suffered a terrible war? Perhaps they even had a war with another species they created? Perhaps they have been seeding the galaxy for millennia before they popped along to earth and one of their earlier creations came to fruition, found the Enigneers and started a huge war that was so bad that the Engineers got scared and decided they should destroy their other creations before the whole thing could happen again?
I think the first scene implies that the Eng started higher life forms on Earth because you see a little plant life but no animal life. Thats way before primates or even mammals. There were no fish in the waters, so closer to your 3.5 billion year figure.
I therefore agree that it doesnt really make sense to seed with human-like DNA billions of years ago and expect it to, even eventually, yield humans. Its too much of a gap, you cannot make a direct jump from plants to humans or even primates and the billions of years evolution would diverge from the Eng DNA to who knows what. Instead of killing an Eng they should have just released some fish DNA to speed things up. Yes I get that its more the ritual symbolic value that an Eng seeded higher life.
Evolution jumps in fits and spurts but has a jump scale on the order of 10000-100,000 years. So perhaps tens of 1000's of big jumps to get from plant life to humans. Of course a near infinite number of little jumps.
The test ran showed 100% match between Eng and human DNA but of course that cannot be completely accurate, so the easiest explanation is that the test Shaw ran is crude and imprecise and is geared toward making gross DNA identifications, with an error, say of 1-2%, accurate enough to distinguish between human and chimp DNA, but not much better than that.
I agree with your point that it is not credible for Eng DNA to seed so long ago and lead to creatures that still retain nearly identical DNA. However we do know that the Eng visited us many times so there could have been multiple interventions to steer evolution towards human development and even subsequent seedings of Eng DNA to insure our outcome. This idea is again similiar to the plot of 2001 by Clarke where aliens guided human evolution.
As to why the Eng changed their minds, I'll be quite disappointed if the answer is as simple as that. It is almost a childish notion that we did something like killed Jesus and the Eng changed their minds -- how old are they? Thats about as sophisticated a thought pattern as the God Yahweh of the Old Testament, complete with jealousy and vengence. Not coincidentally that God also decided to wipe out mankind with the Flood.
I am hoping for a more exciting answer, like there are at least two groups of Engs, one that believes in seeding life and one that thinks it is an abomination, and these two groups are at war and the bioweapons arent just for us but are part of this war.