1) at the beginning of the film, one of the "Engineer" aliens drinks the black sludge found in the ship, apparently dies (very thoroughly dies) but, via microscopic camera shots, it's hinted that a new lifeform is reproducing, and growing, and expanding and replicating cells from the sludge's impact.
Combine this with the later scene -- the Geologist (the one who throws out the 'pups') gets a faceload of the black sludge, and he dies but then morphs into this super-human, with strength comparable to the Engineer seen in the end of the movie. Does this imply humans + black sludge = engineer race?
But then that doesn't make sense either, because the black sludge also has the potential to make a face-hugger: when David poisons Holloway with the black sludge, he looks like he was going to become the same thing as the geologist guy, but dies, but he impregnates Shaw, who then produces a facehugger egg, almost like she was simulating a queen alien. This very same face-hugger eventually impregnates the awoken engineer, and creates what is OBVIOUSLY a predecessor to the xenomorph first seen in 'Alien'.
But if the egg came from Shaw + black sludge infected sperm, this suggests that actually whatever lineage the xenomorphs seen in the Alien series is, it has some common ancestry with the human race?
So now black sludge impregnated humans create xenomorphs?