From a pure science point of view, I thought the plot held together for the most part (I'm claiming intellectual superiority on this subject on the proviso that the movie starts with DNA doing shit and I'm a molecular biologist!).
There is a respectable theory that life on this planet was seeded from space - comets and meteorites apparently contain a lot of amino acids and the process of coming through the atmosphere makes the formation of some of the compounds more likely than if they were expected to spontaneously arise on primative earth. There's another theory that DNA was not the starting point of life. Instead life started with proteins and RNA which are much more volatile and reactive and then life evolved to use DNA as a long term storer of genetic information as it is more stable. So basically the theory goes: amino acids from space --> precursor of all life on earth.
I read an interview with Ridly Scott where he seemed to really get into the idea that the origin of the molecules from space was an evolved life form rather than some chemicals formed by a rock blasting through the primordial atmosphere. He's taken that on to say the alien came down, disintegrated itself down to component genetic parts and that either seeded life on earth or combined with pre-existing life to be engineered or whatever. So far so suspension of disbelief. This molecular biologist can run with that.
Then we get to the planet and the black ooze. Fine, it's hyper evolving primordial slime that responds to whatever biological stuff it's exposed to. Different people/events/environment factors mean that it produces something different each time - geologist with a melted face = psycho spider walking killer, a drop in some champagne followed by sex with barren women = worm in eyeball/octo-embryo. Giant octopus biomass issues aside, I'm chosing to believe that the xenomorph prototype that bursts free at the end will then undergo more hyper-evolution once it is exposed to humans/humanoids to become the apex human killer in the universe. If you notice in Alien 3, the alien that gestates inside the dog is actually a bit different from the previous aliens and I read somewhere Alien 3 related that it was intentionally that way.
So I'm down with the science. My beef is with the fricking scientists. If there was ever a need for a safe-sex-in-space awareness campaign, look no further!
EDIT - another thing that really bugged me is why the hell did Charlize Theron kill Daniel with a bloody flame thrower?!?! Considering he was happy to to be euthanised, you'd think one of them might have said "Hang on a minute, let's not burn him to death, we can shoot him in head instead!"
This post has been edited by Mezla PigDog: 11 June 2012 - 12:28 PM