[QUOTE=Hyperspace05;6476710]The biggest plot hole for me was David's lack of interest in what had happened to Shaw. So he orchestrated the whole thing as an experiment to see what would happen [QUOTE]
He intentionally infected Halloway, yes, but he didn't "orchestrate" anything beyond that. He didn't know what the black goo was. It could have been the engineer quivalent of Gatorade as far as he knew.
The popular theory is that Weyland ordered this done, but I can't think of any reason why, since no one at this point in the film has any idea what this stuff is or what it might do.
Heck, even the film itself doesn't seem to know what this stuff does. A tiny amount will disintegrate you over a period of time. Falling face first into it will turn you into an alien zombie. Little alien worms morph into large aggresive critters. Having sex with someone who has been exposed to a tiny amount will cause a squid to grow in your sterile womb.
Is the black goo supposed to be this unpredictable? Was it once something they had a handle on but eventually lost control of? Were they just going to dump it on Earth, grab some popcorn, and see what crazy stuff happened?