ah ha!!!!! i finally have my answer!!!
them taking their helmets off was a huge key moment in the film!!
the reason is their body temperature changed the atmosphere in that chamber and the vases of black liquid began to melt because of the change in the atmosphere. Worms started to grow because of this and then mixed with this black oil it started to create this new life form.
But the scene with David putting the substance into Halloways drink is left up to interpretation. Did he know what he was doing? Were his intentions evil? You have to decide.
however David discovers that its a weapon because of what happened to Halloway and Shaw getting impregnated and the creature grows inside her.
But this black liquid was intended to be a weapon to destroy the human race because the Engineers created this horrific mutating beast. It keep mutating and mutating to become unstoppable killing machines. this weapon they created to destroy the humans, instead turns against the Engineers. This is where the myth of titan Prometheus comes into play because in the myth he was punished for re-creating the human race.
He DID jump to the conclusion that it was female pretty fast.
you now.
