My (admittedly poor) recollection of the scene is this:
- The camera is doing a visual close-up of the soil. I forget if this was the part showing small, flowing rivulets of black goo.
- The soil is visually barren (except for the goo if that is indeed this part).
- One of the human characters walks across the soil.
- As they lift their boot, a worm appears. I remember it as a centipede rather than a worm, but that's not too important.
So, was the worm in the soil and was exposed by the person walking over it? If so, why hadn't it become mutated at some point in the past? Or was it transferred from the person's boot, perhaps picked up from outside and stuck in the groves?
Answer
"We've changed the atmosphere of the room" - Dr. Shaw
Presumably the door acted as an air lock. Maybe the room was sealed off to halt the biological processes of EVERYTHING in the room (which is why the head is perfectly preserved), and the worms where already in the soil. By breaking the seal for the room, the biological processes are able to continue - maybe there was some sort of cryogenic freezing happening because of the room being sealed.
Once the seal is broken, and the biological processes have started again, the "black goo" begins to ... "unthaw" (for want of a better word), the worms begin to crawl around in the room.
At least, that was my interpretation of it.
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