Why it took so long to figure out it's a parasite. The marine biologists can see it in their tests. These parasites are big and grow very fast. So why the doctors didn't see them . They can see other parasites like tapeworms easy enough.
There was evidence available, but the authorities decided to pull a major cover-up. Even afterwards in the story it was not admitted anything sinister ever officially happened, it was all due to "unusually high water temperatures" or something, as they tried to explain it away.
"Words create lies. Pain can be trusted." ~Audition~
Why the doctors did not see them in their observations and tests?
The local doctor made the parasite connection on the same day he saw the first patient. It was shortly before he died. Most of the crisis in this movie happened in one day.
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