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During the opening scene, it is implied that the shark became more aggressive in attacking the boat of the teenagers because of the blood-like wine that spilled off the boat. But why would a shark mistake the smell of wine for blood? Until you realize that it's thanks to the shark's enhanced brain that it's ignoring its instincts of smell and is relying on things like assumptions, just like a human would!
Wasn't that one of the sharks that hadn't been made super-smart, though?
The scene where Samuel L. Jackson gets eaten was obviously included to subvert expectations, but it could also be Fridge Brilliance. The sharks have clearly been observing human behavior, even if they can't understand human speech; they figured out that the people could cause the station to sink, and how to herd them around so they'd have to make it happen. So why couldn't they have killed Jackson when they did on purpose? If they could detect the vibrations (and erratic neural impulses?) of people who were panicking, and realized that it was Jackson whose we're-getting-out-of-this speech was calming them down, then they may have deliberately taken him out before he could get everyone thinking and potentially derail the makos' Batman Gambit.
Aquatica was constructed by the Navy as a submarine yard. We're honestly supposed to believe that the military (which tends to be procedural to a fault and require safety protocols for everything) put an enormous window in the middle of their underwater complex and never even considered installing blast doors in case something happened? Granted, the glass was shatter-resistant and very thick, but if the sharks were able to crack it, a mishap with a submarine would've been able to as well.
Maybe the blast shield was there, but the very-not-military scientists were too horrified/dumbstruck by what was going on to activate it?
A bigger one was breeding sharks at all, Northern Bluefin Tuna reach a similar size to the Makos, and aren't nearly as dangerous to humans.
Maybe they would be if they had hugely enhanced brains!
They made a big deal out of sharks not dying from cancer. I think they're trying to imply that sharks have scary regenerative abilities. But, as for the Fridge Logic, the crew of this experiment show a surprising amount of Genre Savvy for being a bunch of people that signed on to make super-intelligent sharks in the first place...
Why didnt they breed thier super-sharks somewhere where escaping was impossible? if you shark in is a big tank in the middle of, say, Arizona, the most it can do is kill people near its little pool, who should be able to acount for that risk. the PR disaster of random people getting killed could not occur.
Possibly Shown Their Work, as no aquarium has ever been able to keep a mako shark alive in captivity for longer than five days. Those which have been held in tanks refuse to eat, and gradually beat themselves to death against the walls. Even great whites are easier to maintain than that.
How does a submarine refueling station in the middle of the ocean make any sense? It would still require you to ship millions of gallons of fuel out to the station itself regularly so you've just traded one logistical problem for another.
Logistically, yes. Strategically, not quite as bad. By refueling the submarines out there, it would allow for extended operations, especially if the station was equipped to handle things like minor repairs and other resupply. Instead of all the subs having to come back to base to refuel, resupply and repair, you only need to have them come back when it's time for major repairs and/or shore leave.
Unless your refueling station is also an oil-drilling rig with its own refinery, you'll have to ship in massive supplies of fuel to any such facility, sea-based or onshore. The chief advantage to building the station to float in mid-ocean is probably that it's moveable.
The the entire Batman Gambit of the sharks. Letting them loose wouldn't seem like a big deal to horror audiences on the surface. But any biology expert can tell you that this is a bad idea. Hypothetically, if there were real life Smart-Sharks like the Makos, the first thing they'd do upon escaping would be to mate with the local sharks. Eventually this would result birth to more smart sharks. There were only 3 in the beginning, so multiply that by the natural mating habit and birth rates of the average Mako Shark. To put it lightly, imagine an entire ocean full of sharks that can think and are ten times more aggressive than a rogue Great White.