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The theory of evolution explicitly claims that whales evolved from Very Small Non-Mammalian Organisms. (Yes, I realize there's a lot of steps between there and here.) As such, and in the same way, the theory of evolution cannot preclude the possibility that some race of fruit flies may at some point evolve into something whale-like. A smart boy like you could probably even spell out the necessary mutations to make such a thing come to pass.

I'll even give you the experimental setup to make this come to pass. For the first stage have a food source close to the surface of the water. Gradually, over many many fruit fly generation put the food source closer and closer to the water. Eventually the food source will be below the water and eventually at the bottom of the tank.

You can run thousands of similiar experiements in one room. Eventually through random chance/mutation/natural selection or whatever you would have to have some fruitflies that evolve into a creature that can swim to the bottom of a tank and get food.

Absurd? Doesn't evolution ask us to believe that something similiar has happened (albeit without any invervention) literally trillions of times to millions or billions of different species?

Your experiment is ridiculous. The problem is twofold. Moving the food into water isn't going to turn the flies into fish. What it's far more likely to do is force the flies to go after a different source of food. Those who depend on the food you've moved will simply die out slowly (you'd best be moving the food over a period of a few million years with no other changes to the environment or all the flies will simply die) while those who have an alternate source of food will simply ignore the food moved under the water. Your example also seems to point toward flies turning into whales. The problem there is that you've skipped probably a few tens of thousands of different species that would need to evolve over tens or hundreds of millions of years to get from fly to whale. You're also ignoring the fact that species do not respond exclusively to a single stimuli. Every aspect of the environment in which they live would have to be controlled, and an extreme amount of knowledge and foresight would be required to create an environment that yields the traits necessary to "push" the development of the proper traits at the proper time via natural selection.

It's a monumental task, and not likely one humans will ever manage to approach achieving in a lab or a field.