The mutations in the fruit flies never yielded any evolutionary advances because there was no deciding environmental factor to kill of the "lesser" variations inherent in each generation.
I see the path of each species as a branch on a tree, with each generation a whole collection of new smaller branches are created. Most will have tiny differences (like being slightly larger or stronger) and a select few will have large differences in their appearance and abilities. With time only a few of these many branches continue on and survive to reproduce.
Perhaps we are disagreeing on what constitutes a mutation. To me, every new member of a species has a new mutation. None are exactly like their parents. The differences may be small, perhaps too small for us to detect, but they are there. It is over time that we see underlying benefits of certain traits (extra height, strength, speed, endurance etc) emerge.
If you believe a mutation to be just a fluke that occurs a couple of times per generation then, yes, that wouldn't drive the evolution of a species. If, however, you choose to see every infant born as a mutation, then the logic behind the natural selection theory becomes much clearer.
On "truth": The truth is subjective. You can choose what to believe and you can pick and choose the facts you wish to back up your claim. Neither religion, nor science can be proven "true" because the truth is not objective. What we perceive as "right and wrong" would be better considered as a metaphorical scale. Each person weighs the scale to match his/her own belief.
In some ways this makes debates like this pointless but the continual questioning of what we hold to be true is part of the system that allows personal freedoms to exist. Were we all to accept the words of a scientist or priest without skepticism, we would be no better off than sheep. By always seeking answers, we can help prevent others from taking advantage of our naivety.
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