yeah, but they are still flies, and humans guided the experiment. if it were too happen out there in nature, and a fly became something other than a fly, I would believe in a heartbeat.
I used macro because microevolution is observable and testable. no one denies that animals change to adapt ( like a ll the finches Darwin observed). where most folks like me take issue, is what I said before, changing randomly in nature from one thing to another. so when the fly becomes something other than I fly, I'll have no problem.
This reminds me of a poem, it goes something like this:
A fly is a fly because he flies and flies and flies all day,
And if that fly, didn't fly,
Would we call that fly a stay?
Which is, I think, a good question with regards to what you are saying about the thing changing its nature. I think maybe this is really the crux of the issue for you? What makes a fly a fly? What would it look like for a fly, or something else, to evolve or become another thing?
I don't really think it would look like anything, because the idea of a fly, or a designation of a species, is to a large degree a human creation or convenience. We define a species (usually) as a group of creatures that can potentially breed together. When there are small changes in their genetic profile we say that is variation within the species. If we could pinpoint when a change occurred that stopped two populations from breeding, then we would say that they were two species. (Usually that wouldn't happen in a whole population all at one time. But it would be a bunch of small changes of the sort that meant they could no longer breed together - even something like a change in the time they were fertile so breeding seasons would not match up.)
But I suspect that wouldn't be because their nature had changed in the mind of God - that one fixed entity in his mind became some other thing. Rather, animal life exists in many permutations and variations and ways of being and God knows each one intimately as an individual and perhaps as a category as well.
And we see that we actually do have other categories we create for animal life for convenience, like class or genus. But I don't think anyone believes them to be somehow fixed entities for God that he is limited to - they are ways for us to break things down and hold them in our minds and see how they relate to each other, because we are linear.
To me what you are saying seems similar to the problem of saying something can't go from being a tree to a chair because that is a change in its nature. (Though of course no one seriously believes that because we know we create chairs and can see it. But people have advanced the question in terms of how we understand a thing to have a fixed nature.) But the change there is more in terms of how we relate to the object, or to the outward form of the object at this particular place and time. But if we look at it through its entire existence it could be called tree and seed and wood and chair and boards and maybe eventually trash, and that is all true and accurate and God holds them all together.
I tend to think of the idea of species in the same way. And if that is true, then it puts a whole different complexion on the issue of animals evolving from one thing into another as a problem of changing their nature.
"Get your stinking paw off me you _____ dirty ape!" 
