That's speciation yes, fruit fly experiments have been studied and researched for years but even though observations were as you say the fruit flies were still fruit flies, they used fruit flies because of their rapid mutational rates, but most experiments were not beneficial to the species, also diversity adaptation mutations survival etc is not the central focus point it is the origin of species or where something came from in the very first place, you know as well as most others do that the evolution that is most talked about is origins.
Try to work this one out?
Although there are variations of apples they only come from apple trees, apple trees can only come from the apple seed and the apple seed can only come from within the apple (exactly as Genesis makes the reader aware of this fact)
We know that apples do not fall from the stars nor do apple trees, so with the power of reason and logic and even scientific research we can deduce that the apple seed came first. This is a dillema for evolution
Can anyone explain the existence of the apple seed by evolution's mechanisms, and I mean with factual observable evidence?
Of course they are still fruit flies. We shouldn't expect fruit flies to be anything but fruit flies. If a certain population of fruit fly diverged enough to be so staggeringly different, then we would have to cease calling them fruit flies. Fruit flies will always be fruit flies.... If they are not fruit flies, then they are no longer fruit flies and can't go by that name...
I'm not sure that I believe that MOST mutations are bad. Every single one of us has a ton of mutations inside of them right now as we speak. There are lots and lots of bad mutations of course, but I think many are also neutral. But never mind the bad or neutral ones. They really don't matter and aren't the point. It's the good mutations that give a selective advantage that matters. Think bears for example. A mutation affected the pigment of a bear living in a snowy area and all of a sudden it had a big advantage over it's peers. It was more likely to blend in with the background and camouflage itself and thus not be spotted by animals it would eat and kill giving it a huge selective advantage. It was more likely to live long enough to pass on it's genes (which is all that matters in evolution) than it's alternative friends. After many generations, the white fur mutation become a staple and now we have "polar bears" a separate species of bear altogether, not created independently by God. Go back to brown or black bears and you can find a point where a lineage split as well and it has vastly different looking animals as it's closest living cousins. This is the tree of life. Many branches, many dead ends where extinctions happened.
All you have to do is extend what I just told you about a single, or in some cases, a few mutations, and you can get hugely different creatures. With enough time (though it can happen quite fast), you'll get all the species you see today at the zoo. Lions and tigers are close cousins just as we are close cousins of chimps and bonobos.
Now here is where your question seems to change from evolution to abiogenesis. I don't know where the first living replicating cell came from. I believe God made it. If you ask some atheist biochemistry students, they might tell you that God is not needed and chemical processes led to the first living replicating cell. If you buy that answer (I don't), and say God did not create life, but rather, chemicals did, the next logical question is where did the chemicals come from? If you go to physics students, they will tell you that minerals and the elements and everything on a periodic table came from the Big Bang. So where did the Big Bang come from? They will go on and mention something about multiverse and possibly say they don't know. Now, I'm waaaay out of my league here. But all I'll say is that I'm absolutely convinced that evolution is true and that all animals are related by a common ancestry. I don't know what happened before that. I'm perfectly fine believing God started life. Abiogenesis is NOT an evolution question. Evolution ONLY deals with once you first have life, how do you get such a variety of life. Evolution will not explain how life originated, nor will it attempt to. The furthest back evolution can probably take you is around the EndoSymbiotic Theory of the origin of Eukaryotes. I've just started reading about this myself and can't say much about it. But evolution is not an origins story of life. It's an origin story of species, hence Darwins title, On The Origin of Species (though much of the book he wasn't exactly talking about that and he was also totally wrong about a few things like genetic information)
To get to your apple question, it's kind of a "what came first, the chicken or the egg?" type question, right? That's the crux of it anyway. Seems like a trick question. It's not, and I fully expect a great answer if I took this question to my teachers. I do know that the egg came before the chicken. Reptiles lay eggs. Fish lay eggs. They are slightly different, but they are eggs. You can actually see different spots of egg evolution in modern animals for an idea of how it happened in the past, not unlike the evolution of the eye. Current living animals represent a very good indication of the stages and processes that took a makeshift eye and transformed it into what we have here. I imagine a similar answer for the question of apple trees. The seed came first. No tree is going to magically poof into existence. It needs a seed to grow. The seed we are talking about may not be an apple seed as we know it. And when planted, it may grow something that looks very different from an apple tree. But it was this ongoing process, that evolved all plants and animals. There never was a "first apple tree" or a "first apple seed". Because every parent gives birth to an animal or plant that is the same species of itself. It's slight modification and mutation over generations that build up to copious changes. Again, there was no first apple seed. And there was no first person, either. We are all the same species of our parents. But if you could go back in time, you'd see an unbroken chain of survivors. Not a single one of you, or I, or the apple tree's direct line of ancestors ever died before giving birth. We are all miracles 4.55 billion years in the making!
On a last note, Apple trees are of course very different now than what our ancestors had. They probably barely resembled an apple we would eat now. Through cultivation and hybridization, we've evolved this to be the tasty fruit we enjoy now. It wasn't always like that. It was surely very bitter at one point. We are lucky to be alive right now.
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