So the fly changes to another fly and the bacteria changes to another bacteria. Riiiiightit was still a fly, just a different species of fly. species are literally just gene pools. so for 2 organisms to be of different species, they simply must not be able to reproduce with each other...that's it
i think u completely misunderstand what speciation is, as well as evolution. it's not as absurd as u probably think it is. it just means that organisms adapt and change to their environment. and given enough time and adaptations, they can get to a point where they're unable to reproduce with their original form or ancestors
in other words that bacteria for example that reached the center of the petri dish cant reproduce with the ones from the outermost portions of the petri dish due to all of the adaptations and mutations they went through to get to the center of the dish. and thus it's a new species. get it?