I'm working on a post about CXCL-4, integrins, and cancer, but until I finish that, here's something I wanted to write to Mr. Ray Comfort, but I figured it would be overly long
Examples of species-to-species transitions are:
ring species of Ensatina salamanders
ring species of Larus gulls (kind of; it's really, really complicated)
[More after the fold]
These two examples are BETWEEN speciation by pretty much any biological definition of species. Neighboring populations can hybridize while distant populations cannot. You will rebut this by saying "but they're the same type." Yes, they are still salamanders or birds respectively, but, for example, are crocodiles reptiles? Myself, and many other biologists, say that while they are reptiles, they are a very unique kind of reptile with four-chambered hearts. This is very unlike any other reptile. It has also been established that genetically, crocodiles and turtles are slightly closer related to birds than other reptiles making the class Sauropsida paraphyletic unless you include Aves. Again, you'll say "common designer" but why, oh why, would a common designer include hundreds of sequences of transposons, retrotransposons, and silenced DNA sequences not present in the genetic sequences of animals which are less similar? Your reply will be "we cannot know, because my God works in mysterious ways."
I'll even say to you that evolution DOES have problems, but the ones you are talking about are NOT the problems. By drawing attention to your nonsensical representation of evolutionary biology, the real questions are not addressed. These include:
1) classification of bacteria due to horizontal gene transfer
2) establishing phylogenies of asexual organisms
3) exploring genetic change based upon things such as codon bias and induced mutation.
4) Many others.
Note, these do not conflict with the current model, rather they are additions which need to be made. Most organisms DO evolve by natural selection and genetic drift. Viruses also evolve in this way, but they, and bacteria, are also much more capable of the aforementioned horizontal gene transfer. Viruses also are capable of introducing their own DNA, which is usually done via RNA converted into DNA then inserted into the genome, and thus giving us insight into said virus evolution, as well as the evolution of progeny of the previously infected organism.
Cue "cosmological evolution" argument which neither you nor I are qualified to argue. Unlike you, however, I have a collegiate education in evolutionary biology and have read more publications on genetics and molecular biology than you can pronounce the titles of (granted that may be zero); this makes me, while not inherently smarter, certainly better educated. You can start with Berkeley's kiddy version of an evolutionary biology course. Ernst Mayr's "This is Biology," Mark Ridley's "Evolution," and D.Q. McInerny's "Being Logical" also would be good reads for you.
*note, I could have included pictures and more links, but then you wouldn't have to do any work.