What I usually do is that whenever an I.D.ist claims that something, either a species, or part of an organism (call that something, "X") had to have been "supernaturally designed," I just google up the following: "evolution of X" or "X evolved" (keep the quotation marks) and I add the latest year in the search box as well, say 2005. That usually takes me to the latest information concerning the evolution of "X." *smile*
Have I.D.ists come up with anything new since they began? They appear to be continuing to lose ground as the genomes of more and more species are fully decoded. For instance, we have learned that though mammalian species look and act very different, they all share many similar genes. So, small numbers of genetic changes (relatively speaking) produce large differences in appearance and behavior. So even if there was a supernatural hand involved, it merely had to do some tinkering with some highly conservative genomic molecules. Such a supernatural hand also just happens to let mutations happen at known rates of mutation that match the needs of evolution; and that hand also left behind plenty of duplicated non-functioning DNA, and invasive non-functioning bacterial DNA, and invasive non-functioning viral DNA, inside the genomes it was "working" on (even left some remnants of a second centromere inside human chromosome 2). Recently a huge chunk of repetitious non-protein coding DNA was removed from fertilized rat-egg cells, and the rats developed fine in the womb and grew up just as healthy as other rats.
Another question to ask I.D.ists is why species split and diversify into so many cousins and side-branches, most of which simply become extinct? A "design" is usually defined by how "straightforward" it is, with something specific in mind, reaching directly from point A to point B, but instead we see evolutionary bushes of many related species, many of whose members simply go extinct, which doesn't look like straightforward "design," but looks more like letting nature do her thing, and also letting nature trim her own hedges as well.
And the earliest fish, earliest amphibians, earliest reptlies, earliest birds, earliest hominids, were not like the later ones. The earliest backboned animals in the fossil record were tiny jawless organisms. The earliest fish were also jawless. The earliest amphibians still had fins on their backs and other fishy features (the number of toes on each foot also varied among the earliest amphibians, "five little piggies" wasn't yet the norm for all four-legged creatures at that time, some had "eight little piggies" splayed out, perhaps like fins were once splayed out in a fan?). Many (all?) of the earliest known reptiles also had fins on their backs. The earliest birds were extremely reptilian (the earliest archeopteryx fossil was simply classified as a reptile till someone a few years after the specimen was discovered, noted the ligth feather impressions in the fossilized stone, and now we know that feathers evolved on dinosaurs prior to the evolution of the earliest birds with feathers, and those earliest birds had dinosaurian skeletons too boot), and the earliest birds were not very well adapted for flight at all, too little keel bones to hold flight muscles, and long boney tails that created drag, and heavy triangular reptilian skulls, and unfused wrist bones. Same goes for the earliest cetaceans, not adapted for full lives in the ocean, not by any means. And along the way many of the cousin species of ancient fish, ancient amphibians, ancient reptiles, ancient mammals, ancient primates, ancient hominids, simply became extinct. We even know now that Neanderthal once covered Europe but was wiped out by the species that was to become modern man.
Still, no one can disprove to an I.D.ist, or even disprove in principal, that a supernatural outside influence could be doing things we don't know about, i.e., making certain mutations happen rather than others. Or, it could be working even more subtly than that--it could merely be guiding natural mutagenic substances and activities so that they come into contact with DNA at specific places to cause specific mutations. *smile* Kind of like guiding a bullet so it reaches a highly specific part of a target. Sure the bullet was already headed in the right direction, but how could anyone possibly disprove that the bullet's trajectory was "breathed on"ever so slightly by some supernatural force so that it was "directed" to hit the exact upper left corner of the yellow circle inside the target? How could you disprove that? *smile* Nobody can disprove in fact that an invisible supernatural being is making my hair grow either, directing each molecule and atom in each hair follicle. Scientists used to argue that photosynthesis was a miracle, but then someone analyzed the chlorophyl molecule and found out how it took energy from the sun and converted it into chemical energy inside the cell.
All I say is, let's keep analyzing and comparing genomes, since they hold lots of information about duplicated and old genes and we can build a tree of life on such information alone--a tree that just so happens to compliment the tree of life that was discovered by digging through geological strata of the earth to find information about fossilized life forms of each era.
Another thing we can learn by comparing DNA of living organisms is where certain organisms may have first evolved. For instance studies of the DNA of living passarines (perching birds) from all over the world, reveal that their earliest common living ancestors are species that live in Australia and New Zealand. The species living there today have the most DNA traits in common with all the rest of the perching birds in the world. In other words, scientists analyzed specific DNA strands in many species of perching birds and compared the order of the base pairs, like comparing a large number of near-identical chain letters from the internet, looking at the differences in each one, what periods were added, what commas were taken away, what sentences and paragraphs likewise were added, deleted, or altered. Since we know that chain letters have to start with someone writing the first one, and then others add their own changes, you can indeed work backward to distinguish the earlier variations from the later ones. That's what you can do by comparing the DNA of living species. And that's how they discovered that the perching birds living in Australia had DNA that was of the earliest known type for all the perching birds they studied around the world. So DNA can tell you a lot. You just have to know where to look.
Scientists will undoubtedly discover new and different limiting and instigating factors related to how mutations arise and how the cell processes them, and how they affect development, and how the environment, or an organism's diet preferences lead to changes in it's DNA. Possibly there is even a supernatural force of some sort inherent in each organism, a life force, that directs it in some ways--a "morphogenetic field" as Rupert Sheldrake once put it. But such a force if discovered would be part of that organism itself, like it's DNA, and unlike an outside "Designer" ruling over all mutational changes of all species like an autocratic despot pointing his finger here and there, and moving genes and bases around to suit His Divine whims. Anyway, the arguments are endless. But of one thing I have grown increasingly certain, organisms share common ancestors. The theory of evolution, whether understood purely in a Darwinian fashion, or some other fashion, is not really in dispute today.
And that means maybe it is time for the I.D.ists to stop molly-coddling the creationists in their midst and start interacting in a more friendly fashion with Christian and non-Christian evolutionary biologists round the world.