I periodically get interested in looking at the "debate" between creationists and evolution. I quote the word "debate" as I don't think there is any real debate between religion and science (see other blog posts).
However, the politics of the debate are intriguing. The creationists have succeeded in several fronts with making their minority opinion on Intelligent Design seem like an actual scientific theory. They've done so with marketing in a clever manner. By arguing that schools should "teach the controversy" they are, in fact, creating the controversy out of nothing - very clever marketing. The fact that the Intelligent Design worldview is not present in any significant numbers among scientists is lost in the seemingly fairness-based argument about teaching "both sides" of the issue.
The more insidious plot is the attempt for the creationists to set up a "straw man" arguments that will "kill" evolution as a theory. As a science, evolution is subject to being "killed" through contrary evidence that can't be accommodated in the model, or in revisions of the model. This holds for all scientific theories, and is the actual strength of the paradigm - when evidence is contrary to a theory, the theory must go, either "evolve" to a new theory, or be discarded.
Irreducible complexity is the idea that some aspect of an organism is so complex and interrrelated that removal of any part would destroy the function, and thus it could not have been derived through step-by-step evolutionary methods. Thus, there is a search among creationist-scientists to discover a process or organ that is structured that it doesn't appear to allow for an evolutionary origin. The eye is often cited, as is the flagella in bacteria. Evolutionary arguments supporting the step-by-step development of both the eye and flagella have been produced.
The simple logic of irreducible complexity is compelling, but is based upon two problematic ideas. Firstly, the fact that we can't "see" or understand the evolutionary history of a particular mechanism doesn't infer that it didn't evolve - we just might not be clever enough to deduce the chain of events. The second problem is that some aspects of the evolutionary history may have been completely erased over time. Imagine a suspsension bridge - remove the supports and it collapses. However, there were supporting structures during construction, which are now gone, so it would be difficult to understand how the existing structure was created, only using the observation of the bridge.
Similarly, there may be a convoluted evolutionary path where the current structures are remnants of a more inefficient but easier to understand primitive set of mechanisms. Parts that no longer required in a newer mechanism may be evolved away, assuming they "cost" energy but don't contribute to the organisms' fitness. It would then be difficult to trace or understand the mechanisms of evolution that led to the current state because significant evidence no longer exists. Thus, irreducible complexity creates a logic problem to explain, but no "kill shot" to evolution.
In one of Dawkins' books he talks about the fact that evolution, as a scientific theory, can be disproven by relatively simple evidence to the contrary (e.g. primitive tools from humans with dinosaur bones). I agree that significant departures from the timing sequences of evolution and geological strata would be problematic to account for, I was more worried that some creationist was buying primitive tools and digging into dinosaur bone sites and planting them.
I think the "science" end of the debate should ignore the creationist end, as they tend to do, as any argument does seem to support the "controversy". However, I also agree that Intelligent Design and other pseudo-scientific arguments need to be confronted when they begin to cause damage (e.g. change to science curricula in schools). This paradox shows the cleverness of the current creationist arguments.
In reality, the history of evolutionary change is difficult to find, as fossilization only occurs under unusual circumstances and is best suited for large structures like bones. Evidence of under-utilized structures in living organisms provides hints to evolutionary history as do developmental stages in growth cycles.
The real compelling arguments for evolution are not "back-facing" explorations of what happened to cause the current state, but the predictions of what will happen given current starting point and conditions. Evolution of micro-organisms and viruses are real-world adaptations to the methods we devise to kill them - evolution in action. Also the predictive power of evolutionary theory is what distinguished it as a scientific theory, not just an explanatory fiction.
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