Irreducible complexity is a "god of the gaps" argument: it says: we don't understand yet how this particular feature came about therefore: God did it.
In cases such as the bacteria flagellum, Dr. Behe's famous example of irreducible complexity, we see similar protein structures on different bacteria but with different purposes. For example, with the bacteria that causes bubonic plague, the protein structure that makes up the flagellum is missing some of the parts but acts as a secretory appendage.
With the blood clot cascade, another Behe example of irreducible complexity, in whales and dolphins we observe a reduced complexity and yet clotting still happens.
Just because something "seems" irreducibly complex or designed does not necessarily negate 150 years of evolutionary science. Evolutionary theories have been challenged more vigorously than any other and yet are still the current predominant scientific paradigm.
If Intelligent Design proponents want to be taken seriously by the science community, they need to produce research, conduct experiments which demonstrate the predictions of ID, and publish these findings in peer-reviewed papers. Then, instead of having to go around or avoid the scientific community by using politics to get ID taught in schools, it will simply be the predominant theory taught in schools.
With all due respect, a scientist with anything involving ID theory won't get within 50 miles of a peer-reviewed publication. The science community tends to be very averse to theories associated with spiritual faith. And that is fine, I think that's probably how it should be. But we have to remember that just because physical science doesn't want to look at something, doesn't mean it is invalid or untrue.
One of the best examples I can think of is the discovery of bacteria. When the first scientists found this, they were largely dismissed by the scientific community. It was considered irrational... supernatural... not something to be taken seriously as science. Dr. Ignaz Semmelweis proposed that surgeons wash their hands between digging around in cadavers and operating on live humans... his ideas were kooky and crazy... they locked him up in an insane asylum. Years later, they discovered that ...hey, he was right... who woulda thunk it?
Another example is the Big Bang theory.... Did you know that "Big Bang" was actually a pejorative term used to mock the theory in the early days? Scientists did not want to accept that the universe had a beginning because THAT implies a creation. They wanted to cling to the opinion that the universe had always existed. They called it the "Steady State" model and they held on to this well into the 20th century until the background radiation we discovered pretty much concluded there was a Big Bang event.
Irreducible complexity, from my understanding, is very simple. In fact, the first mention of it is by Charles Darwin in
Origin of the Species, not Dr. Behe. A system that is interdependent upon itself cannot evolve in stages. It simply doesn't function without all it's parts and there is no logical explanation for how all the parts could know what they were developing into.
I have many problems with Darwin's theories because Darwin didn't have all the information in 1859. He lived in a time where a cell was about as complicated as a ping pong ball. We didn't even know what "atoms" were... which is another thing scientists debated for years. The thing you have to realize about Science is, it never stops asking questions or exploring possibilities. MAN draws conclusions. Then we adopt a faith around our conclusions. This is the antithesis of science.