An important point to remember about a theory. If a theory violates the facts, the facts may be wrong. If a theory violates the Second Law of Thermodynamics, the theory is wrong.
Is anyone seriously arguing that the theory of evolution violates the 2nd Law? If they are, I would love to hear it.
The irreducible complexity of bacterial flagellum is often used to support the theory of intelligent design. On the face of it, the fact of irreducible complexity does seem to violate the theory of evolution. Here is the catch. One must always remember that the theory of evolution must obey the 2nd Law.
The 2nd Law states that entropy will be maximized or potentials minimized. There can be billions and billions of different paths and states to choose from, so how does the Cosmos know which one to take?
Add the Law of Maximum Entropy Production to the 2nd Law. It states that the system will take the path or paths, out of all available paths, that maximizes entropy at the fastest rate. Under the laws of our Cosmos, those paths almost always result in the production of ordered states. Stars maximize entropy faster than dispersed ionized gas. Life maximizes entropy on planets faster than atmospheric or geological paths.
The 2nd Law created the stars, planets, and life. It is embedded within the fabric of our Cosmos. In 2005, we do not understand how it created a bacterial flagellum. That does not mean we should throw the 2nd Law out the window and invoke unseen spirits in our science classes.