Want to sound like you've refuted your opponent's position? First, take their idea. Next, make it simpler by removing parts you don’t like. And now here’s the key: Attack the weaker version you created – not the original idea. Voila! Now you can publish your article in a prominent magazine and pat yourself on the back.
That's what happened with Wired's article that allegedly refuted evidence for intelligent design. They shot down a straw man. They erroneously defined irreducible complexity as a system that "can't be broken down into smaller, simpler functional parts." With a definition like that, it's impossible to demonstrate any system is irreducibly complex, even in principle. Why? Because everything can be broken down into smaller, simpler functional parts.
But the definition of irreducible complexity is, well, more complex. Even Wikipedia gives a more accurate definition! (Michael Behe gives and explains his definition of irreducible complexity here). And this sort of misunderstanding about the nature of irreducible complexity has occurred before.
The other odd idea is that Wired believes that the functional subcomponents of this irreducibly complex system existed "before there’s a need for them." Somehow, these complex biological parts can just sit around in a be-functional-or-get-selected-out world, waiting to be repurposed for evolutionary innovations.
So, complex molecular components somehow arise, sit around for eons of time before they’re necessary (while natural selection runs rampant), and then combine to form even more complex machines. Wired believes that when you think of it this way, "Then it makes sense." Maybe to them, but that’s not a refutation of intelligent design.
Check out Discovery Institute's recent blog post for a more scientifically technical response to Wired’s article.