I have Behe's book, and have read most of it, but quite simply he is wrong. His concept of 'irreducible complexity' and his (in)famous example of bacterial flagellum being 'irreducibly complex' has been thoroughly shot to pieces - not just by his critics, but in a US Federal Court... Behe's assertion was that this organelle is 'irreducibly complex' - that it could not work without all of it's constituent parts all being present, and that those constituent parts don't work without all the other parts. That's simply not true, and even Behe now concedes that he made a collossal mistake by saying that. The fact that the subunits that make up the whole organelle are individually functional in a myriad of other organelles is just the tip of the iceberg. For a proper critique of Behe's work, try reading some of Richard Dawkins' work or Niall Shanks' 'God, The Devil and Darwin'
On a more general note, Behe
doesn't explain how evolution doesn't hold up. He merely 'explains' that he cannot see how it's possible or how it works. He goes out of his way to show how 'this can't be so' but then offers no better alternative explanation than 'it must have been Intelligently Designed'...
Atleast Behe has made a genuine attempt, albeit slightly biased by his Creationist leanings, to address some of the problems with evolution theory at the molecular level, but some of his scientific shortcomings (and plain errors) are really shocking. This is why scientists typically do not convey their science through the medium of the popular press - basically because in a book, you can say whatever you like without the all-important process of peer-review. At best, Behe's book should be read with this firmly in mind - at worst, it should probably be best forgotten.
No, it doesn't violate the Third Law of Thermodynamics... there are plenty other examples of 'order arising from disorder' which also do not violate the TLOT - because we're not talking about closed systems. Whenever energy can be put into a system, we have an open system - some everyday examples of order arising from disorder are: Hurricanes - they draw energy from the sea and a 'complex' system is created where one did not previously exist. Amyloid fibril formation in Alzheimer's Disease - random, unstructured sections of soluble protein (peptides) which self-assemble to form highly ordered, insoluble fibres in the brain (the hallmark of Alzheimer's). The formation of a baby from an embryo - again, this wouldn't be 'possible' according to someone who misunderstood the TLOT in the same way as it has been applied to evolution. Crystallisation - crystals form from the self-assembly of molecules, which provide a template for further self-assembly. All these processes require energy input from their environments - in a more abstract way, so does evolution. The contention that 'order cannot arise from disorder because it violates the third law of thermodynamics' is incorrect.
No-one has ever said that hurricane formation is 'impossible' because, clearly, it isn't impossible. It does happen somehow, we just took a while figuring out exactly how it does happen. Similarly, the contention that evolution is impossible is incorrect, especially given that the basis for it's so-called impossibility is completely wrong.
I'll leave that one for the experts...