You can bear with me through a brief discussion of emergence, or jump to my moral (What is the lesson then?) flagged in bold print below.

Emergence refers to phenomena on a given scale of length or time which are not immediately predictable from those phenomena at either a larger or smaller scale.  For example, the remarkable theory of the strong nuclear force based upon quarks and gluons cannot at present be used to produce a comprehensive description of  a proton (although  it can capture many qualitative details, reinforcing confidence in the underlying  correctness of the quark theory).  No theory of individual molecules (or neurons) can at present account for the ability of certain collections of molecules to think about molecules (consciousness). 

The central intellectual question in this is whether emergence is of a weak form (we simply await a better theory) or strong (there is no way to make the leap).  The latter would be on an intellectual par with Goedel's proof if it can shown to be true in any sense, because it would place fences around the scales of observation, and dictate a democracy of theories much as Goedel dictated a democracy of axiomatic systems.  Notably, it would limit the activity of science to developing organizing principles for given length and time scales.  I personally doubt that we can do other but formulate strong emergence as a hypothesis and test it in certain cases, such as whether certain formulations of the Schroedinger equation can predict the existence of the high temperature superconductivity phenomenon  discovered twenty years ago.   At present, the answer appears to be no, but this is merely consistent with strong emergence as a meta-principle.

Natural selection is a remarkable example of such an organizing principle that has spanned many length and time scales, from the smallest organisms at the earliest times of the planet to blue whales and, well, us. It is at the level of a hypothesis by extension that some form of selection underlies both the production of DNA at the molecular level and the immune system at the cellular level.   Behe is right to say that we don't know this.  

 The immune system may be `crackable', in that a few groups have succeeded in generating simple models with natural selection built in that can actually be practically applied to problems such as optimizing flu vaccines or cancer therapy. (Google, for example, `statistical mechanics + flu shot'.)

For DNA, a big part of the problem is that we have no ``molecular fossil record'' .   In the lab, the famous efforts of Urey and collaborators succeeded in generating amino acids, the building blocks of proteins, in experiments which mimicked the conditions of the primordial earth soup, and other experiments have verified the potential for the self assembly of amino acids into protein chains which can initiate the process of natural selection at a higher level of organization than individual amino acids.  Namely, those sequences of amino acids which can fold into useful shapes  for yet higher organization are selected out, and those proteins which cannot aren't.  However, there have been no lab successes at generating nucleic acids from a model primordial soup.  Possibilities abound--perhaps proteins came first and then RNA and then DNA, but at the moment it is all hypothesis with no test through direct lab experiment or observation and no richness of hypothesis generation.

DNA is definitely an emergent phenomenon, and whether it is of the strong or weak sort only time will tell.  But Behe and his crowd have found a niche living between observations and taking potshots at those attempting to construct an overarching and coherent narrative using the tools of science.  They offer only a pallid deconstruction.  

What is the lesson then?  The positive aspect of the IDers work is to provide those who research and teach science with genuine frontier questions to stimulate young minds.  There is no question that the understanding of the immune system or the demonstration that evolution at the molecular level can produce DNA would be remarkable scientific accomplishments.  To this we can add efforts to unite quantum mechanics and gravity, or to explain consciousness. As a mature and successful field of human endeavor, science can, in the classroom or research lab, acknowledge the limits to our explanatory power now and draw upon past examples of successes in eliminating examples of weak emergence (incomplete understanding). 

When they (the ID crowd) play deceptive games we can and must call them out.  However, we can also assimilate those who might fall under the sway of their critiques of evolution by inviting them to work on the questions the IDers identify by using the methods of rigorous science instead of chalking that up as a win for the big Designer.  We need to carry this discourse into the public arena, and it is of course hard.  It is incumbent upon scientists to work at it. 

The lengthy focus upon emergence above is an effort to point a way.  The trouble with a merely harsh reaction against ID is that we trample all over their appeal to mystery.  It seems to me that there is a duality in us all of wanting to know reasons and yet loving it when we bump up against mystery.  Organized religion obviously lives with that tension, and so should science.  When religion oversteps the bounds of cultivating this lovely dualism and into prescriptive practice, the tendency is towards rebellion, as evidenced in the enlightenment and the founding of our republic.  There is certainly a concern amongst the populace that science can become overly prescriptive and circumscribing about the nature of reality as well, and the IDers know this and are exploiting it. 

By healthily embracing mystery within a conceptual framework such as emergence that does not demand we leave the scientific realm but find a way to live with mystery within it, we can beat the IDers at their own game and garner new recruits and supporters in the larger world.   

Postscript:  Behe cites one peer reviewed article on ID in Protein Science. The paper is publicly available at this site.  It contains a mathematical model (`it is just a theory!') and appears to be an effort to bound the efficacy of point mutations (one amino acid in a protein) to engender larger scale adaptive change. I will provide a non-technical synopsis of this on this site later for the afficionados.  A quick observation--the paper nowhere mentions ID.