While the critics are correct that Behe and Snoke (2004) doesn't contain the phrases "intelligent design" or "irreducible complexity" directly, there is a good reason for this: if the authors had mentioned "intelligent design" in the article, there is little chance it would have been published. Nonetheless, Behe and Snoke's article discusses how protein-protein interactions require multiple amino acid residues to be precisely matched in order for interaction to occur. These enzyme interactions have been often described as a "lock and key" fit. As Behe wrote in a New York Times editorial:

"The intracellular transport system is also quite complex. Plant and animal cells are divided into many discrete compartments; supplies, including enzymes and proteins, have to be shipped between these compartments. Some supplies are packaged into molecular trucks, and each truck has a key that will fit only the lock of its particular cellular destination. Other proteins act as loading docks, opening the truck and letting the contents into the destination compartment."
(Michael Behe, "Darwin Under the Microscope," The New York Times, October 29, 1996, Tuesday Final Section A; Page 25; Column 2; Editorial Desk)

In light of this "staggering complexity," Behe believes that “[t]hese complex systems were designed -- purposely arranged by an intelligent agent." ("Darwin Under the Microscope")

Christoph Adami is not an ID proponent. However, his recent Science article uses the same "lock and key" description for proteins, and claims it can provide at least intuitive evidence for design:

"If an elaborate lock fits an elaborate key, we immediately sense purpose of design: The key was crafted with the idea of the lock in mind. When we come across such lock-and-key pairs in nature, it is natural to ask how these pairs could have evolved by Darwinian evolution. At first glance it appears that the key can only fit the lock if the lock is already present, and the lock cannot evolve except in the presence of the key (because without the key, it does not open). ... This concern has been seized upon by proponents of an 'intelligent design' alternative' to Darwinian evolution that proposes that complex systems--like those that display lock-and-key complexity--cannot evolve. The premise for the argument is that systems of a lock-and-key nature cannot evolve and thus are "irreducibly complex" (3), implying that only the lock-and-key combination, but not its parts, is complex. The argument continues that because such systems do exist in nature, and cannot have evolved, they must have been 'designed.'"

("Reducible Complexity" by Christoph Adami in Science, 311: 61 (April 7, 2006))

Adami is a firm believer that Neo-Darwinian explanations can account for the origin of these "lock and key" fits. However according to Adami, these "lock-and-key" enzyme-substrate interactions can indeed be argued as examples of irreducible complexity, and are even used by design proponents to contend for intelligent design. But Behe and Snoke's paper in Protein Science studies this precise phenomenon: the "lock and key" fit of enzyme-substrate interactions. They might not use the words "irreducible complexity" or "intelligent design" but Adami's own words in science show that those issues can be directly implicated in the Behe and Snoke (2004) study.

Adami’s Own Puffs of Political Smoke
Adami is cognizant that by talking about intelligent design, he might imply there is some kind of bona fide scientific discussion taking place here. (You know, he's talking about the controversy that doesn't exist.) Adami tries to persuade readers to remember that “ID isn’t science—so this exercise in refutation is just a drill” by adding superfluous comments at the end of his article that any claims of irreducible complexity must be “purely political:”

"The Bridgham et al. studies are of particular scientific interest, given the political attention given to intelligent design lately. Although these authors have not directly addressed this controversy in their work--because the work itself is intrinsically interesting to biologists--such studies solidly refute all parts of the intelligent design argument. Those "alternate" ideas, unlike the hypothesis investigated in these papers, remain thoroughly untested. Consequently, whatever debate remains must be characterized as 'purely political.'"

("Reducible Complexity" by Christoph Adami in Science 311: 61 (April 7, 2006), emphasis added)

Many pro-ID scientists have already responded to research by Bridgham et al., showing that they are engaging in smoke and mirrors by claiming that their research refutes ID. Given the weak nature of this evidence and the hyperbolic nature of the claims Adami extrapolates from the paper, perhaps it is Adami who is really playing politics here. After all, look at the bottom line of what this research really found:

Adami highlights that the lock and key fit of the glucocorticoid enzyme with the cortisol substrate is based upon the specificity of merely two amino acids, where the precursor molecule was also functional (lacking those 2 mutations).

In other words, one enzyme might have evolved into another via 2 mutations. This would appear to be a fairly simple system--and, assuming it did evolve in this fashion, an unimpresive example of evolution. Two meager mutations (something which even Behe and Snoke's (2004) simulations found could evolve under mutation and selection) is not an impressive evolutionary leap and there seems no reason to assume that many enzyme-substrate interactions might not require the simultaneous substitution of many more amino acid residues in order to function, vastly decreasing the likelihood of their evolution. (In fact, this research would not address the origin of complex molecular machines requiring many interacting parts, like the bacterial flagellum.) Even if we grant that this present system is "reducibly complex" (with regards to at least 2 meager amino acids, that is), why should we assume that all the other enzyme-substrate interactions in biology follow suit?

It seems quite reasonable to conclude that irreducible complexity might very well still exist in many other systems. By labeling anyone who supports irreducible complexity as “purely political” in light of this interesting but ultimately lightweight research, it is clear that Adami himself is the one playing politics.

Adami simply wants to pretend there is no scientific controversy over irreducible complexity. Perhaps Allen Orr was right when he wrote:

“Many scientists avoid discussing I.D. for strategic reasons. If a scientific claim can be loosely defined as one that scientists take seriously enough to debate, then engaging the intelligent-design movement on scientific grounds, they worry, cedes what it most desires: recognition that its claims are legitimate scientific ones.”
(H. Allen Orr, "Devolution: Why intelligent design isn’t,” The New Yorker, May 30, 2005, emphasis added)

But if Adami feels the need to talk about the science of ID, then perhaps Orr is wrong to pretend that ID poses a non-challenge to evolution that real scientists can simply let slide right off their backs. Of course Adami tries to lightly paper over the discussion with "purely political" comments at the end. If this is "purely political" then why all the talk about irreducible complexity?

We’re Not Buying it, Dr. Adami:

If irreducible complexity were simply a "purely political" idea, then Nature wouldn't have published Adami’s Avida paper, which he also proclaims is a refutation of irreducible complexity (see below), which was strangely co-authored by the non-scientist philosopher Robert T. Pennock, who has devoted his entire career to critiquing ID.

If irreducible complexity is "purely political," then why did Adami give talks at AAAS meetings entitled Evolution of Biological Complexity, claiming his Avida paper refuted irreducible complexity:

"It is often claimed that Darwin's theory of evolution is incomplete because it cannot account for the evolution of complex adaptive traits via the accumulation of mutations. At the same time, the concept of biological complexity itself--how it may be defined and whether complexity increases in evolution--is often perceived as controversial. In this talk, Dr. Adami will address both concerns: the definition of complexity and whether there is a trend in its evolution, as well as the mechanisms by which complex traits evolve that appear to be "irreducible". Evidence from experiments that study the evolution of complexity in a digital life form will be shared. These experiments show that complex adaptive traits do emerge via standard Darwinian mechanisms, and that this evolution is accompanied by an increase in a suitably defined measure of complexity." (Abstract of Adami's Evolution of Biological Complexity lecture before the AAAS.)

(This is especially poignant when Adami's Avida paper doesn't refute irreducible complexity.)

If irreducible complexity were simply a “purely political” idea then Adami wouldn't be making such a big deal about the Bridgham et al. paper in Science as a refutation of irreducible complexity.

If irreducible complexity were simply a “purely political” idea then Bridgham et al. would not have opened their paper framing itself as a vindication of the same passage from Darwin’s Origin of Species that Michael Behe cites as the basis for his challenges to Darwin from irreducible complexity. (At least this recent article in Science wasn’t coauthored by Barbara Forrest, and if you would find that strange if it had happened, then you should accept that Adami / Pennock et al.'s Avida paper was clearly politically motivated.)

If this Bridgham et al. paper doesn’t have some political aspirations, then why did the authors issue a sweeping press release entitled “Evolution of ‘Irreducibly Complex’ Features Explained”?

If the Bridgham et al. authors aren't acting politically, why did one co-author recently remove mention of irreducible complexity from his web page, to remove mention of motives to explain the evolutionary origin of "irreducible complex" systems? It looks like Joe Thornton is trying to hide the fact that irreducible complexity is a bona fide scientific idea which he desired to address in his research.

If irreducible complexity is simply a "purely poligical" idea, then why are Adami and others making such overbroad claims of refutation of irreducible complexity based on such skimpy evidence?

By pretending that irreducible complexity is simply a "purely political" idea, it seems fair to ask Adami: Who is the one really playing politics?