I would suggest that the fact that the intermediate forms seem to provide a selective advantage and the fact that the 4 mutations are not so highly specific are the most likely reasons an ID proponent might put forward for this not being a case that demonstrates the evolution of a truly irreducibly complex system, whatever one of those might really be.
They may put that forward, but the fact that the 4th mutation required for the utilisation of OmpF didn't occur without the previous 3 raises an interesting question. What would happen if one of those initial 3 was knocked out, so you had steps 1, 2 and 4 or 2, 3 and 4? Their data suggest that steps 1,2 and 3 are absolutely required for step 4 to take place, but once step 4 is in place, how necessary are the previous steps or can one or other then be discarded? The early mutation that increases the phage's affinity for the rare LamB binding site can possibly be knocked out now that the phage has an alternative, abundant binding site (although I'd like to see this shown experimentally). That also means that further mutations at that site may now be more "survivable"
I think this demonstrates the fault that Behe makes when he starts with a "completed" IR system and then tries to work back. Not every step that resulted in an IR system may still be hanging around. Rather than working backwards, it's more productive to try to work forwards. It's a bit like building something that requires scaffolding to be put up. Once the build is complete, the scaffolding is removed. An IDist would look at the building and suggest that the builders flew up to the higher levels to do the work, a scientist would suggest ladders, hoists and scaffolding to reach the higher levels. While not an ideal analogy, I can't come up with a better one. Feel free to suggest some as analogies are so useful in explaining things.
"An aeroplane pilot commanded to remain in place (aloft) for another hour, replies: 'the machine is not fitted with skyhooks' " ... The skyhook concept is perhaps a descendant of the deus ex machina of ancient Greek dramaturgy: when second-rate play-wrights found their heroes into inescapable difficulties, they were often tempted to crank down a god onto the scene, like Superman, to save the situation supernaturally. ... Skyhooks would be wonderful things to have, great for lifting unwieldy objects out of difficult circumstances, and speeding up all sorts of construction projects. Sad to say, they are impossible." (p74).
Dennett uses the skyhook and crane as a magnificent metaphor. Just like objects can be lifted by imaginary skyhooks or cranes, so can design originate by 'skyhooks' or 'cranes'. The 'skyhook'-explanation of design invokes the supernatural, the 'crane' explanation invokes natural processes. The 'skyhook'-explanation of design is invoked by Creationists, the 'crane' explanation is invoked by 'evolutionists'. Darwin's Dangerous Idea is that all design can be explained without skyhooks: without Mind or God. Dennett gives a good historical overview of the use of these two types of explanation.
Life, don't talk to me about life - Marvin the Paranoid Android
I don't think the sort of strict sequentiality you seem to be describing here really exists.
What the author's conclude is that all 4 mutations are required, the order in which they arise seems irrelevant. In their replicate experiments all of the mutation types arose in the non OmpF infecting strains and at least 2 distinct combinations of 3 mutations arose, in EvoA lacking the A3034G mutation and in F2 and H4 lacking the G3319A mutation. Both of these were just one mutation away from an OmpF infective strain through slightly different evolutionary trajectories.
No doubt it is significant that in both cases it is one of the highly specific mutations that is missing but there is no reason to assume that with a broader sampling strains might not have been found with both the highly specific mutations but lacking one of the broader mutations, such strains are just more unlikely.
Your final point comes back to the lamentable lability of the term 'Irreducible Complexity' which seems to be one of those terms that means whatever a person wants it to mean. Behe himself has given more than 1 distinctly different definition and the main point of difference is precisely whether systems which have prior functional intermediates with a distinct function, as in this case, are IC.
It would certainly be very informative to have some proper analysis of the extent and nature of the fitness benefits of each mutation in isolation. Perhaps all any of the mutations do is increase affinity for LamB up until such a point with all 4 mutations that it can now bind to OmpF which is apparently the most structurally similar E. coli protein to LamB (at least going by crystal structure).
Creationists like Behe and Dembski put ideas out there that they then defend with great energy in the public arena but upon which they conduct no actual research. Dembski is now at a seminary while Behe, because he has tenure, remains ensconced at Lehigh where he has produced 0.2 papers per year over the past decade. Both are just as convinced of their ideas as ever, but ideas in science are measured by how convincing they are to other scientists, and by this measure both creationism generally and ID specifically have been spectacular failures for a long time.
And so it seems incongruous and almost comical to me to see evolutionists giving ID disproportionately far more critical attention than it is receiving from those who should be actively researching ID but aren't.
quote:I stayed on as a full-time Discovery fellow until Baylor hired me in early 2000. But in the intervening twelve years, they’ve provided lots of support, both tangible and intangible. As it is, I’m leaving my present post at Southwestern Seminary and returning as a full-time fellow of Discovery later this year (2012). This will allow me to redouble my efforts at developing ID’s scientific research program.
...the Center explores how new developments in biology, physics and cognitive science raise serious doubts about scientific materialism and have re-opened the case for a broadly theistic understanding of nature.
Design theory promises to reverse the stifling dominance of the materialist worldview, and to replace it with a science consonant with Christian and theistic convictions.
--To defeat scientific materialism and its destructive moral, cultural and political legacies. --To replace materialistic explanations with the theistic understanding that nature and hurnan beings are created by God.
Yup, lots of scientific research there!
Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
Last I saw the Dishonesty Institute didn't have any research program.
The scary thing is that in their own minds they have probably redefined "research" in the same way that they have redefined science. And I'm not entirely kidding here, for the mind that can redefine science to include the supernatural, it is no great leap to redefine research to include personal revelation.
Most of the research side of things, such as it is, has been hived off into the Biologic Institute instead.
Is that some kind of uber-procrastination, where you get someone else to not do what you should be doing?
quote:New Scientist magazine sent a reporter to the Biologic Institute facilities in late 2006 to investigate. The reporter, Celeste Biever, was given a fairly chilly reception and found few willing to speak to her about their research. Although the New Scientist article was somewhat negative, the Discovery Institute touted it as unequivocal evidence that the Biologic Institute is engaging in scientific research.
If I were you And I wish that I were you All the things I'd do To make myself turn blue
This will allow me to redouble my efforts at developing ID’s scientific research program.
Last I saw the Dishonesty Institute didn't have any research program.
Yes. In fact the above quoted statement says that Dembski is going to increase his efforts to develop a research program, and not that he is simply going to do contribute to current research efforts. I see the statement as an honest assessment that DI does indeed consist of flacks, hacks, and apologists, at least currently.
After the big dust up over Dembski's statements about a world wide flood, or lack thereof, nobody should be the least bit surprised that Dembski is involved in new pursuits. The YEC establishment's treatment of Dembski puts the lie to all those fundamentalist efforts at pushing ID in the name of academic freedom.
Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)
Can anyone find a citation that challenges naturalistic approaches to science? Anything that seems like it introduces a "broadly theistic understanding of nature" or that challenges the "materialistic worldview"?