My first-order reaction: get over yourselves. This is a perfect example of academics getting their panties in a twist over the exceedingly trivial (in this case, the propriety of the disclaimer). Second-order: the underlying dispute (theism v. atheism) is really, really boring, but even so, there must be better ways to argue about it than to take offense at editor's notes.
But in poking around in this mess, I noticed something more interesting -- one of the guest editors of the journal issue is James Fetzer, whose name I was vaguely familiar with from the old days because he worked in philiosphy of AI for awhile. But now he seems to have become a full-blown conspiracy theorist, in the most literal sense -- he's published an academic paper on it (Reasoning about Assassinations), which looked interesting at first glance. The issue of how one properly evaluates evidence in such cases is pretty interesting from an epistemological viewpoint, especially to someone like me who likes to dabble with fringe beliefs without losing my mind over them.
But on second glance it looks like he's just become sucked into a rather standard hole, and is now an unquestioning supporter of various Kennedy assassination theories, 9/11 conspiracies, climate change denialism and the like, as well as even kookier-sounding ones like a conspiracy by Johnson & Johnson to murder someone over a dental floss-related invention. He's founded a site called Assassination Science, which might qualify for my Academic Units with Amusing Names series, although it doesn't look recognized by any institution, or likely to be. The paper above doesn't seem like it's meta to conspiratorial thinking as its name suggested; it's just an example of it.
But the really interesting thing is that the initial offense of the original paper was exactly the sort of conspiracy-flavored thinking that Fetzer seems to be promoting, although in a much milder form. Here's an extract:
In addition to the ideological congruences between Dembski's views and those of declared dominionists, there are more direct connections between ID and CR [Christian Reconstructionism --mt]. The CSC has received major funding from Howard Ahmanson, a former board member of the Reconstructionist Chalcedon Foundation... In 1999, speaking at Christian Reconstructionist D. James Kennedy's "Reclaiming America for Christ" conference, Phillip Johnson urged attendees to reclaim the intellectual world "while we're recapturing America ... Kennedy, a staunch ID supporter, produced a 2006 anti-evolution documentary featuring CSC fellows Michael Behe, Richard Weikart, and Jonathan Wells as experts. CSC fellow Charles Thaxton was among the "conference faculty" at a May 2006 CR conference held by American Vision (AV), one of the most extreme CR groups. Journalist John Sugg describes AV leaders Gary North and Herbert Titus: Their imposition of a theocratic state would not, by their standards, be tyranny. Public schools to them are tyrannical. The Southern Poverty Law Center (SPLC) labels AV a hate group because of its virulent anti-gay attitudes. Similarly, Beckwith is listed among the conference faculty of Summit Ministries, which SPLC reports "graduates more than 1,300 students a year--all steeped in "¦Christian dominionism and anti-gay politics" ... [references omitted --mt]Now, I don't see anything particularly wrong with this. Weaving strong networks of ideas, people, and evidence while attacking your opponent's corresponding networks is just how argumentation works. But it does seem to stray a bit from the academic norm into something more journalistic, polemical, personal, and mildly conspiratorial. Doesn't bother me but I can see how it might bother someone with more devotion to the academic ideal. I've argued before that ad hominem is a perfectly valid form of reasoning, or at least close to one. Apparently Charles Taylor and Paul Feyerabend have also defended ad hominem in their own ways, so I'm not alone in this. The passage above is not even all that ad hominem, although that seems to be the basis for why it has offended its target.
Oh well I'm rambling. The interesting thing here I think is the paper Fetzer didn't write, on how to think productively about conspiracies and conflict, how to account for the reliability or bias of sources, how to do ad hominem right. How do we factor in to our world models the revelations of Climategate or Wikileaks, or the fact that intellectuals we might admire or not are bankrolled by the Koch brothers? How do you think about the hugely important role of networks of power and influence without becoming a kook? These are actually useful, indeed crucial questions that professional epistemologists ought to be applying themselves to.