It's wonderful to wake up, have breakfast, and see that the Europeans and N. American early birds have been working on this while I slept. Let me lay out what I now think must have happened, modifying my earlier timeline by taking into account comments on my earlier post, especially from Jim Fetzer, John Pieret, and Reinhard Muskens.
0. Special issue of Synthese published on-line, including articles by Barbara Forrest and Trevor Pennock.
1. EICs receive letters from Alvin Plantinga and Francis Beckwith and worry about the "tone" of some of the contributions, or possibly just the two mentioned above. At this stage, the EICs don't quite know what to do about it, and waver back and forth, but one clear option is to do nothing. They include the Guest Editors in the discussions during this "oscillatory phase."
2. Then Synthese received some kind of legal threat from someone other than a Christian philosopher. (Since Alvin Plantinga is quite clearly a christian philosopher, he is not the author of any kind of legal threat. So the letter from him is separate from this threat. Is Beckwith himself a Christian philosopher? It would be highly evasive of the editors to describe the legal threat simply as not coming from a CP if Beckwith was the author. On the other hand, what grounds would anybody else have for a legal threat? Draw what conclusion you may.)
3. The publisher either directly receives or is apprised by EICs of a legal threat.
4. "Eventually the editors arrived at a shared position, in consultation with the publisher, based on what we judged to be the offending language in two papers." (The use of the definite article is an inadvertent give-away: "the" offending language. Unless this is a linguistic slip, signed by one of the leading modal logicians in the world, it is a back-reference to discussions about "offending language.")
5. In discussions with the publishers and perhaps their lawyers/in-house legal team, the Editors arrive at a decision to do something. They ask Forrest whether she will tone her paper down. This matter is unresolved, but at about this time the publishers advise/order the EICs not to communicate any further with others, including Forrest and Guest Editors. Thus: "We were unable to properly communicate later stages of our decision-making process to the guest editors." (The lack of ability is clearly not some large-scale breakdown of email servers, etc.)
THE ACT At this point the special issue of Synthese goes into print. EICs publish a disclaimer, and an on-line response from Beckwith (to be printed in due course). Beckwith says that the EICs have publicly distanced themselves from some quite specific elements in Forrest's article--which they hadn't, except insofar as they consented to the publication of his statement to this effect.
6. The discussion on this blog, on Leiter Reports, and on a number of other sites takes off. A petition is posted and signed by over 400 philosophers, including most leading philosophers of biology. The editors are more or less forced to write a response, but in order to make it as invisible as possible, they post it as a jpeg image on an island website. No note of the response is made on Synthese's official website.
I have tried to be as non-commital as possible on contested points in the above narrative, and it may contain some inaccuracies, but on the whole it is plausible, in my opinion.
What conclusions should we draw from this narrative? The first is that the publishers played a role in the process. This does not exculpate the EICs: on the contrary. But it shows how commercial factors can get involved in a process that most of us would like to see in academic hands. Readers of blogs such as Leiter's should be alarmed by how professional management has slowly eroded academic control of universities: at KCL, Nottingham, UMSL, and a number of other places. We should similarly be alarmed by non-academic management at scholarly publishing houses.
A while ago, there was a suggestion on Leiter Reports--I forget by who--that academics should not publish in or referee for for-profit journals. It is well worth thinking in a broader context of how we should relate to Springer, North-Holland/Reidel, and the rest. We should remember: exorbitant subscription rates, issues that serve industry, and other problems that have come to light in the last year or two.