On July 31, 2008, I submitted a paper on “Flight mechanics of the Ivory-billed Woodpecker (Campephilus principalis)” to PLoS ONE. The academic editor accepted the paper for publication on the basis of positive reviews by experts on woodpeckers and the flight mechanics of birds. I paid the $1300 publication fee and was formally notified that the paper was accepted for publication on December 5. This notice mentioned a press embargo, which reminded me to prepare a press release. The Ivory-billed Woodpecker is a topic of great interest and controversy, and much of the debate has taken place in the press. My paper would be the third since 2005 to report on sightings and evidence of this critically endangered species, including the first data from Louisiana in decades, and this data should be part of the discussion. Since the work was privately funded, I was not able to issue a press release through my employer. I asked PLoS for assistance, but they claimed there was “a danger that the work will be misinterpreted by the popular media.” I let PLoS know my opinion of this insulting comment, and they immediately pulled the paper (later claiming that this was not done in retaliation). The following week, PLoS claimed that the following “concerns” about the paper had arisen:

1. The work is being presented too strongly as evidence for the existence of the ivory-billed woodpecker
2. The fieldwork and evidence has not been reviewed in sufficient detail (some of this information was added after assessment by the reviewers)
3. Discussion of previous published evidence regarding this bird is not balanced, and does not refer to uncertainties that have been expressed in subsequent literature

After a paper has been through the peer review process and accepted for publication, the decision should not be reversed unless a serious problem is discovered. On December 27, I sent PLoS a compilation of the instances in which evidence is discussed in the paper and pointed out that it is done so conservatively in each case (the phrase “consistent with” is used 23 times in the paper), but PLoS ignored this rebuttal and used the “concerns” as an excuse to send the paper to new reviewers. The other two “concerns” also lack substance. The evidence consists of three videos of birds that were identified in the field as Ivory-billed Woodpeckers, each of which shows a bird with flight mechanics and other characteristics consistent with this species. All of this material was included in the original manuscript and was seen by the reviewers. The academic editor requested major revisions, all of which were made according to his instructions. The academic editor made the perfectly legitimate decision to review the revisions without consulting back with the reviewers. In the Introduction, I mentioned that two independent groups of ornithologists have recently published reports of sightings and evidence of Ivory-billed Woodpeckers. These are clearly the most relevant papers, but I did not discuss them in detail and mentioned them in a neutral fashion. I kept the Introduction concise and did not delve into the controversy, which has been discussed extensively elsewhere. I would have been willing to include additional discussion, but neither the reviewers nor the academic editor requested such changes. It is clear that the “concerns” about the paper are fabrications that were used as an excuse to reverse a publication decision when there was no legitimate reason for doing so. Trumping up these charges against the paper was an exceedingly dishonest maneuver by the editorial staff of PLoS.

On January 13, I was notified that PLoS had received comments from two new reviewers who supported publishing the paper without the data, which is the most important part of the paper and took 84 weeks of fieldwork to obtain. The new reviews were never sent to me, and PLoS refused to provide any specific comments to support their claim of concerns about the data. PLoS also claimed that the data is largely unconnected with the section on “Historical accounts, physiology, and flap rate models,” but each of the videos shows elements of flight that are consistent with historical accounts and/or physiology and/or flap rate models. The 2006 video shows takeoffs with deep and rapid flaps that are consistent with historical accounts and physiology. In addition to showing another takeoff with deep and rapid flaps, the 2007 video shows a swooping takeoff and a swooping landing, which are consistent with historical accounts. This is the first putative footage of the swooping behavior that motivated Audubon to describe the flight of this species as “graceful in the extreme.” The 2008 video shows the first putative footage of the cruising flight, which is consistent with the flap rate models and historical accounts of rapid flaps and a high flight speed. This footage is the strongest quantitative evidence that has been obtained to date, including well-resolved wingtip elevation and wingspan curves that were digitized from the video by the leading expert on woodpecker flight mechanics. This footage provides the first putative new science on this species that has been obtained since Tanner’s work was published in 1942, including the first measurements of the flight speed and flap rate in cruising flight and the discovery of a widespread misconception about the flap style in cruising flight (my paper points out that a Tanner photo from 1939 -- the significance of which had been overlooked -- brings into question the expected flap style but is consistent with the flap style of the bird in the video).

The academic editor did a fine job by sending the paper to appropriate experts who do not have a vested interest in this hotly contested problem. One of the original reviewers is an expert on the flight mechanics of birds, who has published on this topic in Nature and other leading scientific journals. The other original reviewer who identified himself is an expert on woodpeckers, who has published on this topic in the Proceedings of the National Academy of Sciences. The only new reviewer who was identified is Thomas Brooks, whose scientific expertise appears to be irrelevant to evaluating data on the flight mechanics of woodpeckers. How can PLoS justify accepting a paper for publication on the basis of the opinions of established experts in appropriate areas and then reversing the decision on the basis of the opinion of a non-expert? The academic editor made the following positive comments shortly before accepting the paper for publication:

“I realise that this paper covers a topic that a number of research groups have vested and potentially conflicting interests in, and I suspect that there will be heated discussion about some of the points you make and the way in which you make them, but this is exactly the kind of paper that PLoS ONE was set up to publish. I'm satisfied with the responses you've made to the referees…”

Since the academic editor provided detailed instructions for the revisions and then claimed to be satisfied with them, it seems very curious that PLoS claimed on January 13 that he supported the decision to pull the paper, send the paper to new reviewers, and take the responsibility for the paper out of his hands.

Was PLoS influenced by a third party (such as one of the research groups alluded to in the quote by the academic editor above)? There are plenty of candidates. Some of the most vocal critics of Ivory-billed Woodpecker research have openly admitted to a conflict of interest (opposition to funds being diverted from their pet projects into Ivory-billed Woodpecker research), and one of them sent an unsolicited letter to the Louisiana Bird Records Committee in an attempt to undermine my work. Such an unprofessional act is comparable to interfering with the peer review process, which is supposed to be based on the opinions of qualified experts who don't have conflicts of interest. Shortly before my paper was scheduled to appear, I sent a preprint to a member of a powerful consortium that has a major vested interest in Ivory-billed Woodpecker research. I'm not very popular with some of the members of that group, having single-handledly obtained more and better data than their vast enterprise has obtained and having pointed out a serious error in their work (the type of error, in fact, that would justify reversing a publication decision).

A few days after the paper was pulled, I had a phone conversation with Michael Eisen, who is a co-founder of PLoS and a member of the Board of Directors. He agreed that it was wrong to pull the paper and actually laughed about it. He agreed to help, but it does not appear that he took any action. If a co-founder of PLoS allows the editorial staff to get away with such shenanigans, what does that say about this organization? I contacted Eisen in order to give him an opportunity to clarify his position, but he did not respond.