Firstly, Ben Goldacre and Respectful Insolence discuss the case of two papers, recently published in Medical Hypotheses, that were so bad they were withdrawn by publishers Elsevier. Given that Elsevier happily publishes Homeopathy, the fanzine of the Faculty of Homeopathy, this should give pause for thought. Medical Hypotheses is a bit of an oddity: it does not send papers out for peer review. Rather, they are approved solely by the editor of the journal, one Bruce Charlton. It appears that many papers are approved within days, sometimes hours, of being submitted, suggesting that there is very little scrutiny of the papers.
The two papers are one by Duesberg et al., and one by Ruggiero et al., both of which seek to deny the magnitude of the AIDS crisis. Seth Kalichman of the Denying Aids blog did an experiment by sending the manuscript out for blind peer review. All three "reviewers" rejected the manuscript on the basis that it was filled with logical flaws and mis-representations of the published literature.
This Article-in-Press has been withdrawn pending the results of an investigation. The editorial policy of Medical Hypotheses makes it clear that the journal considers "radical, speculative, and non-mainstream scientific ideas", and articles will only be acceptable if they are "coherent and clearly expressed." However, we have received serious expressions of concern about the quality of this article, which contains highly controversial opinions about the causes of AIDS, opinions that could potentially be damaging to global public health. Concern has also been expressed that the article contains potentially libelous material. Given these important signals of concern, we judge it correct to investigate the circumstances in which this article came to be published online. When the investigation and review have been completed we will issue a further statement. Until that time, the article has been removed from all Elsevier databases. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
The second example is a paper published in Proceedings of the National Academy of Sciences, amusingly known as PNAS. This is a venerable and respected journal, but it has a little-known wrinkle: members of the National Academy of Sciences are allowed to bypass formal peer review by "communicating" papers for other researchers. This is how the PNAS "Information for Authors" page describes the process:
An Academy member may “communicate” for others up to 2 manuscripts per year that are within the member's area of expertise. Before submission to PNAS, the member obtains reviews of the paper from at least 2 qualified referees, each from a different institution and not from the authors' or member's institutions. Referees should be asked to evaluate revised manuscripts to ensure that their concerns have been adequately addressed. The names and contact information, including e-mails, of referees who reviewed the paper, along with the reviews and the authors' response, must be included. Reviews must be submitted on the PNAS review form, and the identity of the referees must not be revealed to the authors. The member must include a brief statement endorsing publication in PNAS along with all of the referee reports received for each round of review. Members should follow National Science Foundation (NSF) guidelines to avoid conflict of interest between referees and authors (see Section iii). Members must verify that referees are free of conflicts of interest, or must disclose any conflicts and explain their choice of referees. These papers are published as “Communicated by" the responsible editor.The paper in question is was submitted via this communication process. It was written by Donald Williamson, a retired academic from the University of Liverpool, and suggests that butterflies and caterpillars orginated as different species:
I reject the Darwinian assumption that larvae and their adults evolved from a single common ancestor. Rather I posit that, in animals that metamorphose, the basic types of larvae originated as adults of different lineages, i.e., larvae were transferred when, through hybridization, their genomes were acquired by distantly related animals.
The paper has been criticised on the basis that it contains no supporting data for what is, after all, a fairly extraordinary hypothesis. Not only that, but it turns out that it had previously been rejected by seven different journals.
In both Medical Hypotheses and PNAS, the defence seems to be that there needs to be some mechanism by which speculative ideas that go against current mainstream opinion can be presented and discussed. This seems fair enough, but is anything gained by publishing hypotheses that are not supported by any data, or papers that are logically flawed and contain mis-representations? In both these cases, it seems that the papers would not have been published had they been reviewed properly.