Author of retracted Molecular Biology and Evolution paper explains opaque notice that’ll still cost you $32

A completely unhelpful retraction notice appears in the September issue of Molecular Biology and Evolution for “Investigating the Role of Natural Selection on Coding Sequence Evolution in Salmonids Through NGS Data Mining,” a paper first published in March.

Here’s the entire notice for the paper — which has been removed completely from the journal’s site, we should mention:

This article has been permanently retracted from publication by the authors.

Reading the entirety of that unhelpful notice, by the way, will set you back $32 if you’re not a subscriber. Otherwise, you will learn only that “This article has…”

Has what? Cooties? Been given an award? Too many references? Come on, Oxford University Press. We know times are tough. But you can’t make the whole sentence free?

Lucky for us, the Universite Laval’s Louis Bernatchez, the senior author of the study, was happy to say why the paper was retracted:  

Quite simply, our study targetted specifically a comparative genomics analysis of salmonid species. However, because the whole family went through a relatively recent whole genome duplication event, sorting out paralogs from true orthologs remains a serious challenge. We realised that some targets retained in our analyses were likely to be paralogs, which could cause some biases in our results. We now need to revisit that very carefully using alternative analytical approaches.

We asked Joseph Pickrell, a University of Chicago graduate student in genetics who brought this retraction to our attention, to explain what that meant: 

They wanted to compare the sequences of genes across different species, and thought that’s what they had done. However, in these species, apparently a lot of genes are duplicated, such that there are two relatively similar copies (call them gene 1a and gene 1b). If you’re looking at a copy of a gene in a species, it’s difficult to tell whether it’s gene 1a or gene 1b. So presumably what happened is that they thought they were looking at gene 1a in both species, but realized they were looking at gene 1a in one species, but gene 1b in another species. This is an easy mistake to make, and could definitely lead to major problems. Though again, without the text of the original article, it’s tough to be more precise than that. 

Indeed. We don’t think removing a retracted paper completely from an archive — as opposed to just clearly marking it “retracted” — is the best way to correct the scientific record. (The citation still appears on PubMed, sort of.) And it’s also hard to understand why the journal didn’t just say why the paper was retracted.

We tried to get comment from the journal’s editor, as well as Oxford University Press, and will update with anything we hear back.

Please see an update on this story.