A Senior Editor at PLoS ONE has notified me that the paper I first complained about back in September (“A cautionary tale on reading phylogenetic trees“) has been retracted. I still have lots of questions.
In the December issue of EMBO Reports, Matheus Sanitá Lima and David Roy Smith argue that biologists utilizing next-generation sequencing data should include detailed methods with their submissions to the Sequence Read Archive (the paper is paywalled at the publisher site but available here):
For those who are unfamiliar with it, the SRA is an international public online archive for next-generation sequencing (NGS) data, which was established about a decade ago under the guidance of the International Nucleotide Sequence Database Collaboration (INSDC)…Once there, you will find yourself at a sequencing-read superstore.
I like PLoS ONE. I know a lot of scientists don’t. I think there’s a niche for what my PhD advisor called ‘bricks’: papers that may not be groundbreaking, but present rigorous results that contribute to building a larger structure (he was, BTW, describing one of my papers, and it wasn’t a compliment). It’s also possible that research that may not be obviously important when it’s done turns out to have big implications that weren’t at first obvious. PLoS ONE explicitly aims to ignore the ‘impact’ of a paper in accepting or rejecting papers, focusing only on the rigor of the results:
PLOS ONE will rigorously peer-review your submissions and publish all papers that are judged to be technically sound. Judgments about the importance of any particular paper are then made after publication by the readership, who are the most qualified to determine what is of interest to them.
But a couple of recent developments are worrying. First, as I’ve previously written, a recent article reporting a phylogenetic tree for eukaryotes was published in a form that never should have survived peer review (“A cautionary tale on reading phylogenetic trees,” “PLoS ONE responds“). The article contains numerous misinterpretations of the tree, unexplained contradictions in the inferred divergence times, and, most importantly, a choice of outgroup that pretty much invalidates all of the phylogenetic inferences.
I have contacted the editors by Twitter and by email, and so far I haven’t gotten much more than “we’re looking into it.” I am very interested to see what the journal does about this, because, as I said before,
The only thing that separates a high-volume, open access journal like PLoS ONE from the dark underbelly of scholarly publishing is a rigorous peer review process.
Now there’s a whole new reason to worry.
Okay, that line above is exactly how far I got before reading the paper I’m about to write about. I’m leaving it in as a caution against rushing to judgement.
A reader commented by email about my criticism of the PLoS ONE article that inferred a multigene phylogeny of eukaryotes, with Chlamydomonas reinhardtii as the outgroup (“A cautionary tale on reading phylogenetic trees“).
Although you are of course correct to complain about nearly everything in the paper (esp. re “basal” and node rotations), and I am sure the tree is wrong in more ways than it is right, I think you might reconsider or put in context complaints about the “provides a link between”. My thought is simply that if one has a long branch between two nodes in a tree, if you add a taxon group that branches off in the middle of this long branch, then it does, in a sense, provide a “link” between these two nodes. A more proper way to put it is that it provides information concerning the ancestral state at the two original nodes (i.e., may substantially modify the posterior probability of the states at the two nodes). I doubt that the authors mean it in this sense, but in the general context of teaching people about trees, I would want students to understand this.
PLoS ONE is a strange journal. Until recently, it was the largest journal in the world, publishing as many as 30,000 papers a year. It’s definitely the low end among the Public Library of Science (PLoS) stable of journals, but opinions of its quality vary over a wide spectrum. PLoS ONE‘s mission is explicitly different from most journals, as they say impact (i.e. significance) is not a consideration:
Often a journal’s decision not to publish a paper reflects an editor’s opinion about what is likely to have substantial impact in a given field. These subjective judgments can delay the publication of work that later proves to be of major significance. PLOS ONE will rigorously peer-review your submissions and publish all papers that are judged to be technically sound. Judgments about the importance of any particular paper are then made after publication by the readership, who are the most qualified to determine what is of interest to them.
I see that it’s been nearly three weeks since I posted, maybe the longest gap since I started this. It wasn’t a conscious decision, just a combination of deadlines and life in general.
Back in April, I got an email out of the blue from a ‘Project Manager’ at Research Features, a digital magazine “…born from a passion to break down barriers that exist in the dissemination life cycle from researcher to the mass audience.”
Dear Dr. Herron
I would like to speak with you concerning your work with the Collaborative Research: De Novo Evolution of Multicellularity in a Unicellular Volvocine Alga study.
Biologists have the option of posting preprints, articles that have not yet been through peer review, to bioRxiv. Modeled on the physics preprint server arXiv, bioRxiv is much newer, and its adoption by biologists (unlike arXiv’s by physicists) has been well short of universal. bioRxiv recently got a small boost, though, and I suspect it may be approaching a tipping point.
I’ve been getting a new (for me) form of spam lately. I’m used to invitations to submit to predatory journals and to attend conferences for which I have no relevant expertise, but it’s only in the past few months that I’ve been getting invitations to serve on journal editorial boards. For example:
Most of the articles published in scientific journals report publicly funded research. You can see this in the acknowledgments section, where the authors list their funding sources, which will often include the National Science Foundation, National Institutes of Health, NASA, Department of Defense, Department of Energy, Environmental Protection Agency, etc. (this is obviously a US-centric list, but most countries have similar funding mechanisms). Even if the work isn’t supported by a government grant, much of it is done at public universities, meaning that the facilities and possibly researcher salaries are government supported. And government-supported means taxpayer-supported.