Jeffrey Beall, academic terrorist!

I’ve been fairly outspoken about my support for open access publishing (On paywalls, F paywalls), so you might think that I would naturally be at odds with probably the most prominent critic of (paid) open access publishing, Jeffrey Beall. I’m not, though. I despise scammers of all stripes (This should be interesting, What good is a washing machine on Arrakis?I think Tina/Nora has given up on me), and I think predatory open access publishers are loathsome parasites.

Did Beall miss the mark with his criticism of Frontiers publishing? I think he did. I THINK he did. I hope he did, because I recently agreed to serve as a ‘review editor’ for Frontiers in Plant Science [that’s my full disclosure, folks]. From everything I can tell, they are completely above-board. If someone can convince me otherwise (and I AM listening), I will turn on them like Trump on Cohen. That said, Beall only ever claimed to have identified “potential, possible, or probable” predatory publishers. I think his website was a valuable resource, and I miss it (Say it ain’t so! Beall’s list shuts down).

Beall’s list is archived at https://beallslist.weebly.com/, but of course it’s not maintained, which is crucial given the rate at which predatory publishers spawn. I was looking for that the other day in response to a colleague’s question, and I thought, I’ll just check to make sure the original site is still down. I’m glad I did, because I came across one of the most egregious (and hilarious) examples of cybersquatting I’ve ever seen.

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In defense of preprints

At the end of July, I criticized an opinion piece that Tom Sheldon published in Nature, “Preprints could promote confusion and distortion“:

While the article casts preprints, preprint servers, and scientists who post their work to preprint servers as potential sources of misinformation, its arguments better support the case that science reporters should act more responsibly…What irks me is that I can’t find any hint in the article that Sheldon thinks journalists share the blame when they sensationalize bad science.

The latest issue of Nature includes three more critical responses to Sheldon’s nonsense.

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What’s a DOI?

Whenever possible, I try to link to a publicly accessible version of any scientific article I report on. Sometimes this is on ResearchGate, sometimes on an author’s academic website, sometimes even a course website. The benefit is that anyone can download and read the article; the downside is that these links sometimes disappear. Publishers issue takedown notices, academics change institutions, and courses end.

For these reasons, I usually provide, in addition to a publicly accessible link, a link that I can count on to not disappear (these appear at the end of the post, under “Stable Links”). Almost always, these are DOIs. DOIs are Digital Object Identifiers, persistent handles that are permanently assigned to particular documents. Almost all academic journals assign DOIs to all of their articles (Evolutionary Ecology Research is one exception, much to my annoyance), as do the preprint servers arXiv and bioRxiv and the digital data archive Dryad.

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Don’t dump and run

In the December issue of EMBO ReportsMatheus 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.

Sanitá Lima & Smith

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Not so fast

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.

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A valid point

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.

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PLoS ONE responds

PLoS ONE logo

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.

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Research Features: seems sketchy to me

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.

Research Features

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.

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bioRxiv gets a boost

bioRxiv

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.

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