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


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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Two more tools for (legally) avoiding paywalls


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.

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Say it ain’t so! Beall’s list shuts down

I hate it when a resource I rely on stops working. First it was igoogle, then Google Reader (necessitating a switch to Feedly, which I don’t like as well). Now it appears that Scholarly Open Access, the website that hosts Beall’s List of predatory open-access publishers, has shut down (I found out about this from Retraction Watch).

Screenshot 2017-01-18 08.41.00 [Read more…]


I’m resorting to name-calling, and I don’t even know who I’m talking about.

Retraction Watch carries the story of a peer reviewer who published a paper he or she reviewed as his or her own. Stole the paper, in other words:

…after Michael Dansinger of Tufts Medical Center realized a paper he’d submitted to Annals of Internal Medicine that had been rejected was republished, and the journal recognized one of the reviewers among the list of co-authors, it published a letter from Dansinger to the reviewer, along with an editorial explaining what happened.

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