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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Rediscovered after two thirds of a century: Pleodorina sphaerica

Pleodorina sphaerica

Figure 1 from Nozaki et al. 2017. Pleodorina sphaerica.

There really aren’t enough people looking for volvocine algae. There’s a suspicious tendency for the geographical centers of volvocine diversity — southern Africa, central North America, southeast Asia — to include the home institutions of phycologists studying volvocine diversity — Mary Pocock, Richard Starr, Hisayoshi Nozaki, respectively. I find it much more likely that this is an artifact of sampling effort than that, for example, central Africa and Central and South America are depauperate of volvocine algae.

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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).

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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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Chance favors the minute animalcule: John Tyler Bonner on randomness


A colleague recently (well, not that recently; sorry, Art) lent me a copy of John Tyler Bonner’s latest bookRandomness in Evolution. Dr. Bonner is emeritus faculty at Princeton University, where he has been since 1947, shortly after World War II interrupted his Ph.D. studies. Among many other contributions, Bonner was a pioneer in the development of the social amoeba (or cellular slime mold) Dictyostelium discoideum as a model system for multicellular development and cell-cell signaling. A member of the National Academy of Sciences and a fellow of the American Association for the Advancement of Science, he has published over twenty books and mountains of peer-reviewed papers.

As much as David Kirk’s Volvox, Bonner’s books The Evolution of Complexity and First Signals: The Evolution of Multicellular Development influenced my decision to study Volvox in grad school. I had the pleasure of meeting Dr. Bonner in 2009 when, as a graduate student, I invited him to give a departmental seminar at the University of Arizona. It really was a pleasure; this is someone who thinks deeply about big questions and has made important contributions to understanding many of the answers.

The central argument of the new book is that randomness plays a larger role, relative to natural selection, in the morphology of small organisms than that of large ones. Typically of Bonner’s work, the book is coherent, readable, and full of fascinating examples. Although the cellular slime molds are his primary study organism, Bonner has long had an interest in, and interesting things to say about, Volvox, so I was excited to read his most recent thoughts.

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Wired was more eloquent…


Self-portrait of a female Celebes crested macaque (Macaca nigra) in North Sulawesi, Indonesia. Public domain image from Wikimedia Commons.

…but I think I was more succinct. Ryan Merkley, CEO of Creative Commons, has a new article about Sci-Hub on Wired:

If it wasn’t so well-established, the traditional model of academic publishing would be considered scandalous. Every year, hundreds of billions in research and data are funded, in whole or in part, with public dollars. We do this because we believe that knowledge is for the public good, but the public gets very little access to the fruits of its investment. In the US, the combined value of government, non-profit, and university-funded research in 2013 was over $158 billion—about a third of all the R&D in the US that year. Publishers acquire this research free of charge, and retain the copyrights, even though the public funded the work. Researchers aren’t paid by publishers for their research as it’s sold piece-by-piece or by subscription through academic journals. The reviewers who evaluate the research aren’t paid either. So we pay for it, and then we have to pay again if we want to read it.

My slightly abridged version of this sentiment [PG-13 below the fold]:

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Dual first authors


A forthcoming paper in Philosophy of Science has dual first authors, Kate E. Lynch and Pierrick Bourrat (I’ve written about Dr. Bourrat’s work previously, which is part of the reason this is on my radar):

Author order has been decided randomly, therefore both authors are first authors. KEL and PB contributed equally to the manuscript. KEL’s distinct contribution was the ideas developed in Section 3. PB’s distinct contribution was the ideas developed in sections 4 and 5 and the equations in Section 3. Other sections received equal contributions from both authors.

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F paywalls


Sure, I have $2000 a year to spend on this one journal.

I’ve written twice before about paywalls and how to get around them (On paywalls, Paywalls revisited). Paywalls pop up when you try to read a peer-reviewed article that you don’t have access to. If you work at a university, museum, or other research institution, you probably see these only every once in a while, because most such institutions have subscriptions to most of the big journals. Otherwise, you’re pretty much out of luck. [Warning: PG-13 below the fold]

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