Wired was more eloquent…

Macaca_nigra_self-portrait

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

Thunderdome

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

CritRevPaywall

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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Paywalls revisited

Say you think I’m full of it. Or Larry Moran is. Or ScienceNews, or Scientific American, or PhysOrg. One of us has written about a peer-reviewed paper, and you think maybe we’ve misrepresented it, or cherry-picked the bits we like, or you just want to read a more complete story. There’s good reason to be skeptical: news organizations (and bloggers) misunderstand, misrepresent, or exaggerate scientific studies all the time. But the article is behind a paywall, and you don’t want to have to shell out serious money every time you have your doubts. So you just have to take our word for it, right? Not usually.

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On paywalls

Screenshot 2016-03-03 07.58.23

No, you don’t have to pay to read this blog post. Or most scientific articles.

I often blog about peer-reviewed articles, and some of those articles are behind a paywall. There’s a large and growing trend toward open access journals, which charge the authors a publication fee and make their articles available to everyone for free, but this is far from universal. A lot of the big, high-profile journals, such as Science, Nature, PNAS, Ecology Letters, and Current Biology still charge for their articles. And the charges aren’t trivial. A typical scientific paper might cite 50-100 previous articles, and an author might have to read two or three times that many that don’t end up being cited. If you had to pay $38 for each one of those articles, you’d be a lot less inclined to do a thorough literature search.

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“…of the bignefs of a great corn of fand…”

Van Leeuwenhoek 1700 Figure 5

Figure 5 from van Leeuwenhoek 1700. “I thought convenient to get drawn one such before-mentioned particle, with the particles inclosed within it, as fig. 5 by E F sheweth.”

I usually try to comment on recent papers, but this time I’m going to go back a bit. More than a bit, really: 315 years, to what, as far as I know, is the first published report of Volvox (Van Leeuwenhoek, A. 1700. Part of a Letter from Mr Antony van Leeuwenhoek, concerning the Worms in Sheeps Livers, Gnats, and Animalcula in the Excrements of Frogs. Phil. Trans. Roy. Soc. London, 22:509–518). You know it’s old when half of the s’s look like f’s:

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Evolution of eusociality

Last month, two papers on the evolution of eusociality were published in high-profile journals: one by Karen M. Kapheim and colleagues in Science, the other by Sandra M. Rehan and Amy L. Toth in Trends in Ecology & Evolution (TREE). Social and eusocial insects are an attractive system for studying major transitions, sharing some of the key features that make the volvocine algae so good for this purpose: multiple, independent origins of traits thought to be important to the transition and extant species with intermediate levels of sociality. These features make the social insects, like the volvocine algae, well-suited for comparative studies.
Figure 1 from Rehan & Toth: (A) Overview of phylogeny of aculeate Hymenoptera (with the nonhymenopteran but eusocial termites as an outgroup), highlighting independent origins of sociality (colored branches), groups with species ranging from solitary to primitively social (green), primitively social to advanced eusocial (orange), solitary to advanced eusocial (blue), and all species advanced eusocial (grey). (B) The full range of the solitary to eusocial spectrum (blue) and predictions of which genomic mechanisms are hypothesized to operate at different transitional stages of social evolution (broken arrows).

Figure 1 from Rehan & Toth: (A) Overview of phylogeny of aculeate Hymenoptera (with the nonhymenopteran but eusocial termites as an outgroup), highlighting independent origins of sociality (colored branches), groups with species ranging from solitary to primitively social (green), primitively social to advanced eusocial (orange), solitary to advanced eusocial (blue), and all species advanced eusocial (grey). (B) The full range of the solitary to eusocial spectrum (blue) and predictions of which genomic mechanisms are hypothesized to operate at different transitional stages of social evolution (broken arrows).

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African Volvox in Montana

Ninepipe Reservoir

Ninepipe Reservoir near Charlo, MT. Photo by Aeravi.

Last summer, I hosted Drs. Hisayoshi Nozaki, Noriko Ueki, Osami Misumi, and two graduate students from the University of Tokyo, Kayoko Yamamoto and Shota Yamashita, to collect volvocine algae from Montana lakes. To our surprise, we found a species of Volvox (V. capensis) that had previously only ever been found in South Africa! Dr. Nozaki’s team identified the algae collected in Ninepipe Reservoir based on their morphology and DNA sequencing. South Africa and Montana: this is about as disjunct as a distribution can be. Is Volvox capensis a master of long-distance dispersal? Is its distribution actually cosmopolitan, and if so, why hasn’t it ever been found anywhere else?

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Expression and form: Arash Kianianmomeni on gene regulation

Kianianmomeni Figure 1

Figure 1 from Kianianmomeni 2015. Gene regulatory mechanisms behind the evolution of multicellularity. Model illustrating the role of gene regulatory mechanisms in the evolution of multicellular Volvox from a Chlamydomonas-like ancestor.

Arash Kianianmomeni’s latest paper in Communicative & Integrative Biology addresses the possible roles of gene regulation and alternative splicing in the evolution of multicellularity and cellular differentiation (Kianianmomeni, A. 2015. Potential impact of gene regulatory mechanisms on the evolution of multicellularity in the volvocine algae. Commun. Integr. Biol., 37–41. doi 10.1080/19420889.2015.1017175). The article is an ‘Addendum’ to a 2014 study by Kianianmomeni and colleagues in BMC Genomics. Communicative & Integrative Biology often invites authors to write these addenda after they have published a (usually high impact) paper elsewhere, providing authors the opportunity to publish material that was not included in the original paper due to space limitations or because it was opinionated or speculative. I may address the BMC Genomics article in a future post, but right now there is more new volvocine research than I have time to write about (it should be an exciting Volvox meeting this summer!).

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Evolutionary Transitions to Multicellular Life published

Iñaki Ruiz-Trillo and Aurora Nedelcu have recently edited a new book on the evolution of multicellularity, Evolutionary Transitions to Multicellular Life.  The 22 chapters are divided into five sections: “Multicellularity in the Tree of Life,” “Model-Systems,” “Theoretical Approaches,” “Genomics Insights,” and “Molecular Mechanisms,” and the forward is written by Nicole King. Volvox  shows up in the chapters by Susan C. Sharpe, Laura Eme, Matthew W. Brown and Andrew Roger (“Timing the origins of multicellular eukaryotes through phylogenomics and relaxed molecular clock analyses”); by myself and Aurora Nedelcu (“Volvocine algae: from simple to complex multicellularity”); by Cristian A. Solari, Vanina J. Galzenati and John O. Kessler (“The evolutionary ecology of multicellularity: the volvocine green algae as a case study”); by John O. Kessler, Aurora M. Nedelcu, Cristian A. Solari and Deborah E. Shelton (“Cells acting as lenses: a possible role for light in the evolution of morphological asymmetry in the volvocine algae”); and by Daniel Lang and Stefan A. Rensing (“The evolution of transcriptional regulation in the Viridiplantae and its correlation with morphological complexity”).

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