September 22, 2016
Judgmental readers will recall that I have dabbled in mammal skulls, thanks to the corrupting influence of my friend and colleague, Brian Kraatz. At the end of my last post on this sordid topic, I mentioned that Brian and Emma Sherratt were working on a version 2.0 based in 3D morphometrics. The first volley from that project was published today in PeerJ.
Happily for all of us, Brian and Em confirmed the relationship between facial tilt and locomotor mode that we first documented last year, using more taxa, more landmarks, and two more dimensions (Kraatz and Sherratt 2016: 12):
…in accordance with previous findings by Kraatz et al. (2015), facial tilt angle is correlated with locomotor mode (D-PGLS, F(2,17) = 11.13, P = 0.003), where lower facial tilt angle, meaning more pronounced cranial flexion, is found in cursorial species, and high angles are found in generalist species.
That’s just the most personally relevant tip of a very large, multifaceted iceberg, including a monster supplementary info package on FigShare with, among other things, 3D models of bunny skulls. It’s all free and awesome, so go have fun.
September 18, 2016
I have before me the reviews for a submission of mine, and the handling editor has provided an additional stipulation:
Authority and date should be provided for each species-level taxon at first mention. Please ensure that the nominal authority is also included in the reference list.
In other words, the first time I mention Diplodocus, I should say “Diplodocus Marsh 1878″; and I should add the corresponding reference to my bibliography.
What do we think about this?
I used to do this religiously in my early papers, just because it was the done thing. But then I started to think about it. To my mind, it used to make a certain amount of sense 30 years ago. But surely in 2016, if anyone wants to know about the taxonomic history of Diplodocus, they’re going to go straight to Wikipedia?
I’m also not sure what the value is in providing the minimal taxonomic-authority information rather then, say, morphological information. Anyone who wants to know what Diplodocus is would be much better to go to Hatcher 1901, so wouldn’t we serve readers better if we referred to “Diplodocus (Hatcher 1901)”
Now that I come to think of it, I included “Giving the taxonomic authority after first use of each formal name” in my list of
Idiot things that we we do in our papers out of sheer habit three and a half years ago.
Should I just shrug and do this pointless busywork to satisfy the handling editor? Or should I simply refuse to waste my time adding information that will be of no use to anyone?
- Hatcher, Jonathan B. 1901. Diplodocus (Marsh): its osteology, taxonomy and probable habits, with a restoration of the skeleton. Memoirs of the Carnegie Museum 1:1-63 and plates I-XIII.
- Marsh, O. C. 1878. Principal characters of American Jurassic dinosaurs, Part I. American Journal of Science, series 3 16:411-416.
August 31, 2016
As explained in careful detail over at Stupid Patent of the Month, Elsevier has applied for, and been granted, a patent for online peer-review. The special sauce that persuaded the US Patent Office that this is a new invention is cascading peer review — an idea so obvious and so well-established that even The Scholarly Kitchen was writing about it as a commonplace in 2010.
Well. What can this mean?
A cynic might think that this is the first step an untrustworthy company would take preparatory to filing a lot of time-wasting and resource-sapping nuisance lawsuits on its smaller, faster-moving competitors. They certainly have previous in the courts: remember that they have brought legal action their own customers as well as threatening Academia.edu and of course trying to take Sci-Hub down.
Elsevier representatives are talking this down: Tom Reller has tweeted “There is no need for concern regarding the patent. It’s simply meant to protect our own proprietary waterfall system from being copied” — which would be fine, had their proprietary waterfall system not been itself copied from the ample prior art. Similarly, Alicia Wise has said on a public mailing list “People appear to be suggesting that we patented online peer review in an attempt to own it. No, we just patented our own novel systems.” Well. Let’s hope.
But Cathy Wojewodzki, on the same list, asked the key question:
I guess our real question is Why did you patent this? What is it you hope to market or control?
We await a meaningful answer.
Just posting a few images from my impending talk at SVPCA this Thursday.
I’ve written about the recurrent laryngeal nerve before, in Wedel (2012) and in this post. It’s present in all tetrapods, from frogs and salamanders on up. The frog RLN is shown in ventral view above, and in lateral view below, both from Ecker (1889:plate 1, figures 114 and 115). I’ve highlighted the RLN in red in both. Perhaps not a monument of inefficiency, but still recurrent, and therefore dumb.
And in a giraffe – RLN in blue, nerve path to hindfoot phalanges in red. Hollow circles are nerve cell bodies, solid lines are axons.
And in the elasmosaur Hydrotherosaurus, same color scheme plus the nerve path to the tail in purple, base image from Welles (1943).
That’s all for now!
- Ecker, A. 1889. The Anatomy of the Frog. 478pp. Clarendon Press, Oxford.
- Wedel, M. J. 2012. A monument of inefficiency: The presumed course of the recurrent laryngeal nerve in sauropod dinosaurs. Acta Palaeontologica Polonica 57 (2): 251–256.
- Welles, S. P. 1943. Elasmosaurid plesiosaurs with descriptions of new material from California and Colorado. Memoirs of the University of California Museum of Paleontology 13: 125-254.
Long time readers may remember the stupid contortions I had to go through in order to avoid giving the Geological Society copyright in my 2010 paper about the history of sauropod research, and how the Geol. Soc. nevertheless included a fraudulent claim of copyright ownership in the published version.
The way I left it back in 2010, my wife, Fiona, was the copyright holder. I should have fixed this a while back, but I now note for the record that she has this morning assigned copyright back to me:
From: Fiona Taylor <REDACTED>
To: Mike Taylor <email@example.com>
Date: 15 August 2016 at 11:03
I, Fiona J. Taylor of Oakleigh Farm House, Crooked End, Ruardean, GL17 9XF, England, hereby transfer to you, Michael P. Taylor of Oakleigh Farm House, Crooked End, Ruardean, GL17 9XF, England, the copyright of your article “Sauropod dinosaur research: a historical review”. This email constitutes a legally binding transfer.
Sorry to post something so boring, after so long a gap (nearly a month!) Hopefully we’ll have some more interesting things to say — and some time to say them — soon!
July 18, 2016
As predicted, the popular and useful Social Sciences repository SSRN, having been acquired by Elsevier, is now being destroyed. Papers are being quietly vanished from SSRN, without their authors even being notified. This is happening even in cases when the copyright is held by the authors (who posted them, giving implicit permission for them to be redistributed), and even more astonishingly when papers are under Creative Commons licences. Details at PrawfsBlawg.
These are not the actions of a publisher acting in good faith.
As James Grimmelmann comments:
There’s no longer a point in deterring SSRN. Its new owners at Elsevier have made their true colors clear, and we as a community canot afford to centralize our scholarly communications in the hands of for-profit publishers.
It is time to depublish all of our articles from SSRN and walk away completely. It doesn’t matter if they reverse course now. We can’t trust them in the long run. It’s time to walk away from SSRN.
And as Tony Ross Hellaur puts in, an another comment on the same post (emphasis mine):
Anybody who bought Elsevier’s line that “both existing and future SSRN content will be largely unaffected” following the sell-off should now wake up. Elsevier is aggressive in enforcing copyright, and have the resources and scale to be able to make extreme judgements on what constitutes copyright violation and then to put the burden of proof on individual researchers to show otherwise.
The good news: Brandon Butler points out in the comments that there is a new and open alternative to SSRN: Announcing the development of SocArXiv, an open social science archive. SocArXiv has some very good people behind it. I hope it takes off, and that the zombie SSRN is rapidly defleshed.
July 12, 2016
A few months ago I got an email from Nathan Myers, who asked me:
Do you have advice for someone who wants to spin up a new OA journal? Is there automation for the boring parts? Is someone you know well versed in what to do?
In many ways, I’m the wrong person to ask: I’ve never started a journal, OA or otherwise, nor even served on an editorial board.
But, hey, I’m not one to let something like that stop me. So here’s what I told Nathan. I’m sure I missed a lot of important possibilities: please point them out in this comments. I’ll try to keep this post updated as the landscape changes.
There are several good options at this point.
The simplest and cheapest is probably to use Annotum, a WordPress plugin that helps with the review workflow. I’ve not used it myself, but I know it’s what PLOS Currents uses, so it’s obvious battle-ready. I’m not sure but I think you can use it as a theme in a wordpress.com-hosted free blog.
Open Journals Systems is a widely used software package for running open-access journals — IIRC they have more that 10,000 running installations worldwide. I’ve not used it, but it evidently has what it takes.
If you have some funding to cover production charges, or are able to charge an APC, you can use a full-service option from a low-cost OA publisher such as Ubiquity Press.
PeerJ’s system is widely liked — very easy for authors and reviewers to use. Its software is all on GitHub, though I think some work would be needed to tie it all together. If you have the software engineering chops, this may be the best option for performance/price ratio.