Just launched: a new open-access journal of vertebrate paleontology, brought to you by the University of Alberta, Canada! It’s called VAMP (Vertebrate Anatomy Morphology Palaeontology), and it charges no APC. Here’s a illustration from one of the two articles in its first issue.
VAMP uses the canonical open-access licence, Creative Commons Attribution 4.0 International (CC By), which means it fulfils both the letter and the spirit of the Budapest Open Access Initiative’s definition of OA.
It’s great that we in vertebrate palaeontology can add this journal to the roster of OA journals in our field, already including Palaeontologia Electronica, Acta Palaeontologica Polonica, Palarch’s Journal of Vertebrate Paleontology, The Fossil Record and others. (Plus of course there is lots of vertebrate palaeontology in PLOS ONE and PeerJ.) I think that as a field, we are ahead of the curve in making the transition towards an all-OA literature.
December 23, 2014
Arriving as an early Christmas present, and coming in just a week before the end of what would otherwise have been a barren 2014, my paper Quantifying the effect of intervertebral cartilage on neutral posture in the necks of sauropod dinosaurs is out! You can read it on PeerJ (or download the PDF).
Yes, that posture is ludicrous — but the best data we currently have says that something like this would have been neutral for Diplodocus once cartilage is taken into account. (Remember of course that animals do not hold their necks in neutral posture.)
The great news here is that PeerJ moved quickly. In fact here’s how the time breaks down since I submitted the manuscript (and made it available as a preprint) on 4 November:
28 days from submission to first decision
3 days to revise and resubmit
3 days to accept
15 days to publication
TOTAL 49 days
Which of course is how it ought to be! Great work here from handling editor Chris Noto and all three reviewers: Matt Bonnan, Heinrich Mallison and Eric Snively. They all elected not to be anonymous, and all gave really useful feedback — as you can see for yourself in the published peer-review history. When editors and reviewers do a job this good, they deserve credit, and it’s great that PeerJ’s (optional) open review lets the world see what they contributed. Note that you can cite, or link to, individual reviews. The reviews themselves are now first-class objects, as they should be.
At the time of writing, my paper is top of the PeerJ home-page — presumably just because it’s the most recent published paper, but it’s a nice feeling anyway!
A little further down the front-page there’s some great stuff about limb function in ratites — a whole slew of papers.
Well, I’m off to relax over Christmas. Have a good one, y’all!
November 5, 2014
Last night, I submitted a paper for publication — for the first time since April 2013. I’d almost forgotten what it felt like. But, because we’re living in the Shiny Digital Future, you don’t have to wait till it’s been through review and formal publication to read it. I submitted to PeerJ, and at the same time, made it available as a preprint (Taylor 2014).
It’s called “Quantifying the effect of intervertebral cartilage on neutral posture in the necks of sauropod dinosaurs”, and frankly the results are weird. Here’s a taste:
A year back, as I was composing a blog-post about our neck-cartilage paper in PLOS ONE (Taylor and Wedel 2013c), I found myself writing down the rather trivial formula for the additional angle of extension at an intervertebral joint once the cartilage is taken into account. In that post, I finished with the promise “I guess that will have to go in a followup now”. Amazingly it’s taken me a year to get that one-pager written and submitted. (Although in the usual way of things, the manuscript ended up being 13 pages long.)
To summarise the main point of the paper: when you insert cartilage of thickness t between two vertebrae whose zygapophyses articulate at height h above the centra, the more anterior vertebra is forced upwards by t/h radians. Our best guess for how much cartilage is between the adjacent vertebrae in an Apatosaurus neck is about 10% of centrum length: the image above shows the effect of inserting that much cartilage at each joint.
And yes, it’s weird. But it’s where the data leads me, so I think it would be dishonest not to publish it.
I’ll be interested to see what the reviewers make of this. You are all of course welcome to leave comments on the preprint itself; but because this is going through conventional peer-review straight away (unlike our Barosaurus preprint), there’s no need to offer the kind of detailed and comprehensive comment that several people did with the previous one. Of course feel free if you wish, but I’m not depending on it.
Gilmore Charles W. 1936. Osteology of Apatosaurus, with special reference to specimens in the Carnegie Museum. Memoirs of the Carnegie Museum 11:175–300 and plates XXI–XXXIV.
Stevens, Kent A., and J. Michael Parrish. 1999. Neck posture and feeding habits of two Jurassic sauropod dinosaurs. Science 284(5415):798–800. doi:10.1126/science.284.5415.798
Taylor, Michael P., and Mathew J. Wedel. 2013c. The effect of intervertebral cartilage on neutral posture and range of motion in the necks of sauropod dinosaurs. PLOS ONE 8(10):e78214. 17 pages. doi:10.1371/journal.pone.0078214
October 29, 2014
Just a quick post today, to refute an incorrect idea about open access that has unfortunately been propagated from time to time. That is the idea that if (say) PLOS were acquired by a barrier-based publisher such as Taylor and Francis, then its papers could be hidden behind paywalls and effectively lost to the world. For example, in Glyn Moody’s article The Open Access Schism, Heather Morrison is quoted as follows:
A major concern about the current move towards CC-BY is that it might allow re-enclosure by companies […] This is a scenario suggested by assistant professor in the School of Information Studies at the University of Ottawa Heather Morrison. As she explains, “There is nothing in the CC BY license that would stop a business from taking all of the works, with attribution, and selling them under a more restrictive license—not only a more restrictive CC-type license (STM’s license is a good indication of what could happen here), but even behind a paywall, then buying out the OA publisher and taking down the OA content.”
This is flatly incorrect.
Reputable open-access publishers not only publish papers on their own sites but also place them in third-party archives, precisely to guard against doomsday scenarios. If (say) PeerJ were made an offer they couldn’t refuse by Elsevier, then the new owners could certainly shut down the PeerJ site; but there’s nothing the could do about the copies of PeerJ articles on PubMed Central, in CLOCKSS and elsewhere. And of course everyone who already has copies of the articles would always be free to distribute them in any way, including posting complete archives on their own websites.
Let’s not accept this kind of scaremongering.
September 18, 2014
There is little enthusiasm for CC-BY […] in the field of political studies. […] It is clear that there is serious concern about the potential for work published under a CC-BY licence to be distorted and used inappropriately.
There may be concern, but it’s misplaced. Using CC By does not allow your work to be misrepresented. The human-readably summary of the licence clearly states, in its definition of the attribution clause: [Emphasis added]
You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
What does this mean? It means creationists can’t take our paper on sauropod neck anatomy, change it so that we seem to be advocating Intelligent Design, and post the result as though it’s our work. Instead, the terms of the licence require that they state that changes were made, and that they do not portray us as endorsing their use.
Really, I don’t see how much clearer or simpler the CC By licence could be. It’s 108 words long. For heavens’ sake, folks, go and read it. It’s ridiculous that we have academics, who are supposed to be trained in research and rigour, expressing flagrantly incorrect opinions about a hundred-word-long document that they’ve not even read.
September 2, 2014
A couple of weeks ago, more than hundred scientists sent an open letter to the AAAS (American Association for the Advancement of Science) about their new open-access journal Science Advances, which is deficient in various ways — not least the absurdly inflated article-processing charge.
Today I learn from email that there has finally been a response — of sorts. Editor-in-Chief Marcia McNutt had a long phone-call with Jon Tennant — one of the hundred-plus authors/co-signers. All we know about that call is (and I quote from Jon’s email account) “it became quite apparent that we would have to agree to disagree on many points”.
All I want to say is this. When a hundred scientists co-sign an open letter, it is TOTALLY UNACCEPTABLE for the response to take the form of a private telephone call with one of those authors.
Come on, AAAS. This is all about openness. Let’s see an open response: a substantive, non-patronising one which addresses the actual points made in the original letter.
Meanwhile, you may like to read this article at The New Statesman: Scientists criticise new “open access” journal which limits research-sharing with copyright. In finishes on this very clear note, courtesy of Jon Tennant:
The AAAS should be a shining beacon within the academic world for progression of science. If this is their best shot at that, it’s an absolute disaster at the start on all levels. What publishers need to remember is that the academic community is not here to serve them – it is the other way around.
August 15, 2014
This is an open letter concerning the recent launch of the new open access journal, Science Advances. In addition to the welcome diversification in journal choices for authors looking for open access venues, there are many positive aspects of Science Advances: its broad STEM scope, its interest in cross-disciplinary research, and the offering of fee waivers. While we welcome the commitment of the Association to open access, we are also deeply concerned with the specific approach. Herein, we outline a number of suggestions that are in line with both the current direction that scholarly publishing is taking and the needs expressed by the open access community, which this journal aims to serve.
The first of these issues concerns the licensing terms of the journal articles. The default choice of a non-commercial licence (CC BY-NC) places unnecessary restrictions on reuse and does not meet the standards set out by the Budapest Open Access Initiative. Many large funders, including Research Councils UK and the Wellcome Trust, do not recognise this as an open license. The adoption of CC BY-NC as the default license means that many researchers will be unable to submit to Science Advances if they are to conform to their funder mandates unless they pay for the upgrade to CC BY. There is little evidence that non-commercial restrictions provide a benefit to the progress of scholarly research, yet they have significant negative impact, limiting the ability to reuse material for educational purposes and advocacy. For example, NC-encumbered materials cannot be used on Wikipedia. The non-commercial clause is known to generate ambiguities and uncertainties (see for example, NC Licenses Considered Harmful) to the detriment of scholarly communication. Additionally, there is little robust evidence to suggest that adopting a CC-BY license will lead to income loss for your Association, and the $1,000 surcharge is difficult to justify or defend. The value of the CC BY license is outlined in detail by the Open Access Scholarly Publishers Association.
We raise an additional issue with the $1,500 surcharge for articles more than 10 pages in length. In an online-only format, page length is an arbitrary unit that results from the article being read in PDF format. Can the AAAS explain what the additional costs associated with the increased length are that would warrant a 50% increase in APC for an unspecified number of additional digital pages? Other leading open access journals, such as PeerJ, the BMC series, and PLOS ONE, offer publication of articles with unlimited page lengths. The extra costs create constraints that may adversely incentivize authors to exclude important details of their study, preventing replication and hindering transparency, all of which are contrary to the aims of scholarly publication. Therefore it seems counterproductive to impose this additional charge; it discriminates against researchers’ best effort to communicate their findings with as much detail as necessary.
We feel that the proposed APCs and licencing scheme are detrimental to the AAAS and the global academic community. As such, we recommend that Science Advances:
Offers CC BY as standard for no additional cost, in line with leading open access publishers, so authors are able to comply with respective funding mandates;
Provides a transparent calculation of its APCs based on the publishing practices of the AAAS and explains how additional value created by the journal will measure against the significantly high prices paid by the authors;
Removes the surcharges associated with increased page number;
We hope that you will consider the points raised above, keeping in mind how best to serve the scientific community, and use Science Advances to add the AAAS to the group of progressive and innovative open access scholarly publishers. We hope AAAS will collaborate with the academic community to facilitate the dissemination of scientific knowledge through a journal committed to fully embracing the principles of Open Access.
We kindly request that you allow your response(s) to be made public along with this letter, and look forward to hearing your response soon.
Signatories (please note that we do not formally represent the institutions listed):
- Jonathan P. Tennant, PhD student, Imperial College London (firstname.lastname@example.org, @protohedgehog)
- Timothée Poisot, University of Canterbury (email@example.com, @tpoi)
- Joseph R. Hancock, Montana State University-Bozeman (firstname.lastname@example.org, @Joe_R_Hancock)
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- François Michonneau, University of Florida (firstname.lastname@example.org, @FrancoisInvert)
- Michael P. Taylor, University of Bristol (email@example.com, @MikeTaylor)
- Graham Steel, Open Science, Scotland (firstname.lastname@example.org, @McDawg)
- Jérémy Anquetin, Section d’Archéologie et Paléontologie, Switzerland (email@example.com, @FossilTurtles)
- Emily Coyte, University of Bristol (firstname.lastname@example.org, @emilycoyte)
- Benjamin Schwessinger, UC Davis (email@example.com, @schwessinger)
- Erin C. McKiernan, independent scientist (firstname.lastname@example.org, @emckiernan13)
- Tom Pollard, PhD student, University College London (email@example.com, @tompollard)
- Aimee Eckert, MRes student, Imperial College London (firstname.lastname@example.org, @aimee_e27)
- Liz Allen, ScienceOpen, San Francisco (email@example.com, @LizAllenSO)
- Dalmeet Singh Chawla, Imperial College London (firstname.lastname@example.org, @DalmeetS)
- Elizabeth Silva, San Francisco (email@example.com, @lizatucsf)
- Nicholas Gardner, Marshall University (firstname.lastname@example.org, @RomerianReptile)
- Nathan Cantley, Medical Student, Queens University Belfast (email@example.com, @NathanWPCantley)
- John Dupuis, Librarian, York University, Toronto (firstname.lastname@example.org, @dupuisj)
- Christina Pikas, Doctoral Candidate, University of Maryland (email@example.com, @cpikas)
- Amy Buckland, Librarian, McGill University, Montreal (firstname.lastname@example.org, @jambina)
- Lenny Teytelman, www.zappylab.com, Berkeley, CA (email@example.com), @lteytelman)
- Peter Murray-Rust, University of Cambridge, UK (firstname.lastname@example.org), @petermurrayrust)
- Zen Faulkes, The University of Texas-Pan American, email@example.com, @DoctorZen)
- Robert J. Gay, The University of Arizona/Mission Heights Preparatory High School, AZ, USA (firstname.lastname@example.org, @paleorob)
- Peter T.B. Brett, University of Surrey, UK (email@example.com, @PeterTBBrett)
- Anders Eklund, Linköping University, Sweden (firstname.lastname@example.org, @wandedob)
- Johannes Björk, Institute of Marine Sciences, Barcelona, Spain (email@example.com, @AwfulDodger)
- William Gunn, Mendeley, London, UK, firstname.lastname@example.org, @mrgunn)
- Nitika Pant Pai, McGill University, Montreal, Canada (email@example.com) @nikkiannike
- Philippe Desjardins-Proulx, Ph.D. student (firstname.lastname@example.org, @phdpqc).
- Joshua M. Nicholson, PhD candidate Virginia Tech, VA and founder The Winnower, VA (email@example.com, @thewinnower)
- Scott Edmunds, GigaScience, BGI Hong Kong (firstname.lastname@example.org, @SCEdmunds)
- Steven Ray Wilson, University of Oslo (email@example.com, @stevenRayOslo)
- Stuart Buck, Vice President of Research Integrity, Laura and John Arnold Foundation (firstname.lastname@example.org, @stuartbuck1)
- B. Arman Aksoy, Ph.D. student, Memorial Sloan Kettering Cancer Center (email@example.com, @armish)
- Nazeefa Fatima, University of Huddersfield, UK (firstname.lastname@example.org, @NazeefaFatima)
- Ross Mounce, University of Bath, UK (email@example.com, @rmounce)
- Heather Piwowar, Impactstory, (firstname.lastname@example.org), @researchremix
- Avinash Thirumalai, Ph.D student, East Tennessee State University (email@example.com)
- Jason Priem, Impactstory (firstname.lastname@example.org), @jasonpriem
- Clayton Aldern, University of Oxford, UK (email@example.com, @compatibilism)
- Marcus D. Hanwell, Technical Leader, Kitware, Inc., (firstname.lastname@example.org, @mhanwell)
- Kristen L. Marhaver, NSF Postdoctoral Fellow, Carmabi Foundation (email@example.com, @CoralSci)
- David Michael Roberts, ARC Research Associate, University of Adelaide (firstname.lastname@example.org)
- Brian Hole, Ubiquity Press, UK (email@example.com, @ubiquitypress)
- Alexander Grossmann, University of Applied Sciences Leipzig, Germany and co-founder of ScienceOpen, Berlin/Boston (firstname.lastname@example.org, @SciPubLab)
- David L.Vaux, Assistant Director, The Walter and Eliza Hall Institute, Australia (email@example.com)
- John Murtagh, Repository Manager, London School of Hygiene and Tropical Medicine @LSHTMlibrary
- Alecia Carter, University of Cambridge, UK (firstname.lastname@example.org, @alecia_carter)
- Alex O. Holcombe, University of Sydney (email@example.com, @ceptional)
- Ignacio Torres Aleman, Cajal Institute, Madrid. Spain. (firstname.lastname@example.org)
- Sarah Molloy, Research Support Manager, Queen Mary University of London (email@example.com, @moragm23)
- John Lamp, Deakin University, Australia (firstname.lastname@example.org, @johnwlamp)
- Matthew Todd, The University of Sydney and Open Source Malaria, email@example.com)
- Anusha Seneviratne, Imperial College London (firstname.lastname@example.org, @anushans)
- Guido Guidotti, Harvard University (email@example.com)
- Joseph McArthur, Assistant Director, Right to Research Coalition(Joe@RighttoResearch.org, @mcarthur_joe)
- Carlos H. Grohmann, University of São Paulo, Brazil (firstname.lastname@example.org)
- Jan de Leeuw, University of California Los Angeles, (email@example.com)
- Jung H. Choi, Associate Professor, Georgia Institute of Technology (firstname.lastname@example.org)
- Ernesto Priego, Centre for Information Science, City University London, UK (Ernesto.Priego.email@example.com)
- Brian Pasley, University of California, Berkeley (firstname.lastname@example.org)
- Stacy Konkiel, Impactstory.org (email@example.com), @skonkiel)
- Elizabeth HB Hellen, Rutgers University (firstname.lastname@example.org)
- Raphael Levy, University of Liverpool (email@example.com)
- Paul Coxon, University of Cambridge (firstname.lastname@example.org)
- Nitika Pant Pai, McGill University, Montreal, Canada (email@example.com)
- David Carroll, Queen’s University Belfast (firstname.lastname@example.org, @davidecarroll)
- Jacinto Dávila, Universidad de Los Andes (email@example.com, @jacintodavila)
- Marco Arieli Herrera-Valdez, Universidad Nacional Autónoma de México (firstname.lastname@example.org, @brujonildo)
- Juan Pablo Alperin, Simon Fraser University, Canada (email@example.com)
- Jan P. de Ruiter, Bielefeld University (firstname.lastname@example.org, @JPdeRuiter)
- Xianwen Chen, Norwegian University of Life Sciences (email@example.com, @xianwen_chen)
- Jeanette Hatherill, Librarian, University of Ottawa, Canada (firstname.lastname@example.org, @jeanetteanneh)
- Katharine Mullen, University of California Los Angeles (email@example.com)
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- Lachlan Coin, University of Queensland and founder of Academic Karma (email@example.com @AcademicKarma )
- MooYoung Choi, Department of Physics and Astronomy, Seoul National University, Korea (firstname.lastname@example.org)
- Oscar Patterson-Lomba, Harvard School of Public Health (email@example.com)
- Rowena Ball, The Australian National University, Canberra, Australia (Rowena.Ball@anu.edu.au)
- Daniel Swan, Oxford Gene Technology, UK (Daniel.Swan@ogt.com @DrDanielSwan)
- Stephen Curry, Imperial College London, UK (firstname.lastname@example.org, @Stephen_Curry)
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- Sibele Fausto, University of São Paulo, Brazil (firstname.lastname@example.org @sibelefausto)
- Lorena A. Barba, George Washington University (email@example.com @LorenaABarba)
- Ed Trollope, Director, Things We Don’t Know CIC (firstname.lastname@example.org, @TWeDK)
- Stephen Beckett, Ph.D. student, University of Exeter (S.J.Beckett@exeter.ac.uk, @BeckettStephen)
- Andrew D. Steen, Department of Earth & Planetary Sciences, University of Tennessee, Knoxville (email@example.com, @drdrewsteen)
- Mari Sarv, Estonian Literary Museum (firstname.lastname@example.org, @kaskekanke)
- Noam Ross, Ph.D. Candidate, Ecology, University of California-Davis (email@example.com, @noamross)
- Erika Amir, Geologist, Massachusetts, USA (firstname.lastname@example.org, @geoflier)
- Martin Paul Eve, University of Lincoln (email@example.com, @martin_eve)
- Franco Cecchi, University of Florence (firstname.lastname@example.org)
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- Philip Spear, postdoc, Northwestern University (firstname.lastname@example.org)
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- Graham Triggs, Symplectic (firstname.lastname@example.org, @grahamtriggs)
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- Colleen Morgan, University of York (firstname.lastname@example.org @clmorgan)
- Kara Woo, National Center for Ecological Analysis and Synthesis, UC Santa Barbara (email@example.com, @kara_woo)
- Mathew Wedel, Western University of Health Sciences (firstname.lastname@example.org)