Thursday, October 29, 2009

Buying PDFs: Truth and Consequences

On-line journals are great. You get immediate access to the latest research and can download a fully searchable PDF for later use. Journal digitization has revolutionized the pace of science communication and increased the reach of formerly obscure journals. Through the wonders of the Internet, anyone can get access! Right?

Not so fast. On-line journals offer full benefits only to those whose institution has a subscription. If you don't have a subscription, you're out of luck. . .mostly. Thankfully, it is possible to buy PDFs of individual articles. Right?

Not so fast. It is indeed possible to buy PDFs of articles from most journals. . .if you can cough up the money to do so. Let's face it. PDFs are expensive. Ridiculously so. A three page note from Journal of Vertebrate Paleontology might cost nearly $30! A six page paper from Geology runs $25. [end of this post] Is it really worth it?

Big Problems
I won't pretend that journal sales don't support professional societies I care about. I won't pretend that publishers shouldn't get compensated for their services. I won't pretend that everything is going to turn open access tomorrow.

But, I'm not shy about saying that the current system stinks. No matter how you slice it, $30 for a PDF article is unaffordable for a typical consumer of paleontological publications. The new membership rates for the Society of Vertebrate Paleontology, which include electronic access to Journal of Vertebrate Paleontology, cost $115 for e-journal only. Assuming around 120 articles per year (a rough count for JVP in 2008), this works out to a little less than $1 per article (and remember that this assumes that 100 percent of membership dues go to the journal subscription - certainly not the case). Why is there a 3,000 percent markup for non-members? Wouldn't journals be able to get by with, perhaps, a 500 percent markup over the member rate? [IMPORTANT NOTE: I am not intending to single out JVP and SVP exclusively; nearly all journal publishers are guilty of this problem. . .it just so happens that JVP is the example most relevant to most readers here]

Let's put it another way. At the current costs of PDF articles, buying every single article in the journal would cost an individual around $3,600 per year.

And let's look at it from yet another angle. Institutional paper subscriptions to JVP are $270/year for US institutions (pre-Taylor & Francis switch; we don't yet know what the cost will be post-switch). This works out to an average of$2.25/article. . .for a format that is much more expensive to deliver than an electronic document!

And one last angle. . .the Mesozoic Birds: Above the Heads of Dinosaurs edited volume, which is a beautifully produced and scientifically important work, includes 20 articles, ships in hard cover and retails for $100 new. This works out to $5/article within the book. Contrast this with $30 or more for a single digital file.

Commenting in a recent thread here at the OSP, a librarian noted that libraries are paying between $2-$4 per PDF article when bought in bundles from for-profit publishers like Elsevier (which, incidentally, continues to post profits in the midst of the recession). Although it is certainly fair to have volume discounts (although the pricing schemes and the bundled journals are often rather dubious in practice), it is of dubious benefit to science to charge such a disproportionate rate to private individuals who are just trying to do some science.

Do these pricing schemes serve science? Do these pricing schemes serve the interests of the authors, who just want their work to be read?

Commonly Suggested "Solutions"
When the issue of paying for individual PDFs is brought up, there are often a number of "solutions" proposed. I put the word in quotes because, as explained below, none of these is fool-proof.

Why not write the author for a PDF?
In some cases, this is a good workaround. But it's never a perfect workaround. Sometimes authors are unresponsive, have changed email addresses, retired, or passed into the fossil record. In this case, the researcher in need of the paper is out of luck.

Why not post a PDF request to VRTPALEO or the DML?
In some cases, this is a workaround. . .one need only look at mailing list archives to see that this is a common strategy. But, PDF requests unfortunately carry a small annoyance factor for many list subscribers. Sometimes no one responds. Finally, PDF sharing by anyone other than the author is generally illegal in the eyes of the publishers and societies (but let's not pretend it doesn't happen).

Why not join the society, and then you get all of the articles as part of your membership?
Again, this is a solution in some cases. If you are a paleontological enthusiast or professional who loves (or needs) to follow every bit of the literature, you should probably join the Society of Vertebrate Paleontology and/or the Palaeontological Association and/or the Paleontological Society.

But, let's be realistic. Nobody can afford to join every society to get access to all society publications. In some cases, it's just not necessary. Consider this hypothetical situation. You're a population biologist working for a small nature preserve who wants a little background on the evolutionary history of the coyote. You do a search on Google, and find a citation to Journal of American Paleontology with an abstract that details ecological shifts by coyotes during the Ice Age using isotopic analysis. You click on the link, and. . .paywall! The Society of American Paleontology wants $30 for a five page article. Is it really worth your time and money (as a population biologist) to join a society of paleontology, when you are already stretching your budget to cover dues for two more relevant societies? If the charter for the American Paleontological Society says that they are to promote and advance the science of paleontology, is the society really living up to this mandate? If the society wants to foster cross-discipline appreciation for the relevance of the field, is this happening if the research is not easily accessible? Are the authors who contribute to the journal being well-served by having their research so restricted?

Finally, some journals just aren't sponsored by societies. There is no solution in this case, other than to pay a few hundred dollars per year.

Most of the other journals charge $30 for a PDF!
This is not a solution (or even a "solution"), but an excuse. During the business meeting for a scholarly society to which I belong, I raised a concern about the prices that the society's journal was charging for individual PDFs. Can you guess the answer that I received? I remember something my mother often said to me. . ."If everyone else jumped off a cliff, would you too?" Exorbitant PDF costs may be the norm, but that doesn't mean it's the ethical thing to do (especially for a non-profit society whose stated mission includes phrases like "advance the science" and "serve the common interests").

What Needs to Change?
Science (yes, that's the reason why most research is published) is not being served by the current pricing schemes. Alleged solutions for those beyond the boundaries of the pay-wall are not comprehensive, and again do not serve the interests of science.

PDFs of individual articles need to cost less. There is no way to legitimize charging $25, $30, or more for something that costs less to produce than a printed journal, particularly when it prices out to up to a 3,000 percent markup. The current pricing scheme restricts the readership of articles and creates a hierarchy of have- and have-not researchers, in a time when the Internet is supposed to fix these problems for academia. Also, let's not forget that the research behind these articles is often heavily subsidized by public tax dollars. . .

I would suggest that $5, or maybe $10 in exceptional circumstances (e.g., a 50 page monograph) is a cost that I would be willing to pay for a PDF. I would also submit that many journals would see increased PDF sales (particularly for popular topics, such as dinosaurs) if the price was set at something mere mortals could afford to pay.

Is There a Solution?
Right now, it sounds like I'm doing a lot of complaining and not a lot of problem solving. Well. . .yes. This post is partly a rant. Unless people are aware of the problem, nothing will ever happen.

So what can we do? Here are a few suggestions:
  • Ask journals and professional societies to consider the implications of pricing schemes for PDFs. Speak out to the people who matter. Let them know how you feel, and how it affects you.
  • Don't pay the ridiculous charges. Find low-cost, legal alternatives (e.g., writing to the author or interlibrary loans) whenever possible.
  • Submit your work only to journals with researcher-friendly publishing policies.
  • If you are an author, do everything you (legally) can to get your work out there for free. If the journal allows you to post a PDF, do so. Respond promptly to PDF requests from other individuals.
What are your thoughts?

Addendum 1: As if by magic, this post at The Scholarly Kitchen appeared at nearly the same instant as I hit the "publish" button on this post. I haven't followed up on the service (which essentially offers cheap rental access to articles from various scientific publishers), but will certainly be looking into it.

Addendum 2: Matt over at Protichnoctem has a nice post with more on the issue of buying PDFs. Go check it out!

The Journal List
The Anatomical Record (Wiley): $29.95
Bulletin of the Geological Society of America (GSA): $25 (GSA website)
Bulletin of the Geological Society of America (GSA): $32 (Geoscience World website)
Cretaceous Research (Elsevier): $31.50
Geology (GSA): $25 (GSA website)
Geology (GSA): $32 (Geoscience World website)
Ichnos (Taylor & Francis): $37
Journal of Experimental Biology (The Company of Biologists): $10
Journal of Morphology (Wiley): $29.95
Journal of Paleontology (Paleontological Society): $12 (BioOne website)
Journal of Paleontology (Paleontological Society): $15 (Geoscience World website)
Journal of Vertebrate Paleontology (SVP): $30 (BioOne website)
Nature (Nature Publishing Group): $32
Palaeogeography, Palaeoclimatology, Palaeoecology (Elsevier): $31.50
Paleobiology (Paleontological Society): $12 (BioOne website)
Paleobiology (Paleontological Society): $15 (Geoscience World website)
Palaeontology (Wiley): $29.95
Proceedings of the National Academy of Sciences (NASUSA): $10 ($25/full journal access for seven days)
Science (AAAS): $15

Wednesday, October 28, 2009

A Happy Family of Pachycephalosaurus

ResearchBlogging.orgDistinguishing the skulls of juveniles and adults of the same species, and sometimes different species, can be a prickly thing in the fossil record. The result is that paleontology is littered with juvenile fossils that have been considered adults at some time or another. The crested duck-billed dinosaur Corythosaurus has also been known under names like Procheneosaurus, the famous Monoclonius is actually a juvenile of adult Centrosaurus, Styracosaurus, and kin, and the debate still continues on whether Nanotyrannus is a juvenile Tyrannosaurus.

Yesterday in the open access journal PLoS ONE, paleontologists Jack Horner and Mark Goodwin published a long-awaited paper positing synonymy for a trio of iconic (and melodiously-named) dinosaurs. The bone-headed dinosaurs Pachycephalosaurus, Stygimoloch, and Dracorex are all one and the same animal, according to their work. The latter two are juvenile stages, whereas Pachycephalosaurus represents a full adult.

Skulls of Pachycephalosaurus (top), Stygimoloch (middle; the front of the skull is missing), and Dracorex (bottom; the skull is crushed from top to bottom). In particular, note the changes in skull size and similarities in spike placement. Modified after the original in Horner and Goodwin 2009.

How is this possible? The animals look so different, right? Pachycephalosaurus has this big bowling ball on top of its head, which the other two lack. Stygimoloch has a uniquely-shaped, narrow dome, and Dracorex has a completely flat head. Furthermore, Pachycephalosaurus lacks the elongated spikes that make the other two look so fearsome.

Well, it turns out that this can all be attributed to ontogenetic changes (i.e., change as the animals get older). Horner and Goodwin assemble multiple lines of evidence for this hypothesis.

First, the skulls of Dracorex, Stygimoloch, and Pachycephalosaurus form a size gradation from smallest to largest--exactly what one would expect for a growth series. By itself, this is not irrefutable proof, of course--it could just be that Dracorex had a small adult size compared to Pachycephalosaurus.

Second, many of the knobs and bumps on the skulls can be matched up one for one between individuals of the various specimens. Alternatively, one would also expect that closely related (but different) species might have similar patterns of bumps. As Horner and Goodwin admit, there is some variation between individuals of the different "species"--but, the authors also note that this sort of variation is entirely expected and occurs even within undisputed adult Pachycephalosaurus.

Third, specimens of Stygimoloch, both in CT scans and physically cut specimens, show an open suture between the two frontal bones of the dome. Pachycephalosaurus domes are completely fused up. Open sutures are often strong indications that an animal is still growing--and, it's particularly intriguing that a small "species" has them but a large "species" doesn't!

Finally, microscopic examination of the bones in two of the three "species" (Stygimoloch and Pachycephalosaurus; there weren't any Dracorex available for cutting up) shows that Stygimoloch was still growing (and thus not a full adult)--but Pachycephalosaurus specimens weren't growing much at all (and therefore were probably full adults).

Any one of these lines of evidence might be interesting, but not completely convincing. Taken together, however, they make a pretty compelling case that Dracorex and Stygimoloch are juvenile Pachycephalosaurus. Because Pachycephalosaurus was named first, the first two become junior synonyms. It's a shame, because they're such cool names!

As for duckbilled dinosaurs, horned dinosaurs, and even modern crested birds like the cassowary, the story in the pachycephalosaurs suggests that weird ornaments on the skull were something that happened only as the animals approached full size. The domes practically appeared overnight! The teenage years must have been a real headache for these dinosaurs.

Thanks to the wonders of open access, the article is freely available for all to read. Additionally, it is worth taking advantage of the rating and comment features at PLoS ONE [disclaimer: I am a section editor for that journal]. . .few other scientific publications allow the readers to annotate the papers directly!

Horner, J., & Goodwin, M. (2009). Extreme cranial ontogeny in the Upper Cretaceous dinosaur Pachycephalosaurus. PLoS ONE, 4 (10) DOI: 10.1371/journal.pone.0007626

Wednesday, October 21, 2009

The ODP in Nature

I finally managed to publish in Nature (along with Mike Taylor and Matt Wedel)! Ok, it's only a glorified letter to the editor. But we still won't complain. Our contribution [subscription required; I know, it's ironic] focuses on the issue of data sharing in paleontology. It's partly a plea for greater data availability, and partly an advertisement for the Open Dinosaur Project. For more details, see my post at the ODP project blog.

Farke, A. A., M. P. Taylor, and M. J. Wedel. 2009. Public databases offer one solution to mistrust and secrecy. Nature 461: 1053. [link; subscription required]

Tuesday, October 20, 2009

Open Access Recap

Continuing with our Open Access Week theme, I wanted to highlight some previous posts on the issue here at the Open Source Paleontologist. In other words, I don't have time to write a more comprehensive post right now. So, enjoy these old ones!

Greatest Hits of Open Access at OSP
Open Access Publishing and the Paleontologist
Open Access Journals in Paleontology
Rating Open Access Journals in Paleo - Intro, I, II, III, IV
My Dissertation - Now Open Access
Aetosaurs and the Open Access Dissertation

Monday, October 19, 2009

It's Open Access Week!

October 19 - October 23 is designated Open Access Week, in order to raise awareness of open access publication and scholarship. So, I'll be blogging a little bit more about open access during the next few days.

For my first post, I wanted to clarify a common confusion that I hear from many colleagues: open source vs. open access. Although the terms are related in some ways (indeed, they derive from a very similar philosophy), they refer to two discrete concepts.

Open Access: Focuses on the unrestricted sharing of research results, typically through open access journals (PLoS ONE, Palaeontologia Electronica, etc.).

Open Source: Computer software, typically (but not always) freely distributed, in which the source code is freely available. There are a host of other stipulations in some definitions, which are largely an elaboration upon this point.

Thus, PLoS ONE is open access; 3D Slicer is open source.

Thursday, October 15, 2009

More on JVP's Big Switch

Astute paleontologists are likely aware by now of major changes ahead for the Society of Vertebrate Paleontology's Journal of Vertebrate Paleontology, announced in July and detailed in this blog post. The journal has grown at a tremendous rate, and something needed to be done in order to ensure continued high quality, timely publication, and financial viability into the foreseeable future. After extensive research, the decision was made to partner with commercial publisher Taylor & Francis.

Of course, many questions remained for those of us who follow issues of academic publishing and access to publications. What would happen to copyright of articles? Who gets the profits from sales of the journal? Would authors still be able to post a PDF on their website? So, I drafted an email and sent it along to the relevant folks in SVP's leadership.

I am now happy to say that an extensive list of FAQs, responding to questions from me and other folks, is now posted at SVP's website [link to PDF]. Every single one of my questions (and others) was addressed, in detail. My sincere thanks goes to the individuals at SVP who put this together! Major points (and some commentary) follow:

Copyright will stay with the Society of Vertebrate Paleontology (as appropriate - publications produced by many government workers should be exempted), as has been the case in the past. This is a Good Thing.

Is This Forever?
The contract lasts five years - so, SVP has the option to find another publisher or renegotiate at the end of this period. Again, a Good Thing. This also means, however, that those society members with an interest in commenting on or influencing the renewal process have about three (or at most four) years to wait before springing to action. Mark your calendars for SVP 2012 and 2013. Given the rapid pace at which academic publishing is changing right now, it will certainly be worth taking a close look at the conditions of journal publication in a few years.

Author Benefits
In the new publishing arrangement, authors will benefit from faster publication (by going from four issues a year to six). This is, of course, a major plus. Other benefits are, in my opinion, slightly more mixed. Gone are the days when we can (legally) pay an affordable fee for the right to post the PDF of our published work to a personal web page. We will, however, receive a PDF that can be emailed to colleagues and those who request it. This unfortunately represents a step backwards for the (legal) distribution of paleontological information. As a consolation prize, though, we get 50 free paper reprints of our articles! [editorial note: I had a rant written on this topic, but decided against including it here in the end. Suffice it to say that I personally find paper reprints less than useful in this day and age, recognizing that others may not share this opinion]

Open Access
It is probably no surprise that JVP will not be going to an open access model, even a delayed open access model. On a small positive note, authors now have the option of purchasing complete open access for their article (presently, to the tune of $3,250) through Taylor & Francis's iOpenAccess program.

Final Thoughts
It's still far too early to know for sure how JVP's transition to Taylor & Francis will work out. As mentioned above, the world of academic publishing is changing. Only time will tell if the switch is a Totally Good Thing or not.

Saturday, October 10, 2009

The Paleo Paper Challenge: Roll Call!

The Paleo Paper Challenge, sponsored by Dave Hone of Dave Hone's Archosaur Musings and me, is nearly a month in. At last count, we have 22 23 participants! That's a lot of science going on.

Of course, what's the point of having a challenge without being challenged just a little bit? The whole point of this is to nudge. . .cajole. . .motivate. . .humiliate. . .all of us into finishing up those nagging papers. With less than three months to go, it's time to start kicking things into overdrive.

PPCers: Now it's time to make good on your promises. In the comments below, drop a note to tell us how you're doing! It's upon all of us to make each other finish these papers!

I'll start. I've committed to finishing a paper on a Myledaphus tooth site, as well as finish up revisions on one of my dissertation chapters. Right now, I'm ashamed to say that I haven't done a thing. But, the good news is that the dissertation chapter is on my priority list for the coming week. Readers: if I don't indicate any progress by Friday, you are allowed. . .nay, required. . .to publicly humiliate me. And while you're at it, get to work on your own papers!

That is all.

Sunday, October 4, 2009

The Paleo Paper Challenge in the Blogosphere

The Paleo Paper Challenge is now in full swing! At just under 20 participants (and please let me know if I've inadvertently left you off the list!), some serious science is going to be happening in the next few months. Dave and I are seriously excited about the turnout.

In my casual internet browsing, I've noticed that a few of you have blogged about your efforts on the PPC (or at least mentioned them in passing). Here's a quick run-down of some of the links - once again, please let me know if I've left anyone out! And if you're a blogger, but haven't blogged about your participation, why not give it a try now?

Dave Hone's Archosaur Musings (Dave Hone; only most recent post included here): Return of the PPC, post SVP (& SVPC), OK?
Dinochick Blogs (ReBecca Hunt): Only 88 Days Left
El Pakozoico (Pak): Paleo Paper Challenge!
SV-POW! (Mike Taylor): Electronic Publishing is Inevitable, and Even the ICZN is Beginning to Accept It
Thoughts and Ideas from a Paleo Punker (Tor Bertin): The Paper Paper Challenge

Friday, October 2, 2009

The Paleo Paper Challenge: Post-SVP

In the event that you were trapped under a building for the past two weeks, the annual Society of Vertebrate Paleontology meetings have come and gone. Not only do these meetings provide a nice outlet for ongoing research, they also provided an opportunity for me and Dave to 1) recruit more participants for the Paleo Paper Challenge; and 2) nag everyone to get to work on their papers, already! With the SVP recruits and new volunteers from the comment threads of this blog, the Paleo Paper Challenge is rounding out nicely. Oh yeah, and I finally got to meet Dave Hone in person.

Acceptors of the Paleo Paper Challenge
Brian Beatty
Calvert Formation terrestrial mammals review with Ralph Eshelman

Tor Bertin:

Statistical analysis of evolution of sauropod body size, involving a mystery specimen
Spinosauridae review

Lisa Buckley

Papers to be decided

Andrea Cau:
Description of metriorhynchid from northern Italy

Andy Farke:
Myledaphus paper
Final dissertation chapter

John Foster:
Morrison critter paper

Francisco Gasco:
Master's thesis

Mike Habib:
Pterosaur flight range

Penny Higgins:
Bulk isotopic ratios from tooth enamel and general interpretation of environment

Casey Holliday:
Articular cartilage paper

Thomas Holtz:
Tyrannosaur heterochrony/paleoecology

Dave Hone:
Unspecified paper

ReBecca Hunt:
Mygatt-Moore taphonomy paper

Nick Gardner:
Unspecified paper with Mickey Mortimer

Chris Note and Ari Grossman:
Dinosaur ecomorphology

Bill Parker:
Revueltosaurus manuscript

Heinrich Mallison:
sauropods rearing
sauropodomorph rapid locomotion

Anthony Maltese:
Unspecified paper

Mark Mancini:
Redondosaurus cranial description (with Axel Hungerbuehler)

Eric Snively:
Chicken electromyography and implications for big theropod neck muscles
Atlas of gekkotan lizards of the Paris Basin
Artiodactyl vs. Stegoceras head-strike mechanics

Mike Taylor:
The Archbishop description

Matt Wedel:
Final dissertation chapter

Adam Yates:
Early sauropodomorph pneumaticity
Rauisuchians of the Elliot Formation

Thursday, October 1, 2009

A Veritable Paleo-Blizzard from PLoS ONE

I'm just back from SVP/associated collections visits, enjoying the post-SVP glow of research motivation as well as a big pile of things on my "to-do" list. Among these are an update of the Paleo Paper Challenge, commentary on the new Journal of Vertebrate Paleontology publication contract, and much more.

In the meantime, I wanted to call your attention to a whole blizzard of paleontology-relevant publications that have been unleashed from the on-line, open access journal PLoS ONE during the past two weeks. Although I'm an admittedly biased opinion (I am an academic editor for the journal), it is quite nice to see so many interesting and relevant paleontology publications within PLoS ONE's "pages." I am short on time, and many of these articles were covered in depth by other bloggers, so I'm just posting the references this time around.

The Papers
Arribas A, Garrido G, Viseras C, Soria JM, Pla S, et al. (2009) A Mammalian Lost World in Southwest Europe during the Late Pliocene. PLoS ONE 4(9): e7127. doi:10.1371/journal.pone.0007127

Hocknull SA, Piper PJ, van den Bergh GD, Due RA, Morwood MJ, et al. (2009) Dragon's Paradise Lost: Palaeobiogeography, Evolution and Extinction of the Largest-Ever Terrestrial Lizards (Varanidae). PLoS ONE 4(9): e7241. doi:10.1371/journal.pone.0007241

Kröger B, Servais T, Zhang Y (2009) The Origin and Initial Rise of Pelagic Cephalopods in the Ordovician. PLoS ONE 4(9): e7262. doi:10.1371/journal.pone.0007262

Spaulding M, O'Leary MA, Gatesy J (2009) Relationships of Cetacea (Artiodactyla) Among Mammals: Increased Taxon Sampling Alters Interpretations of Key Fossils and Character Evolution. PLoS ONE 4(9): e7062. doi:10.1371/journal.pone.0007062

Wolff EDS, Salisbury SW, Horner JR, Varricchio DJ (2009) Common Avian Infection Plagued the Tyrant Dinosaurs. PLoS ONE 4(9): e7288. doi:10.1371/journal.pone.0007288 [Note--Ewan Wolff, the senior author on this paper, was my co-author on the "fighting Triceratops" paper that came out earlier this year. Nice to see more paleopathology stuff out there!]