PeerJ—What Does It Mean for Paleontology?

For those following open access issues, the arrival of PeerJ has been hotly anticipated (see this link round-up). We all knew Pete Binfield--someone with years of experience in academic publishing and, until recently, publisher of PLoS ONE--was associated with the project, so it wasn't likely to be a half-baked scheme. The big day of announcement finally arrived yesterday, and things look even more innovative than expected. So, what does this mean for us paleontologists?

First, a little background on PeerJ. It's a new journal, falling squarely in the online and open access (CC-BY) categories. Editorial criteria are similar to those for PLoS ONE (scientific and methodological soundness count; perceived impact or splashiness don't). All of this is pretty typical; but the rest ain't.

Innovation
One of the most common fears of open access publishing is that it can cost a lot of money for authors, a particularly big concern in an underfunded field like paleontology. Free open access journals (like Palaeontologia Electronica) and fee waivers (as for PLoS ONE) can fill the gaps, but most mandatory open access fees are otherwise unaffordable for the typical paleontology lab budget (assuming there is a budget for the lab). PeerJ attempts to fill in this gap, while paying for the costs of open access. Things get pretty interesting as a result.

The conventional open access model is to pay per publication; once a paper is accepted, you pay the $2,000 or $1,350 or whatever to subsidize production costs. PeerJ front-loads this in a unique way; each author pays a one-time membership fee, which is then good for life! Depending on what category of membership you buy, you then can publish one, two, or an unlimited number of publications yearly. These lifetime membership fees are quite reasonable, too. They start at $99, and culminate at $259 (fees go up slightly after September 1). Fee waivers are available for those in developing countries.

So what's the catch? Members are expected to review one paper yearly (either as a full-blown peer reviewer, or as a post-publication commenter). Additionally, each author on a paper (up to the twelfth author) must be a member. How does that translate financially? Let's say I want to publish a paper, and have three co-authors. Assuming each of us is only publishing in PeerJ once a year, that translates to $99 per person. With four total authors, the cost is $396. If one of my co-authors and I later publish another paper, the cost for that one is $0. Same cost for the third paper. That's three open access articles for $132 each. This is definitely an encouragement to continue publishing with PeerJ.

Other good things
PeerJ is pretty savvy, and has covered its electronic bases (see their FAQ). The journal will be edited by an independent academic editorial board, an author's membership category doesn't factor into decisions, and content is archived via CLOCKSS. The journal has plans to get an impact factor (which will take three years) and to get indexed in the major services. These are all carefully thought-out, and within (or exceeding) professional standards for publishing.

As another incentive, PeerJ offers a preprint service (free if you only post one a year). Physicists have arXiv, where they can post unpublished manuscripts for community commentary. However, there isn't really such a central repository for the biosciences (especially since the demise of Nature Precedings). Thus, PeerJ is filling a community need (even if we paleontologists don't yet realize the advantages of preprints).

What's needed now?
This journal is surely within the realm of interest for paleontologists, and those of us who support open access publishing will follow it pretty closely. Because the journal has yet to officially launch, some details are still hazy. In order to be of maximum use to paleontologists, I hope to see the following things (in roughly ascending order of difficulty):

• Clear guidelines for nomenclatural acts. These should follow recommendations from the ICZN and ensure that any new species erected within PeerJ are valid.
• A clearly designed, paleontology-specific ethics policy. Standards should be in line with those used by organizations such as the Paleontological Society and Society of Vertebrate Paleontology, and ideally would mandate that all specimens discussed in PeerJ are reposited in appropriate institutions. The last thing the journal needs is to be filled with papers on illegal Chinese specimens or thinly-veiled advertisements for fossils on the commercial market.
• A strong editorial board with a respected paleontologist (or paleontologists). In order to get community buy-in, we need to see that the person who handles our manuscripts is qualified, trustworthy, and fair. Paleontologists are also rather skittish; we won't publish in a new venue unless someone else tests the waters first (judging by the pattern in PLoS ONE).
• Strong impact factor and community perception. We all hate impact factors (or at least say we do, right before hitting the submit button on that article for Nature which we know will be rejected but hey we have to try anyhow just in case), but it's sadly a reality for those who want to get jobs and grants. Early-career scientists are likely to be a little wary of submitting their very top stuff to PeerJ, at least until the journal is a little more established. It sucks for the researchers and for the journal, but that's just the way it is. PLoS ONE faced a similar hurdle (and still does, to some degree), and only time can defeat it. Positive word-of-mouth will also help immensely.

Given the experience of the staff at PeerJ with academic publishing, I have all confidence that these issues will be addressed when the formal editorial guidelines are announced. Open access is changing the way paleontologists do business; whether directly or by influencing other publishers, PeerJ will surely push that change a little more in the right direction.

A Paleontology-Specific Impact Factor for PLoS ONE

The threads at SV-POW! are hopping right now, particularly with one commenting on open access in Journal of Vertebrate Paleontology. One question that came up is how much, if at all, the impact factor of PLoS ONE (4.411 for 2010) indicates the reach of paleontology papers in that journal. In other words, if PLoS ONE just published paleontology papers, what would its IF be?

Naturally, I had to calculate it out. I used the standard IF formula, and looked just at citations in 2010 for papers published in 2008 and 2009. Citation counts were derived from Web of Science, which is linked to from each individual article at the PLoS ONE website. Articles under consideration from 2008 and 2009 were harvested from the PLoS ONE Paleontology Collection; one or two articles in there were only tangentially paleontological, but I kept them in anyhow just for consistency.

I calculated a "paleontology IF" of 3.317 for 2010 - a little lower than 4.411 for the overall journal but still higher than in other more field-specific publications. So, not too shabby.

This omits the issue of whether or not impact factors are worth anything, but I won't delve into that here. Love it or loathe it, we scientists still like to talk about IF!

Introducing the Dental Microwear Image Library

Dental microwear, seen in the tiny pits and scratches on a tooth, provides lots of detailed data for inferring diet and chewing behavior in animals. Analyses are often conducted by digitizing highly magnified images of the tooth surface and counting up and classifying the various microscopic features. Animals with a certain percentage of pits and scratches may have browsing habits, whereas those with another profile may be grazers. By measuring extant animals with known diet, we can (hopefully) infer the diet of extinct animals.

Dental microwear; modified from figure 3 in Mihlbachler et al., 2012

In this age of increasingly open science, microwear studies can be problematic. A cornerstone of science is reproducibility - yet, inter-observer variation and error can greatly affect measured data. Furthermore, one study alone may generate dozens or hundreds of images. Even if you wanted to re-analyze teeth, it's pretty tough - how could you get access to the necessary images? Ideally, we want a world where anyone can access the raw image data, make their own observations, double-check published analyses, and add new data for comparison.

Thus, a new project - called the Dental Microwear Image Library, or DMIL - may change things. Assembled by Brian Lee Beatty and Matthew Mihlbachler, the website aims to become a clearinghouse for dental microwear images. This will allow greater standardization of analyses and hopefully better interpretations of paleoecology and diet for extinct organisms and modern organisms. The first data (from a recent paper in Paleontologia Electronica) are now posted, along with many other data sets.

Brian Lee Beatty (who blogs at The Aquatic Amniote and tweets as @Vanderhoofius) was kind enough to answer a few questions about the DMIL. Thanks, Brian!

Was there a particular moment or incident that inspired you to build the DMIL? If so, what was it?
As we set out to test and develop the method that Nikos Solounias and Gina Semprebon started, we found ourselves frustrated by not only the lack of information on methods that were given in most microwear papers, but also the inability for people to check their work. Interobserver error is a major cause of problems for microwear, and the only way for anyone to be aware of those differences is if they compare interpretations of microwear surfaces, not just their numbers on a spreadsheet. The DMIL was the only possible solution to the need to share such images.

How has community response been so far? Is there any particular type of skepticism that you're working to overcome?
The DMIL hasn't yet come up against skepticism, but our first paper on this method that uses it has.

What license, if any, are the data housed under? Or is it on a case-by-case basis?
There is no license for the data. We want it to be completely open-access and simply available.

How would you envision the DMIL 10 years from now? What goals might you have for the long-term?
We hope it will be a place that people can use to learn how to use the methods we are continuing to develop. I most sincerely hope that it will not only be home to our own data, but also be a place for others to deposit their data using similar methods so that more work of this sort is available in a similar, comparable format.

Authors of the recent paper in PE, along with a research assistant. Photos courtesy of Brian Lee Beatty.

For more information, check out the DMIL, or read the recent paper (open access) about the work.

Citation:
Mihlbachler, Matthew C., Beatty, Brian L., Caldera-Siu, Angela, Chan, Doris, and Lee, Richard, 2012. Error rates and observer bias in dental microwear analysis using light microscopy. Palaeontologia Electronica Vol. 15, Issue 1;12A,22p.

Open Access in the UK - Comment Now!

The Research Councils UK (an umbrella organization overseeing much of the public scientific funding in that country, as well as funding for the arts and other worthy ventures) is soliciting comments on a new open access policy [PDF]. No matter what your opinion on open access, please comment. Mike Taylor, writing at SV-POW!, has further information and instructions.

Even if you don't live in the UK, it is worth letting the Research Councils know how you feel about the policy. Why? Because science (and scientific publishing) is inherently an international endeavo(u)r. I collaborate with colleagues in the UK all of the time, and many of the best papers I read these days have their origin across the pond. But, as with most scientific literature, access sometimes ain't easy. A more open scientific literature helps all of us, and each accessible paper raises the country's profile in the scientific community. Funding agencies always want more bang for their buck (or pound), and improving accessibility is one great way to do that.

So, drop a line to communications@rcuk.ac.uk by April 10 and use the subject "Open Access Feedback." Even a short sentence of support will do. Or three short sentences, as I did (basically using the argument in the paragraph above). Make your voice heard!

Curators: not just for museums anymore?

"The promise of the Internet-as-Alexandria is more than the rolling plenitude of information. It’s the ability of individuals to choreograph that information in idiosyncratic ways, the hope that individuals might feel invited by the gravitational pull of a broad and open commons to “rip, mix, and burn” — to curate." — Gideon Lewis-Kraus, 2007 [emphasis mine; paywall to original quote]

The internet is a very big place, and it can be exceptionally tough to keep track of everything that's of interest. A typical reader randomly browsing a topic ends up with a fair number of dead-end clicks—articles that just aren't that relevant or important. Fortunately, some individuals out there collate the best stuff, remix it, and push it to the outside world through blogs, news sites, Twitter, Facebook, Google+, and other venues. In a formal sense, these individuals are often termed "web curators" or "content curators".

In a nutshell, the web curator is not necessarily a content creator, but a content editor. I mean "editor" in the broad sense, of course—someone who selects interesting pieces and places them with other interesting pieces in new and meaningful ways. This is similar to what editors of magazines or anthologies do.

Museum Curators
Of course, the term "curator" was around well before the internet -- most notably in the museum profession (Wikipedia provides a pretty good summary, as does the US Bureau of Labor Statistics). In fact, my official job title is curator, so I can speak from some personal, professional experience. What exactly do curators do, then?

• Direct the overall collection strategies for an institution. What to collect, what to deaccession, what to devote resources towards, etc.
• Ensure the long-term survival of the collections.
• Engage in original research (often using museum collections).
• Present the collections to a broad audience, often through physical exhibits but also through various other media.

Depending on the type of institution and the field of study, a curator's duties may vary. For instance, a curator at an art museum may have slightly different tasks from that at a natural history museum, and collections managers may do some of the routine maintenance and preservation stuff at large museums. In any case, curation is a complex job.

Note that there is some overlap between the goals of a typical web curator and a museum curator. Both select and present collections of objects (fossils, or artwork, or blog posts) to a broad audience, but here the resemblance ends.

The British Museum - where curators reside. Image by awv, cc-by-2.0.

Why So Annoyed?
The contemporary usage of "web curator" is fundamentally misleading, at least judging from the above job description of a museum curator. Web curators collect, winnow, repackage, and disseminate information; they may have little role in content creation, and often have no concern for content longevity or archival. By the very nature of the internet, a web curator's work may be ephemeral (but not always). I would argue that this typical absence of the long view is a fundamental difference between most web curators and most museum curators.

Usage of the term "web curator" also muddies the waters around genuine digital curators. These are archivists, preservationists, and conservationists who work to ensure our digital heritage will be extant for the long haul. Digital curators in the pure sense aren't just repackaging links; these individuals ensure that the linked content will be around in 200 years. Calling yourself a curator doesn't mean you are one (similar to how not all museums are really museums, and loose applications of the term paleontologist, no matter how well-intentioned).

In part, I admit that some of my objections to the new usage of curator are a knee-jerk turf defense. I paid my dues, got my Ph.D., have an office in a museum basement. . .what have these internet upstarts done? I recognize this, and realize that such feelings are somewhat irrational. The English language changes constantly, and old words are often repurposed. After all, the web used to be just a product of a spider's backside. I just have to deal, right? On some level yes, but it still doesn't mean I have to like it! Nor does it mean I'm wrong.

The Most Important Objection
Admitting that definitions expand and contract, the fundamental issue here is that the phrase "web curator" is still basically meaningless. It serves to obfuscate, implying some kind of profundity where there may be none. In short, "web curator" is a buzzword.

A buzzword is corporate-speak that gussies up an otherwise mundane concept and makes it more intriguing (and profitable). Consider some examples. Value-added. Holistic. Accountability. All perfectly nice terms whose vague usage gives me a headache.

The big problem here—and a key quality that makes "curator" such a great buzzword—is that most people have no clue what a curator does. At best, folks have some vague notion of a curator as a person with a fancy degree and hipster glasses who hangs paintings on a wall and maybe writes some label copy. "Web curation" fits this stereotype and thus is a masterfully empty use of an important-sounding term (see these links for some choice, typical usages).

A solution?
I'm a big fan of calling a spade a spade. "Web curators" provide a valuable service, but the title unfortunately misleads. Just read the phrase "Real-time curators need to add participation widgets", and tell me it's not slightly silly! Were this statement not from a rather well-known blogger, the phrase could just as easily have originated in the Web Economy Bullsh*t Generator. In fact, the cited example is the perfect storm* of all that is wrong with buzzword-led thinking. 

Mike Taylor has pressed me on my objections to the term "web curator," asking for an alternative. I see nothing wrong with "editor". As outlined above, it's a much more accurate description of what "web curators" do. An editor is a skilled person who practices the art of identifying relevance and distributing the results. At its core, curated content on the web is part of a web anthology, just like an anthology of prose or poetry. The only difference is the digital format. Could we ever find a better, more descriptive term than "editor" for this role? In the digital realm, "curator" should be reserved for those who go beyond a primarily editorial role, to preservation, archival, and conservation.
 
So, ditch the web curator. Web editor, please.

-------------

*perfect storm = buzzword. Yes, I was being ironic by using it. Very meta, huh??
Thanks to Bora Zivkovic, Mike Taylor, Mike Keesey, Tori Herridge, and others for stimulating discussion and feedback that led to this post.

Self-archival: a good start, but not the full solution

We all want our work to be discovered, read and cited. There is little doubt that closed access systems hamper this - a paywall to an article is a hefty obstacle, and we all encounter them at least occasionally no matter how extensive our library access is. From an author's perspective, freely-available PDFs of their work are a major boost.

In recent discussions on Twitter and in the blogosphere, I've chatted with Mike Taylor, Ross Mounce, and others about self-archival as one of many mechanisms to bring about open access. Mike's recent blog post at SV-POW! summarizes much of the discussion to date, and I thank him for helping me to crystalize my thoughts on the topic.

For those who are not familiar with the term, self-archival refers to placing a freely-downloadable copy of a publication (or other work) on one's personal (or departmental, or whatever) web page. In this post, I want to discuss the pros and cons of such an approach.

Pros

• The PDF is freely available to anyone who wants to see it. No paywalls. No hassle.
• Once picked up by search engines, your posting may be the first one web users find - even above the "official" journal page!
• If users browse your website with the PDF, it means that they might discover closely-related work. This can be a big plus for getting the word out about your research program. 

Cautions

• A personal archive is probably not a permanent archive. Barring special arrangements, your personal or institutional web page is not likely to last substantively beyond your lifetime. Free hosting services such as WordPress may not be around in 20 years (remember Geocities?), so it may be worthwhile to pay for hosting. And make sure your descendents pay for hosting, or that your departmental web administrator doesn't delete your page 15 years after you retire. I have little faith that the PDFs I post on my own web page will be around 200 years from now, at least at that website. That sure would stink for that researcher in 2212, who wants to read all about ceratopsian sinuses.
• Author-hosted archives are not independent. There is nothing to prevent someone from removing embarrassing details or adding fraudulent information to their publications, and little that a casual reader can do to detect such fraud. The great majority of academic authors are honest - it's that tiny minority we have to watch out for. An independent archive, hosted by an institution, library, or publisher, provides a firewall protecting the literature from the authors.
• As article-level metrics gain prominence, author-hosted PDFs may skew some statistics. For instance, let's say I publish a paper in PLoS ONE, and also post a copy of the PDF to my site. Because PLoS ONE records and posts view and download statistics for its own site, any downloads or views from my site are not recorded there. Thus, the statistics are spread across several venues. This is not a major issue in my opinion, but some people may care.
• Under the terms of publication, a publisher may not allow you to post a PDF of your paper. Or, they may only allow you to post a pre-review copy. Or a post-review, unformatted copy. Things get complicated quickly, especially for those concerned about following the letter of the law.

The Up-Shot
If you are active researcher, you should be posting whatever PDFs of your own work that you (legally) can.  If you don't, you're missing out on innumerable opportunities to publicize your work and interact with colleagues. However, personal archiving is not enough to ensure permanence. For the long-term, a bigger solution is needed. Institutional archives, journal archives, society archives, whatever. The ultimate answer may take some time to sort itself out.

The Open Museum Notebook - Torosaurus Style

A new paper on the Torosaurus / Triceratops issue was just published in PLoS ONE, bringing some additional analysis to the table. I won't comment on it any more here (I'm saving my thoughts for a formal reply on the PLoS ONE website itself), other than to refer you to my own paper and the Scannella & Horner response.

In any case, I have a pile of notes from my own work on Torosaurus (or whatever we should call it), and figured it was time I distribute them a little more widely. So, I just uploaded my notes on the Yale Torosaurus specimens to figshare.com. There isn't really anything earthshaking in there (most of the meat of it has been previously published), but in any case now other folks can use them. The sketches of real bone vs. reconstruction should be particularly useful.

My sincere hope is that at least a few other paleontologists will follow suit with their own notebooks - there are a lot of unused data that will never see the light of day otherwise. I also have a goal of gradually digitizing and posting my other museum notebooks, but that will probably take some time!

Citation and Link

Notes and Observations on Specimens of Torosaurus at the Yale Peabody Museum of Natural History. Andrew Farke. Figshare. Retrieved 15:40, March 02, 2012 hdl.handle.net/10779/664bf2cb5ac486da32c7fb7261e595cd

Update: Since this posted, I have uploaded a number of other notebooks. Find them on my figshare author page.