Wednesday, November 28, 2012

Mostly moving. . .

Along with Sarah Werning and Shaena Montanari, I have a new blog over at the PLOS blogs network. We're The Integrative Paleontologists - go check it out! For the most part, I'm going to be moving my activity over that-away from here on out. . .the occasional post outside the domain of TIPs will still land here, though.

Wednesday, November 14, 2012

The 2012 Paleo Project Challenge

Everyone has an unfinished project. Most of us have at least a half dozen. Those partly finished manuscripts, paintings, data sets, and preparation projects. Oh, we started out with good intentions. Maybe we even poured a productive week into it. But then, the honeymoon glow faded. Something else got in the way. The field season, or teaching duties, or another more pressing project, or a grant deadline, or just plain old life circumstances, interrupted us.

Luckily, all of that work doesn't have to go to waste. Why not finish up that project? What are you waiting for? Heck, what am I waiting for?

Regular readers of this blog may remember that Dave Hone and I instituted the "Paleo Paper Challenge" (PPC) back in 2009, in an effort to shame all of us into cleaning our (figurative) research plate. We had pretty remarkable success - although not everyone (including ourselves) were able to finish everything we wanted to, most folks made some major progress. Some papers even made it into publication, in venues like Journal of Vertebrate Paleontology and PLOS ONE. Not too shabby.

Not wanting to rest on our laurels, it's time to kick things off for 2012. As before, Dave and I want to pursue a "bigger tent" approach. Why limit the PPC to just academic research? Let's open it up to all paleo enthusiasts! Preparators, artists, researchers, bloggers. . .after all, paleontology does not survive on publication alone. Thus, we are happy to kick off:

The Paleo Project Challenge
Do you have a paper that just needs the finishing touches before it heads off to publication? Is there some half-prepped fossil sitting in a cabinet in the lab? Have you started and finished a big blog post half a dozen times, but never pulled the trigger? Is that masterpiece rendering of a liveTylosaurus still sitting on the easel? Stop sitting around, and finish it!

Here are the rules:
1) Indicate your willingness to participate in the Paleo Project Challenge (PPC) in the blog comment section. You should at a minimum indicate the category it falls under (paper, blog, art, or whatever), and the project (if you can - we totally understand the need for secrecy in some cases!).
2) Do the work! You have until December 31, 2012. Remember, we're all watching.
3) Once you're done, celebrate!

Let's get to work!

My Commitments
1) Write up the ODP results. [yes, for real this time!]

What are you going to do? Chime in below in the comments section!

Note: This post is largely recycled from my post back in 2010. In the interest of laziness--which really is the impetus behind the PPC--that 2010 post is given with only slight modification.

Wednesday, June 13, 2012

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.

Thursday, April 26, 2012

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!

Wednesday, April 18, 2012

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.

Thursday, April 5, 2012

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!

Wednesday, March 14, 2012

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.

Tuesday, March 6, 2012

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.

    Friday, March 2, 2012

    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.

    Wednesday, February 8, 2012

    Restoring that sense of wonder

    These can be depressing times for a paleontologist - funding is poor for most, the job market is dim for many talented friends and colleagues, and rhetoric-ridden battles for scholarly publishing rage. That's enough to suck the joy right out of the field. In instances like this, it's nice to step back for a second and think about the really cool stuff going on.

    So, I've put together a list of wondrous things that have happened in paleontology over the past several years. Why are they cool to me? Mostly because they challenge ideas that I acquired while a little, dinosaur-obsessed kid. And they also challenge ideas I've acquired as an "educated" professional. Sometimes it's nice to have our comfort zone stretched.

    Symbols of the new paleontological revolution: an eye-catching Sinosauropteryx crouches on top of mammoth DNA, overlain on a thin-section of dinosaur bone (sources at end)
    In no particular order:
    • We know what colors were on parts of the body of some dinosaurs. Really. How cool is that? Sure, it's not perfect, and there is lots we'll never know, but the mere fact that you can plausibly reconstruct parts of the pelage of a feathered dinosaur is amazing. Especially because I had always believed the truism that we'd know the texture of dinosaur skins, but never the color.
    • I can download a genetic sequence from a woolly mammoth. Or a Neanderthal. Or any number of extinct organisms. I had always known that Jurassic Park would never be a reality. It probably never will be (at least for non-avian dinosaurs). But to stare at the A's, T's, G's, and C's of an extinct organism still gives me some goosebumps.
    • I can listen to a Jurassic katydid. Yes, yes, there are some assumptions in the reconstruction. But let's suspend criticism for a moment, and accept that it's probably at least a decent approximation. These are noises that haven't been heard in 165 million years.
    • We know the sex of some individual dinosaur specimens. Thanks to studies of medullary bone and comparative anatomy, the seemingly impossible is made real. Wow!
    • Similarly, we know the age of some dinosaur individuals at death (give or take a few years). The notion that sauropods only got big because they grew for a century can't be supported anymore. Once again - wow!

    This is just my personal list - what's on yours?

    Sources for image: Mammoth DNA sequence in background from GenBank Accession FJ655900 (published by Enk et al., 2009); dinosaur bone histological section modified from Woodward et al. 2011 Figure 1C (colors inverted and adjusted); Sinosauropteryx modified from original by Marty Martunuik. Image released under Creative Commons Attribution-Share Alike 3.0 Unported license.

    Tuesday, February 7, 2012

    How Big Commercial Publishers Can Help Themselves

    Big commercial publishers - especially Elsevier - have been getting a lot of flack lately. There's the usual background noise about high costs of institutional subscriptions and individual PDFs for non-subscribers, and now we have concerns over SOPA, PIPA, RWA and the burgeoning Elsevier boycott. I think it's fair to say that the argument has been dominated most strongly by the publishers' critics. Nonetheless, there is invariably someone who pipes up in comment threads (or in posts at sites like The Scholarly Kitchen) in defense of the publishers.

    Pro-commercial publisher arguments almost always include the term "added value" or something similar. In other words, the big publishers add something beyond the raw manuscript and figures that are provided by the authors. I think very few people will dispute this claim, at least at its face*. The publishers:
    • facilitate peer review by paying for a manuscript handling system (either licensing a commercial product or installing an open source product on servers they pay for) [note that this is not the same as doing the peer review, which is done by volunteer referees and unpaid or minimally-paid editors]
    • do some copy editing
    • format the manuscripts into a pretty PDF and web page
    • provide a veneer of respectability with well-known journal "brands"
    • distribute the journals to libraries and interested readers, via subscriptions, web hosting, and proprietary search engines
    • and other miscellaneous things
    [*To forestall the inevitable comments, yes, some of these "services" are of dubious value to many users]

    Look, I appreciate the fact that all of this costs money. Somebody needs to be paid to do the formatting into the appropriate medium (whether web page or PDF), technical staff need to make sure the authors submit the files in the right format, it costs money to run a server, programmers don't come cheap, and all of the various functions of a business/journal aren't free (office space, salaries for necessary employees, etc.).

    But does it really cost so much that publishers have to charge $37.95 for a single PDF file, or $392 for a personal subscription to a journal?

    Maybe the answer is yes (forgetting the 30%+ profits for many major publishers). Maybe it does cost a lot of money to produce an article. Fine. Just do a better job of convincing me that it's worth it. Particularly when some of the most labor-intensive tasks (typesetting and peer review) are provided for free by the authors and their colleagues.

    Many large publishers have an established list of things they do that cost money. They've done a decent job of publicizing these talking points, judging by the facts that they show up so often in comment feeds and that I was able to assemble the bullet points above virtually from memory.

    However, publishers have performed miserably at convincing us that $37.95 is a reasonable price for a PDF download. Elsevier and company could deflect much criticism if they were to be more honest and transparent about the costs behind a journal article. How much time/money actually goes into formatting? How much does it really cost to serve a file to the internet, over multiple years? What is the honest per-article cost for the manuscript submission system? How many people actually buy articles? Instead we're stuck with the broken record of "oh, this stuff costs money, OA advocates just think it all happens for free. . ."

    Finally, here's my most pressing question: If economies of scale apply to publishing, why are the largest publishers providing some of the most expensive services? (in terms of solo journal subscription rates, individual PDF downloads, and open access fees) Wow, would I love the answer to that one!

    Post script: It seems that many folks are having similar thoughts. Check out Bj√∂rn Brembs' round-up here.

    Monday, February 6, 2012

    PLoS ONE 2011 - Final Round-Up

    Back before the new year, I reviewed all 17 of the new fossil taxa that were published in PLoS ONE during 2011. Here, I look at the general trends for paleontology in the journal, both last year and over its entire history.

    Topics and Biases
    Paleontological Topics in PLoS ONE, 2011
    The chart above shows the general topics covered by PLoS ONE papers in paleontology during 2011 (for those of you adding the numbers, a handful were counted in two categories). Just as for new taxa, there is a major skew towards archosaurs. Much as I love dinosaurs, we really need to get a broader diversity of taxonomic coverage. Part of this is probably the result of different cultures of publishing among different groups of specialists - dinosaur workers are comfortable with PLoS ONE, whereas trilobite workers aren't. We need some pioneers in invertebrate paleontology, paleoicthyology, and elsewhere.

    The Big Picture
    By my count, there were around 65 paleontology-related articles published in PLoS ONE last year (2011). This is up from 39 articles in 2010, and reflects a continuing increase since PLoS ONE was founded in 2006.
    Trends in Number of Paleontology Papers at PLoS ONE
    Compare this count of 65 for PLoS ONE with 95 papers in Journal of Paleontology and 120 papers in Journal of Vertebrate Paleontology during 2011. PLoS ONE is still smaller than some "conventional" journals, but I think it is safe to say that it may overtake these alternatives in annual volume within the next year or two. Whether or not this is a good thing for PLoS ONE and paleontology is another question - if the quality of the papers submitted to the journal as well as the editing process can be maintained (or improved where necessary), perhaps yes.

    Many paleontologists clearly are warming up to the idea of PLoS ONE. It is tough to know what factors are behind this - whether it's availability of high-resolution color figures, cost-effective outlets for lengthy papers, frustration with "conventional" journals, the impact factor, broader acceptance of open access, or something else altogether. Other paleontology journals - and paleontological societies that publish their own journals - would be wise to see what they can do to match or improve upon the attractive points of PLoS ONE. As much as I love PLoS ONE, the last thing I want is a publishing monoculture. Unless others journals adapt, though, this may be the result.

    The oldest Eucalyptus in the world - from South America! Modified after Gandalfo et al., 2011



    [note: although I am a volunteer editor at the journal, this post reflects only my personal opinions]

    Sunday, January 22, 2012

    ScienceOnline2012 - Parting Thoughts

    My thoughts on Days 2 and 3 of ScienceOnline2012 are found elsewhere - here I sum up some other impressions.

    Twitter at ScienceOnline
    This is the first time I've actively tweeted through an entire meeting, and found it to be a worthwhile addition. It was cool to see what other folks in my sessions were thinking (at times it was like passing notes in class), and also nice to be able to follow the sessions in other rooms. Over 300 active users participated (on and off-site), and over 17,000 tweets discussed the meeting (see this cool summary map)! It's this broad participation that took Twitter from just being a small piece of the meeting to an essential component - an important observation for groups like Society of Vertebrate Paleontology that might want to acknowledge (or even encourage) Twitter.

    Some thoughts on the state of blogging
    One perception I have after ScienceOnline 2012 is that blogging - as an activity and as a medium of communication - seems to have reached a relatively mature state. Sure, there are incremental advances and changes, but by and large I don't really get the sense that there is much substantively new going on (other than new people joining the blogging fold on occasion). This is somewhat reflected by the blogging-relevant sessions at ScienceOnline2012 - they are much the same kind of stuff you might have seen at ScienceOnline 2010, or 2009, or 2011. Topics like getting students involved in blogging, increasing acceptance of blogging in academia, use of images on blogs, etc., are important but really not much advanced beyond where we were a few years ago. [brief note - this should not be interpreted as me saying that I think things are just OK as they are - in fact, it is a rather sad thing that some of these issues are still issues!]

    I don't mean this as a criticism, but just a state of how things are. In fact, stability is partly a good thing in that someone new to the world of blogging can jump in with clear role models, expectations, and pathways to success (whatever success may be). Many of the broad principles have been laid out, and now we're working on refining the details. Some big issues do remain (we can always increase the acceptance of quality blogging for academic career advancement, for instance), but many of these will probably just require the imperceptible cultural shifts that happen over time.

    Some thoughts on the state of online science
    Perhaps it just reflects my own intellectual trajectory, but it seems like we're approaching some measure of stability for many of the old issues in science  communication. Open access - important, but not really novel anymore. Blogging - same thing. Social media - ditto. As all of these trends started, I took a wait-and-see approach before engaging myself. As such, I have missed out on getting in at the very, very beginning of some trends, but have also avoided wasting time with trends that haven't much gone anywhere or have fizzled out (e.g., SecondLife and GoogleWave, to name just two). Based on my attendance at ScienceOnline 2012, the areas to watch include:
    • Crowdfunding: Small donations can add up to decent funding for a focused project, and present unique outreach opportunities. In a field of shoestring budgets like paleontology, I see crowdfunding as a potentially important new trend.
    • Article-level metrics and data set archival and citation: I've tied these two topics together because they reflect a major advance beyond the old journal-level metrics like Impact Factor. Neither topic is completely new, but I saw plenty of new tools at ScienceOnline that may move the discussions and usage of these metrics forward. Furthermore, there is still a long way to go for community buy-in.
    There may indeed be some major issues to watch in science art or writing that I have missed because I'm not really plugged in to those communities, so please comment if there is something I missed!

    Saturday, January 21, 2012

    ScienceOnline2012 - Day 3

    In Day 3 of ScienceOnline 2012 (my second day), we had a fun mix of split sessions and common gatherings. Areas of interest for me included:
    • Students as Messengers of Science: This discussion focused on how to engage high school and college students in science blogging. There are no easy solutions, but there were some tips to get them started. In particular, planning is key. What is the goal? Who are the potential readers? 
    • Why the Resistance to Science Blogging? This session was pretty much as advertised. Unfortunately, there was little new here - yes, there are downsides to putting yourself out there on a blog, but for the most part it seems like it will just take slow attrition of the skeptics to normalize blogging for non-blogging scientists. Same issues as in 2011, 2010, 2009. . .but little in the way of new solutions. One good piece of advice, though: should we put blogging activity on our CV, and if so how? In many cases, there are impactful ways to describe this activity - online outreach editor, web editor, etc. These or similar terms can be honest, accurate descriptors that are more positive for those who might be instinctively averse to the word "blog."
    • Raising Money for Your Science and Journalism with Crowd Funding: This session filled in many of the details related to yesterday's demo - and was quite interesting. One clear worry is that crowd funding in science could be hijacked by "stodgy" forces that try to impose NSF-style limitations on the crowdfunding community (e.g., layers of vetting by experts, etc. - in fact, I think the odds are quite good that someone will un-ironically submit an NSF proposal in the near future to put together a service to validate and serve as a clearinghouse for crowdfunding science). This could have the chilling effect of squeezing out small players in favor of big institutions that are already comparatively well-funded. Vigilance is required - and the situation will doubtlessly change rapidly over the next few years. Either way, it has cool potential.
    • CyberScreen Science Film Festival: Again, what the label says. I'm hoping to find a link to a list of the films - there were some really excellent ones.
    • Closing Plenary Panel on Scientist/Journalist Relations: This isn't a new topic (see here for one recent post), and is getting a little tiresome for many. Lots of discussion, little movement from either side. My thought is that the real problem is not with the journalists or scientists at ScienceOnline, but the reporters who aren't science specialists, or who just copy press releases, or who throw stuff together without contacting relevant scientists.
    Next. . .parting thoughts.

    Friday, January 20, 2012

    ScienceOnline2012 - Day 2

    ScienceOnline is really one of those unique experiences - explicitly set up as an "UnConference," it encourages freewheeling input from all attendees, bursting the bounds of conventional presentations. In fact there really aren't presentations in the conventional sense. The presenter is only a facilitator; everyone else is encouraged to join in the conversation. As such, it is both a disconcerting and intensely rewarding experience.

    In my second trip to one of these unconferences (see here for my report on the last trip), ScienceOnline 2012 has proven to be worth every instant of invested time. It's been enjoyable to meet the faces behind the websites, interact with science media types (both bloggers and "conventional" reporters), and learn about the current trends in doing science in the internet age.

    Work scheduling meant I had to miss the first day of the conference (disappointing, as there were some good sessions), but I was happy to drop in Day 2. Some highlights of the sessions included:
    • Saying howdy to the infamous Bora Zivkovic - a tireless promoter for science on the internet, and arguably one of the most influential individuals out there in the new science communication landscape (Bora is the reason why I'm involved with PLoS ONE!).
    • Seeing a presentation from the talented high school students behind Extreme Biology Blog. It's tough to balance the demands of being a high school student and being a blogger - but blogging can clearly be a good component of the curriculum.
    • Learning about FigShare.com - a newly revamped way to share all sorts of data (not just figures!). This looks to have some great potential, especially once the long-term archiving is worked out (which seems to be on the near horizon)
    • Learning about ROMEO, a clearinghouse for summaries of publisher policies - a great place to find out whether you can post a copy of your paper on your own site, for instance.
    • ORCID is an upcoming service to assign unique identifiers to researchers. Launching later this year.
    • Annotum is a WordPress plug-in to allow writing, peer-review, editing, and publication of scientific papers.
    • SciFund is a way to crowdfund research projects. But, it's not just about collecting dollars - the most successful fundraisers made a solid outreach connection with the public.
    • I really enjoyed visiting with some of the other paleontologists here. It is nice to see other paleo folks on the ScienceOnline bandwagon, but also a little distressing how out of touch many of our colleagues are with the world of online outreach!
    One interesting observation is the slight change in feel of the conference from 2010. Back then, scienceblogs.com was the reigning champion of science communication - and to be honest, parts of the 2010 banquet felt like a string of in-jokes between a handful of  bloggers. As the landscape has shifted, it feels as if things are a little more inclusive. All in all, a good thing! ScienceOnline2012 is a little bigger, but it has retained all of the charm and good qualities that made ScienceOnline2010 a useful, fun experience. Kudos to the organizers and presenters!