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]