What is the scientific literature used for?

For better or for worse, we paleontologists (and many other scientists) view the use and importance of the literature in terms of citations. Citations are what drives the ever-beloved impact factor, as well as other metrics such as the h-index. Indeed, this focus on citations colors many discussions on access to the literature, such as the relative importance of rapid electronic access. You’ll hear lots of statements along these lines: “If you are in the business of writing a manuscript, but don’t have access to a particular piece of literature, you can always use interlibrary loan or a similar service. Or just got to the university library next door. Patience is a virtue. It won’t kill you (or science) to wait a few extra days.”

Oh, for everyone to have a library like this on their doorstep! Or at least the electronic equivalent. Stockholm Public Library, photo by Samantha Marx, CC-BY.

Oh, for everyone to have a library like this on their doorstep! Or at least the electronic equivalent. Stockholm Public Library, photo by Samantha Marx, CC-BY.

Although I don’t completely discount this idea (indeed, we all have seen our share of PDF requests that could have been fulfilled with a few extra seconds of Googling), I think it reflects a rather anemic view of how the scientific literature is used by scientists. Citations are certainly an easily trackable mode of literature use, but (as noted time and time again by advocates of “alternative metrics”) the literature is used for more than just writing papers. Particularly in a field like paleontology, which has a strong record of public interest and public engagement, these non-citeable uses can be myriad.

So, I decided to put together a quick list of the different ways that I use the scientific literature on a day-to-day basis. In particular, I’ve noted some areas where timely (i.e., near-immediate) access is highly desirable.

How do I use the literature?

  • Background research for teaching. I teach a one month introduction to paleontology / evolution in the fossil record course for high school freshmen, and this is a topic for which there isn’t a good textbook for all of the content we cover (although Neil Shubin’s Your Inner Fish does an excellent job with talking about homology, development, and the fossil record). And even if there was a comprehensive textbook, I still want to sprinkle my lectures with examples from the literature, images from papers, and the like, as well as bring in relevant material from recent publications. Thus, I not infrequently turn to the primary literature.
  • Background research for a media interview. Every once in awhile, I’m contacted by a member of the news media to provide an opinion on a piece of new research. Although I do not generally accept interview requests for topics outside my area of expertise, even for topics within my area of expertise I sometimes want to brush up on a particular fact or research some of the context behind a particular story. For instance, I’m quite comfortable talking about horned dinosaurs–but if it’s a horned dinosaur from a place I don’t know much about, I might head to the literature to brush up on the overall context. This may or may not come up in the interview, but I want to be prepared to represent the science as accurately and completely as possible. Time is of the essence here!
  • Research for public talk. When developing a talk for a public audience (I give between 5 and 10 annually, for museums, community groups, and other events), I sometimes need to delve into a new topic. Maybe it’s to see what else has been found in a particular formation (it’s always nice to throw in “local color”), or just to understand a particular point on a related topic.
  • Reviewing manuscripts. Although I only accept review requests for manuscripts within my area of expertise, I frequently refer back to the literature to double-check claims made by the authors, suggest additional references, and refresh my memory on relevant details of anatomy, statistics, or geology. Review turnarounds are usually between 10 and 30 days, and it is not uncommon to be polishing a review a few days (or hours) before it is due. Waiting two weeks for an ILL isn’t a good use of time, or fair to the authors and editors who expect timely reviews. I’m certainly not going to drop $40 for a PDF in this case, either (particularly because publishers don’t reimburse for these kinds of expenses).
  • Reviewing grant applications. The same logic as for reviewing manuscripts applies to reviewing grants.
  • Writing manuscripts. I’ve buried this one in the middle of the list to emphasize that it is only one of many uses. There are few things more frustrating than being in the final push to finish a manuscript, and finding out there is a seemingly critical paper tantalizingly out of reach behind a paywall.
  • Identifying specimens in a museum collection. In the process of curating a museum collection, I am called upon to ensure that all of our cataloged specimens are identified as precisely and accurately as possible. In some cases, past experience guides me and others who work in the collections. However, parts of our collections (particularly historically collected ones) are somewhat outside my expertise (e.g., oreodonts and trilobites). Off to the literature! A well-illustrated paper can be invaluable for pinning down an identification. (how well some papers achieve this, though, is the topic of another post)
  • Providing information on a topic to a colleague or member of the public. At our museum, we’ll sometimes have folks drop by for a fossil identification, or we might get a question about a particular paleontological topic. If it’s something that’s outside the realm of popular books (and let’s face it, if it’s not a dinosaur, it’s probably not in a book), off to the literature!
  • Writing museum exhibit text. I am fortunate to have the opportunity to assemble temporary exhibits for my museum sometimes, focusing on fossils from our collection that tell a story about Earth’s history and our connection to it. But, I am not necessarily an expert on every fossil that I think is exhibit-worthy. So, off to the literature I go! Temporary exhibits here are frequently the result of reading or skimming at least a few papers on the topic.
  • Reference for artistic project. Every once in awhile, I’m lucky enough to work with an artist to illustrate a new discovery made by my museum and colleagues, or I am contacted by an artist who wants an opinion on a particular piece of work. My extensive photo library comes in handy, but I also rely extensively on the literature. If there’s a question about the plants found in a particular environment, or the scale pattern on the skin in a particular group, or the types of non-dinosaurs that lived at a relevant time in history, I’ll often turn to previously published work.

I’m sure I’ve probably missed something–how do you use the literature? Sound off in the comments section!

Category: Open Access, Publishing | Tagged , , , , | 5 Comments

The Open Access Dinosaurs of 2014

As we enter 2015, it’s a good time to reflect on the state of paleontology and the state of open access. Because I’m a dinosaur paleontologist (my apologies to the other 99% of life that ever lived), this post will of course address that clade in particular!

<i>Ziapelta</i>, one of the new open access dinosaurs named in 2014. Illustration by Sydney Mohr, from Arbour et al. 2014. CC-BY.

Ziapelta, one of the new open access dinosaurs named in 2014. Illustration by Sydney Mohr, from Arbour et al. 2014. CC-BY.

Thirty-eight new genera or species of dinosaur were announced in 2014 (according to my count based on a list at Wikipedia and the Dinosaur Genera List), spanning everything from sauropods to tyrannosaurs to horned dinosaurs. Seventeen of these were published in open access or free-to-read journals. This works out to around 45%.

PLOS ONE continues to dominate the world of open access dinosaur species–9/17 were published here. I will be very interested to see if this trend continues into future years, particularly as more open access journals enter publication. Seven other journals hosted open access or free-to-read papers on new taxa. These included publications hosted by professional societies, “big publishers,” museums, and the like.

You’ve probably noted by now that I’ve been parsing a difference between “open access” and “free to read.” The former category includes those that are fully BOIA-compliant; usually this means publication under a Creative Commons Attribution (CC-BY) license. This freely allows redistribution, repurposing, translation, and other uses, as long as the author is credited (interestingly, I note that many critics of CC-BY conveniently forget that authors must always be attributed). 11 out of 17 species were published under a CC-BY license. The remainder were under a variety of licenses (e.g., CC-BY-NC-SA). I will confess a certain amusement at the “NC” (non-commercial) clause, particularly when used by very much for-profit and very much commercial publishers (to their credit, a strict CC-BY license is now the default offering for NPG’s Scientific Reports).

Overall, 2014 (17/36 new taxa are free-to-read) doesn’t reflect a big change from 2013 (16/38 free to read). I would be interested to see what percentage of the overall paleontology literature (not just alpha taxonomy) is freely available–anyone up to collating this?

Full disclosure: I was an author on one of the papers naming a new dinosaur this year, and was handling editor for some of the other papers naming new dinosaurs. 

Appendix: The Data

Taxon Freely readable CC-BY? Journal
Adelolophus No No
Arcovenator No No
Augustynolophus No No
Changyuraptor No No
Daurosaurus No No
Eousdryosaurus No No
Gobivenator No No
Gongpoquansaurus No No
Kulindadromeus No No
Kulindapteryx No No
Laquintasaura No No
Mercuriceratops No No
Panguraptor No No
Pentaceratops aquilonius No No
Plesiohadros No No
Qianzhousaurus No No
Quetecsaurus No No
Rhinorex No No
Vahiny No No
Zaraapelta No No
Zby No No
Allosaurus lucasi Yes No Volumina Jurassica
Datanglong Yes No Acta Geological Sinica
Dreadnoughtus Yes No Scientific Reports
Fosterovenator Yes No Volumina Jurassica
Rukwatitan Yes No Journal of Vertebrate Paleontology
Huangshanlong Yes No? Vertebrate PalAsiatica
Anzu Yes Yes PLOS ONE
Aquilops Yes Yes PLOS ONE
Chuanqilong Yes Yes PLOS ONE
Leinkupal Yes Yes PLOS ONE
Nanuqsaurus Yes Yes PLOS ONE
Tachiraptor Yes Yes Royal Society Open Access
Tambatitanis Yes Yes Zootaxa
Torvosaurus gurneyi Yes Yes PLOS ONE
Yongjinglong Yes Yes PLOS ONE
Zhanghenglong Yes Yes PLOS ONE
Ziapelta Yes Yes PLOS ONE

Note: The taxa Camarillasaurus and Oohkotokia were published “officially” in 2014, but made their initial (pre-print) appearance in past years, so I don’t include these open access dinosaurs on the list.

Category: Dinosaurs, Open Access, PLOS ONE, Publishing | Tagged , , , , | 5 Comments

2014: A Great Year for Hupehsuchia

Hupehsuchus, in silhouette. Public domain image by Neil Kelley via PhyloPic.

Hupehsuchus, in silhouette. Public domain image by Neil Kelley via PhyloPic.

I just can’t get enough of those bizarre hupehsuchians! These ancient marine reptiles–known exclusively from ~248 million year old rocks in China–had a tubular, bone-encased torso, toothless jaws, and flippers often sprouting an extra finger and toe or two. In a previous blog post, I noted that they’re probably best described as a “swimming sausage topped with armored mustard”.

Formerly a poorly-known group (both in the literature as well as in general paleontological awareness), Hupehsuchia underwent a scientific transformation in 2014. A wave of newly described specimens has washed through the literature, highlighting the diversity of species and body plans in this group. Additionally, recent studies and new discoveries have clarified their relationships–these animals were probably most closely related to the famous icthyosaurs, or fish lizards. Just in time for the holidays, yet another hupehsuchian has been announced.

Skeleton of Eohupehsuchus; the head is at the left of the image. Modified from Chen et al. 2014. CC-BY.

Skeleton of Eohupehsuchus; the head is at the left of the image. Modified from Chen et al. 2014. CC-BY.

Our newest character is called Eohupehsuchus brevicollis, and it’s a tiny thing (full disclosure: I was the handling editor for this paper). The whole body, when complete, might have been less than 30 cm (~1 foot) long, and the head is a little shorter than a typical human thumb. The animal had a relatively shorter neck than many of its close cousins (hence the species name “brevicollis“, which means “short neck”), and its limb bones also happen to be much more ossified than is typical for a hupehsuchian. This feature, among others, suggests that Eohupehsuchus probably isn’t just a tiny juvenile of some larger, better known species; juveniles of most animals tend to have less densely ossified bones than do adults.

There are now a total of four named species of Hupehsuchia, and at least one more is on the way. Remarkably, all of them lived within a fairly small geographic area (<80 km separation between all known fossils) and within a limited time interval (2 or 3 million years, max). Chen and colleagues, the authors on the study naming Eohupehsuchus, speculate that all of these species were able to coexist so happily due to differences in body size and shape–thus indicating different lifestyles that ensured ecological separation.

So…in the year 2014, Hupehsuchia doubled the number of named species. Long-hazy details of anatomy were resolved, and as a result, the evolutionary relationships of hupehsuchians to other marine reptiles are now more certainly known than ever before. Not bad for an armored swimming sausage!

Still craving some hupehsuchian action? Check out my previous posts on other discoveries from 2014!

Skull (photograph and interpretive drawing) of Eohupehsuchus. The tip of the snout is to the left of the image. From Chen et al. 2014. CC-BY.

Skull (photograph and interpretive drawing) of Eohupehsuchus. The tip of the snout is to the left of the image. From Chen et al. 2014. CC-BY.

Citations
Chen X-H, Motani R, Cheng L, Jiang D-Y, Rieppel O (2014) A carapace-like bony ‘body tube’ in an Early Triassic marine reptile and the onset of marine tetrapod predation. PLoS ONE 9(4): e94396. doi:10.1371/journal.pone.0094396

Chen X-H, Motani R, Cheng L, Jiang D-Y, Rieppel O (2014) The enigmatic marine reptile Nanchangosaurus from the Lower Triassic of Hubei, China and the phylogenetic affinities of Hupehsuchia. PLoS ONE 9(7): e102361.doi:10.1371/journal.pone.0102361

Chen X-H, Motani R, Cheng L, Jiang D-Y, Rieppel O (2014) A small short-necked hupehsuchian from the Lower Triassic of Hubei Province, China. PLOS ONE 9(12): e115244. doi:10.1371/journal.pone.0115244

Category: Paleontology, PLOS ONE | Tagged , , , | Comments Off on 2014: A Great Year for Hupehsuchia

Assembling the Aquilops Paper

In my previous post, I introduced Aquilops, a new little dinosaur from ancient Montana, and talked about some of the science behind establishing its identity. Here, I want to step back (or is that look down?) for a little navel-gazing about the process behind the paper (and you can read the paper here).

Reconstruction of Aquilops, by Brian Engh. CC-BY.

Reconstruction of Aquilops, by Brian Engh. CC-BY.

I was a real latecomer to the project. Scott Madsen, a wonderfully skilled paleontologist and fossil preparator, found the fossil back in the late 1990s. This was on a National Geographic Society-funded expedition headed up by Rich Cifelli (Sam Noble Oklahoma Museum of Natural History) and Des Maxwell (University of the Pacific). After Scott found the skull, he did the preparation on it, and passed it on to Des and Rich. They, in turn, set to work on the research and formal description. Life and work caught up with everyone, so the manuscript aestivated for a time. Matt Wedel (who was Rich’s graduate student) ended up moving to the same town as me, we became good friends (and babysitters of each other’s kids–thanks, Matt, for helping out last night!), and Matt thought he’d suggest bringing me on board for the project [read more of Matt’s side of the story here]. By that point, I had personally seen many of the Chinese ceratopsians that weren’t described at the time of the discovery of Aquilops, so I could genuinely contribute to the research and provide broader context. Des and Rich agreed to bring me on, so in the fall of 2010, Matt and I drove up to Des’s town to pick up the specimen, and we all got to work.

Thankfully, Des and Rich had done a bang-up job with the original manuscript–in fact, their diagnosis of Aquilops is largely unchanged from the original manuscript to the published paper, as are the basics of the description. Because the manuscript was originally formatted for a short-paper journal, we made the decision to expand it into a monograph-type treatment of the fossil. This would allow us to really do justice to an amazing fossil. Thus, we had to take the basics of the first manuscript and plunk in additional comparisons and figures, as well as add some detailed biogeographic analyses.

For me, this project was fun for several reasons. First, I got the opportunity to work on a cool fossil. There had been rumors and rumors of rumors of an Early Cretaceous ceratopsian skull from Montana, so it was rather awesome to hold the thing in my hands and be involved with the scientific research. Second, this paper stretched my writing abilities. I learned much from my co-authors, particularly Rich, about tightening prose and presenting a scientific story for a broad audience. Because Rich’s expertise is mainly in fossil mammals, he was constantly pushing me to make the tale of Aquilops and its biogeography accessible to non-dinosaur workers. Des Maxwell and Matt Wedel in turn added their own text and polish to my text. I also greatly enjoyed getting to see Scott Madsen’s handiwork up close. As a paleontologist usually removed from the prep lab, it is easy to forget how much we really owe to preparators. Without Scott, Aquilops would still just be some teeth sticking out of a lump of rock.

Another thing I greatly enjoyed was delving into the realm of biogeographic analysis. Although some of my previous papers have had a biogeographic slant, I’ve never really had cause to use some of the more advanced analytical techniques that are becoming the standard for paleontology. Thus, the Aquilops project pushed me into a new scientific realm. Along the same lines, I also did a lot of hard thinking about paleogeographic reconstructions–those pretty maps showing past connections between continents. As I delved into that literature, particularly for the Lower Cretaceous, I learned more and more just how much uncertainty there was. I had always had a rough feeling for this, but the Aquilops project really drove the point home.

Phylogeny of horned dinosaurs, from Farke et al. 2014. CC-BY.

Phylogeny of horned dinosaurs, from Farke et al. 2014. I am really quite proud of this figure, which summarizes a great deal of information in a compact space. That includes everything from what the dinosaurs looked like, to when they lived, to how they were related to each other, to their biogeography. This final product was produced only after many consultations between the various authors. CC-BY.

Random Thoughts
To finish out this post, I thought I’d throw out a few random thoughts that are useful to share, but don’t really warrant their own post. Here goes!

  • PhyloPic is awesome. This website hosts silhouettes of various organisms, all of which are explicitly licensed for reuse by other workers. A variety of CC-BY ceratopsians were already available, and I generated a few other images where necessary.
  • Open source software was invaluable for this paper. All of the figures I produced were generated within GIMP or Inkscape, and then exported as TIF files. For the figure of the digital surface scans, the initial images were captured in Meshlab. All bibliographic work, except for the final polish, was completed in Zotero.
  • It was nice to put multiple 3D formats of surface scans in as supplemental information with the paper. Although 3D PDFs are handy on some levels, they can be…quirky…within various browsers and operating systems, so OBJ and STL files are a little more universally guaranteed to work. Plus, if we were going to all the work of scanning the specimen, we might as well make it so people can easily find and use the darned scans.
  • One nice use of the 3D scans was that we could produce color-free surface models that could then be annotated to produce a figure of the specimen. This removes discolorations in the specimen that obscure details, and is a trick I first learned from Joe Sertich on our Dahalokely paper. This was also done the “old fashioned way” for the teeth, by Rich and the folks at the OMNH. In that case, an ammonium chloride-coated cast showed the detail much better than the digital scan could (due to limits in scan resolution). See also this post on figuring fossils for more on why removing color is a good thing sometimes.
  • I am really pleased that we had the space to document the specimen so completely, including multiple photographic views, interpretive drawings, and measurements. On the latter point, it all traces back to Matt Wedel’s classic post, “Measure Your Damned Dinosaur.” Although aspects of our interpretations and analyses will inevitably be superseded by future discoveries, the data will always stand.
  • The folks in Oklahoma are working on a really, really nifty museum exhibit to highlight the fossil of Aquilops, which permanently resides in their collections. Digital artist and exhibit technician Garrett Stowe, in collaboration with preparator Kyle Davies, has been doing some amazing stuff to reconstruct the skull of Aquilops as well as the entire animal. Get a sneak peek at the Sam Noble Oklahoma Museum of Natural History website!

That’s all for now! I highly recommend checking out any number of other posts related to this article, including Matt Wedel on the history of the project, Brian Engh on the artwork, and a nice web page from the folks in Oklahoma on their fossil specimen. You can also read the original paper at PLOS ONE.

Category: Dinosaurs, Navel Gazing, Open Access, Paleontology, PLOS ONE, Publishing | Tagged , , , , , , | 1 Comment

Aquilops, the little dinosaur that could

Today, several colleagues and I named a really cute little dinosaurAquilops americanus. At around 106 million years old, Aquilops turns out to be the oldest “horned” dinosaur (the lineage including Triceratops) named from North America, besting the previous record by nearly 20 million years. Even more interesting is the fact that Aquilops is not at all closely related to later horned dinosaurs from North America, but is mostly closely related to forms that lived in Asia around the same time. This is in line with a growing body of evidence showing an exchange of animals between the two continents at that time.

Aquilops in life, by Brian Engh. CC-BY.

Aquilops in life, by Brian Engh. CC-BY.

To learn the major details, you can of course check out the paper in PLOS ONE or read any number of news articles and blog posts on the find. For the rest of this post (and probably one or two other posts), I instead want to talk about some things that weren’t necessarily discussed in the paper or the press. [note: I should definitely add that the fossil is housed at the Sam Noble Oklahoma Museum of Natural History; Matt Wedel has more over at his blog, and I’ll add some on the history of the project in an upcoming post]

What’s with that bump on the front of the beak?
The rostral bone, which forms the upper beak and is a feature that unambiguously identifies Aquilops as a horned dinosaur, has a funky bump on the front of it. I spent a lot of time up-close with the specimen in hand and under a microscope, trying to convince myself that it wasn’t just some piece of bone displaced by crushing. In the end, I’m pretty certain that it’s a “real” feature; i.e., something the animal had while it was alive. Perhaps it’s pathological (abnormal) bone, but once again the texture doesn’t look ugly enough for that to be my preferred explanation.

At any rate, this animal had a funky bump on the front of its face. No idea what it was for (fighting? digging? something else?), but it sure was cool.

Skull and lower jaw of Aquilops, in my hand for scale. CC-BY.

Skull and lower jaw of Aquilops, in my hand for scale. CC-BY.

That animal is pretty small! How do you know it’s not just a baby?
It is indeed small! Based on Matt Wedel’s estimates, it was probably about the size of a large raven and body mass of a bunny rabbit (we only have a skull, so this was based off scaling from more complete skeletons of closely related species, such as Archaeoceratops [body mass statement corrected after initial post]).

As you can see from the picture, the skull could fit pretty neatly into your hand. The overall head is a little less than two-thirds the size of the largest published skulls of its closest relatives (Liaoceratops and Archaeoceratops), so based on size alone I suspect it’s not fully grown. The bone texture is also consistent with a young-ish animal.

But…other features (such as the development of the teeth and the comparatively close fusion between some bones) suggest that although the animal was young, it probably wasn’t a baby (or even a kid). I imagine it something like the Aquilops equivalent of an adolescent or maybe a teenager.

Can’t you just slice up the bone to determine the age?
Unfortunately, we don’t have any limb bones, which are the gold standard for determining dinosaur age. Skull bones are a possibility (and have been used for some dinosaurs, at least to determine relative age), but…the growth and changes in skull bone are very poorly characterized (especially relative to calendar age), and virtually nothing is known about skull bone growth in early ceratopsians. Thus, microanatomy of skull bones probably wouldn’t be that informative.

Why name a new species if it the animal is not fully grown?
It is no secret that dinosaurs change–sometimes radically–as they grow up. So, this can raise some concerns about whether or not species should be established based on young specimens. However, I am pretty comfortable naming Aquilops as a new species, even if the skull is from a young individual. Several features of the skull–including the unique shape of the beak as well as some combinations of features in the skull–distinguish Aquilops from other animals. Many of these features seem to be fairly stable through the life of an animal in species where we have large samples (e.g., beak shape). Thus, there is little to suggest that we wouldn’t recognize a larger and older Aquilops when and if we find one.

Aquilops to scale next to a human. They look like they would make cute pets, but don't let that fool you--those beaks would have been sharp! Illustration by Brian Engh, CC-BY.

Aquilops to scale next to a human. A dinosaur at this size looks like it would make a cute pet, but don’t let that fool you–those beaks would have been sharp! Illustration by Brian Engh, CC-BY.

If you only have a skull, how do you know what the rest of the dinosaur looked like?
Even though we only had the skull, we did want to attach that head to the rest of the body for the artwork that is being used to publicize this find. The body plan of early horned dinosaurs such as Aquilops was fairly conservative–large head, long hindlimbs, shorter forelimbs, mostly bipedal, long tail. Decent skeletons are known for close relatives of Aquilops (such as Archaeoceratops) and quite fine skeletons are known for slightly more distant relatives (such as Psittacosaurus. Thus, although some details may be shown to be slightly off if a complete skeleton of Aquilops is found, we are pretty confident in the overall reconstruction.

Coming up…more behind the scenes tidbits
Update: Want to learn more? Check out this blog post from co-author Matt Wedel and a behind-the-scenes look at the artwork from Brian Engh.

Citation
Farke, A. A., W. D. Maxwell, R. L. Cifelli, and M. J. Wedel. 2014. A ceratopsian dinosaur from the Lower Cretaceous of western North America, and the biogeography of Neoceratopsia. PLOS ONE 9(12):e112055. [read the paper – open access!]

Category: Dinosaurs, Paleontology, PLOS ONE | Tagged , , , , | 14 Comments

Lungfish brains ain’t boring

I tend to think of fish brains as fairly unremarkable. Too simple relative to mammal brains, too un-dinosaur-y relative to dinosaur brains. Shark and perch brains get a brief nod in many comparative anatomy classes, but mostly to lament how “primitive” they are. Check ’em off the list, make a sketch, pass the quiz, and let’s see how fish brains evolved into something more interesting.

But, I only just learned that my callousness is more than a bit unwarranted. Researchers Alice Clement and Per Ahlberg, both from Uppsala University, Sweden, last week published a fascinating look at the reconstructed brain of a 380 million year old lungfish from Australia, Rhinodipterus. In conjunction with previously published work, a fascinatingly complex picture of lungfish brain evolution emerges.

Lungfish are particularly interesting to study due to their long fossil record–over 400 million years–as well as their key position within vertebrate evolution. Today, there are three main lungfish genera–Neoceratodus (the Australian lungfish), Lepidosiren (South American lungfish), and Protopterus (African lungfish). Only Protopterus has more than one species. Lungfish as a group are probably the fish most closely related to limbed vertebrates (tetrapods, including salamanders, turkeys, and humans, to name a few), and thus are an important reference point for understanding tetrapod evolution. 

The modern African lungfish Protopterus, probably even less tasty than it sounds. Image in the public domain, modified from Ray 1908.

The modern African lungfish Protopterus, cursed with a mostly cartilaginous cranium. Image in the public domain, modified from Ray 1908.

The problems with studying lungfish brains, though, really occupy two levels. The first is that brains don’t generally fossilize well–so, paleontologists have to rely on a “cheat code” to view the brains in extinct animals. Brains are encased in brain cases, a skull structure that often preserves at least the basic contours of the brain. Use a CT scanner to look inside the braincase, make a spinning digital model of the brain. But…the braincase is mostly cartilaginous in modern lungfish as well as many fossil species. Thus, even the basics of brain anatomy are essentially unknowable for much of lungfish evolution.

Thankfully, many early lungfish did have bony skulls. Nonetheless, many of the known fossils were crushed, incomplete, or incompletely studied. We are fortunate to have the fossil resources of the Gogo Formation, a 380 million year old set of rocks that preserves the remains of a marine reef. The specimens from here are spectacular (including an embryonic fish still connected to its umbilical cord), uncrushed, and beautifully freed from their rocky cradles using advanced preparation techniques. One of these fossils included a partial skeleton of the lungfish Rhinodipterus kimberleyensis. The braincase was CT scanned, and then a digital model of the inside contours was created to approximate the brain. This digital model, in turn, was then compared with published data from a few living and a fossil lungfish.

The ancient lungfish Dipterus, a close relative of the Rhinodipterus studied by Clement & Ahlberg (2014). Image from Ray 1907, in public domain.

The ancient lungfish Dipterus, a close relative of the Rhinodipterus studied by Clement & Ahlberg (2014). Image from Ray 1907, in public domain.

One of the most striking findings is that the reconstructed brain of Rhinodipterus is more similar to that of Neoceratodus, the modern Australian lungfish (picture at end of post), rather than that of the other modern lungfish (i.e., those from Africa and South America, Protopterus and Lepidosiren). Because Neoceratodus and the ancient lungfish Rhinodipterus share this “primitive” shape, Clement and Ahlberg hypothesized that the brain shape of other modern lungfish probably evolved as a unique evolutionary innovation. Other researchers have noted that the brains of today’s amphibians share some similarities with those of Protopterus and Lepidosiren. Looking at the entire evolutionary tree, it is now apparent that this was simply convergent evolution.

Clement and Ahlberg also looked into what brain says about function and behavior. They note that lungfish probably developed an enhanced sense of smell through their evolution, based on changes in the size and shape of the part of the brain associated with olfaction. Some differences in the inner ear–which is related to sensing changes in body position, movement, as well as sound–are also apparent across species, but the specific implications of these differences are a little hazier.

Digital endocast and interpretive drawing of the endocast from Rhinodipterus. The front of the brain is on the right, and the back (spinal cord) is at the left. Modified from Clement & Ahlberg 2014, CC-BY.

Digital endocast and interpretive drawing of the endocast from Rhinodipterus. The front of the brain is on the right, and the back (spinal cord) is at the left. The inner ear region is shown in orange, the hindbrain (including base of the spinal cord) in yellow, the midbrain in blue, and the forebrain in green and red. Modified from Clement & Ahlberg 2014, CC-BY.

Lungfish brains are surprisingly interesting! My congratulations to the authors on producing a very accessible piece of work. If a dinosaur paleontologist can understand it, that’s an achievement! Yet, even with this new study, there is so much more to learn. Hopefully studies of other well-preserved specimens will provide additional information on the noggins of these fascinating animals.

The modern Australian lungfish Neoceratodus. Public domain, modified from Flower 1898.

The modern Australian lungfish Neoceratodus. Public domain, modified from Flower 1898.

Citation
Clement AM, Ahlberg PE (2014) The first virtual cranial endocast of a lungfish (Sarcopterygii: Dipnoi). PLOS ONE 9(11): e113898. doi:10.1371/journal.pone.0113898

Category: Fish, Open Access, Paleontology, PLOS ONE, Zoology | Tagged , , , , | 2 Comments

Give the Gift of Paleoart!

One of my favorite things about the Internet Age, among many favorite things, is the way in which it facilitates access to some incredible paleontology-themed art. The talented artists who illustrated the dinosaurs of my childhood reached their audiences through books or magazines. Now, a quick Google image search, or a brief stint on Twitter, or a browse through deviantART, turns up countless creative and compelling works by artists around the globe. We are living in an age of incredible abundance. Yet, as noted by many paleontologists and paleontological artists, it is still incredibly difficult even for well-known artists to be compensated appropriately for their talents.

Want to make a difference? Support artists by purchasing their work! During this time of the year when many have their eyes towards mass-produced “stuff”, find something a little more unique for someone in your life. What paleontology fan wouldn’t want a compelling print to hang on their wall, or a t-shirt depicting their favorite prehistoric beastie?

Support Original Palaeoart: accuracy, creativity, history

A cause I can get behind! From Witton et al. 2014

Towards this end, I’ve put together a list of a few artists whose work I think is worth highlighting! Of course, this list is not intended to be comprehensive, and I’ve generally gravitated towards people whom I know in real life or on social media, and who have a strong web presence with easy ways to order their work. If I missed anyone, it is not intended as a personal slight–in fact, please add more artists in the comments!

Acheroraptor, by Emily Willoughby. CC-BY, via Wikimedia Commons.

Acheroraptor, by Emily Willoughby. CC-BY, via Wikimedia Commons.

The List (Alphabetical Order, with Twitter handles when available)

Raven Amos (@alaskanime) has a fun, almost Art Nouveau style to her work. I love the clean lines and bright colors that she brings to the table. Check out her stuff on her deviantART page or her RedBubble page.

Michelle Banks (@artologica) focuses on squishy cells rather than paleontological topics, but her science-themed work is so compelling that I have to include it here! Check out her website or her Etsy shop for more.

Biscuithead and the Biscuit Badgers (@biscuitbadgers) also are not paleoartists per se, but captured my heart with their musical ode to dinosaurs. The video is something special, and the rest of their tunes (available via their website, iTunes, or Amazon) will appeal to anyone who likes quirky, geeky music.

John Conway (@nyctopterus) is well-known to many as one of the core people in the “All Yesterdays” movement. His work captures mood in a way that few do (an unhappy Hypsilophodon is one great example). Visit his website here.

Julius Csotonyi (@JCsotonyi) blends “traditional” and digital media for breathtaking renderings that frequently reach a global audience. My personal favorite is his collage of ceratopsian heads. See more work at his website.

Scott Elyard (@notdeadorgone) creates some truly delightful, original work; perhaps my favorite is his robotic, electronic Triceratops. But, he also has pterosaurs, and…well, just check out his Redbubble shop.

Rebecca Groom (@PixelMech) has gained fame as the creator of Paleo Plushies–prehistoric animals in cuddle-able form! She recently had a successful Kickstarter campaign for a stuffed Velociraptor, and has a variety of other stuffed organisms here.

Doug Henderson painted many of the dinosaurs of my childhood, and has done more than just about anyone else to set high standards for reconstructing dinosaurs within their environments. Look at one of his works, and you are transported to the Mesozoic. See his amazing portfolio here.

Glendon Mellow (@FlyingTrilobite) has established himself as someone who does “Art in Awe of Science” (to quote his website), and is also a positive advocate for artists. As you might guess by his Twitter handle, trilobites hold a special place in his repertoire (and his “baby trilobite” graphic is totally adorable on a onesie).

David Orr (@anatotitan) has produced a series of fun, whimsical logos–dinosaur family crests, as well as Protoceratops rendered in a vaguely tiki-bar motif. Learn more at his website or his Redbubble store.

Niroot Puttapipat (@himmapaan) brings a Victorian sensibility to paleontological art, and it is delightful! Picture Triceratops on a tricycle, or the fable of the tortoise and the hare recast with Cretaceous characters. You can order prints via his Redbubble or deviantART shops.

Sharon Wegner-Larson (@Omegafauna) has work that spans a variety of zoological subjects in paint and textiles, including some gorgeous interpretations of Dimetrodon and Triceratops. See more at her website or her Etsy store.

Emily Willoughby (@eawilloughby) captures the birdy nature of carnivorous dinosaurs–in no small part due to her hours spent observing and photographing today’s birds. And a “Caffeinated Raptor“? Sounds like a recipe for trouble (and some fun art)! See here for links to original art, prints, and shirts.

Mark Witton (@MarkWitton) is widely known as a pterosaur researcher and illustrator, as well as an advocate for high-quality paleoart (err…palaeoart). Just about everyone I know loves his “Quetzalcoatlus chowing down on baby sauropods” piece (below). This link tells you how to get prints of this and other work by Mark.

Pterosaurs feasting, in a classic image by Mark Witton. CC-BY, from Witton & Naish 2008.

Pterosaurs feasting, in a classic image by Mark Witton. CC-BY, from Witton & Naish 2008.

What else can you do to support artists?

Supporting artists isn’t just something for the holiday season–you can (and should) do it all year long! Here are a few ideas:

  • If you’re a researcher, commission an artist whose work you like to depict your latest fossil discovery. Great artwork can be key to capturing media attention, as well as telling your scientific story to a broad audience. Original, high-quality art is worth the investment!
  • Tell your friends about the great art that you’ve seen. Spread the word on social media, and encourage others to support artists.
  • If you are giving a public presentation, use work by up-and-coming artists to illustrate your points (of course, make sure that you have permission to use it, and credit it appropriately!).
  • Decorate your office or home with paleontological art!
  • If you’re looking for something really special for yourself or someone special to you, consider commissioning a piece of original art. This might be a painting, a t-shirt, a logo, or maybe even a tattoo!
  • Be a good citizen — always credit work appropriately, make sure you have permission to use art, pay fair prices for original work (“exposure” doesn’t pay the bills!), and encourage others to do the same. Remember: “Wikipedia” or “The Internet” isn’t a proper citation.

Citation
Witton, Mark P., Naish, Darren, and Conway, John. 2014. State of the Palaeoart. Palaeontologia Electronica Vol. 17, Issue 3; 5E: 10p.

Update: David Orr has a fantastic gift guide over at Love in the Time of Chasmosaurs, with some overlap, and a few great artists not mentioned here. Go check it out [and part 2 also]!

Category: Art, Dinosaurs, Paleontology | Tagged , , , | 9 Comments

Can penguins tell us how far the Cretaceous diving bird Hesperornis wandered?

Don’t mess with Hesperornis. It was a flightless, aquatic Cretaceous bird that measured up to six feet long, had a beak lined with sharp teeth, and was partially responsible for the downfall of at least one scientific career*. It superficially resembled a loon or a penguin–unlike penguins, though, Hesperornis probably propelled itself using its feet rather than its stumpy wings. Hesperornis also had a wide range–fossils within North America are known from Arkansas up to the Arctic Circle. Even during the comparatively balmy Mesozoic, winters would have been cold in the far north. Today’s birds (including many penguins) with this kind of geographic range are often migratory–so was Hesperornis migratory with the changing of the seasons, or did it stay put year-round?

Hesperornis, by Nobu Tamura. CC-BY.

Hesperornis, by Nobu Tamura. CC-BY.

For living species, you can track migration with banding or radio tracking devices. There’s no such luxury for fossil birds, which are sort of…stationary. Bones are all we have. Two major possibilities exist to parse out possible migration patterns: isotopic analysis (looking at the chemical makeup of the bones, which can be affected by where an animal gets its food and water) and bone histology (microanatomy).

Map showing locations of Hesperornis fossils studied by Wilson and Chin (2014; figure from the paper, modified from original by Blakey).

Map of North America during the Late Cretaceous, showing locations of Hesperornis fossils studied by Wilson and Chin (2014; figure from the paper, modified from original by Blakey).

Paleontologists Laura Wilson and Karen Chin set out to determine if bone histology might hold a record of ancient migrations by Hesperornis and its closest relatives. Bone tissue is affected by the way an animal grows–if an animal grows quickly and without pause, the bone shows one pattern, and if an animal grows quickly but experiences pauses in growth (or if it grows slowly), another pattern of bone shows up. Studies in non-avian dinosaurs have reached varying conclusions about what bone anatomy says regarding potential migrations, although an overall opinion seems to be that dinosaurs at high (Arctic) latitudes might show more prominent growth marks than their more southerly relatives, due to sharply distinguished seasons. If an animal stayed put for the winter, the cold temperatures (and associated decrease in food availability) would have slowed down its growth. An alternative viewpoint suggests that sharp growth marks resulted from the stress of migration, and still another viewpoint posits that you can’t really tell much of anything about migration from bone microanatomy. At least part of the conflicting story resulted from a dearth of studies on modern migratory and non-migratory animals that were good analogues for Mesozoic animals.

Penguins to the rescue! Conveniently, today’s penguins are rather aquatic animals (similar in this respect to Hesperornis), some of which are quite migratory during their lifetimes and others of which stay fairly close to home. Some species grow fairly quickly, and others grow slowly by comparison. Because we can understand the generalities (and many specifics) of modern penguin behavior, they make good lenses through which to interpret the past.

Gentoo Penguin Colony

A day at the beach for Gentoo Penguins. “Gentoo-Colony” by Ben Tubby – IMGP8815. Licensed under Creative Commons Attribution 2.0 via Wikimedia Commons

Wilson and Chin sampled four specimens of Hesperornis (three from Kansas in what is now the Midwestern United States, one from Nunavut in the Canadian Arctic) as well as a spectrum of individuals from three different penguin species with a variety of migratory behaviors (Adélie, gentoo, and chinstrap penguins–all members of the genus Pygoscelis). Hind leg bones were cut up, glued to a microscope slide, polished, and examined under high magnification.

"What are you looking at?" Chinstrap penguin, photo by Jerzy Strzelecki. CC-BY.

“What are you looking at?” Chinstrap penguin, photo by Jerzy Strzelecki. CC-BY.

None of the penguin bones–for migratory or non-migratory species–showed evidence of growth marks; thus, this feature isn’t reliable for inferring migration patterns. Interestingly, the non-migratory gentoo penguin showed some differences in the basic fabric of the bone from its migratory kin. These features included more radial bone and higher vascular canal densities (related to the number of blood vessels permeating the bone). Wilson and Chin suggest, based on comparisons with other animals as well as growth rate data for penguins, that these features are related to a very rapid growth rate in gentoo penguins. This may be related, in part, to the need for the penguins to reach full size prior to the start of the harsh Antarctic winters. More study is needed, they note, particularly to see if these patterns hold throughout the rather larger range of gentoo penguins (the sample used here was from the southerly limits).

Overall, the Hesperornis from north and south didn’t differ in any substantive way that couldn’t be attributed to differences in the age of the animals at death. Importantly, it looks like the animals reached skeletal maturity (adult size and a cessation of major changes in the skeleton) within a year of hatching. Thus, even if migration patterns caused stresses to the body that could show up in the skeleton, they probably wouldn’t be visible in Hesperornis. They just didn’t grow enough after the first year to show this kind of seasonal skeletal marking, similar to penguins today. This could be interpreted two ways: 1) the animals got big enough, quickly enough, to be able to migrate long distances soon after hatching; or 2) the animals got big enough, quickly enough, to be able to tolerate long, cold winters. Unfortunately, we can’t tell from the evidence at hand.

This uncertainty might be frustrating to some (did Hesperornis migrate, or not?!), but that shouldn’t overshadow the major accomplishments of this study. First, there is now a lot more information about how one ancient bird grew–the study by Wilson and Chin greatly expands the previously published sample for Hesperornis, particularly in terms of geographic representation. Secondly, the study provides a major new dataset on the bone of extant penguins, which helps interpret both life in the past and life in the present. Bone histology may not hold the keys to tracking ancient migrations after all.

The research was published in a new open access journalRoyal Society Open Science. It’s excellent to see an expanding number of open access venues, and equally excellent to see scientists using these venues!

The hypnotic patterns of gentoo penguin bone, under high magnification and cross-polarized light. The image here is <2 mm across. Modified from Figure 6 in Wilson and Chin 2014. CC-BY.

The hypnotic patterns of gentoo penguin bone, under high magnification and cross-polarized light. The area shown here is <2 mm across. Modified from Figure 6 in Wilson and Chin 2014. CC-BY.

*When O.C. Marsh published his United States Geological Survey monograph on toothed birds (including Hesperornis), it was decried by some in the Washington establishment as evidence on the boondoggle of federally funded science (among other things–the full situation was quite complex and ugly). That controversy led, in part, to funding cuts for the USGS, including the loss of Marsh’s position with the survey. The more things change, the more they stay the same.

Citation
Wilson, L. E., and K. Chin. 2014. Comparative osteohistology of Hesperornis with reference to pygoscelid penguins: the effects of climate and behaviour on avian bone microstructure. Royal Society Open Science 1:140245. http://dx.doi.org/10.1098/rsos.140245

Category: Birds, Dinosaurs, Paleontology, Zoology | Tagged , , , , , | 4 Comments

Which (non-open access) journals can paleontologists access?

In a previous post, I detailed the various ways in which paleontologists access the non-open access literature. Institutional subscription was the most commonly-used method (but not for all people who answered a survey on the topic!), followed by accessing author-posted PDFs or requesting PDFs over social media.

A logical follow-up question is which non-OA journals are most commonly available to paleontologists via their institutions, at least when institutional subscriptions are available. Which subscription-based journals are least available?

To evaluate these questions, I posted a survey and advertised it via Facebook and Twitter. The sample shouldn’t be considered scientific, but it probably can be considered at least a general picture of the state of things for many paleontologists.

Here are the results! A total of 115 responses were submitted. One minor note: due to the nature of the survey form, there may have been some small errors in how some individuals responded, and some did not answer particular questions. Note, for instance, that 78% of respondents reported institutional access, but 24% reported no access at all to Nature. I do not expect, however, that these kinds of errors would have greatly influenced the reported percentages. Note, also, that individuals could report both a personal subscription as well as institutional access. [click table to enlarge — a text-based table didn’t present well, so I include the results as a graphic]

Type of electronic access, if any

survey

Some general observations:

  • I am somewhat surprised by the rate of inaccessibility reported for some journals. For instance, a quarter of all respondents indicated no access to Science or Nature, journals which have a reputation as being widely accessible. Now, the survey did include respondents from small museums, government agencies, and amateur collectors; this is probably where many of those without access reside.
  • Society journals are doing reasonably well, for the most part–if you are a vertebrate paleontologist wanting to reach an audience of vertebrate paleontologists, JVP is one of the better options in terms of accessibility. I speculate that some folks keep their memberships at least in part for the journals.
  • Some journals that are anecdotally considered “top tier” (and which I personally consider to often publish very solid science) are not terribly easily accessible. This should be given some consideration for those cases when having to submit to a non-open access journal.
  • Best quote from the survey, regarding a journal I shall not identify [edited for punctuation]: “If I was going to publish something I didn’t want someone to see, I’d put it there.

How to use these results?

Firstly, the only way to guarantee easy electronic access to one’s research is to publish in open access or free-to-read journals. Barring that, institutional repositories or personal PDF posts can be a secondary measure (although I suspect that the activation energy required for many readers to locate such sources outside journal websites is a significant barrier).

However, based on conversations with colleagues at various stages in their career, publishing in certain non-OA journals is important. But, that still doesn’t absolve a researcher from working to ensure that their work has at least a minimum level of easy accessibility. We can say “just use ILL” or “just write to the author”, but every barrier to immediate access reduces even cursory skimming of a paper by potential readers. If you absolutely have to publish in a non-OA journal, it is worth your time (and career) to publish in one that is more widely available than not.

So, if you have to submit to a non-OA journal, give some consideration to these survey results. If many of your colleagues and other potential readers won’t be able to read your work easily, you may want to submit elsewhere.

Category: Open Access, Paleontology, Publishing | Tagged , , , | 2 Comments

How do paleontologists access the (non-open access) literature?

It is no secret to those who know me that I am strongly supportive of open access (OA)–published data and personal experience alike show that OA is strongly beneficial to science. That said, it’s not as if we can ignore the “non-open” (call it paywalled or subscription based or whatever) literature. Some really great research is published there, and it is often necessary to get access to it one way or another.

One thing I have been really curious about is how paleontologists and paleontology enthusiasts access the non-OA literature. Is literature access even a problem for most people? If you don’t have institutional subscriptions, what other methods work?

Mostly for my own curiosity, and partly so I can be better informed on the issues, I put together an informal, non-scientific survey. The survey asked questions about how people access the literature, the kinds of journals they can access most easily, and basic demographics. I advertised the survey via Twitter and Facebook. I wouldn’t count it as a scientific sample by any means, but I do feel that I got reasonably good coverage of various types of paleontologists at various types of institutions (as well as non-paleontologists who follow the literature). 115 individuals responded, during the course of about a week. I’ll be exploring these results in the this and a few upcoming posts.

How do you access the literature?
The first survey question focused on the methods that people use to access the literature–institutional access, personal subscription, requests via social media, etc. The question was specifically worded as, “In which ways do you electronically access full text articles from the scientific literature that require subscription?”

Which methods do you use to access the literature? Results from a recent survey.

Which methods do you use to access the literature? Results from a recent survey. Note: “Author-posted PDF” includes sites like academia.edu.

These results show that people, as a whole, use a whole variety of options to access “paywalled” literature. There’s a surprising amount of variety–but which methods are most commonly used? To assess that, I asked the same question in a different fashion, asking survey-takers to indicate the three methods they most commonly used.

Most commonly used methods to access literature.

What are the top 3 methods you use to access the subscription-based literature? Results from a recent survey.

This, I think, is a much more informative set of results. Perhaps unsurprisingly, “institutional subscription” was rated as one of the top methods for accessing literature by 76% of those who answered the question–after all, 60% of the respondents indicated they were at a college or university.

was a bit surprised by the next most highly rated category–author-posted PDF (as worded, the question included authors’ personal websites, institutional websites, and external sites such as academia.edu). A full 40% of respondents indicated this as frequently-used. More on the implications of this below.

The third most-indicated method was requests over social media–Facebook, Twitter, and the like, selected by nearly 30% of those who responded.

There are also a few interesting “mismatches” between the two survey questions, suggesting that some methods are widely but infrequently used. This would include contacting authors for the PDF and getting PDFs from colleagues with subscriptions, in particular.

What does this mean?
So, with this information in hand, what can we do as scientists and other folks interested in the paleontology literature? If there are cases where we have to (or feel we have to) publish in non-open access literature, how can we maximize availability of our work?

1) Don’t assume that an institutional subscription will necessarily get your work into the hands of interested readers. Nearly a quarter of the respondents don’t list this as their primary source of literature access! In an upcoming post, I’m going to talk about access to specific journals, which will illuminate the issue even more. Without giving too much away, some choices are far better than others.

2) Author-posted PDFs are quite important for distribution of scholarly literature. So, if you’re an author, get that PDF out there! And if the journal doesn’t allow it, consider another journal (read your publication agreements–once you sign that piece of paper, you may not have all of the rights you think you do!).

3) A large percentage of people use “unauthorized” methods (i.e., those explicitly not allowed by journal terms of use and publication agreements) to access literature. This includes requests over social media, bumming PDFs from colleagues with access, and internet forums. One could argue that these folks should just use “legitimate” methods like ILL, writing the authors, etc., but the reality is that people don’t, and this is at least in part a factor of convenience as well as necessity (once an author dies, it’s hard to get in touch with them). As an author I would much rather my work be convenient and easy to access than not. I’d also rather my work be convenient, easy, and legal to access by multiple methods.

Coming Up…
Which subscription-based journals are most widely available? Which journals most guarantee that your work is hard to find? The answers may surprise you.

Final note…source data will be posted once I’ve concluded with the series!

Category: Open Access, Paleontology, Publishing | Tagged , , , , | 5 Comments