Tuesday, 16 September 2014

Theropod envy?

When giving conference or public presentations, I often use the opportunity to take a swipe a theropods: after all, most of my career has been spent working on dinosaur herbivores, which often end up in the capacious guts of their carnivorous relatives. However, it's not because I genuinely hate theropods per se - some are amazing animals, and even though Tyrannosaurus is, without doubt, over-exposed and over-rated it is still a neat animal. I've even found myself working on theropods from time-to-time, though admittedly I still have a strong preference for the more diverse and disparate herbivores. The main reason I feel I have to insult theropods (and by extension theropod workers) is simply the hyperbole that surrounds these animals. A mouthful of sharp teeth, claws, and endless speculations over dino-celebrity death matches seems to get people weak at the knees, clouding all sensible judgement regarding new claims about their palaeobiology. Who really cares if one giant theropod was 50 cm longer than another? Such trivia has no real effect on our knowledge of theropod biology and evolution. Although the media might be blamed for fanning the flames of theropod adoration, this would be unfair - they simply give people what they want and there are plenty of people out there, both professionals and public, who idolize theropods in ways analogous to 'A'-list celebrities. This manifests every year at Society of Vertebrate Paleontology meetings, for example: theropod talks are often packed to the rafters (thanks mainly to work on feeding and behaviour: big fluffy killer death lizard syndrome), whereas the room feels distinctly emptier when similar talks start on herbivorous dinosaurs.

A cast of Giganotosaurus in the Museo "Carmen Funes" Plaza Huicul, Argentina
More seriously, this idolatry extends to scientific publication too. I'm frequently teased by colleagues in other disciplines about how easy it must be to get dinosaur papers into top journals like Nature and Science - after all, dinosaur papers appear in both venues regularly, despite the fact that dinosaur workers represent only a tiny fraction of scientists worldwide. However, while vertebrate palaeontology clearly punches above its weight in this regard, there is a bias - almost all dinosaur papers in these journals are on theropods, while the other two-thirds of dinosaur diversity do far less well (and analytical papers dealing with dinosaurs as a whole are exceptionally rare). These theropod papers generally fall into two categories - announcements of new dinosaurs with feathers, or some other aspect of the dinosaur/bird link - or discoveries of non-feathered theropods with potentially interesting palaeobiological features or geographical/temporal range extensions.

This is perhaps exemplified by the new paper in Science published last week on the iconic North African theropod Spinosaurus (Ibrahim et al., 2014). In this widely reported paper, the authors describe a new articulated skeleton of this animal and use it to update various aspects of the animal's anatomy. The hook for the paper was that Spinosaurus might have been a largely aquatic animal - and when not aquatic might have been quadrupedal - an unusual (and potentially interesting) adaptation for a theropod. This news flashed around the world on the media, Facebook and Twitter, with few critical voices. However, the hype generated by the release (in no small measure due to the heavy involvement of National Geographic) overlooks some important details.

Importantly, most dinosaur workers had already accepted that spinosaurs were probably unusual dinosaurs that did spend a lot of time in water. This was based on numerous lines of evidence:
1. Snout and tooth morphology: convergently looking like a crocodile and potentially engaged in croc-like feeding behaviour. Those teeth aren't for slashing, but could have been good at holding slippery prey;
2. Weird forelimbs: the big claws have long been suggested as tools for gaffing fish from the water, and it has even been suggested that the robust humerus might have been associated with quadrupedality;
3. Gut contents: the British spinosaur Baryonyx has fish remains in its gut contents (the only gut content known for a spinosaurid);
4. Oxygen isotopes: these suggest that spinosaurs ate far more aquatic prey than other dinosaurs and may have spent more time in/near water as a result;
5. Palaeoenvironments: the North African localities yielding Spinosaurus have long been though to be very wet - with wide meandering channels, which, coincidentally are full of big tasty fish.

This work was all done previously by palaeontologists going back to Strömer, most notably by Angela Milner, Alan Charig, Andrew Cuff, Emily Rayfield and colleagues in their work on Baryonyx and Spinosaurus (Charig & Milner, 1986, 1997; Cuff & Rayfield, 2013) and by the isotopic work of Romain Amiot and colleagues on Spinosaurus (Amiot et al., 2010), as well as numerous other less detailed accounts. Although these papers are cited in the recent Science contribution, they are not given due credit for establishing the idea of aquatic spinosaurs – the new observations made on the additional material are really only the icing on the cake for the story of spinosaur habitat preference. Moreover, doubts have emerged over the proportions of the new skeleton (see the excellent blog entry by Scott Hartman) and given the vagaries associated with the collection of the material (which was  collected by professional fossil dealers who did not  keep or provide detailed field notes to corroborate the association of the skeleton) additional assurances are needed to support the claims of the authors in the Science article. If the new specimen is genuinely associated and the problems noted thus far can be accounted for this would be a neat discovery (even if it is a theropod): a new, good specimen of an animal known otherwise from published images and isolated material. However, extraordinary claims merit extraordinary levels of evidence.

Given the foregoing I'm left wondering why the editors thought that this might be suitable for Science - a journal that wants to publish transformative research. Is it a new taxon? No. Does it tell us something distinctive about evolution or dinosaurs that we didn't know before? No. This is really a specialist paper, updating our knowledge of a single taxon that was named nearly a century ago, although one with an interesting history. My theory? It's a big scary theropod ... I doubt very much that anyone working on a new sauropod or ornithischian skeleton belonging to a named taxon would stand much chance of getting similar papers published. That's why I'm envious of theropods ...


Amiot, R. et al. (2010). Oxygen isotope evidence for semi-aquatic habits among spinosaurid theropods. Geology 38: 139–142 doi:10.1130/G30402.1.
Charig, A. J. & Milner, A. C. 1986. Baryonyx, a remarkable new theropod dinosaur. Nature 324: 359–361.
Charig, A. J. & Milner, A. C. (1997). Baryonyx walkeri, a fish-eating dinosaur from the Wealden of Surrey. Bulletin of the Natural History Museum London 53: 11–70.
Cuff, A. R. & Rayfield, E. J. (2013). Feeding mechanics in spinosaurid theropods and extant crocodilians. PLoS ONE 8(5): e65295. doi:10.1371/journal.pone.0065295.
Ibrahim, N. et al. (2014). Semiaquatic adaptations in a giant predatory dinosaur. Science DOI: 10.1126/science.1258750.

Monday, 1 September 2014

Opening up on Open Access

I'm a huge admirer of the hard push we're currently witnessing to make published research freely accessible to all who need it. The move towards universal Open Access (OA) is going more slowly than some would like, but there has been a huge shift in perception among academics, publishers and funders, most of it positive. Many of the issues in this debate have already been aired extensively, but I have a few brief observations (well, mini-rants) based on my own biases and experiences, both as a journal editor (both for commercially and society published journals), someone with a hand in running academic societies, and as an author. This is going to be a stream of consciousness, so apologies in advance ...

1. OA costs authors money. Please don't lambast people for not publishing their papers with Gold OA - they may not be able to afford it. Average fees for Gold OA are high (around $2.5K on average in my field) and at a time when budgets are tighter and tighter finding money to support publications gets trickier. RCUK recently provided the institutions that they fund with block grants to pay for work done via their grants to be published OA. However, these block grants are inadequate: one recently completed NERC grant of mine (which was funded prior to the new rules coming in) generated nine papers - the costs of making each of these Gold OA would have exceeded my institution's entire RCUK annual block grant. In this case, the funding body has imposed a knee-jerk response to a call for more OA, without providing the people that it funds adequate resources to do so. The situation for people in small institutions in developing counties is likely to be even harder.

2. OA costs publishers money. It could be argued that OA fees should be lower (and some places like PLoS and PeerJ manage this, which is admirable), but there is a fixed minimum cost of publishing a paper in any format due to the need to employ people to run journals. Even online journals require IT  and editorial staff, as well as the staff needed to look after their pay and pensions, legal issues,  maintaining their offices, etc. Costs start to balloon further when printing physical copies and distributing them. Although many large commercial publishers might have slack in their accounting lines to offer lower fees, thanks to economies of scale, many smaller publishers will not. Let's not forget many excellent journals are published by small academic societies, which serve niche communities well, and that are entirely financed by membership dues or small investment portfolios. Many small academic societies could not exist or promote new work without the revenues generated by publications, which are usually fed back to benefit the members of those societies directly. Give these guys a break, at least.

3. Green OA is great. Authors retain copyright over the final versions of their publications in their original form - i.e. the non-formatted final version they submit to the publisher. Posting of this after an embargo period is free, legal and gets the data out. It might not allow access to the beautiful proofed version of the article, but it does the job. Although access to the article isn't instant - it's still free after a relatively short lag. Please remember OA and instant access are not necessarily the same thing. Except in a few very rare instances, does it really matter if you have to wait six months for public access to a paper? (Especially given point 4, below). Admittedly the world might benefit from rapid medical or technological advances based on immediate OA, but let's be honest - it's 99.9% likely that the people with the insight and training to make those advances will have instant access to it through an institutional library or professional network anyhow.

4. Rediscover some scholarly skills. To some extent, I regard the need for instant gratification with some amusement. I did my PhD at time when email was just starting to be used widely (I had to go to a university computer centre to use it!) and PDFs did not exist. Amazingly, I still managed to access all of the material I needed, essentially for free, through libraries, interlibrary loans, requesting reprints, and asking colleagues if they had copies of particularly hard to get publications that I could borrow from them. Getting away from Google and asking a human being for help might actually have some side benefits for your research. All of these are forms of free information exchange that existed for centuries before exchanging PDFs. Ask the author for a PDF of that paywalled paper. You might actually learn something else by accident.

5. A historical perspective is interesting. Originally all scientific publication was funded by private patronage - authors had to pay to publish their work, either directly (often via the historical equivalent of crowd-sourcing) or via high membership dues to a handful of elite societies. Handing over publication to commercial publishers actually removed the need for authors to pay - scientists swapped the initial cash outlay for the fact that commercial publishers would profit from their work. So, the rise of academic publishers allowed people who formerly couldn't pay to get their research published. Free to the author at the point of submission. We've now come full circle, with authors again expected to pay upfront for Gold OA. We're effectively arguing for a nineteenth century financial model, though admittedly a better version of it in which papers are much easier to find for everybody...

In conclusion, it would be great if we could publish everything instantly for everyone and - ulimately - I would be totally in favour of this approach. Where possible, I currently use Gold OA for some of my work but, frankly, pressures to publish in certain venues (in terms of career advancement and visibility) and lack of ready funds often prevents this. However, until we work out where the money to pay for Gold OA  will come from we will have an extended period with a mixed model of Green and Gold OA, as well as paywalls for some publishers that hold out for profits either because they want to or simply have to in order to survive. The main ways this might happen are reductions in OA fees associated with a total abandonment of print journals (saving on printing and posting), less reliance on editorial offices (e.g. less proofing - as happens with PLoS ONE - which has pros and cons), some unprecedented drops in expected profit margins for commercial publishers (good luck with the shareholders on that one), and/or governmental intervention to either cap profits on relevant publications or to provide the money to make up the shortfall between the two.