Friday, 19 August 2016

Favourite figures from papers

My last few posts have been been a bit serious, so thought it was worth having a fun post to break it up again. I'm proud that most of my papers to date have figures I've made in them, and a few of them even have one's I've drawn. I do not claim to be an artist, but think they do a good job for explaining the science. As the cliche goes, a picture says a thousand words. The rest of the post will focus on some some of my favourite figures included in papers, normally because they are interesting, beautiful or just plain old fun. Without further ado:

1. Pandas falling into caves where their remains are preserved
Figure 7 from Jablonski et al., 2012. Remains of Holocene giant pandas from Jiangdong Mountain (Yunnan, China) and their relevance to the evolution of quaternary environments in south-western China.
This has been going around the web for a while due to its brilliance and what's not to love about it? Pandas, cartoon speed lines showing it falling and flood waters washing bones to their final resting place where they were discovered.

2. A thunder thighed dinosaur kicking a pesky theropod.
Figure 12 from Taylor et al., 2011. A new sauropod dinosaur from the Lower Cretaceous Cedar Mountain Formation, Utah, USA. Acta Palaeontologica Polonica 56, 75-98.
This amazing piece of art by Francisco Gasc├│ shows the recently described Brontomerus mcintoshi kicking an Utahraptor whilst protecting its baby. Why kicking? Well the dinosaur had massive blade like thighs (hence the Brontomerus name which means thunder thighs) so it was suggested they had evolved these massive legs for kicking as a defence mechanism.

3. This random thing
Figure from The Natural History of Oxfordshire (1677). Taken from 
The odd bulbous structure in the middle is the earliest known scientific figure of a dinosaur bone in the publication by Robert Plot. Plot thought it was from a giant human, and Richard Brookes was to name it Scrotum humanum in 1763 for somewhat entertaining reasons even though it is the end of the thigh bone. Officially that is the first name of a dinosaur ever (note the term dinosaur wouldn't arrive until 1842), but because the name fell out of common usage, the dinosaur it came from is now called Megalosaurus (a name that came about in 1824). There is talk that Megalosaurus is actually a bunch of different species and possibly genera, and if that is the case I am hoping that someone finds a reason to resurrect the original name for one of the new species.

4. Reptile in a tree just watching the world burn.
Fig 4 from Falcon-Lang and Calder, 2004. UNESCO world heritage and the joggins cliffs of Nova Scotia.
Painting of Hylonomus lyelli by Steve Greb showing the earliest known reptile sheltering in a tree trunk to avoid a fire. The hypothesis extends from the first finds of reptiles (dating back to 310 million years ago) remains in erect trees from Dawson (1882), although there is still discussion over whether the reptiles were sheltering or fell into the tree trunks and couldn't escape.

5. When hunting things from another realm, make sure you can actually eat it
Fig. 1 from Frey and Tischlinger 2012. The Late Jurassic pterosaur Ramphorhynchus, a frequent victim of the ganoid fish Aspidorhynchus?
The paper is a tale of fish eat pterosaur eat fish. They have the small Rhamphorhynchus with fish remains in its throat, but more spectacularly, 4 fossils of fish having their revenge by hunting these flying reptiles whilst the pterosaurs were probably catching fish at the water's surface. The problem comes from the fish having tiny teeth which get caught in the wing membranes causing the demise of both fish and flying reptile.

6. Mortichnium
Fig. 1 from Lomax and Racay. 2012. A long mortichnial trackway of Mesolimulus walchi from the Upper Jurassic Solnhofen lithographic limestone near Wintershof, Germany.
First things first, a "mortichnium" is a fancy way of saying a trackway created by an animal that then died and is preserved at the end of it. In this case, a 9.7m long trackway was created by an ancient horseshoe crab, that for whatever reason died at the end of it (left side, little blob) with the whole harrowing march preserved for us to see. Trace fossils are the only fossils we have created from ancient organisms that show behavioural patterns, and the death traces are the rarest with most being created by horseshoe crabs and other invertebrates, but they do exist for fish as well (see Schweigert et al., 2016).

7. Land vs sea creature huddles
Hawkins 1854. On visual education as applied to geology.
One of the figures from Hawkins (1854) that shows early reconstructions of the the first known dinosaurs (L-R: Iguanodon, Hylaeosaurus and Megalosaurus), and some marine reptiles including Plesiosaurus and Ichthyosaurus. Anyone who has ever studied dinosaurs has probably seen the famous Crystal Palace dinosaurs and the author was the sculptor himself. The paper describes the issues with reconstructing animals from limited evidence, and the designs as they are were to be the foundations of how dinosaurs were reconstructed for many years (down to the tail dragging).

8. Deinonychus
Cover figure from Ostom 1969. Osteology of Deinonychus antirrhopus, an unusual theropod from the Lower Cretaceous of Montana.
This famous drawing of Deinonychus by Bob Bakker in the Deinonychus monograph is probably the most important in regards to how we view dinosaur today. They were no longer those tail-draggers of old, they could now be fast and active hunters. 

9. Fuzzy wuzzy was a dinosaur (not a bear)?
Fig 2. from Chen et al., 1998. An exceptionally well-preserved theropod dinosaur from the Yixian Formation of China.
Sinosauropteryx was discovered and theropod dinosaurs were never to be the same again. Just like Deinonychus making dinosaurs active, Sinosauropteryx was to make them feathery. The first non-avian dinosaur to have feathers would lead the the discovery of hundreds of new specimens over the next 20 years, mainly from China's Jehol biota. The figured specimen was also to be one of the first to be tested for fossil pigmentation (in melanin) with the dark banded regions in the tail and along the back probably being orange, and the "gaps" being white.

10. Therizinosaur just hanging out
Fig. 1 from Nessov 1995. Dinosaurs of Northern Eurasia: New data about assemblages, ecology, and paleobiogeography.
After a series of serious figures, I bookend the post with another funny one that is one of the best figures I've ever had the delight of seeing from a paper. I first saw it sat above a colleague's desk who was working on the group of dinosaurs - therizinosaurs (also known as segnosaurs). With their big claws, the author believed that they climbed trees like sloths. Looking at the drawing he also believed that they had a prehensile tail. Fossil wasp nests were found in trees of similar ages, and therizinosaurs had weak jaws and small teeth, so the logical jump was to propose therizinosaurs in trees were eating wasp nests. Work by many authors since suggests that they were plant eaters, and probably not climbing trees. It is shockingly difficult to see how 26 years after the Deinonychus paper, that dinosaur reconstructions had backtracked so far, but then if they hadn't I probably would not be posting this one.

Bonus 11. Dinosaur vomit
Martin 2014. Dinosaurs without bones. Pegasus Books, New York.
After I wrote my 10, I asked my lab colleagues if they could think of any other good ones and this one was suggested showing the potential impact from vomited material and the resulting trace. There are additional papers looking at urine/faecal material and their traces that have been identified in the fossil record (e.g. Fernandes et al., 2004) was suggested, but sadly there were no great images.

That wraps up this ten figures. Do let me know if you have any favourites that I've not included, whether they show ground breaking science, beautiful illustrations, or are just hilariously brilliant. Feel free to add links in the comments or tweet me (@AndrewRCuff). If I get enough I will do a part 2 (through however many). 

Wednesday, 10 August 2016

Extraordinary claims need extraordinary evidence

As the post's title says, extraordinary claims need extraordinary evidence and when it comes to palaeontology this couldn't be more true. If you have spent any length of time reading palaeontological literature, you may think that nearly all extinct animals did only one thing all the time. However, to realise how ridiculous that is, all you have to do is observe any living animals. Yet some palaeontologists seem to happily to ignore these facts, or unwilling to correct the media if things are misquoted. Either way the media love a snappy headline so it often makes big news.

Claim 1. T. rex was a scavenger. 
This all started with Jack Horner giving a talk around 1993 where he discussed the idea that T. rex was a very strange build for a predatory dinosaur with its tiny arms. Through the years it keeps re-appearing as a common question, and Jack Horner himself happily will raise it as a debate starter although there is no evidence he truly believes it. *There was an extensive chapter in a book in 2008 by Thomas Holtz that critically appraised this field (and covers many of the same points I do here, although I must admit I hadn't read it at the time of first publishing this article).* Brian Switek has written a great blog post on the whole debate back in 2013, shortly after a paper in PNAS described fossils of two fused hadrosaur vertebrae with a T. rex tooth crown embedded in them. The vertebra in question had regrowth around the damage showing the hadrosaur had survived its hunting and lived for at least a while longer, although the regrowth and trauma may well have led to its ultimate demise.

Figures 1 and 2 from  DePalma et al., 2013. Top showing the fused vertebrae. The horrific change in shape is a result of the trauma from the tooth (probably infection accompanying regrowth). The tooth crown is circled in white. Bottom images show CT scans of the crown embedded within the bone.
This is a case where a cool fossil find gets far more value as a publication than it should do (no offence to the authors as the fossil and science are both cool), because it is putting the nail in the bed of T. rex being a scavenger. But let's think about this in terms of terrestrial animals today. If I told you to think of a large scavenger, you'd almost certainly think of a hyena in Africa (and most likely a spotted one). I will forever remember being taught in a university course that spotted hyenas hunt 60% of their food! Equally shocking was being taught that for lions, they often scavenge more than they hunt! Of course I hear you all being sceptical (as was I), so I've done some research and indeed spotted hyenas across Africa always hunt more of their food than scavenge. The link is to a BBC article I accept, but the scientist interviewed has published many papers on the matter (e.g, Holekamp et al., 1997). As for the lion fact there is far less data out there, however it is widely accepted that lions can, and do, scavenge large percentages of their food. The reason for this is blatantly obvious: lions are the largest carnivores in their environment, if they stumble across a kill from another smaller predator (single hyena, leopard, cheetah etc.) they can easily scare it away and eat the food with no energy expenditure of the hunt (and their hunting success rate is low: 10-20%), so why wouldn't they? So why do we think that dinosaurs would be any different? T. rex was the largest carnivore in its environment so it will almost certainly have done both to varying extents depending on prey and carrion availability.

Claims 2-many. Spinosaurus.
Where to start with this one. I've worked on spinosaurs as part of my MSci project and have published on their snouts and convergences so am potentially biased from that work, but I hope I can walk through my reasoning on many of the issues with publications in the last few years. Just a quick background (if you don't know), spinosaurs are a crazy group of theropod dinosaurs that evolve incredibly elongate snouts. The group has gained its name from the first species found, Spinosaurus aegpytiacus which was discovered in Africa, and remains the largest known of the spinosaurs (and length-wise one of the biggest theropods ever) and possessing the biggest sail on its back. It only really came to global fame with Jurassic Park 3 as the big dinosaur that chased around the actors and killed a T. rex.

Spinosaurs being big and weird, with a global following garner a lot of interest in publications. This is further helped by the fact the original Spinosaurus specimen were destroyed during WW2 in a bombing raid of Munich so new fossils help inform us on this enigmatic group.
The original Spinosaurus specimen found by Stromer in 1912, now lost.
They also have evolved an unusual expansion of the premaxilla (the tip of the snout) called a terminal rosette.
Dal Sasso et al., 2005. The largest known Spinosaurus snout showing the highly elongate snout.
These unusual morphological features got them very quickly compared to lots of crocodiles, particularly the equally unusual and long snouted gharial.

Gharial skull showing the elongate narrow snout, with terminal rosette expansion (photo from Glasgow Museum Collections)
The gharial is a crocodile from India which uses its unusual snout to slash through water and to stun/capture fish. As such it follows that because things look the same, they eat same things and in pretty much all Spinosaurus papers discuss it eating fish (e.g. Ibrahim et al., 2014). Some of this is backed up by findings of acid-etched fish scales in the gut region of Baryonyx (Charig and Milner, 1997), and the skull shape of Spinosaurus performing similarly to that of the Gharial in finite element models (Rayfield et al., 2007).

However, everyone fails to take into account size.

Whilst the biggest gharials are 970kgs, the biggest spinosaurs are amongst the largest theropods to have ever lived with mass estimates between 7-20 tonnes. This is where my research came in. Spinosaurs do have incredibly rubbish snout morphology for relative strength as they are effectively solid cylinders. Alligators flatten their snouts so have big, flat, wide ones which are much stronger than similar sized cylinders. However, when size is taken into account, all crocodiles snouts were less strong than the Spinosaurus and Baryonyx snouts. Again I know people may argue that it means they are just able to take bigger fish, and there were indeed 6ft long saw-fish in the regions where Spinosaurus lived. However, that argument comes under the Tyrannosaurus only scavenging. Why would a super-massive predatory dinosaur with a strong skull (due to size over shape) only eat fish in an environment that would have had loads of other prey items, whether to hunt or scavenge? Many crocodiles are known to change diets as they get bigger shifting from mainly fish and amphibians to increasing amounts of terrestrial vertebrates. In the case of alligators, they shift from invertebrates and amphibians, to fish, then turtles and ultimately large terrestrial prey as they grow up. Whilst impossible to prove for Spinosaurus at present, a tooth from a South American spinosaur was found embedded in a pterosaur vertebra and an Iguanodon bone was found in proximity to the Baryonyx remains which may have also been consumed.

Due to spinosaurs consuming at least some fish in their diets, it is assumed they must have lived at least partially in the water to catch them. The first major paper attempting to scientifically prove this was Amoit et al. (2010) which used isotopes from their teeth (particularly the apatite - the stuff that makes bone and enamel hard). Some important things to know about the isotopes in question (in this case ╬┤18Op): 1) they vary with body size; 2) they vary with diet; 3) they vary location you are living (whether in actual location or water vs land). That being said, the authors test isotopes of teeth for spinosaurs, theropods and crocodiles (and their osteoderms) as well as isotopes of turtle shells from the same rock layers.

To compensate for the first issue, they get teeth of the same size for the spinosaurs and the theropods. They do not say though how they ensured the teeth all come from the same sized individuals and teeth in spinosaurs are notoriously different sizes in one individual, with big teeth in the terminal rosette, followed by some small ones, followed by some more big ones. The small sample numbers also worry me (most 3-4, but up to 9 teeth) were tested for each site/time as this size issue may come into play more. In addition they do not specify that they compensate for the size differences between the turtles and crocodiles compared to the spinosaur teeth, which when there conclusions are that the spinosaur isotope numbers are similar to that of turtles and crocodiles thus they are at least semi-aquatic, worries me greatly.

The second issue, with diets influencing isotopes, is tricky. Spinosaurs, as a group, are known to eat fish and terrestrial prey but we only have this data for one individual from England, and one from South America. Species and individuals in Thailand and Africa may have different preferences and proportions of each in their diets. For the other theropods, the diets are unclear as not all species are listed, but for the specimens that can be identified to taxa like Carcharodontosaurus presumably most prey was terrestrial. For crocodiles, presumably diet varies with body size like in modern crocodilians, but with no data even on the size of the crocodile teeth, this is tough to even guess at. So again let's assume their assumptions are fine.

The final issue is what is being tested. The authors assumed that they covered issue 1 with same sized teeth, and for sake of argument let's also assume that. They cover issue 2 by saying that spinosaurs eat at least some terrestrial prey so their isotopes should be similar to other theropods on that ground. Thus differences between the other theropods and spinosaurs must be down to where they are living. In this case, it is suggested that it is the water, as the spinosaur isotopic numbers are not statistically different to that of crocodiles and turtles. The problem with that is that spinosaur numbers are expected to be completely different to crocodiles and turtles living in the same environment (e.g. the water at least part of the time), as their body sizes are completely different. Secondly, the results are really heavily biased by the first three locales (all Thailand) where there is an enormous difference between spinosaurs and other theropods whereas in the other locations spinosaurs are not that different to other theropods. In fact, I carried out Mann-Whitney tests on their data and found that six sites are not statistically different (although sample size may well play a role, but can only work with what they've given), and one of the the other three is statistically "more terrestrial" than the other theropods. Brazil, Thailand and one site in Morocco (of the five) are the only places where spinosaurs are statistically different from other theropods. I am not sure how these issues escaped the reviewers, particularly as this completely changes the result of their whole paper. From the isotopes, it would be safer to say there may be a few locations where spinosaurs are doing something different to other theropods (and possibly semi-aquatic) but the rest are indistinguishable from any other theropod. So in this case the exceptional claim does not withstand scrutiny of their own data.

I had fun picking this apart as a first year PhD student, but have only now gotten around to writing it down, and sadly don't have any additional data to put it into a proper rebuttal. Hopefully someone might be able to add to this to either prove or disprove the original hypothesis, but presently it does not withstand statistical testing.

This paper has been used, in addition to the fish feeding spinosaur papers, to help support the new reconstruction of Spinosaurus by Ibrahim et al., 2014. The story of the new fossils has been well publicised by National Geographic and TED talks featuring Ibrahim but involves purchases by museums of some fossil bones that would be identified as Spinosaurus because of the big neural spines. When the original collector was traced, he led the authors to a site where additional Spinosaurus material was collected. They combined their newly collected material, the previously purchased stuff in the museum, and various other specimens including estimates from the original destroyed specimens. The result is a short legged theropod they propose spent a lot of its time in the water. 
Ibrahim et al., 2014 reconstruction of Spinosaurus.
Again an extraordinary claim and why the paper hit the front cover of Science, full size reconstructions were made by National Geographic and there were countless news and popular science articles and talks about it.

Does the evidence back this up? Well, not yet. The problem with reconstruction is they are based on lots of different specimens, so the reconstruction is a chimera. If any part of these comes from a different species the reconstruction will be wrong. Since the new Spinosaurus reconstruction in 2014, Evers et al., 2015, and Hendrickx et al., 2016 suggest there are at least 2 spinosaur species found in the same deposits, and some of the second - Sigilmassasaurus was used in the reconstruction of Spinosaurus. Even worse, we don't even know the specimens in the museum and the newly collected fossils from the field are from the same individual despite the word of the professional fossil collector in Morocco. There is no collection map that would be typical for any fossil collection to show how the specimens were found. The biggest oddity remains the legs. They are so short compared to any other known theropod. An older, African spinosaur for which a single specimen exists showing a lot of the skeleton (Suchomimus, Sereno et al., 1998) shows relatively normal leg sizes.
Sereno et al., 1998 reconstruction of Suchomimus showing the discovered specimen.
There have been suggestions that small legs would be ideal for swimming around in water particularly if it evolved webbed feet (no evidence) so it could catch fish. Funnily one of the original authors presented work at SVP 2015 showing their reconstruction tipping onto its side when put in water, but more recently Don Henderson presented work at ICVM 2016 showing the reconstruction would be stable in water, but then so was a T. rex model. The short legs don't make it better at being in the water in a static test, but I suspect longer legs would be better to counterbalance the large sail to prevent Spinosaurus being top heavy.

The extraordinary claim really is going to have to wait for a more complete publication of all of the original authors' finds. Unfortunately Science only publishes short papers, so the full monograph description has yet to happen. Whether it will, or gets caught up in never ending peer review due to some of the issues that are now being raised in other publications we shall have to wait and see. Ultimately, we really need an exceptionally complete individual fossil to back it up (like the Suchomimus fossil). Undoubtedly there is one out there, quite possibly in the Kem Kem of Morocco, but it needs a proper excavation and not a piecemeal extraction and selling by a commercial dealer who may have ulterior motives.

In science, the extraordinary claims make the big headlines, lead to publications in the highest impact journals, and this in turn often helps make researchers' careers. The problem in palaeontology, like all sciences, is this leads to overstatements or overreaches for the data that we have (particularly for small sample sizes). I have been lucky to work in labs that have been very good at helping me tone down my language to accept that there are uncertainties in our work, and really extraordinary claims do require extraordinary evidence. I hope anyone reading considers this when writing their next manuscripts.

*Update. It has been pointed out to me that I missed an important reference in the T. rex scavenging debate which I have now included. My apologies. Please continue to add further reading/comments with regards to the topic.

Amoit R, et al., 2010. Oxygen isotope evidence for semi-aquatic habits among spinosaurid theropods

Charig AJ, Milner AC, 1997. Baryonyx walkeri, a fish-eating dinosaur from the Wealdon of Surrey. Bulletin of the Natural History Museum of London 53, 11-70.

Cuff AR, Rayfield EJ, 2013. Feeding mechanics in spinosaurid theropods and extant crocodilians. PLoS One 8, e65295.

Dal Sasso C, et al., 2005. New information on the skull of the enigmatic theropod Spinosaurus, with remarks on its sizes and affinities. Journal of Vertebrate Palaeontology 25, 888-896.

DePalma et al., 2013. Physical evidence of predatory behaviour in Tyrannosaurus rexProceedings of the National Academy of Sciences USA 110, 12560-12564.

Evers S et al., 2015. A reappraisal of the morphology and systematic position of the theropod dinosaur Sigilmassasaurus from the “middle” Cretaceous of Morocco. PeerJ e1323.

Hendrickx C et al., 2016. Morphofunctional Analysis of the Quadrate of Spinosauridae (Dinosauria: Theropoda) and the Presence of Spinosaurus and a Second Spinosaurine Taxon in the Cenomanian of North Africa. PLoS e0144695.

Holekamp KE, et al., 1997. Hunting rates and hunting success in the spotted hyena (Crocuta crocuta). Journal of Zoology 242, 1-15.

Holtz Jr, T.R., 2008. A critical reappraisal of the obligate scavenging hypothesis for Tyrannosaurus rex and other tyrant dinosaurs. Tyrannosaurus rex the Tyrant King, 371, p.396.

Ibrahim N, et al., 2014. Semiaquatic adaptations in a giant predatory dinosaur. Science 345, 1613-1616.

Rayfield EJ, et al., 2007. Functional morphology of spinosaur 'crocodile-mimic' dinosaurs. Journal of Vertebrate Paleontology 27, 892-901.

Monday, 1 August 2016

The job search

For people who don't know, the early part of an academic career (after the PhD at least), is usually at least one postdoctoral position. These are short term contracts, usually 1-5 years but commonly 1-3, that run for the length of the funding (either a specific project or a specially funded postdoc). Originally, the postdoctoral position was supposed to be a one off position intended to be the stepping stone where young researchers go out and develop important new skills before getting a permanent position such as a lectureship. However, with the rise of increasingly large numbers of PhDs being completed, and increasingly few permanent positions opening (due to declines in funding, and something many scientists in the UK fear with Brexit), many scientists go through multiple postdoctoral positions before finding some level of permanency and I work with several people on their 3rd and 4th postdoctorates.

I, like most PhDs, suffered from imposter syndrome where I didn't feel like I belonged in the programme and didn't know as much as others. It was particularly tough for me as I was self-funded (thanks to my parents), and believe that far better people who wanted to do PhDs never managed to because they couldn't afford it/get funding. Nowadays, it feels much the same as I apply for jobs that I think there are better applicants for. I was spoilt by applying for only 2 jobs last time, getting 1 interview, and that one leading to my current job which is rapidly coming to an end.

I cannot really complain as I am a young person (both age and career wise) on the scene, but at the same time I am finding the whole process disheartening. The worst moment (so far) was when the grant I helped write was rejected, as it is the area I want to work on when I get a permanent job/my own lab. Otherwise it's much the same as other careers, lots of applications (and lots of rejections), maybe a few interviews, and hopefully a job at the end. The big difference is the few jobs are scattered around the world, on a range of subjects, so trying to find one that is a good fit is exceedingly difficult. It would also be nice though to have a permanent job and consider settling down as well, but all things take time, and I can't be so fussy. I saw this cartoon today, and it made me chuckle:
Credit to an unknown Facebook user for this
The question is what happens if I don't get a job? I am busy planning the next grants that need writing that hopefully will be more successful, and there will always be more job advertisements. If it all goes horribly wrong and cannot find a job, I will probably return home for a few months to save money, but for me that will be the ultimate feeling of failure. I can still work and have a bucket load of papers to read and write, and I am planning fun projects I might be able to do whilst back home (with a lot of speaking nicely to a lot of people to gain access to facilities that I won't have not being attached to a university), but it will put a sobering moment for me. I had a month off after my PhD, but that was arranged so I could come back fresh into a new job, but this may be the first real time since I was about 4 (when I had just started school) that I won't know what is next.

I appreciate this has been an unusual post compared to most of my blog, and thanks anyone who has read these musings and worries. I guess I should stop writing the blog with my fears and worries, and get back to work and job applications!