Archive for May, 2011

Diplodocus skulls again

I did feature one of these a while back – though one that was bolted onto a Mamenchisaurus skeleton. Here we have a cast from the same collections in Ireland as yesterday’s Stegosaurus cranium. This has the mandible separate from the skull, but I’ve put in back on for some shots to show off how they fit together. Diplodocus has a rather iconic skull shape when seen side on, but actually the dorsal view is the one I always find most interesting. It’s so regular with very square sides and just a slight curve to the very front. It seems almost too geometric to be quite natural.

Stegosaurus skull

This cast is rather less than perfect, but it’s quite a bit better than nothing and having it free means it’s easy to manipulate and take some decent photos from multiple angles. It’s always nice to be able to handle things freely like this and see into corners and check out awkward features. This is the first time I’ve really got my hands on a stegosaur skull so while ornithischians do not really feature in my research, it’s good to take a look and learn a few little things.

This cast is from the collections at the National Museum in Ireland and my thanks to them for letting me show it here.

This article has been translated into Estonian here.

Taxonomic practice and publications

Thanks to some reviews I have been writing, papers I’m working on, conversations with colleagues and a recent blog post, I’ve been thinking much about the practices of myself and my colleagues when it comes to taxonomy. Obviously I’ve written about the how-s and what-s to a degree in the past, but this is a little more specific.

The main point I’d make (as a referee / editor and recipient of referee reports) is one roughly in the line of Voltaire. I disagree with your taxonomy, but I defend your right to publish it.

Now obviously this has limits. You’re specimen must be genuinely diagnostic. You’ll have to use consistent characters. They must be well defined and not vary ontogenetically or be subject to excessive intraspecific variation (or be so massive as to not make this an issue). Or if you are trying to synonymise a bunch of taxa then you’ll need to show that other diagnoses were flawed or didn’t stick to these rules etc.

However, I may think you are overly splitting or lumping something, but I still think you should be allowed to publish (as indeed, so should I). There really are no hard or fast rules as to exactly what constitutes a genus or species. Exactly how many characters you need for one or the other, or whether some are better than others. Taxonomy really does work by consensus and the starting point of any discussion will be the publication of a new taxon / synonymy of an old one. Not allowing such a paper actively inhibits discussion / research.

A paper that on balance few people agree with will soon fall by the wayside. But it’s mere existence will allow a greater depth of discussion by getting people to examine and evaluate the characters at hand and compare them more thoroughly. So let these be published. The authors get a paper, the journal gets a paper, and the worst thing to happen is that a few people quibble about it, everyone gets some citations and we move on, but with a better understanding of the issues.

Here is something I wrote in a review of a paper that intended to name a new species (and has now been published):

I actually tend towards ‘splitting’ over ‘lumping’ myself, and I would not wish to prevent the author erecting a new taxon here if he feels it is necessary, but I would say that I do not think it is required and in the same position I would not erect one myself…. The author does effectively concede all of these points in his text, and clearly still feels the erection of a new taxon is necessary and appropriate and I am happy for him to make that call from a superior position of knowledge, but I do offer a contrary position.

This is a position I wish far more people would take. Make your points and give your opinion, but let the author make their decision and allow for the fact that they have been putting more time and effort into this that you have and know the material better.

On a similar note, I notice a tendency by some (admittedly often online rather than necessarily with respect to the literature, either published or at the review level) to second guess people working on specimens. Now for sure, people with detailed anatomical knowledge of specimens can see certain errors that others will miss (or that at least need to be verified more carefully) based on photos or drawings or descriptions alone. There is nothing wrong at all with making that clear. But I have seen people in the past second-guess authors based on things that haven’t seen. It is most frustrating to be told by someone 5 thousand miles away that you have got something wrong when you have the material in your hands and have been looking at it for months and all they have is a black and white photo of it. (And on that note, there’s a huge difference between asking someone to recheck and telling them it’s wrong. Ultimately the message is the same but the first is polite and the second isn’t. And of course you risk looking very foolish if you are wrong).

This is something raised by Larry Witmer in his excellent recent blog post about the tiny Tarbosaurus. His team commented extensively on the potential taxonomic issues of their work and explicitly which specimens / taxa this might effect and even how. But they also pointedly didn’t make any revisions. With none of them having looked in detail at any of the key specimens, they felt it unwise (and I would suggest, even impolite, impertinent, or maybe even unprofessional) to have done so. I wholeheartedly agree (as you probably guessed form the contents of those parentheses).

Yes there are exceptions to every rule, but as with the above point, I think you have to be careful before messing around with taxonomy and however much you disagree, respect the interpretations and work of your colleagues. If there are huge and obvious errors, then point them out do. But I’d avoid any kind of formal synonymy without having seen critical material first hand. There is, after all, nothing quite like seeing a fossil.

Advice to students writing science essays and answering exams

I’ve just come off the back of marking a quite sizeable pile of exams and coursework for my job. While I have done bits in the past (and earlier this year) this was the first time I had to deal with a large and concerted mass of the two and it allowed me to spot a series of things that irked me. While I am easily irked, the issue is not trivial, good clear writing is essential to communicate your ideas and if you are not doing that right, then this is a problem. It matters not that this is zoology or even biology, in any job or field, precise communication is critical. And not just accuracy but ease of reading – the information can be 100% accurate but if it’s buried in waffle or phrased badly it makes it hard to follow.

I know that I have a fair few regular student readers on here and others find me on occasion so I hope this will be useful. I’m only sorry I wasn’t able to think of this before the last round of exams or this might have been posted in a rather more timely occasion. So, here’s a few things I kept seeing that I’d quite happily never see again. They are all stylistic and people would probably not mark you down for using them, but they are at best, clumsy and inelegant and you want your work to appear astute and well produced. Helping someone to follow the thread of your work and ideas when they are reading their 37th five page long essay on the subject will help your cause.

-       Long and flowery introductions. There is noting wrong at all with a bit of craft to your writing (indeed, it is a good thing) and a little (a little) hyperbole can be good. But having to read a whole half a page before we get anywhere with actual detail is pointless and especially so in an exam. I don’t want, nor need to be told about how magnificent birds are and how they being joy to all who behold them. Write about them.

-       Repeating the question. It if helps you to focus, then feel free to write out the question before answering it. But if the question is “Define the 4 features of X and why their function is important”, don’t write “X has 4 main features, and their functions are important. These are…”. I know there are 4 and they are important, it’s the damned question!

-       The I’s have it. Science is really supposed to be about dispassionate reporting. Don’t talk about yourself. “I think”, “I am saying”, “I will show that”. Even when a question says something like “What do you interpret Smith et al.’s 2004 paper to mean….” you can avoid the first person. Say “It can be shown” or “This can be interpreted to mean”. It’s obviously your interpretation, you are writing it.

-       Don’t describe what you are describing. This seems to go hand-in-hand with the point above. I read far too many things that went “I will now describe the following features of X”. This sentence is pretty much absolutely redundant. Just describe X.

-       An alternative version of this is repeating information in reverse. Where it is pertinent, there’s nothing wrong with reminding the reader of a key point later in the answer. But writing “There are four feature of X” describing them and finishing with “…and these are the four features of X” at the end of the same 2 or 3 sentence paragraph is nonsense. I even saw it done in the same sentence a few times.

-       Try to avoid repetition of phrases. I lost count of people who needing to make similar points over a number of paragraphs would start each section with “Another point / idea / function is…”. About the 4th time you read that it gets very, very boring. Just add a smidge of style. “A further function is”, “The next function to be considered is”, “X is another key function, “In addition, function X”, “Furthermore, X” and so on.

-       Avoid ‘believe’ like the plague. Ideas can be supported, though of, understood to be, have a consensus behind, be agreed upon and others, but not believed. Yes, the vernacular use is one of genera “I accept that” but it really should be kept out of science. It’s even worse when you say it about other people “Smith et al. believe that X…”. Not they don’t, on the balance of the evidence, that’s the hypothesis they support.

-       Unsuitable anthropomorphism or odd terms. Something like an ankylosaur was slow, and heavy, and didn’t move very fast. But to call it ‘ponderous’, ‘clumsy’ or ‘lumbering’ is to give it something close to emotive or descriptive characters that just aren’t suitable for animals.

And finally, on a related note, answer the question. That one really seems to have gone past far too many people.

“Any jackass can trash a manuscript….”

“….but it takes good scholarship to create one.”

This title is taken from an editorial in Molecular Biology in the Cell which basically admonishes poor refereeing techniques and lays out how these should be done and how both editors and authors should deal with them. It’s all very, very good stuff, I just hope people pay attention to it. If only more people or journals went with this kind of thing.

It’s always nice when you shout about various things quite loudly (like this, this and this) and then see that quite independently in a rather branch of study the same problems are being felt and the similar solutions proposed.

Thanks to Graeme Lloyd for putting me onto it.

The framing of scientists

The other night I caught the second half of a documentary about science shows on the TV. It covered a bit of Sci-Fi and drama but mostly the actual science and technology shows and how they were presented, what they covered, how they were made and styled and so on. It was quite light and breezy but did include some classic clips and was a decent summary of the cultural attitude towards science and how it featured on television.

One feature was the use of quite a few talking heads of various researchers who are also well known as TV presenters or similar. One thing absolutely struck me however, so much so that I actually grabbed my camera and took some photos of it (so they are mostly not very good). And here they are. Let’s see if you can spot the ludicriously obvious and annoying trend.

Continue reading ‘The framing of scientists’

Where to stop?

One under appreciated feature of almost any paper is the incredibly difficult problem of where to draw line under the work and just stop. Every aspect of science is of course completely interconnected with other things and if you follow every possible tangent or lead everything you write will swell to dozens or even hundreds of papers.

Even something as simple as describing an isolated tooth or bone will have further implications for other branches of work. It could be the first record of something in a formation / time / place, extending the range of a group, or may be in association with another species, or have a pathology with implications for diagnosis of the species or clade or, or, or….. When you’re doing a more complex paper that integrates a number of major lines of evidence then this gets harder and harder as more and more important things have to be cut off somewhere, or at least not followed up to the depth you want.

This means inevitably that the paper will to a certain degree have a truncated feel. If you have an interest in a particular area it’s frustrating to see a paper that leads up to a significant point and then shies away and leaves it unsaid or doesn’t explore things, or give you quite the depth you wanted. Or of course, fails to make the link with something you have said in another paper or work you are very familiar with.

This can on occasion be a real issue with referees on papers. It’s very annoying when they demand you remove what they consider a tangent to the main work, and you consider an important extension of the thesis. It’s even more annoying when they do they opposite and demand you massively expand one section you don’t want to (or can’t if it lies beyond your expertise). Indeed, following up from yesterday’s post and the first half of this paragraph, there are few things more annoying than people complaining that basically you didn’t write the paper they wanted you to write. It’s your paper and you’re probably already compromising on a page length limit from the journal, desires from co-authors, and your own limitations of what you want to write about now and what you have brewing further down the line.

Just making a point really

This post is, perhaps rather obviously, tinged with a small touch of bitterness, but there are some commenters out there in blog-land who might do well to recognise the reality of research. Following some behind the scenes discussion with fellow palaeo-bloggers it seems this sentiment is far from limited to me. Science is, to a degree, all about criticism and the ability of hypotheses to pass tests of criticism. However, bearing that in mind…

Do you know what’s easy? Criticising someone’s work.

Do you know what is hard? Publishing a paper.

Do you know what’s next to impossible? Publishing a paper with no mistakes in it.

Do you know what’s actually impossible? Publishing a paper that everyone is happy with.

Being less catty, seriously, it’s impossible. I don’t know of any paper that doesn’t have a mistake in it somewhere. Now there are mistakes and mistakes, but typos, miss-citations, missing citations, bad phrases and odd little mistakes are rampant. Get over it. We try hard to eliminate them, but they will slip through. I know of people who have spelled the name of their own taxa wrong, I know someone who produced a conference poster with their university and their coauthor’s name both spelled wrong, and a colleague once published a paper with ‘Cretaceous’ wrong in the title.

In short, there is, in essence, nothing wrong with criticism. But an understanding not just of what you are attempting to criticse, but appreciating how and why it came to be, in the manner in which it did is integral to that. So don’t be a jerk and try points scoring because you spotted a missing reference or think there’s a better citation than the one given. Seriously try writing your own paper. It’s not that hard, but you might well find it an absolute ton harder than you think.

Pterosaurs alive!

No, not those ones, but human-pterosaurs. These come courtesy of palaeoartist Brian Choo and feature him as a Pteranodon longiceps with his friend Paul Kidd as Ornithocheirus. These are, frankly, awesome and if I had the time and motivation i might try to make one myself. Good work and great fun.


Neck multifunctionality

Following on from my post on sauropod neck lengths (and indeed that of the SV-POW! boys and Tet Zoo too), at the end I made the inevitable comment that necks (and indeed other structures) can be multifunctional. A long neck can be an indicator of sexual selection at the same time as providing increased reach for food. As noted before, analogy plays an important role in working out (or at least hypothesising) palaeo behaviour, so are there any animals out there that seem to do this. Indeed there are, so step forward, the Galapagos giant tortoise.

Tortoise neck use - above, reaching for food, below, challenging rivals. By Darren Naish, from Taylor et al., 2011.

Research shows that those animals with longer necks do gain a distinct advantage in reaching higher placed food. The neck provides a genuine basis for natural selection based on neck length. However, it has also been shown that when tortoises stand off in dominance battles, the individual with the longer neck tends to win. So, necks would also appear to be under some measure of sexual selection / dominance as well.

So what about the giraffes? They have long necks and the males fight with their heads, so what’s going on there. Well males do have longer necks than females, but there’s not really anything to say that longer necked males do better. Bigger males do better (no surprise) but not through a longer neck per se. Plus of course the males are actively fighting with their heads. (And tortoises can be quite vicious if you’ve ever seen them fight, then bite and butt with their shells).

Posturing only gets you so far in nature. Sure, there are cheats out there (false cleaner fish, milk snakes, female mimic salmon etc.), but they can only prosper as long as they are in the minority. This is because sooner or later someone is going to square up to you in one way or another and find out if you really can back the bark with bite. If you can’t, you’re going to lose. And if say most of the population were lying, once a dominant animal (or predator etc.) finds out, then that is going to take over damned fast. So lying only works when there are few liars, and most things are honest. In other words, if they are advertising that they can win a fight, it’s because they can and will.

What does this mean for sauropods? Well is has been suggested in the past that sauropods might fight one another, with their necks. Now if this was going to happen you’d expect to see some evidence of this in sauropods. Like the especially tough and thick skulls of male giraffe, or the prow-shaped rams of some tortoises, or robust necks and heads in male sauropods and you’d see injuries from some serious sauropod neck-on-neck action. Only of course there aren’t any.

Instead sauropod skulls are incredibly weak and fall apart if you look at them funny, let alone ram them into something else at speed. And while the neck as a single unit might be quite tough, it has those lovely wafer-like lamina and those oh-so-thin cervical ribs. If they were fighting we’d see breaks, pathologies, healed bones and the rest. And you can’t cheat by just having a big neck and expecting the others to back down, you have to back that up or someone will realise it’s all talk.

I’m sure sauropods did fight on occasion, sooner or later animals of pretty much any species will come into competition and of course it is members of the same species that tend towards the fiercest competition. There will come times when accessing that water hole, or harem, or territory is critical and combat becomes inevitable. But was it with the neck? No. The neck might have been a *symbol* of the power of the individual even if it wasn’t used (pheasants and cockerels show off their colours to demonstrate their fitness, but they fight with their spurs).

The end of the Hayashibara?

In yesterday’s Tarbosaurus post I noted that the Institute housing the specimen may not be much longer for this world. This is a serious and deeply unfortunate turn of events with major consequences for dinosaur palaeontology that could last for a very long time. I’m somewhat personally involved too as I have friends and colleagues based there and have collaborated on research with them (like this famously ‘gnawed’ bone) and have more things lined up.

So what’s happening and what does it mean? (Note this is my interpretation of events based on my conversation with friends and colleagues in the know or whoa re directly involved, I may have got things wrong with the specifics, but in general I believe this is all accurate. There’s a mail archived here from some of the people involved). The short version is that the Hayashibara Museum of Okayama, Japan was ultimately funded mostly by it’s parent company Hayashibara. Despite being a multinational company (they manufacture sports drinks, medicines and other things) they have recently gone bust. The museum was founded and sponsored by the company because the chief executive / owner had an abiding passion for dinosaurs and anthropology and so paid for a museum that did just that (and in that respect it is really rather odd, they work on chimp behaviour and Asian dinosaurs and basically nothing else). Though additional funds were also present through research grants from various bodies.

While considered a museum, the ‘galleries’ as such never really materalised owing to planning issues. However, hordes of schoolchildren and other visitors were still welcomed through the doors to see various display specimens and the prep labs at work. There’s no doubt that this was a valuable educational tool, but the research side of things were especially important.

The Hayashibara had a superb working relationship with Mongolian researches that was of great mutual benefit. The Japanese provided funding and expertise and of course Mongolia (unlike most of Japan) has great fossils. Thus the Japanese teams would go prospecting in Mongolia with their local colleagues to collect material which would be taken to Okayama and prepared and studied on long term loans before the material was returned.  Thus the museum got access to great research materials and the Mongolians got funding and exhibition quality specimens. In addition, the museum was building up quite a collection of specimens of North American specimens that had been purchased.

However, with the parent company going under (and still great economical issues with the recent natural disasters in Japan) the museum is under dire threat. They are likely to have their funding pulled from a company who (understandably) don’t necessarily see the value in paying for a dinosaur museum when they are bankrupt. If they do then things get really bad really fast.

For a start the partly prepared and unprepared materials will be going back to Mongolia, but of course to a place that largely cannot afford to prepare them themselves and (I would guess) might not even be in a position to take a warehouse full of material at short notice. Then there’s the question of the North American material with a less certain fate, but it’s equally likely to be at best inaccessible for a long time and not useful for research. With that owned by the Museum (unlike the Mongolian material) it may even be sold off (there’s not much point in keeping it if the museum is forced to close).

We then risk losing specimens, outright research being put back years or even decades and the loss of a superb collection, as well as the human cost of jobs for preparators, curators and researchers. The loss of a great education tool and of course one of the few really successful partnerships between a real philanthropist and palaeontology, and a long term commitment between two countries and research teams.

All is not yet lost. No formal decision has yet to be made about the future of the museum, and under the threat of closure, many researchers rallied and wrote appeals to the company to save the museum. However, dark clouds are hanging over it and it would be true shame if this ultimately ended the place. Even the threat is causing problems as the researchers struggle to deal with the possibility of closure and contingency plans have to be made about the removal of material when of course more research is exactly what they need to be doing right now. There is hope, but the situation is very far from rosy.

Tiny Tarbosaurus

By now I’m sure most readers will have picked up on the new paper describing the skull of a tiny Tarbosaurus. It’s estimated to have been just 2 years old when it died and was around 2 m in length – that’s rather smaller than the 10-12m long adults! A few images of this hit the news when the specimen was first announced around three years ago and can be hunted down if you look. There is one above of me with a cast of the specimen as it was when discovered (it’s now been fully prepared out) which gives you a pretty good idea of just how small it was.

While above is just the cast, I was lucky enough to see some of the material while it was undergoing preparation. Even better I was allowed to take some pictures for my own research and have been told I can show off a couple of them here now that the paper is finally out. My thanks for this to Mahito Watabe and his team for this generosity. Though perhaps inevitably with Larry Witmer on the team, there are even better pictures and 3D animated scans of the skull out there too!

This is post is (a little) more than just a couple of photos though as the paper itself has some interesting things to say about tyrannosaur ontogeny. This is the smallest / youngest tyrannosaur we have and coming from an especially big genus makes the size discrepancy even greater. This is pretty handy as there are a variety of problematic tyrannosaurs specimens out there that may or may not represent distinct taxa but being known only from juveniles make this hard to work out. However, if you have a really good handle on how some characters do (or do not) change as individuals get older and bigger then you know what you can and cannot rely on when looking for unique characters in other juveniles.

For me the most interesting characteristic was that of the number of teeth. While there is a little intraspecific variation in tooth numbers, there are also some discreet differences between taxa too – the big tyrannosaurines like Tarbosaurs and Tyrannosaurus have fewer teeth than do smaller ones like Daspletosaurs or Alioramus. In the past it’s been suggested that this number actually changed during ontogeny with the number starting relatively high and the number of teeth reducing as the animal got bigger. However this little guy has exactly the same number of teeth as an adult Tarbosaurus. While this doesn’t exactly disprove the hypothesis, it does at least show that at best it’s not always true, and so a smaller tyrannosaurine skull with lots of teeth could grow into a big adult with lots too.

All in all a very revealing paper (and superbly illustrated I should add) and with more to come on the postcranium, this is going to be an important specimen for many a long year. Sadly, it’s parent institution may not be able to say the same as I will talk about tomorrow.


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