Archive for the 'Practical Palaeontology' Category

How do I become a palaeontologist?

This question comes round and round again online and I regularly get e-mails asking exactly this from people who are interested in becoming palaeontologists. There is plenty of good advice out there in various formus and answers to questions, but I don’t think I’ve ever seen a really long and detailed answer and as much as anything, having something like this will hopefully serve as a one-stop shop for people who have this question.

For anyone who has come to this blog because of this post and doesn’t know me, I am a palaeontologist working on dinosaur behaviour and have been for over a decade (I got my PhD back in 2005). Though I’m British and based in the UK, I’ve had palaeo jobs in Ireland, Germany and China and I’ve got numerous colleagues in the US, Canada, all over Europe and in places like Japan, Brazil, Mexico, Australia and South Africa that I have talked to about working there, so I have a decent picture of what issues are relevant wherever you are from and where you want to be. There will of course be things I don’t cover below or that vary significantly (e.g. the duration of various degree programs and what they specialise in etc.) but this should cover the basics.

Hopefully this will help answer the major questions, and clear up some big misunderstandings and offer some advice to get into palaeontology. There are also some harsh truths here but I’m trying to be open and honest about the realities of trying to make a career of this competitive branch of science. So, with that in mind…

What do you think a palaeontologist does?

A lot of people asking about getting into the field seem to be seduced by the apparent image of the field as a glamorous science. There’s fieldwork in exciting places, media coverage (you can be on TV, in movies!), new discoveries, naming new species and generally being a bit cooler than the average biochemist or experimental physicist. But if this is what you think, it’s actually pretty misleading. You are only seeing the very top people and most of us don’t get much time in the field or travelling in a given year, and spend most of their time in an office and while that might include writing papers, there’s plenty of grant writing, admin and less exciting stuff. I rarely get into the field and probably >90% of my time is spent teaching and doing admin work for my university. A fair chunk of my research and outreach output is done in my own time taking up evenings and weekend and even vacations. I don’t get to sit around and play with fossils all day and there are very, very few people with senior enough research positions who get perhaps even 50% of their time to do real research and fieldwork – there will always be paperwork and admin that needs doing and even writing research papers or planning a field season can be really quite tedious at times. Real joy comes from discoveries in the field or in research but these are moments you work for, there’s not a constant stream of them.

So it’s worth making sure you have a realistic impression of real life as a palaeontologist and ask yourself if you have realistic expectations of what the job might entail and where you may end up. That said…

Do you know what jobs are available?

Palaeontology tends to be thought of as people digging up fossils and then maybe researching on them and / or teaching about them. Palaeontologists are scientists and they work in museums or maybe universities. That’s not wrong, but it masks a pretty wide range of careers and employers. It goes back to my point above, there are lots of jobs for palaeontologists or people working in the field of palaeontology and in addition to researchers and lecturers, there are science educators, museum curators and managers, exhibition designers, specimen preparators, photographers, science writers, palaeoartists and consultants of various kinds. People can work for media outlets, national parks and other government bodies, companies that mount or mould specimens, that monitor building sites and roads for uncovered fossils, and others. One of these might be more what you are interested in – you don’t have to end up as the senior researcher in your national museum to have ‘made it’ and similarly, that can mean you have a very different set of requirements to get a different kind of job. You pretty much have to have a PhD to teach at a university, but you can potentially get a job working preparing fossils with little more than a good high school education. Experience and engagement with the field can always lead to you changing paths and I know of people who started out in science without a degree that are now full professors or have some senior palaeontological position.

There are also lots of opportunities in various places to be a volunteer and you certainly don’t need a PhD or even a degree to get involved in scientific research and i know of high scoolers who have managed to publish papers – some drive and knoweldge can go a long way. There are opportunities to engage in the science without actually holding a professorship at a big university. If some of the information coming up is a bit daunting, there are options and alternatives.

Do you know what the job market is like?

Despite the above listed variety of jobs out there, there are still not a huge number of jobs in palaeo, and fewer still for academic positions. Worse, there a lot of people who want them. If you are desperate to get into an especially sexy area like dinosaurs or carnivorans then it’s even worse. For every academic job there are likely to be 10 well qualified candidates (and quite possibly 20 or more) and these are all people who have held at least one postdoctoral position (maybe 1 available for every 5 people) and have a PhD (maybe 1 available for every 20 or 30 people who want to do it). It’s very common for people for slowly drift out of the field simply because they cannot find a job even after years and years of training and experience and a good record of research. I know of colleagues who did their PhD around the same time I did and have yet to find a permanent position. Others are stuck in jobs they would rather not be in, hoping for something better and, sadly, when finances are tight, palaeontology is often a field which suffers cuts more than other sciences. As with the point above, I’m not saying this to put people off (though I’m sure it does) but it is worth knowing the reality of the situation. Getting on a degree program, even coming top of the class will in no way ensure you get on a doctorate program, let alone in the field you want to study, let alone a job at the end of it.

Do you know what the career trajectory is?

As noted above this can vary enormously depending on what you may want to try and do, but I’ll focus here on academic positions since that’s what most people do want to do, and it’s generally the longest and most involved pathway. First off you will need an undergraduate degree, increasingly this tends to be in the biological sciences though there are lots of people with a background in geology. You’ll need to know at least some of each but it’s perfectly possible to forge a palaeontology career (depending on what you do) with a very heavily biased knowledge in favour of one or the other. Most people don’t specialise seriously until later so don’t worry about doing one and assuming it’s a problem, and don’t get hung up on doing a palaeontology degree – there simply aren’t many of them about and it’s not a deal at all if you have not done one. With a good degree you can get onto a Masters program which will obviously increase your knowledge further and improve your skills, and then onto a doctorate which will be anything from 3-6 years depening where you do it. It could take a year or two to get onto this programs if there is something specific you want or of course you may need to work to get the funds necessary for tuition fees etc. Most people will also then go on a take one or two positions as a postdoctoral researcher or similar before finding a job. Some of these are short term (a year or so) and some can be much longer (5 year special research fellowships are rare and great if you can get them, a one or two year contract is more common). You may end up taking some short-term jobs (parental leave cover, or for a sabbatical etc.) and can bounce around on contracts for a while before landing a permanent position/ All told, it’s likely to be at least 10 years and could easily be 15 or 20 between starting at university and a first year undergraduate and having a permanent position at a university as an academic. This can also involve moving round the country or between countries (and continents) to find a job. Again. if you are dead set on working on taxon group X at university Y, be aware that it’s likely to be a very, very long shot or needs to be a very long-term career goal.

How do you start?

So assuming that this is still something you think you want to go for, how do you actually start on the road to becoming a palaeontologist? Well, the short version is go to university and do well. That’s what I did, at least in part because I wasn’t any more interested in palaeo than some other fields in biology and I kinda drifted this way (this is really common, even people who start absolutely dedicated to working on one particular area get sidetracked by new interests or simply the available opportunities). Of course with so much more information out there now online there are much better ways to get started and to learn something about possible careers, universities, current research, museums to go to, etc. etc. You may be surprised to find that a what of what you know is not that relevant or important for getting into the field. Knowing a whole bunch of facts isn’t a bad thing, but understanding principles, being good at absorbing knowledge and interpreting things and coming up with ideas and testing them are more important. You can always look up a fact if you forgot it or don’t know it, but if you can’t effectively come up woith ideas to test, collect good data and organise your thoughts then it’s obviously hard to do good science. Learning things like names of species and times and places they are from is obviously a good start, but don’t think it’s a massive head start on potential peers. Obviously you’ll want to focus on palaeontology, but biology and geo sources are important too, a wider knowledge base will be better than a narrow one. So, in sort of an order that will lead to you learning and understanding more and getting better:

  • Read online. There are tons of good sources out there – follow people on Twitter, join Facebook groups, listen to podcasts, read blogs etc. etc. Absorb information on biology, geology, current research trends, the history of the subject and the fundamentals of science. Engage and discuss things with people.
  • Read books. Build up your knowledge base with some good popular science books and then if you can access them, get hold of some university level books that are introductory for subjects you want to engage in. There are good books out there on palaeontology generally and various branches like invertebrate palaeo, mammals, human origins etc. Public libraries can often get even very technical works in for free and there are others online. Some books can be very cheap second hand.
  • Get more practical experience and engage with the field and fossils if you can. Visit museums and go fossil hunting. If you can, volunteer at a museum and get some experience and training no matter what form it might be.
  • Read papers. Large chunks of the scientific literature are online and available. You won’t get everything you want, but you will be able to see a lot of things. Learn from them, not just the science being done, but look at patterns and trends and look at how papers are written and delivered, how hypotheses are produced and tested. See what makes a good argument and a good peice of work.
  • Get to a scientific conference if you can. As with reading papers, it may be hard to dig into technical material given by experts aimed at other experts but you will learn something from it and get to see scientific discourse in action and meet people. Speak to students about how they got started in the field and speak to academics about their programs and what finding or positions may be available.
  • Try to get involved in scientific research if you can. Offer your services to academics with whatever your current skills and knowledge you have and see if you can help. It might be very peripheral sorting out specimens, or merely collating data or drawing things for a figure and it might not end up in authorship on a paper, but it would get you actively engaged and see the process of research up close. I have had people assist me from Germany and Australia so you don’t need to be physically in the smae building to collaborate and get valuable experience and training.

Any, though in particular all, of these will give you a huge advantage when it comes to getting started for real on a degree or with a new palaeontology job or internship. The best students know what they know and what they don’t, and have the initiative and drive to seek out opportunities to learn and get experience and are not put off by setbacks. You may not be able to get to a conference or find an academic looking for help, but you really should be able to start at least reading papers and developing your knowledge and understanding. That will massively appeal to people looking to recruit to positions or studentships and can make a big difference.

TLDR

Palaeontology is a hard field to break into, most don’t make it even if they are hard-working and talented and deserve it. But if it’s what you really want to do, then be aware of the risks and go into it open eyed but also hopefully armed with a bit of knowledge and advice as to what you can do to stand a better chance. Be prepared to have to move, be prepared to have to sacrifice a great deal, be prepared to end up somewhere very different to what you might have expected or planned, but also be prepared for the possibility of a fantastic job. All of it is of course up to you, but I wish you the best of luck and I hope this is some useful advice.

 

To finish off, here’s a bunch of links to other related resources I’ve generated over time on getting along in research and getting hold of papers etc. etc. that should be useful: https://archosaurmusings.wordpress.com/2009/10/04/the-complete-how-to-guide-for-young-researchers-so-far/

and: https://archosaurmusings.wordpress.com/2012/02/09/online-resources-for-palaeontologists/

 

Constructing hypotheses on behaviour in the fossil record

Those keeping up with papers on palaeoethology may well have noticed that a number of papers have gone online in the Journal of Zoology of late with a common theme. Darren Naish has a paper on the behaviour of fossil birds, Andy Farke has one on combat in ornithischians, and Pete Falkingham has a paper on interpretation of trackways. This is not a coincidence, but part of a special issue of the journal out today on behaviour in the fossil record and all of these contributions will eventually be published together with a number of others in a collection I have assembled as a guest editor. The volume has ended up rather dinosaur-biased which is unfortunate as a number of other papers were promised from other fields (including on whales and the Burgess shale) which never appeared and giving the set a more dino-centric appearance than I had planned or hoped for.

Adding to this is in fact my own paper in the volume. This was something I had been working on for a while before being asked to compile the special issue (indeed the fact that I was working on it, and it was intended got the journal may have precipitated the invitation) and in the context was the perfect home for the paper. As with similar cases I had nothing to do with my own manuscript and it was submitted separated and edited and refereed independently by the journal, and only after acceptance could it be added to the list. Most of the papers are reviews of one form or another, and in my case the paper written with my friend Chris Faulkes looks primarily at issues of hypothesis creation on behaviours for fossil taxa.

Our main contention is that in the past palaeontologists have been a bit over zealous in the production of hypotheses and the way in which they have been generated has made them difficult to assess or even simply discuss and in at least a few cases hould probably not have been suggested at all. We don’t think it inappropriate to generate hypotheses that cannot be immediately tested, or those that are difficult generally to assess, but a hypothesis must have at least some support behind it to make it valid in the first place, and poor uses of terms, lack of specificity, or even use of fundamentally flawed concepts have meant that there are problematic ideas in the scientific literature.

Mutual sexual selection is perhaps a good example here. I’ve now penned a number of papers with various authors about the issues surrounding this idea and how it may fit into archosaur evolution. The point is not whether or not we are right about this, but more the fact that this was something hinted at by Darwin, written about by Huxley and extensively studied by numerous ethologists for decades, and yet many palaeontological papers discussed sexual selection purely in terms of dimorphism, or the fact that sexually selected features should feature on only one gender, or indeed that sexual selection should be mutually exclusive of other functions. None of these things are true, so hypotheses that rely on one of these as are starting point are going to be fundamentally flawed, or at least problematic.

Thus the paper sets out to identify some key areas where we feel mistakes have tended to be made (myself drawing on examples from dinosaurs and pterosaurs, Chris from his area of expertise the mammals) and to also then try to find a set of guidelines that might help the better generation of hypotheses allowing for reduced confusion and better testing. Naturally we think this is going to benefit researchers, but given the rampant hypothesising that often accompanies any online discussions of the behaviours and ecology of extinct animals online and in other informal venues, it might just help clean up some of the more egregious suggestions that can be put forwards based on the most tenuous of links. Some of it may sound excessively simple and even obvious, but that doesn’t mean it hasn’t been an issue in the past. I actually had a chat with an ecologist the other day who bemoaned a similar set of problems in her field, and I think the issue is more one of advancement and general improvement that systematic errors or poor science.

Naturally we did try hard not to pick on individual papers (or people) but we did also want to point to some specific examples of the kinds of problems we were discussing and so a few things get the finger pointed at them, but they have mostly had specific rebuttals in the literature already, or were very much generic issues. Hopefully then, we’ve not bent any noses out of joint. I was certainly grateful to Andy Farke for reading an earlier version to check for overall tone and to see if it was working the way we wanted. Anyway, here are a few of the things we looked at.

Terms need to be more specific. Talking about ‘parental care’ say in general terms isn’t very helpful when this can encompass pre- or post-natal care, or both, and differing degrees of commitment from parents over very different timescales. So a statement like ‘X showed parental care and Y didn’t’ may not mean much if the parental care shown was minimal, or two papers might say this where one is referring to all parental care, and the other only post-natal, making them hard to compare.

Overlooking counterexamples or complexity. Descriptions of species or clades as ‘social’ has been creeping into the literature on dinosaurs and yet even if you do somehow have super evidence for sociality in a species, applying that to other taxa, or even other member of the same species is not necessarily a great idea. While we do have highly social species that basically can’t function when not in a group (like some molerats) even famously social animals like lions often spend part or much of their time apart, and some like cheetahs can be incredibly plastic, switching from social to solitary multiple times in their lives, and yet it would be a big mistake to suggest tigers are fundamentally social because their nearest relatives the lions are.

Extreme examples or oddities are useful to provide context or even limits on ideas. Some species have incredibly specific requirements or only live in certain environments, while others are much more adaptable. You don’t really find sand cats outside of deserts or dry environments, and while lions show up in quite a few places, you can get puma in everything from high mountains to praries, deserts and rainforests, yet there’s not especially obvious about their osteological anatomy that they could occupy so many more environments.

Make sure the analogy or reasoning behind it is actually correct. Not too long ago it was suggested that azhdarchids had long necks to reach into carcasses of large dinosaurs. However, given that the heads of the biggest azhdarchids (estimated at getting on for 2 m) are longer already than the longest sauropod ribs we know of (2 m) then any kind of neck is redundant in this context, let alone a long one, and vultures do fine with absolutely short necks and heads while feeding on carcasses of animals many times their size. The analogy that the hypothesis is being based on is fundamentally false and if that is the sole support for it as a concept, then it’s really not much of a hypothesis.

The short version of much of this could well be summarised as “look more at the behaviour of extant organisms”. I know Darren bangs this drum a lot on TetZoo and I’ve said it in plenty of talks and to lots of people if less so online. It is confounding when people say that such-and-such behaviour isn’t seen in reptiles when it plainly is, or that only animals with feature Y can do this behaviour when it’s known in numerous species, that are just less specialised towards it (or even show no obvious adaptations – like tree-climbing crocs). True this may not be common or normal, but to assume that it’s impossible, or that there is a perfectly consistent correlation is incorrect.

Part of the difficulty is a lack of good data on many of these things. Ethologists can simply observe behaviours and therefore don’t necessarily go looking for osteological or other correlates that we might be able to detect in the fossil record. That does make things harder, but we need to try and avoid getting trapped by ‘we don’t know if this correlates therefore this hypothesis is valid since we don’t know’. I am actually not against (in principle) hypotheses that are difficult if not currently impossible to test, but as with the azhdarchid neck example, there is a difference between something that can’t be tested, and something which is not even supported at the most basic of level. A hypothesis has to have some support, and some specificity about that will go a long way to making things much more clear and amenable to testing and allow a great fit of existing and future data.

What is most remarkable is how far things have come so quickly. So many modern analyses are using things like FEA and functional morphological analyses, are looking for correlates of behaviour (or aspects of ecology that link to behaviour), and more and better comparisons to extant forms and their anatomy are being used. Such important work or our understanding of the biology of extinct animals should not be let down by poor hypotheses and we do hope that, while things are improving already, this will help better communication and understanding of ideas.

 

D. W. E. Hone and C. G. Faulkes 2014 A proposed framework for establishing and evaluating hypotheses about the behaviour of extinct organisms (292: 260–267)

 

 

 

 

Pterosaur ontogeny

 Not too long ago, Matt Wedel had an SV-POW! post that talked about ways of diagnosing an adult vs non-adult sauropod. Inspired by this and the fact that I have recently been playing around with issues of ontogeny in pterosaurs, I decided to write something similar for the non-avian Mesozoic fliers. If you have a pterosaur specimen in front of you, just how do you know if it’s an adult or not?

Obviously there are some general indicators that are pretty good for vertebrates as a whole that will get you quite a long way (even if this is a new species). Size is obviously rarely a great indicator, but if you have a pterodactyloid with a 20 cm wingspan then it’s going to be a juvenile, and likewise if you have a rhamphorhynchoid coming in close to the 2 m mark it’s very unlikely to be anything but a big adult. Young animals (and especially very young animals) tend to have big heads compared to their body and especially very big eyes compared to the size of the head. A bunch of fusions are absent in young pterosaurs that are present in adults too, just as you’d expect for most animals. The sutures between the centrum and neural arch of the vertebrae will be open in juveniles and closed in adults, and similarly the elements of the pelvis and sacrum, and the scapula and coracoid will be separate in young animals and fused together in adults.

Pterosaurs also have some characters of ontogenetic change that are rather more peculiar to them than vertebrates in general. Very young pterosaurs also tend to have a very grainy texture to the surfaces of their longbones, despite the fact that even embryonic pterosaurs have a pretty ossified set of bones (unlike many young animals). Smaller pterosaurs also tend to have various parts of the skeleton being less ossified and rather amorphous compared to those of adults. The tarsals are often not well ossified and can be missing (well don’t preserve) and if present may be very simple shapes. The carpals tend to look more ‘blobby’ and lack the detailed morphology seen in adults and will be separated into multiple elements whereas in adults the wrist will primarily be formed of just two massive elements (plus the pteroid). Finally, while obviously you would expect skulls to fuse up during ontogeny, pterosaurs do tend to take it one step further than most. Rather like birds, in adult pterosaurs the sutures all but disappear, or even go entirely, such that the skull looks like a single smooth piece of bone. Also as in some birds, bigger pterodactyloids have a notarium and this only fuses up and fully develops in adults. Similar to the point above about absolute size, the presence and development of some form of head crest is indicative, but not a great indicator of age. Yes a massive and elaborate crest in an animal is indicative that it’s an adult, but there could be a fairly well developed crest in an animal that is close to becoming and adult and of course there are taxa without crests and in at least once case it appears that females don’t have crests.

As in mammals, but unlike dinosaurs and birds, pterosaur also have epiphyses. The growing plates at the ends of the long bones physically separate the main shaft of the bone from the proximal and distal ends, so things like the femur can appear to be in three pieces. Obviously as growth slows towards maturity these epiphyses slowly disappear as they fuse into the single element that you would expect to see.

So in short, something that is small, with grainy textured bones, a big head, with big eyes, unossified tarsals, amorphous carpals, no crest, clear sutures in the skull, no notarium, and separated scapulocoracids, pelvis, epiphyses and neurocentral sutures is going to be a young juvenile. And the close these various features get to the opposite condition the closer the animal is likely to be to adulthood.

As ever with such things these are not absolutes, but merely guides. Good guides, certainly – you simply won’t see a notarium in a very young pterosaur, or open neurocentral arches in a big, old adult. However, in terms of determining more subtle difference in age it will be tricky – one animal may have fused up the notarium, but may have incompletely ossified tarsals and another could have the reverse. Although at least some characters do seem to have a bit of a pattern (the scapulocoracoid seems to fuse pretty early in most things) a general lack of numerous specimens of different ages makes it hard to do any more detailed analysis. Still, in terms of gross age (hatchling – young – adolescent – adult) even for a specimen of a previously unknown species with no obvious close relatives, it should be relatively easy to determine the approximate age of the animal.

On publications

 It can’t have escaped the notice of most readers that there is currently a rather major rumble going on in the world of scientific publishing. Huge numbers of blog posts, editorials, tweets, and more are going on about quite what researchers should and shouldn’t do with their work and with regards to their interactions with various publishing houses and the knock-on effects of access to research for the reader.

If you’ve not been keeping up or are not familiar with the general set-up for publishing papers I’ll try and give this the briefest of introductions. In short as a researcher once you have completed your work, you’ll need to get it published in a journal if people are going to read it. That means submitting it to a journal where an editor will read it and select referees. They’ll report back to the editor who’ll sift the results and send them to you. You’ll make corrections and send it back and hopefully it’ll go to publication if it’s deemed good enough for the journal.

So much so simple (well, over simplified). What is causing the stir is that in most cases when you give your work to the journal, they aren’t just publishing it for you, but you sign the copyright of the work over to them. In short, you do all the work and they then sell the papers onto people who want to read it, potentially including the university or museum you’re already working for… This to many doesn’t seem right or fair and in the internet age researchers are in a position to complain and organise and do something about it.

The battle, such as it is, is ongoing. I’ve not been drawn on this before as, while I do have some strong opinions, it’s largely not the kind of thing I want to blog about on here. What is relevant to this blog however is the process involved from the perspective of the academic. While I have written a couple of posts before about the mechanics of writing and reviewing papers, I wanted to provide more of a summary of everything that a researcher can end up doing in the chain to publication.

Obviously I’ve published my fair share of papers both as a lead or sole author and co-author across a variety of platforms. I’ve also been an editor for volumes of papers produced by museum journals, and I’m an editor for a ‘mainstream’ palaeo journal with one of the big publishers. I’ve also reviewed dozens of papers over the years for all kinds of books and journals, at least 50 or so and probably much more though I’ve never kept a close count. In short, I’ve seen things from all sides a good few times each. What I’m putting down here is purely from my own experiences and while it therefore certainly anecdotal, I don’t think it’s anything other than entirely normal. I’m not complaining or criticising it, just saying what I have done and experienced. I think that’s worth adding to the mix.

As a researcher I come up with the ideas for papers. I do the research. At the moment that includes doing things on my own time and money, though before it’s been (mostly but not always) covered by a grant or my employers. I do the work, write the paper, format it, create the figures and the rest. I don’t get any help with any of this from the journal at any point. Indeed oddly enough quite a lot of effort can go into formatting and arranging things to the very exacting specifics they require, even if the paper is later rejected or even if the journal itself doesn’t print things in that format (yes, really, they make you format things to a standard for them to read them but which they will change later if they ever do print it). The odd journal still requires you to submit multiple hardcopies which are not necessarily cheap to print or post. I get no pay for this and typically (but no, not always) hand over the copyright of the work. One journal did send me free issues for a year for publishing with them, but in a lot of cases I don’t even get access to my own paper at the journal and in more than a few cases I’ve never even gotten a free PDF of my own work. Rarely am I even informed if something has been printed, and on more than one occasion things have been done against my express wishes (e.g. publication of advanced un-proofed copies of papers).

As an editor I take papers submitted, read them, check them and pick referees. I send the papers to the referees and ask for their comments, hassling them where necessary. When the reviews are back I collate them and make a decision and send them comments out to the authors. There may be further dialogue with the authors, referees or other editors. When the corrections come back I need to check them again against the referee’s comments before making a decision. Speaking for myself, I don’t get paid for any of this, and nor have I had any training or received any benefit from doing the job (like access to other journals in the care of the publishers) or copies of the journal itself.

As a referee I take on papers to read and review. Some can be very long, or complex or just badly written and require a lot of time devoted to them (one I recently reviewed twice was about 150 manuscript pages with about 50 figures as well). I might even have to read other papers too and check analyses etc. in addition to writing the actual report. I don’t get paid for this. I don’t get free copies of the paper when it comes out or (most of the time) even notification it’s been published.

Those are all the things I do with regards to publishing a paper and are therefore in the main what I think happens to a typical palaeontology paper with regards to the input from academics. The main thing the journal does is actually format and arrange the words and images into their own format and to proofread it. Don’t forget though that I’ve already formatted much of the manuscript (titles, numbered headings, reference formatting) and scaled images etc. according to their layouts and I often have to correct errors introduced by the journal (generic names have a nasty habit of becoming un-italicised). Oh yeah, and they will eventually publish it and of course send it out to subscribing libraries, museums, universities, societies and individuals and sticking it up online so people can find it.

So what do I generally get out of this? Well as an author, a paper in a journal, hopefully a good one that will (theoretically at least) enhance my reputation, and with luck a free PDF. As a referee, I get to see things in advance of publication (assuming the get published of course) and I know I’m doing a job of helping keep science on an even keel (however small the role). As an editor I see what’s going on and can generally get access to these and other papers in the journal, and hopefully influence and improve the devlopment of the journal. That is, however, about it. Certainly a good paper in a good journal will help my profile and can count for things in research reviews and the like and it can be worth a lot, but it’s still no guarantee that the people who need to see my paper will or even can.

The trade off does therefore vary enormously from journal to journal with the prestige of the journal, the access it grants to others, the promotion it gets, and the ease and help that can accompany the submission and review process (some are far more tortuous than others, some are blessed with excellent editors, others cursed). However, I think most would note that for many journals it does seem like they get an awful lot (all my time, efforts, the actual science itself since I give them the copyright) for not a huge amount in return (it gets published and many, but not all people can see it). Of course how this affects individuals and institutes can only really be talked about in a case-by-case basis (what is this paper worth in this journal?) but based on my own experiences I can’t help thinking that in the future I should be more selective about what I do with my work once it is finished and before I formally hand it over. In my mind the trade off is certainly worth it in some cases, but far from all.

Online resources for palaeontologists

I was chatting to Mike Taylor the other day about Cladestore as I couldn’t find the page I needed and was surprised he didn’t know of it. To be fair it did start off well and then rather sank, but the principle is sound and it seemed relevant enough that he might know of it. It is, in short, an archive for the various files and datasets used for phylogenetic analyses. Obviously these are generally published alongside any paper that they feature in, but typing these out again or taking the raw data and formatting it into a useable manner can be a pain, and it’s not always easy to get things out of the original authors. The idea therefore was to create and archive for these files so they were easily accessible to all. Since this does seem little known, it’s well worth advertising. And I should add that despite it’s slight antiquity, I believe they still take submissions so send ‘em your nexus and tre files.

Coupled with my reference to the Paleobiology Database earlier and it got me thinking. It would be nice if there was a single, simple, one-stop-shop for all manner of palaeo websites and online resources that are useful to researchers and those interested in the field. So I’ll try and create one, as it’ll help me learn and I expect, help my colleagues. So, anything you can think of, do submit it below. I’m thinking general stuff – a database of tyrannosaur specimens, or pterosaur papers is fine but it won’t be of much use to too many people so it’s not really worth putting here. I’m thinking of major resources that cover whole fields or are simply so vast with the data collection that they are must-know-abouts.

Here’s the few I can think of, add yours below and I’ll package them all up. And do spread the word please – blog and tweet this. This could, I think be very useful to a lot of people.

Cladestore – archived phylogenetic datasets

Morphobank – more phylogentic datasets

FigTree – creates phylogeny diagrams for publication

Palaeobiology Database – data of fossil specimens, deep and wide set of data

Tree of life – phylogenetic tree of the whole diversity of life

Palaeotology Journals – Jerry Harris’ lists of journals, major and minor, that publish palaeo papers

Rankings of Palaeo Journals – Kenneth de Baets’ list of journals and things like IF, SJR, OA etc.

Polyglot Paleontologist – translations of non-English papers

The Marsh Archive – PDFs of papers by Marsh

Stratigraphy.net – archive of stratigraphic data

Phylogeny programs – list of phylogenetics software

Morphometrics – various resources for morphometric analyses

Morphobank -hmm, link doesn’t load for me…

Digimorph – digital anatomy archive of extant and extinct taxa

Comparative osteology database – mostly mammals and a few birds, but very good

3D skulls – Witmer Lab visualisations and scans of various taxa extant and extinct

Paleoportal – search museum collections for specimens

Data Dryad – data of all kinds from published papers

Figshare – data of all kinds from unpublished studies.

Biomesh – FEA models and properties.

Biodiversity library – huge archive of books and paper.

Microstrat – stratigraphy database

I’ve started adding these as the comments come in so it’s easier for people to see and avoid duplicates rather than have to hunt through the comments to see if they have been suggested or not.

Dinosaurs labelled

Inspired by the posters featured in this post of mine Mike Taylor has gone and made this picture comparing a sauropod and theropod to show the homology of all the elements.  He’s stuck it up on SV-POW, but is encouraging people to use it in their teaching so I thought I’d repost it here. Thanks Mike and great job.

Who said what? Diving into papers

Yesterday I was talking about authorship lists on papers and what this can mean, or rather imply, for who did what within a paper. An important extension of this is appreciating who has what responsibility for which parts of a paper and who intends what.  Obviously papers do not state exactly who was responsible for which parts of a given manuscript, but if you are familiar with the filed and the researchers then at least some parts are probably obvious or pretty clear such as the appearance of a specialist on histology or taphonomy on a paper which includes elements of this but doesn’t focus on it.

This can tell you who is responsible for things in the sense of their creation, but true responsibility and intent can be rather different. By tradition and for practical purposes the lead author has responsibility for the content of the paper and any mistakes in there or other issues. In theory he has control over the manuscript and as such gets the credit for the work and thus also takes the blame for its failings. Naturally however, the truth can be rather different.

There could have been a lot of help from a supervisor if the work is by a young researcher, and various issues can mean that actually the first author may not have had full control over the paper. I can think of a few papers where I know the first author is working in a second language or well outside their normal field and they are not sufficiently blessed in them to have possibly had much to do with the manuscript as a whole, let alone take credit or responsibility accordingly. Equally, if the lead author is likely relying on a specialist for some aspect of the paper, that person should be held responsible for the issues there. Yes the criticism could be directed to the Smith of Smith et al., but if it’s pretty obvious he didn’t put together that part of the manuscript then don’t judge him harshly and take the issue up with the person most likely concerned.

On a different note, if it is a long and complex paper with many authors then don’t be surprised if not everyone agrees with everything in the paper. As before, many people can be credited on papers for different reasons. If I put in a substantive amount of effort into a project, I’d want credit on the paper (and of course to show to my funders etc.) but I might not agree with or be happy with the final outcome. Profound disagreements can lead to people taking their name off of papers, but that isn’t always a practical issue for all concerned. Even the lead author may not agree with everything said in his paper if he writes democratically and gets outvoted by his colleagues or again he’s relying an expert and trusts his judgement on interpretation even if he disagrees.

Ultimately for me this all comes down to the inaccuracies of authorship lists and so on. Clearly there is a practicality issue and I’m not advocating that they change. As things stand these issues are not really very big, and if you have a problem or are curious a quick e-mail to the lead author will generally clear things up (Did you write this bit? Do you really think that? Does Jones agree with that statement, he said the opposite in his last paper?). Still it’s worth remembering and bearing in mind both how papers are put together and what that can mean for people’s take on even their own work and the implications of having your name on a given paper.

Authorship lists

Some time ago I muttered something along the lines of “there are lies, damn lies and authorship lists”. It is really one of the more contentious sides of research and an endless source of strain to some people (and to everyone on occasion) as with more than one author there has to be some kind of order of authors on the paper (Jones and Smith, or Jones, Smith and Smythe), and at least one person is probably going to be less than 100% happy, and it is almost certainly not going to really represent quite who did what on the manuscript.

Moreover, who even gets on the paper and for what reason can vary from field to field (lab techs seems to regularly be included as authors on molecular papers, whereas fossil preparators are rarely included on palaeo ones) and certainly within fields too, and there are some arcane rules hidden away in those lists. Indeed I’m sure there are others that I’m unaware of even within biology/ palaeontology and certainly beyond.

Things also vary according to the structure of a paper too. If you already have half a dozen or more authors on a small project and someone comes in with an important point or can add an extra analysis or whatever, then it’s unlikely to upset the applecart to add them in as an author, and it probably represents a reasonable approximation of the contributions with so many involved. If however you’re refining a 50+ page monster you constructed yourself then the same amount of help will likely only get you into the acknowledgements: it’s not really fair to split the credit as Smith & Jones as opposed to Smith alone for that (proportionally) little. Some people probably will of course, when others might not go that far in the first example, but such is life.

It’s also the reason why younger researchers (I think) get more concerned about this, when you only have a handful of papers to your name, missing out on one, or dropping down the authorship list a few places can make a big difference to your overall record, whereas seasoned researchers will have this effect balanced out over a number of papers and are generally more generous with credit (and can afford to be). Certainly it can be frustrating when some people seem to endlessly get added to work by their colleagues or supervisors or there are 20 authors on a 3 page paper, it looks like someone(s) isn’t pulling their weight and are getting undue credit. To be honest I think this is a pretty open, if dirty, secret but it survives because really there’s no demand by journals for authors to justify exactly what they did, and in any case people can (and I suspect at least some would) simply lie.

Obviously the order generally reflects the level of work committed to a project. The first author did the most, the last author the least, but it’s rarely that simple. In palaeo at least and certainly most fields of biology I know, it’s common for the last author in a string to have been in some kind of supervisory role. Senior researchers at the head of labs are often in this position though they might have made a considerable contribution to the paper. In know that in China however, this is generally not the case and authorship lists there tend to more reflect levels of contribution, though confusingly this can also integrate levels of seniority (so Professor X might be listed above researcher Y even though the latter did a bit more).

Certainly different people can be on papers for very different reasons and it’s certainly not uncommon for people to be in papers for which they have written not a word. That of course doesn’t mean they didn’t contribute – they could have collected important data, run analyses, found or prepared the original material, been involved in discussions or generated the ideas the work is founded on, generated funding to support the work or a host of other technical and academic contributions without necessarily being involved in the actual writing. In some cases the final paper contains none of the persons’ contributions because it was cut out, but they remain on their in reference to their efforts and time (and quite probably money) devoted to the project.

All of this adds up to a confusing picture and while some papers can be read and each author’s contributions laid bare, others are rather more complex. If nothing else, there is a huge difference between a genuine collaboration between ‘Smith and Jones’ where each did 50% of the work (and you can even see joint first authored papers these days) and a ‘Smith and Jones’ where the latter was the former’s supervisor who helped the project into being, and deserves his credit, but did perhaps 10% or less of the paper. Hence the inevitable issues when you get to 5 or even 10 authors and the conflicts that can arise and of course, the confusion that can arise when reading a paper.

 

Reserving Specimens

A while back I mentioned that I had sort of ‘reserved’ the new pterosaur specimens in Toyko to work on. This practice is pretty normal in vertebrate palaeontological circles – there are only so many specimens available and it can take a lot of time and money to go and see something. If you spend that only to discover that someone else is already publishing on that material then it’s rather wasted and your funding body may not be too impressed.

As such if you have an invitation to work on something or have seen something and the curator has agreed that you can work on it, the unwritten rule / general consensus is that this is your ‘exclusive’ specimen and no one else should work on it without permission until your work is done. This can apply as much to revisions of old material as new specimens but the general idea is the same. Obviously if you come across something and are informed that someone else has ‘reserved it’ then you need to get in touch with the ‘owner’. Naturally, many people are happy to collaborate on something, or are happy for people to do minor work like code something for a phylogenetic analysis, or even carry on as normal if the work is completely non-overlapping (say you want to take a histological sample and the other guy is only interested in skeletal proportions or doing and FEA analysis of the skull). In theory at least this also means that if you can’t get the work done for whatever in a ‘reasonable’ amount of time, then you should make it clear and let any circling people into the fold and let them do their work (and if they are being generous, they should try to involve you).

When this all works, it works well. People can guarantee they won’t be gazumped after writing a grant or spending all their cash to do a piece of work, and others know what they can and can’t do in advance. People can collaborate or tailor their projects to build up a piece of work or avoid toe treading and feelings can avoid being hurt. Of course there are those who either cling on to stuff they can’t (or won’t) work on and there are (true) horror stories of specimens being withheld for decades while someone (allegedly) works on them and at the other end, some people try (and even succeed) in publishing on things they have been told other people are working on. It is imperfect, but in my experience at least it generally leads to much better working practices and less confusion and paranoia, than simply declaring anything up for grabs.

Darren Tanke’s Gorgosaurus preparation 32: Removing the field jacket 2

Some pieces come off in large sections. A block of wood is useful as a fulcrum with the screwdriver(s) to pry up the plaster bandages. After 1.5 days of pulling and tearing, most of the jacket was off, rock was showing and the ilium uncovered in the field was also seen again for the first time in several years. The skull was outlined again with a red felt pen using the drilled holes. As the jacket got thinner, a quite large piece wanted to lift off the skull area. This was too big, so I used a cast cutter to cut two parallel lines through the jacket and pulled out the plaster and burlap in between.

This separated the remaining jacket into two pieces and the plaster/burlap covering the skull section was lifted off easily. By doing this, the jacketed skull was seen. The rags and black plastic sheeting was exposed and removed- the latter with a razor blade. The skull jacket looks odd with white sandstone and dark brown mud, but the latter was a poultice I mixed up and put on the exposed snout to protect it from the jacket- I did not want the jacket pressed right against the skull.

The poultice of dried mud was removed and preparation on the skull begun again. The skull is definately incomplete on this side and the bone seems more poorly preserved- the bone is very splintery. Several of the teeth show white meandering markings (root etchings) made by modern plants as they grew against the specimen. It is thought the roots leach minerals out of the fossil with possible negative effects on the fossil. The rest of the exposed rock was allowed to dry out and when done, glue was squirted into the cracks, etc to stabilize it for the upcoming preparation.


Fieldwork for me starts very soon so these will likely be the last postings from me for some time. [Actually Darren has already gone I think, I’ve just had this sat waiting for a while].

Darren Tanke’s Gorgosaurus preparation 31: Pulling off the jacket 1.

Dave writes: I’m nearly over my jetlag and am now settling down to the business of working at the IVPP. Sadly there’s nothing on display I haven’t shown off before and I’m still behind on writing some posts of m y own. So for now you’ll have to settle for yet more Gorgosaurus prep.

Now comes the “fun” part, taking the original field jacket off. Often we use power tools such a reciprocating saws and remove large pieces of the jacket, but the specimen is too fragile and nice to risk it as these tools cause vibrations. First the bolts were removed. Usually with a field jacket, the first few layers (there are about 6-7 on this in total) come off easily by hand, so the edge of the burlap is found and simply pulled away one piece at a time. Because the pieces overlap and are covered in plaster it is hard to see where one piece starts and end and sometimes you end up pulling on a lower piece and it tears into smaller bits. On average, the pieces here came of in hand-sized bits. A couple large flat-headed screwdrivers were good to get under the burlap and lift it up and separate the layers.

All the supporting 2 X 4 timbers used as splints in the field jacket were removed and saved- they can be used in another jacket someday. Once I got down to the harder plaster I used a water spray gun to soak the plaster/burlap. This softens the plaster and makes removal easier. Many people uses water-soaked rags for this step, but the water hose was close by so I just sprayed it lightly. After soaking in for 10-15 minutes the pieces came off more easily. Removal of a plaster jacket piece by piece by hand is tough on ones fingers and hands and time consuming- the better part of one day (7.5 hours work) was needed to get this far.

Darren Tanke’s Gorgosaurus preparation 30: turning the block 2

The block is lifted off the table by a large overhead crane (it runs on tracks mounted near the ceiling and can move 4 directions) and lowered onto a pallet jack. Then it was taken to a larger empty work area nearby. The red lifting straps are readjusted so when the block is lifted it now stands vertically, then the whole crane is moved over and simultaneously the cable lowered so the jacket comes to rest “upside-down”. Actually it is now in its original field orientation. The flipped block is put back on the pallet jack, wheeled over to the work desk, the straps readjusted a final time and the block lifted back onto the table. This work is always done with others helping for safety reasons.

Once the block was on my work table I was able to refind the holes I drilled through days ago and “connect the dots” with a red marker pen. Now I  know exactly where the skull is positioned inside. Now the manual labor of pulling the jacket off begins!


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