Saturday, 31 December 2016

Year in review 2016

2016 was best described as a busy year. It started incredibly well with 4 publications in the first four months starting off in January with my first publication on a fossil I found:

Halliday TJD, Cuff AR, Prasad GVR, Thanglemmoi MS, Goswami A, 2016. New record of Egertonia (Phyllodontidae, Elopiformes) from the Late Cretaceous of South India. Papers in Palaeontology. DOI: 10.1002/spp2.1040. Paper link, blog.


The following month the PhD student on the project, Marcela Randau, published the first of her papers on the vertebral column of cats:

Randau M, Goswami A, Hutchinson JR, Cuff AR, Pierce SE. 2016. Cryptic complexity in felid vertebral evolution: shape differentiation and allometry of the axial skeleton. Biological Journal of Linnean Society. DOI: 10.1111/zoj.12403. Paper link, blog.


The early part of they year would also involve various efforts in the field with different cat species as a student and I attempted to gather force plate data (with varying levels of success).


March was a slow publishing month, but April was to be a double whammy with both the papers on cat muscle scaling across the postcrania:

Cuff AR, Sparkes EL, Randau M, Pierce SE, Kitchener AR, Gosawmi A, Hutchinson JR, 2016. The scaling of postcranial muscles in cats (Felidae) I: forelimb, cervical and thoracic muscles. Journal of Anatomy 229, 128-141. Paper link, blog

Cuff AR, Sparkes EL,Randau M, Pierce SE, Kitchener AR, Gosawmi A, Hutchinson JR, 2016. The scaling of postcranial muscles in cats (Felidae) II: hindlimb and lumbosacral muscles. Journal of Anatomy 229, 142-152. Paper link, blog


Also in April I joined Anjali (as well as Ryan and Carla from the lab) on another trip to Argentina where we joined up with our Argentinian colleagues for continued explorations of the Salta area looking for more fossils. It was a largely unproductive trip in terms of finding many new fossil locales, but we did rule out large areas, revisited the site I discovered previously and found another very promising site. Hopefully Anjali is successful with a large grant that would allow for a longer term exploration of the area with a bigger crew.


April was to be the final month of publishing for a while, but in May my blog passed the 10,000 view mark (or at least as far as blogger's tally count goes) so at least that publishing kept going strong. 

At the end of June and into early July I attended the International Congress of Vertebrate Mophology - ICVM. It was another fabulous conference with an abundance of cool science. It made up for not being able to make SVP this year, the first time I haven't attended in 6 years. In years gone by I've heard stories of the attendees who haven't missed on in 40+ years. Guess that won't be me!

The summer would lead to publishing my two most popular blog posts of all times, the first on why extraordinary claims need extraordinary evidence (still surprised there haven't been many comments on it), and the second on some of my favourite figures from palaeontological papers. Both posts got over a thousand hits in their first month which no other posts before or since have matched.


August was a particularly crazy month as I was expecting to be unemployed when September got around. Applications had gone into various places with a fair few rejections before interview, one failed interview (although a friend got the job so can't be too upset about it), and eventually an interview at RVC which was successful in getting me three more months employment as a technician whilst searching for something longer term.

In September I started my technician role, and whilst filling in the paperwork to start was invited to interview for postdoc on John's massive European Research Council (ERC) grant looking at the evolution of pseudosuchians (the crocodile line), and dinosaurs in the Triassic. After a tricky interview and encountering what I now think is a brilliant question on who I would invite to a symposium about the project (although hated it at the time as I blanked on names), I would eventually be offered the position which I gladly accepted. I would be returning to dinosaurs in December, learning some new techniques, and having a couple more years at the RVC.

After a six month hiatus, October would bring the next publication with Marcela again publishing on felid vertebral columns and her kindly writing a blog post for me becoming the first guest blogger on my site.

Randau M, Cuff AR, Hutchinson JR, Pierce SE, Goswami A. 2016. Regional differentiation of felid vertebral column evolution: a study of 3D shape trajectories.Organisms, Diversity & Evolution
DOI 10.1007/s13127-016-0304-4. Paper link, blog

November would result in my paper on felid brains (in combination with Anjali and our summer student/Imperial Uni undergrad) being accepted, and at present it has a DOI, but we are awaiting proofs before it gets published fully. I was hoping it would be fully online before the end of the year to count as published in 2016 and take my final total up to 6 for the year but it has not made it. At the start of the year I had hoped for 7-10 papers to be published this year. The 2 papers in review (one should be accepted after this round), a few failed projects (like digital image correlation on cat bones) and collaborations that are completed from my end, but not submitted are where I fell short. All of these should add to the expectation of at least 5 more by the end of 2017.

Ultimately December would bring the start of my second postdoctorate on the ERC project (expect many, many posts over the next few years on it), as well as leaving the UK for a much needed 3 week break having not had time off since Easter and feeling exhausted from work.

Across the year I have been practicing what I preach in regards to reviewing papers, with 12 reviews completed for 5 papers across 6 journals (one I got for 2 different journals when it wasn't deemed suitable for the first journal). Somewhat crazily, I have accepted another review across the Christmas holidays, so will be reviewing another one early in 2017.

It has been another good year for me, although maybe not so much politically for science in the UK with Brexit threatening large amounts of funding and collaborations. It shall be interesting to see where things go and I live in the optimistic (and probably vain) hope that it is not the doom and gloom we all fear,

A final amazing figure for the year from an undergraduate research project at Leicester (and a great example of how to get students thinking about science at all levels). I have to say I have nothing to do with the research, but it is a fun studying into whether the satellite phone swallowed by the Spinosaurus in Jurassic Park 3 could really have been heard by the main characters.
Childs et al., 2016. Dinosaur in-dial-gestion. Journal of Physics Special Topics.
Fig 1. A rough model of the path travelled by the sound, with Z-values from the literature.
Happy New Years and best wishes to all for 2017!

Wednesday, 23 November 2016

The cat's backs - a guest post

Two papers recently have come out that I have been involved in, and am thankful to Marcela Randau (the primary author) for giving up time between finishing a PhD, postdoc hunting and preparing for lecturing to write this post. If anyone reads whatsinjohnsfreezer.com regularly, you will see an identical post there as Marcela, understandably, didn't have time to write two similar but different posts for us both as we clambered for her expertise in felid vertebral columns.

The cat’s back.
by Marcela Randau (m.randau@ucl.ac.uk)
It is often said that all cats are very similar in terms of their skeletal morphology (“a cat is a cat is a cat”). But is this really the case? It may be if only gross, qualitative anatomy is taken into consideration, i.e., if you just eyeball the skeletons of tigers and lions you might find yourself not knowing which one is which. But with huge advances in technology that allows for extracting detailed shape information off a structure (e.g., a skull) and for analysing this information (‘Geometric Morphometrics’), it has become more and more possible to distinguish between relatively similar forms – which may be from distinct species, separate sexes, or even just different populations of the same taxon.

And it is reasonable to think that cat skeletons might be a lot more different than what meets the eye, as for a lineage of apparently similarly built animals, with not that much variation in diet (all cats are hypercarnivores) there is substantial variation in body mass (over 300-fold just in living species!) and in ecology across cat species. From the cursorial cheetah to the arboreal clouded leopard, felids present a wide range of locomotory adaptations. Yes, all cats can climb, but some do it better than others: think lion versus margay (yes, they do descend trees head-first). As hypercarnivores, all cats are meat specialists, but they also change with regards to how big their prey is, with a general and sometimes-not-so-black-and-white three-tier classification into small, mixed and large prey specialists. The rule of thumb is ‘if you are lighter than ~20-25kg, hunt small stuff. If you are heavier than that, hunt BIG BIG things, much bigger than yourself. And if you are in the middle ground, hunt some small-ish things, some big-ish things, and things about your size. Well, -ish’ – their prey size preference has a lot to do with energetic constraints (have a look at Carbone et al. 1999; and Carbone et al. 2007, if you're interested in this). But the fun bit here is that form sometimes correlates quite strongly with function, so we should be able to find differences in some of their bones that carry this ecological signal.

Indeed, for a while now, we have known that the shape of the skull and limbs of felids can tell us a lot about how they move and how big their prey is (Meachen-Samuels and Van Valkenburgh 2009, 2009), but a large proportion of their skeleton has been largely ignored: we don’t know half as much about ecomorphology and evolution of the vertebral column. Well, it was time we changed this a bit! As the PhD student in the Leverhulme-funded ‘Walking the cat back’ (or more informally, “Team Cat”) project, I’ve spend a big chunk of my first two years travelling around the world (well, ok, mainly to several locations in the USA) carrying a heavy pellet case containing my working tool, a Microscribe, to collect 3-D landmarks (Fig. 1) across the presacral vertebral column of several cat species. And some of first results are just out! Check them out by reading our latest paper, “Regional differentiation of felid vertebral column evolution: a study of 3D shape trajectories” in the Organisms Diversity and Evolution journal (Randau, Cuff, et al. 2016).

Fig. 1: Different vertebral morphologies and their respective three-dimensional landmarks. Vertebral images are from CT scans of Acinonyx jubatus (Cheetah, USNM 520539).
Building from results based on our linear vertebral data from the beginning of the year (Randau, Goswami, et al. 2016), the 3-D vertebral coordinates carry a lot more information and we were able to describe how this complex shape-function relationship takes place throughout the axial skeleton (in cats at least) in much better detail than our prior study did. One of the difficulties in studying serial structures such as the vertebral column is that some clades present variation in vertebral count which makes it less straightforward to compare individual vertebrae or regions across species. However, mammals are relatively strongly constrained in vertebral count, and Felidae (cats; living and known fossils) show no variation at all, having 27 presacral vertebrae. So adaptation of the axial skeleton in mammals has been suggested to happen by modification of shape rather than changes in vertebral number.

Using a variety of geometric morphometric analyses, under a phylogenetically informative methodology, we have shown that there is clear shape and functional regionalisation across the vertebral column, with vertebrae forming clusters that share similar signal. Most interestingly, the big picture of these results is a neck region which is either very conservative in shape, or is under much stronger constraints preventing it from responding to direct evolutionary pressures, contrasting with the ‘posteriormost’ post-diaphragmatic tenth thoracic (T10) to last lumbar (L7) vertebral region, which show the strongest ecological correlations.

We were able to analyse shape change through functional vertebral regions, rather than individual vertebrae alone, by making a novel application of a technique called the ‘Phenotypic Trajectory Analysis’, and demonstrated that the direction of vertebral shape trajectories in the morphospace changes considerably between both prey size and locomotory ecomorphs in cats, but that the amount of change in each group was the same. It was again in this T10-L7 region that ecological groups differed the most in vertebral shape trajectories (Fig. 2)
Figure 2: Phenotypic trajectory analysis (PTA) of vertebrae in the T10 – L7 region grouped by prey size (A) and locomotory (B) categories.
So in the postcranial morphology of cats can be distinguished, changing its anatomy in order to accommodate the different lifestyles we see across species. But the distinct parts of this structure respond to selection differently. The next step is figuring out how that might happen and we are working on it.

While Team Cat continues to investigate other biomechanical and evolutionary aspects of postcranial morphology in this interesting family, we’ve been able to discuss some of these and other results in a recent outreach event organised by the University College of London Grant Museum of Zoology and The Royal Veterinary College. We called it “Wild Cats Uncovered: movement evolves”. Check how it went here: (https://blogs.ucl.ac.uk/museums/2016/11/17/cheetah-post-mortem/) and here (http://www.rvc.ac.uk/research/research-centres-and-facilities/structure-and-motion/news/wild-cats-uncovered), with even more pics here (https://www.flickr.com/photos/144824896@N07/sets/72157676695634065/ ).

References used here:
Carbone, C., Mace, G. M., Roberts, S. C., and Macdonald, D. W. 1999. Energetic constaints on the diet of terrestrial carnivores. Nature 402:286-288.
Carbone, C., Teacher, A., and Rowcliffe, J. M. 2007. The costs of carnivory. PLoS biology 5 (2):e22.
Meachen-Samuels, J. and Van Valkenburgh, B. 2009. Craniodental indicators of prey size preference in the Felidae. Biol J Linn Soc 96 (4):784-799.
———. 2009. Forelimb indicators of prey-size preference in the Felidae. Journal of morphology 270 (6):729-744.
Randau, M., Cuff, A. R., Hutchinson, J. R., Pierce, S. E., and Goswami, A. 2016. Regional differentiation of felid vertebral column evolution: a study of 3D shape trajectories. Organisms Diversity and Evolution Online First.
Randau, M., Goswami, A., Hutchinson, J. R., Cuff, A. R., and Pierce, S. E. 2016. Cryptic complexity in felid vertebral evolution: shape differentiation and allometry of the axial skeleton. Zoological Journal of the Linnean Society 178 (1):183-202.

Friday, 11 November 2016

11/11/2016

This post has a cryptic date as a title, but it signifies that two years from the blog's inception, I am still here and people are still reading it. I've never really gone into why the blog started and credit/blame goes to John Hutchinson at the RVC who, at one of his weekly team meetings, was talking about our online presence and encouraged us to get a researchgate and academia profile, as well as twitter and consider starting a blog. I have always enjoyed outreach so the blog was an obvious step, although I haven't always enjoyed writing and it is the one thing I struggle with most when it comes to my own research.

My blog started with a simple post on a SVP conference I had just attended in Berlin and it was a simple starting point for me. I enjoy conferences to meet and mingle with people and talk science, and I was expecting the Berlin SVP to be the last one I attended for a while as my work was looking mainly at modern species. That turned out to not be the case as I attended last year having managed to work on scaling of extinct cats. This year I didn't make SVP as I was finishing my contract with UCL and starting a short-term technician role at the RVC and there were no travel funds, but I managed to attend the very amazing ICVM in July instead. It is still a bit weird for me going to conferences and people knowing your name from work you've done.

The blog has developed covering topics such as my postdoc research, and stuff on ornithomimosaurs - the group of dinosaurs I did my PhD on. I even ventured out of my comfort zone of the strictly scientific into a bit of historical things on how cats and human interactions have evolved and changed through time. It was an eclectic mix of topics as I was finding a direction for the blog. To be honest, the blog remains an eclectic mix of topics as it covers things I am interested in and working on.

I've also spent a lot of time talking about my publications. It helps that I had a productive few years in my first postdoctorate in terms of publications with 8 papers in the last 2 years, 2 in review, 1 about to be submitted, and about 5 more in the works across various collaborations. However, I make a particular effort with the blogs on the papers as I know many of my friends and family aren't experts and can only understand one in every 3-5 words (apparently in some papers, my parents get even fewer) due to the specialist nature of some of our research. I'm still trying to get my first guest blog post from one of my colleagues who was the lead author on two of the most recent papers looking at felid vertebral columns. If anyone does ever want a copy of a paper, just give me a shout and I'll get you a .pdf as soon as I can.

I've particularly enjoyed getting to show off some of the field work I've been lucky enough to work on, whether it was digging for fossils in India or Argentina, or the postdoc work on cats (1 or 2). A lot of my work is done in labs/my office but I cannot ever fail to emphasise how much I think field work is vitally important for palaeontologists for collecting fossils, or actually getting hands on animals to see how they actually work.

One of the Cat Survival Trust leopards having a yawn
There are some bloggers who are very active in showing the human side of the science in terms of their emotions and feelings, and to that end I've tried hard to show myself in my writing, but have kept a lot of my personal life out of my blog (although kind of got close discussing the job hunt). That aspect is not likely to change even though work and personal life are sometimes tough to tell apart right now. I am hopeful that some of the things I publish are helpful particularly to others in terms of advice and guidance whether that is for people interested in getting involved in palaeontology or young career researchers going through similar things in their academic careers.

I like numbers so there has been a change from how I monitor visitors from just using the blogger details (about 18,250 page views in the last 2 years), and got Google analytics. It's only been active since mid-June but allows me to see better who is reading and what is being read. Each post still has a variable number of reads, but I did have two since June hit 1000 reads already. Unsurprisingly, dinosaurs do better than job search chat. In that time, I've had readers from 79 countries (I have regular readership from about 30 countries each month), with the USA being the largest readership and all 50 states and DC have had people read the blog.

Readership of the blog since June from Google Analytics. Darker colours are higher numbers of views.
I'd like to thank everyone who has been reading, and particularly those who keep widely sharing my blog and the posts so widely. I know with my Twitter and personal Facebook I don't reach more than about 700 people with a high overlap across the two so getting as many viewers as I have is largely thanks to them.

What changes can people expect in the next 2 years? There will be a general winding down of cat chat as I move away from the project (although there is probably a year or so worth of research that I am involved in). That being said there may be one shortly about the outreach event we did on the evening 9 November where we carried out a postmortem on a cheetah that was donated to us via a museum for science and outreach. The animal had passed away at a UK zoo and we were lucky enough to be able to use its unfortunate death for science and teaching the general public.

Picture preview of the postmortem. Myself in the middle working on the forelimb. Photo from the RVC link above, Photo credit: Oliver Siddons
What comes next for me? Well, I've been offered and accepted a job at the RVC as a postdoc in John's lab for another 2 years and I will be returning to dinosaurs and crocodiles looking at the evolution of the two groups' locomotion. Expect lots of posts showing "Team Dawn Dino" at work with live crocodiles and tinamous (fairly primitive birds from Central and South America), as well as work on fossils. I am hoping to still sneak out on field work from time to time to get dirty in the field. The quest for a new species is ongoing! If anyone has any digs upcoming and are looking for volunteers, do give me a shout.

The blog is never going to become a massive thing like IFLS (which became click baity and designed to make money). I am going to keep posting my research and things that interest me. I am hopeful to get a few colleagues who I have worked with share their knowledge, particularly on collaborations where I am not the first author. I will do my best to make sure everything I publish is accurate and up-to-date, but feel free to call me out on mistakes or missed citations as I will happily update the blog accordingly.

Thanks again to everyone reading and do let me know in the comments if there are things you like/dislike or think I could do differently.

Friday, 28 October 2016

Early career advice time

Its been almost 3 years since I handed my PhD in, and I've completed my first postdoc. I've thankfully gotten another one offered (although awaiting my contract) so should be continuing in academia. 2 months ago I wasn't sure this would be happening so I am very thankful to have one less thing to worry about. I thought I'd chuck out some of the advice I'd give to anyone who wants to read.

1) Academia is a great career
People laughing please stop now. It is. Flexible work hours, doing something you love, discovering new things out about the world, travelling the world for free (or cheap), amazing conferences etc etc.

2) Academia is an awful career
People who were laughing before can laugh again. The early career part is tough. Short term jobs lead to a lack of permanence. There is a never ending need to publish and prove yourself, whilst also balancing applying for grants and permanent positions. Throw in all the other odds and sods which come with it (relatively low pay for such high qualifications, sometimes working stupidly late to get stuff done etc.).

3) Make sure you are doing it for the right reasons
PhDs are major commitments and take at least 3 years of your life. In the USA and Canada it can be 5 or 6. Make sure you are ready and able to one. Do it because you love it, not because someone said you should. Everyone goes through ups and downs in work (even when you love it most of the time), but if you aren't in it for the love of it, the bad will heavily outweigh the good. This applies for postdoc positions too.

4) Find a work/life balance
I have no idea how anyone really manages this properly but everyone should try. I struggle as what I am doing has been my dream for so long it becomes tough to untangle it from who I am. Work often comes home with me, and even on weekends if I am not doing it, my brain is often thinking about work. It is tiring. Academics in general find their coping mechanisms and have to long term. Many of my friends are crazy fit, running 10km (or more) regularly, climbing weekly, gyms regularly, that sort of thing. Additionally nearly every one I know is in a serious relationship. I know people have said that maintaining a relationship during your PhD is hard (I never managed to), but I think it is definitely helpful for those who have/can.

5) Don't do work you wouldn't try to publish
Ok, so this needs clarification. Don't do primary research you wouldn't try to publish (do outreach though, see below). This was something Mike Benton taught all masters level students at Bristol. If your research question isn't going to be publishable, why are you doing it? It is a symptom of academia and the publish or perish mentality. Jobs look at your publications, and particularly those in the high impact journals. This means you need to be thinking of new and interesting questions that are worthy of publication.

6) Try to get in lecture experience
It will be good on so many levels. You can't teach unless you understand things, so spending the time planning a lecture should ensure you know and understand all of the material. In the UK particularly, with such short PhDs, we don't do the typical teaching assistant roles found in many North American universities and lecturing experience is hard to come by. In addition, postdocs (in the UK at least) get very limited teaching experience as that generally falls to the permanent staff - the first permanent post many in the UK get is a lectureship (lecturer). It's a trade-off as UK academics tend to have more publications than a person the same number of years since the start of their PhD, but they miss out on many countless hours of lecturing experience. But to get to the next step you need teaching experience. How can you prove you can lecture, without lecturing? But at the same time how get lecturing experience when you can't lecture? Take advantage of any and all chances. Volunteer if there is a chance, do practicals, do anything you can.

7) Do outreach
I beat this drum all I can (for example, see here). The world needs scientists, not just the current generation, but the future ones. Our ability as academics to inspire the next generation is vital (I smiled when I was told that a young family friend was visiting the American Natural History Museum and told them her friend [me] was digging for dinosaurs in Argentina). Our ability to explain to the public what we do and why they should care, and want to keep funding us is of the utmost importance for our ability to ever expand human knowledge. In addition to those obvious points, on a somewhat selfish level, it gives you a chance to do lectures to the general public, and work on your communication and understanding of your science. Einstein was a great proponent of being able to explain things simply (and usually so a child could understand), whether it was racing a light beam, or the bending of space-time, and so should we. Try it! We have our next big outreach event coming up in November which I will almost certainly blog about.

8) Get involved in side projects
This adds to the list all the things you should do, and thus flies in the face of the work/life balance points above. If you get spare time, or a chance to work on a project that doesn't hamper your own project you should do it. It is useful to collaborate lots, and who knows when one of those collaborations may lead to something major (even a job) down the line. If nothing else, it helps the publication count which we all know is a big deal.

9) Supervise students
Fits with lots of the above themes: you learn lots; get involved in side projects; and get experience in supervising which will hold you in good stead for future careers. It should be noted that having someone doing work for you doesn't actually reduce your work load unless you get a highly competent student. I've had a spectrum from those I had to walk through absolutely everything, to those who needed minimal assistance. Sometimes it is a good thing if they don't need help, but often in means they aren't pushing themselves. I was lucky enough to get a student who managed to turn my project into 2 papers I was directly involved in, and an additional one beyond the scope of my project, but he required help because he was pushing his limits all the time and getting the most out of the research. Suffice to say he is now working towards a PhD and I think has as many publications as I do.

10) Read lots
This is obvious, but finding time for it is tricky. At the start of a project it is always useful to write a literature review to get an idea of the main literature for the research. It comes in very handy for introductions in papers, and gives you a quick catch up to the literature for the project. Inevitably you will miss things, but can expand out from your core literature to fill in the gaps. Thankfully I've always been part of groups that do reading groups and that really helps to motivate you to read papers, particularly in areas you may not normally read.

11) Use your advisers/advisors 
They are useful for so many things, whether it is guidance in reading, improving writing, reading CVs, advice for grants, helping supervise etc. They've been through it all before, have many years of experience and are worth listening to. I've been lucky to have had lots of involved supervisors and feel sorry for those who miss out on that.

12) Apply for things, regularly and often
This advice comes from Anjali Goswami who encourages her group to apply to lots of jobs, particularly permanent positions. You can't get a job if you don't apply after all. Even if you don't get the position it helps to get your name out there and hopefully they keep you in mind for the future. Obviously don't apply outside of your field, but for jobs you are qualified/able to do.

13) Review papers
This is a multi reasoned thing. Reviewing is vital for science to function. It's why there are 2 reviewers for every manuscript (minimally). Help the community out and review what you are qualified to review (see advice here). In addition reviewing for journals looks good on your CV as it shows you are considered an expert, and also it gives you a chance to potentially become an editor one day. From what I am told, good reviewers at more senior levels get invited to become editors for the journals which again looks great on CVs. Additionally it helps with point 10) reading lots. What better way to read cutting edge research, than to help edit it (obviously you need to understand the research to review, but the principle applies).

*14) Broaden your horizons
Don't just focus on your skill set. I did lots of finite element stuff for my PhD, but it meant starting my postdoc I was a long way behind on coding (both R and Matlab, and soon to be C++). Obviously I am not saying do all of them, or indeed do coding, but take additional courses that may be beneficial. In palaeontology it is worth doing field work, in other fields it may be worth spending time in industry. These things may come in incredibly useful later in projects, or even for spawning new ones, and your skills and drive to learn look great on the CV.

*15) Go to conferences, and speak to people
I debated splitting this into 15 and 16, but lumped them together as lots of the speaking to people outside of your groups happens at conferences. Going to conferences allows you to broadcast your work to a wide audience, whether that is just by talking to people, giving a talk or presenting a poster. Giving a talk will get lots of people listening (although at my only SICB the room probably had only 20 people in it), but only a few will ask questions during your allotted time (assuming you've not gone over) and is considered more prestigious. Giving a poster lets lots of people see your work, and with you being there allows a lot more interaction, although your method for attracting people may not be the same as mine. I will suggest getting a few friends to come over every once in a while to ask you to explain things (even if they've heard it hundreds of times before), as groups tend to attract more attention to people. Conferences also have the benefit of  allowing you to see loads of research that may or may not be applicable to you, interact with the presenters, and job hunt. It is worth getting to know the big names in your field and find them at conferences to talk work whether in a coffee break, or in the case of palaeontologists more likely over a drink. You never know what may happen.

I'm sure there are many other things that are worth talking about/adding to this list, so if you have any feel free to message me/comment and I may add them. Thanks for reading!

*Added advice post original publication. Thanks to those who have suggested them.

Friday, 30 September 2016

Reviewing for journals

Reviewers are the most important people in the whole academic publishing process. They are (theoretically) unbiased, impartial and are there to make sure the paper is correct, everything is clear and the science is of high quality. Reviewers are doing the work for free (or occasionally reduced publishing costs) on top of their usual work, so there is often a struggle for editors to get reviewers so there will come a time where all young academics eventually get asked to review for journals. The first time I got asked was a bit of a shock, and I turned down the first couple as I didn't feel qualified enough to review the papers. Looking back I probably could have done one of them, but the other I definitely wasn't able to do to a high standard. I'm still a newbie when it comes to reviewing having only reviewed for 6 journals so far (and turned down a couple of others).

The review process is much the same across journals (at least for the few I've done) and follow the following format:

A few sentences summing up the paper showing they have at least read some of it. e.g. The authors of this new paper on tyrannosaurs, using new phylogenetic methods to prove that tyrannosaur arms aren't really small. That sort of thing but obviously with some more details about all of it.

Next is major issues and this is normally in paragraph format. What is really wrong with the paper? What analyses are missing or are the analyses run badly? Is there missing data that means you cannot be sure of the results?

Then comes minor issues. How detailed you get depends on the journals and your willingness to catch all typos/grammar issues. This is line by line errors/typos/grammar/missed references etc. Those sort of things. E.g. P4 ln 10: Missing ref from Author, year (incredibly useful to also give title of the paper too if not the full reference. Amazing how many people have multiple papers from the same year).

There is also normally a section to the editor where you put in your comments that are not seen by the author. Is it novel and high enough impact for the journal? Are there things you cannot say about the paper to the authors or issues that need raising to the editor (e.g. plagiarism)? Increasingly journals are moving towards a series of tick boxes instead of this section, but many still have it.

What advice would I have for any person just starting to review?
  1. Review a manuscript with a supervisor or colleague first to see how it is done. At university, we actually did reviews for published papers which was very informative. To review something for a journal, you've probably published before and seen your paper reviews to give you an idea of how it is done.
  2. Make sure you are qualified to review the paper. Does the title/abstract read like something you can fairly review? If not, don't be afraid to turn it down, but be prepared to suggest some other reviewers that might be able to do it.
  3. Read the manuscript, scribble down notes on things that immediately catch your eye, then walk away and come back to it. Big errors are easily caught, but taking some time away helps you think over aspects of the manuscript that you might miss first.
  4. Remember this is someone's work, and be professional. There are huge swathes of the internet devoted to demeaning insults in reviews about the manuscript (e.g  this particularly famous tumblr) that are neither helpful nor clever.
  5. At the same time, don't be afraid to be harsh. If something isn't right, call the people out. If the data doesn't support the conclusions say it.
  6. But, don't be that reviewer. You know, reviewer 2. The one who hasn't read the paper fully, is pedantic about nothing, and writes a review that is longer than the paper because they've had a crappy day and need someone to take it out on.
  7. Be helpful in your reviews! Sometimes people are working across fields. I am one of those who works on biomechanics, phylogenetics, physiology and anatomy in a vast array of groups. I will not know as much as a specialist in any one of those fields so despite my best efforts may miss papers, or might not have read the newest methods that came out last month.
  8. Do it in the length of time requested. We've all sat around waiting for reviews (see this earlier post), and early career researchers in particular need published papers to advance their careers. Don't sit on your reviews until the prompts start arriving (I've not found out what those emails are like yet). Most journals give 3-4 weeks to review the paper although a few are 14 days. If you can't make that deadline, don't take the review.
Hopefully that gives a quick insight into the review process, and help anyone just starting. There undoubtedly are lots of other opinions on how exactly to do a peer review, although I'm optimistic that most of those will be the same as those stated above. If you have any suggestions of things to include/do differently/methods that work for you, do let me know and I will, as always, happily add them to the list.

Friday, 23 September 2016

Favourite figures from papers 3: The eating edition

After the edition a fortnight ago, I've had no further suggestions for favourite figures so thought I should do a few themed topics. Today's theme is eating, not just because I love eating, and I've already featured a couple of cases of fossils with taxa eating each other (be it pterosaurs with fish being eaten by fish, or the fighting dinosaurs), but because of this specific fossil which caught my eye last week and has featured heavily in lots recently:

 Fig 1. from Smith and Scanferla 2016.
Fig. 2 from Smith and Scanferla 2016.
The second author (Agustín Scanferla) is a colleague we've done field work with in Argentina and the fossil is amazing. The fossil is from Messel (48 million years old) in Germany, and shows a snake (Fig 2a grey) with a lizard (Fig 2a orange),  in its gut. In the gut of the lizard is a beetle (Fig 2a turquoise).

1) Fish within a fish
Fig 4. from Walker and Everhart 2006. The impossible fossil - revisited.
This famous fossil shows a 14ft long Xiphactinus fish with a 6ft long Gilicus fish inside it. It was collected by George F Stenberg (a relative of the famous Sternbergs known for the many fossils, particularly dinosaurs in Canada) in 1952. Xiphactinus is a famous fish species for its love of eating other big fish, with about 13 known specimens showing other large fish inside.

2) Dinosaur eating mammal
Fig 3. from Hu et al., 2005. Large Mesozoic mammals fed on young dinosaurs
Whilst everyone always assumes that during the Mesozoic mammals are small and hiding from the dinosaurs trying to eat them, this fossil proves otherwise. Repenomamus robustus was a badger sized mammal that has the remains of dinosaurs in its guts.

3) Dinosaur eating dinosaur

Fig 1 and 5 from Xing et al., 2012. Abdominal Contents from Two Large Early Cretaceous Compsognathids (Dinosauria: Theropoda) Demonstrate Feeding on Confuciusornithids and Dromaeosaurids
Jurassic Park may have skewed people's opinions of which dinosaurs were likely to eat other dinosaurs. Compsognathids are presumed to be small chicken sized dinosaurs, and dromeosaurs are the big terrorising creatures. This fossil shows that is not always the case, with a large compsognathid (Sinocalliopteryx gigas) preserving gut contents including dromeosaur limbs and feathers.

4) Birds have long eaten seeds
Fig 1a. from Zhou and Zhang, 2002. A long-tailed, seed-eating bird from the Early Cretaceous of China
This large early bird from the Jehol of China (Jeholornis prima) preserves a mass of over 50 seeds (the small round things lower centre of the image) in its guts. Whilst this may not seem that exciting, new research this year suggests the ability to process seeds may be important in the survival of birds when the dinosaurs died out.

5) Deinocheirus ate fish?
Extended data Fig 7 from Lee et al., 2014. Resolving the long-standing enigmas of a giant ornithomimosaur Deinocheirus mirificus
Anyone who has read the blog for a while knows I've got a soft spot for ornithomimosaurs because I did my PhD on them. They are an incredibly strange group that loses their teeth and evolve beaks, and this change (and a bunch of others) has been linked to a change in diet from carnivory to herbivory. The massive, and now with a body, Deinocheirus seems to have gastroliths for eating plant materials, but also preserves fish bones within its stomach. Whether this was deliberate hunting of fish, accidental ingestion of them, or one of the many other ways for fish remains to end up there, is still uncertain. With more fossils will hopefully be more clarity on the matter.

There are countless other ones I could have picked. Whether it was ichthyosaurs with belemnite hooklets, or other dinosaurs and mammals with their various prey/flora gut contents. If you have any amazing ones, let me know and I am happy to add them in after. 

Friday, 2 September 2016

Favourite figures from papers 2

Due to the popularity of the last post with over 1000 people viewing the post, I thought it was worth doing a second. The first two were pointed out to me by comments on the last blog post, and are compliments of a tumblr that showed them, although sadly that tumblr seems to have gone inactive after 2 months. Please keep suggesting other figures that are worth being more widely seen

1. Dinosaur pain thresholds
McCrea et al., 2015. Vertebrate Ichnopathology: Pathologies Inferred from Dinosaur Tracks and Trackways from the Mesozoic. Ichnos 22, 235-260.
A set of tracks were discovered showing several deformities of the toes in theropods, including loss of the second digit on the foot. The authors showed a sense of humour by adding a speculative dinosaur pain scale  to the various toe deformities. Using what metric? Who really cares. If it is that brilliant there is nothing to not love.

2. Phytosaurs were not sniffing each like dogs
Senter 2002. Lack of pheromonal sense in phytosaurs and other archosaurs, and its implications for reproductive communication. Paleobiology 28, 544-550.
This weird group of animals look superficially like crocodiles (but are only somewhat closely related), but instead of having their nostrils at the front of the skull like in modern crocodiles, their nostrils are near their eyes. This has implications for their ability to use scent like other animals to detect reproductive pheromones by either sniffing the ground or cloacae (the shared urogenital opening found in most non-mammal terrestrial groups) without breaking their necks or getting their noses/heads squished as beautifully indicated by the figure.

3. The fighting dinosaurs
Figure 1 from Carpenter 1998. Evidence of predatory behavior by carnivorous dinosaurs. Gaia .
Found in 1971 and first described in 1974 by Barsbold (I couldn't find the paper to get the original figures) during the Soviet-Mongolian expeditions it remains one of the most famous fossils ever discovered. It preserves a Velociraptor and Protoceratops forever locked in combat, with the Protoceratops biting down on the right forearm of the Velociraptor, whilst the Velociraptor is kicking its famous sickle claw into the throat region of the Protoceratops. The Velociraptor probably killed the Protoceratops with this kick, but was trapped when its right leg ended up under the Protoceratops. The death scene may have been scavenged explaining the loss of the front limbs of the Protoceratops before ultimately being buried under a sand dune and fossilised. I was lucky enough to see the specimen in Mongolia and it truly is amazing, although having been transported around the world a lot in the last 40 years it is now particularly fragile and hidden in a basement, not the place for a Mongolian national treasure. Hopefully the new dinosaur museum being built in Ulanbataar will put it back on display.

4. Big mamma
Figure 1 from Norell et al., 1995. A nesting dinosaur. Nature 378, 774-776. 
Big mamma is a beautiful skeleton of an oviraptor (Citipati) sitting on its nest brooding its eggs. Oviraptors got their name "egg theives" when Roy Chapman Andrews first found them close to eggs and assumed they were stealing them from Protoceratops. Turns out it was an incredible misnomer and these dinosaurs (with their feathered bodies) brooded their eggs just like modern birds do. There is another specimen (Big Auntie) preserved in the same position as well.

5. T. rex described
Figure 1 from Oxborn 1905. Tyrannosaurus and other Cretaceous carnivorous dinosaurs. Bulletin of the AMNH 21, 259-265.
Possibly the most famous of all dinosaurs, and shamefully/shamelessly one of my favourites. What's not to love from its massive head to its tiny arms. The figured reconstruction shows it tail dragging but we know now that it held its tail out behind it in a far more active posture (see the last blog of favourite figures showing the transition from the Crystal Palace dinosaur reconstructions to the Deinonychus reconstruction by Bakker). It's also sad we no longer have skeletal humans for scale next to our dinosaur reconstructions.

6. The claw...
Figure 4 from Altangerel et al., 1993. Flightless bird from the Cretaceous of Mongolia. Nature 362, 623-626.
T. rex always gets a lot of abuse for its tiny arms, but it doesn't have the smallest or most reduced arms of the dinosaurs. This ridiculously tiny arm belongs to Mononykus (one claw), an alverezsaur which has reduced its arm to basically nothing with one finger. The morphology has been suggested to be linked to breaking into termite mounds although whether it could has not been tested.

7. Pterosaur meets cat
Figure 6 from Martin-Silverstone et al., 2016. A small azhdarchoid pterosaur from the latest Cretaceous, the age of flying giants. Royal Society Open Science.
In the Cretaceous most known pterosaurs (the flying reptiles) are huge creatures, with species like Quetzalcoatlus reaching giraffe sizes. The paper describes a new species of pterosaur from the late Cretaceous of Canada which shows itself to be nearing maximum size, but yet is still small. Mark Witton (an author and very accomplished palaeo-artist) shows its size relative to a cat, and for me (and the internet as a whole) that is a winning combination. Check out the paper as it is open access too!

8. How do you make a chicken walk like a dinosaur?
Figure 1 from Grossi et al., 2014. Walking like dinosaurs: Chickens with artificial tails provide clues about non-avian theropod locomotion. PLoS One 9, e88458.
In response to the question of how do you make a chicken walk like a dinosaur, you stick a plunger on its butt. Well, not exactly a plunger, but a weight that resembles a plunger. As your chicken grows you increase the weight and the result is a more upright posture in their legs relative to the control and the control weight groups. Whilst there are issues with the assumptions as a whole, mostly due to a lot of the muscles that control the leg movements in dinosaurs attach in the tail which isn't the case in birds (as they don't have a long tail), it is an interesting experiment and result.

9. The upside down hallucination inducing animal
Figure 2 from Conway-Morris 1977. A new metazoan from the Cambrian Burgess Shale of British Columbia. Palaeontology 20, 623-640.
Hallucigenia is a weird and wonderful creature from the spectacular Lagerstätten (site of exceptional fossil preservation) of the Burgess Shale. When first found there was much debate over which way round the animal goes, and Conway-Morris speculated it went spikes down. Funnily he even went as far as to speculate about the hypothetical arrangement of muscles (parts B and C of the figure) that would allow the animals to walk on the spines. Recent papers suggest that he got it upside down, and it walked on the soft legs, and had spines on its back to protect itself.

10. Lucy in the sky with broken bones
Figure 2 from Kappelman et al., 2016. Perimortem fractures in Lucy suggest mortality from fall out of tall tree. Nature
Lucy is perhaps the most famous of the fossil hominins due to the remarkably well preserved skeleton (as far as hominins go). New research out suggests that this famous Australopithecus has a bunch of fractures similar to those found in modern humans falling from height and have linked the fossil breaks to Lucy falling out of a tree. Based on the news reports, this is highly controversial and it will be interesting to see whether this hypothesis withstands the test of time.
This one also comes with a bonus video:


That rounds off this next set of 10 favourite figures, across the spectrum from of categories from funny pictures to interesting science. Please let me know yours as I quite enjoy doing these posts!