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!