Manuscripts: reviews, rejections and acceptance

I am still a very early career academic being only two and a bit years through my first postdoctorate (and 5.5 years on from the start of my PhD). As such I don't have the ability to write an amazing CV of failures like Johannes Haushofer did that hit the news recently. However, it did inspire me to go through my publication list and my record of revisions I've had to help remind early researchers and PhD students it's not all bad.

Papers:
2009

• Diversity of chondrichthyans since the K-Pg mass extinction. Reject with lots of corrections Palaeontology. Sadly I never found the time to get back around to it as it was a literature review as part of my undergraduate third year and would require more work and time than I had to learn the techniques. A PhD project on the topic appeared during my time as a PhD but I remain unsure what happened to it.

2011

• Feeding Mechanics in Spinosaurid Theropods and Extant Crocodilians. Major corrections at PLoS one (functionally a rejection)

2012

• Feeding Mechanics in Spinosaurid Theropods and Extant Crocodilians. Major corrections at PLoS one (functionally a rejection)

2013

• Feeding Mechanics in Spinosaurid Theropods and Extant Crocodilians. Minor revisions and then accept in PLoS one.
• Validation of a finite element model of an ostrich (Struthio camelus) skull. Reject with encouragement to resubmit Journal of Anatomy

2014

• Functional anatomy and feeding biomechanics of a giant Upper Jurassic pliosaur (Reptilia: Sauropterygia) from Weymouth Bay, Dorset, UK. Reject from Proc. Royal Soc. B. Minor, minor then accept at Journal of Anatomy.
• Complex rostral neurovascular system in a giant pliosaur. Minor corrections and accept Naturwissenschaften.
• Validation of a finite element model of an ostrich (Struthio camelus) skull. Reject and don't resubmit Journal of Anatomy.

2015

• Big cat, small cat: reconstructing body size evolution in living and extinct Felidae. Reject and accept Journal of Evolutionary Biology.
• Retrodeformation and muscular reconstruction of ornithomimosaurian dinosaur crania. Major, major  and accept PeerJ.
• Validation experiments on finite element models of an ostrich (Struthio camelus) cranium. Major and accept PeerJ.
• Cryptic complexity in felid vertebral evolution: shape differentiation and allometry of the axial skeleton. Reject, minor Zoological Journal of the Linnean Society.
• The scaling of forelimb, cervical and thoracic muscles across cats (Felidae). Major Journal of Anatomy
• The scaling of hindlimb and lumbosacral muscles in cats (Felidae). Major Journal of Anatomy
• The endocranial morphology of the extinct North American lion (Panthera atrox). Major Scientific Reports.
• New record of Egertonia (Elopiformes, Phyllodontidae) from the Late Cretaceous of South India. Moderate, accept Papers in Palaeontology. (Only out in 2016 though)

2016

• Cryptic complexity in felid vertebral evolution: shape differentiation and allometry of the axial skeleton. Accept Zoological Journal of the Linnean Society
• The scaling of postcranial muscles in cats (Felidae) I: forelimb, cervical, and thoracic muscles. Accept Journal of Anatomy
• The scaling of postcranial muscles in cats (Felidae) II: hindlimb and lumbosacral muscles. Accept Journal of Anatomy.

So there you have the list so far. 30 decisions, 10 publications and 1 dead paper. The longest time between submission and acceptance was the ostrich validation, first submitted 26  August 2013, published 13 October 2015. For those of you counting that is 2 years, 1.5 months or 778 days. In that time, there were reviews that took 3 months and 4 months which is ridiculously long especially to just get rejected. It was good data, just wasn't the for the journal as the results were negative.

What have I learnt from all of it?

1. Publishing remains an enigma. In some ways it gets easier with experience, in others it never does. Your publications are your work, and it is always a little hard when you think you've done an amazing piece of work to get back reviews saying you've got lots to do. My spinosaur paper had pages of revisions! At the same time you get used to it, and with experience paper writing gets easier so generally there are fewer corrections as you avoid falling into the same pitfalls, and the time to turn around revisions decreases even with major corrections.
2. Reviewers, whilst the bane of my publishing, are very good at making sure the science is good and the methods are up to scratch. Sometimes they get things wrong or miss things, but for the most part they give incredibly useful suggestions that will improve your paper. Listen to them.
3. Reviewer two always seems to always dislike my papers...
4. Reviews should only take 1-2 months. I've had some really short ones that are returned within a month (PeerJ was 3 weeks normally) and some shockingly long reviews (see above 3-4 months), but after about two months you are well within your rights to chase it up.
1. A follow on from this is that if you are unhappy how long reviewers are taking, you can't be fussy and turn down the chance to review for journals (assuming you are qualified to review the paper). I have now reviewed for PLoS one and Naturwissenschaften, two of the journals I've published with.
2. I also remain unsure why I seem to acquire 3 reviewers regularly for papers when 2 normally suffices.
5. If at first you don't succeed, try, try again. Whether it's revisions, refocussing, or sending to a different journal where your paper might be better suited. In the case of the ostrich validation paper, it needed to go to a journal that accepted negative results.
6. Some journals have really harsh standards for what constitutes reject, major and minor corrections. I've never had such minor corrections as I did for the Big cat, small cat paper, but that was a rejection, and similarly minor corrections for the muscle scaling papers were major corrections. This is never personal, but I'm informed sometimes the decisions to reject are made to keep the journal's time between submission and acceptance down (as a resubmission from a reject resets the clock). It's annoying, but the quicker you turn around corrections, the quicker you get it back into review.

"Publish or Perish" remains an awful motto of academia due to the never ending requirements to keep publishing, and this being the standard to which most academics are judged. It is something that gets easier and the longer you spend in academia the more avenues for collaboration and publication appear (I think at any point in the last 2 years I've had at least four papers on the go, with up to 7 at one point). I was told during my MSci that any work you really are doing at that point you want to be trying to publish and ultimately that helps guide ongoing work and decide on what future work I do. At the end of it saying all of that, find what enthuses you, what works for you, and get on with it!

10,000 blog views

My blog started off 1.5 years ago as a way of communicating my science, mainly to my friends and family who don't understand most of my work, but has grown into a globally viewed entity. This is in no small part due to Facebook, Twitter and being linked to by some other popular blogs (e.g. What's in John's Freezer).

For those of you who are nerdy and interested, here's how the viewer statistics (as given by Google) break down:

Overview stats for the blog. I have set it so my page views aren't tracked but cannot guarantee I am not responsible for quite a few views.

The distribution of views is somewhat skewed by me not having been blogging since 2010, but the blog is now consistently picking up 500 views a month, which is helped by me trying to keep publishing once a month this year.

The blogs themselves make for interesting viewing with an exponential decay for the blog views, although this may be down to being able to see the newest ones by just going to the homepage rather than the individual blog posts.

The location stats are the most interesting (in my opinion). The USA and the UK being the top two view locations doesn't surprise me due to where my friends and  palaeontology readers in general are, but the Ukraine and Russia being in the top 5 surprise me. I can't remember when they peaked, but recently there have been far less viewers from those countries, so I have suspicions they were caused by some dubious linking from websites (they still count right?). That aside, I suspect Apple will be very sad that I don't have more Mac users viewing my blog with 70% of my viewers from Windows operating systems.

What have I learned?

1. That despite 10,000 views, my blog doesn't even feature in the top 5 pages of Google searches for palaeontology blog (I was vain and checked). Impressively a friend's is number one although she has since moved it from blogspot to wordpress so hopefully the new site gets back up the search list soon!
2. Blogging has been lots of fun, and actually somewhat stress relieving. It is much easier than writing the papers...
3. It doesn't take much time, and means a lot more people read my research than would otherwise through just papers. However, despite not taking much time, it requires some time to actually do some research or put together some ideas to talk about on here.
4. My blog readers love dinosaurs more than cats. My top blog post was on ornithomimosaurs, and almost three times the number of views (with the caveats that 6 months separated the two, and that readers of my blog get the most recent blogs without having to click on a specific one).
5. Not many people leave messages. Having seen YouTube comments I assumed people would be more engaged with my blogs. A wish I may yet regret...

Most importantly I want to thank anyone who has read my blog, shared links, or even offered advice and ideas for being part of it. I have a few more papers in the works, some draft blog posts on other topics ready, and hopefully my first guest blogger lined up. Make sure you check back regularly or subscribe (there should be a link below).

How do muscles scale in cat species?

Two new papers out, and as the title of the blog post suggests, they are on the scaling of muscles in cat species:

The scaling of postcranial muscles in cats (Felidae) I: forelimb, cervical and thoracic muscles
The scaling of postcranial muscles in cats (Felidae) II: hindlimb and lumbosacral muscles

As you can probably guess, they are two closely related papers covering most of the post-cranial muscles of different felids. Surprisingly it has never really been done, with the only data before these papers were published on cat muscles covering cheetahs, which we used. Another paper has come out since my papers were accepted on the Eurasian lynx (Lynx lynx) which would have been great to incorporate and I'm hoping someone builds on my research and incorporates more individuals and more taxa.

So first a bit of background. This was a collaboration with a lot of people - all of team cat (myself, John, Anjali, Marcela and Stephanie Pierce), plus Andrew Kitchener (National Museums Scotland) and Emily Sparkes (the invaluable technician in Structure and Motion in RVC who suffered many hours dissecting with me). We obtained all of the specimens from zoos and private collections when they had died from natural causes. None were killed for the research, and none were wild. This does have implications for the muscles and the condition of the animals, but it's the best we can do. Funnily it was easily to get a snow leopard (we got 2 in 4 months) than it was to get a domestic cat (we only got 2 in the year we were working on it), due to the levels of consent and ethics required for animals that were pets.

After lots of dissections, which in my case were back breaking (in my case almost literally as I ended up with sciatica for a while from all of the dissections), we had collected data on the muscle body (the bit without the tendon attached) mass and lengths, tendon (where there were) mass and lengths, fascicle lengths (roughly the muscle fibre lengths) from black-footed cat, caracal, ocelot, domestic cat, snow leopard, leopard, tiger, lion. We also measured the pennation angle (the angle of the fascicles to the line of action of the muscle), and combined with the fascicle length and muscle mass we can calculate the physiological cross-sectional area (PCSA: an approximation for force production).

Tiger-forelimb by Andrew R Cuff on Sketchfab

As we were testing to see how these metrics scale, it is worth considering the expected relationships. We were scaling everything relative to body weight, so unsurprisingly the isometric (where things scale as expected from the geometry) scaling for tendon and muscles masses is 1 (i.e. if a cat gets twice as heavy, a given muscle or tendon gets twice as heavy). If the metric differs from that statistcally, we say it scales allometrically (either positively if bigger than expected, or negatively if smaller). Moving onto the other measures, we have to consider masses approximate volumes, so mass is proportional to length³, therefore isometry for the length against mass is 1/3 (when both values are logged), and for the PCSA isometry is 2/3 (area being length²).

The results show that most of the muscle metrics that we studied scaled indistinguishably from isometry whether it be forelimbs, hindlimbs or vertebral muscles. Below are the figures that show which muscles scale allometrically (they are all the pretty colours).

Cuff et al., 2016a. Figure 2. Muscles displaying potential allometry (prior to phylogenetic analysis) in the studied felid species are shown in colour; others as white; for a representative left forelimb. A) Lateral superficial muscles of the shoulder; B) Lateral muscles of the lower forelimb; C) Medial muscles of the lower forelimb. Colour codes for allometries: Red = muscle belly length; orange = tendon length; purple = fascicle length; navy blue = muscle belly mass; light blue = tendon mass; green = PCSA. Stippling pattern indicates negative allometry; lack of stippled colour indicates positive allometry. Muscles not shown, but displaying allometries: M. serratus ventralis cervicis (Table 2), M. biceps brachii (Tables 1,3), M. pectoralis superficialis (Table 7). After phylogenetic correction, only the M. brachioradialis remains significant.

Cuff et al., 2016b. Figure 1. Muscles displaying potential allometry (prior to phylogenetic analysis) in the studied felid species are shown in colour; others as white; for a representative right hindlimb. A) Lateral superficial muscles of hip and knee; B) Lateral, deeper muscles of the hindlimb; C) Medial muscles of the thigh and shank; D) Lateral muscles of the lower leg; E) Medial muscles of the lower leg. Red = muscle belly length; orange = tendon length; navy blue = muscle mass; light blue = tendon mass; green = PCSA. Stippling pattern is for negative allometry. Muscles not shown: M. psoas majorum (Table 6); M. vastus intermedius (Table 4,5); M. lateral digital extensor (Table 4), , M. superficial digital flexor (Table 6); M. peroneus brevis (Table 2).

Whilst there are lots of colours, the one I am going to focus on are the greens, PCSA (remember this is linked to force production). As isometry for PCSA scales proportional to body mass^2/3, if PCSA scales with isometry big animals become relatively weaker. In fact, even with positive allometry, unless the scaling is greater than 1, the biggest species still become relatively weaker than their smaller relatives. It might be quite obvious where I am going with this if you look at the figures, but ultimately the results show that the felids get relatively weaker as they get bigger. Thus for it's size, a domestic cat is relatively stronger (and previous work shows relatively faster) than its bigger relatives. Some interesting patterns do show up for the PCSAs in the forelimb: muscles linked to shoulder stabilisation generally scale with positive allometry, as do those linked to prey capture (whether it is those active whilst gripping prey, or those responsible for the claws being unsheathed).

Beyond just looking at the muscles, we put the data through a principal components analysis (PCA - not to be confused with PCSA). A PCA works by effectively regressing all of the data against the other data simultaneously, so instead of the standard x vs y graph you end up with each axis potentially representing many variables (e.g. a-z vs a-z but to differing contributions on each axis) to see if the data groups. We tested for both body size (big cat vs small cat - see earlier post), and also locomotor mode (those that basically do nothing but stay on the ground vs those that also regularly climb) after removing the effects of size from all of the data to see if there are any differences.

Cuff et al., 2016a Principal component analysis of the forelimb architectural metrics, grouped by body size and locomotory mode. (A,B) Body size, with blue for small felids, orange for large felids (Cuff et al. 2015). (C,D) Locomotory mode, with red for terrestrial, pink for scansorial. (A,C) PC1 (25.32% of total variance) vs. PC 2 (20.86% of total variance). (C,D) PC3 (14.08% of total variance) vs. PC 4 (12.04% of total variance).

Cuff et al., 2016b. Fig. 3 Principal component analysis of hind limb muscle architecture metrics. (A,B) Body size groups, with blue for small felids and orange for large felids (groupings follow Cuff et al. 2015). (C,D) Locomotory mode groups with red for terrestrial and pink for scansorial. (A,C) PC1 (28.48% of total variance) vs. PC 2 (15.39% of total variance). (C,D) PC3 (12.83% of total variance) vs. PC 4 (11.24% of total variance)

Whilst it appears that there is separation of the groups on some of these groupings, statistically there is no difference between any of the pairings we compared. It may ultimately boil down to the fact that cats are very conservative across all species and their muscles aren't scaling that differently to what we expect, and ultimately their physiology and ecology means they are high speed, ambush predators but for most of their time, they do very little. Is this ultimately how big cats can get away with being relatively weaker than their small relatives?

Full references
Cuff et al., 2016a. The scaling of postcranial muscles in cats (Felidae) I: forelimb, cervical and thoracic muscles. Journal of Anatomy DOI: 10.1111/joa.12477

Cuff et al., 2016b. The scaling of postcranial muscles in cats (Felidae) II: hindlimb and lumbosacral muscles. Journal of Anatomy DOI: 10.1111/joa.12474