Talk for CCMB, Hyderabad

21 February 2018

Talking at the Centre for Cellular & Molecular Biology, Hyderabad

I gave a talk at the CCMB main campus in Hyderabad about our approach to invasive amphibians in southern Africa.

The talk was well received, although attendees were as interested in the functioning of the CIB network, in addition to the work that we've done on invasive amphibians in southern Africa. 

Thanks to Milind Mutnale for taking this pic!


Why critical reading is critical for your writing

07 February 2018

Why critical reading is critical for your writing

It is hard to emphasise exactly how important your reading will be, when it comes to your writing. If you are sitting with a blank page in front of you and feel that you have nothing to draw on, then think again. All of the reading that you have done to get to this point has already helped you more than you think. As I’ve pointed out elsewhere (formula writing blog) your chapter or manuscript is likely to resemble the formula that many others already follow, and standing on the shoulders of those giants (citation blog) will help you again. But it’s possible that your reading isn’t helpful if you aren’t being sufficiently critical.

When you read, it’s worth making all sorts of comments about what you’re reading. Of course you should be trying to follow the story that the authors are trying to tell, but you should also be using it as an opportunity to learn tips and tricks of writing. Once you are actively writing, and I’d suggest that this should have been right from the very beginning of your studies, you should be actively thinking about how the authors are writing. Are they writing well? Are parts written poorly? Then the critical part is to cogitate, albeit briefly: what works, what doesn’t and why.

When I started reading papers, I made photocopies (1 sided was as sophisticated as it got) from volumes of books and made notes in pencil on back and front of those pages as I read. I understand that most of you will be working on pdfs which offer possibilities to add notes in text boxes that go alongside. I question whether the cognitive advantages that you get from writing by hand will be achieved by typing, and if I ever find out I’ll link to this blog. But I did learn many years back in my psychology classes at Liverpool University that making handwritten notes on what you read will help build them into your memory. Thus, if you make notes on style, you are likely to remember them in the same way that you remember the paper and its contents. An alternative to typing everything is to make notes in a notebook. That way you get the advantage of building your memory with your own writing, and you can easily find everything in the same place when you forget where you read the fascinating insight.

 It’s important to emphasise that you should not copy and paste parts of someone’s paper that you like. It’s easy to do, but any copying could be your undoing if you later forget and paste your ‘notes’ into your manuscript. It’s so easy to plagiarise like this that the only way to really avoid it is by being very strict with yourself. Making notes by hand will force you to look away from the written text while you write, and you’ll be unlikely to inadvertently copy anything. The advantages of writing notes by hand then make it greatly advantageous to restricting yourself to your computer (tablet or cell!).

 So how should you read critically in order to help with your writing? I’d suggest that this is as simple as highlighting or making a quick note each time you see something that you like, or dislike. I used to underline text in pencil, and then make an illegible comment in the margin. What was singled out? For example, instead of using a taxonomic list (I don’t like lists) and long citation string to describe lots of different studies that had previously made the same point, a co-author (in a recent review study) organised them all into the same categories we were presenting in a review. The result was that the reader was reminded of our categories at the same time as seeing how well others had already covered these same topics. Another example is the way in which one of my students imaginatively linked the subjects between their paragraphs (I do like links). Lastly, it may be a theme that the author manages to develop over several paragraphs or pages, but if you’ve spotted what it is that you like, write it down and commit it to memory. The very fact that you start to see things in other people’s writing that you like and admire means that you’ve managed to start reading critically. Keep this up, and it will help your writing no end as you open up your mind to critical reading.

 You don’t have to restrict yourself in what you can learn while reading other people’s papers. Think about the stages in writing a paragraph (blog entry here). Look at the paragraphs you are reading and see if you can spot the subject and summary sentences. Maybe they are absent from the entire paper, or maybe they are present in every paragraph. Does it help enhance the readability of the paper? What about the times when authors break the rules? Can you see in your reading that the majority of authors follow rules? Do they follow the formula? What is the power in shaking it all up? If it works, try and analyse why it works. Then you will be reading critically.

What if I’m having problems recognising anything good or bad in what I read?

It’s going to be hard for me to teach you how to read and think at the same time. A little like walking and chewing gum, it comes with experience. And if you do fall over, stop chewing for a while and wait until you’ve got into your stride before having another go. Thinking is all part of the reading process, and while I agree that it might be hard to think on multiple levels while you read, it is possible. For example, consider what other worthy things you’ve thought about while reading this blog. If you’ve not stopped to check your phone, or think about eating or drinking something, well done. It might be worth creating an atmosphere with less other stimulants while you read. If you only have your reading material and notebook, you’ll be able to concentrate all of your thinking on them instead of getting distracted.

 There is also a possibility that you are struggling to get insight with your reading because English isn’t your first language. The subtleties of some of the usage of English may be passing you by. Because of the large number of words, it is possible to write something in English in many different ways. The overall aim is to convey the largest amount of information possible in the smallest number of words, while enhancing the context, meaning and readability. It’s not easy, but the only way you’ll ever get good is by starting, and reading and writing as much as possible.

 If you are still struggling, a really good way forward is to start a journal club with your colleagues. It is probable that you aren’t the only one who is having difficulties. There may already be a journal club in your institution which may (or may not) be a good place to go. What you do need is a safe space in which you aren’t afraid to say when you don’t understand. Think of it as a book club for scientific papers. After all, it may be that no-one understands and the paper is badly written. Alternatively, it can be that someone is able to help you quickly and easily. They can then give you extra insights into how and why they think the author is crafting their paper. This will then help you with your reading as well as your writing.

  Lab  Writing

SAIAB trip on the Krom

19 January 2018

Invasive fish on the Krom

I spent a couple of days with Olaf Weyl's group on the Krom River, Cederberg, prior to the extirpation of invasive fish. Olaf's group has been monitoring the Krom for 2 years prior to the removal of alien fish by CapeNature. The trip was organised to train Honours students from all over South Africa by Olaf's post-graduate experts.

This stunning locality has invasive trout, bass and bluegills. The monitoring consists of assessments of current fish stocks before the extirpation. Olaf's group uses GoPro cameras, snorkling swim counts and fyke nets to assess current fish abundance. Once the Krom has been treated they will be able to track its recovery. 

Thanks to Olaf's group for organising the trip.

  Frogs  Lab

Nitya's popular article

16 January 2018

Scientists in the field: the ways around the indignities we suffer

In this popular article for The Wire, Nitya Mohanty explores the life of a field biologist. It’s not always possible to feel comfy in the field, and many would be explorers find that they are better suited to lab studies.

I can think of numerous leaches (wear wellies – they can’t climb up), wasps, bees (sweat bees annoy to the appoint of distraction), bottle-ass flies, and bot flies that have made field work more arduous than it could have been.

The bot fly, Dermatobia hominis, lays its eggs on the legs of mosquitoes. They hatch when the mozzie bites and the young maggot crawls across your skin looking for lesions to gain access. I was in denial about my first bot fly maggot that I acquired on a field trip to the South of Belize in 1991. I didn’t feel it for a few weeks. One day we were attending the opening of a new power generator for the local village, Sarteneja. I could feel an uncomfortable poking of something at the back of my leg, behind my knee. At first, I thought it was a fly landing there. I swatted and found that my hand was wet with puss. I tried not to think about it for the rest of the very long speeches, but my mind would not allow me to think of anything except the poking I could feel in the back of my leg.

That night, I resolved to rid myself of the maggot. I knew that they relied on maintaining an active air hole to the surface. The poking I had felt was the maggot trying to reach fresh air from inside my leg with its posterior spiracle (breathing tube). If you deepen the distance the tube has to move, by smearing the skin with a thick layer of Vaseline, you can entice the maggot to leave your body. Sadly, in 30C heat and 100% humidity the chances of balancing a blob of Vaseline on the back of my knee was zero. Hours of frustrating contortion later, I gave up.

The solution was simply to allow the maggot to grow much larger, and then squeeze it out with maximum pressure applied to both sides of its body. Before I could get that far, I had to admit that I’d been infected, and once that was out of the way I felt much happier about letting the maggot grow large inside me. Yes, there was some discomfort, but the denial had been far worse that the reality.

Later I got more maggots in my shoulders and then one last one below my left eyebrow. This was acutely uncomfortable, in part because it stretched out the skin of my forehead and I was acutely aware of every move. I sort help straight away. In those days the British Army had a base in Belize, and someone thought that this was my best chance for removal. I’m not sure really why it came about, but I found myself in a military operating room with local anaesthetic being injected around my eye socket. The sapper whose expertise included bot fly removal was a very large guy. I swear I could feel my skull contorting as he applied maximum pressure either side of the maggot. Sadly, again, it was far too small to be popped out, and I left with a numb head and one of the blackest eyes I’ve ever possessed.

Within a couple of weeks I was snorkelling on the Belize barrier reef. The maggot could not take the prolonged exposure to the salt, died and got hauled out dead. I still remember the hooks around its body dragging along the hole as it was pulled out. Happy days.


Ending my time as AJH editor

31 December 2017

Reflections on editing African Journal of Herpetology 2009-2017

Today is my last day as editor of African Journal of Herpetology. In this blog post, I reflect on 9 years of being editor in chief.

In 2009, I had already published 37 papers so had a pretty good idea of the author side of the publishing game. I had been outraged at decisions that I felt had been unfair, surprised at others which I had felt were too easy, and often mystified at the rejection without review for manuscripts that I had prepared for journals. And when reviewers disagreed about my manuscripts, why did the editor came down on the side of rejecting or calling for major revisions? In essence, what I didn’t know was how editors made their decisions.

Don Broadley started the Journal of the Herpetological Association of Africa in 1965 and edited it for 20 years. The name changed to African Journal of Herpetology in 1996 with many prestigious names in African herpetology having been editors (see Measey 2011 for a detailed retrospective). I had submitted manuscripts that had been both rejected and accepted under two different editors. The editor in 2008 was Alex Flemming who had taken over from Graham Alexander in 2006 but had already resigned so that the Herpetological Association of Africa (HAA) committee was looking for a replacement editor. I realised that this was an opportunity I had been looking for and volunteered. I was proposed and in the absence of any other interest was made editor.

I have already written about the huge workload that I took on at that time not only editing, but also publishing the journal (you can find that blog entry here). Together with that added workload, I had the dubious honour of typesetting a manuscript of my own, already accepted by Alex Flemming (Ngawa et al 2009). The decision to hand over the publishing to Taylor & Francis was taken after long discussions with the HAA committee, but finally resulted in Volume 59 issue 1 (see cover above). One of the enjoyable tasks I undertook was to redesign the journal logo. The old journals carried a map of Africa with political boundaries, so I decided to retain the theme but replace politics with outlines of herps. I selected images representing as many groups of herps as I could (yes - there is a caecilian covering much of Algeria and an amphisbaenian in Namibia), and drew simple outlines around them. It was fun to do and I was proud of the result, and surprised when I received complaints from HAA members that they preferred the old version. But I shouldn't have been surprised as there will always be those who don't like change.

Of huge significance to my life as editor was the move to an editorial online platform which allowed simple tracking of manuscripts in which both Associate Editors and I could visualise the peer review process. Trying to maintain a personal, professional and editorial inbox all in the same place was quite a challenge, and so the editorial online platform was very welcome.

Acting as editor for my own manuscripts

Early on, I had to make a decision about what to do when I wanted to submit my own manuscripts to AJH, or if I was a co-author. The conflict of interest was clear and my decision was to have any such manuscripts handled by a designated Associate Editor and to recuse myself from the review and decision making process. I was very strict with this, even though it resulted in one unhappy episode when a review for a manuscript I had submitted was withheld until a rival paper had been submitted, accepted and published in another journal. My co-authors felt particularly unhappy that our paper had spent so long in review. I felt let down by the Associate Editor who had allowed the reviewer to sit with our manuscript for months.

Policies old and new

This was not the only policy decision that I took for AJH. I decided on a double-blind peer review process. In retrospect I still think that this was a good decision, although many authors appeared incapable of removing their names from a manuscript, and persuading them to do so caused a surprising amount of delay. African Herpetology is a small world, and I didn’t really think that reviewers would not guess who senior authors were for most of the papers. However, there was evidence at the time that women authors could be disadvantaged by open peer-review (Budden et al 2008), and I didn’t want this to happen to any of our student authors. The other option would have been to have both reviewers and authors revealed, but this seemed less likely to be workable as anonymous reviewers were already hard to come by. Occasionally, reviewers would insist that their anonymity be waived. Although noble, this would have been against the spirit of double-blind reviewing and so reviewer names were systematically removed. Thus, double-blind review became (and remains) a headache for the editorial process, but one that I think is worth keeping, even though authors and reviewers alike couldn’t follow instructions.

The inability of especially authors to follow comprehensive instructions was perhaps the major theme that ran through my time as editor of AJH. Early on in the process, I revised the Instructions to Authors, making it as comprehensive as I could. I’ve never been someone who enjoys formatting manuscripts for a particular journal style, and so did not insist that manuscripts adhered to the peculiar referencing style of AJH on first submission. I was also happy for this first submission to have embedded figures and tables. However, it isn’t possible to submit such files to the publishers, and if the manuscript passed the first round of reviewing, formatting of text and files would need to be done by the authors. Many found this difficult and producing the figures in an acceptable format appears particularly problematic for many authors. Some seemed to think that this was something that the editor would do for them!

AJH received many manuscripts that were outside its scope: African herpetology. The instructions to authors couldn’t have been more explicit in this regard and I do wonder how often some authors consult them at all. It would be nice to think that being a ‘chancer’ in this respect might have a pay-off somewhere down the line. However, one fault of the editorial platform is that it takes a very long time to enter all the meta-data required for the publisher to place accepted manuscripts online. Authors, especially older authors, grumble about this a lot, but it is a reality of modern publishing. More and more meta-data is expected to be displayed separately to the printed paper, and this requires that authors enter it. That they do this on initial submission means a whole lot of work when the scope of the journal is completely wrong, thus I don't see any pay-off for being a chancer in this case.

Another policy change occurred in 2013 when AJH moved to use ZooBank to safeguard against taxonomic theft. You can read more about that change here.

AJH for African herpetologists

I also wanted to encourage authors from more countries in Africa to submit their work to the journal. Although I didn't get the numbers of manuscripts I would have wanted, the journal did see an increase in the number of papers published from authors outside of southern Africa. More recently, the journal has published a number of papers from north Africa, including the first paper in AJH on African salamanders. 

Thus in my time as editor, AJH published on all three Orders of Amphibia: Anura, Gymnophiona and Caudata, as well as a lot of papers on reptiles.

How easy did it turn out to make decisions?

Decisions were much easier than one might think. For the majority manuscripts that were sent out to review, the reviewers did a good job of assessing the worthiness of publication. The difference between minor and major revisions was determined by whether or not another review was likely to be needed on resubmission. My suggestion to Associate Editors was that manuscripts that had already received a decision of Minor Revision shouldn’t be sent out to review again unless something major had changed. Probably the most difficult decisions were where I could see that useful data had likely been collected, but the manuscript lacked pertinent detail to know whether or not it was ever likely to be accepted. The decision to Reject and Resubmit often results in a great amount of time for the Associate Editor involved to wade through poorly written manuscripts. Reviewers were also burdened. However, in some cases, authors did eventually publish their work in the journal and these were sometimes good additions to the literature that would otherwise have been lost.

Another policy was to prevent more than 2 rounds of review. It can be very frustrating for authors to go through multiple rounds of peer review, especially if additional reviewers are brought in on later rounds as they inevitably have new comments. My policy was that once a paper had received two decisions as Major to Minor Revisions, the third submission should be handled by the Associate Editor, and not sent out to review again. For the most part, I think this policy worked well. There were, and always will be, exceptions to any such editorial procedure. 

The peer in peer review

During my time as editor, I co-authored an editorial that appeared in many of the world's herpetological journals: The 'peer' in 'Peer Review'. The basis of this editorial is something that I'm sure all editors are finding, that increasingly our colleagues are all too happy to turn down conducting peer reviews. Sadly, this is not an affliction of only herpetological journals, and I see the same problems in my work editing for PeerJ. I find it especially distressing when the peers themselves are authors who rely on the process of peer review for their publications. While we can't always conduct every review we are asked to do, we can make the effort at least to reply and make a suggestion of another reviewer to the editor. 

Should everyone be an editor at least once?

I do feel that everyone should participate in the peer-review process. You should expect to review something equal to the work that you produce for other reviewers. The role of editor is a massive burden on top of reviewing. Some of this is carried by Associate Editors who I found did a sterling job of helping authors get their manuscripts published. If you feel inclined to become an editor then you should volunteer to become an Associate Editor for a set period. Ask up front how many manuscripts you’ll be asked to handle each year and what turn-around time the editor expects. Do this before you sign up to be an editor, as it’ll give you most of the information you need before you decide.

Personal happiness

In July 2013 a would be author wrote to inquire whether her research on fossil African frogs would be appropriate for AJH. I responded positively and also that I had a keen interest in the subject. Thalassa and I met up to talk about it later in the year. Unexpectedly, it transpired that editing the journal had led directly to me meeting my wife. We married in December 2016 (see blog post here). It's not something that I would have predicted when I took on the job back in 2009.

There has been more happiness as editor of AJH. I have headed a team which has helped many first time authors get their work publised in a scientific journal. The team work of associate editors and peer reviewers cannot be underestimated and has led to the direct improvement of every manuscript that AJH has published in my time as editor. I am very grateful for all of the work that associate editors (past and present) have put into the journal. I am thankful also for all of the authors that have chosen to submit their work to the journal.

It’s all about helping authors

I am happy that in my time as editor of AJH I’ve been able to contribute to helping many authors produce decent peer review publications. The team of Associate Editors that I’ve been privileged to work with has always managed to assist authors produce something better. Most reviews have been constructive and in the spirit that we all benefit from good literature.

Read editorial reports published in African Herp News:

Measey, J. (2017) African journal of herpetology editor’s report 2017. African Herp News 64: 4-6. pdf

Measey, J. (2015) African Journal of Herpetology Editor’s report. African Herp News 62: 6-8. pdf

Measey, J. (2013) Taxonomic publishing, vandalism and best practice: African Journal of Herpetology makes changes that will safeguard authors. African Herp News 60: 2-4. pdf

Measey, J. (2013) Journal Editor’s report. African Herp News  59: 8-10. pdf

Measey, J. (2011) Journal Editor’s report. African Herp News 53: 5-7. pdf

  Lab  Writing