An example of progressive peer-review in a scientific journal

Almost all scientific papers are peer-reviewed.  This means (typically) that between one and three researchers from the same field as the paper’s topic offer (sometimes constructive) criticism and a judgement as to whether or not the paper merits publication.  There is a strange ritual to it, whereby the authors submit, the reviewers critique, then the authors rebut or acquiesce to the reviewers’ demands, while the editor acts as ringmaster and makes the final decision.  The main problems are that (i) there is a lack of dialogue (you only get a very small number of opportunities to engage), and (ii) your manuscript is in the hands of a very small number of reviewers with their own particular foibles and hobby horses.

A solution to this is to have either (i) open pre-publication peer-review, or (ii) open post-publication peer-review.  This means that the paper is discussed by more people and in a medium which encourages dialogue, such as a blog comments section.  Even better, each element of the dialogue can feature as a subsection of the paper itself, making each section citable in its own right.  This encourages reviewers and commenters alike to produce high-quality criticisms and has been implemented in some journals. Here’s an example of the process in action in a particularly controversial climate paper at Atmospheric Chemistry and Physics:

Screen Shot 2018-08-10 at 13.44.05

This is certainly the way forward for open science.

One quick trick to increase visibility and citations of research papers

digitization-of-library-3068971_640Since I’m “young” (whatever that means) I sometimes get asked to advise on how to disseminate research outputs through new-fangled doohickies like “the social media” (like writing click-baity headlines). This came up in a School Management Group meeting today, in the context of trying to increase visibility and citation rates for papers published by our faculty. It was something that I was quite interested in, so I spent about an hour doing some quick literature searches and then implementing some of what I found. Here’s the gist:Read More »

My run of luck

It is easy to look back and see those little (and sometimes not so little) moments that have caused great changes in your life. Being in academia (and having survived this far) means that I have been immensely lucky. There is no other way to describe it. Some of that luck has been self-made, or at least I have seen and taken opportunities when they presented themselves. However, there were a lot of cases where I benefitted from sheer serendipity. I thought it might be useful to highlight some of those:

  1. I was born this way – Straight off I need to acknowledge my privilege. I’m white and male (among other awesome things) and that gives me a massive headstart straight away.
  2. A casual conversation with a lecturer – After an ecology lecture in 2004 I approached my lecturer and asked about PhDs. In my mind, he asked “How do you feel about dragonflies?” although I have a feeling I have made that up. He wrote a PhD project up, I applied, and started working with him the next year.
  3. A transoceanic link – My PhD supervisor happened to have a former student working at a university in Canada. He put me in touch, we found a slightly unusual funding source, and I ended up moving over shortly after finishing my PhD.
  4. Helping out around the lab – As the senior postdoc in the lab in Canada, I chipped-in with supervision of MSc and PhD students. The upshot was that I was helping a student analyse and write-up her data. That analysis produced a Nature paper.
  5. Government policy on research assessment – Because I hadn’t held a faculty position before, if I joined a UK university and was a part of their Research Excellence Framework submission I would only have to submit one paper. The fact that I was looking for a faculty position just as our Nature paper came out made me very attractive as a new hire.
  6. Having a big mouth – Someone in the department realised that I never say “no” to anything. One day I was called into my Head of School’s office and shown an email from Random House publishers saying that the chair of a local event had pulled out and could they suggest someone to fill in. The event was an Evening With Richard Dawkins (of whom I am a massive fan) in front of a sell-out crowd at the West Yorkshire Playhouse. I said yes (inevitably), met Richard, we shared a couple of hours on stage, and I have been told that the evening went extremely well (it was hard to tell from under the spotlight!).

That’s not saying that I haven’t worked hard. I’ve done what most academics do, which is to sacrifice a degree of work-life balance until reaching a permanent position. I have published a LOT and the ideas that I have been nurturing for a number of years (urban pond research networks, projects on environmental education, pedagogical research, and dragonfly evolution) are coming to fruition. However, there were key points in my career when luck was a deciding factor. There are probably academics out there who had no luck and got to where they are purely on the basis of hard work. However, I imagine they are in the minority!

Who are “Adjacent Government”?

Having just given a talk on science communication and the merits of public engagement to a group of undergraduate students, I was delighted to receive a phone call out of the blue from someone asking me to write about my research for “Adjacent Government Main Document”. The gentleman who called (and who spoke with a delightfully posh English accent) assured me that it was read by 145,000 key decision makers, politicians, and research councils, with a >30% read rate on their email and 28,000 views of each email in the previous issue. I was informed that Miguel Cañete, the EU Commissioner for Climate Action, had specifically requested a piece to go opposite his editorial on climate, to highlight “climate change impacts nature’s mimicry system research”. That sounds a bit strange, I thought, but fine – the EU had just published a short piece on my work (which they fund) and so I figured this was some sort of follow-up. I was asked if I could provide 1,000 words by 10th January 2017 for inclusion in a later issue. I said “yes” – I can eat 1,000 words for breakfast! Then I was informed that this was wonderful and that all that was left was to negotiate the fee. There was discussion of fees in the £1000s, and possible discounts. A bargain!Read More »

Community Collaborative Science (CoCoSci) as an alternative model for scientific collaboration?

G.Mannaerts, CC BY-SA 4.0,
G.Mannaerts, CC BY-SA 4.0,

I went to a fascinating talk by a colleague at Leeds, Dr Mark Davis, a few weeks ago. Mark works on Alternative Finance (“altfin”), which involves a shift in economic thinking away from traditional big banks (with low interest and risky investments) towards peer-to-peer and community-based lending. You can read more about Mark’s ideas in his recent Conversation article: “How alternative finance can offer a better banking future“. Mark had a lot of fascinating insights which (to a lay person like me) resonated strongly. The notion that banks are inherently risky and create the circumstances for economic collapse, and the idea that all of our money that we give to banks ends up going far away into large, complex economic systems, rather than helping closer to home. Mark also made the point that there is a parallel between the “Big Society” notion promoted by the UK Conservative Government under David Cameron, and the Alternative Finance concept that he promotes. Under the Big Society, it is assumed that everybody has a little bit of spare time here and there and that we can volunteer that time to solve social problems. This means lower investment from the government because we are (in theory) capable of taking over from public services. Some people are skeptical… Altfin, on the other hand, takes the same approach to capital: almost everybody has a small amount of capital sitting around that is doing nothing productive, and if we pool our spare capital then we can do good things with it. This got me wondering whether the same thing was true for research…

Read More »

A hat-full of academic how-tos

Dipping in and out of the stream of tweets, there are always fascinating links to excellent resources for academics at all stages of their careers. I just spotted another, and thought it might be about time to aggregate some of these for posterity. Here’s the quick list (to which I will add if people suggest links), and details are below

  1. “How to find a postdoc”
  2. “How to get started with R”
  3. “How to use Github and RStudio”
  4. “How to use Github effectively”
  5. “How to respond to reviewers’ comments”
  6. “How to write a literature review”
  7. “How to help fight sexism in academia”
  8. “How to make your publications more accessible”
  9. “How to make your work reproducible”

Read More »

Making my research more open using Kudos

I’ve always tried to make sure that my academic work wasn’t tucked away on a dusty shelf (or paywalled in an obscure academic journal, which is the equivalent in the digital age) and that has meant that my digital footprint is huge. I have accounts on ResearchGateTwitterSlideshareLinkedInFigshareGoogle ScholarAcademia.eduFlickr, and Google+ (as well as probably a few more that I’ve forgotten!). I don’t think I have lost anything by “scattering my wild oats” across a huge swathe of the internet, because I assume that it increases visibility. Indeed I get a few views across all platforms:

However, what I have been looking for is a service that allows me to aggregate all this content. Ideally it would have (i) a single page per publication, where I could bring together all the bits of information relating to that paper (data, preprints, press coverage, and a lay summary), and (ii) a personal profile page that brings all of those publication pages together under my profile. Well, I think I’ve found it!Read More »

How to write a scientific paper

writing-427527_1280When we teach students how to write papers, we take it for granted that they have already absorbed the basic format of a scientific article from their reading of the primary literature. They should be familiar with abstract-intro-methods-results-discussion-references, for example, and the content that goes into each section in order to lead the reader through the work. However, it is easy to see how students might fail to grasp the general structure of a scientific paper. For example, we often hold up the high impact journals as models of scientific research, but journals such as Nature, Science, Current Biology and PNAS have a structure and a style that is really quite different from other journals (referenced abstracts, methods at the end, extremely brief structure). I have been teaching undergraduate and postgraduate students how to write scientific papers and theses for a few years now, and I thought I would share my personal method (I think I can credit Phill Watts, now at the University of Oulu, for suggesting this to me years ago):

I hope it’s useful and please do let me know if it helps, either in the comments here or on the YouTube page. The video is released under Creative Commons.

More toxic frogs live longer, but more venomous snakes do not

frog-284044_1280Background: It is thought that all animals age: they show an increased probability of death at greater ages. However, the lifespans of many animals vary widely. What is it that determines whether or not an animal lives for one year or one hundred years? One of the key drivers is thought to be how likely you are to be killed by something else. Those animals that that are unlikely to be eaten, whether that is because they are very large (elephants), well armoured (tortoises) or poisonous (poison dart frogs), tend to evolve lower rates of ageing. After all, if you are going to live for a long time anyway, you might as well make the most of it. On the other hand, if you live precariously from day to day then there isn’t much point in investing later in life because you probably won’t get that far.

What we did: We compared lifespans of amphibians and snakes that either had a chemical defense (in amphibians) or venom (in snakes) with those that did not have those traits. We showed that (accounting for their evolutionary history) poisonous amphibians had a significantly longer lifespan than non-poisonous amphibians, but there was no difference in venomous and non-venomous snakes.

Importance: This study has two major implications. The first is that it is vital to incorporate evolutionary history into these sorts of analyses. We had built our study on the findings of an earlier piece of work (which did not account for evolutionary history) that suggested that the snakes also showed a longer lifespan when they were venomous, but our results refute that earlier finding. Second, our findings offer yet more evidence for an offensive role for the origins of snake venom, which has been suggested in other recent studies.

This is part of a series of short lay summaries that describe the technical publications I have authored.  This paper, entitled “Species with a chemical defense, but not chemical offense, live longer”, was published in the Journal of Evolutionary Biology in 2013. You can find this paper at the publisher or for free at Figshare.

Image credit: Ephraimstochter,, Public Domain.