On Pre-Prints, Publishing and Peer Review

Hallo readers, it’s James here again to announce the release of another new manuscript written by the FEZ group! This one is something we’ve been working on for quite some time, and it’s also the result of a really exciting collaboration with Pia Merete Eriksen, a guest researcher with the FEZ lab here at the NHM in Oslo. You can find it below:

https://f1000research.com/articles/12-945

It’s also the first time I’ve ever submitted to a Journal with Public Peer Review! So it’s probably a good opportunity to talk about the whats and hows of publishing an academic paper. We’ll publish a piece on the science of Scoutknife once the manuscript has passed peer review, which is the topic of this ‘blog. You’ll also be able to follow along with the peer review of Scoutknife in the coming weeks by keeping track of the manuscript in the link above (or by listening to my running commentary on Twitter).

What really is a Journal, and why do they even need to exist?

When you’ve finished your scientific work, and you’re happy with your results, the first thing you might do is go around and share it at conferences. You’ll give a talk, present a poster, or just discuss research with colleagues. But that isn’t really useful for the community at large: if they want to reference back to your work, it needs to be in words on a page that they can point other researchers towards. This is called a citation – citing your work gets increasingly important the further you go from accepted common knowledge, and the deeper you get into big controversies. Other researchers will always want to see controversial claims backed up by strong evidence.

You could, in theory, write a blog, like I’m doing now. Researchers could cite your work that you release there. Except I could write a blog about anything. I have very strong opinions on a great many things, from scientific topics to the best Star Trek (it’s Deep Space Nine, and I won’t apologise). Some of my opinions are backed up by the research of others, some my own research and some are unjustified subjective beliefs that exist in the back of my head.

So for a researcher to be able to truly cite something, they need some security that the claims made are robust. That means that even if it is controversial, and even if other scientists might disagree with their own robust scientific claims, that it isn’t just drawn from nowhere. Which is what we use journals for.

When I finish a bit of scientific work, after presenting a poster or giving a talk about it, I’ll submit it to a scientific journal. Journals are academic magazines – they come out monthly, quarterly or half-annually and contain all the hip new science that you should be excited about. Some of them are general in their approach – a journal like Nature or Science will publish across many scientific disciplines. Some are incredibly specific – I eagerly await new issues of Arthropod Structure and Development, but I have the self-awareness to realise that this is a niche interest. Some lie somewhere in the middle – Molecular Biology & Evolution, for example, is restricted to a sub-field of biology, but a pretty large one.

You might have noticed that all the journals I have mentioned have very plain titles. This isn’t necessarily true: Proceedings of the Royal Society B has a slightly opaque name, but is the life sciences journal of the British Royal Society (Proceedings A is for physical sciences and maths, so the B doesn’t even stand for Biology). However, the vast majority of journals use very clear descriptors of what they are about. This is because journals are often used as citations, as mentioned earlier. That means when I read a paper about Chemical X that uses a reference from Plant Science rather than Zoology I can easily tell that it is an article about Chemical X in plants rather than in animals. Practicality overcomes art.

The other thing you might have noticed is that all of these titles are in English. This wasn’t always the case, but in the present day, English has come to dominate academic journals as a common language. This might not be a good thing – some research indicates it might be a barrier to doing good science as a global community, and discouraging non-native speakers of English from participating. There’s been a lot of great work on this (notably, recently here: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002184), with some concrete suggestions on what we can do to improve, but it is also a huge topic in itself, so I won’t dwell too long on it here.

Journals, thereby, act as gatekeepers for what is valid and useful scientific research and what isn’t. What stuff can be cited and used as evidence to back up an argument, and what can’t. The way journals achieve this is through a process called Peer Review.

So Who Even Are My Peers? And Why Are They Reviewing Me?

To submit something to a journal, we write a description of our research called a manuscript, and send it to a journal we think would like to publish it. Some of my predecessors stared, blank-eyed, telling tales of when this process used to involve posting huge stacks of paper all over the world, but thankfully these days we just send it to them through a submission website.

After the Journal receives your manuscript, the editor looks at it to see if they are interested, and if they are, they send your manuscript to two other researchers in the same field. These are the Peers of Peer Review. They’ll look over your manuscript in detail, and see what they think.

An Academic Manuscript normally consists of a series of sections:

  • Abstract (where you summarise the whole manuscript)
  • Introduction (where you introduce the concepts and background)
  • Materials & Methods (where you talk in detail about what you did)
  • Results & Discussion (where you present what you found and try to explain the implications of what that might mean. This is where the meat of the new science exists)
  • Conclusions (where you wrap everything up)

As you might expect, peer reviewers are especially vigilant around that Materials & Methods section, and in the Results & Discussion. They want to make sure your results support the claims that you want to make. They might even repeat some of your methods to make sure your results can be replicated. Normally, alongside the manuscript, you submit something called “Supplemental Information” which is also available to the reviewers – this includes your original data, and important bits of software that you’ve written, to make it easier for them to double check your work.

The Peer Reviewers come back with an answer. Peer Reviewers are normally anonymous, so you don’t know who is checking your work (though in very small fields you might be able to guess from a colleague’s writing style – I, apparently, overuse commas and asides). When you submit your manuscript, many journals let you suggest 3-5 possible reviewers, but since the editor tends to sensibly assume you will select people who you think will be favourable towards the research, it is very likely that at most one of your recommendations will be picked, and you won’t know which one. Still, it does help to have someone in your corner, as the reviewers get to give a verdict, a bit like a jury. They can tell the editor that they think the manuscript should be:

  • Rejected (The worst result, but happens to every scientist once in a while. You go home, go to sleep, and try to rework it later)
  • Revised & Resubmitted (This is the most common result for a first submission in my experience. Basically a “try again next time”. They want to see the work again, but they don’t think it is great yet)
  • Revised (This is great – it means they only think minor changes are needed)
  • Accepted (The unattainable holy grail for a first submission.)

The editor looks at the two reviewers verdicts and comes to their own final verdict. They will also need to consider the specifics of the reviewer’s arguments, concerns and queries about the manuscript. If two reviewers are really conflicted about a manuscript, the editor might even send it out to a third or fourth reviewer to get more opinions about it. But once the editor has enough information to make a decision, they will send it back to you, complete with the reviewer’s comments so that you can act on them. You get these comments even if you get rejected, which is nice – I wish I got detailed feedback from job application rejections!

Sometimes these comments are buoyant words that will inspire you to get right back to work improving the manuscript. Sometimes these comments will incisively pierce the depths of your soul and leave you staring into the middle distance for the next hour. Receiving reviewer’s comments is the source of a lot of academic gallows humour. These comments are often about a page from each reviewer, but they can be far more: I once got a set of reviewer’s comments that was 20% the length of my manuscript!

Normally, a manuscript will go through two or three rounds of this process. I mentioned earlier that “Revise & Resubmit” was the most common. I tend to expect to hear R&R twice before acceptance, or R&R, then just Revise, then acceptance. This whole process can take anywhere between about 3 and 18 months, depending on the speed of the reviewers, the scale of the changes requested by them, and many other factors. Often, a manuscript finishes review looking very different from the first submission, but that is, hopefully, a good thing.

Once a manuscript is accepted, it gets properly referred to as a “paper”. Then you work on the layout and proof with the layout editors at the journal and pay the article processing charge. It’s important to note that scientists pay journals to publish their research (often from our research funds), not the other way around! It tends to cost even more if you want to make it “Open Access”. That means it will be freely available to anyone rather than only available to people with a subscription to the journal. After all that effort, eventually you get to see your work in print!

So Why Write This Blog Now?

For most journals, all of this work goes on behind closed doors – the initial submission, the reviewer’s comments, the back and forth between reviewer and author and editor. As I mentioned earlier, peer reviewers are normally anonymous, too!

However, the journal we’re submitting to this time does things a bit differently. F1000 Research posts your initial submission (which is what has just appeared this week), then also posts the (non-anonymous) reviewers comments. If the manuscript needs revisions, they also publish your response to the reviewers comments, and then the new version. By making the whole process public, F1000 hopes to make the process more transparent, and I thought that was a really cool approach. At the very least, it gives everyone an inside look at the workings of one of the more peculiar parts of the academic machine.

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