I was recently interviewed by Daniel Shea for his podcast Scholarly Communications — you can listen to the interview here: https://newbooksnetwork.com/how-to-write-a-scientific-paper

We discussed my writing book and writing in general. This was a very enjoyable discussion & Daniel had plenty of good points and new perspectives that I could immediately agree with — do have a listen, highly recommended!

This post continues directly from part 1/2.

One way of making the referees happy is to always acknowledge that they have been heard, whatever it is that they say. Never treat a referee with disrespect, even when what they propose is wrong, or when they have misunderstood things because they obviously didn’t bother to read your manuscript carefully enough. Always give them something.

If the referee misunderstood something that is obvious, write another sentence on whatever the obvious issue is and add it somewhere. Thank the referee for pointing out that your paper was not clear enough on the issue, and tell her that you have now added a clarifying sentence. If the referee’s comment or question is so confused that you cannot even figure out what it is that the referee wants from you, do something about it nevertheless. Pick some sentence or paragraph that might be related to whatever is confusing the referee. Then rewrite it: try to make it more clear, or at least rearrange the words… Finally, write a polite answer to the referee: tell that to the best of your understanding, her problem was probably related to the issue discussed in this sentence or paragraph, and that you have now tried to make it more clear. At times, the referee is confused enough not to know herself what the original issue was, and gladly accepts this act of repentance from you.

The above does not mean, however, that you should always do what the referee tells you to do. If the referee asks you to do something that you feel is wrong or doesn’t make sense, don’t do it. You should, however, explain in detail in your rebuttal letter why you chose not to do it. But, if possible at all, change something in the text, however small. Then, the referee will feel that she has been heard.

It is common for the referees to get speculative and to come up with so-called bright ideas. While this may be genuinely helpful, it can also be a nuisance if those ideas are tangential to whatever it is that you are doing. If the referee asks you to do something that sounds sensible but is clearly outside the scope of your paper, insert a sentence into your discussion section where you mention that it would be useful to do in the future whatever it was that was suggested by the referee.

It may also be that the referee is both hostile and wrong: you know that your results hold, but the referee does not believe you and does not want to believe you. In this case, you must make your stand and defend your results. Be polite, constructive, and firm. Why does the referee act this way? If it is because you have not provided enough evidence to support your conclusion, apologise for lack of evidence and provide more (even if there was enough already). If it is because the referee feels left out (often indicated by requests to cite some of her own work), you can give her credit for some earlier work in the introduction or discussion, but you should not cite papers only because you are forced to do so.

There may even be more nefarious reasons for referee hostility – the referee trying to block competition for instance – that may be hard to detect or disentangle from general grumpiness: perhaps the referee simply had too low blood glucose levels, you never know. Even if you suspect something like an attempt at blocking, be polite but firm while writing your responses in a way that they are also meant for the editor’s eyes. If someone has decided to block your work, you cannot turn that person’s head, but the editor might be able to spot what is happening. And if a referee is clearly being unethical, you should confidentially let the editor know this.

But most of the time your referees have good intentions: being critical is not the same as being mean. If you treat your referees with respect, if you make sure that they feel that they have been heard, and if you always give them something, they will be happy or at least happier, and because of this, they will accept your paper more willingly.

This concludes the series (for now). I may post summaries, cheat sheets etc later. Thanks for reading!

Breaking news: the ebook based on this series is out! Go get it!

Previously in the series: how to write the cover letter. 

After several weeks or months of letting your paper out of your hands and into the cold and hostile world of scientific publishing, the dreaded moment of judgment finally arrives—if you haven’t been desk rejected by the editor in a few days, that is. There is a letter from the editor in your inbox, telling that you are either rejected outright or requested to revise your manuscript so that it can have a second chance. This statement is followed by detailed referee comments that may or may not make sense to you (or anyone else, for that matter). In theory, it is also possible to have the paper accepted as it is, but this is very rare: it has happened only once or twice during my career. Therefore it is safe to assume that there is more work to do now and that you have to get back to your paper. Often, this feels, at least to me, inexplicably painful, because the submitted paper has been neatly wrapped up and archived in my mind. I’ve gone on to think of other things, and now that perfect and beautiful wrapping has to be torn open – what a pain!

When receiving the letter, my suggestion would be to first take a few deep breaths and to try to calm yourself. This gets easier after dealing with tens of rejections and criticisms, but it never gets easy. Especially to PhD students who have put a lot of effort into their work and to whom this manuscript may represent 100% or 50% of their publication record, the moment of realising that someone is critical of their work is a difficult one.

What often happens at this stage is that you directly rush to the referee comments, and read through them at top speed. This is because you want to know RIGHT AWAY what it is that the referees find wrong with your beautiful work. And because you really speed through the comments, you only see the surface, and only pick up words that criticise your work. Your view is distorted.

Then, being a human, you get all emotional: angry, embarrassed, frustrated, depressed, or any linear combination of these. You may feel that your work is worthless, and therefore you are worthless. Please do not worry, feeling like this is as normal as it gets. You are certainly not worthless! We have all felt like this. This is what a career in science is about. Those who survive learn to persist and to deal with these emotions. It will get easier, and part of why it gets easier is that you learn that the process of peer-review can be very noisy and the referees can be wrong (they often are). And when they are not, you can use their criticism to learn and to improve your work.

When faced with a letter from the editor where referees UNJUSTLY criticise your work, my recommendation is to take a few more deep breaths, relax, calm down, and maybe do something else for a while. In particular, if the reviewers are very critical, your fight-or-flight-response prevents you from seeing what is really being said and what the really important problems are, and from assessing how difficult it would be to fix them for a revised version. So, get some distance first. Breathe, get a cup of coffee, look at a video of playing kittens or cute animals, and only then read the letter again, this time more slowly and analytically.

First, focus on what the editor says because this is the most important thing of all. As an example, I and my colleagues successfully got an article published where the referee hated the paper and asked for a total rewrite from a different and quite alien perspective. This rewrite would have been impossible for us to do. But the editor seemed to like the paper and told us that only a few minor things remain to be done. These two requests were completely at odds, but we chose to listen to the editor instead of the referee (nevertheless, we picked some of the referee’s points and cosmetically revised a few sentences, just in case). The paper was immediately accepted after resubmission.

So always listen to the editor! If the editor encourages you to submit a revised version, she is already on your side. Do it. If the editor uses less encouraging words like “should you wish to resubmit a revised version”, do it nevertheless, because even in this case the door is still open. Sometimes what you receive is a standard, copy-pasted response, and the editor takes no stance but leaves you to deal with the referees. In this case, just move on to the referees’ comments. But if there is anything in the editor’s words that you can use, use it.

Next, read through the referee comments carefully and with an analytical mind. First, look at the science and look at the positive side of things: did the referees spot any obvious flaws in your work? If so, great, now you can fix those flaws! Did they misunderstand your results? If so, great, this shows that you need to be more clear in your writing (even though referees often miss explanations that are already there in the manuscript…) Do the referees require some extra experiments or calculations to back up your conclusion? Do these make sense? If so, great, these experiments or calculations will make your paper more solid and you should do them, even if this takes time.

After you have gleaned useful and actionable information from the referee comments, look at what is left. There may be comments that you do not understand, comments that you understand but that you know are wrong, and all kinds of weird debris. The worst comments read like “I am sure that I have seen a similar result somewhere but cannot be bothered to find a reference”. Now, take off your scientist hat for a while, and put on your psychologist hat. You don’t have one? Get one, it’s tremendously useful. It pays off to realise that the referees are human. Humans are not analytical machines; humans have feelings. Your referees have feelings too. Figure out how they feel and what to do about it.

It is really worth the while to try to see the world through the eyes of the referees. Read the negative comments again, and try to understand what the referees think, feel, and expect from you. Do they feel irritated? Left out? Bored? Insecure, needing to bolster their confidence? Confused? Just plain cranky?

The key to getting your revised paper accepted is to understand what makes the referees happy, and then to give them this (while maintaining your scientific integrity, of course).

TO BE CONTINUED…

Previously in this series on how to write a scientific paper: ten tips for editing your sentences.

Now that you have revised and polished your draft and are the happy owner of a shiny new manuscript, one more step remains before you can submit it to a journal: writing the cover letter.

The cover letter is, in my view, mostly a historical remnant. Having to write one is, consequently, rather annoying. I can see that there may be some reason for cover letters for journals where the papers are too long to be skimmed by the editors, but even then, I doubt whether cover letters are of any use. Let me explain.

The point of the cover letter is to convince the editor that your manuscript is solid and important and that it fits their journal. But this is something that the abstract should do in the first place, especially if it follows the broad-narrow-broad formula outlined earlier in this series. The paper itself should do the job, too. In particular, the paper’s introduction should contain all the information that the editor needs to decide whether the paper is in the journal’s scope. It should also be enough for gauging whether the results sound believable and important enough for the paper to be sent to referees, instead of bluntly desk rejecting it. So why repeat all this information in a redundant letter?

So a big thank you to those journals who no longer ask for a cover letter.

Was I an editor, hard pressed on time, whose journal demands cover letters, I would highly appreciate a cover letter that is focused and short, say three to four paragraphs, max one page, preferably less. Here are two ways to write a short cover letter with only a few paragraphs and less than a page of text.

The better but slightly more adventurous way is to follow the inverted-pyramid schema that journalists commonly use for news stories. Most scientists are not used to writing this way! When following the inverted pyramid, you should begin with the most important thing and then proceed towards less important things, the nice-to-know details of the story, one by one and in order of decreasing importance. Tell what you have found in the very first sentence or two, then tell why your finding matters, and only then say something about how you obtained your results. Do not write a detailed explanation of your methods unless they are the key point of the paper; the editor is probably too busy to care, and if not, the details can be found in your manuscript. This way of structuring the letter is particularly suitable for those top-tier journals whose editors desk-reject most of the papers that they receive— they do not have the patience to search for the main point if it is buried somewhere on page two of your letter. They want to hear it first and then decide.

As a side note, the inverted-pyramid structure should always be used for press releases; those are read by journalists, not scientists, and journalists only get confused if they have to wade through lengthy introductory material before the main point arrives.

The other, more traditional way is to structure your cover letter in the same way as the abstract, or the Introduction section. Begin with the broad context, and then narrow the scope down and proceed towards your specific research question. After stating the question, tell what you have found out and how, and why what you have found out matters. But please be swift and move quickly: the first paragraph for context and question, second paragraph for the key result, and the third paragraph for significance.

You can also consider writing a hybrid version of the traditional cover letter and the inverted-pyramid lede. First, state your key result in a single-sentence paragraph: “In this manuscript, we show that X”. Then, follow the structure of the abstract and explain the context and the question in the second paragraph, a more detailed explanation of the result in the third paragraph, and an account of its significance in the fourth paragraph.

Whichever structure you choose, put emphasis on the implications and impact of your results. The why-does-it-matter part matters more than the how-did-you-do-it part, even if you have used particularly inventive methods. Do not exaggerate; rather, tell honestly what your work means. Whenever you feel like typing the word “very”, take a deep breath, command your fingers to stop, and jump directly to the next word.

Cover letter: if you have to write one, keep it simple, keep it short, put important stuff first, tell why your work matters.