Monthly Archives: November 2007

I’ll be the judge of that…

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Josh’s blog a long time ago now on how to write a cover letter made me think it might also be useful to provide some thoughts on how to referee a paper – hopefully we can again get some other editors, as well as you guys as authors and referees, to chime in on what is helpful/successful (or not).

First, to clarify what we do before we send the paper to referees: we evaluate whether the manuscript is within the scope of the journal (that is, assuming the results are true, would our journal be the right place to publish it?), whether it’s likely to be of broad interest (does it have larger implications, or is it in a big field that everyone is thinking about?), and whether it’s likely to be a significant advance (this one is certainly most difficult for us, as non-experts, to evaluate, but if the vast majority of the ideas have already been published, it’s probably not a big advance). It is not our job to evaluate the data, although we do consider whether the right data are present (if the author is trying to make a conclusion about a biological process, for example, there usually needs to be biological data in the paper). With the exception perhaps of the first point (journal scope), we do need feedback from our referees on these same issues, in addition to evaluating the data and determining whether the data support the conclusions (and whether they are sufficient to support the conclusions). There is also more information available here.

In addition to those general ideas, there are a few specific tips I thought I would pass along. I’ll go from most to least obvious, if I can figure out which ones are which:

1) If you are asked to referee a paper, and are really too busy to take it on, then decline. You may think that the editors will be annoyed with you if you say no, but we find it much more annoying to have to send 8 emails to someone to get them to provide a report that’s already 3 weeks late. Even more annoying is when that 8th email still does not produce any response, and we have to either make a decision on the paper without all the facts we need or find someone else, which then delays the process for at least another 2 weeks. A quick, polite ‘no’ will let us move on to someone else.

2) Similarly, if you do agree to look at a paper, a 3 sentence report (“This paper seems really good”) is usually not helpful. However: if you have truly assessed the paper on all conceptual and technical merits within your expertise, and found NO problems at all, it is fine to say something to that effect without belaboring the point.

2b) We identify referees based on their knowledge of some particular field or technique, but are often pleasantly surprised by their comments on an additional aspect of the work. While this is not necessary or standard, I think it would be super cool if referees would tell us in the confidential (editor-only) comments which methodology/techniques they felt qualified to evaluate. This would especially be helpful in cases like #2 above, where no specific comments are provided.

3) Please do not make personal attacks on the author/coauthors. If you have some reason to dislike them on a personal level at the outset, don’t agree to review the paper. If you discover in the process of reviewing the manuscript that they have not included the 12 references that make their work completely uninteresting, please just say something like, ‘The authors have unfortunately failed to reference several pertinent papers (refs 1, 2, n as necessary). As a result, the novelty of this particular contribution is not clear.’ Or if they have missed several important control experiments, please just point them out without suggesting that the authors are stupid or hiding information, etc.. It is possible they are stupid or hiding something, but it’s more likely that the experiment was just overlooked. I guess the summary here is: write a report that you would be happy to receive, even if the overall message is a negative one. Similarly, keep in mind that you serve a valuable role not only in assessing the paper, but improving it, which often makes for the most exciting papers we publish.

4) Please use the ‘remarks to the editor’ field – that’s where you can tell us confidentially that you have a paper in press on the same topic, or that you don’t feel qualified to comment on a particular aspect of the work; additionally, we often find that referees make their most candid assessment of the manuscript within the confidential comments. However, please do include some measure of your overall assessment of the paper in the remarks to the authors. Our authors can get quite confused when we reject papers because, from what they can see, there were not any problems (‘the work seemed well done’, etc.) when in reality the referees told us confidentially that the paper was not an advance, not appropriate for the journal, or similar. If you hate it, but are worried about hurting the author’s feelings, you could say something like ‘I was not convinced that this paper represented an important advance in this field.’ After all, it is/should be the authors job to convince you of just that.

5) If you find that there are technical problems, please suggest specific experiments/controls that the authors could/need to do to conclusively prove whatever it is that they are trying to prove. If there are conceptual/logic problems, please suggest alternate hypotheses that would need to be ruled out, or factors they have not taken into consideration, in addition to just noting that the paper is flawed or not conclusive. This is helpful for you, too: If we don’t know exactly what the authors need to do to merit another round with the referees, we will be more likely to send the paper back to you (thus taking up more of your time) than if we (and the authors) have better guidelines about how to revise.

6) Finally, please keep in mind that, if you agree to look at a paper, you have signed on for life. It is extremely disruptive for the process if we have to find new referees at the second or third round, etc., both because we have to actually find someone new and because that new referee has a significant extra burden of trying to figure out what the history of the paper is. As I implied above, we do strive to limit the amount of time that referees need to spend with a particular paper, and we do limit the number of times we will contact you with new manuscripts. So unless you have come down with pneumonia or have moved to the arctic circle where no internet is available, please stay active in the process.

Well, that’s what you need to know – at least, as far as I can judge. What have I forgotten?

Catherine (associate editor, Nature Chemical Biology)

Reactions – Ben Davis

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1. What made you want to be a chemist?

A sense of being able to explore the beauty of nature at its most fundamental level. That and parents who had a day-to-day approach to exploration and a cracking teacher when I was in the sixth form.

2. If you weren’t a chemist and could do any other job, what would it be – and why?

(Modern) art collector/curator – it evokes similar excitement and the same sense of yet-to-be discovered wonder and awe.

3. How can chemists best contribute to the world at large?

I think by taking on big questions, fundamental questions that have the potential to be translated. There is often a false opposition created regarding ‘blue skies’ and applied research. I’m personally interested in new knowledge (the real definition of science) no matter how obscure. It’s hard to know beforehand what might or might not be technologically useful.

4. Which historical figure would you most like to have dinner with – and why?

I shall cheat and invite two people. Firstly, William Blake – he was a remarkable man who seems to have had a connection with life and the joy of life that was more keenly felt than most. He created this magical world; he had this fantastic walled garden in London and wandered and roamed through the city as a source of inspiration. His ‘Songs of Innocence and Experience’ gives you a glimpse of what he saw – ‘Jerusalem’ is majestic and still makes me weep. Even the illustrations in ‘Songs’, which despite being in some cases technically unrefined and even occasionally clumsy are something that one could stare at for hours on end.

The second guest would be Emil Fischer – he had such vision and almost a supernatural instinct for the interactions of biomolecules decades ahead of his time. Genuine chemical genius.

5. When was the last time you did an experiment in the lab – and what was it?

On the sly I’ve been fiddling with something that I call ‘sugar PCR’. It’s either deeply naïve or could be freakily fun. It’s a biocatalytic cascade based on thermal switching that could allow general amplification of minute quantities of glycans up to measurable levels. I like to give the group odd projects and so it’s rare that we have one that I play with first. However, this one is pretty speculative even for us and so I’m creeping in late at night and giving it a pop.

6. If exiled on a desert island, what one book and one CD would you take with you?

Book is easy – Shakespeare’s collected works including sonnets. It’s a cliché, but it really is true that therein lie the best descriptions of the human condition. We often take his talent too much for granted, probably through familiarity, but every time you pick any of his stuff up it strikes such a resonant chord. He knew people.

If I had to take just a single novel though, it would be Jane Eyre.

CD is tough. I’m obsessive about music, cycle with it on and usually itching to listen to new stuff. This means that picking just one is a bit odd. At the moment, something I keep coming back to is “Because of the Times”, Kings of Leon – genuinely heartfelt in an unashamed way. Having said that, if it was something that I had to listen to forever, then I’d pick “Heart and Soul” Joy Division – an 81 track collection masterpiece that would allow me to practice my Curtis-style dancing. All sing: “To the centre of the city in the night…”.

Ben Davis is in the Department of Chemistry at the University of Oxford and works on the chemistry and chemical biology of sugars and proteins.

Sugar Daddy: Do not pass ‘Go’, do not collect $200

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The qualifying exam.

If there is ever a moment in graduate school that usually receives about 100 times more preparation and 100,000 times more anxiety than necessary, it is the qualifying exam. For those of you who are not in grad school (or those that have been through it and somehow, shockingly, blocked the thing from your memory), here’s a primer. Of course, it depends on the school, but the basic scenario is that as a second- or third-year student, you have to stand up in front of three or four professors and defend your research. Or so you think. It actually, I think, usually goes something more like this:

Student: “I’ve been interested in studying the mechanistic details of how [some enzyme that is inexplicably fascinating to you, your advisor, and maybe four other people on the face of the earth] is involved in the biosynthesis of [some natural product that sounds like a really nasty infection and always looks misspelled]. The locus for the gene was identified in—”

Professor 1: “Draw the structure of cytosine.”

Student: [Starts to draw structure of cytosine correctly]

Professor 2: [Interrupting] “Which is higher, the intracellular or extracellular concentrations of potassium in the central nervous system?”

Student: [Begins to answer, but stumbles]

Professor 2: “Why don’t you draw a neuron. What is the action potential? How do ion channels function in its propagation? What different types of ion channels exist? Which ions are the principal players, and what are their functions? What structural information exists on ion channels and what is the functional significance of the structural studies? What are the major classes of ion channel-blocking compounds? What are their relative affinities for different classes of ion channels?”

Student: “The action potential is—”

Professor 3: “Draw the mechanism for the Horner-Wadsworth-Emmons reaction.”

And so it goes… I guess what I can say is that you don’t really know what the professors will ask, and they will probably form an opinion of your ability in the first five minutes (if they hadn’t already by reading or hearing what your advisor had to say about you prior to your exam). So much for a blind audition…

Today, we will conclude with a haiku, in the poetic style that seems to be all the rage on the Sceptical Chymist:

Study as you wish

but predict the questions you

won’t. Good luck, sucker!