Do you really have to reformat for each new submission?

There was a fascinating conversation at the blog of neuroscientist Dorothy Bishop recently. As a side point in a post on getting replication studies published, she says:

…if a journal commonly rejects papers without review, then it shouldn’t be fussy about the format in which a paper is submitted. It’s just silly for busy people to spend time getting the references correctly punctuated, or converting their figures to a specific format, if there’s a strong probability that their paper will be bounced. Let the formatting issues be addressed after the first round of review.

Palaeontologist Mike Taylor agreed in the comments:

…it seems unbelievably stupid that when preparing my research output for the world, such a huge proportion of the effort is dedicated to inserting and removing commas.

He blogged about this issue back in 2010, commenting that the value of this work by researchers is zero but its cost is enormous. In a recent article in Discover, he says:

Most journals have stringent formatting guidelines that authors must follow in submitted manuscripts. (A colleague of mine recently gave up attempts to submit his manuscript to a particular journal after it was three times rejected without review for trivial formatting and punctuation errors, such as using the wrong kind of dash. Seriously.)

I found it hard to believe that some journals are this strict. When I was an in-house editor (for Elsevier and BioMed Central), I always ignored the formatting of newly submitted papers. I was trained to focus on whether the topic of the manuscript fitted the scope of the journal and whether it would be interesting enough for the readers. I have never seen an article rejected because it was in the wrong format.

But it does seem that there are journals that reject because of formatting before they even decide whether to send a paper to referees. Mike mentions The Journal of Vertebrate Paleontology as being one, and Dorothy describes similar procedures at Journal of Neuroscience and Psychophysiology.

This seems to me to be a great waste of authors’ time. It is an insult to an author to ask them to reformat, only to then reject their paper on grounds other than the formatting – grounds that were presumably clear in the first version. If an editor is sure that they are not going to send a manuscript out to referees, why not just reject it straight away, so that the author can submit it quickly somewhere else?

I know how much time it can take to reformat from one journal style to another. In fact I quite enjoy doing this, though it helps that I am generally being paid to do it and that it is part of my job, not a distraction from important research. And I also have lots of practice in macros, wildcard searches and other tricks that make reformatting far quicker. If you’re a scientist whose main expertise is research, reformatting will be much harder and more frustrating. Scientists are good at research, and copyeditors are good at house style – why don’t journals get their (usually freelance) copyeditors to do this reformatting? The only reason I can think of is that we will charge for the work.

The best time for reformatting to journal style is after a paper is accepted. The second best is when revisions have been requested: given that there is now a good chance that the journal will publish the paper, it seems reasonable at this point to ask the author to get the formatting close to the journal style. Major things, in particular, such as whether the methods section is before or after the results, or keeping to overall length limits, are best done by the authors in revision.

I’d like to put together a list of journals that do or don’t require perfect formatting at first submission, so that authors can find out before submission what will be expected of them. This information isn’t easy to find. Of course, instructions for authors always imply that formatting should be done before submission, because (I suggest) the editors would love every author to do this, as it makes an editor’s job easier. But detailed formatting issues, like the kind of dash used (or other examples given by Mike Taylor)? I don’t believe any editor really needs this kind of thing to be sorted out by authors. If they do, they must frequently be disappointed!

If you feel that it would help your paper to get published if you reformat it precisely to the journal style before submission, I won’t stop you – after all, you will be making the job of the in-house editor easier, which might, you never know, tip the scales in your favour. And if you want to pay me to do the reformatting for you, I probably won’t say no. But at the risk of doing myself out of some work, I would recommend that authors don’t spend too much time or money on reformatting before the paper has been first submitted. And if a journal asks you to reformat when they haven’t promised to send the paper out to referees, I suggest asking why.

Your experience

Journal editors, do you expect papers to be formatted to your house style before you will consider sending them to reviewers? How strict are you about this? Why?

Researchers, which journals have asked you to reformat before they decide whether to send your paper to reviewers? Which journals don’t mind the formatting being incorrect?

The really dangerous formatting errors

No journal editor expects submitted papers to be perfectly formatted. But there are different types of error that cause different problems.

  1. Common formatting errors that are easy to spot and easy to fix, like double spaces at the end of sentences
  2. Things that aren’t really errors, which will be ignored when the paper is typeset, such as spacing between paragraphs
  3. ‘Errors’ that are really matters of house style, such as italicisation of the ‘p’ in ‘p-value’
  4. Things that are hard to spot and that could cause the reader to misunderstand something crucial.

It is this last category that I would like to focus on here. These are the kinds of errors that every scientific copyeditor should know to look out for, but not all do. If you do one of these things, you will cause extra work for whoever copyedits your paper. Not a major problem, you might think. But if the copyeditor is not experienced in this kind of problem, or is rushed or underpaid, or if the journal doesn’t copyedit it at all, the error might not be spotted. As you will see from the examples below, this could have serious consequences.

Misuse of underlining

OK, so you want to quote a mean and standard deviation. But that symbol you want to add between the two, that ‘plus or minus’ sign (±), where is that in your wordprocessor? It’s not always obvious where to find the symbol you want. So some clever authors think ‘I know, I’ll put in a plus sign and underline it! It looks the same, doesn’t it?’

Well it looks the same as long as the underlining never gets lost. But the journey from the author’s wordprocessed file to the final published article is a long one, and the underlining could be stripped out at various points: preprocessing, copyediting, typesetting or conversion to XML or HTML. Some typesetters, I’m told, remove all formatting from documents and add it back manually by looking at a pdf of the original. Sure, proper professional scientific typesetters used by journals are unlikely to do this, but can you be sure? Underlining is generally not used in published work, so some copyeditors also remove it – again, they should always check first for any underlining that means something, but can you be sure that they will see your clever underlined plus sign?

Similar logic also leads to the underlined less than sign, or greater than sign, to give a version of ≤ or ≥.

So I wonder, now, how many papers there are out there that quote the mean + standard deviation not the mean ± standard deviation because of this error. I haven’t actually seen any myself – have you?

Greek letters

A similar difficulty presumably leads some authors to fudge Greek letters. Take microliters, an extremely commonly used unit in molecular biology papers. The correct symbol is ‘µl’, but I’ve lost count of the times I’ve seen ‘ul’. Maybe this wouldn’t cause too much misunderstanding if left in, but the fact remains that it is incorrect.

More dangerous is to put in an ‘m’ and change the font to Symbol. This can lead to the same kind of problem as underlining – the Symbol font can all too easily be stripped out by mistake during processing. And do you really want the amounts to be given in milliliters rather than microliters? In some rare cases this could actually be dangerous, if someone took a drug at 1000 times the intended dose because of this kind of error.

Another surprisingly common error is to use the German ß instead of β. ß means double-s and is completely unrelated to β, despite its surface similarity.

Degrees

This one I find even more surprising than those mentioned above: using the wrong symbol for the degrees sign (°). This symbol isn’t hard to find in the Insert Symbol dialog in Microsoft Word, or in the LibreOffice equivalent. Superscript lower-case letter o or superscript zero aren’t good substitutes, again because the formatting might be stripped out. There is a very similar looking symbol called ‘Masculine ordinal indicator’, which is used in languages such as Italian to abbreviate ‘primo’ (‘first’). If you use this it probably won’t cause any harm, but it will still be incorrect.

Finding the right symbol

The best way to insert any symbol in Microsoft Word is to find out its character code in Unicode and then type the code and then press ALT+X to convert it into a character. For example, type 2265 and then, with the cursor just to the right of the 5, press ALT+X – this gives ≥. This site has a convenient search function – type in ‘greater than or equal to’ and you get a list of possible characters, of which U+2265 (ie Unicode 2265) is at the top. In Open Office or Libre Office, the process is similar but slightly more complex and is explained here.

Thanks to @nfanget, @EndoMetabPub, Katherine Timberlake and Kathleen Lyle (the latter two of SfEP) for suggestions for this post.

Your experience

Editors, have you seen any other formatting errors that are as dangerous as those mentioned here? Researchers, have you seen any examples that got through to the published version of a paper?

Choosing a journal V: impact factor

This the fifth post in my series on choosing a journal, following posts on getting your paper published quickly, getting it noticed, practicalities, and peer review procedure.

It is all very well getting your paper seen by lots of people, but will that lead to an increase in your reputation? Will it lead to that all-important grant, promotion or university rating?

The impact factor of a journal is a measure of the average number of citations of papers published over the previous two years in the year being measured. A very common view among academics is that having your paper published in a journal with a high impact factor is the most important thing they can do to ensure tenure, funding, promotion and generally success. And in fact the impact factor of the journals your papers are in still has a big influence on many of those whose job it is to assess scientists (as discussed recently on Michael Eisen’s blog). It is also a factor in whether librarians choose to subscribe to a journal, which will affect how widely your paper is seen.

So even if the impact factor has flaws, it is still important. However, remember the following caveats:

  • Citations are only a proxy measure of the actual impact of a paper – your paper could have an enormous influence while not being cited in academic journals
  • Impact doesn’t only occur in the two years following the publication of the paper: in slow moving fields, in which seminal papers are cited five or ten years after publication, these late citations won’t get counted towards the impact factor so the journal’s impact factor will be smaller than justified
  • The impact factor measures the average impact of papers in the journal; some will be cited much more, some not at all
  • There are ways for journals to ‘game‘ impact factors, such as manipulating types of article so that the less cited ones won’t be counted in the calculation
  • The methods used for calculating the impact factor are proprietary and not published
  • Averages can be skewed by a single paper that is very highly cited (e.g. the 2009 impact factor of Acta Crystallographica A)
  • Although impact factors are calculated to three decimal places, I haven’t seen any analysis of the error in their estimation, so a difference in half a point may be completely insignificant
  • New journals don’t get an impact factor until they have been publishing for at least three years.

So although it is worth looking at the impact factor of a journal to which you are considering submitting your paper, don’t take it too seriously. Especially don’t take small differences between the impact factors of different journals as meaningful.

Other new metrics are being developed to measure average impact of journals, such as the Eigenfactor and Source Normalized Impact per Paper (SNIP) and SCImago Journal Rank (SJR). These might be worth looking at in combination with the impact factor when choosing a journal.

Your experience

How important is the impact factor of a journal in your decision to submit there? Have you taken other measures of impact into account? Do you think the impact factor of journals you have published in has affected the post-publication life of your papers?

And journal editors, how much difference does the impact factor of your journal make to how many papers are submitted to it, or to your marketing? Do you know the Eigenfactor, SNIP or SJR of your journal?

Journal news 28 January to 3 February

Your journal-related news for the week.

F1000Research

Faculty of 1000 (F1000), the well established post-publication peer review service, has announced a new service that will publish original research papers. According to the initial announcement, this will differ from traditional journals in that all papers will be published immediately, before peer review (as long as they pass a ‘sanity check’), and peer review will happen openly after that. Publication of datasets will also be encouraged. Fees are still under discussion. Retraction Watch discussed the proposal and received many comments, including from two members of F1000 staff, Rebecca Lawrence and Sarah Greene, who thanked commenters for helping them to develop the idea further. This looks like an experiment worth watching – if it takes off it could herald a big change in publication of peer-reviewed papers. (Via @F1000Research.)

Arsenic Life (or not) in arXiv

Microbiologist Rosie Redfield has been trying to replicate the experiments presented by Felisa Wolfe-Simon et al. in late 2010 about a bacterium (called GFAJ-1) that could apparently grow using arsenic instead of phosphorus. Redfield has now submitted a manuscript to Science and at the same time uploaded it to the preprint server arXiv. She has found that there is no arsenate in the DNA of arsenate-grown GFAJ-1 cells. She is inviting comments on the manuscript on her blog, as an experiment in open peer review. (Via @RosieRedfield.)

More on the boycott of Elsevier

See my post earlier this week for the background on this. The list of researchers who have pledged not to support Elsevier journals has now reached over 3800. An article by Josh Fischman in The Chronicle of Higher Education on Tuesday included responses from Elsevier (Alicia Wise and Tom Reller). Kent Anderson of the Scholarly Kitchen criticised the boycott, saying that other publishers have prices as high as Elsevier, bundling of journal subscriptions is useful rather than being wrong, and other publishers also support the Research Works Act. Elsevier also put their case in this blog post by Chrysanne Lowe. Meanwhile, Michael Eisen, one of the founders of the Public Library of Science, gives some historical context in his blog. (Various sources.)

Launch of Cell Reports

In an announcement that got rather lost in the furore about the boycott, Cell Press (part of Elsevier) launched a new open access journal, Cell Reports. According to its information for authors (pdf), it publishes ‘thought-provoking, cutting-edge research, with a focus on a shorter single-point story… in addition to a longer article format’ and also ‘significant technical advances’ and ‘major informational data sets’. Authors can choose between two Creative Commons licences for their papers: Attribution (CC BY) and Attribution-Noncommercial-No Derivative Works (CC BY-NC). Are there now any major scientific publishers left that don’t have any open access journals? Possibly not. (Via @WiseAlic.)

Gyrations in Life

A controversial paper was published this week in the little known open access journal Life, apparently after peer review, that claims to explain just about everything using a simple geometric figure, the gyre. It has been taken to pieces by John Timmer in Ars Technica and PZ Myers in Pharyngula. Following these and other criticisms, the editor has now responded, saying that peer review was thorough, and Retraction Watch has discussed the response. (Via @tdechant and @leonidkruglyak.)

Mind your Editorial Board

Evolutionary biologist Jonathan Eisen pointed out something not quite right about the biography of an editorial board member on a journal called Molecular Biology, published by OMICS Publishing Group. The expert in ‘oximological microbiology, non-linear submorphological endosaccharomorphosis, applied endoplutomomics’ turned out to be a fictional creation of the German satirical magazine Titanic. How the journal administrators could take him seriously when his biography says that he ‘has successfully completed his Administrative responsibilities as vice president of the universe for scientific publication ethics and spamology’, we may never know. His name is still on the editorial board page as I write. It may be relevant that OMICS has been described as a ‘predatory open access publisher‘. (Via @phylogenomics.)

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