AcWriMo: The journey of a paper after submission to a journal

So you did great science, got exciting results, and after probably quite a steep learning curve, you got a manuscript together that was approved by all co-authors. Excellent! That means you need to let go of the paper by submitting it to a journal, and it disappears in a black hole for several weeks/months. So what happens during that time? Here I will discuss my experiences as (senior) editor at two microbiology journals, and will give some tips about submission, revision and the sometimes inevitable rejection stages. There will be differences between fields and journals, but many of the things discussed here will be relevant for the journey from submission to publication.

When a paper arrives at a journal, the editorial office usually has a checklist whether everything is accounted for, authors have been included etc. They sometimes identify problems with the submission and unsubmit it, so authors can make corrections. Once the paper passes that stage, it goes to a senior editor responsible for the section where the manuscript fits, mostly chosen by the authors. The senior editor will check whether the manuscript is within the scope of the journal, whether it is the type of paper it is interested in, and whether it matches the scientific requirements. Some examples of checks I do: when there is DNA sequencing involved, I check for Genbank/EMBL or SRA/EMBL accession numbers, without which the manuscript will not be reviewed. These are the minimum requirements for data availability nowadays! I will also check whether it is more than just a data deposition or incremental advance, i.e. does it make a significant contribution? Can the work be used by other scientists for replication or comparative studies? I regularly get manuscripts which are based on work that can not be replicated, does not have reference materials/strains needed for comparison, or lacks controls. Such manuscripts get a “pre-screen reject” or “desk reject”, with some explanation in the decision email on why.

You may say this sounds very harsh, as it hasn’t even gone through peer review. But from the point of view of the journal, it is essential. Peer review and handling cost resources and time from reviewers and editors, why spend that at manuscripts that have deficiencies? Also, is it fair to authors to have to wait for months for an inevitable rejection? Better send it back quickly, with explanation, so the authors are free to decide on what they want to do next. Papers that cannot be used by other scientists will not be cited, and this is one of the things that journals require to sustain themselves, so articles that won’t make such a contribution are not good for a journal.

If the manuscript passes that stage, it gets assigned to a handling editor, who will deal with the peer review. Usually they will invite peer reviewers (which can be difficult nowadays, with no one having time!), which submit a report. The authors will usually only see the public part, but not any confidential comments or assessments. Be aware that some reviewers may make statements about acceptance, revision or rejection in the report; this is frowned upon as it is the editor that decides, and may disagree with the reviewer. If your manuscript is rejected while a reviewer said “revise” publicly, please note that it isn’t sufficient for an appeal.

So what are the usual types of decisions:

Revision or minor revision. That is good, it usually means that only textual/presentation changes are required, but no major work required.

Reject/resubmit or major revision. This usually means some additional work or analysis is required, together with significant changes to the text and presentation. Do not underestimate what is required. Don’t be dejected if you get a “Reject/resubmit” decision, that is now more and more the common phrasing used for major revision. It means the journal is interested in the work!

Reject. This means they do not invite a resubmission, and usually will not take a resubmission into account unless permission is given. Don’t despair if a paper is rejected: many papers are at least rejected by one journal, and some people say that if your paper is not rejected by the first journal, you aimed too low! Just regroup and consider the next possible journal.

The revision stage: dos and don’ts, and a strategy

Negative or critical comments from peer reviewers often elicit very strong reactions. Sometimes these comments are outright wrong or even worse, sometimes it is based on a misunderstanding, and some are pointing at issues you were aware of, but hoped the reviewers wouldn’t spot. Don’t worry, this is perfectly normal!

Remember the goal of submitting a paper: getting it published. So if that means making changes to satisfy the comments, just do it. My personal approach is:

1) draft a quick response to the comments. Don’t worry about language, this is only meant to be discussed with the co-authors. Indicate how the comment can be addressed, i.e. textual changes, figure change/addition, or extra work required

2) identify the one or maximum two points that you really don’t want or can’t address. Those are the ones you will fight, and make a strong case on why you disagree/won’t do the extra work, etc. Go with all guns blazing if necessary!

3) all the other points: swallow your pride and just do it, whether you like it or not. You can’t go back to the editor saying “the reviewer was wrong most of the time”, so get over it. Again: don’t lose sight of the ultimate purpose, so be strategic.

When you prepare the revision, remember that editors (and reviewers) are often scientists that do this next to their day job. So don’t antagonise them by making them do unnecessary work. Make sure that you include the following:

– a marked copy with all changes indicated. This allows the editor to check whether you actually did make the required changes. The “compare changes” function of MS-Word can be used for this.

– a point-by-point response, even the small ones or typo corrections. I usually include the original comment in italics, so the editor can see what I respond to. Make sure you include line numbers (or line numbers + page numbers) in your response, for example “We changed this sentence (P3, L15-18)”. Use the line numbers in the revised final document, and indicate this at the top of the rebuttal. Again, this makes it easy for the editor to check. Make sure you use visible line numbers.

– figures in the correct format, size and resolution. You can get Powerpoint to export TIF-files at 300 dpi resolution, but it requires a change in the registry of the computer, which may require admin rights. Make sure that figures are made in the size they will be in the final version in the journal, and make them 7.5-8 cm wide for a single column figure, and 15-16 cm wide for a double column figure.

It may go through a second round of review, or not. Often, the better the job done at revision, the easier it gets through. But it will all be worth it in the end, I hope. I have published >125 papers, and I am still really happy when I see another one published that I contributed to.

The aim is to get a workshop organised that combines the experiences of different people who have been author, editor and peer reviewer in different disciplines, which can be used for those about to submit to a journal. Watch out for the announcements.

Dr Arnoud van Vliet, Surrey Vet School