This is the final installment in a four part series on writing your first paper. For the first part in the series, click here, for the second part, click here, and for the third, click here.

After what has potentially (likely?) been years of data collection and a month or two of writing, re-writing, wailing and gnashing of teeth, your first paper has been hammered into shape. Hopefully the process has yielded something metaphorically closer to Michelangelo’s David than Mr. Potato Head. Either way, it’s time to send your creation out into the word and see your hard work in print. Here is a brief description of the publication process

The cover letter
In the old days, manuscripts were submitted by mail, and one wrote a cover letter so that the person who opened the package didn’t have to figure out the contents on their own. Nowadays, manuscripts are submitted electronically, but cover letters are still part of the package in one form or another. For some journals it still looks like a letter, and for others the various elements are entered into fields on a webpage.

The purpose of the cover letter is three-fold: to explain to the editor the significance of the work (ie – why their journal should publish your work), to suggest other experts in your field to review the work, and to exclude other scientists that may have competing projects or other conflicting interests. (There are some other legalities that are taken care of here, but they aren’t all that interesting.) The latter two areas are strictly between you and the editors at the journal, but know that these are only suggestions – if the editor feels that you have “stacked the deck” by excluding all of the most qualified scientists, they have the right to send it out to those that you have requested not review the work. The significance of the work may or may not be confidential – some journals now send this statement along with the abstract when asking potential referees if they are willing to review the work. From what I have seen, however, the journal will explicitly state which sections are confidential and which will be shared with the referees.

The importance of the cover letter grows, generally speaking, as the impact factor of the journal rises. At the top of the heap, journals like Cell, Science, and Nature are only interested in publishing novel, ground-breaking research and they receive far more manuscripts than they can publish. The cover letter for these journals needs to convince the editors that your manuscript fits the bill, otherwise your manuscript may never even be read. Well, it will, but not by them…

The editors
Different journals are organized differently, but in general terms there are at least two levels of editors – ones at the top that have the final say on publications, and a second tier of editors that actually handle the review of the manuscripts, often called managing editors. At the top journals these positions are all filled by full-time PhDs that work for the journal, while most journals have a much larger staff of academic lab heads (PIs) who volunteer a portion of their time to the journal as editors.

Once you and your mentor submit your manuscript to a journal, somebody takes a look at the cover letter, abstract, and key words and tries to decide which of the managing editors has the expertise to manage the review of the manuscript. This editor doesn’t need to have the level of expertise that the referees’ posses, but he or she must be familiar enough with the field to know who to ask to be a referee, and to make educated decisions when there is a difference of opinion between two referees or between a referee and the authors.

Once the manuscript (with cover letter) has been sent to the managing editor and that editor has agreed to handle the paper (if the editor is a volunteer), then the first decision that he or she makes is if the manuscript is suitable for the journal. If this editor feels that your work isn’t consistent with the journal’s mission, then he or she can reject the paper without it even going out for review. This is called an editorial rejection, and there isn’t much you can do about it. It could be because:

  • they don’t believe your topic is “sexy” enough for their journal,
  • they don’t think it constitutes a significant enough advance in the field even if the topic is sexy,
  • they think the discipline is wrong (trying to publish a biochemistry paper in The Journal of Cell Biology, for example),
  • or they feel that the work is derivative (it has already been published before).

The only good thing about an editorial rejection is that it generally happens quickly. If the editor is undecided about a manuscript’s suitability for their journal, he or she may send out “feelers” to lab heads, which consists of an e-mail containing the title, authors, abstract, and possibly a significance statement and solicit their opinion.

The referees
Well, you have just found out that your manuscript has been sent out to review. So what is actually happening? Remember the “feelers” sent out above? If the lab head contacted feels that the work belongs in that journal, feels qualified to review the work, doesn’t have any conflicting interest, and has the time, then he or she will be asked to review the work. Now what is supposed to happen is that this scientist receives the manuscript and reviews it, keeping the information in strict confidence. Some lab heads do this, but some farm out the paper review to their senior graduate students and postdocs. You should keep this in mind – once you send the work out the door, the question isn’t “Does anybody in my field know about my work?”, but rather “How many people in the field know about my work?” Even if the lab head has farmed out some of the legwork of the review, almost all will read the manuscript themselves and come to their own conclusions.

When the referees submit their reviews, there are parts that are relayed back to the authors, and parts that only the editors see. In addition to a field where you can enter editor-only comments and concerns, there are also a series of statements that the referee must choose from. They are some form of the following:

  • Publish without revision
  • Publish with minor revisions
  • Consider for publishing upon major revisions
  • Reject

As the author, you never actually see what the referee recommended – you receive the recommendation of the editor. The editor’s recommendation is influenced by the referee’s recommendations, but the editor has the freedom to come to his or her own conclusions. It’s good to bear this in mind, because sometimes a referee will be held responsible for killing a manuscript, when he or she actually recommended publication (almost certainly with revisions) but the editor disagreed. (We’re not supposed to know who reviews our papers, of course, but speculation on referee identity is a favorite pastime of many scientists, and raised to the level of an art by some.)

Dealing with the reviews and writing your response

Your manuscript wasn’t rejected, but the referees did have some criticisms, though. Don’t worry about that – we all get them. I think criticisms are how scientists prove to others that they actually read something. Referee comments can fall into one of several different categories, though.

– The referee has no idea what is going on. Sometimes the editor just picks a bad referee, and the referee either didn’t want to admit ignorance or truly believes they can review papers outside of their discipline. The best example of this that I’ve heard was a friend that had a math-intensive paper reviewed by somebody that didn’t know what basic mathematical symbols were, mistaking them for variables which were left undefined, to their great outrage. When you get these types of comments (and you will, eventually), the hardest thing to do is to write a polite response, but you should. Remember, you don’t know who the referee is, but they know who you are, and scientists have excellent memories.

-The question that you already answered – in the manuscript. The referee probably just missed the fact that you explicitly addressed this question/issue. Or maybe you didn’t address the issue as clearly as you could have. Read over what you wrote again to make sure it’s clear, and if it is find a polite way to say “we already said that” in the response letter.
-You didn’t cite my favorite papers. If you have the space to add a couple sentences and/or a couple references, add them. This person spent their valuable time helping you publish your paper, so do as they ask. Chances are that you should have cited them in the first place, and citations are one criteria that is used to evaluate established scientists, so it isn’t just an ego thing. Now if they ask you to rewrite your entire introduction, it may be a different story.

-The nitty-gritty details question. These are usually asked by the people right in your field, and they can go one of two ways. Some are so specific and detailed that trying to incorporate the information that the reviewer requests into the manuscript itself is difficult to do while keeping the paper accessible to the average reader. In this case, it may suffice to just answer the question in the response letter and the referee will be satisfied that the work is solid. On the other hand, the issue may be a more important point than you originally thought, so if the information can be incorporated without confusing the average reader, incorporate it into the manuscript.

-This is nice, but I would rather have read your next paper. This one is tough – you’ve put together ~6 figures (and a bunch more in supplemental), and all the referee wants are the next 6 figures, which you thought would be your second paper. Re-read your title and conclusions – does your data solidly support these statements? Sometimes referees ask for the next paper because the authors promised more with the title than they delivered with the data. If this isn’t the case, then politely state in the response that you agree that the next 6 figures/experiments would be very interesting and exciting – so exciting that they will get their own paper.

-You did it all wrong. This is the toughest. The referee doesn’t like your reagents, your experimental design, your interpretation of the data, or all of the above. I think the most important thing to do is try to distance yourself from the experiments and ask if there is any validity to what they are saying. Keep an open mind and try doing the experiments their way and see what the results are. If the results are different, then they may have saved you from having to retract the paper in the future. If the results are the same, then your work and the conclusions have only gotten tighter. If their requests are completely off-base or unfeasible (the experiment that costs millions of dollars or uses an instrument with specifications that hasn’t been invented yet), then you need to communicate this politely in the response letter.

One thing that you should bear in mind when writing the response to the reviews is that the editor is obliged to communicate the referee’s review to you, regardless of whether the editor agreed with it or not. Your response may only be read the editor, or it may also be forwarded back to the referee for additional comment. This is why I emphasized politeness so many times above. You also have to strike some balance between rebuttals to a referee’s criticisms and changes to the manuscript. If the editor requests additional comments from the referee and all you have done is argue the validity of the referee’s comments without changing anything in the manuscript, then the referee isn’t going to be very happy about the situation. On the other hand, you should never weaken, diminish, or reduce the clarity of your manuscript just to appease every comment of a referee.

Page Proofs
You have survived the review gauntlet, and the journal has accepted your creation. You aren’t quite done yet, but don’t worry, the next step is pretty painless. After accepting your manuscript, the journal shipped it off… someplace… where they format it for publication. (I like to think it is a Keebler-esque tree-house full of elves with laptops rather than the cubical-farm that it likely is.) These formatted files are called the page proofs, and these files will show up unannounced in you inbox with a ~48 hour deadline for you and your mentor to review and return them. After you return them, that is it. That is what is published, warts and all. Fail to return them? They might publish the paper as-is. So pay attention to your inbox and the details!

Remember that list of words that your mentor hates? Well the journal/line editor has their own list, and they have edited your text. The best advice I was given is to read the paper backwards, one sentence at a time. This forces you to read what is written, and not to start reciting the manuscript you wrote in your head. This can allow you to catch any typos that have snuck through, and to catch the edits that the line editor has made. If the edits that have been made don’t change the meaning or clarity of the statement, let them go – learn to pick your battles. Don’t forget to check the references, either. It may be a good idea to bribe a grammar/spelling gifted friend to help you out, as well.

Scrutinize the figures both printed at actual size (preferably on several different printers) and enlarged on your computer screen. Has the resolution changed? Are the brightness and contrast acceptable? Are there any typos/misspelled words in the figure itself? This is your last chance to fix it in the manuscript without the potentially embarrassing publication of a correction.

Congratulations! You have published your first paper! Now how far are you along on the next manuscript?

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