Friday, September 11, 2015

How to publish your first scientific paper

I get a lot of email asking me for advice on paper publishing. There’s no way I can make time to read all these drafts, let alone comment on them. But simple silence leaves me feeling guilty for contributing to the exclusivity myth of academia, the fable of the privileged elitists who smugly grin behind the locked doors of the ivory tower. It’s a myth I don’t want to contribute to. And so, as a sequel to my earlier post on “How to write your first scientific paper”, here is how to avoid roadblocks on the highway to publication.

There are many types of scientific articles: comments, notes, proceedings, reviews, books and book chapters, for just to mention the most common ones. They all have their place and use, but in most of the sciences it is the research article that matters most. It’s what we all want, to get our work out there in a respected journal, and it’s what I will focus on.

Before we start. These days you can publish literally any nonsense in a scam journal, usually for a “small fee” (which might only be mentioned at a late stage in the process, oops). Stay clear of such shady business, it will only damage your reputation. Any journal that sends you an unsolicited “call for papers” is a journal to avoid (and a sender to put on the junk list). When in doubt, check Beall’s list of Potential, Probable and Possible Predators.

1. Picking a good topic

There are two ways you can go on a road trip: Find a car or hitchhike. In academic publishing, almost everyone starts out a hitchhiker, coauthoring a work typically with their supervisor. This moves you forward quickly at first, but sooner or later you must prove that you can drive on your own. And one day, you will have to kick your supervisor off the copilot seat. While you can get lucky with any odd idea as topic, there are a few guidelines that will increase your chances of getting published.

1.1 Novelty

For research topics as with cars it holds that a new one will get you farther than an interesting one. If you have a new result, you will almost certainly eventually get it published in a decent journal. But no matter how interesting you think a topic is, the slightest doubt that it’s new will prevent publication.

As a rule of thumb, I therefore recommend you stay far away from everything older than a century. Nothing reeks of crackpottery as badly as a supposedly interesting find in special relativity or classical electrodynamics or the foundations of quantum mechanics.

At first, you will not find it easy to come up with a new topic at the edge of current research. A good way to get ideas is to attend conferences. This will give you an overview on the currently open questions, and an impression where your contribution would be valuable. Every time someone answers a question with “I don’t know,” listen up.

1.2. Modesty

Yes, I know, you really, really want to solve one of the Big Problems. But don’t claim in your first paper that you did, it’s like trying to break a world record first time you run a mile. Except that in science you don’t only have to break the record, you also have to convince others you did.

For the sake of getting published, by all means refer to whatever question it is that inspires you in the introductory paragraph, but aim at a solid small contribution rather than a fluffy big one. Most senior researchers have a grandmotherly tolerance for the exuberance and naiveté of youth, but forgiveness ends at the journal’s front door. As encouraging as they may be in personal conversation, a journal reference serves as quality check for scientific standard, and nobody wants to be the one to blame for not keeping up the standard. So aim low, but aim well.

1.3. Feasibility

Be realistic about what you can achieve and how much time you have. Give your chosen topic a closer look: Do you already know all you need to know to get started, or will you have to work yourself into an entirely or partially new field? Are you familiar with the literature? Do you know the methods? Do you have the equipment? And lastly, but most importantly, do you have the motivation that will keep you going?

Time management is chronically hard, but give it a try and estimate how long you think it will take, if only to laugh later about how wrong you were. Whatever your estimate, multiply it by two. Does it fit in you plans?

2. Getting the research done

Do it.

3. Preparing the manuscript 

Many scientists dislike the process of writing up their results, thinking it only takes time away from real science. They could not be more mistaken. Science is all about the communication of knowledge – a result not shared is a result that doesn’t matter. But how to get started?

3.1. Collect all material

Get an overview on the material that you want your colleagues to know about: calculations, data, tables, figures, code, what have you. Single out the parts you want to publish, collect them in a suitable folder, and convert them into digital form if necessary, ie type off equations, make vector graphics of sketches, render images, and so on.

3.2. Select journals

If you are unsure what journals to choose, have a look at the literature you have used for your research. Most often this will point you towards journals where your topic will fit in. Check the website to see whether they have length restrictions and if so, if these might become problematic. If all looks good, check their author guidelines and download the relevant templates. Read the guidelines. No, I mean, actually read them. The last thing you want is that your manuscript gets returned by an annoyed editor because your image captions are in the wrong place or similar nonsense.

Select the four journals that you like best and order them by preference. Chances are your paper will get rejected at the first, and laying out a path to continue in advance will prevent you from dwelling on your rejection for an indeterminate amount of time.

3.3. Write the paper

For how to structure a scientific paper, see my earlier post.

3.4. Get feedback

Show your paper to several colleagues and ask for feedback, but only do this once you are confident the content will no longer substantially change. The amount of confusion returning to your inbox will reveal which parts of the manuscript are incomprehensible or, heaven forbid, just plainly wrong.

If you don’t have useful contacts, getting feedback might be difficult, and this difficulty increases exponentially with the length of the draft. It dramatically helps to encourage others to actually read your paper if you tell them why it might be useful for their own research. Explaining this requires that you actually know what their research is about.

If you get comments, make sure to address them.

3.5. Pre-publish or not?

Pre-print sharing, for example on the arxiv, is very common in some areas and less common in others. I would generally recommend it if you work in a fast moving field where the publication delay might limit your claim to originality. Pre-print sharing is also a good way to find out whether you offended someone by forgetting to cite them, because they’ll be in your inbox the next morning.

3.6. Submit the paper

The submission process depends very much on the journal you have chosen. Many journals now allow you to submit an arxiv link, which dramatically simplifies matters. However, if you submit source-files, always check the complied pdf “for your approval”. I’ve seen everything from half-empty pages to corrupted figures to pdfs that simply didn’t load.

Some journals allow you to select an editor to whom the manuscript will be sent. It is generally worth checking the list to see if there is someone you know. Or maybe ask a colleague who they have made good or bad experience with. But don’t worry if you don’t know any one of them.

4. Passing peer review

After submission your paper will generally first be screened to make sure it fulfills the journal requirements. This is why it is really important that the topic fits well. If you pass this stage your paper is sent to some of your colleagues (typically two to four) for the dreaded peer review. The reviewers’ task is to read the paper, send back comments on it, and to assign it one of four categories: publish, minor changes, major changes, reject. I have never heard of any paper that was accepted without changes.

In many cases some of the reviewers are picked from your reference list, excluding people you have worked with yourself or who are in the acknowledgements. So stop and think for a moment whether you really want to list all your friends in the acknowledgements. If you have an archenemy who shouldn’t be commenting on your paper, let the editor know about this in advance.

Never submit a paper to several journals at the same time. Also don’t do this if the papers have even partly overlapping content. You might succeed, but trying to boost your publication count by repeating yourself is generally frowned upon and not considered good practice. The exception is conference proceedings, which often summarize longer paper’s content.

When you submit your paper you will be asked to formally accept the ethics code of the journal. If it’s your first submission, take a moment to actually read it. If nothing else, it will make you feel very grown up and sciency.

Some journals ask you to sign a copyright form already with submission. I have no clue what they are thinking. I never sign a copyright form until the revisions are done.

Peer review can be annoying, frustrating, infuriating even. To keep your sanity and to maximize your chance of passing try the following:

4.1. Keep perspective

This isn’t about you personally, it’s about a manuscript you wrote. It is easy to forget, but in the end you, the reviewers, and the editor have the same goal: to advance science with good research. Work towards that common end.

4.2. Stay polite and professional

Unless you feel a reviewer makes truly inappropriate comments, don’t complain to the editor about strong wording – you will only waste your time. Inappropriate comments are everything that refers to your person or affiliation (or absence thereof), any type of ideological arguments, and opinions not backed up by science. All other comments you should go through and address them one by one, in a reply attached to the resubmission and by changes to the manuscript where appropriate. Never ignore a question posed by a referee, it provides a perfect reason to reject your manuscript.

In case a referee finds an actual mistake in your paper, be reasonable about whether you can fix it in the time given until resubmission. If not, it is better to withdraw the submission.

4.3. Revise, revise, revise

Some journals have a maximum number of revisions that they allow after which an editor will make a final decision. If you don’t meet the mark and your paper is eventually rejected, take a moment to mull over the reason of rejection and revise the paper one more time before you submit it to the next journal.

Goto 3.6. Repeat as necessary.

5. Proofs

If all goes well, one day you will receive a note saying that your paper has been accepted for publication and you will soon receive page proofs. Congratulations!

It might feel like a red light five minutes from home when you have to urgently pee, but please read the page proofs carefully. You will never forgive yourself if you don’t correct that sentence which a well-meaning copy editor rearranged to mean the very opposite of what you intended.

6. And then…

… it’s time to update your CV! Take a walk, and then make plans for the next trip.


  1. "stay far away from everything older than a century" The Equivalence Principle (mass and weight being in constant proportion) is Galileo, 1638. Present two marbles having local non-identical minimum action vacuum free fall trajectories, then Phys. Rev. Lett. Easy!

    Somebody credible must drop and measure. 21st century diddling is embezzlement of research funding. Working off hours in France earns administrative vivisection. "foundations of quantum mechanics" Milgrom acceleration. Unlimited opportunities are imprisoned within wisps of proper procedure.

    "Modesty" Toujours l'audace! Modesty after victory.

  2. "But simple silence leaves me feeling guilty for contributing to the exclusivity myth of academia, the fable of the privileged elitists who smugly grin behind the locked doors of the ivory tower."

    "Pre-print sharing, for example on the arxiv, is very common in some areas and less common in others. I would generally recommend it if you work in a fast moving field where the publication delay might limit your claim to originality."

    Another reason is that, in many fields, a paper which is not on arXiv will be read much less than if it were on arXiv.

    It is at least unclear if "anyone" can submit to arXiv, especially someone submitting their first paper. For someone at a real institute, this shouldn't be a problem, but above you claim that the exclusive ivory tower is a myth. You need at least an "endorsement" to submit to arXiv if you haven't submitted anything before. This is necessary, but not sufficient.

  3. Phillip,

    You are right, sorry for the omission. Honestly, I just forgot about the endorsement requirement because when I was a student that simply didn't exist.

  4. I have a problem with a couple points. First, I don't agree that you shouldn't submit to more than one journal at a time. In my experience, it can take months and even years before anyone even gets back to you with a response, and in some cases the response is equivocal -- i.e., "we'll consider your paper if certain requirements are met" -- meaning more months or even years of waiting. While most journals "forbid" multiple submissions, if they really want your paper they'll publish it anyhow and if they don't they won't, regardless. Also what they don't know won't hurt them -- or you. I have no problem with the first come first serve approach -- the first editor to get back to me with a meaningful response is the one I'll take seriously. As for the rest, I don't feel sorry for them for being forced to embrace some degree of competition at the other end of the great power divide.

    Also, I see no reason to cede copyright to any journal or any publisher, at any time during the process. If this is a "work for hire," that's different, but if it's an original piece of research it belongs to the author not the publisher. The only time I was asked to sign such a release I refused, and was promptly sent another release, permitting the publisher to reprint my work but NOT handing over copyright privileges. In most cases, that's all the publisher really needs, but they are too lazy/insensitive to bother with the distinction.

  5. " I just forgot about the endorsement requirement because when I was a student that simply didn't exist."

    Yes, Sabine, we are old. :-|

    When they introduced the endorsement system, arXiv sent an email saying that those who already had put something there would be "grandfathered in". :-) OK, I'm not THAT old, yet. (I suppose I could become a grandfather any day, but it's not something I can control. As speakers of German will understand, "ich stecke nicht darin".) Of course, it's more important to remain mentally young. Mick Jagger is a great-grandfather and still manages to expend more energy at a concert than many people a quarter his age, and can still wear the same clothes he wore 50 years ago.

  6. DocG,

    I don't know which journals you publish in, but at least in my field pretty much every journal requires you to confirm that you have not at the same time submitted your paper elsewhere. Anecdotically I hear that in the social sciences this isn't so.

    As to the copyright, same thing. I don't have a huge problem with the copyright on scientific papers because it's not normally content I want to reuse elsewhere anyway. Except possibly figures, but this usually isn't an issue, I've never had a problem with a publisher to reuse my own figures.

    I sometimes do have a problem with copyright forms for other text. I literally just refused signing a "work for hire" contract. (An unpaid one in addition. Makes me wonder what they are thinking.) Best,


  7. Yes, in physics it is submit to one journal at a time and if one submits elsewhere after rejection, mention this. But the turnaround is not years. These days, there are a few weeks between acceptance and publication. If there are more than a few weeks between submission and acceptance, it's because revision is necessary.

    Copyright? I prefer to retain it unless the person or organization who wants it hired me to do the writing involved. That is essentially never the case. In practice, one retains the copyright but gives the journal an exclusive license for actual publication, or signs over the copyright but retains a non-exclusive license to post it on an open-access archive, one's own website, institutional website, etc. I prefer the former but can live with the latter.


    Luboš was exhaustive mathematical certainty. Quantum gravitation is empirically sterile. Luboš abandoning validation is Tommy Aquinas versus Baruch Spinoza, decorated with witch burnings.

    Come in from phenomenology. Embrace classes of failure as diagnostics. Reach out orthogonal to failure. Chemistry offers outstanding tests of Official impossibility. Look. CENPA/Eöt-Wash Group, priests, and now Luboš say "it's OK if it doesn't work."
    It's not OK - Pyrex, steel, or vacuum.

  9. Uncle,

    Thanks for the pointer. Lubos, as always hilarious, apparently didn't fully realize my blogpost is soaked in cynicism. Which should have been obvious by point 2 at the latest, or if not this should help.

  10. And what is the recommended approach for someone who needs an arXiv endorsement for their first paper but who is not academically affiliated?

    I sympathise with both sides: the serious and conscientious unaffiliated author and the serious and conscientious endorser whose time and goodwill are, if not already consumed, in jeopardy if they don't automatically ignore all approaches from unknown authors? After all, valid contributions from independents are rare.

    But, if the author is claiming a suitably modest result, can write, argue, calculate and cite properly (though not necessarily without error), how does he or she cut the Gordian knot - even if only to seek corrections or rebuttal?

  11. Hi Julian,

    You don't need an arxiv endorsement to publish a paper in a journal. I would suggest the independent researcher wanting to prove their work is interesting for the community first publishes a few papers in peer-reviewed journals. Then they can attend conferences giving talks about their work, which is really important to get into a new community. Almost all conferences will accept talks about published papers. Conference talks typically lead to some seminar invitations. And once you know a few people who think your work is interesting, who might maybe want to work with you and so on, you should have no problem finding someone to endorse you.



  12. Hi Sabine,

    So, as Sean Carroll once put it, there's no substitute for really LaTeX'ing it all up (and submitting to journals) ;)

    I suppose that if someone is prepared to put the intellectual effort into the intellectual content they should also be prepared to do the same for the presentation - but don't journals have (sometimes quite high) processing charges?

    Institutions would normally cover the journal fees for their own researchers but independents would have to pay this themselves. Is the cumulative height of the barrier to publication reasonable?

    The process you describe is, however, sensible (not that I expected any less)

    Best regards


  13. I basically agree with Sabine. The only problem is that many people read papers only from arXiv. However, if the paper has been accepted by a respected journal (note: not all peer-reviewed journals are respeced), try to find an endorser as soon as it is accepted. If the referee is not anonymous, you could ask him, or ask the journal editor to recommend an endorser.

    There are some journals which won't consider papers from unaffiliated researchers, but there are enough which do.

  14. Julian,

    What you say is actually the main reason I am opposed to author fees, which is what I believe you are referring to. However, at least in my field, the vast majority of journals do not charge the author. Unless, that is, you want extras like color printed figures, supplements, or an open access option. I have never have to pay a fee for my publications. Best,


  15. "- but don't journals have (sometimes quite high) processing charges?

    Institutions would normally cover the journal fees for their own researchers but independents would have to pay this themselves."

    As Sabine says, most journals don't have page charges, at least in some fields. In astronomy/astrophysics/(astronomical/astrophysical) cosmology, the leading journals are MNRAS, A&A, ApJ and AJ. The first two have no page charges at all (except for colour figures in the printed version), the second do.

  16. What would your advice be that might help me write/publish a paper when my idea is "one of the Big Ones"? I try to show simulations that show that my idea is at least worth listening to but I'm simply ignored. All I need is one chance. I know I sound like a mad man... I really do.

    Should I show up on some University's doorstep with whatever proof I can? Knock on Professors' doors until someone gives me 2 minutes of their time?


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