Copyright © 2011 by Stephen G. Lisberger. All rights reserved. This book was purchased for your personal use.  It may not be redistributed in printed or electronic form, nor posted on a website or elsewhere on the internet. Content herein may not be reproduced without permission of the author: Steve.Lisberger@gmail.com

First edition: published in 2011 in the United States of America

ISBN 978-1-4507-8666-9

Acknowledgements

I am especially grateful to my wife, Chieko Murasugi, without whose support I would not have completed this book. She tolerated my travels, during which I conceived the idea for this book, she encouraged me to develop and complete the project, and her extensive editorial work clarified and polished my writing.  I thank Graig Donini, Fiona Stevens, and Jeff House, friends who are or were publishers, for their enthusiastic endorsement for the idea for this book and for their advice on publication strategies.  Graig read an early draft of the text and his enthusiasm for “what goes on inside the sausage factory” encouraged me to develop the project to a greater extent than I first envisioned. I am grateful to those who had enough confidence in me to appoint me to editorial posts. Special recognition goes to the chief editors at the journals where I have (or have not) been an editor, who mentored and taught me about the ways of a good editor: Drs. Gary Westbrook, David van Essen, John Maunsell, Peter Strick, and Ole Petter Ottersen all deserve mention. I thank Floyd Bloom with whom I have shared the joys and challenges of editorial work, “from one editor to another.” I owe a tremendous debt to the publisher of Neuroscience, Elsevier Ltd, and to Paul Carton, my friend and colleague at Elsevier, who supports me as the Chief Editor of Neuroscience. Paul arranged for me to be invited to the venues at which the idea for the book was hatched. I feel honored by the trust placed in me by my longtime friend and colleague Piergiorgio Strata, and the International Brain Research Organization or IBRO for appointing me to a lead editor’s role at Neuroscience.  Finally, I must acknowledge the forbearance of Emika and Theodore, my teenage children, for enduring many conversations about the book at the dinner table, for pretending to be amused by my jokes about the project, and for accepting that parents need to have their own pet projects outside of their daily jobs, along with the freedom to pursue and complete those projects.

Preface

In 2009, I was asked to speak at an “Authors’ Workshop” at the annual meeting of the Chinese Society for Neuroscience,and also at Sun-Yat Sen University in Quangzhou, China. The lecture I presented was entitled How to Write a World-Class Paper. I was stunned by the massive attendance and the thirst of the attendees for the information I presented. The level of interest inspired me to write a short book that covers the substance of my talk, plus answers to the questions I was asked.

As I thought about the challenges of writing and publishing a successful scientific paper, I had several realizations. First, because the process of writing a paper is embedded within a scientific career, the paper will be more successful if the career as a whole is managed properly. Second, fluency in written English is only a small part of a quality scientific publication; good science and an effective structure for the paper are the essential ingredients. In fact, imperfect English is acceptable as long as the writing is easily understood and the content is strong. Third, for a paper to be published it is not enough to submit a first-rate paper. As authors, you have to successfully navigate the process of submission, review, revision, rejection, and appeals. Fourth, you need to consider many ethical issues before publishing a scientific paper. In my capacity as a reviewer and editor for multiple journals, I have seen many apparent errors in ethics. I have dealt with enough of them to know that most (but, alas, not all) arise because of misunderstandings rather than malicious intent. Because proper scientific conduct is so important, I discuss ethical issues in this book.

Why should you listen to my advice? First, I am a successful scientist with well over 100 peer-reviewed publications in major journals in the field of neuroscience. Second, I have mentored many junior scientists at all levels, from graduate students to junior faculty, both at my own institution and others. Third, I have been an editor of major journals in the field of neuroscience for many years. I was a Reviewing Editor and then a Senior Editor for the Journal of Neuroscience for a total of eleven years. I was the Associate Editor of Neuroscience for four years, and am currently its Editor-in-Chief. I have read more reviews of papers than almost anyone else in the world, and I have seen the operation of the review and decision process from the perspective of an editor for more than 12,000 papers.  I haven’t yet “seen it all,” but I am getting close.  My experience has allowed me to formulate advice on many aspects of scientific publication. I hope my advice helps you.

Chapter 1: Features of a “successful” paper

The title of this book may make you wonder what it means to publish a “successful” paper.  Everyone has a different idea of what makes a paper successful.  Here is what I mean:

1)

The paper provides a clear explanation of the problem it sets out to solve.

2)

The research methods are described clearly and thoroughly, the data are presented in sufficient detail, and the analyses are appropriate and employ meaningful statistical tests.

3)

The experimental design leads to new knowledge that is believable, and supported by proper control experiments.

4)

The Discussion section provides a succinct and clear explanation of how the paper has moved the field forward conceptually.

5)

The Figures and Tables are neat and professional, detailed but not too detailed.

6)

The research is performed and published within the bounds of acceptable ethical behavior.

7)

The paper is published in a journal where it will come to the attention of interested readers. The correct journal for a paper may not be the journal with the highest impact factor or the best reputation. It is more important for the paper to appear in a journal where it will be seen and read.

8)

The paper is read by other scientists and cited in their papers. The best test of a paper’s success is not whether it appears in a journal where papers are cited frequently, but rather whether it is cited frequently.

Chapter 2: Manage your career

Scientific publications do not spring out of thin air; they emerge from a career of scientific inquiry. They represent milestones in discovery. To create a steady stream of successful scientific publications, think about your papers in the context of a scientific career that you plan and manage, from the day you decide to acquire education and training in science, to the day you retire.

Many succeed in science, but few do so without advice and encouragement from mentors and role models. No matter where you are in your career, you can profit from interactions with others who have successfully progressed past your current level. Seek mentorship.

Mentors

It is your responsibility to seek mentors throughout your career, and to use the mentoring that is available to you. It also is the responsibility of your institution to provide professional guidance to scientists at all levels of their careers, from first-year graduate students to senior professors. This point is very important and I will repeat it; it is the responsibility of the institution to provide mentorship for scientists at all levels, from the novice graduate student to the most senior professor. If your institution does not provide the mentorship you need, work with your superiors to set up a suitable system.

If you are a graduate student or a postdoctoral fellow, the head of your home research laboratory is your primary mentor. But you can benefit from having additional mentors. If you are a woman, you may wish to find a mentor who is a successful woman scientist. In spite of how far we have come in recognizing the unique challenges faced by women in science, we have not completely overcome the problems women face in their scientific careers. A successful woman scientist can give you crucial advice. But no matter who you are, you benefit from the advice of a broad set of people.

If you are a junior faculty member, you need to seek mentors aggressively. Find one or two senior faculty whose advice you trust, and talk with them about the various challenges you face. You don’t have to follow all the advice you receive, but remember that your senior colleagues have cleared many of the hurdles you face.

Seek the advice of your mentors on how to deal with problems, or potential problems, in your laboratory. Use your mentors as sounding boards as you ponder whether to offer positions to prospective students or postdoctoral fellows. Solicit your mentors’ help in deciding when to finish a project and write a paper, or whether to abandon a project that is not succeeding at the level you had hoped it would. Ask them if you are doing too much teaching, or if you are serving on too many committees.

I encourage you to learn to say “no.” Remember that you do not hurt the person who asked you when you say “no” to a request for your time. Someone else will do the task you were asked to do. Sometimes, you will be asked to do some things that could be important to do and that are good for your career. Ask your mentors how you should respond to various requests for your time before you say “yes” when asked to do something. Rely on your mentors to help you identify the assignments that are a good use of your time.

Mentoring committees

Graduate students usually have a thesis committee to oversee their research. In my research center, we extend this idea by having research advisory committees for each postdoctoral fellow as well. Graduate students must meet with their committees annually for their yearly stipends to be renewed. Postdoctoral fellows are encouraged to meet with their committees once a year but do not face a stringent requirement. Both the thesis and postdoctoral committees provide a structure for scientists-in-training to receive valuable advice on their research from a diverse group of experienced scientists.

Another benefit of the research committee is that it helps to protect students and postdoctoral fellows from being exploited, even subtly, by their research advisors. Research advisors may not always be objective about the work performed in their labs because they benefit directly from the work of their students and postdoctoral fellows. The advisor’s desire to promote his/her own success could color their advice, even at a subconscious level.

The advisory committee has benefits for its members as well. The thesis and postdoctoral committees promote interaction between faculty members by educating them about the research being performed in their colleagues’ laboratories. The fostering of intellectual interactions between labs could lead to productive collaborations.

If you are a junior faculty member and are running your own lab, your institution may not have a formal mentoring program. It should. I advocate the formation of a mentoring committee for each junior faculty member or junior research scientist. The committee should consist of senior researchers who stay in regular contact with the particular junior scientist and monitor his/her progress. Graduate study usually does not include a course entitled, How to Run a Laboratory 101, but the material covered in such a course would be valuable to starting scientists. A mentoring structure that consists of a formal committee plus other informal contacts should guide you through the early challenges of your career and help you to:

- Establish a functional and happy laboratory

- Obtain your first grants

- Create a research program and portfolio of publications that allows you to be promoted to the next level

Mentors for grant writing

If you are writing a grant proposal, you will benefit from the constructive criticism of someone who has successfully applied for a similar type of grant. Do not underestimate the value of experience in grant writing. You can save yourself an enormous amount of time and grief if you seek advice from experienced grant writers and listen to their advice. To receive feedback in enough time to help you, prepare a good draft of the grant sufficiently ahead of the deadline so that your reader can read and comment on it and you can incorporate their suggestions.

It is worthwhile to prepare your grant in two stages. In the first stage, set out both the long-term goals and the “Specific Aims” of your grant in one page of text. Only after the Specific Aims is nearly finished and has been approved by your mentors should you embark on the second stage, which consists of writing the entire proposal.

The “Specific Aims” of your grant is a vehicle for refining the goals and scope of your application in a short, clear document that you can revise many times without managing a large amount of text. Because of its brevity, you can ask your mentors to read the Specific Aims several times and give you helpful feedback on the structure and content of your application. If you revise the Specific Aims until you and your mentors are satisfied with it, then you will have a much easier time writing the main narrative of the grant proposal.

Role models

The year I started as a graduate student, two very important sets of papers were published in my field. I read the papers carefully and decided that I wanted to write papers of comparable quality and thoughtfulness. The papers were exceptional in many ways: they investigated important research problems, used state-of-the-art data analysis, contained clear figures, and were well organized and written. Even a first year graduate student could appreciate them on many levels.

To write successful papers, I recommend that you do what most effective researchers have done: learn from exemplary scientists who are in your field but may be outside your institution. You can benefit from these role models even without taking any of their time, by reading their papers thoroughly. Study the papers. Evaluate what makes them successful. Analyze how the authors designed their research projects, and how they organized their papers for publication. You hasten you own progress if you find various people you can emulate in different ways, even if you do not know them personally.

Chapter 3: Ethics

Science is supposed to be a pure pursuit of knowledge. It used to be that way, sort of.  Nowadays, science is very competitive and everyone feels the stress of trying to succeed in a difficult field. As a result, there are many temptations for unethical behavior.

Competition is fierce for jobs, grants, journal space, and recognition. Regulations for experiments on humans and animals, and for work with biohazards, stem cells, and radioactivity are expanding and becoming more and more intrusive of our professional lives. Some scientists are in a position to profit monetarily from their research, which raises the specter of financially motivated conflicts of interest.

Proper ethical behavior is critical. Make sure that you are in complete ethical compliance. Scientific misconduct, if detected and proven, can destroy your career and have a serious negative impact on your life.

My professional society, the Society for Neuroscience, has developed a thoughtful guide to ethical practices in publication. The guide, found at the following website, should be helpful to all scientists:

http://www.sfn.org/index.aspx?pagename=responsibleConduct

Ethical issues should be discussed widely. Many institutions, including my own, have extensive training programs for students, employees, and faculty alike in various areas of ethics. Even with training, sometimes we are unsure about what constitutes ethical behavior. If you are uncertain about what to do in a situation that involves ethics, ask your mentors or colleagues.

As the editor of a journal, I see many instances of seemingly unethical behavior. In my position, I must, and do, respond to every allegation of ethical misconduct. In some cases, I am persuaded that the apparently unethical act resulted from a misunderstanding or lack of knowledge of what constitutes correct behavior. Many actual ethical violations are relatively minor and can be resolved and/or corrected without severe consequences to the offender. But, once in a while, I encounter truly shocking behavior. I suspect that the violations we detect make up only the tip of the iceberg of transgressions that occur. Fortunately, the internet is making it easier to detect ethical violations.

I investigate and sometimes verify the following forms of ethical misconduct, which I discuss in detail below:

- Disagreements or errors of author inclusion, exclusion, and order

- Improper use of animal and human subjects

- Multiple submissions, duplicate publications, and re-packaging of previous work with only minor changes

- Plagiarism, data fabrication, and data falsification

- Breeches of confidentiality

Choice and order of authors

The assignment of proper authorship is critical. We give credit for advances in research on the basis of authorship. Our record of authorship on scientific publications is of major importance when we apply for grants, compete for a job, are considered for promotions, and for attaining recognition in the field. Even if it takes considerable trouble and energy, you should select and order the authors of your paper to correctly reflect the relative contributions of each collaborator.

The order of authorship has different meanings in different disciplines. In my field of neuroscience, the first author is the lead scientist who did the research with his/her own hands, and who made the primary intellectual contribution to the paper. Frequently, the first author is a student or postdoctoral fellow for whom the research was his/her primary project and/or his/her thesis project. The last author on the paper is usually the head of the lab who guided and directed the research, and provided space and funding so that the other authors could do their work. Therefore, in neuroscience the first and last authors are the most significant. Authors with middle positions generally made lesser contributions to the research described in the paper.

You and your colleagues as a group need to discuss the questions of who should be an author on the paper, who should not be, and what the order of authorship should be. When there are only two authors, as in a collaboration between student and advisor, decisions about authorship are straightforward. In larger collaborations, the order of authorship can be more difficult to negotiate but it needs to be discussed openly and in good faith. In general, all the authors on a scientific publication should have made an identifiable intellectual contribution to the paper, and should be familiar enough with the material to read and comment on the paper. Usually only the scientists are authors. Technical staff who work for everyone in the lab can be mentioned in the Acknowledgements. When choosing the identity and order of authors, use good judgment and make sure that everyone who is on or off the list of authors is satisfied with their position.

I believe that the first author of a paper should be the person who writes the first draft of the paper. Increasingly, however, papers can have quite a few authors, and more than one junior scientist may have made major contributions to a given paper.  It is now common to encounter situations where two students or postdoctoral fellows make equal contributions to the science and possibly to the writing. When two people have made equal independent contributions to a paper, you should use asterisks to indicate that “the first two authors contributed equally” to the paper. This is now an accepted procedure. Committees that make decisions that affect the careers of young scientists understand that papers often include strong independent contributions from two junior scientists.  And, they know and accept the significance of the asterisk.

In collaborations across laboratories, the authors of a paper might include one or more junior scientists and the heads of the two laboratories. If the two laboratory heads contributed equally to the paper, then I suggest extending the asterisk system used in the case of two equal authors, but with the statement that “the two senior authors contributed equally.”

Even with the asterisk system, I think that the first and last authors of a paper get a little more credit than the other authors who “contributed equally.” This means that it is necessary to negotiate the order of the first two and last two authors. In cases where the authors are two junior scientists and two laboratory heads involved in a collaboration between two laboratories, one of my colleagues has adopted a sensible strategy for the ordering of authors.  He puts the junior author from one lab first on the list, and the senior author from the other lab last. This ensures that the two labs receive equal credit for the paper. In addition, he indicates equal contributions with asterisks, as outlined above.

As a general rule, you should decide on authorship, non-authorship, and the order of authors at the time you conceive of the collaboration. If, in the middle of a project, you ask a colleague in the lab to contribute some of his/her data or to participate in the project, then you should renegotiate the order of authors at that time.

Ethical infractions in authorship

It is an infraction of ethics if someone who deserves to be an author is omitted, or if someone who does not qualify for authorship is included. Most complaints I receive are from scientists who allege that they did not receive proper credit for their contributions to a paper. There are instances where a student discovers, after a paper is published, that his/her PhD thesis is the basis of the paper but s/he is not on the list of authors. I also have seen cases where a student publishes work without giving deserved authorship to his/her advisor. It is scientific misconduct when a collaborator is deprived of authorship without his/her express consent.

All authors must read the final draft of the paper and approve it before the paper is submitted for publication. This is important both because it is the right thing to do, and for your own protection. I see a remarkable number of cases where a co-author complains after publication that s/he is unhappy about something in the paper. I have even seen instances where a co-author alleges after the paper is published that the work was done incorrectly and the paper was submitted without his/her knowledge and/or approval. You can protect yourself from these problems if you are thoughtful and careful when you put together your list of authors, and if all authors read and approve the final version of the paper before it is submitted to the journal.

Different journals and editors handle grievances about authorship differently. If I receive a complaint about authorship, I stop the process, wherever it is. When a disagreement comes to my attention, I contact the authors immediately and ask if they can settle the issues amicably amongst themselves. If they can document within a day or two that everyone agrees with the identity and order of authors, then we move forward in the publication process. If the authors cannot settle the dispute very quickly, then I take more formal steps. If the paper is in review, I interrupt the review process. If the paper is accepted but not yet published, I take it out of the publication queue. If the paper is already published, I retract it from the journal. If the authors cannot resolve the disagreement themselves, then I direct them to seek the help of their institution to mediate and resolve the dispute. I tend to be forgiving. If the authors provide me with documentation of complete and unanimous agreement among the authors about both the choice and order of authors, then I allow them to resubmit their paper, or restart a halted review process, Other editors may be less forgiving than I am.

Proper use of animal and human subjects

You have three responsibilities with respect to the ethical treatment of your research subjects.

- You must know the regulations in your country and at your institution.

- You must have an appropriate, approved protocol for your research before you begin any experiments.

- You must know and follow the detailed procedures outlined in your protocol.

The Declaration of Helsinki in 1964 mandated the ethical treatment of human research subjects.  Most countries have laws and regulations to ensure the ethical treatment of animal subjects. The United States adopted its requirements in the Animal Welfare Act, amended in 1985.

A good source for websites on the regulations pertaining to animal use in many countries is:

http://www.aaalac.org/resources/internationalregs.cfm

My professional society, the Society for Neuroscience, has developed an excellent guide to the proper use of animal and human subjects. It makes for informative reading:

http://www.sfn.org/index.aspx?pagename=guidelinesPolicies_UseOfAnimalsandHumans

All institutions now have a system in place to review and approve protocols for research on human and animal subjects, and to ensure compliance with those protocols. Scientists ought to follow accepted regulations, but some researchers disregard regulations even when they are well established and widely known. I believe the most common violation is to perform procedures that are not described in the protocol, or in a way that is different from how it is described in the protocol.

Documentation of the ethical use of human and animal subjects

Most journals expect you to state in the Methods section that you followed the procedures outlined in a protocol, and that the protocol has been approved in advance by the responsible committee at your institution. If a journal reviewer questions your treatment of human or animal subjects, you are expected to provide proof that you complied with regulations.

As a general rule, include enough detail in your Methods section to show that you were sensitive to the well being of your subjects. For research using human subjects, you can state that they gave their “informed consent.” For research with animals, state the guidelines that you followed, and also that the research was approved in advance by a suitable institutional committee. You can explain very briefly how you prevented undue pain or distress in your subjects. If the animals were euthanized, describe the humane methods you used. Some organizations advocate that you give a full description in the Methods section of how you complied with the regulations pertaining to your animals’ welfare. For example, see:

Osborne NJ, Newman ML, Payen D (2009) Journal Editorial Policies, Animal Welfare, and the 3Rs. American Journal of Bioethics 9: 55.

http://www.bioethics.net/journal/j_articles.php?aid=2093

Misconduct in use of human or animal subjects

It is scientific misconduct to perform research without an approved protocol, or to perform procedures that are outside the boundaries of the approved protocol. A failure to follow your approved human or animal procedures is more likely to be discovered by your institution’s regulatory groups, or by outside inspectors, than by reviewers of a paper submitted to a journal. A reviewer usually does not have enough details of the researchers’ procedures to uncover a serious breech of protocol in the use of animal or human subjects. Unlike instances of ethical misbehavior of other types, the internet is not likely to help detect ethical violations in the use of subjects.

In a small percentage of the papers I have handled as an editor, reviewers have questioned whether the experiments complied with reasonable ethical standards. Different journals respond differently to the reviewers’ doubts. I prefer to let the local institution determine whether an experiment was allowed or not. Unless the procedures in question are clearly inhumane, I ask only that you, the author in question, provide proof that your local committee approved the experimental procedures before you initiated your research. Other journals and editors may have more stringent requirements.

If you are found to be out of compliance with your protocol, at the very least, your laboratory’s work will be suspended. If the offense is serious, as when human rights or animal welfare are compromised, the lab might not be permitted to do similar research in the future.  In any event, you will be not be able to publish research that is found to be out of compliance with an approved protocol, or that was performed without an approved protocol.

I recommend that you become familiar with the regulations in both your country and in the United States. To be certain you are in compliance, you should strive to establish and follow procedures that would be approved by a reasonable ethics committee in the United States, as well as at your own institution.

Multiple submissions and duplicate publications

You may not submit your paper to two journals at the same time, and you may not publish work that has been published previously in a peer-reviewed journal. If you try, you are likely to be caught. In the case of a duplicate publication, there is a good chance that your paper will go to a reviewer who is familiar with the prior paper. Multiple submissions of the same paper generally are detected quickly because different journals often will ask the same people to review the paper. Due partly to the internet, attempts at dual publication frequently come to light very early in the publication process. When two very similar or identical papers are accepted and appear on the internet, the transgression is discovered with short latency.

If a journal discovers that you published the same material twice, then at least one, and sometimes both, of the offending publications are retracted. Even though retraction removes the dual publications, it does not erase the offense. When a paper is published, it receives an indexing number called a “digital object identifier” that is irrevocable. Even after the retraction, a record of the paper remains on the internet and in the printed journal. In the place of the published paper, the journal publishes a brief notice stating that the paper was retracted and why. Any searches that lead to the paper are directed to that retraction note. The blemish remains forever.

Most journals allow you to submit work that was published in brief in a symposium volume or as an abstract at a meeting. Full disclosure is a good policy. You should indicate in the last sentence of your Introduction that “this work has been presented in preliminary form (references),” and you can ask a journal about its policy in specific cases.

A more complicated situation arises if you wish to take a figure that was published previously and place it in your current manuscript to present a context for your research. To use a published figure in your paper, you first need to obtain permission from the journal in which it appeared. As a general policy, however, it is better to use previous figures, with permission, only when you write review articles.

Plagiarism

Plagiarism is defined as the act of copying the work of others or oneself without proper attribution, either verbatim or with minor modifications. Do not do it. It is not flattery to copy the words of someone else without stating your source. It is scientific misconduct.

It would seem that nothing more need be said. Still, I see instances where authors have cut and pasted their own published text or the text of others into their papers. If you are writing a new paper, then you need to rewrite your Methods and Introduction. You may not repeat your old text.

It is plagiarism to copy the figures of others, or to clip out parts of their figures and represent them as your own. It is plagiarism to redraw a graph that appeared in one of your own papers. With permission from the publisher, which is actually quite easy to get, you can reproduce some or all parts of a previously published figure. Most journals have a form on their websites that you can use to request permission to reproduce a published figure. Permission frequently can be obtained within 24 hours via the internet. If the figure belongs to another author, then you also need to receive that author’s permission to reproduce his/her figure.

Data fabrication and falsification

If you make up data or alter data to make it look better, you commit an offense that is as bad as plagiarism. And one, I suspect, that is more frequent.

I can easily imagine how one could be tempted to make up data or to improve existing data. It is simple to do. Reducing the error bars increases statistical significance. Changes in the exact position of a few data points on a graph can enhance an experimental effect. Perhaps your motive is to raise the level of your project so that it will be published by a journal with a higher profile. Or perhaps you wish to curry favor with your lab head by providing data that substantiates his/her favorite hypothesis. Or perhaps the lab head has applied some pressure on you, directly or indirectly, to find the “right” answer.

There are three important points regarding data fabrication and falsification.

1)

If the misbehavior is discovered, it will destroy your scientific career, and the careers of your lab head and your collaborators.

2)

If you know that someone is fabricating or falsifying their data, then you need to report it to your institution. You should also inform your institution if you, or others you know, feel even subtle pressure to fabricate or falsify data, or to “get the right answer.” Your institution should provide an avenue for you to report the pressure or the wrongdoing without incurring retaliation. A quick internet search should show you what to do.

3)

You can protect yourself against allegations of data fabrication or falsification by keeping very careful records of your experimental progress, and complete results of every experiment. Save the individual data points and keep records of how you obtained them. Write continuously in your experimental log as you perform your research, and keep notes of dates and times. Write in pen to show that your notebook could not have been altered after-the-fact.

Confidential material

If you are given material that is unpublished, either for your information or for review for a journal, you must keep it confidential. Remember that everything is a confidential document until it is published. Don’t break confidences. If you review a paper or grant, you may not use the material in that confidential document to get a head start on your own research. Indeed, you must “bend over backwards” and go out of your way to make sure that you do not abuse the confidentiality of any information you receive.

Chapter 4: When to publish

Scientists are judged by their entire careers rather than on the basis of any single paper. Try to develop a career based on a steady stream of successful papers. Do not focus entirely on producing the one paper that will be a “home run.”  Concentrate on doing good science. Publish your work at regular intervals.

I am asked frequently what kinds of papers we publish in “my” journal.  I answer, “successful papers.” A successful paper is structured correctly and describes sound scientific research in correct English. You will write successful papers if you:

- Choose important problems

- Perform experiments that are technically rigorous and properly controlled

- Make good choices about when and how to break up your research program into publishable segments

- Structure your papers logically

- Write in good English

Choice of research problem

The first step in doing sound science is to choose an important problem. Make sure that you are genuinely interested in the question you choose so that it will continue to intrigue you through a period of several years. Choose a question that breaks new conceptual ground. Try to seek the answer to an open question, not merely to fill in some missing data in the literature. I frequently see papers where the rationale given by the authors for doing the research is that something “is not fully understood,” or that some fact is “not known.” Design your research career so that you can go one step further. When you write your papers, you should be able to present the question you wish to answer, and describe how your approach has helped you answer it.

Your goal is to convince the reviewers chosen by the journal that people will want to read your paper because it is important and has been performed well. What you wish to hear from the reviewers is that your paper “is an important advance” in the field,” not that it is a mere “incremental” advance, or even worse, that your research is “repetitious” and covers well-trodden ground.

If you are working in someone’s lab, you are probably engaged a problem that is related to the lab head’s broader research program. You may have a strong urge to do something “original,” but it is usually a mistake to stray too far from the research that is going on in your advisor’s laboratory. You ought to profit from the experience of others in the lab. It is prudent to work on a topic in which your advisor is an expert so that s/he can help you solve problems. In my lab, I have sometimes allowed postdoctoral fellows to pursue questions that were outside my area of expertise. Good science resulted from their efforts, but I believe that these young scientists would have produced more and better results if they had worked in areas or with techniques that I knew better.

If you are starting your own laboratory, strive to create a research program that is original, and is different from those of other laboratories in the field. If you can avoid it, try to find a niche that does not compete with other labs that are doing similar research. At the same time, you need to evaluate the probability that your research will be successful, and the time it will take to succeed. If you develop a research program that is far from the mainstream, or is very innovative or risky, it has a low chance of success within a reasonable period of time.

As you plan your research program, think about when you expect to be writing your first papers. If your proposed research is risky and technically challenging, prepare for a long delay before your first publication. I suggest that you do the risky work concurrently with research that is almost assured to produce original, publishable results within a known period of time. You should be pleased if your first papers, indeed many of your papers, are solid and original contributions to the field. They don’t have to shake the earth. It is important to be productive early in your career so that you can get grants, be promoted, recruit good students and postdoctoral fellows to your lab, and so on. With luck and insight, an earthshaking paper will come along now and then.  For almost all scientists, this is the most we can expect.

Phases of a research project

Plan your publications in the context of the overall goals and progress of your research program.  A scientific project goes through three phases: exploration, refinement, and completion. At all times, make sure you and your students know what phase you and they are in.

Exploration: During the exploration phase, you conduct your first experiments. Your goals are to get a preliminary result, to test the overall feasibility of your project, and to obtain the results that will form the basis for expansion of your research program. You reach the end of the exploration phase when your results tell a story that can develop into a paper. Depending on the nature of your research, the exploration phase could consume anywhere from 10 to 50% of the time you spend on the project. The exploration phase is very important in the development of your research career. It is when you can be creative in the questions you ask. The scope of your research could widen during this phase; you can test different approaches that have the potential to add to the project. Remember to analyze your data as you go through the exploration phase. It is important to know whether you have a result that stands up to the rigor of quantitative analysis, or an ephemeral effect that vanishes after a more thorough analysis.

Refinement: During the refinement phase, you cease to widen the scope of your research and instead, undertake a full set of publishable experiments with appropriate controls. You enter the refinement phase when you can predict the main outcome of your project, and you are ready to turn a set of novel observations into a complete and rigorously controlled research project. You need to plan carefully at this stage. Outline exactly what experiments and controls you need, as well as how many repetitions, and what additional avenues of research you should follow. Collect enough data but not too much. If you plan your data analysis in the refinement phase, you can calculate the number of observations you need to achieve statistical power. Design your data analysis so that it will convince others of what you observe in the data without being overly detailed. The refinement phase ends when you collect enough data to visualize, with preliminary figures, the papers that result from your research project.

When is it time to stop performing experiments and to write a paper? This is a good question and one you should consider often during the refinement phase. On one hand, you wish to have a complete story before you write a paper, but on the other hand, you should strive to write and publish on a regular schedule. One of the worst, and most common, mistakes made by scientists at all levels is to wait until a project is 100% finished before writing a paper, or to wait until a paper is 100% perfect before submitting it to a journal. Of course, you want to make your research and papers as good as you can, but you must know when to stop and move on. During the refinement phase you make the decision to combine some your experimental results into a paper. You then move into the completion phase for the publishable part of your project. In a large project, one line of research can move to the completion phase while the rest of the project remains in the refinement phase.

Completion: During the completion phase, the scope of your efforts narrows to the single goal of producing a publishable paper. You finalize your preliminary figures, complete your data analysis, gather any incomplete or missing data, and prepare to write the paper. You should have a list of tasks that need to be accomplished and work single-mindedly to check off each item on the list as you complete it.

Do not wait too long to publish

One of the most common mistakes that scientists make is to wait too long to publish. It is unwise to set your standards too high in terms of what constitutes sufficient content for a paper. It could take you three years to get a project and its paper to even 95% of the quality you wish it to be.  Then it might take three more years to reach 98% of your ideal. You need to know when to publish and move on. Your mentors can help with this.

If you hold onto a paper for too long, you deprive yourself of a publication to add to your list, and you deprive your field of knowledge that could help it progress. At the same time, you should not publish too soon. A very brief paper can be unsatisfying to the reader unless it tells a complete story. A set of results that is barely enough to publish and falls short of a full “story” is negatively perceived as a “least publishable unit.” Brief papers can be effective vehicles for advancing knowledge, but they should be used in exceptional cases and not as a general rule.

In summary, there is a stage at which a project has revealed enough information. At this point, you should write a paper that is “good enough” and submit it for publication. Look for that narrow window between too soon and too late to publish. Try to publish successful papers, but do not hold out for perfection. In that rare instance when you obtain a result that is so exciting and solid that you want to publish it in one of the highest profile journals, you can hold the paper to a higher standard to increase your chance of a receiving a favorable decision from the editors.

Documentation

Good science requires complete documentation. In the world of science as we know it today, you need to keep careful records of your work because it is an integral part of the scientific process, but also to protect yourself in case any questions arise about your research. You should keep a thorough log of your work, either on paper or in computerized form. If you use the computer to analyze your data, keep careful records of intermediate results and meticulously document your computer code. If you record what you did in your research, when you did it, and how you did it, you will be able to answer anyone who asks to check what you did, or questions your results after they are published. In your notebook, you should fully document the results from each day’s experiment, as well as the summaries of the results derived from repetitions of each experiment. Of course, your publications do not disclose all the details that are present in your laboratory notebooks.

In the future, I believe it is likely that the funding agencies will require you to put your data on-line and make the data available for other scientists to view (and possibly use) once your paper is published. I also predict that some journals will require you to make your original data accessible on-line as a condition of publication, much as scientists are now required to deposit gene sequences into a public data bank. When scientists have widespread access to original data, we and the public will be able to better judge the quality of the data, and the validity of the “knowledge” contained in our published papers.

Chapter 5: Journal choice

The correct journal for your paper is the one that publishes related and similar papers, where your paper will come to the attention of scientists who want to read it, and where your paper has a good chance of being published. Your goal is to find a good match between your paper and the journal. To make the right choice, examine the different journals, understand their style and requirements, and ask yourself some hard questions about your paper.

Differences among journals

There are hundreds of journals for each subfield of science. Each has its own personality and specific readership. Your job as author is to select the journal that is suitable for your paper. There are two reasons why you should submit your paper to the right journal. First, if your paper is a good fit for the journal, the process of submission, review, and revision is smoother and more efficient. Second, if your paper appears in the right journal, then you maximize the number of interested scientists who see, read, and cite your paper.

There is a hierarchy, or “food chain” of journals, a different hierarchy for every field. In neuroscience, the most prestigious journals are Nature and Science, both of which draw a large readership from all areas of science. These two elite journals are followed, arguably, by Neuron, Nature Neuroscience, and the Proceedings of the (U.S.) National Academy of Sciences. Below these journals lie a number of journals that publish excellent papers of general interest to many sub-fields of neuroscience but lack the high status of the top journals: these include Neuroscience, the Journal of Neuroscience, the European Journal of Neuroscience, and many others. Finally, there are the specialist journals. Some specialize in papers about a particular anatomical structure, such as Cerebral Cortex, Hippocampus, and Cerebellum. Others publish papers about a single system, such as the Journal of Motor Behavior, Vision Research, or Vestibular Research, or about a research technique, such as Neural Computation, the Journal of Neurophysiology,or the Journal of Computational Neuroscience.

Journals are ranked implicitly according to their “impact factor,” defined as the average number of citations received by papers published in the prior two years.  The general interest journals reach the top of the hierarchy because they have the highest impact factors, while the specialist journals tend to have lower impact factors. I find impact factor to be a flawed criterion for ranking journals or papers. But we are stuck with it, at least for now.

Differences among papers

Before you select a journal for your paper, you need to ask some questions about your paper’s features and structure.

- Does your paper present an exciting new story of general interest that can be described in four figures and 4,000 words?

- Is your paper a detailed analysis of a complex subject that is of interest to a limited number of specialists and requires ten or more figures and 12,000 words?

These two types of papers represent opposite ends of the continuum and their correct audiences are found in the readership of different journals.

Your paper can be extremely successful even if it does not appear in a high-profile journal that garners many citations for its papers. I have published a few papers in journals that are read by researchers in many subfields of neuroscience. However, most of my papers are long and detailed and therefore unsuitable for the highest-profile, general-interest journals. For this reason most of my papers are published in specialist journals that are read by the people in my field, and not by people outside my specific area of research. Nonetheless, many of the papers I have published in specialist journals have been highly successful.

What journal is right for your paper?

You have a much greater likelihood of having your paper published if you choose the right journal. Several criteria need to be considered before you choose your target journal. These are:

- The degree of match between the readership of the journal and the readers who might be interested in your paper

- The length, number of figures, and amount of detail in your paper

- How much your paper advances the concepts in your field of research

First, look for a match between your paper and the readership of a journal. Because it is critical for your paper to come to the attention of the scientists who want to read it, select a journal in which similar work is published. If, for example, your paper is about the mechanisms of cancer in brain cells, submit it to a cancer journal that is read by people who are interested in brain cancer rather than to a general neuroscience journal. If you submit your paper to a journal that receives many papers on your topic, you can expect the review process to be smooth and insightful. Reviewers can be found quickly, and the editors and reviewers are sufficiently knowledgeable to make a fair decision.

You can see whether a particular journal is a good fit for your paper if you visit the on-line website of the journal and look at the Table of Contents of recent issues. Check whether there are papers on topics related to yours. Readers are more likely to read and cite your paper if it is surrounded by other papers on related topics. Remember that part of what defines a successful paper is the number of readers and citations it receives.

Second, consider the specific requirements for publishing in a particular journal. Plenty of information from the publishers is available on the internet, and every journal provides detailed Instructions for Authors on its website. Examine the journal’s requirements and limitations for the length of text, the number of figures, and for color figures. Note also the journal’s conditions for allowing free and open access to your publication, and the cost (if any) of publishing in that journal.

Third, honestly and critically evaluate the importance of the contribution your paper makes to the field. In my experience, almost all scientists overestimate the significance of their research and try to publish their papers in journals that are too high in the publication food chain. Try to be critical and reasonable in judging your work. A clear-eyed assessment will save you time in the publication process, and will add to the level of respect you command among your peers. Be sure that you are realistic and not simply optimistic.

Keep in mind that it may not make sense to compress your ten-figure paper into one with four figures for the sole purpose of submitting it to a high-profile, general-interest journal such as Nature or Science. By condensing your paper, you could remove important details that were needed to allow the reader to fully appreciate your research. Once in a while, however, you could have results that you think deserve a broader audience, and that fit neatly into the shorter format of a high-profile journal. Discuss the research with your mentors and colleagues, and ask them if they also think that your research should be published in a top journal. If they agree with you, then you definitely should try for it.

Should you aim high and hope to get lucky?

Why not simply aim to publish in the top journal of your field and work your way down the food chain until your paper is accepted? In my field, this strategy means that you compress your story into a paper with four figures and a couple of thousand words, and submit it to Nature or Science.

The strategy of blindly aiming for the top journal wastes your time. Because simultaneous submissions to multiple journals is not allowed, you need to go through the entire submission and review process with one journal before you submit your paper to another journal. It usually takes one to two months for your paper to be reviewed at one journal. If it is rejected, then you need to rewrite your paper according to the requirements of another journal. Beyond simple formatting issues, some journals require more details on your research than others. The months you spend submitting your paper to journals that are clearly too high on the food chain consume valuable time that you could use to perform new research or to prepare other work for publication.

The strategy of blindly aiming for the top journal also wastes the time and efforts of reviewers and editors. As a field, we already spend an inordinate amount of time evaluating our colleagues’ work. If you submit your paper in sequence to two journals that are too ambitious before you send it to the right journal, then your paper receives at least six reviews—two from each journal. The first four of these reviews are a waste of the reviewers’ time.

The strategy of blindly aiming for the top journal could undermine your credibility. It is remarkable how frequently the editors end up choosing the same reviewers when you submit your paper to a succession of journals. If you submit your paper to several journals before finding a place to publish it, the reviewers who encounter your paper multiple times will recognize your tactic. They may resent your disregard of their time and think less favorably of you and your paper. In contrast, if you submit your paper from the start to the most suitable journal for your research, even the most expert and knowledgeable reviewers are inclined to respect your judgment. It will help your career if you make thoughtful choices about the target journals for your papers, and it could hinder your career if you always aim too high.

Resist the pressures to aim too high

Not everyone agrees with my strategy of how to choose the right journal for your paper. I am aware that increasingly, our scientific culture evaluates researchers on the basis of where they publish, rather than what they publish. There is pressure to publish in the journals with the highest impact factor. Many institutions rank a scientist’s research according to the impact factors of the journals in which his/her work is published. According to this formula, a successful scientist is someone who publishes many papers in journals with a high impact factor. I disagree with this practice. I believe that a paper is successful if it contributes to knowledge in its field. A successful paper is cited by other scientists. It is cited even when it appears in a lower-impact journal where the other papers in it are not frequently cited. Finally, it is important to remember that the number of citations a paper receives is not the only measure of its influence. Even though I have included citations as one criterion for a successful paper, a paper can be influential, and therefore successful, even if it is not cited often. In my own list of publications, some of my best and most influential papers are cited infrequently.

It could take a long time to change the practice of judging scientists by the quantity of papers they publish in journals with high impact factors. In the meantime, I hope you will try to be part of the solution: evaluate other scientists by the content of their papers, not simply by the prestige of the journals in which their papers are published.

Chapter 6: Get started on your paper

It is an imposing task to write a scientific paper, especially your first one. It is easy to stand on the brink of starting for a long time and not write a word. It feels a little like standing on the shore with cold ocean-water lapping at your feet while you figure out how to take the plunge and begin swimming. Different people have different strategies for writing a paper. I will outline mine.

The parts that make up your paper

- The Title Page states the title of the paper, and the names of the authors with their affiliations and contact information. Frequently, keywords and acknowledgements appear beneath the authors’ names. Acknowledgments recognize the people and funding agencies that helped accomplish the research. A short version of the title runs along the tops of all pages of the paper.

- The short Abstract summarizes the content of the paper.

- The Introduction is the first section of the main body of the paper, and presents the context or background for the research.

- The Methods section describes how the research was performed. It contains enough information about how the experiments were done to allow interested researchers to repeat the research. In many journals the Methods section is the second section in the main text of the paper, but in some journals the Methods appears at the end of the paper, or even as supplementary material that is not part of the main paper.

- The Results section describes the findings of the research.

- The Discussion gives an interpretation of the new findings and places the work in the context of the research and conclusions of other scientists who asked the same or related questions.

- Graphical material, such as Figures and Tables, can be inserted into any part of the paper, but are most commonly found in the Results section. Figures frequently are composed of multiple graphs.

- Legends appear alongside each figure and table.

- References to publications cited in the paper are included in the list of References, which follows the main body of text.

Draw your figures first

When I write a paper, I usually start by making figures. The graphics are the heart of most scientific papers and create the structure of the paper. To make my writing time the most efficient, I first produce figures that are nearly perfect and complete. This does not mean that the figures are in final form; what it means is that they look professional and contain the information I need to plan and write the paper. I use the sequence of figures to help me develop the key points in my paper. As my paper takes shape, figures are often added, modified, or deleted. If I find that my order of figures does not follow the direction of my logic, I shuffle the figures. In high school, our teachers taught us to make an outline of a paper before you write it. Your figures can serve as your outline.

I expect my lab members to show me excellent drafts of their figures as a first step in writing their paper. I can imagine their final paper from a set of well-prepared figures. The figures help me identify areas in the prospective paper where the data are not as strong as they could be, or where the presentation is illogical, or the logic is flawed. From seeing a draft of the figures I can suggest the additional figures, experiments, or data analyses that are needed to complete the paper.

Number and order of figures

What is the right number of figures for your paper? The figures should tell a logical and complete story. They need to be complete but concise. Most scientific papers have at least one figure and few papers have more than ten. Still, the number of figures is dictated by the message of the paper. You could have a result that is expressed better with equations rather than figures, or a finding that requires fifteen figures to convey. You are the best judge of how many figures you need. Neither too many, nor too few.

Make your figures, look at them, and ask yourself some questions.

- Do your figures contain so much information that their components could be difficult to see when they are published in a paper? If so, break up your figures into smaller pieces.

- If a figure has more than one panel, are the panels related?  I am in favor of figures that include multiple, related graphs and pictures. However, I also like to keep each figure simple enough so that it is visually pleasing and easy to understand. I advocate that you present only one result in each figure.

- Can you explain your results using only the figures? You should be able to. If you use a lot of text to describe the results contained in a figure, you may need to add more content to the figure.

- Do you have little or nothing to say about one of the figures? If so, the figure is probably dispensable, and you can describe the result in a few words of text. For example, the following figure can, and should be replaced with the simple sentences: “For stimuli A and B, the mean and standard deviations of the response were 14.5+2.5 and 8.5+1.5. The difference in the means was statistically significant (p=0.02).”

What is the right order for your figures? Almost all scientific papers have one or two main ideas or results that provide the most important and novel advances, plus several related control experiments or more minor points. Once you make your figures, examine whether the main point of your paper is shown clearly and efficiently in one or several figures. Be sure that the most important result in your study appears early in the paper.

When I read a draft of a paper written by my colleagues or students, the most frequent mistake I see is in the ordering of the figures and results. Your reader does not want to plod through your methods, controls, and minor results before finally coming to the most important point of the paper.

Your reader also does not want to read through material that repeats prior experiments before getting to the new material. Instead of starting your paper with a figure that sets the context by showing a repetition of a prior experiment, summarize the work that preceded yours in a few sentences. It is better to place the most important and newest material from your current research at the start of your paper. Your paper should showcase your latest research and results.

It may seem sensible to present your results from the bottom up, by starting with the foundations, verifying that the methods work, and describing controls. It is logical to build up to the final and most important element, the main result. But think about your readers. You want to capture their attention and show them what is important early in the paper. If you do not, your readers could lose interest before they get to the important figures at the end of the paper. Often when I start to write, it seems impossible to organize the paper in a way that brings the important results to the front of the paper. But it is possible. Look critically at the order of your figures. Find a way to present the most important findings early in the Results section; it will create a more interesting and more successful paper.

Order of writing

Once I have a good set of figures, I begin to write the paper. In chronological order, I write the Methods, Results, Discussion, Introduction, and Abstract.

- I start with Methods because this section is a straightforward report on how I did the research and is easy to write.

- I then turn to the Results section and write about the figures I already made.

- Next, I write the Discussion. The first draft of my Discussion is an important test of my thoughts and conclusions. I always think that I have well-formed ideas about my conclusions before I start to write, but the act of writing challenges the strength of my ideas. The actual words in the first draft of my Discussion can reveal instances of fuzzy thinking or leaps in logic.

- After I finish the Discussion and am satisfied with its content, I write the Introduction, which sets the stage for the entire paper and anticipates its conclusions.

- I write the Abstract last, to make sure that it summarizes the paper accurately.

As you write your paper, think about your reader. Your goal is to maximize the number of scientists who read your paper in hopes that they will incorporate your ideas into their own work and cite your paper. Write with your audience in mind. Make your paper coherent and logical, but also as succinct as you can. Write a text that is long and detailed enough to be clear, but short enough to spare the reader unnecessary details. Keep your Discussion section from being overly long, and come to directly to your main point.

We live in a café culture. Your reader should be able to digest your paper in an hour over a cup of coffee.  Write your paper so this is possible.

Chapter 7. Graphics and tables

I follow three rules when I make figures for my papers:

“A picture is worth a thousand words.”

“Variety is the spice of life.”

“Neatness counts.”

A picture is worth a thousand words

Use your figures to illustrate your story. When I view the figures and figure legends of a paper in my research area, I understand the results without reading the main text. Figures should be self-explanatory. A colleague in your lab should be able to comprehend your results simply by studying the figures.

Variety is the spice of life

There are many different ways to present the same data. Mix it up. Because everyone’s data are different it is impossible to give an exhaustive set of examples. Again, here are just a few rules:

Create figures that look different from one another. If you present four consecutive figures that look very similar but have different data, you could dull your readers’ minds so that they do not discriminate between the figures. Insofar as it is possible, consecutive figures should be distinct from each other. Use scatter plots, bar graphs, histograms, color and grayscale images, and continuous data traces to present data in a variety of ways.

Look for ways to graph your data to emphasize similarities and differences across experiments. For example, supposed you ran 40 experiments and in each experiment you measured response amplitude right after you delivered a drug and 10 minutes later. You could present that data in a scatter plot where each point shows data for a different experiments and plots the response amplitude right after you delivered the drug versus the response amplitude 10 minutes later.  If you also want to show the shape of the distribution of the responses, you can use “marginal” histograms that run parallel to the two axes of the scatter plot, as I have done in a figure that appears later in this chapter.

If you made your measurements at different times or after delivering different doses of a substance, then plot the results as a function of time or dose instead of presenting separate plots for each time point or dose. For example, the figure below shows two different ways or presenting the same data.  The histograms in panels A and B show distributions of response amplitude at two different doses.  The graph in panel C contains the same data plus more by plotting the mean and standard deviation of response size for the two doses illustrated in the distributions, plus more.

Neatness counts

Remember that you are writing a paper for a professional scientific journal. Make the figures look polished; they should be impeccably neat, tasteful, and readable. Create them with a computer program that is designed to make figures. Unfortunately, it is easy to find poorly made figures in the published literature – just leaf through any journal in your field. To avoid their shortcomings, here is a set of positive guidelines you can follow to create aesthetically pleasing, professional quality figures.

- Compose your figures. Think about how the different panels fit together; do not just throw them together. Both content and appearance are important.

- Create your figures so that each presents one result clearly. If a figure presents two distinct results, separate it into two figures.

- Create each figure in the size you wish it to be published in the journal. This approach allows you to manipulate the size of the fonts and the panels in the figure. Print your figures to see what they will look like in the journal and decide if you want to change them.

- Throughout your paper, use the same font size, and the same line weights for each type of attribute in your figures. For example, all the axes in your graphs should have the same line thickness in every figure of the paper. You can use a different line thickness for the lines or arrows inside the graphs. Remember that you can control the font size and line weights in the final publication, but to do so you will need to make your figures in the size you wish it to be published in the journal.

- When a figure contains multiple graphs, align the edges of the all the graphs.

- Use only necessary text in each figure, and make the text understandable to your reader. Minimize the use of titles in your figures, and avoid using abbreviations in the axis labels. Place statistical data and values of “n” in the figure legend rather than on the graphs.

- Include a short and clear “key” so the reader can interpret your figure without referring to the longer Figure Legend.

- Center your axis labels on the middle of the axis.

- Make the ticks on your axes long enough to be visible, and align your tick labels on the ticks.

- Align all your text horizontally and vertically, both within each graph and across the multiple panels of your figure.

- Use color only when it enhances the presentation. Try to distinguish between the symbols, lines, and other features of your figures without using color. In many cases you can differentiate the features of your figures with different line weights, line types, symbol shape, and gray scale.

- In a micrograph or photograph of an original image, indicate size with a calibration bar. Do not use a magnification scale.

- Make sure your images are in focus and of sufficient contrast so that your readers can easily see the features you report. I frequently encounter the criticism that a claim made in the paper is not easily discernible in the photomicrographs, or worse, that the image contradicts the statement.

In the figure above, the three graphs (panels A-C) present identical results in three different styles for comparison. Note the key features:

- Tick marks are evenly spaced and their labels are centered on the ticks (A-C).

- Different symbols (A, B) are at least as distinct as different colors (C).

- Key to symbols is present in each panel.

- To save space, axis labels appear only as needed. For example, the y-axis label in panel A is not repeated in panels B and C. It is not necessary to include the x-axis label on A and C, but is allowable.

- Compare the error bars in panels A (uncrossing) and B (crossing). The vertical error bars that project either upwards or downward in panel A provide a nice clean look that is easy to read, unlike the overlapping error bars in panel B. In A, some points do not have error bars because they would overlap with the error bars from other points.  This is allowed.

Key features of the above figure:

- Tick marks on axes are evenly spaced and neatly labeled.

- To save space, the x-axes of the two histograms are not labeled since they are identical to the corresponding axes on the scatter plot.

- The y-axes of the scatter plot and the upper histogram are aligned, as are the labels “Measure #2” and “Percent.”

- The two histograms give a summary of the distributions of “Measure #1” and “Measure #2” and make the figure more interesting.

Key features of the above figure:

- Panel A illustrates several ways to show the deviation about a continuous mean, or other measure. Starting from the top, the three techniques are: a gray “ribbon” around the mean; vertical bars above and below each point; and two fine lines above and below the mean.

- Panel B illustrates several ways to summarize the variation about a mean, or other measure. Starting from the left, the three techniques are: error bars above and below the mean; inclusion of all data points; a “box” plot with a symbol for the mean, error bars for the range, and a box to indicate plus and minus one quartile.

- To save space, the y-axis is not labeled in panel B because it is identical to the y-axis in panel A.

- One label is sufficient for the two identical x-axes, and it is centered between the “0” on the x-axis of panel A and the “100” on the x-axis of panel B.

Key features of the above figure (reproduced with permission from Li and Lisberger, Neuron 69: 159-169, 2011):

- Each panel presents data using a different format, making for a varied and interesting figure.

- Color is only used in panel B to render the diagonal stripe more vividly than is possible in black-and-white.

- In both columns of the figure, the vertical axes and labels are aligned.

- The top and bottom, and the left and right boundaries of the graphs are aligned even though the different panels are of different sizes and shapes. The result is a figure that is balanced and neat.

- The key in panel D explains the meaning of the symbols.

- Panel E does not require a key because the two curves are clearly labeled.

- Another alternative is to present panels A-C in one figure, and panels D-E in a second figure.

Chapter 8: Methods

The Methods section should contain enough detail so that someone who is working in your field can reproduce your experiments and analyses. Methods is a dry and formulaic part of the paper, and there is no reason to try to make it more exciting. Describe in succinct language how you did your research. For procedures that are well documented in the literature, you can limit yourself to a brief statement of what you did with references to prior papers that contain more detailed descriptions.

Getting started

I usually start my Methods section with a brief summary paragraph that describes the subjects or the material used for the research, and states in a general way what we measured. My goal is to give my readers an idea of what we did and how we did it. The summary paragraph is a good place to state that you have received institutional approvals for your research; journals require that you put this statement in the Methods section. If your research involves animal or human subjects, you should state that your research followed procedures that were approved in advance by the overseeing review panel. Needless to say, your statements must be true. Below are some examples of how these statements are written.

To quote from one of my papers on research that used animal subjects:

“All procedures had been approved by UCSF's Institutional Animal Care and Use Committee and were in compliance with National Institutes of Health's Guide for the Care and Use of Laboratory Animals.” (from J. Neurophysiol. 102: 2013-2025, 2009).

To quote from one of my papers on research that used human subjects:

“The Committee on Human Research, which is the Institutional Review Board for UCSF and its affiliates, approved all experimental procedures in advance, and the subjects gave their informed consent.” (from J. Neurosci. 26: 12479-12486, 2006)

As I discuss in the Chapter 3 on Ethics, the publishers of scientific journals usually do not question the ethics of how you did your research. They are satisfied with your statement that you have followed the accepted ethical procedures. If a reviewer or editor doubts that you abided by the correct protocols, the editors may ask you to provide a copy of the documents that show you were permitted to perform the procedures described in your paper. Be prepared to provide these documents if requested.

One or two times in my career as an editor, I have rejected a paper without review solely because the methods strayed so far from acceptable ethical standards that I was not prepared to publish the paper under any circumstances. But this is a very rare occurrence.

Body of the Methods

I try to divide the Methods into logical chunks or subsections. Below are descriptions of what you can include in the different subsections, in order from the beginning to the end of the Methods.

- In the first part of Methods, give details of the experimental preparation or the substrate for the experiment. If the experiment was performed on cell lines or on tissue taken from an animal, describe how you obtained the tissue. If the research was performed on intact animals or on humans, outline the experimental protocol and/or the behavioral task the subjects were trained to perform.

- Provide details on how you conducted your experiments, outlining the experimental design and how you made your measurements.

- Describe how you controlled the independent variables in your experiments.

- Detail how you acquired and documented your data.

- Present the details of your data analysis and statistical methods.

Before you start to write the full Methods section, you can create an outline by choosing section headings for each of the chunks you think you will write, and then placing them in a logical order.

The best way to learn how to organize your Methods is to study papers from another good laboratory in your field or from your own laboratory. Just remember that you cannot plagiarize content from another paper, even from your own. You must use original words. When you write your Methods be careful not to repeat information that is already published, such as descriptions of standard experimental procedures. You can refer the reader to these details by citing the correct source in the literature.

Scientists tend to write their papers in the passive voice. I do not favor the use of passive language, as in: “Data were analyzed using procedures described in Smith et al., (1999).” It is better to write: “We analyzed the data using procedures described in Smith et al., (1999).” Use the active voice. Do not be afraid to sound less formal and to take responsibility for what you did. Your writing is more direct and alive if your voice is active.

Illustrations in the Methods section?

If your experimental approach is novel and/or complex, you may include a figure to help describe your methods. For example, you can use a figure to illustrate a new behavioral task. Or, if your experiments involve a complex sequence of treatments on cells or tissue extracted from an animal or human, it may be helpful to the reader if you provide a schematic figure that outlines the experimental protocol.  A schematic figure may be especially valuable if you are describing the protocol for the first time, or using known methods in a novel way.

Papers on methods

If the purpose of your paper is to present a new method, you must describe the procedures in great detail. Most scientific journals are more interested in the advances you made with your new method than in the method itself. If you have novel results to report along with your new method, you can report the method and findings together in the same paper, and submit it to a journal that accepts long papers with detailed Methods sections. I favor publishing the new method along with a scientific advance in a single paper. This approach brings your paper to the attention of more scientists. Because the paper includes a scientific advance, you are likely to receive more recognition.

If your paper is solely about a new method, submit it to a journal that specializes in papers about new methods, or to a journal with a special section for novel methods. To learn whether your methods paper is suitable for a particular journal, visit the journal’s website and read its Instructions for Authors.

Methods versus results?

Sometimes, you may be uncertain whether a particular method should be presented in the Methods section or in the Results. My general rule is that you describe a method only once in a paper, usually in the Methods section. But if you feel strongly that the reader needs to know the details of an experimental or analysis method while s/he is examining the data in Results, describe the method in the Results alongside the data. Be cautioned, however, to avoid cluttering the presentation of your data with details on how you did the research. You want the Results section to read like a story. Your presentation could be unwieldy and difficult to follow if you include methods in the Results section when they belong in the Methods.

Some journals put detailed descriptions of methods at the end of the paper, following the Discussion, or even in Supplementary Material that is posted only on the internet. In either case, you could write something in the Results section about how you did the research. However, be brief, and tell only the bare minimum the reader needs to know so that s/he can understand your techniques and experiments. Reserve your detailed methods for the location the journal designates in (or outside) the paper.

Chapter 9: Results

The Results section tells a story about your figures. By the time your reader reaches the end of your Results, s/he should know what you did, what you found, what control experiments you included, and what analyses you performed to support your claims.

Figure 9-1. Effect of stimulus strength and duration on the amplitude of EEG responses. Filled and open symbols show the data for weak and strong stimuli. Each set of connected points summarizes the results of 17 experiments; error bars show the standard deviation of the response amplitude across experiments. Dashed lines show linear regression fits to the two sets of data points.

How to write Results

Consider the data illustrated in Figure 9-1 (above). There are wrong and right ways to write about them (note that the different text styles used below is for the purpose of illustrating different features of correct and incorrect writing):

A right way:

“The amplitude of the EEG responses increased as a function of stimulus duration for both strong and weak stimuli (Figure 9-1). Stimulus duration had a much larger effect for strong stimuli (open symbols) than for weak stimuli (filled symbols). Each symbol shows the average response amplitude across 17 experiments, so that the relatively small error bars, which report standard deviations, indicate that the response amplitudes were genuinely different for the two stimuli. We confirmed the different magnitude effects for the two stimuli by regression analysis, which revealed regression lines (dashed lines) with slopes of 0.05 and 0.45 mV/second for the two stimuli. Note that we calculated the response amplitude in Figure 9-1 by averaging across the entire stimulus duration, so that the analysis interval differed for different stimulus durations. We obtained nearly identical response amplitudes when we used the same 100 ms analysis interval for all stimulus durations.”

What is right about the above paragraph?

1)

The first two sentences (in bold font) state the most important effects.

2)

In the next two sentences (in italics), we refer to the error bars to discuss the statistical differences between strong and weak stimuli, and we describe how we did the analysis.

3)

The paragraph ends with two sentences (underlined) to describe an analysis that is an important experimental control but an inconsequential result. Because it is of low significance as an experimental result, the analysis takes the position of lowest priority within the paragraph.

Note that in example of a “right way,” I present a story about Figure 9-1. I refer to the important features of the figure, the open and filled symbols and the dashed lines, in parentheses.

A wrong way:

“Each symbol in Figure 9-1 plots the average EEG amplitude as a function of the stimulus duration. The error bars show standard deviations calculated across 17 experiments.  Response measures were based on averages of the response across the entire stimulus duration and therefore the analysis interval differed for different stimulus durations. We obtained the same results and nearly identical response amplitudes when we used the same 100 ms analysis interval for all stimulus durations. Comparison of the open and filled symbols shows that the two stimuli had different effects on response amplitude. For both, increases in stimulus duration caused increases in response amplitude. At each stimulus duration except 100 ms, the mean response amplitudes were statistically different (P<0.05).  We conclude that strong and weak stimuli have very different effects on EEG activity, an effect that we understand in terms of non-linearities in the sources of the EEG potentials.”

What is wrong with the above paragraph?

1)

The first two sentences (in bold font) belong in a figure legend, not in the first sentence of Results.

2)

The third and fourth sentences (in italics) report an important, but small, result that should follow, not precede, a description of the main effects shown in Figure 9-1.

3)

The fifth and sixth sentences (underlined) report the most important effects discussed in the paragraph and should appear at the top of the paragraph.

4)

It is better to perform statistics on the regression lines than on the individual points (sentence in bold italics).

5)

The final sentence (underlined italics) interprets the results and belongs in the Discussion, not the Results section.

Compare the contents of the “right” and “wrong” paragraphs with the figure legend for Figure 9-1. The right way to write the Results section complements the information provided in the figure legend. The figure legend contains point-by-point descriptions of components of the figure and the paragraph tells the story created by your experiments and data.

Note that the figure legend does not give a description of the data. For example, it does not state that the response increases as a function of the duration of the stimulus, or that there was a difference between the results for strong and weak stimuli. The material written in the Results and the figure legend provide fundamentally different perspectives to your reader. Do not write your Results section as a set of figure legends, or the figure legends as Results.

Choice of content

How much detail about your original data should you include in your paper? The answer to this question is a compromise between various competing forces. The desire to provide the most complete documentation of your results pushes you towards including more data and more figures. The wish to keep your paper readable and within the length limit of your target journal, pushes you towards a more concise presentation.

Every paper is different, and different fields have different standards. All good scientific papers, however, meet an important criterion: the data presented in the figures, tables, and Results section provide sufficient evidence for the authors’ conclusions. A successful paper contains clear, representative examples of the raw data, and quantitative (when possible) analyses that demonstrate the repeatability of the findings. Both the raw data and the quantitative summaries support and illustrate legitimately the main trends reported in the paper.

To avoid the criticisms I often see from reviewers about the standard of evidence presented in a paper, try to observe the following:

- Your figures present raw data that are clear enough, and with resolution good enough, for the reader to see the main effects. When you submit your paper through an on-line application, you should verify that there is adequate resolution in the PDF of your figures (see Chapter 18).

- The quantitative analysis you present in your paper is sufficient to convince the reader that your observations are reliable and reproducible.

- All examples of raw data illustrate the results of your quantitative analysis and the conclusions of your paper.

Your goal in the Results is to illustrate and summarize your data using the correct quantitative measures. To make your main point you should analyze your data thoroughly, but it usually is not necessary to show that several types of analysis produce the same result. One class of errors is to report on an excessive number of data analyses that all lead to the same conclusion. To avoid this mistake, assess whether your figures and tables contain too much data, or whether you have too many figures, and edit if needed.

You also need to decide how much to say about control experiments. For some controls, you can state in a single sentence that they were successful. For others, the details could be important enough to show your readers. Imagine what you would like to see if you were the reader. Would you be satisfied with a simple declaration that the control worked? Or would you like a full documentation because the control is critical to the conclusions of the paper?

Supplementary material

With the shift from paper journals to on-line publication, journals have begun to use their websites as a place to post “supplementary material.” Many papers now provide additional figures and text that are not included in the main paper, but that are available on the internet for readers to download and view. Supplementary figures and text can provide content that some readers may wish to see, such as analyses of secondary importance, or controls.  Supplementary material also can include audio clips and videos that cannot be included in the PDF of the main paper.

In my field, some journals no longer post supplementary material, or post only file formats that cannot be included in a PDF. The reasons for this trend are complicated and will not be discussed here. I predict that we will see a continuing movement away from supplementary material posted on the journals’ websites, or at least restrictions on what is allowed.

I would rather not read or write “on-line supplementary material.” My reluctance to read it stems from my perception that the supplementary material frequently is not prepared as carefully and professionally as the main paper, nor is it reviewed as rigorously as the main paper. I prefer not to write supplementary material because I think that the published paper should give a full account of the research, and should cover all the important material. Although many people (and journals) disagree with me, in my opinion the “supplementary material” should be omitted if it is not essential to the presentation, or should be included in the main paper if it is essential.

Keep in mind that your paper is not supposed to include all of your data, although in rare cases this is necessary. If it is important to make your raw data available to the reader, I encourage you to post the data on your personal website. Scientists who work with technologies such as gene sequencing and functional imaging sometimes are required to deposit their original data into on-line data banks. I think this practice will expand to other fields, especially as governmental agencies increasingly allow the public free access to the scientific knowledge acquired though their funding.

Order of presentation

Present your most important, interesting, and novel finding early in the paper. Follow it with information that bolsters your story, presents controls, and reveals secondary features of your experimental findings. I elaborate below.

Frequently in scientific research, a story evolves from the results of a logical sequence of experiments, with each finding arising from the preceding one. Sometimes the first findings are the most important, but often the initial findings turn out (by design or by accident) to be the foundation or controls for a future finding. It is more common for the final experiments, or the last set of data analyses, to deliver the most significant and novel observations. Given the typical course of research, it is tempting to present your data in the order you obtained them. The logic behind a chronological presentation is that it allows the reader to experience the same build-up of ideas as the authors.

In the development of your project, you may have performed a long series of experiments to learn the strengths and weaknesses of your experimental system. It is not a good idea to present the results of your early investigations on the validity of your methods before you report your novel results. You could lose impatient readers if your most important data appear near the end of your paper. If you can put your main experimental finding in the front of the paper, you should do so. Supporting material, such as controls, can appear later in the paper.

The most common error I see in the papers of my colleagues is that the main finding appears too late in the Results section. A consequence of this error is that the paper is likely to be criticized unfairly by reviewers for lacking findings that are sufficiently novel. Reviewers generally assume that you put your most important results in the first, rather than the last half of the Results. You can avoid misleading your readers if you document your most important findings in the front of the Results.

Consistency

As you write the Results, make sure that your presentation is consistent across your entire paper. The specific examples you give of your data should agree in detail with the quantitative summaries of them. If repetitions of the same experiment or measurement produce wide variations in the results, you should address the possible, or known causes of the variation. You also should be attentive to logical inconsistencies, such as when the results of two related experiments disagree. Reviewers and readers are alert to inconsistencies in your data and in your paper. The presence of inconsistencies of any kind undermines the reviewer’s confidence in the quality of your research, and can result in major criticisms of your paper.

Passive versus active voice

I prefer to write scientific papers in the active voice because I think it leads to a crisper and more engaging style. In the example earlier in this chapter of the “right way” to write a paragraph of the Results, I use the active voice:

“Stimulus duration had a much larger effect for strong stimuli (open symbols) than for weak stimuli (filled symbols).”

It is equally accurate and correct, but less compelling, to write in the passive voice:

“The effect of stimulus duration was larger for strong stimulus (open symbols) than for weak stimuli (filled symbols).”

Although the choice of active or passive voice is a matter of style and both are correct, your writing is more engaging when you use the active voice.

Introduction or Discussion in the Results?

How much material that is typically part of the Introduction or Discussion can you include in your Results section? Only a little, and only in rare cases. Editors, reviewers, and readers rightly expect the content in a section of a paper to be consistent with its heading. However, there are times when your readers can benefit from a broader explanation of your data in the Results. In these exceptional cases, you can include a small amount of material that is usually associated with the Introduction or Discussion into the Results section of your paper.

- Introductory statements in the Results allow you to explain your reasons for presenting a particular set of data, or to establish a context for understanding the data. Your statements, however, should be brief and infrequent. Limit your introductory remarks to a single sentence or at most two, and do not include similar statements in every paragraph or even in every section. The inclusion of introductory statements in the Results section is the exception rather than the rule.

- You also can include a single, brief concluding sentence in the Results that discusses or interprets a set of complex data. The purpose of the sentence is to illuminate a concept or idea that is important for the reader to grasp before s/he proceeds to the next section of Results. Do not insert a concluding sentence if you sense that the text would be just as effective in the Discussion.

The emphasis here is on necessity. Be sure that any sort of introduction or discussion in the Results is absolutely necessary for the clarity of your paper. Furthermore, do not insert broader statements in the Results to bypass the journal’s word limits for the Introduction and Discussion sections. The journal’s goal is to produce a paper that is short enough to be readable and structured in a way that is clear. Work with the journal, not against it.

Methods in the Results?

When, and to what extent should you include the details of your experimental methods in your Results section? The standard answer is that methods should appear in the Methods section, but there are two exceptions to this rule.

- You could encounter a situation when you feel that that it is essential to describe particulars of your experimental design or analysis to your reader at the time you present your data. When this occurs, you can include the details of your method in the relevant section of the Results. But be sure that you report your methods in detail only once in your paper. If you describe a procedure in the Results, do not do so again in the Methods.

- Some journals do not have a Methods section in their papers and put descriptions of methods into the supplementary material. For these journals, you can describe your methods in just enough detail in the Results section for your reader to understand your experimental design and measurements. You are expected to present the full description of your methods in the Methods section, which is part of the paper’s supplementary material.

Again, the emphasis here is on necessity.  Details of your methods may appear in the Results section only to the extent that they must be in that location for the reader to understand your data.

A final check

When your Results section is complete, I suggest that you perform the following exercise. Copy and paste the first sentence of each paragraph into a single “summary” document. You, or better yet a colleague should grasp the main message of your paper by reading the summary document. The order of the topic sentences should make sense. The Results section should start with the most important findings and present all your results in a logical order.

If your summary document is a coherent synopsis of your findings, then you know that the sequence of your topic sentences produces a well-ordered and effective Results section. You can be confident that your readers will navigate easily through your paper and grasp its main points. Conversely, if your summary document fails to tell the story of your findings, then you should rework the structure, the order, and/or the content of your paragraphs.

Chapter 10: Discussion

Think of your Discussion as an essay about your science. It is the place where you say what you think your findings mean.

There are usually four elements to a Discussion. They are:

1)

An introductory statement that gives a brief summary of the key findings in your paper.

2)

An evaluation of possible artifacts and/or ambiguities in your data.

3)

A comment on the consistencies and/or inconsistencies between the main findings of your paper and the results of previous research.

4)

An explanation of what your results mean and what you conclude from your findings. You also can present the broader implications of your results and conclusions.

The Discussion is not the place for an extensive review of the literature, or a rehash of your results, or an occasion for wild speculation. Review previous work only if the review is required to understand your research. Do not introduce new data or draw conclusions that go beyond your results. You could arouse suspicion if you cite “unpublished” or “preliminary” results to support your conclusions. You can pose some questions for future research, but you should end your Discussion with your conclusions, not with a paragraph that outlines your next research project. You are writing a paper, not a grant application.

If there is controversy in the field, or if there are inconsistencies within your data, or if your results disagree with the results of others, discuss the differences and resolve them if you can. If you steer away from controversy and disagreement, you risk criticism from reviewers who are aware of the discrepancies. Instead of sweeping inconsistencies under the rug, embrace them. Discrepancies between your work and others could be due to differences in experimental design or other factors that you can explore. Inconsistencies within your data could drive you to modify your initial reasoning and might lead you to a new conclusion that explains your full set of data.

Make your Discussion interesting and keep it a readable length. Journals vary in the word limits they set for their Discussion section, but 1,500 words is a reasonable goal for a full-length paper. If you feel the need to write a much longer Discussion, consider writing a review paper as an adjunct to your research paper. Reviews follow different “rules” from the research papers described here.

After you write a draft of your Discussion, ask yourself whether the material you presented in your Results supports the conclusions you draw in the Discussion. Reviewers often criticize a paper for presenting “conclusions not supported by the data.” It is a major flaw to make claims that are not justified by your results, and is grounds for an outright rejection of your paper.

If you approach your Discussion with a sense of self-criticism, it will help you assess the true importance of your research. Does your work move the field forward and fill an important gap in knowledge?  Or is your work “incremental,” in that it tells us only a little more about something we already know? If it is difficult to find something to say in your Discussion beyond repeating your experimental findings, perhaps you should do more experiments to address additional problems or goals. If your finding supports only a weak and uninteresting Discussion, you could have problems getting your paper published. At the very least, you will need to lower your expectations when choosing the right journal for your paper.

If English is not your native language, then you may find it difficult to express your thoughts fluently, even when your ideas are valid, important, and well-formed in your mind. If you have a hard time writing your Discussion in English, write it first in your native language. Look at what you wrote, and ask whether you expressed your ideas more clearly than you could in English. If you did, then translate the Discussion from your mother tongue to English. The new Discussion should be an improvement over your first effort.

Another avenue to a successful Discussion section is to talk about your research to a colleague. The act of speaking about it, in English or in your native tongue, can free up your thinking. While your thoughts are still fresh, create an outline that you can expand to write the full Discussion.

Chapter 11: Introduction

After you write your Discussion, you know how your paper concludes. You can now step back to the Introduction, and explain the concepts the reader needs to grasp so that s/he can understand and appreciate your work. Like the Discussion, the Introduction should be brief.  It is neither a detailed literature review nor a complete summary of your results.

Organize your Introduction into three or four short paragraphs:

- The first paragraph introduces the problem. What does your research set out to learn?  How do the goals of your research relate to the bigger questions of the field?

- The second and third paragraphs provide essential details about the specific system and problems under study. These two paragraphs cite key references and inform the reader about the current state of knowledge. They do not contain a detailed review of the literature in your field.

- The fourth (and shortest) paragraph says what you did, what you found, and presents your main conclusion. Even though you give a summary of your findings and your conclusion, this last paragraph should no duplicate or replace the Abstract.

The Introduction helps the reader appreciate the significance of your paper by educating the reader about the issues you cover in the paper and explaining their importance to the field. If your conclusions or your approach deviate from established views or paradigms, use the Introduction to prepare the reader for your new ideas. If there are one or two key concepts in your paper, mention them in the Introduction.

Be short and succinct in your Introduction. Because so much is known about any topic, it is not possible to write an Introduction that is both compact and complete. Do not describe the entire background for your research. I think 500-600 words are sufficient for this section. Some journals allow more words, in which case you could use them to cover more background. But if your Introduction contains a lot more than 500 words, consider how much is necessary. In our world of tweets and SMS text messages, we expect concise communication. Most of your readers do not have the patience to read an excessively long paper.

Chapter 12: References

You have to make some difficult choices about what papers to cite. First, consult the journal’s Instructions for Authors for guidelines or restrictions on the number of references you are allowed. It is then helpful to look through an issue of the journal you have targeted for your paper and examine the number of references in typical papers.

Here are some of the questions you need to consider, and my answers to them.

- Should you cite original research papers or review articles?  Cite the original literature whenever possible. The importance of a scientific paper is often judged by the number of times the paper is cited by subsequent researchers. We should give credit to the originators of knowledge if possible, rather than to the authors of review articles that cite the original works.

- Should you cite the paper that was first to report a phenomenon, the most compelling report, the most recent one, or all of these? Cite the first paper that authoritatively demonstrates the phenomenon of interest. The scientists who discovered the phenomenon should receive credit. This is preferable to choosing arbitrarily from a list of relevant, but more recent papers. In cases where there are, for example, ten papers that could be cited, include the most relevant two or three.

- How many times should you cite yourself? Avoid too much self-citation. Only rarely will you be the main person who works in the area your paper explores. Usually there are other researchers who you can and should cite. Also, avoid disproportionately citing your friends, and/or colleagues at your own institution. Even if you wish to bring attention to relevant papers written by friends or colleagues, do not do so to the exclusion of equally deserving papers by others.

- How many papers should you cite? Between forty and eighty citations is a reasonable number for a full-length paper in a journal that has no restrictions on the number of citations. The number can be fewer if the topic of the paper is very narrow. If you have more than eighty citations, ask yourself whether you are including too many.

If you have, say, over one hundred references, reexamine your Introduction and Discussion to see whether you unintentionally wrote a literature review, or compiled too many facts from past studies. If your paper examines an entire area of research and extensively cites prior work, you should consider writing a review article. It is common for a review article to have hundreds of references.

Use the Information for Authors to format your references in the style dictated by the journal you choose for your paper. If you submit your references in the correct format, you avoid having to make editorial changes in the revision, or even later, in the copy-editing stage.

Chapter 13: Figure legends

A figure legend helps the reader grasp quickly the meaning of each of the various elements in the figure. A figure legend does not describe the findings. You should restrict the data in the legend to just a few numerical details, such as the values of the means and standard errors of a few measurements, the values of regression parameters, or the number of repetitions of the experiments.

Figure 13-1. Effect of stimulus strength and duration on the amplitude of EEG responses. Each set of connected points summarizes the results of 17 experiments. Filled and open symbols show the data for weak and strong stimuli. Error bars show the standard deviation of the response amplitude across experiments. Dashed lines show linear regression fits to the two sets of data points.

When I write figure legends, I have all my figures in front of me. I then proceed using the following formula for each figure in the order shown, and I recommend that you do so also.

- Start by writing a single sentence that serves as the title of the figure. The title states what the data illustrate; it does not describe the conclusions from the data. Consider, for example, Figure 13-1. A good title for the figure legend is: “Effect of stimulus strength and duration on the amplitude of EEG responses.” A poor title is: “Stimulus duration controls the amplitude of EEG responses.” The second title is a poor choice because it draws a conclusion between cause and effect, an interpretive statement that does not belong in a figure legend.

- Examine the figure systematically and write a sentence about each element, such as the symbols, lines, colors, and so forth. Start with the more general features of the figure and get more and more specific. For example, the legend to Figure 13-1 states the meaning of each point first, next indicates the significance of filled versus open symbols, and then defines the error bars. The meaning of the dashed lines appears last.

As a second illustration of how to write figure legends, below is a figure from one of my papers.

Figure 13-2. The effect of complex spike probability in learning trials on learned changes in simple spike activity in probe trials.  Each point plots the results of one learning experiment on one Purkinje cell and shows averages across all the trials in the learning block. Filled and open symbols indicate data from group 1 (n=11) and group 2 (n=6) Purkinje cells; blue and red symbols indicate learning in the on-direction and off-direction of the Purkinje cell under study. Filled, black squares connected by lines indicate the mean values in bins along the x-axis; error bars shown standard deviations of the measurements along the y-axis. (Figure and slightly revised legend reproduced after prior publication in Nature Neuroscience 11: 1185-1192, 2008)

The figure legend contains:

- A title sentence.

- A statement of what the points in the graph indicate.

- Statements of what the different symbol shapes and colors indicate.

There is a difference in the style of writing between the figure legend and the Results. Below is the part of the Results that corresponds to what is shown in Figure 13-2. Direct references to the figure are enclosed in parentheses.

“Across Purkinje cells, the probability of a complex spike during learning was a good predictor of the size and direction of the learned change in simple spike firing in each individual Purkinje cell (Fig. 13-2). For learning in the off-direction, group 1 Purkinje cells had a high probability of emitting a complex spike in the learning trials and showed large learned decreases in simple spike firing in probe trials (filled red circles); group 2 Purkinje cells were less likely to emit a complex spike during learning and showed learned increases, rather than decreases, in simple spike firing (open red circles).  For learning in the on-direction, neither group of Purkinje cells emitted very many complex spikes in the learning trials and both showed learned increases in simple spike firing during the probe trials (open and filled blue circles). Averaging the response measures in bins (black symbols) indicates that the probability of a complex spike had to at least triple from baseline to be consistently associated with a learned decrease in simple spike response.”  (modified slightly from Nat. Neurosci. 11: 1185-1192, 2008)

Notice that the figure legend states what the symbols and lines indicate, whereas the paragraph from the Results tells a story about the data in the figure.

I repeat the same exercise below on another of my figures:

Figure 13-3. Comparison of trial-by-trial variation in smooth pursuit eye movements and the vestibulo-ocular reflex. A: Mean and variance of eye velocity for pursuit of target motion at 20 deg/s as a function of the time from the onset of the response. B: Mean and variance of eye velocity for the vestibulo-ocular reflex evoked by head motion to the left at 20 deg/s. Black curves show the mean eye velocity and the gray shaded areas indicate the trial-by-trial variance of eye velocity. (Figure and legend reproduced with permission from Neuron 66: 477-491, 2010)

Note that the figure legend contains:

- A title sentence.

- A statement of what each panel shows.

- Statements of what the curves and shaded areas indicate.

Again, compare the figure legend above with the corresponding text in the Results section:

“Because neural responses are quite variable, there is a risk that motor behavior also could be quite variable. In pursuit, this is true. The mean eye velocity of smooth pursuit (Figure 13-3A, black curve) increases as a function of time and has an impressive trial-by-trial variance (gray ribbon). In contrast, the eye velocity of the vestibulo-ocular reflex (VOR) is about 7 times more precise for a similar mean eye velocity trajectory (Figure 13-3B). Because pursuit and the VOR use the same brainstem interneurons and extraocular motoneurons, the variation in the initiation of pursuit cannot be attributed to noise added by the final motor pathways.” (Modified from text in Neuron 66: 477-491, 2010).

One approach is to study the way I write my figure legends, and follow the same guidelines to write yours. You also can learn from looking at the figure legends in papers written by other members of your lab, or by other labs that do similar research.

Chapter 14: Abstract

The Abstract is an art form. Special care is needed to accurately represent the content of your paper with the small number of words the journal allows.

The Abstract is a very important part of your paper and can affect the outcome of the review process in several ways:

- Journal editors use the Abstract to decide whether or not to send your paper out for peer review.

- Journal editors use the Abstract to select the editor who chooses reviewers for your paper.

- Potential reviewers use the Abstract to decide whether or not they should agree to review your paper.

- After it is published, potential readers use the Abstract to decide whether or not your paper is worth reading.

- Since many people do not take the time to read an entire paper, it is likely that some scientists cite a paper after reading only the abstract. I do not endorse this practice, but it happens.

Your abstract is the primary advertisement for your paper.  Take the time and effort to make it really good.

Before you write your abstract, choose a target journal for your paper. Read several of the abstracts published in your target journal, especially abstracts of papers on topics similar to yours. Ask yourself which abstracts are more or less successful, and model your abstract on the successful ones. Remember to consult the journal’s “Instructions for Authors” to find out how many words you are allowed. With the movement to electronic submissions, journals can and do enforce the restrictions they place on length. Word limits on abstracts can be as short as 100 words, or as long as 250 or 300 words.

The contents of an abstract vary by journal. Some journals prefer a short abstract that summarizes a paper in a few sentences. Other journals prefer a longer account of the main results and conclusions.

For a short abstract, be informative but succinct. Use the following structure:

- One or two sentences to describe the gap in knowledge that your research fills.

- One or two sentences to state your main findings.

- One sentence to present your main conclusion.

Below is a fictional example of an effective, short abstract that contains only eighty words:

“Multiple genes are involved in the rare familial ataxia, SCA747, but their distribution in the central nervous system is not known. We surveyed the genome of affected patients, identified the 25 genes with the highest likelihood of mutation and developed probes for their gene products. In post-mortem material from affected patients, the gene products are absent from Purkinje cells in four specific lobules of the vermis of the cerebellum. Our findings localize the cerebellar regions where malfunction leads to ataxia.”

A longer abstract for the same paper is more like an outline or a Table of Contents. It has the following structure:

- The first sentence describes the gap in knowledge that the research fills.

- There is one sentence for each of the five major findings in the Results section of the paper.

- The final sentence presents the main conclusion.

Below is an example of a longer abstract that uses 185 words to give an outline of the paper:

“The rare familial ataxia SCA747 involves many genes, but we do not know their anatomical pattern of expression in the central nervous system or how that expression changes in affected patients. We have identified 25 genes that have a high likelihood of mutation in SCA747 by genotyping of the affected patients. Probes then were created for the products of the 25 genes and we used in-situ hybridization to localize gene products in post-mortem tissue from affected patients and non-symptomatic, age matched controls. Different genes had subtly different expression patterns in non-symptomatic controls. In general most gene products were found in Purkinje neurons throughout the cerebellum, and with some gene products restricted to a subset of lobules. Different genes showed different patterns of expression. In affected patients, the products of all 25 genes were absent in lobules IV, V, VI, and VII of the cerebellar vermis.  The loss of gene products selectively in certain lobules of the vermis points to those lobules as essential for preventing ataxia, and focuses attention on them for further analysis of the neural circuit basis of ataxic symptoms in cerebellar disease.”

The middle sections (in italics) of the two examples demonstrate the main difference between the two styles of abstracts. The shorter abstract uses one or two sentences to summarize only the main results of the paper. The longer abstract summarizes every major finding, using one sentence for every result.

No matter how hard you try, the first draft of your abstract will be too long. The first drafts of my abstracts are frequently 100-200 words longer than the journal allows. But this is fine. The act of choosing which words, phrases, and sentences to remove is an important part of the process of perfecting the abstract. Refine the abstract to say everything you want to say within the word limit.

You can use the following strategy when you write your abstract. Begin by writing the abstract the way you wish and let your word processing program count your words. If as expected, the abstract is too long, ask yourself how you can shorten it. Can you omit whole sentences or phrases? Can your sentences be more succinct? You can always make your piece shorter. A good science writer can summarize your entire paper in one or two sentences. With effort you can write an abstract that conveys the message of your paper within the allowed word limit.

Finally, I mention two forms of digital abstracts that have come into use with the predominance of on-line publishing.

- Some journals require a “structured digital abstract” that organizes the content of your paper to allow digital searches to be more productive. More journals will add this requirement in the future. If your journal uses structured digital abstracts, then you could be asked to fill out a text box for each part of your paper: purpose, methodological approach, main results, and conclusions. If you provide a structured digital abstract, it is worthwhile to write it with care. An effective digital abstract helps potential readers find your paper.

- Some journals offer the authors the opportunity to provide a graphical abstract that appears in the Table of Contents of the on-line journal. The graphical abstract should be simple and direct, consisting perhaps of a single simplified data figure that shows your main result, or of a schematic diagram that summarizes your conclusion. A good graphical abstract can be excellent advertising for your paper. How your graphical abstract looks, rather than the details it contains, may be the most important factor in determining the graphical abstract’s success.

Chapter 15: Title page

The title page contains essential information about your paper: the title, authors, affiliations, and keywords. It takes some thought to get these correct.

Title

The title describes the content of your paper and should be brief but informative. It should also be professional and specific, but not too specific. Your title is an advertisement that draws readers to your paper. You should have confidence that your title will be accurate and true in twenty years, and it will be if it describes the work you did rather than your interpretations or conclusions.

An example of a good succinct title is:

Relationship between gene expression in the hippocampus

and memory of a spatial task in mice (15 words)

A more provocative, but interpretive title is risky unless the contents of the paper establish a firm and undeniable relationship of cause-and-effect. An example is:

Gene expression caused by acquisition of a spatial memory (9 words)

You should avoid needlessly long titles such as:

Quantitative analysis of the gene expression in the hippocampus in mice

trained to perform a task involving spatial learning and memory (21 words)

The above title can be shortened successfully to:

Gene expression in the hippocampus of mice trained to perform

spatial learning and memory (13 words)

Authors

Authorship is an ethical issue that is treated in detail in  Chapter 3. Your list of authors must include all the authors in the correct order, even in the first submission of your paper. You displease journal editors if you add to, subtract from, or reorder the list of your authors’ names in your revisions. You can avoid making such changes if all your authors read and approve the manuscript that is to be submitted for publication. In addition, the professional affiliations of the authors should be accurate and complete, because this information is used to determine potential conflicts of interest when the editors select reviewers for your paper.

Acknowledgments

Different journals have different stipulations about where to put the Acknowledgements in the paper; sometimes they appear at the end, sometimes on the cover page. The Acknowledgments is the place to recognize people and institutions that aided your research. You should acknowledge the following: people who gave technical support; participants in discussions you found especially helpful; colleagues who read drafts of your manuscript; providers of resources such as computer code, antibodies, chemicals, or specially-prepared animals; and the sources of funding for your research. You should be thorough in giving credit where it is due, but do not go overboard.  The Acknowledgements of a scientific paper is not the place, for example, to thank your family for their support. It is where you recognize the contributions of people who did not qualify for authorship (see Chapter 3).

Keywords

Give more than cursory attention to the keywords you put on your title page. The journal uses your title and keywords to index your paper, and digital search engines also employ them. Given how important search engines have become in our quest for information, choose keywords that make it easy for potential readers to find your paper. Keywords should be different from the words in your title, since the title will be used automatically for indexing and searches.

Chapter 16: Writing in English

Your paper needs to be understandable. The English does not have to be perfect, but it should at least be very good. You do not want your paper returned by reviewers with the comment that: “the English writing is so poor that I cannot evaluate the scientific content of the manuscript.” On the other hand, I have never seen an editor reject a paper written in competent English, solely because the language is not perfect. Indeed, it is rare for even native speakers to write in perfect English.

If your paper is written in clear and coherent language, it will receive fair and thoughtful reviews even if the grammar or usage is flawed. If the written English is competent, then most reviewers judge your paper on the basis of the science.

I have encountered two types of problems in communication that arise when non-native speakers write scientific papers in English:

The more serious problem occurs when the logical structure of the paragraphs and sentences suffers because of the writer’s poor command of written English. If your thoughts are poorly expressed, then your paper can appear scientifically weak even when the research is strong and your ideas are good. You can rectify this problem by seeking help from someone who can both understand the science and help with the writing. Someone who knows about the science can help you express your thoughts and ideas about your research. A scientist, not a professional editor, is most qualified to help you with this problem.

The more frequent, but less serious problem concerns English grammar and usage. If the science in your paper makes sense to the reader but the writing is poor, then a professional scientific writer or editor can help you improve the paper.

Place your science in the best possible light by making your paper clear and readable. Invest in your paper. You already have put considerable time, effort, and grant money into doing the experiments and preparing your data for publication. It is worth paying a professional to make the English in your paper excellent, even if slightly imperfect.

Chapter 17: Cover letter

The cover letter allows you to speak directly and confidentially to the editor. But depending on the paper or journal, a cover letter is not always required when you submit your manuscript. If you are confident that the journal will send your paper out for review, and there are no potential controversies or conflicts of interest, your abstract alone gives the editor sufficient information about your paper

For some journals, the contents of the cover letter can determine whether your paper is reviewed or returned without review. Even though the editors read your abstract, the cover letter is another opportunity to convince them that your paper belongs in their journal. In two or three brief paragraphs, you can outline what is significant about your paper, provide more background than you can fit into the abstract, and state how much your paper advances the field.

You can also use a cover letter to alert the editors to the biases they could encounter with your paper. For example, you can forewarn them about controversies in your area of research so that your paper is sent to impartial reviewers. You can inform the editors about the disagreements you have with your competitors, or name one or more competitors who could be prejudiced against your paper. If you believe your paper was reviewed unfairly in the past, either at the current journal or at another one, you can explain the situation to the editors.

Do not dash off a cover letter at the last instant. Write it carefully and keep it short, informative, and unemotional.

Here is a fictional example of a cover letter. It includes:

An introductory statement

A description of the research reported in the paper

A statement of how the paper moves the field forward

An explanation of the controversies that could taint the review process.

Dear Dr. <name of editor>:

My colleagues and I would like to submit the enclosed paper to be considered for publication in the Journal of Truly Exceptional Science. The paper is entitled: “Neural sites of spatial learning”.

In our paper, we have trained mice to find their way around a complex maze that contains many obstacles and a large number of orienting landmarks. As they learned the maze, we recorded the activity of up to 100 neurons at a time in the CA3 and CA1 regions of the hippocampus. We also used a fluorescent indicator that emits light when a synapse undergoes long-term potentiation so that we could visualize cellular plasticity during behavioral learning. We found that plasticity occurs in the CA3 region early in learning, and in the CA1 region later in learning, while the neural responses change in each region throughout the learning process.

The field has understood for some time that the hippocampus is a locus of spatial learning and that long-term potentiation (LTP) was a likely cellular mechanism of plasticity that would support spatial learning. The contribution of our paper is to actually measure cellular plasticity directly during learning, and to be able to relate that cellular plasticity to changes in the electrical activity of neurons. The ability to measure cellular plasticity in vivo, the finding that LTP occurs in a temporal sequence in CA3 and CA1, and the disconnection between LTP and changes in neural responses provide a completely new kind of observation that will reshape how we think about the complex process of behavioral learning.  We think these advances are quite novel, and that they merit publication in a high-profile journal such as yours.

There are a couple of controversies in the field that may come up in the reviews of our paper. Some groups think that tasks such as ours are too complex for constraining a mechanism of learning. We disagree, and have provided some control experiments to defend our position.  We also are aware of some skepticism about our ability to measure LTP definitively. In prior papers that are cited in the present paper, we have provided controls that defend the validity and veracity of our technology.  We hope you will take these issues into consideration in evaluating the reviews of our paper.

Thank you in advance.

Yours sincerely,

Jane Scientist

Chapter 18: Submission

The majority of journals accept submissions only in electronic form through a specialized web interface. The interface allows the journal staff, editors, and reviewers to communicate electronically with each other and with the authors to process papers. Most submission websites require authors to provide information about the paper and the authors, and to upload original files for the main text of the paper and the figures. The websites guide you through the submission process, which is simple and self-explanatory.

Using the on-line submission website

Before you submit your paper to a journal, visit its “Instructions for Authors.”  Journals vary in their requirements for submission. For example, some journals require a cover letter that contains specific disclosures and statements on ethical issues. Other journals require particular documents or text in addition to the manuscript. Have everything ready before you log on to the submission website of the journal you choose.

Most journals expect you to upload several files when you submit a paper: one file for the main text, one for each figure, and possibly a cover letter. Once you upload all the files and complete the on-line forms, the submission system creates a PDF file for you to review. Examine the PDF file for your paper carefully to make sure that everything is correct. The editors and reviewers use this PDF file in the review process. You should be particularly attentive to equations and figures, as the programs that create the PDF sometimes introduce errors into the PDF for files made on certain computers.

The PDF should represent your paper accurately to the editors and reviewers, but this PDF is not used to create the published version. Most journals produce the published paper from the original files you submit with your final revisions. There is no need to worry about inconsequential errors in the PDF, as long as the errors are not present in your original files. The “help desk” on the submission website can help you with technical problems, such as difficulties in handling a particular file. If you have a problem, someone else has probably faced the same problem before and the help desk usually knows how to fix it.

Recommending or excluding reviewers

Almost all journals have a form on their submission websites that allows you to recommend particular reviewers, and to exclude some people from serving as reviewers. Take advantage of this opportunity to voice your preferences.

There are several reasons why you should provide the names of possible reviewers:

- Editors follow your recommendations if they are good.

- Editors respect you and your paper if you recommend names of qualified scientists who are leaders in your area.

- You are more likely to receive an expert review if you recommend scientists who are knowledgeable in your field of research.

Some people will tell you that editors do not use authors’ recommendations. This is not true, as long as they are reasonable suggestions. Do not suggest collaborators, former students or postdoctoral fellows, close friends, or people who do not work in your specific field of research.

Editors also honor reasonable requests from authors not to select certain people to review their paper. You may not exclude every expert in the material your paper covers, for the editors obviously need some of these experts as reviewers. When I submit a paper, my list of scientists who should not review my paper is usually short. They are people with whom I have a direct conflict of interest, or those who I believe are prejudiced against my work.

You may try to exclude your direct competitors and other scientists with whom you have real conflicts of interest from reviewing your paper. But in the final analysis, you reduce the quality of the reviews you receive when you try to “stack” the system in your favor. If you recommend reviewers because you expect them to be supportive and exclude qualified people because you expect them to be critical, you compromise the review process.

As you think about who to recommend or exclude as reviewers for your paper, keep in mind that the author’s guesses about the identities of the reviewers often are wrong. As an editor, I frequently receive a thoughtful, helpful, and fair review from someone whose impartiality the authors questioned. I also receive unfair and very negative reviews from people the authors expected to be sympathetic to their work.

Chapter 19: The review process

When you click on the “submit” button, you set in motion a series of steps behind the scenes. The first step is the approval of your submission by the journal’s office staff. The staff looks at the mechanics of your submission, checks that you followed the Instructions for Authors, and verifies that your paper is ready to send out for review. Then, they direct your paper to the editors. The flowchart below illustrates a plausible decision tree for a typical, hypothetical journal.

Every journal has its own criteria for deciding whether to send a paper out for review.

Some journals, especially the high-profile journals, send only a small fraction of papers out for peer review.  An editor will read your paper and decide whether it seems to be of high enough priority and quality to appear in the journal. If the editor decides that your paper is not important enough for their journal, then they will return it to you without further review, usually in 10-14 days.

Most journals send 90-95% of papers out for peer review.  In most cases, the editors do not make decisions about scientific quality or about the conceptual advance in the paper. Instead, they decide whether the topic of the paper is appropriate for their journal.  If it is, they send the paper out for review.  If it is not, they reject the paper without further review.

Many journals have two levels of editors. The top-level, or “main” editor directs your submission to a second-level editor who has the scientific expertise to handle your paper; this “expert” editor is sometimes called a “Section Editor” or “Reviewing Editor.” The expert editor chooses reviewers, reads the reviews once they are complete, and recommends a decision to the top-level editor. During the electronic submission of your paper, you have the opportunity to choose, or at least recommend, the editors who handle your paper at each level. You can also state whether you have a conflict of interest with any of the editors.

When you recommend editors for your paper, follow the same guidelines you use to suggest reviewers. Suggest an editor who is knowledgeable about your area. S/he can understand the reviews of your paper, advocate for your paper with the main editor, and mediate effectively between you and the reviewers. An editor who knows about your area of research is more likely to provide your paper with helpful reviews and an appropriate decision.

When the editors send a paper out for peer review, they solicit at least two independent reviews. “Independent” means that the two reviewers are at different institutions and do not collaborate with each other.  The two reviewers are not allowed to discuss the paper or collude in any way to try to influence the editor towards a specific decision. It takes time for the editors to find people to review your paper, to receive the reviews, and to make a decision. You may wait as little as two weeks, as long as two months, or in rare cases even longer, to receive the editors’ decision.

If the first two reviews of your paper have widely different opinions and recommendations, then the editors could seek one or more additional reviews. The additional review helps you if it is favorable towards your paper, or if takes an intermediate position between the first two reviews. If the third review agrees with the more negative of the first two reviews, it favors a decision to reject your paper.

Some journals find three reviewers when they first decide to have your paper reviewed. The presence of a third expert review helps editors make better decisions and probably leads to published papers of a higher quality. But, there are major disadvantages to this approach, which prevent many journals from adopting it. It requires more of a precious resource – reviewers – and frequently means that it takes longer to reach a decision.

If, after many weeks you do not receive the reviews of your paper, you should make polite inquiries with the appropriate editor. When a journal takes a long time to process a paper, the bottleneck almost always is a tardy reviewer. Sometimes a note from the author provokes the editor to contact the overdue reviewer, who in turn could deliver the review in a day or two. When you are invited to review a manuscript, remember your own frustration at waiting for the reviews of your own papers. Complete your reviews on time.

If you are meeting a deadline for a grant or promotion, it is your responsibility to write and submit your paper to the journal with enough lead-time for it to be peer-reviewed, processed, and included in the material you submit to the granting agency or your institution. You cannot expect or request special consideration or a quicker turnaround for your paper because you have a grant or promotion deadline to meet.

Chapter 20: Your decision e-mail

When the editor sends an e-mail with his/her decision on your paper, the first paragraph informs you of the main outcome of the reviews. Read on. Crucial information can appear anywhere in the letter. Embedded in a sentence somewhere, the editor could provide information that is important in guiding your next step.

No matter what the decision letter says, do not use the reply button to respond immediately to the editor. If your paper is rejected, whatever you write is likely to be emotional, angry, and does not help your cause. Wait, sleep on it, think about it. Read and digest the decision letter and the reviews, and make a plan. One of my close friends, who is also an editor, once reacted to my hasty use of the reply button with the following advice: “Go home, have a glass of wine, and write me in the morning.” I advocate that you wait longer than overnight before you reply (see Chapter 21).

The decision you receive from the editor vary from an outright rejection without apparent recourse, to an immediate acceptance of your paper. In the next few paragraphs, I discuss the most common decisions and explain what they mean. You need to read your decision letter carefully to understand exactly what the editor is telling you.

Provisional acceptance with minor revisions requiring re-review by the editors only

This is a very favorable decision. If you discern from the wording of the letter that your paper does not require re-review, then you need to respond to what the editors consider to be a reasonable and minor set of criticisms, and your paper is very likely to be accepted. The editors will look at the revised paper to check that you have made the requested changes.

Revise and re-review

You can be pleased, but you cannot be certain of success. The reviewers are generally supportive of your paper, and the editors believe that you can successfully revise your paper to meet the reviewers’ criticisms. Most papers that are eventually accepted go through this step. Often you can determine from the letter whether the editors plan to check the revisions themselves, or return the paper to one or more of the reviewers for re-review. If your revised paper goes back to one or more of the original reviewers and you have responded to the criticisms with suitable improvements in the paper, then the reviewers will probably endorse publication.  However, the reviewers need to be satisfied with your changes. They will recommend further revisions or even rejection if they think that you have not responded adequately to what they consider to be fundamental criticisms.

As an editor, I prefer to consult only the original reviewers after a decision of revise and re-review. Authors should feel that their papers will be closer to being accepted if they respond thoroughly to the comments in the reviews. New reviewers are likely to raise new issues. Additional comments from fresh reviewers could help improve the paper, but it is unfair to the authors to make the review process a moving target. Other editors could feel differently about this issue, and there are times when we need to bring new reviewers into the process.

Rejection with an invitation to resubmit

Almost all journals have this type of “soft” rejection letter, which is clearly different from a decision to revise and re-review. In a soft rejection, the editors are not willing to publish your paper in its current form, and believe that you cannot make your manuscript acceptable through simple revisions. However, the editors acknowledge that if you make extensive changes to your paper, you could get favorable reviews in a resubmission. A soft rejection letter could say:

“We are sorry to report that we will be unable to publish your paper. The reasons for our decision appear in the comments from the reviewers, which are appended to this e-mail.  If you are able to make extensive revisions to the paper that address all the substantial concerns of the reviewers, then we would be willing to consider a resubmission of your paper.”

Editors use the soft rejection for many different reasons. Try to identify the reason that applies to your paper by reading the reviews carefully. Some reasons are:

- You need at do more experiments or add considerable data analysis.

- The editors think that the reviewers’ concerns are serious, and they doubt that revisions can resolve the issues. But they give you the benefit of the doubt, and the opportunity to overhaul your paper.

- The editors think that the reviewers’ concerns are legitimate and that you can address them. But they worry that your responses to the reviews could reveal other, perhaps bigger, problems, or confirm the weaknesses identified by the reviewers.

- The two reviewers give conflicting recommendations for your paper. The editors think your paper will fare better if you improve the manuscript before they submit it to a third, adjudicating reviewer.

- You receive a very negative set of reviews but the editors have reservations about them. The editors’ soft rejection letter does not directly admit this, but you can figure it out from the decision e-mail and the reviews.

- Most editors give a soft rejection if they have any other reasons to seek new reviewers if/when the paper is resubmitted. For example, a very negative reviewer may have indicated an unwillingness to review a revision of the paper.

Rejection without an invitation to resubmit

The editors and the reviewers are unenthusiastic about your paper. The editors, possibly by reading the paper themselves, do not think that you can make sufficient changes to the paper to change the reviewers’ negative opinions. The letter can subtly disclose the editors’ reasons for their negative decision. For example, they could think that your paper lacks enough originality or significance, and therefore fails to meet the journal’s standard for moving the field forward. Or they may be persuaded that your paper has serious scientific or technical flaws.

Everyone has papers rejected. Even Nobel laureates have papers rejected. It is part of the practice of science. I know it is hurtful and you feel angry when your paper is rejected, but try not to take it personally. Regard the rejection as one step in the process that leads you to improve your paper, and ultimately to publish it in a suitable peer-reviewed journal.

Editorial rejection

Some top journals such as Nature and Science have professional editors who screen the submissions and choose the papers they send out for review. If your paper is not selected, you receive an “editorial rejection.” In my field, most of the other journals solicit peer review for the overwhelming majority of papers they receive.

For most journals, however, a small fraction of the submissions are rejected without review. The most common reasons for an editorial rejection are that the editor believes the subject or scope of the paper is incompatible with the audience of the journal.  In some cases, the editors decide that the paper has little or no chance of receiving positive reviews.

Chapter 21: Revisions and resubmissions

In the previous chapter, I caution you to not hit the “reply” button on your e-mail program to complain to an editor immediately after you receive the decision on your paper. One of my former postdoctoral fellows said after his paper was rejected that, we should “get even, not angry.” He is right. Respond to your reviews rationally, thoughtfully, and professionally. Use the feedback you receive to do better science and to write a more successful paper.

Whether your decision e-mail rejects your paper or asks you to revise and resubmit, you need to take the following steps. I explain each of them in more detail below:

1)

Understand the main issues that concern the editors.

2)

Understand the real questions the reviewers have raised.

3)

Choose your general plan of action. Will you plan a revision, submit an appeal to the editors, or shift to another journal?

4)

Write a draft of your point-by-point response to the reviews.

5)

If necessary, perform new experiments or analyses.

6)

Revise your paper.

1) Understand the main issues that concern the editors.

Editors create decision e-mails from a small number of templates that already exist in the web applications used for processing manuscripts. The editor can choose a standard e-mail that is applicable to your paper and send it to you unmodified. Or they can customize the letter for you simply by typing into a text window. If the editor uses this easy means of customization, the letter is likely to contain information or advice that can help you take your next step.

If your paper is rejected, try to understand why. A paper can be rejected because of the reviewers’ criticisms, or because the editors thought the paper was not a good fit for their journal. Occasionally, it is rejected because the review process fails and the editors decide that the paper should be submitted to another journal. Read the decision e-mail carefully several times, and try to spot the subtle points the editors are trying to convey.

If your paper is rejected with an invitation to resubmit it after extensive revisions, try to determine what sorts of changes the editors expect. Do they require more experiments or fresh analyses? Do they request that you rewrite your paper in a style that is more like the other papers in their journal? Did you fail to convince the editors that your paper is of general interest and high priority?

If your paper is rejected after a long delay, or on the basis of a single review, or despite highly disparate reviews, perhaps the reviewers did not provide a fair assessment of your paper. If you believe that your paper was reviewed unfairly, this can affect how you proceed. Your options are to:

- Submit a revised paper to another journal.

- Appeal the rejection and ask for permission to resubmit an extensively revised paper.

As you read the editors’ letter, take advantage of whatever hints they give you. Remember that the editors are not trying to be obstructive; they are trying to help you navigate the publication process successfully. If the decision e-mail appears to be a standard letter, then the editors endorse the reviewers’ comments. In this case you need to address the reviewers’ criticisms and questions in full.

If you receive a decision asking for revision, the editors may have added personalized text to the decision letter to offer guidance on what they expect. Do they say whether they agree with the reviewers’ comments?  Do the editors tell you to add data or do additional analyses? The editors may have customized the decision letter to amplify some of the reviewers’ comments.  If the editors ask for specific changes or additions to your paper, then they expect you to comply with their requests. If the editors use a stock letter, then they endorse the reviewers’ comments fully and you need to comply.

2) Understand the real questions the reviewers have raised

You have to make some difficult choices about how to respond to the reviews. Your first step is to understand what those choices are.

Some reviews are understated and gentle, other are aggressive and demanding. Some reviewers even write in a style that is nasty and hurtful. Ignore the emotional tone of the reviews and focus on their substance. Ask yourself these questions:

- If the reviewers are critical, do they disbelieve the data, or simply require more documentation or controls?

- If the reviewers ask for additional experiments, do they make reasonable requests that would resolve important issues in the paper?

- Do the reviewers ask for new experiments that would exceed the scope of the paper by extending the results in a new and different direction?

- Can you address fully the reviewers’ concerns?

Do not underestimate the seriousness of the reviewers’ concerns. You may need to read between the lines to learn what the reviewers really want you to do with your paper. If the reviewers have serious, legitimate concerns, then you must respond to them in a substantive manner. If you believe that the reviewers’ concerns are not particularly relevant or reasonable, then you need to convince the editors of your view. Ultimately, the success of your revision or resubmission depends on how well you respond to the reviews.

3) Choose your plan of action

Your plan of action will depend on the decision you received.

Revise and resubmit

If the decision letter asks you to revise your paper and resubmit it for re-review, then your plan of action is simple. Revise your paper and resubmit it. Do as best you can what is required and recommended by the reviewers.  But do not be tempted to expand the focus of your paper unless the reviewers or the editors require you to do so.

Rejection with an invitation to resubmit

If your paper is rejected with an invitation to resubmit, assess whether you can respond successfully to the reviews. This decision is not the more lenient “revise and re-review” decision; your paper is deemed not acceptable. But because the editors think that it is possible for you to meet the criticisms, they invite you to reply to the reviewers and resubmit your paper. If you believe you can satisfy the reviewers, make the required changes and resubmit your paper to the same journal. If you doubt that you can settle the contentious issues, do not persist at the journal. Excessive optimism or enthusiasm for your paper can impede you from following a productive course of action. Be realistic, and move on to another journal. To submit your paper to another journal, rather than to persist after a rejection, benefits you and the review process in several ways:

- It saves you the time of waiting through a review process that is likely to lead to another rejection.

- It saves you the time and effort of revising your paper twice, instead of once.

- The journal that rejected your paper is not burdened by having to solicit additional reviews or reviewers for your paper when the likely outcome is another rejection.

Rejection without an invitation to resubmit

If your paper is rejected without an invitation to resubmit, your best option is to submit it to another journal. But do not just submit the original paper. Take advantage of the reviews you received to improve your paper. When you submit your paper to a second (or subsequent) journal, the same people could be asked to review it, and it is better for these reviewers to see a revised version. If you resubmit the original paper and the reviewers discover that it is identical to the one they recommended for rejection at another journal, then your paper probably will be rejected again.

People frequently inform the editors of their previous decision if they are asked to review your paper for a journal after they had rejected the paper at another journal. Such knowledge can prejudice the editors against your paper and put you in a defensive position. If you are able to respond fully to the reviews and decide to send the paper to another journal, than you can pre-empt some of the editors’ negative bias and strengthen your position by directly inform the editors of your previous submission. State in your cover letter that your paper was rejected previously, but that the reviews were helpful and that you responded substantively to many, or all of the reviewers’ concerns. I return to this issue towards the end of the chapter.

If you believe that your paper was rejected on the basis of an unfair review process or criticisms that you can address fully, then you can appeal to the editors for permission to resubmit your paper. You need to appeal only if your paper is rejected without an invitation to resubmit. If you received a rejection with an invitation to resubmit, then you already are allowed to resubmit.

Before you send an appeal for a paper that was rejected without an invitation to resubmit, think carefully about your chances of success. Do not reflexively appeal for permission to resubmit each time you have a paper rejected. At most journals, the editors take the authors’ appeal seriously, but it must be substantial, complete, and professional. I describe the appeal process at the end of this chapter.

If you are relatively inexperienced in publishing scientific papers, or in submitting to the journal you chose for your paper, solicit the advice of a more experienced colleague. Although you should not persistently contact editors for advice, you can approach them for answers to specific questions about the changes they expect to see in your resubmission.

4) Write a draft of your point-by-point response to the reviews\

When your paper receives a revise decision, or some level of rejection, you have to modify your paper. You also need to write a reply to the reviewers and/or editors that explains in detail the changes you have, and have not, made. This document, a point-by-point response to the reviews, is a potentially useful tool whenever you revise a paper. It is the roadmap that guides your revisions and any additional work you perform. Even if you plan to appeal rejection of your paper, you need to go through this step.

Before you do anything – more experiments, more analyses, revisions of your paper—write a draft of your point-by-point response to the reviews. Here is a useful procedure to follow:

- Enter copies of the two (or more) reviews into a word processor.

- Create a separate paragraph for every criticism.

- Write a brief response to each criticism. Your response should not be a simple rebuttal to the criticism, but rather, explain how you plan to modify the paper to resolve the criticism.

Drafting a point-by-point response to the reviews can help you plan your revisions. The process allows you to organize your thoughts and make a check-list for the work you need to do to improve your paper. As you write the first draft of your response to the reviews, look for themes or general concerns that appear throughout one or both reviews. You can create a separate section at the top of the draft for the themes you find. In this section, summarize the reviewers’ general concerns and state how you plan to respond to them.

When my students and I revise a paper together, I expect my students to start by writing a draft of our point-by-point response to the reviews. The resulting document is a collaboration tool that allows us to discuss the proposed responses and to make a plan for how to proceed.

For more information on how to write a response to the reviews, see Chapter 22.

5) Perform additional work

Reviewers may ask for additional analyses, or new experiments.

- If the reviewers think that the scope of your paper is too limited for the journal you have chosen, then you need to broaden the appeal of your paper by adding new experiments.

- If the reviewers think that the data analyses are incomplete or incorrect, then you need to reanalyze your data.

- If the reviewers think that control experiments are required to confirm that your results are valid, then you need to perform the experiments.

Usually, you need to perform the additional analyses and/or experiments requested by the reviewers. However, there are some situations in which you may not need to do so.

- If the reviewers suggest a data analysis that is incorrect, then you may decline to provide it. However, read between the lines of the comments.  The reviewers could still want additional analyses, and there could be a more appropriate analysis that you can provide.

- If the reviewers request a whole new line of experiments that you think is “beyond the scope of the paper”, try to persuade the editors that the additional experiments would dilute the tight focus of the paper.  Read between the lines, again.  The reviewers may have asked for additional data because they think your paper is too brief and needs to be more substantial.  Depending on the journal you have chosen, this could be a very reasonable request.

6) Revise your paper

This is the easy part. Make new figures if necessary.  Edit the paper. Make every change you propose in the draft of your point-by-point response to the reviews. I find it helpful to color the text red in the draft of my point-by-point response for all the changes I have to make. Once I respond fully to a criticism and incorporate the change into the paper, I restore the text to black. When the entire point-by-point response is in black font, I am finished.

After you respond completely to the reviews, treat the paper as you would an original submission. Read through it carefully and critically, polish the English, and confirm that the paper covers what it should without excess words. Finally, complete your point-by-point response to the reviews according to the guidelines presented in Chapter 22.

Chapter 22: Point-by-point response to reviews

The point-by-point response to the reviews is your most important correspondence in the process of publishing your paper. Whether you respond to a simple set of constructive comments, or appeal to the editors for permission to resubmit a rejected paper, this document has a significant role in determining your success.

In Chapter 21, I recommend that you write a draft of the point-by-point response as a tool to organize your thoughts, decide how to proceed, and to plan your revision. Once you complete the revision of your paper, or are ready to appeal to the editors, it is time to turn the draft of your point-by-point response into a finished document.

When you write the final version of your point-by-point response, avoid unnecessary words or emotion. Even if the reviewer of your paper is angry or harsh, keep the tone of your reply matter-of-fact and professional. Your response should also be clear and complete, but not lengthy. Neither the editors nor the reviewers wish to read a wordy ten-page, single-spaced reply to the reviews. Keep your explanations concise.

Your point-by point response to the reviews is a statement of how you changed the paper. Do not burden the editors and reviewers with information that does not appear in the paper. When the reviewers make a critical comment, they expect you to respond to it with a change in your paper, not merely in your written response to the reviews. If you choose to rebut some points of criticism, give valid reasons why you think the reviewer is wrong. But you may not dispute all, or even most of the criticisms you receive. If you do, then the reviewers and editors could think that you are unable to accept constructive feedback from your peers, and decide to reject your paper.

Examples of replies to reviews

Below are some examples of criticisms from reviewers and the authors’ responses to them. Some examples are reviews that papers from my laboratory received, and some are fictional. In some instances the authors agree with the reviewers and do as they are asked, and in others the authors disagree either partially or entirely, and decline to follow the reviewers’ requests. Although it is difficult to fully understand the comments without the papers, the examples demonstrate the style of a successful point-by-point response by the authors to the reviews.

Example #1: (Agree with reviewer and make change)

Reviewer: The paper lacks a clear hypothesis. It is not clear why the authors expect that neurons involved in motor learning would be active at a certain time.

Authors: We have rewritten the Introduction to make our hypothesis clearer.  Basically, the idea was to ask whether temporally-specific learning was related to the prior observation that different neurons seem to contribute to behavior at different times.  We agree that this issue was not adequately covered in the prior Introduction and we now have remedied that.

Example #2:  (Agree with reviewer and make change)

Reviewer: Some parts of the paper should be written more clearly. For example the last paragraph of the Intro states "We have recorded changes in the responses." it is not immediately clear that the statement refers to the current paper, rather than to the citations at the end of the sentence.

Authors: We have rewritten this sentence and looked for other places where we could improve the writing.

Example #3: (Agree and added data to comply)

Reviewer: It seems to me that two key controls are missing from Figure 4.  First, the authors need to show that the effects are specific for the locus of the injection and not for the surrounding tissue.  Second, they need to show that the inactive version of the antibodies do not have the same effects.

Authors: For the first control, we have analyzed the data from injections that missed the center of the target area and have found that the effects were quite modest.  These data have now been included in an additional panel from Figure 4.  For the second control, we wish to argue that the presence of this control in several of our prior papers is enough and that we do not need to add the control here.  We have, however, rewritten the text to point more clearly to our prior papers.

Example #4: (Agree, admit errors, and change)

Reviewer: The claim in the abstract that “the results support a role for calcium channels in short-term adaptation” seems unsubstantiated by the data in the body of the article.  Perhaps I missed this point, if so clarify which data supports this claim.

Authors: Both reviewers completely missed this part of the paper.  Clearly, we failed in the prior version of the paper to write clearly about these issues.  We have reorganized the paper completely and rewritten the paper in a way that we think makes this and other points more clearly.

Example #5: (Disagree and do not change)

Reviewer: In Figure 3, the data from the various groups was averaged and displayed (black line and error bars).  The statistical significance of the averages is never described.  For example, which points represent significant changes in the responses of the neurons?

Authors: We have decided not to comply with this request for two reasons.  First, we do not see a legal way to test for the statistical significance of responses that occur so infrequently.  Second, we view the consistency of the relationship across neurons as the strongest statistical statement about the data. We argue that the consistency of the trends is valid, independent of the statistical significance of the effects in any individual neuron.

Example #6: (Disagree but comply partially)

Reviewer: Regarding the vestibular inputs to the floccular complex, there is competing evidence that suggests different roles of different parts of the structure for different kinds of eye movements. In this view, firing rate modulation of the "floccular complex" might not be due to vestibular inputs, but rather to the visual inputs for pursuit during VOR suppression. You should clearly mention the difference of both regions with respect to the anatomy and inputs by citing the following:

Nagao, S. (1992) Different roles of flocculus and ventral paraflocculus for oculomotor control in the primate. Neuroreport 3, 13-16.

Glickstein, M., Gerrits, N., Kralj-Hans, I., Mercier, B., Stein, J. and Voogd, J. (1994) Visual pontocerebellar projections in the macaque. J Comp Neurol 349, 51-72.

Author: With all due respect to the reviewer, this issue was resolved by a prior lesion paper from my laboratory by Rambold et al., (2002). Here, we showed that VOR learning deficits and pursuit deficits scale together in proportion to the amount of the floccular complex that was removed, without regard for the exact location of the lesions. The paper by Rambold et al. put this controversy to rest and led to the use of the term “floccular complex” to describe the functionally relevant part of the structure.  Because this may still be an issue for others, I’ve added the references given by the reviewer and also added a short paragraph on this issue.

Example #7: (Disagree with concerns about priority, make changes to clarify message)

Reviewer: The main concern about this study for this journal is that the message largely reinforces that of previous publications from these authors, and there is not much dramatically new.  There are lots of good data and rigorous analyses presented here, including a number of internal consistency checks that are appealing.  That said, some of the main sections of results seem to lack a clear punch line (examples below).  At some points, the story seems to get a bit lost in the analyses, and one has to ask themselves what they have just learned.  In general, this is a very solid piece of work, but it is a judgment call as to whether there is sufficient novelty and impact here for publication.  The result in Figure 6 is the main thing that I will remember from this paper 6 months from now.

Authors: We certainly hope that in a year, readers and this reviewer will recall more the result in Figure 6.  We take full responsibility for the fact that this one point came to the front for the reviewers, while the full, integrated picture we see in the paper didn’t come through clearly.  We have reorganized the Results, removed extraneous material, rewritten key sentences of the Abstract, Introduction, and Discussion, and produced a paper that we hope is more memorable.

Seven rules to follow when writing your point-by-point response to the reviews:

1)

Be professional and polite, even if the reviewers are not.

2)

Address any broad issues at the beginning of your response.

3)

Address every point raised in the reviews.

4)

Be concise.

5)

Change your paper and state the changes you made.

6)

Take responsibility for your errors in the previous version of your paper.

7)

You can disagree, but politely, and on only a minority of the criticisms.

Chapter 23: Appeals

You should not make it standard practice to appeal a rejection. But if your paper is rejected without an invitation to resubmit and you wish to appeal the editors’ decision, there is a process you must go through that is similar to the process for revising your paper and responding to the reviews.

1)

Understand the main issues that concern the editors.

2)

Understand the real questions the reviewers have raised.

3)

Write a draft of a point-by-point response to the reviews.

4)

Use the draft point-by-point response to write a letter of appeal to the editors.

Once you understand the reasons for your paper’s rejection, you can write the editors to ask them to reconsider their decision. Explain how you would change the paper to address each criticism. You may succeed with your appeal if you have understood correctly the issues that led to the decision to reject your paper, and if you are able to address those issues thoroughly. Appeal only if you can respond to all the criticisms with substantial changes that will satisfy the reviewers and absolve the editors’ negative decision. Your appeal could succeed even if you receive two critical reviews, but your changes are better if the rejection was based on disparate reviews, one positive and one negative.

Once in a while, you could suspect that your paper was reviewed unfairly and on this basis decide to appeal the rejection. In your appeal, inform the editors about disagreements that exist between the labs in your field that could have led to a prejudiced review of your paper. You could receive permission to resubmit your paper if there is evidence of biases in the review process. Editors usually know when this occurs, and are predisposed to be sympathetic to the author’s concerns. Even so, editors allow resubmissions only if you carefully and thoroughly argue the merits of your case.

A final caution: unless you are sure that you address the true reasons for the rejection of your paper, it is a waste of time to appeal the decision or to resubmit it to the same journal. Your paper probably will not be accepted. Furthermore, if you get a reputation as an author who appeals all rejections, then your future appeals will be taken less seriously.

An example letter of appeal

Here is the skeleton of a letter that was used successfully to appeal a rejection. The editors allowed us to submit an extensively revised version of the paper.  It was reviewed, and ultimately rejected again, but for new reasons having to do with the perceived significance of the paper.  The paper ultimately was published in a journal that was one notch lower on the “food chain”.

Dear Editors:

After considerable thought and two months of additional experiments, we have decided to appeal to you for permission to resubmit an extensively modified version of our previously-rejected paper (XX-XX-nnnn-08).

As we understand the reviews, there were three major issues that led to your decision.  We can make changes in the paper, including the addition of new data, to address each of these major issues completely.

1)

Both reviewers expressed concern that we had conducted our behavioral experiments and our neural recording experiments using different stimulus forms.  This was a legitimate and particularly apt concern given that a recent paper has shown that the nature of the neural adaptation depends to a large degree on stimulus form.  We have addressed this issue fully by conducting new experiments using targets of multiple forms to probe adaptation.  We have found that the pattern of adaptation does not depend on the form of the target.  We have added these data to the paper, and we think this issue is now resolved and that the reviewers will agree.

2)

One of the reviewers disagreed with us about whether our study was enough of a conceptual advance over prior work to be published in your journal.  The reviewer’s opinion is an honest disagreement with our opinion, formed by the reviewer after reading (and thinking about) a paragraph we wrote to defend the advances in our work. But, we think it was not a fair assessment of the situation. [Here, I included a brief account of 3 papers that had gone before and argued that our paper represented a qualitative advance over each.]

I realize that this is a matter of opinion and we are prepared to write about the advances of our paper more clearly in a revision, and to address these issues in our rebuttal.

3)

The third key issue was that our analysis of the neural responses provided a qualitative but not a quantitative accounting of the effects of adaptation on motor responses. We think it is unreasonable to expect that pooling the recordings from <0.1% of the sensory neurons will mimic the actual data perfectly. We propose to take this question up explicitly in our Discussion, evaluating the reasons why pooling the adapted population response we recorded provides only a qualitative explanation for the changes in motor behavior. I think the reviewers you chose for our paper are knowledgeable and reasonable, and I am hopeful that they will agree that this is a reasonable remedy.

There are quite a few minor issues, but we would be able to address them easily in a revision. We have included a separate point-by-point response to the specific comments in the reviews, to indicate the changes we would plan to make.

Yours sincerely,

[Authors]

Five rules to follow when writing your appeal

1)

Be professional and polite, even if the reviewers were not.

2)

Identify the major reasons your paper was rejected and address them with care.

3)

Treat the minor issues very briefly. You can say that the other issues were minor and can be addressed with simple modifications of the paper. Or, you can do as I did in the example letter above and include a separate detailed response to the reviews.

4)

Explain how you plan to change the paper to address the criticisms.

5)

Be concise.

Chapter 24: Neuroscience Peer Review Consortium

In my field of neuroscience, we recently implemented an agreement among many journals that allows them to reuse the same reviewers when a paper is rejected by one journal and submitted to another. The agreement among this group of journals is called the “Neuroscience Peer Review Consortium,” or the Consortium. A list of the member journals and the rules of the Consortium are described on the website:

http://nprc.incf.org/

Here is how the Consortium works. You, as author can choose to tell a journal that the paper you are submitting was rejected by another journal in the Consortium. You identify the prior journal. Your new submission consists of your revised paper and your detailed response to the previous reviews, as if you were submitting a revision to the prior journal. The journal then requests the reviews and the names of the reviewers from the previous journal. The reviews are transmitted to the new journal without questions. But, the previous reviewers are identified if (and only if) they gave permission to release their names to other Consortium journals. At this stage, the journal that receives your new submission has several options.  It can:

- Accept your paper on the basis of your revisions.

- Ask one or both of the reviewers who read your paper at the previous Consortium journal to review your revised paper.

- Ignore what happened at the previous Consortium journal and initiate a new review process.

The Consortium has the potential to reduce the time and effort that reviewers spend on manuscripts, and to speed up the review of some papers. The Consortium also allows journal to share constructive and helpful reviewers, and promotes greater consistency in the review of papers.

The Consortium protects the wishes and rights of all parties with the following principles:

- Authors can choose whether or not to use the Consortium. You can submit your paper, revised or not, to a new journal without revealing that it was reviewed and rejected before.

- Reviewers can choose whether or not to reveal their names to other Consortium journals. However, their reviews always are sent upon request.

- Editors can choose whether or not to use the prior reviews or reviewers, and are free to initiate a fresh review process.

I am a strong advocate of the Consortium. Although it has its limits, it is successful. More than 40 journals in the field of neuroscience are members of the Consortium, with the result that some papers are processed more efficiently by journals, and with less stress for authors, reviewers, and editors. The Consortium is becoming an increasingly effective part of the review system as more authors, reviewers, and editors start to appreciate how it can help the review process.

Chapter 25: How to talk to editors

Be polite and respectful to editors, and honor their time. In many instances, an editorial position is voluntary community service. Do not treat editors as if they work for you, or owe you something. Editors cooperate with you to achieve a fair outcome for your paper if you approach them in a professional manner. Write to editors only when you are ready to provide complete information, or when you need one-time advice or help. They do not appreciate long, elaborate explanations of detailed technical or conceptual issues outside their areas of expertise. Keep your correspondence simple and direct.

Editors know how to do their jobs; you do not need to tell them. They know the identity of the reviewers and often know more about what happened with your paper than you do. If you think you can correctly guess who the reviewers are, you will almost always be wrong. Editors have a plan for your paper that they intend to execute. Your best approach is to respond productively to the criticisms you receive and work within the guidelines the editors set for you.

Perhaps the worst news you can receive from editors is that your paper is rejected. You may be emotional and upset, but try to remain calm. Do not use the “reply” or “reply-all” button on your e-mail program to respond immediately to the decision letter. Do not write a rash note to the editors claiming that the reviews are biased, wrong, or stupid. Experienced editors anticipate these e-mails and learn to ignore them. But, some editors are annoyed by impulsive, emotional reactions to their decisions and such outbursts could temper their future good will towards you.

If you write a clear, respectful, and concise letter to an editor, you should receive a timely and helpful answer. If you make an editor’s job difficult, s/he will be less inclined to be generous with his/her time in helping you.

Chapter 26: Authors’ rights

As an author, you have the right to:

- A timely decision.

- Fair and professional reviews.

- A consistent and reasonable review process.

- A hearing from the editors about resubmitting your paper and recourse if you have been treated unfairly.

A timely decision

You can expect a decision from the editors within 30-40 days of submitting your paper. This interval gives time for the editors to find suitable reviewers, and allows the reviewers two to three weeks to read the paper and write their reviews. You should not expect a decision in less than 30 days. Do not badger the editors for an earlier decision, even if you need to know the status of your paper to complete a grant review or to apply for a promotion. Instead, plan ahead and get your papers submitted with enough lead-time to have the decisions when you need them.

If your paper is in review for six weeks or longer, you can send a note of inquiry to the editor. Write in your e-mail that six weeks have lapsed since your paper was submitted, and ask whether the editor can contact the reviewers to try to accelerate the return of the reviews. At most journals, over half the papers receive a first decision within six weeks of submission, and editors like to see decisions processed in that time. You should not pester the editor with premature inquiries, but occasionally papers get lost. An e-mail to the editor can rectify the situation.

Fair, professional reviews

The reviews of your papers should be thorough, thoughtful, and respectful. They should show that the reviewer read and understood the paper, and the criticisms should be politely stated. The reviews should not reveal the antagonism of the reviewer. Even if your paper receives harsh criticisms and is rejected without an invitation to resubmit, the tone of the reviews should be professional and courteous.

If the reviews are written in an abusive or overly negative manner, you can bring this to the attention of the editors. But, however mean-spirited the reviews are, editors try not to let the inflammatory tone affect their judgment. An objectionable tone in a review is not enough reason to allow you to resubmit a flawed paper. As an editor, I usually state in the decision e-mail that our decision was not influenced by the harsh tone of the reviews. Your appeal of the editors’ decision should be based on sound scientific reasoning and the intent to address the major criticisms. But it is worthwhile to point out the negative tone of reviews.

It is unfortunate that some reviewers berate authors. Editors should send abusive or insulting reviews back to the reviewers with a polite request to eliminate the nastiness and to deliver their criticisms in a professional tone. When I make this request as an editor, most reviewers realize they have erred and are glad to rewrite their review.

A consistent and reasoned review process

The review process should be predictable and logical. Your paper should not be rejected after a revise decision if you have addressed the reviewers’ main comments. If the editors change their initial decision without consulting the reviewers, you have the right to ask the editors to consult the reviewers again and let you know their responses.

You are entitled to continuity in the review process. This means that you can expect the editors to retain the same reviewers throughout the course of reviewing your paper. It the editors decide to introduce new reviewers for any reason, as they have the right to, the editors should alert you of the change.

If the first two reviews of your paper are split between two decisions, the editors could posess enough expertise themselves to take a side. If you are unhappy with the decision after split reviews, you could offer to wait a few more weeks while the editors consult a third reviewer. The editors may not comply with your request, but it is worth asking. If the editors are not familiar with the issues covered in your paper, they should find a third reviewer and inform you of the new addition in their decision letter.

If your original submission receives two reviews with disparate opinions followed by a third that is positive, who reviews your revision? If you are invited to resubmit your paper on the basis of the third review, the editors should ask the two positive reviewers to read your revision. The editors can also obtain a re-review from the negative reviewer, but they should not base their decision solely on his/her recommendation. If the editors reject your paper without consulting the opinions of the two more supportive reviewers, you can ask that your paper be returned to the third reviewer. The editors should reassess their decision according to his/her review.

A hearing from the editors, and recourse if you have been treated unfairly

If you have a strong basis for appeal, and you argue your case well, and you are courteous and respectful, you can expect the editors to hear your appeal of their decision. You usually have only one chance to voice your disagreement with the editors, so assemble persuasive arguments and materials before you send your letter . Do not waste your time or anyone else’s if you do not have compelling grounds for appeal. You may not succeed even if your case is strong. You surely will not if it is weak.

Keep in mind that life is not always fair.  If the editors sustain a decision that you think is unjust, you have no choice but to move on and submit your paper to another journal.

Conclusion: Top ten tips to writing a successful scientific paper

1. Build a career path with the guidance of good role models and suitable mentors.

2. Ask important questions.

3. Adhere to ethical standards.

4. Provide sufficient, but not excessive documentation of your data.

5. Structure your paper properly, with an acceptable balance of figures, tables, and words.

6. Know when it is the right time to write a paper, and choose the right journal.

7. Write in English that is good enough, seeking help if necessary.

8. Respond thoroughly and constructively to reviews.

9. Know your rights as an author, and be courteous but direct with editors.

10. Know when to give up with one journal and move on to the next.

Table of Contents

Acknowledgements

Preface

Chapter 1: Features of a “successful” paper

Chapter 2: Manage your career

Chapter 3: Ethical issues in scientific research

Chapter 4: When to publish

Chapter 5: Journal choice

Chapter 6: Get started on your paper

Chapter 7: Figures and tables

Chapter 8: Methods

Chapter 9: Results

Chapter 10: Discussion

Chapter 11: Introduction

Chapter 12: References

Chapter 13: Figure legends

Chapter 14: Abstract

Chapter 15: Title page

Chapter 16: Writing in English

Chapter 17: Cover letter

Chapter 18: Submission mechanics

Chapter 19: The review process

Chapter 20: Your decision e-mail

Chapter 21: Revisions and resubmissions

Chapter 22: Point-by-point response to reviews

Chapter 23: Appeals

Chapter 24: Neuroscience Peer Review Consortium

Chapter 25: How to talk to editors

Chapter 26: Authors’ rights

Conclusion