How to Write and Publish a Scientific Paper PDF

How to Write and Publish a Scientific Paper How to Write and Publish a Scientific Paper Eighth Edition Barbara Gastel and Robert A. Day Copyright © 2016 by Barbara Gastel and Robert A. Day All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, except for the inclusion of brief quotations in a review, without prior permission in writing from the publisher. Library of Congress Cataloging-in-Publication Data Names: Day, Robert A., 1924– author. | Gastel, Barbara, author. Title: How to write and publish a scientific paper / Barbara Gastel and Robert A. Day. Description: Eighth edition. | Santa Barbara, California : Greenwood, | Authors’ names in reverse order on previous editions. | Includes bibliographical references and index. Identifiers: LCCN 2015045511| ISBN 9781440842627 (hardcover : alk. paper) | ISBN 9781440842801 (pbk.) | ISBN 9781440842634 (ebook) Subjects: LCSH: Technical writing. Classification: LCC T11.D33 2016 | DDC 808.06/65—dc23 LC record available at http://lccn.loc.gov/2015045511 ISBN: 978-1-4408-4262-7 (hardcover) ISBN: 978-1-4408-4280-1 (paperback) EISBN: 978-1-4408-4263-4 20 19 18 17 16 1 2 3 4 5 This book is also available on the World Wide Web as an eBook. Visit www.abc-clio.com for details. Greenwood An Imprint of ABC-CLIO, LLC ABC-CLIO, LLC 130 Cremona Drive, P.O. Box 1911 Santa Barbara, California 93116-1911 This book is printed on acid-free paper Manufactured in the United States of America Contents Preface xv A Word to International Readers xix Acknowledgments xxi PART I: SOME PRELIMINARIES 1 What Is Scientific Writing? 3 The Scope of Scientific Writing 3 The Need for Clarity 3 Receiving the Signals 4 Understanding the Signals 4 Understanding the Context 4 Organization and Language in Scientific Writing 5 2 Historical Perspectives 6 The Early History 6 The Electronic Era 7 The IMRAD Story 8 3 Approaching a Writing Project 11 Establishing the Mindset 11 Preparing to Write 12 v vi Contents oing the Writing 14 D Revising Your Work 16 4 What Is a Scientific Paper? 18 Definition of a Scientific Paper 18 Organization of a Scientific Paper 20 Shape of a Scientific Paper 22 Other Definitions 22 5 Ethics in Scientific Publishing 24 Ethics as a Foundation 24 Authenticity and Accuracy 24 Originality 25 Credit 26 Ethical Treatment of Humans and Animals 27 Disclosure of Conflicts of Interest 28 6 Where to Submit Your Manuscript 29 Why Decide Early, Why Decide Well 29 Prestige and Impact 31 Access 34 Avoiding Predatory Journals 34 Other Factors to Consider 35 Using Instructions to Authors 36 PART II: PREPARING THE TEXT 7 How to Prepare the Title 41 Importance of the Title 41 Length of the Title 42 Need for Specific Titles 42 Importance of Syntax 43 The Title as a Label 44 Abbreviations and Jargon 45 More About Title Format 45 8 How to List the Authors and Addresses 47 The Order of the Names 47 Definition of Authorship 49 Contents vii Defining the Order: An Example 50 Specifying Contributions 51 Proper and Consistent Form 51 Listing the Addresses 52 A Solution: ORCID 53 Purposes of the Addresses 54 9 How to Prepare the Abstract 55 Definition 55 Types of Abstracts 57 Economy of Words 59 Akin to Abstracts 60 10 How to Write the Introduction 61 Guidelines 61 Reasons for the Guidelines 62 Exceptions 63 Citations and Abbreviations 65 11 How to Write the Materials and Methods Section 66 Purpose of the Section 66 Materials 67 Methods 68 Headings 68 Measurements and Analysis 68 Need for References 69 Tables and Figures 69 Correct Form and Grammar 70 12 How to Write the Results 72 Content of the Results 72 How to Handle Numbers 73 Strive for Clarity 73 Avoid Redundancy 74 A Supplement on Supplementary Material Online 74 13 How to Write the Discussion 75 Discussion and Verbiage 75 Components of the Discussion 76 Factual Relationships 76 viii Contents Noting Strengths and Limitations 77 Significance of the Paper 78 Defining Scientific Truth 78 14 How to State the Acknowledgments 80 Ingredients of the Acknowledgments 80 Being Courteous 80 15 How to Cite the References 82 Rules to Follow 82 Electronic Aids to Citation 83 Citations in the Text 83 Reference Styles 84 Name and Year System 85 Alphabet-Number System 85 Citation Order System 86 Titles and Inclusive Pages 87 Journal Abbreviations 87 Some Trends in Reference Format 88 Examples of Different Reference Styles 88 Citing Electronic Material 89 One More Reason to Cite Carefully 89 PART III: PREPARING THE TABLES AND FIGURES 16 How to Design Effective Tables 93 When to Use Tables 93 How to Arrange Tabular Material 96 Exponents in Table Headings 99 Following the Journal’s Instructions 99 Titles, Footnotes, and Abbreviations 100 Additional Tips on Tables 100 17 How to Prepare Effective Graphs 101 When Not to Use Graphs 101 When to Use Graphs 103 How to Prepare Graphs 104 Symbols and Legends 106 A Few More Tips on Graphs 107 Contents ix 18 How to Prepare Effective Photographs 108 Photographs and Micrographs 108 Submission Formats 108 Cropping 109 Necessary Keys and Guides 109 Color 111 Line Drawings 113 PART IV: PUBLISHING THE PAPER 19 Rights and Permissions 117 What Is Copyright? 117 Copyright Considerations 118 Copyright and Electronic Publishing 119 20 How to Submit the Manuscript 121 Checking Your Manuscript 121 Submitting Your Manuscript 122 The Cover Letter 122 Sample Cover Letter 124 Electronic Cover Letters 125 Confirmation of Receipt 125 21 The Review Process (How to Deal with Editors) 126 Functions of Editors, Managing Editors, and Manuscript Editors 126 The Review Process 128 The Editor’s Decision 132 The Accept Letter 133 The Modify Letter 133 The Reject Letter 136 Editors as Gatekeepers 138 22 The Publishing Process (How to Deal with Proofs)— and After Publication 140 The Copyediting and Proofing Processes 140 Why Proofs Are Sent to Authors 141 Misspelled Words 141 Marking the Corrections 143 x Contents Additions to the Proofs 143 Addition of References 145 Proofing the Illustrations 145 When to Complain 146 Reprints 146 Publicizing and Archiving Your Paper 147 Celebrating Publication 149 PART V: D OING OTHER WRITING FOR PUBLICATION 23 How to Write a Review Paper 153 Characteristics of a Review Paper 153 Preparing an Outline 154 Types of Reviews 155 Writing for the Audience 156 Importance of Introductory Paragraphs 157 Importance of Conclusions 157 24 How to Write Opinion (Letters to the Editor, Editorials, and Book Reviews) 158 Writing Informed Opinion 158 Letters to the Editor 158 Editorials 159 Book (and Other Media) Reviews 160 25 How to Write a Book Chapter or a Book 162 How to Write a Book Chapter 162 Why (or Why Not) to Write a Book 163 How to Find a Publisher 163 How to Prepare a Book Manuscript 165 How to Participate in the Publication Process 166 How to Help Market Your Book 168 26 How to Write for the Public 170 Why Write for General Readerships? 170 Finding Publication Venues 170 Engaging the Audience 172 Conveying Content Clearly 173 Emulating the Best 174 Contents xi PART VI: CONFERENCE COMMUNICATIONS 27 How to Present a Paper Orally 177 How to Get to Present a Paper 177 A Word of Caution 178 Organization of the Paper 178 Presentation of the Paper 179 Slides 180 The Audience 181 A Few Answers on Questions 182 28 How to Prepare a Poster 183 Popularity of Posters 183 Organization 184 Preparing the Poster 185 Presenting the Poster 187 29 How to Write a Conference Report 188 Definition 188 Format 189 Presenting the New Ideas 190 Editing and Publishing 190 PART VII: SCIENTIFIC STYLE 30 Use and Misuse of English 195 Keep It Simple 195 Dangling Modifiers 196 The Ten Commandments of Good Writing 197 Metaphorically Speaking 198 Misuse of Words 198 Tense in Scientific Writing 200 Active versus Passive Voice 202 Euphemisms 202 Singulars and Plurals 203 Noun Problems 204 Numbers 205 Odds and Ends 205 xii Contents 31 Avoiding Jargon 208 Definition of Jargon 208 Mumblespeak and Other Sins 208 Mottoes to Live By 210 Bureaucratese 210 Special Cases 212 32 How and When to Use Abbreviations 214 General Principles 214 Good Practice 215 Units of Measurement 216 Special Problems 216 SI (Système International) Units 217 Other Abbreviations 217 33 Writing Clearly across Cultures and Media 218 Readable Writing 218 Consistency in Wording 220 Serving International Readers 220 A Few Words on Email Style 221 Writing for Online Reading 222 34 How to Write Science in English as a Foreign Language 223 English as the International Language of Science 223 The Essentials: Content, Organization, and Clarity 224 Cultural Differences to Consider 225 Some Common Language Challenges 226 More Strategies for English-Language Writing 227 More Resources 228 PART VIII: OTHER TOPICS IN SCIENTIFIC COMMUNICATION 35 How to Write a Thesis 231 Purpose of the Thesis 231 Tips on Writing 233 When to Write the Thesis 234 Relationship to the Outside World 235 From Thesis to Publication 236 Contents xiii 36 How to Prepare a Curriculum Vitae, Cover Letter, and Personal Statement 237 What’s a CV? What’s It Good For? 237 What to Put In (and What to Leave Out) 239 Other Suggestions 239 Preparing a Cover Letter 240 Writing a Personal Statement 241 37 How to Prepare Grant Proposals and Progress Reports 243 Preparing a Grant Proposal 243 Identifying Potential Sources of Funding 244 Preliminary Letters and Proposals 244 Common Parts of a Proposal 245 Preparing to Write the Proposal 246 Writing the Proposal 246 Common Reasons for Rejection 249 Other Problems to Watch For 249 Resubmitting a Proposal 250 Two Closing Comments 251 Writing a Progress Report 251 Basic Structure 251 Some Suggestions 252 38 How to Write a Recommendation Letter—and How to Ask for One 254 Deciding Whether to Write the Letter 254 Gathering the Information 255 Writing the Letter(s) 255 A Light Aside 256 If You’re Seeking Recommendation Letters 257 39 How to Work with the Media 258 Before the Interview 258 During the Interview 260 After the Interview 261 40 How to Provide Peer Review 263 Responding to a Request for Peer Review 263 Peer Reviewing a Scientific Paper 264 Providing Informal Peer Review 266 xiv Contents 41 How to Edit Your Own Work 269 Preparing to Edit Your Work 269 Items to Notice: 8 Cs 270 A Good Choice: Checklists 271 Finding and Working with an Author’s Editor 272 42 How to Seek a Scientific-Communication Career 276 areer Options in Scientific Communication 276 C An Admittedly Unvalidated Quiz 277 Career Preparation 278 Entering the Field and Keeping Up 279 Appendix 1: Selected Journal Title Word Abbreviations 281 Appendix 2: Words and Expressions to Avoid 285 Appendix 3: SI (Système International) Prefixes and Their Abbreviations 293 Appendix 4: Some Helpful Websites 295 Glossary 297 References 303 Index 311 Preface Criticism and testing are of the essence of our work. This means that science is a fundamentally social activity, which implies that it depends on good com- munication. In the practice of science we are aware of this, and that is why it is right for our journals to insist on clarity and intelligibility. —Hermann Bondi Good scientific writing is not a matter of life and death; it is much more seri- ous than that. The goal of scientific research is publication. Scientists, starting as graduate students or even earlier, are measured primarily not by their dexterity in labo- ratory manipulations, not by their innate knowledge of e ither broad or narrow scientific subjects, and certainly not by their wit or charm; they are measured and become known (or remain unknown) by their publications. On a practical level, a scientist typically needs publications to get a job, obtain funding to keep doing research in that job, and gain promotion. At some institutions, publica- tions are needed to obtain a doctorate. A scientific experiment, no matter how spectacular the results, is not com- pleted until the results are published. In fact, the cornerstone of the philosophy of science is based on the fundamental assumption that original research must be published; only thus can new scientific knowledge be authenticated and then added to the existing database that we call scientific knowledge. It is not necessary for the plumber to write about pipes, nor is it necessary for the lawyer to write about cases (except brief writing), but the research scien- tist, perhaps uniquely among the trades and professions, must provide a docu- ment showing what he or she did, why it was done, how it was done, and what xv xvi Preface was learned from it. The key word is reproducibility. That is what makes sci- ence and scientific writing unique. Thus, the scientist must not only “do” science but also “write” science. Bad writing can and often does prevent or delay the publication of good science. Unfortunately, the education of scientists is often so overwhelmingly com- mitted to the technical aspects of science that the communication arts are neglected or ignored. In short, many good scientists are poor writers. Certainly, many scientists do not like to write. As Charles Darwin said, “A naturalist’s life would be a happy one if he had only to observe and never to write” (quoted by Trelease, 1958). Most of today’s scientists did not have a chance to take a formal course in scientific writing. As graduate students, they learned to imitate the style and approach of their professors and previous authors. Some scientists became good writers anyway. Many, however, learned only to imitate the writing of the authors before them—with all its defects—thus establishing a system of error in perpetuity. The main purpose of this book is to help scientists and students of the sci- ences in all disciplines to prepare manuscripts that will have a high probability of being accepted for publication and of being completely understood when they are published. Because the requirements of journals vary widely from discipline to discipline, and even within the same discipline, it is not possible to offer recommendations that are universally acceptable. In this book, we present certain basic principles that are accepted in most disciplines. Let us tell you a bit about the history of this book. The development of How to Write and Publish a Scientific Paper began many years ago, when one of us (Robert A. Day) taught a graduate seminar in scientific writing at the Institute of Microbiology at Rutgers University. It quickly became clear that graduate students in the sciences both wanted and needed practical information about writing. If a lecture was about the pros and cons of split infinitives, the stu- dents became somnolent; if it addressed how to organize data into a table, they were wide awake. Therefore, a straightforward “how to” approach was used for an article (Day 1975) based on the lecture notes. The article turned out to be surprisingly popular, and that led to the first edition of this book. The first edition led naturally to the second edition and then to succeeding editions. Because this book is now being used in teaching programs in many colleges and universities, it seems especially desirable to keep it up to date. We thank those readers who kindly commented on previous editions, and we invite suggestions that may improve f uture editions. Please send suggestions and comments to Barbara Gastel at b-gastel@tamu.edu. This edition, the eighth, is the third for which Barbara Gastel joins Robert A. Day—and the first for which Gastel is first author. Gastel remains grateful to Day for asking her to collaborate. We are delighted that our previous editions Preface xvii together have been translated into at least five languages, and we hope the cur- rent edition will be widely translated too. In keeping with its title, this book has always focused primarily on writing and publishing scientific papers. It also has long provided broader advice on scientific communication. Beginning with the first edition, it has contained chapters to help readers write review papers, conference reports, and theses. Over time, chapters were added on other topics, such as how to present a paper orally and how to prepare a poster presentation. Recent editions also included chapters on approaching a writing project, preparing a grant proposal, writing about science in English as a foreign language, communicating science to the public, and providing peer review. The current edition maintains this scope but has been substantially updated and otherwise revised. The electronic world of scientific communication has continued to evolve, and we have revised this book accordingly. Thus, for example, we now discuss using ORCID identifiers, avoiding predatory journals, and giving digital poster presentations. We have added a chapter on editing one’s own work before submission, and we now include a section on publiciz- ing and archiving one’s paper a fter publication. The list of electronic resources has been expanded substantially. Cartoons have long been a popular feature of the book; we have retained favorites from previous editions and added several new cartoons by Jorge Cham (of PHD Comics), Sidney Harris, and others. This book remains a “how-to book” or “cookbook,” focusing mainly on points of practical importance. As in past editions, the book also contains some other items, such as cartoons and examples of humorous errors, intended to lighten the reading. Readers wishing to explore topics further are encouraged to con- sult works noted in the text or cited as references and to look at websites men- tioned in this book. Good scientific writing is indeed crucial. We hope this book w ill demystify writing and publishing a scientific paper and help you communicate about your work effectively, efficiently, and even enjoyably. Your success will be our great- est reward. A Word to International Readers For researchers throughout the world, communicating in English in standard Western formats has increasingly become the norm for sharing information widely. Thus, over the years How to Write and Publish a Scientific Paper has had many readers for whom English is not a native language. We hope the current edition will serve an even wider readership. Aware of the diversity of our readers, we have tried especially hard in the current edition to present the main content in language easily understood by non-native speakers of English. One issue that we faced, however, was w hether to retain the jokes that enlivened the book for many readers but sometimes confused readers from linguistic or cultural backgrounds other than our own. Because these jokes have been a distinctive feature of the book and one of its appeals, we have retained most of them in those chapters updated from early editions. However, because humor often does not translate well cross-culturally, we have limited its use in the more recently added chapters. If, as an international reader, you occasionally encounter a silly-seeming story or comment in this book, do not worry that something is wrong or that you have missed an important point. Rather, realize that you are seeing some examples of American humor. We welcome readers from throughout the world and hope they will find our book helpful in communicating science internationally. Suggestions for mak- ing the book more useful are appreciated at any time. xix Acknowledgments Over the years and over the editions, many colleagues and o thers have contrib- uted directly or indirectly to this book. Those we have worked with in scientific publishing and academia have shared information and ideas. So have fellow members of the Council of Science Editors and the Society for Scholarly Pub- lishing. Students and other users of the book have made suggestions. Many colleagues read and commented on manuscripts for early editions. Wura Aribisala, George Hale, Daniel Limonta Velázquez, Arkady Mak, Nancy Day Sakaduski, and Roberto Tuda Rivas read recent editions and offered thought- ful suggestions. Editors and production staff brought the work to publication. We thank all these people. We also thank our families for their support, encouragement, and counsel. As preparations for this edition were beginning, life was ending for Sophie B. Gastel, m other of Barbara Gastel. It is to her memory that we dedicate this edition. xxi PART I Some Preliminaries CHAPTER 1 What Is Scientific Writing? State your facts as simply as possible, even boldly. No one wants flowers of eloquence or literary ornaments in a research article. —R. B. McKerrow THE SCOPE OF SCIENTIFIC WRITING The term scientific writing commonly denotes the reporting of original research in journals, through scientific papers in standard format. In its broader sense, scientific writing also includes communication about science through other types of journal articles, such as review papers summarizing and integrating previously published research. And in a still broader sense, it includes other types of professional communication by scientists—for example, grant propos- als, oral presentations, and poster presentations. Related endeavors include writing about science for the public, sometimes called science writing. THE NEED FOR CLARITY The key characteristic of scientific writing is clarity. Successful scientific exper- imentation is the result of a clear mind attacking a clearly stated problem and producing clearly stated conclusions. Ideally, clarity should be a characteristic of any type of communication; however, when something is being said for the first time, clarity is essential. Most scientific papers, t hose published in our pri- mary research journals, are accepted for publication precisely because they do contribute new knowledge. Hence, we should demand absolute clarity in scien- tific writing. 3 4 How to Write and Publish a Scientific Paper RECEIVING THE SIGNALS Most people have no doubt heard this question: If a tree falls in the forest and there is no one t here to hear it fall, does it make a sound? The correct answer is no. Sound is more than pressure waves, and indeed there can be no sound without a hearer. And similarly, scientific communication is a two-way process. Just as a sig- nal of any kind is useless u nless it is perceived, a published scientific paper (signal) is useless unless it is both received and understood by its intended audience. Thus we can restate the axiom of science as follows: A scientific exper- iment is not complete until the results have been published and understood. Publication is no more than pressure waves unless the published paper is understood. Too many scientific papers fall silently in the woods. UNDERSTANDING THE SIGNALS Scientific writing is the transmission of a clear signal to a recipient. The words of the signal should be as clear, simple, and well-ordered as possible. In scientific writing, there is little need for ornamentation. Flowery literary embellishments—metaphors, similes, idiomatic expressions—are very likely to cause confusion and should seldom be used in research papers. Science is simply too important to be communicated in anything other than words of certain meaning. And the meaning should be clear and certain not just to peers of the author, but also to students just embarking on their careers, to scientists reading outside their own narrow disciplines, and especially to those readers (most readers today) whose native language is other than English. Many kinds of writing are designed for entertainment. Scientific writing has a different purpose: to communicate new scientific findings. Scientific writ- ing should be as clear and simple as possible. UNDERSTANDING THE CONTEXT What is clear to a recipient depends both on what is transmitted and how the recipient interprets it. Therefore, communicating clearly requires awareness of what the recipient brings. What is the recipient’s background? What is the recipient seeking? How does the recipient expect the writing to be organized? Clarity in scientific writing requires attentiveness to such questions. As communication professionals advise, know your audience. Also know the conventions, and thus the expectations, for structuring the type of writing that you are doing. What Is Scientific Writing? 5 ORGANIZATION AND LANGUAGE IN SCIENTIFIC WRITING Effective organization is a key to communicating clearly and efficiently in sci- ence. Such organization includes following the standard format for a scientific paper. It also includes organizing ideas logically within that format. In addition to organization, the second principal ingredient of a scientific paper should be appropriate language. This book keeps emphasizing proper use of English because many scientists have trouble in this area. All scien- tists must learn to use the English language with precision. A book (Day and Sakaduski 2011) wholly concerned with English for scientists is available. If scientifically determined knowledge is at least as important as any other knowledge, it must be communicated effectively, clearly, in words of certain meaning. The scientist, to succeed in this endeavor, must therefore be literate. David B. Truman, when he was dean of Columbia University, said it well: “In the complexities of contemporary existence the specialist who is trained but uneducated, technically skilled but culturally incompetent, is a menace.” Given that the ultimate result of scientific research is publication, it is sur- prising that many scientists neglect the responsibilities involved. A scientist will spend months or years of hard work to secure data, and then unconcern- edly let much of their value be lost b ecause of a lack of interest in the commu- nication process. The same scientist who will overcome tremendous obstacles to carry out a measurement to the fourth decimal place will be in deep slum- ber while a typographical error changes micrograms per milliliter to milligrams per milliliter. English need not be difficult. In scientific writing, we say, “The best English is that which gives the sense in the fewest short words” (a dictum printed for some years in the Journal of Bacteriology’s instructions to authors). Literary devices, metaphors and the like, divert attention from substance to style. They should be used rarely in scientific writing. CHAPTER 2 Historical Perspectives History is the short trudge from Adam to atom. —Leonard Louis Levinson THE EARLY HISTORY uman beings have been able to communicate for thousands of years. Yet H scientific communication as we know it today is relatively new. The first journals were published about 350 years ago, and the IMRAD (introduction, methods, results, and discussion) organization of scientific papers has developed within about the past century. Knowledge, scientific or otherwise, could not be effectively communicated until appropriate mechanisms of communication became available. Prehistoric people could communicate orally, of course, but each new generation started from essentially the same baseline because, without written records to refer to, knowledge was lost almost as rapidly as it was found. Cave paintings and inscriptions carved onto rocks were among the first human attempts to leave records for succeeding generations. In a sense, t oday we are lucky that our early ancestors chose such media b ecause some of t hese early “messages” have survived, whereas messages on less-durable materials would have been lost. (Perhaps many have been.) On the other hand, communi- cation via such media was incredibly difficult. Think, for example, of the dis- tributional problems the U.S. Postal Service would have today if the medium of correspondence were 100-lb (about 45-kg) rocks. It has enough troubles with 1-oz (about 28-g) letters. 6 Historical Perspectives 7 The earliest book we know of is a Chaldean account of the Flood. This story was inscribed on a clay tablet in about 4000 BC, antedating Genesis by some 2,000 years (Tuchman 1980). A medium of communication that was lightweight and portable was needed. The first successful medium was papyrus (sheets made from the papyrus plant and glued together to form a roll sometimes 20 to 40 ft [6–12 m] long, fastened to a wooden roller), which came into use about 2000 BC. In 190 BC, parchment (made from animal skins) came into use. The Greeks assembled large libraries in Ephesus and Pergamum (in what is now Turkey) and in Alexandria. Accord- ing to Plutarch, the library in Pergamum contained 200,000 volumes in 40 BC (Tuchman 1980). In AD 105, the Chinese invented paper, the dominant medium of written communication in modern times—at least u ntil the Internet era. However, because there was no effective way of duplicating communications, scholarly knowledge could not be widely disseminated. Perhaps the greatest single technical invention in the intellectual history of the human race was the printing press. Although movable type was invented in China in about AD 1100 (Tuchman 1980), the Western world gives credit to Johannes Gutenberg, who printed his 42-line-per-page Bible from movable type on a printing press in AD 1455. Gutenberg’s invention was immediately and effectively put to use throughout Europe. By the year 1500, thousands of copies of hundreds of books were printed. The first scientific journals appeared in 1665, when two journals, the Journal des Sçavans in France and the Philosophical Transactions of the Royal Society of London in England, began publication. Since then, journals have served as the primary means of communication in the sciences. As of 2014, t here were nearly 35,000 peer-reviewed journals in science, technology, and medicine, of which more than 28,000 were in English. Altogether, these journals were publishing about 2.5 million articles per year (Ware and Mabe 2015, p. 6). The number of scientific papers published per year has been increasing exponentially (Born- mann and Mutz 2015). THE ELECTRONIC ERA When many older scientists began their careers, they wrote their papers in pen or pencil and then typed them on a typewriter or had a secretary do so. They or a scientific illustrator drew graphs by hand. They or a scientific photographer took photographs on film. They then carefully packaged a number of copies of the manuscript and sent them via postal service to a journal. The journal then mailed copies to the referees (peer reviewers) for evaluation, and the referees 8 How to Write and Publish a Scientific Paper mailed them back with comments. The editor then mailed a decision letter to the scientist. If the paper was accepted, the scientist made the needed revisions and mailed back a final version of the manuscript. A copy editor edited the paper by hand, and a compositor re-keyboarded the manuscript. Once the paper was typeset, a copy was mailed to the scientist, who checked for typographical errors and mailed back corrections. Before the paper was published, the scien- tist ordered reprints of the paper, largely for fellow scientists who lacked access to libraries containing the journal or who lacked access to a photocopier. Today the process has changed greatly. Word processors, graphics programs, digital photography, and the Internet have facilitated preparation and dissemi- nation of scientific papers. Journals throughout the world have online systems for manuscript submission and peer review. Editors and authors communicate electronically. Manuscript editors typically edit papers online, and authors elec- tronically receive typeset proofs of their papers for inspection. Journals are available online as well as in print—and sometimes instead of in print; increas- ingly, accepted papers become available individually online before appearing in journal issues. At some journals, electronic extras, such as appendixes and video clips, supplement online papers. Many journals are openly accessible online, either starting at the time of publication or a fter a lag period. In addition, readers often can access papers through the authors’ websites or through resources at the authors’ institutions, or the readers can request electronic reprints. Some of the changes have increased the technical demands on authors, but overall, the changes have hastened and eased the publication process and improved service to readers. Whereas much regarding the mechanics of publication has changed, much else has stayed the same. Items that persist include the basic structure of a sci- entific paper, the basic process by which scientific papers are accepted for pub- lication, the basic ethical norms in scientific publication, and the basic features of good scientific prose. In particular, in many fields of science, the IMRAD structure for scientific papers remains dominant. THE IMRAD STORY The early journals published papers that we call descriptive. Typically, a scientist would report, “First, I saw this, and then I saw that,” or “First, I did this, and then I did that.” Often the observations were in simple chronological order. This descriptive style was appropriate for the kind of science then being reported. In fact, this straightforward style of reporting still is sometimes used in “letters” journals, case reports in medicine, geological surveys, and so forth. By the second half of the nineteenth century, science was beginning to move fast and in increasingly sophisticated ways. Microbiology serves as an example. Historical Perspectives 9 Especially through the work of Louis Pasteur, who confirmed the germ theory of disease and developed pure-culture methods of studying micro-organisms, both science and the reporting of science made great advances. At this time, methodology became all-important. To quiet his critics, many of whom were fanatic believers in the theory of spontaneous generation, Pas- teur found it necessary to describe his experiments in exquisite detail. Because reasonably competent peers could reproduce Pasteur’s experiments, the prin- ciple of reproducibility of experiments became a fundamental tenet of the phi- losophy of science, and a separate methods section led the way toward the highly structured IMRAD format. The work of Pasteur was followed, in the early 1900s, by the work of Paul Ehrlich and, in the 1930s, by the work of Gerhard Domagk (sulfa drugs). World War II prompted the development of penicillin (first described by Alexander Fleming in 1929). Streptomycin was reported in 1944, and soon after World War II the mad but wonderful search for “miracle drugs” produced the tetracy- clines and dozens of other effective antibiotics. As these advances were pouring out of medical research laboratories after World War II, it was logical that investment in research would greatly increase. In the United States, this positive inducement to support science was soon (in 1957) joined by a negative factor when the Soviets flew Sputnik around our planet. In the following years, the U.S. government (and others) poured addi- tional billions of dollars into scientific research. Money produced science, and science produced papers. Mountains of them. The result was powerful pressure on the existing (and the many new) journals. Journal editors, in self-defense if for no other reason, began to demand that manuscripts be concisely written and well organized. Journal space became too precious to be wasted on verbosity or redundancy. The IMRAD format, which had been slowly progressing since the latter part of the nineteenth century, now came into almost universal use in research journals. Some editors espoused IMRAD because they became convinced that it was the simplest and most log- ical way to communicate research results. Other editors, perhaps not convinced by the simple logic of IMRAD, nonetheless hopped on the bandwagon because the rigidity of IMRAD did indeed save space (and expense) in the journals and because IMRAD made life easier for editors and referees by indexing the major parts of a manuscript. The logic of IMRAD can be defined in question form: What question (prob lem) was studied? The answer is the introduction. How was the problem studied? The answer is the methods. What were the findings? The answer is the results. What do these findings mean? The answer is the discussion. It now seems clear that the simple logic of IMRAD does help the author organize and write the manuscript, and IMRAD provides an easy road map for editors, referees, and ultimately readers to follow in reading the paper. 10 How to Write and Publish a Scientific Paper Although the IMRAD format is widely used, it is not the only format for scientific papers. For example, in some journals the methods section appears at the end of papers. In some journals, t here is a combined results and discus- sion section. In some, a conclusions section appears at the end. In papers about research in which results of one experiment determine the approach taken in the next, methods sections and results sections can alternate. In some papers, especially in the social sciences, a long literature review section may appear near the beginning of the paper. Thus, although the IMRAD format is often the norm, other possibilities include IRDAM, IMRADC, IMRMRMRD, ILMRAD, and more. Later in this book, we discuss components of a scientific paper in the order in which they appear in the IMRAD format. However, most of our advice on each component is relevant regardless of the structure used by the journal to which you will submit your paper. Before writing your paper, be sure, of course, to determine which structure is appropriate for the journal to which you w ill submit it. To do so, read the journal’s instructions to authors and look at papers similar to yours that have appeared in the journal. T hese actions are parts of approaching a writing project—the subject of our next chapter. CHAPTER 3 Approaching a Writing Project Writing is easy. All you do is stare at a blank sheet of paper until drops of blood form on your forehead. —Gene Fowler ESTABLISHING THE MINDSET The thought of preparing a piece of scientific writing can intimidate even the best writers. However, establishing a suitable mindset and taking an appropri- ate approach can make the task manageable. Perhaps most basic, remember that you are writing to communicate, not to impress. Readers of scientific papers want to know what you did, what you found, and what it means; they are not seeking great literary merit. If you do good research and present it clearly, you will please and satisfy readers. Indeed, in scientific writing, read- ers should notice mainly the content, not the style. Realize that those reading your work want you to do well. They are not out to thwart you. Journal editors are delighted to receive good papers; ditto for the scientists they enlist as referees (peer reviewers) to help evaluate your work. Likewise, if you are a student, professors want you to do well. Yes, these people often make constructive criticisms. But they are not d oing so b ecause they dis- like you; rather, they do so because they want your work to succeed. Do not be paralyzed by the prospect of criticism. Rather, feel fortunate that you w ill receive feedback that can help your writing to be its best. 11 12 How to Write and Publish a Scientific Paper PREPARING TO WRITE In the laboratory, careful preparation helps experiments proceed smoothly and efficiently. Much the same is true of scientific writing. By preparing carefully before you start to compose a manuscript, you can make writing relatively easy and painless. Of course, in our unbiased view, preparing to write should include reading this book and keeping it on hand to consult. (Our publisher suggests buying a copy for your office or lab, a copy to use at home, and maybe one to keep in your car or boat.) But using this book is only a start. The following also can help. Good writing is largely a m atter of effective imitation. Therefore, obtain cop- ies of highly regarded scientific papers in your research area, including papers in the journal to which you plan to submit your current work. Notice how these papers are written. For example: What sections do they include, and in what order? How long do the various sections tend to be? What types of sub- headings, if any, tend to be included? How many figures and t ables, and what types thereof, are typical? Especially if you are a non-native speaker of English, what seem to be some standard phrases that you could use in presenting your own work? Using published papers as models can prepare you to craft a man- uscript that will be suitable to submit. Successful writing also entails following instructions. Essentially every sci- entific journal issues instructions to authors. Following these instructions takes much of the guesswork out of writing and can save you from the unpleas- ant task of rewriting a paper because it did not meet the journal’s specifica- tions. If instructions are long (some journals’ instructions run several pages or more), underline or highlight the key points to remember. Alternatively, you may list, on colored paper so you can easily find them, those points most rel- evant to the paper you will write. Also consider bookmarking on your computer the journal’s instructions to authors, especially if the instructions encompass links for accessing different parts of their content. For more detailed guidance—for instance, on nomenclature, reference for- mats, and grammar—instructions for authors often refer readers to standard style manuals. Among style manuals commonly used in the sciences are the following: The ACS [American Chemical Society] Style Guide (Coghill and Garson 2006) AMA [American Medical Association] Manual of Style (Iverson et al. 2007) The Chicago Manual of Style (2010) Publication Manual of the American Psychological Association (2010) Scientific Style and Format (Style Manual Subcommittee, Council of Science Editors 2014) Approaching a Writing Project 13 New editions of these manuals come out from time to time. Increasingly, such manuals are available in online versions as well as in print. Look for the most recent edition of the style manual you will use. Commonly, you can find such style manuals in the reference sections of academic and other libraries. Many libraries also offer online access to style manuals. If you lack easy access, con- sider investing in the style manual(s) most commonly used in your research field. In any case, be ready to consult such manuals. If you do not have reference-management software—for example, EndNote, Reference Manager, or RefWorks—now may be a good time to obtain it. Many universities make such software readily available and provide instruction in its use. Further information about such software appears in Chapter 15. While you are gathering scientific content, ideas for your paper may occur to you. For example, you may think of a point to include in the discussion. Or you may come up with a good way to structure a table. Write down these ideas; con- sider creating for each section of your paper a file—either paper or electronic— in which to place them. Not only will recording your ideas keep them from escaping your memory, but having such ideas readily available to draw on can get your writing off to a quick start. Once you have gathered and analyzed your data, speaking can be a fine transition to writing. If possible, present your work at a departmental seminar or local research day. Perhaps give an oral or poster presentation at a confer- ence. Preparing to speak can help in formulating your article. Also, questions from listeners can help you to shape what you will write. Research typically is a team endeavor. So is reporting on research. In the writing as in the research, different team members commonly take different roles. Sometimes one member drafts the whole paper and the others review and revise it. Other times, different members draft different parts of the paper and then circulate them for review. Whatever the case, clarify beforehand who will do what, and perhaps set a timetable. Maybe consider what software, if any, you will use to facilitate collaboration. W ill you share drafts via Dropbox? W ill you be using Google Docs? Will you use software designed specifically for aca- demic collaboration? Discuss such matters before starting to write. To facilitate writing, do lots of pre-writing. For example, stack copies of pub- lished papers in the order in which you plan to cite them. Make outlines. List points you wish to make in a given section, and sort and re-sort them u ntil you are pleased with the order. Perhaps make a formal outline. By doing much of the thinking and organization beforehand, you can lower the activation energy needed to write a paper. In fact, such pre-writing can catalyze the writing pro cess so well that you find yourself eager to write. In preparing to write, realize that sometimes ideas must percolate for a while. If, for example, you cannot come up with an effective way to begin your paper 14 How to Write and Publish a Scientific Paper or to structure a section, take a break. Exercise for a while, take a nap, or maybe discuss your work with someone. A solution may then occur to you. DOING THE WRITING oing the writing means making time to do it. Most of us in science are busy. D If writing must wait until we have extra time, it might never get done. There- fore, block out times to write. Indicate on your calendar or in your personal organizer the times that you have reserved for specific writing projects. Except in emergencies, do not let other tasks impinge on those times. Also, set dead- lines. For example, promise yourself that you will draft a given section by Thurs- day. Or make clear to yourself that you w ill not leave for vacation u ntil you have submitted a given item. One highly published professor advocates the following approach (Zerubavel 1999): On a sheet of paper showing your weekly schedule hour by hour, cross out the times you are regularly unavailable—for example, times that you teach, have laboratory meetings, or have personal commitments. Then choose from the remaining times some to reserve for writing. In d oing so, consider what times of day you tend to write most effectively. For example, if you are a night person, block out some evenings during which to write each week; perhaps save some morning time for more routine writing-related tasks, such as check- ing references. If you are a morning person, do the reverse. When writing, you can start with whatever part of a manuscript you find easi- est; there is no rule that you must write the introduction first. Many researchers like to begin by drafting the methods section, which tends to be the most straight- forward to write. Many like to begin by drafting the figures and tables. Some like to start by drafting a preliminary reference list—or even the acknowledg ments. And many authors leave u ntil last the writing of the title and abstract. Once you have drafted one section, the momentum that you have established can facilitate writing the o thers. Feel f ree to draft the remaining sections in what ever order works best for you. Although the structure of Part II of this book parallels that of a scientific paper—with the first chapter addressing “How to Prepare the Title” and the last “How to Cite the References”—you can draft the parts of a scientific paper (and read these chapters) in whatever order works best for you. Once you have established momentum, beware of dissipating it by inter- rupting your writing to search for small details. Rather, make notes to find the missing information; to identify them easily, write them in boldface type in your manuscript or use the “new comment” feature in Word. Also, if a manu- script will take more than one session to draft, consider how you can best main- tain your momentum from session to session. Some authors like to stop in the Approaching a Writing Project 15 (© ScienceCartoonsPlus.com) iddle of a section while still going strong. Before ending their writing session, m they jot down the next few points they wish to make. Thus, at their next writing session they can start quickly. Consider taking this approach. Much like d oing a piece of scientific research, crafting a scientific paper typi- cally entails solving a series of problems in order to achieve the overall objective. In writing, as in research, often the problems have more than one reasonable solution, each with advantages and disadvantages. Yet writers sometimes worry that there is “one right way” (Becker 1986). Just how should a given item be worded? In just what format should a given illustration appear? How should a given part of the paper be organized? Often such questions have more than one good answer. Find one that seems reasonable and go with it. If it seems inadequate, or if a better solution occurs to you, you can make changes when you revise your manuscript. 16 How to Write and Publish a Scientific Paper REVISING YOUR WORK Good writing tends to be largely a matter of good revising. No one will see your early drafts, and no one cares how rough they are (a comforting thought to those facing writer’s block). The important thing is to revise your writing u ntil it works well. First revise your writing yourself. Then show it to o thers and, using their feedback, revise your writing some more. Revision is not just for students or other beginners. Researchers with long success in publishing revise the papers they write. After a presentation to a scientific-writing class, a well-known scientist and journal editor was asked, “Do you revise your work?” He answered: “If I’m lucky, only about 10 times.” In revising your work, ask yourself questions such as the following: Does the manuscript include all the information it should? Should any content be deleted? Is all the information accurate? Is all the reasoning sound? Is the content consistent throughout? Is everything logically organized? Is everything clearly worded? Have you stated your points briefly, simply, and directly? In other words, is everything concise? Are grammar, spelling, punctuation, and word use correct throughout? Are all figures and tables well designed? Does the manuscript comply with the instructions? Information that can aid in answering some of t hese questions appears in l ater chapters of the book. For example, Chapters 10 through 13 describe the appro- priate content and organization of the main sections of a scientific paper, and Chapters 30 through 34 address word usage and related subjects. In addition to reading these chapters before you write, consider consulting them as you revise your manuscript. Also, for further guidance, please see Chapter 41, which focuses mainly on editing one’s own work. Once your manuscript is nearly the best you can make it, show it to others and request their feedback. Years ago, scientists w ere advised, “Show your manu script to a guy in your lab, a guy in a lab down the hall, and your wife.” These days, such advice would rightly be viewed as inaccurate and sexist. Yet the con- cept remains valid. So, consider following this advice: Show your manuscript to an expert in your research specialty, who can help identify technical prob lems. Also show it to someone in your general field, who can note, for example, items that may be unclear to readers. And show it to an intelligent general reader—for instance, a friend in the humanities—who may identify problems Approaching a Writing Project 17 that those interested mainly in the content tend to miss. In addition, consider also showing your manuscript to a professional scientific editor, as discussed in Chapter 41. After receiving feedback from those reviewing your manuscript, consider how to apply it. Of course, follow t hose suggestions that you find useful. Even if a suggestion seems unsuitable, keep it in mind. Although you may disagree with it, it may alert you to a problem. For example, if a reader misinterpreted a point, you may try to state it more clearly. Comparing the various readers’ com- ments may aid in this regard. If only one reader had difficulty with an item, you might dismiss it as a fluke. If, however, multiple readers did so, improve- ment probably is needed. Revise your writing thoroughly. But avoid the temptation to keep revising it forever. No manuscript is perfect. Be satisfied with mere excellence. Journal editors and o thers will be pleased to receive the fine manuscripts you prepare by following the advice in this chapter and the rest of this book. CHAPTER 4 What Is a Scientific Paper? Without publication, science is dead. —Gerard Piel DEFINITION OF A SCIENTIFIC PAPER A scientific paper is a written and published report describing original research results. That short definition must be qualified, however, by noting that a sci- entific paper must be written in a certain way, as defined by tradition, editorial practice, scientific ethics, and the interplay of printing and publishing pro- cedures. To properly define “scientific paper,” we must define the mechanism that creates a scientific paper, namely, valid (that is, primary) publication. Abstracts, theses, conference reports, and many other types of literature are published, but such publications do not normally meet the test of valid publication. Further, even if a scientific paper meets all the other tests, it is not validly published if it is published in the wrong place. That is, a relatively poor research report, but one that meets the tests, is validly published if accepted and published in the right place (a primary journal or other primary publication); a superbly pre- pared research report is not validly published if published in the wrong place. Most of the government literature and conference literature, as well as institu- tional bulletins and other ephemeral publications, do not qualify as primary literature. Many people have struggled with the definition of primary publication (valid publication), from which is derived the definition of a scientific paper. The Council of Biology Editors (CBE), now the Council of Science Editors (CSE), arrived at the following definition (Council of Biology Editors 1968, p. 2): 18 What Is a Scientific Paper? 19 An acceptable primary scientific publication must be the first disclosure containing sufficient information to enable peers (1) to assess observa- tions, (2) to repeat experiments, and (3) to evaluate intellectual processes; moreover, it must be susceptible to sensory perception, essentially per- manent, available to the scientific community without restriction, and available for regular screening by one or more of the major recog- nized secondary services (e.g., currently, Biological Abstracts, Chemical Abstracts, Index Medicus, Excerpta Medica, Bibliography of Agricul- ture, etc., in the United States and similar services in other countries). At first reading, this definition may seem excessively complex, or at least verbose. But those who had a hand in drafting it weighed each word carefully and doubted that an acceptable definition could be provided in appreciably fewer words. Because it is important that students, authors, editors, and all others concerned understand what a scientific paper is and what it is not, it may be helpful to work through this definition to see what it really means. “An acceptable primary scientific publication” must be “the first disclosure.” Certainly, first disclosure of new research data often takes place via oral pre sentation at a scientific meeting. But the thrust of the CBE statement is that disclosure is more than disgorgement by the author; effective first disclosure is accomplished only when the disclosure takes a form that allows the peers of the author (either now or in the future) to fully comprehend and use that which is disclosed. Thus, sufficient information must be presented so that potential users of the data can (1) assess observations, (2) repeat experiments, and (3) evaluate intel- lectual processes. (Are the author’s conclusions justified by the data?) Then, the disclosure must be “susceptible to sensory perception.” This may seem an awk- ward phrase, b ecause in normal practice it simply means published; how- ever, this definition provides for disclosure not just in terms of printed visual materials (printed journals and the no longer widely used media called micro- film and microfiche) but also in nonprint, nonvisual forms. For example, “pub- lication” in the form of audio recordings, if that publication met the other tests provided in the definition, would constitute effective publication. And, certainly, electronic journals meet the definition of valid publication. What about mate- rial posted on a website? Views have varied and can depend on the nature of the material posted. For the most current information, consult materials from professional organizations and journals in your field. Regardless of the form of publication, that form must be essentially perma- nent (often not the case for websites), must be made available to the scientific community without restriction (for example, in a journal that is openly accessi- ble online or to which subscriptions are available), and must be made available to information-retrieval services (Biological Abstracts, Chemical Abstracts, 20 How to Write and Publish a Scientific Paper MEDLINE, etc.). Thus, publications such as newsletters, corporate publications, and controlled-circulation journals, many of which are of value for their news or other features, generally cannot serve as repositories for scientific knowledge. To restate the CBE definition in simpler but not more accurate terms, primary publication is (1) the first publication of original research results, (2) in a form whereby peers of the author can repeat the experiments and test the conclu- sions, and (3) in a journal or other source document readily available within the scientific community. To understand this definition, however, we must add an important caveat. The part of the definition that refers to “peers of the author” is accepted as meaning prepublication peer review. Thus, by definition, scien- tific papers are published in peer-reviewed publications. This question of definition has been belabored here for two reasons. First, the entire community of science has long labored with an inefficient, costly system of scientific communication precisely b ecause it (authors, editors, and publishers) have been unable or unwilling to define primary publication. As a result, much of the literature has been buried in meeting abstracts, obscure conference reports, government documents, or books or journals of minuscule circulation. Other papers, in the same or slightly altered form, are published more than once; occasionally, this is due to the lack of definition as to which conference reports, books, and compilations are (or should be) primary publi- cations and which are not. Redundancy and confusion result. Second, a scien- tific paper is, by definition, a particular kind of document containing specific kinds of information, typically in a prescribed (IMRAD) order. If the graduate student or the budding scientist (and even some of those scientists who have already published many papers) can fully grasp the significance of this defini- tion, the writing task might be a great deal easier. Confusion results from an amorphous task. The easy task is the one in which you know exactly what must be done and in exactly what order it must be done. ORGANIZATION OF A SCIENTIFIC PAPER A scientific paper is organized to meet the needs of valid publication. It is, or should be, highly stylized, with distinctive and clearly evident component parts. The most common labeling of the component parts, in the basic sciences, is introduction, methods, results, and discussion (hence the acronym IMRAD). Actually, the heading “Materials and Methods” may be more common than the simpler “Methods,” but the latter form was used in the acronym. Some of us have taught and recommended the IMRAD approach for many years. The tendency toward uniformity has increased since the IMRAD system was prescribed as a standard by the American National Standards Institute, first in 1972 and again in 1979 (American National Standards Institute, 1979a). Some journals use a variation of IMRAD in which methods appear last rather What Is a Scientific Paper? 21 than second. Perhaps we should call this IRDAM. In some journals, details regarding methods commonly appear in figure captions. The basic IMRAD order is so eminently logical that, increasingly, it is used for many other types of expository writing. W hether one is writing an article about chemistry, archaeology, economics, or crime in the street, the IMRAD format is often the best choice. This point is generally true for papers reporting laboratory studies and other experiments. There are, of course, exceptions. As examples, reports of field studies in the earth sciences and many clinical case reports in the medical sci- ences do not readily lend themselves to this kind of organization. However, even in these descriptive papers, the same logical progression from problem to solu- tion is often appropriate. Occasionally, the organization of laboratory papers must differ. If a number of methods were used to achieve directly related results, it might be desirable to combine the materials and methods and the results into an integrated exper- imental section. In some fields and for some types of results, a combined results and discussion section is usual or desirable. In addition, many primary journals publish notes or short communications, in which the IMRAD orga nization is modified. Various types of organization are used in descriptive areas of science. To determine how to organize such papers and which general headings to use, refer to the instructions to authors of your target journal and look at analo- gous papers the journal has published. Also, you can obtain general informa- tion from appropriate source books. For example, types of medical papers are described by Huth (1999), Peat and others (2002), Taylor (2011), and contribu- tors to a multiauthor guide (Hall 2013); types of engineering papers and reports are outlined by Michaelson (1990) and by Beer and McMurrey (2014). Indeed, even if a paper will appear in the IMRAD format, books on writing in one’s own discipline can be worth consulting. Examples of such books include those in biomedical science by Zeiger (2000); the health sciences by Lang (2010); in chemistry by Ebel, Bliefert, and Russey (2004); and in psychology by Sternberg and Sternberg (2010). In short, the preparation of a scientific paper has less to do with literary skill than with organization. A scientific paper is not literature. The preparer of a scientific paper is not an author in the literary sense. As an international col- league noted, this fact can comfort t hose writing scientific papers other than in their native language. Some old-fashioned colleagues think that scientific papers should be litera ture, that the style and flair of an author should be clearly evident, and that varia- tions in style encourage the interest of the reader. Scientists should indeed be interested in reading literature, and perhaps even in writing literature, but the communication of research results is a more prosaic procedure. As Booth (1981) put it, “Grandiloquence has no place in scientific writing.” 22 How to Write and Publish a Scientific Paper Today, the average scientist, to keep up with a field, must examine the data reported in a very large number of papers. Also, English, the international language of science, is a second language for many scientists. Therefore, scien- tists (and of course editors) must demand a system of reporting data that is uniform, concise, and readily understandable. SHAPE OF A SCIENTIFIC PAPER Imagine that a friend visits your laboratory or office. The friend is unfamiliar with your research and wants to know about it. To orient your friend, first you identify your general research area and say why it is important. Then you state the specific focus of your research, summarize how you gathered your data, and say what you found. Finally you discuss the broader significance of your find- ings. The friend now has a new understanding—and, if you are lucky, he or she might buy you lunch. Although intended for readers who are more knowledgeable, a scientific paper should take much the same approach: first providing broad orientation, then focusing narrowly on the specific research, and then considering the find- ings in wider context. Some have likened this shape for a scientific paper to an hourglass: broad, then narrow, then broad. Keeping this overall structure in mind can aid when writing individual parts of a paper and integrating them into a coherent whole. OTHER DEFINITIONS If scientific paper is the term for an original research report, how should this be distinguished from research reports that are not original, are not scientific, or somehow fail to qualify as scientific papers? Some specific terms are commonly used: review paper, conference report, and meeting abstract. A review paper may review almost anything, most typically the recent work in a defined subject area or the work of a particular individual or group. Thus, the review paper is designed to summarize, analyze, evaluate, or synthe- size information that has already been published (research reports in primary journals). Although much or all of the material in a review paper has previously been published, the problem of dual publication (duplicate publication of orig- inal data) does not normally arise because the review nature of the work is usually obvious—often from the title of the periodical, such as Microbiology and Molecular Biology Reviews or Annual Review of Astronomy and Astrophysics. Do not assume, however, that reviews contain nothing new. From the best review papers come new syntheses, new ideas and theories, and even new paradigms. What Is a Scientific Paper? 23 A conference report is a paper published in a book or journal as part of the proceedings of a symposium, national or international congress, workshop, roundtable, or the like. Such conferences commonly are not designed for the definitive presentation of original data, and the resultant proceedings (in a book or journal) do not qualify as primary publications. Conference presentations often are review papers, presenting reviews of the recent work of particular scientists or recent work in particular laboratories. Material at some conferences (especially the exciting ones) is in the form of preliminary reports, in which new, original data are presented, often accompanied by interesting speculation. But usually, these preliminary reports do not qualify, nor are they intended to qualify, as scientific papers. Later, often much later, such work may be validly published in a primary journal; by this time, the loose ends have been tied down, essential experimental details have been described (so that a competent worker could repeat the experiments), and previous speculation has matured into conclusions. Therefore, the vast conference literature that appears normally is not primary. If original data are presented in such contributions, the data can and should be published (or republished) in an archival (primary) journal. Otherwise, the information may essentially be lost. If publication in a primary journal follows publication in a conference report, permission from the original publisher may be needed to reprint figures and other items (see Chapter 19, “Rights and Permissions”), but the more fundamental problem of dual publication normally does not and should not arise. Meeting abstracts may be brief or relatively extensive. Although they can and generally do contain original information, they are not primary publications, and publication of an abstract should not preclude later publication of the full report. Traditionally, there was little confusion regarding the typical one-paragraph abstracts published as part of the program or distributed along with the program at a national meeting or international congress. It was usually understood that many of the papers presented at these meetings would later be submitted for publication in primary journals. Sometimes conference organizers request extended abstracts (or synoptics). The extended abstract can supply almost as much information as a full paper; mainly it lacks the experimental detail. How- ever, precisely because it lacks experimental detail, it cannot qualify as a scientific paper. Those involved with publishing t hese materials should see the importance of careful definition of the different types of papers. More and more publishers, conference organizers, and individual scientists are agreeing on these basic definitions, and their general acceptance will greatly clarify both primary and secondary communication of scientific information. CHAPTER 5 Ethics in Scientific Publishing [A]ll scientists have an unwritten contract with their contemporaries and those whose work will follow to provide observations honestly obtained, recorded, and published. —CBE Style Manual Committee ETHICS AS A FOUNDATION Before writing a scientific paper and submitting it to a journal—and indeed, before embarking on your research—you should know the basic ethical norms for scientific conduct and scientific publishing. Some of these norms may be obvious, others not. Therefore, a basic overview is provided below. Graduate students and others seeking further information on ethics in scientific publish- ing and more broadly in science may do well to consult On Being a Scientist: Responsible Conduct in Research (Committee on Science, Engineering, and Public Policy 2009), which contains both guidance and case studies and is accompa- nied online by a video. Other resources include ethics chapters in style manuals in the sciences. AUTHENTICITY AND ACCURACY That research reported in a journal should actually have been done may seem too obvious to mention. Yet cases exist in which the author simply made up data in a paper, without ever d oing the research. Clearly, such “dry-labbing,” or fabrication, is unethical. Fiction can be a g rand pursuit, but it has no place in a scientific paper. 24 Ethics in Scientific Publishing 25 More subtle, and probably more common, are lesser or less definite devia- tions from accuracy: omitting outlying points from the data reported, preparing figures in ways that accentuate the findings misleadingly, or doing other tweak- ing. Where to draw the line between editing and distortion may not always be apparent. If in doubt, seek guidance from a more experienced scientist in your field—perhaps one who edits a journal. The advent of digital imaging has given unethical researchers new ways to falsify findings. (Journal editors, though, have procedures to detect cases in which such falsification of images seems probable.) And ethical researchers may rightly wonder what manipulations of digital images are and are not valid. Sources of guidance in this regard include recent sets of guidelines for use and manipulation of scientific digital images (Cromey 2010, 2012). For research that includes statistical analysis, reporting accurately includes using appropriate statistical procedures, not t hose that may distort the findings. If in doubt, obtain the collaboration of a statistician. Enlist the statistician early, while still planning the research, to help ensure that you collect appropriate data. Otherwise, ethical problems may include wasting resources and time. In the words of R.A. Fisher (1938), “To consult the statistician a fter an experiment is finished is often merely to ask him to conduct a post mortem examination.” ORIGINALITY As discussed in the previous chapter, the findings in a scientific paper must be new. Except in rare and highly specialized circumstances, they cannot have appeared elsewhere in the primary literature. In the few instances in which republication of data may be acceptable—for example, in a more extensive case series or if a paper is republished in another language—the original article must be clearly cited, lest readers erroneously conclude that the old observa- tions are new. To republish a paper (either in another language or for readers in another field) permission normally must be obtained from the journal that originally published the paper. Beginning scientists sometimes wonder whether they may submit the same manuscript to two or more journals simultaneously. After all, a candidate can apply to several graduate programs at once and then choose among those offering acceptance. An analogous situation does not hold for scientific papers. Simultaneous submission wastes resources and is considered unethical. There- fore, begin by submitting your paper only to your first-choice journal. If that journal does not accept your paper, you can then proceed to the next journal on your list. Originality also means avoiding “salami science” (or, for vegetarians, “cucum- ber science”)—that is, thinly slicing the findings of a research project, as one 26 How to Write and Publish a Scientific Paper might slice a sausage or cuke, in order to publish several papers instead of one (or, in the case of a large research project, many papers instead of a few). Good scientists respect the integrity of their research and do not divide it excessively for publication. Likewise, good hiring committees and promotion committees look at the content of publications, rather than only the number, and so are not fooled by salami science. CREDIT Good scientists build on each other’s work. They do not, however, take credit for others’ work. If your paper includes information or ideas that are not your own, be sure to cite the source. Likewise, if you use others’ wording, remember to place it in quotation marks (or to indent it, if the quoted material is long) and to provide a reference. Otherwise, you will be guilty of plagiarism, which the U.S. National Institutes of Health defines as “the appropriation of another person’s ideas, processes, results, or words without giving appropriate credit” (National Insti- tutes of Health 2010). To avoid inadvertent plagiarism, be sure to include infor- mation about the source when you copy or download materials others have written. To avoid the temptation to use o thers’ wording excessively, consider drafting paragraphs without looking directly at the source materials; then look at the materials to check for accuracy. In journal articles in most fields of science, it is unusual to include quota- tions from o thers’ work. Rather, authors paraphrase what o thers have said. Doing so entails truly presenting the ideas in one’s own way; changing a word or two does not constitute paraphrasing. On rare occasions—for example, when an author has phrased a concept extraordinarily well—quoting the author’s own phrasing may be justified. If you are unsure whether to place in quotation marks a series of words from a publication, do so. If the quotation marks are unnecessary, an editor at the journal can easily remove them. If, however, they are missing but should have been included, the editor might not discover that fact (until, perhaps, a reader later does), or the editor might suspect the fact and send you an inquiry that requires a time-consuming search. Be cautious, and thus save yourself from embarrassment or extra work. Resources to educate oneself about plagiarism, and thus learn better how to avoid it, include a tutorial from Indiana University (Frick and o thers 2016), an online guide to ethical writing (Roig 2003), and a variety of materials posted on websites of university writing centers. Another resource to consider is plagiarism-checking software. Such software helps identify passages of writ- ing that seem suspiciously similar to text elsewhere; one can then see whether it does indeed appear to be plagiarized. Such software, such as Turnitin, is Ethics in Scientific Publishing 27 (© ScienceCartoonsPlus.com) available at many academic institutions. Free plagiarism checkers, seemingly of varied quality, also exist. Many journal publishers screen submissions with plagiarism checking software, such as CrossCheck. Consider pre-screening your work yourself to detect and remove inadvertent plagiarism. Also be sure to list as an author of your paper everyone who qualifies for authorship. (See Chapter 8 for more in this regard.) Remember as well to include in the acknowledgments those sources of help or other support that should be listed (see Chapter 14). ETHICAL TREATMENT OF HUMANS AND ANIMALS If your research involves human subjects or animals, the journal to which you submit your paper is likely to require documentation that they were treated ethically. Before beginning your study, obtain all needed permissions with regard to human or animal research. (In the United States, d oing so entails having your research protocol reviewed by a designated committee at your institution.) 28 How to Write and Publish a Scientific Paper Then, in your paper, provide the needed statement(s) in this regard. For guid- ance, see the instructions to authors for the journal to which you are submit- ting your paper, and use as models papers similar to yours that have appeared in the journal. You may also find it useful to consult relevant sections of style manuals in the sciences. If in doubt, check with the publication office of the journal. DISCLOSURE OF CONFLICTS OF INTEREST Authors of scientific papers sometimes have conflicts of interest—that is, outside involvements that could, at least in theory, interfere with their objectivity in the research being reported. For example, they may own stock in the company mak- ing the product being studied, or they may be consultants to such a company. Increasingly, it seems, journals are requiring authors to report such conflicts of interest. Some have checklists for doing so, and others ask more generally for disclosure. Journals vary in the degree to which they note conflicts of inter- est along with published papers (Clark 2005). Ethics requires honest reporting of conflicts of interest. More importantly, ethics demands that such involvements not interfere with the objectivity of your research. Some scientists avoid all such involvements to prevent even the possibility of seeming biased. CHAPTER 6 Where to Submit Your Manuscript I’ve always been in the right place and time. Of course, I steered myself there. —Bob Hope WHY DECIDE EARLY, WHY DECIDE WELL Too often, authors write scientific papers and then consider where to publish them. The decision, however, is best made early, before the writing begins. That way, the paper can be geared appropriately to the audience (for example, read- ers of a general scientific journal, a journal in your discipline as a w hole, or a journal in your specialized research field). Also, thus you can initially prepare your manuscript in keeping with the journal’s requirements, rather than having to revise it accordingly. Of course, if your first-choice journal does not accept your paper, you might need to revise your manuscript to suit another journal. But at least you will have avoided a round of revision. In addition to deciding early on your first-choice journal, decide well. Choos- ing a journal carefully helps you to reach the most suitable audience, gain appropriate recognition, and avoid needless difficulties with publication. The decision where to submit the manuscript is important. Because of poor choices, some papers are delayed in publication, fail to receive sound review and revi- sion, or lie buried in inappropriate journals. If you submit your manuscript to a poor choice of journal, one of three things can happen—all bad. First, your manuscript may simply be returned to you, with the comment that your work “is not suitable for this journal.” Often, however, this judgment is not made until after review of the manuscript. A “not suitable” notice after weeks or months of delay is not likely to make you happy. 29 30 How to Write and Publish a Scientific Paper (PEANUTS © 1982 Peanuts Worldwide LLC. Dist. By UNIVERSAL UCLICK. Reprinted with permission. All rights reserved.) Second, if the journal is borderline in relation to your work, your manu- script may receive a poor or unfair review because the reviewers (and editors) of that journal may be only vaguely familiar with your specialty area. You may be subjected to the trauma of rejection even though the manuscript would be acceptable to the right journal. Or you could end up with a hassle over sug- gested revisions that you do not agree with and that do not improve your manu- script. And, if your manuscript really does have deficiencies, you would not be able to benefit from the sound criticism that would come from the editors of the right journal. Third, even if your paper is accepted and published, your glee w ill be short- lived if you later find that your work is virtually unknown b ecause it is buried Where to Submit Your Manuscript 31 in a publication that few in your intended audience read. Talking with colleagues can help prevent this situation. Think about the appropriate readership. If, for example, you are report- ing a fundamental study in physics, of course you should try to get your paper published in a prestigious international journal. On the other hand, suppose that your study relates to management of a disease found only in Latin Amer ica. In that situation, publication in Nature will not reach your audience—the audience that needs and can use your information. You should publish in an appropriate Latin American journal, probably in Spanish. To start identifying journals to consider, recall what journals have published work similar to yours. The journals publishing the papers that you w ill cite are often journals to consider. Perhaps ask colleagues to suggest potential publica- tion sites. To help determine w hether a journal indeed seems to be a possibility, look in the journal or at its website for statements describing its purpose and scope. Look at some recent issues of the journal to see w hether the journal publishes research such as yours and whether the papers are of the type you envision writing. PRESTIGE AND IMPACT If several journals seem suitable, does it matter which one you choose? Perhaps it shouldn’t matter, but it does. There is the matter of prestige. It may be that progress in your c areer (job offers, promotions, grants, e tc.) will be determined largely by the number of papers you publish. But not necessarily. It may well be that a wise old bird sitting on the faculty committee or the grant review panel will recognize and appreciate quality factors. A paper published in a “garbage” journal simply does not equal a paper published in a prestigious journal. In fact, the wise old bird (and t here are quite a few of t hese in science) may be more impressed by the candidate with one or two solid publications in presti- gious journals than by the candidate with 10 or more publications in second-or third-rate journals. How do you tell the difference? It isn’t easy, and of course there are many gradations. In general, however, you can form reasonable judgments by just a bit of bibliographic research. You w ill certainly know the important papers that have recently been published in your field. Make it your business to determine where they were published. If most of the real contributions in your field were published in Journal A, Journal B, and Journal C, you should probably limit your choices to those three journals. If Journals D, E, and F, upon inspection, contain only the lightweight papers, each could be eliminated as your first choice, even though the scope is right. 32 How to Write and Publish a Scientific Paper You may then choose among Journals A, B, and C. Suppose that Journal A is an attractive new journal published by a commercial publisher as a com- mercial venture, with no sponsorship by a society or other organization; Journal B is an old, well-known small journal published by a famous university, hospi- tal, or museum; and Journal C is a large journal published by the principal scientific society in your field. In general (although there are many exceptions), Journal C (the society journal) is probably the most prestigious. It will also have the largest circulation (partly b ecause of quality f actors, and partly b ecause society journals are less expensive than others, at least to society members). By publication in such a journal, your paper may have its best chance to make an impact on the community of scholars at whom you are aiming. Journal B might have almost equal prestige, but it might have a very limited circulation, which would be a minus; it might also be very difficult to get into, if most of its space is reserved for in-house material. Journal A (the commercial journal) might well have the disadvantage of low circulation (because of its comparatively high price, which is the result of both the profit aspect of the publisher and the lack of backing by a society or institution with a built-in subscription list). Publi- cation in such a journal may result in a somewhat restricted distribution of your paper. Be wary of new journals, especially t hose not sponsored by a society. (In par ticular, avoid predatory journals, which are discussed later in this chapter.) The circulation may be minuscule, and the journal might fail before it, and your paper, become known to the scientific world. Be wary of publishing in journals that are solely electronic unless you know that those evaluating your work for purposes such as promotion consider those journals as prestigious as journals with printed versions. On the other hand, be wary of publishing in the increas- ingly few journals that appear only in print, as scientists today expect important scientific literature to be accessible online. One tool for estimating the relative prestige of journals in a given field is the electronic resource Journal Citation Reports, commonly available through academic libraries. With this resource, you can determine which journals have recently been cited most frequently, both in total and in terms of average num- ber of citations per article published, or impact factor (Garfield 1999). Although not all good journals have impact f actors computed, impact f actor can be worth considering in judging the prominence of journals. If, in a given field, the aver- age paper in Journal A is cited twice as frequently as the average paper in Journal B, it is likely that researchers find Journal A the more important jour- nal. In some countries and institutions, impact factors of journals in which papers appear are among criteria considered when candidates are evaluated for promotion. However, limitations of the impact f actor also should be noted. The impact factor indicates how much the papers in a journal are cited on average— not how much your paper w ill be cited if it appears in the journal. It does not Where to Submit Your Manuscript 33 indicate how much impact other than on citation the papers in a journal have— for example, how much they influence policy or clinical practice. And because different scientific fields have different citation practices, impact factors should not be used to compare importance of journals in different fields. For instance, in biochemistry and molecular biology, in which papers tend to cite many recent papers, the impact f actor of the top-cited journal was 32.2 in the year 2014, but in geology it was 4.9. In short, although knowing a journal’s impact-factor rank- ing in its field can help you assess the scientific importance of a journal, the impact factor does not say everything about the journal’s quality and its suitabil- ity for your work. In journal selection as in much else in life, a multidimensional concept cannot validly be reduced to a single number. Increasingly, experts have emphasized the need to include indicators other than impact factor when assessing the importance of a person’s research. For example, the San Francisco Declaration on Research Assessment (2012), com- monly called DORA, calls for using more varied approaches in evaluating research output. These approaches include—in addition to, most importantly, evaluating the scientific content of the article—using multiple journal-based metrics (rather than only impact factor) and looking at article-level metrics. Examples of the latter include how many times an article has been viewed, (© ScienceCartoonsPlus.com) 34 How to Write and Publish a Scientific Paper downloaded, or bookmarked; how much attention it has received in social media and mass media; and how many times and where it has been cited (Tananbaum 2013). Noticing which journals’ articles in your field tend to receive such atten- tion can aid in identifying suitable journals for your papers. ACCESS Other items to consider when choosing journals can include open access—that is, the provision of articles online free of charge to all who may be interested. One consideration is whether to choose a journal (termed an open-access journal) that immediately provides open access to all its content. At such journals, which do not have subscriptions and so lack this source of income, the costs typically are defrayed at least in part by fees charged to authors. In some countries, t hese fees commonly are paid from grant funds; it can be wise to consider expected publication costs when preparing the budget for a grant. When authors, such as those in developing countries, cannot afford to pay the fees, the journal may waive or reduce them; if you cannot afford the normal publication fee for an open-access journal in which you hope to publish, contact the journal. Access-related considerations for publishing in traditional journals can include whether to seek a journal for which the electronic version, initially avail- able only to subscribers, becomes openly accessible relatively fast, for example, in a few months. Also, some journals give authors the option of making their articles freely accessible upon publication in return for paying a fee. Another consideration when publishing in a traditional journal is w hether the journal allows rapid posting of articles on authors’ or their institutions’ websites. The website SHERPA/RoMEO (www.sherpa.ac.uk/romeo/) provides information about journals’ policies in such regards. AVOIDING PREDATORY JOURNALS As noted, open-access journals typically charge authors fees as t hese journals lack income from subscriptions. Some dishonest people take advantage of this model by claiming to publish valid journals while instead just trying to get authors’ money. These publishers of predatory journals may, for example, post all the papers that they receive, without peer review or editing. Or they might take authors’ money and publish nothing. Submitting papers to such journals advances neither science nor one’s career. Such journals often market themselves vigorously, filling researchers’ email with invitations to submit papers. How can you recognize, and thus avoid, pred- atory journals? Clues that a journal might be predatory include promises that Where to Submit Your Manuscript 35 seem too good to be true (for example, a guarantee to publish all submissions within a week), a website with many typographical and other errors, inclusion of what seem to be fake metrics (such as “impact index”), and lack of good articles (or any articles at all) on the journal’s website. On the other hand, indi- cations that a journal is likely to be valid include publication of good articles that you already have seen and inclusion of the journal in major bibliographic databases. If you think that a journal might be predatory, consider consulting Beall’s List (scholarlyoa.com/publishers/), compiled by academic librarian Jeffrey Beall. This list of “potential, possible, or probable predatory scholarly open-access publishers” can aid in evaluating one’s suspicions. Especially if you are inexperienced in publishing, perhaps consult a mentor or senior colleague if you think a journal that you are considering might be predatory. In fact, in any case, such consultation can be wise before finalizing one’s choice of a journal. OTHER FACTORS TO CONSIDER In choosing a journal, other f actors also can merit consideration. One such f actor is speed of publication. Increasingly, journals have been publishing papers online before they appear in print or are included in a

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