How to Write A PaperIris Lindberg 3/05

What Is a Paper?

• Communicates a linked series of observations in a logical fashion

• Interprets data neither too much nor too little

• Provides historical and biological context

• Tells a story• Moves the field forward

Assemble Your Data

• Most often present in the order it was obtained

• Re-order if this makes a more logical presentation

• First step: get a list of figures ready with the conclusions from each figure– Figure 1. Compound X lowers the

amount of compound Y in HEK cells.

When to Write Up?

• After you think you have a good story

• All critical experiments are finished• Before you finish tying up all of the

loose ends– Writing up will show you clearly what

controls/additional experiments still need to be performed

Choose a Journal

• Select before you start so format is appropriate

• Focus of journal should be appropriate• Best journal that the work is appropriate

for– Availability and readership– Ranking (“impact factor”)– Time to publication

In What Order Should Paper Be Written?

• Figures and Legends• Results• Methods (easy part!)• Introduction• Discussion• Abstract• Referencing• Letter to the Editor

Figures

• Easy to read and logically presented,• Can be reduced severely without loss

of legibility (use the reducing Xerox machine) with little white space

• Try different types of format: bar graphs vs. figures- which is easiest to interpret?

• Figures should not need legends to be comprehensible if at all possible

Results• Succinctly describes each major finding,

grouping appropriately in figures/panels.

• Every statement made in the results should be supported incontrovertibly by the data in the paper.

• Make sure results are internally consistent!

• There is no substitute for beautiful data (to convince the reader)

Methods

• Easiest part to write if you have kept a good notebook

• Enables the reader to actually repeat the experiments

• Skip methods that can be found in Current Protocols- just cite

• Cite the source of all reagents used and where QC information is to be found

• Cite previous your papers whenever you can

Introduction

• Orients the reader as to why the work is important

• Should provide fair and comprehensive referencing of the field

• Should cover all required subjects in a logical order

• Concludes with a brief summary of what was done (BRIEF!)

Discussion

• Does not repeat the Results but rather takes each major finding presented in the results and discusses it in the context of how it relates to previous and future work, with comprehensive and appropriate literature citation.

• Ends with a brief speculative statement or idea for future work

Abstract- write last!

• Summarizes the major findings in the broad context of the work.

• Consists of two or three sentences of topic introduction

• Selected results (not all but the most important)

• Concludes with implications of work

Tips

• Save the journal space by writing concisely and by eliminating unnecessary or negative figures and tables

• Proof all text carefully for errors-– typos, omissions, inconsistencies in the

data, redundancies, or errors in referencing.

• Expect to revise again and again- 10 times ? Until language is perfect

Writing Good Sentences

• Omit all unnecessary words- the shortest phrasing is usually the best

• Use active voice when possible• Use the correct tense- present means

it is true while past means it is true under a specific set of circumstances

• Do not switch tenses frequently

Common Mistakes

• Data= plural; datum= singular. DATA ARE!!

• Effect vs Affect (both are nouns and verbs. But you will seldom use “affect” as a noun unless you are a psychologist)– We studied the effect of different

concentrations of X on Y– Compound Z effected a large change in Y– The inclusion of compound Z affected the pH

of Y.

Common Mistakes• Dependent, not dependant; ensure, not

insure, principle vs principal – The principal of the school had 3 principle

reasons for not allowing gum in class

• Dangling participle: – Running for the bus, a package fell out of

my arms

• Use of commas instead of semi-colons: – “however” is almost always preceded by a

semi-colon

Common Mistakes• Inconsistent use of abbreviations• Colloquial language: contractions,

“some”; “done” vs “performed”; “spun” vs “centrifuged”

• Redundant language (e.g. use of “excellent” twice in two neighboring sentences)

Rebuttal Letter

• Thank the reviewers for their time. They did not have to spend it on your work!

• Address each criticism in numbered order• Repeat or include the criticism in your

answer• You are allowed to argue one or two items

but most items should be addressed precisely the way the referee indicates

• Conclude by saying that you feel the paper is improved and you hope it is now acceptable for publication

Reviewing the Work of Others

• You cannot review a paper if you are simultaneously engaged in identical work

• You cannot review a paper if you have strong feelings (hate or love) for the authors; or have recently collaborated/mentored/been mentored

• Golden Rule applies- apply the standard you would apply to your own work (neither be too critical nor too soft)

• Be helpful rather than pejorative; soften criticisms with an initial positive statement

Reviewing- General • Read the manuscript with a pencil in

hand, making notes on the margins• Is the English used up to par?

(suggest editorial revision by a native speaker; do not edit for them)

• Is it sloppily done? (referencing wrong, many typos etc)

• Is the content appropriate for the particular journal audience?

Reviewing, continued

• Set down your thoughts in a numbered order – cite figure and/or page for each

• Introduction– Is it sufficiently comprehensive and fair?– Does it provide a good rationale for the

work?– Are all abbreviations clear or is there

jargon?

Reviewing Methods

• Are the methods neither too detailed (common methods not described) nor insufficiently described? (primers)

• Could the work be repeated by an outside group? (amounts of starting material given etc)

• Are the methods clearly written?

Reviewing Results

• Are the figures cited in order?• Is the rationale for each experiment

given? • Do the text conclusions agree with

the result you see in each figure? – Watch for over interpretation

• Are all of the figures really necessary?

Reviewing Figures• Accuracy

– are stated results really present and really significant?

– Does the figure number correspond to the correct figure?

• Presentation– is there a minimum of white space?– are figures sharp and clear? Are

legends readable?• Is the legend neither too long nor too

short?

Reviewing Discussions

• Does it simply repeat the introduction?• Does it provide alternative explanations for

the data/ introduce necessary complexities?

• Is it about the same length as the results?• Does it put the work in context and

suggest further lines of experimentation?• Most importantly: does it go too far?

Review Format• State ms. number, title, authors• Review the major findings of the authors• Give major problems in numbered order• Give minor problems in numbered order• Do not state whether paper is

acceptable- this is not your decision