How to Write A Paper

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• How to Write A Paper
• Iris Lindberg 3/05

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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

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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.

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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

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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

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In What Order Should Paper Be Written?

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

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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

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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)

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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

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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!)

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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

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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

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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

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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

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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.

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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

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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)

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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

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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

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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?

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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?

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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?

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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?

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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?

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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?

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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