09/02/2010

Scientific Paper Writing:

Guidelines and Tips

A. S. M. A. Haseeb
Dept. of Mechanical Engineering
University of Malaya
Office: Room 13, Level 5, Engineering Tower Bldg.
Tel: 7967 4492, E-mail: haseeb@um.edu.my

References
(all from internet sources)

Elsevier, Author Workshop 2008-11-6, How to prepare a manuscript for an international journal, Xiamen
University
K. E. Barrett, How to Write (and Review) a Scientific Paper, http://www.the-
aps.org/careers/careers1/mentor/workshop/2001/Barrett.doc,
S. Bloomer and M. J. Haas, How to write a scientific paper, inform, Volume 15 (12), December 2004.
Sami K. Solanki, How to Write a Research Paper, Internet Source
K. E. Barrett, Publishing 101, Chair, APS Publications Committee, Internet Source
Ed BullmoreHow to Write a Scientific Paper, Internet Source
WRITING A RESEARCH PAPER: Some general guidelines
for students and postdocs, Internet Source
S. Cordova, How To Write a Scientific Paper, http://www.nmas.org/JAhowto.html
Daniel J. Jacob, HOW TO WRITE AN EFFECTIVE SCIENTIFIC PAPER
K. Gaafar, How to write a scientific paper
R. Elvik, How to write a successful paper, Institute of Transport Economics, Oslo, Norway, Young researchers
seminar, May 10-13, 2005
W. A. Zin, HOW TO WRITE A SCIENTIFIC PAPER
M. Mallia, How to Write a Scientific Manuscript, Scientific Publications, Texas Heart Institute, Houston, Texas,
USA, Cardiology Rounds, February 19, 2008
T. H. Adair,Writing and publishing a research article, Center of Excellence in Cardiovascular-Renal Research,
University of Mississippi Medical Center
Barbara Gastel, Writing a Scientific Paper: Basics of Content and Organization Texas A&M University

Contents

Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Ethical issues
Submission to a journal
Language
Conclusions

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Gerard Piel: co-founder and the long-term publisher of the

modern incarnation of Scientific American magazine

Origins of Scientific Writing

Knowledge is lost without written records

Cave paintings and inscriptions first attempts to leave
records
2000 BC Papyrus paper as a medium of communication
190 BC parchment made from animal skin
105 AD Chinese invented paper
1100 AD Chinese invented movable type
1455 AD Gutenberg printed his 42-line Bible from movable
type on a printing press
By 1500 thousands of copies of hundreds of books (called
incunabula) were printed
1665 the first scientific journals were published

What is a scientific paper

a written and published report describing original research

results
an addition to human knowledge
the first publication of original research results
peers can repeat the experiments and test the conclusions
published in a journal readily available within the scientific
community

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IMRaD Story
I = Introduction , what question was studied
M = Methods, how was the problem studied
R = Results, what are the findings
a = and
D = Discussion, what do these findings mean

Early journals descriptive papers

By second half of 19th century reproducibility of experiments
constitute a fundamental principle of philosophy of science
The methods section became all important
IMRaD format slowly progressed in the latter half of the 19th
century

Why write scientific papers?

A scientific career expansion of human knowledge

Academic and public sectors scientific papers ARE the means
for this expansion
Publish or Perish You dont publish, youre out
Quality of a scientific paper? (now routinely- perhaps unfortunately
measured by the citation index)

Originality and importance of ideas

Effectiveness of communication, particularly when it comes to
planting the flag for new ideas

Before you
start

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Before you start

Before you start

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Before you start

Before you start

Authorship

Decide on authors, and their order, as early as possible

Authors
- made a substantive intellectual contribution
- participate sufficiently to take responsibility for the content
- can defend the data and conclusions publicly

Before you start

Criteria for authorship

Generate at least part of the intellectual content

Conception or design of the work All three
Data analysis and interpretation criteria
Draft, critically review, or revise the intellectual content
should be
Approve the final version to be submitted
satisfied

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Before you start

Before you start

Contents

Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Ethical issues
Submission to a journal
Language
Conclusions

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General

The paper is not a description of the

work, it IS the work
Richard Feynman

Paper Writing:
A part of your research, not a post-research
activity !

Start writing papers as soon as possible view it as a tool of

your research
Iterate and agonize over the paper as part of your research

Starting Out

Know your working style <pencil and

paper> versus computer, time, place

Set a deadline

Just put something down and edit it

afterwards

Easiest to start MATERIALS and

METHODS and RESULTS

Start writing the data as if you were

describing them to your colleagues

Lay out general arguments and then go

into details

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Starting Out

Decide on the key conclusions - the important

message that you want to put across
Do you have all the data AND the figures to prove
your point ?
If possible, give an informal ORAL presentation of
the work before you start to write the paper

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Contents

Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Ethical issues
Submission to a journal
Language
Conclusions

Title

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The Title

Extremely important and must be chosen with great care will be

read by thousands
Good title fewest possible words that adequately describe the
contents of the paper.
Accuracy of the title Indexing and abstracting
Concise, specific and informative
Contain the keywords that reflect the contents of the paper
Capture the fundamental nature of the experiments and findings
Waste words (studies on, investigations on, a, an, the etc) should
not be used

The Title

How to Prepare the Title

Make a list of the most important keywords
Think of a title that contains these words
Could state the conclusion of the paper
NEVER contains abbreviations, chemical formulas,
proprietary names or jargon
Think, rethink of the title before submitting the paper
Be very careful of the grammatical errors due to faulty word
order
Avoid the use of the word using

The Title

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The Title

Abstract

Very important part of the paper many

readers will read just that

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Abstract

An abstract is a brief summary of each of

main sections (IMRAD) of the paper

A good abstract should contain in a very very precise form the

following elements:

Introduction: State the principal objectives and scope of the

investigation

Method: Describe the methods employed

Results: Summarize the results

Discussion/conclusion: State the principal conclusions

Abstract

No figures, no tables
No references (usually), no footnotes
Avoid abbreviations, equations and symbols
Make sentences short

It should not exceed about 250 words

Written usually in one paragraph
Written usually in the past tense as it refers to work done
Should never give any information or conclusion that is not
stated in the paper
Focus on what is new - essential ideas, essential numbers

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Keywords

Contents

Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Ethical issues
Submission to a journal
Language
Conclusions

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Introduction

Sets the scene for your unique contribution and place it in context

Not meant to be an exhaustive review

Formulate the problem to be addressed

Introduction

Introduction

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Introduction

Why was the problem undertaken? Historical and current relevance

What is its significance?
What is known or has been done before?
- Be selective and critical
- Give credit to intellectual pioneer as well as to best prior work
- Some criticism of earlier work may be necessary be mild
and very respectful, and show professional manners
- Cite peer-reviewed scientific literature or scholarly reviews
Avoid general reference work such as textbooks
Say why the present work needs to be done
Definitely needed: Goals of your paper. If similar papers exist: what is
new in the method or results

Introduction

Often done, but not necessary: give structure of remaining

paper in last paragraph of introduction

Important: The sentences within a paragraph should follow

a logical sequence

Introduction

Signalling the research question at the end of Introduction

To determine whether . . .
The purpose of this study was . . .
Therefore, we tested the hypothesis . . .
This report describes experiments designed to determine
whether . . .
Therefore, our first objective in these studies was to
determine whether . . .
In this study, we sought to extend our observations and to
specifically test . . .

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Contents

Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Responding to reviewers
Ethical issues
Submission to a journal
Language
Conclusions

Methodology

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Methodology

Clear and sufficiently complete other scientists, even

those not familiar with your specialty, could repeat the
Work
Assembe a simple collection of procedural outlines turn
this into prose
Use past tense
Provide references as necessary
Use subheadings if necessary
Do not include results in Methods
Often a figure can illustrate and clarify the method

Methodology

Find the balance between: Describing everything important and

Leaving out everything not needed.
Rule of thumb:
- New method, new instrument, new type of data Describe
in detail, since required for reproducibility
- Known method or instrument, previously used and
described in other paper(s) Often a reference is sufficient
Do not repeat descriptions
For chemicals exact technical specifications and source or
method of preparation
Avoid trade names of chemicals

Methodology

Examples of alternative titles:

Computational technique (appropriate for a numerical

paper)
Instrument and measurements (e.g. if a new
instrument is being described or used, or an instrument
is used in a non-standard mode)
Data and analysis technique (e.g. if the special
technique of analysing the data is essential for the
results)

Often studied carefully by the referee

Decides whether the results can be trusted or not
The paper will be rejected based on methodology

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Results

John Wesley Powell (March 24, 1834 September 23, 1902): a

U.S. soldier, geologist, and explorer of the American West

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How to write the Results

Written in the past tense

Heart of the paper needs to be clearly and simply stated
orderly and logical sequence, without interpretation
guide the reader through the findings, stressing the major points
Do not describe methods that have already been described in
the Methodology section
structure this section is to write it around the figures. However,
do not forget to make a logical order

Results

The core of the paper, where the results obtained during

the long labour of research are presented.
Be concise. Pre-select the results (i.e. identify the
important and new results) before writing about them in
the results section
Keep in mind: The fool collects facts, the wise man selects
them (John W. Powell)
Avoid repetition!

Assemble draft FIGURES and lay them out in order on a table

or desk
Decide what are the key points that you need to make, and
write them out

More Results

Decide on what to put into the Results section and what to

move to the Discussions section
General rule (but not a very hard and fast one)
Results section only describe the results, but do
not interpret them very much
Discussion section provide the interpretation and the
comparison with the literature, without repeating all the
results

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Results: Figures

Each figure must be referred to in the text must have a

caption
Captions short, but self-explaining
only clarify what is plotted and not try to interpret the
figure
For photomicrographs Dont forget scale bars!

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Axes
- Minimize tick marks
- Dont number each tick
Lettering
- Uniform, lower case
- Minimize, avoid bold
- After reduction, 2-3 mm high
Legend
- Gives message

Results: Tables

Make a table if you have multiple numbers to show and

you cannot put them into a figure, or if the exact
numbers are important
Remember, figures are generally easier to read than
tables.
Each table must have a title. Keep it short.
must be referred to in the text.
Never put the same data in the form of both table and
figure

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Contents

Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Ethical issues
Submission to a journal
Language
Conclusions

Discussion

Hardest section to write !

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How to write the Discussion

Primary purpose interpretation, synthesis, predictive speculation
Interpret your results present the principles, relationships,
and generalizations shown by the Results
How your results and interpretations agree or contrast with
previous work
Theoretical implications of your work, and any possible
practical applications
Point out any exceptions or any lack of correlation and define
unsettled points Present ambiguity and discrepancies
objectively
Explain what is new without exaggerating
Discuss key studiesonly those relevant to your work

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Structure and contents

First paragraph
- State major findings
- Paraphrase abstract

Middle paragraphs
- Base each on a major result
Always focus on your results
Never discuss prior work without
reference to your work
Refer Tables and Figures

Last paragraph
- In summary (2-3 entences)
- In conclusion (biggest
message, return to Intro, avoid
speculation, avoid need more
work

Contents

Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Responding to reviewers
Ethical issues
Submission to a journal
Language
Conclusions

Conclusions

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Conclusions
can wait to be written until rest of paper is
mature

First paragraph: focus on what you did. Begin with We have

used, We have investigated
Following paragraphs: one major finding per paragraph. First
sentence states the finding, following sentences elaborate.
Final paragraph should have some forward-looking
perspective. Dont let paper finish on a whimper!

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Reference

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A few words about references

Extensive referencing scholarly and ethical thing to do

useful to readers
makes your paper more accessible by search engines!
Be serious about literature search and reading papers
devote a bit of time to this each day
Never cite a paper for which you havent read at least the
relevant part
Cite papers in a context that makes it clear what the paper did
Dont cite textbooks
Theres nothing wrong with citing yourself or your group
extensively. But dont ignore what others have done!

Contents

Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Ethical issues
Submission to a journal
Language
Conclusions

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Dealing with
reviewers

Dealing with referees reports

anticipate revision: it is almost inevitable and generally beneficial

Complete additional experiments if needed
At first sight referees reports often look more negative than
they really are.
Read the report and then put it away for a week before looking at it
again (to calm down).
Discuss it with your supervisor and make the changes to the paper
asked by the referee
Point by point reply to the referee how you have taken his/her
comments into account
If you disagree with the referee and havent taken one of his/her
suggestions into account you explain why.organise the final version
of the paper and all ancillary data carefully before submission
Referees are not always stupid. If the referee does not
understand something, then it is likely that the paper is not
clear on this point. Make it clearer.

Do not respond to reviewers while upset

try not to take criticism personally or as a reflection of
incompetence on the part of reviewers
their failure to understand is your lack of clarity
be respectful, exact and direct in responding to the editor
Remain polite. Even if the referee is nasty, there is usually
nothing to be gained by showing your anger.
If you feel that you are being unfairly treated by the
referee you can ask for a second opinion.
Sincerely thank the editor and reviewers for helping you to
improve your work
They have invested a lot of time, mostly on a voluntary basis
Ask a neutral colleague to review your response

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Ethical issues in
publication

Ethical responsibilities of a scientist

Intellectual honesty
Accurate assignment of credit
Fairness in peer review
Collegiality in scientific interactions
Transparency in conflicts of interest
Protection of human and animal subjects

Common ethical issues

Redundant publication
Authorship disputes
Duplicate publication
Human welfare concerns
Data fabrication/falsification
Increasingly, includes inappropriate manipulation of
figures
Plagiarism
Conflicts of interest
Others (e.g., reviewer bias, submission
irregularities)

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Prior publication

Defined as:
Data
Extended verbatim text passages
Tables or illustrations

Redundant publication
Definition How to avoid
Using text or data from Do not include
another paper/prior material from a
publication (usually previous study in a
your own) in a new new one, even for
paper statistical analysis
Also called auto- or Repeat control groups
self-plagiarism as needed

What constitutes redundant publication?

Data in conference abstract? No

Same data, different journal? Yes
Data on website? Maybe
Data included in review article? OK if later
Expansion of published data set? Yes

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Authorship disputes
Definition How to avoid
Disputes arising from Agree on authors and
the addition, deletion, their order before
or change in the order starting the study
of authors Ensure all authors
meet criteria for
authorship
Sign publishers
authorship forms

Duplicate publication
Definition How to avoid
Submission of or Do not submit a paper
publication of the to more than one
same paper or journal at a time
substantial parts of a Wait until your paper is
paper in more than rejected before
one place submitting elsewhere
Withdraw a paper if
you decide not to re-
submit after being
invited to do so

Data fabrication/falsification
Definition How to avoid
Changing or making Present the exact
up data in a results obtained
manuscript
Do not withhold data
Intended to improve that dont fit your
the results hypothesis
Includes digital Dont try to beautify
manipulation of images with
images (blots, Photoshop any
micrographs, etc.) manipulations must
apply to the whole
image

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Unacceptable figure manipulation

Improper editing
Improper grouping
Improper adjustment
Authors should not:
Move
Remove
Introduce
Obscure
Enhance
any specific feature within a image. Images
should appear as captured in the lab

Improper editing
Boxes revealed during processing for publication; removal reveals debris

Bottom image from Rossner and Yamada, J. Cell Biol. 166: 11-15 (2004)

Plagiarism
Definition How to avoid
Taking the work of Provide citation to the
another work of others
Copying a figure, Obtain copyright
table, or even wording permission if needed
from a published or Do not copy exact
unpublished paper wording from another
without attribution source, even if
referenced, unless in
quotes

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Conflicts of interest
Definition How to avoid
Real or perceived Disclose all potential
conflict due to conflicts to the Editor
employment, and within the
consulting, or manuscript
investment in entities
with an interest in the
outcome of the
research

The Seven Deadly Sins

1. Data manipulation, falsification
2. Duplicate manuscripts
3. Redundant publication
4. Plagiarism
5. Author conflicts of interest
6. Animal use concerns
7. Humans use concerns

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ACKNOWLEDGMENTS

Include

Intellectual assistance
echnical help, including writing and data
analyses
Special equipment or materials
Outside financial assistance (including
grants, contracts, or fellowships)

Contents

Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Ethical issues
Submission to a journal
Language
Conclusions

Submission to
a journal

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Completion of research

Preparation of manuscript

Submission of manuscript

Assignment and review

Decision
Rejection Revision

Resubmission

Re-review

Acceptance Rejection

PUBLICATION!

Adapted from a figure by Dale Benos

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Most common reasons for rejection

of a manuscript

Major reasons for rejection

Inappropriate for the journal
Do your homework
Merely confirmatory/incremental
Avoid LPUs
Describes poorly-designed or inconclusive
studies
Focus on your hypothesis
Poorly written
Great science in an ugly package can still be rejected

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What makes a good research

paper?

Good science
Good writing
Publication in good journals

What constitutes good science?

Novel new and not resembling something
formerly known or used (can be novel but not
important)

Mechanistic testing a hypothesis - determining

the fundamental processes involved in or
responsible for an action, reaction, or other natural
phenomenon

Descriptive describes how are things are but

does not test how things work hypotheses are
not tested.

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What constitutes a good journal?

Impact factor
average number of times published papers
are cited up to two years after publication.

Immediacy Index
average number of times published papers
are cited during year of publication.

Outline
originality and
important
findings

Language

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Contents

Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Ethical issues
Submission to a journal
Language
Conclusions

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A scientific paper clear, objective, to the point

Strive for logical, linear flow. Put yourself in the perspective of the
reader
Be as short as possible. Every word must hurt
Be on the lookout for unnecessary words and sentences
Use short words (e.g., use vs. utiilize)
Remove value judgments: Surprising, interesting,
unfortunately have no place in a scientific paper.
Use scientific words as much as possible but with their precise
meaning
Avoid slang and jargon
Use the active voice whenever possible usually less wordy and is
unambiguous
First person is acceptable when the meaning is clear

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Avoid Wordiness Delete Unnecessary Words

Delete phrases which do not contribute to the

meaning of a sentence

Tense

Past or present tense preference is to some extent personal

Past tense is OK for describing results of an experiment but use

present tense for a general conclusion

WHATEVER TENSE IS USED, BE CONSISTENT AND

DONT SWITCH BACK AND FORTH IN THE SAME
PARAGRAPH !!!

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Some Common Problems

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Use of suggest that ; hypothesize that possible that

These phrases do not need may, might

Examples

Not correct: Our results suggest that Hoxa3 may be involved in

thymus development
Correct: Our results suggest that Hoxa3 is involved in thymus
development

Not correct: It is possible that Shh in the endoderm may regulate

Bmp4 expression in the mesoderm
Correct: It is possible that Shh in the endoderm regulates
Bmp4 expression in the mesoderm

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Proofreading Unimportant details tend to

be overlooked

BEFORE GIVING THE DRAFT TO YOUR

SUPERVISOR

Check the Figures versus the text

Check the References versus the text
Check the Figure legends

In general, edit a paper after printing it out and reading it

as a whole, rather than editing it on a computer screen

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Contents

Introduction
Before you start
General
Sections: Title, Abstract, Keywords, Introduction,
Methodology, Results, Discussion, Conclusions,
Acknowledgements, References
Submission to a journal
Ethical issues
Submission to a journal
Language
Conclusions

Signatures of a Professional Attitude

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Membership in a professional society
Subscription to at least one scientific
journal (Journals are available on
the web, but do you browse regularly,
as you would with a hard copy
issue?)
Familiarity with literature not directly
related to research.
Continually enlarging library with basis
reference books, e.g. physical,
inorganic, theoretical, etc.
Attendance at seminars, scientific
meetings; discussion with colleagues;
helpfulness. Presentation of research
results.
Eagerness to publish findings.

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