Scientific Writing: 

Journal articles & research 
papers
Dr Phil Stevenson
Dr Phil Stevenson
[Link]@[Link]

[Link]/adappt
 What do you want from your 
What do you want from your
published scientific paper?
• You want:
– To report scientific findings
– Recognition at work
g
– Peer recognition
– Recognition by a wider (global) audience
Recognition by a wider (global) audience
 Report scientific findings
Report scientific findings
•PPaper must be published!
b bli h d!
• Paper should reach a wide audience
Paper should reach a wide audience
p y
–Choose publication carefully
–Highest impact?
–Widest reach?
 Recognition at work
Recognition at work

• Enhance reputation.
Enhance reputation
• Help promotion prospects
Help promotion prospects
• Help career prospects
p p p
 Peer recognition
Peer recognition
• High quality paper ‐ enhanced reputation & 
external esteem.
• Research calibre assessed by publications 
Research calibre assessed by publications
– international level playing field.
• High quality comes from well written paper 
and high quality data
and high quality data.
 Recognition by a wider audience
Recognition by a wider audience
• Paper must be of high quality
• Paper must be readily found 
Paper must be readily found
using an electronic  search engine.
 Where do I start?
Where do I start? 
Research idea????
Is it novel/original?
g In a big
g or small
way?
C
Check Literature/Discuss
/ with
colleagues/Peers

Reference data bases

(Web of Science/Science Direct/PubMed
Google Scholar/Infoseek/Journals/etc)
 What is novel 
• Stevenson et al., 2007 evaluated effects of 
C i
Cassia sophera
h l
leaves on Sitophilus
Si hil zeamais i in 
i
Maize in lab and on station.
1. Effects of Cassia sophera on Sitophilus oryzae on 
rice? 
2. Identification of toxic compounds in C. sophera
against S zeamais?
against S. zeamais?
3. Farmer participatory trials of C. sophera to control 
storage pests of Maize
storage pests of Maize
4. Effects of Cassia sophera against S. zeamais in 
Z bi
Zambia
Can the “research”
Can the  research  be carried out 
be carried out
by you?
yy
Nature of research

Laboratory based: Literature/survey based

If something's worth doing – its worth

doing properly
properly.
Can the “research” be carried out 
b
by you at your
t i tit t ?
institute?
What are the requirements:
i) Scientific expertise
ii)) Available facilities /resources
(equipped laboratory + computing)
iii) Time frame (make a GANNT chart)
iv) Group project/collaborations through networks
v) Multi-disciplinary teams
vi) Collaborative approach
vii) Management/end goals
viii)) Financing
g – increasingly
g y the driving
g force.
The steps of the Scientific Method

Observation of phenomenon

Research Hypothesis

Prediction

Experimentation

Conclusion (s)

PAPER WRITING!!!!!
 Research Design

Materials, samples, chemicals

Equipment & instrumentation

Experimental protocols (complexity/diversity)

Methods of data analysis (e.g. statistics)

Seek advice – cooperate and collaborate

Th enemy is
The i ignorance
i nott your colleagues
ll
Research Design
g

Remember:
1) Health
H lth and dSSafety
f t rules
l and d regulations
l ti fforms
e.g. In UK Control of substances hazardous to
health (COSHH) – Health and Safety Exec
2) Ethics
3)) Consent forms
4) Are “ licences” required?
(e.g. Insects? GM materials? Material Transfer
A
Agreements? t ?CContract
t t agreements?) t ?)
5) Safety issues
6) Requirements of regulatory bodies
Institutional, National, International

Keep Voucher specimens!!!!

 Research Design

Where is the research to be “published”

p ((?):
)
i) “in–house news letter”
ii) internal report
iii) professional
f i l jjournal/publication
l/ bli ti
iv) scientific journal
a) impact factor
b) refereed
c)) p
printed/electronic
d) pure electronic “journals” (payment?)
v) book chapter
vi)
i) conference
f proceedings
di
vii) Poster at national/international conference
Major
M j considerations
id ti b
before
f embarking
b ki
on report of Research findings

•Research
Research, content and conclusions of manuscript
must be evidence based and statistically robust
• Avoid excessive conjecture
• Avoid assumptions
• But see the broader picture

•Use peer reviewed research methodologies and

statistical analysis

•The pleural of anecdote is NOT evidence!

 What to include
in your article?
This will depend on journal
This will depend on journal.
• Title
• Abstract
• Introduction
• Materials and Methods
• R lt ( ith T bl
Results (with Tables and Figures)
d Fi )
• Discussion
• Acknowledgments
• References or Literature Cited
References or Literature Cited
 Authorship 1
Authorship 1
• Establish co‐authors & who will write what

• Don’t have more authors than facts!

• Order of authorship
– 1st place usually to the principal author or 
investigator 
– Last place traditionally of second most 
significant spot – often taken by HoD
significant spot – often taken by HoD or PI
or PI
– Corresponding authorship often used to indicate 
overall project or research team authority.
 Authorship 2
Authorship 2
• Ethical guidelines on authorship
– All authors should be able to say what they 
y y
contributed constructively to the paper
– This is a requirement for many journals now
This is a requirement for many journals now
– Running the department doesn’t count! 
– Being someone’s boss doesn’t either!
i ’ b d ’ ih !
– Designing experiments & developing concept 
might
 Key approaches to writing: 
being read successfully
• Clear & Concise with Critical thinking (of your 
own research and other cited work). )
• Put yourself in the readers (referees) position
– Don’t make assumptions about readers knowledge
D ’t k ti b t d k l d
– Establish in‐house editorial groups 
– Get colleagues to read your work ‐ feedback
– Read colleagues work in return. 
Read colleagues work in return.
• Put manuscript in drawer for 2weeks and re‐read 
it helps to give new perspective
it – h l t i ti
What are you Writing and who for?
What are you Writing and who for? 
• Research papers
R h
– refereed journals
– conference papers
• Research/technical reports
Research/technical reports
– Press, Policy papers, technical reports for 
f di
funding agency.
• MSc /PhD Theses
• Read successful examples – critically.
• Don’t publish same work twice.
D ’t bli h kt i
 Choosing a Journal
h l
• Read journal aims and scope to determine if 
your work fits with the journal and readership
your work fits with the journal and readership.
• Can reject papers outright if outside scope. 
– Don’t waste your time
– rejection is deflating and resubmission requires a 
rejection is deflating and resubmission requires a
lot of work – re working style, references etc.
• R
Read recent papers from the chosen journal to 
d t f th h j lt
check content, style and length.
 Crop Protection Aims and Scope
Crop Protection – Aims and Scope
• The Editors of Crop Protection especially welcome papers 
describing an interdisciplinary approach showing how 
different control strategies can be integrated into practical
different control strategies can be integrated into practical 
pest management programmes, covering high and low input 
g y p p
agricultural systems worldwide. Crop Protection particularly  y
emphasizes the practical aspects of control in the field and for 
protected crops, and includes work which may lead in the 
near future to more effective control. The journal does not 
f ff l h ld
duplicate the many existing excellent biological science 
journals which deal mainly with the more fundamental
journals, which deal mainly with the more fundamental 
aspects of plant pathology, applied zoology and weed science.
p
Crop Protection covers all practical aspects of pest, disease 
p p p
and weed control, including the following topics:
 Impact and readership
Impact and readership.
• Impact factor (ISI‐Thomson Reuters)
Impact factor (ISI Thomson Reuters)
– mean annual citations per article in most recent two years 
following publication i e in 2010 and 2009 for 2008 papers
following publication.  i.e.,  in 2010 and 2009 for 2008 papers.
• Nature IF = 34 
• Current Biology IF = 10
• Pest Management Science = 2.2
• Crop Protection IF = 1.3
• African Journal of Biotechnology IF = 0.6
African Journal of Biotechnology IF = 0 6
• African Journal of Agricultural Research IF = 0.08 (<10%)
– Can look these up on web for individual journals
C l k h b f i di id l j l
– Many new journals (especially on line) don’t yet have them. 
 Instructions for authors
Instructions for authors
• Read them thoroughly 

• They are provided for a reason.
– Uniformity
– Economy  of space.
y p
– suggested length of sections, things to include, 
options for supplementary information, style –
options for supplementary information, style 
particularly references etc
 Plagiarism in publishing
Plagiarism in publishing 
• Plagiarism
Plagiarism is a very serious academic and 
is a very serious academic and
publishing offence. 
• In UK – students get suspension from the 
d f h
University and a mark of zero. This could lead 
to course failure 
• Professional staff can be sacked
Professional staff can be sacked
• Submitted manuscripts rejected (authors 
names noted). 
• Loss of academic integrity. 
Loss of academic integrity
 Plagiarism what is it? 
Plagiarism – what is it?
• Copying others work (even if you cite)
– Entirely copied work
y p
– Word for word sections of others work
– Concepts and ideas process (intellectual property)
Concepts and ideas process (intellectual property)
– Crude paraphrasing
 Plagiarism avoiding it.
Plagiarism – avoiding it
• Keep careful and complete track of sources. 
• Distinguish between your ideas and others.
Distinguish between your ideas and others.
– intellectual honesty
– if you use other’s conclusions, acknowledge them 
if h ’ l i k l d h
even if you came to same conclusions yourself. 
• Distinguish carefully your own words and 
p
experimental work and those of others. 
 Plagiarism avoiding it.
Plagiarism – avoiding it
• Organizing your writing in an original manner.
– Avoid mimicking pattern or order of argument 
gp g
used by others. Remember: this is YOUR 
contribution
• As you weave others ideas into your work, 
make clear choices about the use of quoted
make clear choices about the use of quoted 
material. 
• Avoid close paraphrasing or purely cosmetic 
changes.
 Plagiarism avoiding it.
Plagiarism – avoiding it
• Write an initial draft without actually looking 
y
at your source material.
• add specific facts later once own 
comprehension written
comprehension written.
• effective paraphrasing is not the same as 
substituting synonyms and rearranging words 
– this is plagiarism even where the source is 
this is plagiarism even where the source is
cited!
Original:
If the existence of a signing ape was unsettling for linguists, it was also
startling news for animal behaviorists. ---Flora Davis (1978), Eloquent
Animals, p. 26

Version 1:
According to Flora Davis (1978), linguists and animal behaviorists were
unprepared for the news that a chimp could communicate with its trainers
through sign language (26).

Version 2:
The existence of a signing ape unsettled linguists and startled animal
behaviorists (Davis, 1978).

Version
V i 3:3
If the presence of a sign-language-using chimp was disturbing for
scientists studying language, it was also surprising to scientists studying
animal
i lbbehavior
h i (D (Davis
i 1978)
1978).

(Sa p es ta
(Samples taken
e from
o Diana
a a Hacker’s
ac e s Rules
u es
for Writers, 3rd ed. p. 356)
 So what do you write first?
So what do you write first? 

• Title
• Abstract
• Introduction
• Materials and Methods
• R lt ( ith T bl
Results (with Tables and Figures)
d Fi )
• Discussion
• Acknowledgments
• References or Literature Cited
References or Literature Cited
 But what do you write first?
But what do you write first? 
• Title 6
• Abstract 5
• Introduction 4
• Materials and Methods 3
• Results (with Tables and Figures)
Results (with Tables and Figures) 1
• Discussion 2
• Acknowledgments 7
• Literature Cited
Literature Cited 17
1‐7
 Choosing a Title
Choosing a Title
• Make the title specific:
– A good title should describe the contents of the 
g
paper in the fewest possible words.
– Keep to 12 words or less.
Keep to 12 words or less
• The title should be appropriate for the 
intended audience (particularly the referee).
d d d ( l l h f )
• It should make people want to read  the 
p p
paper. 
 Compare
• A study of the effects of chaos as a source of 
p y y y
complexity and diversity in evolutionary 
processes.
• Chaos as a source of complexity and diversity 
Chaos as a source of complexity and diversity
in evolution
 Title Guidelines
Title Guidelines
• Titles contain key words. 
• Some are more important than others.
Some are more important than others.
• Place key words near the start of the title 
– makes it easier for reader to determine what 
paper is about.
 Title Guidelines
Title Guidelines
• Insert searchable keywords in your title.
• This makes it easier for your work to be found 
This makes it easier for your work to be found
using web‐based engine.
 Compare word search
Compare – word search

• Interim Technical Report on progress from the 
ADAPPT project
ADAPPT project.

• Optimising use of Pesticidal Plants against 
cattle ticks and maize pests in Africa: ADAPPT 
cattle ticks and maize pests in Africa: ADAPPT
Project interim report. 
 Title Guidelines
Title Guidelines
• Suit the title to your audience.
 Compare

• Fat Rats: What Makes Them Eat?
at ats at a es e at
– New Scientist.
• Th
The role of Luteinising Hormone to Obesity in 
l fL t i i i H t Ob it i
the Zucker Rat
– Journal of Neuroendocrinology
• Rats hold the key to a gorgeous body. 
Rats hold the key to a gorgeous body
– The Daily Mail.
Scientific names in title help clarity about content and
with citations.
But avoid overdoing it! – e.g. Family names etc
 The Abstract
The Abstract
What did I do in a nutshell
• The abstract should provide a very short 
summary of your work
summary of your work.
• It should stand on its own and it should not be 
too technical or 
h l
bulging with data
bulging with data
• It should state 
your main findings
and conclusions.
and conclusions.
 Reality of Abstracts
Reality of Abstracts
• ITS OFTEN THE ONLY PART OF YOUR PAPER 
THAT WILL EVER BE READ.

• Publications databases 
provide abstracts only

• Shouldn’t be unintelligble
– Even if nice to look at
 The Abstract: What it should 
The Abstract: What it should
contain

• Very briefly (check word count with journal 
and guidelines) write:
– What you did,
– Why you did it
Why you did it
– What are the results implications
Background information and 
why we did the work 
What we did and 
the results
the results
Conclusions and 
implications
In some journals abstracts
are limited to record the
experimental work only
 The Keyword List
y

• opportunity to add words used by indexing 
t it t dd d db i d i
and abstracting services 
• They are often but not exclusively additional 
to those in the title
to those in the title. 
• Helps others find your work and cite it. 
• All research quality now determined by 
citation indices.
 The Introduction
The Introduction
• The purpose of the introduction is to:
– Establish the context of the work being reported. 
g p
– This is accomplished by discussing (as briefly as 
possible) the relevant primary research literature 
possible) the relevant primary research literature
(with citations) and
– Summarizing current understanding of the 
Summarizing current understanding of the
problem you are investigating.
 The Introduction
The Introduction
• State the purpose of the work in the form of 
yp q p y
the hypothesis, question, or problem you 
investigated.
 Background to subject

From Stevenson et al., 2009 Journal of Agricultural and Food Chemistry, 57, 8860
 Reason for this particular work

From Stevenson et al., 2009 Journal of Agricultural and Food Chemistry, 57, 8860
 Background to research in paper

From Stevenson et al., 2009 Journal of Agricultural and Food Chemistry, 57, 8860
 Aim of present study

From Stevenson et al., 2009 Journal of Agricultural and Food Chemistry, 57, 8860
 The Introduction
The Introduction
• Briefly explain your rationale and approach 
p p
and, whenever possible, the possible 
outcomes your study can reveal. 
 Experimental Details 
(Materials and Methods)
• This section of the paper ought to contain the 
g pp p
following details where appropriate:
– Materials used;
– Organisms used
Organisms used
– Instruments used
– Experimental protocols
 Experimental Details
Experimental Details
• These experimental section should contain 
g p
enough details that a competent researcher 
could repeat your experiment.
• The cornerstone of good science is 
The cornerstone of good science is
reproducibility and repeatability.
Materials
 Experimental Methods
Experimental Methods
Manufacturer Instrument 
used
Use tables where 
they help clarify 
y p y
the narrative 
Use diagrams 
g
to help clarify 
experimental 
experimental
details
 Be precise
Be precise
• When giving details of measurements such as 
g g
the temperature of the oven be precise.
• Accurate methods allow your work to be 
A t th d ll kt b
repeated and verified by others. 
• Which is better?
– The experiment was carried out at room 
The experiment was carried out at room
temperature!
– The experiment was carried out at 23 ±
The experiment was carried out at 23 ± 1°C
 Grammar : Use 
G U
the third person 
p
past passive voice.
 Results
• Present your results clearly and HONESTLY
• When possible use tables and figures 
When possible use tables and figures
effectively
 Results
• Do not repeat all of the information that 
pp g
appears in a table or figure in the text; but do 
summarize it. 
• Draw out key points
Draw out key points
 Using Tables
Using Tables
• For example, if you present a table of 
p
temperature measurements taken at various 
times, describe the general pattern of 
temperature change and refer to the table
temperature change and refer to the table. 
• "The temperature of the solution increased 
rapidly at first, going from 50º to 80º in the 
l f f h
first three minutes (Table 1)."
 Using graphs
Using graphs
• Make graphs clear and provide them with a 
p
suitable caption.

• They need to be 
able to stand alone
able to stand alone
 Results only
Results ‐
• Make sure you keep the results section just for 
results
• Some journals combine Results and Discussion
 Discussion
• It is not enough to simply present your data 
again in a slightly different way
• Discuss their significance and implications.
Discuss their significance and implications
• Discuss the meaning of individual results in 
this section; but wait until the conclusions 
y g g
section to tie everything together
• Conclusions are sometimes a 
separate section.
 Issues that need discussion
Issues that need discussion
• Were the results consistent with your 
p
expectations?
• Does experimental error account for any 
deviations between the results and your
deviations between the results and your 
expectations?
 Issues that need discussion
Issues that need discussion
• What underlying patterns or relationships 
y
exist in your results?
• Do these results support the hypothesis that 
you were testing?
you were testing?
• Do these results support the 
predictions/expectations in the literature?
Don’t try to gloss over problems in 
your results.
• If your results show a smooth curve with an 
p p
unexpected dip in the middle, avoid the 
temptation to gloss over the unexpected 
deviation – it may turn out to be the most 
deviation  it may turn out to be the most
important part of your data.
 Discuss data treatment
Discuss data treatment
• There are times when you have may 
p y gy
developed a novel way of treating your data. 
This can go in the discussion section. Though 
sometimes it may go into a separate section
sometimes it may go into a separate section.
 What has 
been found 
and 
achieved?
 Acknowledgements
• If you received any significant help in thinking 
p g g y g
up, designing, or carrying out the work; or 
received free materials from someone you 
must acknowledge their assistance and the
must acknowledge their assistance and the 
service or material provided. 
• Although usual style requirements (e.g., 1st 
lh h l l (
person, objectivity) are relaxed somewhat 
here – “Acknowledgments” are always brief 
and never flowery.
and never flowery.
 References
• All the citations in the corpus of the text need 
p
to be identified in the reference list placed at 
the end of the paper.
 References
• Ensure that the formatting of the citations in 
the text and reference list conform with the 
style of the journal your article will be sent to.
style of the journal your article will be sent to.
• This really bugs editors – get it right!
• Laziness here could tempt a referee to assume 
y g
laziness elsewhere in carrying out the work or 
even collating results. 
• Every part of your written work gives an 
Every part of your written work gives an
impression of your overall scientific calibre. 
Name and 
date
 List in 
alphabetical order
l h b i l d
Numbered 
references
f

List in numerical 
Li i i l
order
 Reviewers guidelines ‐
Phytochemistry
• Please examine the paper with reference to the 
q
questions on this form

(1) Does the paper fall within the scope of the 
(1) Does the paper fall within the scope of the
journal? 

(2) Is it a new and original contribution? 

(3) Are there any assumptions made which you 
consider unjustifiable? 
 Reviewers guidelines –
Phytochemistry 2

(4) Are there any apparent errors of fact or logic? 

(5) Is the length of the paper in keeping with its 
(5) Is the length of the paper in keeping with its
importance? 

( )
(6) Are the Titles and Abstract informative? 

(7) Is the English satisfactory?

(7) Is the English satisfactory? 
 Reviewers guidelines –
Phytochemistry 2

Please add below any additional

COMMENTS th thatt you may h
have
for the Editor:
 Phytochemistry
• REJECT

• This paper describes three new benzofurans from Anotherus plantus The
This paper describes three new benzofurans from Anotherus plantus. The 

structures are secure but represent trivial variants of known compounds. Since the 

authors have already published two papers in this series and announce their 

intention of looking at other parts of this plant I suggest that they include these
intention of looking at other parts of this plant I suggest that they include these 

compounds in a subsequent publication of more substance. 
 Bichemical Systematics and Ecology
Bichemical Systematics and Ecology
• REJECT
C
• Larvicidal effects of essential oil and methanolic extract of A plant…...
• Bloggs et al. 
• This manuscript describes a single bioassay of essential oil and methanolic extract 
against Echinococcus granulosus.  Despite being a new biological activity the 
manuscript is too insubstantial for BSE and lies outside the scope of the journal.  
p p j

• The abstract gives the impression that the authors have actually analysed the 
essential oil but in fact authors simply include write data published elsewhere
essential oil but in fact authors simply include write data published elsewhere   
(Ahmadi 2010). (Plagiarism).  (Hood winking editors)

• The bioassays are presented with no statistical analysis to demonstrate variation in 
Th bi t d ith t ti ti l l i t d t t i ti i
the data and no scientific evidence is provided to substantiate claims about the 
compounds purported to be responsible for the biological activity.  
 BSE / 10‐XXX  Major revision (probably should have 
been reject )
been reject...)
• Hydroxywithanolide as a chemical resistance of Cape Gooseberry against 
herbivory. 
• Bloggs et al. 

• This manuscript describes a comprehensive analysis of cape gooseberry for 4‐beta 
This manuscript describes a comprehensive analysis of cape gooseberry for 4 beta
hydroxywithanolide. 

• The paper has demonstrated this compound occurs in the plant at higher 
h h d d h d h l h h
concentrations in roots than in leaves in mature plants but at lower concentrations 
in roots than in leaves in seedlings and asserts this is to do with their role in 
resistance
it

• The paper is far too long and makes what is a fairly simple outcome is made too 
complicated.  
•
 BSE / 10‐XXX  Major revision (probably should have 
been reject )
been reject...)

• The introduction. 
The introduction
• The introduction needs to be shortened by at least half and the text needs to be 
relevant to the research activities that will be covered in the text.  Presently it is 
more like a review of strategies to reduce resistance costs.  
lik i f t t i t d it t
•
• The methods
• Similarly, the methods are far too long. Attempt to reduce by at least half. The 
introduction spills over in to methods.  The authors need to shorten this to the 
absolute minimum.  E.g. cite previous uses or combine repeated uses of same 
method
•
• The methods contain results and introduction.
The methods contain results and introduction. 
•
• NMR data for 4beta hydroxywithanolide and physapruin has been already 
published elsewhere so not required here.  It is welcome as supplementary 
published elsewhere so not required here It is welcome as supplementary
information but not for publication. 
 BSE / 10‐XXX  Major revision (probably should have 
been reject )
been reject...)

• Results:  
l
• Results should be much more concise.  Combine sections. 
• Logic fails with insects pests chosen to test Physalis resistance compounds because 
they are not pests of Physalis.  Epilachna is a specialist bean beetle, Tribolium 
castaneum feeds on flour and grain (not Physalis) no record of Spodoptera littoralis
being a pest of Physalis.  
•
• Discussion 
• Again too long by at least half A simple result is over‐complicated
Again too long by at least half.  A simple result is over complicated.   The 
The
extrapolation of the results to highly significant implications is largely unconvincing 
and may be made more so by a considerable reduction in the text to the salient 
points. 
points.
• Figures are excessive and most can be described in the results without the need 
for a table. E.g. Table 1 to 5 could be omitted and simply described in a few words 
in the text as could Figure 5 Figures need indication of statistics used including
in the text as could Figure 5.   Figures need indication of statistics used including 
error bars.  
 Accepted with revision
Accepted with revision
• Address the comments of the referee
• Be conciliatory
Be conciliatory
• Be assertive
• Do what you’ve been asked if it means the 
p g
difference between publishing and not.
• Provide the editor a clear inventory of changes 
t
to original manuscript.
i i l i t
– Thoroughness here is a helpful for the editor
 Proofs proof reading
Proofs – proof reading
• And just when you thought you couldn’t read 
dj h h h ld ’ d
a page of the work one more time…….   …..the 
galley proofs arrive with 24 hours to return 
them

• If
If you miss a typo now it now it will be ever 
you miss a typo now it now it will be ever
thus!

• Proof read your manuscript at least twice 
 Key approaches to writing: 
being read successfully
• Clear & Concise with Critical thinking (of your 
own and cited work). )
• Put yourself in the readers (referees) position
– Don’t make assumptions about knowledge
D ’t k ti b tk l d
– Establish in‐house editorial groups 
– Get colleagues to read your work – get feedback
– Read colleagues work in return. 
Read colleagues work in return.
• Put manuscript in drawer for 2 weeks and re‐
read it –
d it helps to give new perspective.
h l t i ti
 More information
More information
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• Colorado State University
Colorado State University
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