1. Dr Margaret Cargill, for Bogor Agricultural University 2017
Incorporating article writing into science methods courses: 1 day workshop

2. Margaret Cargill BA, DipEd, MEd(TESOL), DEd
Writing and publication skill development for research students and staff in the sciences for 25 yrs
Collaborative paper writing workshops for universities and research institutes in Australia, Asia and Europe
Past editor of the journal TESOL in Context; active reviewer for international journals and conferences
Adjunct senior lecturer, University of Adelaide
Principal Consultant: SciWriting: Communicating science effectively in English
Delivers training in publication skill development to University departments, research institutes (government and private), attendees of scientific conferences and individual clients/ research groups

3. Participant introductions
Name and IPB Department
The methods course you teach
Your two top aims for this workshop

4. A note on ppt slide arrangement
Slides with the heading in red, as above, are directed at you, the lecturers
Slides with the heading in blue can be copied and used directly with students
In these, ‘you’ means the student (or anyone taking the course as a participant), as well as you, the lecturer participating in this workshop
Margaret Cargill, University of Adelaide

5. A method for developing international publication skills
Use your existing research skills on the problem of getting articles published
Analyse successful articles – and journals
Use results of applied linguistics research to highlight key points for focus
See ‘Writing scientific research articles: strategy and steps, 2nd Ed.’ (M. Cargill & P. O’Connor 2013, Wiley-Blackwell
Develop strategies for ‘playing the game’

6. Two ways to manage integration of article writing into methods courses
Teach the methods content first, then add on the article writing material as a separate segment
Teach the article writing material at suitable points within the methods content
This can reinforce the methods content
It allows you to make specific points about writing that are relevant to your own discipline/field of research
Your choice: what works best for your context?
Margaret Cargill, University of Adelaide

7. For both options
Students need one or more example published article/s to consult during the course
Supplied by you, if one article can be understood by all class members (helpful for writing assignment questions)
Or – each student selects and brings their own example article, using selection criteria decided by you
Possible selection criteria
SCOPUS listed journal, cited internationally, native English speaker author, relevant to their own research
Margaret Cargill, University of Adelaide

8. Book overview
Chapter 15 (p. 109) gives a concise list of steps to take in writing a manuscript (ms) for international submission
Table of Contents (p. v) highlights the order in which students should learn about the components
3 full published papers are included as Chapters 19-21, but may not be suitable for your students
In this short workshop I skim through the article writing process, emphasising teaching strategies you can consider
Margaret Cargill, University of Adelaide

9. What about the English skills?
IPB English teachers are trained and interested to collaborate with you
They can introduce your students to tools and strategies by presenting guest lectures
They can work with you to co-teach some lectures, e.g on Introductions
See also Chapter 17 for specific guidance on relevant English language features
Section 7.3 (p. 39) gives guidance on active/passive verbs – useful for Methods sections
Section 8.9 (p. 54) has tips on teaching students to edit their writing for flow and linking.
Margaret Cargill, University of Adelaide

10. An image to consider
A diagrammatic representation of the written presentation of an experimental study (Weissberg and Buker 1990)
the ‘driver’

11. From Results to paper outline
Our experience suggests that a productive way to begin preparing a paper is to focus first on your results
With your co-authors, identify a ‘package’ of results that tell a single ‘story’ and support a clear ‘take-home message’ (THM)
Then identify a journal for which this THM is relevant and interesting
This becomes your ‘target’ journal

12. Choosing your target journal
Balance needed between several factors:
How important is Impact Factor to you?
If you aim too high, rejection could lead to delays in getting the work published
Who do you really want to read this paper?
Which journals do you cite most in the paper?
Is the contribution of the paper of local or more global significance?
Talk about this and get advice from supervisors early
(See pp. 6-9)

13. Instructions to Contributors
Seek them out early in the preparation period
Read Overview/Scope/ Aims section in particular and check for a close match with your research
Check for downloadable template of required format for manuscript
Note table/figure requirements in detail
Submissions are often returned without review if instructions are ignored

14. Instructions to Contributors
Seek them out early in the preparation period
Read Overview/Scope/ Aims section in particular and check for a close match
Check for downloadable template of required format for manuscript
Note table/figure requirements in detail
Submissions are often returned without review if instructions are ignored

15. What sort of papers get into New Phytologist?
Papers must focus on timely research that provides new insights into the broad principles of plant biology.
The research should be original, addressing clear hypotheses or questions and be of general interest to our readers.

16. The AIMRaD article structure
A historical artefact that has grown out of a tradition begun in 1665
Provides a structure to enable authors to tell the story of their research:
Not the story they thought they would tell when they planned the research, but
The story they can tell now the results are analysed and the implications thought through.
Some variation occurs – always check your target journal

17. The AIMRaD article (Weissberg & Buker 1990, Cargill & O’Connor 2009)
Abstract
Introduction
Materials and Methods
Results
Discussion

18. For many chemistry or ‘molecular’ papers: AIRDaM
Abstract
Introduction
Results
Discussion
Materials and Methods

19. AIM(RaD)xC: With combined R&D sections

20. For theoretical/modelling/computing/review papers: AIBC
Abstract
Abstract
Introduction
Body of paper (with content-based subheadings)
Conclusion
Introduction
Development of model/ validation, or problem/ solution or theory/ algorithm, etc.
Conclusion

21. Task: Students analyse their example published paper
Analyse the example article you brought with you from your target journal:
Note down the headings and subheadings of your article, including their relationship to each other (i.e. levels of headings).
Which of the structures presented in the preceding slides best matches your example?
Which structure will you use for writing your own article?
Best answer to this question is “It depends on the target journal and my results ‘story’”

22. Notes on the AIMRAD Diagrams
These are conceptual diagrams: It is the width and shape of the boxes that is important, not their depth (i.e. no reference to the length of the section)
The whole structure is governed by the Results or outcome of analysis
Introduction begins much ‘broader’: making firm contact with the selected audience, at the logical contact point

23. Notes on the AIMRAD Diagrams 2
Between start and end of Introduction, background information and previous work are woven together to justify the study
Introduction ends with the aim of the present study OR a summary of the main activity of the study/paper OR findings of the study (depending on the research field and the journal conventions)

24. Notes on the AIMRAD Diagrams 3
M&M establishes credibility for Results by showing how they were reached and why they should be trusted
Discussion begins at same ‘width’ as Results, but by the end is the same width as start of Introduction – addressing the same ‘big picture’ issue as was the focus at the beginning
Even when Results and Discussion are not combined, the paper may have a Conclusion section to address the ‘big picture’

25. Gatekeeper requirements
How do the AIMRaD structures relate to what editors and referees want to publish?
The structure has survived because it can allow scientist authors to tell the stories they need to tell, within an understood set of conventions.
“I can only jump because I know where to look.” (Burrough-Boenisch, 1999)

26. A collated Referee Report Form (sciences)
Is the contribution new?
Is the contribution significant?
Is it suitable for publication in the Journal?
Are all conclusions firmly based in the data presented?
Do the methods and the treatment of results conform to acceptable scientific standards?
Is the organization acceptable?
Is the length of the paper satisfactory?

27. A Referee’s Report Form cont.
Are all illustrations required?
Are all the figures and tables necessary?
Are figure legends and table titles adequate?
Do the title and abstract clearly indicate the content of the paper?
Are the references up to date, complete and the journal titles correctly abbreviated?
Is the paper Excellent, Good or Poor?

28. Task: Students try to think like journal referees
Work in pairs
For the first 4 criteria on the preceding slide, decide where in the manuscript (i.e. in which section/s) you think a referee would expect to find evidence on which to base their answer
Be ready to report when asked

29. Using results as the key ‘driver’
Strategic approaches to preparing results for papers
Decide on the ‘take-home messages’
Refine the tables and figures to tell those messages clearly
Write captions (titles and legends) to capture as much of the message as possible
Write the related subheadings, paragraphs and sentences for maximum effect
Ensure your paper title reflects the key message/s

30. Strategic refining questions
Are these data essential to the ‘story’, or could they be in an appendix/supplementary material?
What message do I want the reader to get from this table/figure?
Therefore, is a table or figure better?
(Why?)

31. Tables are useful for: Databases - recording data (raw or processed)
Explaining calculations or showing components of calculated data
Where the actual numbers are important
Where there are numerous individual comparisons to be made, in many directions
See handout for an effective example

32. Figures are more useful where:
The overall picture is important
The results can be comprehended more rapidly through shape than through number
The comparisons between elements are relatively simple

33. This material can be taught best when teaching research methods
Chapter 5 contains guidelines that are relevant for most disciplines and data analysis methods
You can adapt these guidelines for your specific types of analysis
A good task is to give students a set of relevant results and ask them to prepare a table or figure that clearly highlights the THM of the dataset
Include the task of writing the caption
Margaret Cargill, University of Adelaide

34. Reference to tables and figures in the text
All tables and figures should be
presented sequentially
referred to in that order in the text,
preferably before the table/figure appears on the page (not applicable when files are uploaded separately for submission to the journal)

35. Figure legends A title that summarises what the figure is about
Details of results or models shown in the figure
Additional explanation of the components of the figure, methods used, or essential details of the figure’s contribution to the results story
Description of the units or statistical notation included
Explanation of any other symbols or notation used
Table titles can include same elements – Parts 2 and 3 usually brief, no Part 5

36. Relation to the ‘take-home messages’
Once you have refined the data presentation
Decide on an optimal grouping and order for them, to highlight the appropriate number of ‘take-home messages’
Think: evidence for the points to be presented in the Conclusions
And: meeting the Objectives given in the Intro.
You are answering the question ‘What do my results say?’

37. Task: students refine their figures/tables
Work on your own figures/tables to refine their effectiveness
Then, for each one, write dot-points that capture the key messages presented
Next to each dot-point, indicate whether the point will be written about in the Results of Discussion section of the paper
If this process suggests points for Methods or Introduction, note these down as well.
Check that the dot-point information is clearly visible in the text you have written in the relevant sections – if not, redraft!

38. Writing Results: The “Story” of the paper
You present your Results in the tables and figures
In writing about them, highlight the key points…
…but don’t restate everything.
Concentrate on the important results (the ones you want to focus on in the Discussion)
You should be able to reduce results to a series of “dot points” before you start writing the sentences

39. Writing about Results: Information elements
A statement that locates the figure/s or table/s where the results can be found (L)
Statements that highlight the most important findings (H)
Statements that comment on (but do not discuss) the results (C) (Weissberg and Buker 1990)

40. Which elements are present in each sentence?
1A total of 53 samples were examined. 2Direct microscopic examination of the samples showed 20 different fungal strains, which were isolated by culture and identified to the level of genus and/or species (Table 1). 3These findings show that fungi can tolerate adverse environmental changes in the vegetative form. 4Table 2 shows the results of the tests applied to the isolates. 5None of the fungi strains was able to grow in culture media with 500 to 5000 mg L-1 of anionic surfactant. 6An inhibitory effect on fungal growth and activity might be expected from the anionic surfactant level found in the ponds. (cited in Weissberg and Buker 1990)

41. Tense usage in results writing 1
Present tense = ‘always true’
Use when the sentence focuses on the document, e.g.
Here we present …
Table 5 shows the results of …
Use also when the result is claimed as being a fact that is always true, e.g.
The protein identified on the PBM-enriched protein fraction is approximately 10 kDa larger than that predicted by the amino acid sequence of GmDmt1.

42. Tense usage 2
Simple past tense = completed at a specified time in the past
Use when the sentence focuses on what was done or found in the study
There were no significant differences in the amplitude of contractions during any of the infusions.

43. Tense usage 3
Present perfect tense = completed over a time range in the past, or time not known or not important; has an effect in the present
We have identified an Nramp homologue, GmDmt1, which is expressed in soybean nodules and encodes a divalent metal ion transporter located on the symbiosome membrane (Kaiser et al., 2003)
It has been suggested that AtNramp has an intracellular localisation (Grotz and Guerinot, 2002).

44. Which tenses and why?
1A total of 53 samples were examined. 2Direct microscopic examination of the samples showed 20 different fungal strains, which were isolated by culture and identified to the level of genus and/or species (Table 1). 3These findings show that fungi can tolerate adverse environmental changes in the vegetative form. 4Table 2 shows the results of the tests applied to the isolates. 5None of the fungi strains was able to grow in culture media with 500 to 5000 mg L-1 of anionic surfactant. 6An inhibitory effect on fungal growth and activity might be expected from the anionic surfactant level found in the ponds. (cited in Weissberg and Buker 1990)

45. Use your Introduction to justify your study in a compelling way – argument ‘stages’
To recap: Introductions are important to show
novelty
significance
suitability for the target journal readers
Analysis has shown that there is a set of very common ‘stages’ that appear in published science article introductions
Focus here after your results ‘story’ is clear

46. Introductions: the argument ‘stages’
1. Statements about the field of research which provide the reader with a setting or context for the problem to be reported and claim its centrality/ importance
2. More specific statements about the aspects of the problem already studied by other researchers, laying a foundation of information already known
3. Statements that indicate the need for more investigation, to create a gap or research niche for the present study

47. Introductions: the argument ‘stages’ 2
4. Statements giving the purpose or objective of the author’s study OR its principal activity OR its main results (depending on field/journal)
5. Optional statement(s) that give a value or benefit of carrying out the study (all fields)
6. A ‘map’ statement to show how the rest of the article is arranged (some fields only, and most review articles)

48. Task
Read the Introduction on the following 3 slides. Identify the stages present and their order. Remember that stages and sequences may recur. Discuss with your neighbour.

49. Spatial Distribution of Litter and Microarthropods in a Chihuahuan Desert Ecosystem
1In most deserts of the world, transitions between topographic elements are abrupt and watercourses which are dry most of the time tend to dissipate their occasional waters within local basins. 2Occasional torrential rainfall, characteristic of most desert regions, washes loose debris into watercourses or transports this material, depositing it in and along the shores of ephemeral lakes. 3These physical processes result in a redistribution of dead plant material (litter), affect the distribution of soil water and create a heterogeneous biotic community. 4Therefore, before the dynamics of desert ecosystems can be adequately understood, the spatial relationships must be clarified.

50. 5There have been few studies of litter distribution and/or soil fauna in any of the world’s deserts (Wallwork, 1976). 6Wood (1971) surveyed the soil fauna in a number of Australian arid and semi-arid ecosystems. 7Wallwork (1972) made some studies of the microarthropod fauna in the Californian Mojave desert and Edney et al. (1974, 1975, 1976) studied abundance and distribution of soil microarthropods in the Mojave desert in Nevada.

51. 8In the Chihuahuan desert, Whitford et al
8In the Chihuahuan desert, Whitford et al. (1975, 1976, 1977) described the spatial relationships for many groups of organisms, but soil micro-arthropods remain unstudied. 9The lack of such information represents a gap in our knowledge of desert ecosystems. 10As part of our continuing program of studies of the structure and dynamics of Chihuahuan desert ecosystems, we designed the study reported here to understand the relationship between litter redistribution and the spatial distribution and composition of the soil microarthropod community. (Cited in Weissberg and Buker, 1990)

52. Task: students analyse argument stages in their own published Introduction
Read the introduction to the article you have selected for analysis. Decide if all stages are present, and where each one begins and ends.
Be ready to report when asked

53. Drafting an Introduction for known results
To draft your own introduction (after the results story is clear), our suggested order for drafting is Stages 4, 3, 1, 2, (5) – then combine and refine to produce the best logical order for the audience.
Tip:
First ensure that your Stage 4 is complete, including all necessary parameters of the study
Then draft Stage 1/Stage 2 combinations to justify each part
Each may need a Stage 3 component at the end

54. What about starting with Methods?
You can write methods any time after you know which results will be part of the paper
Every piece of method information you write must connect with a result in your Results section
Content and organisation of Method sections differ for different disciplines; important to work from published examples in relevant fields
3 basic components:
Contextualising study methods
Describing the study
Establishing credibility

55. (Materials and) Methods
Stated purpose is that the work can be repeated
True in your experience?
A key purpose of the M section is to establish the credibility of the Results
Cite methods if they are previously published
Describe in full if readers lack access to the original publication
All novel methods must be described in full
Passive voice verbs are commonly used throughout – but check recent examples of the journal!

56. A Methods paragraph for analysis: 2.3 Protein analysis
Protein content of meals was measured by nitrogen combustion (LECO Corporation, St.Joseph, MI). The proportions of polymeric protein, gliadin, albumin/globulin, and the unextractable polymeric protein (UPP) were measured by SE-HPLC using a Hewlett Packard system equipped with automatic injector according to the procedure of Gupta et al. (1993). Proteins were separated on a Biosep-SEC-S-400 column (300 x 7.8mm, Phenomenex, Torrance, CA) preceded by the respective guard column. The eluting solvent was acetonitrile/water (1:1 v/v) containing 0.05% TFA (v/v). All analytical tests were performed at least in duplicate. Analysis of variance was carried out using the Statistical Analysis System (SAS Institute, Inc., Carey, NC).
(J. Cereal Sci. 48 (2008) )

57. Using information categories instead of terms
(NP=noun phrase)
2.3 Protein analysis
Protein content of NP1 was measured by NP2 [method] ([company], [city], [state]). The proportions of NP3, NP4, NP5, and NP6 were measured by NP7 [method] using a [company] system equipped with NP8 according to the procedure of Gupta et al. (1993). Proteins were separated on a [company] column ([specifications], [company], [city], [state]) preceded by the respective NP9. The NP10 was [chemical]/water (1:1 v/v) containing 0.05% NP11 (v/v). All analytical tests were performed at least in duplicate. Analysis of variance was carried out using the [statistics package] ([company], [city], [state]).

58. Written as a protocol … Do all tests at least twice
Measure protein content of meals by nitrogen combustion
Measure proportions of polymeric protein, gliadin, albumin/globulin, and unextractable polymeric protein (UPP) by SE-HPLC (Gupta et al. 1993).
Separate proteins using guard column, then Biosep column – eluting solvent acetonitrile/water (1:1 v/v) containing 0.05% TFA (v/v)
ANOVA using SAS

59. Group discussion
What information is in the Methods paragraph that is not in the protocol?
Why is it needed in the Methods paragraph?
What does this mean for the work of student researchers? (What extra things will you need to do?)
Be ready to report when asked

60. Examples for discussion
Ten micrograms of total RNA or 1 µg of Poly(A)+-enriched RNA was size-separated on a denaturing 1x MOPS 1.2% (w/v) agarose gel containing formaldehyde (Sambrook et al., 1989)…
We used an integrodifference equation (IDE) model to describe the spatial spread of an S. muticum population.
Why do you think the underlined features in each example are used?
Are you more likely to use passive or active verbs in your M section?

61. Being ‘reader-friendly’ in M&M
Start from the macro level – e.g. project design, then experimental design …
Always include Site Description (if relevant)
Show how individual steps fit in:
e.g. In order to ensure …, two additional steps were included.
Use informative subheadings
Avoid ‘Experiment 1’
Consider tables for lists, etc.

62. Discussion Sections: Information elements (Weissberg and Buker1990, Cargill & O’Connor 2009)
A reference to the main purpose or hypothesis of the study
A review of the most important findings, generally in order of importance:
whether they support the original hypothesis/ how they fulfil the study’s aim, and
whether they agree with the findings of other researchers
Possible explanations for or speculations about the findings

63. Discussion elements cont.
4. Limitations of the study that restrict the extent to which the findings can be generalised
5. Implications of the study (generalisations from the results)
6. Recommendations for future research and/or practical applications

64. Discussion, cont.
Elements 2-5 are often repeated for each group of Results
As you draft, concentrate on the ‘take home messages’ (THMs) to be drawn from your study
Use a subheading or a topic sentence to show where each THM begins
Finally, check for a good link between take home message/s and the paper title

65. Strength of claims
The match between the strength of the claims made in the writing and the strength of the data presented is a key concern of referees.

66. Negotiating strength of claim in writing
In sentences using that, authors have two opportunities to show how strong they want their claim to be:
In the choice of vocabulary and tense in the main verb;
In the choice of verb inside the that clause.

67. Negotiating strength – example of a strong claim
This work
demonstrates experimentally
that the
hypervariable subdomain of SRK is
responsible for ligand
binding.
Strong verb
Present tense = always true
Present tense = always true

68. Negotiating strength 2: less strong claim
Researcher Development International
19-23 January 2009
Negotiating strength 2: less strong claim
Work by Loveys et al. (2003)
indicated
that this
may also be
true for root systems, …
Vocabulary choice less strong
Past tense = in stated context only
Modal verb ‘may be’ is less definite

69. Suggest alternatives to the underlined words: stronger or weaker claim?
The results
indicate
that nonequilibrium effects
may become
more important as polydispersity
is increased.

70. Abstracts/summaries: information elements
B some background information
P the principal activity (or purpose) of
the study and its scope
M some information about the
methods or methodology used
R the most important results of the study
C statement of conclusion or
recommendation

71. Task
Not all the elements appear in all abstracts; check the abstract of your example paper
Which elements are present?
If some are missing, why do you think the author omitted them?

72. Constructing titles for effect
Titles can be noun phrases, sentences or (sometimes) questions; which is yours?
Important to place keywords up-front
Don’t begin with ‘An investigation of…’
Choose keywords with the key audience in mind (remember the search engines)
Take advantage of the colon to allow more ‘mundane’ information to be included later
‘Removal of dissolved organic matter by anion exchange: Effect of dissolved organic matter properties’

73. Thinking about titles New Phytologist Author Guidelines say:
a concise and informative title (for research papers, ideally stating the key finding or framing a question)

74. In your example paper
Check the reference list: how many papers can you find with colons in the title?
How do the titles in the list match with the recommendations I have made today?

75. Conclusions Does your example paper have a headed conclusion?
If not, look at the last paragraph of the Discussion – does it ‘conclude’?
Strong conclusions are becoming more common in the journals I see
Try to avoid word-for-word repetition of Abstract sentences

76. The SciWriting Content Check
Once your draft is complete, compare the following parts to ensure they are telling a consistent and convincing story:
Title
Abstract
Introduction Stage 4
Start of Results
Start of Discussion (if separate)
Conclusion

77. Checklist for review of paper drafts
Table 15.1, Cargill & O’Connor (2013)
See handout for a re-typed version
If you are happy with your draft, use the questions in this list to revise the content again.
The reverse side contains Table 14.2 – some advice about responding to reports from reviewers and editors. Keep this for future reference.
Margaret Cargill, University of Adelaide

78. Submitting a Manuscript

79. The Editor’s Role (PART 1)
The editor is responsible for maintaining the reputation and competitiveness of the journal.
The editor is responsible for the initial decision as to whether a submitted manuscript will be sent to reviewers.
Sometimes the editor returns the manuscript to the author at this stage.

80. What does the editor want to publish?
Important - significant and important research work
Interesting - appropriate and interesting work for readers of the journal
Quality - experimental and statistical methods are valid
Meaningful - literature review, discussion and conclusions are relevant and correctly interpreted
Clear - understandable and readable
Presentable - presentation undertaken with care (spelling, grammar etc.) and instructions to authors followed closely

81. The contributor’s covering letter
Often now this is a message typed into an online form
State that the paper is in the field of the journal
Emphasize that the paper is new & original and fits the journal’s desired emphasis (use key terms from the Aims and Scope section on the webpage)
Highlight specific points which may raise questions for the editor e.g. –
Your belief that a longer paper is justified, not two short ones
Photographs are necessary rather than drawings
Express hope that the presentation is satisfactory; and
Say that you look forward to the referees’ comments.

82. What are reviewers asked to do?
Manuscripts are commonly sent to at least two peer referees
Each journal has its own set of instructions for reviewers – sometimes these are available on the journal’s website
Check to see if this is the case for the journal you are targeting

83. What are reviewers asked to do? (cont.)
In addition to ‘ticking the boxes’, reviewers are asked to write their comments about any problems with the manuscript or any suggestions for improvement that need to be followed before the manuscript can be considered suitable for publication in the journal
Reviewers return their comments to the editor

84. Recommendation  Accept without alteration
 Accept after minor revision
 Review again after major revision
 Reject

85. The Editor’s Role (PART 2)
The editor receives the reports from the referees and decides what response will be made to the author/s
If the first two referees disagree, sometimes the editor will send the manuscript to a third referee for an additional opinion
The editor then writes to the corresponding author, telling her/him of the decision

86. Dealing with comments of editors and reviewers
If paper is accepted
If paper is rejected
If paper needs revision

87. Paper accepted +/- revision
Respond quickly
Try to make all the changes
Don’t start any unnecessary arguments

88. Who gets rejected?
Survey of scientists who had published at least 10 papers in 5 top ecology journals between *
22% of papers eventually accepted had been rejected at least once
Every author had at least one paper rejected
Senior scientists & scientists with more publications had higher rejection rate
EVERYONE
*Cassey & Blackburn (2003) Trends in Ecology and Evolution 18:

89. Why a paper might be rejected:
high ranking journals need to reject a high proportion of submitted manuscripts even if the reviews are (mostly) positive
the paper may not fit the scope of the journal
referees may not read or understand the paper thoroughly enough to appreciate it (remember: the review process is unpaid work for busy people)
something may have annoyed the referee – they are unpredictable: can be helpful or (sometimes) rude
the recommendations from the referee to the editor may be clear or unclear

90. Paper rejected Determine why the manuscript is rejected:
Not suitable for the journal – submit to another journal
Problems with design or method – try to publish the good parts
Research not new or ‘important’ enough – submit to lower ranking journal
If submitting the same manuscript, make changes recommended by reviewers

91. You are asked to revise the paper: Rules of thumb
Rare that the referee is completely right and the author completely wrong
Object is to accommodate the referee by addressing their comments without compromising the message of the paper
Always show the editor you are doing the right thing – be polite
If editor’s comments are not clear, get advice locally or journal to get clarification

92. Example: letter from editor to author after review
“Based on the comments and recommendations of the two reviewers (included) and my own reading of the manuscript, it is my view that some revision is required before this paper would be acceptable for publication. If you wish, you can send me a revised version of the manu-script, with a covering letter outlining how the reviewers’ comments have been addressed. I have also included an annotated copy of the manuscript with some corrections to grammatical, typographical and formatting errors. Please attend to these as well in the manuscript revision.”

93. Example: response from author to editor after revision
“Please find enclosed a revised version of the manuscript, a letter outlining how the reviewers’ comments have been addressed and the annotated copy of the first version. Sorry for the delay, but some … measurements were required… . The manuscript has been thoroughly revised in order to address the valuable suggestions of the editor and the two reviewers.”

94. Your response document to editor
Make it very easy for the editor to see what you have done
Heading: Referee 1
Then copy all the comments, one by one, perhaps in italic type
Underneath each one, in plain type, say what you have done in response
If you have not followed the referee’s suggestion/ advice in some cases, give your reasons
Then do the same for Referee 2

95. Teaching response strategies
Table 14.2 (pp ) summarises research conducted by my co-author Patrick O’Connor
Analysed the correspondence between Editors, Authors and Reviewers for ~200 manuscripts from 3 international journals and 20 extra papers from a range of journals
Looked at letters from editors, reviewer comments and author response
Categorised reviewer comment types and author response strategies for successful approaches
Margaret Cargill, University of Adelaide

96. Main types of comments from referees
1. The aims of the study are not clear
2. The theoretical premise or “school of thought” on which the work is based is challenged.
3. The experimental design or analysis methods are challenged
4. You are asked to supply addition data or information that would improve the paper
5. You are asked to remove information or discussion
6. The conclusions are considered incorrect, weak or too strong
7. The referee has unspecific negative comments – e.g. poorly designed / written / organised

97. Your letter to editor
Point out supportive comments by referees and disagree-ments between them (try to get editor on your side)
Say you have also corrected minor errors (e.g. English)
Defend your conclusions if referee is factually wrong
Say you believe the paper is important research and is now acceptable
Hope for the best!

98. Training for responding to reviewers
See Section 16.5 (p. 121) for a way to coach students to develop capacity to respond to reviewers appropriately
Margaret Cargill, University of Adelaide

99. Q & A Work in groups of 2-3 What questions remain for you?
What parts would you like more information about?
What additional assistance do you need to help you incorporate article writing into your methods courses?
How do you think this support should be provided?
List your group’s responses in order of importance
Be ready to report when asked
Margaret Cargill, University of Adelaide

100. Evaluation and future development
Please complete the anonymous questionnaire that will be distributed
Please do not write any identifying information on the page
If you are willing to be part of a future research study following up the outcomes of this training, please me directly at
Margaret Cargill, University of Adelaide

101. Writing a scientific paper for publication: Strategy and steps
8 September 2008
References/Suggested reading
Cargill, M. & O’Connor, P. (2013). Writing scientific research articles: Strategy and steps. 2nd edition. Oxford, UK: Wiley-Blackwell
Lindsay, D. (2011). Scientific Writing = Thinking in Words. Melbourne: CSIRO Publishing
Olsen, L. A., & Huckin, T. N. (1991). Technical Writing and Professional Communication (Second Edition ed.). New York, USA: McGraw-Hill.
Weissberg, R., & Buker, S. (1990). Writing Up Research: Experimental research report writing for students of English. Englewood Cliffs, New Jersey, USA: Prentice Hall Regents.