ISSN:1978-3019 E-ISSN:2086-4094

Journal of Biosciences

Berry Juliandi

Teknis Penulisan Artikel dan

Korespondensi di Jurnal Ilmiah
 Berry Juliandi
bjuliandi@ipb.ac.id
bjuliandi@gmail.com

• Sekretaris, Departemen Biologi FMIPA IPB

• Kepala, Laboratorium Veterinary Stem Cells, Pusat
Penelitian Sumberdaya Hayati dan Bioteknologi IPB
• Chief Editor, HAYATI Journal of Biosciences
(Elsevier)
• Anggota, Akademi Ilmuwan Muda Indonesia (ALMI)

Journal of Biosciences
S1, Jurusan Biologi, FMIPA, IPB
S2, Program Studi Biologi, IPB
S3 dan Postdoc,
Lab. Molecular Neuroscience,
Nara Institute of Science & Technology,
Jepang
Postdoc,
Dept. Stem Cell Biology & Medicine,
Kyushu University, Jepang
Daur Penciptaan Ilmu Pengetahuan
Reference
Under translation and
modification by Juliandi
et al. and will be
published by IPB Press
on 2017
 Choosing your target journal
• Balance needed between several factors:
– Which metrics are important for you? (e.g. Impact
Factor, SCI)
– 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/applied or
more global/ theoretical significance?
• Talk about this and get advice early
 Selecting target journals
• Check if the journal:
– normally publishes the kind of work you have done
– referees the papers
– publishes reasonably quickly
– has no page charges – or will waive them
– provides an affordable open-access option (if you need
it)
– is NOT suspected ‘predatory journal’
 Instructions to Contributors
• Find them early in the preparation period
• Seek out Overview, Scope or Aims section
in particular to help decision re target
choice
• Once chosen, check for downloadable
template of required format for manuscript
• Note table/figure requirements in detail
• Submissions are often returned if
instructions are ignored
 Implications ...
• Once you have chosen your target journal, you
are aiming to convince the editor and referees
that your paper fulfils the criteria stated in the
Aims and scope/Journal overview
• Analyse multiple examples from this journal to
see how and where they signal both level and
type of contribution in their writing.
The AIMRaD article: Abstract, Introduction,
Methods, Results and Discussion
Abstract

• Abstract
Introduction
• Introduction

Materials and
methods • Materials and Methods

Results • Results

• Discussion
Discussion
For many ‘molecular’ papers
(AIRDaM)

• Abstract
Abstract

Introduction

• Introduction

Results
• Results

Discussion
• Discussion

Materials and
• Materials and Methods
methods
 Structure of articles that combine
Results and Discussion (AIM[RaD]XC)
Abstract • Abstract
Introduction

• Introduction
Materials and
Methods

• Materials and methods

Result/ etc. etc.

discussion
Results Results Results

Conclusions • Combined Results and

Discussion

• Conclusions
 For theoretical/modelling/
computing/argument papers: AIBC

• Abstract
Abstract

Introduction
• Introduction
Development
of model/
validation, or
• Body of paper (with
problem/ content-based
solution or
theory/
subheadings)
algorithm, etc.

• Conclusion

Conclusion
 Start from your Results/findings
• To begin a paper, focus on your results/ findings/
argument
• Everything in the paper must relate to the data
and analysis you present
• Talk with co-authors and get agreement:
– Which data/analysis belong in the paper?
– What story do the data/evidence tell?
• The questions on the next slide help with this
task
 Your results
• What do my results/arguments ‘say’?
• What do they mean in their context? (what
conclusions can be drawn from these
results/findings?)
• Who needs to know this? (= audience for the
paper)
• Why do they need to know? (what
contribution do these results make to the
field? – or why would it matter if researchers
never read your paper?)
 Presenting data
• What data are essential for the ‘story’ of the
paper?
• Prepare tables and/or figures that present the
key data that form your story
• Present data in the order that builds the story
and refer to each data element in the text
• Check if the journal will accept other data as
appendices/supplementary material
 Key role of figures/tables in drafting
• Initial planning meeting held of co-author group
• Lead author (student) presents data
figures/tables
• Beneath each are bullet-points stating the key
findings shown in the figure/table
• Points are labelled according to where in the
paper the information will be written (e.g. R, D)
• Team agrees on data, presentation and story
• Lead author then drafts paper in English
 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
 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
 Additional considerations
 Be consistent with the styles of tables and
figures
 Figures should tell the story with little
reference to the text
 Keep the figure free from clutter (= many
different items, distracting reader from main
point/s)
 Figure legends: beneath the figure
Description or Declaration?
• Usually one descriptive line, tells you what the figure is
about, e.g. “Shell thickness of PDA capsules as a function of
the DMDES concentration.”
• Maybe one sentence about the method
• Explain key results or observations
• Key – explain the different treatments for different points
• Explain statistical and other notation
• Check that the figure ‘stands alone’ (do not need the reader
to consult the rest of the text in order to understand them) –
check target journal examples for specific guidelines
 Tables
 Design the table around the point you wish
to illustrate most strongly
 Keep tables free of clutter
 Don’t box tables, use horizontal lines as
separators
 Use space to distinguish columns
 Define abbreviations in the table using
footnotes and the title legend
 Sort data to best show the main correlations
 Materials and Methods
• Stated purpose is that the work can be
repeated
• Additional purpose 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 (e.g. it is only published in
Bahasa Indonesia)
• All novel methods must be described, but avoid
excessive detail (use supplementary material?)
 Organising the M&M effectively (1)
• Readers come to the Methods from many
directions; make it easy for them to find what
they are looking for
• It can be useful to use similar or identical
subheadings or order of information for the
Results and the M&M
• For the reviewer, it can be useful to include an
overview of the experimental design first
• Investigate your example paper to see if the
authors have used these strategies
 Organising the M&M effectively (2)
• Consider using introductory phrases to explain why a
method was used, e.g.
To generate an antibody to GmDmt1;1, a 236-bp DNA
fragment coding for 79 N-terminal amino acids was
amplified using the PCR. (Kaiser et al. 2003)

• Or use the first sentence in a paragraph to introduce the

method and then give details, e.g.
Mineralisable N was estimated using an anaerobic
incubation assay as described by Keeney (1982). This
involved …
 Argument ‘stages’ of an Introduction
1. Statements about the field, providing the reader with a
setting or context for the problem to be reported and
claiming its centrality or 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,
a gap, need for extension, or research niche for the
present study
4. Statements giving the purpose or objective of the
author’s study OR its main activity OR findings
5. Optional statement(s) that give a value or benefit for
carrying out the study
6. A map of the rest of the article (some fields, and reviews)
 Task:
• Read the introduction of your example article
and decide if all stages are present, and where
each one begins and ends. (It is possible that
stages may be repeated or come in different
order to that suggested above!)
• Tip: identify Stage 4 first, then look for Stage 3
(gap, need). Then identify Stage 1 and where it
moves into Stage 2. Are there repeated sets of
Stages 1, 2, 3?
 Stage 4: Format?

• Look at the last paragraph of the

Introduction in your example paper
• Does it contain a statement of aim/
objective? A statement of principal activity
(what the study did, or the paper does)? A
summary of results?
• Look at verb tenses – how do they reflect
the specific focus of the Stage 4?
• Will your ms follow the same pattern?
 Stage 3:
The research ‘gap’ or ‘niche’
• There are special ‘signal’ words that often
appear in this Stage.
• One type of signal points to an upcoming
contrast (eg ‘however’)
• Another type indicates a problem or a lack.
• Check in your example article for words that
serve these purposes.
• Consider the relative strength of the wordings,
in terms of the significance of filling the
gap/niche.
 Strategic questions on Introductions
• Does Stage 1 match the interests of the target
readers (journal editor/referees)?
• Does the start of Stage 1 reflect the points
made at the end of the Discussion/Conclusion?
• Does every component of Stage 4 have a Stage
3 gap/need somewhere in the Introduction?
• Is all the Stage 2 literature review necessary to
justify why the study was done?
• Could a referee answer ‘yes’ to the questions ‘Is
this work new?’ and ‘Is this work significant?’
 Suggested process for drafting an introduction
(after Results „story‟ is clear)
• Begin with Stage 4
• Draft Stage 3 next – the ‘gap’
• Then think about how to begin Stage 1 – the
setting (think about your audience)
• Next arrange the information you have
collected from the literature into Stage 2
• Then, combine the stages and add any
additional sentences needed to connect them
into a coherent Introduction.
 Discussion: Making meaning
• The Discussion relates to the Introduction
– the aim/purpose statement
– the evidence leading to the ‘gap’, and
– the ‘Universe’ where the Introduction began
• It highlights the key points from the Results
‘story’
• Does your target journal allow a separate
‘Conclusion’? If not, use the last paragraph of
the Discussion to conclude.
 Information elements to include
1. Reference to the main hypothesis, aims
(purpose) or research questions of the study
2. Review of the most important findings,
whether they support the original hypothesis,
and/or agree with the findings of others
3. Possible explanations or speculations about
the results
4. Limitations that restrict the generalisability of
the findings
5. Implications of the study
6. Recommendations for further research or
practical applications
 Discussions, cont.
• First 4-5 of these often repeated for each
group of Results
• Concentrate on ‘take home messages’
(THMs)
• Use a subheading or a topic sentence to
show where each THM begins
• Check for link between ‘take home’
message/s and paper title
 Why are Abstracts important?
• Often the only thing busy readers read – its job
is to get readers to download your paper
• May be all that is available to some readers
• What about ‘additional keywords’?
– Choose words your target audience might use to
search under; avoid general words (e.g. growth)
– Check if they are used in other papers in your field
(or in the database index, if available)
– Strategic repetition of words in title/abstract can
maximise search engine results
– Editors use your keywords to select reviewers
 Abstracts: Typical information
elements
B = some background information
P = the principal activity (or purpose) of the study
and its scope
M = some information about the methodology used
in the study
R = the most important results of the study
C = a statement of conclusion or recommendation
 Abstracts, cont.

This list can sometimes be compressed (in a so-

called reduced abstract) to:
P + M = purpose and method of the study
R = results
C = conclusion (and recommendations)
 Thinking about titles
• Title is the first thing a reader reads
• Can be a Noun Phrase (NP), a sentence, or
sometimes a question
• Can be in two parts, separated by a colon or a
dash
• Should provide as much information as possible
but be concise
• Important to avoid ambiguity if using long and
complex noun phrases
 The Title: examples describing the same work

Effects of added calcium on salinity tolerance of tomato

Calcium addition improves salinity tolerance of tomato
Calcium addition has differential effects on salinity tolerance
of three varieties of tomato
Calcium addition has differential effects on salinity tolerance
of three varieties of tomato grown in solution culture
Calcium addition improves salinity tolerance of tomato by
increasing the K/Na ratio in plant tissues
Enhancing the salinity tolerance of tomato: calcium addition
increases the K/Na ratio in plant tissues
 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.
Follow Guide For Author
 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
 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
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
 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
 Recommendation
 Accept without alteration

 Accept after minor revision

 Review again after major revision

 Reject
 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
Dealing with comments of editors and
reviewers

1. If paper is accepted
2. If paper is rejected
3. If paper needs revision
 Paper accepted +/- revision

• Respond quickly
• Try to make all the changes
• Don‟t start any unnecessary arguments
 Who gets rejected?
• Survey of scientists who had published at least 10 papers
in 5 top ecology journals between 1990-1999*
• 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 18:375-376

 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
 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
 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 email journal to get clarification
 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 manuscript, 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.”
 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.”
 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
 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
 1. The aims of the study are not
clear
What to do:
 check the aims are clearly stated in the
Introduction
 check the aims are consistent with the
experimental design
 check that the Discussion refers back to the
aims
 1. The aims of the study are not clear
EXAMPLES:

R: “The purpose of the research is not clear”

A: “Regarding the purpose of the research, a
sentence has been added at the end of the
introduction…viz „This should provide a better
basis for understanding and
predicting…change…”
2. The theoretical premise or “school of thought” on
which the work is based is challenged

What to do:
 check that the Introduction shows the diversity of
theories (cite the literature) and demonstrate that you
are testing one of these theories
 if you are challenging accepted wisdom, use theory,
references and structure (e.g. section headings)
 include caveats in the discussion
 3. Experimental design or analysis methods are
challenged

What to do:
 defend the design or analysis on its merits
 refer to previously published examples using the
design or analysis
 include additional information on the design or
analysis if available
3. Experimental design or analysis methods are challenged
EXAMPLES:
R: “I think it is not appropriate to conclude that „without
employing such a technique, [method] is qualitative”
A: .“…without proof that [method] is quantitative, it should be
considered qualitative. A sentence has been added to state
this explicitly in the text.”

R: “No explanation is given for the [pre-treatment]

procedure”
A: “Two paragraphs are added justifying the use of [the
procedure]. Two recent references are included which show
that the procedure [works].
 4. You are asked to supply additional data or
information that would improve the paper
What to do:
 do it if you can
 if you cannot, consider whether you are
expected to make major or minor corrections by
the editor.
 if you think the paper will not be improved with
the suggested additions, make your case to the
editor
 4. You are asked to supply addition data or
information that would improve the paper
EXAMPLES:

R: “One possible approach is to run replicate

analyses…see [suggested reference]”
A: “Taking the ideas of [suggested reference], we ran
duplicate measurements…” [new data included]
 4. You are asked to supply addition data or
information that would improve the paper
EXAMPLES:
R: “It would also be valuable to have [experimental
results] calculated for the [duration of experiment].
Can this information be calculated from the data
collected?”
A: “Unfortunately, [extra experimental results]
cannot be extracted from our data. A study
concerning the long term effects of [experimental
conditions] has been published elsewhere
[reference].”
 4. You are asked to supply addition data or
information that would improve the paper
EXAMPLES:
R: “I think it would help if the authors were to suggest
where we should go from here. In the final sentence it is
suggested that analyses of this type provide the insights
needed for a more targeted approach in the future. What
might this more targeted approach be?”

A: “We have revised the manuscript in accordance with the

suggestions…”
 5. You are asked to remove information or
discussion
What to do:
 do it if you can, without changing the „story‟
 ask a colleague to make suggestions on where
to make cuts
 if you don‟t want to cut, see if one referee is on
your side and make your case to the editor
 5. You are asked remove information or discussion
EXAMPLES:
R: “…section contains unnecessary repetition of
previous work”
A: “As (other) reviewer points out, …sufficient
explanation is required to make sense of and
interpret the results.”

R: “This area of research is well known and does

not need this exhaustive review section.”
A: “We have reduced the size of this section and
referred to critical reviews by [references]”
 6. The conclusions are considered incorrect,
weak or too strong
What to do:
 make sure the discussion is tied to the aims at the beginning
of the paper
 reassess the literature you have cited and make a case to
the editor if there is adequate supporting literature
 check that all your statements are justified & the strength is
appropriate
 include caveats in the discussion
 6. The conclusions are considered incorrect, weak or
too strong
EXAMPLES:
R: “…you need to say what magnitude differences you
believe to be significant, and provide some
justification…”

A: “We accepted the comment completely.” [new data and

supporting statistical analysis presented]
 6. The conclusions are considered incorrect, weak
or too strong
EXAMPLES:
R: “…the paper is far too descriptive and speculative…”
A: “After doing some statistics, much of the „cloud‟ surrounding the
descriptive analysis…has disappeared…. The paper was also
shortened and some too speculative paragraphs were omitted”
 6. The conclusions are considered incorrect, weak or too
strong
EXAMPLES:

R: “This is hardly astonishing. A similar accumulation was

reported by [References]”

A: “The comments of the reviewer were profoundly appreciated

and taken into consideration. Two references referred to by the
reviewer were included…”
 6. The conclusions are considered incorrect, weak
or too strong
EXAMPLES:
R: “I do not believe the conclusion that [specific
conclusion] is a valid one, based on the data presented.”

A: “Regarding the conclusion that [specific conclusion], we

changed the text in the abstract, results and discussion. We
omitted the conclusions on the possible role of [conditions]
but we would like to keep Figure 8a, just to maintain
[conditions] as a working hypothesis for future studies.”
 7. The referee has unspecific negative comments
eg. poorly designed / written / organised
What to do:
 show the referees‟ comments to a peer and discuss
them
 think about what the referee has a specific problem
with; restate it and respond
 point out to the editor all the work you have done to
improve the paper
 build up a body of positives – eg. “ I have addressed
point 1 by….”
 7. The referee has unspecific negative comments
eg. poorly designed / written / organised
EXAMPLES:
R: “The English is not good and needs to be greatly improved.”
A: “Grammatical points of the language were reviewed to improve
readability….None of the authors is an English native speaker. …we tried
to improve it as far as we could.”
R: “The logic and circumstantial evidence for [results] is very clear up to
p.16:line5. The next section…was difficult for me to wade through…I
can not offer any suggestions to simplify this section.”
A: “I take this as a comment”
 7. The referee has unspecific negative comments
eg. poorly designed / written / organised
R1: “… improves our understanding and is interesting to a wider
audience. That said, it must be stated that the paper needs
substantial improvement in language and also in correcting sloppy
formatting such as typos in the title, inconsistency of spelling and
use of abbreviations, presentation of units, quotations in incorrect
order etc.”

R2: “The scientific content of the manuscript is poor and results do not
represent any innovative progress…”

E: “Probably none of these [design & analysis] shortcomings are, by

themselves, grounds for rejection. However, their combined effect, and
the fact that the reviewers found very little positive to say about this
paper, leads me to recommend rejection”
 Re-submit (same journal), with letter to editor
 Point out supportive comments by referees and disagree-ments
between them (try to get editor on your side)
 List the main changes individually, referring to referees‟ reports
(copy each individual referee’s comment (e.g. in BOLD text) and
address each comment directly underneath (e.g. in plain text)
 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!
ISSN:1978-3019 E-ISSN:2086-4094

Journal of Biosciences

Terima Kasih!
https://www.journals.elsevier.com/hayati-journal-of-biosciences

http://www.sciencedirect.com/science/journal/19783019