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It is late at night. You have been strug-
gling with your project for a year. You gen-
erated an enormous amount of interesting
data. Your pipette feels like an extension of
your hand, and running western blots has
become part of your daily routine, similar
to brushing your teeth. Your colleagues
think you are ready to write a paper, and
your lab mates tease you about your “slow”
writing progress. Yet days pass, and you
cannot force yourself to sit down to write.
You have not written anything for a while
(lab reports do not count), and you feel you
have lost your stamina. How does the writ-
ing process work? How can you fit your
writing into a daily schedule packed with
experiments? What section should you start
with? What distinguishes a good research
paper from a bad one? How should you re-
vise your paper? These and many other
questions buzz in your head and keep you
stressed. As a result, you procrastinate. In
this paper, I will discuss the issues related
to the writing process of a scientific paper.
Specifically, I will focus on the best ap-
proaches to start a scientific paper, tips for
writing each section, and the best revision
strategies.
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Whether you have written 100 papers or
you are struggling with your first, starting
the process is the most difficult part unless
you have a rigid writing schedule. Writing
is hard. It is a very difficult process of in-
tense concentration and brain work. As
stated in Hayes’ framework for the study of
writing: “It is a generative activity requiring
motivation, and it is an intellectual activity
requiring cognitive processes and memory”
[1]. In his book How to Write a Lot: A Prac-
tical Guide to Productive Academic Writing,
Paul Silvia says that for some, “it’s easier to
embalm the dead than to write an article
about it” [2]. Just as with any type of hard
work, you will not succeed unless you prac-
tice regularly. If you have not done physical
exercises for a year, only regular workouts
can get you into good shape again. The same
kind of regular exercises, or I call them
“writing sessions,” are required to be a pro-
ductive author. Choose from 1- to 2-hour
blocks in your daily work schedule and con-
sider them as non-cancellable appointments.
When figuring out which blocks of time will
be set for writing, you should select the time
that works best for this type of work. For
many people, mornings are more produc-
tive. One Yale University graduate student
spent a semester writing from 8 a.m. to 9
a.m. when her lab was empty. At the end of
the semester, she was amazed at how much
she accomplished without even interrupting
her regular lab hours. In addition, doing the
hardest task first thing in the morning con-
tributes to the sense of accomplishment dur-
ing the rest of the day. This positive feeling
spills over into our work and life and has a
very positive effect on our overall attitude.
Rule 1: Create regular time blocks for
writing as appointments in your calendar
and keep these appointments.
Now that you have scheduled time, you
need to decide how to start writing. The best
strategy is to start with an outline. This will
not be an outline that you are used to, with
Roman numerals for each section and neat
parallel listing of topic sentences and sup-
porting points. This outline will be similar
to a template for your paper. Initially, the
outline will form a structure for your paper;
it will help generate ideas and formulate hy-
potheses. Following the advice of George
M. Whitesides, “. . . start with a blank piece
of paper, and write down, in any order, all
important ideas that occur to you concern-
ing the paper” [3]. Use Table 1 as a starting
point for your outline. Include your visuals
(figures, tables, formulas, equations, and al-
gorithms), and list your findings. These will
constitute the first level of your outline,
which will eventually expand as you elabo-
rate.
The next stage is to add context and
structure. Here you will group all your ideas
into sections: Introduction, Methods, Re-
sults, and Discussion/Conclusion (Table 2).
This step will help add coherence to your
work and sift your ideas.
182
Kallestinova: Your first research paper
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Now that you have expanded your out-
line, you are ready for the next step: dis-
cussing the ideas for your paper with your
colleagues and mentor. Many universities
have a writing center where graduate stu-
dents can schedule individual consultations
and receive assistance with their paper
drafts. Getting feedback during early stages
of your draft can save a lot of time. Talking
through ideas allows people to conceptualize
and organize thoughts to find their direction
without wasting time on unnecessary writ-
ing. Outlining is the most effective way of
communicating your ideas and exchanging
thoughts. Moreover, it is also the best stage
to decide to which publication you will sub-
mit the paper. Many people come up with
three choices and discuss them with their
mentors and colleagues. Having a list of
journal priorities can help you quickly re-
submit your paper if your paper is rejected.
Rule 2: Create a detailed outline and
discuss it with your mentor and peers.
After you get enough feedback and de-
cide on the journal you will submit to, the
process of real writing begins. Copy your
outline into a separate file and expand on
each of the points, adding data and elaborat-
ing on the details. When you create the first
draft, do not succumb to the temptation of
editing. Do not slow down to choose a bet-
ter word or better phrase; do not halt to im-
prove your sentence structure. Pour your
ideas into the paper and leave revision and
editing for later. As Paul Silvia explains,
“Revising while you generate text is like
drinking decaffeinated coffee in the early
morning: noble idea, wrong time” [2].
Many students complain that they are
not productive writers because they experi-
ence writer’s block. Staring at an empty
screen is frustrating, but your screen is not
really empty: You have a template of your
article, and all you need to do is fill in the
blanks. Indeed, writer’s block is a logical
fallacy for a scientist ― it is just an excuse
to procrastinate. When scientists start writ-
ing a research paper, they already have their
files with data, lab notes with materials and
experimental designs, some visuals, and ta-
bles with results. All they need to do is scru-
tinize these pieces and put them together
into a comprehensive paper.
If you still struggle with starting a
paper, then write the Materials and Methods
section first. Since you have all your notes,
it should not be problematic for you to de-
scribe the experimental design and proce-
dures. Your most important goal in this
section is to be as explicit as possible by pro-
viding enough detail and references. In the
end, the purpose of this section is to allow
other researchers to evaluate and repeat your
work. So do not run into the same problems
as the writers of the sentences in (1):
1a. Bacteria were pelleted by
centrifugation.
1b. To isolate T cells, lymph
nodes were collected.
As you can see, crucial pieces of infor-
mation are missing: the speed of centrifug-
ing your bacteria, the time, and the
temperature in (1a); the source of lymph
nodes for collection in (b). The sentences
can be improved when information is added,
as in (2a) and (2b), respectfully:
2a. Bacteria were pelleted by
centrifugation at 3000g for 15 min
at 25°C.
2b. To isolate T cells, medi-
astinal and mesenteric lymph
nodes from Balb/c mice were col-
lected at day 7 after immunization
with ovabumin.
If your method has previously been
published and is well-known, then you
should provide only the literature reference,
as in (3a). If your method is unpublished,
then you need to make sure you provide all
essential details, as in (3b).
183Kallestinova: Your first research paper
3a. Stem cells were isolated,
according to Johnson [23].
3b. Stem cells were isolated
using biotinylated carbon nan-
otubes coated with anti-CD34 an-
tibodies.
Furthermore, cohesion and fluency are
crucial in this section. One of the malprac-
tices resulting in disrupted fluency is switch-
ing from passive voice to active and vice
versa within the same paragraph, as shown
in (4). This switching misleads and distracts
the reader.
4. Behavioral computer-based
experiments of Study 1 were pro-
grammed by using E-Prime. We
took ratings of enjoyment, mood,
and arousal as the patients listened
to preferred pleasant music and un-
preferred music by using Visual
Analogue Scales (SI Methods). The
preferred and unpreferred status of
the music was operationalized
along a continuum of pleasantness
[4].
The problem with (4) is that the reader
has to switch from the point of view of the
experiment (passive voice) to the point of
view of the experimenter (active voice).
This switch causes confusion about the per-
former of the actions in the first and the
third sentences. To improve the coherence
and fluency of the paragraph above, you
should be consistent in choosing the point
of view: first person “we” or passive voice
[5]. Let’s consider two revised examples in
(5).
5a. We programmed behavioral
computer-based experiments of Study
1 by using E-Prime. We took ratings of
enjoyment, mood, and arousal by using
Visual Analogue Scales (SI Methods)
as the patients listened to preferred
pleasant music and unpreferred music.
We operationalized the preferred and
unpreferred status of the music along
a continuum of pleasantness.
5b. Behavioral computer-based
experiments of Study 1 were pro-
grammed by using E-Prime. Ratings
of enjoyment, mood, and arousal
were taken as the patients listened to
preferred pleasant music and unpre-
ferred music by using Visual Ana-
logue Scales (SI Methods). The
preferred and unpreferred status of
the music was operationalized along
a continuum of pleasantness.
If you choose the point of view of
the experimenter, then you may end up
with repetitive “we did this” sentences.
For many readers, paragraphs with sen-
tences all beginning with “we” may also
sound disruptive. So if you choose ac-
tive sentences, you need to keep the
number of “we” subjects to a minimum
and vary the beginnings of the sentences
[6].
Interestingly, recent studies have re-
ported that the Materials and Methods sec-
tion is the only section in research papers
in which passive voice predominantly over-
rides the use of the active voice [5,7,8,9].
For example, Martínez shows a significant
drop in active voice use in the Methods sec-
tions based on the corpus of 1 million
words of experimental full text research ar-
ticles in the biological sciences [7]. Ac-
cording to the author, the active voice
patterned with “we” is used only as a tool
to reveal personal responsibility for the
procedural decisions in designing and per-
forming experimental work. This means
that while all other sections of the research
paper use active voice, passive voice is still
the most predominant in Materials and
Methods sections.
Writing Materials and Methods sec-
tions is a meticulous and time consuming
task requiring extreme accuracy and clar-
ity. This is why when you complete your
draft, you should ask for as much feed-
back from your colleagues as possible.
Numerous readers of this section will
help you identify the missing links and
improve the technical style of this sec-
tion.
184
Kallestinova: Your first research paper
Rule 3: Be meticulous and accurate in
describing the Materials and Methods.
Do not change the point of view within
one paragraph.
For many authors, writing the Results
section is more intimidating than writing the
Materials and Methods section . If people are
interested in your paper, they are interested in
your results. That is why it is vital to use all
your writing skills to objectively present
your key findings in an orderly and logical
sequence using illustrative materials and text.
Your Results should be organized into
different segments or subsections where
each one presents the purpose of the ex-
periment, your experimental approach,
data including text and visuals (tables, fig-
ures, schematics, algorithms, and formu-
las), and data commentary. For most
journals, your data commentary will in-
clude a meaningful summary of the data
presented in the visuals and an explanation
of the most significant findings. This data
presentation should not repeat the data in
the visuals, but rather highlight the most
important points. In the “standard” re-
search paper approach, your Results sec-
tion should exclude data interpretation,
leaving it for the Discussion section. How-
ever, interpretations gradually and secretly
creep into research papers: “Reducing the
data, generalizing from the data, and high-
lighting scientific cases are all highly in-
terpretive processes. It should be clear by
now that we do not let the data speak for
themselves in research reports; in summa-
rizing our results, we interpret them for the
reader” [10]. As a result, many journals in-
cluding the Journal of Experimental Med-
icine and the Journal of Clinical
Investigation use joint Results/Discussion
sections, where results are immediately
followed by interpretations.
Another important aspect of this section
is to create a comprehensive and supported
argument or a well-researched case. This
means that you should be selective in pre-
senting data and choose only those experi-
mental details that are essential for your
reader to understand your findings. You
might have conducted an experiment 20
times and collected numerous records, but
this does not mean that you should present
all those records in your paper. You need to
distinguish your results from your data and
be able to discard excessive experimental
details that could distract and confuse the
reader. However, creating a picture or an ar-
gument should not be confused with data
manipulation or falsification, which is a
willful distortion of data and results. If some
of your findings contradict your ideas, you
have to mention this and find a plausible ex-
planation for the contradiction.
In addition, your text should not include
irrelevant and peripheral information, in-
cluding overview sentences, as in (6).
6. To show our results, we first
introduce all components of exper-
imental system and then describe
the outcome of infections.
Indeed, wordiness convolutes your sen-
tences and conceals your ideas from readers.
One common source of wordiness is unnec-
essary intensifiers. Adverbial intensifiers
such as “clearly,” “essential,” “quite,” “ba-
sically,” “rather,” “fairly,” “really,” and “vir-
tually” not only add verbosity to your
sentences, but also lower your results’ cred-
ibility. They appeal to the reader’s emotions
but lower objectivity, as in the common ex-
amples in (7):
7a. Table 3 clearly shows that …
7b. It is obvious from figure 4
that …
Another source of wordiness is nomi-
nalizations, i.e., nouns derived from verbs
and adjectives paired with weak verbs in-
cluding “be,” “have,” “do,” “make,”
“cause,” “provide,” and “get” and construc-
tions such as “there is/are.”
8a. We tested the hypothesis
that there is a disruption of mem-
brane asymmetry.
185Kallestinova: Your first research paper
8b. In this paper we provide
an argument that stem cells repop-
ulate injured organs.
In the sentences above, the abstract
nominalizations “disruption” and “argu-
ment” do not contribute to the clarity of the
sentences, but rather clutter them with use-
less vocabulary that distracts from the mean-
ing. To improve your sentences, avoid
unnecessary nominalizations and change
passive verbs and constructions into active
and direct sentences.
9a. We tested the hypothesis
that the membrane asymmetry is
disrupted.
9b. In this paper we argue that
stem cells repopulate injured or-
gans.
Your Results section is the heart of your
paper, representing a year or more of your
daily research. So lead your reader through
your story by writing direct, concise, and
clear sentences.
Rule 4: Be clear, concise, and objective
in describing your Results.
Now that you are almost half through
drafting your research paper, it is time to up-
date your outline. While describing your
Methods and Results, many of you diverged
from the original outline and re-focused
your ideas. So before you move on to create
your Introduction, re-read your Methods and
Results sections and change your outline to
match your research focus. The updated out-
line will help you review the general picture
of your paper, the topic, the main idea, and
the purpose, which are all important for
writing your introduction.
The best way to structure your intro-
duction is to follow the three-move approach
shown in Table 3.
The moves and information from your
outline can help to create your Introduc-
tion efficiently and without missing steps.
These moves are traffic signs that lead the
reader through the road of your ideas.
Each move plays an important role in your
paper and should be presented with deep
thought and care. When you establish the
territory, you place your research in con-
text and highlight the importance of your
research topic. By finding the niche, you
outline the scope of your research problem
and enter the scientific dialogue. The final
move, “occupying the niche,” is where
you explain your research in a nutshell
and highlight your paper’s significance.
The three moves allow your readers to
evaluate their interest in your paper and
play a significant role in the paper review
process, determining your paper review-
ers.
186
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Some academic writers assume that the
reader “should follow the paper” to find the
answers about your methodology and your
findings. As a result, many novice writers do
not present their experimental approach and
the major findings, wrongly believing that
the reader will locate the necessary infor-
mation later while reading the subsequent
sections [5]. However, this “suspense” ap-
proach is not appropriate for scientific writ-
ing. To interest the reader, scientific authors
should be direct and straightforward and
present informative one-sentence summaries
of the results and the approach.
Another problem is that writers un-
derstate the significance of the Introduc-
tion. Many new researchers mistakenly
think that all their readers understand the
importance of the research question and
omit this part. However, this assumption
is faulty because the purpose of the sec-
tion is not to evaluate the importance of
the research question in general. The goal
is to present the importance of your re-
search contribution and your findings.
Therefore, you should be explicit and
clear in describing the benefit of the
paper.
The Introduction should not be long. In-
deed, for most journals, this is a very brief
section of about 250 to 600 words, but it
might be the most difficult section due to its
importance.
Rule 5: Interest your reader in the Intro-
duction section by signalling all its ele-
ments and stating the novelty of the work.
For many scientists, writing a Discus-
sion section is as scary as starting a paper.
Most of the fear comes from the variation in
the section. Since every paper has its unique
results and findings, the Discussion section
differs in its length, shape, and structure.
However, some general principles of writ-
ing this section still exist. Knowing these
rules, or “moves,” can change your attitude
about this section and help you create a com-
prehensive interpretation of your results.
The purpose of the Discussion section
is to place your findings in the research con-
text and “to explain the meaning of the find-
ings and why they are important, without
appearing arrogant, condescending, or pa-
tronizing” [11]. The structure of the first two
moves is almost a mirror reflection of the
one in the Introduction. In the Introduction,
you zoom in from general to specific and
from the background to your research ques-
tion; in the Discussion section, you zoom
out from the summary of your findings to
the research context, as shown in Table 4.
The biggest challenge for many writers
is the opening paragraph of the Discussion
section. Following the moves in Table 1, the
187Kallestinova: Your first research paper
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best choice is to start with the study’s major
findings that provide the answer to the re-
search question in your Introduction. The
most common starting phrases are “Our
findings demonstrate . . .,” or “In this study,
we have shown that . . .,” or “Our results
suggest . . .” In some cases, however, re-
minding the reader about the research ques-
tion or even providing a brief context and
then stating the answer would make more
sense. This is important in those cases where
the researcher presents a number of findings
or where more than one research question
was presented. Your summary of the study’s
major findings should be followed by your
presentation of the importance of these find-
ings. One of the most frequent mistakes of
the novice writer is to assume the impor-
tance of his findings. Even if the importance
is clear to you, it may not be obvious to your
reader. Digesting the findings and their im-
portance to your reader is as crucial as stat-
ing your research question.
Another useful strategy is to be proac-
tive in the first move by predicting and com-
menting on the alternative explanations of
the results. Addressing potential doubts will
save you from painful comments about the
wrong interpretation of your results and will
present you as a thoughtful and considerate
researcher. Moreover, the evaluation of the
alternative explanations might help you cre-
ate a logical step to the next move of the dis-
cussion section: the research context.
The goal of the research context move
is to show how your findings fit into the gen-
eral picture of the current research and how
you contribute to the existing knowledge on
the topic. This is also the place to discuss
any discrepancies and unexpected findings
that may otherwise distort the general pic-
ture of your paper. Moreover, outlining the
scope of your research by showing the lim-
itations, weaknesses, and assumptions is es-
sential and adds modesty to your image as a
scientist. However, make sure that you do
not end your paper with the problems that
override your findings. Try to suggest feasi-
ble explanations and solutions.
If your submission does not require a
separate Conclusion section, then adding an-
other paragraph about the “take-home mes-
sage” is a must. This should be a general
statement reiterating your answer to the re-
search question and adding its scientific im-
plications, practical application, or advice.
Just as in all other sections of your
paper, the clear and precise language and
concise comprehensive sentences are vital.
However, in addition to that, your writing
should convey confidence and authority.
The easiest way to illustrate your tone is to
use the active voice and the first person pro-
nouns. Accompanied by clarity and suc-
cinctness, these tools are the best to
convince your readers of your point and
your ideas.
Rule 6: Present the principles, relation-
ships, and generalizations in a concise
and convincing tone.
Now that you have created the first
draft, your attitude toward your writing
should have improved. Moreover, you
should feel more confident that you are able
to accomplish your project and submit your
paper within a reasonable timeframe. You
also have worked out your writing schedule
and followed it precisely. Do not stop ― you
are only at the midpoint from your destina-
tion. Just as the best and most precious dia-
mond is no more than an unattractive stone
recognized only by trained professionals,
your ideas and your results may go unno-
ticed if they are not polished and brushed.
Despite your attempts to present your ideas
in a logical and comprehensive way, first
drafts are frequently a mess. Use the advice
of Paul Silvia: “Your first drafts should
sound like they were hastily translated from
Icelandic by a non-native speaker” [2]. The
degree of your success will depend on how
you are able to revise and edit your paper.
The revision can be done at the
macrostructure and the microstructure lev-
els [13]. The macrostructure revision in-
cludes the revision of the organization,
content, and flow. The microstructure level
188
Kallestinova: Your first research paper
includes individual words, sentence struc-
ture, grammar, punctuation, and spelling.
The best way to approach the
macrostructure revision is through the out-
line of the ideas in your paper. The last time
you updated your outline was before writing
the Introduction and the Discussion. Now
that you have the beginning and the conclu-
sion, you can take a bird’s-eye view of the
whole paper. The outline will allow you to
see if the ideas of your paper are coherently
structured, if your results are logically built,
and if the discussion is linked to the research
question in the Introduction. You will be
able to see if something is missing in any of
the sections or if you need to rearrange your
information to make your point.
The next step is to revise each of the sec-
tions starting from the beginning. Ideally, you
should limit yourself to working on small sec-
tions of about five pages at a time [14]. After
these short sections, your eyes get used to
your writing and your efficiency in spotting
problems decreases. When reading for con-
tent and organization, you should control
your urge to edit your paper for sentence
structure and grammar and focus only on the
flow of your ideas and logic of your presen-
tation. Experienced researchers tend to make
almost three times the number of changes to
meaning than novice writers [15,16]. Revis-
ing is a difficult but useful skill, which aca-
demic writers obtain with years of practice.
In contrast to the macrostructure revi-
sion, which is a linear process and is done
usually through a detailed outline and by
sections, microstructure revision is a non-
linear process. While the goal of the
macrostructure revision is to analyze your
ideas and their logic, the goal of the mi-
crostructure editing is to scrutinize the form
of your ideas: your paragraphs, sentences,
and words. You do not need and are not rec-
ommended to follow the order of the paper
to perform this type of revision. You can
start from the end or from different sections.
You can even revise by reading sentences
backward, sentence by sentence and word
by word.
One of the microstructure revision
strategies frequently used during writing
center consultations is to read the paper
aloud [17]. You may read aloud to yourself,
to a tape recorder, or to a colleague or friend.
When reading and listening to your paper,
you are more likely to notice the places
where the fluency is disrupted and where
you stumble because of a very long and un-
clear sentence or a wrong connector.
Another revision strategy is to learn
your common errors and to do a targeted
search for them [13]. All writers have a set
of problems that are specific to them, i.e.,
their writing idiosyncrasies. Remembering
these problems is as important for an aca-
demic writer as remembering your friends’
birthdays. Create a list of these idiosyn-
crasies and run a search for these problems
using your word processor. If your problem
is demonstrative pronouns without summary
words, then search for “this/these/those” in
your text and check if you used the word ap-
propriately. If you have a problem with in-
tensifiers, then search for “really” or “very”
and delete them from the text. The same tar-
geted search can be done to eliminate wordi-
ness. Searching for “there is/are” or “and”
can help you avoid the bulky sentences.
The final strategy is working with a
hard copy and a pencil. Print a double space
copy with font size 14 and re-read your
paper in several steps. Try reading your
paper line by line with the rest of the text
covered with a piece of paper. When you are
forced to see only a small portion of your
writing, you are less likely to get distracted
and are more likely to notice problems. You
will end up spotting more unnecessary
words, wrongly worded phrases, or unparal-
lel constructions.
After you apply all these strategies, you
are ready to share your writing with your
friends, colleagues, and a writing advisor in
the writing center. Get as much feedback as
you can, especially from non-specialists in
your field. Patiently listen to what others say
to you ― you are not expected to defend
your writing or explain what you wanted to
say. You may decide what you want to
change and how after you receive the feed-
back and sort it in your head. Even though
some researchers make the revision an end-
189Kallestinova: Your first research paper
less process and can hardly stop after a 14th
draft; having from five to seven drafts of
your paper is a norm in the sciences. If you
can’t stop revising, then set a deadline for
yourself and stick to it. Deadlines always
help.
Rule 7: Revise your paper at the
macrostructure and the microstructure
level using different strategies and tech-
niques. Receive feedback and revise
again.
It is late at night again. You are still in
your lab finishing revisions and getting
ready to submit your paper. You feel happy
― you have finally finished a year’s worth
of work. You will submit your paper tomor-
row, and regardless of the outcome, you
know that you can do it. If one journal does
not take your paper, you will take advantage
of the feedback and resubmit again. You will
have a publication, and this is the most im-
portant achievement.
What is even more important is that
you have your scheduled writing time that
you are going to keep for your future publi-
cations, for reading and taking notes, for
writing grants, and for reviewing papers.
You are not going to lose stamina this time,
and you will become a productive scientist.
But for now, let’s celebrate the end of the
paper.
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