Lecture 3

Writing the Introduction Section of a Paper

Chao Song

College of Ecology
Lanzhou University

September 28, 2023

Scientists and writing

You do not succeed as a scientist by merely getting papers published. You

succeed by getting them cited. Writing is not only something a scientist
does. Being a writer is something a scientist is.

Writing can be a painful process of rewriting, rewriting, and more rewriting

until your work gets good enough to be sent off.

“Writing: the most impossible short distance in the history of humanity.”

Some references on scientific writing

Gastel and Day book: comprehensive cover of the fundamentals;

Glassman-Deal book: useful language tips for non-native speaker;
Schimel book: techniques for cohesive and intriguing writing.
Scientific writing as story telling

The role of scientists is to collect data and transform them into

understanding. Their role as authors is to present that understanding.
Scientific writing is not merely outlining what you did and present what you
found, its essence is to extract and distill a story.

(Schimel 2012, Writing Science: How to write papers

that get cited and proposals that get funded)
Structure of a story

Stories usually have the OCAR structure:

• Opening: Whom is the story about? Who are the characters? Where
does it take place? What do you need to understand about the situation
to follow the story?
• Challenge: What do your characters need to accomplish?
• Action: What happens to address the challenge?
• Resolution: How have the characters and their world changed as a
result of the action?
OCAR structure in the scientific writing context

Opening: what is the larger problem you are addressing?

Challenge: what specific question do you propose to answer?
Action: what did you do to address the question?
Resolution: what did you learn from your work?

(Schimel 2012, Writing Science: How to write papers

that get cited and proposals that get funded)
Structure of a scientific paper

A typical scientific paper contains the introduction, methods, results, and

discussion sections, commonly referred to as the IMRaD structure.

(Glasman-Deal 2010, Science Research

Writing for Non-Native Speakers of English)
Mapping story structure to paper structure

The OCAR structure corresponds well with the typical IMRaD structure of
scientific papers.

(Schimel 2012, Writing Science: How to write papers

that get cited and proposals that get funded)
Combining story and paper structure in writing

Establish basic structure of writing based on the conventional IMRaD

structure; Refine the writing based on the OCAR story structure.
General guidelines for the introduction

The introduction should have the following essential components:

• Present the nature and scope of the problem investigated;
• Review pertinent literature to orient the reader;
• Identify current knowledge gaps;
• Make clear the question or hypothesis of the research;
• State the methods of the investigation briefly;
• If necessary, state the principal results of the work.
A general model for introduction

In general, the introduction section may comprise the following:

• Introduce the general background and establish the significance of the
problem (1–2 paragraphs);
• Review literature relevant to the focal problem (1–3 paragraphs)
• Identify knowledge gap and specify the questions/hypothesis to be
addressed (1 paragraph)
• Describe your own research briefly (1 paragraph)
A general model for introduction

We can divide the writing of the introduction into four stages, going from
general to specific.

(Cargill and O’Connor 2013, Writing Scientific Research Articles)

A general model for introduction: example
A few comments on the example

The example in the previous slides has a few notable features:

• The introduction was written with a very clear logical order using the
common structure of the introduction section;
• The authors used the topic sentence of each paragraph to guide the
readers through the logic flow;
• An effective way of drafting the introduction, or more generally a
manuscript, is to write down the first and/or last sentence of each
paragraph before filling up all paragraphs.
Back to story writing

Opening: what is the larger problem you are addressing?

Challenge: what specific question do you propose to answer?
Action: what did you do to address the question?
Resolution: what did you learn from your work?

(Schimel 2012, Writing Science: How to write papers

that get cited and proposals that get funded)
Opening

What is a good opening for a scientific paper?

• A good opening of a scientific paper should define the general problem
and indicate or hint at the direction of the paper.
• The opening typically encompasses the first paragraph and sometimes
several more.
Good opening

This is the openning for a synthesis paper on nitrogen processing in soils

(Schimel and Bennett 2004, Ecology).

Since the late 1800s, N mineralization has been perceived as the center
point of the soil N cycle and the process that controls N availability
to plants.

Comment: This opening is effective for two reasons:

• The opening hints at the readers the direction of the paper. The word
“perceived” draws readers’ attention and makes it clear that the paper
will challenge that perception.
• The opening also indicates that there will be a historical element, which
is suitable for a synthesis paper on how understanding of N processing
in soils changed over time.
Good opening

This opening comes from a paper evaluating the effects of timing, dose, and
source of folate during pregnancy on childhood asthma (Whitrow et al 2009,
American Journal of Epidemiology).

Current public health guidelines in the United States, the United

Kingdom, and Australia recommend that women consume a supple-
mental dose of 400 µg of folic acid per day in the month preceding
and during the first trimester of pregnancy to reduce the risk of neu-
ral tube defects in children.

Comment: This is an effective opening as it introduce the general problem

and hint at the reader that the paper is going to evaluate and potentially
challenge the current recommendation of taking 400 µg folic acid during
pregnancy.
Good opening

This opening comes from a review paper on conjugated polmyers as

molecular materials (Schwartz 2003, Annual Review of Physical Chemistry)

Conjugated polymers are novel materials that combine the optoelec-

tronic properties of semiconductors with the mechanical properties
and processing advantages of plastics. . .Thus, conjugated polymers
offer the possibility for use in devices such as plastic LEDs photo-
voltaics, transistors, and in completely new applications such as flex-
ible displays.

Comment: The first sentence frames the overall topic while the last sentence
set the story in concrete terms, making it clear what this paper is going to
focus on.
Good opening

This opening is from a paper on Arctic soil organic matter chemistry

(Weintraub and Schimel 2003, Ecosystems).

The arctic has become a focus of attention because global warming is

expected to be the most severe at extreme latitudes. The thick organic
soils of the tundra contain large stocks of carbon and these soils may
act as either a source or a sink for atmospheric carbon dioxide. . .Thus,
the direction the C balance of the arctic will shift with warming is
unclear and depends on in- teractions between soil C and N cycling
that we still do not understand in the tundra

Comment: When you need to engage a wider audience, open with a general
issue that engages your target audience, but then modulate it to the one you
want to work with.
Bad opening

Misdirection: this paper is about how plant transport CH4 , but the opening
talks about how plant-derived carbon drives CH4 dynamics. The opening
does not point to the direction where the paper is heading to.

Plants are a critical control of CH4 dynamics in wetland ecosystems.

They supply C to the soil methanogenic community both through
production of soil organic matter, and as fresh exudates and residues.
Fresh plant material may be an important CH4 precursor even in
an organic matter-rich peat soil. Strong correlations between net
primary productivity and system-level CH4 fluxes across a wide range
of ecosystems highlight the importance of plant C inputs.

Vascular plants, however, also transport CH4 out of soil and sediment,
effectively bypassing the aerobic zone of CH4 oxidation.
Bad opening

No direction: the opening talks about common knowledge of meiosis but did
not indicate what the paper will focus on. It offers no direction to the reader.

In meiosis, genes that are always transmitted together are described

as showing “linkage”. Linkage, however, can be incomplete, due to
the exchange of segments of DNA when chromosomes are paired.
This incomplete linkage can lead to the creation of new pairings of
alleles, creating new lineages with distinct sets of traits.
Changing styles for your audiences

For specialists, one can use more technical terminology.

Larry Pameroy’s seminal paper revolutionized our concepts of the

ocean‘s food web by proposing that microorganisms mediate a large
fraction of the energy flow in pelagic marine ecosystems. Before 1974,
bacteria and protozoa were not included as significant components of
food web models. Pomeroy argued forcefully that heterotrophic mi-
croorganisms, the “unseen strands in the ocean’s food web,” must be
incorporated into ecosystem models.
(Azam et al 1994, Microbial Ecology)

For non-specialists, use characters that are familiar to the general readers.

Antonie van Leeuwenhoek (1632–1723), the first observer of bacteria,

would be surprised that over 99% of microbes in the sea remained
unseen until after Viking Lander set out to seek microbial life on Mars.
(Azam and Worden 2004, Science)
How wide should your opening be?

The opening should have similar “width” as your resolution. If you err, it is
better to err slightly onthe wider side.

(Schimel 2012, Writing Science: How to write papers

that get cited and proposals that get funded)
The challenge

General guidelines for writing the challenge of a story:

• Define the challenge as a question, not merely describing your objective.
• Some scientists, particularly those in biology, suggest stating clearly
your hypothesis is a necessity for scientific paper.
• After posing the question, a good challenge briefly lays out the research
approach. This is where you tell us about specific objectives and the
information you will generate.
• The challenge should be logically motivated. Statements like “something
has not been done” or “something has not been done at this location”
are weak and not persuasive.
Good challenge

The authors lay out the problem explicitly first. The literature review, coupled
with logic, makes a strong case for the current study (del Pilar Gomez and
Nasi 2015, Journal of Biological Chemistry).

Despite the tantalizing evidence for DAG and/or its downstream prod-
ucts in visual transsuction and the synergistic role of calcium, in no
instance has application of such chemical stimuli fully reproduced the
remarkable size and speed of the photocurrent. This may imply that
yet another signal may be missing from the proposed schemes. In other
systems PIP2 has been shown to possess signaling functions of its own,
independent from those of its hydrolysis products. These observations
prompted the conjecture that in microvillar photoreceptors PIP2 may
help keep the channels closed and its hydrolysis could promote their
opening. In the present report, we examined the consequences of manip-
ulating PIP2 on membrane currents and light responsiveness in isolated
photoreceptor from Pectren and Lima.
Good challenge

The authors laid out their hypotheses and provided justification for them
(Bengtson and Bengtsson 2007, Ecology Letters).

The experiment was set up to test three hypotheses: first, DOC was
hypothesized to be the source of respired CO2 in forest soils. There are
several reasons to justify that: (i) DOC consists partly of sugars and
amino acids that are readily amenable to microbial uptake; (ii) being es-
sentially aquatic, micro-organisms would be expected to use compounds
dissolved in the soil water and (iii) models of DOC dynamics indicate
that microbial–DOC relationships are important in regulating C fluxes
in surface soil horizons. However, one can raise the objection that the
DOC pool of forest soils is small relative to the CO2 fluxes, and that at
least a part of the DOC pool is old and slowly turned over. Therefore,
our second hypothesis was that the rate of DOC production, rather
than the DOC concentration, was the rate-limiting step for microbial
respiration. Finally, given that enzymes catalyse the DOC production
and enzymatic activity depends on temperature, the rate of respiration
was hypothesized to be dependent on the temperature rather than on
the size of different C pools.
Good challenge

It is common to find signal words or phrases that indicate the existence of

knowledge gap, such as however, remain a major challenge, rarely, not well
understood, and presently unclear.

However, understanding how these processes interact to regulate inva-

sions remains a major challenge in ecology.

Despite its acknowledged importance, propagule pressure has rarely

been manipu- lated experimentally and the interaction of propagule
pressure with other processes that regulate invasion success is not well
understood.

It is presently unclear how different disturbance agents influence long-

term patterns of invasion.

(Britton-Simmons and Abbott, 2007, Journal of Ecology)

Bad challenge

The specific question of the study was not clearly defined here.

Some T-cells may be anergic–that is, unable to proliferate after be-

ing restimulated with an antigen. Some anergic T-cells are unable to
link to the T-cell-antigen presenting cell (APC) interface. Here we
examined the structural characteristics of anergic mouse T-cells and
we tested their functional response to being rechallenged with antigen-
loaded APCs

This can be improved by simply stating what the researchers intend to

achieve. The “To learn X, we did Y” template is an effect way to do this.

To determine what causes mouse T-cells to be anergic, we evaluated the

structural characteristics of T-cells and how they responded to being
rechallenged with antigen-loaded APCs
Bad challenge

The authors presented the challenge in chronological order, but the core
question came in second.

The study had two goals. First, we aimed to constrain our estimates of
grassland plant production by comparing measurements based on two
techniques: maximum biomass at the end of the season and periodic
measurements of photosynthesis. Second, we examined the response of
grass growth to a combination of elevated CO2 and increased temper-
atures, conditions that are expected to occur with climate warming.

To fix this problem, we highlight the core question first.

The primary goal of this study was to evaluate how grass growth re-
sponds to a combination of elevated CO2 and increased temperatures,
conditions that are expected to occur with climate warming. To val-
idate the plant growth measurements, we used to approaches: maxi-
mum biomass at the end of the season and periodic measurements of
photosynthesis.
Connecting the opening and the challenge

The opening of a paper identifies a large problem, while the challenge

defines a specific question. The main body of the introduction narrows the
focus and leads readers from the general to the specific, drawing them along
the story and framing in the knowledge gap
Effective connection: an example

Dissolved organic carbon (DOC) undergoes numerous transformations as

it flows from land to ocean, with both positive and negative effects on
ecosystem services. Mineralization of DOC into greenhouse gases con-
tributes to climate warming but also removes organic contaminants from
potable water reservoirs. Simultaneously, DOC that escapes mineraliza-
tion may contribute to carbon sequestration and, thus, climate change
mitigation, for example, via sedimentation. Thus, DOC turnover and
fate are critical to both society and the global carbon cycle.
There are three main pathways of DOC transformation–biological re-
actions, sunlight-induced photochemical reactions, and immobilization
by flocculation–each controlled by the intrinsic chemical composition of
the DOC but also by extrinsic physical, chemical, and biological fac-
tors. However, despite recent advances in the conceptual understanding
of large-scale DOC turnover and how to model it, the combined intrinsic
and extrinsic controls on these transformation pathways are inadequately
described. Thus, the fates of DOC inputs from land to water in a chang-
ing environment remain unclear.
(Berggren et al 2022, Ecology)
Introduction vs. literature review

Although the introduction usually involves literature review, they are different
in purpose and thus in how we approach them in writing:
• A literature review builds a solid wall—describing knowledge—whereas
an Introduction focuses on the hole in that wall—describing ignorance.
• Pointing out lack of research in a important topic or inconsistencies
in existing literature is an effective way to present knowledge gap.
Introduction vs. literature review

This example points out inconsistent results from existing research on the
temperature sensitivity of whole ecosystem metabolism, thus giving strong
motivation to the current work.

Given the complexity of ecosystem–level temperature sensitivities and

the challenges associated with quantifying them, it is not surprising
that various patterns have been reported. Some studies have found
consistent temperature sensitivities of ER at the ecosystem and the
cellular levels, but others have demonstrated considerable deviation of
ecosystem–level activation energies of GPP from the values of their
cellular analogs. In studies that simultaneously examined the tem-
perature dependence of GPP and ER in streams, a shift toward het-
erotrophy with warming has been observed in some instances, but a
recent synthesis based on geothermal streams concluded that warming
increases GPP and ER to the same extent and results in no net change
in metabolic balance.

(Song et al 2018, Nature Geoscience)

Tense

A few general principles on using tense in the introduction section:

• Present or present perfect tense are common in the introduction to
describe existing knowledge;
• Past tense should be used to describe past actions;
• Pay attention to the meanings different tenses convey. The difference
can be subtle, but correct use of tense can make it more effective to
convey the desired meaning.
Tense

Past tense indicates that the phenomenon only applies to when the
experiment was done.

We found that the pressure increased as the temperature rose, which

indicated that temperature played a significant role in the process

Present tense indicates that the findings are generally true and thus provide
a much stronger statement.

We found that the pressure increases as the temperature rises, which

indicated that temperature plays a significant role in the process.
Tense

Past tense indicates that little attention was paid over two years ago but did
not hint at what happened after that.

However, although the effect of the rubber particles on the mechanical

properties of copolymer system was demonstrated over two years ago,
little attention was paid to the selection of an appropriate rubber
component.

Present perfect tense indicate that not much attention was given to the
question ever since two years ago. It thus offers a stronger motivation for the
current study.

However, although the effect of the rubber particles on the mechanical

properties of copolymer system was demonstrated over two years ago,
little attention has been paid to the selection of an appropriate
rubber component.