Course Title: Scientific Research
Week 10: [Scientific writing part 1]
Instructor: [Mahmoud Salah]
Date: [22/11/2025]
License: CC BY-NC-SA 4.0
Scientific writing, though an essential part of the scientific process, is usually neglected
in academic courses. After all, it is the ability to communicate findings that completes
the research cycle.
Why Publish?
For many professionals, publication is essential for career advancement, securing
funding, or for academic qualifications such as a master’s or doctoral thesis. A scientific
paper is the formal and durable record of a research process, intended to document
protocols, methods, results, and conclusions.
• Purpose of Scientific Writing: Scientific writing aims to update the scientific
community with new data developed from hypotheses, which furthers understanding in
a particular field.
• The Challenge: Scientific writing has a format and structure that is quite different from
most other classes you have taken (e.g., English or History). The process may seem
overwhelming at times.
• The Benefit: Good writing can actually increase your learning of the subject, since
writing requires you to tell a coherent and logical story backed by research and results.
The Standard Format: IMRAD
Clear scientific writing generally follows a standard format, which aids in moving
information from author to reader efficiently. This standard format is often referred to by
the acronym IMRAD:
• Introduction
• Methods (or Materials and Methods)
• Results
• And Discussion
The Hourglass Analogy
The structure of a scientific paper often resembles the shape of an hourglass
1. It starts broadly in the Introduction - setting context.
2. It narrows down to the specific question, hypothesis, methods, and results of your
study.
3. It broadens again in the Discussion and Conclusion, relating your research back to the
literature that already exists and describing how you addressed a "knowledge gap".
Scientific Writing vs. Other Writing
You can easily become attached to your research and, frankly, convinced that your
work is very important. Scientific writing calls upon you to step back and communicate
your work in a clear and understandable manner so others, perhaps well outside of your
expertise, can recognize your findings. You want to focus on what you want your readers
to understand, rather than what you did or learned.
Important aspects that needs to be considered before writing a paper:
1. Research Your Work's Context Familiarize yourself with previous research done
on your topic to decide how your work compares to existing studies.
• Ask: What do we already know about this topic? What open questions-the "knowledge
gap"-exist? Why is this information important?
• This will provide an understanding of the style others use and how your research builds
from prior work to help you create a compelling story.
2. Know Your Audience (and Write for Them) You need to know your audience and
determine what story you want them to understand.
• Ask: Who is my audience? What are their goals in reading my writing? What message do
I want them to take away?
• Writing effectively implies consideration for the readers' needs.
3. Identify Your Target Journal This is a very important step, which you need to do
even before you begin writing.
• Checking the journal's instructions helps not only with formatting, but more importantly
with the orientation and style of your writing to match the target readership.
• Make sure your paper falls within the scope of the journal you choose.
Introduction Section
Introduction: It includes relevant background information and should clearly state the
problem you intend to solve.
Structuring the Introduction (The Funnel)
1. Start Broad: Set your research in a broad context intelligible to a person outside the
field.
• Include only material directly relevant to your research and your story; avoid giving
an entire history of the field.
2. Narrow Down (The Gap/Niche): Reach the very specific focus of your research.
• Identify the knowledge gap, a specific area of the literature containing an unknown
question or problem. Justify the usefulness of your work by stating what explicit
gap your study wants to fill.
3. Statement of Your Study (Occupy the Niche): Clearly state the problem your paper
addresses.
• Explicitly state how your work will contribute to filling that knowledge gap.
• Define your hypotheses and give a brief synopsis of your experimental design in 1-
2 sentences.
A hypothesis: is a testable explanation of an observed occurrence in nature; it relates
directly to a research question and it is an educated guess that attempts to explain the
mechanism underlying a pattern.
The CARS Model One framework for structuring the Introduction is the CARS model
(Create A Research Space):
1. Establish the Territory: Set the general intellectual context, that is, the broad facts and
prior work.
2. Niche: Situate your work within the context by showing what isn't known - the
knowledge gap.
3. Occupy the Niche: In this space, stating your objectives or hypotheses of study
possibly by starting with the expression, “Here we show…
Introduction and Citation Basics
In writing, you should select one formulation for your objective and use the identical
wording in the entire paper, including the Introduction, Results and Discussion sections,
Abstract, and Title.
In-Text Citations
You need to include in-text citations for every paper you cite. This shows how your work
is situated within the literature that already exists.
• Format: Usually (Author, publication year).
• Good Practice: Avoid using an author's name as the subject of a sentence.
• Example (Avoid): "Kilner et al. (2004) found that.".
• Example (Preferred): "Cowbird nestlings use host offspring to procure more food
(Kilner et al. 2004)".
Drafting the Materials and Methods Section
The Materials and Methods section should describe exactly what you did, and how, in
sufficient detail that any average reader could reproduce your study.
Structure and Content:
• Organization: Divide this section into subsections with appropriate headings for
each procedure.
• Study Design: Outline the design, including whether prospective/retrospective,
randomized, etc., and justify any unusual methodology.
• Study Population: Summarize whom or what you studied; human subjects, cells
and animals. Specify the inclusion and exclusion criteria.
Reproducibility Details:
Clearly state the steps you took procedurally in chronological order.
• Equipment: Include model numbers and specific settings of all equipment used,
such as temperature of incubation, speed of centrifuge.
• Procedure: If a procedure was followed from another paper, then cite the source
and describe it generally. Repeat every detail only if you modified the procedure
from the original source.
• No Interpretation: In general, save subjective qualifiers and sources of error for the
Discussion section; do not include them in Methods.
Ethics and Responsibility:
In human studies, you need to assure the reader that:
1. The project was approved by your Institutional Ethics Review Board (IRB).
2. Subjects gave full and informed consent.
• Most journals require you to specify the name of the ethics committee and the date of
approval.
Statistical Analysis:
The last paragraph of the Methods section should describe the statistical analysis. When
designing the protocol, consult a biostatistician, not afterwards when the experiments
are completed.
• Data Presentation: Define how data are presented (e.g., means ± standard
deviation for normally distributed data).
• Specific Tests: Indicate specific statistical methods involved, such as ANOVA or
linear regression.
• Sample Size: Provide sample size justification and calculations.
• Significance: Define the chosen significance level/alpha risk and statistical
software applied.
Tense in Methods:
The Materials and Methods section should be written in the past tense.
Example: “on birth date, enfants were measured their tibia length, and calculated the
instantaneous growth constant K”.
N.B. This lecture would include an online tutorial for using In-text citation software
Mendely.
References:
1. Drake, J. M., & Han, B. A. (2025). How to write a scientific paper in fifteen steps.
PLOS Computational Biology, 21(9), e1013505.
2. Delvin, E., Pillay, T. S., & Newman, A. (2014). How to write a scientific paper:
Practical guidelines. eJIFCC, 25(3), 259-268.
3. Turbek, S. P., Chock, T. M., Donahue, K., Havrilla, C. A., Oliverio, A. M., Polutchko,
S. K., Shoemaker, L. G., & Vimercati, L. (2016). Scientific writing made easy: A
step-by-step guide to undergraduate writing in the biological sciences. Bulletin of
the Ecological Society of America, 97(4), 417-426.
4. Ecarnot, F., et al. (2015). Writing a scientific article: A step-by-step guide for
beginners. European Geriatric Medicine.
License
This document is licensed under a Creative Commons Attribution. 4.0 International
License.