BIOL 2010U

How to Read a Scientific Manuscript

The main purpose of a scientific article is to:

1. Describe, document, and communicate the ideas and results obtained from
experimental work, and
2. To relate these results to prior knowledge in the field.

It is through written (and oral) dissemination of results that scientific knowledge
advances.

Reading a scientific article takes practice. Do not attempt your initial read of a paper
when you are tired. It will be challenging enough, without getting frustrated. Find a
quiet space where you will not be disturbed or distracted, have a pencil and notepad at
hand, and importantly know exactly what you want and expect to get from reading this
article. During your reading, stay calm, write down your questions and try to decide if
your question(s) comes from not understanding a technique, or the basic science. Be
patient, with yourself and with the authors. Finally, realize that everyone struggles to
read articles, especially in the beginning. Starting early in your career, while frustrating
now, will place you at an advantage in the future, especially if you stay in science.

Before you can competently read a scientific manuscript it is important to understand
the format of manuscripts and where information is located in a manuscript. For this
reason, we will begin with a brief overview of how a paper is organized.

In most scientific journals, manuscripts follow a standard format. They are divided into
several sections, and each section serves a specific purpose in the paper. We first will
examine the standard format and end with selected variations on that format.

A standard scientific manuscript is usually divided into the following sections; Abstract,
Introduction, Materials and Methods, Results, Discussion and References/Literature
Cited. For a more detailed guide, visit Writing a Scientific Manuscript located in the
laboratory folder of this course on webCT.

Abstract

Purpose: to briefly introduce some background information, concisely summarize the
experiment performed and the primary results obtained. It also often relates these
findings to the field of study. In some journals this section is called a Summary.

The following questions are typically answered in the abstract:
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What is the subject of the study and what is the central or most important
hypothesis or question?
What approach was taken and what methods were used?
What were the rationale and significance of the study?
What were the most important findings?
What were the main conclusions?
What are the meaning and implications of the study?

Introduction

Purpose: summarizes the current knowledge, by providing background information, on
the topics investigated. This allows the reader to understand why the findings
presented in the paper are an advance on the prior knowledge in the field of study.
Typically, the introduction begins with a broad introduction to the field and then focuses
more specifically on a particular aspect, usually describing results that led to the
research described in the paper. This section is usually concluded by a statement of
purpose and a brief explanation of the rational and possible outcomes of the study
investigated.

The following questions are typically answered in the introduction:

Why was the study conducted, or what is its purpose or importance?
What problem, question or hypothesis does the study address?
What is the basic science or significance of the study?

Materials & Methods (M&M)

Purpose: describes, in a narrative way, the experimental procedures used to collect the
data presented in the manuscript. It also describes the specific materials used in those
experiments.

The following questions are typically answered in the M&M:

What is the study population (i.e. age, gender, size), and the organism or system
under study?
How was the animal maintained or how was the organism cultured (i.e. media
composition, temperature, light-dark cycle)?
What equipment and chemicals were used (name, city and state of the
manufacturer, and the model)?
What specific methods were used?
Which statistical methods were used to analyze your data?

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Results

Purpose: present the key results obtained using written paragraphs and Figures and/or
Tables. The order in which the results are presented should be logical; it should
describe the step by step results that allowed the investigators to answer the question
posed in the Introduction.

The following questions are typically answered in the Results:

What were the findings of the investigation?
What were the trends observed in the results?
Were there any significant differences observed?

Discussion

Purpose: interpretation of the results presented in the paper. In addition to the
presentation of what the authors believe the data show it should compare and contrast
the results obtained with data published by other researchers. The discussion is where
the authors explain how the findings improve the general knowledge/understanding of
the topic.

The following questions are typically answered in the Discussion:

What are the main finding(s) of the study;
How do the data and findings compare to other published data?
What is the significance or importance of the findings?
What are the limitations of the present study?
What are the implications of the findings?
What future studies should be undertaken?

Reference/ Literature cited

Purpose: to provide full citations of all peered-reviewed articles and books that were
cited in the text of the manuscript.

In most scientific journals, the above format is followed. However, the formats for two
high-impact, widely-read journals, Science and Nature, differ markedly from the format
outlined above. In both journals, other than a short abstract and a reference list,
discrete sections do not exist. In Science, the abstract is self-contained; in Nature, the
abstract also serves as a brief introduction to the paper. Experimental details are often
given either in endnotes (Science) or in Figure and Table legends and a short Methods
section (Nature). In addition, common practice is now to place a substantial fraction of
the less-important information, and much of the methodology, into Supplemental Data
that can be accessed online.
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Reading Scientific Articles

Now that we have a general understanding of the material that exists and the questions
typically answered within each section of a manuscript, we can move onto developing a
strategy for accurately and even critically reading a manuscript. Remember that each of
the sections introduced above normally contains recognized conventional features, and
if you read with an anticipation of these features, you will read an article more quickly
and hopefully with better comprehension.

Reading a scientific article is a complex task. Unlike reading a short story or a novel and
letting the plot unfold as you passively sit back, when reading a scientific paper, you
must become an intellectual participant by methodically processing the information. You
will probably find it tempting to read the paper straight through from the first word of
the title to the list of references as you would do with most texts. However, reading an
article in this manner; digesting every word along the way without any reflection or
criticism is not recommended. Rather, it is suggested that you begin by skimming the
article to identify its structure and features. As you read, look for the authors main
points and any unknown vocabulary. Generate questions before, during, and after
reading. Draw inferences based on your own experiences and knowledge. And to really
improve understanding and recall, take notes as you read (Effective readers take
notesit improves recall and comprehension). The remainder of this document
discusses each of these strategies in more detail.


Before reading one word of an article, first ask yourself:
What am I looking for in this article?


Reading primary research papers is partly a matter of experience and skill, and partly a
matter of learning the specific vocabulary of a field. If you approach the paper step by
step, even an impossible-looking paper can be understood. Different people approach
reading scientific literature a little differently. This is a guide that you may find helpful
as you develop your own strategy for reading, understanding, and even critiquing
scientific literature.

Modified from How to Read a Scientific Research Paper: a Four-Step Guide for
Students - developed by Dr. Ann P. McNeal (School of Natural Science, Hampshire
College).

1. Skimming.

Skim the paper quickly, noting basics like headings, figures and the like. This takes just
a few minutes. You're not trying to understand it yet, but just to get an overview. Do
not linger on the abstract (if present)!
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2. Vocabulary.

Go through the paper and,
a. Underline or highlight every word and phrase you don't understand. Don't
worry if there is a lot of underlining; you are not yet trying to make sense
of the article.
b. Underline or highlight the authors main point(s). Because scientific
articles contain so much information, it may be difficult to distinguish the
main points of an article from the subordinate points. Fortunately, there
are many indicators of the authors main points: at the whole document
level, examine the title, keywords, and visuals (i.e. table and figure titles).
In addition, look at the first sentence and the last couple of sentences of
the introduction. While reading through the manuscript, look for words or
phrases like the following:
Surprising
Unexpected
In contrast with previous work
has seldom been addressed
We hypothesize that
We propose
The data suggest
We develop
The data shows

Now you have a choice with these vocabulary and concept (main point) questions,
depending upon the question each poses. You can:

Look up simple words and phrases. Often the question is simply vocabularyfor
example, what is chemiosmosis, a cytochrome, or auxin? A science dictionary,
textbook glossaries, or an on-line reference is a good place to find definitions.
(One good on-line reference is the Encyclopedia Britannica website; dictionaries
and encyclopedias of science, chemistry, biology, environmental science, and
other sciences can be found in the UOIT Library). For more complete
explanations, a textbook may be a good source. (An ordinary shelf dictionary is
not a good source, because the definitions may not be precise enough or may
not reflect the way in which scientists use a word).

Gain an understanding from the context in which a word or phrase is used. Often
words that are used to describe procedures used in an experiment can be
understood from the context, and may be very specific to the paper you are
reading. Examples are the "lithium-free control group" in a rat experiment or the
"carotene extraction procedure" in a biochemical experiment. Of course, you
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should be careful when deciding that you understand a word from its context,
because it might not mean what you think.

Flag phrases belonging to one of the major concepts of the paperthese are
phrases you believe to be more important than a relatively simple vocabulary
question. For example, a paper about diet and cancer might refer to "risk
reduction," which you would need to understand in context and in some depth.

3. Comprehension

This should be completed section by section. Try to deal with all the words and phrases,
although a few technical terms in the Methods and Materials section might remain.

Abstract and Title Read the Title and the Abstract and then review in your mind
what you know about the topic. If there are phrases or terms that are foreign to you,
scan the Introduction section of the paper to determine if they are clarified. If not,
return to section 2 Vocabulary.

Why?

a. Clarify whether you have the background knowledge to appreciate the paper.
If not, you might/should read the required background information in a
review article or textbook, as appropriate.
b. Refreshes your memory about the topic.
c. Helps you integrate the new information into your previous knowledge about
the topic.

Introduction - note how the context is set. What larger question is this a part of? The
author should summarize and comment on previous research, and you should
distinguish between previous research and the actual current study. What is the
hypothesis of the paper and what are the ways this will be tested? If you are very
familiar with the field, the Introduction can be skimmed or even skipped. The logical
flow of most manuscripts proceeds straight from the Introduction to Results;
accordingly, it makes sense to read the manuscript in that sequence as well, skipping
Materials and Methods and referring back to this section as needed to clarify what was
actually done.

Results carefully examine the figures and tables, as they are the heart of most
papers. To understand a figure, you should be able to redraw it and explain it in plain
English words. Be sure you understand the set-up of the experiments shown in each
figure (refer to the Methods and Materials to clarify and to understand experimental
design).

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Discussion - contains the conclusions that the author would like to draw from the
data. In some papers, this section has a lot of interpretation and is very important. In
any case, this is usually where the author reflects on the work and its meaning in
relation to other findings and to the field in general. Ask yourself, do the data presented
in the results section support the authors interpretation?

Methods and Materials if necessary, try to get a clear picture of what was done at
each step. What was actually measured? It may be beneficial to make an outline
(flowchart) and/or sketch of the procedures.


4. Reflection and criticism.

After you understand the article and can summarize it, then you can return to broader
questions and draw your own conclusions. It is very useful to keep track of your
questions as you go along, returning to see whether they have been answered by your
comprehension in step 3. Often, the simple questions may contain the seeds of deeper
thoughts about the work. For example, "Why did the authors use a questionnaire at the
end of the month long study? Wouldn't subjects forget, or have trouble recalling?"