Scientific Writing and Publication DR Gan Lim

11/22/21
Scientific Hello and welcome to this lecture.

Writing and
Publication Before we start this lecture, I would like to
announce that this online session will be
recorded as soon as the lecture begins.
We will start in a few minutes…
- Laurence A. Gan Lim, PhD -
-Gan Lim- 1
Scientific
Writing
and
Publication
Laurence A. Gan Lim, PhD
1
11/22/21
What is scientific writing?

Why publish?
What is a scientific paper?
Organization of a Scientific Paper
Ethics is Publishing
Topics to Choosing Where Publish
cover Listing of Authors

ORCID
Style Manuals
Reference Manager
Preparing the Abstract
Writing the Different Sections of a Paper
-Gan Lim- 3
What is scientific writing?

Writing that involves reporting of original research in journals, through scientific papers in
standard format.
[broadly speaking]: Can include communication about science through other types of journal
articles, such as review papers summarizing and integrating previously published research.
[broadly speaking]: Can also include other types of professional communication by

scientists—for example, grant proposals, oral presentations, and poster presentations.
(Writing about science for the public??)
Key ingredients:
Ø Clarity and/or Simplicity
Ø Organization (follow a standard format)
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Why publish?
Publication is the ultimate goal of scientific research.
Researchers, professors, scientists, (graduate) students, are measured

primarily not by their technical skills in the laboratory and not by their
knowledge about their research areas; they are measured, and become known
(or remain unknown) by their publications.
…To publish, a researcher or scientist must not just “do” science but also “write” science.
-Gan Lim- 5

The Council of Biology Editors (CBE), now the Council of Science Editors (CSE), arrived at the
following definition (Council of Biology Editors 1968, p. 2):
An acceptable primary scientific publication must be the first

disclosure containing sufficient information to enable peers
(1) to assess observations,
(2) to repeat experiments, and
(3) to evaluate intellectual processes;
moreover, it must be susceptible to sensory perception,
essentially permanent, available to the scientific community
without restriction, and available for regular screening by one or
more of the major recognized secondary services (e.g., currently,
Biological Abstracts, Chemical Abstracts, Index Medicus,
Excerpta Medica, Bibliography of Agriculture, etc., in the United
States and similar services in other countries).
http://www.councilscienceeditors.org/wp-
content/uploads/v37n2p68-69.pdf
[14 November 2021]
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The Council of Biology Editors (CBE), now the Council of Science Editors (CSE), arrived at the
following definition (Council of Biology Editors 1968, p. 2):
“peer-reviewed”
An acceptable primary scientific publication must be the first
disclosure containing sufficient information to enable peers
(1) to assess observations,
(2) to repeat experiments, and
(3) to evaluate intellectual processes; “published”
moreover, it must be susceptible to sensory perception,
essentially permanent, available to the scientific community
without restriction, and available for regular screening by one or
more of the major recognized secondary services (e.g., currently,
Biological Abstracts, Chemical Abstracts, Index Medicus,
Excerpta Medica, Bibliography of Agriculture, etc., in the United
States and similar services in other countries).
http://www.councilscienceeditors.org/wp-
content/uploads/v37n2p68-69.pdf
[14 November 2021]
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A scientific paper is a peer-reviewed and published report that has been written in order to
describe the original research results.
The publication of a scientific paper must be:

• essentially permanent,
• must be made available to the scientific community without restriction,
• and must be made available to the information retrieval services (Biological Abstracts,
Chemical Abstracts, Index Medicus, etc.).
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Related Terms
Review Paper
A review paper is a technical paper that summarizes, analyzes, evaluates, and/or synthesizes
various published work on a particular topic or related topics. New paradigms, new ideas, and
new theories can come out from a good review paper.
Conference Report
A conference report is a paper published in the proceedings of a conference, symposium,
congress, or something equivalent. Conference proceedings usually do not qualify as
primary publication due to possible inclusion of papers containing only preliminary results
of on-going studies and are sometimes accompanied by interesting speculation.
Meeting Abstracts and Extended Abstracts or Synoptics

Abstracts are “compressed” versions of papers. The extended abstract can contain as much
information as a full paper minus the experimental detail and therefore cannot qualify as
a scientific paper.
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Organization of a scientific paper
The acronym for the “conventional” scientific article structure:
IMRaD
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IMRaD
Introduction
Materials and Methods
Results
and
Discussion
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is f
stract part o
AI M R a DR
Ab ays r
The t alw l pape
s a
almo echnic
ny t
a Abstract
Introduction
Materials and Methods References

Almost
all
technic
Results have a
al pape
rs
list of
referen
ce
and the end s at
.
Discussion
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Shape of a Scientific Paper

(a) The whole structure is governed by the Results box;
everything in the article must relate to and be
connected with the data and analysis presented in the
Results section.
(b) (1) The Introduction begins with a broad focus. The
Fig. 2.1 AIMRaD: the starting point you select for your Introduction should
hourglass ‘‘shape’’ of a be one that attracts the lively interest of the audience
generic scientific research you are aiming to address: the international readers of
article and key features your target journal.
highlighted by this shape.
M Cargil and P O’Connor, “Writing Scientific Research Articles,
(3) The Introduction ends with a focus exactly parallel
Strategy and Steps.” Wiley-Blackwell (2009). to that of the Results; often this is a statement of the
aim or purpose of the work presented in the paper, or
its principal findings or activity.
(2) Between these two points, background
information and previous work are woven together to
logically connect the relevant problem with the
approach taken in the work to be presented to address
the problem.
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(c) The Methods section, or its equivalent, establishes

credibility for the Results by showing how they were
obtained.
Fig. 2.1 AIMRaD: the
hourglass ‘‘shape’’ of a
generic scientific research (d) The Discussion begins with the same breadth of focus
article and key features as the Results – but it ends at the same breadth as the
highlighted by this shape. starting point of the Introduction. By the end, the
M Cargil and P O’Connor, “Writing Scientific Research Articles, paper is addressing the broader issues that you raised
Strategy and Steps.” Wiley-Blackwell (2009).
at the start, to show how your work is important in the
‘bigger picture.’
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(a) The Methods section, often renamed

Fig. 2.2 AIRDaM (Abstract, Procedure or Experimental, is presented
Introduction, Results, after the Discussion, sometimes in a
Discussion, and Methods smaller type face than the rest of the
and materials): a structure paper.
variation that occurs in
articles in some journals (b) This change means that more details
with a focus on molecular may need to be given in the Results
biology. section to explain how the results were
obtained.
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(a) The Results and Discussion are presented together

in a single combined section; each result is
presented, followed immediately by the relevant
discussion.
(b) This change means that a separate section is needed

at the end to bring the different pieces of discussion
together; it is often headed Conclusions.
Fig. 2.3 AIM(RaD)C (Abstract, Introduction,

Materials and methods, repeated Results and
Discussion, Conclusions): a structure variation
that is permitted in some journals, usually for
shorter articles.
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Ethics in Scientific Publishing
Definiton of ‘Ethical’ (adjective)
1: involving questions of right and wrong

behavior : relating to ethics
2: following accepted rules of behavior :
morally right and good
https://www.merriam-webster.com/dictionary/ethical
[19 Nov 2021]
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Authenticity and Accuracy
“Dry-labbing” or fabrication of experimental results or findings is

obviously unethical.
Omitting outlying points from the data reported, preparing

figures in ways that accentuate the findings misleadingly, or
doing other tweaking are similarly unethical.
Statistics should be used properly or appropriately and not to

distort the findings.
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Originality
Findings in a scientific paper must be new.
Credit
Proper citation is very important when including information or
ideas from others.
Plagiarism is a mortal sin in scientific publishing. The U.S.
National Institutes of Health defines as “the appropriation of
another person’s ideas, processes, results, or words without
giving appropriate credit”
It is unusual to include quotations from others’ work. Rather,
authors paraphrase what others have said.
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Credit
Plagiarism checking software such as Turnitin or CrossCheck

can be used to pre-screen your work and avoid inadvertent
plagiarism.
List of authors: include only those who qualify
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Ethical Treatment of Animals and Humans
Publishers usually require a form to be filled out.
Disclosure of Conflicts of Interests
May interfere with the objectivity of research
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Choosing Where
to Publish
Things to consider:
• Relevance to your
topic/field
• Impact of publication
• (Avoid) Predatory
journals
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Estimating Journal
Impact or Prestige
Journal Metrics
Journal Impact Factor (available through

Thompson Reuters' Journal Citation
Reports).
CiteScore ,
Eigenfactor,
Google Scholar Metrics,
SCImago Journal & Country Rank (SJR),
and Source Normalized Impact per Paper
(SNIP)
Scopus Journal Analyzer (includes
CiteScore, SJR. and SNIP)
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Important Comments about I.F.

While the impact factor (I.F.) is used in many institutions as among the criteria in
evaluating the research performance of a candidate, limitations of the impact factor
also should be noted.
The impact factor indicates how much the papers in a journal are cited on
average— not how much your paper will be cited if it appears in the journal. It does
not indicate how much impact other than on citation the papers in a journal have—
for example, how much they influence policy or clinical practice.
And because different scientific fields have different citation practices, impact factors
should not be used to compare importance of journals in different fields.
For instance, in biochemistry and molecular biology, in which papers tend to cite
many recent papers, the impact factor of the top-cited journal was 32.2 in the year
2014, but in geology it was 4.9. th
B. Gastel and R A Day. “How to Write and Publisha Scientiﬁc Paper,” 8 edition, Greenwood.
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Listing of Authors
There is no universally accepted rule or convention on how to list the
names of authors of a scientific paper.
Traditionally, the most senior person (Professor or Head of Laboratory)

always occupied the last position in the list while the name of the
primary author (usually the student) is listed first.
Scientific papers produced from collaborative research tend to list more

authors and this trend is increasing.
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Listing of Authors
Who should be included in the list of authors?
The list of authors should only include those people who actively
contributed to the overall conceptualization, design, and execution of
research.
An author takes the intellectual responsibility for the research results

presented in the paper.
Intellectual
Authorship
Responsibility
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Introducing ORCID
ORCID à mechanism that can unambiguously identify an author
https://orcid.org/
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Style Manuals
Successful writing also is also about following instructions. Practically every scientific
journal issues instructions to authors.
Listing of Style Guides

Type/Subject Area Association/Organization Style Guide
General Modern Language Association MLA Style Manual: 3rd Ed.
General American Psychological Association APA Style Manual: 6th Ed.
General University of Chicago Press Chicago Manual of Style: 16th Ed.
Physics and Astronomy American Institute of Physics AIP Style Manual: 4th Ed.
Chemistry American Chemical Society ACS Style Guide: 3rd Ed.
Biology Council of Science Editors CSE Manual: 7th Ed.
Mathematics American Mathematical Society AMS Handbook
Engineering Institute of Electrical and Electronics 2009 IEEE Style Manual
Engineers
Medicine American Medical Association AMA Manual of Style: 10th Ed.
Meteorology American Meteorological Society AMS Style Manual
https://www.enago.com/academy/different-scientific-writing-style-guides/
[Nov 20, 2021]
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Basics of the IEEE Style

In-text Citing
It is not necessary to mention an author's name, pages used, or date of publication in the
in-text citation. Instead, refer to the source with a number in a square bracket, e.g. [1], that
will then correspond to the full citation in your reference list.
• Place bracketed citations within the line of text, before any punctuation, with a space
before the first bracket.
• Number your sources as you cite them in the paper. Once you have referred to a source
and given it a number, continue to use that number as you cite that source throughout
the paper.
• When citing multiple sources at once, the preferred method is to list each number
separately, in its own brackets, using a comma or dash between numbers, as such: [1],
[3], [5] or [1] - [5].
https://pitt.libguides.com/citationhelp/ieee
[Nov 20, 2021]
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In-text Citing
The below examples are from Murdoch University's IEEE Style LibGuide.
Examples of in-text citations:
"...end of the line for my research [13].”
"This theory was first put forward in 1987 [1].”
"Scholtz [2] has argued that...”
"Several recent studies [3], [4], [15], [16] have suggested that....”
"For example, see [7]."
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Creating a Reference List
The Reference List appears at the end of your paper and provides the full citations for all
the references you have used. List all references numerically in the order they've been
cited within the paper, and include the bracketed number at the beginning of each
reference.
• Title your list as References either centered or aligned left at the top of the page.
• Create a hanging indent for each reference with the bracketed numbers flush with the
left side of the page. The hanging indent highlights the numerical sequence of your
references.
• The author's name is listed as first initial, last name. Example: Adel Al Muhairy would
be cited as A. Al Muhairy (NOT Al Muhairy, Adel).
• The title of an article is listed in quotation marks.
• The title of a journal or book is listed in italics.
[Nov 20, 2021]
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Creating a Reference List
The below examples are from the IEEE Citation Reference Guide, IEEE Reference
Guide, and Murdoch University's IEEE Style LibGuide.
Material Type Works Cited

Book in print [1] D. Sarunyagate, Ed., Lasers. New York: McGraw-Hill, 1996.
Chapter in book [2] G. O. Young, "Synthetic structure of industrial plastics,"
in Plastics, 2nd ed., vol. 3, J. Peters, Ed. New York: McGraw-Hill,
1964, pp. 15-64.
eBook [3] L. Bass, P. Clements, and R. Kazman, Software Architecture in
Practice, 2nd ed. Reading, MA: Addison Wesley, 2003. [E-book]
Available: Safari e-book.
Journal article [4] G. Liu, K. Y. Lee, and H. F. Jordan, "TDM and TWDM de Bruijn
networks and shufflenets for optical communications," IEEE Trans.
Comp., vol. 46, pp. 695-701, June 1997.
[Nov 20, 2021]
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Basics of the APA Style

APA à American Psychological Association
APA 7th Citation Examples

Material Type In-text Citation Bibliography
A book (Sapolsky, 2017) Sapolsky, R. M. (2017). Behave: The
biology of humans at our best and
worst. Penguin Books.
Chapter in an edited book (Dillard, 2020) Dillard, J. P. (2020). Currents in the
(If the chapter is from an study of persuasion. In M. B. Oliver,
authored book, use the book A. A. Raney, & J. Bryant (Eds.), Media
citation) effects: Advances in theory and
research (4th ed., pp. 115–129).
Routledge.
An article in a print journal (Weinstein, 2009) Weinstein, J. (2009). “The market in
Plato’s Republic.” Classical
Philology, 104(4), 439-458.
https://pitt.libguides.com/citationhelp/apa7
[Nov 20, 2021]
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Basics of the APA Style

APA 7th Citation Examples
Material Type In-text Citation Bibliography
An article in an electronic (Grady et al., 2019) Grady, J. S., Her, M., Moreno, G., Perez, C., &
journal Yelinek, J. (2019). Emotions in storybooks: A
comparison of storybooks that represent ethnic
and racial groups in the United
States. Psychology of Popular Media
Culture, 8(3), 207–
217. https://doi.org/10.1037/ppm0000185
A website (Bologna, 2019) Bologna, C. (2019, October 31). Why some
people with anxiety love watching horror
movies.
HuffPost. https://www.huffpost.com/entry/anxiet
y-love-watching-horror-
movies_l_5d277587e4b02a5a5d57b59e
https://pitt.libguides.com/citationhelp/apa7
[Nov 20, 2021]
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Reference Management Software

The most popular ones…
Purchased and maintained by the academic

publisher Elsevier
Produced by Clarivate Analytics (previously by

Thomson Reuters)
Corporation for Digital Scholarship, previously

Center for History and New Media at George
Mason University
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Reference Management Software

Citation Manager Comparison Table
Zotero Mendeley EndNote EndNote Web
Access Zotero software with Desktop software, but can sync Desktop software with Web-based
browser add-on (Firefox with an online account which is an online version
and Chrome). editable (EndNote Web)
Where is my Local computer with Local computer with web based Local Computer with Web-based
database stored? optional web based syncing between computers cloud storage and
syncing between syncing via EndNote
computers Web
Word-processor MS Word, Google Docs, MS Word, Open Office, LaTex Microsoft Word, MS Word
compatibility Open Office OpenOffice (EndNote
X3+), Pages (X4+)
Ability to work Yes Yes Yes No

offline
Cost Free to anyone Free. $80 via On the Hub Free to UChicago
UChicago faculty, students, and website (students) faculty, students, and
staff can register through Web staff
Departments
of Science for more features
can purchase EndNote
for $75.
https://guides.lib.uchicago.edu/c.php?g=297307&p=1984557
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An abstract is like a miniature version of the paper.
The abstract should provide a brief summary of each of the main
sections of the paper: introduction, materials and methods,
results, and discussion.
The abstract should not exceed the length specified by the
journal (commonly, 250 words), and it should be designed to
define clearly what is dealt with in the paper.
Typically, the abstract should be typed as a single paragraph.
Some journals, however, run “structured” abstracts consisting of
a few brief paragraphs, each preceded by a standardized
subheading.
Most or all of the abstract should be written in the past tense
because it refers to work done.
B. Gastel and R A Day. “How to Write and Publish a Scientiﬁc Paper,” 8th edition, Greenwood.
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The abstract should never give any information or conclusion
that is not stated in the paper.
Literature must not be cited in the abstract (except in rare
instances, such as modification of a previously published
method).
Likewise, normally the abstract should not include or refer to
tables and figures. (Some journals, however, allow or even
require the abstract to include a graphic.)
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Types of Abstract
An informative abstract is designed to condense a paper.
…It can and should briefly state the problem, the method
Informative used to study the problem, and the principal data and
conclusions. This is the type of abstract that precedes the
body of the paper (thus serving as a “heading”) in most
journals.
Abstract
The indicative abstract is designed to indicate the
subjects dealt with in a paper, much like a table of
Indicative or contents, making it easy for potential readers to decide
whether to read the paper. However, because of the
Descriptive descriptive rather than substantive nature, it can seldom
serve as a substitute for the full paper. Thus, indicative
abstracts should not be used as “heading” abstracts in
research papers, but they may be used in other types of
publications, such as review papers, conference reports,
and government reports. Such indicative abstracts are
often of great value to reference librarians.
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Writing the Introduction

Some experienced writers write their title and
abstract after the paper is written.
Statements in the introduction should be written

in present tense because you are referring
primarily to your research problem and the
established knowledge relating to it at the start of
your work.
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Guidelines for a good introduction are as follows:
(1) The introduction should present first, with all possible clarity,
the nature and scope of the problem investigated. For example,
it should indicate why the overall subject area of the research is
important.
(2) It should briefly review the pertinent literature to orient the
reader. It also should identify the gap in the literature that the
current research was intended to address.
Some journals even make this literature review a separate section after the introduction—
yielding what might be considered an AILMRAD structure.
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Guidelines for a good introduction are as follows:
(3) It should then make clear the objective of the research. In some
disciplines or journals, it is customary to state here the
hypotheses or research questions that the study addressed. In
others, the objective may be signaled by wording such as “in
order to determine.”
(4) It should state the method of the investigation. If deemed
necessary, the reasons for the choice of a particular method
should be briefly stated.
(5) Finally, in some disciplines and journals, the standard practice is
to end the introduction by stating the principal results of the
investigation and the principal conclusions suggested by the
results.
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Writing the Materials and Methods Section

This is where you discuss the Methodology or Experimental
Procedures
Majority of statements should be in past tense.
The main purpose of this section is to describe (and if
necessary, defend) the experimental design and then provide
enough detail so that a competent worker can repeat the
experiments.
Other purposes include providing information that will let
readers judge the appropriateness of the experimental
methods (and thus the probable validity of the findings) and
that will permit assessment of the extent to which the results
can be generalized.
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Writing the Materials and Methods Section

For materials, include the exact technical specifications,
quantities, and source or method of preparation.
In general, avoid the use of trade names; use of generic or
chemical names is usually preferred. This approach avoids the
advertising inherent in the trade name.
If human subjects were used, the criteria for selection should
be described, and an “informed consent” statement should be
included in the manuscript. Likewise, if human or animal
subjects were used, approval by the appropriate committee
should be noted.
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Writing the Results Section

There are usually two ingredients of the results section.
• First, you should give some kind of overall description of the experiments,
providing the big picture without repeating the experimental details
previously provided in the materials and methods section.
• Second, you should present the data.
Your results should be presented in past tense.
You should present representative data rather than endlessly repetitive

data.
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Writing the Results Section

The results need to be clearly and simply stated because it is the results that
constitute the new knowledge that you are contributing to the world.
The earlier parts of the paper (introduction, materials and methods) are
designed to tell why and how you got the results; the latter part of the paper
(discussion) is designed to tell what they mean.
Introduction
Materials & Results Discussion
Methods
Obviously, therefore, the whole paper must stand or fall on the basis of the
results. Thus, the results must be presented with crystal clarity.
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Writing the Discussion

1. Try to present the principles, relationships, and generalizations shown
by the results. And bear in mind, in a good discussion, you discuss—you
do not recapitulate—the results.
2. Point out any exceptions or any lack of correlation and define unsettled
points. Never take the high-risk alternative of trying to cover up or
fudge data that do not quite fit.
3. Show how your results and interpretations agree (or contrast) with
previously published work.
4. Discuss the theoretical implications of your work, as well as any
possible practical applications.
5. State your conclusions as clearly as possible.
6. Summarize your evidence for each conclusion.
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Writing the Discussion

Much as the methods and the results should correspond
to each other,…
Introduction
…the introduction and the discussion should function
as a pair.
Methods At least implicitly, the introduction should have posed

one or more questions.
Pair Pair
The discussion should indicate what the findings say
about the answers.
Results
Discussion
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Thank you for listening…
laurence.ganlim@dlsu.edu.ph
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Scientific Writing and Publication DR Gan Lim

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11/22/21

Scientific Hello and welcome to this lecture.

We will start in a few minutes…

- Laurence A. Gan Lim, PhD -

Laurence A. Gan Lim, PhD

What is scientific writing?

cover Listing of Authors

What is scientific writing?

[broadly speaking]: Can also include other types of professional communication by

(Writing about science for the public??)

Ø Clarity and/or Simplicity

Ø Organization (follow a standard format)

Researchers, professors, scientists, (graduate) students, are measured

What is a scientific paper?

An acceptable primary scientific publication must be the first

What is a scientific paper?

What is a scientific paper?

The publication of a scientific paper must be:

Meeting Abstracts and Extended Abstracts or Synoptics

Organization of a scientific paper

The acronym for the “conventional” scientific article structure:

Organization of a scientific paper

Materials and Methods

Organization of a scientific paper

Materials and Methods References

Shape of a Scientific Paper

Shape of a Scientific Paper

(c) The Methods section, or its equivalent, establishes

Shape of a Scientific Paper

(a) The Methods section, often renamed

Shape of a Scientific Paper

(a) The Results and Discussion are presented together

(b) This change means that a separate section is needed

Fig. 2.3 AIM(RaD)C (Abstract, Introduction,

Ethics in Scientific Publishing

Definiton of ‘Ethical’ (adjective)

1: involving questions of right and wrong

Ethics in Scientific Publishing

“Dry-labbing” or fabrication of experimental results or findings is

Omitting outlying points from the data reported, preparing

Statistics should be used properly or appropriately and not to

Ethics in Scientific Publishing

Ethics in Scientific Publishing

Plagiarism checking software such as Turnitin or CrossCheck

List of authors: include only those who qualify

Ethics in Scientific Publishing

Publishers usually require a form to be filled out.

Disclosure of Conflicts of Interests

May interfere with the objectivity of research

Journal Impact Factor (available through

Important Comments about I.F.

Traditionally, the most senior person (Professor or Head of Laboratory)

Scientific papers produced from collaborative research tend to list more

An author takes the intellectual responsibility for the research results

ORCID à mechanism that can unambiguously identify an author

Listing of Style Guides

Basics of the IEEE Style

Basics of the IEEE Style

Examples of in-text citations:

"...end of the line for my research [13].”

"This theory was first put forward in 1987 [1].”

"Scholtz [2] has argued that...”