The document provides comprehensive guidelines on scientific writing, emphasizing the importance of clarity and conciseness. It covers various aspects of writing, including the use of active voice, eliminating jargon, structuring paragraphs, and ensuring logical flow, alongside specific tips for composing sections such as the introduction, results, and discussion. It also includes recommendations for proper citation, revision, and the effective use of tables and figures to enhance the presentation of research findings.

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Notes on Scientific Writing
Presentation · December 2017
DOI: 10.13140/RG.2.2.19566.31041
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2. NOTES ON SCIENTIFIC
WRITTING
By: Essam Munir

3. Overview, principles of effective writing
 Nouns make sentences slower; verbs make it flow (thus use verbs more than nouns).
 Avoid using vague words.
 Avoid using jargon and unnecessary acronyms.
 Passive voice makes it harder to understand the sentence.
 Putting too much distance between the subject and the main verb is a problem.
Cut the clutter
 Always try to cut out the words and see whether your sentence looks good or not.
 Common clutter: -
o Dead weight words and phrases: as it is well known, as it has been shown, it can be
regarded that, it should be emphasized that.
 Provide citations instead of these.
o Empty words and phrases (vague unnecessary).
o Long words or phrases that could be short.
o Unnecessary jargon and performance.
o Repetitive words or sentences: studies/examples, illustrate/demonstrate,
challenges/difficulties.
o Adverbs.
Cut the clutter, more tricks
 Eliminate the negatives: instead of writing “not, no” try to make a positive construction
instead of it.
 Eliminate “there are/is”.
 Omit needless prepositions: for example, “that” and “on” are often superfluous.
Use the active voice
 The active voice follows the format: subject, verb, object.
o I read the book  active voice (agent, verb, recipient of the action).
o The book was read by (me)  passive voice (recipient of the action, verb, agent
which can be omitted).
 Recognizing the passive verb: -
o Passive verb = a form of the verb “to be” + p.p. of the main verb.
o The main verb must be a transitive verb (i.e. takes an object).
 Passive voice takes out the responsibility.
 Steps to turn the passive voice to active voice:
o Recognize the passive verb first.
o Ask “who did the action? And to whom?”.
o E.g. the activation of calcium channels is induced by the depletion of endoplasmic
reticulum calcium stores (passive)  depleting calcium from endoplasmic
reticulum activates calcium channels (active).
 Advantages of the active voice: -
o Emphasizes author responsibility: no attempt was made to contact non-
respondents because they were deemed unimportant to analysis (passive)  we

4. did not attempt to contact non-respondents because we deemed them
unimportant to analysis (active).
o Improves readability: a strong correlation was found between use of the passive
voice and other sins of writing (passive)  we found a strong correlation between
the use of passive voice and other sins of writing (active)  use of passive voice
correlates strongly with other sins of writing (more direct).
o Reduces ambiguity: general dysfunction of the immune system at the level of
leukocytes is suggested by both human and animal studies (passive)  both
human and animal studies suggest that diabetics have general immune system
dysfunction at the level of leukocytes (active).
 Is it ok to use the passive voice?
o A: Yes, use it sparingly and purposefully. For example, use it in the method section
as what’s done is more important than who’s done it.
Write with verbs
 Use strong verbs: -
o Pick the right verb (The WHO reports that approximately two-thirds of the world's
diabetics are found in developing countries, and estimates that the number of
diabetics in these countries will double in the next 25 years.  change reports to
estimates and estimates to projects).
o Use “to be” verbs sparingly and purposefully (highlight them and try to replace
them with strong verbs).
 Avoid turning verbs into nouns: it slows the reader and creates ambiguity.
 Don’t bury the main verb: keep the main verb (predicate) close to the subject.
A few grammar tips
 “Data” is a plural word (“data are” not “data is”).
 “Compare to” is different from “Compare with” (the first is used to show similarities and
the second to show differences).
 That and Which: -
o “That” is used with restrictive (defining) pronoun. “Which” is used with
nonrestrictive pronoun.
o To differentiate, look at commas (no commas with “that”).
o The key question: is your clause essential or non-essential? (if essential, you can’t
eliminate it without changing the meaning).
o The bike that is broken is in the garage (identifies which bike of many). The bike,
which is broken, is in the garage (adds a fact about the only car in the garage).
 Don’t use “they” or “their” when the subject is singular. Change to plural and use them.
Experiment with punctuation
 Increasing power to separate: comma, colon, dash, parenthesis, semicolon, and period.
 Increasing formality: dash, parenthesis, others (comma, colon, semicolon, and period).
o Less formal marks (dash, parenthesis) should be used sparingly.
 Semicolon: -
o The semicolon connects two independent clauses.

5.  (a clause always contains a subject and predicate; an independent clause
can stand alone as a complete sentence).
o Semicolon are also used to separate items in lists that contain internal
punctuation.
 Example: it happened because people organized and voted for better
prospects; because leaders enacted smart, forward-looking policies;
because people’s perspectives opened up, and with them, societies did too.
 Parentheses: -
o Used to insert an afterthought or explanation (a word, phrase, or sentence) into a
passage that is grammatically complete without it.
o If you remove the material within the parentheses, the main point of the sentence
should not change.
o Parentheses give the reader permission to skip over the material.
 Colon: -
o Use a colon after an independent clause (it must be preceded by a subject and
verb) to introduce a list, quote, explanation, conclusion, or amplification.
o Use a colon to joint two independent clauses if the second amplifies or extends the
first.
 Dash: -
o Use dash to add emphasis or to insert an abrupt definition or description almost
anywhere in the sentence.
o Don’t overuse it, or it loses its impact.
Parallelism
 It means “pairs of ideas joined by “and”, “or”, or “but” should be written in parallel form.
 Lists of ideas should be written in parallel form.
Paragraphs
 Each paragraph must have one idea.
 Make it short.
 Give away the punch line early.
 Paragraph flow is helped by:
o Logical flow of ideas (sequential in time, general to specific, logical arguments)
o Parallel sentence structures
o If necessary, use transition words.
Overview of the writing process
 Prewriting:
o Collect, synthesize, and organize information
o Brainstorm take-home messages
o Work out ideas away from the computer
o Develop a road map/outline
 Writing the first draft
o Putting your facts and ideas together in organized prose
 Revision

6.  Read your work out loud
o Get rid of clutter
o Do a verb check
o Get feedback from others
 Invest your time in the prewriting and put what you need at your fingertips.
The pre-writing step
 Get organized first!
o Don’t try to write and gather information simultaneously.
o Gather and organize information before writing the first draft.
 Develop a road-map
o Arrange key facts and citations from the literature into a crude road map/outline
before writing the first draft.
o Think in paragraphs and sections.
 Brainstorm away from the computer
o Write on the go! (on your way home!)
o Work out take-home messages
o Organize your paper
o Write memorable lines
 Compositional organization:
o Like ideas should be grouped.
o Like paragraphs should be grouped.
o Don’t “bait-and-switch” your reader too many times.
The writing step
 Tips for writing the first draft:
o Don’t be a perfectionist!
o The goal of the first draft is to get the ideas down in complete sentences in order
(the sentences don’t have to sound good, they have to be grammatically complete
and in the right place).
o Focus on logical organization and take-home messages more than sentence-level
details.
o Write the first draft quickly and efficiently! (it is a pain…).
o Break your writing task into small and realistic goals (I’m going to write 400 words
today.)
Revision
 Read your writing out loud (the brain processes the spoken word differently than the
written word!).
 Do a verb check:
o Underline the main verb in each sentence.
o Watch for:
 Lackluster verbs (e,g, there are many students who struggle with
medicine.)
 Passive verbs

7.  Buried verbs (long distance between the subject and verb)
 Don’t be afraid to cut
o Dead weight words and phrases (it should be emphasized that)
o Empty words and phrases (important)
o Long words or phrases that could be short
o Unnecessary jargon and acronyms
o Repetitive words or phrases
o adverbs
 Do an organizational review
o In the margins of your paper, tag each paragraph with a phrase or sentence that
sums up the main point.
Then move paragraphs around to improve logical flow and bring similar ideas
together.
 Get outside feedback
o Without any technical background, reviewer should easily grasp:
 The main findings
 Take-home messages
 Significance of your work
Checklist for the final draft
 Check for consistency: making sure that you don’t have things that are contradictory in
different sections of the paper.
o “we followed participants for a minimum of 2 years” (methods section)
o “the average follow-up time was 1.5 years” (results section)
 Check for numerical consistency:
o Do the numbers in abstract match the numbers in tables/figures/text?
o Do the numbers un the text match those in the tables/figures?
o Do the numbers in each table/figure match those in other tables/figures?
 Check the references: do you have “references to nowhere”?
o References does not provide the indicated information/fact.
o Authors misinterpreted or exaggerated the findings from the original source.
o References cites a secondary source rather than a primary source. (citation
propagation)
o Authors mis-numbered the references.
Tables and Figures
 Recommended order for writing a manuscript:
o Tables and figures
o Results
o Methods
o Introduction
o Discussion
o Abstract
 Figures and tables should stand alone and tell a complete story. The reader should not
refer back to the text to understand.

8.  Tips:
o Use the fewest figures and tables needed to tell the story.
o Do not present the same data in both a figure and a table.
 Tables vs. Figures
o Tables:
 Give precise values
 Display many values/variables
o Figures:
 Visual impact
 Show trends and patterns
 Tell a quick story
 Tell the whole story
 Highlight a particular result (most important)
 Table title:
o Identify the specific topic or point of the table.
o Use the same key terms in the table title, the column headings, and the text of the
paper.
o Keep it brief!
o Example: Descriptive characteristics of the two groups.
 Table footnotes:
o Use superscript symbols to identify footnotes, according to journal guidelines
o Use footnotes to explain statistically significant differences (e.g. *p<.01)
o Use footnotes to explain experimental details or abbreviations (e.g. amenorrhea
was defined as 0-3 periods per year).
 Table formats:
o Model your tables from already published tables. Don’t re0invent the wheel!
o Follow journal guidelines:
 Roman or Arabic numbers
 Centered or flush left table number, title, column, headings, and data
 Capital letter and italics
 The placement of footnotes
 The type of footnote symbols
o Most journal use three horizontal lines: one above the column headings, one
below it, and one below the data (you can use gray shading).
o Watch out for alignment.
o Give units for your variables.
o Use one decimal.
o Omit unnecessary columns.
 Types of figures:
o Primary evidence: electron micrographs, X-rays, pathology slides...etc. (indicates
data quality and “seeing is believing”).
o Graphs: line graphs, bar graphs, scatter plots...etc.
o Drawing and diagrams: illustrate an experimental set-up or work-flow
 Indicate flow of participants

9.  Illustrate cause and effect relationships or cycles.
 Give a hypothetical model.
 Represent microscopic particles or microorganisms as cartoons.
 Figure legends:
o Allows the figure to stand alone.
o Contains:
 Brief, informative title
 Essential experimental details
 Definitions of symbols or line/bar patterns
 Explanation of panels (A, B, C, D, …etc)
 Statistical information (tests used, p-values)
Results
 Results do not equal raw data.
 The results section should:
o Summarize, at a higher level, what the data show
 Point our simple relationships
 Describe big-picture trends
 Cite figures or table that present supporting data
o Avoid simply repeating the numbers are already available in tables and figures
 Tips for writing results:
o Break into subsections, with headings (if needed “long and complex results”)
o Complement the information that is already in the tables and figures
 Give precise values that are not available in the figure
 Report the percent change or percent difference if absolute values are given
in the table
o Repeat/highlight only the most important numbers
o Don’t forget to talk about negative and control results
o Reserve the term “significant” for statistically significant
o Reserve information about what you did for the methods section
 In particular, do not discuss the rationale for statistical analyses within the
Results section
o Reserve comments on the meaning of your results for the discussion section
 What verb tense do I use?
o Use past tense for completed actions:
 We found that…
 The average time was…
 Women were more likely to….
o Use the present tense for assertions that continue to be true, such as what the
tables show, what you believe, and what the data suggest:
 Figure 1 shows…
 The findings confirm…
 The data suggest….
 We believe that this shows…

10.  Use the active voice.
Methods
 Give a clear overview of what was done
 Give enough information to replicate the study (like a recipe!)
 Be complete, but make life easy for your reader!
o Break into smaller section with subheadings
o Cite a reference for commonly used methods
o Display in a flow diagram or table where possible
 You may use jargon and the passive voice more liberally in the methods section
 Verb tense:
o Report methods in past tense “we measured”
o Use present tense to describe how data are presented in the paper “data are
summarized as means...”
Introduction
 Typically, 3 paragraphs long (recommended range: 2 to 5)
 It is not an exhaustive review of your general topic (should focus on the specific
hypothesis/aim of your study).
 Tips for writing an introduction:
o Keep paragraphs short
o Write for a general audience (clear, concise, non-technical)
o Take the reader step by step from what is known to what is unknown. End with
your specific question. (known  unknown  question/hypothesis)
o Emphasize how your study fills in the gaps (the unknown)
o Explicitly state your research question/aim/hypothesis:
 “We asked whether”; “Our hypothesis was”; “We tested the hypothesis
that”; “Our aims were”
o Do not answer the research question (no results or implications)
o Summarize at a high level! Leave detailed descriptions, speculations, and criticisms
of particular studies for discussion.
Discussion
 Invert the cone of the introduction:
o Answer the questions asked
o Support your conclusion (your data, others’ data)
o Defend your conclusion (anticipate criticisms)
o Give the “big-picture” take-home message (implications)
 Tips on the discussion:
o Showcase good writing!
 Use the active voice
 Tell it like a story
o Start and end with the main finding
 “we found that…”
o Don’t travel too far from your data

11.  Focus on what your data do prove, not what you had hoped your data
would prove
o Focus on the limitations that matter, not generic limitations
o Make sure your take-home message is clear and consistent
Abstract
 It gives and overview of the main story
 Gives highlights from each section of the paper
 Limited length (100-300 words, typically)
 Stands on its own
 Most often, the only part the people read
 Don’t write it prior to the paper
 Contents:
o Background (one-sentence statement)
o Question/aim/hypothesis (explicitly state that)
 “We asked whether,” “We hypothesized that,” …. etc
o Experiment (quick summary of key materials and methods)
o Results (key results found, minimal raw data)
o Conclusion (answer the question, take-home message)
o Implication, speculation, or recommendation
 Two forms of abstracts:
o Structured (with subheadings)
o Free-form
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