6 Thesis

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This chapter will give some guidance and resources for thesis writing.

Sections in this chapter

Get organized

The thesis is the largest document that graduate students need to write! Efficient writing requires organization, not just while writing but also in your scientific practice.

  • Keep your lab notebook updated and organized
  • Don’t write on scraps of paper, write everything in a notebook!
  • Compile good records of literature references (use a Citation Manager)
  • Use a system to name all your files
  • Keep your electronic files organized and properly named
  • If you like to save many drafts, keep an “archive” folder for old drafts
  • Always have a backup!!!
  • Consider syncing your OneDrive to allow for auto-save
  • Become familiar with the “Versions” features in Word
  • Become familiar with Styles in Word
  • Become familiar with the graphics programs (e.g., ChemDraw)


Who is the audience of your thesis? Many students struggle with this question and this creates challenges with writing. The answer is that it depends on the section of the thesis!

Your graduate research, which culminates in the thesis, was at least in part funded by taxpayers in the general public. You owe it to the general public to have some part of your thesis that is accessible to their audience. This can be accomplished in the first few paragraphs of the Introduction and helps to ground all readers at the same level before getting into the high-level details.

By the time you are writing your thesis, you are the foremost expert in the research you have done (wow!). However, the downside of this expertise is that you can forget that others, even other experts, don’t have your level of knowledge. If you don’t keep the audience in mind, you will write your thesis in a way that is only understandable by you (and maybe your supervisor). For almost all thesis revisions, examiners request that the author explain in more detail what was done and use simpler language.

Structure of a thesis

There are also two possible forms of a thesis (Table 9.1): Traditional or Manuscript. The main difference is that in a Manuscript thesis, traditional chapters are replaced with verbatim copies of manuscripts (with the publisher’s approval). The manuscript format saves time for students who published several papers throughout their degree and prevents self-plagiarism.

A thesis has a different structure from a journal article, one main difference being that the experimental details are often left until the end in the Appendices (similar to the Supplementary Matierlas in an article).

Table 9.1 Forms of thesis
Traditional Form Manuscript Form  
Title Page Title Page Front Matter
Abstract Abstract
Co-authorship (if necessary) Co-authorship (if necessary)
Acknowledgements Acknowledgements
Statement of originality (PhD only) Statement of originality (PhD only)
Table of Contents Table of Contents
List of Tables List of Tables
List of Figures and Schemes List of Figures and Schemes
Chapter 1: Introduction Chapter 1: General Introduction Body
Chapter 2: Literature Review Chapter 2: Literature Review (optional)
Chapter 3 to n: Results and Discussion Chapter 3 to n: Manuscripts
Chapter n+1: Summary and Conclusions Chapter n+1: General Discussion and Conclusions
Bibliography or References Permissions from publishers End Matter
Appendices Appendices

How to start?

Begin writing your thesis early, from the very start of your graduate program. First, you can begin by organizing literature references. Once a month compile your group meeting and conference presentations, annual progress reports, candidacy exam reports, conference abstracts, and early results into a draft. Write a few lines a day or week, whenever you think of something, and this will quickly grow into a large document that will become your first thesis draft.

There are many resources to help you along the way. The School of Graduate Studies has thesis templates, writing retreats, and mental health resources. Student Academic Success Services has a lot to offer for graduate students including a Thesis ManagerDissertation Bootcamp and Writing Lab, as well as one-on-one consultations.

Seriously, start now!

Do not wait until you are 3 months from finishing to create the first draft of your thesis, or you will quickly get overwhelmed. Start now:

  1. Open a file in your word processor (Word, Latex, Google Docs)
  2. Write a ‘quick & dirty’ paragraph about your research plan
  3. Title your file “Thesis Working Document”
  4. Download a citation manager and it’s word processor plug-in

Later on, build up your working document into a draft:

  1. Create an outline using headings
  2. Create a Table of Contents and learn how to link it to document headings
  3. Organize the document into chapter and sections
  4. Add references and a bibliography
  5. Learn to use fields to automatically update compound numbers and Figure/Table/Scheme numbers.
  6. Learn how sections work in the word processor

Give yourself 3-6 months for the final thesis writing and defense process. Check the deadlines for submission for Spring/Fall convocations and tuition fees on the School of Graduate Studies Website.

As early as possible check the Queen’s University guidelines for theses. You should also look at past theses from your research group for guidance and format.

Common mistakes to look out for:

  • no general introduction
  • the incessant use of jargon
  • unnecessary fancy words (e.g., “employed” rather than “use”)
  • not following Graduate School guidelines for format
  • incomplete reporting of the literature
  • inconsistencies in format, spelling, abbreviations, symbols, references, numbers, facts, etc., especially from chapter to chapter
  • no conclusions/suggestions for future work
  • no thought was given to the meaning of the results
  • too much subdividing of Chapters (e.g. The …)
  • the use of “we” instead of “I” – it is your thesis
  • failure to proof-read before submitting to supervisor
  • not backing up your computer files


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Principles of Scientific Communication Copyright © 2020 by Amanda Bongers and Donal Macartney is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License, except where otherwise noted.

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