A.2 General Thesis Writing Advice

This section is not specific to LaTeX. Some of the points have already been mentioned in asides or footnotes. Remember that each college or university or even school within a university may have different requirements, and requirements will also vary according to country, so some of this advice may not apply to you. I am writing from the point of view of an English scientist, and am basing it on my own experience and on the comments of English science-based PhD examiners and supervisors. I cannot guarantee that your own department or university will agree with them. If in doubt, check with your supervisor.

Find out the thesis style requirements from your supervisor or your department's website. Many universities still require double-spaced, single-sided documents with wide margins. Double-spacing is by and large looked down on in the world of typesetting, but this requirement for a PhD thesis has nothing to do with æsthetics or readability. In England the purpose of the PhD viva is to defend your work^A.1. Before your viva, paper copies of your thesis are sent to your examiners. The double spacing and wide margins provide the examiners room to write the comments and criticisms they wish to raise during the viva, as well as any typographical corrections. Whilst they could write these comments on a separate piece of paper, cross-referencing the page in the thesis, it is more efficient for the comments to actually be on the relevant page of the thesis. That way, as they go through the manuscript during your viva, they can easily see the comments, questions or criticisms they wish to raise alongside the corresponding text. If you present them with a single-spaced document with narrow margins, you are effectively telling them that you don't want them to criticise your work!
Don't try to pad your thesis with irrelevant information. This includes adding items in your bibliography that are not referenced in the text, adding figures or tables that are not explained in the text, and supplying all the source code you have written. The outcome of your viva will not depend on the physical size of your thesis, but on the clarity of your writing and on the quality of your work.
Clearly delineate your thesis through the use of chapters and sections, outlining your original aims and objectives, an overview of the subject matter including references to other people's work in the area, the methods you employed to extend or innovate the field, your results and conclusions.
Make sure your references include some recent journal or conference papers to illustrate that you are aware of new developments in your field. Remember that due to the nature of publishing, most books are dated by the time they reach the book shelves. Journal and conference papers are likely to be more up-to-date^A.2.
Always explain acronyms, technical terms and symbols. It is a good idea to include a glossary of terms, list of notation or list of acronyms to avoid confusion (see §6. Generating Indexes and Glossaries).
If you have equations, make sure you explain the variables used, and how you go from one equation to the next. Depending on your field, you might also consider clarifying the mathematics by providing graphical representations of the equations^A.3.
If you include any graphs, bar charts, pie charts or any other form of data plot, make sure it is clearly labelled and no distortion is introduced (such as using three-dimensional bar charts or pie charts^A.4.)
If you have used a computer application to generate numerical results, make sure you have some understanding of the underlying process and what the results mean. This doesn't necessarily mean that you need to understand complex computer code, or complex algorithms, but what you shouldn't do is say something along the lines of, “well, I clicked on this button, and it said .” What is the purpose of the button? What does represent? What does the result signify? What value were you expecting or hoping to get? Numbers on their own are meaningless. If I ran into a room shouting “I've got 42!” What does that mean? Forty-two what? Forty-two brilliant reviews? (Great!) Forty-two percent in an exam? (Not good.) Forty-two spots on my face? (Very bad!)
Don't waste time worrying about the best way to word your thesis in your first draft. Write first, then edit it later or you will never get started.
If your supervisor offers to critique chapters of your thesis, don't say no! Such offers are not made out of politeness, but a desire to ensure that you pass. Don't be embarrassed and worry that it's not good enough, that's the whole point in your supervisor helping you improve it^A.5.
Write in a clear concise manner. A thesis is a technical document, not a novel, so don't be tempted to write something along the lines of: “I awaited with bated breath, my whole body quivering with excitement at the eager anticipation that my algorithm would prove superior to all others, and, oh joy, my experiments proved me right.”
Don't decorate your thesis with irrelevant clip art. It is unprofessional and highly inappropriate in the sciences.
Make regular backups of your work. Be prepared for any of the following: accidentally deleting your thesis, accidentally overwriting your thesis with another file, software failure, hardware failure, viruses, fire and theft. Consider using at least a two-tier system where you keep one backup in a safe place where you live and ask a close relative or friend to take care of another backup.

Items 9 and 10 above were supplied by Dr Gavin Cawley^A.6 who has been both a PhD supervisor and examiner.

Footnotes

... work ^A.1: I gather this is not the case in some other countries, where the viva is more informal, and the decision to pass or fail you has already been made before your viva.
... up-to-date ^A.2: Having said that, I know someone who submitted an article to a journal, and it took three and a half years before the reviewers came back with comments. In the end, the author withdrew the manuscript because by that time the topic was out of date.
... equations ^A.3: When I was a PhD student, I was once rendered speechless when asked to provide a graphical illustration of an equation involving a quadruple summation that had no graphical meaning from my point of view. Perhaps this was a drawback of being a mathematician doing a PhD in an electronics department.
... charts ^A.4: The sole purpose of 3D pie charts or bar charts appears to be to look pretty and impress people who have no understanding of mathematics.
... it ^A.5: but don't expect your supervisor to actually write your thesis!
... Cawley ^A.6: School of Computing Sciences, University of East Anglia

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