Writing A Phd Dissertation

Writing and publishing a scientific paper

Getting Started

When you are about to begin, writing a thesis seems a long, difficult task. That is because it is a long, difficult task. Fortunately, it will seem less daunting once you have a couple of chapters done. Towards the end, you will even find yourself enjoying it – an enjoyment based on satisfaction in the achievement, pleasure in the improvement in your technical writing, and of course the approaching end. Like many tasks, thesis writing usually seems worst before you begin, so let us look at how you should make a start.

An outline

First make up a thesis outline: several pages containing chapter headings, sub-headings, some figure titles (to indicate which results go where) and perhaps some other notes and comments. There is a section on chapter order and thesis structure at the end of this text. Once you have a list of chapters and, under each chapter heading, a reasonably complete list of things to be reported or explained, you have struck a great blow against writer's block. When you sit down to type, your aim is no longer a thesis – a daunting goal – but something simpler. Your new aim is just to write a paragraph or section about one of your subheadings. It helps to start with an easy one: this gets you into the habit of writing and gives you self-confidence. In an experimental thesis, the Materials and Methods chapter is often the easiest to write – just write down what you did; carefully, formally and in a logical order.

How do you make an outline of a chapter? For most of them, you might try the method that I use for writing papers, and which I learned from my thesis adviser (Stjepan Marcelja): Assemble all the figures that you will use in it and put them in the order that you would use if you were going to explain to someone what they all meant. You might as well rehearse explaining it to someone else – after all you will probably give several talks based on your thesis work. Once you have found the most logical order, note down the key words of your explanation. These key words provide a skeleton for much of your chapter outline.

Once you have an outline, discuss it with your adviser. This step is important: s/he will have useful suggestions, but it also serves notice that s/he can expect a steady flow of chapter drafts that will make high priority demands on his/her time. Once you and your adviser have agreed on a logical structure, s/he will need a copy of this outline for reference when reading the chapters which you will probably present out of order. If you have a co-adviser, discuss the outline with him/her as well, and present all chapters to both advisers for comments.

Organisation

It is encouraging and helpful to start a filing system. Open a word-processor file for each chapter and one for the references. You can put notes in these files, as well as text. While doing something for Chapter n, you will think "Oh I must refer back to/discuss this in Chapter m" and so you put a note to do so in the file for Chapter m. Or you may think of something interesting or relevant for that chapter. When you come to work on Chapter m, the more such notes you have accumulated, the easier it will be to write.

Make a back-up of these files and do so every day at least (depending on the reliability of your computer and the age of your disk drive). Do not keep back-up close to the computer in case the hypothetical thief who fancies your computer decides that s/he could use some disks or membory as well.

If you thesis file is not too large, a simple way of making a remote back-up is to send it as an email attachment to a consenting email correspondent; you could also send it to yourself. In either case, be careful to dispose of superseded versions so that you don't waste disk space, especially if you have bitmap images or other large files. Or you could use a drop-box or other more sophisticated system.

You should also have a physical filing system: a collection of folders with chapter numbers on them. This will make you feel good about getting started and also help clean up your desk. Your files will contain not just the plots of results and pages of calculations, but all sorts of old notes, references, calibration curves, suppliers' addresses, specifications, speculations, notes from colleagues etc., which will suddenly strike you as relevant to one chapter or other. Stick them in that folder. Then put all the folders in a box or a filing cabinet. As you write bits and pieces of text, place the hard copy, the figures etc in these folders as well. Touch them and feel their thickness from time to time – ah, the thesis is taking shape.

If any of your data exist only on paper, copy them and keep the copy in a different location. Consider making a copy of your lab book. This has another purpose beyond security: usually the lab book stays in the lab, but you may want a copy for your own future use. Further, scientific ethics require you to keep lab books and original data for at least ten years, and a copy is more likely to be found if two copies exist.

If you haven't already done so, you should archive your electronic data, in an appropriate format. Spreadsheet and word processor files are not suitable for long term storage. Archiving data by Joseph Slater is a good guide.

While you are getting organised, you should deal with any university paperwork. Examiners have to be nominated and they have to agree to serve. Various forms are required by your department and by the university administration. Make sure that the rate limiting step is your production of the thesis, and not some minor bureaucratic problem.

A note about word processors

One of the big FAQs for scientists: is there a word processor, ideally one compatible with MS Word, but which allows you to type mathematical symbols and equations conveniently? One solution is LaTeX, which is powerful, elegant, reliable, fast and free from http://www.latex-project.org/ or http://www.miktex.org/. The standard equation editor for MS Word is point and click, so extremely slow and awkward. In many versions, Word's equation editor can be reached via hotkey Alt-equals, and takes pseudo latex typed input (eg X_1 converts to X subscript 1) upon the next space or operator. It uses some different formats - eg () rather than the {} of latex to group things and interprets divisions rather than having to use \frac. Here's a link: http://blogs.msdn.com/b/murrays/archive/2008/02/17/hidden-math-features-in-word-2007.aspx
It has been useful to know these as it seems biologists and latex don't mix!

A timetable

I strongly recommend sitting down with the adviser and making up a timetable for writing it: a list of dates for when you will give the first and second drafts of each chapter to your adviser(s). This structures your time and provides intermediate targets. If you merely aim "to have the whole thing done by [some distant date]", you can deceive yourself and procrastinate more easily. If you have told your adviser that you will deliver a first draft of chapter 3 on Wednesday, it focuses your attention.

You may want to make your timetable into a chart with items that you can check off as you have finished them. This is particularly useful towards the end of the thesis when you find there will be quite a few loose ends here and there.

Iterative solution

Whenever you sit down to write, it is very important to write something. So write something, even if it is just a set of notes or a few paragraphs of text that you would never show to anyone else. It would be nice if clear, precise prose leapt easily from the keyboard, but it usually does not. Most of us find it easier, however, to improve something that is already written than to produce text from nothing. So put down a draft (as rough as you like) for your own purposes, then clean it up for your adviser to read. Word-processors are wonderful in this regard: in the first draft you do not have to start at the beginning, you can leave gaps, you can put in little notes to yourself, and then you can clean it all up later.

Your adviser will expect to read each chapter in draft form. S/he will then return it to you with suggestions and comments. Do not be upset if a chapter – especially the first one you write – returns covered in red ink (or its electronic equivalent). Your adviser will want your thesis to be as good as possible, because his/her reputation as well as yours is affected. Scientific writing is a difficult art, and it takes a while to learn. As a consequence, there will be many ways in which your first draft can be improved. So take a positive attitude to all the scribbles with which your adviser decorates your text: each comment tells you a way in which you can make your thesis better.

As you write your thesis, your scientific writing is almost certain to improve. Even for native speakers of English who write very well in other styles, one notices an enormous improvement in the first drafts from the first to the last chapter written. The process of writing the thesis is like a course in scientific writing, and in that sense each chapter is like an assignment in which you are taught, but not assessed. Remember, only the final draft is assessed: the more comments your adviser adds to first or second draft, the better.

Before you submit a draft to your adviser, run a spell check so that s/he does not waste time on those. If you have any characteristic grammatical failings, check for them.


What is a thesis? For whom is it written? How should it be written?

Your thesis is a research report. The report concerns a problem or series of problems in your area of research and it should describe what was known about it previously, what you did towards solving it, what you think your results mean, and where or how further progress in the field can be made. Do not carry over your ideas from undergraduate assessment: a thesis is not an answer to an assignment question. One important difference is this: the reader of an assignment is usually the one who has set it. S/he already knows the answer (or one of the answers), not to mention the background, the literature, the assumptions and theories and the strengths and weaknesses of them. The readers of a thesis do not know what the "answer" is. If the thesis is for a PhD, the university requires that it make an original contribution to human knowledge: your research must discover something hitherto unknown.

Obviously your examiners will read the thesis. They will be experts in the general field of your thesis but, on the exact topic of your thesis, you are the world expert. Keep this in mind: you should write to make the topic clear to a reader who has not spent most of the last three years thinking about it.

Your thesis will also be used as a scientific report and consulted by future workers in your laboratory who will want to know, in detail, what you did. Theses are occasionally consulted by people from other institutions, and the library sends microfilm versions if requested (yes, still). More commonly theses are now stored in an entirely digital form. These may be stored as .pdf files on a server at your university. The advantage is that your thesis can be consulted much more easily by researchers around the world. (See e.g. Australian digital thesis project for the digital availability of research theses.) Write with these possibilities in mind.

It is often helpful to have someone other than your adviser(s) read some sections of the thesis, particularly the introduction and conclusion chapters. It may also be appropriate to ask other members of staff to read some sections of the thesis which they may find relevant or of interest, as they may be able to make valuable contributions. In either case, only give them revised versions, so that they do not waste time correcting your grammar, spelling, poor construction or presentation.

How much detail?

The short answer is: rather more than for a scientific paper. Once your thesis has been assessed and your friends have read the first three pages, the only further readers are likely to be people who are seriously doing research in just that area. For example, a future research student might be pursuing the same research and be interested to find out exactly what you did. ("Why doesn't the widget that Bloggs built for her project work any more? Where's the circuit diagram? I'll look up her thesis." "Blow's subroutine doesn't converge in my parameter space! I'll have to look up his thesis." "How did that group in Sydney manage to get that technique to work? I'll order a microfilm of that thesis they cited in their paper.") For important parts of apparatus, you should include workshop drawings, circuit diagrams and computer programs, usually as appendices. (By the way, the intelligible annotation of programs is about as frequent as porcine aviation, but it is far more desirable. You wrote that line of code for a reason: at the end of the line explain what the reason is.) You have probably read the theses of previous students in the lab where you are now working, so you probably know the advantages of a clearly explained, explicit thesis and/or the disadvantages of a vague one.

Make it clear what is yours

If you use a result, observation or generalisation that is not your own, you must usually state where in the scientific literature that result is reported. The only exceptions are cases where every researcher in the field already knows it: dynamics equations need not be followed by a citation of Newton, circuit analysis does not need a reference to Kirchoff. The importance of this practice in science is that it allows the reader to verify your starting position. Physics in particular is said to be a vertical science: results are built upon results which in turn are built upon results etc. Good referencing allows us to check the foundations of your additions to the structure of knowledge in the discipline, or at least to trace them back to a level which we judge to be reliable. Good referencing also tells the reader which parts of the thesis are descriptions of previous knowledge and which parts are your additions to that knowledge. In a thesis, written for the general reader who has little familiarity with the literature of the field, this should be especially clear. It may seem tempting to leave out a reference in the hope that a reader will think that a nice idea or an nice bit of analysis is yours. I advise against this gamble. The reader will probably think: "What a nice idea – I wonder if it's original?". The reader can probably find out via the net or the library.

If you are writing in the passive voice, you must be more careful about attribution than if you are writing in the active voice. "The sample was prepared by heating yttrium..." does not make it clear whether you did this or whether Acme Yttrium did it. "I prepared the sample..." is clear.

Style

The text must be clear. Good grammar and thoughtful writing will make the thesis easier to read. Scientific writing has to be a little formal – more formal than this text. Native English speakers should remember that scientific English is an international language. Slang and informal writing will be harder for a non-native speaker to understand.

Short, simple phrases and words are often better than long ones. Some politicians use "at this point in time" instead of "now" precisely because it takes longer to convey the same meaning. They do not care about elegance or efficient communication. You should. On the other hand, there will be times when you need a complicated sentence because the idea is complicated. If your primary statement requires several qualifications, each of these may need a subordinate clause: "When [qualification], and where [proviso], and if [condition] then [statement]". Some lengthy technical words will also be necessary in many theses, particularly in fields like biochemistry. Do not sacrifice accuracy for the sake of brevity. "Black is white" is simple and catchy. An advertising copy writer would love it. "Objects of very different albedo may be illuminated differently so as to produce similar reflected spectra" is longer and uses less common words, but, compared to the former example, it has the advantage of being true. The longer example would be fine in a physics thesis because English speaking physicists will not have trouble with the words. (A physicist who did not know all of those words would probably be glad to remedy the lacuna either from the context or by consulting a dictionary.)

Sometimes it is easier to present information and arguments as a series of numbered points, rather than as one or more long and awkward paragraphs. A list of points is usually easier to write. You should be careful not to use this presentation too much: your thesis must be a connected, convincing argument, not just a list of facts and observations.

One important stylistic choice is between the active voice and passive voice. The active voice ("I measured the frequency...") is simpler, and it makes clear what you did and what was done by others. The passive voice ("The frequency was measured...") makes it easier to write ungrammatical or awkward sentences. If you use the passive voice, be especially wary of dangling participles. For example, the sentence "After considering all of these possible materials, plutonium was selected" implicitly attributes consciousness to plutonium. This choice is a question of taste: I prefer the active because it is clearer, more logical and makes attribution simple. The only arguments I have ever heard for avoiding the active voice in a thesis are (i) many theses are written in the passive voice, and (ii) some very polite people find the use of "I" immodest. Use the first person singular, not plural, when reporting work that you did yourself: the editorial 'we' may suggest that you had help beyond that listed in your acknowledgments, or it may suggest that you are trying to share any blame. On the other hand, retain plural verbs for "data": "data" is the plural of "datum", and lots of scientists like to preserve the distinction. Just say to yourself "one datum is ..", "these data are.." several times. An excellent and widely used reference for English grammar and style is A Dictionary of Modern English Usage by H.W. Fowler.

Presentation

There is no need for a thesis to be a masterpiece of desk-top publishing. Your time can be more productively spent improving the content than the appearance.

In many cases, a reasonably neat diagram can be drawn by hand faster than with a graphics package, and you can scan it if you want an electronic version. Either is usually satisfactory. A one bit (i.e. black and white), moderate resolution scan of a hand-drawn sketch will be bigger than a line drawing generated on a graphics package, but not huge. While talking about the size of files, we should mention that photographs look pretty but take up a lot of memory. There's another important difference, too. The photographer thought about the camera angle and the focus etc. The person who drew the schematic diagram thought about what components ought to be depicted and the way in which the components of the system interacted with each other. So the numerically small information content of the line drawing may be much more useful information than that in a photograph.

Another note about figures and photographs. In the digital version of your thesis, do not save ordinary photographs or other illustrations as bitmaps, because these take up a lot of memory and are therefore very slow to transfer. Nearly all graphics packages allow you to save in compressed format as .jpg (for photos) or .gif (for diagrams) files. Further, you can save space/speed things up by reducing the number of colours. In vector graphics (as used for drawings), compression is usually unnecessary.

In general, students spend too much time on diagrams – time that could have been spent on examining the arguments, making the explanations clearer, thinking more about the significance and checking for errors in the algebra. The reason, of course, is that drawing is easier than thinking.

I do not think that there is a strong correlation (either way) between length and quality. There is no need to leave big gaps to make the thesis thicker. Readers will not appreciate large amounts of vague or unnecessary text.

Approaching the end

A deadline is very useful in some ways. You must hand in the thesis, even if you think that you need one more draft of that chapter, or someone else's comments on this section, or some other refinement. If you do not have a deadline, or if you are thinking about postponing it, please take note of this: A thesis is a very large work. It cannot be made perfect in a finite time. There will inevitably be things in it that you could have done better. There will be inevitably be some typos. Indeed, by some law related to Murphy's, you will discover one when you first flip open the bound copy. No matter how much you reflect and how many times you proof read it, there will be some things that could be improved. There is no point hoping that the examiners will not notice: many examiners feel obliged to find some examples of improvements (if not outright errors) just to show how thoroughly they have read it. So set yourself a deadline and stick to it. Make it as good as you can in that time, and then hand it in! (In retrospect, there was an advantage in writing a thesis in the days before word processors, spelling checkers and typing programs. Students often paid a typist to produce the final draft and could only afford to do that once.)

How many copies?

Talk to your adviser about this. As well as those for the examiners, the university libraries and yourself, you should make some distribution copies. These copies should be sent to other researchers who are working in your field so that:
  • they can discover what marvellous work you have been doing before it appears in journals;
  • they can look up the fine details of methods and results that will or have been published more briefly elsewhere;
  • they can realise what an excellent researcher you are. This realisation could be useful if a post- doctoral position were available in their labs. soon after your submission, or if they were reviewers of your research/post-doctoral proposal. Even having your name in their bookcases might be an advantage.

Whatever the University's policy on single or double-sided copies, the distribution copies could be double-sided paper, or digital, so that forests and postage accounts are not excessively depleted by the exercise. Your adviser could help you to make up a list of interested and/or potentially useful people for such a mailing list. Your adviser might also help by funding the copies and postage if they are not covered by your scholarship. A CD with your thesis will be cheaper than a paper copy. You don't have to burn them all yourself: companies make multiple copies for several dollars a copy.

The following comment comes from Marilyn Ball of the Australian National University in Canberra: "When I finished writing my thesis, a postdoc wisely told me to give a copy to my parents. I would never have thought of doing that as I just couldn't imagine what they would do with it. I'm very glad to have taken that advice as my parents really appreciated receiving a copy and proudly displayed it for years. (My mother never finished high school and my father worked with trucks - he fixed 'em, built 'em, drove 'em, sold 'em and junked 'em. Nevertheless, they enjoyed having a copy of my thesis.)"

Personal

In the ideal situation, you will be able to spend a large part – perhaps a majority – of your time writing your thesis. This may be bad for your physical and mental health.

Typing
Set up your chair and computer properly. The Health Service, professional keyboard users or perhaps even the school safety officer will be able to supply charts showing recommended relative heights, healthy postures and also exercises that you should do if you spend a lot of time at the keyboard. These last are worthwhile insurance: you do not want the extra hassle of back or neck pain. Try to intersperse long sessions of typing with other tasks, such as reading, drawing, calculating, thinking or doing research.

If you do not touch type, you should learn to do so for the sake of your neck as well as for productivity. There are several good software packages that teach touch typing interactively. If you use one for say 30 minutes a day for a couple of weeks, you will be able to touch type. By the time you finish the thesis, you will be able to touch type quickly and accurately and your six hour investment will have paid for itself. Be careful not to use the typing exercises as a displacement activity.

Exercise
Do not give up exercise for the interim. Lack of exercise makes you feel bad, and you do not need anything else making you feel bad while writing a thesis. 30-60 minutes of exercise per day is probably not time lost from your thesis: I find that if I do not get regular exercise, I sleep less soundly and longer. How about walking to work and home again? (Walk part of the way if your home is distant.) Many people opine that a walk helps them think, or clears the head. You may find that an occasional stroll improves your productivity.

Food
Do not forget to eat, and make an effort to eat healthy food. You should not lose fitness or risk illness at this critical time. Exercise is good for keeping you appetite at a healthy level. I know that you have little time for cooking, but keep a supply of fresh fruit, vegetables and bread. It takes less time to make a sandwich than to go to the local fast food outlet, and you will feel better afterwards.

Drugs
Thesis writers have a long tradition of using coffee as a stimulant and alcohol (and, in the old days, marijuana). Used in moderation, they do not seem to have ill effects on the quality of thesis produced. Excesses, however, are obviously counter-productive: several espressi and you will be buzzing too much to sit down and work; several drinks at night will slow you down next day.

Others
Other people will be sympathetic, but do not take them for granted. Spouses, lovers, family and friends should not be undervalued. Spend some time with them and, when you do, have a good time. Do not spend your time together complaining about your thesis: they already resent the thesis because it is keeping you away from them. If you can find another student writing a thesis, then you may find it therapeutic to complain to each other about advisers and difficulties. S/he need not be in the same discipline as you are.

Coda

Keep going – you're nearly there! Most PhDs will admit that there were times when we thought about reasons for not finishing. But it would be crazy to give up at the writing stage, after years of work on the research, and it would be something to regret for a long time.

Writing a thesis is tough work. One anonymous post doctoral researcher told me: "You should tell everyone that it's going to be unpleasant, that it will mess up their lives, that they will have to give up their friends and their social lives for a while. It's a tough period for almost every student." She's right: it is certainly hard work, it will probably be stressful and you will have to adapt your rhythm to it. It is also an important rite of passage and the satisfaction you will feel afterwards is wonderful. On behalf of scholars everywhere, I wish you good luck!


A suggested thesis structure

The list of contents and chapter headings below is appropriate for some theses. In some cases, one or two of them may be irrelevant. Results and Discussion are usually combined in several chapters of a thesis. Think about the plan of chapters and decide what is best to report your work. Then make a list, in point form, of what will go in each chapter. Try to make this rather detailed, so that you end up with a list of points that corresponds to subsections or even to the paragraphs of your thesis. At this stage, think hard about the logic of the presentation: within chapters, it is often possible to present the ideas in different order, and not all arrangements will be equally easy to follow. If you make a plan of each chapter and section before you sit down to write, the result will probably be clearer and easier to read. It will also be easier to write.

Copyright waiver
Your institution may have a form for this (UNSW does). In any case, this standard page gives the university library the right to publish the work, possibly by microfilm or other medium. (At UNSW, the Postgraduate Student Office will give you a thesis pack with various guide-lines and rules about thesis format. Make sure that you consult that for its formal requirements, as well as this rather informal guide.)

Declaration
Check the wording required by your institution, and whether there is a standard form. Many universities require something like: "I hereby declare that this submission is my own work and that, to the best of my knowledge and belief, it contains no material previously published or written by another person nor material which to a substantial extent has been accepted for the award of any other degree or diploma of the university or other institute of higher learning, except where due acknowledgment has been made in the text. (signature/name/date)"

Title page
This may vary among institutions, but as an example: Title/author/"A thesis submitted for the degree of Doctor of Philosophy in the Faculty of Science/The University of New South Wales"/date.

Abstract
Of all your thesis, this part will be the most widely published and most read because it will be published in Dissertation Abstracts International. It is best written towards the end, but not at the very last minute because you will probably need several drafts. It should be a distillation of the thesis: a concise description of the problem(s) addressed, your method of solving it/them, your results and conclusions. An abstract must be self-contained. Usually they do not contain references. When a reference is necessary, its details should be included in the text of the abstract. Check the word limit. Remember: even though it appears at the beginning, an abstract is not an introduction. It is a résumé of your thesis.

Acknowledgments
Most thesis authors put in a page of thanks to those who have helped them in matters scientific, and also indirectly by providing such essentials as food, education, genes, money, help, advice, friendship etc. If any of your work is collaborative, you should make it quite clear who did which sections.

Table of contents
The introduction starts on page 1, the earlier pages should have roman numerals. It helps to have the subheadings of each chapter, as well as the chapter titles. Remember that the thesis may be used as a reference in the lab, so it helps to be able to find things easily.

Introduction
What is the topic and why is it important? State the problem(s) as simply as you can. Remember that you have been working on this project for a few years, so you will be very close to it. Try to step back mentally and take a broader view of the problem. How does it fit into the broader world of your discipline?

Especially in the introduction, do not overestimate the reader's familiarity with your topic. You are writing for researchers in the general area, but not all of them need be specialists in your particular topic. It may help to imagine such a person – think of some researcher whom you might have met at a conference for your subject, but who was working in a different area. S/he is intelligent, has the same general background, but knows little of the literature or tricks that apply to your particular topic.

The introduction should be interesting. If you bore the reader here, then you are unlikely to revive his/her interest in the materials and methods section. For the first paragraph or two, tradition permits prose that is less dry than the scientific norm. If want to wax lyrical about your topic, here is the place to do it. Try to make the reader want to read the heavy bundle that has arrived uninvited on his/her desk. Go to the library and read several thesis introductions. Did any make you want to read on? Which ones were boring?

This section might go through several drafts to make it read well and logically, while keeping it short. For this section, I think that it is a good idea to ask someone who is not a specialist to read it and to comment. Is it an adequate introduction? Is it easy to follow? There is an argument for writing this section – or least making a major revision of it – towards the end of the thesis writing. Your introduction should tell where the thesis is going, and this may become clearer during the writing.

Literature review
Where did the problem come from? What is already known about this problem? What other methods have been tried to solve it?

Ideally, you will already have much of the hard work done, if you have been keeping up with the literature as you vowed to do three years ago, and if you have made notes about important papers over the years. If you have summarised those papers, then you have some good starting points for the review.

If you didn't keep your literature notes up to date, you can still do something useful: pass on the following advice to any beginning PhD students in your lab and tell them how useful this would have been to you. When you start reading about a topic, you should open a spread sheet file, or at least a word processor file, for your literature review. Of course you write down the title, authors, year, volume and pages. But you also write a summary (anything from a couple of sentences to a couple of pages, depending on the relevance). In other columns of the spread sheet, you can add key words (your own and theirs) and comments about its importance, relevance to you and its quality.

How many papers? How relevant do they have to be before you include them? Well, that is a matter of judgement. On the order of a hundred is reasonable, but it will depend on the field. You are the world expert on the (narrow) topic of your thesis: you must demonstrate this.

A political point: make sure that you do not omit relevant papers by researchers who are like to be your examiners, or by potential employers to whom you might be sending the thesis in the next year or two.

Middle chapters

In some theses, the middle chapters are the journal articles of which the student was major author. There are several disadvantages to this format.

One is that a thesis is both allowed and expected to have more detail than a journal article. For journal articles, one usually has to reduce the number of figures. In many cases, all of the interesting and relevant data can go in the thesis, and not just those which appeared in the journal. The degree of experimental detail is usually greater in a thesis. Relatively often a researcher requests a thesis in order to obtain more detail about how a study was performed.

Another disadvantage is that your journal articles may have some common material in the introduction and the "Materials and Methods" sections.

The exact structure in the middle chapters will vary among theses. In some theses, it is necessary to establish some theory, to describe the experimental techniques, then to report what was done on several different problems or different stages of the problem, and then finally to present a model or a new theory based on the new work. For such a thesis, the chapter headings might be: Theory, Materials and Methods, {first problem}, {second problem}, {third problem}, {proposed theory/model} and then the conclusion chapter. For other theses, it might be appropriate to discuss different techniques in different chapters, rather than to have a single Materials and Methods chapter.

Here follow some comments on the elements Materials and Methods, Theory, Results and discussion which may or may not correspond to thesis chapters.

Materials and Methods
This varies enormously from thesis to thesis, and may be absent in theoretical theses. It should be possible for a competent researcher to reproduce exactly what you have done by following your description. There is a good chance that this test will be applied: sometime after you have left, another researcher will want to do a similar experiment either with your gear, or on a new set-up in a foreign country. Please write for the benefit of that researcher.

In some theses, particularly multi-disciplinary or developmental ones, there may be more than one such chapter. In this case, the different disciplines should be indicated in the chapter titles.

Theory
When you are reporting theoretical work that is not original, you will usually need to include sufficient material to allow the reader to understand the arguments used and their physical bases. Sometimes you will be able to present the theory ab initio, but you should not reproduce two pages of algebra that the reader could find in a standard text. Do not include theory that you are not going to relate to the work you have done.

When writing this section, concentrate at least as much on the physical arguments as on the equations. What do the equations mean? What are the important cases?

When you are reporting your own theoretical work, you must include rather more detail, but you should consider moving lengthy derivations to appendices. Think too about the order and style of presentation: the order in which you did the work may not be the clearest presentation.

Suspense is not necessary in reporting science: you should tell the reader where you are going before you start.

Results and discussion
The results and discussion are very often combined in theses. This is sensible because of the length of a thesis: you may have several chapters of results and, if you wait till they are all presented before you begin discussion, the reader may have difficulty remembering what you are talking about. The division of Results and Discussion material into chapters is usually best done according to subject matter.

Make sure that you have described the conditions which obtained for each set of results. What was held constant? What were the other relevant parameters? Make sure too that you have used appropriate statistical analyses. Where applicable, show measurement errors and standard errors on the graphs. Use appropriate statistical tests.

Take care plotting graphs. The origin and intercepts are often important so, unless the ranges of your data make it impractical, the zeros of one or both scales should usually appear on the graph. You should show error bars on the data, unless the errors are very small. For single measurements, the bars should be your best estimate of the experimental errors in each coordinate. For multiple measurements these should include the standard error in the data. The errors in different data are often different, so, where this is the case, regressions and fits should be weighted (i.e. they should minimize the sum of squares of the differences weighted inversely as the size of the errors.) (A common failing in many simple software packages that draw graphs and do regressions is that they do not treat errors adequately. UNSW student Mike Johnston has written a plotting routine that plots data with error bars and performs weighted least square regressions. It is at http://www.phys.unsw.edu.au/3rdyearlab/graphing/graph.html). You can just 'paste' your data into the input and it generates a .ps file of the graph.

In most cases, your results need discussion. What do they mean? How do they fit into the existing body of knowledge? Are they consistent with current theories? Do they give new insights? Do they suggest new theories or mechanisms?

Try to distance yourself from your usual perspective and look at your work. Do not just ask yourself what it means in terms of the orthodoxy of your own research group, but also how other people in the field might see it. Does it have any implications that do not relate to the questions that you set out to answer?

Final chapter, references and appendices

Conclusions and suggestions for further work
Your abstract should include your conclusions in very brief form, because it must also include some other material. A summary of conclusions is usually longer than the final section of the abstract, and you have the space to be more explicit and more careful with qualifications. You might find it helpful to put your conclusions in point form.

It is often the case with scientific investigations that more questions than answers are produced. Does your work suggest any interesting further avenues? Are there ways in which your work could be improved by future workers? What are the practical implications of your work?

This chapter should usually be reasonably short – a few pages perhaps. As with the introduction, I think that it is a good idea to ask someone who is not a specialist to read this section and to comment.

References (See also under literature review)
It is tempting to omit the titles of the articles cited, and the university allows this, but think of all the times when you have seen a reference in a paper and gone to look it up only to find that it was not helpful after all.

Should you reference web sites and, if so, how? If you cite a journal article or book, the reader can go to a library and check that the cited document and check whether or not it says what you say it did. A web site may disappear, and it may have been updated or changed completely. So references to the web are usually less satisfactory. Nevertheless, there are some very useful and authoritative sources. So, if the rules of your institution permit it, it may be appropriate to cite web sites. (Be cautious, and don't overuse such citations. In particular, don't use a web citation where you could reasonably use a "hard" citation. Remember that your examiners are likely to be older and more conservative.) You should give the URL and also the date you downloaded it. If there is a date on the site itself (last updated on .....) you should included that, too.

Appendices
If there is material that should be in the thesis but which would break up the flow or bore the reader unbearably, include it as an appendix. Some things which are typically included in appendices are: important and original computer programs, data files that are too large to be represented simply in the results chapters, pictures or diagrams of results which are not important enough to keep in the main text.


Some sites with related material
Some relevant texts
    Stevens, K. and Asmar, C (1999) 'Doing postgraduate research in Australia'. Melbourne University Press, Melbourne ISBN 0 522 84880 X.
    Phillips, E.M and Pugh, D.S. (1994) 'How to get a PhD : a handbook for students and their supervisors'. Open University Press, Buckingham, England
    Tufte, E.R. (1983) 'The visual display of quantitative information'. Graphics Press, Cheshire, Conn.
    Tufte, E.R. (1990) 'Envisioning information' Graphics Press, Cheshire, Conn.

Distribution

If you have found these documents useful, please feel free to pass the address or a hard copy to any other thesis writers or graduate student organisations. Please do not sell them, or use any of the contents without acknowledgement.

Suggestions, thanks and caveats

This document will be updated occasionally. If you have suggestions for inclusions, amendments or other improvements, please send them. Do so after you have submitted the thesis – do not use this invitation as a displacement activity. I thank Marilyn Ball, Gary Bryant, Bill Whiten and J. Douglas, whose suggestions have been incorporated in this version. Substantial contributions will be acknowledged in future versions. I also take this opportunity to thank my own thesis advisers, Stjepan Marcelja and Jacob Israelachvili, for their help and friendship, and to thank the graduate students to whom I have had the pleasure to be an adviser, a colleague and a friend. Opinions expressed in these notes are mine and do not necessarily reflect the policy of the University of New South Wales or of the School of Physics.

A FAQ and some observations about the web

Why and how did I write this document? The need for it was evident so, as one of my PhD students approached the end of his project, I made notes of everything that I said to him about thesis writing. These notes became the plan for the first draft of this document, which has been extended several times since then. I am surprised that it has hundreds of readers each day. However, this is an important message about the web. It takes time and thought to make a good resource but, if you do, it can benefit a lot of people. When this document was first posted, the web was relatively new and feedback showed that people were often surprised to find what they sought. Now there is a tendency to take the web for granted: one is almost disappointed not to find what one is seeking. However, the web is only as good as the collective effort of all of us. The readers of this document will be scholars, experts and educators: among the many contributions you will make to knowledge and your communities, there may be contributions that should be made freely available, all over the world. Keep this observation about the web in the back of your mind for later, when you are not writing a thesis.

How to Write Up a Ph.D. Dissertation
(for computer scientists and the like)

by Jason Eisner (2006)

This page is about how to turn your research (once it's done) into a readable multi-chapter document. You need to figure out what to include, how to organize it, and how to present it.

Following this advice will make me happier about reading your submitted or draft dissertation. You may find it useful even if I'm not going to read your dissertation.

Many others have written usefully on this subject, including someone in the Annals of Improbable Research. There's also advice on writing a thesis proposal. However, this page focuses on what a finished dissertation should look like. You could also skim good dissertations on the web.



What Goes Into a Dissertation?

A typical thesis will motivate why a new idea is needed, present the cool new idea, convince the reader that it's cool and new and might apply to the reader's own problems, and evaluate how well it worked. Just like a paper!

The result must be a substantial, original contribution to scientific knowledge. It signals your official entrance into the community of scholars. Treat it as an chance to make a mark, not as a 900-page-tall memorial to your graduate student life.

Beyond stapling

The cynical view is that if you've written several related papers, you staple them together to get a dissertation. That's a good first-order approximation -- you should incorporate ideas and text from your papers. But what is it missing?

First, a thesis should cohere -- ideally, it should feel like one long paper. Second, it should provide added value: there should be people who would prefer reading it to simply reading your papers. Otherwise writing it would be a meaningless exercise.

Here's what to do after stapling:

  • integrate the pieces
    • craft a substantial introductory chapter that ties the work together and highlights the novel contributions
    • reorganize the remaining presentation into a series of chapters that support and develop your story from the introduction
    • write a (brief) concluding chapter that recapitulates your story and summarizes what was learned
    • make the notation, terminology, and style consistent throughout
    • do keep good ideas, text, and results from your previous papers (giving credit to any co-authors)

  • expand the text
    • make the text clearer, more tutorial, and more thoughtful
    • add more examples and intuitions to help the reader
    • add new experiments/theorems/significance tests to leave no stone unturned
    • consider counterarguments, variations, and alternative explanations
    • give enough details to allow a reader to replicate the work or apply it in new settings

  • contextualize the ideas
    • open the thesis with a page or two that sells the work to a general audience (e.g., a science reporter)
    • mention all obviously related work and explain how it relates to yours (warning: finding, reading, and contemplating additional work may take a while!)
    • discuss alternative solutions that you rejected or are leaving to future work
    • point out connections to other areas, including other possible applications of your ideas
    • describe possible generalizations (and try them if possible)
    • lay out future work for yourself or others

  • acknowledge help (usually in a preface)
    • acknowledge any collaborators on this work, such as your advisor
    • acknowledge financial support on this work, and perhaps also other financial support you've received as a grad student
    • thank other people who have helped you technically, administratively, socially, or emotionally over your grad student career
    • state which parts of the thesis text (if any) have appeared in your previous publications; get permission to republish if you are no longer the copyright holder of those works, or if you had co-authors

Taking Responsibility

Don't expect your advisor to be your co-author. It's your Ph.D.: you are sole author this time and the responsibility is on your shoulders. If your prose is turgid or thoughtless, misspelled or ungrammatical, oblivious or rude to related research, you're the one who looks bad.

You can do it! Your advisor and committee are basically on your side -- they're probably willing to make suggestions about content and style -- but they are not obligated to fix problems for you. They may send your dissertation back and tell you to fix it.

In the following sections, I'll start with advice about the thesis as a whole, and work downward, eventually reaching small details such as typography and citations.


Know Your Audience

First, choose your target audience. That crucial early decision will tell you what to explain, what to emphasize, and how to phrase and organize it. Checking it with your advisor might be wise.

Pretty much everything in your thesis should be relevant to your chosen audience. Think about them as you write. Ask yourself:

What does your audience already know?

A computer science thesis can freely invoke basic ideas like hash tables and computational complexity without defining or even citing them. (After all, do biologists read a computer science thesis? Not unless they are pretty comfortable with computer science.)

You can also safely assume that your readers have some prior familiarity with your research area. Just how much familiarity, and with which topics, is a judgment call -- again, you have to decide who your intended audience is.

In practice, your audience will be somewhat mixed. Up to a point, it is possible to please both beginners and experts -- by covering background material crisply and in the service of your own story. How does that work? As you lay out the motivation for your own work, and provide notation, you'll naturally have to discuss background concepts and related work. But don't give a generic review that someone else could have written! Discuss the background in a way that motivates and clarifies your ideas. Present your detailed perspective on the intellectual landscape and where your own work sits in it -- a fresh (even opinionated) take that keeps tying back to your main themes and will be useful for both experts and beginners.

In short, be as considerate as you can to beginners without interrupting the flow of your main argument to your established colleagues. A good rule of thumb is to write at the level of the most accessible papers in the journals or conference proceedings that you read.

What do you want your audience to learn from the thesis?

You should set clear goals here. Just like a paper or a talk, your dissertation needs a point: it should tell a story. Writing the abstract and chapter 1 at the start will help you work out what that story is.

You may find that you have to do further work to really support your chosen story: more experiments, more theorems, reading more literature, etc.

What does your audience hope to get out of the thesis?

Why does anyone crack open a dissertation, anyway? I sometimes do. Especially for areas that I know less well, a dissertation is often more accessible than shorter, denser papers. It takes a more leisurely pace, provides more explicit motivation and background, and answers more of the questions that I might have.

There are other reasons I might look at your dissertation:

  • To better understand your cool idea: your grand vision, how you think about it, and what you did.
  • To look up details, clarification, or further results after reading a shorter version of your work.
  • To get a sense of what your field or area is all about.
  • To read a thorough summary of work in your area, via your literature review.
  • To describe your work accurately in a paper I'm writing.
  • To check whether a paper I'm writing (or reviewing) needs to cite you.
  • To decide whether to give you a Ph.D. :-)
  • To help me write a recommendation or promotion letter.

For students, reading high-quality dissertations is a good way to learn an area and to see what a comprehensive treatment of a problem looks like. Noah A. Smith once ran a graduate CS seminar in which the students read 8 dissertations together. Each student was also required to select and summarize yet another dissertation and write a novel research proposal based on it.

Readers with different motivations may read your thesis in different ways. The strong convention is that it's a single document that must read well from start to finish -- your committee will read it that way. But it's worth keeping other readers in mind, too. Some will skim from start to finish. Some will read only the introductory and concluding chapters (so make sure those give a strong impression of what you've done and why it's important). Some will read a single chapter in the middle, going back for definitions as needed. Some will scan or search for what they need: a definition, example, table of results, or literature review. Some will flip through to get a general sense of your work or of how you think, reading whatever catches their eye.


High-Level Organization

Once you've chosen your target audience, you should outline the structure of the thesis. Again, the convention is that the document must read well from start to finish.

The "canonical organization" is sketched by Douglas Comer near the end of his advice. Read that: you'll probably want something like it. A few further tips:

Keep your focus

Keep your focus. Length is not a virtue unless the content is actually interesting. You do have as much space as you need, but the reader doesn't have unlimited time and neither do you.

Use space as needed for clarity and to flesh out and support your story. If you feel like your thesis is too short, it may need more ideas or thoughtful discussion or experiments (talk to your advisor), but it doesn't need more padding.

Get to the good stuff

A newspaper, like a dissertation, is a hefty chunk of reading. So it puts the most important news on page one, and leads each article with the most important part. You should try to do the same when reasonable.

Get to the interesting ideas as soon as possible. A good strategy is to make Chapter 1 an overview of your main arguments and findings. Tell your story there in a compelling way, including a taste of your results. Refer the reader to specific sections in later chapters for the pesky details. Chapter 1 should be especially accessible (use examples): make it the one chapter that everyone should read.

The same strategy works within a chapter. Start by telling your readers what the chapter is about and why they should read it. Then unfold your ideas and results. The order of your presentation should be natural and logical (e.g., motivation before experimental design before results), but try to keep the reader turning pages; seek reasonable ways to move the boring bits to later sections or later chapters.

Include a road map

Chapter 1 traditionally ends with a "road map" to the rest of the thesis, which rapidly summarizes what the remaining chapters or sections will contain. That's useful guidance for readers who are looking for something specific and also for those who will read the whole thesis. It also exhibits in one place what an awful lot of work you've done. Here's a detailed example.

Where to put the literature review

I recommend against writing "Chapter 2: Literature Review." Such chapters are usually boring: they're plonked down like the author's obligatory list of what he or she was "supposed" to cite. They block the reader from getting to the new ideas, and can't even be contrasted with the new ideas because those haven't been presented yet.

A better plan is to discuss related literature in conjunction with your own ideas. As you motivate and present your ideas, you'll want to refer to some related work anyway.

Related work that didn't meld naturally into that presentation can be acknowledged soon afterwards in its own section -- where you should still focus on how it relates to your ideas and fits into your framework, which you have already presented.

Each chapter might have its own related work section or sections, covering work that connects to yours in different ways.

Where to define terminology and notation

Basic terminology, concepts, and notation have to be defined somewhere. But where? You can mix the following strategies:

Retail. You can define some terms or notation individually, when the reader first needs them. Then they will be well-motivated and fresh in the reader's mind. If you use them again later, you can refer back to the section where you first defined them.

Wholesale. On the other hand, there are advantages to aggregating some of your fundamental definitions into a "Definitions" section near the start of the chapter, or a chapter near the start of the dissertation:

  • Sits readers down and gets them oriented all at once.
  • Makes the definitions harder to overlook.
  • Highlights how the definitions are related to one another.
  • Gets the definitions out of the way, so they don't have to interrupt the flow of your argument later.
  • Gives readers a place to check if they forget what you meant by
or the "bumptiousness" of a model. (An alternative is to include a summary of notation and a glossary at the back of the dissertation, and advertise their existence.)

The downside is that such sections or chapters can seem boring and full of not-yet-motivated concepts. Unless your definitions are novel and interesting in themselves, they block the reader from getting to the new and interesting ideas. So if you write something like "Chapter 2: Preliminaries," keep it relatively concise -- the point is to get the reader oriented.

Thrift shop. Use well-known notation and terminology whenever you can, either with or without a formal definition in your thesis. The point of your thesis is not to re-invent notation or to re-present well-known material, although sometimes you may find it helpful to do so.


Make Things Easy on Your Poor Readers

Now we get down to the actual writing. A dissertation is a lot to write. But it's also an awful lot to read and digest at once! You can keep us readers turning pages and following your argument. But it's a bigger and more complicated argument than usual, so you have to be more disciplined than usual.

Break it down

Long swaths of text are like quicksand for readers (and writers!). To keep us moving without sinking, use all the devices at your disposal to break the text down into short chunks. Ironically, short chunks are more helpful in a longer document. They keep your argument tightly organized and keep the reader focused and oriented.

If a section or subsection is longer than 1 double-spaced page, consider whether you could break it down further. I'm not joking! This 1-page threshold may seem surprisingly short, but it really makes writing and reading easier. Some devices you can use:

subsectioning
Split your section into subsections (or subsubsections) with meaningful titles that keep the reader oriented.

lists
If you're writing a paragraph and feel like you're listing anything (e.g., advantages or disadvantages of some approach), then use an explicit bulleted list. Sometimes this might yield a list with only 2 or 3 rather long bullet points, but that's fine -- it breaks things down. (Note: To replace the bullets with short labels, roughly as in the list you're now reading, LaTeX's environment lets you write .)

labeled paragraphs
Label a series of paragraphs within the section, as a kind of lightweight subsectioning. Your experimental design section might look like this (using the LaTeX command):

Participants. The participants were 32 undergraduates enrolled in ...

Apparatus. Each participant wore a Star Trek suit equipped with a Hasbro-brand Galactic Translator, belt model 3A ...

Procedure. The subjects were seated in pairs throughout the laboratory and subjected to Vogon poetry broadcast at 3-minute intervals ...

Dataset. The Vogon poetry corpus (available on request) was obtained by passing the later works of T. S. Eliot through the Systran translation system ...

footnotes
Move inessential points to footnotes. If they're too long for that, you could move them into appendices or chapters near the end of the thesis. (Here's my take on footnotes.)

captions
Move some discussion of figures and tables into their captions. Figures and tables should be clearly structured in the first place: e.g., graphs should have labeled axes with units. But a helpful caption provides guidance on how to interpret the figure or table and what interesting conclusions to draw from it. The figure or table should itself include helpful labels (axis

(In LaTeX, you can write . The optional argument will be used for the "List of Tables" or "List of Figures" at the start of the thesis.)

theorems
Even simple formal results can be stated as a theorem or lemma. The theorem (and proof, if included) form a nice little chunk, using the LaTeX enviroment.

Breaking down equations

Long blocks of equations are even more intimidating than long swaths of text. You can break those apart, too:

  • Intersperse short bits of text for guidance (perhaps using LaTeX ). You might introduce line 3 of your formula with

    A change of variable from x to log x now allows us to integrate by parts:
  • Distinguish conceptually important steps from finicky steps that just push symbols around. You can even move finicky steps to a footnote, like this:

    Some algebraic manipulation5 allows us to simplify to the following:
  • Use visual devices like color, boldface, underlining, boxes, or to call attention to significant parts of a formula:

  • Simplify the formulas in the first place by defining intermediate quantities or adopting notational conventions (e.g., "the t subscript will be dropped when it is clear from context").

Now tie it back together

Now that you've chopped your prose into bite-sized chunks, what binds it together?

Coherent and explicit structure

Your paragraphs and chunks have to tie together into a coherent argument. Do everything you can to highlight the structure of this argument. The structure should jump out at the reader, making it possible to read straight through your text, or skim it. Else the reader will get stuck puzzling out what you meant and lose momentum.

Make sure your readers are never perplexed about the point of the paragraph they're reading. Make them want to keep turning the page because you've set up questions to which they want to know the answers. Don't make them rub their eyes in frustration or boredom and wander off to the fridge or the web browser.

So how exactly do you "highlight the structure" and "set up questions"?

  • Ask questions explicitly and then answer them, as I just did. This is a great device for breaking up boring prose, communicating your rhetorical goals, and making the reader think.

  • Explicitly refer back to previous text, as when I wrote, "So how exactly do you 'highlight the structure' and 'set up questions'?"

  • Use lots of transitional phrases (discourse connectives). Note that it's fine to use these across chunk boundaries; that is, feel free to start a new subsection with "For this reason, ...", picking up where the previous subsection left off.

  • Section and subsection titles pop out visually at the reader. So use them to provide explicit, helpful guidance. Not Analysis, but Error Analysis: Why Conditional Likelihood Usually Beats Large-Margin Training on Vogon Poetry. (That's on the long side, but still shorter than the chapter titles in old-fashioned novels ...)

  • As you start a section, explicitly state how it will be organized, or how it fits into the larger organization.

  • As you come to the end of a section, remind the reader what the point was. If possible, this should lead naturally into the next section.

  • If a section is skippable, or chapters can be read out of order, do say so. (But don't use this as an excuse for poor organization or long distractions. Some readers tend to read straight through, and in particular, your advisor or committee may feel that they must do this.)

Lots of internal cross-references

A thesis deals with a lot of ideas at once. Readers can easily lose track. Help them out:

  • Use plenty of references to your equations, sections, figures and tables. This is really helpful to a reader who might be getting confused, or who is skimming the thesis or reading it piecemeal or out of order.

    • Don't just say "as defined earlier" or "we will see below"; give the section number.
    • Don't say "divide by Z"; say "divide equation (3.22) by Z from (3.19)."
    • Don't say "footnote 22"; say "footnote 22 on p. 99" (if it's far away), by using both the and commands in LaTeX.
    You'll probably want define some LaTeX macros for frequent reference styles.
  • Each figure or table should be mentioned in the main text, so that the reader knows to go look at it. Conversely, the figure's caption may point the reader back to details in the main text (stating the section number). A caption may also refer to other figures or tables that the reader should be sure to compare.

  • Boldface terms that you are defining, as a textbook would. This makes the definitions easy to spot when needed. You may also want to generate an index of boldfaced terms.

  • Be very consistent in your terminology. Never use two terms for the same idea; never reuse one term or variable for two ideas.

  • Be cautious about using pronouns like "it," or other anaphors such as "this" or "this technique." With all the ideas flying around, it won't always be obvious to everyone what you're referring to. Use longer, unambiguous phrases instead, when appropriate.

  • Try saying "the time t" instead of just "t" or just "the time." Similarly, "the image transformation T," "the training example xi," etc. This style reminds the reader of which variables are connected to which concepts. You can further do this for expressions: "the total probability Σipi" instead of just "the total probability" or "the sum."

  • Give the reader some clue about the type of each variable. This makes it easier to interpret formulas. State the type (range) when you introduce the variable: "let x∈ [1,N] be an index." The name of the variable should also be a clue to its type. You may want to adopt naming conventions and state them explicitly, e.g.,

    • i, j, k ... for integers in the range [1,N]
    • a, b, c ... for characters
    • A, B, C ... for sets of characters
    • α, β, γ ... for strings
    • X, Y, Z ... for random variables
    • script X, Y, Z, ... for the ranges of random variables
    • x (or x with an arrow above it) for a vector
    • x(n) for an n-tuple
    • SMALL CAPS for the name of a model or system
  • Feel free to lavish space where it confers extra understanding. Don't hesitate to give an example or a caveat, or repeat an earlier equation, or crisply summarize earlier work that the reader needs to understand.

Be concrete

As I read a thesis, or a long argument or construction within a thesis, I often start worrying whether I am keeping the pieces together correctly in my head. Something that has become deeply familiar and natural to you (the world expert) may be rougher going for me. If I can see some concrete demonstration of how your idea works, it helps me check and deepen my understanding.

  • Examples keep the reader, and you, from getting lost in a morass of abstractions. Example cases figured in your thinking; they can help the reader, too. Invented examples are okay, but using "real" examples will also show off what your methods should or can do.

  • Running examples greet the reader like old friends. The reader will grasp a point more quickly and completely, and remember it better, when it is applied to a familiar example rather than a new one. So if possible, devise one or two especially nice examples that you can keep revisiting to make a series of points.

  • Pictures serve much the same role as examples: they're concrete and they share how the ideas really look inside your head. A picture is worth at least a thousand words (= 2.5 double-spaced thesis pages).

  • Pseudocode is a concrete way to convey an algorithm. It is often more concise, precise, and direct than a prose description, and may be closer to your own thinking. It will also make other people much more likely to understand and adopt your methods.

  • Theorems, too, are concise and precise. They are also self-contained chunks, because they formally state all their assumptions. A reader sloshing through a long, complicated, contextual argument can always grab onto a theorem as an island of certainty.

  • Experimental results are also concrete. You don't have to wait for the experimental section: it is okay to foreshadow your experiments before you present them in full. When you are developing the theory, you can say "Indeed, we will find experimentally in section 5.6 that ..." You can even showcase an example from your experiments or give some summary statistics; these might not even show up later in the experimental section.

  • Commitments keep the reader anchored. As noted earlier, your dissertation should discuss alternative solutions that you rejected or are leaving to future work. That's scholarship. But make it clear from the start what you actually did and didn't do. Don't have section 2.3 chatter on about everything one could do -- that reads like a proposal, not a thesis! -- while waiting till section 4.5 or even 2.5 to reveal what you actually did.

Placing these concrete elements early is best, other things equal. Either embed them early in the section or just tell the reader early on to go look at Figure X. (If you continue the section by discussing Figure X, the reader is more likely to actually go look. Figure X or its caption can refer back to the text in turn.)

For example, consider pseudocode. Some readers prefer code to prose, and it's concise. So you may want to give pseudocode early in the section, before you ramble on about why it works. An alternative is to intersperse fragments of pseudocode with your prose explanation, as in literate programming. Of course, the pseudocode itself should also include some brief comments; where necessary these can just point to the text, as in "implements equation (5)" or "see section 3.2."


Mechanics

Sentences. The previous section dealt with sections and paragraphs, but how about sentences? Yours should read well. The best advice in The Elements of Style: "Omit needless words. Vigorous writing is concise." To learn how to improve your sentences, read Style: Lessons in Clarity and Grace, by Joseph M. Williams, and do the exercises. Another classic is On Writing Well, by William Zinsser.

Typography. It's nice to get the typography right. This might be a good time to read a LaTeX tutorial or book, if you don't know

  • the differences among , , and , and whether to put spaces around them
  • the differences among spacing commands like , , , , , and
  • why , , , and look ugly and how to fix them
  • what to use for multi-line equations or groups of equations (not !)
  • how to use other improved math commands and environments (shorter guide)
  • where to browse through obscure math symbols (or look one up by drawing it!)
  • how to make complicated tabular environments
  • how to include graphics (via the package)
  • how to define macros to make your life easier
  • that pdflatex (in place of latex) directly produces a PDF file with nice fonts

Margins, spacing, title page, etc. Read JHU's submission and formatting requirements, then use these LaTeX style files provided by the library.

Citations.BibTeX is definitely worth using to manage your bibliographic database. Then I recommend formatting your citations with (accompanied by to format the actual bibliography). The package ordinarily produces reader-friendly citations such as

Computers are getting exponentially faster (Moore, 1965). However, Biddle (1971) showed ...
and is blessedly flexible enough to handle more complex forms that you'll probably need somewhere in your thesis:
Bandura's (1977) theory ...
... (e.g., Butcher, 1954; Baker, 1955; Candlestick-Maker, 1957, and others).
The work of Minor (2001, pp. 50-75; but see also Adams, 1999; Storandt, 1997) ...
According to Manning and Schütze, 1999 (henceforth M&S), ...
(It can also switch to numerical citations like [34] if you really want.)

(Another option is the package, which precisely follows the style manual of the American Psychological Association. It is nearly as flexible in its citation format, but APA style has some oddities, including lowercasing the titles of proceedings volumes. One nice thing about APA style is that if you have multiple Smiths in your bibliography, it will distinguish them where necessary, using first and middle initials. Another nice thing is the use of "&" rather than "and" in author lists; however, you can easily hack to mimic this behavior.)

Hyperlinks within your PDF file. I recommend including this in the LaTeX preamble:

\usepackage[colorlinks]{hyperref} \usepackage{url}

Notes to yourself. I like to use !!! to mark something that I have to come back and finish or fill in. For longer "to do" notes to yourself, try using the cool latex package. Or for a lightweight alternative, define a macro so your note appears as highlighted text in the document:

\usepackage[usenames,dvipsnames,svgnames,table]{xcolor} \usepackage{soul} \newcommand{\todo}[1]{\hl{[TODO: #1]}} \todo{Either prove this or back away from the claim. I think Fermat's Last Theorem might be the key ...}
To suppress all notes, change the definition to
\newcommand{\todo}[1]{}
Not all notes to yourself are to-do items that should jump out at you. You may also want to include TeX comments as documentation for your own use:
... only 58 words in the dictionary have this property. % to get that count: % perl -ne 'print if blah blah' /usr/share/dict/words | wc -l

Version control. It's probably wise to use git (or CVS or RCS or Subversion or mercurial or darcs) to keep the revision history of your dissertation files. This lets you roll back to an earlier version in case of disaster. Furthermore, if you host the repository on your account, it will be backed up by the department.

Sharing your thesis. When you're willing to open up for comments from fellow students, your advisor, or your committee, give them a secret URL from which they can always download the latest, up-to-date release of your thesis, as well as earlier versions. (This is probably friendlier than just pointing them to your git repository.)

Keep this URL up to date with your changes. Each distinct version should bear a visible date or version number, to avoid confusion. For each new version (or on request), you should probably also supply a PDF that marks up the differences from an appropriate earlier version, using the wonderful latexdiff program (available here or as an Linux package; plays nicely with git via latexdiff-git or other scripts) or a similar technique. (Note: If you use a makefile to build your document by running latex, gnuplot, etc., then you can also make it run latexdiff and update the URL for you.)


Planning Your Dissertation

Every dissertation is a little different. Talk to your advisor to draft a specific, written plan for what the thesis will contain, how it will be organized, and whom it will address. Discuss the plan with each of your committee members, who may suggest changes. They might disagree with advice on this page; find out.

As the dissertation takes shape, your plan may need some revision. Your advisor and committee may be willing to provide early feedback. But no one will want to slog through more than a version or two in detail. So ask them each how many drafts of each chapter they're willing to read, and in what state and on what schedule. Some of them nmay prefer to influence your writeup while it's still in an early, outline form. Others may prefer to wait until your prose is fairly polished and easy to read.

In addition to your advisor's goals and your committee's goals, you may have some goals of your own, e.g.,

  • settle some open questions that are bugging you
  • reach out to a related field
  • present ideas so that you can cite them in future work
  • provide useful reference material for your own future students
  • make it easy to turn the thesis into a job talk or a book
  • make it easy to turn individual chapters into journal articles
  • establish a particular identity in the research community
  • convince certain senior researchers to read your thesis
  • graduate by a particular date

GOOD LUCK!!! Now, download that LaTeX template, and take the first step toward filling it in today ...


Time Management

A little helpful advice from PhD Comics:


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