This book is about the overview of the article-based thesis. It is written for graduate students mainly in the “hard” sciences, such as biology, medicine, and technology. The best time to read this book would be when you are finishing your individual papers.

However, you must find out at an early stage whether your university allows you to use the article-based format. If not, you have to write a traditional monograph thesis. Then, the contents of this book would be helpful to you as well. Listed below are those parts that are also valid for the traditional monograph.

1. Front cover picture

2. Title

3. Abstract

4. Quotations

5. Abbreviations

6. Acknowledgment

7. General introduction

8. Aims

9. General discussion

10. Copyright

To a certain extent, the content of the methods and results sections could also prove beneficial.

This chapter is not included in the thesis of the sandwich format, but it contains tips on how to make illustrations and to write figure legends which can be useful when you write papers in the future.

Begin by referring specialist readers to the individual papers (Tapio Kurki, 1992).

Then, in the overview, try to synthesize data from more than one paper. For example, one overview presented the results of all four individual papers in one single page; we can call it Results at a glance (Carin Staland Nyman, 2008). Another one summarized the findings of Papers III and IV in one illustrative drawing (Daniel Bexell, 2008). After such summaries, only the main points need to be highlighted. This approach may be better than a tedious repetition of the results paper by paper.

Data from the studies are often assembled in figures made especially for the overview and have thus passed no editorial scrutiny. Some representative figures will be scrutinized here. If the figure has a message, and most figures do, the message should be conveyed in the legend.

You open your general discussion in either of two manners: (a) by answering the questions or suggestions put forward in the aims, or (b) by discussing the methodology – the latter because one of the goals of a thesis is to learn how to use scientific methods and to get to know their limitations, not primarily to make discoveries.

Which of these you choose depends on the purpose, the direction, and the results of your research. We begin with the first alternative.

General discussion

Discussion of the results

Open this section by explaining how you achieved your aims. In one thesis (Anders Bergström, 1994), two of the aims were to determine:

• a technique for subretinal transplantation of retinal cells

• the survival … of donor cells

… and the discussion of the results began with subheadings for each aim:

1. Transplantation procedure

2. The subretinal transplantation technique that we have developed has turned out to be easy and [has given] good and consistent results.

1. Transplant cell survival

2. The survival rate was …

What makes the writing of these sentences especially good is that the author used almost exactly the same wording as in the sentences describing the aims. Here is no place for synonyms. The readers must know for certain what you mean. Remember that more than half the scientists worldwide have English as a second language, and such readers may become uncertain if you use synonyms.

If papers included in your thesis have several authors, you must indicate which portions of the papers are your own work and which are the work of your co-workers. Some universities require that all authors sign a statement of their contribution. In other universities, especially in Scandinavia, the candidates themselves write a contribution list stating what each person did, as described in the following.

Every research project is divided into four main parts: designing the project, collecting the material, analyzing the results, and writing the paper. Because writing the paper is a major intellectual part of the research work, it is what counts most in the eyes of the examiner at the oral defense of a thesis.

Some graduate students have not written all the individual papers on their own – or, even worse, written none of them. They may indicate their contribution to the writing in different ways. Consider this:

1. I. The author … wrote most of the manuscript.

2. II. The author … wrote a major part of the manuscript.

3. III. The author … assisted in writing the manuscript.

4. IV. The author wrote a significant part of the manuscript.

5. V. The author … wrote a substantial part of the manuscript. [Emphasis added.]

This appendix is written for those universities that do not yet allow article-based theses but are contemplating introducing them. If you decide on this alternative format, the discussion below may give you hints on what to add to the doctoral guidelines of your university.

Article-based theses vs. traditional monographs

In the article-based thesis, the accepted papers have “been scrutinized by international peer review, probably more prestigious than local committees” (Carlino, 2006). The article-based thesis gives students the opportunity to begin publishing early in their academic careers. One candidate put it this way: “You can graduate with a degree and a publication record. This is a wonderful kick-start to an academic career” (Kumpulainen, 2008). After all, one goal of a university is to produce scientific papers publishable in refereed journals.

After graduating with a traditional monograph, the graduates can be stricken with “Post-Dissertation Burnout,” meaning that few journal publications will eventually grow out of their thesis. Important research findings may therefore languish on the shelves of libraries. That does not happen after graduation with an article-based thesis, because most or all of its papers are already published, are in press, or have been submitted. Candidates who publish throughout their candidacy receive ongoing peer review, improving their writing skills.

Thesis at a glance first appeared in a thesis by Elke Theander in 2005, at Lund University (Figure 7.3). Although this section has become popular in the local region, it has not yet – in 2011 – been recognized at other universities.

A Thesis at a glance could be described as an abstract of the abstracts and is extremely helpful to the reader. However, avoid including drawings, graphs, or tables in the one-page variant. They will be reduced too much to be readable (Figure 7.1). If you really need illustrations, you may want to use two pages, where pictures and tables can be made large enough to be legible (Figure 7.3). In the two-page variant, the pages should face each other, to allow readers to see the content at a glance.

No instructions for writing a Thesis at a glance exist. Its layout depends on the subject and the results obtained. On the following pages you will find four examples of Thesis at a glance. They are illustrative with respect to the layout.

List of publications is intended to cover both published manuscripts (articles) and unpublished ones (papers).

Normally, you do not have the copyright to your own publications and must seek permission from the publishers to reproduce them. As some publishers are probably unaware of compilations, you have to inform them. The following example is fictitious.

1. To the Publisher:

2. I am preparing my doctoral (PhD) thesis, which is intended to be a compilation of an overall summary (overview) and research papers – bound together.

3. I would greatly appreciate your permission to include:

4. Andersson A, Pettersson, P. Smoking as a risk factor for cancer of the lungs. Journal of Significant Results, 2011;12:34–56.

5. I would also like your permission to use Figure 1 from this article in my overview of the thesis.

6. Yours sincerely,

The reference figures (2011;12:34–56) may be changed to in press, as appropriate. If the publisher has no electronic form to fill out, you may send the letter directly to the permissions department of the publisher; you will find the email address on the journal’s homepage. If the publisher has its own permissions form (most publishers have), you may use it, of course. However, you are advised to paste the above permission letter into the appropriate box – so that all details are included, for example, the permission to use Figure 1.

Quotations from famous individuals such as Socrates, Leonardo da Vinci and Charles Darwin occasionally appear on one of the opening pages before the text itself. However, what these people said seems to have less to do with the content of the thesis than to express more general views of research work, like the following popular one:

I have only found one citation that illustrated the essence of the actual findings, formulated by the graduate student himself (Adad Baranto, 2005).

Try to avoid citing someone, unless the quotation is exactly to the point with respect to your subject.

I will show you a dissertation with a layout that may be worth considering. Some aspects of the presentation are in line with those emphasized in this book. That is a dissertation (by Christopher James Clark, published 2009) at the University of California, Berkeley. Excerpts are presented on the following pages, with comments.

At the time the dissertation was filed, that is, submitted to the Graduate Division at Berkeley, two chapters were published as articles, the third was in revision by the author, and the fourth had been submitted for publication.

Sorry to say, the author was not allowed to orally defend his dissertation, because Berkeley seems to be unique in having no dissertation defense. Actually, for papers still in manuscript, an author could benefit from feedback during a defense process when making the final revisions of the articles before submission for publication.

This chapter is a review of the article-based thesis, also called compilation thesis. The compilation is increasingly encouraged, especially in the hard sciences such as biology, medicine, and technology.

Compilations

Compilations are of two types. In one, the reprinted articles are appended to an overall summary of their content, here called the Scandinavian model. In the other, the reprinted articles are sandwiched between introductory and concluding chapters, here called the sandwich format.

Scandinavian model

Common to theses of the Scandinavian model is that an overall summary (overview) is followed by research papers – bound together in a single volume. Published articles are reproduced as exact copies of the articles as they appear in the publishing journal (including title pages with original letterheads, logotypes, typefaces, and so on) – in short, as reprints; papers in press are reproduced as preprints.

In contrast with the research papers, which are highly structured, the overview of the Scandinavian type of compilation has no formula for arranging its various parts, not even regarding which parts to include.

Preface

Before writing this book, I looked into a couple of thousand theses based on published (and ready-for-publication) papers. Most of them I viewed on the Internet, but several I surveyed while on location in various university libraries. Merely seeing an image of a thesis on the Internet is not the same as having a paper version in your hands; to smell and feel the paper – I love it!

Although the examples shown are real (if not otherwise stated), bad ones are given without revealing the source. When I wanted to include a figure, I sought permission from the author. If the example was bad, the author was informed of the changes suggested and of the form the credit line would take, for example: Reproduced from a thesis published in 2008, with permission. All the authors asked gave me permission. I am grateful for your generosity, which has provided the readers with authentic examples from which to learn. Thank you!

This book is about the overall summary of a thesis (also called the overview). It is thus not about the research papers which were dealt with in my book How to Write and Illustrate a Scientific Paper (2nd edition, Cambridge University Press, 2008). Such research papers authored by the degree candidate have passed editorial scrutiny; the overview has not. As a former editor of a scientific journal, I had the experience of giving this overview a closer look.

In the thesis overview, abbreviations are often defined in a list (headed: “Abbreviations used”) and also in the text when they first occur. Nevertheless, you should redefine them in the aims section.

Abbreviations in the aims section

In the aims section readers are often bombarded with undefined forms of abbreviations. Redefine them, as in this example (Raimo A. Lahti, 2005).

The cumbersome abbreviation

Try to replace a long and cumbersome abbreviation with a reader-friendly substitute. In one thesis the subject was hereditary nonpolyposis colorectal cancer. The accepted abbreviation, HNPCC, was used frequently throughout the thesis. However, the list of abbreviations tells us that Lynche syndrome is synonymous with HNPCC. So, as a non-specialist, I suggested in my course on scientific writing that the abbreviation could have been replaced with Lynche syndrome; alternatively with the/this syndrome. How much easier the text would have been to read with such a substitute.

However, in my May 2011 course, one participant (apparently an HNPCC expert) said that Lynche syndrome is no longer in use. So, to correct myself, instead of the words for this syndrome, you can use, for example, this type of cancer or the cancer form studied or just the/this cancer.

Also called Background or just Introductory chapter. Some universities use an Introduction followed by a Review of the Literature. Consult the guidelines of your university to see what they recommend.

The general introduction is often far too long; occasionally up to 100 printed pages. About 10 printed pages may be sufficient. Brevity is a basic rule of scientific writing. Therefore, your general introduction should not include all papers that touched on your subject, but only those that could contribute to solving your problem. Try to avoid the usual platitudes in the opening sentences.

Openings

Avoid platitudes:

This could open any introduction, whatever the subject. Could you guess what it comes from? The answer is the Institute of Analytical Chemistry.

… and avoid general statements: