Welcome

Welcome to my course on how to write your thesis and publish the contents in the biological sciences. This guide is pitched at postgraduate students, but is applicable to anyone who is writing scientific papers and wants to know more. It is not going to tell you what to write, but to open and examine the black box of scientific writing and publishing, and more broadly explore how this impacts the academic context. My intention is to demystify writing and publishing in the biological sciences, so that you will become aware of what to expect when you prepare to publish your thesis chapters.

Class times and Venue

In person classes will be held:

  • Time: every Friday (from 30th August to 25 October - 9 weeks) sessions 1 (8:30-9:15am) & 2 (9:25-10:10am). The ten minute break between the lectures will be observed. Attending class is compulsory and it is a requirement that you sign the class register every week. Students not attending classes will have a period of 6 days to submit a written explanation.
  • Venue: Room 2507, Gewu Building (Building 2), Chenggong Campus.

Online activities and workshops:

  • All online activities will be posted in this guide. If you have difficulties accessing this site or any of the content, please let me know immediately.
  • Within each online activity there are Exercises listed which are obligatory activities for every student. These must be individual to the student (no groups and no duplicate results).
  • Use of AI. Any students using AI to compose their submitted work will have to repeat the exercise within 24 hours and have 10% deducted for any mark awarded.

Course outline

  1. The philosophy of science – why we need to record what we do; standing on the shoulders of giants; publication
  2. The hypo-deductive model in science – big questions in your field; reviewing the literature; how to write a hypothesis; citing the literature
  3. A formula for thesis writing – introduction; methods; results; discussion
  4. Nuts and bolts of writing – sentences; paragraphs; logical arguments; examples; citation databases
  5. When science goes wrong – publication bias; the evolution of bad science; rewards and retractions
  6. Open Science – transparency; the movement for Open Science; data curation
  7. Time management and Mental Health – structuring your working days; improving your working environment; tracking your mental health
  8. Submitting to a journal and Peer Review – submission framework; writing a rebuttal; how to conduct peer review
  9. Your future in science – scientific living; in and out of academia; networks; careers

Before you start

Many of the exercises in this course will rely on you having an active research project that you are starting or working on. The idea is that you will use skills learned in this course directly on your own project. If you do not have a project, or your project is at such an early stage that you are unfamiliar with the literature, you should ask your advisor now for five papers that will be important for your project (preferably not all by your advisor).

If you don’t get five of your own papers, then you will be using five papers on topics that I choose: i.e. you will be working for me! It will be much better for you if you do the work in this course for yourself.

Text books

Depending on just how early you are in your career, there is a lot missing from this book that has been provided in two other books How to write a PhD in Biological Sciences and How to publish in the Biological Sciences. Those books should be consulted whenever you feel that you want more information - you should also consult articles, papers and other literature that is cited in this guide and those books. Whenever possible, I have put links to chapters in these other books. They have the look and feel of this guide, so watch out and don’t get lost!

The course will be pulled from the two course texts:

How to write a PhD in Biological Sciences: A guide for the uninitiated

This is an Open Access book by John Measey, and published in 2022 by CRC Press, Boca Raton.

You can read this book for free online at http://www.howtowriteaphd.org/, or purchase print or ebook edition from CRC Press.

Please note - How to write a PhD in Biological Sciences is currently being translated into Chinese (completion date will be 31 January 2025). Right now, you can help with this translation by talking to Dr. Measey about your experience as a MSc or PhD student in China. Please make the effort to help with this project so that it can be the best guide possible for you and other future students.

请注意 - 如何写生物科学博士学位 目前正在翻译成中文（完成日期为 2025 年 1 月 31 日）。现在，您可以通过与 Measey 博士讨论您在中国攻读硕士或博士学位的经历来帮助进行翻译。请努力帮助完成这个项目，以便它成为您和其他未来学生的最佳指南。

View open-source code for source text and templates at here

and

How to publish in Biological Sciences: A guide for the uninitiated

This is an Open Access book by John Measey, and is also available in print from CRC Press (2022)

You can read this book for free online at https://howtopublishscience.org/, or purchase print or ebook edition from CRC Press here.

View open-source code for source text and templates at https://github.com/johnmeasey/Thesis-Writing-Guide

You can contribute

This book is written in bookdown (Xie 2016) specifically to make it a ‘live project’ that will be open to anyone who wants to contribute, improve, or use as the basis for their own book. The easiest way for readers to contribute content directly is through a GitHub pull request. At the repository for this book, you will find Rmd files for each chapter, and as a GitHub user, you can simply edit the Rmd file and submit the changes. If I am happy with the changes proposed, I will merge your content with that of the book and add your name to the Acknowledgements.

One of the amazing potentials for bookdown books is that because all the files for this book are hosted in a repository on Github, you have the opportunity to fork this repository and write your own version for a different discipline, a different language or for a different region of the world. It is also my hope that this guide can grow to become a community of practice for those conducting MScs or PhDs in Biological Sciences. It will not be possible to cover every aspect of writing an MSc or PhD in Biological Sciences, but it may be that I have missed out ones that are very important to you. Equally, parts of what is currently written will become obsolete as new initiatives begin, and old problems are resolved. For this reason, this guide needs to be a ‘living document’, and anyone who wants to provide feedback or contribute new sections is more than welcome. Please feel free to open an issue, or make a Pull Request if you spot a typo, or see anything else that you want changed or added. If you aren’t up to that, then you can simply contact me by email.

Acknowledgments

There are a great many people that I need to thank. First and foremost are the members of my lab, past and present, who have inspired me to put together first the blog posts and then the book. It is because you wanted more that I put this together. This book contains lots of links to blogs and articles written and posted freely on the internet by others who also aim to demystify and help. I thank this greater academic community (especially #academicTwitter) for sharing and inspiring.

Disclaimer

Although I have tried to make the information is this course as accurate as possible, it is provided without any warranty. The author has neither liability nor responsibility to any person or entity related to any loss or damages arising from the information contained in this course.

John Measey
Yunnan University Kunming

References

Xie, Yihui. 2016. Bookdown: Authoring Books and Technical Documents with R Markdown. CRC Press.