Category Archives: Writing a thesis

10 stages of the PhD journey: advice from many experts


Designing, executing and writing up a PhD study takes a large chunk of your time and energy. Here is an overview of each stage of the PhD journey, along with links to excellent articles that will help you along the way. Some of the advice offered here may be specific to a discipline, country or university, or may be heavily dependent upon some author’s experience and background. Nevertheless, you are likely to find most of this advice and instruction helpful.

 1. Consider what you hope to achieve by completing a PhD

It is important to seriously consider why you are undertaking a PhD and what you hope to achieve by completing a PhD. Completing a PhD can be extremely useful even for those who may not continue doing research later on.

*   A successful PhD student will be expected to possess key research skills and knowledge as listed here: Researcher graduate qualities for the PhD by the University of Sydney.

2. Write a research proposal 

You might be offered a PhD project where the research proposal is already planned or you might need to devise a research proposal yourself, either before or after you have chosen a supervisor. This proposal and confirmation of candidature will need to be approved by your university’s research committee.

*   What is confirmation? – University of Melbourne

3. Choose a PhD supervisor

Some students have one key supervisor with one or two additional supervisors, while it is not unusual for some students to have three or four. It is important to remember that your supervisor may have many students under their direction, so their time may be strictly limited. At many Australian universities supervisors need to be accredited

*   You and your supervisors by the University of South Australia

4. Design your project budget

An essential project management skill when conducting research is the ability to effectively design and manage research budgets. If you need to request finances through a grant application, ensure you thoroughly investigate the necessary guidelines.

*   Developing a Budget for Your Research Application by Western Sydney University
*   How to make a simple research budget by Jonathan O’Donnell

5. Start writing in the early stages of your project

Don’t wait until you have collected and analysed your data before you start writing. Most universities encourage students to write about their project while they are conducting their research. Project proposals can be rewritten and methods sections developed as data is collected and analysed. Literature reviews can be updated and conference talks and posters can be prepared even before you have started to collect data. 

6. Consider the structure and the format of your thesis

Exactly how to structure and format your thesis will vary greatly depending upon your project, your discipline, your department and your university and your discipline. Always refer to your university’s guidelines for thesis format requirements. For example:

*   Formatting your thesis' by the Edith Cowan University
*   Structuring your thesis by the University of Queensland
*   Thesis Format Guide (PDF) by the University of New South Wales 

How to find completed PhD theses

It is always a good idea to check other PhD theses that are similar to your topic, have been completed recently and have been produced by your university department. You can gain a wealth of ideas about structure, size and overall thesis design.

*   Discover Our Theses Collection by Macquarie University


How to write a literature review

Reviewing the literature is important to assist your knowledge and understanding of your topic and integral to establishing your position in the academic landscape. Writing good literature reviews is crucial to show your examiners how well you know the literature and how well you are able to explain the importance of your project. It is a common requirement that you write a separate chapter as a stand-alone literature review. However, for those theses that are predominantly composed of complete published papers, there might not be a requirement for a separate review section.

7. Get feedback on your writing

In addition to your supervisor, seek feedback on different aspects of your writing from appropriate advisors: accuracy, clarity and brevity. Increasingly, projects are written for a variety of aim to get academic audiences so ensure that your writing is clear and succinct.

*  Getting Feedback – University of North Carolina (USA)

8. Learn how to publish peer-review papers

Increasingly, students are expected to submit a large proportion of their thesis as published papers. Not every PhD project can be easily prepared as separate papers; however, remember to look at recently submitted theses within your discipline and within your department to see how people have completed their thesis.

*   What is a ‘thesis by publication’? by the University of Newcastle

9. Submit your thesis

The process of submitting your thesis may include preparing additional tasks and preparation of paperwork (i.e. the Originality Statement).

*   Prerequisites for Submission by Melbourne University

10. Understand the examination process

Usually there are three examiners. However, the process of thesis examination will vary widely according to discipline and university. Broadly speaking, your examiners will recommend that your thesis be accepted without alteration, accepted with minor alteration, accepted providing major changes are made or rejected. Usually your supervisor will choose who your examiners are and you may have the opportunity to choose one of your examiners.

*   Thesis examination by Victoria University

An oral examination for a PhD is necessary in some Australia universities.
*   Guidelines for the oral defence of the thesis by James Cook University

If there are any problems...

Most problems with your project are surmountable and remember that your supervisors and your university are there to help you. If things go drastically wrong at any time, it is essential that you seek assistance as early as possible. There are people within your university administration who are there to help you. To help dealing with problems, document any issues as they arise. It is essential for you to have excellent time-management and record-keeping skills.

*   Resolving Issues by the University of Melbourne
*   Student Complaints Resolution Procedure by the University of Adelaide

and remember...

*   Be aware of, and develop, sound project management skills including risk management protocols to identify alternative actions in unforeseen circumstances.
*   Keep records and extra copies of everything: for example, data, thesis drafts, email, meeting agendas, fieldwork notes. Ensure you have excellent electronic version control of your documents and extra backups of all your data and work.
*   Ensure you develop and maintain a support network of friends and colleagues who may give important advice and help you deal with any obstacles.
*   Get plenty of exercise, rest and sleep.


© Dr Marina Hurley 2026 www.writingclearscience.com.au

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10 reasons (from ChatGPT) why science writers should not use AI to write their papers


I have written a few blogposts about the problems with using AI for writing. This time I asked ChatGPT to list 10 reasons why science writers should not use AI to write their papers. I thought it would be interesting to see how/if AI criticises itself. The following is verbatim:

My prompt: Can you give me 10 reasons why science writers should not use AI to write their papers?

"Yes. If your audience is scientists, it's important to make nuanced arguments. AI is a useful tool for some tasks, but there are strong reasons not to rely on it to write a research paper. Here are ten reasons you could use in a workshop, article or discussion.

1. AI cannot take responsibility for the research
AI did not conduct the experiments, collect the data or make the scientific decisions. The authors are responsible for every claim in the paper, regardless of who or what drafted the text.

2. AI can invent information
Large language models sometimes generate incorrect facts, citations, statistical interpretations or methodological details that sound convincing. These errors can be difficult to detect, particularly outside the author's area of expertise.

3. AI can weaken scientific thinking
Writing is part of the research process. As scientists write, they clarify their arguments, identify gaps in their reasoning and refine their interpretation of the results. Outsourcing the writing can also outsource some of this thinking.

4. AI often produces generic writing
Scientific papers need to communicate the novelty and significance of the work. AI tends to produce safe, conventional language that can obscure what is genuinely original about the research.

5. The writing may no longer reflect the authors' understanding
A paper should represent what the authors know and can defend. If AI introduces concepts, interpretations or terminology the authors do not fully understand, they may struggle to answer reviewers' questions or explain their conclusions.

6. AI can introduce subtle inaccuracies
Even when the overall text appears correct, AI may change the meaning of a sentence, oversimplify complex ideas or overstate the certainty of findings. These changes can alter the scientific message.

7. Confidential information may be exposed
Depending on the AI system and its settings, uploading unpublished data, grant applications, patient information or confidential manuscripts may conflict with institutional policies, journal requirements or privacy regulations.

8. Journal and institutional policies are still evolving
Many publishers and research organisations have specific guidelines about the disclosure and acceptable use of AI. Using AI inappropriately could create ethical or compliance issues.

9. Scientists need to develop their own writing skills
Clear writing is an essential research skill. It influences publication success, grant applications, collaboration and career progression. Relying heavily on AI may slow the development of these skills, particularly for early-career researchers.

10. Good scientific writing requires judgement
Choosing what to include, what to omit, how to organise evidence and how strongly to interpret results all require expert judgement. AI can imitate these decisions but cannot replace the scientific expertise behind them.

A balanced perspective
Rather than saying scientists should never use AI, a more defensible position is:
- Don't use AI to generate the scientific content, interpretation or conclusions of your paper.
- Do consider using AI for low-risk tasks such as brainstorming titles, checking grammar, suggesting alternative wording, summarising your own notes, or identifying awkward sentences—provided you verify every suggestion and comply with your journal's policies.

This distinction encourages scientists to retain ownership of the intellectual work while using AI as an editing or productivity aid rather than a substitute for scientific writing
."

While I agree that it's ok to use AI for 'low risk tasks', I do not include summarising in this category. Whatever you use AI for, consider it the first author or a co-author if you use it's exact wording or summary points.

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How to write when you don’t feel like it


There are many obstacles that can prevent us from being productive and efficient writers, especially procrastination. Even if there is a looming deadline and we are well aware of what needs to be written, sometimes we simply don’t feel like writing. And if we don’t feel like writing, procrastination can creep in, and we might put off writing until the last minute and then produce something that is substandard or incomplete.

Here are four ways to set you on the path of writing, even when you don’t feel like it.

1. Write intensively for short blocks of time

Set a timer and commit to writing for only 30 minutes. Thirty minutes of writing might seem achievable when you don’t feel like writing. Tell yourself that after the 30 minutes is up, as a reward, you will allow yourself to do whatever you want for one hour. Commit to only write for 30 minutes and make sure that you don’t do anything else during that period: no re-reading what you wrote previously, no stopping to google something, no telephone, no talking. Just write. If you find this too hard, start with ten minutes.

If you are normally a productive writer, 30 minutes might not seem like a long time, yet 30 minutes writing is much better than not writing at all. We can write a lot within short time periods if we don’t allow ourselves to get distracted, especially with other work tasks.

Avoid setting the timer for too long a period. Avoid setting unrealistic goals for yourself as you will feel unproductive and unsatisfied if you don’t meet them.

When you set a timer, try placing it out of reach so you have to get up from your computer to turn it off. After 30 minutes, stand up and walk around, print out what you have written so you have physical evidence of your productivity. You may find that you want to reset the timer for another 30 minutes and keep going. Ultimately, you may find that setting these short writing sessions allows you to break through the barrier of just getting started.

2. Don’t switch between writing tasks during a designated writing session

During your writing sessions, only compete one type of writing. Switching between different writing tasks will sap your energy more quickly than completing one task. If you are getting your thoughts down, just write freely and don’t switch to editing or proofreading halfway through. If you are rewriting a section of your document, don’t switch to writing new material on a related topic. 

3. Take a break from the computer: print your document out and use a pen

We spend a large proportion of our time in front of a computer for all sorts of work activities, especially writing. Periodically take a break from writing on a computer, even if it is for a short time. Try printing out the latest draft of your document and take it to a café or a lounge chair with a pen and a notebook. Edit your draft by hand and use a notebook to write fresh material. You might find that the change in environment allows you to relax yet you can still work on your document.

I always print my document out whenever I complete a draft so that I can see how my writing looks on paper and then plan what writing I will do for the next draft. With a paper printout, I can see my whole document at a glance, without having to scroll through a digital version on a computer screen. Moving to a lounge, or a comfortable environment, gives me a break from staring at a computer screen and sitting on an office chair.

4. Find a friend to write with

Writing is usually a solitary activity but you might it more enjoyable if you organise writing sessions with a friend or colleague. Try taking your laptops to a park or a café and set up 30-minute writing sessions followed by 30 minutes social chat. You could also read and give feedback on each other’s work.

And remember…

Avoid creating unrealistic expectations that create stress and reduce our work satisfaction. It is unrealistic to expect that we can be super-productive writing machines that can write anything, anywhere and at any time. Aim to write in intensive pre-organised, short blocks of time in an environment that is as comfortable and distraction-free as possible.

© Dr Marina Hurley 2026 www.writingclearscience.com.au

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6 steps to drafting a grant application


Applying for grants is a time-consuming process. Deadlines can loom suddenly, leading to stress and long days. Success rates can be low, meaning that considerable effort is often not rewarded. 

At the outset, you need to form a realistic timeline to work on the grant application. In addition to identifying your funding source, researching the specific requirements of the grant application and formulating your project budget, you will need to start planning your written proposal. Careful planning and early feedback from your colleagues will maximise your chances of a successful outcome. 

In addition to the detailed advice you will receive from your grant body, following the 6 steps outlined in this article will help you develop the core content of your application. 

Step 1: Identify your audience

Will the grant be reviewed by specialists in your field and will the panel include non-specialists or lay people? In reality, you may have two types of audience:

- Non-specialist or non-scientific reviewers who will require background information to judge whether your project is worthwhile.

- Specialist reviewers within your discipline that will be more familiar with your research.

Depending upon the funding organisation, some of your reviewers may not be familiar with the terminology or the current research problems of your discipline or immediately appreciate why your project is so important. Therefore, it is imperative to make sure your proposal outlines the relevancy of your topic to current issues and that it is clear and concise.

Step 2: Summarise the key research problems overarching your project

Before you can think about convincing people how good your project is, you need to build a picture about the current problems facing your research community.

Successful grant applications clearly define the area of need and how it is relevant to your potential funding source. In addition to outlining the scientific importance of your project, describe how your work might affect society, the environment and the economy. For example, if you are researching a disease, highlight the burden associated with that disease. Outline how many people it affects and the costs to society.

Step 3: Summarise the key problem your project will solve

This is where you focus on the key problem your project will attempt to solve. Clearly articulate what specific problem needs to be investigated and why. Avoid promising to solve too many problems or problems that are too large in scope, otherwise your project will seem unrealistic and unachievable. Describe how the key problem is connected to the broader scope of the research problems outlined in Step 2. Once you have outlined your research problem, then you can clearly state what you aim to achieve (step 4).

Avoid writing vague or generalised statements, for example: “To date, little research has been conducted in this area.” To help you keep your application short, also avoid obvious statements, for example: “This topic was investigated through an extensive search of the literature.”

Step 4: Articulate your aim, hypotheses and outcomes

While directly referring to your key research problem, outline what you aim to achieve, including your hypotheses and what outcomes you can expect from your completed project.

Once the overall aim is stated, the project should be broken down into sub-aims, each with a defined outcome. This approach helps you to define realistic timelines, ensures that the project description is concise and will improve the likelihood that the grant will be successful.

Step 5: Summarise how you will do the work (methods)

A major factor in grant success is being able to convince the reviewers that the project is feasible and important and that the work is likely to be completed within the proposed timeframe. Clearly outline what methods you will use and what experience you have in this area. If you need to develop new methods, clearly explain what is required and provide evidence of your ability to develop other methods in the past.

Outline the scope of the project. How long it will take to complete each component? Is the size of your project feasible within the set time frame? Do you have access to suitable equipment and operational facilities?  Promote yourself. Provide evidence (such as previous publications or unpublished data) to demonstrate that you are capable of successfully completing the project.

6. Seek feedback from colleagues

Give your draft proposal to your colleagues for feedback. They may provide valuable feedback on what is feasible, which aspects are the most interesting and what might be missing.

This early feedback will help you focus on what you want to achieve, why it is important and how likely the project is to succeed. It can be helpful to talk to people who have already received funding from a particular source; what feedback did they receive and what aspects did they think helped them to secure funding? If appropriate, it might also be helpful to seek feedback from colleagues who have recently been unsuccessful in winning a grant from the same funding body.

What to do next?

- After receiving feedback from your colleagues, rework the application so that it is clear, compelling, concise and flows well.

- Finalise your budget and ensure all aspects of your project are justified.

- Seek at least two more rounds of feedback from your peers as you proceed through the writing and submission process. Grants that are peer-reviewed prior to submission are more likely to be successful.

- Pay close attention to the small details in the submission process. You don’t want to have your grant rejected on a technicality or an unchecked box on a submission form.

© Marina Hurley 2026  www.writingclearscience.com.au

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When to cite and when not to

What information should be cited? Where do I place the citation in a sentence? These two questions are commonly asked during my writing workshops and online courses. Other problems I regularly see are too many citations to support a piece of information or statements of fact that should be supported by a citation. This blogpost reviews the basic concepts of citation and discusses the importance of always citing your sources.

What is a citation?

Authors of scientific documents use citation to indicate when information comes from another source: who wrote (or produced) the information being discussed and when it was published.

The standard method of citation is to insert in-text citations directly before, or after, the information that is attributed to another source or author. These citations are then listed at the end of the document, within either a bibliography or reference list. A reference list includes only the references that are cited, whereas a bibliography is both a list of the references cited and additional references used when researching and writing the document.

There are many different referencing styles, including the APA style which is commonly used in science publications. The Author – Date in-text citation is where the authors surnames and dates of publication are written within brackets at the end of a sentence or phrase. For example. “Aquatic air breathers periodically break the water surface to gulp air but never leave water (Gonzales et al. 2006).” (Magellan 2016, p 452)

If there is more than one citation for a particular statement, the citations are separated by semicolons. For example: “The conflicting requirements for aquatic and terrestrial life are perhaps most pronounced in air-breathing fishes (Sayer & Davenport 1991; Graham 1997; Sayer 2005).” (Magellan 2016, p 452). This example also demonstrates the convention of ordering citations from earliest year published (1991) to latest year published (2005). If two publications were cited from the same year, then the order of citation would be in alphabetical order of the first author (Sinclair & Ryan 2019; Smith 2019).


Where should in-text citation be placed?

I am often asked whether to place the citation at the end of the sentence, in brackets, or at the beginning where it forms part of the sentence.

Often the citation is made after a statement of fact. If there are three statements within a sentence, there will be three separate citations lists within that sentence; An example from Magellan (2016, p 452), “Amphibious animals are adapted for both aquatic and terrestrial habitats and divide their lives periodically (e.g. Yeomans 1995; Dall’Antonia & Sinsch 2001) or ontogenetically (e.g. Martin et al. 2004; Blob et al. 2007) between water and land (Sayer & Davenport 1991; Sayer 2005).”

Alternatively, the authors of a publication can appear in the beginning of a sentence when they are is used as the subject of the sentence, while the date of publication is written in brackets. In this case, the previous citation example of Gonzales et al. 2006 by Magellan 2016 could be rewritten as ‘Gonzales et al. (2006) found that aquatic air breathers periodically break the water surface to gulp air but never leave water’. However, this type of citation increases the length of the sentence as the verb phrase ‘found that’ needs to be added.

As a general guide, if you use the findings of a study to develop your reasoning, it is easiest and more concise to place the citation at the end of the sentence. That way you can easily list more than one study as a list of citations in brackets, as in the example above. However, if you are discussing a particular study over more than one sentence, it is easier for the reader if you first introduce the authors as the subject of the sentence.
Irrespective of where the citation is placed, hyperlinking can used with electronic publications to link a quote or citation directly to the document being cited, as with the Fensham et. al (2017) paper cited below.

Ideas, quotes and paraphrasing should be cited

You must include a citation if you quote, paraphrase or summarise someone else’s information or ideas. Quoting is writing the exact words used by another author and enclosing the text in double quotation marks; for example: Fensham et. al (2017) concluded that “The findings of the current study support the importance of rainfall variability as the major influence on the demography of E. melanophloia, the dominant tree in a semi-arid savanna” (p. 780). The page number where the quotation appeared should always be included.

Paraphrasing is rewriting someone else’s writing using your own choice of words; for example, I would both summarise and paraphrase this previous quote as, ‘Fensham et. al (2017) concluded that rainfall variability is the major factor influencing the demography of E. Melanophloia.’ or ‘The demography of E. melanophloia is most strongly influenced by rainfall variability.’ (Fensham et. al 2017).

When using quotation marks, whether you use single or double quotation marks, be sure that you are consistent. Note that I used single quotes here to distinguish my wording and double quotes for the direct quotation.

Why do we cite?

The main reasons we cite is to clearly distinguish our work from others and so the source of information can be located and verified. Citation also honours the work or intellectual property of the author. Researchers most often cite other studies when developing their reasoning for their own studies, when comparing their work with other researchers and to indicate when authors reach similar or dissimilar conclusions. In this way, the citation process maintains and further develops the scientific discourse and shows how authors place their work within the published scientific literature.

What information can be cited?

It is a good idea to only cite information that has been published or made publicly available. Be cautious about referencing information from documents that are not publicly available or have not been peer-reviewed.

Unpublished research is referred to as grey literature. Grey literature is defined as “…research that has not been published commercially and is therefore not necessarily searchable via the standard databases and search engines. Much grey literature is of high quality and can be an excellent source of up to date research in certain subject areas. Examples of grey literature: government reports, conference proceedings, theses / dissertations, research reports, maps, policy statements, clinical trials, technical standards, interviews and newsletters” (UNSW Library).

If it is necessary to cite unpublished information, the integrity of this information may be questioned if no other sources are provided. Be cautious about generating conclusions or inferences solely on the basis of unpublished information or uncitable 'facts'.

How to cite different types of publications

Most Australian university library websites will list guides to different referencing styles; for example, Queensland University and Victoria University have in-depth guides on different referencing styles and how to cite and reference different types of publications. Also refer to Colin Neville’s book, The Complete Guide to Referencing and Avoiding Plagiarism (2016) for an in-depth guide on how to reference and cite a wide range of published material including books, papers, newspaper articles and audio-visual material.

What doesn’t need to be cited     

Information that is commonly known to be true is not cited. Common knowledge is information that is widely accepted as being true and does not need to be cited. However, what is common knowledge depends upon the knowledge of the audience: what is commonly known to some groups of people would not necessarily be commonly known by another group of people.

As readers, we trust that the author’s knowledge of what is commonly known, is true. For example, the quote from Fensham (see above) included an unreferenced statement that E. melanophloia is a dominant tree in a semi-arid savanna (Fensham et al. 2017, p. 780). I assume that this statement is common knowledge as it was uncited. Another example is that it is common knowledge to entomologists that (most) beetles have only one pair of flying wings, with the second pair of wings evolved to form protective covers to the flying wings. This fact would not need to be cited in entomology publications, not only because it is commonly known, but because it is easy enough to find out.

Avoid inadvertent plagiarism

Remember that unreferenced statements might be considered plagiarism. If you continually make unreferenced statements, you can mislead the reader into thinking that your un-cited information is either common knowledge or that you generated this information yourself.

Publications cited
- Magellan, K. (2016) Amphibious adaptations in a newly recognized amphibious fish: Terrestrial locomotion and the influences of body size and temperature. Austral Ecology 41,452-460
- Fensham, R. J., Freeman, M. E., Laffineur, B., Macdermott, H., Prior, L. D., & Werner, P. A. (2017). Variable rainfall has a greater effect than fire on the demography of the dominant tree in a semi-arid Eucalyptus savanna. Austral Ecology, 42(7), 772– 782
- Gonzales T. T., Katoh M. & Ishimatsu A. (2006) Air breathing of aquatic burrow-dwelling eel goby, Odontamblyopus lacepedii (Gobiidae: Amblyopinae). J. Exp. Biol. 209, 1085–92.

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