PhD Comprehensive Exam Guidelines
Overview
The PhD Comprehensive Exam (PARA 701) evaluates the candidates' suitability to continue in the Parasitology PhD program. The examination consists of two parts: a Proposal Document and an Oral Exam. Both must be submitted before the end of PhD 3 with the proposal document submitted 6 weeks before the end of PhD3. Students with an MSc, typically enter as PhD 2, which means the proposal must be submitted before the end of the second year. Students who enter as PhD 1 must complete the Exam during their third year.
Proposal Document
Overview
The Proposal Document must be submitted at least six weeks prior to the date of the Oral Exam. The document will be examined by at least three members of the advisory committee plus one examiner who may be from outside Parasitology who holds a PhD and has no involvement with the student or their project. Each examiner will provide a grade for the written document and the average will contribute 40% to the final grade for the Exam.
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The Proposal Document must convince the examiners that the student is sufficiently aware of the background and basis for the proposed work, that they understand the concepts of scientific enquiry, that they can formulate an appropriate hypothesis and objectives that will lead to specific tests of this hypothesis, that they understand the methodology required to achieve these objectives, and that they have made sufficient progress in their first two years of research. One essential skill required at the PhD level is critical decision making and there is a 30 page limit for the Proposal document that will require judgement of what is relevant and what is not. The document should be a coherent body of work that makes a clear and convincing argument that the student has the skills required to continue in the PhD program. Pages devoted to each section are for guidance rather than strict limits.
- The document should be prepared in a 12pt font that is easy to read.听
- Margins should be at least 2cm on all sides
- Text should be 1.5 spacing
- No more than 30 pages for the body of the document
Title (one sentence)
The title should be concise and informative, indicating the main subject of the proposed research
Contents (1 page, not included in the page limit)听
List of the major sections of the document as well as figures and tables and the pages where they are found.
Abbreviations (not included in the page limit)
List any abbreviations used frequently in the document. Abbreviations listed here should be written in full the first time they are used, followed by the abbreviation in brackets.
Abstract (1 page)
The abstract should be a single stand-alone paragraph that covers all key elements of a research plan including background, the hypothesis and objectives for the work, expected outcomes and a statement of the relevance of the research in a wider context.
Background (9 pages)
In this main section of the Proposal you should lay a foundation for the proposed research and provide a coherent narrative that is logical to follow. You should assume that the examiners are familiar with the general research area and common techniques used in your particular field. You should set out current knowledge, highlighting particular problems or barriers that you will be addressing through your objectives. You need not discuss general information about your particular model system, such as the life cycle of the parasite, the numbers of people infected, the global impact of the parasite unless it is specifically relevant to the objectives you set out to achieve. You will be expected to know this kind of information for the Oral Exam but it need not be in the Proposal document.
There should be a coherent story explaining how you arrived at your hypothesis and why your specific objectives are necessary. Decide, before you start writing, what this story should be and maintain your focus on it throughout the writing process.
You should provide sufficient details of the backstory for your project to justify why your proposed research is important and relevant to the broader field. Space is limited. Only include things that are directly relevant to your proposed research. If something is not needed to justify and understand your project, do not included it. Part of the assessment of your Proposal will be based on how well you judge what to include and what to exclude. Include sufficient details needed for an examiner who is not an expert in the field, but a knowledgeable researcher, to understand what you propose to do. While the Proposal document should be concise, you will be expected to answer questions that lie outside the contents of your Proposal in the oral exa.
Do not simply combine relevant sections in any order. Follow the story you are trying to tell. In the last paragraph of each section, provide a logical link with the following section and why it is relevant so that the text becomes a single coherent story.
Hypothesis and Specific Aims (1 page)
State the hypothesis and your rationale for this hypothesis. List the objectives, describing each in three to four sentences.听
The Scientific Method is based on a foundation of setting up hypotheses that can be tested. The hypothesis should be based on previous research and a statement of something that you believe might be true that is still uncertain. This hypothesis should then lead to specific predictions that can be tested to either confirm or refute the hypothesis. Your objectives should be specific tests of your hypothesis. Your objectives should be ideas and concepts, they should not be the application of a specific method. Avoid objectives that are simply statements of something you will do. Specific details of how you will achieve those objectives will come in the next section.
Research Strategy, Implementation and Methods (8 pages)
This section should explain how you will combine the different methods you propose to use to achieve your objectives. Explain how the different techniques will achieve steps towards your overall goals. Show that you are aware of variability within your experiments, how you decide what controls will be used and explain how you will determine reliability of the results. You need to present sufficient details of each method to convince the examiners what you propose is feasible and that you are familiar with the techniques, that you know the time and effort involved and which aspects of the different techniques are critical and what the major pitfalls are. Too many trivial details will suggest a lack of understanding, show that you can see what is relevant and what is not.
Troubleshooting (3 pages)
Something always goes wrong. In fact, you could argue that most of the time and effort spent doing scientific research is to make sure things don't go wrong.
Explain what the biggest challenges will be to achieving your objectives. Convince the examiners that you are aware of the problems and that you have a strategy in mind for how you will overcome those problems. Do you have a back up plan or an alternative strategy if your first idea proves impossible?
Perhaps the most fundamental building blocks of the Scientific Method are controls. In order to be certain that you know the cause of a particular effect, you must establish what to expect in the absence of a particular treatment. You must also establish that the system you plan to use does produce the results you expect. You must also establish the reliability of, and expected range of observations produced by a particular system. Only when you have these can you make an informed interpretation of your particular investigations. Many times, most of the things you do will not test any specific idea but lay a solid foundation that a test is not influenced by something unknown, outside your control. You should demonstrate in this section that you know what scientific controls are and how to use them. You should also demonstrate that you understand the concept of experimental variability, what can cause this variability and that you have strategies in place to take this into account.
Results (4 pages)
To convince the examiners that you will be successful in the PhD program, you must provide preliminary data and demonstrate that you are able to carry out research successfully. To do this, you must show that you have, in fact, completed some part of your proposed work by the time of the Exam. You should present the outcome of experiments that you have completed and how these relate to your objectives. Explain what these results mean and their significance. Be concise, use tables and figures to present the information efficiently.
Significance (1 page)
In this section summarize how these results go towards achieving your specific objectives? How will others in the field be affected once you have achieved your objectives at the end of your PhD? What types of research could be done when your project is finished that is not possible when you started?
Research Plan (3 pages)听
You should aim to complete a majority of your PhD work by the end of PhD 5, that means four years of focused work. By the time you take the Comprehensive Exam, you are almost half way there. The first two years include coursework and preparing for the Comprehensive Exam. After this, you can focus full time on your research. You should present a timeline for your research, explaining what you plan to do. Be realistic and include aspects of troubleshooting and data analysis that will be required. You may wish to present your timeline in the form of a .
One essential requirement to graduate with a PhD is that you demonstrate original thinking. During your final PhD defence, at the end of your degree, you should be able to explain an aspect of your research that you developed beyond what was laid out at the beginning, showing your originality. In this section of the Proposal, you can speculate on areas of your research where you might be able to demonstrate these aspects. Is there a specific area that could be developed in more depth, expanded in a different direction during your research?
Figures and Tables (included in the page limit)听
Figures and Tables should be embedded in the text of the Proposall close to the first time the text references the Figure or Table. They should be numbered sequentially. Each should have a concise legend that explains what the Figure or Table contains and what it shows. They do count towards the overall limit of 30 pages.
References (not included in the page limit): The source of any supporting evidence, or ideas taken from elsewhere must be cited in the text. You should use a citation format that uses all the author names, not simply numbers in brackets or superscript. The bibliography at the end provides the full details of each citation and is not included in the Proposal page limit. You can obtain the citation management software, Endnote for free through 不良研究所.
General Comments
Avoid sentences that are vague and do not mean anything specific, such as "this work will greatly advance the field of drug discovery in this parasite". Be specific, say something like "Detailed knowledge of protein interactions for this activator means that a drug screen based on the concept of targeted interface disruption could be developed, something that is currently impossible".听
Be practical. If you argue that your research will lead to improved drugs, explain exactly how. Be prepared to answer questions during the Oral Exam on specific details of what the drug development process looks like from initial concept to the final clinical trials. Explain how your research will benefit any one specific aspect of that process. If you make any vague, general claims in the Proposal you will be asked questions in the Oral Exam on specific details. In the Proposal Document, explain exactly what you mean, be precise about what is possible and what is not.
Develop a single unifying story that runs through your Proposal, something it will be easy for the examiners to remember that captures the entire concept. When editing the proposal document, ask yourself for each paragraph, does this contribute to my unifying theme, if it doesn't, ask yourself why you included it. Consider removing it entirely. Be convinced that every sentence you include in the Proposal contributes something that is required for understanding the research you propose to do. If it isn't, remove it. If it now doesn't make sense, rewrite the sentence more clearly.
Scientific writing should be as clear as possible. Do not try to build suspense by hiding part of the story to be revealed later. By the end of the Background and Significance section, the examiner should already have your objectives as obvious questions that need to be asked. That means that when reading the objectives section, the examiner is thinking "of course", not "why are they doing that?".听
Make sure you describe methods in the methods section. Do not explain a method in the results section because you forgot to do it there. Put the results in the results section but save a discussion of what the results mean and why for the Significance section.
Oral Exam
The Proposal Document must receive a passing grade before the candidate can proceed with the Oral Exam.听
The Oral Exam follows a similar format to a PhD Defence and contributes 60% to the final grade.听
- At the beginning, the student will be asked to step outside the room while the examining committee discusses anything arising from the document and decides on the order in which the examiners will answer questions.
- The student will be invited back into the examination and will make a 20 minute presentation.听
- Following the presentation, there are typically two rounds of questions. Ten minutes for each examiner in the first round followed by a second round of five minutes.
- The student will be asked to step outside while the examining committee arrive at a final grade for the oral exam
- The student will be invited back to hear the grade and sign the report form
General Comments
You should assume that all examiners have read the Proposal Document and so are knowledgeable in your research area. Critical thinking is an essential, required skill, and you should demonstrate this by deciding on an appropriate level for your presentation, what to include and what not to include. The presentation should refresh the examiners on the content of your Proposal. You should not explain things as though they are being heard for the first time. Only present material that is relevant. If you show the life cycle of your parasite, explain why you need to know that in order to carry out your proposed objectives successfully. Justify why you have chosen your hypothesis, your objectives and the strategy you will use to achieve your objectives. Highlight any area you believe could be expanded to demonstrate an original contribution.
The goal of the question period is to judge if you have sufficient background knowledge in your discipline, if you understand what will be realistically required to achieve your objectives, if you have made sufficient progress with your research and if you understand how to approach a scientific question. You should be prepared to answer questions beyond the content of your Proposal Document and demonstrate a general knowledge of the proposed research area. The examiners will try to find the limits of your knowledge. For this reason, the questions may quickly focus on aspects you have the most difficulty with. This is normal and is not a sign that there is a problem. If you are asked a question where you do not know the answer, use this as an opportunity to show how you think. What do you know that could contribute towards an answer? How would this question impact your research if you never find an answer? What would you need to do to find an answer?
Failure Policy
Students who do not submit a Proposal document before the end of PhD 3 will be awarded a failing grade and will have an additional 6 months to submit their Proposal document.听
If the Proposal document is not passed by any one of the examiners, the student will not proceed to the Oral Exam. The student must receive a clear explanation of why the document has failed and what is required to achieve a passing grade. This will constitute a first failure and a grade of HH will be entered until the student resubmits their Proposal. The student then has 6 months from that date to submit a revised Proposal Document for evaluation. If the document is now acceptable, the student may then proceed to the Oral Exam.
If any examiner evaluates the Oral Exam as not passed, this will be considered a failure. If this is the first failure, a grade of HH will be entered, the student will receive a written explanation of why a failing grade was awarded and what must be done to achieve a passing grade. A second Oral Exam will be scheduled six months from the date of the first failure.
Failure of the Proposal Document twice, failure of the first Proposal Document and failure of the Oral Exam, or two failures of the Oral Exam听will result in a failure of the Comprehensive exam and the student will be required to Withdraw from the University.
