How to write a PhD thesis your committee will NOT approve

Sometimes it takes 7 years to get back to square one…

Jesse was a bright and ambitious student in a Biochemistry PhD program. She was always ready to learn new techniques, and she diversified her skill set by working in the animal facility, cell culture room, and also in a mass spectrometry lab.

Her supervisor picked up on Jesse’s talents, and he frequently assigned younger students to shadow her, and he also volunteered her to work with collaborators on joint projects.

As the years went on, Jesse was spread thin between her own PhD thesis project, mentoring, and collaborations.  Jesse tried to reduce her load by asking her advisor to take her off collaborations. However, several projects were in advanced stages already and Jesse’s expertise was indispensable to the completion of the projects.

Jesse spent a good portion of her days mentoring younger students and walking across campus to her collaborators’ labs, and her PhD thesis writing was not coming together.

Over the course of 7 years Jesse had collected a lot of data, but most of the projects were dead-end or too small for a publication. As a 7th year student, Jesse had only one publication, and she was only 2nd author on it. Nevertheless, Jesse scheduled what she hoped to be her final committee meeting.

Her presentation was a “hodgepodge” of all the different projects she worked on. The projects were related, but there wasn’t a cohesive story that pulled all her data together.

write-a-phd-thesis-simply

After 7 years of working 60-80 hour weeks, mentoring younger students, and being a key person on collaborations, Jesse’s committee denied her proposal for a PhD thesis defense. “I am back to square one” – she declared walking out of her committee meeting, feeling more defeated than ever before in her lifetime. Should she quit, after devoting 25% of her life to her doctoral program?

Fortunately, Jesse’s story has a happy ending, but she had to take a different approach than what she had been used to. Given her diverse skill set, companies started to approach her with employment opportunities but she could not start interviewing until she had a defense date scheduled.

Motivated by the companies that were trying to hire her, Jesse became laser-focused on how to write a PhD thesis. She had several heated meetings with her supervisor to get off collaborations that were not supporting her thesis, and she also asked for clarification on what she had to do in order to be allowed to defend.

Over the next few months, Jesse collected enough data to complete and defend her PhD thesis, which allowed her to interview for jobs and get an offer.

What is the lesson from Jesse’s story? She thought she was doing all the right things for seven years (working long hours and pleasing her supervisor, collaborators and group members), yet her committee did not approve her PhD thesis, until she started doing things differently.

Without realizing it, Jesse (like many other graduate students) was practically following portions of a recipe to write a PhD thesis that a committee would NOT approve. Perhaps you will recognize some of these patterns in your own workflow.

Recipe to write a PhD thesis your committee will NOT approve

(Anti-dotes included)

1. Do what you think your advisor and PhD thesis committee wants you to do, and avoid conflict at all cost

Miscommunication is the #1 reason for unpleasant surprises at committee meetings. Many students think they know what they need to do to graduate. They put a lot of work into collecting and analyzing data without communicating frequently enough with their supervisor to see whether they are on the right track.

The frequency of meetings with your supervisor depends on his or her management style (hands-off vs. hands-on). In either event you need to make sure that you have sufficient communication (in person, phone, email) that you know with 100% certainty that you are on the right track.

Fear is a major reasons that students don’t approach their PhD supervisors frequently enough.  “What if my supervisor thinks less of me because I made mistakes, or I don’t know what I should do next?”

Conflict can be scary, and some students will go out of their way to avoid confrontations with their supervisors. This was Jesse’s strategy for 7 years, but once companies started reaching out to her, she became more assertive in setting boundaries for her role in collaborations and the requirements for her graduation.

Anti-dote: Always know what your supervisor’s and committee’s expectations are for you to write a PhD thesis. In some cases, getting clarification will involve disagreements and heated discussions.  (Good practice for working with others in your career).

As research evolves, expectations will change over time, but you always need to know what you are supposed to be working on now.

What if the expectations of your supervisor are not clear? Read more to learn a simple 3-step method to help you get the mentoring you need to put you PhD thesis back on track. 

Write a PhD thesis y no

 2. Assume that all the hard work that you do will turn into a PhD thesis eventually

Jesse collected lots of data, but she was missing the most important ingredient of a finished thesis: a central question or hypothesis. With her time scattered among collaborations and mentoring other students, Jesse lost focus.  Her projects were related, but not closely enough for a comprehensive doctoral thesis.

The way she turned her “hodgepodge” into a PhD thesis, was that she picked one question (for which she had already collected a significant amount of data), and she set up a research plan to answer that question in sufficient detail for a doctoral thesis.

Jesse’s story is extreme in the sense that even in her 7th year she did not have a clear thesis question. However, many students in their 5th years don’t know the exact question that their thesis is asking.

Anti-dote: Define clearly the question that your PhD thesis will answer. Once you have a question, you can set up a long-term research plan, with well-defined milestones and deadlines. Students are hesitant to this approach because the thesis question sometimes changes as more data is collected.

Check this post on how to manage a large research project.

What’s the point of a plan if it keeps changing? Given the uncertain nature of research, your initial plan will most certainly change. However, you always need to have a plan to start with, and milestones to measure your progress.

You might need to develop this plan on your own, but be sure to get your supervisor’s and committee’s approval, so you can turn your hours at work into tangible progress on your PhD thesis writing.

More hours at work do not automatically translate into a finished thesis. Here is how I became more productive in graduate school by reducing my work hours. 

 3. Do research that you think is interesting

This is related to #1 and #2, but it is so common that it deserves a category of its own.  Going off in a research direction that you think is interesting (while neglecting your actual thesis topic) is a type of “shiny object syndrome.” Perhaps you come across a paper, or a new technique, and you want to try it on your own.

As an independent researcher, you don’t always need to consult with your supervisor before you try something new. The problem occurs when this new “side-project” starts to become a significant time-sink.

Students pour in a lot of their resources without checking whether it complements their PhD thesis research.

Anti-dote: If you come across a novel idea that you think could complement your thesis, run it by your advisor before spending a significant amount of time (or money) on it. You might need to do literature research or collect preliminary data before presenting your idea to your supervisor.

Don’t assume that just because you think this research is interesting, your advisor will too. (Perhaps he/she has tried it in the past and chose not to pursue it for a good reason).

Difficult PhD supervisor angry

4. “Hope” that experiments or studies to turn out the way you want them to

There are few things more disempowering than “crossing your fingers” for your results to turn out a certain way. When you “hope” that you will finally get the results that you need to graduate, you are sending a subconscious message to yourself that someone else has power of your thesis. There are two problems with this approach.

The first problem is that you are stripping you of your self-confidence to be able to write a PhD thesis. The second one is that you cannot dictate how your results turn out – your data is what it is. In fact, sometimes unexpected results are more interesting and can lead to new research directions.

 In order for your committee to approve your PhD thesis, your research needs to be “solid” with reproducible results.

If you doubt your own methods and data, your committee will probably pick up on your lack of self-confidence and ask you to repeat your studies until your data is more robust.

Anti-dote: Think about possible outcomes in advance. How will each outcome effect the interpretation of your results? Many successful graduate students also have several backup plans in case they reach a dead-end, either in the direction of their research or in the development of their methods.

Having a Plan A, B, and C, will give you a peace of mind, so you no longer need to stress and “hope” for a certain outcomes. You probably know by this point that “hoping” and “crossing fingers” are not effective tools to help you finish your thesis.

Here are 7 other habits that keep you lingering in graduate school, and simple tips for breaking them so you can finally complete your degree.

 5. Jump into conclusions or the next phase of research before rigorous data analysis

Did you ever make preliminary conclusions by eye-balling your results? 

Unfortunately many students jump into conclusions too soon, go off in a certain direction, and then realize that they are back to square one.

I learned this lesson the hard way in graduate school when I had to determine whether certain conditions improved the survival of cell in my culture system. The plots in Excel suggested that one experimental setup was superior to the other.

When we did rigorous statistical analysis on the data, there was no significant difference between the two conditions.  This was great news as the setup that I suspected was more effective, cost 10 times more than the other system!

Anti-dote: In order to have confidence in your data so you can move to the next phase, examine your results from different angles. For example, try plotting it in different ways and do rigorous statistical analysis to determine if any of your results are significant.

Write a PhD thesis data

6. Cram as much data as possible into your PhD thesis to show how much work you have done

I will never forget a certain job talk by a candidate for a faculty position.

The applicant had just finished his PhD thesis and his 45 minute job talk had 149 slides. Half of the audience walked out after 20 minutes, because it was impossible to follow him. The problem was not only that he went through his slides at the speed of light, but his talk did not have a central question or hypothesis.

Your thesis needs to be a cohesive story beginning with a question or hypothesis and ending with conclusions that supported by data.

Don’t try to cram in unrelated data just to show how much work you did. An incoherent presentation will probably frustrate your thesis committee. Many students joke that when they look at their thesis it seems like only 1-2 years of work not 4 or 5.

Due to the nature of research, there is a good chance that a significant portion of your data will not make it into the final phase of your thesis, and you need to make peace with that.

Anti-dote: Make an outline of your thesis, including bullet points for the data or arguments you will make in each section. This outline (or skeleton) will change over time, but it will help to guide you in what data you need to collect or what information to include in each chapter.

As you go through your research and are unsure about the relevance of some of your data sets, check with your supervisor before your committee meeting to avoid surprises and heated debates.

 7. Cherry pick or massage your data to fit your story

  • Cherry picking: means that you are choosing to emphasize only the data that supports your story, while ignoring findings that contradict your proposed conclusions.
  • Data massaging: can refer an a spectrum of questionable analysis methods, ranging from elimination of obvious outliers to “tightening” up your data set by excluding all points outside certain error bars.  (Some consider fabrication a type of data massaging, but I will not go into that as the consequences of such misconduct are much more serious than just having to schedule yet another committee meeting).

Outliers can be extremely frustrating if you have spent months or years designing your study. In some cases outliers can be excluded for good reasons, such as animal or human volunteer had a certain underlying condition that interfered with your study.

In other cases, there is no good explanation of the outliers, which can be even more irritating, because you have no scientific reason for excluding them and they can have a negative impact on your statistical analysis.

Both cherry picking and massaging data are questionable scientific practices.

If your committee finds out that you were trying to “hide” your original data set, they might even take you off the project or suspend you from the program. Cherry-picking or massaging can lead to serious (even legal) consequences in certain areas of research, particularly those involving human volunteers.

 Anti-dote: Most data sets will not be perfect, and an outlier does not invalidate your results. If there is an outlier, make a note of it. The take-home message is that you need to be completely transparent on what data you collected and how you analyzed it. If you chose to eliminate an outlier, you need to be clear why you did it.

Your supervisor’s experience can be particular helpful here, as he/she might be able to suggest scientifically valid reasons to exclude certain points.

Also keep in mind that in most experimental sciences, data is not expected to be 100% reproducible. A 20% variation between sets is considered reproducible in many fields. Of course, you need to check with your advisor on how much variability is acceptable in your specific field.

Do you want to know what to do with not-so-exciting data and results? Check this post on how to document your scientific mistakes.

Write a PhD thesis perfectionist

 8. Rewrite the same paragraphs over and over until they are perfect

Perfectionism is one of the most common causes of writer’s block. Some students are worried that their writing is not good enough, or they may be too afraid to put any thoughts on papers. The result is write a PhD thesis with only bits and pieces and there isn’t enough material for their committee to approve their thesis.

Anti-dote: Get everything on paper: your data, your ideas, your references, and your proposed data interpretation. You cannot pull a thesis together while all of this information is in your head.

Rewriting the same paragraphs until they are perfect will not bring you much closer to a finished thesis.

Instead, focus on putting a story together, even if you don’t have all the pieces of your puzzle in place.

During the active writing phase, put your attention on the content: what questions you are asking, the validity of your methods, the quality of your data, and any gaps in your story that you might need to fill before handing in your thesis.

To write a PhD thesis seems intimidating (which could be a reason that some students re-edit the same paragraphs repeatedly). Keep in mind that the more you write, the easier it will be to keep writing.

 

Make writing a daily practice until you have a complete story.

Leave the editing (word choice/style/formatting) until the very end. Some universities have writing centers that offer editing services, or you can also hire someone to do a copy editing polish on your thesis if you are concerned about your writing style.

Are you experiencing writer’s block? Click here for 12 strategies that will help you become a more effective writer, so you can complete your theses and manuscripts by their deadlines. 

9. Use secondary references without checking primary references

When you come across a paper by a Smith et al, who cites data from Johnson et al., do you cite Smith or Johnson when you refer to this data?

It is tempting to just cite Smith et al., to save yourself the trouble of having to look up Johnson et al. However, citing secondary references (in this case Smith et al.) is a questionable practice because you are trusting someone else to interpret the original data set, which was published by Johnson et al.

It is also not enough to just cite both Smith and Johnson, without looking up Johnson, because some papers give incorrect citations. The journal name, page number, or year of publication might have been typed incorrectly in their bibliography, and if you just copy it verbatim, you will be held responsible for an invalid citation.

Anti-dote: If you refer to an original data set, you need to look at the data set yourself. Always cite the primary paper, but only after you have confirmed that the conclusions made by the secondary paper are valid.

You can also cite the secondary paper if you want to refer to their interpretation of the data, or any follow-up experiments that they have done.

 

10. “Lift” off information from other papers

When you review 50-100 papers for a literature review, it is tough to keep all your references straight. As you begin writing, the text in your literature review might sound very close to some of the papers you read.

Your sentences and word choice might be so close that your advisor might question whether you “lifted” off some paragraphs, or worse, he or she may accuse you of plagiarism (one of the worst offenses in an academic environment).

Whether it was intentional or not, if your paper is too close to someone else’s, it will reflect very poorly on your performance and could ruin your reputation for years.

 Anti-dote: Keep all the information from your references organized electronically. Since most of your references will be in electronic format such as pdf’s, you can highlight or box the information within the pdf itself.

You can group your references by category in different folders. This way, whenever you come across a new reference you can highlight the necessary information in the pdf, and then save it right away in the appropriate folder.

This practice will ensure that when it is time to write your literature review, you can pull up the corresponding files right away and see what information you want to use. You can then paraphrase this information appropriately (and include the references) so that  you avoid any chances of being accused of “lifting” off or plagiarism.

Check this post if you want to improve your literature review in just 4 hours.

Where is Jesse today?

Jesse is the director of a group in a biotech company.

While the 7 years she spent in graduate school were frustrating and stretched her to her limits, the lessons she learned helped her to advance her career quickly.

Jesse’s first job after graduation was in a small company, which downsized soon after she was hired. Just a few months after being hired, Jesse was working three people’s jobs – for no extra pay. By then Jesse was married, and she was no longer willing to put in unreasonable hours.

In order to reduce her workload, Jesse had several meetings with her supervisor. By applying the same communication skills that helped her to resolve conflicts with her PhD advisor, Jesse was able to reach an agreement with her new boss so she could have better work-life balance.

Her increased in self-confidence also motivated her to seek out new opportunities at different companies where the work environment was a better fit for her.

Jesse received several job offers in the next few years before she accepted her current position as a high level manager. The lessons that she learned as a PhD student have also helped her to mentor junior scientists in her group properly, so they could become more productive and support her company’s mission.

 3 actions for you

  • Find which of these 10 mistakes you make and fix them using the proposed antidote
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About Dora Farkas

Dora Farkas, Ph.D received her PhD from MIT and worked in the pharmaceutical industry for several years. Dora is a thesis and career coach for graduate students and postdoctoral fellows. She is the Founder of www.FinishYourThesis.com, a site devoted to help graduate students complete their degrees. Dora is launching her online "Finish Your Thesis Program" soon. Click here to get a copy of Dora's FREE report “Secrets to Success in Graduate School”, which includes her favorite productivity tips based on coaching over 200 students in the last 5 years.

Comments

  1. Jafra D. Thomas says:

    This was a very helpful article. As a first year Ph.D. student, the lessons on how to write a thesis you Ph.D. committee will not approve are extremely valuable and will help me have a better start as I begin work on my dissertation. As a major within the social scientists, we typically spend a bit less time completing our degree than basic science disciplines, but the information I say equally applies. I’ tend to be a perfectionist in my writing and the anti-dote really resonated with me. Getting back to basics: the advice to focus on telling a story I resonated with me as I often set that as my main goal to say something meaningful and that can make a positive impact. Remembering that as I sit down to write will be helpful by encouraging me to get down on paper all my thoughts. The tip of finding a professional copy editor is a great advice. I’ll be sure to look into the services provided by my university to see if they offer review and editing help. The other tip that resonated with me is with conducting a literature review. It can become very easy to “lift” off others’ ideas when you read so many articles. I want to do my best job to avoid this by keeping the advice of the author in mind and create sub-folders organized by content or how it helps answer a specific research question; I’m becoming savvy with using online file stores and their tagging tools seem to be very helpful, as well as other features. All in all, this was a great article. Thank you for writing it!

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