Train PhD students to be thinkers not just specialists

By Gundula Bosch
Taken from
Under pressure to turn out productive lab members quickly, many PhD programmes in the biomedical sciences have shortened their courses, squeezing out opportunities for putting research into its wider context. Consequently, most PhD curricula are unlikely to nurture the big thinkers and creative problem-solvers that society needs.
That means students are taught every detail of a microbe’s life cycle but little about the life scientific. They need to be taught to recognize how errors can occur. Trainees should evaluate case studies derived from flawed real research, or use interdisciplinary detective games to find logical fallacies in the literature. Above all, students must be shown the scientific process as it is — with its limitations and potential pitfalls as well as its fun side, such as serendipitous discoveries and hilarious blunders.
This is exactly the gap that I am trying to fill at Johns Hopkins University in Baltimore, Maryland, where a new graduate science programme is entering its second year. Microbiologist Arturo Casadevall and I began pushing for reform in early 2015, citing the need to put the philosophy back into the doctorate of philosophy: that is, the ‘Ph’ back into the PhD. We call our programme R3, which means that our students learn to apply rigour to their design and conduct of experiments; view their work through the lens of social responsibility; and to think critically, communicate better, and thus improve reproducibility. Although we are aware of many innovative individual courses developed along these lines, we are striving for more-comprehensive reform.
Our offerings are different from others at the graduate level. We have critical-thinking assignments in which students analyse errors in reasoning in a New York Times opinion piece about ‘big sugar’, and the ethical implications of the arguments made in a New Yorker piece by surgeon Atul Gawande entitled ‘The Mistrust of Science’. Our courses on rigorous research, scientific integrity, logic, and mathematical and programming skills are integrated into students’ laboratory and fieldwork. Those studying the influenza virus, for example, work with real-life patient data sets and wrestle with the challenges of applied statistics.
A new curriculum starts by winning allies. Both students and faculty members must see value in moving off the standard track. We used informal interviews and focus groups to identify areas in which students and faculty members saw gaps in their training. Recurring themes included the inability to apply theoretical knowledge in statistical tests in the laboratory, frequent mistakes in choosing an appropriate set of experimental controls, and significant difficulty in explaining work to non-experts.
Introducing our programme to colleagues in the Johns Hopkins life-sciences departments was even more sensitive. I was startled by the oft-expressed opinion that scientific productivity depended more on rote knowledge than on competence in critical thinking. Several principal investigators were uneasy about students committing more time to less conventional forms of education. The best way to gain their support was coffee: we repeatedly met lab heads to understand their concerns.
With the pilot so new, we could not provide data on students’ performance, but we could address faculty members’ scepticism. Some colleagues were apprehensive that students would take fewer courses in specialized content to make room for interdisciplinary courses on ethics, epistemology and quantitative skills. In particular, they worried that the R3 programme could lengthen the time required for students to complete their degree, leave them insufficiently knowledgeable in their subject areas and make them less productive in the lab.
We made the case that better critical thinking and fewer mandatory discipline-specific classes might actually position students to be more productive. We convinced several professors to try the new system and participate in structured evaluations on whether R3 courses contributed to students’ performance.
So far, we have built 5 new courses from scratch and have enrolled 85 students from nearly a dozen departments and divisions. The courses cover the anatomy of errors and misconduct in scientific practice and teach students how to dissect the scientific literature. An interdisciplinary discussion series encourages broad and critical thinking about science. Our students learn to consider societal consequences of research advances, such as the ability to genetically alter sperm and eggs.
Discussions about the bigger-picture problems of the scientific enterprise get students to reflect on the limits of science, and where science’s ability to do something competes with what scientists should do from a moral point of view. In addition, we have seminars and workshops on professional skills, particularly leadership skills through effective communication, teaching and mentoring.
It is still early days for assessment. So far, however, trainees have repeatedly emphasized that gaining a broader perspective has been helpful. In future, we will collect information about the impact that the R3 approach has on graduates’ career choices and achievements.
We believe that researchers who are educated more broadly will do science more thoughtfully, with the result that other scientists, and society at large, will be able to rely on this work for a better, more rational world. Science should strive to be self-improving, not just self-correcting.

Nature 554, 277 (2018)

doi: 10.1038/d41586-018-01853-1

The Not-So-Secret Guide to Dissertating

By Jenny J. Lee
Taken from
As a professor for nearly 15 years, I have advised more doctoral students than I care to count. I’ve had my fair share of national award winners, those who gave up and vanished, and countless students in between. I have referred them to books, manuals, articles, and advice columns that provide no shortage of step-by-step guidance on how to embark upon the pinnacle of their studies — the doctoral dissertation.
Published advice can be helpful. But it often portrays the research-and-writing process as neutral and predictable, and it hardly takes into account the pitfalls and mishaps that can affect whether, and how soon, you finish. Yet it’s also a mistake to view the dissertation — as many students do — as a challenge so cryptic and clouded in ambiguous idealism that it seems insurmountable.
In fact, the dissertation process should not be a mystery at all, given that the most common problems can be easily avoided. That it is mysterious for so many means that faculty members need to better communicate those problems.
As advisers who probably wrote our own dissertations decades ago, we may too easily forget what it was like to be a student to offer the clearest advice. Or, to avoid seeming too autocratic, we may see a professional value in not directing our students’ ideas too firmly. And sometimes we may simply forget what we told which student, mistakenly assuming that the advice will somehow inevitably spread from one advisee to the next.

Despite your attempts to find the right experts to guide you, you may find that you still know more about your topic than your adviser and committee members do. However, knowledge alone does not guarantee a Ph.D.

Here, then, are maxims that some of us may neglect to spell out clearly enough — and that students may be too afraid to ask about.
Some dissertation topics are pretty good and others are really, really bad. The onus here is on you, the student, but a successful proposal is most often a collaboration between student and adviser. We aim to nurture your ideas, but the reality is: Some are better than others. The really, really bad topics are those that fail to establish relevance to the field, do not appear to be genuine inquiries, or are unconvincingly masked as a shortcut to your educational credentials.
We have our research biases, but please don’t believe you can make a career as our clone (however much we may privately wish it). To make your dissertation worthwhile, think about an ideal — yet realistic — job you might apply for upon obtaining your Ph.D.
If you are considering a faculty job, how will your dissertation make you stand out from 100-plus other applicants seeking the same position? What are some conferences where you can start sharing your results and expanding your academic connections? If you are seeking a nonacademic career, how might your research findings inform your day-to-day work? What will you say about your dissertation during a job interview?
In this tough job market, don’t be afraid to tell us your career plans, whether or not they are in academe. If we know what you want to do, we can better advise on a career strategy. Also, keep in mind that, while you might be limited to one dissertation adviser, you are not limited in the number of mentors you can approach for job advice. So if you’re interested in nonacademic careers but your dissertation adviser doesn’t have any such expertise, find someone who does.
We do not expect you to change the world with a single study. In an ideal world, a student’s thesis would revolutionize the field and forever change how we think about a topic. But I have witnessed many students’ repeatedly extending their timeline because they are stuck on coming up with the “perfect” proposal idea.
People who pursue a Ph.D. do not, by nature, lack ambition. As an adviser, I spend far more time helping overly ambitious students scale down their research designs to make them more feasible than I do revving up the aspirations of laid-back students whose research goals are underwhelming. The bottom line: A dissertation that you can actually finish — with good-enough scholarship — can still offer something meaningful to the field.
What we perhaps don’t emphasize enough in our advising is that the dissertation is not just an end product. It’s also a process of learning how to become an independent scholar. Your dissertation probably won’t change the world, but with the skills you gain in writing it, you will be better equipped to do that down the road, or at least to make a bigger splash in your field.
We will probably come up with ideas when you have none. That’s not necessarily a good thing. Too many students sit silently, feverishly taking notes on ideas that I offer — whether on the topic, the methodological approach, or something else — without telling me what they want to do or what their ideas are.
There are pitfalls in relying on your adviser’s ideas alone. Just remember: Your adviser has a strong say here but not above your own. The dissertation is not a passive process, and so it is important that you speak up if there is something you want to do instead of what we are advising.
Otherwise we may assume you don’t care or are not thinking at all. We have no shortage of ideas, but they should not be taken as commands. And occasionally we might forget the details of our last conversation unless you remind us. Worst case, we might suggest a different topic or approach every time we meet. Idea generation is a two-way process and should come mostly from you.
We do not know everything. In rare cases, the scholarly interests of both student and adviser may align. Most of the time, however, they don’t. Your adviser may have only peripheral knowledge to guide your specific research project. Your dissertation committee then supplements the knowledge and methodological bases. That’s important to keep in mind in assembling your committee.

Dissertations are supposed to be specialized and, despite your attempts to find the right experts to guide you, you may find that you still know more about your topic than your adviser and committee members do. However, knowledge alone does not guarantee a Ph.D. As mentioned, the finished product exhibits your ability to do independent scholarly work. A reasonable expectation is that your adviser will suggest where to locate the relevant literature, recommend how best to design the study, offer feedback on your drafts, and provide some professional advice along the way.
Face-to-face meetings can give a false sense of progress. It’s vital to communicate with your adviser, especially in formulating the research proposal and making critical decisions along the way. But your dissertation is not “real” unless it is in writing. I have wasted many hours with students who wish to meet regularly to discuss their ideas — with different ideas in each meeting — but have not committed so much as a sentence to text.
Meetings between you and your adviser are not intended to be academic confessions to absolve your guilt for not writing. And we can’t provide feedback on written work that doesn’t exist.
Make writing a regular habit. Consider drafting as early as possible while still fleshing out your ideas. Then go back to your document as you continue to rethink and refine your topic.
On a related note, don’t be a writing hoarder. I mean, be prepared to toss pages of what you have already written. There is no prestige in a long dissertation if the organization is confusing and the writing unclear. Be willing to let go of your own words and use the delete key as needed to make your arguments coherent.
The finished manuscript is typically not a biographical narrative of your research journey, with unexpected twists and turns (except on those rare occasions when your personal narrative is the dissertation). In most cases, the dissertation should offer a logical stream of thinking rather than a torrent of internal consciousness.
We are not sitting by our computers waiting for your next draft. Unless, of course, the two of us have agreed to a specific timeline, in which case we expect to hear from you on certain dates.
The lack of a time-oriented structure in the dissertation process means that weeks, or even months, can go by before I hear from most of my students. And then I get an email that begins, “I am sorry I took so long.” Some have even admitted to postponing their correspondence out of fear that I would be upset with them for taking too long to update me on their progress.
Most professors are not staying up at night thinking about your dissertation or why we have not heard from you. Rather, we are juggling many other dissertations in addition to grading papers, managing our own research projects, meeting writing deadlines, and drowning in email.
More often than not, your email updates remind us that you are our student. The takeaway here is that much of your timeline and progress depends on you. Come up with a writing schedule and stick to it. And keep your adviser informed every now and then, but do not hide with guilt if it has been a while.
We sometimes forget to write back. If we do not respond to your email or latest draft after a couple of weeks, it is OK to remind us. Rather than stewing in anxiety because you have not received any response, simply email us again.
But please do not give us immediate deadlines. If you take months to write your latest version, you shouldn’t expect us to turn your draft back to you in two days. Timelines vary and should be discussed upfront, but our taking a couple of weeks to provide you with feedback is reasonable.
Your dissertation will probably never be read once it is filed. Too much anxiety has gone into perfectionistic writing that might never be seen by more than the few people on your dissertation committee. A professor of mine once said: “Put $1 in your dissertation on file at the library and check back 10 years later, and the $1 will still be there.” Dissertations are digitized nowadays, but it is still quite likely that your work may never be downloaded, except by your family members.
With that in mind, have concrete plans to publish from your dissertation, so that your hard work will have more than a few readers. Consider it a goal, not an option, to publish at least one scholarly article or book based on your dissertation research. By the time you finish, most of your work has already been done. It’s well worth the added effort, both professionally and personally, to make your work accessible to a wide pool of readers.
We work for you. It is our job to get you to graduate. We do not enjoy making your lives difficult (most of us, anyway). We challenge you because we have high standards. Regardless of rank or reputation, helping you succeed is what we are paid to do.
Too many students are afraid to ask for help when they need it. No, we will probably not offer to edit your manuscript line-by-line to fix your grammar. But we can refer you to resources if you ask. We cannot read your minds, but we can respond when you ask for clarification or request more support.
Be mindful of your own expectation biases. Some students unfairly expect more — or less — based on a faculty member’s gender, race, or other personal factors. Also, be consistent in how you address your professors. Men are not the only “Dr.s” on the faculty. I have worked with some students who decided to call me by my first name while referring to my male colleagues as “Dr.” It’s fine to ask us our preference about that.
Producing a dissertation is a process of discovery, but not only an academic one. The journey involves discovering yourself as a scholar. It helps to know the difference as you encounter obstacles along the way. Your path may not be easy, but I hope these suggestions will make it a little more clear. Just tell yourself every day: I got this.
Jenny J. Lee is a professor of educational policy studies and practice at the University of Arizona’s Center for the Study of Higher Education.