One of my most formative experiences in the PhD was being a member of the MIT Biological Engineering Resources for Easing Friction and Stress (REFS), a student-run peer conflict coaching program part of the larger REFS program across MIT. The BE REFS offered a privileged window into the realities of PhD experiences through on-demand, confidential conflict coaching sessions for students and exit interviews of all students defending their thesis, carried out to better understand the pressure points of the PhD program. After running 27 coaching sessions and 23 exit interviews between 2018 and 2024 (plus my own unhinged, rambling, 4-session-long exit interview run by the brilliant and endlessly patient Ellen Kan), common motifs in the life cycle of a PhD in STEM start to appear.
The Three Chapters of a PhD Life Cycle
In my eyes, the challenges and experiences of a PhD break down into three chapters, each characterized by positive and negative feelings that stem from the central struggles of each stage. They include:
The Jump (years ~1–2): excitement and anxiety when evaluating possible paths
The Slog (years ~3–4): freedom and disorientation in self-directed research
The Push (years ~5–6): mastery and overextension while concluding work and eyeing next steps
Of course, these three chapters and their experiences are all rough averages, and every PhD will deviate from them one way or another: some might have an advisor who micromanages their work constantly during The Slog, stifling freedom but perhaps providing clear orientation. Others might have a sudden end to their PhD due to funding problems, an unexpected and exciting job opportunity, or a personal event, changing the tenor of The Push in myriad different ways. Many PhD programs, particularly in the European system, require no initial classes, admit students directly into labs, and often have predetermined projects, compressing The Jump of the PhD. And of course, PhD programs in the humanities and social sciences have radically different funding structures, relationships to labor, and research activities, all bringing their own sets of unique challenges. However, on average, the most common themes I heard when asking graduating bioengineering students the question “What was the most stressful part of your PhD, and why?” clustered around the struggles of the three chapters outlined above, and the positive and meaningful experiences underlying the reasons why we pursue PhDs fall neatly into each stage as well.
The Three Chapters of a PhD Thesis
The three chapters in the life cycle of a PhD are also marked by different prioritization of research projects, which end up becoming the literal chapters in a PhD thesis document. There’s obviously no single right way of structuring research projects in a PhD. However, I’m very interested in experimenting with strategies and structures at MsEE Lab. Based on experience and observation, the archetypal PhD at MsEE Lab will have three projects (resulting in a 3-chapter thesis):
A Starter Project that culminates or complements an existing project currently underway in the lab, maybe even one close to the finish line. The starter project is closely mentored by a more experienced lab member or a collaborator able to provide direct mentorship. The objectives of this project are to provide an opportunity to learn about the state of the art and technical craft of research in the field, as well as a secure training ground within which to build confidence.
A Straightforward Project with a clearly defined hypothesis or design objective that can be addressed using expertise that the lab currently has access to, either internally or through collaborators. This project is not necessarily easier, less ambitious, or less impactful than more risky projects, but it is more certain. The objectives of this project are to provide a well-defined pathway to contributing new knowledge to the field, and thus, a PhD, relieve anxiety about the uncertainty and open-ended nature of a PhD. It also provides an opportunity for mentorship: a senior student’s Straightforward Project can contain a younger student’s Starter Project.
An Exploratory Project with a more preliminary and/or risky character and no expectation of being completely finished during the student’s time in the PhD—or perhaps ever. Often driven by research questions without clear hypotheses or design objectives requiring new technical advances, this includes “fishing expedition” and “pie in the sky” projects. The objectives of this project are to explore a potential new line of research in the lab, to provide a source of excitement for the student and a second shot on goal for advancing knowledge in the field, and to train the student in how to navigate uncertain, open-ended research challenges. In lucky cases, an Exploratory Project might advance fast enough to be completed by the student who started it, but if it doesn’t, it may be continued by another student as their Exploratory Project. If the unfinished Exploratory Project at least advances to a point of greater technical certainty, it might become another student’s Straightforward Project or even Starter Project.
Students focus on each of these three project types in different ways as they progress through different chapters of the PhD life cycle, according to each chapter’s goals and circumstances. It’s worth noting that the same project can (and often should) be worked on by multiple students, both in different moments and concurrently. Thinking about the life cycle of a project rather than a PhD student, a project will commonly start as one lab member’s Exploratory Project before being handed over to a second lab member’s Straightforward Project and serving as a Starter Project of a third lab member who helps wrap it up.
Let’s take a guided tour through the arc of grad school. We’ll examine practical strategies for each stage along the way.
1. The Jump: How does a PhD start?
The first chapter of a PhD is defined by the excitement —and anxiety— of picking a research group, advisor, and research project, all while balancing advanced coursework and teaching duties (at least in the US system). For many, this is piled on top of learning to live in a new city, country, culture, and/or language.
On the bright side, this is a period full of energy and enthusiasm. You’re riding a sense of achievement at having gotten into a PhD program, you’re supercharged with the excitement that pushed you to apply to a PhD in the first place, and you’re being exposed to all kinds of new ideas and people through classes, laboratory rotations, and other activities. It feels like you’re on the right track, immersed in a world of people with similar interests, ambitions, and ideas. Furthermore, the blank slate of your PhD career and beyond is full of a sense of opportunity. The exercise of imagining possible futures branching from potential advisors, research groups, and types of projects can be invigorating.
On the other hand, this can also be a period riddled with anxiety. Entering into an environment full of extremely capable people when you’ve previously been accustomed to being singled out as “the smart one interested in research” is a jolting experience for many. Feelings of imposter syndrome begin to rear their head, fueled by comparison with peers and evaluation by mentors in classes and research rotations. Competition for coveted open positions in research groups or for available projects within them can reinforce these feelings. Furthermore, the “blank slate” of your PhD can be a source of anxiety and decision paralysis. What if you choose your advisor, research group, or project wrong? What criteria should you choose them based on? How are you even supposed to know as a first-year PhD student just beginning to learn a field?
Strategies:
Choosing an advisor and research group:
Projects change, people don’t: Although I have seen people’s interests and mentorship style change dramatically on occasion, betting on a working environment, advisor relationship, and general scientific interest is much more reliable than betting on a specific project. How do you know if you can have a good relationship with an advisor? Speak to other lab members and try the next few bullets.
Potential MsEE Lab students: Prof. Jen Heemstra encourages advisors to try personality tests in her book on lab leadership. If you’re a student considering MsEE Lab, I’m patient, outgoing, creative, extremely easy to get along with, and generally determined (if reckless and not very self-disciplined) according to the extensively studied Big Five personality traits.
Good advisors advise: STEM PhD students report that the aspects that most increase job satisfaction include having a good relationship with their supervisor, with at least 1 h of contact per week, and having independence and flexibility in their work. Search for advisors who are available as mentors, but not overbearing as supervisors.
Communicate openly: If you have goals, expectations, or requirements for your PhD experience, communicate them clearly with a potential advisor. What do you want to do with your PhD? What kind and amount of work do you hope to do? What mode or frequency of communication works best for you? More importantly, be direct about asking them for the same clarity: understanding an advisor’s expectations is not a privilege that you should feel ashamed to ask for. Ask about how they select PhD students and available funding as well.
Collaboration is organic: Every other PhD student starts off wanting to be coadvised, myself included. Most often, this is fear of missing out that you shouldn’t heed. You can get the scientific benefits of coadvisement through collaborations that grow organically over the course of your work without the pressure of having two bosses. Formal coadvisement isn’t a thing to avoid either, but is often done for administrative or financial purposes. Regardless, don’t worry about having to establish all the connections right at the start of your PhD; let them happen when they do.
It takes a village: The lab environment will be a defining feature of your next half-decade, so talk to as many members of the lab in different stages as you can. The experiences of senior students will likely be similar to yours, so pay attention to their achievements and their struggles. Furthermore, the engagement of senior lab members in mentorship is more predictive of your skill development than your advisor’s engagement, so look to them as sources of guidance. If the lab is new (like MsEE Lab in 2026), look for external mentorship opportunities in collaborator labs that can complement your expertise.
Choosing research projects:
The focus of this chapter should unsurprisingly be your Starter Project. However, learning and planning for future Straightforward and Exploratory Projects is an important part of this era as well.
Join a Starter Project: Join an existing project in the lab or a collaboration where you can receive firsthand training in the techniques and questions that you intend to learn during the PhD.
Learn what is possible: Speak with your advisor, lab members, and collaborators to understand the state of the field, the technical capabilities and expertise available to you, and the lab’s ongoing projects. This will later be the source material for your Straightforward Project.
Brainstorm what is not yet possible: Imagine pushing beyond what is available for the purposes of possible Exploratory Projects. Write down all the ideas you have and brainstorm extensively! These will be exciting things to return to throughout your PhD, and indeed, your entire career.
Morale:
Lean into exploring new areas of research: Even if you don’t join the lab of a professor you’re taking a class or rotating with, these professors could be your committee members and external mentors later on. They may also show you new paths for collaborations or ways to look at a problem you hadn’t considered.
Science needs all hands on deck: Remember you’re defined not only by the magnitude of your abilities, but also by the specific combination of them, as well as by the combination of your interests, experiences, and perspectives. Science is a democracy of effort, and you are an asset to science for caring about whatever you care to put your effort into. Comparing yourself to others only makes you distressed or arrogant: everyone’s path is different, and you only get to see fragments of other people’s. It’s far more productive (and encouraging!) to compare yourself to past versions of yourself.
Course-correcting is always a possibility: If you have decision anxiety or find yourself regretting a decision, remember that although switching projects, labs, and advisors is a stressful experience and never the original goal, it is always an option and is far from abnormal. Successful careers come in all shapes and forms. The seemingly straight arrows of others’ career trajectories are usually narratives we all construct in retrospect.
2. The Slog: How do you get through the middle of a PhD?
The second chapter of a PhD is defined by the lack of external structure, for better or for worse. There are no more classes for you to take, fewer or no classes for you to teach (for some), and once you’re done with your qualifying exams and thesis proposal, there’s no meaningful objective for you to achieve other than defending your thesis somewhere down the road in a diffuse future. Yearly thesis committee meetings sometimes punctuate this desert landscape.
For many, this is a sigh of relief. You finally get to be in charge of your own schedule, defining how you organize your days, weeks, months, and years. You can make time for new interests or old ones you may have neglected. You have the breathing space to immerse yourself in your research problem, retreating into the cocoon that will see you reemerge magically transformed into an expert in your field.
This lack of structure is, of course, a double-edged sword. Without clear external cues, it can be easy to lose interest in a routine. Without additional activities, research projects become an all-consuming endeavor that dictates our emotional well-being. When they inevitably run into roadblocks, staying motivated becomes challenging. The feeling of spinning one’s wheels while feeling in a rut is common enough that it has a name, “The Slump”, and it has been written about for decades.
While The Slog is when The Slump happens, it doesn’t have to be defined by or reduced to the negative experience of The Slump, hence the different name. The Slog will see you develop ideas, questions, and expertise that will define your career and keep you up at night —in the best of ways— for years to come.
Strategies:
Conducting research projects
During this chapter, students split their focus between their Straightforward and Exploratory projects. Setting regular project goals and milestones with the advisor becomes key in this period. A key skill is recognizing when one of these projects is not serving its intended purpose and adjusting accordingly.
Backwards design: Use the principles of backwards design to chart a path to completion for your projects. What is the overall objective of the project? What do you need to achieve to get there? When can you achieve these subgoals, and how?
Regular feedback: Meet regularly with your advisor and collaborators to check in on progress and adjust your backward-designed goals and plans. This is key to maintaining engagement as well, and advisors can provide structured ways of doing so. Ideally, this should be a space to give your advisor feedback on mentorship style as well.
Your Straightforward Project is there to provide stability: If your Straightforward Project runs into a critical problem that puts its reliability into question, something must be done. Resolve the uncertainty quickly if possible; don’t shy away from the killer experiment that will make or break your project. Learning to fail fast is a skill! The faster you find out that your Straightforward Project isn’t straightforward, the better. Once you find out, adjust it, abandon and replace it, or upgrade it to an Exploratory Project (abandoning your current Exploratory Project) and find a new Straightforward Project.
Your Exploratory Project is there to provide enthusiasm: If your Exploratory Project is proven hopelessly unfeasible, find a new one. If your Exploratory Project stops bringing you excitement, find a new one. If your Exploratory Project proves definitely feasible and you hate your current Straightforward Project, congratulations, it’s now your new Straightforward Project, and you need to find a new Exploratory Project.
Morale
Savor your science: When people look back and say, “I wish I had all the time I used to have to read papers and just understand something in depth”, this is that time. Enjoy it! If you’re in a PhD program, you’re doing it because you enjoy learning and research. Dive down the rabbit holes of obscure papers from the 60s, take a moment to go to the seminar that seems interesting even if it’s not related to your project, and never stop writing down your ideas.
Cultivate your professional interests beyond your research projects: This will not only keep you sane and excited about work, but can also open doors when it becomes time to look beyond the PhD during the next chapter. Pursue an internship in industry, branch out into a different area of research, try consulting or government advocacy, enroll in a teaching class or conflict coaching program, explore science communication, outreach, philosophy of science, art... the world is full of options. There’s no time to pursue them all at the same time, but finding one or two that are meaningful to you can go a long way.
Share the wins and the struggles: You’re not alone. I promise your classmates in the PhD program are going through the same challenges. If it brings you happiness, keep in touch with them and share the highs and the lows of the experience.
Find multiple sources of mentorship: Your advisor is expected to be your primary mentor, but having different people you can turn to for different types of challenges is crucial. Senior lab members more directly involved in your area of work can be fundamental for technical help, other faculty members can provide scientific expertise on a different area of study, someone with connections in a certain type of industry or line of work can give you career advice, someone with authority can advocate on your behalf when needed, someone with a background similar to yours can serve as a role model for personal advice. If a mentor isn’t serving their purpose, look for new ones (this includes your thesis committee!).
Mentor others: Taking up an undergraduate student or a rotation student at this stage can be valuable for everyone involved. Your student gets the benefit of being exposed to the practice of research in general and an area of research in particular, helping them shape their career. You get a sense of routine and accountability amidst the lack of structure, a sense of purpose for yourself and your work amidst the lack of milestones, and a chance to hone your skills by teaching them.
3. The Push: How does a PhD end?
The third chapter of a PhD is defined by trying to squeeze all you can out of your training while also trying to squeeze yourself out of your training program.
On the bright side, this is the period of your PhD in which you’re reaping all the benefits of the training you have sown with years of effort. Hours upon hours spent immersed in papers, seminars, and conversations about the questions and methods in a field have made you able to recall who works on what and which paper explains what technique. Countless repetitions have made technical procedures or analyses second-nature to you: what took you months to achieve during The Jump, you can now get done in a matter of days. It’s said that all the data that ends up being shown in a PhD thesis is generated in the last year—an exaggeration, but not by much. The expertise of a PhD is a small niche of science, but within your small niche, you become almost omnipotent.
Ah, if only there were time to let that feeling of omnipotence sink in. Finishing the PhD is reported as the most stressful part of grad school by 35% of MIT BE alumni as of 2025, the highest single response. Writing manuscripts, finishing experiments, dealing with reviewer comments, training other lab members to pass on the torch, organizing a cogent thesis document, preparing a thesis defense, and all the paperwork associated with graduation are all activities that need to get done before the looming deadline of your defense date. Now that you have the skills and knowledge to do things “the right way”, there’s a feeling of frustration that your project isn’t everything that it could have been if only you had more time. Maybe the main project of your PhD led to a dead end, and you find yourself either pivoting rapidly or grappling with a thesis of negative results. As if that weren’t enough, your life somehow must go on after graduation, and you have to figure out how to get a job. There’s anxiety about what your next steps will be after spending so long in the same environment. Finally, there’s also burnout after years of sustained effort. A PhD is a marathon, and the last lap can feel harrowing. For some, the process is made worse by seeing the finish line run away from you as you approach it, as some advisors are unclear or mercurial about their expectations.
Strategies:
Concluding research projects
Focus on a project: During The Push, push to finish whichever project is closest or most exciting to you. The time has come to cut your losses and transition Exploratory Projects to others as you focus on making sure whatever your Straightforward Project ended up being gets over the finish line.
Agree on a clear finish line: Push your advisor to define and commit with you to clear goals that your projects will need to reach for you to be able to graduate. Use backward design approaches to do so. Don’t be afraid to start these conversations early—graduation can sometimes feel like a taboo topic, but it’s a natural part of every PhD experience. Your thesis committee should ideally be there to support you in this regard.
Looking ahead
Take advantage of informational interviews: Most people are much more willing to sit down and chat about their jobs and careers than you’d think, even with complete strangers. One MIT BE alumnus I interviewed scheduled an informational interview with a different person every week for the entire year before she graduated. While she admitted that it may have been a lot, she and others all found informational interviews to be an underappreciated resource when considering different career options.
Tap into alumni networks: Firsthand connections, for better or worse, are invaluable ways to open doors. Especially in the age of AI recruiting, having a human being refer you to recruiters can give you the chance you need. Don’t be shy when cold-emailing alumni you had little or no interaction with.
Sometimes, the best way to graduate is to get a job first: It’s important to maintain good communication with your advisor regarding job applications and plans. That said, I witnessed more than one instance in which, after a student tells their noncommittal advisor that they’re applying to jobs, the advisor stops dragging their feet on graduation when a job offer actually materializes. It’s not a universal solution, but if it presents itself, don’t let your PhD defense get in the way of your career.
Morale
You have become an expert: With such an overwhelming volume of work on your plate, it’s easy to lose sight of how much you’ve learned throughout the PhD by the time of The Push. Even if your project hasn’t (or doesn’t) achieve its objectives, the skills and knowledge it has taken for you to ascertain this are the same.
Self-advocacy is key to graduation: Over 80% of MIT BE alumni reported that the reason for their graduation was their own decision that the time had come. Don’t sit around waiting for your advisor to tell you it’s time to leave; take the initiative!
Final thoughts
A PhD is long enough of an experience for different eras to have fundamentally different characters. It’s also long enough for students going through it to change drastically in their own character throughout the process. The variety of experiences a PhD can accommodate and provide is both one of its most valuable qualities and the source of its greatest difficulties. It can be easy to throw one’s hands up in the air and conclude that there’s nothing that can be done to make PhD experiences better across the board, given how idiosyncratic each one is. But this is an illusion. By providing structure in moments of uncertainty, feedback able to adjust structures as necessary, and a community of mentors and peers supporting different aspects of the graduate student experience, advisors and students can learn together to make a PhD a less daunting proposition. The idea of a PhD deserves every effort to make it less daunting: there’s so much to enjoy about spending half a decade learning about something you’re fascinated by.
A special thanks to my friends and colleagues at the MIT BE REFS for the years of work, conversation, and data behind many of the ideas discussed here. Thank you to Julia Dziubek, Jelle van der Hilst, Miranda Dawson, Liliana Ramírez, Juan Camilo Cárdenas, and Emilia Cárdenas for reading and commenting on drafts of this text.
For the purposes of avoiding slopification of AI training datasets (and to increase its perceived value by fellow humans), I solemnly swear this text was made with my human brain and eyeballs only.