Summer is for snoozing, meeting new people, taking a swim, exploring historic cities and it's for sciencing. How might all of that go together? I did a story for Nature Methods on summer courses--it's here and an openly accessible link is here.
There were so many lovely responses when I queried people about these courses that I wanted to share more of what people kindly shared with me. Yes, there are many courses to choose from but these are thoughts and impressions from two of them:
The summer course 'Physiology: Modern Cell Biology Using Microscopic, Biochemical and Computational Approaches’ at the Marine Biological Laboratory in Woods Hole, Massachusetts, which is affiliated with the University of Chicago and
the summer course Cold Spring Harbor Asia ‘Advanced Technologies for 3D Genome Research’ in Suzhou, China.
Enjoy!
These courses are essential components of a greater effort to train and improve science here in the United States, says Zach Geisterfer, a post-doctoral fellow in the lab of Duke University researcher Amy Gladfelter who currently co-leads the course.
The courses and scientists who call the MBL home are world renowned, with some of these courses having been taught for 140 years. They have been central to the development of a great number of scientists who have returned to benefit the global community. “My own career is proof, along with many others in my own lab and associated labs,” he says.
The MBL is a bastion for curiosity driven science - and the loss of such a valuable resource would mean the end to a legacy of cutting-edge research and development.”
Typically, says Geisterfer, trainees in the course differ in their experience levels, some may be early graduate students and others are university level faculty who wanting more wet lab training. Though applicants from all over the world, “there is usually a higher number of Western applicants’ he says.
Says Xiangyi Ding, who is a PhD student in the Starr-Luxton Lab at University California Davis, the lab that that Daniel Starr and G.W. Gant Luxton run jointly at the University of California, Davis. “I hoped to open myself up to new perspectives, learn how to communicate across disciplines, and build friendships.” She believes that a supportive community makes for better science and “This course embodied that,” she says. After returning from Physiology, she shared the experience with as many peers as possible and was surprised that many didn’t know much about the course.
“I hope more people learn about it and are encouraged to apply—it’s an incredible opportunity and truly a unique community.”
Every year at MBL, something new and exciting emerges — it’s part of what makes the course so special. “The MBL Physiology course has led to many existing discoveries, one of my favorites being the work on P granule condensation in C. elegans,” says Raghavan Thiagarajan, postdoctoral fellow at the University of Copenhagen. “What fascinated me was not just the outcome, but the pace and the conducive environment offered by the course for such discoveries.” For example, he says. The concept of phase separation that underlies the process of P granule condensation was done and realized over a matter of days, which is astonishing given that people spend months-to-years to observe and contemplate ideas.
“I see the course not only as a training ground, but also as a hub for building lasting collaborations with fellow scientists who will be part of my research journey for years to come,” says Thiagarajan.
This course offers an exciting ride into how science can and should be done. It offers an ideal environment for asking bold and unconventional questions that one might hesitate to pursue in a traditional academic setting. “It showed me ways to think freely and experimentally,” he says.
“The community is so supportive and collaborative,” says Veronica Farmer, a postdoctoral researcher in the Gladfelter lab. She has attended MBL courses since her time in graduate school and became an instructor in the course. “I have met scientists I never would have met, and was educated from perspectives I do not have.”
Stanford University researcher Manu Prakash has taught in the course “It’s an incredible, incredible course,” he says. And, he says, “it can also become a place for all of us to come collectively and address and discuss the big challenges in science that exist in the near and far future - specifically climate change,” which is a subject he things about plenty these days.
“I cannot speak highly enough about the course,” says Ben Larson, assistant professor at Rensselaer Polytechnic Institute.
“I would say that these summer courses are essential for promoting interdisciplinary science, in contrast to the canonical syllabus taught in subject-specific graduate programs,” says Arnold Mathijssen who is an assistant professor of physics and astronomy at University of Pennsylvania.
His lab works on biophysics, “but our graduate students have a lot of required courses on electromagnetism and quantum mechanics, which are often not as relevant as physiology,” he says. “Our PhD students hugely benefit from these summer schools to learn new techniques, to meet new people, and to exchange ideas across different fields of science. “
“It’s no overstatement to say that the course was the single most influential experience of my career and transformed my approach to science,” says Jonathon Nixon-Abell who is a principal investigator at University of Cambridge.
Says Jennifer Lippincott-Schwartz, the Physiology course at MBL, Woods Hole “is a super special experience for those fortunate enough to have attended.” Seven weeks of intensive lab exposure and the chance to use cutting-edge instruments to focus on ground-breaking questions transformed the lives of many in the course, including her and her postdocs who attended as students or served as teaching associates.
“The environment was unlike any in the world,” says Jennifer Lippincott-Schwartz.
One can scoop up creatures from the ocean, such as A. Victoria for looking at green fluorescent protein or octopus or barnacles to study them. “Many projects started in the MBL course led to major subsequent breakthroughs- from the discovery of cell cycle proteins to liquid-liquid condensates,” she says. Lippincott-Schwartz heads 4D Cellular Physiology and a senior group leader and Howard Hughes Medical Institute investigator at Janelia Research Campus.
“The course has already given me so many great connections,” says Julia Martin, who took the course as a PhD student. One of those connections, she says, “has helped me secure my dream job of working with and building custom microscopes!” Martin is about to start a position at UC San Francisco at the imaging core facility.
Duke University researcher Amy Gladfelter took the course as a graduate student and now co-directs it. Taking the course “absolutely transformed my life.” Applicants are from all over the world and are mainly graduate students and postdocs. There’s a wide spectrum of applicants, she says, “from people who have never picked up a pipette to expert cell biologists who have never written a line of code.”
**
Here is a podcast about the course with Dr Daria Ivanova, a postdoctoral fellow at the University of Geneva, University of California San Francisco staff scientist Dr. Sam Lord, who is a course manager and Dr Will Ratcliff, a principal investigator at Georgia Institute of Technology who was an instructor in the course for two summers. And the story continues below this...and a transcript of the podcast is pasted way at the bottom of this blog post.
This is also on Spotify here, on Apple podcasts here on Amazon Music here. And you can find it on other streaming platforms, too.
**
Why they attended, future plans.
As a graduate student Zach Geisterfer, says he attended a microscopy course in 2019 – that was Analytical and Quantitative Light Microscopy – AQLM and it was “ where I felt like I had finally found my people.“ He felt he could root himself more in the community as a summer researcher in 2022 and then by helping the course as a Teaching Associate in 2023 and 2024. He is now a postdoctoral fellow in the lab of Amy Gladfelter who co-leads the course and he focuses on cell and molecular biology, and biophysics. He would like to continue his career with an emphasis on scientific training and trainee career development. His focuses include cell and molecular biology, and biophysics. Helping teach the physiology course has been invaluable to my training as a leader and a mentor.
Zach Geisterfer feels he has been able to ‘try on’ being a PI since he led trainees through a rigorous research program and he learned “how to develop individual mentorship plans on the fly.”
Ben Larson is assistant professor at Rensselaer Polytechnic Institute and works in cellular biophysics and evolutionary cell biology. He was once a student and several times—likely four times--as a teaching associate for the Physiology Course. “Most of all, I enjoy the scientific atmosphere of the course,” he says. It’s intense and rigorous but also supportive, creative, and fun in a way that is difficult to put into words.
“Being able to just focus on doing science with other passionate people, guiding students on an unpredictable journey all while having access to some of the best microscopes and a revolving cast of some of the brightest minds in cell biology is an amazing experience and an immense privilege,” says Ben Larson.
It also doesn't hurt to be able to easily run off to go for a swim or to fish for striped bass at just about any time of the day or night as well. “My time in the course has been disproportionately scientifically productive, and it has been some of the most fun I have ever had doing science.” He’s made and strengthened enduring friendships through the course. “In many ways, the course feels like my natural habitat for doing science.”
Larson met his postdoc advisor in the course and made connections that have advanced his career. “I met a ton of wonderful people who have helped me feel a part of and supported by my scientific community,” he says.
Without this, he may have decided not to continue on his current career path. An important related realization that came through the course was to reveal to him that he has a unique scientific perspective--as we all do--and that that perspective does seem to have a place in science.
He learned technical as well as less technical, most importantly, “probably a specific attitude toward doing science.” Larson took the course relatively early in his PhD, and “I came away with a new understanding of just how much can be accomplished in a relatively short period of time,” he says. This reduced my psychological barriers to trying out new ideas “even somewhat wacky ones” in order to quickly see how things would work out. And that is opposed to spending time thinking or worrying about doing things
In addition, says Larson, both as a student and TA,” I made scientific discoveries that have significantly advanced my research.”
It was pretty transformative for him, it led to a bunch of scientific breakthroughs, it was fun also very intense, but in a good way, says William Ratcliff who taught the Physiology course for two years and directs the Interdisciplinary Graduate Program in Quantitative Biosciences at the Georgia Institute of Technology.
Jonathon Nixon-Abell is a principal investigator at University of Cambridge, I was a teaching associate on the Physiology course for from 2015-2018 and has continued to revisit in various capacities since.
The course “was the single most influential experience of my career and transformed my approach to science,” says Jonothon Nixon-Abell. The course offers, in his view uninhibited science and engaged people, which in the ‘real world’ is hard to achieve.
Budget restrictions, funder targets and life commitments, can often distract from the purity of doing uninterrupted and innovative science, he says. “The summer courses at the MBL provide the opportunity for students, teaching assistants, and faculty alike to unshackle themselves from many of these practical concerns and really focus on creative solutions to hard problems.”
Another key point is interdisciplinarity, which in the context of the physiology course, this is far more than just a buzz word, it’s a driving principle, he says.
Biologists, physicists, engineers, and computer scientists interact in ways he hasn’t haven’t seen elsewhere, which may perhaps be due to the freedoms provided by the course. “The resulting productivity of these collaborations is clear, with the numerous projects, manuscripts, and grants that have been birthed from the course,” he says. Nixon-Abell remembers NIH researcher Clare Waterman saying “It’s a special feeling when you meet somebody else who has been on the course, and you share a brief look, both knowing the magic of that very special place”.
Debraj Ghose who is a postdoctoral ‘Sloan Matter-to-Life’ fellow in the lab of Donald Ingber at the Wyss Institute at Harvard University, took the Physiology course in 2024. “I loved the course's emphasis on having fun and being non-judgmental while pursuing rigorous science,” he says. Academia often presents challenges and isn't perfect, but the MBL courses and the MBL more generally represent academia at its best, in his view, filled with genuinely curious, motivated individuals collectively driven by a desire to understand nature’s puzzles, especially in biology.
“I enjoyed the community's brazen openness to diverse approaches,” says Debraj Ghose.
In the course he learned a wide range of techniques, from microinjection and advanced microscopy to physical modeling. And he gained experience working with diverse organisms such as Hydra, phytoplankton, and Xenopus eggs. One valuable takeaway for him was that his ‘indoor-lab centric interests,’ which broadly center around biological self-organization, relate to how marine lifeforms harness the sun's energy.
“An especially rewarding aspect was becoming close friends with people who shared a similar scientific philosophy that was rooted in understanding mechanisms underlying biological processes,” she says.
Coming away from the course, he realized many practical things have to be considered in science such as publications and grants. “These are important for progress, but they are not the primary objective,” says Ghose. “The Physiology course focuses on what motivated many of us in the first place—curiosity about how nature works.”
Raghavan Thiagarajan is a postdoctoral researcher in the lab of Jakub Sedzinski lab at the University of Copenhagen. He took the Physiology course in 2023. He hopes to become an independent group leader with a lab based in India for research that focuses on the emergence of self-organization in biological systems, in particular how sub-cellular dynamics and organization give rise to tissue-scale processes.
This course offered him a way to meet some of hiscompetitive international peers. He got to know their interests and passion.
“I was excited about the opportunities arising from the post-course interactions which have already led to concrete outcomes,” says Raghavan Thiaagarajan.
He spent a month after the course in Sebastian Lourido’s lab at the Whitehead Institute where he explored the biophysical basis of host-pathogen interactions, which was a completely new direction for him.
Solving a problem starts by posing questions, reading literature, designing experiments, making observations, gathering data and finally contemplating the mechanisms – and that all can take three to four years, he says.
The delay comes ab out because when they enter a PhD program or beginning a postdoc people are excited, open minded and full of enthusiasm. “This enthusiasm has a decay time which I believe is roughly 3-4 years,” he says. In the three to four years, the researcher spends most of the time exploring, designing new experiments and analysis pipelines that involves out-of-box thinking and a lot of learning. It’s what he calls ‘honeymoon phase’. Then, when this phase is over the pressure to publish tends to shift the focus towards documentation and away from open-ended exploration. “I recognised that lack of learning and excitement kills scientific enthusiasm,” he says.
When those “mind-blowing observtions and solutions’ come about such as those related to P-granule condensation, the course participants were given the scientific freedom to explore, learn for excitement, without any pressure of producing results, “that is, an environment that celebrates learning for its own sake,” says Thiagarajan. “In other words, they were re-offered the first few years of their PhD or postdoc.” It allowed “bold and tangential science without fear of failures,” he says. Spending a few months working on new problems and with new people in an environment designed for intellectual risk-taking is an unique opportunity.
Veronica Farmer is a postdoctoral researcher in the Gladfelter lab at Duke University. She has attended the summer courses since she was a graduate student at Vanderbilt University and progressed over time from being a student and is now an instructor in the course.
“Each year it teaches me a new lesson in mentoring different personalities,” says Veronica Farmer.
The course gives her the opportunity to focus on something besides just her research. Julia Martin is finishing her dissertation at University of California, Berkeley in chemistry. She was a 4th year PhD student when she applied for the Physiology course. “I was interested in learning new microscopy techniques to apply to my research,” she says.
“I was excited to go because of the rich history at MBL and its notoriety for having state-of-the-art microscopes at our disposal during the course,” says Julia Martin.
Martin is about to start a position at UC San Francisco at the imaging core facility. “I am excited to stay within the microscopy field, but now with a focus on developing custom optics and supporting other researchers with their own imaging experiments,” she says. Her career trajectory is to be an independent investigator and train the next generation of scientists.
The mindset of research at the course was different from doing thesis work, she says. Instead of worrying about getting data to graduate with, which often means one sticks with ‘safe’ experiments, “I was able to be more daring with the experiments and focused more on trying new techniques and approaches that I haven't done before.”
What was also invaluable, in her view was the diversity of disciplines. Martin has a background in chemistry and got to interact with microbiologists, neuroscientists, physicists and more. They all had unique insights and perspectives on developing scientific questions and experiments.
“Everyone was supportive of trying out new things that no one has ever done before, and that is what makes MBL so special,” says Martin. The course is seven weeks long and has an intense schedule. “Nonetheless I graduated from the course with some very special friendships and memories that were quite literally life changing to my career goals and approach in science. “
Veronica Farmer’s first course was Analytical and Quantitative Light Microscopy, which she wanted to take to get holistic light microscopy training. She then applied to Physiology because she wanted to have the chance to interact with leaders in the field, and collaborate with people from different scientific backgrounds
Teaching in the Physiology course has given her the opportunity to teach students from diverse scientific backgrounds and a spectrum of personalities, says Farmer. “I hope this experience gives me the confidence and the experience to be the best mentor possible.”
Austin Lefebvre is a senior data scientist at Calico where he works on image analysis tools. He helped to manage and teach the image analysis portion of the 2024 course. “It was incredibly exciting and fun to participate in,” he says. There is plenty to juggle, especially when everyone has microscopy datasets that they've never dealt with before, “so everyone is coming to me asking how to quantify their images,” he says. “But you can tell all the students are excited by it, and want to learn from it. “
In general, Lefebvre sees people’s eyes glaze over when conversation is about image analysis. In a way “they just want to see the pretty pictures but the students actually wanted to know the theory, and the math behind it, it was great,” he says. By the end of the the course some had even built their own custom pipelines, either in Python with Napari or in FIJI.
He wishes every PhD student got to have this kind of broad exposure to model organisms, microscopy profiling methods, and visualization and quantification techniques, especially early on in their studies. “Often times, just knowing the variety of techniques or methodologies out there opens up researchers' minds to what is possible,” says Lefebvre. Some of the students came in to the course with no microscopy or image analysis knowledge and now routinely apply it to their research because of this course.
Ed Wheeler has just started his PhD at the University of Oxford and is a member of the lab of Karina Pombo-García at the Rosalind Franklin Institute. When I interviewed him, he was getting ready to head to the course and looking forward to it.
“I hope to get to first-hand experience working with a wide range of different microscopy techniques,” says Ed Wheeler.
Learning about advanced analysis pipelines will give him skills back to the lab and his own work with stimulated emission depletion (STED) microscopy and light-sheet microscopy. He hopes to broaden his understanding of the microscopy field through the lectures and meetings. “I expect this will inform my career choices both in terms of the remainder of my PhD and future research” he says.
Andrew Countryman, who is a fifth year PhD student in biomedical engineering at Columbia University where they study developmental mechanics in Drosophila applied for the MBL Physiology course to improve their ability to form and answer research questions and to become part of a community of scientists.
They were particularly interested in the Physiology course because of the way it emphasizes building a research mindset. “I thought that having the opportunity to come up with scientific questions and design experiments for systems that were completely unfamiliar to me would sharpen my scientific thinking and experimental design abilities,” says Countryman.
Additionally, they hoped to gain experience with an array of techniques and microscopy approaches that they otherwise would not have had the opportunity to work with at their home institution.
Before Physiology, says Andrew Countryman, “I had had few opportunities to build my scientific network beyond my lab or university, and taking part in the course really made me feel like I was connected to a worldwide community of scientists.”
“Through my experience in Physiology, I grew to feel empowered as a researcher,” says Countryman. They entered the course thinking that they could only make useful contributions in their specific subfield, and “I left feeling that my expertise and skills uniquely positioned me to contribute intellectually to a range of research topics across many model organisms,” says Countryman.
Daria Ivanova who just completed her PhD at University of Geneva and took the course in 2023 and is now a post-doctoral fellow at the university. It was a "mind-blowing, life-changing experience, she says.
Xiangyi Ding is graduate student at UC Davis, she took the Physiology Course in 2024 “and found it to be a truly transformative experience.” At first she was intimidated by the idea of taking on a completely new research project—learning the background, conducting experiments, analyzing data, and preparing a presentation—all within two weeks. The course showed her how this can be done, with a combination of collaboration and independence, supported by teaching associated and peers. “It completely changed how I work.”
She liked that the course stated with Skill Week to familiarize them with the tools and the people we’d be working with. The course involved balancing intense lab work with community-building and that was both was essential and rewarding. “It fostered friendships and networks that made the experience even more meaningful, says Ding.
The joy of it
Geisterfer is now a post-doctoral fellow in the lab of Duke University researcher Amy Gladfelter who currently co-leads the course. Mentorship is to him, the most rewarding part of science. Heping to teach the Physiology course is a concentrated form of mentorship, where one teaches and mentors trainees through a project over the term of the course.
“It's intense and exhausting, but the reward is seeing amazing scientists make discoveries and connections that will stay with them for the rest of their scientific journey,“ says Zach Geisterfer.
His own career and his journey in life have both benefited from this community.
Overcoming hurdles
Hurdles do occur, says Amy Gladfelter, “but I’d say for the most part where there is a will, there is a way and these situations so far have been rare,” she says. “ I hope that continues.”
It happens that people who want to attend the course do not end up being able to do so. “This is certainly a large issue for international students,” says Geisterfer. Some courses can last nearly two months and thus visa issues are common amongst international applicants. It’s also true that the course is not free. Not all principal investigators can afford to send a trainee to a course for two months. In his observation if applicants can find financial support it helps ensure that applicants from well-funded labs as well as newly established labs can attend.
As a U.S. citizen, Countryman didn’t face any visas issues. Their participation in the course was funded around 70% by a NSF grant to MBL and around 30% was covered by their home advisor's funding.
Martin was worried that she would not be able to attend the course due to funding “but I just asked and I got the funding I needed,” she says. “All tuition and accommodations paid for by MBL.”
Veronica Farmer is a postdoctoral researcher in the Gladfelter lab at Duke University knows that the worry about not being able to get a visa is a big problem for some participants. “Financial aid for students is imperative to ensure cost does not inhibit students from applying,” she says. She knows that some principal investigators can be reluctant to spend this money.
Ed Wheeler from the University of Oxford says the US visa application process was lengthy but quite simple. It took about two months to sort out, but he planned to reapply in case there are any issues. One hard task for him as a British citizen was to identify a good health insurance provider. “In terms of grants, I was subsidized through the generosity of Woods Hole, plus travel grants from my University, College and program.” He looked around for other grants, too, “but it turned out to not be necessary.”
A postdoctoral fellow at a university in the UK and who will not be named, tried to get a visa to do a post-course stint in a US lab with one of the course organizers. The plan was to continue work started during the course. The student is from a South American country. Even after nearly a year, he was unable to get the visa approved and had to abandon this project and his plans to do a postdoctoral fellowship in the US.
Ding heard from several people who were interested in taking the course but discouraged by the cost, even though they had scholarships. “The course is also seven weeks long, which means stepping away from ongoing work in their home labs—a commitment not everyone can make,” says Ding.
This course, says Gladfelter, has had probably the most impact on generations of cell biologists because it does not teach content or even technology, “it is a way to set a culture for the field that values collaboration, humility, exploration, risks and imagination. “
It shows the value of relationships and builds connections across the planet that last a lifetime. “These values are what people take from it for the rest of their lives and this has an indelible impact on the field of cell biology because these are values that people bring to their classes, their labs and their communities for the rest of their careers,” she says.
“The course is vulnerable to the current financial crisis in science and I am deeply worried about its future.”
-
The summer course Cold Spring Harbor Asia ‘Advanced Technologies for 3D Genome Research’ in Suzhou, China is a little over a week long. Here are some comments from participants and organizers.
Yijun Ruan from Zhejiang University is a co-founder of the 3D genome biology field. He started and co-runs the course. He thinks that 3D genome analysis techniques are often seen as tough to do and learn, so this course can help change this perception. His research interests have been about developing advanced tools to study the underlining genomic mechanisms that relate gene transcription during development of healthy and disease cells. "Specifically, my group pioneered a number of sequencing-based methods for the mapping of long-range chromatin interactions in 3D genome folding and helped establishing the filed of 3D genome biology," says Ruan.
Most of the course participants are students from mainland China. A few international students from South Korean and Europe take part and there have been more experienced researchers, too. One of them from the US took the course to plan 3D genome mapping approaches in his research program.
From an organizer’s perspective, he says, the first summer course on this topic was a good success. There were an overwhelming number of applications, the evaluations were good and scientists in the field had good things to say about the course.
We therefore decided to continue this summer course in the next several years and plan to cover some of the most advanced technologies including single-cell 3D genome mapping methods," says Yijun Ruan.
The cost to attend the CSH Asia summer courses are reasonable, says Ruan. "Most labs with normal supports should not have financial issues to send students to attend," he says. "In fact, our course is limited with only 30 spots due to restricted lab space allowed, and we have to decline many applicants."
Many were interested in taking the course but could not attend due to the limited number of spots, says Yi Zhang, who took the course as a PhD student The organizers offered scholarships to help cover tuition fees for those with financial difficulties.
Cyang Li took the course in 2024. He is a PhD student at Tsinghua University developing tools to manipulate 3D genome structures.
Although he had theoretical knowledge from textbooks and papers, he was eager to sharpen his lab skills and integrate sequencing approaches into his own research. The CSH Asia summer course with its valuable hands-on practice seemed to him as a great opportunity .
Participating in the course was an amazing experience, says Li. The surroundings were beautiful, I met many interesting people, and I learned a lot in a smooth and supportive environment. It was a refreshing break from the lab that helped me clear my head and refocus.
His advisor had recommended the course and encouraged him to participate because establishing a platform for these sequencing techniques aligns with the lab's interests. "I've always been interested in 3D genomes since I began my journey as a scientific researcher," he says.
HIs advisor also actively encouraged his participation, says Li Qinghua. Each day included lectures from leading experts in 3D genomics, followed by hands-on lab sessions where they practiced techniques like Hi-C and ChIATAC, says Qinghua, who is a PhD student at Peking University's department of medical biochemistry and molecular biology. He works 3D genome organization and chromosomal structural variations in cancer.
He applied to the CSH Asia course to get a deeper understanding 3D genomics methodologies and refine his analytical workflows.
"The program’s emphasis on integrating single-cell technologies with 3D genomic approaches particularly resonated with me, as these innovations hold immense potential for studying tumor microenvironments, " says Li Qinghua.
He wanted to explore synergies between epigenomic data and 3D genomics to advance cancer epigenetics. The structured curriculum, combining expert lectures and hands-on training, gave a robust foundation for designing interdisciplinary projects. "Ultimately, I aimed to translate the acquired knowledge into establishing a comprehensive experimental-analytical platform in our lab, enhancing our capacity to address complex research questions," he says.
"The schedule was demanding but incredibly enriching," says Li Qinghua.
He was glad that the course let him link new knowledge with practical skills in a short timeframe. It "left a lasting impression," he says.
The course gave him with advanced technical expertise in 3D genomics, specifically hands-on training in ChIATAC and Hi-C methodologies. He now uses these skills to study tumor heterogeneity and chromatin spatial organization.
"These techniques have significantly enhanced my ability to map chromatin interactions and integrate these findings with epigenomic datasets—a skill pivotal for uncovering mechanisms in cancer progression," he says.
The practical sessions also gave him a deeper understanding of experimental design and data interpretation in 3D genomics. The collaborative environment and discussions with peers inspired him to explore interdisciplinary approaches, broadening his perspective on applying these tools to address complex biological questions in oncology.
The course was an unforgettable experience. Beyond gaining cutting-edge knowledge through lectures and lab sessions, I formed lasting connections with peers who share a passion for 3D genomics, says Li Qinghua.
The collaborative environment and exposure to emerging technologies have profoundly influenced my research approach, he says.
I would eagerly participate again and highly recommend the program to others in the field.
Yi Zhang took the course as a PhD student and he is now a postdoctoral fellow at the Center for Interdisciplinary Research in Biology, Collège de France. "I truly enjoyed the cutting-edge scientific lectures during the course, says Zhang.
Zhang's supervisor supports participation in international workshops and training courses. "She quickly approved and encouraged my application," he says. The same kind of encouragement is what he experienced, says Qi Tian, a PhD student t Sun-yat sen University. His y supervisor values training in emerging technologies and actively encourages him to pursue opportunities that foster interdisciplinary growth. "I’m deeply grateful for his generous support and trust."
Zhang had applied to learn the advanced technologies and the highly skilled techniques needed to use them. His research focuses on the pathogenic mechanisms of fusion proteins in leukemia, and he wants to use these 3D genomic methods to address transcriptional regulation questions.
The organizers invited leading experts from around the world in the 3D genomics field to share their latest findings and ideas, which he found inspiring. He appreciated the hands-on lab sessions, which guided the group step-by-step through complex techniques and had the opportunity to discuss technical details with instructors and fellow participants.
"Additionally, the social activities and cultural events outside of the classroom created unforgettable memories," he says.
To get to know one another, says Zhang, there was a gathering and everyone introduced themselves first in terms of their academics and their personal lives. After that, everyone got together to drink and play games.
Qi Tian, a PhD student from Sun-Yat-sen University is a newcomer to the 3D genome field. He seeks to use new tools for detecting three-dimensional genomes to study the fate determination and transcriptional regulation mechanisms of stem cells from a new perspective. Participating was a way to gain a solid foundation in the core principles, the leading technologies and analytical methods used in 3D genome research.
"I also hoped to connect with peers from diverse scientific backgrounds and explore how 3D genome technologies can be applied across disciplines in life science," says Qi Tian.
Structure dictates function, but when it comes to the cell nucleus, it remains an open question how chromatin architecture influences or even determines transcriptional events. He hopes to build the the experimental and computational methods taught in this course into his own research on stem cell fate and transcriptional regulation. He also took part to expand his understanding of the field and gain new perspectives that can inform the design of future projects. "And I hoped to meet potential collaborators who share both curiosity and joy in doing science," he says.
This was Tian's first summer course, "and it has fundamentally reshaped how I think about academic communities," he says.
The course lacked the formal atmosphere of large conferences and felt more like a close-knit family. The professors were approachable and generous in sharing their expertise, offering extensive hands-on training and thoughtful guidance.
The course participants come rom different regions, fields, and career stages became friends through the course’s well-planned social activities.
We learned new things together, discussed our career paths, got excited about new ideas, and explored a new city as a group. It was not just a course—it was a beautiful journey we shared, both in science and in life.
(Credit: PhotoDisc/Getty Images)
Transcript of the podcast Science summer: The MBL course 'Physio'
Note: These podcasts are produced to be heard. If you can, please tune in. Transcripts are generated using speech recognition software and there’s a human editor. But a transcript may contain errors. Please check the corresponding audio before quoting.
Daria Ivanova
It was really, the experience I would count in like three top of the best summers of my life.
Vivien
That's Dr Daria Ivanova, a postdoctoral fellow at the University of Geneva, talking about her summer. One of the three best summers of her life. Okay, that sounds pretty great, right? Hi and welcome to Conversations with scientists. I am science journalist Vivien Marx. I have not produced a podcast in a long while. I had health reasons, mainly and unfortunately, but I'm back and happy to be back. This episode is about summer and how some scientists spend their summer. Here's another sneak peek. This is University of California San Francisco staff scientist Dr. Sam Lord, who is a course manager.
I think people come back with a more collaborative and collegial outlook on science. These are courses that can change you just briefly, though, before we get to those courses about these podcasts and thank you for tuning in when I do stories, a lot falls on the proverbial cutting room floor, and these podcasts are a way to share more of what I find out and hear this podcast is about summer courses. Yes, I know summer is for chilling and snoozing in the shade, taking a swim, maybe having a chat on the beach at sunset and into the night.
For many scientists, this kind of Summer Chill Out is not easy to come by, but there is a way to combine chilling and sciencing. Well, true, what people will be talking about in this podcast is probably more sciencing than chilling, but they still manage to combine the two a little. And just in case, you are not yet a scientist and maybe have never touched a microscope because you are more of a theory person, these courses can be for you too, and if you are not at all a scientist, that's totally fine. Please come along and hear how some researchers spend their summer. I did a story for Nature Methods and a blog post about summer courses.
One of them is the course physiology at the Marine Biological Laboratory MBL in Woods Hole, Massachusetts, which is part of the University of Chicago, and the other is a course at Cold Spring Harbor Asia, and it's called advanced technologies for 3d Genome Research, and it's in Suzhou, China.
There's a link in the show notes to the story and the blog post about these courses. People told me so much about what they experienced in these courses as participants, as teaching, associates, instructors and organizers. In this podcast, I want to share more of what I heard about the MBL summer course, Physiology is the shorthand.
The full name is physiology, modern cell biology using microscopic, biochemical and computational approaches. There are lectures, there's time in the lab, but in many ways, it's not exactly a typical course. This podcast talks about the course some practical things, what it's like when you are there, and what it feels like afterwards, what it teaches you about yourself and about working in a community. Please come along for some summer sciencing, you will meet a few people you've heard from already. Dr Daria Ivanova, who just completed her PhD at the University of Geneva, and she is now a postdoctoral fellow at the University of Geneva. Dr Sam Lord is also in this podcast. He's a staff scientist at the University of California San Francisco. He's in the lab of Dr Dyche Mullins, and you will meet Dr Will Ratcliff, a principal investigator at Georgia Institute of Technology in 2023 Daria Ivanova took the physiology course, and the course organizers were Dr Nicole King from the University of California Berkeley, and Dr Daniel Fletcher, also from UC Berkeley. And when I spoke with Daria, she was just about to defend her PhD, it's too early.
Vivien [4:00] Congratulations, though, anyway, for what's about to happen.
Daria Ivanova Thank you.
Vivien Take me back to 2023. What was that, course like, I mean, and why did you decide to do it. Like, I mean, that's a seven, seven weeks, six weeks. Yeah, it was like, what was it? Two months?
Daria Ivanova
I think, yeah, almost two months. Wow, okay, and you were in Geneva also, or were you also...? Yeah, yeah, I was in Geneva at this point. And actually, my boss has encouraged me to apply, yeah, because we have, well, you know, the physiology course is really meant to for you to become independent in the way you think about science. And we already had one lab member who went few years back.
Vivien
Oh, I see that. How cool. I've been hearing that a lot, that it really depends on your PI, but also people being supportive, because two months, that's a lot of time, well, they're like, shouldn't you be at the bench?
Daria Ivanova
Yeah, for sure, yeah. But I mean, I was lucky. My PI is very understanding. Also, like, he would like us to be, you know, to continue science. Vivien And so who is this again? Just, is your PI on your page? Yes?
Daria Ivanova
Patrick Meraldi, yeah.
Vivien Okay. Ah, nice. I see. So there was support. Still. You decided you wanted to kind of take your project and put it on ice or in the freezer or wherever, for a moment. And do this that takes a lot of courage so…
Daria Ivanova Well, you know, my project was, actually still is going very well, and I was in a very good track. I'm actually was collaborating very closely with another PhD student, so I didn't really have to put completely everything apart, but she was able to take a bit care of the project. And then when I came back, she went for an exchange program, so we, like a bit coordinated, and it was okay.
Vivien That's nice, I see. And so were there others from outside the US in the course, or was it International? Or were you the only person from outside the US?
Daria Ivanova
So, yes, it was International. It was we had few. So I think maybe two people that was, there was for sure, one person from Japan, maybe two people from UK. Well, yeah, someone from China, one person. But actually, when I came back and I was telling about the course, then my PI said that actually it used to be much more international. So when this other PhD person went in 2018 maybe he said that there was like 10 other people from Europe.
Vivien Wow that's a real change. I mean, it's expensive, but it's also time. Did you have a you had a fellowship later, but did you have a fellowship for this too? Or how were you paid? I mean, and somebody had to pay the course fee, of course, and the flight and all that.
Daria Ivanova
So first, the first, of course, I was able. So there was, like, partial scholarship from MBL, actually, even two, I believe. So my course fee was reduced, like, to 3000 euros, maybe. And then my, well, I applied for two other scholarships, but so one, my boss actually got it because he applied for something else, and I so I didn't get it the same lab, and the other one I didn't got, so he paid for it.
Vivien
Oh, that's so great. Yeah, okay, so, so what was it like? I mean, obviously, it's very intense. I mean, it's like, morning to night, it's lectures, but it's also time in the lab, what, you know, and there's freedom, but it's also, like, very intense. So what was it like for you?
Daria Ivanova
It was the last year of Nicole King and Dan Fletcher. It was really , the experience, I would count it in like three top of the best summers of my life.
Vivien Wow. Summer is supposed to be beach and sunshine. No, I'm kidding, no,
Daria Ivanova
But really it was great. It's I spent, you know, so much time really thinking about fundamental things in life, and, you know, being able to tackle them in a very simple way, or also having other people thinking about it too, is really very inspiring. And it's like, also like, having this community, which actually is really supportive, is not something I mean, despite the my lab being a very good lab, I've never really experienced it in this way, right?
Vivien And I mean, it's a lot of people, you know, talking science in the in the hallways and next door, there's another course going on, right? So it's like, Daria Ivanova Yeah, yeah. And also, like, just this feeling of being able to do what you are interested in and what you want, just you know, for a few weeks, because you know not, not to be working on your own project, but just to think outside of all those things you're doing, and then, you know, do something completely different, it's really nice. Vivien And did you feel like you learned something that you didn't like you could try something that you didn't normally try? I know they have a lot of fancy microscopes there, and there's probably also other things.
Daria Ivanova
Yeah, yeah. I think the biggest thing I learned is really like to be very it gave me a lot of courage. So, like before, I used to, you know, before I do something, I would search the protocols, and then I would talk to people. And maybe I would prefer that people actually. Actually teach me how to do things. But like when I came there is, you know, you also don't really have so much people around who can teach you, you know, so you have to really learn by yourself. And it's, yeah, it's really this, you know, feeling that, you know, there's also this microscope, you know, a bunch of, like, different microscopes, which you can try, but also which are all really, really expensive.
And I used to be really frightened by it here the university, like, you know. I mean, when something costs $1 million for example, it's not something you want to break.
Vivien No. And then, of course, you have a limited time there, right? And the core facility is a big place, and they're looking at their watch a little bit, and it's not the same kind of environment as where they say, oh, go sit over there.
Daria Ivanova
Right, right, for sure. Yeah. And, but, you know, I found that, you know, I could try any, I could try things. And it was, you know, I didn't really feel like I could break anything. I mean, I could break, probably things, but it was not really, I mean, I could always ask for help, and, yeah, I just really learned a lot of things very fast, just like trying things. This was something which I learned. Then, in terms of science, of course, I learned a lot of things in lectures. This was also it helped me a lot here, because I noticed it when I came back, I started to ask myself much more fundamental questions.
Because, you know, like before I would ask, maybe, if I would go to seminar, I would ask things like, oh, you know, how did you do this technique, or something like this. But now my question really goes, usually beyond the techniques, but really goes to maybe more evolutionary points.
Vivien It sounds like the course really changed her approach to science, and I had heard this from other course participants too. It certainly seems like a powerful summer. I asked a bit about how the course unfolded, which was organized by Nicole King and Dan Fletcher, and had many different lecturers.
Daria Ivanova [12:05]
Yeah, there was like every day. So we had six days a week, a lecture in the morning, from 9am yeah. And so every day there was a new lecture. They usually would invite really, really interesting people, and it was really all over places, evolutionary biologists, it would be biophysics. I mean, everything whom they I don't know how they invite people, but I guess people they knew would do good science or, I mean, they would invite them. And this was well, you know, and also the fact that we were there alone, just us and the lecture, you know, gave me the possibility just to ask all the time. We would ask all the time, every time there was like, 10 questions after the lecture.
Vivien It was encouraged right? It's not just like your lecture, where you're like, supposed to sit and take notes or just listen.
Daria Ivanova
Exactly. Yeah, yeah, you you ask questions. You even ask questions during the talk. And like, then we had the, really a chat only with a like us and the lecture, because so the lectures itself are usually were open to other people. Not so many people would come. But still and but after that, we had, like, really, a coffee session with, with a speaker, and there you could ask, like, anything you want, like, also about career or, you know, personal things.
Vivien Nice so you, I mean, you're learning about what it could be like to be an academic, have a lab, but maybe also, as you mentioned, you know, do the post-course research, wow, I see. I mean, it sounds like a really creative time, intense time. Did you also have time to do things like, have a glass of wine, go for a swim or no?
Daria Ivanova
Totally. Yeah, we went. It was really, as I told you, it was a really great community. So in the evening, at 10, we had the beer session. And it we had really, like, a beer. And sometimes you had the car, okay, you know, it's was a lot of fun. Sometimes people will still go to the lab after the beer session. Like, I know that some people stayed, like, in the lab, sometimes until morning. I'm not this kind of person. I have to sleep.
Vivien Yeah, sleeping is good. But I guess, because it's open, you could, you know, go and do something, or maybe, you know, passage cells or whatever you need to do. So are you still in touch with your I guess you could say, is there like an alumni group, or is it like a, maybe something loose-knit, that you may be people you see or talk to?
Daria Ivanova
So, I mean, most of people were in US, so I was not, I mean, I didn't see them after I have met the person in Japan, because I went to Japan last year. Actually, I met him, yeah, and I met also Amy. Just out weeks ago. She came to Switzerland to give a lecture. So we had a little chat also.
Vivien The Amy she mentions is Dr Amy Gladfelter from Duke University, who is the current physiology course co-organizer at the MBL after the course participants can sometimes get the option to spend time in a lab of one of the course instructors. And Daria Ivanova wanted to do that specifically she wanted to go to the lab of Dr Wallace Marshall from UCSF, but the visa didn't work out for that. She also wanted to do her postdoctoral fellowship in the US, but that didn't work out either. In Woods Hole she got to know a different side of science that really appeals to her.
Daria Ivanova [15:40]
Yeah, I would have done the post doc in the US. I really like the way science and us is made. It's really, I mean, yes, okay, maybe MBL is also very like completely different place and the very like special place. But also feel like people at the MBL, they come from different institutions, and really the way they do science, but also the way they have the open mindedness about science is really special. And, yeah, I wanted to do postdoc in US. Yeah.
Vivien The post-course research thing is basically not a postdoc, but it's like a phase, maybe three months or six months somewhere, which a lot of people do, and you tried to do that, right?
Daria Ivanova So actually we it's because we started the project. So in one of the rotations with Wallace, and we discovered something really cool. So his PhD student wanted to continue working on it, and I really wanted to be part of the story. So, yeah, I first presented it actually they, I was Nicole as they select me to present my work for this symposiums I make every year at Woods in Woods Hole. It's called Shinya Inoue imaging symposium conference. So yeah, and then I went, when I finished the course, I wrote to Wallace saying I would really like to come. I would like to apply for the for the money from the MBL to come. And he was really glad, because the project, they continued the project and will happen and well, it went really nowhere. I tried everything
Vivien She truly wanted to experience working in the US as a post doctoral fellow. And I should say, Daria Ivanova is Russian, and living with her family in Switzerland. Daria Ivanova So I'm from Volgograd, you know, on the south border with Kazakhstan, really south. Vivien In an academic trajectory, it's viewed positively to go elsewhere for a post doctoral fellowship after your PhD.
Daria Ivanova [18:00]
If you want to become professor, you really have to have postdoc mobility, additional point points. And basically, if I would stay in Switzerland, there will be no mobility. So there's not even point of trying in academia, honestly, because, because then it's really easier to go in the company.
Vivien That's hard. I mean, you know what company R&D is like, right? And you know probably where to look. But you know that, of course, it would be nice if you had an opportunity to to go elsewhere,
Daria Ivanova Yeah, of course, yeah. But yeah. I mean, I guess sometimes I think that, like, you know, really, academia sometimes is something for for people who have a stronger passport.
Vivien Ooh, a stronger passport. Hearing that made me pretty sad. I do hope that the world of science can be a global place of exchange and growth, which is not easy to say right now, Daria Ivanova had a dream that she could not fulfill.
Daria Ivanova
I really wanted to do the postdoc in us, and it was really my dream when I also came and also when I went to the physiology course, it was really like, I saw how the science is made. And I really wanted to do this, and I can't find it like really anywhere else I've been also to Germany and to France before, and it's not really the same thing.
Vivien It would be great if an opportunity comes through for her. National borders shouldn't really present barriers in science, but they do. The combination of her dream and her experience with the summer course are perhaps both why she cherishes the course experience so much.
Daria Ivanova [19:40]
It's a very special place, yeah, and it's, you know, I so, I think it was something which is, really was one of in a lifetime opportunity, and I'm so happy I took it. It's, it's really beyond my words, really to say how much I'm thankful. For them to accept me, because, honestly, I didn't even think they would.
Vivien Did you also work with Will Ratcliff by any chance?
Daria Ivanova Yeah, yeah.
Vivien Ah, okay, because I interviewed him too. Daria Ivanova He's so nice. He's really cool, and I love really this evolutionary aspect of his work. It really made me very interested in evolutionary studies. I've never thought before that I would be interested in evolution so much. Vivien You will hear about Will Radcliff in a bit. Next is Dr Sam Lord during the year. He is a staff scientist and microscope specialist in the lab of Dyche Mullins at UCSF. He was a teaching associate in the physio course in 2018 and 2021 when Dr Mullins taught the course and then Sam Lord became the course manager.
Sam Lord
This is Sam.
Vivien Hi, Sam, this is Vivien. Strike the iron while it's hot. Is that ok?
Sam Lord
Yeah, sure. Hi.
Vivien From my teeny experience in a course I audited for one summer at the MBL, and I hopped around in other courses and labs too. My observation was that being a teaching associate is a long day, and I just wanted to say, I apologize for the sound quality I caught Sam Lord on his cell phone, and I didn't want to miss the opportunity to chat with him.
Sam Lord
Yeah, no, it's ton of work. And, you know, I've had people say at the end, why do I do this? But I don't know why I did it the first time. But my professor was like, you know, he took the course, and
Vivien I see, and this is so in 2018 were you also in? Who were you then? Just say,
Sam Lord [21:15]
At that time, well, I'm still now I'm the microscope specialist in the lab, right? So I did a postdoc, my post postdoc. But he, yeah, so he invited me to ta with a few other grads, another grad student and a postdoc from the lab. okay?
Vivien And just because you know simpleton here, can I call you a staff scientist? Is that okay?
Sam Lord
Sure, that's fine.
Vivien Awesome
Sam Lord
So I work for Dyche Mullins. He took the course when he was between graduate school and postdoc, and it like changed his sort of career.
Vivien Really, huh.
Sam Lord
Yeah, well, he was like an engineer, and took the course and ended up doing a postdoc for one of the professors that he had worked with in the course. That happens to a lot of people.
Vivien Huh, I mean, that's a big switch, right? When you kind of think, yeah, Huh, interesting. I mean, I've heard that before, but it's always cool when that happens. I mean, it's unsettling, I guess, in that moment where you're like, Wait, I thought I was going to do B, I don't know, x.
Sam Lord
And then directors, usually, at least these current directors, the previous directors that I worked with, they were usually, they tried to find, like, a diversity of people that are coming. So not only people that have a lot of experience in cell biology or at the bench top with microscopy, but some people have never touched a pipette, or theorists, you know, people that are don't know anything about biology, to help them sort of bridge from grad school to postdoc.
Vivien But that means that you have a wide as a TA, you have some people who are like, 'this isn't, I don't know, the microscope isn't set up, right, or some parameter that I usually use isn't set up.' And then there are other people who are like, Okay, where's the on button?
Sam Lord
Exactly.
Vivien Good for you.
Sam Lord
Yeah. So it's pretty exciting to get people, and by the end of the two weeks, they're like, you know, doing the experiment, and super excited about a new skill that they never had.
Vivien
If you are thinking about acquiring a skill you didn't have, or if you are thinking about applying more generally, you should. It's definitely competitive. And it's true that it is seven weeks, which is a long time. And days, well, they can last from eight to midnight. Vivien Eight to midnight, okay, fine.
Sam Lord
Yeah, yeah. TAs work a lot. Yeah, eight to midnight, that's right, and the students work even harder. The TAs also have to prepare for weeks or months ahead of time, right? To bring a project that's going to work, have all the materials like express proteins that they need, so you have a tone of work. And so I think that is part of, you know, that's probably one reason why there's a lot of like, you know, I came from a lab whose professor had experience in the course, took the course and then as a director for the course for five years. That, you know, because then they encourage their people like, I know that. Sounds crazy, like you're gonna work really hard, but you should do it, and so that's great, and also that the professor's willing to take time out of their summer to go and work and bring people with them. And you know, it's two weeks that it's only two weeks, but it sort of on either end, takes some time, a lot of prep work and oh, why
Vivien The course is shorter, shorter than the other ones. I didn't realize that because
Sam Lord
There was two week rotation. The whole courses is seven weeks, right? But the professor's only there for two weeks with TAs.
Vivien Oh, I see.
Sam Lord And then they rotate out, and there's new ones that come in there. The students are there the whole time.
Vivien So you, you're basically there to set up. And then I guess you come back later to,
Sam Lord
Oh I'm there the whole time.
Vivien Yeah, oh, you're the whole time. Wow. Okay, did you have time go swimming. Sam Lord Oh yeah, you go swimming every day, but yeah, everyone has time to do that. We're there a lot but there's breaks. Vivien Sam Lord encourages people to apply for the course.
Sam Lord [26.05] The courses are very well known, and you know, they do get a lot of applications, but they're not like flooded with applications, I think partially because, unless you've had some experience with the course, I think a lot of professors are reluctant to send their grad student away for seven weeks.
Vivien Oh, right, because that's really an absence that'll be felt in in the home lab, wherever it is, if it's in the US or wherever, it doesn't matter, it's
Sam Lord
Yeah and and often the home lab pays tuition and stuff, so sure, like, you have to be motivated to send your person, your people. So I know, you know, I remember when I was in grad school, I did chemistry, so it wasn't really like in the same realm. But my friend wanted to do the course asked her professor multiple times, and every year he said no.
Vivien Yeah, so it's about the time, but it also, I guess this is maybe important for me to really highlight, is that it can, I mean, without wanting to sound like New Age or something, but it's like, it does change your outlook, and that you bring stuff back to others and for yourself, right?
Sam Lord
Sounds so motivating. You come back and you're like, I mean, maybe not the first week you come back, but you come back with, like, all these new ideas, all these new techniques, scientific ideas that you had never been exposed to, and you come back and apply them to your work. And a lot of professors come back with, like, Hey, you use that really cool microscope for that really cool cell sorter, or that really cool, you know, cell country, something. Maybe we should write a grant for that. A ton of a ton. It's such concentrated exposure to science and, yeah, so you come back, students always come back with, like, a new lease on life to take their project places where I hadn't gone before. And there's this post course research opportunity that you can apply to, and a handful of students get to, like, continue their project after the summer is over, no time. Throughout the next year, they come, they go to the home lab with one of the professors that I've worked with over the summer, and they finish up a project or continued along.
Vivien Oh, that is super cool. I did not know that. So that is really, like, I can see how where that energy comes from. I mean, I felt it myself when I was there, but for different reasons, because I'm one of those what's a pipette people. I mean, but what I felt was great was just that people sounded like and I observed this, or at dinner table, they're like, do you want to come watch or doing this thing with sea urchins? And I was like, Sure, it was always interesting.
Sam Lord
Hmm. I think, I think people come back with a more collaborative and collegial outlook on science. So much collaboration during the course. And you see professors coming in at professors and TAs coming with so much. They're giving so much, you know, their time, their their reagents, their expertise. And you walk away with this idea that, okay, that one, you know, that's what you do in science. You help other people, you get your stuff going, and then you stand other people, and they have new ideas that you had never thought of, because the TA has come come home also saying, like, oh, we had this student who was great. They had all this experience in like, who knows, whatever you know, like sequencing, and we don't do that. But they decided to sequence our programs, and we hadn't done that before, and it can open up a new project that the TAs have never thought of either. I think people come home with just a lot of collaborative ideas and and reach out to people that they worked with on the course, but also, just like anytime someone comes up to you and says, hey, I'm interested in your technique, it kind of like sparks a little memory of of that, like with whole experience and you're much, I think people are much more likely to say yes and help out new faculty and stuff.
Vivien Yeah, that's, I mean, it's not probably, you know, impossible. I mean, I suppose at UCSF, it's maybe even daily, but it's, it is difficult, if you're a graduate student, to just go up to somebody and say, Can I hang out here for a few days? And they'll probably look at you like, right? Yeah, sit in the corner at a camp rise, or, I don't know, whatever I see, huh? Well, that's important. So then it's like, I mean, I'm getting, like, this transformative vibe that is different from, say, you know, just it's exciting to be in grad school and all that, and at an important Institute, but there is kind of a structure that is there, and then in Woods Hole, it's about, you know, I don't having dinner or breakfast or just hanging out and talking and maybe looking at a neighboring lab or something falling into conversation that really then says, Oh, you guys are doing that. Let me Yeah, the course changes you. And that is not just true for participants. It also is true for teaching associates like him. Here's Sam Lord,
Sam Lord [31:40]
From my perspective, as a TA and seeing other TAs. I do think it opens up new avenues I know I know multiple dogs who basically started projects at Woods Hole. They like, come out of the woodwork, and then they continue them for years.
Vivien Ah, okay. And are you in touch with, I mean, obviously, with people who you know from the course. But are you staying in touch with people that. Sam Lord Way, yeah. It's like, yeah. It gives you this little community. You know, you go to a conference and like, you're just like, walking down the hall, and you're constantly, like, waving at people that you took the course with, or TA with, or Vivien Nice, nice, nice, nice,
Sam Lord
met at a party. Yeah, there's a lot of and it opens up collaborative ideas
Vivien
One word that kept coming up in interviews about this summer course is the word transformative.
Sam Lord [32.40]
You got the word right, transformative. It really transforms before and after, pushes them on a different path, and career wise too, because, like, they meet all these people, and often they go and do a postdoc, I know as many people, like, just interacting with other people, then they say, Hey, remember I took the course you or I was a TA for so and so you were there. And it just helps people connect
Vivien right in a way that you can't if you're going to a cell biology meeting or even the more
Sam Lord
Tat helps too, but it also lets you move out of your field, because, because you go, you're like, Yeah, I was doing, like, cell culture, but you were doing atomic force microscopy, and I learned how to do that cool. Now, I had never thought of that, but now I want to do it that kind of
Vivien thing. And just briefly, I'd be curious person here, but like so as a chemist, how did you end up in biology kind of but also microscopy?
Sam Lord
I was doing single molecule imaging and microscopy. And we had some collaborations with some cell biology people like image single molecules in cells. And then I did a postdoc where I was kind of imaging cells with collaborating with a biologist, but I realized I want to do more the microscopy side. And I just chatted with Dyche, my current PI, and he was looking for someone to help, you know, maintain microscopes. And I was like, Well, I like doing that. That's like, what I like doing day to day.
Vivien Oh, cool. So you crafted your own kind of a spot based on sort of things you learned and things you had an affinity for,
Sam Lord I slowly moved into this, like biology field.
Vivien It's always interesting to hear how people transform themselves and their careers. So if you take the course something like that, something transformative might happen to you too.
Next you will hear from Dr Will Ratcliff, an evolutionary biologist from Georgia Institute of Technology, who taught in the physiology course for two years at Georgia Tech. He directs the Interdisciplinary Graduate Program in Quantitative biology, and he studies the evolution of multicellularity.
He sent me a cover image from Nature in March of 2025 and it's a striking image. It's a study he did along with colleagues at Georgia Tech and other institutions. Yes, this is a podcast, so you can't see it, but it's beautiful, and you can take a peek because it's in the blog post. I can just say here it's willowy branches of green and yellow. The study is about how whole genomes duplicate themselves for various evolutionary reasons. In the case of yeast, the organisms start out diploid and become tetraploid in his lab, Radcliff runs something called the Multicellularity Long Term Evolution experiment, hello.
Vivien
Um, yes, hi there, Dr Radcliff.
Will Ratcliff [36:00] Hello. How’s it going.
Vivien I think this is going, wow. How amazing that cover. Gosh, that's pretty cool. It is. I mean, I don't know the paper, unfortunately, because I'm just like a hoppity hop, but I'll look for it for sure. So this is from a past course, I guess, right? But is that led to a paper or, okay, so, Will Ratcliff Well, yeah, actually, that interestingly, those that cover was the microscope was, you know, one of the super nice ones they had at the institute. But the paper wasn't actually directly based on something we did during during our time there, I see, but we have, we do have other papers that, like were effectively inspired by our time there. And one of them was just updated this week at Science Advances, and another one in progress.
Vivien
Will Radcliff taught modules in the physiology course for two years, and explains a bit about the menu of ideas he brings to the lab.
Will Ratcliff
Nicole King was the organizer when I went, she's a multicellularity person, I'm a multicellularity person. They made good sense. So I came twice, 2022, and 2023, then Nicole. People turned it over and to Amy and Cliff, and they're doing something pretty different. And so, you know, they didn't have me back, which was both too bad, but also totally cool. You know, everyone wants to have their own sort of prerogative.
Vivien The Amy and Cliff he mentions, that's Amy Gladfelter at Duke University, and Cliff Brangwyn at Princeton University. They are both the Co-leaders of the Physio course these days. Will Radcliffe shares a bit about how he prepares the course because there is not a lot of time, and he wants people to have enough time to do some interesting experiments.
Will Ratcliff [37:50]
Well, I came in 2020, in, 2022, and 2023 for a couple weeks per summer. And, you know, you basically, kind of bring ideas for, like, experiments that the students could do that are sort of, like crazy ideas or things that would work really well if they're incredible microscope core, and they have to be, like doable in like a week because, you know, because you're going to do troubleshooting, and you're going to get, you know, like, so they have to be like, but, but the students are willing to work like insane, like, 18 hour days, you know, they're really, really good, and they're really hard working. But you only have two weeks for your module, so, oh,
Vivien So you have to prepare. I was talking to Sam on about this, like, prepare everything from reagents to tweaking the parameters and settings on microscopes in order for this to be doable, otherwise, people are still futzing with,
Will Ratcliff
Oh, yeah, and you want to give them some scope to, like, define their own ideas, too. So, like, what I typically do is, or what I did the two times I went, I brought, like, a menu of cool ideas, a whole bunch of strains from our so you know what we do is we're evolving in multicellularity, like multicellular life, from from scratch, over really, really long evolutionary timescales in our laboratory at Georgia Tech. So we're about 10,000 generations in right now. And yeah, it's and we've been working on this for 15 years. And so, you know, I basically have like, a life's mission to, like, push these organisms as far as they can go before I retire or die 20,30, years,
Vivien And then others can take it out 10,000 generations. My goodness,
Will Ratcliff
Yep, yep, it's really cool. And so, you know, we bring strains from like, across the entire scope of the experiment, right? And we bring strings to all these labels already built in genetic, genetic reporters and stuff. And we have some ideas of, like, I things that would be cool to look at. And we just kind of present these to the students, and then they take in their own direction. You know.
Vivien see So, but you have, and I mean, others have mentioned this too. So for I guess some people might be coming, let's say might be only computer people, or physics people or biophysics people. Others might be really advanced in sort of biosciences, but haven't used this particular microscope, so you have to kind of really dance.
Will Ratcliff
Oh yeah, but that's also a lot of the fun, right? Is those you're both you know, like, yes, you don't really know where someone's strengths and where their knowledge gaps are, because you're just getting to meet a group of 10 people. But at the same time, the fun of that, if someone will be like, Hey, you don't be cool, we should try doing this technique. Like, I've never thought of that before. Like, yeah, I've done this before, and it turns out it's awesome, right? That, to me is, like, a lot of the fun is having this collection of brilliant, diverse people that are just like, throwing stuff at the walls and, like, when things stick, it's really exciting, right? Because you wouldn't have tried doing that.
Vivien Yeah, no. And I'm looking at your site now, wow, biophysical toughness and all this population genomics, my goodness. So you're really also inviting people who might be, let's say they're in a grad program thinking about their postdoc. They might and they might be thinking, wow, I need to switch to something that is more focused on, say, multicellularity, or biophysics of it, or how to measure I don't know. I'm making this up because I don't know enough about your field.
Will Ratcliff
Yeah, and I'm very used to this interdisciplinary thing, because I work at the interface of physics and biology, evolutionary biology. I've directed a PhD program that's an Interdisciplinary Graduate Program in, like, quantitative biology. So it's got math, people, physics people, chemists, biologists, all in one program. So to me, that's, like, very comfortable, right? Like, I love that. I love being in those waters.
Vivien
Then people have been telling me how they like that experience that might be different from their lab, of like meeting someone who is sort of as a physics thing going on. And I know, and I've been hearing a lot about how great these courses are, but it is also true that there is competition between labs, traditionally, right? And it's not always easy to learn. How to collaborate and share and stuff with people who aren't in your lab. Is there any kind of issue with people who are like, wait, I maybe shouldn't. I don't know, like a, I guess, a culture thing that can come up because they're like, wait, I should really be focused on how I get ahead and be a little egotistical. Or am I just, do you mean in the course? Yeah, in the course, if there's, like, a, you know, it's a different culture, right? So people who are competing with one another in a way, yeah, first to get in, but then, you know, later on, they might be hesitant, or is it, is it just kind of, is the vibe?
Will Ratcliff
Vibe is, like, very collaborative, you know, I don't think anybody works independently, right? Everyone works in small teams, right? And that really helps, right? It's not like you have like, three or four people that are independently working on the same question, and, like, one of them could answer it, and that would mean the others don't get to, like, they're working in small groups. They're making really fast progress. They're having a lot of fun, and everyone's doing something different. And like, they get to see what other people are doing. And like, are very supportive and excited by that, you know. Like, there's a lot of like, mutual like, picking up, like, dude, that result is super cool. Hey, have you thought about this? Have you tried this?
Vivien Nice? Yeah, yeah. So it just engenders that kind of behavior. Instead of, okay, I'm just going to be quiet at my microscope and not say anything, yeah, I've noticed that. And I, as I moved around labs, when I was there, it was kind of like that. I see very cool. And how about like? I know that people have. Some people have told me that, you know, it is expensive, so they need to find funding. And in some cases, you know the former course, TAs, or people who've taken the course are very supportive. But I do think it isn't easy to say you want to go for how long? As a bi How do you feel about that?
Will Ratcliff
I've never been in that position. I've never sent a student. I've only taken people with me. And I don't even know what the cost is, but I would assume it's expensive. So let's say it's $10,000 because I think just based on, like, what I was paying for food and housing, for the TAs that I brought with me, it was like 2000 bucks per person for two weeks for housing and food, and that's not even including registration costs, travel costs,
Vivien right? No, of course, yeah, no, it's involved. So you add, you add things, and then people, yeah,
Will Ratcliff
So it's going to be a lot of money. And then, of course, you have issues of, like, you know, perceived unfairness within the lab, right? Like, hey, why did so get to do this? I don't get to do it right. Like,
Vivien or I didn't get to go to cell biology meeting or some Keystone, or Gordon, or, yeah,
Will Ratcliff
Yeah. Whereas, you know, like, I try to be fairly even when I'm when people want to go go to summer conferences, it's like, yeah, everybody gets to go to at least one, right? Like, for sure, everyone gets, you know, if you want to do more than one, sure, let's justify it.
Vivien. Will Ratcliff thinks about all of his lab members as he plans letting people go to Courses and conferences. But it still seems rather special to help someone go to a course for seven weeks. You know, you you've experienced it so, you know? So someone who maybe hasn't done or hasn't been to Woods Hole or felt what it's like to be there might have a harder time saying you want to do what for how long?
Will Ratcliff [45:40]
Yeah, you know, what I think is a very common rationale for the students that do go there is like they're in the lab, and that lab is doing, you know, high end cell biology of the kind that Woods holes are really good at, right? They're doing tons of imaging. They're, you know, like they're, they are microscope like masters, and maybe the students coming from a physics background or coming from a genetics background, they don't really have that expertise. And the pi is, like, I want you to go learn these skills and bring them back, all right? Like,
Vivien Oh, so you're doing something for the lab, ultimately,
Will Ratcliff
That's common. I think that's really common, right? And I can see that being really, actually quite useful. Like, especially if your lab is changing changing modes, you're going into your area, you don't already have the expertise in house, or you've gone through a bottleneck in funding so that a lot of intellectual knowledge is gone, because those people departed, right? It's like, All right, yeah, go spend your summer at Woods Hole. You're going to come back. You're going to bring all these new techniques. We're going to teach everyone lab how to do it. Yeah, I could justify that for 10,000 Yeah, go for it. That'd be great.
Vivien yeah, because they see it's one person, but then it multiplies to everyone in the lab, and then it also will enable people even after beyond this person graduating or finishing their postdoc, huh? I see Exactly,
Will Ratcliff
Yeah. So I think those are and I did see that. A lot when I was teaching, there was, like, a lot of people were coming in, and they were like, Yeah, you know, I have a physics background, but I'm now. I'm like, in the cellbio lab like, yeah, I see why you're here.
Vivien Yeah. It's like finding, finding your community. And ultimately, I mean, some people have been so abusive, and I'm like, it totally changed my career outlook and what I wanted to do. So this is really powerful. So I understand this might be hard, but like this summer, so you don't do this. Are you doing something like this or, Oh,
Will Ratcliff
Not hard at all. Not really. I this summer, I'm doing a lot of travel for talks. I've got like, four European trips scheduled for different conferences, and it's pretty crazy, actually. And I'm spending two weeks in California with my family in between, so basically for two months and traveling for all but one or two weeks.
Vivien But it's not the same, like you're not, it's not like you have people coming along and you are hanging out and maybe tinkering in somebody's lab as a, I don't know, I guess what they call visiting someone? Yeah, no,
Will Ratcliff [48.30]
Not at all. Not at all. In fact, if I was, if I was like, given the opportunity to go back to physio, I would turn down a keynote talk in Paris kind of thing to do that, because it's really, it's it's incredibly valuable. I mean, you've heard the you've heard what the students have said. But like, from, from a professor perspective, it's both, like, really fun, because you don't really get to roll your sleeves up and get dirty in the lab very often. You know, I'm on my computer all day, every day. I'm managing, I'm writing grants and dealing with MTAs. So, yeah, that's my job. My job is like, make sure everything is running. But I don't really get to be in the trenches on the front lines very often, right? That's usually filtered through a few steps of students that then do a bunch of stuff and come talk to me, and I look at their data, and we discuss their data.
They go back to the lab and I stay in my office, you know, like, that's kind of life for most professors. So this is the opposite this. You're in the lab, you're, you're like, dude, let me get on the microscope. Show me how to do this. You're like, I got an idea we should do this. Let me collect data.
Vivien Aren't you also, like, I don't know. I mean, I this whole setup of thing, and the lasers that don't, aren't constant and all that stuff. I mean, you guys have a lot of, as we say in New York, futzing to do. It's so it's not. It might not. The trenches are not that fun all the time, but I guess it's problem solving, huh? Okay,
Will Ratcliff
It's problem solving. It's also, you know, yes, it's if I had to choose to be in the lab all the time, or in the office all the time. I'd probably choose the office because I get to have a kind of like, the scope of things I work on is so broad, the impact that I can have is so large, because I can leverage my time so efficiently. You know, I get a lot of joy out of that, a lot of satisfaction. But I spent a decade in the lab all the time. And going back to that feels like coming home
Vivien I see: so Paris, and no, but yes to the lab. Wow, that's yeah, that's a draw,
Will Ratcliff
Yeah. And then, and then secondarily, this would be hard to, like, appreciate till I've actually gone through it. But like, when I'm working on project with students. I think in a certain even though we try not to be we're naturally a little conservative. We work. You know, when a new student joins the lab, we work on ideas that we think are going to work. They're the logical next step, right? Hey, this is an important topic. We have preliminary data. Why don't you do a PhD on it? That'd be really cool. It's gonna work. You're gonna get your PhD. You're gonna get big papers.
Vivien You're trying to help them not sink their life. You know, 10 years later or seven years later, it's not coming together, and they're freaking out because you
Will Ratcliff [51:00]
Can't do that. That's not, that's not like a responsible thing to do, right? You want to give them projects that are very likely to work. Woods, hole is like, very different, right? You are just doing you have one or two weeks to explore and to play, and if it doesn't work, that's fine. If it works, that's great. But the goal is not that it works. The goal is to just try exciting things, and you'd be great if it works. But like, that's their success isn't dependent on whether or not, like, the idea is like a publishable unit at the end of it, it's like we're able to get data, we're able to explore, are we able to test hypotheses, learn, learn new techniques, learn conceptual domains. Research has taken, like, fundamentally exciting new pathways that are, that are now things that we're working on for like, five years. Well, let's see for three for the last three years, a couple of major projects in our lab are things that started at Woods Hole, ideas we kind of had ahead of time but wouldn't have really invested in, and then really congealed at Woods Hole, like, wow, this is exciting, and going to work. That's crazy. That's cool. Let's keep going. And honestly. Of you probably wouldn't have ever done them if not for having those two weeks to, like, try them full, full strength, try them right?
Vivien And also, you're not alone there or in a core facility, but you're sitting at a scope and you've got, you know, you're three hours booked, but you can't talk to anyone, and you certainly can't feel any excitement around you because you're alone in that room.
Will Ratcliff [52:40] That's right. That's right. And you know what? Also, the microscope staff are awesome, and on this paper, we just had accepted last week one of their core staff members, Tanner Fadero. I don't know if you met or talked to Tanner, but he's like the core physios, microscopist. He's a co author on the paper, because he, like, had such good ideas for, like, what to do. They were like, You should be.
Vivien Oh, well. So basically, they're there for the summer, or they're they're also staff. They're full time.
Will Ratcliff He's, uh, only there for the summer. He's only there for the course. I see, Vivien wow, I see, so you really have someone that you can constantly ping, but also, who's really interested in what you're doing? So it kind of is like a contagious, I mean, good, contagious, hmm, neat. More Will Ratcliff Even than that, like, so, you know, we wanted to image, you know, we work on this multicellular yeast, which, in a in the first physios Summer, summer school, we found, like, wow, they create these, like, they overcome diffusion, like, you know, diffusion limitation by making flows like a sea sponge that, like, suck in from the outside, from the outside.
Vivien Yeah, I'm watching the video now that you, I mean, you have lovely gifs. Wow. I'm like, this is drawing me in, and I'm not even
Will Ratcliff That gif was taken, and that's what this paper, that was just accepted last week, is on. And in the second year we came back and we got these beautiful Tanner was like, we need to image these things from the side so you can really see the volcano in action. And really, yeah, it's cool.
Vivien And oh, because it's not flat, obviously. Ah, okay, yeah, yeah,
Will Ratcliff
The first ones are all looking down at the top. Really, you want to see it from the side. So Tanner was like, Yeah, let's go from the side. Let's buy these, buy these mirrors. And so, you know, you can just buy them from store labs have them shipped here. And so I just bought some with my credit card, and I come back the next day, and Tanner is like, Hey, we got it working, but it wasn't quite the right mirror. So, like, I just bought some more, like, with my own credit card, you know, was like, bullshit, man, you've just earned yourself authorship.
Vivien
And it's also so creative, too, right? Because they're saying, oh, you know, this is the type of mirror that we need, because I could see how it wasn't distorting in some way or something, huh? Exactly.
Will Ratcliff She came up with core ideas then even was just like, so invested in the project. He was like, you know, spending his own money to make it move along. You know, wouldn't take any any payment back. I was like, Can I reimburse? He's like, totally cool. Just so excited about the science
Vivien And that, of course, is also good for the students too, who are all of a sudden, really enabled in that, in that moment. If the course sounds like All work and no play, well, that is, as you have heard from others, not completely true. Here's Will Radcliffe
Will Ratcliff
Because all that other stuff really adds to the social bonding dynamic, right? We're going to the beach together, going on hikes or Martha's Vineyard or whatever.
Vivien I realized well into the conversation, I wasn't sure what discipline will Radcliffe was in and how he self defined himself. Labels, what do I call you? Do I call you a quantitative biologist, or, I know labels are so boring, but, oh yeah,
Will Ratcliff [55.50]
You could do that, or evolutionary biologist, because that's like, really, I see myself is primarily an evolutionary biologist. Everything. I think about it through the lens of evolution, but I use many tools, right physics, math, computation, synthetic biology, like classic directed evolution, like kind of use it all, but it's in the service of thinking about evolutionary questions.
Vivien
That was conversations with scientists. Today's episode was about summer courses, in particular, the course physiology at the Marine Biological lab, MBL in Woods Hole, Massachusetts. Today's guests were Dr Daria Ivanova from the University of Geneva, Dr. Sam Lord from the University of California, San Francisco, and Dr Will Ratcliff at Georgia Tech. The music in this podcast is Watercolor Beach by Kitrano, licensed from artlist.io.
And I just wanted to say because there's confusion about these things, sometimes the participants and their institutions didn't pay to be in this podcast. It was also not paid for by the MBL. This is independent journalism that I produce in my living room. I'm Vivien Marx, thanks for listening.