Category Archives: arts & culture

CMDB and Genetics Programs Come Together in Portland, Maine

For the first time, the Genetics and CMDB programs came together for a retreat in Portland, Maine for the snow and slush-filled weekend of April 1st. The retreat brought together students from different programs to interact and learn more about one another’s’ research, as well as students from different campuses. Both the Boston and the Bar Harbor Jackson Laboratories contingents made it to Portland to join the Scarborough Maine Medical Research Center Institute (MMCRI) folks for a weekend of science and camaraderie. Students and faculty gave brief talks on their work, followed by a poster session and a fantastic keynote speech on storytelling was given by Christine Gentry. Read on for details on the weekend, written by Jessica Elman (CMDB, Boston Campus), Jessica Davis-Knowlton (CMDB, MMCRI), and Alexander Fine (Genetics, JAX).  

We kicked off the retreat with a marathon of 16 talks given by students in year four and up from the CMDB and Genetics programs. Given the challenge to present a summary of their work in seven minutes or less, the students delivered with presentations that were brief but pointed. Three winners were selected by Philip HInds, Ira Herman, and Rajendra Kumar-Singh for their exceptional clarity, creativity, and concision.

In third place, Melissa LaBonty, a 5th year CMDB student in Pamela Yelick’s lab, presented on her work studying Fibrodysplasia Ossificans Progressiva (FOP). In this rare and severely understudied disease, an abnormal wound repair mechanism results in bone ossification in soft tissue after damage or injury. LaBonty is working with zebrafish to create a model of FOP, which will help to better characterize the disease and understand the underlying mechanisms that drive its progression. In her presentation, LaBonty spoke clearly and at an even pace, with assisting powerpoint slides that displayed only the most essential words: together this style helped keep the group focused on her story and contributed to her ranking as one of the best speakers of the day.

 

Siobhan McRee, a 5th year Genetics student in Philip Hinds’ lab, came in second among the student presenters. McRee talked about her work in which she is elucidating the roles of different Akt isoforms in BRAF-mutant melanoma. Though this cancer is initially responsive to the drug Vemurafenib, which specifically targets cells with a BRAF-mutation, cells with other driving mutations manage to survive the drug treatment and clonally expand, resulting in significant and potentially deathly relapse of disease. Ultimately, McRee’s work will help to better understand how the Akt signaling pathway is involved in this disease and may result in more therapeutically targetable molecules. McRee’s story logically built from general facts and understanding of BRAF melanoma to ultimately culminate on more specific data showing her findings thus far as well as their implications. Furthermore, her even pace and well-organized slides made her an especially great presenter that day.

Coming in first place was Kayla Gross, a 4th year CMDB student in Charlotte Kuperwasser’s lab. Gross’s work involves understanding how aging contributes to the breast cancer development, and why certain subtypes of breast cancer are more prevalent in the aging population. Given the prevalence of breast cancer, the impactfulness of Gross’ research is immediately obvious. She worked with an aging mouse model to characterize their mammary tissue as well as performed an RNAseq experiment to uncover molecular mechanisms that might be differentially expressed in young and aging mouse tissue. Gross presented her data in a logical progression, and used illustrative cartoons and animations to her advantage to keep her audience focused and to get her point across. Besides for her brilliant and captivating powerpoint, Gross stood out for her speaking style: she had clearly chosen her words to be concise and to the point, which allowed her to make the most of the seven minutes allotted to her.

All in all, the student presentations were remarkably impressive: in just seven minutes, all the participating students managed to convey the most critical and interesting components of their research. This was a great opportunity for everyone to learn a little bit more about what our colleagues are working on, as well as a chance to practice our “flash talk” skills, which will come in handy whether it’s at a job interview or at Thanksgiving table when your uncle asks you to explain what you’re doing in graduate school for the third time.

The Story Collider’s Christine Gentry, PhD as keynote

It was suggested by Terry Pratchett, Ian Stewart, and Jack Cohen in The Science of Discworld II: The Globe that perhaps Homo sapiens as a name for our species is a bit of a misnomer considering we are not omnipotent beings. They suggest Pan narrans, the storytelling ape, because we gain understanding by fitting facts into a larger narrative rather than collecting and storing millions of pieces of disparate information.

As communicators of new knowledge to the world (i.e. our scientific findings), it is important for us to keep the nature of our listeners in mind. In her keynote presentation to the retreat, Story Collider’s Christine Gentry, PhD encouraged us all to think about how to frame our narratives to be more approachable and demonstrated some methods of drawing in an audience.

She immediately captured our attention and sympathy by describing the challenges she faced in a wending career path that started with her geek excitement to bring a black widow spider to her Texas elementary school show-n’-tell, traversed through public outreach on the topic of zoology, and has landed at teacher/storyteller in Boston.

She required us to engage with her material by highlighting snippets of stories that we examined in small groups to find the element that made them compelling. We saw that admitting to vulnerability helps to humanize us to our audience in the story from a researcher who relies on fresh donor tissue, that self identity makes us more honest in the story from a researcher who decided not to cover her tattoos, and that we can surprise our audience by not sticking to script in the story from David who refused to tell the inspiration arising from conflict story that reporters sought to box him into. The thread tying all these stories together is that at the core they are about relationships with others, ourselves, our work, and with the larger community.

Perhaps the most memorable take-home point from her talk is that anecdotes do not equal stories. The response to most anecdotes is naturally “so what?” In order for an event or experience to be a story, it must have changed you: “I was callus, this event happened, and now I am more thoughtful” rather than “I am amazing, I did this, and I am still amazing!”

Scientific inquiry must be done in an objective manner and it is imperative that we remain unbiased as possible when we review scientific evidence, but there is room for us to inject our personalities into our presentations and relate our findings to the people who care. Now it remains to us to decide when to do so and to what degree.

On Sunday morning, we took a break from data and lectures; it was time to start working together. The purpose of this retreat was cross-program cooperation, and in our final event of the weekend, we put that goal into action. We separated into breakout sessions, not by program or campus, but by what we are interested in. These small group discussions were designed to get people together with various strengths and experiences to think about how to solve some of the challenges that graduate students face.

So what are graduate students at Sackler interested in discussing? The topics of these breakout sessions varied. Some sessions focused on day-to-day problems that a graduate student might face, like using CRISPR/Cas9 or selecting a sequencing platform. In the CRISPR discussion, participants came to the conclusion that there are no specific shared standards for all the applications of CRISPR and identified strategies to address potential off-target effects.

Other discussions centered on how to accomplish broader training goals, including grant writing, mentoring, and communicating in science. The grant writing section reviewed general writing strategies, like setting short-term, realistic goals, and shared a need for a formalized grant-writing course at Sackler. The mentoring/leadership session discussed existing programs at Sackler where a student can find a mentor, like the Tufts Mentoring Circles and the Tufts Biomedical Business Club. Students expressed a need for a more accessible alumni network, including cross-institutional resources. In the scientific communication group, students were urged to get on social media platforms like LinkedIn, Twitter, and ResearchGate.

In two of the largest breakout sessions, participants concentrated on solving larger scale problems: designing coursework for a modern graduate program in biology and bridging the gap between science and medicine. To help bridge the gap between scientific research and medicine at Tufts, the discussion group recommended that faculty members be identified that can connect labs with clinicians and tissue banks. In addition, access to a course that provides a basic orientation to clinical research would benefit many students at Sackler. In the session on coursework for a modern graduate program, one topic became the clear center of the discussion: computational biology! Whether students had struggled through teaching themselves or were currently stuck with a dataset they didn’t know how to analyze, everyone in the room agreed that coursework in computational biology was crucial for a graduate student’s success in modern biology. In addition to new coursework, students from both programs expressed a need for a revision and update of their first year coursework.

While all of the breakout sessions at the retreat were productive, they are meant to be starting points for continued discussion and collaboration. This retreat should be the springboard that leads to action across programs and institutions. Sackler students are lucky to be in programs that span multiple states, campuses, and research focuses. The cross talk between these groups will make each of our programs stronger and better prepare us for our careers in the future.

What Scientists Can Learn From Fiction Writers

Scientists don’t often think of themselves as writers. Our employment responsibilities do not include crafting characters or building worlds from words, nor investigating the latest political scandal, nor travelling the globe and composing reflections on our experiences. Yet, we do write: grants, reports, manuscripts. It is how we distribute our knowledge and the science we have done, because graphs and images and data have little impact if not shared. We write and revise as much as any journalist or novelist; still, writer isn’t an identity most scientists would primarily claim.

We are, though. Scientists are writers. Scientists are storytellers. Each graduate student, post-doc, faculty member has a story they are telling through their science. The scale and impact differs, but the fact remains: we must spin a tale convincing enough for our science to be funded, to be published, to matter. We are  writers, and we don’t even realize it.

I was trained to be a writer in the classical sense, specifically fiction writing. There were certain lessons that we learned over and over again, because they were fundamental to crafting even the most basic story. What fascinates me is that I have encountered these components informally in my graduate school training, just in the guise of doing good science.

We use basic story structure in writing articles: our beginnings ask a question, which we then try to answer in the middle, and our ends show how we have changed our little corner of the science world with our answer. There may even be a cliffhanger in there–alluding to a sequel coming soon to a journal near you!–if we’ve created even more questions with our answer. Grant writing uses a similar structure, with more emphasis on the cliffhanger. Leaving your reader on the edge of his seat, wondering what could come next, is something both scientists and fiction writers want (equally for the validation of having intrigued your audience and the satisfaction that such engagement often results in financial investment).

Show, don’t tell. Rather than telling a reader that a character is angry or sad, a writer should describe the character’s balled-up fists or tear-stained cheeks. For scientists, our equivalent of ‘telling’ is ‘data not shown’–and we all know how much we should avoid that. We do our showing in our figures. A scientist knows that the more data you can include, all the better. A scientist also knows that the more visually appealing your data is, the better it represents your conclusions. No one likes to read tables, right? Those data become so much more interesting as a pie chart, a graph, or a schematic. We show as much as we can, and tell as little as possible, because the best case scenario is when the data speaks for itself, instead of the scientist speaking for it.

Stories are much more interesting when they start in media res, or in the middle: no boring leadup, no extensive exposition. It is why publications often start with describing a hit or two they discovered from a screen, instead of the million little steps that led up to and happened during the screen itself. Good papers do that, and so does good fiction. The first Harry Potter book does not walk the reader through Harry’s childhood; it just starts right at the moment his life is about to change. Relevancy and immediacy are key components to telling any story, and scientists know and practice these principles to the best of their ability.

Crafting things out of thin air to make a story is a staple of fiction, but we know that as data fraud in the science world. The ‘characters’ in our scientific writing, the ‘plot’, the ‘setting’, the ‘rising action’, the ‘falling action’, all of those things have to be based on facts and evidence, on carefully planned and painstakingly executed experiments. They are based on reality. We know this; every scientist knows this. What we as scientists may not realize, however, is the extent to which fiction writing is also rooted in reality. Creating characters or worlds out of thin air is in actuality rarely done. The foundation of so many characters–ordinary or fantastical–come from experiences and observations within the writer’s own realm. It is a different way of collecting and representing evidence, a different way of asking or answering a question about the world. This reality-turned-fiction is one of the best ways a novel writer can build a sense of believability even in the most far-fetched fiction. It also builds trust between author and reader, one of the most important–and difficult–parts of fiction writing. Scientists have these components within their works as well, though constructed and strengthened in a different manner. Trust in science is built through executing proper and thorough controls, validating via different experimental methods, and considering (and hopefully, systematically eliminating) alternate theories or explanations. So regardless of the method in which they are built, that believability and that trust are critical components to any story, be it science or fiction.

Fiction writing, creative nonfiction writing, journalistic writing are all still very different beasts than scientific writing. Still, it would benefit scientists to focus less on the differences and more on where our often polarized fields actually do intersect. So much of our work is to provide convincing answers to difficult questions, and that type of evidence-based persuasion can be drastically more powerful if we use the same tools that traditional writers do. Scientists need to learn these tools as undergraduate and graduate students through formalized, structured, specified, and required coursework. That training will carry us, and our work, miles farther in graduate school and in our careers beyond. We need to be trained as writers, maybe as much as we are trained as scientists. Communicating our work in a persuasive and captivating manner is more important the ever, given the disturbing loss of faith in evidence-based arguments. We, as scientists, need to win that trust back, and to do so, we better be able to tell one hell of a story–to our funding institutions, to our public–about our science. For science to progress, we need our stories to be loud, to be spellbinding, to be believed and trusted by the public. We need to be writers, otherwise we might one day read a story about science that starts with once upon a time…

 

 

 

 

 

 

 

 

 

 

 

On the Shelf…

For Work

Effective Data Visualization

Effective Data Visualization: The Right Chart for the Right Data, by Stephanie D.H. Evergreen

Location: HHSL Book Stacks, Sackler 5, P 93.5 E937 2017

This book shows you how to select the best type of chart for your data, design an easily readable chart, and create effective charts and graphs in Excel.

For Leisure

The Undoing Project

The Undoing Project, Michael Lewis

Location: HHSL Book Stacks, Sackler 5, WL 103.4 L675 2017

Michael Lewis, the author of The Blind Side and The Big Short, describes the working relationship between two psychologists, Daniel Kahneman (author of Thinking Fast and Slow) and Amos Tversky, whose work changed how we think about decision making, and catalyzed the creation of the field of behavioral economics.

Opposites Attract: The Unlikely Marriage of Science & Fiction

Science, as a subject of study, often comes into conflict with other ways of thinking about the world. Religion. Philosophy. Art. The caricature of science as an opponent to these ‘humanitarian’ endeavors obscures the real relationship: symbiotic. In the case of science and literature, science provides fiction with an intriguing playground to muck around in, while fiction gives science a more human voice. This give-and-take between the two is what makes the genre of science fiction so rich, so enduring, and above all, so entertaining.

Science fiction more often than not uses science as a tool to explore other subject areas versus the science itself. It is not the engineering of the 20,000 Leagues submarine or the bioelectricity behind the monster in Frankenstein that makes these books long-standing members of high school reading lists. Readers are not likely spellbound by Margaret Atwood’s MaddAddam series mainly because of the intricacies of the genetic engineering catastrophe that ended her version of our world. No one likes Star Wars because of its explanations of the physics behind inter-galaxy travel. Fiction is not a mirror that reflects science to readers so that they can understand its most basic aspects. Instead, fiction is a prism that refracts science, fractioning and expanding it into its ripple effects and societal implications. It bends the bleached starkness of the discipline into a million different shades, spattering dark implications and bright hope for humanity in equal measure.

It is not always a fair coloring. Dystopia walks hand-in-hand with science fiction more times than not. Those stories do speak well of the perseverance of the human condition but often at the cost of vilifying some aspect of science. (Everything becomes a villain if left unchecked long enough, after all.) Still, fiction doesn’t just take from science; it gives as well. Science fiction is always ahead of its time, more audacious in imagining what human hands are capable of creating than what we believe is achievable at the time. With that creative inspiration, our history has shown it is inevitable that science fiction becomes science fact, from endeavours as incredible as space travel to tools as mundane as credit cards. And as such, science fiction has the privilege of not just asking can we, but also should we, and it has the added advantage of most times asking it first.

The audacious pushing of boundaries beyond the confines of the contemporary scientific knowledge within science fiction also creates a unique and rich environment for rebellion. Because in that type of story, in an imagined world that both is and is not this real one, what else could be different? Who else could become something more than what they are, or what society tells them they are?

This type of rebellion is what led to the existence of the genre itself. In 1666, the English duchess Margaret Cavendish published The Blazing World, a prose piece often considered one of the first utopian fictions and the precursor to ‘science fiction’ (a term not officially coined until 1926) as we know it today. Cavendish was an anomaly of her time, publishing plays, essays, and prose that tackled philosophy, rhetoric, and fiction, all under her own name instead of anonymously. She also was the first woman to attend a meeting of the Royal Society of London, despite fierce protest, and did not hold back in commenting on and even criticizing the scientific presentations and practices she observed. Her novel dove into discussions tackled by male authors of the time period–the conflict between imagination and reason or philosophy and fiction–but also was groundbreaking in two ways. First, she explored these topical areas within an alternate universe entirely of her own making but one that still used contemporary science of the era; second, her story strikingly centered on herself as the main character, where she traveled in between the two worlds. In a time where women were not considered capable of studying complex topics such as science, the Duchess of Newcastle used her writing to boldly carve herself a space in which she could defy that notion. In the process, she wrote into existence the first examples of many science fiction tropes still widely used today.

Her actions paved the way for other rebels, such as Mary Shelley, the mother of the first science fiction horror novel, Frankenstein. While a grey, depressing summer and a writing challenge born out of boredom provided an opportunity to craft her terror-filled story, her imagination was ultimately sparked after a firelit evening conversation with the controversial Lord Byron about what life is and how to create it. Despite being supported in her endeavours by her companions and her husband, Shelley ran into criticism upon publishing her work–incidentally most strongly from the specific publishers who knew the author was a woman–because it challenged the entrenched ideology of God being the only conceivable creator, not Man (or, in her case, Woman). In the deeply religious society of Victorian England, this was a revolutionary act.

Cavendish and Shelley may have been the some of the first authors to use sciene in fiction to challenge the social and moral status quo, but it was a tradition that persisted in the genre throughout the twentieth century. Starting in the 1960s, female authors were among the first to interrogate the definitions, implications, and biases associated with gender, class, and race. Ursula Le Guin’s sci-fi novel The Left Hand of Darkness–with its gender-fluid alien race dissecting what exactly gender and sex means outside of its Western civilization confines–led the charge. This breakthrough was followed by Joanna Russ’ 1975 matriarchal parallel-universes utopian novel The Female Man, then by Octavia Butler (who was the only African-American woman publishing in the genre at the time) and her late-1980s space trilogy Xenogenesis which explored race in addition to sexuality.

These revolutionary works also represent a broader theme within the genre: the influence of contemporary events of the era in which they were written. Science fiction is as much a reflection on the scientific knowledge of the day–and what could come of it–as it is on the historical and political backdrop of the time. Many early science fiction novels from the eighteenth and nineteenth centuries focus on stories of exploration and the technology that allows journeys into lands unknown. Most notable of these are Gulliver’s Travels (Jonathan Swift, 1726), 20,000 Leagues Under the Sea (Jules Verne, 1870), and The Time Machine (H.G. Wells, 1895). Historically, these centuries were flooded with exploration expeditions by European countries, and later the United States and Russia. While discovery for political and economic gain was the main purpose of most 18th century explorations, those carried out in the 19th century were more focused on deepening knowledge of the world, often through scientific observation and analysis. So, it is little wonder that the science fiction of the era reflected that desire to know more about the surrounding environments.

In the early 20th century, the domination of exploration themes in science fiction gave way to playing around in other subject matters–such as technology, biology, and medicine–which would later become genre staples. The early half of the century was one of rapid scientific advancement as much as it was political upheaval, and the collision of these two jarring phenomenons is reflected in the science fiction of the day. It was during this era that some of the seminal works of the genre were produced, including the post-Bolshevik revolution novel We (Yevgeny Zamyatin, 1924) and the science fiction classics Brave New World (Aldous Huxley, 1932) and 1984 (George Orwell, 1949). These novels each address how uncurbed scientific advances lead to a dystopian political society, and their thematic commonality clearly demonstrates the lasting impact several world wars and fast-paced science had on the public psyche of the time.

While dystopia strongly persisted within science fiction in the middle of the 20th century, the worlds crafted within genre novels did begin to grow a little less dire. As technological development continued to accelerate and started infiltrating daily life in the Western world–thus ‘normalizing’ it–likewise did the role of technology grow in fiction as androids and robots appeared on the genre scene. Authors of the time such as Isaac Asimov and Philip Dick couldn’t help but ask–and then answer through their writing–questions pertaining to the human condition in relation to the (imagined) creation and existence of non-human life. This philosophical bent echoed the early origins of the genre, going all the way back to Cavendish’s precursor work, demonstrating how far the genre had progressed.

Glancing back and paying homage is all well and good, but science fiction also found new ways to move forward at the end of the 20th century. In 1979, The Hitchhiker’s Guide to the Galaxy added a little laughter and good humor to the genre, breaking ground for many others to follow across even until today. The gloom of the war-torn early decades also seemed to have worn off, with a revitalization of the previously ‘tired’ utopian sci-fi tradition by Kim Stanley’s Mars trilogy in the 1990s. This trend of revitalizing and redefining the genre has persisted into recent years, with the semantic alteration by Margaret Atwood, who calls her novels not ‘science’ fiction, but speculative fiction. In her MaddAddam series, she reaches for what might be just possible in the realm of science and society, instead of the complete impossible. In some ways, this approach brings about an even more imaginative (and frightening, and wonderful) vision of what the human mind can create when challenged in the perfectly right and wrong ways.

Ultimately, the fiction of science is as elusive and ever-changing as the real thing. It circles itself: thought and action, can and should, might and will and have done. Whether we as scientists today use science fiction as inspiration–or as a warning–only time will tell.

Humans of Sackler: Nafis Hasan, “I Refused Determinism”

Humans of Sackler, 30 January 2017

Nafis Hasan, Cell, Molecular & Developmental Biology, Fourth-Year Student: “I Refused Determinism”

This month I present, for your reading pleasure, excerpts from my interview with Nafis Hasan from CMDB. Nafis and I had a remarkably wide-ranging conversation covering existential philosophy, cultural differences between Bangladesh and the US, the exquisite symmetry between ecology and cell biology, and current controversies in carcinogenesis research. I can only hope to capture in the space below a mere whisper of his deeply-considered intellectual convictions and passion for social justice. Fortunately, Nafis has also authored an editorial on Science Activism in this very issue, and I strongly urge you, dear reader, to check that out next!

 

Having a grand time in Dhaka
Having a grand time in Dhaka

AH: Where did you grow up?

NH: I grew up in the house that my father and his brothers built in Dhaka, Bangladesh, and moved to the U.S. when I was 18. Most of my dad’s siblings and their families lived with us in Dhaka. As kids, we didn’t really have the notion of “privacy” for the longest time: the elders would each get a room and the kids would sleep in the living room on a big mattress. My cousins and I would all get into trouble at the same time… it was fun!

 

On the road with college friends
On the road with college friends

AH: Have you had any opportunities to travel around the States?

NH: For F1 visa (student visa) holders, you have a 3-month window where you have to find a job or get into school. After graduating from Lafayette College [in Easton, Pennsylvania], I thought, “If I have to leave the country, I might as well see it.” So when one of my friends said, “Let’s do a road trip,” I said “Let’s do it!” We started from Pennsylvania, went down to Virginia, our first stop was Shenandoah – I had actually never been camping before that, it was all a very new experience. We had two American kids, a Colombian kid, and a kid from South Africa… It was very liberating, and I started to see the country as it really is. At the same time, on the road, I was interviewing for jobs. I remember doing a job interview [by video phone] at a McDonalds in Idaho. I borrowed a shirt from one of my friends who dresses nicer than I do, since the interviewer could only see the top half of me… Over the course of two months, I think I applied to 200 jobs. Finally, I ended up getting a research tech job at Thomas Jefferson University in Philly.

 

Basking in the beauty of nature at Yellowstone
Basking in the beauty of nature at Yellowstone

AH: What was it like adjusting to American culture?

NH: When I came to America, I had no idea what to expect, I had only heard things from my cousins who came here for college and what was on TV. One thing that I had in my mind was that I was going to try and meet as many people of different nationalities as I can. But there was a big cultural divide, how they grew up versus how I grew up. I think the road trip really helped me to understand the diversity of American people and especially during these times when people are so polarized, I reach out to that experience. We grew up seeing this version of America as the land of opportunity, the land of freedom, but America is not the government, is not their foreign policy, is not the consumerism that has taken over the world… America is more about the people that you meet here, and that’s how I see the country. America encapsulates the dichotomy of homogeneity versus heterogeneity, and I think that’s so beautiful.

 

The scholar/activist as a young man
The scholar/activist as a young man

AH: When did you begin to discover your interest in biology research?

NH: In Bangladesh I went to a private school that taught everything in English. The division of sciences starts in 7th grade, and biology was definitely the most interesting to me. At the same time, I was caught up in the process of deconstructing my religious identity, because I was reading biology which has hard facts about how your body works, which calls into question how life was created… I found that more fascinating than having a set answer imposed by some superior being.

 

Positive work environment!
Positive work environment!

AH: How did you choose your field of study for grad school, and why is it so interesting?

NH: I started reading a lot of scientific nonfiction, presenting cancer as a very complex biological phenomenon, which was fascinating to me. I also had a solid foundation in breast cancer by the time I applied for grad school and I wanted to pursue that… I had seen lots of tumors, but no mammary glands. The more I learn about the mammary gland, the more I am fascinated by it. It develops throughout life: initially it’s just a branched structure that looks like sticks; when you get pregnant, it almost flowers, with grape-like clusters that come up through alveologenesis and these alveoli then revert back to the branched structure after weaning. It’s comparable to how trees shed leaves in the Fall, except in reverse: this course of nature – the seasons that you see – the same dynamic is there in animal tissue. And all of this is happening through the lifetime, after the majority of the organs are already fully developed!

 

100 miles?!
First Century – Repping Sackler at 2015 Tufts Century Ride

AH: What is one of the big challenges or controversies in your field at the moment?

NH: Traditionally, cell culture is done in two dimensions, on plates that are usually plastic – and plastic is not a natural substrate for cells to grow on, so you can’t recapitulate the same 3D environment where the cells are growing inside an organism. You can either try to mimic the natural environment as much as possible, or try to make a scaffold that is biocompatible… Cells need to be able to manipulate their environment, just as the environment should be able to provide them with physical or chemical cues to make them grow or organize in certain ways. Our lab has a very organic approach to it: we do 3D cultures in type 1 collagen, the predominant structural protein found in the mammary gland stroma. We believe that “organicism is greater than reductionism.” This is where we’re at odds with a lot of others in the cancer field, where reductionism is still the predominant philosophy. And we’re not saying it’s bad! It’s just insufficient to explain carcinogenesis.

Feature: Humans of Sackler

Do you have fun and interesting hobbies?  Have you traveled to fascinating places?  Held unusual and challenging jobs?  Do you use cutting-edge technology to conduct biomedical research of earth-shattering importance?  Are you a human?  If you answered “yes” to any of these, you could be the next Human of Sackler!

Humans of Sackler is a monthly blog featuring individual Sackler students’ firsthand accounts of their path to the Graduate Biomedical program.  Inspired by Brandon Stanton’s “Humans of New York” blog, the aims of this project are to highlight the Sackler School’s rich diversity of backgrounds, interests, and personalities, and to engage with the public by revealing the human side of scientists.

If you are interested in contributing to or nominating someone for the Humans of Sackler blog, contact Andrew Hooper (andrew.hooper@tufts.edu, Subject: Humans of Sackler) to set up a brief interview at your convenience.  We look forward to hearing your story!

Read the first issue here: Humans of Sackler, 25 July 2016

Humans of Sackler: Jaclyn Dunphy, “Good Things Come to Those Who Waitress”

I’m Andrew Hooper, a fourth-year student in Dr. Jamie Maguire’s lab in the Neuroscience program.  For as long as I can remember, I’ve been fascinated by the stories of how scientists came to be scientists.  Where are they from?  When did they recognize their passion for science?  How did they get their foot in the door?  What is it about their topic of interest that so captivated them?  And what breakthroughs just over the horizon would most excite them?  There are as many compelling, eye-opening answers to these questions as there are scientists, and I decided to highlight the diversity of backgrounds and perspectives at the Sackler School by gathering and sharing some of these stories.  Inspired by the format of Brandon Stanton’s wonderful “Humans of New York” blog, I called this project “Humans of Sackler”.

Recently I had the opportunity to sit down with Jaclyn Dunphy, a fourth-year Neuroscience student in Dr. Phil Haydon’s lab.  We discussed the questions above and many more, and I’m very happy to share with you a small sample of our conversation in this, the first issue of “Humans of Sackler”.  Enjoy, and please look me up if you’d like to share your story and be the next Human of Sackler!

 

Humans of Sackler, 15 June 2016

Jaclyn Dunphy, Neuroscience, Fourth-Year Student: “Good Things Come to Those Who Waitress”

Humans_Image1
Graduating from the Masters program at Kent State NEOMED

AH: Did you come into college with a biology major, knowing that that’s what you wanted to study?

JD: I wanted to be a teacher when I started college because I had a really great biology teacher in high school. I went to Xavier, a private Catholic college, so I also thought I might want to be a religion teacher. For the first couple years I took biology, education classes, and theology classes. But I had a ‘coming to terms moment’ with what my major was going to be around sophomore year, and so I just went through the bulletin of all the courses that were offered and picked the ones I liked the best – and they tended to be related to biology, so I figured that’s what I should be doing. I didn’t know what I could do with the degree. I had never heard of graduate school until after I graduated!

Humans_Image2
At an air show with dad

AH: Were your parents interested in science, or did your interest develop totally independently from family?

JD: I think my interest in science definitely goes back to roots that I have with my dad. He has a workbench in the basement, and some of my earliest memories of us spending time together were us building rockets in the basement. He was very into space and stuff, so we would build rockets down there. Also, I was in this program for gifted students when I was in fourth and fifth grade, and we were assigned weird projects – like if you’ve heard of the ‘egg drop’ project, where you have to drop an egg off of a roof and get it not to crack? I would get assignments like this and take them home. I was really excited about them, but my dad was even more excited! So we would work on those things together, and I would go back to school with something that was, like, 80% his idea and 20% mine. So in those couple of years we had five or six things we worked on together in the workshop downstairs, and that was really fun… We built a bridge with Popsicle sticks, and I could stand on it. I could stand on it to this day! We made I-beams – not my idea. I’d never heard of that, but he was like ‘We need to build I-beams!’ We even sanded them – it was intense.

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After a day of kayaking on the Charles

AH: After you finished undergrad, what did you do for work and how did you transition eventually to grad school?

JD: I was working at an upscale restaurant called Bistro on Main, close to Kent State’s campus, where Kent State professors take their seminar speakers out for dinner. So I had seen a couple groups of them come through, but one night I was waitressing for a table of four people: three people from NEOMED/Kent State and their invited speaker, Wendy Macklin. When I came to the table they were talking about prion disease, and I said, ‘Oh, that’s odd dinner conversation’. And they asked ‘How do you know what that is?’ in a very accusatory but jovial tone, and I said ‘Well, I just graduated with a degree in biology’ and they were like ‘Then what are you doing here?’ and I said ‘Waiting on you, what does it look like?’ So after that, all four of them took turns harassing me, they asked ‘Do you need a job?’ and I said ‘No, I have a great job, I’m making a lot of money doing this, I’m just trying to figure out what I want to do.’ And they said ‘Well, if you figure it out, then here’s my card.’ They put the card in the bill and they said, ‘Give us a call if you want to work as a technician.’ And I didn’t even know what that meant. At that point, I thought I was going to be cleaning rat cages. So I interviewed with one of the professors at the dinner, Bill Lynch, a few weeks later. It was the worst interview I’ve ever had, it was terrible! He’s a virologist: he asked me whether viruses are living or not. I didn’t know it at the time, but that’s a controversy among virologists. So I just picked a side, and then he argued me all around in circles until I switched sides, and then he asked me why I switched sides..! I left feeling so defeated; it was the first experience I’d had of someone who really, really questioned my thought process. I felt terrible, I felt like I had done such a bad job. But he ended up offering me the job because he liked that I didn’t give up, he liked my enthusiasm.

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Demonstrating the Blind Spot at the Museum of Science, with Alex Jones (right)

AH: What was it about glial cells that made them so interesting to you?

JD: I fell for astrocytes – I liked that they were so abundant but they were so under-studied. There was so much to learn. What are they doing? There has to be more to the story. Later on, when I met Phil Haydon, he said that in the field of glia, there’s a lot of low-hanging fruit, and I felt like that was very much the case. Glia are… I hate the word ‘support’ cells, but they are support cells for neurons. Neurons are like actors in the big play that is the brain, so the glia are stagehands, directors, producers, writers – they’re the ones that actually control the show. But the ones that you see and you care about are the neurons.

 

Notes from the North – The Science of Lobster

The other week my family and I were driving home from an afternoon on the beach playing in the waves, poking through tide pools, and eating seaweed (only Ronan indulged in this last pursuit) when we IMG_20160713_204129_894[1]made a spur of the moment stop at a local farm to pick up lobster and a couple pounds of steamers1. Standing at the counter in flip-flops and a swimsuit as the lobsterman weighed out our “bug”, I began to ponder this quintessential Maine summertime treat. In preparing and eating whole lobster the consumer becomes acutely aware of the animal’s physiology; an experience most of us are divorced from for most of the produce we eat.

 To start with, you have to decide as you are making your purchase whether you would like a hard-shell or a soft-shell lobster. A soft-shell lobster is one that has recently undergone ecdysis, a shedding of the exoskeleton. The lobster does this by inflating a newly grown exoskeleton with water within the old carapace causing it to pop open and expose the soft new shell. The reason these soft-shell lobsters cost less per-pound than the hard-shell lobsters is that a good proportion of their weight comes from that water rather than meat.

When you get your lobster home and are facing the decision of how to cook him or her2, you might begin to wonder “why on earth do I need to buy it live?” In part this goes back to the molting cycle again: powerful proteases (four members of the calpain family) induce muscle atrophy in the claws in order to reduce the volume of tissue that will need to be withdrawn from the old shell. When the lobster is dead, these proteases cause rapid degradation of the flesh. The other part of the answer lies in the presence of metabolites from micro-organisms. The combination means a much shorter shelf-life for raw lobster meat than you might otherwise imagine.

This inconvenient brevity of freshness forces the chef to consider the question of lobster nociception.  The avoidance behaviors (tail-flipping) exhibited by lobsters upon being placed in boiling water clearly demonstrate that at the very least lobsters have evolved to respond to noxious stimuli. Pain is typically understood to be comprised both of physical sensation and emotional distress, but since it is difficult to observe or define emotion in non-humans using only our experience of human emotion it seems reasonable to minimize the animals’ exposure to noxious stimuli. In Europe this is accomplished by electrocuting crustaceans prior to cooking, but the best compromise I have seen in the US is to make a cut through the lobster’s brain while it is still cold from the fridge before cooking.

There is a huge body of scientific literature out there both utilizing lobster as a model organism and studying it directly (the lobster fishery just in Maine is worth over $1 billion!), but I’ll leave you with just one last lobster physiology anecdote. Ed Kravitz, one of my grandmentors (mentor’s mentor) demonstrated that GABA is a neurotransmitter using lobster (the shell apparently makes a convenient receptacle in which to bath the muscle and nerves), but I was always told that Ed’s favorite part of studying lobster was the taste test!

  1. Scrumptious little soft shell clams that are cooked by steaming. In our family we bring the cooking brine to the table so we can rinse each clam clean of sand before dipping in butter to consume whole.
  2. The most infallible method to determine the gender of your lobster is by looking at the first pair of swimmerets that appear on the ventral surface of the animal where the tail joins the cephalothorax. In females these are soft and flattened while in males they are stiff and curve to form a tube through which spermatophores are deposited in the female during mating.Lobster anotomy

From the Shelf…

For work…

Sackler School Biomedical Resources Guide

Electronic Resource: Sackler School Biomedical Sciences Resource Guide

Location: http://researchguides.library.tufts.edu/biomedical_research

The redesign of the library’s website eliminated pages dedicated to each school in favor of individual ‘guides’.  You can access the Sackler School Biomedical Sciences Resource Guide either directly via the link above or by choosing ‘Biomedical Sciences’ from the Find drop-down menu on the HHSL homepage (http://hirshlibrary.tufts.edu/).  This guide includes resources for finding journal articles, chemical and drug information, and protocols.  The guide also links to other library guides of interest.  I will be modifying this guide over the summer to ensure that it provides easy access to library resources.  Please contact me (laura.pavlech@tufts.edu) with any questions or suggestions!

And leisure…

Letters to a Young Scientist

Letters to a Young Scientist, by Edward O. Wilson

Location: HHSL Book Stacks, Sackler, 5th Floor, QH 31 W64 S4 2013

Pulitzer-Prize winning biologist and Harvard emeritus professor Edward O. Wilson shares advice and autobiographical anecdotes from his long career.  The author of several books on entomology and conservation, as well as memoir, Wilson was name one of Time magazine’s 25 most influential Americans in 1995.

On the Shelf…

For work…

Essential Science Indicators

Electronic Resource: Essential Science Indicators

Location: Search for ‘Essential Science Indicators’ in Databases search box on the HHSL homepage (http://hirshlibrary.tufts.edu/).

This research analysis tool, integrated with Web of Science, provides performance statistics for authors, journals and articles for 22 subject fields.  Essential Science Indicators can answer questions like: who are the most-cited authors in my field; what journals publish the top papers in my field; what is the average number of citations per article in my field; or what is the minimum number of citations that my article needs to receive to be in the 10% percentile in my field?

And leisure…

All the Light We Cannot See

All the Light We Cannot See, by Anthony Doerr

Location: HHSL Leisure Reading, Sackler, 4th Floor, Fiction D652

Winner of the 2015 Pulitzer Prize for fiction and numerous other awards, this book tells the parallel, and eventually intersecting, stories of a girl in France and a boy in the German army during World War II.