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Humans of Tufts Boston: Najah Walton, “The power of the mind is not a joke!”

Humans of Tufts Boston, 15 Oct 2020

Najah Walton, Neuroscience, Second-year Ph.D. Student: “The power of the mind is not a joke!”

JH: How did you get started in science and what were you doing before graduate school?

NW: I’ve always had a fascination with science as an extension of trying to learn more about the world around us. In elementary school I spent a lot of time with my grandma who lives in a rural part of Massachusetts and she always encouraged my siblings and me to get outside and appreciate nature. At the time I was a mini-lepidopterist, but when her sister was diagnosed with ALS my interest in the biomedical field became more of my focus.

As a first-generation student I had no idea what “wet lab” was or the prospect of getting a PhD. Luckily, I was fortunate enough to have friends working in research labs that introduced me to bench research as well as science mentors that inspired me to pursue science on a deeper level. One of my friends that was already doing research encouraged me to apply to the U54 Program which was a collaborative summer research training program between UMass Boston, Dana Farber Cancer Institute and the Harvard Cancer Center.  I got to work on a public health outreach project aimed at increasing healthy lifestyle choices in faith-based organizations in the Boston area, as well as increasing the inclusivity of underrepresented individuals in biobanking. By the end of the summer I was captivated by research and wanted to continue pursuing research in conjunction with the clinical work that I was doing as a nursing student. To my benefit, one of the PIs that was on the grant for the summer program, Dr. Tiffany Donaldson, offered me a position working in her Neuroscience lab at UMass, where I started off studying a potential therapy for a birthing complication known as hypoxic ischemic brain injury.

When I graduated from UMass I received my license to practice as an RN but I chose to pursue a neuroscience graduate degree to continue the exciting work that I was doing as a research technician in the Maguire lab at Tufts. Dr. Maguire’s lab is now the lab where I will be working on my thesis and I’m looking forward to using my training to one day treat patients with neuropsychiatric disorders.

Summer students in the Maguire lab

JH: What drew you to neuroscience?

NW: “The power of the mind is not a joke!” (Quote from world-renowned philosopher Drake Aubrey Graham.) The brain literally controls every aspect of our beings: how we think, how we move, how we breathe, how we laugh, how we love, how we manage illnesses, and how we help those around us.  Seeing how devastating both neurodegenerative and neuropsychiatric diseases can be for individuals drew me to want to know more about the brain and how scientists may be able to combat these diseases with their discoveries.

JH: Have you been following any fascinating new scientific developments (in or out of your field)?

NW: In quarantine it’s been hard not to follow the news about the coronavirus vaccine (s/o Dr. Kizzmekia Corbet!). Dr. Corbet has been leading the NIH’s Vaccine Research Center in its push to develop a vaccine for coronavirus. Once the sequence for the virus was published, she and her team moved from vaccine development to a Phase 1 clinical trial…in just 66 days! To say it in plain terms she is a FORCE of nature and a true inspiration for all pursuing science careers.

Tufts Black Student Alliance

JH: What do you like to do outside of lab? (This is a great place to plug BSA and I would love love love to link to a website or social media account if you have one!)

NW: Outside of lab I am currently co-president for Tufts Black Student Alliance (follow us on Instagram @tufts_BSA)! The Black Student Alliance was founded serendipitously as myself, Udoka, and several of our board members met by passing each other in the hallways or eating lunch in similar locations in the Biomedical Sciences Building. Udoka and I went to undergrad together and benefitted greatly from the community that was offered at UMass Boston and hoped that the same community could be formed at Tufts to ensure graduate school was just as fruitful. Since Black biomedical graduate students account for less than 10% of the STEM graduate student body it made more sense to create a community that spanned all of the health sciences campus to ensure that all Black students from each of the graduate programs were represented and could have a place of refuge/support during their time at Tufts.

I also host science workshops for youth in the Greater Boston area through Bethel Institute for Social Justice.

JH: Are you taking up any new hobbies during COVID times?

NW: Not necessarily a new hobby but my dogs definitely received a lot more attention in quarantine. We’ve had more time for long walks and they love getting off leash and going for hikes.

Connect with Najah on LinkedIn:
https://www.linkedin.com/in/najah-walton/

Humans of Tufts Boston: John Ribis, “Think about how far you’ve come and how much you’ve learned”

Humans of Tufts Boston, 12 Jul 2020

John Ribis, Microbiology, Rising fourth-year Ph.D. Student: “Think about how far you’ve come and how much you’ve learned”

JH: How did you get started in science and what were you doing before graduate school?

JR: I had a circuitous path to grad school, and I came from some very humble beginnings. Both of my siblings are quite a bit older than I am (9 and 11 years), and I remember my sister talking about her high school chemistry class when I was 6 years old. It sounded pretty cool to me, even then. I’ve definitely had interest in science since I was a young child.

Unfortunately, for a variety of reasons, I faced a few challenges throughout my primary education and once I finished high school, I had no real plans to start college. No one else in my immediate family had gone beyond high school, so there wasn’t much pressure or expectation to continue on. After graduating, I got a job working at a local hospital where I worked first bringing food to inpatients and then I worked as an orderly for around 6 years. Being an orderly mostly entailed transporting patients, but we did a number of other things as well; EKGs, responding to violent situations, and providing support during medical emergencies. Twice a day, we would round through the ICU and to assist with various things (helping patients get out of bed, repositioning sedated patients, and sometimes doing chest compressions during codes). I enjoyed asking questions to the nurses and physicians and I got to have a lot of interesting and unforgettable experiences during my time there.

After working at the hospital for a few years, I got motivated to continue my education and started working towards my bachelor’s degree at the suggestion of my girlfriend and some co-workers. I started off by filling in a couple of prerequisites at a local community college over the course of a semester, but I eventually enrolled in classes at the University of Vermont. I did this through a special program that would guarantee admission as an undergraduate as long as you maintained a certain GPA. My high school transcript was dismal to say the least, so I felt very fortunate to have an opportunity like this. I was initially a biology major, but I changed that to microbiology after a year. I toyed with the idea of pursuing a career in medicine, but I was also open to the prospect of a basic science career. I first stepped foot into a research lab in the second semester of my junior year (late I know) and I wasn’t sure what to expect from working in the lab, but I immediately loved it. I was (and still am) very fortunate to have an awesome mentor! I had a ton of fun working in lab learning how to do research, and I spent a ton of time there. I also made friends with a bunch of the grad students and felt like I fit in well with them, so I started seriously considering grad school. I started at Tufts shortly after I graduated.

JH: Looking back, what would you tell someone on a similar path as you about making the decision to go to college and choosing science?

JR: I’d remind them that it’s normal to feel intimidated when making the transition back to school, especially if you had a difficult time previously. It’s also easy to get discouraged at times, feel like you’ve made the wrong decision, and think you’ve wasted a huge amount of money. Make sure to check in with yourself, take a step back and think about how far you’ve come and how much you’ve learned. I’d also suggest starting in a lab as early as possible, and if you have a bad time in the first lab, move on and don’t let that shape your view of science. I’ve seen so many people have a bad experience in their first lab, and they decide to never work in a lab again.

JH: What drew you to microbiology?

JR: This goes back to my time in the hospital, where I was able to see firsthand how incredibly destructive some pathogens were. The thought that something so tiny could wreak such havoc on the body amazed me. It was also crazy to me how prevalent antimicrobial resistant organisms were like MRSA and VRE (vancomycin-resistant enterococcus). I also got to see a ton of people infected with C. difficile, which is the bug I work on now. In addition to pathogens, I thought the fact that we have co-evolved with a huge number of commensal bacteria, which we rely on for what seems like everything, was fascinating as well. It’s pretty wild that the gut microbiota has an impact on pretty much everything, including our brain since some bugs actually produce neurotransmitters that probably impact our mood and behavior. They also protect us from other bacteria that can cause really severe disease. For example, the bacterium I study only makes people sick when gut commensals get wiped out.

JH: Have you been following any fascinating new scientific developments?

JR: Well, if you ask anyone that knows me, they will tell you that I have a slight, maybe unhealthy, obsession with microscopy. It’s the main thing that I’ve missed about being away from the lab. Fun fact: I’m color blind, so my love for microscopy often causes a lot of confusion amongst my peers! I then tell them that GFP doesn’t have to be green and mCherry doesn’t have to be red.

Microscopy pretty much dominates my twitter feed. It’s a hugely innovative field and it’s hard to pick a single fascinating development. I am a bit of a sucker for any super-resolution technique, so the fact that we can now use light microscopy to see single fluorophores and separate them within a couple nanometers of each other in living cells just blows my mind.

On the image analysis side, things seem to be developing even faster. Machine learning/deep learning is making image processing and analysis insanely fast, more accurate, and super high-throughput. There’s a huge open source community that is constantly developing new tools.

If you want to learn the basics, I’d definitely recommend the iBiology microscopy videos on YouTube, the Microcourses YouTube channel, the Nikon Microscopy U website, and the book Fundamentals of Light Microscopy and Electronic Imaging is fantastic. If you’re in a lab that will pay for you to go to a short course, do it. It’s exhausting, but you truly get immersed in everything related to microscopy.

Also, follow microscopy people on twitter.

JH: What do you like to do outside of lab?

JR: Outside the lab I enjoy running, staring at things in museums, spending time with my dog Lucy and my girlfriend, enjoying craft beer, and more recently brewing beer completely from scratch; grain to glass. I also like travelling to cool places when possible and was lucky to do a pre-pandemic trip to Spain and Portugal. I’m also a big fan of horror movies. I definitely recommend The Witch, Hereditary, and Midsommar. They are all fantastic. Like Ramesh, who was previously featured, I keep a planted aquarium as well.

JH: What does that grain to glass process look like?

JR: You steep malted barley (and other grains sometimes) in heated water. You have to control the temperature and pH to activate enzymes in the malted barley to convert starch into simpler sugars for the yeast to eat. Once that’s, done, you boil the wort (unfermented beer), add hops, cool it down, and then add yeast. While its fermenting might have to dry hop, add fruit, coffee or other things. After its fermented you bottle it or keg it to carbonate. Bottles take longer because you have to get a little fermentation started again to generate the CO2 to carbonate the beer. It all can take anywhere from a couple weeks to months (sometimes years) to finish a beer depending on the style!

Homemade New England IPA!

Racist Science: Books on How We Got Here

When I originally began writing this – my next article for the Insight – it was going to be about things to read during a pandemic. George Floyd hadn’t been murdered yet. Protests hadn’t begun. And originally, I was going to put an extra section at the beginning of my article on racism in science and medicine.

That’s not enough; this topic really needs its own article and more. Speaking here as a white person, I can’t stress enough how critical it is for people like me to self-educate and do some thorough self-examination, and this article meant to be a point from which people can start.

Racism is endemic in our society, and it’s endemic in our sciences. It’s something that the scientific community has passively accepted and ignored for years, and it’s high past time to end that. If you’re new to this, welcome! Reading about racism is a great way to open your mind and determine where your own biases lie. It’s also a great way to keep yourself moving and thinking if you feel you’ve hit a standstill in your progress on this important and evolving topic. Identifying and uprooting biases and racism is a continuous learning process, one that I’m committed to being better at.

The title of each book on this list is linked to The Frugal Bookstore, Boston’s only Black-owned independent bookstore, where possible. Please join me in picking one (or more!) to read, and let’s start educating ourselves and doing better!

The Immortal Life of Henrietta Lacks (Rebecca Skloot)

The scientist that obtained Henrietta’s cells did so without her consent. More than 20 years after her death in 1951, her family finally learned the truth: that scientists had been using her cells for years, that people had made a lot of money from discoveries using those cells, and that they themselves never saw any of the profits.

Most students in the biological sciences are familiar with HeLa cells. Here, Skloot presents the reader with the story of Henrietta Lacks herself, as well as the results of race exploitation in scientific discovery. If you have a few hours to spare, check out the 2017 movie adaptation, featuring Renée Elise Goldsberry (of Hamilton fame) as Henrietta Lacks and Oprah Winfrey as Deborah Lacks.

Medical Apartheid: The Dark History of Medical Experimentation on Black Americans from Colonial Times to the Present (Harriet A. Washington)

The story of Henrietta Lacks is the tip of the iceberg when it comes to the history of exploiting African Americans for medical and scientific progress. It starts long before that, at least as far back as the 17th century. Medical Apartheid presents the first comprehensive history of medical experimentation on African Americans.

This is going to be an uncomfortable book to read. What we now think of as racism in the medical system – racial disparities in access to health care, morbidity, and mortality rates – began with horrific and nonconsensual experiments (a quick Google search on James Marion Sims, the so-called “father of modern gynecology” should do the trick, for anyone curious). And while we have made much progress in that regard, there is so much more left to be done.

Already read this one? Check out one of Washington’s other books on the intersection of race and medicine: A Terrible Thing to Waste details environmental racism and its contribution to racial disparities in disease.

Superior: The Return of Race Science (Angela Saini)

For many white people, the story of overt racism in science may end with the end of World War II and the Holocaust, when people realized the consequences (putting it quite lightly) of the mass implementation of eugenics. But science did not truly let go of racism. Society hadn’t (and still hasn’t) abandoned the idea. It just took on an even more insidious nature.

Superior covers racism throughout known history. It is a book exposing the way scientists cling to an idea of race as a biological truth, as something that is encoded in our genes. This is a book that reveals the propensity of science to look for genetic differences in races as a convenient way of explaining away a difference in disease risk, poverty, and other things, when so much more goes into an individual than genetics.

The Mismeasure of Man (Stephen Jay Gould)

And there is much more to an individual than genetics. Published in 1981, The Mismeasure of Man systematically dismantles the idea that differences between groups of people (such as races) comes from genetics, a malpractice often referred to as biological determinism.

While Gould received great reviews in the popular press, the scientific community gave him the cold shoulder with claims of historical inaccuracy and political bias.

We all have a lot of work ahead of us to successfully strip our communities of racism. The above works touch only on the highly visible aspects of racism in science; microaggressions and other vastly overlooked racist practices are yet another area in which the sciences need to get a whole lot smarter.  It’s not going to happen overnight, but it does need to happen. If you’re looking for more resources, please consult this #STEMforBLM Resource List. It contains more books on racism in science, as well as links to general resource lists (which contain titles like How to Be an Antiracist by Ibram X. Kendi, White Fragility by Robin J. Diangelo, and Between the World and Me by Ta-Nehisi Coates).

Books may not be everyone’s speed, but there are plenty of podcasts to check out if that’s more your style. There are two episodes of NPR’s Short Wave, a podcast on the science behind various news headlines, that might be particularly interesting. “Coronavirus and Racism are Dual Public Health Emergencies” details how systemic racism causes health disparities, such as during the Coronavirus pandemic. In “Science Is for Everyone – Until It’s Not” Brandon Taylor tells his heartbreaking story of why he had to leave science – because of how his fellow scientists treated him, as a Black person.

Which book will you be reading? Have you read any of these, and if so, what did you think?

Black Lives Matter: In STEM and Everywhere

Black lives matter. Derek Chauvin, the police officer who killed George Floyd, knelt on Floyd’s neck for 8 minutes 46 seconds; Eric Garner said “I can’t breathe” 11 times before he died in the chokehold put on him by a NY cop. It took 74 days to arrest Travis and Gregory McMichael, the shooters of Ahmaud Arbery. Amadou Diallo was shot 41 times by the NYPD, Michael Brown was shot 6 times by Ferguson police officer Darren Wilson, Philando Castile was shot 5 times by a cop from St. Anthony, Minnesota, Ezell Ford was shot 3 times in the back by LAPD even when he had his hands up in the air. It took Cleveland police officers less than 2 seconds to shoot Tamir Rice from the time of their arrival at the playground where 12-year-old Rice was playing. Rayshard Brooks, killed by an ex-Atlanta cop at a Wendy’s drive-through, left behind four children aged 1, 2, 8 and 13. Breonna Taylor would have been 27 years old last week. 

Between 2013-2019, police killed 7,666 Black people in the US. 

Black health matters. Black people are dying at ~2.4 times higher rate from COVID19 than white people in the US. Black Americans have the highest incidence AND mortality rates from lung, breast, prostate, colorectal and cervical cancers. Black women are 4-5 times more likely to experience treatment delays and less likely to receive proper treatment for cancer. Black women suffer more often from inadequate pain management. Black women of higher wealth and resource brackets suffer worse outcomes at childbirth compared to white women with fewer resources. According to the Centers for Disease Control and Prevention, 15.3% of Black children suffer from asthma compared to 7.1% of white children; Black people are ~3 times more likely to die from asthma. Racial bias in the form of “race correction” in diagnostic tools used for kidney transplants, kidney stones, urinary tract infections, childbirth, cancer, osteoporosis and bone health, and lung function risk Black patients’ lives through discriminatory clinical practices. 

In Boston, between 2008-2012, Black residents have consistently shown higher emergency department visits and hospitalization rates due to asthma, higher hospitalization rates and mortality due to diabetes, and higher hospitalization rates for chronic heart disease and hypertension compared to all other ethnicities. All of these indicators were observed at the highest quartiles in Roxbury and Dorchester, predominantly Black and poorer neighborhoods of the city.  

Approximately 50% of white medical students and residents in the US have misconceptions about the biology of Black people.

Black futures matter. In 2017, across more than a dozen STEM subfields, not a single doctoral degree was awarded to a Black person in the US; that same year, Black faculty made up 2% of full-time professors in the US. Between 2002-2017, the percentage of Black PhD earners rose from 5.1% to only 5.4%. In 2003-04, 40% of Black undergraduate students switched out of STEM majors compared to 29% of white students; 26% Black STEM majors dropped out of college compared to 13% of white students. In the 2015-16 academic year, Black faculty made up 0.7% and 1.4% of all faculty in Biology and Chemistry across top 40 US institutions, respectively, compared to 83.3% and 81.7% white faculty in those fields. A 2011 study reviewing NIH R01 applications submitted between 2000-06 found that applications from Black scientists constituted only 1.4% of all applications; only 16% of applications from Black scientists were funded compared to 29% of applications from whites. Between 2014-2016, applications from Black scientists constituted 2.2% of all R01 applications; overall award rate for Black applicants was 10.2% compared to 18.2% for white counterparts, resulting in a 45% funding gap. ln 2018, Black scientists received 1% of total R01 grants awarded. 

At Tufts, as of Fall 2019, Black students make up 3.8% of all graduate students and Black faculty constitute 2.7% of all faculty. In STEM fields, Black graduate students range from 0.7% (School of Dental Medicine) to 6.5% (School of Medicine, Public Health & Professional Degrees). At the Graduate School of Biomedical Sciences, there are 7 Black graduate students (3.4%); there are only 2 Black faculty members at Tufts School of Medicine and 3 Black faculty members at School of Engineering. 

It is often assumed that scientists care more about data than individuals. While that assumption is possibly wrong, the obsession with statistical significance as a proxy for significant biological phenomena cannot be understated. But when it comes to Black lives, both statistical and biological significance are tied together – the numbers show us the immense disparity in health outcomes, each death shows us the complexity of a life that is lost. Black people are dying at the hands of police and physicians at higher rates than other races/ethnicities in the US. The vicious cycle of misconceptions of Black bodies, that they have thick skins, or that they are “monsters” as Darren Wilson alleged, stem from the other-ization of Black people – the same racist ideology, so ingrained in every aspect of US culture including academia, that drives racial disparities in STEM education and careers of Black academics. From the Tuskegee Syphilis Experiment to HeLa cells to Black women vivisected to establish the field of gynecology, Black bodies have been used as disposable commodities throughout the history of biomedical research. Diversity and Inclusion efforts in academia are largely performative, as the #BlackInIvory stories on Twitter show; faculty hiring committees end up reproducing whiteness in their pursuit of diversity. 

Over 6,000 scientists across the world participated in #ShutDownSTEM and #Strike4BlackLives on June 10 in solidarity with the ongoing #BlackLivesMatter protests nation-wide. Yet, this outpouring of solidarity is not enough – one day of recognition is not going to undo centuries of racist ideology that permeates biomedical research and rest of academia. But this serves as a stepping stone to recognizing the racist history of the fields we work in, the subjects we study, the places we work at. Biomedical scientists need to grapple with the fact that health disparities ravaging Black populations are due to racism, rather than race. Faculty and universities need to recognize that “promoting diversity rather than substantive structural change will not create equal opportunity and equal outcomes.” The work to undo the racism within our own ranks require us to stand in solidarity with Black people, whether at our workplaces or neighborhoods, and to educate ourselves on the intersectionality between the diseases we study, the history of such research and the material conditions of Black lives.

Thoughts on the book “Bad Blood: Secrets and Lies in a Silicon Valley Startup”

I began to read more than usual because of social distancing, going through the list of books I had been planning to read for a while. One of the books that was recommended by a friend was “Bad Blood – Secrets and Lies of a Silicon Valley Startup” by John Carreyrou [1], based on the rise and fall of the blood-testing company, Theranos. I was especially interested in it given its relevance to the biotech industry and on recently finishing the book, I realized GSBS students might also find it interesting and thought of sharing a little bit about it. While there are plenty of resources out there that help you understand how to search for a job, determine if it is a good fit and notice red flags, this book paints a picture of life in the biotech industry, both as an entrepreneur and as an employee. I think students interested in careers in industry, entrepreneurship, venture capital, or science policy will gain some perspectives from reading this book. For instance, the book portrays the harsh reality of working in industry when a team of engineers were laid off because the research was headed in a new direction and they were not needed there anymore.

In January 2003, a 19-year-old Elizabeth Holmes founded Theranos with the vision of enabling multiple diagnostics tests to be run from a small volume of blood obtained from a finger-prick rather than the traditional venous blood draw, using the company’s small, portable, automated devices. In October 2015, a reporter from the Wall Street Journal, John Carreyrou, published an article [2] revealing that the company has been misleading investors and consumers, that the blood tests analyzed by Theranos devices were inaccurate and unreliable, and that a lot of the tests were actually performed by third-party commercial analyzers. Expanding the article into a book, Carreyrou walks us through how the company was formed, how it grew to become one worth over $9 billion, and finally, how it dissolved in September 2018 [1]. It is common knowledge that most, if not all, companies in Silicon Valley have skeletons in their closets that make headlines when they are revealed. However, fraud and irresponsibility by a health technology company like Theranos, and at such a massive scale at that, is even more dangerous considering the direct harm to patients’ lives. It is shocking that a company could get so far with technology that never performed as promised, and Carreyrou lays out the various scenarios and circumstances that contributed to it.

This book exemplifies the importance of validated and peer-reviewed data, the need for rigorous testing and quality-control checks, and the need for adhering to regulations – things we already know and are trained to practice. The book also highlights the need for communication within and between different departments in a company, so employees are aware of what stage of development the product is in, identify what exactly is holding up progress and work together to solve the problem. This lack of communication and the unusually high level of secrecy was frustrating to the employees at Theranos [1]. It is therefore important to find a balance between protecting proprietary information and facilitating communication to ensure highest productivity. Besides the need for effective communication between employees, the book also shows how there is a need for open, honest communication and understanding between the employees directly involved in developing the product and higher-level management. Without it, as a leader, you risk facing the dangers of being surrounded by yes-men – a false sense of security that you are doing things right, that the technology is working perfectly, experiments are returning expected and reliable results, and experiments that are not actually feasible can be done – hence wasting both time and money. You do not improve because you do not know where improvements are needed. However, at Theranos, the yes-men were not the only ones contributing to this culture. Holmes was not only a bad listener; she seemed to consider anyone who challenged her as disloyal [1]. She was surrounded by yes-men because she did not foster an environment that welcomed ideas, suggestions, and opinions opposite her own. Employees did not come forward with concerns because they did not want to get fired. This may be especially true of employees with H1-B or other work visas who have much more to lose, considering how their ability to stay in the country is tied to their employment. Abuse of H1-B visa workers is not unheard of; a recent example is Cloudwick Technologies Inc., based in Newark, California, paying their H1-B employees a much lower salary than what was agreed upon, and making illegal deductions from their salaries.

A negative (and savage!) review on the Glassdoor website (a website where employees can leave information about a company they work or worked in, such as CEO approval ratings, company reviews, salary reports) mentioned in the book prompted me to look at what else the ex-employees of the company had to say. Many of the reviews for Theranos are very detailed, with some ex-employees especially taking the time and effort to explain the “Pros” and “Cons” of working there. The most common “pro” mentioned was free food and snacks – something we, as grad students, can easily relate to. The “Cons” part of the negative reviews is where things got interesting. You could get an insight into how the employees felt and how they were treated. Most of them were overworked and underappreciated. It may be typical of employees to put in extra hours or feel like they have no work-life balance at a start-up firm, but at Theranos, they would not only track the number of hours the employees would spend at work, but would also monitor their social media activity [1]. The employees’ dedication was measured by how long they stayed at work and whether they would come in during the weekends. I imagine such a working environment would be suffocating and counterproductive, and it was no surprise that the employee turnover was high. What you can also glean from the reviews is the shattered hopes and dreams of the employees who were inspired by Holmes’s visions and dedicated their time to actualize it. As scientists, we all hope to contribute to making this world a better place. On top of not being able to do that at Theranos, they also feared that their time in the company will work against them in future applications. The book also mentioned how the HR department would post fake positive reviews on Glassdoor, and some of the reviews did spin the “cons” in a way to show Theranos in a positive light. For example, one of the reviews listed the cons as “truths” with statements like, “If you are unable to work in a highly self-directed environment where you are counted upon to create clarity from ambiguity, you will not be successful at Theranos.” This reminded me of reading about people answering the common interview question “What is your biggest weakness?” with “I work too hard.”

All things considered, Theranos did not really ruin the prospects of a biotech-startup in Silicon Valley. As a couple of articles in Wired mentioned, investors may be more skeptical now and that may actually be better. The increased scrutiny will hopefully mean rigorously tested data and more valid claims. Carreyrou points out how tech companies usually exaggerate about how their devices perform, but the same cannot be done with a medical device. No one ever died from a buggy Candy Crush app, but a misdiagnosis can be potentially fatal.

It is also interesting how Elizabeth Holmes and her downfall (from a net worth of $4.5 billion to zero) is discussed by the public. After she and her company were exposed for fraudulent practices, the focus skewed towards her appearance rather than her transgressions. They talked about how her unblinking stare (described as a “hypnotic” gaze in the book) is “sociopathic”, how she is not naturally blond, how her makeup is weird, and her deep, baritone voice is fake. Also, concerns about Theranos’ technology and the company’s practice were brought forward to some highly intelligent and experienced investors. Granted, they were not experts in the field of medical technology, but it would not be difficult to get an expert’s opinion and some of them were indeed alerted about Theranos by experts. If they genuinely did not have the power, even as a member of the company’s board of directors, to do anything about Holmes, why continue to be investors and not step down? Were they all simply manipulated and “bewitched” [1] by Holmes’s charm?

People have lots of ideas and opinions on where things went wrong, what Holmes could have and should have done, but the bottom line is, she blew the chance to be an inspirational leader and a role model. The struggle of female entrepreneurs, especially women of color, is no secret. Holmes did have a better chance than most women to become the “first female billionaire tech founder” [1] – she is smart, motivated, hard-working, charismatic and understands how Silicon Valley operates. She comes from a privileged family, had access to opportunities and was well-connected enough to benefit from the support of famous investors at a very early stage of the company. It is unfortunate that what was going to be a huge success story is now in the news for all the wrong reasons.

This book is a cautionary tale for biotech start-up founders and venture capitalists interested in biotech start-ups – providing insight into what makes an effective leader and the responsibilities that come with it, and what employees and venture capitalists should look for when looking to work or invest in a biotech firm. In my opinion, the story of Theranos could be an interesting case study for discussion in an ethics class or at the Tufts Biomedical Business Club. Regardless of whether you are interested in the biotech industry, I think anyone who is a fan of thrillers will enjoy this book. For those interested in something more visual and/or sensationalized, there is an HBO documentary covering this story called “Inventor: Out for Blood in Silicon Valley” and a movie based on Carreyrou’s book is set to release sometime this year.

References:
[1] Carreyrou, John. Bad Blood: Secrets and Lies in a Silicon Valley Startup. New York, Knopf Publishing Group, May 21st, 2018.

[2] John Carreyrou, “A Prized Startup’s Struggles,” Wall Street Journal, October 15, 2015.

Coffee and Conversations with Professor Madeleine Oudin

One of my favorite Boston GWiSE events is the monthly Coffee and Conversations with female faculty, alumni, and post-docs from Tufts. “Coffee and Convos” allows GWiSE members and other GSBS students to have a casual conversation with these successful professionals. Past guests have included Malavika Raman, Claire Moore, Trina Basu, Georgina Kontou, and Parisa Kalantari. We learn about what got them into science, their career trajectory, and advice for navigating academia. Unfortunately, work-from-home and stay-at-home advisories have brought all student-led events to a halt. So today, I would like to bring the coffee and convo directly to our work-from-home office. Start brewing your favorite caffeinated drink and grab a snack if you haven’t already!

This month’s Coffee and Conversation is with Dr. Madeleine Oudin. She has been an Assistant Professor in the Department of Biomedical Engineering at Tufts School of Engineering since 2017. Since coming to Tufts, she has generated a lot of interest in her lab, which works on the role of tumor microenvironments in cancer metastasis and drug resistance. I sat down with her over Zoom and started off with the question that we start all “Coffee and Convos” with: 

What got Madeleine into science?

Growing up in a suburb of Paris, France, Madeleine enjoyed her Biology and Chemistry courses in high school. None of her family members were scientists, so she fostered that growing interest by herself. She majored in an accelerated Biochemistry path at McGill University in Montreal because it combined these two interests and left out plant biology (a sentiment this author fully supports). She didn’t get into research until her senior year because she didn’t think undergraduates could do research!

What was Madeleine’s career trajectory after University?

With her new-found love for scientific research, she pursued a Master’s degree in Pharmacology at King’s College London. The one-year master program led to her to complete her PhD in Neuroscience in the same lab. The senior PI, Dr. Patrick Doherty, was studying stem cells from the subventricular zone of the brain in the context of adult neurogenesis. Meanwhile, the junior PI studied the migration of these cells in the stage after neurogenesis. What Madeleine learned from the junior PI is what got her into imaging cell movement, which is still a staple of her research today. “Let the cells tell you what they are doing.” 

Madeleine loved neuroscience but craved a medical aspect that her research had been lacking up to that point. When she met Dr. Anne Ridley, who studies Rac and Rho signaling in cancer cell migration and metastasis, at a conference, Madeleine realized she could translate her skills in imaging cell migration to a field with more biomedical relevance. Her post-doc lab was a perfect place to tie her neuroscience training in with cancer biology. Dr. Frank Gertler at MIT studies Ena/VASP proteins involved in axon guidance that are also upregulated in cancer. This essentially divided the lab in half: a neuroscience group and a cancer group. Madeleine loved this! Additionally, the lab was in a new engineering building at MIT intended to foster collaborations with cancer research. When Madeleine looks back at her time at MIT, she admits that it was really cool to see the collaborations and new tools that came from this unique union of fields.

When it came to applying to faculty positions, Madeleine looked at both engineering and biomedical departments. She came to the Tufts School of Engineering in 2018. If you were to ask her at the beginning of her research training, she never would have imagined she’d end up in this field.

How can we change predominantly male science environments to be accepting of women?

Madeleine wants to see more representation in seminars, in faculty, and at conferences. Biology historically has had a higher representation of women than Engineering as a field. When Madeleine got to Tufts, the Biomedical Engineering seminar series was 90% men. She raised this issue with her colleagues. “A woman would’ve noticed the discrepancy in minority representation pretty quickly, but my male colleagues hadn’t. I think it’s important to promote awareness.” She then organized the seminar series and increased minority and women representation from 10 to up to 80%. Stepping up to this task reflects on Madeleine’s belief that more women in leadership roles will facilitate necessary changes to predominantly white, male environments.

Other areas that Madeleine thinks need more support are childcare, maternity leave, and time to apply for grants during maternity leave.

Has Madeleine ever experienced discrimination as a woman in the work place?

Madeleine wishes people would focus less on her appearance and more on her abilities as a scientist and mentor. Colleagues of hers have commented on how young she looks in front of students and have even mistaken her for an undergraduate student. To set a more professional tone and reduce confusion, she introduces herself as Professor Oudin. Conversely, she tries not to assume when asking other people what their role is at seminars and conferences. Despite these challenges, Madeleine has been extremely successful in her first 3 years as a professor. The Oudin lab has produced 3 published papers and been awarded a handful of grants since coming to Tufts. Make no mistake: Professor Oudin kicks ass as a scientist. 

How does Madeleine foster an inclusive lab culture?

Madeleine’s students see her advocating for inclusion in her role as a mentor. Her lab consists of a majority of women and a diverse group of students. Interestingly, mostly female undergraduates apply to work in her lab. Some have told her it is because they are inspired by seeing a woman in her position. Madeleine enforces a respectful, collaborative, and supportive lab environment; no bullying or bad behavior is tolerated. She circulated an anonymous survey of lab culture, which opened the door to having a conversation about it. “As PIs, we aren’t taught how to manage. We aren’t always going to be perfect, but getting honest feedback from the lab on our work culture seems like the easiest step to take in that direction.” 

As a mentor, Madeleine encourages her students to expand their professional network and try new things. As a baseline, she has younger students interact closely with older students in the lab. She also introduces her students to the people she knows in Boston. These are the steps she actively takes in fostering an inclusive and successful lab setting. However, she emphasizes there is only so much she can do. “Students can put themselves out there to get the information they need.”  Madeleine provides excellent resources to her students and it’s their decision to utilize them.

Does Madeleine participate in outreach programs?

Outreach is another avenue in which Madeleine exemplifies her commitment to fostering an inclusive science community. Some of her favorite local outreach programs are the Cambridge Science Festival, Tufts Community Day, and the Girl Scouts Science Fair. She also participates in panels where she can raise awareness about the obstacles women still face in the fields of biology and engineering. The Biomedical Engineering and Chemical Engineering Graduate Student Society (BEaChES) at Tufts acknowledged Madeleine’s advocacy by voting her as an Exemplary Engineer among the Biomedical Engineering faculty in 2019 and 2020.

What new hobbies has Madeleine taken up during quarantine?

Madeleine recently got a Peloton! She says it’s a fun way to stay active while staying indoors. She’s also taken up more household projects like painting and gardening. And since Madeleine is gluten-free and has had little issue finding gluten-free flour at the market, she’s been baking cakes during quarantine.

Learning to love quaran-TEA-ne

Sorry for the terrible pun, but during these times of stress something that I have found to be very relaxing is to drink a lot more tea during the day than I previously had. While I always enjoyed various black, green, and oolong teas (more on the different types later), I discovered vastly more types and varieties of tea that exist while locked up in my apartment these past two months. Fortunately there are many reputable companies selling tea online, allowing you to get your fix without having to leave the apartment (not like you could anyways). Let’s discuss the different types of teas, their characteristics, and some places that I have gotten really great teas from in the past two months.

The types of tea

Camellia sinensis is the humble plant that has provided humans with tea for thousands of years. Originally drank in ancient China, tea cultivation spread to Japan, India, Southeast Asia, and Africa. The Assam and Darjeeling regions of India produce vast quantities of black tea each year. The Japanese produce almost exclusively green tea, what is known as sencha, which has a distinctive aroma of freshly cut grass and a nice vegetal taste. What makes a green tea different from a black tea? A white compared to an oolong? It comes down to how long the picked leaves are allowed to oxidize before being heated, a process which denatures the enzymes present in the leaves halting the oxidation reaction. As oxidation occurs for longer, the leaves take on a darker color.

White tea: What is considered the most delicate and unprocessed form of tea, white tea usually consists of the earliest leaf buds of the tea plant that are picked and either dried right away or heated before drying. While there is no agreement among the tea growing community, white teas are typically not oxidized or rolled, creating much lighter flavors when brewed.

Green tea: Consisting of many varieties and processing methods, green teas are minimally oxidized and can be heat-inactivated through either steaming (typical of a Japanese sencha) or pan-roasted (common in Chinese green tea). These different methods impart greatly different final flavors and aromas in your cup. Green teas are typically very vegetal and grassy in flavor.

Oolong tea: Halfway between a green tea and a fully-oxidized black tea is oolong (or wulong). These can be either lightly oxidized or closer to fully oxidized. I have come across hundreds of oolong teas while shopping online, and I’m sure there are hundreds more. These are fascinating to me as you can experience so many different flavors and aromas based on where the tea was grown, how much it was oxidized, how it was heated, and the final rolling and drying. Oolongs are best for gongfu style brewing described below.

Black tea: Consisting of fully oxidized leaves, black tea is probably most familiar to Westerners. While produced in many tea growing regions around the world, I believe the majority of black tea is grown in India for the international markets. Most black tea is destined as “dust” for tea bags and large distributers, but there are many full leaf black teas with great flavors that don’t need milk or sugar to make palatable. I do enjoy Twinnings or Taylor’s for bagged breakfast teas, such as Scottish or Irish breakfast.

Pu’er tea: I had not heard of pu’er tea until just recently. This tea is fermented over various periods of time (decades is better) allowing bacteria and various fungi to do what they do best. This imparts complex earthy aromas and flavors from the tea. While I have only tried one pu’er tea that was produced in Malawi, I’m sure there is a rich variety of flavors that can be enjoyed. For me, I think it is more of an acquired taste. The pu’er I had smelled exactly like dirt in a forest, during a large storm, and there were definitely worms and fungus involved. The flavor was mild and not bad, but the smell took some getting used to.

How to brew tea

A gaiwan for gongfu cha brewing

Each type of tea requires different brewing processes to allow for the optimal flavor extraction without causing the tea to become too bitter from the tannins present in the leaves. A general rule of thumb is that for black and pu’er teas you must use water just off the boil. Let the leaves steep for 3-5 minutes. For oolongs the temperature varies depending on the oxidation level, but typically brew from 175-195 degrees Fahrenheit for 3 minutes or so. Green and white teas taste best at lower temperatures, from 160-176 Fahrenheit or even 150 for more delicate teas. The brew time can be from 30 seconds to 3 minutes depending on the type of tea.

Gongfu cha style: A brewing style that I learned about during my time in home confinement is the gongfu cha method. This involves a ritual preparation of the tea encompassing many short, low volume, steeping of the tea leaves. Traditionally, the leaves are brewed in a gaiwan, a vessel consisting of a saucer, cup, and lid. You use the lid as a strainer when you pour out the tea liquor. Naturally, I acquired such a device over the internet and love using it. This process allows you to focus on making the tea, experience how the flavors and aromas change during subsequent infusions, and achieve a feeling of calm and mental clarity I did not think possible during a PhD.

My favorite tea venders

I have bought tea from several venders and have enjoyed many different types that are mentioned above.

Harney and Sons King of Bai Mudan. Delicious sweet white tea

Harney and Sons are based out of New York and have an expansive selection of teas at a good price. I enjoy their Bai Mu Dan white tea, Scent of the Mountain Sencha, and Ali San Oolong.

What-cha is a UK-based company sourcing many great teas. I sampled many different teas from here, but my favorites were the Yunnan Pure Bud Golden Snail black tea, Obubu Kabuse sencha, Taiwan GABA oolong, and a Taiwan Mi Xiang honey black tea. The owner also includes a hand-written note with each order, which I think is a nice touch and shows his devotion to fair and sustainable tea trade.

MEM Tea: Right in our own backyard located between Porter and Davis square is MEM Tea. I await some of their teas in the mail, but they have a great selection of teaware. I received some gongfu cha tea brewing essentials from them and the quality is good.

Rare Tea Company: Another UK-based company, the founder of Rare Tea searches the globe for unique and well, rare, teas that are unlike anything else. From here I have sampled teas from Malawi, Nepal, China, and Japan. They are truly unique and delicious but rather pricey for a graduate student. My favorites are a White Peony from Malawi, a Sofu Sencha (smells like summertime and happiness), and a silver tip jasmine white tea.

I hope you discover a new tea that you enjoy brewing and tasting to help you cope with the research shutdown.

Humans of Tufts Boston: Ramesh Govindan, “Our ingenuity will pull us through”

Humans of Tufts Boston, 7 May 2020

Ramesh Govindan, CMDB, Fourth-year Ph.D. Student (Sixth-year M.D./Ph.D.): “Our ingenuity will pull us through

JH: How did you get started in science and what were you doing before medical/graduate school?

RG: I always had an interest in science, although I had a brief stint in college where I wanted to be a history major (my parents were terrified). I went to college thinking that I wanted to become a biomedical engineer, because my big interests at that time were in tissue engineering. Growing synthetic organs for transplantation seemed like the coolest thing on Earth (and it might be), and I wanted to be the guy to make it a reality. As I learned more biology and physiology as part of my major coursework, as well as a lot of the humanities courses I was required to take, I also became a lot more interested in the human elements of disease and medicine. So, on top of working in a biomedical engineering lab, I started volunteering at a local hospital in a Medical Specialties ward, through a program where we would visit patients who had been, or were anticipated to be, on the ward for a long time (weeks, months). I’d spend a few days a week there for a couple of hours at a time going on walks, playing board games, and chatting with the patients. I got to know a few people pretty well, including a particularly memorable guy who had poorly-controlled schizophrenia and type I diabetes, the combination of which prevented him from being discharged on his own. By the time I hit senior year, I was pretty confused as to what I wanted to do – science or medicine. I ended up taking a gap year at the NIH in a basic science cancer research lab, where we studied the mitotic kinetochore, a protein-chromatin-microtubule complex that forms during metaphase to regulate chromosome segregation. I had two projects there, first looking for substrates of Aurora B kinase, which orchestrates numerous processes in the kinetochore. The second was to study the role of a specific histone methylation (H3.3S31me) in mitosis. Our model system was Xenopus laevis frog eggs, which are highly mitotic and are great for immunoprecipitation. I applied to MD/PhD programs during that time.

The MD/PhD team at the 2018 Relays

JH: Why did you choose to do an MD/PhD?

RG: People ask this of MD/PhD students a lot, and I’m not sure if it’s out of a concern that we’re all secretly insane, or whether they actually think there’s some hidden driving motivation behind each person’s choice. I’ve come to realize over the years that I really don’t have a single reason why I chose this. There are a lot of small reasons, though. The first, probably, is that I was really torn between two professions. I enjoy science and the lab, but I also like helping people directly, with my own hands. To find out at the age of 20 that there was a career path that would allow me to do both of those things, even if it was only in theory, was something I had to jump at. The second reason I chose this is maybe more nebulous – I didn’t really see the downside. It was a challenge that only a relative few chose, and it opened up potential without closing any doors. In my mind, the regret of not having tried to do both would far outweigh the regret of having tried and failed. So I applied, then I got in, and, six years later, I’m still doing it. And yes, I still have two more years of medical school, five-ish years of residency, and then one or two more years of a fellowship, but I take it one step at a time and so far I’m really enjoying it!

The third reason was that medical school is free.

Waiting in line at the 2018 Extreme Beer Festival

JH: What drew you to microbiology for your thesis research?

RG: My interest in microbiology was not a deciding factor in any choice I’ve ever made. I’m not sure I even knew what a virus was before John Coffin and Katya Heldwein told me about them during lectures in my first year of medical school. And even then, I only wrote down enough information to pass whatever exam I had coming up. I didn’t realize that viruses would become such a big part of my life until I decided to join James Munro’s lab, and I only really joined because I liked his mentoring style and pew-pew lasers. But in the last four years, I’ve come to realize that viruses are maybe some of the coolest biological phenomena on the planet. They’re the only known replicating pathogen that is, by most definitions of “life”, dead. They’re nature’s freak killer robots. From a structural biology perspective, they are macromolecular machines perfected by evolution with only the goal of efficiency. They’re insanely amazing as research and therapeutic tools, and equally terrifying as agents of human disease. So I’m pleasantly surprised to have found virology as a PhD student, and I’m hoping to maintain a level of engagement with it as I move on my career.

Setting up a new hot pepper garden at Ramesh’s parents’ house in central MA

JH: Obviously COVID-19 has been getting a lot of press lately. As a future doctor, what do you think? Are there any questions that aren’t being asked that should be?

RG: These are truly terrifying times. The looming specter of COVID-19 has, I think, become a defining challenge for society. As a virologist-in-training, I hope that this pandemic helps us re-evaluate the ways in which we interact with the ecosystem and each other, and, as a doctor-in-training, I hope that we find new ways to organize ourselves to respond to emerging viral pandemics. The gut-wrenching part of this is that this entire pandemic, on nearly every level, is a product of human activity. From the encroachment of humans on untouched wilderness, to our inability to deal with global poverty, to our complacency in letting free market forces dictate the makeup of our healthcare systems, simultaneously all of us and none of us are to blame for this. For instance, while the lack of infectious disease (ID) doctors in this country isn’t specifically anybody’s fault, experts have been pointing out this shortage for decades. A root of the problem is that training in ID is financially devastating – you pay ~60k a year through medical school, then slog through a low-paying internal medicine residency, and then train for 2-3 years as a fellow in ID. As an ID doc, you make less than you would have if you had just stayed in internal medicine – you take a pay cut to get more training. Your salary as a doctor is tied to how much you can bill insurance, and if you don’t do any surgeries or procedures (like an ID doc), you bill less, and you make less. It’s ridiculous. We were able to fight HIV in the ’80s and ’90s because at that time, there were many more ID doctors in the country. Today, we’re out-gunned. 

So, this has been a classic conversation with Ramesh where it gets really dark once he gets going. But it’s not all bad. I am, surprisingly, still an optimist, and I really do believe that our ingenuity will pull us through. Vaccine trials are already underway, and drugs like remdesivir are showing some promise. But we need to keep up our momentum once this pandemic is over, and rethink our preparedness for viral pandemics, because SARS-CoV-2 is just one of many pathogens to come.

Ramesh’s fish tank with Saruman, the betta fish

JH: What do you like to do outside of lab?

RG: Foremost, seeing my friends is my favorite thing to do. The friends I’ve made at Tufts have helped me in more ways than I can describe. Even if I somehow failed out of two doctorate programs, I know I’ll walk away with some of the best friendships I’ve ever had. If you’re asking after hobbies, then I think an easier question would be, ‘What doesn’t Ramesh like to do outside of lab?’ I think most people who know me know of my strange obsession with The Lord of the Rings, the greatest story ever told. More recently, I finished another fantasy series, the Wheel of Time, via audiobook on my drives out to UMass and my lonely nights in lab. I can’t recommend that series enough. During the final book (50-ish hours long) I had to periodically look up to the ceiling to let the tears drain back into my sinuses so that they wouldn’t splash into my ELISA plate. This was besides the tears I normally shed in lab. I also really enjoy gardening. I worked eighteen years a slave in my family’s yard, and then left home to realize that I actually enjoyed it the whole time, so besides heading home to work my parents’ garden I also have a small yard in Cambridge that I’ve been working on. Hand-in-hand with gardening, I’ve started keeping a freshwater fish tank with real plants that’s been pretty fun to maintain, especially in the winter when there’s no gardening to be done outside. I also enjoy cooking – I use the guides on Serious Eats and America’s Test Kitchen to try out new things when I can. It seems like during this pandemic there’s been a huge explosion of cooking on the internet, and I’m really enjoying that. I also can’t wait till summer rolls around so I can start smoking meats again. I generally think that people of our generation need more hobbies that are not Netflix, and I’m very grateful to have found hobbies that I enjoy and can share with my friends.

Humans of Tufts Boston: Logan Schwartz, “I am interested in helping an aging population”

Humans of Tufts Boston, 9 Apr 2020

Logan Schwartz, Genetics (JAX), Second-year Ph.D. “I am interested in helping an aging population”

JH: Thank you so much for agreeing to answer some questions! What were you doing before graduate school?

LS: I started my scientific career as a summer intern at Regeneron Pharmaceuticals for three summers right after high school and through college. I worked in the VelociGene Department aimed at developing genetically modified mammalian models of gene function and disease! I attended the University of Rochester and studied Molecular Genetics and Chemistry. After completing undergrad, I was working for Dana Farber Cancer Institute and MGH as a research technician studying the functional genetics and molecular mechanisms of chronic lymphocytic leukemia and cystic fibrosis.

The Trowbridge lab

JH: What drew you to the JAX program?

LS: I was drawn to the JAX program by the opportunity to work with Dr. Jennifer Trowbridge and the novel mouse models for studying clonal hematopoiesis (CH). The Genetics program at JAX is a unique graduate program with the freedom to take courses at The Jackson Laboratory in topics ranging from systems genetics to different computational languages. I really enjoy the close and collaborative community at JAX and I am happy to be a part of it!

Dr. Trowbridge is a leader in the field of hematopoietic stem cell (HSC) research and she is fearless with respect to developing and employing the new and best techniques to address scientific questions. She is an inspiring investigator to be mentored by, having navigated herself the challenges of achieving success as a woman in science.

The Trowbridge lab hikes in Acadia

I am particularly excited to work in this field of research because I am interested in helping an aging population. With the growing population of elderly individuals worldwide, preventative strategies to reduce aging-associated diseases are urgently needed. We acquire somatic mutations in our HSCs as we age, some of which can confer a competitive advantage and cause clonal HSC expansion, known as clonal hematopoiesis (CH). This is present in 10-15% of individuals aged 70 years or older. My thesis work in the Trowbridge lab strives to identify novel mechanisms that can be used as interventions to prevent aging-associated diseases and disorders of the hematopoietic system, with a specific focus on HSCs, which are responsible for the lifelong maintenance of a functional hematopoietic system.

Riding a camel with Rebecca Brown (Genetics program) in Israel

JH: Is there anything you think is under-appreciated in the field of genetics?

LS: Genetic Diversity! Many diseases are studied by using models on a single genetic background when no two humans with the same disease are genetically identical. My lab is using genetically diverse mice to determine if inherited genetic variants increase the likelihood of developing CH and that there are population differences in clonal advantages gained by specific mutations in particular genetic and environmental contexts. CH is most commonly driven by somatic mutations in the gene encoding DNA methyltransferase (DNMT3A), so we are testing the hypothesize that variation in genetic background dictates whether DNMT3A-mutant HSCs acquire a selective advantage. The work is still in progress so we will have to wait and see!

Logan’s cat, Eugene!

JH: What do you like to do outside of lab?

LS: Outside of the lab, I enjoy hiking/exploring Acadia national park, running, painting and trivia nights, and taking care of my fifty house plants! A couple of years ago, my friend gave me my first house plant, a snake plant. He told me they were impossible to kill, and somehow I still managed to kill it. I decided to try again, and somehow I was able to keep it alive. After that, it has become a sort of obsession, although I still kill succulents from time to time. The thing I love most about having plants is how much life they can bring into your home. I also love watching them grow and change over time!

Some of Logan’s many house plants!

How Do You Figure?: Graphic Design Software For Scientists

As I sit at home writing what will (hopefully) be my very first first-author manuscript, I began to wonder how scientists go about making their figures for a paper. Like many things in academia, it was probably going to be lab-specific: someone would have started using a particular software, taught the next graduate student how to use it before they left, and that student would teach the next. And so on, and so forth.

With this in mind, I took to Twitter to ask students (and @AcademicChatter), how, exactly, were they figuring?

BioRender (@vanesque89, @Nicole_Paulk)

Price: Free for personal/educational (limited) use, various paid plans
Platform: Web-based

Think of BioRender as your scientific clip-art library. BioRender has a collection of over 20,000 different icons covering more than 30 fields of the life sciences. The colors of each icon can be customized, and the drag-and-drop functionality makes figure creation very quick. Even better, there’s nothing to download! It’s right there in your browser, ready whenever and wherever you are working.

CorelDraw (@AdemaRibic)

Price: $249/year or $499 (one-time purchase)*
Platform: Windows, Mac

Originating in Ottawa, Canada, CorelDRAW touts vector illustration, layout, photo editing, and typography tools. It works on both Windows and MacOS.

*Editor’s note: Corel Education Edition is a one-time payment of $109 (thanks to Adema Ribić for this correction!)

Adobe Photoshop and Illustrator (@Nicole_Paulk)

Price: $20/month for the first year, $30/month after that (student pricing, includes all Adobe apps)
Platform: Windows, Mac, some apps available for iOS and Android

Almost everyone is familiar, at this point, with Adobe Creative Cloud, Adobe’s suite of software for designing things (literally, any and all of the things). Photoshop is useful for raw images (such as overlaying fluorescent images and stitching together microscope images). Illustrator, in contrast, is for creating vector art and illustrations, but it’s also useful for aligning the different panels for a cohesive figure. The most updated version of Illustrator seems to have kept this in mind: the Adobe website specifically mentions its use in making infographics, including the ability to edit data through a charts function.

GraphPad Prism
Price: $108/year (student pricing)
Platform: Windows, Mac

Prism is less for making figures and more for making graphs, but it’s worth mentioning here since many of us include graphs in our figures. In Prism 8, you can draw lines or brackets on graphs to indicate significance. A centered text box is automatically included for your asterisks! These graphs can be exported as images and then arranged easily in another application as panels of a figure.

Affinity Photo and Designer (@SimonWad)
Price: $50 per app, one-time purchase
Platform: Windows, Mac, iPad

These are popular alternatives to Adobe Photoshop and Illustrator. One of the major complaints about Adobe was its movement to a cloud-based subscription model. Affinity uses a one-time purchase model, and is also considerably more affordable. The company also has an alternative to Adobe InDesign (called Publisher).

This is by no means an exhaustive list of all the possible software you could use to make a figure. Many people swear by PowerPoint as their favorite way of assembling figures. Here are a few other pieces of software to check out that are free to all:

Gimp
Price: Free!
Platform: Windows, Mac, Linux

Gimp is a high-quality raster image editor. Think of this as the free version of Photoshop. It can do a lot of the same things, but it’s missing some of the advanced tools, such as using adjustment layers to non-destructively edit images.

Inkscape
Price: Free!
Platform: Windows, Mac, Linux

Inkscape is a vector graphics editor with shapes, layers, text on paths, and the ability to align and distribute objects. If you’re looking for something like Illustrator to handle vector graphics but don’t want to shell out the money, this is a great option!

Scribus
Price: Free!
Platform: Windows, Mac, Linux

Scribus is an open-source alternative to Adobe InDesign. It has many of the same features as InDesign, but unfortunately can’t open InDesign files.

Thank you to everyone who responded, and happy figuring!

Cover image by Mudassar Iqbal from Pixabay

Sources:
biorender.com
coreldraw.com
adobe.com/products/photoshop.html
adobe.com/products/illustrator.html
graphpad.com
affinity.serif.com
products.office.com
gimp.org
digitaltrends.com/photography/gimp-vs-photoshop/
inkscape.org
scribus.net