The greatest show on earth

“We are going to die, and that makes us the lucky ones. Most people are never going to die because they are never going to be born. The potential people who could have been here in my place but who will in fact never see the light of day outnumber the sand grains of Sahara. Certainly, those unborn ghosts include greater poets than Keats, scientists greater than Newton. We know this because the set of possible people allowed by our DNA so massively exceeds the set of actual people. In the teeth of these stupefying odds it is you and I, in our ordinariness, that are here. We privileged few, who won the lottery of birth against all odds, how dare we whine at our inevitable return to that prior state from which the vast majority have never stirred?”

-Richard Dawkins, Unweaving the Rainbow: Science, Delusion and the Appetite for Wonder

This powerful passage signs off a wonderfully unique song by the Finnish symphonic metal band Nightwish from their album Endless Forms Most Beautiful. Drawing on works from Charles Darwin and evolutionary biologist Richard Dawkins (who’s book The Greatest Show on Earth inspired the song name), this 24-minute magnum opus explores the major events of life’s evolutionary history to present day. The song is broken up into four larger parts that tell the tale of Earth’s unique history. This has quickly become one of my favorite songs. Let’s now take a closer look at how Nightwish set out to marry heavy metal with evolutionary biology concepts (link to a live version with guest appearance by Dawkins will appear at the end of this article).

Part 1: Four Point Six

The song opens with a repetitive and fluid piano melody accompanied by orchestral components that signify whatever “existed” before the Big Bang . At 1:33 the Big Bang arrives, and the music shifts to convey the resulting chaos and energy of a nascent universe being born. At 1:55 we are introduced to the main melodic theme that we will revisit throughout the song. Several more explosions are heard (2:40) which I imagine as our solar system coming together from the ensuing bombardment. The first lyrics are sung as a haunting ephemeral wailing.

 Archaean horizon, The first sunrise
On a pristine Gaea
Opus perfectum, somewhere there, us sleeping

Geologic time is broken into distinct eons, and the Archaean signified the earliest emergence of life. In Greek mythology, this life arose from Gaea the Greek goddess of the Earth. Life has now been established (opus perfectum- “perfect work”) and eventually mankind will appear from this starting template billions of years later. We are reminded that all the elemental building blocks are present in this early Earth, “waiting” to be reorganized into the human species. Next is another Dawkin’s excerpt:

“After sleeping through a hundred million centuries
We have finally opened our eyes on a sumptuous planet
Sparkling with color, bountiful with life
Within decades we must close our eyes again
Isn’t it a noble, an enlightened way of spending our brief
Time in the sun, to work at understanding the universe
And how we have come to wake up in it?”

The song then erupts into fanfare (5:46), life is here and begins its unending 3-billion-year journey.

Part 2: Life

The cosmic law of gravity
Pulled the newborns around a fire,
A careless cold infinity
in every vast direction
Lonely farer in the Goldilocks zone
She has a tale to tell
From the stellar nursery into a carbon feast
Enter LUCA

Here is the birth of our solar system with Earth becoming one of the nascent planets circling our Sun. Outside the solar system, there is a vast and cold emptiness for light years in all directions. Earth is the lucky one in the Goldilocks zone (not too hot, nor too cold, but just right). The early Earth contains all the building blocks leading to the eventual evolution of our Last Universal Common Ancestor from which all current life sprang.

The tapestry of chemistry
There’s a writing in the garden
Leading us to the mother of all

In my mind tapestries evoke “weaving” which makes me think of the endless strands of double helical DNA connecting all forms of life through history. Life is commonly referred to as a garden and this can be interpreted as reading the fossil record showing us snapshots of the interconnectedness of all life in the past.

We are one,
We are a universe
Forebears of what will be Scions of the Devonian sea.
Aeons pass, writing the tale of us all
A day-to-day new opening
for the greatest show on Earth

Naturally what follows is that all life is connected as one. The band highlights the Devonian era which was a time period of massive radiation of fish (this era is termed The Age of Fishes) as well as land colonization of plants. We are all scions, descendants of a notable family (family tree of life), from this time period. Looking back even earlier to the Cambrian explosion, the earliest known chordate, Pikaia, is the ancestor to all vertebrates.  We now roll credits for the mention of the song’s title. Since life is always changing and evolving, each day is different. Thus, the story of life has a day-to-day new opening.

Ion channels
welcoming the outside world to the stuff of stars
Bedding the tree of a biological holy,
Enter life

There is a reference here to Carl Sagan who coined the term “starstuff” referring to all of life being made up of elements formed from the dying explosions of exhausted stars. Another beautiful connectedness of all life, arising not only from a common ancestor, but incorporating all matter born in the belly of long-gone stars. The focus on ion channels here is striking when you think about what they are trying to convey. Elements from dead stars were eventually combined into living forms that evolved proteins capable of generating action potentials in our neurons which allowed ourselves to become aware of the universe. Essentially through ion channels, the universe is able to learn about itself.

We are here to care for the garden
The wonder of birth of every formmost beautiful
Every form most beautiful

Chronologically humans have not appeared yet in the history of life, nor the song. I am unsure of the “we” that is referred to here, but it could be the general responsibility of all life due to our connectedness. Of course all lifeforms are beautiful, an homage to the final sentences of Darwin’s Origin of Species.

Part 3: The Toolmaker

Humankind has arrived. Animal grunts and other savannah creatures can be heard during our early days of trying to survive amongst animals that could easily kill us. The song explodes into another heavy riff signifying our eventual dominance over all life on Earth (11:53).

After a billion years
The show is still here
Not a single one of your fathers died young
The handy travelers out of Africa
Little Lucy of the Afar

This stanza makes us remember that we are all here because each one of our ancestors going back billions of years successfully reproduced itself to the next generation. An unyielding unbroken chain avoided life’s dead ends of extinct genera and species. We know that early humans migrated out of Africa and the earliest known mother of humankind was an Australopithecine named Lucy found in eastern Africa.

Gave birth to fantasy
To idolatry
To self-destructive weaponry
Enter the god of gaps
Deep within the past
Atavistic dread of the hunted

As the human brain developed it gave rise to religion and mythology to fill in gaps of missing knowledge, attributing that which was not known to deities. We also strive for continual and never-ending progress, as atavism is the fear of returning to a more primitive ancestral state (how could any of us live without the Internet?!)

Enter Ionia
The cradle of thought
The architecture of understanding
The human lust to feel so exceptional
To rule the Earth

Man has settled into civilizations and frees up time to think and discover how the world works. We elevate our status as greater than all other life forms, set to inherit the Earth.

Hunger for shiny rocks
For giant mushroom clouds
The will to do just as you’d be done by

Here is the self-explanatory human lust for gold and money, but also dominance over other humans through creation of super weapons. Weapons that have the capability of destroying ourselves.

Enter history
The grand finale
Enter ratkind

A warning of what may come. A reference to another Dawkin’s work, The Ancestor’s Tale. Here Dawkins imagines a post-apocalyptic world where rats survive and feast on the remains of human corpses and our agriculture/food products. As the population of rats explodes, they resort to cannibalism. Natural selection, always running in the background, allows rats to diverge and radiate out into different carnivorous and herbivorous species. Eventually through enough geologic time, intelligence arises in one species to that of humans. They then study human fossils and ponder how we had driven ourselves extinct.

Man, he took his time in the sun
Had a dream to understand
A single grain of sand
He gave birth to poetry
But one day’ll cease to be
Greet the last light of the library

I especially appreciate this passage as all scientists can relate to devoting our life’s work to a very small esoteric topic. Each of us has or could have their own “grain of sand” that they seek to fully understand. This is a unique attribute of human beings, but this facet of life may not always exist forever, ending with the destruction of the human race.

There is a notable section highlighting the evolution of humans through that of our music (starting at 13:55). Early tribal drumming and chanting can be heard. This is followed by throat singing and a famous Bach snippet. A rocket blast sets off the Modern Age and a banjo depicting country music. Then the unmistakable main riff from Enter Sandman by Metallica can be heard followed by a short measure of techno or electronic music.

Finally, the climax of the song. A desperate loud exclamation, “We were here!” emphasizes the desire that all humans have the need to be remembered, to leave their mark. I see this section as a warning as well. This proclamation ends with an explosion and crumbling rock. If continued on its current path, human society will be been destroyed. “We were here!” is an audible fossil to record how the human race once evolved to dominate the planet but like countless species before it, has gone extinct.

Part 4: The Understanding

Another gentle piano melody appears and allows us to reflect and take in the previous 17 minutes. We did just play out the entire history of life on Earth after all.

The song ends with the passage from The Greatest Show on Earth that began this article, and then the closing excerpt from Origin of Species.

There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one. And that whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

I hope you enjoy the song as much as I do. It has quickly become one of my favorite songs, combining my love of biology, the works of Dawkins and Darwin, and metal music. Check out a live version with guest appearance by Richard Dawkins below:

The Next Frontier for Diagnostic Imaging

The advent of Magnetic Resonance Imaging (MRI) revolutionized the way medical practitioners diagnose and track diseases throughout the body. MRI utilizes magnetic properties of ions in the body along with computer-generated radio waves to create detailed images of the body’s organs and tissues4. This allows for the detection of cancers, traumatic brain injury, strokes, aneurysms,  spinal cord disorders, and other  ailments, without exposing patients to radiation or necessitating the use of intravenous dyes as required in other forms of diagnostic imaging. While many advances in MRI technology have been made to implement artificial intelligence for image reconstruction, increasing magnetic field strengths, optimizing receiver coil arrays, and enhancing imaging gradients, there remains an ongoing need to prioritize expanding access of these technologies on a global scale.

One area of advancement in MRI research that has received recent attention is the use of lower field-strength (0.2 Tesla) MRI systems2,3. These systems were once thought to provide suboptimal imaging quality as they utilize a substantially lower magnetic field strength compared to modern MRI systems. Integration of artificial intelligence for low-field MRI systems provides the capability for its images to compete with the resolution of that of a high-field MRI2. There are several advantages to low-field MRI that directly impact healthcare facilities and the patients they serve. Importantly, low-field MRI does not require a cooling system nor a large energy source in order to function properly1,2,3,5. This allows for a reduction in the ongoing costs associated with MRI systems in addition to a reduction in the high maintenance fees (~$10 thousand per month) and acquisition costs (~$1million/T) that are required of high-field MRI systems1,3,5. For under-resourced healthcare centers, these fees can be the determining factor for whether or not a patient receives a lifesaving diagnostic scan.

The utility of low-field MRI systems extends beyond cost savings, however. Due to the smaller magnetic field, noise produced by these systems is reduced which favors its use among pediatric populations1,3,5. In 2020, the FDA approved the use of the first portable point-of care low-field MRI (Below is a video of Dr.Kevin Sheth, a critical care neurologist at Yale School of Medicine discussing the advent of a the world’s first portable low-field MRI). Its small footprint and open design allows for family members to remain at the bedside with patients as they receive their scan1,2,3,5. The small footprint of these systems also makes its use in preclinical research settings more accessible. The open design of these systems is an additional benefit for patients with claustrophobia as well as obese patients that have difficulty in high-field MRI systems. Widescale clinical use of low-field MRI would expand access for patients that have metal implants such as pacemakers or shunts, who otherwise would not receive such diagnostic imaging2. Given the ability of a portable low-field MRI system to provide cost savings to healthcare facilities, expand access to patients in need, and further diagnostic capabilities for practitioners, low-field MRI systems are posed to pioneer a new era of medical diagnostic imaging.

Incorporating artificial intelligence into low-field MRI diagnostic imaging stratifies the detection of disease by combining the observer-based image interpretation currently in practice with an artificial intelligence generated semi-quantitative approach (please see observer-based and semi-quantitiative decision making diagram below). In doing so, as larger datasets of diagnostic images are collected, artificial intelligence algorithms become more reliable in detecting disease pathology. Such measures may be used to not only detect disease but to better inform clinicians of potential treatment responses and health outcomes of their patients.

  1. Cooley CZ, McDaniel PC, Stockmann JP, Srinivas SA, Cauley SF, Śliwiak M, Sappo CR, Vaughn CF, Guerin B, Rosen MS, Lev MH, Wald LL. A portable scanner for magnetic resonance imaging of the brain. Nat Biomed Eng. 2020 Nov 23. doi: 10.1038/s41551-020-00641-5. Epub ahead of print. PMID: 33230306.
  2. Ghadimi M, Sapra A. Magnetic Resonance Imaging Contraindications. [Updated 2020 May 24]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2020 Jan-. Available from:
  3. Grist, T. M. (2019). The Next Chapter in MRI: Back to the Future? Radiology, 293(2), 394-395. doi:10.1148/radiol.2019192011
  4. J.P. Hornak, The Basics of MRI, Interactive Learning Software, Henrietta, NY, 2020,
  5. Sarracanie, M., & Salameh, N. (2020). Low-Field MRI: How Low Can We Go? A Fresh View on an Old Debate. Frontiers in Physics, 8. doi:10.3389/fphy.2020.00172
  6. Sheth KN, Mazurek MH, Yuen MM, et al. Assessment of Brain Injury Using Portable, Low-Field Magnetic Resonance Imaging at the Bedside of Critically Ill Patients. JAMA Neurol. Published online September 08, 2020. doi:10.1001/jamaneurol.2020.3263

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:

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.

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!

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


COVID-19 and Your portfolio

Dow Jones Industrial Average, Feb-March 20th, 2020. Source:

Investing in a time of turmoil

The uncertainty of the novel coronavirus pandemic has left global stock markets reeling, erasing gains from the past 3 years. Massive selloffs have occurred over the past month that have not been seen since the 2008 financial crisis. For those of us young enough to be long-term investors (many year horizon) this is not a time to panic sell. I would argue the opposite and to continue your monthly contributions practicing dollar cost averaging. I caution against trying to “catch a falling knife” in trying to time this market volatility with large sums of uninvested cash. This is a trial-by-fire for testing an individual’s tolerance to risk and unrealized loss, so do not throw money in now that you are not comfortable seeing potentially decline another 50% or more in the coming months. Even if that does occur, ride out the bump however long it lasts and eventually you will see the value increase. Historically, market downturns are followed by a recovery, and over the long term still provide the best returns on investment. While the past is no guarantee of future results, the two hundred years of US stock market history would indicate this is still the best way to generate wealth.

Anyone near retirement age should have already reallocated their assets to consist mostly of lower-risk fixed income securities as appropriate for their age. For those of you who have parents who are concerned by this crisis, assure them that unless they need their capital within the next few years, they should not sell holdings at a significant loss. The hit to the economy during this pandemic is uncertain but will definitely be deep. In the coming weeks, unemployment will skyrocket as most sectors grind to a halt. This is certain to continue for the coming months as more and more state-wide lockdowns will go into effect. However, the extent to which this is mitigated depends on the actions of Congress as they continue to debate different stimulus measures.

Choosing stock investments

So, what investments should be considered during this current market discount (and at all times when investing)? I would not feed into frenzy of any “hot stocks” because by the time you have heard about it in the media, they are likely already overvalued. Similarly, companies with promising COVID-19 treatments may end up disappointing investors. The principles I would recommend for those beginners wanting to invest a percentage of their savings would be to dollar cost average into an index fund that tracks the total stock market. These provide the safety of diversification that picking individual stocks do not. Essentially each month, no matter what the price of the fund is, buy the same dollar amount of that fund. Some months you can buy more when the price is low, and other months you buy less when the price is high. Over time, this averages to a lower cost-per-share than jumping in all at once. This is a great way to passively invest in stocks, as you don’t need to do deep analysis of a company that you want to invest in (and feel the pain when it turned out you were wrong). The S&P500 tracks 500 large companies in the US and SPY is a great low cost fund tracking it. Be sure to chose a fund with a low expense ratio (fees), and many popular ones can be found for under 0.1%. Anything charging over 1% eats away at your return and is not worth your money.

For those who want to be more active in their investments and buy individual stocks, you must do your homework. If you don’t want to take the time and discipline to invest in individual stocks, follow the investment strategy in the previous paragraph. Your principal will be much safer that way. There are two main schools of thought for picking stocks, technical analysis and fundamental analysis. Technical analysis looks at volume trends of buying and selling of shares and other metrics on how to predict which way a particular stock will move. In my opinion, this is essentially gambling and should not be followed. Fundamental analysis looks at the fundamentals of a business. All things from its financial health, growth prospects, dividend payments, management team, and advantage over competition are looked at. This is the best way to determine which companies have true staying power over the long run.

Fundamental Analysis and Value Investing

The best-known proponent of fundamental analysis is the investor Warren Buffet, who learned his strategy from the “father of value investing”, Benjamin Graham. Value investing seeks to buy stock at a safe discount, as the investor has determined this stock to be mispriced by the market in her favor. Eventually, she hopes the strong fundamentals of the company place it in the good graces of Wall Street and as more investors buy in, the share price increases. Value investing requires patience, as you could wait many years before your favorite picks become the favorites of Wall Street. But when they do, you will be happily rewarded.

You can read hundreds and hundreds of pages from many books and take many classes on how to learn fundamental analysis. Personally, I feel a great starting off point for those who are interested is to read Ben Graham’s, The Intelligent Investor. My perspective on investing, risk, and emotional responses were completely changed for the better after reading that book. Honestly if I had not read this only a few months ago, I probably would have sold my investments completely at the first whiff of this virus. (I believe time in the market is superior to timing the market). Briefly, the definition Graham gives for investment is the following:

  1. Investment, upon thorough analysis, promises safety of principal and a satisfactory return. Not meeting these requirements is speculation
  2. An investment operation is one that can be justified on both qualitative and quantitative grounds.

In another earlier work by Graham, Security Analysis, he sets criteria that should be met by a company before consideration of purchasing their stock:

  1. a suitable and established dividend return
  2. a stable and adequate earnings record
  3. a satisfactory backing of tangible assets

Essentially this boils down to the company should distribute profits (and they should have for many years prior), they actually have earnings, and their debt does not exceed their assets. If you follow the advice in The Intelligent Investor you will do well. If you want to speculate, avoid doing so with more than you are comfortable seeing disappear to zero. I would strongly urge against gambling with all derivatives (buying on margin, puts, calls, futures etc.) unless you REALLY know what you are doing and are also ok with losing your initial investment, or in some of those cases, owing MORE than you originally had.

Where can you buy stocks?

After putting down your copy of The Intelligent Investor and carefully analyzing a stock that looks attractive to you, you decide to go ahead and buy that stock. But how is this accomplished? Today it is even easier to buy and sell stocks than in the past. A stock broker is authorized to handle this task and there are many companies offering this service online. Fortunately many commission fees for doing this have been eliminated. Some popular brokers are TD Ameritrade, Fidelity, Vanguard, and E-Trade. These companies have different minimum investment amounts so be careful to check the requirements before choosing.


Many of us are not trained in finance, economics, or security analysis (I certainly am not), but I hope that investing does not have to be scary to those in other disciplines and is seen as a valuable way to grow wealth over the long run. It is fun to learn more about a field completely different than your own. This could also be a good skill for scientists, as familiarizing yourself with a prospective company’s 10-K filing (yearly financial report) will teach you a great deal about that company and if they have the financial health to ensure you don’t need to look for a new job in 6 months. This only applies to publicly traded companies however. Startups and established private companies don’t have to disclose as much to the public. Whether or not you decide to take a passive or active approach, you will be able to achieve your financial goals through sound and disciplined investment.

Disclaimer: These views are my own and I am not qualified to give financial or investment advice. Please seek out certified financial planners from trusted institutions. I own shares in SPY and other individual stocks and index funds as of this writing.

Can you find artist among the scientific community?

Can you find artist among the scientific community? If you ask someone off the street if they consider a scientist an artist many may answer no; perceiving scientist as dull people in lab coats. This early March serval scientist at the Tufts Boston Campus where challenged to strut their artistic skills in the Sci-Art Competition helping break down the dull scientist persona people often perceive.

Jacob Klickstein, a Neuroscience student won first place with his “Brain Storm” piece. The piece was part of his current lab work in which he was looking at a cluster of iPSC-derived lower motor neurons stained for a cytoskeleton marker (TuJ1-cyan), a nuclear marker (dapi-blue) and a motor neuron-specific transcription factor (Hb9-red).

For second place, we had a tie between graduate students Ashlee Junior and Linus Williams. Ashlee is a Genetics student, her piece titled “INVADERS!” showcases Candida albicans filaments invading an agar plate.

Linus Williams is an Immunology student, his piece “A heart, broken by rejection”, is a Maisson’s Trichrome of a rejected mouse heart (Blue is fibrosis, red is muscle).

Eric Link is a technician in the Zeng lab. His piece “B-CHP Metatarsal on glass slide”, is a collagen hybridizing probe highlighting cartilage remodeling in the growth plate of a developing mouse metatarsal.

Quentin Bernard is a Microbiology student, his piece “Five, six, pick up Tick”, is an oxide’s scapularis tick stuck on its back before it was microinjected.

Alyssa DiLeo is a Neuroscience student. Her piece, “Possibilities: what went wrong with my western blot”, showcases the unfortunate results from a botched western blot.

Rachael Ryner is a CMDB student. Her piece, “Mermaid Mouse Brain”, is a fluorescent mouse brain section that has been immune-stained for beta-catenin and GABA in a CaMKII-Cre:Ai9 background.

Surendra Sharma is a CMDB student. His piece “The Dark Side of the Genome”, describes the long considered “dark matter” of genomes, regulatory noncoding RNAs like miRNAs and lncRNAs which are now recognized as key drivers and/or regulators of a variety of cellular processes.

Dominique Ameroso is a Neuroscience student. Her piece “Alien Astrocytes”, showcases astrocytes in culture – or an alien waiting for host.

Pragya Singh is a CMDB student. Her piece” A network of collagen”, exhibits collagen bundles forming in 3D, specifically a collagen1 gel as a result of LOXL2 treatment.

As scientists we have characteristics that by any dictionary definition would categorize us as artists. Naturally most scientists are curious. Our daily work requires us to be creative, take risks, and have a sense of passion for the work we do. The muse of a scientist lies in the continuous sense of adventure that comes from trying to uncover the unknowns in our projects. We don’t have to look too far for an example of an established scientist who struts his scientific muscles regularly. In our own Tufts community, our very own Dean, Dan Jay, is a visual artist who combines art and science to create pieces that express inspiration in science. This art competition was definitely a testament to our communities vibrant artistic abilities. Thank you to all those who participated and keep a look out for upcoming events and competitions.


“Daniel Jay.” Daniel Jay | School of the Museum of Fine Arts | Tufts University,

Humans of Tufts Boston: Noell Cho, “Representation Can Have a Broader Impact”

Humans of Tufts Boston, 12 Mar 2020

Noell Cho, Neuroscience, Second-year Ph.D. “Representation Can Have a Broader Impact”

JH: Thank you so much for taking the time to answer some questions! How did you get your start in science?

NC: My start in science harkens back to my high school on the island of Guam, when I volunteered to work at its endangered species lab under the direction of our AP Bio teacher Dr. Hauhouot Diambra-Odi. For decades, invasive species have completely destroyed Guam’s ecosystems. Of particular interest to our group was the introduced Philippine collard dove, which is threatened by the invasive Brown tree snakes. In the lab we designed experiments to learn more about existing bird migration patterns and behaviors. We delved into “field work,” which involved several camping trips on an uninhabited islet called Alupat island (approximately 200 meters off the western coast of Guam). We eventually presented the data at the International Student Science Fair in Kyoto, Japan. Unfortunately, some of Guam’s endemic bird populations, such as the Guam rail are deemed extinct in the wild and extirpated from the island. I was surprised to find that the New England Aquarium had these birds, a little piece of home right in Boston!

Cetti Bay in the southern region of Guam

JH: What drew you to neuroscience?

NC: I worked as a tech in several different labs and research areas, including cancer biology, immunology, and translational neuroscience. I worked in Clive Svendsen’s lab at Cedars-Sinai in Los Angeles, where I became involved in stem-cell transplantation studies in animal models of neurodegeneration, specifically the SOD1G93A rat model of ALS. I was fascinated that a neurodegenerative disease phenotype was able to be recapitulated in rodents harboring a mutated human ALS gene. Through these studies, I joined Gretchen Thomsen’s lab, whose particular focus was studying the link between repetitive TBI and ALS. My previous experience in immunology research motivated my investigation of selective inflammatory responses related to TBI-induced neurodegeneration. I fully credit working in the Thomsen lab as where I discovered my passion for neuroscience research.

The Thomsen lab at Cedars-Sinai. From left to right: Gretchen Thomsen (PI), Mor Alkaslasi, Patricia Haro-Lopez, Noell Cho

JH: What is your favorite technique that you use in lab?

NC: I’ve become an apprentice of electrophysiology since I joined the Moss laboratory here at Tufts. Tarek Deeb has been profound in imparting his knowledge of ephys and its many applications for neuroscience research. It’s intriguing to use the patch-clamp technique to measure the electrical properties and functional activity of neurons. My research experience has been primarily focused on looking at biochemical changes in neurological disease, so it has been refreshing to learn a new technique and observe electrophysiological changes in the brain. I remember that first moment, not too long ago actually, when I patched onto hippocampal neurons in mouse slices and observing action potential firing patterns. Seeing those spikes is so satisfying!

Members of the Moss lab representing at Relays

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

NC: More recently, I’m trying to stay updated on new ephys systems in vivo and ex vivo. There are so many cool videos and photos that pop up on my feed of some of the most insane multipatch ephys rigs. Ed Boyden’s group has made tremendous advances in automated in vivo multipatch recordings. Automated multipatch rigs not only allow for ease of recording multiple neurons simultaneously, but also provide large-scale mapping of brain circuits. Multipatch clamp recordings also reveal more about connectivity between specific cell types in the brain, and automation provides a huge advantage in terms of time and feasibility. It’s always exciting to see the latest innovations that come out from the Boyden lab, but also it seems that robots are an inevitable part of scientific developments.

Noell presenting her repetitive TBI model at her first SFN!

JH: What do you do outside of lab?

NC: Because I’m a Boston transplant from Los Angeles, it was important to me to foster an environment at school that would feel like home. Thankfully, student organizations such as GWiSE and SPINES provided just that. Currently, I am the GWiSE secretary and operate media and communications for our group. As a first-year, I enjoyed the GWiSE coffee & conversations events that feature a woman in STEM and learning of their school and career experiences. I am so thankful for my former PI, mentor and friend, Gretchen Thomsen, who believed in me and is one of the reasons why I am in grad school today. I definitely benefit from the efforts of GWiSE and SPINES that provide programming surrounding diversity and inclusion, because ultimately representation can have a broader impact. You can follow GWiSE and SPINES on Twitter (@TuftsGwise and @TuftsSPINES)!

Checking out the East Coast surf in Montauk, NY

“We Ball Outrageous”

Did you know that GSBS has a basketball team?

The Tufts Medical campus has had a long-standing basketball league that historically consisted of medical and dental student teams. It wasn’t until October 2019 that GSBS contributed its first team to the league. The Contaminators was founded by team captain Linus Williams (#6) and was made up of both PhD and MD/PhD students. With financial aid from the Graduate Student Council, The Contaminators bought green and gold jerseys.

The 2019 season started in October and ended in January with 9 Saturday games. The Contaminators started out their season strong, winning their first 3 games. The competition started to heat up later in the season, and The Contaminators entered the playoffs with a record of 4-5. This league’s playoffs were a double elimination tournament running through mid-February. The Contaminators won their first playoff game, but lost the following game, sending them to the loser’s bracket. They were eliminated in their very next game by the eventual champions, Nothing but Netters. Overall, The Contaminators ended their 2019-2020 campaign with a respectable 5-7 record.

Williams, who is known for scoring with his signature one-handed floater, said he was happy with how the season went: “We learned how to defend with man-to-man and with zones, and were able to adapt to whatever the situation called for.” One of the team’s weaknesses was dealing with defensive pressure, especially when Liam Power (#2), Point Guard and MVP, was not on the court. This resulted in more turnovers due to the restricted court vision of the ballhandler.

Team member Daniel Fritz (#11) said “The league was a perfect balance between fun and competition.” He wants to encourage other students to join who may be wary of a team sport that they’ve never played before.

The team recruited students with a wide range of experience in the sport, from first-timers who wanted to learn the fundamentals of the game to seasoned veterans who were lifelong basketball players. Regardless of skill, each teammate was a valued asset in a sport that requires cardiovascular fitness. Lack of female substitutes was especially felt with only 3 women on the team. The co-ed league required that one female player be on the court at all times. That meant one female player would have to play the entire game if the other two female teammates couldn’t make it (shout-out to Sasha Smolgovsky #12, Patriots fan). One of The Contaminators’ goals for future seasons is to increase the recruitment of players.

Although the season is over, there are upcoming opportunities to get involved. During the spring and summer, there will be pick-up games hosted by Williams and future team captain for 2020, Joshua Man (#24—Kobe). If you are interested in participating in pick-up games or the 2020 season, please contact Williams or Man via their Tufts email.

Other team members of The Contaminators:

#3, Zemplen Pataki—Valuable tall person who can shoot.

#4, Rachael Ryner—Author of this article.

#7, Zoie Magri—Played middle school b-ball and it shows.

#14, David Jetton—An owner of the Green Bay Packers who plays b-ball on the side.

#32, Mike Rist—Secret weapon when he’s not at a wedding in New Hampshire.

#33, Mike Thorsen—Team morale booster and team mascot.