Wednesday, March 03, 2021

On Dr. Mavis Agbandje-McKenna


“I am not really looking for a graduate student. I guess I will take one”, said Mavis in a thick British accent at the Biochemistry faculty talks to recruit fresh graduate students to their labs as the fresh meat looked back at her blankly. So, naturally, Dr. Mavis Agbandje-McKenna followed through in her usual style and took THREE sincere and hardworking graduate students who expressed the desire to work with her after an 8-week rotation stint in her lab. And then she took in a fourth one. A raw, playful Indian kid with infinite enthusiasm but limited skills, focus and tact (yours truly). He had done a rotation with her husband Dr. Robert McKenna and the latter offered him a chance to work as a shared student with Mavis, “We like your personality”.

Over the next 5 years, I managed to exhaust Rob and Mavis’ patience as they chipped away at me with hammer and chisel (only occasionally literal) to somehow extract meaningful research effort. They were successful, however, and I went from being a bouncy platypus to a salable research duck (Rob loves collecting them) that almost looked like a swan. I expressed the desire to join one of their best friends’ labs as a post-doctoral fellow and they risked their reputations to recommended me to Dr. Adam Zlotnick, who hired me quickly. I wonder if it may have been my personality again, but it had to be because I had the “Mavis’ graduate student” stamp. Because this is not my story.


Dr. Mavis Agbandje-McKenna was born in her grandmother’s hut in Nigeria. She moved to live with her parents in England at the age of 11 and needed to be tutored to speak in English. Just 10 years later Mavis started a PhD in Dr. Stephen Neidle’s lab at the University of London where she met a tall, long-distance running, introverted mathematics nerd with flaming red hair - Robert McKenna. They managed to get their PhDs, fell in love and got married, all in 3 years and before the age of 25, they were post-doctoral fellows in Dr. Michael Rossmann’s lab at Purdue University. They were younger than most of the graduate students around them, one of them, the aforementioned Adam Zlotnick. But they were talented and hardworking and had very productive post-doctoral stints. Soon enough, they were able to start their own lab at the University of Warwick. Shortly after, the McKenna lab moved to its permanent home at the University of Florida.


Mavis’ lab fit her personality. She was very tough on the outside and very warm inside. She built a strong, diverse, thorough-minded crew that worked crazy hard and played just as hard. Everything that she did had an extra challenge to it - it was whole virus capsid structure determination, not just one protein; it was Adeno-Associated Virus - the gene therapy vector - and not another easy-to-work-on virus (“That virus is a piece of rock” - Adam Zlotnick); it was cryo-electron microscopy with 10Å resolution and messy film data collection, at a time when the resolution revolution had not yet happened. But Mavis was tenacious and never gave up. She charged at the problem again and again with a new approach or a new collaboration each time until the science simply had to yield. This had to be Mavis’ most defining trait and her team loved her for it. It was never a small team; it was heterogenous and diverse in ethnicity and ideas; even running a team had to be a larger-than-normal challenge to fit Mavis’ plate.


And boy did she run it well. Her undergrads were talented and they were rewarded with publications that helped them to successful medical school admissions and research careers. Her graduate students and post-doctoral fellows had to be extremely hardworking to catch up with her expectations. If you were caught napping, you were done. I struggled to somehow keep my naps just under the bar, so my tendency to slack passed off as more of an annoyance. But Mavis did not give up on me. She would never hold back on expressing high expectations or critical feedback. It would be quick, tough and final.


Her expectations, however, were no more than what her own performance matched. She would work on grants like a machine, locked in her office for days. We would drive the 25-hour stretch each way to Ithaca, NY to collect synchrotron data at Cornell (a continuous 48-96 hour shift) regularly. These were the days before we shipped protein crystals in those fancy pucks for remote data collection. Mavis would do a bulk of the driving and data collection herself as we would try to get the most data collected in the allotted time. Between us, we would average a few hours of sleep through those days (I would sleep the most while Mavis’ would barely yawn).


These trips were also the best time to get to know Mavis’ other side and how her thoughts worked. She shocked me when her pronunciation of ‘Jalfreizi’ was more accurate than my own. I only got to know on one of these trips that she overcame great personal tragedy when her father was murdered in Nigeria and she could not travel there to see him. She had profound, yet practical thoughts on feminism, culture and third-world sensibilities. This was significant especially for those of us that came from diverse backgrounds seeking acceptance. Mavis’ thoughts have significantly influenced my own views and values. Despite the pressures of running her lab, a wonderful family and a constant scientific drive, Mavis would find time like this to sustain her inclusive environment. 


Mavis’ personality and work ethic have won her many fans outside the lab. She was a stand-out member of the structural virology community and her collaborators always became close friends soon enough. We would have about two conference trips each year (another larger-than-normal Mavis special). We would nervously smile at the professors that we recognized at the conferences even though they would coldly stare straight through us and not reciprocate our unspoken request to connect. Mavis was never one of them. She would always be surrounded by friends but still take time to engage with students that were not her own. She would always join the dance floor, be a voice in the birthday song and share wisdom without restrain. She had big accomplishments and a big team but operated with regular sized sensibilities, a tough act to pull off.


A few months after I left the McKenna lab, I got the call. Mavis had been diagnosed with Amyotrophic Lateral Sclerosis (ALS). It struck me like a free-electron laser. I had lost a very dear uncle to that dreaded disease a decade before and I knew what it meant; what it would do to her. But ALS was not going to have it easy with this one. She fought it for almost a decade, while her scientific empire flourished. She continued to churn out students, structures, publications and even gene-therapy companies. She would still travel to all the meetings, do interviews and stay in touch with her science-children.


Mavis’ larger-than-normal life stands as a stellar example of almost every kind of struggle that one overcomes. Barriers of gender, race, nationality, language, bureaucracy, health or fate could not hold back this mountain of a woman. Her science-children (as she refers to us) take pride in knowing her and calling her our own. As someone who now has a meaningful scientific career with a short mentorship journey of my own, I hope to live up to her standards in my professional and personal life. Late last year, she sent me a text, “Rob and I are SO proud of you” - something I will hold in memory (and in screenshot form) for as long as I live. It is my privilege to have had Mavis guide my journey thus far as her story and principles will take over from here on.


Rest in peace my dear mentor.



Note: In eulogizing Mavis, I hope not to have minimized Rob’s partnership in Mavis’ achievements and central role in molding me as a graduate student or Adam’s mentorship that I have modeled my own mentorship on. I am grateful to have them all.

Wednesday, January 11, 2017

Basketball student sections

In the spirit of college football being is officially over for the season, I present my collated (incomplete) list of college basketball student section names. It took me a couple of weekends to put this together; some of these are tough to find and others are quite fluid with their names. Additions and corrections are warmly welcomed. Help me complete this list!






Saturday, October 04, 2014

Google Cardboard

I tried out google's cardboard virtual reality (VR) system this week. It was awesome!

I have always been a big google fanboy, mostly because they make life cheaper and easier. And most of their applications are free. What is to really be admired though is their commitment to lateral thinking and cool science. For the uninformed, google cardboard is one such project. A couple of google employees took some time out to write an application that ports google maps, photos and youtube to a stereo display format on supported android devices. They then designed a simple cardboard mount to hold the phone to be viewed through lenses on the mount. They even put a cute little magnet contraption on the side of the mount to act as a switch detected by the phone. And then they released the app and the mount schematics for free. 

I had heard of some upcoming sophisticated VR devices that are apparently poised to take humanity a lot closer to The Matrix. So when google announced this cheap cardboard app, I wanted to try it out. I was skeptical however. You see, most of my specialized viewing experiences have been less fun than expected. Stereo images make my eyes water and 3D movies give me a headache. I still grieve the day I spent $17 on a that awful remake of Clash of the Titans (in 3D!) that looked better without the glasses. I spent a weekend playing Super Mario 3D land on the 3DS console and it was OK because I turned off the 3D function. But a gadget-geek coworker encouraged me to try it out just as a craft project, so I bought in. The schematics were simple enough and in no time I had the pieces ready. Getting the lenses was a little tricky but I managed to find what I needed ($2.52) from the local hipster hardware store. I had a couple of spare magnets lying around for the switch contraption.


Assembly was a breeze and I had the mount ready in ten minutes. The phone app was quite big and I was concerned if my faithful old galaxy nexus would handle the beast but it loaded fine. 


I turned on the app and a playstation-like menu popped up and I could navigate through it by looking around. The dual viewing paired with the lenses worked well enough and I could see just one image; the measurements from the schematics weren't too shabby. I magnet-contraption-clicked on the street view (street vue) option and within seconds my mind was blown. 

It put me on a car driving through a European city in full speed where I was free to look around and it rocked! I am a big google maps user and I spend about half hour everyday taking virtual tours through the world on it. This was that experience on steroids. I spent a good ten minutes on the ride after which I tried the other options, that were mercifully slower paced. The earth option puts you on a stationary spot in a few selected locations and surrounds you with google's 3D building models to look at. You can even fly off to space and look at the earth from above. Tour guide does the same with some select spots in Versailles and adds voiced descriptions. Photosphere allows you to explore you own photosphere images. While all these options were more like trial versions than full fledged virtual worlds, the youtube app seemed more open. It put you in a theater-like surrounding with the video of choice running on the big screen and more videos on the side to look at and click on. Some of the videos seemed related to my viewing history on youtube, so I suspect that it may have a longer lifetime than the other app options. 

It was a fun home project. Overall, the experience was brilliant cheap fun and has me lauding the google engineers that came up with it for their smart work. Thumbs up gentlemen, keep up the good work!


Monday, July 21, 2014

Cedar Bluffs

There are a good number of established trails and state parks around south-west Indiana. Cedar Bluffs remains one of the less discovered locations. I like trails that are less manufactured and more rugged and Cedar Bluffs gets a 8/10 for that. It is lush green, has water bodies, plenty of small creatures and hardly any noise.


It was a nice warm day and we drove south along S Ketcham Rd until we saw a tiny black board marking the entrance to Cedar Bluffs. It is basically a protected nature preserve and you are cautioned to not go off trail and ruin its delicate fauna. 

Ramya had been there before so she was to guide me through the trail. 

The trail started out pretty and innocuous. I let Ramya lead our party and used my camera to cover the walk in google glass-like fashion.


We walked until we hit the stream that goes along the trail. A number of people seem to come here for fishing.

 






On the other side of the trail was this rocky cliff that we had to get to later. 

At one point the trail turned to the left but we decided that we knew better and ended up making our own trail. That is when the fun started.


The trail got a lot less trail-like and we had to now find a way to get to the cliffs from there. So we turned left and headed uphill. 


The place was now a maze of spiderwebs and trees. Note: You will have to leave your arachnophobia at home to come here.

Lost. Yes.


No we were totally off.

After unwillingly and unintentionally destroying a dozen spider homes, we compass-ed our way back to the true trail and we decided to stick to it from that point on. 

Win. And we learnt something.

The trail is actually a smaller stream that joined the one we walked along.

Trail 

Not trail

A little farther on, Ramya found some parts of the trail that she actually remembered!


Like Ariel's grotto but with snakes.

We stayed along the trail until we could get back on the hillock we had seen and walked down the other side of it back to our car. Overall a pretty fun place. I recommend it.



Wednesday, February 12, 2014

Crapstallography

I spend a good amount of time at work wading through microscopy images of concentrated proteins soaking in salt syrups that should hopefully tease them into forming innocent pretty crystals (that I can mercilessly shot with X-ray guns but that part is another story). It takes just a glance to figure an image out. So with a few thousand conditions and a few images per condition the whole process takes just a few thousand times a few glaces.

Rarely do you get to see something that has crystal written across the image with zoom-in zoom-out effects. The image on the right is a UV light image of the same drop.


Less rarely, you get to see misshapen gunk that has meh written across the image with sound effects that say 'really'?


Then you can spend some time perfecting the syrup recipe until you have something that is workable.


What you see most of the time is either clear boring drops or drops that contain what looks like shredded snakes or alien foetuses.


This one actually looks like the alien from alien.


An that is the scary part. You wade through enough of these crap-drop images that you start seeing mind-game things. Like smiley faces.




Or flirty botched plastic surgery-lips.


Or hand-bags.




Spend enough time and you really start seeing crazy things. Like stars.





Or the Batman.


Must...focus...



I am headed out for some soup, sports and grounded sanity. Peace.






Monday, September 09, 2013

Tennis the menace

I secretly love sports. Watching football and basketball is fun but playing just about any sport is awesome (except for when you play with competitive killjoys). I signed up for a new intramural league sport every semester in grad school and that turned out to be quite useful in a jack of all trades sort of way. I blew my knee out a couple of years back though, as a result of which there is a narrower range of sports that I can play now. No cutting-jumping motions - so no badminton, football, ultimate frisbee, soccer, basketball, and sprinting. Unfortunately those were my favorite sports and now I was forced to find new ones that fit better. I can still play racquetball, racquetball is fun.

I have been trying to get a grip on tennis for close to six years now and most of my best cricketing shots have happened on a tennis court. The muscle memory from playing other racquet sports makes you even more clumsy on the tennis court. Only recently I have managed to get enough of touch that I can actually return a hittable ball to the opponent. But my play is not of exhibition quality, so I mostly pick late evenings and hidden courts to do my dance.

This week, we started playing at the apartment complex court at about 8:30 pm. Twenty minutes in, I was starting to find a groove. A couple of rallies happened. 'I must be getting better at this', I reflected. Just that moment, a balding man with a white t-shirt and frayed shorts walked up to the enclosure. He said something inaudible, so I moved closer. And then the horrifying thing happened.

"Can my son play with you guys?", he requested. He moved aside to reveal a scrawny 8-year old kid clutching a racquet, his pockets bulging with tennis balls. Ignoring all niceties, I inquired seriously, "how good are you?". "Actually, I'm really good", the kid replied nervously. I spat inside my mouth and probably made a face too. "Why not?" my wife said and the kid propped open the gate and entered the enclosure. "Thanks", said the dad and stayed outside to watch.

Now I don't really hate kids and I definitely don't mind playing with them. I just have some scars from my past. I remember playing a reluctant chess game with my (then) 6-year old cousin when I was about 17. He beat me in less than ten moves. Thrice. It hurt bad. I am a pretty competitive person, it is just that I am also simply incompetent. The sensitive ego makes it worse. From then on, I restricted myself to handicap games that still look fair.

So I now had to manage this crisis. I signaled for my wife to join my side of the court. The kid held two balls in his hand. It was surprising that he could fit one in those tiny hands but he held one firmly and bounced the other one on the ground in preparation. He arched back in a perfect semi-circle and let loose his cannon serve at me as I skipped slightly in my spot so nobody would notice me shivering.

BANG! It rammed into the net. I smiled in relief. BANG! The second serve hit the net too. And a third. And a fourth. "Can I just serve like this instead?", the kid asked nervously and motioned to make an underarm serve. "Is that allowed?", I asked my wife with a grin. She ignored me and nodded at the kid.

It was not too bad a game as things turned out. I let the wife serve the entire time. This kid had a talent for apologizing for everything. He raced around the court to take my erratic returns, often with a sorry when he missed (and I chuckled). The dad got his workout around the court enclosure as he picked up and returned balls from my home runs back to the park. I noticed that my wife was a better player than I thought. With a proper opponent, she was able to hit the ball back with a lot of zip on it (though she did not get as many apologies as I did. Ha!). I mostly stared at them play, occasionally chipping in and making the kid run more. Half hour later, it was over and we walked home. I was still grinning.

Lets do this again sometime kid.