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.

Saturday, April 22, 2017

The march of ides

The spouse and I will participate in the march for science on April 22nd, joining thousands of others who will. The march hopes to represent diversity in the scientific community and in that, diversity of ideas is most important. So, as we do march with a large group, our reasons and expectations from the march may differ from our fellows, and the ones listed in websites and community pages. This post elaborates on our personal agenda.

WE HAVE NO POLITICAL PURPOSE: I am an alien to America and I have not been around for an election in my home country; making me a non-partisan observer irrespective of stated beliefs, because I have no actions to back them up. Ethically, that should tell you that my political ideas are not to be respected beyond a basic measure. Even if my political ideas are obliged, and even if I may have stances that require protest and attention, our march is not for them this time. Our rights in this country are provided by treaties and ties between America and our home country, we do not march for them either. This march, despite its claims of non-partisanship, will be laughably partisan; that's just how the setting is. That is why it is very important that we do not draw lines in the sand and make 'us versus them' points in this process; liberals and conservatives do that every day on social media to heavily divisive effect. We do not wish to add to that. Partisan ideology is, at least partly, based on belief and science isn't.

WE DO NOT WANT TO BEAT OUR OWN SCIENCEY DRUMS: A substantial set of people of science tend to believe strongly in their intellectual exceptionalism and superiority. This has impacted their dialogue and their social responsibility, triggering a reaction where intelligence is treated as an elitist sin. They air their opinions, either in a hit-and-run fashion or in spaces that only serve to confirm their biases. They patronize more and empathize less. They may choose this platform to validate their feelings of intellectual superiority. We do not wish to be part of that set; it is not helpful. We also do not intend to impress other members of the scientific community with our genius signs (pun may be taken as intended) and nimble brains; the world and this march will have enough narcissism without our indulgence.  We believe that holding a post-graduate degree or working in science does not make one smarter, better or more noble, it just assigns your roles and responsibilities. Speaking of which...

WE WISH TO EMBRACE OUR PUBLIC ROLE AS SCIENTISTS: One of the main purposes of this march is to draw attention of the role of science in policymaking - we share that. We feel that the lack of empathetic communication between the scientific community and everyone else is responsible for the confusion over what constitutes science and what its role ought to be; the scientific community should take a majority of the blame in that. We wish to engage positively and learn as much as we teach. We wish to humanize scientists so they are looked upon as experienced in a specific subject rather than unfriendly wizards and witches in ivory towers. Scientists forget sometimes that the humanities are also an essential method of inquiry. Only a joint application of the two is useful to society; we should be aware of that as we make our point. 


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!

Monday, July 11, 2016

Election selection

Conservative elements in America have recently protested that Facebook may have a liberal bias. The social media company has defended itself and said that Facebook's functioning is not influenced by the political choices of its management or employees. While this is probably true, with Facebook being equally accessible to all people irrespective of their political leanings, I argue that social media, by virtue of it being on a (currently) free internet, is a liberal tool; irrespective of what its management may say and do to keep looking independent. 

Social media has revolutionized social interaction in two general ways:

1. Interaction is between crafted representative avatars rather than real people. Our airbrushed, free-thinking, like-awarding, social commentator avatar interacts with other cartoons of the same make in a sandbox world of finite means. Our perceptions based on these interactions, however, are in the real world. This gives us a heavily cognitively biased set of conclusions to react to and our real world reactions sometimes are the opposite of what we choose to evoke in the sandbox. 

2. Your interaction is your presence. Social media is not a place for introverts. You cannot smile warmly and hope that it counts as a social action on the internet. You share anything between a supportive +1,  to a high-definition live video of your life to mark your presence. That has not been the human way for a good chunk of us; how I dress up is not a social interaction (though some rapists differ) but uploading a photo of myself on Facebook is. Social media, therefore, does a poor job in mimicking and substituting for real social interaction leaving a lot of us dissatisfied or depressed. 

This is not to say that social media is bad. It acts as a good compliment to true social interaction rather than a replacement, and that is what we ought to take it as. The human condition cannot evolve to keep up with the freedom and framework of social media, making this a social experiment that nobody really understands well enough to predict an outcome. For a lot of us, it is jarring for sure. 

Back to politics, conservative thinking places its faith on a traditional lifestyle of choice (or conditioning) and strives to not move away from it. At times, this is a logical choice - you have faith and comfort in a tried and tested method that has worked for generations before you and has stood strong against the test of time. What it is not good against though, is changed evolutionary pressure, and different circumstances may demand a more case-defined approach than a formulaic one. 

The conservative approach relies on the recirculation of traditionalist ideas rather than the free sharing of ideas in an unweighted manner. The liberal school of thought however chooses to engage such ideas aligning it perfectly with the rules of social media on a free internet. So Facebook is not liberal because of the views of its makers. It is not liberal because it is populated by more liberals than conservatives (hypothetically). It is liberal because it attempts to be unweighted on a free-access internet. And that cannot be fixed; unless you violate net neutrality...

Tuesday, July 05, 2016

The thathuva padam

In a time when opinions are rained through free and porous internet mouth pieces, some still choose to collate their opinions and present them as fictional, but exemplary motion pictures. This remains a smart strategy because of how powerful motion pictures still are and how they have a longer lasting impact than the average mouthpiece. I personally enjoy deconstructing a good issue/message driven movie, even if I may disagree wholly with its content; just good food for semi-productive parts of the brain. However, for consideration at the present time, are some basic rules to be a quality moral-instilling motion picture that deserves at least grudging respect. If they do not fit these rules, they haven't met the bar.

1. They must satisfy the Bechdel-Wallace test.

Not because these rules are inspired by the Bechdel-Wallace test (which they are) but because if you are not going to trouble yourself with content that appeals to roughly one half of your target audience, potentially alienating them, then your message needs more work.

2. There is no prize for being good.

So the person that chose to be kind to the beggar on the street does not get rewarded with a sexy girlfriend halfway through the movie. That is not the world we live in.

3. Target stereotype may not have unrelated flaws.

Your movie probably involves some straw characters that you will tear apart and burn to fuel the smoke of your fiery message. Do not make him boring and whiny (and ugly) just because he also decided to extol the virtues of some form of badness. Bonus positive points for your movie though, if target stereotype has other potentially redeeming (but unrelated) virtues. That makes things fun.

An optional (essential) fourth - Your concept must have some validity outside your straw universe.

Otherwise your discussion is a mountain of an expense for a molehill of an issue. We have social media for that.


Note to Alison Bechdel: Alien may have passed this test but the underlying message has been elusive.

Friday, April 08, 2016

On Sci-Hub

If you are not a first world researcher you definitely know what it is. For the rest of us, Sci-Hub is a free (as in beer) repository of scientific articles; articles that would normally cost you upwards of approximately $30 (USD) each, or a slightly less-cost (but still expensive) annual membership with the publisher. Sci-Hub achieves this by accessing these articles with voluntarily (though discreetly) provided proxy accounts that subscribe to these journals and publishers. Once accessed, these articles are available to download from Sci-Hub for all visitors. So naturally it is illegal, because piracy. Thievery is bad. Shame.
More details add wrinkles and grey shades to the picture. The publishers opposing Sci-Hub's activities are registered non-profit organizations but do not function so selflessly. They do not pay for the research in their publications. They do not pay the scientists who critically review and edit these articles for their time and effort. They separately charge submitting authors for printing costs. The also have revenue from ads. So in being a record for scientific data, publishers do not add any real value to the product. However, the system of science has anointed them the gatekeepers and power-brokers of achievement and progress. We have come to unofficially define science as something that is peer-reviewed and published in an established scientific journal. 'X papers in journals with an impact factor of at least Y' is a requisite for most any research position and this dogma gives a lot of power to the middleman publisher (who, I repeat, adds little or no scientific value). Over time, it has created an artificial brand of which the publisher is an under-deserving owner. It is not to say that there is not a sound logic in the concept of scientific publishing and valuation, merely that this brand-based system is extremely vulnerable to greed and outdated in in the internet age. 
The central issue with the publisher's monopoly on science is the cost. The publisher owns the window and so, both the producers of scientific information and the consumers have to pay him to access the window. The system has also created an unspoken rule that if you create your own window, it is not as good as the publisher's branded window. The tax-payer who funds the whole machine is unable to access this information that he paid for, unless he pays for it again, which he should not have to. $30 is not a nominal cost, even in the first world, especially considering that the seller pockets all of it and does not pay the producer or even the quality-control crew. If I need to access a conservative average of 60 articles for a report that I am writing, the cost becomes big. Any reasonable research requires access to hundreds of articles and if I belong to a country or system where funds are at a premium, this barrier becomes unbreakable. Local scientific progress is therefore held back because of the cost of brand value. And that is not good. It is this environment that creates and nurtures Robin-hood elements like Sci-Hub. The poor are definitely very happy about it. Sci-Hub has, in short time, revolutionized scientific access in places like India and is of major value to Indian academia. 
It could be argued that the poor are just lazy folk that want handouts. The thing is, most of the people accessing scientific data do not intend to sit on it, they will use for science. They are not begging for things they do not deserve, they pay for the research, as tax payers and sometimes as the people that created the data. The publishing company profits big from the whole system. This is not wrong if these profits were directed back to science in some way, by paying for new research. It is, when publishers behave like unbridled, greed fueled, selfish corporations (like you Elsevier). As long as the system of excessively rewarding a publisher who gives back little exists, rebel endeavors like Sci-Hub will keep getting created and celebrated underground. 
Am I promoting piracy? No, merely the need for reform in scientific publishing. The onus is on the scientific community to take science back from extreme capitalism. The cost of scientific access should equate to the running cost of publication and no more. There should be less focus on brand value on more on scientific value. The scientific community must actively boycott profit-oriented publishers and use and promote open-access methods. The law must weigh on the wrongs of monopolistic practices by publishers as much as it weighs on Sci-Hub's methods. When a community that prides itself on its intellect and ethical quality is exploited, that, is a shame. 

Friday, January 09, 2015

Moderate and extremely clueless

Apparently extremism has no religion. So I guess religion gets to wash its hands clean every time someone bad invokes it. In a different way, that thought makes religion even more scary. Extremism could hijack any religion! Like computer viruses that work on Windows, OSX and Linux (Yes they exist). All one needs is a good hole and both operating systems and religions have plenty. 

Holes in computer operating systems can be fixed however; and people are expected to work on that everyday. The big problem with organized religion is their holes don't get fixed easily, if ever. People try to not talk about them, jump over them, walk around them, ignore that they exist, and sometimes they fall into them because they are told that it is not a hole. A common tie across all levels of religious fandom is the belief that their texts and the so-called "word of god" are perfect and infallible. It is not amendable to fit new sizes and you do not question it. This tying tenet is THE oath of religious membership. None of them invite open questioning; they are challenged by it. So you are expected to get married drinking sweetened milk on a swing because that is how they performed child marriages in the dark ages, and by the gods, that is how you will be wed. No questions. 

While most religion followers faithfully refuse to ask or answer questions that carry logic, the occasional apologist will present semi-logical ideas. He will deny the official membership of extremists and state that moderate followers - the teeming millions of them - are the majority and their membership is truly for inner peace and salvation, as is said in the texts. The extremists, the zealots and the evildoers are a handful and are not exemplary of the religion, which is pure and beautiful.

Like Windows 8.1

Here is the problem with that line of thinking. Religious membership exists as a hierarchy defined by how far you are willing to take your fandom with your actions.
I call this a hierarchy of support. Each level supports the next tier, even though they may not support the levels beyond. The support may be open or a non-verbal nod to their ideas. At the base you have the apologist who suggests that religious membership is truly an innocent experience, exemplified by the pious and gentle moderate follower, who strives to make his life more beautiful with his religion. The moderate follower supports the political follower who will use his position of power to influence others to also enjoy this wonderful mission to peace and bliss. The political follower takes his religion and his job very seriously. He believes that he can enlist ideas from his religion to do his job. Through this, he hopes to provide good governance to the people who are of his religion and the people who aren't. He supports the chief religious body that fashions the guidelines of his religion. The chief religious body strives to preserve the identity of the religion and ensure that members adhere to the tenets of the religion properly and non-members maintain good respect. And for that, they accept the existence of the extremists.      

Each of these levels have increasing amounts of power even if their numbers decrease. And just having that power makes them dangerous and disquieting. Should they choose to move away from ethical behavior, standing up against them could spell doom. The extremist could be willing to sacrifice thousands to ensure success for his holy mission of supremacy. The chief religious body holds the rulebook on the religion and their interpretation and direction could alter the fates of all followers. The religious body could threaten followers (and others) with damnation if they did not buy into its policies. The political follower holds all other rulebooks that could make or break the world around him. It could be argued that the meek and modest moderate follower poses no danger as he holds no such power. Certainly, all apologists make good mention of it. But if you consider how these higher tier bodies are empowered, we get the reverse hierarchy of hijacking to hide away evil intentions and deeds. 

The extremist is empowered by the approval of the religious body; he does not question the ethics of his deeds anymore. The religious body is empowered by the approval of the political follower; now even its questionable actions under the guise of religious self-preservation can be cleaned away by use of political power. The political follower is voted in by the moderate, so abuse of the power is acceptable because the people enabled him to do it. The moderate follower never doubts his choices because there is an apologist over the shoulder validating him on the news and social media. It does not matter if the apologist is religious or non-religious. However, it does matter that you might be one of these.

This hierarchical model suggests that religion is a general subscription. If you buy in, you have bought in all the way and the extremists become your people even if you don't like it. It may be too radical to suggest that all individuals quit religion in an instant. It challenges your identity and a way of life that defines you. It may take away what gives you inner peace. But think about what you follow and what it can lead to. Think about the relevance of archaic practices and how they stand in the way of humanism. Think about who truly deserves your respect and support. Think about who they support. Think about where your values come from. Offer a hand, not blind fandom. Is the preservation and resurrection of dark-age remains of your organization truly more important than humanity?

 You are afraid of breaking out of this system of fear, hate and blind following. Don't be. 

Je Suis Charlie

P.S. This