Monday, 25 June 2018

On fallibility, humility, and responsibility in science

It has been a rough seventy two hours in the lab. Things have gone very very wrong. We have lost a lot of animals to an unknown illness that is swift and lethal. All day we have felt powerless, and the day ended in a succession of necropsies. More dispiriting, this is the second attempt we have made at this particular experiment. It started out much more promising than the last, but very suddenly, we were once again confronted with how little power we have over biology.
We work on an animal model of infant physiology, which means we work on infant animals. Few people do. It is difficult and demanding work. Infants have care needs beyond what a university animal facilities can provide (though ours have accommodated ours to an astounding degree). So we must step in to feed animals and care for them. Our bigger problem is this: there is little data on infant mammalian physiology, particularly for large farm animals like we work on. I remember a few years ago when we were having problems with our anesthesia procedure. Every vet and textbook in the country swore by tylezol for inducing our animals. It may have worked in adults, but it was useless in infants.
For the past two years we have increased the complexity of our experiments. We now raise the animals from birth, when they are most vulnerable. With full term animals, we had good luck. We got all the data we needed, and felt confident we knew what we were doing.
The grant that was funded however, called for doing the project in premature animals.
There is a very good reason for this. Human premature babies have a host of complications, in particular with regard to feeding and respiration function, which is what we study. Yet it is almost impossible to do the type of research we do on human babies, because it requires X rays. This is doubly the case for premature babies. Crucially, only babies diagnosed with problems can be enrolled in research studies for what we do. As a result, we have no idea what non pathological physiology in this system looks like for newborns, either full term or premature. The work we do addresses a critical gap in pediatric physiology.
Nor did we rush into this blind. We have years experience caring for young animals. Before this project, my PI found a team of researchers who do research in our model on animals far more premature that we were planning. They have come to visit us and us them. We discuss our problems with them regularly. And, thanks to them, our care of full term animals was a resounding success. We were cautiously confident.
The first preterm litter was a disaster. Only a single individual survived past 48 hours. It was pretty much our worst case scenario. We sat back, took stock. We bought better incubators. We developed new protocols for cleanliness and care. We settled on a slightly less premature age for our animals, scaling back our ambition in the face of how much more delicate these preterm animals were.
Again, we thought we were ready.
The delivery of the litter went amazingly. Sixteen healthy newborns in two used medical incubators. For 48 hours, we felt good.
Then they started to fall ill. By Saturday evening, two were refusing food (a very bad sign). By sunday morning, they had started dying. Today was almost like being in a hospital during an outbreak. It was utterly heartbreaking, and sobering.
We pay for our experiments in effort. I have been working well over fifty hours since Wednesday, like everyone in the lab. And we care. Our animals are helpless. And so we try to marshal all our resources to help them when they are ill.
And today I was reminded that we too are helpless.
We are working on a animal model of an incredibly vulnerable patient population. That vulnerability is baked into the very experiments we proposed to undertake.
I understand a little what working in a neonatal ICU must be like now. I understand what realising how little you know, and how little you can do, must feel like now.
As scientists, we plan experiments. We anticipate contingencies. We think about physiology, experimental conditions, confounding factors. Yet when we create animal models of disease, we create, in effect, patients. And we are suddenly faced with the maddening, terrifying, awe full power of illness. The limits of medical science, laid bare in our own research labs.
Hopefully, the remaining animals will survive. We will get data. We will feel our bargain with our animal subjects has been at least partially fulfilled.
But today, I think, I confronted the limits of what I do. Today, I think, we all felt, perhaps, we were getting close to the point where the price of the bargain is too high.

Friday, 2 February 2018

On the vastness of friendship

We had nowhere to go.

We were on holiday in a part of France where we knew no one, in a decidedly less than glamourous rental cottage, 1000km from the nearest family, when the phone rang. It was my father, calling to say that he wouldn't meet us in Alsace later in the summer, that he wouldn't be at the house in London when we got back. Finally setting fire to a year and a half of hope and wishful thinking. Detonating, as my sister puts it, our too perfect party of five.

We were alone, and already the maelstrom of pain and incomprehension started spinning, so that we were alone even from each other. And we had nowhere to go.

My mother did not have much of a family. Partly as a result of being the very youngest, but mostly because her own mother, not being a very nice woman, had atomised the family, reduced it to constituent parts that repelled each other. As far as I can tell, from the age of roughly 18 to 29 when she married my father, my mother's contact with her own family was minimal, and strained. There was little pleasure in it. But my mother instead busily built herself an army of friends. To this day she maintains the ability to find kindred spirits and make friends with them, so that she has true friends, spanning multiple generations and multiple continents. But it is in the crucible of her twenties that she forged her deepest friendships. She sought out lifelong friends at bad concerts, yoga retreats, one off mountain activities, as well as in her university courses. My mother built herself an family of friends that probably helped her survive her twenties, in much the same way, I realise, that my brother's, my sister's, and my friends helped us survive the disintegration of the first version of our family.

One of my mother's best friends was a painter she met at a (apparently very bad) concert in Strasbourg as a student. This women was fifteen years older than my mother. A mother of two, a wife, a free spirit, and an exceptional, talented, thoughtful painter with no gift for self-promotion. By the time of that fateful summer she was a widow, and lived, in her own way, as bohemian a life as the middle class widow of a company doctor living in a rather stayed provincial town could. She had turned two whole rooms in the large, XIXth century apartment she rented into her studio. There was a magnificent winter garden filled with ancient houseplants in large cracked pots. She had, years ago, repainted a whole wall of the long hallway. As she had been in geometric phase at that point, it was in fact a mural of bold geometric shapes. And on every wall in the house hung her canvases. A rotating cast of her latest works (she painted prolifically). Abstract, unframed, untitled composition in rich textures of black and grey, with flecks of red paint and gold dust. Throughout her life she challenged herself as an artist, subtly but continuously so that year on year her paintings became an evolving text of her own thoughts about her art.

The only picture I have of one of her paintings. Uncharacteristically pink.
That summer, my mother called that friend. And she told us to come and stay with her. Not at the apartment, but at her other house. I had been to that house a few times as child, and remembered it as a remote and beautiful place. Returning there that summer, lonely, afraid, distraught, angry, I rediscovered it, and found it was a dream. The house was an old farm in one of the less beautiful valleys of the Vosges mountains, nestled up against the mountainside on a dirt road. But, in a fit of whimsy, a previous owner had had the meadow in front of the house landscaped into a magnificent garden centered around a lilly pad covered lake. There was a stone terrace by the like surround by intricately carved old topiaries. There was an island, accessed by a little wooden bridge on which stood a wisteria covered boathouse with an open air dining area attached. There were huge magnolias, yew trees, Japanese maples. The place was an effervescence of life and greenery.

The house itself was not grand to match the garden. But over the years my mother's friend had added there what was important. A well stocked kitchen. A large fireplace in the dining room. A bookcase full of an eclectic and thoughtful selection of books. She always said she did not paint at that house, because nature was too distracting there. But I also think that her art took a different form in that house: where her paintings explored her ideas about life and humanity in the abstract, in that house, she put her humanism into concrete action. Or at least, that is how it feels to me now. Because what happened that summer was simple, but immense: my mother's friend opened her house to us, and kept it open, so that we could grieve, forget, and eventually heal. There was no time limit to the gift. We went back summer after summer after summer, and she welcomed us with the warmth of her hearth and her heart.

Our society does not really know what to do with friendship. It is rarely the topic of any films other than war movies. It is not protected by any legal status. Would we classify friendship as an institution, like we do marriage or parenthood? Yet, its gift, when given, transfigures uur world. All the more so because it is compelled by nothing more than the friend's own love. My mother's friend, who became my friend, saved our family, for no other reason than she loved my mother.

I remember waking up in that house one summer. It had heavy french shutters so the room was pitch black until I opened the window, then the shutters, and let the bright sun of an Alsatian August burst into the room. In the distance was the blue sky between grey green mountainsides, a backdrop to the symphony of vibrant green coming from the garden. And below me, on the dew soaked lawn, I heard my mother and her friend, who had been up for hours, laughing and talking as they helped themselves to bread and honey from the beehives up the hill. I called down to them from the freshness of my well rested youth, and they called back to me from the freshness of their friendship, not needing me to join them but glad for me to come. It was art, a poem in the morning light, a gift beyond value.

In memoriam.

Wednesday, 3 January 2018

Professor PaleoGould's completely unvetted guide to surviving five day conferences

Five day conferences are fun, and intellectually stimulating, and will provide you with experiment and grant ideas for months. They are also an absolute physical and mental marathon, not to mention a financial black hole, that can leave you a drained zombie surviving on complimentary SouthWest peanuts by day three. I have been doing five day conferences since I started graduate school, and after ending up as said zombie one too many times, I have developed a few ideas to help. These ideas primarily work for a man travelling alone without children who is comfortable navigating big cities, and is a pretty extroverted and social person. I understand that there are challenges for others that I don't address. If there's anything you think I have missed that is important, please weigh in in the comments. The focus here is not on how to get the most out of the talks (though I touch on that), but how to manage your physical and mental energy to make it through tfive days without needing a holiday to recover.

1) Travel is exhausting, recognize this. If you're travelling more than two hours to get to the conference, you will be exhausted by the time you get there. Doubly so if you're flying through multiple time zones. Don't plan to go out or catch up with friends the day you arrive. Register, attend the plenary, shake a few hands, drink a lot of water and have a light quiet meal and get to bed. Start day one on the right foot.

2) Plan ahead. Both for the science, and the practicalities. Figure out how to get from the airport to the hotel. Does the public transit system run when your flight lands? How long does the journey take? Both before hand (google maps is your friend) and on the first day, do some quick reconnaissance. Find the nearest coffee place that is not in the conference hotel, the nearest chemist (for my UK friends) or drugstore (for my US friends), and the nearest grocery store. The aim here is to emancipate yourself from the conference hotel's amenities. That will save both your pocketbook, and your sanity when it comes to dealing with milling crowds of grumpy, jetlagged academics waiting to order theirs first coffee.
As for the science, go through the talk titles and circle the ones you are interested in. This is a great use of airplane time. Get a rough idea of what days are full of things that might be important, and what days less so. Identify conflicts between concurrent sessions in advance, and only read abstracts closely in that case. Write down clearly when your poster or talk is, and recognise the restrictions that places on what you can do. This will help you when dealing with the rush and panic of finding a talk to see among a dozen concurrent sessions.

3) Once you get to the meeting, accept serendipity. Talks will run over, you will miss sessions you wanted to see. You will oversleep. Lunch will take too long. You will run into a old friend/collaborator who is leaving that evening right as you're about to enter the most interesting session of the day but you haven't seen this person in two years. It's fine. The plan you did was to help guide you through the chaos of talks. It is not a map of your actions. Conferences are about serendipity and happy accidents that result from concentrating a bunch of people with shared interests in one space. There's actually research on this stuff.

4) Pace yourself, and take downtime. Don't force yourself to go to an entire afternoon if you only saw one talk you were interested all afternoon (in my case, invariably, because it was Fish and Dinosaur day at SVP). Go up to your room, sit, read a book, call a loved one, take a nap.

5) Exercise, but differently. The hotel will have amenities but not the ones you're used to. And your body is not in the state you're used to. Now is not the time to try to break your rep max on deadlifts. Pick an easy half hour workout. A good body resistance circuit if the hotel has a fitness center. A three mile run if weather permits. Swimming if there is a pool. A simplified vinyasa if all you have is your room. The aim here is to exercise and stretch your body, and take your mind out of the crowd and conference space.

6) Don't party every night. Conference parties are fun. Hanging out with old friends at the hotel bar until 2am is fun. But do not do it every night. That way lies missing out on the conference. And even if you stay up until 2am, stop drinking alcohol much earlier. Go to bed tired, sober, and well hydrated.

7) Vary your diet. Don't eat at the nearest sandwich place every day. Find the food trucks. Explore. Your body will thank you.

8) Say yes to random invitations, but learn to eat alone. If you're chatting enthusiastically with someone you've just met, and their friends turn up, and they invite you to join them for lunch, say yes. Good things may come of it and you'll have more friendly faces in the crowd. On the other hand, learn to eat on your own. Sometimes you won't find anyone to go with. And sometimes you'll want to be as far away from people as possible. Take a chance: pick a restaurant you like the sound of, go there, sit at the bar with a good book and order a meal by yourself. It is a very calming experience in the middle of a meeting.

9) take time off. Remember that afternoon with almost no relevant talks? Take it off. Go to a museum, or exploring, or to a slightly further away but well regarded restaurant. Some meetings include afternoons off in their schedule. If your meeting doesn't, schedule your own.

10) If your hotel has a 39th floor bar with panoramic views of the city, go there. Part of meetings is embracing what the moment brings.

Wednesday, 25 October 2017

What goes into a paper

I'm currently analysing data on what will probably be the final paper from the project I joined the lab to work on four years ago. This project was to look at the effect of a specific nerve lesion on behavior and function at multiple levels. We've looked at performance (how well the function is achieved), kinematics (how the structures which perform the function move), and neuromuscular physiology (when the muscles which perform the function are active). For this last paper I'm attempting to synthesize these different strands of data to understand something about mechanisms, and if they could potentially be targets for intervention.
On my end, the synthesis has taken months of lining up different data sets, verifying they are properly synchronized, figuring out discrepancies. It's been painstaking. Most days I've had between two or four spreadsheets open, generally half of which are metadata telling me how two different data sources line up. As I was reaching the end of this process, finally getting close to the dataset I needed for my analysis, it struck me that this was data we'd gathered two years ago. I'd been working on it for over a year. Furthermore, the datasets I was working with weren't raw data, they were themselves measurements of muscle activity and performance that former techs and summer students had also spent months to years working on. Cumulatively, the person hours spent on the data set I was assembling was staggering.
There is a paper in review from our lab right now whose entire results section is summarized in one very simple, very elegant graph. Six means with error bars. Those six means with error bars represent two months of caring for over twenty baby animals. Hours of understanding what our measurements meant. Hours of students and techs pouring over videos and chart recordings. Cross checks and visualizations and arguments and sick animals and broken equipment, all distilled down to one figure, six points.
My dissertation papers are the result of four years of work. I know this because I'm the only person that worked on them, and they took me four years. But if that is true, then this paper, that has in some ways also taken me four years, yet builds on the work of close to half a dozen people, is the result of two or three times that many years. And it will be maybe eight pages long, at most?
Academic papers, with their brevity and elisions, their straightforward narratives, are poor monuments to the sheer time consuming, physical work that goes into their production. The only clue in an academic paper of how many hours have been spent on it lies in the length of the author list. Those unsung middle authors are the only monument we allow to the effort that goes into our sleek, polished productions. And maybe, that is not good enough.

Friday, 29 September 2017

Stravinksy and inspiration

Yesterday evening, I went to do something I love and have not done in a long time. I went to the orchestra. The performance was of one of my favorite pieces of music: Stravinsky's the Rite of Spring. It was a piece so controversial in its day it managed to start both a riot (at its first performance in conjunction with Diaghilev's ballet), and a standing ovation (when performed as a standalone piece a few years later). Even now, after nearly one hundred years, there are few repertoire pieces like it. It is a stew of ideas that would influence all the major currents of classical music in the 20th century (minimalist composition, dissonance, even elements of serialism). And it inspired one of the greatest, strangest meetings of high art, popular culture, and science: the magnificent Rite of Spring sequence from (of all people) Walt Disney's bizarre flawed masterpiece Fantasia:

That sequence is, for obvious reasons, close to my heart. And in its daring combination of science, imagination, and revolutionary music, let it be my inspiration for the coming months.

Wednesday, 30 August 2017

Continental drift of the heart

The Mistress of the Animals has a new series of posts up, on dealing with less than ideal job situations. Go read them, they are useful, and make good points. And, as is Potnia's wont, a very important meta-point: what, at any given point in your life, is important to you, and what, at any point in your life, is worth putting up with?

The twist is that what matters, what is important, what you need, want and value, does not remain constant, nor is it always clear to oneself. Some of our values and priorities are like the Hawaiian volcanic hotspot, arising straight from our core and remaining fixed even as immense changes pass over our surface. Yet these hotspots are few. More often, things we think are massive and perennial are like the summit of Everest: superficially imposing, but in actuality a temporary wrinkle on the surface of our ever changing selves. We often change without knowing it, only recognising much later that things we once valued, were once utmost priorities, have shifted to peripheral importance and we are in fact organising our lives and decisions around new mountains.

Ten years ago this month, I moved to America for the first time. What did I want ten years ago? What was important? So important that to pursue a PhD I could have pursued at home in less time, I traveled to America, willingly moving to a city I had never even visited to start a PhD with an advisor I had never met? I remember why I did it: a desire for adventure, and a fear of getting bogged down. I lived in central London. I had good degrees and a good job and I could easily see myself never moving far from where I had grown up, devoting all my efforts to keeping a toe hold in the immensely comfortable, yet predictable life I had in London. I looked at the life my mother had led, which, while far from easy, had involved travels around the world by the time she was thirty, who had lived in three countries, and I balked at how stayed the profile of my own twenties was becoming. The furthest I had moved from home was Cambridge, a 45 minute train journey from King's Cross. In my master's degree, I met a diverse cohort of people from all over the United Kingdom and further, whose path to that masters, while more winding, and perhaps less easy than mine, still had given them a host of life experiences that made me stop and think. So, I resolved to have my own adventure, and to go pursue all my dreams at once: America, a fresh start, and a Ph.D. I applied to four programs, was interviewed at two, got into one, and with the blessings of my friends and family, boarded a plane and landed in Baltimore airport on August 20th 2007, with two suitcases, an address, and the name of a person I'd never met who was going to pick me up and take me to my first apartment I had rented without seeing.

And what a fresh start it was. For the first week I slept on an air mattress on the floor, and had only my laptop perched on my suitcase as furniture. The very first day I had my first encounter with how little London had prepared me for an American city. I left my apartment in Mount Vernon in search of food and some basic housewares. Despite walking from North Avenue, to Lexington Market, to the inner Harbour, I could not find a home ware store, and returned home with four cheap glasses, and a an overpriced saucepan from the convenience store down the road. It wasn't until the middle of the week when my new fellow graduate students took me to the Target on the outskirts of the city I was actually able to buy what I needed. The first five years I lived in America were the  adventure I hadwanted. I lived in and discovered a whole new city. I made many new friends. I did field work in India and Wyoming, and travelled all over the United States collecting data, spending weeks in San Francisco, Pittsburgh, New York city. And yet, by the time the adventure ended, already, subtly, the need for adventure had been replaced by other priorities. The desire for some stability, to be able to build a life with my partner, and the growing realisation that my increasing desire to be back home with my old friends and family was getting less and less likely to be easily combined with my desire for a fulfilling personal and professional life.

Ten years later, America is no longer an adventure, even though I have moved away once, and moved back to a new part of the country. America is a reality in my life, a part of it far more profoundly than I ever thought, at twenty three, it would be. It looms like mount Everest, or like the width of the Atlantic Ocean, in my decision making. My priorities now do not feature America, they must accommodate it. My desire to see my husband happy and fulfilled professionally means we are likely here at least another six year, probably more. My desire to be a good son, brother, and uncle, means I must continue to find ways to fly home often. My desire to have a successful career in academics mean I must continue to work hard, travel, be flexible and take opportunities. America is the geographic and political chess board on which I try to make my moves. And I know it now, I know it well. But whereas once, the fact I lived in America was a goal in itself, that time is long gone.

Tuesday, 22 August 2017

Why your society should have an LBGT+ science event

I don't normally blog in direct response to twitter, but this thread from the wonderful Alex Bond invites a response from personal experience.
Please read this thread to learn what not to do when approached by LBGT+ scientists asking for greater representation in the societies they are members of. Specifically, I want to address this point with a personal story to illustrate how wrong headed an attitude this is. As I've mentioned elsewhere in this blog, I had only recently come out when I started graduate school. From the beginning, navigating outness in my career and navigating the world of science were intertwined. When I came to Johns Hopkins, the LBGT association at the school of medicine was more or less moribund (a good friend of mine who came along a few years later has since kickstarted it and then some). And my department, while I had an out colleague, did not really discuss these things. For my first year in graduate school, I was out to my fellow graduate students, and that was it.
So, when in the fall of my second year I went to my first meeting of my society, I associated being professional in science with being in the closet. But I was uncomfortable with this. Such feelings put a distance between you and fellow attendees, particularly at a conference where out of hours socialising is important (and enjoyable). Being professionally closeted involves eliding a lot of questions.
On the second night of the conference, I noticed a little sign on the noticeboard: "LBGT members dinner will be tomorrow evening at this location, at this time". And suddenly I knew I was not alone. I knew there were others like me in this place, in this society, and that they were welcome.
Ironically, I didn't go to the LBGT dinner that year. I wasn't ready for it. Wasn't ready to be identified as a gay scientist. But even without going, it mattered. And when I went back two years later, I definitely went, and have gone every year since. Each time, a new grad student, or indeed someone more senior, turns up slightly sheepishly, and they are welcome, and they are made a little more comfortable.
But even then, the LBGT dinner (which has been running for years) has always been held at a distance. It was the initiative of one or two people, who have organised it for over a decade, and maintain the mailing list. Getting it listed on the website as an official society event has been a struggle. And every so often you hear someone grumble when they notice the sign "why do they need one?". Which is really the answer to that question.
There is, among a certain generation of scientists, a belief that things were better when we didn't discuss these things. And they'll often say: "well everyone knew X was gay, he (it is invariably a he) just didn't make a fuss about it". If you believe this, I urge to ask X how they felt. You will probably hear a different story, of getting invited to considerably fewer social events, and never with a partner. Of being passed up for promotions and committees, of advisors suddenly becoming frosty and distant. Not talking about it was not about decorum, it was about protection, and being resigned to lesser treatment.
Every time an LBGT person enters a new space, they look for clues as to how out they can be. The older and more establishment a crowd (so most scientific conferences), the more they will assume they have to be reserved. This is difficult, isolating, and honestly just damned unpleasant. And all it takes to start to make it better is a sign on a noticeboard. Is that really so much?*

*No, it isn't and you should do more, but start with that.