Friday, 5 December 2014

From the trenches of experimental biology

I remember a conversation I had in undergrad with my two best friends, both of whom where studying physics. We were discussing the relationship between scientific equations and the actual natural world over cups of tea (as you do when you're a bunch of over-achieving Cambridge students). As physicists, they were of the opinion that the equations had meaning, and that error was just that: the result of experimental imperfection. I was unconvinced: I could not perceive of any situation in which all biological observations would line up neatly with the predicted curve. There would always be error. Here lies a big division between the physical sciences and biology: we cannot get away from variation in biology. It it structured at the most fundamental level into the data we work with.
And sometimes, that variation is the dominant signal in your data. And that variation is both biologically relevant and analytically intractable. Which brings me, quite neatly, to my data. I'm currently working on a poster for the upcoming SICB meeting in West Palm Beach this January (conference location win, incidentally).  I'm looking at whether or not our experimental treatment is related to changes in how the tongue and jaw move in feeding. Our preliminary results (and these were reasonably robust preliminary results) showed a clear pattern. And then we added more sources of variation.
There was a point earlier this week where I feared the whole study would collapse, and that the interesting result was simply an artefact. As it turns out, elements of that pattern are consistent, but the variation between individuals and even between feeding bouts, is huge. Yet interestingly, within an individual and within a feeding bout patterns are highly consistent. The variation is non random. The variation is data.
The whole point of this project is to attempt to understand a system that is both highly integrated functionally and anatomically, and yet also highly variable. What's more, clinical prognosis for injury to the part of the system we're studying right now is also highly variable: symptoms of varying severity, duration and response to treatment efforts. We do work in a animal model precisely so that we can create reproducible, controlled injuries to the system. These are ceteris paribus (to use my PI's favorite expression) experiments. And, all things being equal, the system responds differently. This might lead some to look for some other systematic difference, and maybe there are some (stage of neural maturation, variation in anatomical patterns innervation, changes in spontaneous brain activity, or simply different strategies to adapt to the perturbation are all avenues we're looking at). And yet, at the base of it, I don't think there is any equation that we could make, even in an ideal world, that would result in our data lying exactly on the predicted line. Because variation in biology isn't noise, it's signal.

Wednesday, 26 November 2014


I grew up in a family that was quite synchretic in its attitude to traditions. My mother is French, but from Alsace, which celebrates Christmas in the Germanic style (on the 24th of December in the evening, with cured meats, choral music, and white wine). My father is English, which means church on Christmas morning, stockings, roast goose, plum pudding and plenty of brandy. We lived in Belgium for four years, and there picked up yet another Christmas variant (December 6th, St Nicolas, chocolate coins in slippers laid out by the fire). And we did Hallowe'en long before it was widely observed in the UK, I now realise, because my mother's neighbour in West London when my brother and sister were young was an American women with two young daughters. Thus, my family collects holiday traditions, and as a rule, sticks to them.
Thanksgiving is not a holiday in the United Kingdom or in France. This is obvious if you know its history, but the traditions we are raised with seem so natural to us that I have more than once had to explain this to Americans. In much the same way, I am still not used to not having a four day weekend for Easter (in England, both Good Friday and Easter Monday are public holidays). Yet as I have now been in the US for six years, and have a American fiance, Thanksgiving is very much part of my own branch of the family's holiday traditions. In the years I have been here, I have had the good fortune to enjoy many different thanksgivings varieties: a gathering of international waifs and strays in a small apartment on the upper East Side of Manhattan, in a room barely big enough to hold us all was my first. The next year, it was a huge clan of Connecticut Jewish Americans in an old house outside Phili (hosted by that same former American neighbour who'd introduced our family to Hallowe'en).  For the past few years, it's been at my soon-to-be-in-laws house outside DC, where they make two turkeys (one roasted, one smoked). We'll be headed out there shortly. And I'll be spending next week in the gym.
Thanksgiving is an oddity in the American calendar. A day held holy, where everyone must find somewhere to go and belong. Uniquely, it is a time when the ordinary and day to day must be suspended. It's as if all the energy and focus that Europeans spread across a year's worth of holidays is shoved into one weekend, where it is considered normal to fly across the country, or drive 12 hours, all to eat the same food with the same people. The tradition of hospitality attached to Thanksgiving, which requires that you invite anyone in your home who may have nowhere to go, is a wonderful thing. It's very clear to me why it is such an important holiday to so many here, in a way that sterotyped movies focused around turkey mishaps never quite capture.
Throughout graduate school, my mother would come to visit for Thanksgiving. She would spend a week with me in the US. We built a series of traditions around that week, just the two of us. A day wandering around DC, a trip to Phili to visit her friend, dinner at a particular restaurant in Baltimore. Thus, in that week, we re-affirmed each other's place in our lives, even though we were an ocean apart.
Each family, each person, each group of friends, builds a personal narrative of traditions with the holidays, places and times that we encounter throughout lives. Some of these traditions survive almost unchanged throughout huge chunks of our lives. The 24th of December in my family is merely a slight modification of the Holiday my mother learnt from her parents. Some are entirely new, arriving with new people or new places entering our lives. Some are abandoned, or modified. Some are created to mark new life stages. In this pattern of shared traditions across time and space, the ebb and flow of our lives, and our connections to our history, both personal and larger, are made explicit. A year full of public and private holidays to be celebrated in particular ways is a marker of a life lived in the company of others.
Happy thanksgiving.

Tuesday, 18 November 2014

Rekindling the fire

After I finished my master's degree, about nine years ago, I was at a loss as to what to do next. A Ph.D. seemed too much of a commitment at that age. I wanted to get a proper job, and see what the real world had to offer and if I could be content there. Problem was, I had no idea what one did in the real world.
I had almost no professional experience. I wrote amateurish, over eager cover letters and sent my woefully short CVs out to scientific publishing houses. I wrote clumsy mock articles for science journalist internships. I was basically directionless. I eventually took a job as a website content editor and translator for a half arsed start up animation and comic book company based in London county hall. I learnt a lot on that job, mostly that anything that looks too good to be true on paper probably is, and that throwing everything  at the wall to see what sticks can work great for management, but is a great way to fuck over enthusiastic young people.
The job offered no guidance. I had no idea what I was doing, how well I was doing, and what was expected of me. I felt out of my depth, frustrated, and unhappy. That's when I found the web forum fo a popular webcomic dedicated to graduate students. I leapt in. I checked threads at all hours of the day, and late into the night. Within a few months, my posting was through the roof. I have a lot to thank that forum for. It gave me a community when I felt isolated professionally, encouraged me to overcome my fear of graduate school, and taught me a lot about passionate and intelligent people. It was also an emotional minefield, that would at roughly three to six month interludes erupt into belligerent arguing. Those forum fights were emotionally exhausting to those involved, and seemed difficult to contextualise to those outside the forums. Sound familiar? The forum became a crutch to escape my dissatisfaction with my professional life. The six month I spent unemployed, and the nine months I spent in that job with no clear direction and no idea what was going to happen the next day, let alone in a month, destroyed what had up to then been a pretty solid work ethic and discipline that had successfully carried me through high school, college and my master's degree.
Eventually, I realised that the job was bad for me, so I didn't even wait to hear whether or not I got into graduate school. I found another job, one that was more focused and more serious, with a much better boss. I rediscovered some (though not all) my work ethic. And eventually, I was accepted into graduate school in the US and left. The forum faded and was eventually disbanded, though I found I had lost interest sometime shortly after starting my PhD. During my PhD, I was stressd, but overall happy. I almost never had trouble motivating myself to do what needed to be done. I was an independent adult for the first time, and it felt great. Seriously, balancing my own budget at the end of every month made me feel like a kid imagines being a grown up feels like.
Five years later, I was back where I had been after my masters. I had finished the PhD, and was looking into a gaping unknown. My visa had expired and in focusing on finishing my dissertation I found myself without publications and without a job. I had to move back to the UK, leaving behind a life I had spent five years building, including a four year relationship. My partner and I agreed to go long distance, but it was terrifying to do that with no set end date, and no idea under what circumstances we could be back together.
So, at 29, I moved back in to my mother's house in London. After five heavily goal directed years, in which I had grown as a person and a scientist, in which I had begun to achieve some degree of professional recognition, suddenly nothing. The result was a return to that feeling I had had in my first job of frustrated aimlessness, combined with a fair dose of humiliation. Amid that frustration and isolation, a good friend and fellow scientist introduced me to science twitter. It was great. I found colleagues and scientists I could chat to in almost real time. I kept abreast of developments in my field. I found out about job opportunities. I commiserated about the job market. And I got involved in many large twitter spats that were emotionally draining. I found a voice yes, but man I used it a lot.
That year of my life was not, in many ways, a good one for me. It contained many good things (the birth of my nephews and niece, time with my family, time to rediscover my home town), but professionally, despite submitting my first two papers (and getting one accepted), giving several invited seminars and getting four postdoc interviews, it felt like stagnation, if not regression. And, as before, my work ethic went to pot. I was listless and unmotivated. I drank too much. And I spent a lot of time on twitter. It was clear to me that I was angry, and burned out. Yet I couldn't muster the willpower to change my slew of bad behaviors. I was in licking my wounds mode. This scared me: I've always prided myself on my willpower. Yet suddenly, I couldn't stop myself from tweeting when I should be working, from not wasting my days playing Skyrim, and from not engaging in alarmingly regular drinking. Don't get me wrong, I love twitter, love video games and enjoy a good beer, but even I could tell this was no longer quite healthy.
Eventually, through networking, good luck and some people willing to go to bat for me in a big way, I landed my current postdoc. And as soon as I started, things started to change. The first three  months, I was in the office at 8 every day and staying til six. I probably achieved more in those first few months than I had in the entire previous year. In January, my now fiance came to join me out here. Suddenly we had our life back.
But my bad habits hadn't left. I had the energy for work again, but everything else was still off kilter. I'm one of those people who's always on top of his paper work (taxes filed a month before the deadline, paperwork submitted with weeks to spare), but things were still slipping through my fingers. I missed bills (something I NEVER do). I also had almost zero energy to do anything outside of work. I've always been a voracious reader, but I suspect this year I've read fewer books that at any other time in my life. And limiting my drinking has proved harder than I had wanted.
And then there's twitter. Its use as a crutch in that year in the wilderness made it difficult to shake the habit, but there's no denying that I tweet more than is sensible, given all the other things I need to do.
A year in I finally feel myself returning to a better version of me. As the winter is settling in, I'm looking forward to making my way through a backlog of books. I'm exercising regularly again. I'm making a concerted effort to be more disciplined about non work tasks, and the drinking is finally getting under control. And then last week, after the turmoil of shirstorm, and the wonderful response to my post, I realised I was also ready to reboot my relationship with twitter. So I'm taking a twitter break (I'm still lurking, so no saying mean things about me thinking I won't find out). I need to devote this new energy to tasks closer to hand: my research, my papers, my impending wedding.
A friend of mine told me, as I was entering my final year of graduate school, that six months to a year of unemployment was getting increasingly common between completing a PhD and starting a postdoc in palaeontology. Even if we disregard the economic lunacy and unsustainability of this arrangement, the psychological and emotional toll it takes on young researchers is huge. If you are in this situation, be honest with yourself about how exhausted you are, and be aware of any bad behaviors you may have accumulated as coping mechanism. Give yourself time, and be gentle, and you will find your way back to a version of you you prefer. It's taken me a year. And that means next year can only be better.

Wednesday, 12 November 2014

Confessions of a teenage dirtbag: Thoughts on shirtstorm

When I was in my late teens and early twenties, I went through a bit of a skater boy/snow bum phase. It was the closest thing I ever got to a teenage rebellion: wearing baggy jeans, big graphic T shirts, skater boy trainers. I went to a rather prim French school in central London, and then to university at Cambridge - a place that for all its charms is the definition of stuffy englishness - so in those middle class settings, my look was enough to raise a few eyebrows.
Picture 1: Snow Bum PaleoGould

Part of my collection,some of my favorite shirts, had 'classic' fifties and sixties pin ups on them. One of them, my favorite T shirt for many years, was a red Von Dutch number with a girl in an 8-ball bra holding a monkey wrench on the back. I still have it. It's faded with the years, and has now been relegated to a gym shirt. And maybe, after today, it won't even be worn as that.
The purpose of this post is not to whine that Matt Taylor of the European Space Agency has ruined forever my ability to wear pin up shirts. It is rather to ask the question about why he, and I, would choose to wear such a garment. Irrespective of your stance on the artistic value of Pin Up art, questions can fairly be asked about wearing what amounts to mild erotica to work.
The truth of the matter is, I always wore those shirts to provoke.  As I mentioned, I went to stuffy environments. And wearing these shirts that skirted lines of decency (and make no mistake, I knew they did), was a form of provocation. I distinctly remember there were times and places I would not were them. Is it not odd that these commercially available garments of mild provocation should use as their weapons women's bodies? Isn't it odd that I would never go to lecture wearing a T shirt with a Tom of Finland image on it? No, it isn't actually odd at all.
When Matt Taylor put on that shirt today, it was not, as has been suggested, that he doesn't care about clothes. It is clear that he has given his aesthetic great thought. He put on that shirt to provoke the stuffy media perceptions of scientist. He put on that shirt to loudly proclaim that he wasn't part of the Establishment. He put on that shirt for the same reason I used to put on my graphic Ts of pin up girls to lectures at Cambridge university. And, in doing so, he abused and belittled women. He probably didn't even realise it. He probably just thought he was being cheeky.
Our aesthetic choices are not free. That applies to subcultures like Rockabilly as much as it does to mainstream preppy campus outfits. The imagery of rockabilly and classic sci-fi, by reaching into the past, necessarily dredges up sexism with it. These images and styles cannot be worn uncritically. You have to interrogate your aesthetic choices. Otherwise you end up wearing a sexist shirt on a world platform, and casting a shadow over a great scientific achievement.

There's another issue I want to address, which I think resonates more in the UK than it does to American audiences. Because there is a class aspect to this too. Americans looking and listening to Matt Taylor hear a white dude with a British accent. Brits hear someone who's from a social background that doesn't normally get to speak for British science. People who got to speak for British Science when I was growing looked like this.

Sir Patrick Moore, late astronomer royal

Sir David Attenborough
 Matt Taylor was being presented as a working class hero, and that's important. With Britain the most unequal society in Europe, we need to encourage people from non traditional backgrounds into science, and we need to break the snobbery that makes people think that scientists look and sound, well, like me. But that doesn't mean we get to give Matt Taylor a pass. Today he failed as an ambassador for science. In doing so, he failed not only young women, but young working class children too. The solution is not to gloss over Matt Taylor' mistake. The solution is to find more working class people, men and women, to speak for science in the public eye. The solution is to expect more.

When you stick it to the man, be careful that you don't throw women, or anyone else under the bus in the process. And when you become the head of a major international space project, remember that you are no longer quite the underdog you once were. In fact you have power, and visibility, and a platform. You will be judged on how you make use of them.

Wednesday, 5 November 2014

Spell. It. Out.

Last night, a twitter fight erupted on where one should encourage trainees to publish. Specifically, whether it was appropriate to encourage trainees to publish in a trendy but untested open access journal, given that publication venues counts in hiring and promotions. Proflikesubstance wrote a thoughtful response (read the comments, for once).
I am very invested in this conversation. I am a postdoc in neurophysiology with two publications. Not two publications from my postdoc. Two publications period. One is in PLoS ONE, one is a decent society journal from my old field, vertebrate palaeontology. Here's the thing, my old field doesn't have high impact journals. I'm trying to get a third paper in what vertebrate palaeontology considers a high impact journal. The IF is less than five. My decent society journal is less than 2. In my new field, that shit don't fly. Compared to the neuroscientist I share a department with, my publication record is a joke.
Now, here's where I get annoyed. There are people in my field who would, and have told me, that I am already at a huge disadvantage compared to my peers. People who would tell me to seriously look at alternative careers. People I respect who've tweeted such advice. I am aware of this. I am not playing games anymore. I need to know what I need to do to restack the deck in my favour. So I am tired of people, well intentioned people whose advice on many things I trust, pussy footing around the issue of where I should publish.
Whenever the topic of open access comes up, proponents argue that they have placed postdocs into faculty positions without glam pubs. Detractors then darkly mutter about the selection committees' expectations and promotions and tenure requirements. Yet when it comes to specifics, nada. No one is willing to say HOW they whittle down those three hundred applications to a shortlist of five. I've yet to see anyone go on the record and say "yup, I chucked everyone who didn't have a CNS paper" or conversely "I looked up the candidates' H index and ranked them that way". Or, "our process is opaque, and I'm not sure how I came up with shortlist, but looking back on it, yes most had a CNS paper". Or "actually, it was the K99/R00 that did it".
Our department has NSF type comparative primatology people as well as neuroscientists in it. Recently, we had a seminar speaker meet the postdocs. He was a neuroscientist. The anthropology postdocs on NSF money talked about how, after two years, they were heading onto the job market. The neuro postdocs, and the speaker, all did a double take, as for them, no one was job market ready with less than five years of postdoc and at least a dozen papers, not even considering journal impact. This is the complex quagmire of tacit expectations a postdoc is supposed to navigate as they gauge where to publish and how much.
I'm currently awkwardly straddling paleontology, physiology and neurology, and I'm competitive for anatomy teaching positions. I know what the standards in many different fields are, and they change a lot. As I mentioned, in my old field, it's almost impossible to reach the kind of impact that neuroscientists get. And NIH money is out of the question. So I know for a fact that paleontologists have very different publication profiles to neuroscientists. As a trainee, I need you, as senior people who have been on hiring committees and tenure and promotion committees to level with me. Tell me what I need, what you expect in terms of publication. Spell it out by field, by university, by department. Tell me how you deal with people from radically different background when you do broad searches (like a ecology and evolutionary biology position, for example). Stop it with the dark hints.

Wednesday, 29 October 2014

Even on Anarres

There are few greater pleasures in life than chancing upon in the stacks of a second hand bookshop something hard to find  you'd forgotten you wanted. And so it was that few months ago I got half a dozen books by Ursula LeGuin. Among them was The Dispossessed. If you haven't read it, I highly recommend you track down a copy.
The Dispossessed is difficult to classify. Perhaps the best description of it is a science fiction socio political fable, but that doesn't do it justice. As an author of science fiction and fantasy, LeGuin stands out for her world building. The Dispossessed is admirable in this regard. It presents us with two societies based on a planet and its moon. The planet, Urras, is a complex, rich, highly unequal society of property ownership, and elaborate social hierarchy. It is place that is presented as both attractive and appalling, and very, very familiar. It is a society of plenty, but where access to that plenty is unequal. The moon Anares, on the other hand, is a political experiment, an anarcho-socialist society founded by idealist refugees from Urras, who follow the teachings of the political philosopher Odo. Urras is an almost barren world, the population low, and cooperation both a virtue and a necessity for survival. There is no ownership on Urras, and no hierarchy or state or economic compulsion. All actions are undertaken voluntarily, and the only accepted form of punishment is social exclusion by the immediate group. 
Our guide through the worlds and culture of Urras and Anares is an Anaresti called Shevek, who ultimately becomes the first of his people in 200 years to travel back to Urras. What is interesting is that Shevek is a theoretical physicist, and it is precisely because he is a physicist that he is able to communicate with the Urrasti, as physics is a shared universal interest between the two societies.Yet, as Shevek discovers, the political ideas, values and organisation of the two societies lead them to conceive of fundamental problems in physics differently. Thus he travels between the two worlds to synthesise their views. 
What is interesting to me as a scientist is that Le Guin uses the organisations and institutions of academic pursuit as our main way of understanding Urras and Anares. I don't think this is an accident. The university world of Urras is familiar to anyone who has visited a prestigious American or British university. It is opulent, high minded, cloistered and deeply steeped in hierarchy and social prestige. It is, in essence, indistinguishable from what we have here on Earth. There are prizes with large sums of money attached; there are prestigious publications; there are junior academics bowing the pressures of senior academics and administrators, and there are senior academics unused to being contradicted. 
Anarres is more interesting. The Anaresti philosophy is that each individual should seek of their own accord to fulfill his or her organic function, that is that role they feel is most useful to Anaresti society as a whole. Thus, people become scientists because they are drawn to it. There is no career structure, no hierarchy,  no expectation of work. Indeed, people drift in and out of science, as they drift in and out of all the possible jobs that one can do in Anaresti society. And yet, it is in Science that we first experience the corruption of the Anaresti ideal. Shevek goes to work with a great physicist in the capital, only to find that he is secretly communicating with Urras, and that all his great works are in fact Urrasti ideas that he plagiarised and passed off as his own because he alone could read Urrasti. Shevek suddenly finds that he cannot get access to the facilities that he needs without playing along with his new collaborator. Suddenly, Shevek is confronted with what is not supposed to exist on Anarres: ambition to dominate and control, institutional forces, the desire to own. It is in physics, what the Urrasti and Anaresti call the Noble Science, that the idealistic vision of  a society free of control, coercion and covetousness is found.
Thinking about Anarres has made me think that the problems of career incentives we face in science are far more deeply rooted than we often like to think. As I mentioned in an earlier post, I feel that a certain naivety attaches to the open access movement, or the post pub peer review movement. They pursue the idea that the pernicious incentives of prestige, status, hierarchy in academic pursuits can be defeated by these technical fixes. But expensive journals, the pursuit of glam, the addiction to personal and institutional status are not causes, they are symptoms of the fact that science is an exclusive, competitive pursuit existing in highly hierarchical, status obsessed societies.As Shevek comes to realise, the Urrasti university is completely anathema to Anaresti ideals.Yet Le Guin warns us that even on Anarres, personal ambition and institutional inertia can create an embryonic version of the academic system we are all fighting. 

Monday, 20 October 2014

Fat Lesbians need more NIH funding

The usual suspects are going after NIH funding in light of Francis Collins' political own goal on ebola research. As a non US citizen, despite being paid out of an R01 NIH grant, I often feel like my voice is not the most useful in these debates. But as a gay man living in rural Ohio, I can tell you this. Contrary to what fair and balanced news coverage may have you believe, fat lesbians need more NIH funding, not less.
LBGT people are an understudied population in all aspects of clinical intervention, yet what research we have clearly indicates that, as a group, gay and lesbian people have worse health then straight people when you control for income and socio-economic group. Compared to straight men in their thirties, I am more likely to smoke, binge drink, and show signs of psychological distress. Although I am less likely to be overweight, lesbian women are more likely to be so than their straight counterparts. (data from CDC survey of health differences among gay and lesbians).
Crucially, that survey was conducted in 2013, and its results only published this year. It was the first of its kind. We have almost no population wide, systematic data on differences in the health of gay and lesbian individuals. What is more, we know they are less likely to have medical coverage (in part owing to problems with spousal coverage), less likely to have a regular healthcare provider, less likely to seek out medical help regularly and less likely to discuss LBGT specific issues with their healthcare providers.
Conversely, we know that most physicians receive almost no education in LBGT specific healthcare issues in four years od med school. I have a couple of gay doctor friends, and I have watched them advocate tirelessly for years to get LBGT health issues on the medical school radar. It is tough going and change is slow. The medical profession in the US is surprisingly conservative on these matters. LBGT men and women have long known that they have to be their own advocates in the doctor's office. Ask any gay friends you may have, and you're bound to hear some cringe worthy stories. But patient advocacy requires privilege. With my PhD and middle class background and white maleness, I can talk back to a doctor (especially when it comes to anatomy). I can demand treatment. I can argue. A latina teen lesbian who'se been kicked out of her house has no such recourse. A closeted twenty something gay farm boy visiting the same family doctor his whole family and town sees isn't going to be comfortable asking for an HIV test.
The HIV crisis fundamentally damaged the (already shaky) relationship between LBGT people and the medical profession. Not helped by the fact that homosexuality was considered a disease until 1973. Many gay men and lesbian women in big cities set up parallel networks of healthcare providers, because they neither trusted the medical establishment, nor had access to insurers. These voluntary outfits do amazing work for outreach, education and testing, but they do not provide the follow through a established family doctor does. And in the rural areas of the US, these services are few and far between. I know this first hand. In my old city, I could get free HIV tests several times a week at several locations. Here in Ohio, my family doctor seems surprised when I order one, and my other options are a monthly clinic half an hour away, or planned parenthood, which my insurance will not cover.  And again, I am an out, educated, financially independent male. I'm not afraid of my doctor's looks, or the village gossips, or who sees me come in and out of the planned parenthood offices. I don't think that experience generalises to my LBGT friends who grew up here.
When Fox news goes after the paltry amount of money NIH is willing to give to investigating LBGT health issues, they are attacking vulnerable men and women in precisely the place where they are most exposed: their relationship with their healthcare provider. It is low and callous even by their standards. Fat lesbians and gay men who drink too much deserve NIH money. And remember, one day you may be grateful on behalf of your son or daughter that they got it.
PS: Hat tip to drungmonkey for alerting me to this.

Thursday, 16 October 2014

Silver bullets, snake oil and software patches

My computer's operating system is updated every month with various patches. Patches, by definition, are work arounds, fixes to problems that were missed in initial software development. I'm a Windows user, which means I am used when going to help forums to being told "the problem is Windows, it's fundamentally broken". In the eyes of linux and UNIX users, no amount of patching can ever make Windows a good operating system. There is no silver bullet to fixing its myriad flaws. That being said, 80% of the time, my computer works fine.
A couple of weeks ago, this brilliant article on the limits the open access amount is encountering came out. The key here to me is that Elsevier's actuaries don't view OA as a threat to Elsevier's business model. Actuaries are terrifying people: no one will puncture your views of 'oughts' more thoroughly. (As an aside, this is why I really want to know what insurance companies' actuaries are doing about global warming). In their discussion of why OA isn't a threat to Elsevier, the actuaries hit the nail on the head. Open access claims to be able to solve too much. All the ills in science (glamour chasing, the under representation of developing world scientists, the unfairness of taxpayers not having access to the research they fund, science communication) can be fixed if we just switch to open access. In response, opponents trot out their line of perfectly valid critiques (junior scientists need glam pubs to get jobs, who will pay for publication charges, how will we judge publication quality). And the same argument happens all over again, while, incidentally, Elsevier's bottom line stays healthy and scientists continue to chase publications that will win them job security. 
Does this pattern seem familiar? It sure resembles what happened last week in a twitter discussion of the usefulness of crowdfunding for scientific research. On the one side, the young Turks, denouncing the corrupt and anti-innovative nature of the NIH and NSF. On the other, the Established Scientists, arguing that no one was covering overheads, and that none of this funding scaled to reach the levels of the government funded scientific enterprise. Same debate, same rhetoric, same failure to reach a conclusion. 
I have no issue with open access, or crowdfunding. I am no fan of the status quo. Paywalling research is problematic. My dissertation research, unfunded by NSF, would have been funded several times over by the amounts that opponents of crowd funding deride as insignificant.  Yet I feel that the proponents of both are all making a fundamental mistake. They are viewing technocratic, process changes as solutions to much deeper, sociopolitical problems with the way modern science is run. Open access won't solve the issue of prestige, because prestige is deeply rooted in the social networks that underlie scientific hiring decisions, amplified by the hyper- competitive nature of the job search in  modern science, Crowdfunding won't solve the current funding crisis, because it cannot counter the increasing instability and uncertainty associated with science funding. More fundamentally, neither of these mechanism, nor many other solutions put forward by scientists, explicitly engage with the socio-political dynamics at the roots the problems they propose to solve.
Open access makes research available for consumption by all. It neither opposes profiteering (just look at the amount that AAAS thinks it can charge for its open access publication), nor prestige based publishing (ask any junior scientist). Crowdfunding may help you collect preliminary data, but it won't pay your salary if you're on a soft money position.
Technocratic fixes are software patches: they fix local problems in a broader system. But fixing the deep problems requires rewriting the code. That difficult, political work cannot be replaced by a silver bullet. And if you keep claiming your patch will be a silver bullet, you'll end up looking like you're peddling snake oil.

Tuesday, 7 October 2014

Scale, rotate, translate: on moving between fields of biology

I'm currently writing up abstracts for our lab to submit to a clinical meeting. Writing abstracts for a clinical meeting, especially as we work on an animal model, is a very different thing that writing abstracts for a basic science meeting. It's reminded me that my background is unusual compared to the people at this meeting (which I will be attending for the first time). As it turns out, the most active people I follow on twitter are also more clinically oriented, and in a discussion yesterday about animal models, the differences in our scientific backgrounds became stark. To put it simply, I think sea slugs are probably just as interesting and worth studying as humans. If you don't agree, go and read up on how they co-opt the poisonous organs of sea anemones for their own defence. Furthermore, as a evolutionary biologist, the answer to "does knowing about sea slugs help us understand humans" is "of course it does!"
In fact, until I started this postdoc, I'd never worked with live animals. My undergraduate research had involved a little collection of ecological field data (staring at birds through a telescope). My masters and PhD work, however, were all palaeontology. My research was collections based, meaning I spent my time in dusty museums rummaging through drawers pulling out fossilized bones and measuring them. The questions I was interested covered increasingly large time spans (several thousand years for my masters, several million for my PhD). Taxonomically, I looked at the European wide distribution of an entire species for my masters, and several entire orders of mammal for my PhD. It is big questions that excite me. Questions like: how do entire faunas respond to major episodes of environmental change? What is the role of functional specialization in the evolution of goups? How does variation in shape change through time? And, for me, the big one: how does variation in shape of body parts (mostly teeth and bones) relate to how animals function in their environments? I've spent a lot of the past five years thinking about these questions. They are, to me, fundamental to biology, and relevant to understanding organism function at any level. After all, every thing we observe in any organism (yeast, mouse, sea slug, hairless bipedal ape) is a product of evolution. Yet I now find myself writing for an audience that not only doesn't think about things this way, but actually views such thinking as suspect or frivolous. I am not saying they are wrong to think that way (I would only do that after a couple of pints). However, it does require that I learn a new way of talking and thinking about research, about organismal function, about biology, about science.
Given the above, you might reasonably ask what the hell I am doing in my current position. Well that brings us right back to the question of the relationship between organism shape and function. Most paleontological work doesn't test this relationship experimentally. Instead, we establish correlations between variations in shape and differences in ecology, often broadly categorized. A complex and elaborate suite of techniques for quantifying shape variation, correlating it with ecology, accounting for confounding variables such as shared evolutionary history and body size exist to look at this problem. Initially, this approach seemed very promising, allowing me to reconstruct functionally important behavior in fossils, and use it to understand evolutionary change on a macro (millions of years or more) scale.
Ultimately though, this approach became frustrating, because the fundamental premise remained untested. Specifically, I was looking at joints. Although I established that mammals that live in certain habitats have joints of a certain shape, I had no real data on why that might be. This is a major limitation of the comparative approach. And I realised that to fill that missing gap, I had to get data on how animals actually work. I would have to become an experimentalist. So, when through a stroke of luck, I was offered a postdoc in a lab that did just that, even though it was in a different system to what I was initially interested in, and was more clinically oriented than my previous research (admittedly, not difficult), I jumped at the chance.
The transition hasn't been hard, exactly, but it has been challenging. I have met people who are experimental biologists studying evolutionary questions who openly scoff at methods I have used and considered gold standard in my old field. Researchers who express serious misgivings about the validity of methods used to ask those big questions I was so interested in. I've had to learn that big questions can be different types of questions. Questions about complex systems, questions about organismal function, questions about disease etiology.
Ultimately, the research program I would like to pursue requires me to learn to think about questions at both these levels, and hopefully integrate them meaningfully. I've already lost my naivety with regard to many of the questions I wanted to ask about mammalian evolution. Answers will be partial, clues gleaned from the fossil record illuminating clues gleaned from detailed experimental work illuminating clues gleaned from broad comparative studies of living mammals. And many researchers are studying these systems with very different end goals in mind, to do with human health, that make them suspicious of my intentions and my seriousness if I harp on about the shared evolutionary history of all living mammals. It is a valuable experience I think to learn the complex languages of biological research, for all that it is uncomfortable at times.
But I assure you, as animals, humans are not special.

Tuesday, 30 September 2014

How far we've come

This past weekend I was at the wedding of one of my best friends. We met in graduate school. She helped me find a flat before I even arrived in North America. She picked me up at the airport and helped me move in. But most importantly, she was an out lesbian in the department. She had blazed the trail I would follow, and by her presence and actions, made my life as an only recently out gay man less difficult, and less lonely.
She and her wife married, surrounded by friends and family, at a beautiful, touching, fun and definitively ORDINARY wedding. How far we'd come from our tumultuous days only seven years ago. Same sex marriage was not legal in Maryland back then, DOMA and DADT were still in place. Our families (we both have old parents) were still grappling with our sexualities. WE were still grappling with our sexualities. Grappling with how to live honest lives, while protecting ourselves. Learning to deal with our fears real and perceived.
Many people from my graduate school days were at the wedding, including my advisor, which took me somewhat by surprise. He and his wife greeted my fiance and me warmly. They asked how we were doing. We talked about life in Ohio, about my job, about our futures. Again, an intensely ordinary moment. Later I remembered something that made smile. Years before, in my third year in graduate school, when my boyfriend and I had been together for about nine months, I was agonizing over a problem. The departmental Labor day party was about to happen, and as always significant others were invited. I wanted to invite my boyfriend, it seemed insulting not to. And so, my stomach twisted into knots, I went to tell my advisor that I would be bringing my boyfriend to the labor day party. I outed myself to my advisor at 5pm on a friday in his office. I was nervous beyond belief, even though I knew my friend had brought one of her girlfriends to the labor day party years before. She was not his student, I thought, maybe he would react differently.
My advisor's reaction was splendid. He simply asked how long I'd been with my boyfriend. The next day, when we arrived at the party, he greeted my partner with "So nice to finally meet you. I've heard so much about you". Even though he'd only learnt of his existence the day before. We laugh about it now, but at the time, all I felt was relief. *
So here we are, seven years later. I am an out gay scientist living in rural Ohio. I have a wonderful supportive boss and department. We are planning our wedding with the full excitement of both our families, immediate and extended. The marriage will be legal in all three countries that it needs to be. We will have as much chance at happiness as everyone else, and we will be free to celebrate that happiness openly.
There is still much to do, yes. There is still no employment protection for LBGT individuals. Gay marriage is still not legal in all states. There is still intolerance, covert and overt. There is the tragedy of homeless LBGT youth. There is the horror of persecution of LBGT individuals in much of the rest of the world. Yet for this scientist who stepped off a plane in Baltimore seven years ago unsure he would be able to be happy as a gay man, who stood with butterflies in his stomach outside his advisor's office waiting to ask if he could bring his partner to a barbeque, who wondered if he would be ever able to legally reside in the same country as the love of his life for that reason alone, the change is breathtaking. I will take a moment to celebrate how far we've come as a society, and how far I've come as an individual.

*As an aside, even though the purpose of this post is not to teach lessons, this is why you must be pro-active in creating a gay friendly environment. Be inclusive in your descriptions of couples. Invote succesful LBGT scientists to seminars. You cannot assume your students know the department is gay friendly, and given the potential risks if they make a mistake, they will be cautious.

Tuesday, 23 September 2014

Well meant and freely given (mostly)

There's all out Generationenkonflikt in the science corners of the internet these days. And, as with many disagreements in life, it is couched in terms of money. Who has it, who wants it, and who deserves it. Nothing nice or pretty will come out of a conversation like that. I got very upset and frustrated. It is not a pleasant feeling to be judged and found wanting based on a collection of vague impressions about entitlement.
There have been many versions of this post playing around in my head. Initially, it was going to be all righteous anger, a Phillipique against the older generation. But I have long since learnt I am no Cicero. My righteousness sounds great in my head. On the page, it more often than not comes off as peevish. Yet the attacks felt too brutal to go for my usual spiel and try to synthesise the argument, take the measure of both sides and achieve some sort of resolution. When you've engaged in a multi day, multi post, hundred comment long bout of circular onanism on the stoic resilience of your generation and the myriad failures and frailties of mine, I am fucked if I am going to be reasonable. I had a couple more ideas, each more terrible than the last.
Finally, I said sod it. Life is too short to try to craft the perfect post for a bunch of internet curmudgeons.  Here, in no particular order, are my thoughts on the matter. Take them or leave them.
1) Life is hard. This is a truism. It is also mostly unhelpful. It gives neither advice on how to proceed with life, nor does it provide emotional support. "Suck it up, Buttercup" is not advice, it's a cop out.
2) No amount of being told something will be difficult can fully prepare you for the reality of that difficulty. Thus, people make choices with incomplete information and also, things like hope and self belief (stupid stupid people). Encountering full on quite how hard the reality of a situation will be will cause howls of anguish. It is unhelpful to raise your eyebrows and say "you didn't know?" I knew going into grad school that it would be difficult to hit my goal of a faculty position. I did not know quite how far away the goalpost would be, how small the opening would be, that I would be kicking against a strong wind and that the ball was made of concrete. Also, I managed, despite my best intentions, to turn up wearing ballet slippers instead of cleats (to continue this tortured metaphor). That was my bad mostly. It still sucked.
3) Most of my cohort are angry, they have taken to writing about this anger. Unlike previous generations that were limited to poetry slams and self printed 'zines, we have the internet. Thus, you are encountering a lot of this anger. Much of it comes across as whining. It is poorly written and badly argued. It is inadequate in its analysis of the problems. It is sarcastic. It is incendiary. It lobs verbal molotov cocktails that massively miss the mark. It attempts to lob verbal molotov cocktails and lobs verbal pina coladas instead. This results in a sticky mess. Then again, have you read any of the lyrics to Joan Baez songs? My point is, the arguments are uneven, there is dross. The anger is real, and you should probably pay attention to it. Or not, your choice.
4) Most of my cohort are terrified. This is more important than the anger. They are terrified daily that they may not have a job in a month, six months, a year, two years. They are terrified it will all be for naught anyway because they won't get a faculty career. They are terrified that they need a plan B. They are terrified that they will have to move again, sell their meager belongings on the stoop, end up somewhere they know no-one, without a car. living in student halls, through one of the worst winters in memory, at the age of thirty. They are terrified that one day, their partner whom they love and are engaged to and wish to spend the rest of their lives with, will say "seriously, we moved to Ohio for you, what are you going to for me?" This is getting oddly specific, but you get the gist.
5) Most of my cohort feel guilty all the time. We feel guilty for choosing a career that was interesting rather than safe. We feel guilty because we were in grad school during the 2008 financial crash and while all our non academic friends lives were collapsing around us we coasted through, We feel guilty because we left our families for five years. We feel guilty because our significant other chose a long distance transatlantic relationship when we went home. We feel guilty for accepting help from our parents when we didn't finish before our stipend ran out, and then again when we didn't get a postdoc. Again, the list goes on.
6) Most of my cohort take the postdocs they bloody well get. I had the choice between two, one that would have been career suicide, one that was great for my career, more than I deserved, but that involved leaving my family and heading to Ohio. Oh, and making my partner leave his and move to Ohio. The one that was career suicide was in Chicago, fyi. So I did all the right things and I don't grumble much. Can I get a fucking cookie please. And here's the dirty little secret (let's talk about choice, shall we?). I would have taken either of those postdocs rather than give up on a science career. Not because OMG science, but because that had been my job for five years by that point and I literally had no idea what else I could do.
8) A postdoc is a commuted sentence, no more. It is a reprieve from failure, but a distinctly temporary one, It does not instill you with confidence, nor calm, not a sense that you any sort of control over your life.
9) "entitled young people" are the kids I went to school with whose parents' had invested a fortune in the NASDAQ for them. They would ostentatiously point out to the teachers in class that they could afford not to pay attention because they already had more money than the teachers ever would have. Yes, I went to that sort of school. Reality check: these kids are correct to be entitled. Trust me, I know the grades they got at A-level and I know what universities they went to. Thirty somethings in precarious short term contracts working long hour for between thirty five and fifty grand a year, with no guarantee of benefits and no job security, are not entitled. No not even when they occasionally opine that they wish things could be better. At this point, we should all just agree to stop using the word entitled. It has merely come to mean "people who appear to want something I don't think they should have", and it's unhelpful. Also, please stop relying on anecdotes when characterising an entire generation. That would be a characteristic of the #allegedprofession, would it not?
10) Sometimes, people talk about money as a proxy for all these other things, because money is grown up, serious, quantifiable, and because our society is so fucked up we have decided money is only valid locus of political and social activism. So use your humanity.
11) It is not controversial to assert that an employer is responsible for informing an employee of their terms of employment. This is true for fast food workers. It is true for magical not-really-employee science trainees too.
12) My mother threw paving stones at cops and ran from tear gas. There were valid, important serious reasons for the May 1968 riots in France. But the main rallying slogan for the youth was a poster of De Gaulle' silhouette muzzling a French student with the tag line "soi jeune et tais toi". "be young and shut up".

My mother (who was an PhD student at the time) also tells the story of attending a symposium of the condition of funding for Early Career Researchers, asking a question about the provenance of funds, and receiving the answer "Ca n'a pas trente ans et ca dit 'je penses'". Translation " It isn't thirty years old and it says 'I think' ". Plus ca change, eh?
13) Yes, there are worse problems that being a postdoc, but it presents real problems none the less. To the three year old, failing to get up the slide is a real problem, and her frustration is understandable, justifiable, and worthy of our compassion.

I will leave you with two quotes about judgment and advice, because I'm pretentious that way:

Atticus: 'You never really understand a person [...] until you climb inside his skin and walk around in it' (To Kill a Mockingbird, Harper Lee)

Dream King: "And you, your actions have been rash and unconsidered. You will scarcely last another hundred years if you continue in this manner"
Thessaly: "I don't recall asking for your advice, Dream King"
Morpheus: "it was well meant, and freely given" (Sandman: A Game of You, Neil Gaiman).


Monday, 15 September 2014

Sins of the fatherland

My birthday this year will coincide with the referendum on Scottish independence. So forgive me if I make this momentous event a little more about me then perhaps I should.
I've stayed silent throughout most of the debate. Not because I have any delusions that my ill-formed and ill-informed ideas might have any influence on the outcome of the vote. The stage is already crowded with English people heckling Scots on how they should vote. More because I am conflicted about this debate. And mostly, because, as an English person, this debate has been uncomfortable.
It is difficult for people from outside the British Isles to understand that this debate could be so fraught. We are a small island. The Act of Union was signed before the USA became an independent country, before France was a Republic. Throughout Europe, countries have merged and broken apart countless times in the same time span that the United Kingdom has been persisted. Heck, Ireland has undergone more changes in that time period. It would seem strange therefore, that a Union that has persisted so long could conceal a desire for independence strong enough to break it now. Yet, here we are, with a vote that looks like it will be as narrow as the independence referenda in Quebec, despite the fact the differences between Quebec and the rest of Canada are more obvious.
It is not my place to legislate on the validity of the Scottish feelings of independence, to argue about which parts of Scottish culture are true and authentic, which are reflections of recent political differences, and which are recent fabrications. I will say that nationalist sentiments of all stripes are mostly mythology of some sort. That is why historians have so little patience for them. I'm half French, half English. I have more than enough of that baggage to deal with.
This is, of course, where my discomfort begins. For, with the best will in the world, it is almost impossible, as an English person - worse, as a Londoner - not to feel slightly hurt by much of the rhetoric coming out of Scotland. The most optimistic, hopeful writings about Scottish independence, that avoid saying that everything will be better if we just ditch the English, still contain the implicit message that, well, England is doing a lot of things wrong. The worst, well, they fit into a long narrative of painting the English as the devil.
My first response to this was to highlight the unfairness of the political critique. Scotland is not unique having suffered under Tory rule; so has much of Northern England. Without Scotland in the Union, it will become harder for left-wing Labour governments to form a majority, thus condemning England to more years of post Thatcherite crisis economics. The fact that the Labour party has consistently failed to convince the Scots that it has their interests at heart is one problem with this narrative. The other is that it is not mine. I do not come from one of those parts of the UK ravaged by Tory rule. In fact, I come from the one part of the country that has consistently done well since the recession. When I talk about Wales or the North of England to argue a case for Scottish solidarity, am I not simply using that history as an argument to avoid, well, looking at the content of the Scottish critique of ruling class Englishness? Most crucially, when I point to mine and my friends in London's desire for a more equitable government, our disgust with the Tory policies, our hope for a better future, am I not, in fact, trying to hide my own complicity with the dominant narrative? After all, none of us have left London. None of us would seriously consider redistributing the art budget more equitably ("but the Royal Opera is so wonderful it would be such a shame to lose it"). As has been pointed out, it is difficult to take the critique of Scottish nationalism seriously, when what is being propped up against it, in all seriousness, is a jingoistic take on British history that would make Churchill blush with embarrassment. 
As I mentioned before, I am half French, half English. Until the middle of the twentieth century, both those countries subjugated half the world. French colonialism was horrible, and despite better PR, British colonialism was no better. For complex reasons owing to my French parent's background, I am somewhat on the periphery of the French power establishment (protestant background, and from a region of France often deemed insufficiently French). Yet my Englishness, with my central London upbringing, my accent that sounds like what you here from the green baize of Parliament, my private schooling, and my Cambridge degree, is pretty damned Establishment. And the Establishment has managed to portray itself as very close to the caricature it claims the Scots have leveled at it. In the end, my discomfort in the face of Scottish independence is more to do with the disturbing possibility that I may in fact have some of the traits of the cold, callous, dismissive, and arrogant Englishman of those narratives.

Tuesday, 9 September 2014

Great expectations?

"The job for life is dead; long live the job for life".
This was the slogan on advertisements a management consultancy firm had taken on the underground back in the late nineties, possibly early 2000s. I remember them distinctly as a teenager riding the tube. British advertising is a thing of wonder, and these ads tapped into the ambient Zeitgeist with dreadful precision. The changing nature of London's job market for young people was sufficiently topical that it had made its way into the mind of a teenage boy still at least half a decade from his first "real job".
"The job for life is dead; long live the job for life". A rebuttal to a debate that was occupying the op-ed columns of the broadsheet newspapers. An attempt to make the uncertainty of job prospects for young graduates into an opportunity. A warning that things had changed. Nearly 20 years ago, yet it could have been written yesterday.
I had a long conversation with a friend of mine today. He's several years older than me, a late genXer where I am an early millennial. He's Californian, but has lived in the UK for nearly ten years. I've now lived in the US for nearly six. We regularly trade notes on each other's countries, attempting to help each other understand their idiosyncrasies. You can live in a place many years as an adult, yet still find its inhabitants hard to understand sometimes. Today he helped me realise something: part of that is due to the emotional impact of formative experiences from youth which shape what people come to expect from life, what they do. And here, I think, lies a major faultline in how American and British young people view the world.
There is much talk of the entitlement of the millennial generation in the US from Boomers and gen X ers. Conversely, Millennials will regularly point out that their start in life is hard, burdened with student debt and the worst job market in living memory. I have little patience for older generations berating younger. Historically, it's not generally a position that has shown itself to have much merit. Each generation comes to being with certain expectations and certain baggage, and deals with it as best it can. My mother's (late greatest) generation faced challenges I can barely imagine, but benefited from an economic miracle I will never experience. My brother and sister (late gen X ers) benefitted from a welfare state far more generous that I will, yet have had the middle of their careers hard hit by the financial crash. Me? I grew up in a globalised world, trained and poised to take advantage of all that had to offer. Yet I would have no security. Ever. I would have to be permanently on the move, getting better, hunting new opportunities. No rest, no relaxation. I learnt that lesson before I ever went to university, looking at those posters on underground carriages, learning what my professional life would be. Precarity framed as opportunity for growth, again, and again, and again.
The UK when I was growing up was in its post Thatcherite heyday. New Labor, Cool Britannia, Britain relevant on the world stage again. What the past few years have laid bare was how much of a sham that all was. Long term observers had noted it: the manufacturing regions ravaged by decades of failed industrial policy before being brutally culled by Thatcher never recovered. Instead, something else was created, a place that has virtually become synonymous with everything that's wrong with the UK today: London. And those adverts I mentioned were the ethos of the city I grew up in. Hustle, hustle every day all the time. There is nothing else to do, nothing else to build.
London's post thatcherite growth had never been predicted by her government, nor the sudden explosion of the UK financial sector, driven by a glut of foreign capital from increasingly unsavory locations. I suspect now that, in the aftermath of the winter of discontent and the destruction of most of the country's economy, the attitude that developed in London was one of Post apocalyptic survival. We had somehow made it out. In fact we were doing better than ever, Yet, deep down, we knew this was down to luck, and we suspected it would not last. After all, everyone else was screwed, when would the other shoe drop?
Thus, when I went to university, I already knew that I was playing a game. I knew the odds were stacked against me. I knew the name of my university was my way of stacking the deck back in my favor. I expected nothing from the world of employment (when I went there after my masters), other than a paycheck that would be insufficient to let me live. And I suspect that teenagers in the rest of the country, who didn't even have the fever dream of finance doped London to look to, were even more cynical.
What I have come to realise is that I don't think anything as traumatic happened in the US until much later. The dot com boom and the Asian financial crisis didn't eradicate entire sectors of the economy for good. Outsourcing was a more gradual process, rather than the traumatic destruction of the entirety of heavy industry in the UK in just a few years. Even the automobile industry in Detroit limped along until 2007. Britain's car industry ended in national ignominy in 2005, after an agonising decade long decline. Thus, an American teenager my age would never have encountered with such force the message I saw on that tube train.
This explains what I cannot help but perceive as a certain naivety from recent American college graduates. As they work for years as bartenders, baristas, and so on, as they are paid peanuts for short term jobs, or working unpaid internships for experience, they express a sense of betrayal, an idea that they had been promised more. To my 90's London upbringing, this seems hopelessly naïve.
In the UK, it was my brother's generation, graduating in the late 90s, who went through those growing pains, the certainties of an older world order swept away. My generation of young Brits has never expected anything from the world, other than a sunny slogan to hide a grim reality. In that way, we truly are the children of Blair.

Wednesday, 3 September 2014

The unspoken art of publication (why I suck at it)

My PI has set ambitious publication goals for our lab following the summer of data collection. Knowing her track record in the past, I have no doubt they are achievable. This is in fact one of the main reasons I came to work with her. For I also have no doubt I will find this just as difficult, if not more so,  than learning the technique of our experiments.
I've been doing scientific research off and on (at this point, mostly on) for nearly ten years now. The first piece of research for which I thought "I would like to publish this" was my master's thesis back in 2004. It wasn't published. I entered my PhD, after a 2 year break from academia, knowing that I should have three publications by the time I was done to be competitive on the job market. I never published anything until after I submitted my dissertation, and I still don't have three publications (one in print, one in press, one revise and resubmit I need to both revise and resubmit). So I've been intending to publish for as long as I've done research. But good intentions only take you so far.
My lack of publications has already nearly cost me a career in science. I was unemployed for just under a year after completing my PhD. As I asked about jobs, and for advice on getting them, my non existent publication record was always the thing that stumped people. I gave seminars, I led workshops, I presented at conferences. I got a lot of encouragement about my research, and always the same warning: none of that was worth much as long as none of it was published. At my first interview, the first thing I mentioned was that I had just submitted a paper. My interviewer's relief was palpable. In fact, my lack of publications was held against me even earlier: one of the comments from my unfunded NSF DDIG was that, as I had no publications, I was an unknown quantity when it came to research. At the time, I felt the comment was unfair. After all, I was only a third year graduate student. With time, I have come to see the comment for what it was: a warning to me from the reviewer.
If I'm going to make it in this gig, I need to understand why, despite having the intention to publish, I've been so bad at it so far. And I think a lot of that boils down to learning a set of skills that are specifically relevant to publication, distinct from research. Coincidentally, as I was begining to write this post, this very topic of discussion was brought up by the esteemed Drs Isis and Drugmonkey. So, at the risk of repeating what has already been, here are my thoughts on things I've come to understand have hampered my ability to publish.
I do not find writing hard. I don't particularly like writing papers (or my dissertation), but I write well, and quickly, and generally produce first drafts that are pretty solid from a basic readability point view. I do hate making figures (I really really do), but as I become better at using ggplot, that's getting less of an issue. Yet writing has, so far, probably constituted a relatively minor portion of my time as a researcher. Why is that the case?
1) Re-learning how to write. This one only occurred to me recently, as a result of the discussion over at Drugmonkey's. It struck me that learning to write collaboratively, to accept and embrace criticism, to be willing to submit anything less than your best work for comment, is not taught when writing undergraduate or high school essays. You don't get a do-over for those: no matter how constructive the comments of your teacher, errors in style, argument, structure, analysis amount to lost grades. Certainly in the British University system, one has no opportunity to have one's written work critiqued and fix the errors before marking. Thus, succesful undergraduates are the ones who have learnt to go over their work with a fine toothed comb and anticipate all possible critiques. It makes sense they will be prickly in their response to criticism: any thing they missed or overlooked is a rebuke of their hard earned skills. I know people will respond "but you're not undergrads anymore". To which my response is: you were there too once. Recognise the patterns and help the trainee unlearn them. For what's it's worth, that process for me started outside academia, when writing website copy. My initial reaction to being critiqued was not great. I've learnt, finally, to view writing as a cooperative exercise, to embrace critiques and view my drafts as suggestions. It's taken a long time to get there.
2) Knowing when what you have is publishable. This, I think, is the one that stumped me for many side projects. I simply had no idea what "publication standard" was. My master's thesis was probably borderline publishable as it was at the time, yet I didn't know it. My first year rotation project in graduate school, I was told, was unpublishable. Yet a paper came out just a few years ago asking the same question, using the same methods, with the same conclusion, though looking at a different taxon. Maybe my project wasn't publishable as was, but it was clearly a damn sight closer than my rotation advisor thought. This, I think, is one where advisors are crucial. As graduate students in particular, I think we tend to assume our work is sub par. It takes encouragement to realise that no, our work is decent.
3) Publishing what you have, not what you want to have. I submitted five conference abstracts while in Grad school. All had good data, most of which will be part of the publications I will eventually get out of my dissertation. Yet, of the ones that would eventually be part of my dissertation, I wrote none of them up as I went. Why? Because I had a plan for the papers I wanted to publish, and until I had all the pieces of that plan, I wouldn't publish anything. Unfortunately, one of the pieces of that plan didn't come together until my last ten months in grad school. Thus, I delayed publishing results that were publishable until after everything was done. This was foolish.
4) Don't worry that your paper will be bad. If you have spent time developing your hypothesis, if you can argue your methods, if you have done your background reading (which, if you have defended your thesis proposal you should be able to do), your paper will not be bad. It may not be the best. It may only be worthy of a society level journal. That doesn't matter. It will exist, and it will be OK, Don't worry about some journal club somewhere tearing it apart. And remember that, at some point, you will find someone who will demolish a paper you have held as a paragon of scientific integrity. 5) Do not seek "accepted with minor revisions". Don't, it isn't worth the effort, Trust me, I've done it. I much prefer the paper I have that was accepted with major revisions than the one that was almost accepted as is. I am excited about my revise and resubmit. Peer review, as much as it can be jarring, is an occasion to make your paper better. "Major revisions" is just another round of editing.
6) Speaking of which: find mentors who will read and critique your drafts constructively. Reach out to a broad circle of people. Thank each person willing to read your draft. Remember you are the author, so have final say, but give each commenter a fair and judicious hearing.
7) Middle authorships are important. My advisor in grad school had few side projects to share with me. I carried the weight of all my research and my papers. This makes me proud of my dissertation, but being middle author on a lab paper early on would probably have made me more comfortable about publication. So mentors: involve your newbie trainees sufficiently in projects that they can be middle authors. It's a great, low stakes way for them to learn the arcana of publication. And trainees: god damn it, ask. Find some skill you can offer for a project and ask if you can be involved. Get that middle author paper.
8) Seek out and be grateful for collaboration. Two people can work faster on all aspects of a paper than one. You must do the heavy work of your dissertation and postdoc projects, yes. It does not follow you must do all the work, and do it alone.
9) Don't chase glam. Your first paper should be aimed squarely at a respectable journal in your field. Don't sell yourself short, but don't pin your hopes on a longshot, not until you have a few good pubs under your belt. Again, a published paper in a decent society journal is worth more than a CNS paper in prep.
To mentors, I would say this: none of this is obvious to your trainees. Nor will they learn it by osmosis. Talk to them, sit them down, explain the process to them. Demand drafts of them. Give them drafts to edit. This is the very definition of tacit knowledge. If you do not seek to make it explicit, you cannot expect your trainees to know it,

Wednesday, 20 August 2014

The many faces of Leviathan

In his treatise on the ideal form of government, the philosopher Thomas Hobbes articulated the idea of the State as an entity with a monopoly on the use of power, in particular, violence. The right to use such violence as was necessary to maintain peace was to be vested in the Sovereign, and a social contract between subjects and Sovereign would abdicate to the Sovereign all rights of the subject to determine themselves. Most strikingly, the Sovereign (a monarch, an aristocracy or a democratic group) could never be accused of injuring his subjects. Though Hobbes argued that his Leviathan (a state vested with absolute power) was preferable to a State of Nature he described as a war of All against All, it was never particularly appealing to those outside of power. Never more so then when the State wields its monopoly on power against its own citizenry. At such a time one may justly ask if an implicit social contract that is so far reaching is truly a sensible philosophy.
Ferguson, MO, has occupied a lot of my mental energy this past week. I was glued to twitter on the night of the first heavy SWAT response. As a white European man living in a rural area of the US, I feel that it is not my place to discuss the specificities of Ferguson. I have retweeted many of the observations made by African American and other people of color from around the US. This is their story to tell, not mine.
That being said, coming from a country with a mostly unarmed police force, the shooting of Mike Brown is a particularly jarring reminder that I am not in Kansas anymore. I can only view the gunning down an 18 year old unarmed man in the street as evil, cruel, and excessive act. Having lived for five years in Baltimore, I have learned a lot about the context of oppression of inner city black populations by the state in which these shootings and subsequent riots happen. I also have friends in law enforcement who have patiently shared their perspective with me, despite my strong a priori distaste for sanctioned police violence. I have come to realise that, in the context of a racist and oppressive system of institutions, these events end up playing out as a kabuki theater where roles are pre-determined by a greater narrative. It is difficult to see a way forward sometimes. I believe shit is fucked up.
There is a tendency for transatlantic comparison to occur whenever these incidents happen in the US. The fact is always brought up (as indeed I just did) that policemen in the UK  are unarmed. The resulting statistics from this are pretty striking. And yet, if you look at the UK police force's history of dealing with civil unrest, it's less lethal perhaps, but seems hardly edifying. In the 1970s and 1980s,  police charged striking coal miners with batons, severely wounding many. Towards the end of the 80s, the poll tax riots and protests were challenged by policemen on horseback riding into the crowds. When a crowd panicked at Hillsborough football stadium in 1989, the police's refusal to open the stadium doors led to the death of 96 people. The subsequent attempt by the police to cover up their action and smear the dead as drunken hooligans was only uncovered in 2012 following a public enquiry. Getting that enquiry set up took 20 years of campaigning by the survivors against an uncaring establishment. Those events were marked by the clear class distinction between those being attacked (working class men and women in the North), and those in power.
More recently, the Metropolitan Police (London's police force) has come up for repeated criticism for its handling of protests and anti-terrorism measures. There was the routine containing of globalisation protestors for hours in the street without access to water or toilets. There was the shooting of Brasilian plumber Jean Charles de Menezes on the Underground at point blank range by armed anti terrorism officers, despite a complete lack of evidence that he had anything to do with any bombings. No officers were convicted or even disciplined for this, though the police commissioner eventually resigned. In 2010 following the shooting of Mark Duggan by the police, rioting erupted throughout the country. In 2009, during anti-G20 protests, Ian Tomlinson died as a result of being struck by a police officer. The Met police initially tried to claim he died of natural causes, yet video footage soon surfaced showing the police violence. Eyewitness accounts directly contradicted the police narrative, which is a recurring theme throughout all these events.
In 1999 the McPherson report came out on the wake of the murder of Black British teenager Stephen Lawrence. The Metropolitan Police had made a mockery of the investigation, convinced that the perpetrator had to be black (they were both white), that the murder was not racially motivated (it was), and that Lawrence had been involved with drugs (he wasn't). The report accused the met police of institutional racism, a term I suspect few White British people fully understood. And despite that, Stephen Lawrence's killers were only convicted in 2012, after years of campaigning by Stephen Lawrence's mother. The met police still has a difficult time with ethnic minorities, and accusations of police brutality (particularly in custody). The fact most police officers are unarmed does not reduce the level of mutual distrust between police and some communities. The Leviathan in the UK may wear a slightly different mask, but its actions are surprisingly similar, even if the targets are somewhat different.
Yet, what Ferguson really reminds me of is the police in my other home country, France. In France, the police doesn't even really pretend to deal fairly with French citizens of North African descent in the suburban projects (banlieues) around the big cities. In fact, after several years of annually escalating unrest, a minister of the interior who would later become president famously declared he would clean out the suburbs with a pressure hose. In 2005, two children died while running into an electric fence to escape the police. Rioting, looting, protesting followed. France's dedicated, quasi military riot police, the CRS, rolled out in their distinctive black vans. CRS cops are armed with water canons, batons, tear gas, black visors and the more or less complete support of the State to do whatever they want. My mother was involved in the 1968 student uprising, and from her I learnt that if you see the CRS coming, you run. For days running battles raged in the suburbs of Paris and other major cities, while life continued as normal in the city centers. The comparison with the situation in the US is all the more chilling when you remember that French Algeria essentially operated under Jim Crow-like laws until the war of independence in the '50s. Again, the detail of Leviathan's actions are shaped by a State's history, but in the broad behavior there are repeating patterns.
I can see these patterns in all these places. When Leviathan strikes, it does so with brutality, and with a disturbing precision in its targets. Knowing the specific histories of oppression in France, the UK and the US, one can predict with a fair degree of confidence who will be on the receiving end of physical violence wielded by the State. Another pattern is therefore also clear. In all three cases, I and people like me are never the target. In all three countries, I can walk mostly unaware of Leviathan. I see these patterns affect others. If these others did not have means to make me see them, I might never even notice the cost of Leviathan, I might think this arrangement was for the greater good. I might think all was well in the best of all possible worlds,
I am glad that I do not. I am thankful that enough people have raised their voices, their camera phones, their keyboards so that I can see these patterns wherever I live. I do not yet know what I can do about them, but it is good not to be blind.

Monday, 11 August 2014


Since July, our lab has been running experiments non stop. The way our protocol works, this is an all hands on deck, round the clock situation, as it involves bottle feeding very young mammals by. The data we need requires lengthy surgeries on USDA animals. The procedures are sterile, the animals are intubated and have IV lines. The surgeries themselves take four hours. The success of the surgery is only known afterwards, when the electrodes are connected up to the EMG system. Prior to surgery, our electrodes must be built by hand, and then be sent off for gas sterilization as they cannot go through a standard autoclave. Other parts of our system are also made in house, and require testing for electrical faults. Between surgeries, tools have to be washed, packed and sterilized. None of the materials we use are easy to come by, many of them have lengthy lead times on orders and all of them are expensive. Suffices to say, there are many, many, MANY things that can go wrong in our experiments. And, after six weeks of solidly being part farm, part electrical shop, and part hospital, I can say with some confidence that almost everything did.
Among the things that went wrong, the worst was losing an animal in surgery. In this case, the dominant emotion is not frustration. It's sadness, anger, disappointment. As we had three young summer students from the medical school in the lab, all of whom where involved in the surgeries to some degree, the priority was making sure that they were ok. Loosing an animal in surgery is too serious a matter to focus on your frustrations with the science. And, because my PI is awesome, she knows this. Those events exist in a separate space from the other things that went wrong this summer. They are matter for sober reflection, and no matter how much you want to get data that summer, you pause when that happens, and figure out what you can do better.
However, there were myriad other things that went wrong, of greater and lesser importance. Electrode placement in surgery failed to yield adequate results. Intermediate cables broke and had to be resoldered, sometimes as a surgery in which that cable would be needed was progressing. An inaccurate channel map of all the connections meant that two whole EMG channels were wasted (my fault). The lab was not finished, meaning our lab server could not be set up, resulting in all the data being fragmented across multiple 3TB external hard drives. Tools had to be autoclaved during surgery. IV lines were ripped out. Animals stopped breathing in the middle of surgery. Injectible aneasthetics everyone swore would make our surgery smoother had only bad effects on our animals. A vomiting and diarrhea bug tore through all our animals one by one. A cable came partially unplugged, resulting in us losing half our EMG channels. An xray c-arm we'd already had repaired twice failed again. Every day started at 8 and ended at six, if not seven. Most weekends involved data collection of some sort. As the summer wore on, everyone's reserves were ground down. Everyone's patience began to wear thin. As one of the chief surgeons, I began to be concerned about my ability to do the surgeries. I was, and am, exhausted.
In such a situation, frustration quickly comes to dominate your feelings. Every thing that hasn't been done, every logistical snafu that comes from something having slipped through the cracks, becomes an issue. Surely, someone was supposed to be on top of it. Surely this had been mentioned three weeks ago. Surely we had agreed it would be done (just not by me). The productive response in these situations is to figure out how the situation can be fixed here and now. The frustrated response is to huff, to use a sharp tone, to bitch. In reality, the best you can hope for is that both will happen, the frustrated response to let off steam, the productive response to keep things moving.
The worst aspect of frustration is how it blinds you to simple solutions. After a few weeks of experiments like these, it is most tempting, when faced with a glitch, to reach for the explanations that involve people, not things or simple stochasticity. Thus days are lost remaking cables, rather than checking that all the cables of the set up are still plugged in. The solution that involves people, work, effort, not accidents, is more appealing to the frustrated mind grappling with how little control it has over the situation.
Dealing with frustration is hard. It requires calm and perspective, in rare supply when surrounded by screaming animals and beeping machines. This is why we can't do our research year round. During experiments, the best that can be done, I think, is to take small breaks when it all gets to much. Send the med students home early if you can. Cancel a day's data recording, if you need to. Be kind to each other. Make sure that night shift burdens are spared.
I am thankful that the two people in charge of personnel planning (my PI, and SuperTech), have a good eye for how everyone else is doing. On one particular day, SuperTech noticed that after a long surgery, I was a mess. My hands were shaking, my motor control gone, my mood frazzled and incoherent. After I messed up a (not life threatening) routine procedure, I think she went to find the PI. The PI sent me home (in a nice way). Sometimes, that's the best thing you can do.
Frustration is friction: energy wasted as heat. At the end of long experimental bouts, or long field seasons, energy is at a premium. Managing an exhausted, frustrated team takes tact and sensitivity. That's not something you realise until you experience it. I hope that, when the time comes, I will be able to look past my own exhaustion and frustration and make the right decisions for the people and the science in my lab.

Monday, 4 August 2014

The Stakhanovite tendency

When the former Soviet Union was at the height of its productivity war with the West to demonstrate the superiority of Marxist-Leninist forms of production over capitalism, a myth emerged of the worker Stakhanov. Aleksei Stakhanov was a miner who allegedly dug up 102 tons of coal in 6 hours (14 times his quota) (source Wikipedia). Soon, Stakhanov was praised throughout the USSR. His example was one to be emulated, for the greater good of the people, the Soviet Union, and the cause of Marxism-Leninism. Medals were awarded by the Party to workers who lived up to stakhanovite ideals. Men and women worked hard and long in fields and factories to win honour for themselves, their collectives and the nation. The aim was always to do more, do better, to beat the previous record set by the workers in your collective. Like many of the impulses that drove the early Soviet Union, the Stakhanovite movement was both impressive in its achievements and appalling in its costs. Many people lost their health, even their lives in their pursuit of Stakhanovite goals. Many more simply cheated, adding a dark twist to the suffering of those striving to achieve impossible targets.
Especially today, the nature of scientific research means that sometimes we have a huge amount of repetitive work (data processing) to do in a short period of time. This is sometimes unavoidable. The Stakahnovite tendency haunts us at such times. When we brag about how long our experiments are. When we build overly ambitious schedules despite the voice in our head whispering "this is too much". When we power through the night editing data files on coffee and beer, convincing ourselves we have a strict deadline no one is imposing but ourselves. We come to pride ourselves on our ability to do these tasks. "I spent 14 hours yesterday writing my third chapter" (never mind that the last third of what I wrote is almost unintelligible stream on consciousness). "I was up until 3am editing these video data for analysis" (never mind that I have a nagging suspicion the last dozen or so are less than rigorous).
The Stakhanovite tendency is ingrained, and difficult to budge. It is at its most dangerous however, when dealing with members of the research group who have not bought in wholesale to the ideology of sacrifice for science. When we apply it to ourselves, we mostly have ourselves to blame for not checking our own destructive behaviour. When we expect it of others in our lab, especially those whose backgrounds and career directions are different from ours, we are being exploitative, and fostering unnecessary resentments in the group.
Our lab group for the summer has accumulated a significant amount of data throughout a series of exhausting and complicated experiments. Much of the work, in particular the grunt work of feeding animals, cleaning and wrapping tools for surgery, building electrodes and generally keeping track of things has been done by our three amazing summer students and my colleague SuperTech. Our daily experiments require out of hours commitment, long hours and a willingness to go above and beyond. This is understood and accepted by all parties, and all of us, regardless of position in the lab, chip in where we can.
As the experimental run reaches a close, however, we are faced with the need to begin to analyse the data from the summer, in part to answer broad questions from the grant, in part so that the summer students can complete their research projects. In a lab meeting last week to discuss how best to organise the analysis of a summer's worth of data in a few days, I went into full Stakhanov mode. I explained how all the data we needed could be prepared in a weekend, and I suggested task distributions by project, regardless of size discrepancies between projects. One of the summer students (as I mentioned above, these guys have already gone above and beyond), exhausted and anxious, eventually was coaxed by my PI into explaining that he felt the division of labor was unfair, the expectations too high. He was right. There was no need for me to put forward the grueling schedule I'd suggested. A day or two more would not hurt. I was channeling my graduate school experiences of processing all my data in a few days, and it was unnecessary, and insulting to the effort everyone had already put in.
The Stakhanovite tendency is destructive precisely because it undervalues the work already done. It demands endlessly more sacrifice from people, often when they've already given more than was required of them. For our own sanity, we should check it in ourselves. In order to be decent human beings, we must never let it govern our relationships to others.

Tuesday, 29 July 2014

Perspectives and expectations

There's an interesting thing about the place I now work. Almost everyone who isn't faculty is from here. By from here, I mean from this state, and in most cases from this region. People have lived their whole lives within three hours drive of this small town, and in many cases, so have their parents and grand parents.
In contrast, almost no one is from the city I grew up in. And even people like me, who lived there long enough to almost qualify, have only been there for one generation. Furthermore, my city looks to the world. It's one of those places of which people say that's it's more similar to New York or Tokyo than to towns an hour away.
In graduate school, almost no one I knew was from the city itself (for complex, difficult and unpleasant socio-economic reasons). It was a private R1 institution (in fact, pretty much the R1 institution) in a heavily socio-economically deprived area. As a rule, places like that aren't so good on representing the local community.
So to be somewhere where most people's perspective is limited to the State, and even to an area of the State, is an adjustment. Well meaning efforts at improving diversity at the university come across as naïve and ham-fisted. Awareness of broader world issues is limited. Knowledge of either of my home countries (which are not particularly obscure places) is limited to stereotypes and, in some cases, gross falsehoods resulting from right-wing political discourses about the depravity and lack of freedoms in the old country. The oddest comment yet was when one of our summer students asked me how I felt about my home country having presumption of guilt rather than presumption of innocence. I was slightly baffled by this, as it was news to me.
In spite of this, everyone in the lab is very open to discussion about political and social issues. This could be tense, but I have to say that these are the most respectful and least awkward such conversations I've ever had. Which is good, as they tend to occupy much of the 5 hour surgeries we've been doing lately. The group mix covers several decades of age difference, several thousand miles (mostly due to me) of geographic distance, and a fair breadth of socio-political views on most issues.
Today was an interesting challenge of my assumptions though. In a conversation about gay rights, I mentioned the Stonewall riots. At least one of our summer students is involved in the local LBGT community as an ally, but even he had no idea what the riots where or how they related to the modern gay rights movement. More surprising to me was that when explaining the history of the riots, the students were amazed to discover that the police used to regularly raid gay bars in cities across the country. My advisor then reminded them that, when she was a child, there was nowhere in her home town for her mother and her African American friends to have coffee together.
In some ways, I guess I should be heartened that a new generation should be so far removed from that time that they would have no concept that such overt, state sanctioned discrimination should happen. On the other hand, I cannot help but slightly fear that such a degree of unawareness of where we have come from explains much of our erstwhile allies lack of urgency in joining us in the struggle for a better world.