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.