A Playful Tone

Like a lot of my fellow early-stage grad students, I just submitted an application for a grant from the National Science Foundation. It’s a curious grant; more like a college application than your typical description of a research project in search of funding. Applicants aren’t bound to actually perform the research that they propose, and where ordinarily you might be prompted to include a list of publications, presentations, and accolades, instead this application includes a personal statement.

Here’s what a lab mate wrote on the personal statement I asked him to review: “There is a playful tone to your writing.” Coming as it did on the heels of a critique of the preceding paragraph, and a rejoinder to pay at least a little attention to the prompt, I don’t think he meant it in a good way.

It’s true. I admit it. There is a playful tone to my writing. I wrote the essay in the spirit of a college application, in hopes of being liked. I aimed for a voice, a confident and fun-loving one, instead of just a list of achievements and accomplishments. I told a story about my mentor in college, and another story about the Science Question Box in a classroom I volunteered in, and I was only narrowly dissuaded from telling a third story about a girl I met at a dance performance. The question is, was the playfulness out of place?

I hope not. I hope there’s room for a light-hearted, fun-loving approach to science in the highly competitive world of research, because that’s how I seem to be wired, and that’s where I would like to work. I guess, this time, the funding committee will decide.

What I’ve been reading

I love this introspective post by Robert Krulwich on what it means to collect a ton of data about yourself, and whether that’s the same as being observant.  Myself, I tend to side with the poets and with Bill Bryson. (H/T Ed Yong)

“Numbers are really the only reason you’re writing your paper, and you don’t want your readers to think that you’re into something as lame as words”  –Adam “you don’t write like a scientist” Ruben, whose Experimental Error blog at Science I can stand to read only one post at a time.  He’s also the author of Surviving your stupid, stupid decision to go to graduate school, which I have avoided on principle; I’m saving it for a crisis.  Possibly the one that happens when my love-affair with words is uncovered.

I’m enjoying the Wellcome Trust’s series on scientific writing that science writers admire.  It’s good to hear from experts on how to do a thing well.  If you’re in the UK or Ireland and have any interest in science writing, consider submitting a piece to their contest!  I’m told there is a prize.

And on the lighter side Scicurious’s jumprope rhymes: possibly worth getting a Twitter account for.

Some like it hot: temperature-dependent sex determination and sea turtle conservation

Sea turtles are among the most charismatic of megafauna.  They have fans everywhere, and more than their share of outreach programs designed to make more fans. Even locals who don’t much see the appeal can tell you that turtle ecotourism is big business.

And it’s not hard to see why.  Sea turtles are one of conservationists’ big success stories. Almost extinct before anyone even noticed, their numbers plummeted in the face of conservation efforts, recovering at what seemed the last possible minute thanks to heroic efforts and one important discovery about their physiology that came not a moment too soon.  The story of the Kemp’s ridley sea turtle, at one time the closest to the brink, is a story of science at work in real time.

At the beginning of the 20th century, when Kemp first put his name on the species, female Kemp’s ridleys flocked to beaches by the tens of thousands, laying their eggs all at once in a phenomenon known as arribada, or arrival. But humans caught on to this, and thanks to a brisk trade in turtle eggs, not to mention the help of other predators, the arribadas had disappeared by the time the Endangered Species Act was passed.

In 1977, Mexican and American wildlife agencies began a collaboration to protect nesting habitat at Rancho Nuevo, a park near the border that was the last known nesting site for Kemp’s ridleys. The conservationists knew that if they left nests where they were laid, they’d lose eggs to raccoons, foxes, and opportunistic humans. So when beach patrols found eggs, they dug them up and removed them to either nest areas near a base camp and inside of a fence, or Styrofoam boxes filled with sand.  Around hatching time, in a move that must have looked very strange to anybody not in on the reasoning, researchers allowed the hatchlings to crawl down the beach into the ocean, then scooped them up with nets to raise in captivity and release after about a year. This was called head-starting, and the thinking behind the nets was that females were more likely to return and lay eggs on beaches they had successfully imprinted on.

Researchers didn’t know, until head-started females returned to lay their eggs, how many females and how many males they were raising. It’s hard to tell the sex of hatchling sea turtles; they keep the relevant organs inside a shell, and at such a young age their blood hormone levels are not very high.  After they disappear into the ocean, it’s some years until females reach maturity and return to lay eggs, and many hatchlings don’t make it so long. Sea turtles are difficult to research in general: there aren’t many of them, they live most of their life cycle well out of the reach of land-bound humans, and if you want to study their hatching, you had better be prepared for a swashbuckling adventure from a pirate novel, racing to find buried treasure deposited on the beach at night before a poacher snatches it up. For the most part, researchers incubating eggs for release into the wild had to rely on the findings of studies of captive populations (like the Cayman Turtle Farm), because to count sex ratios of their own hatchlings would mean sacrificing precious live turtles.

Researchers knew, from a paper published in 1979, that sex determination in turtles (as with other reptiles) depends on temperature. Instead of being genetically determined at conception, as sex is for humans, birds, and other chromosome-dependent species, sex among turtles is determined by the temperature at which the egg is kept.

To say that a trait as fundamental as an organism’s sex can come from outside factors like the temperature sounds crazy.  It cuts to the heart of the genes-versus-environment question in development (the question being, “which is more important?” and the answer being, “it appears to depend on what trait you measure”). Fortunately for turtle researchers, the concept of temperature-dependent sex determination had been floating around evolutionary biology circles for some two decades, in such strange and wonderful organisms as the nematode, and the orchid, and evolutionary theories on the benefits of temperature-dependent sex determination (or TSD) abounded.  Unfortunately, the pivotal temperature, at which an even number of males and females develop, differed from species to species, and for sea turtles like the Kemp’s ridley, no one knew the key temperature.

It was only after about six years of head-starting that researchers could even begin to determine the pivotal temperature; they needed to wait for adult females to return, then determine using some careful statistics just how many males and females they had released some years before.  In 1988, Donna Shaver, a ranger at Padre Island National Seashore, published the results of about ten years’ worth of study on head-started hatchlings’ sex ratios, identifying the pivotal temperatures.  Over 30.8 C (roughly 87 degrees F), all of the hatchlings turned out female; under 29.0 C (87 F) they all turned out male. This was a terrifyingly tiny temperature range; it was lucky that artificial hatching and head-starting efforts had produced any males at all. This publication roughly coincided with the lowest Kemp’s population (in 1985, just 518 wild females nested), and knowing how to produce a natural sex ratio was key to conservation and repopulation efforts.

Nearly thirty years later, we still don’t know exactly what gene or network of genes in turtles determines sex in response to temperature. There may even be different pivotal temperatures for different subpopulations within the species that nest on different beaches. Although the head-starting program was shut down amidst debates about its cost-effectiveness just ten years after it began, the practice of moving nests to more protected areas until they hatch is still widespread.  And nowadays, when nests are re-located, volunteers take care to move the eggs quickly, to avoid placing them on hot sand or in direct sun, keeping conditions as natural as possible. While the Kemp’s ridley is still on the critically endangered list, it survives; we have the work of conservationists to thank for that.

For one more thought on temperature dependent sex determination: maybe it killed the dinosaurs.  I ask you.

Bioinformatics and the importance of curation

I recently finished a class on bioinformatics, the study of how best to use all the information scientists have accumulated and are accumulating in databases scattered around the world and web. And there’s a lot of information out there. Sometimes you hear the word “inventory” used to describe massive studies that characterize a lot of cellular components at once, as in, at some point in the future we will have a complete inventory of all proteins in all cancer cells, or stages of embryonic development, or what have you. I have to confess, I always picture an attic full of boxes, with structures and sequences and expression patterns, all minimally labeled, gathering dust.

Huge aggregations of information are scary.  Even just in one database for just one field of study—say, the NCBI website—even that tiny slice of All The Knowledge in the World makes us face that no one person will ever be able to assimilate it all. My feelings about bioinformatics are a lot like my feelings as a child, when I realized I would never be able to read all the books in the world: a crestfallen sense of having to miss out on something really, really interesting.

And at this point, maybe everyone is missing out. Even the authors of big-data studies, say, microarrays that assay expression levels of every gene in the genome in disease and non-disease tissues, can’t follow every lead to its source; often a few differently-regulated genes get followed up, but the rest just get put out there for others to work with. Sometimes I suspect that we (that collective, Internet-era “we”) have all the information to answer any cell-level biological question we could ask, but no idea of what the questions will be or how best to frame them.

One of the solutions to this problem is data mining—enlisting a computer’s help to sift through the masses of information with a program that looks for connections a human might see, if a human had the time and brainpower. Reading up on the art of data mining, I stumbled across a company called Narrative Science with a novel idea on how to present the results of data mining. Instead of making graphs from data, it makes sentences or even short passages, computer-generated but composed so that they read like something a human wrote. The company calls it a novel kind of visualization.  I think it’s absolutely brilliant, both as a way forward for handling a huge amount of information, and for the amount of cleverness that must have gone into programming a computer to take scores from a game and generate something like this:

WISCONSIN appears to be in the driver’s seat en route to a win, as it leads 51-10 after the third quarter…

As I’ve mentioned, I like my science in story form; decontextualized data, however useful they may be, are automatically less compelling to me.  So I’m glad that, in this age when the gestalt seems to be moving from the longform newspapers of the past to the Twitters of the future, that there’s still some consensus that narrative is a good vehicle for understanding the world.  According to some neuroscientists, perhaps it is the best vehicle.

When I think it over, I realize that nature has, or is, exactly as staggering a dataset as anything they’ve got at NCBI, with considerably more information much better encrypted. People have been trying to extract laws and trends from it for generations. All we’ve accomplished with our microarrays and our high-throughput proteomic studies is removing one step between the framing of a question and finding out the answer. Plenty of work of interpretation and meaning-making remains to be done.