Category Archives: science

Science online, best model kit ever edition

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111/365 - You’re My Boy, Blue The whale today. Photo by djwtwo.
  • This week at The Molecular Ecologist: How to pick a programming language.
  • Also, why biologists still speak Latin. How the North American turkey was, indirectly, named after the Eurasian nation-state Turkey.
  • Not-bad news, everyone! Americans will, sometimes, vote for better funding of public universities.
  • Terrible news, everyone. The climate change prognosis is looking a lot worse.
  • No word about the squid, though. How the American Museum of Natural History built a life-size blue whale before anyone involved had actaully seen a whole blue whale, in two parts.
  • Yes, there’s oxytocin in nematodes. It’s called nematocin.
  • It’s just not as easy to see. Black people do, in fact, get sunburns.
  • Tiny pamphlets about abstinence? What do you do when a protected species is about to interbreed itself to extinction?
  • Go ahead, break a leg. (Not really.) Raising a baby doesn’t necessarily have to be bad for a woman’s bones.

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The Molecular Ecologist: Which programming languages should I learn for bioinformatics?

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Over at The Molecular Ecologist, Mark Christie runs down the considerations to take into account when you’re thinking about making the effort to learn a programming language — he focuses specifically on bioinformatics, but his points really apply for just about anything you’d do with a script.

Perl and Python programs are (typically) compiled each time before they run and they are often not compiled to the same extent as C and C++ (but see PyPy for Python). This means that C and C++ typically run faster and require less memory after a program has been completed. Like most things in life, however, there is a tradeoff in that C and C++ programs usually require more lines of code because there are more details that have to be specified in each program. Thus there is a tradeoff between time spent developing, writing, and debugging code and the time that the program takes to run through completion.

Planning your first bioinformatics project? You should probably go read the whole thing.◼

Dying young? Better live fast — if you’re an ant.

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Myrmica scabrinodis. Photo by Myrmecophilie.

Cross-posted from Nothing in Biology Makes Sense!

Among the many things I hope you’re thankful for — whether you’re U.S.-based and celebrating Thanksgiving this week, or you’re feeling generally grateful regardless of geography and time — you can add to the list the fact that you’re not an ant. Worker ants are essentially enslaved to the task of helping their mother, the queen, reproduce. Any individual worker is disposable, in support of that broader task of the whole colony.

And it’s not as though the workers don’t seem to be aware of this — to the extent that a worker ant can be “aware” — at some level. An experiment described in the current issue of The American Naturalist demonstrates pretty clearly that, when workers are injured, they take greater risks — as you’d expect if they’re trying to give the colony the greatest possible benefit from their shortened lives.

The study itself sound logistically tricky, and maybe a bit mean-spirited, but as an experiment it’s elegant. A team of Polish researchers started by going out into the forest to collect ants — Myrmica scabrinodis, a common European species — and setting them up in artificial colonies. In each case, the team set up pairs of artificial colonies with equal numbers of workers collected from the same natural source colony, and supplied these transplanted workers with a queen and some larval ants to tend. Which, apparently, the captured workers were perfectly happy to do after about a day of acclimation.

Within each artificial colony, then, the researchers injured half of the workers. They did this either by exposing the ants to carbon dioxide for an hour and a half, or by breaking off their propodeal spines — pointy projections from the rear-ward part of the ants’ thoraxes. Neither of these treatments left the workers unable to work, but they both have the effect of shortening their lifespans.

Within each pair of artificial colonies, then, the team chose one colony to present with a “risky” condition. All the colonies were connected via a PVC passageway to a small foraging arena where the ants could gather food. Risky conditions, in this context, were one of three possible variations on the basic colony design. First, there could be a much longer passage to the foraging arena; since, in the wild, more time spent outside the nest means more time vulnerable predators. Second, the passage could be heated up to a temperature that would be uncomfortable to ants. Third, the foraging arena might contain workers of a competing ant species — which were kept from actually attacking by a mesh barrier, but still able to interact with the ants from the experimental colony.

So, for each pair of colonies, one had a riskier path for workers to take to collect food. And in each colony within the pair, half the workers had been gassed or maimed. The collaborators allowed the ants a couple days to acclimate to the artificial colonies, then closed off the foraging arenas to capture the ants that were out collecting food, and tallied up how many were injured (individual ants were identifiable by dots of paint).

And, consistently across colonies and the three different kinds of risk, the foraging arena in the riskier colony of each pair contained a larger proportion of injured workers.

How this might actually work is beyond the scope of the experiment. It seems unlikely that an individual worker ant has anything like the train of thought: “Hmm. I seem to be injured. I guess I can walk through this hot tunnel to go find food, since the Colony needs me to, and I don’t have much productive life left anyway.”

So maybe the injuries the researchers inflicted on the workers made them poorer judges of risk — less able to detect the risky conditions, or less able to respond when they did. But the end result is the same, from the perspective of a whole colony: workers who are closer to death are more expendable, and they act accordingly.◼

Reference

Moroń D., Lenda M., Skórka P., Woyciechowski M. 2012. Short-lived ants take greater risks during food collection. The American Naturalist. 180:744–750. DOI: 10.1086/668009.

Science online, antediluvian itch edition

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Coral Photo by Romain Bochet.

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Knowing what I know now: Let’s make it a carnival!

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County Fair Photo by Justin in SD.

Cross-posted from The Molecular Ecologist.

So, not long after I posted my advice for grad school, and said I hoped that The Molecular Ecologist ultimately collect similar posts from a whole bunch of people, Scicurious e-mailed to point out that there’s a thing we do in the blogosphere when we want to collect a bunch of posts on a particular topic: we hold a carnival!

So the plan is now that The Molecular Ecologist will host a “Knowing What I Know Now” carnival on Monday, December 10, and if you’re working in science at any career stage, you’re invited! All you need to do is write up a few things you wish you’d known in your previous career stage that would’ve helped you prepare for your current career stage. (i.e., grad students, write about undergrad; postdocs, about grad school; and so on.) In my original post I may have over-emphasized the academic career track — we’d love to hear advice about preparing for work in industry, or with a non-academic nonprofit, or in government, too.

If you have a blog, write up your advice as a post and either e-mail the link to me or post it in the comments below. If you don’t have a blog, we’ll be happy to post your contribution at The Molecular Ecologist — again, e-mail me to set that up. Please send all your links and post contributions by Saturday, December 8, and I’ll pull them together for the carnival post on the 10th.

Ready? Set? Start your advice-ing.◼

The Molecular Ecologist: Knowing what I know now (about grad school)

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2007 - Day 113 - This England Tea. It’s important. Photo by Jonathan_W.

In what I hope will be the start of a whole series of posts about careers in science, I’ve taken a stab at writing down what I wish I’d known to do (and what I’m glad I did) during graduate school, over at The Molecular Ecologist:

I can’t claim to have any blinding new insights — my own career is very much still under construction. But I’ve been interacting with a number of freshly-arrived graduate students this semester, and I’ve found myself thinking, after conversations with them, about what I might have done differently back when I was looking ahead to five (oops, six) years of grad school — and about what I did that worked out pretty well.

And no, I will not apologize for the choice of videos I’ve used to illustrate the complete post.◼

Science online, what’s in your genome? edition

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Cape Ground Squirrel (Xerus inauris) Cape ground squirrel. Photo by Ian n. White.

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Evolve the vote?

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Barack Obama in Lima - November 2nd President Obama at a rally in Lima, Ohio, on Friday. Photo via Barack Obama.

You may have heard that there’s an election happening in the United States today. It’s been ten months of “campaign season” since the early Republican party primary elections in Iowa and New Hampshire, and the two presidential campaigns and their various allies have raised and spent going on two billion (billion!) dollars on advertising and campaigning and probably also consultants’ fees.

This seems like an awfully expensive and inefficient way to choose someone to run a government, which is to say an awfully expensive and inefficient way to work together to decide upon and achieve common goals. Winston Churchill famously noted that democracy is the worst form of government “except all those other forms that have been tried from time to time.” But Churchill was really only talking about democracy in comparsion to other human forms of government. The living world contains all sorts of examples of individuals coordinating their actions for mutual benefit, and none of them need political action committees to do it.

Is there a better approach to group organization somewhere else on the tree of life? Let’s consider a few options:

Flock of starlings Starlings flocking together don’t communicate via attack ads. Photo by t.klick.

Flocking: Many animals forage and travel in groups that coordinate their movements. This may be best studied in birds: individuals within the flock watch and react to other nearby individuals, which lets them spend less effort watching for predators [$a] or finding food [$a].

This seems like it might have an obvious application to human government — we’ll just all agree to take our cues from the people nearest us to decide whether we need to subsidize agriculture or preemptively invade an oil-producing nation. Actually, now that I think about it, this sounds pretty much like what we’re doing already.

Dominance hierarchy: Many animals establish some sort of hierarchy within social groups, which decides who gets precedence in conflicts over food, or preference for mates. In wolf packs, for instance, social rank seems to be strongly related to age and reproductive status [$a], with relative ranking mediating food sharing or division of labor within the pack.

Wolf Noble-looking, sure, but no basis for a system of goverment. Photo by Tancread.

Unfortunately for human governance, dominance within wolf packs is structured by familial relationships — so it’s not going to translate very well for decision making at any level greater than individual precincts, or maybe individual school districts in some of the more rural parts of the country. Which is just as well, because I don’t particularly want to share this elk I’ve just caught. Mmm, elk.

Quorum sensing: Many species of bacteria change their behavior and activity when they’re in big groups [PDF]. To achieve this, individual cells produce signalling molecules at a predictable rate. As they detect more signalling compound, they can “know” that there are more cells of their species nearby, and can begin to do things that only make sense when there are lots of cells in one place. Different bacterial species use this approach to “decide” whether to begin a growth phase that harms an infected human, to start making chemicals that kill off competitors, or to generate bioluminescence for squid.

So, what would government by quorum sensing look like? Well, clearly we’d just all gather at some location, and, when there were enough of us present, we’d build a bridge or start a school or whatever it is that needs doing. I foresee no complications whatsoever with this approach.◼

Seriously, though, people. If you’re a U.S. citizen, you should go find your fucking polling place, and please vote Sensible.

References

Clark, C. and M. Mangel. 1984. Foraging and flocking strategies: Information in an uncertain environment. American Naturalist 123:626–641. DOI: 10.1086/284228.

Krebs, J., M. MacRoberts and J. Cullen. 1972. Flocking and feeding in the great tit Parus major-an experimental study. Ibis 114:507–530. 10.1111/j.1474-919X.1972.tb00852.x.

Mech, L. D. 1999. Alpha status, dominance, and division of labor in wolf packs. Canadian Journal of Zoology 77:1196–1203. DOI: 10.1139/z99-099.

Miller, M. and B. Bassler. 2001. Quorum sensing in bacteria. Annual Reviews in Microbiology 55:165–199. DOI: 10.1146/annurev.micro.55.1.165.

Powell, G. V. N. 1974. Experimental analysis of the social value of flocking by starlings (Sturnus vulgaris) in relation to predation and foraging. Animal Behaviour 22:501–505. DOI: 0.1016/S0003-3472(74)80049-7.

Waters, C. M. and B. L. Bassler. 2005. Quorum sensing: Cell-to-cell communication in bacteria. Annual Review of Cell and Developmental Biology 21:319–46. DOI: 10.1146/annurev.cellbio.21.012704.131001.

Science online, ovulate the vote edition

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Voting Apparently there’s an election coming up. Photo by KCIvey.

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