Category Archives: science

The Molecular Ecologist: Using R to model the spatial distributions of species

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Environmental variation across the range of Joshua tree. Image via The Molecular Ecologist.

This week at The Molecular Ecologist, I’m showing how to use the popular open-source statistical programming language R to estimate species distribution models.

Species distribution models (SDMs) are handy any time you want to extrapolate where a species might be based on where you know it actually is. Maybe you’re trying to figure out where would be fruitful to do more sampling; maybe you want to know where your favorite critters probably lived back during the last ice age; maybe you want to know what regions will be suitable for your favorite critters after another century of global climate change.

Given how widely useful SDMs are, it’s very nice to be able to estimate them using multiple methods implemented within a single open-source framework. To get a taste of the capabilities provided by R and a select set of add-on packages, go read the whole thing.◼

Science online, two months to Snowbird edition

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Cecret Lake - Alta Utah Are you going to Snowbird? Photo by Al_HikesAZ.
  • This week at Nothing in Biology Makes Sense! We’re looking ahead to the Evolution meetings.
  • And, at ProfHacker: I review a book about teaching science.
  • Maybe! Does your brain know whether you’re reading a piece of paper or a screen?
  • Not that we couldn’t do a lot better. U.S. policies for reducing carbon pollution are a scattershot mess, but they seem to be working.
  • No, really. Why we should treat science and math literatcy more like basketball.
  • With a lot of money on the line. The U.S. Supreme Court heard oral arguments this week in a case that could decide whether it’s legal to patent a human gene.
  • So to speak. Even when you have all your publication-ducks in a row, how do you decide which ducks go first?
  • Yum! Scicurious review’s Mary Roach’s new book Gulp.
  • In a lineage this young, are we surprised? Human origins are turning out to be more of a mosaic than a clean-cut family tree.
  • No kidding. For more students to go into science careers, maybe there need to be more science careers?
  • Well, Earth-scale-ish. Kepler space telescope finds evidence of not one but two Earth-scale planets orbiting in another star’s “habitable zone.”
  • More on E.O. Wilson vs. math. Maybe what he really doesn’t understand is how collaboration works.
  • Aww. Zoobooks! The journey to field studies of lions in Kenya starts with a subscription to Zoobooks.

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I read a book!

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Scheikundeles / Chemistry class Chemistry lab. Photo by Nationaal Archief of the Netherlands.

It’s called Making Scientists: Six Principles for Effective College Teaching (buy it over on Indiebound). It’s about teaching science to undergraduates, which is a thing I’ve been trying to do, lately. And I wrote a review for ProfHacker.

In their new book Making Scientists: Six Principles for Effective College Teaching, (Harvard University Press, $24.95) Light and Micari argue that undergraduate education in the sciences should go beyond imparting a basic set of knowledge, and make learning science more like the experience of doing scientific research.

If teaching science to undergraduates is also a thing you do, may I suggest you go read the whole thing?◼

Science online, advice that doesn’t add up edition

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math outside Math, in the field. Photo by Wanda Dechant.

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Science online, plight of the honeybees edition

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Honeybees Bees. Photo by wondermac.

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Carnival of Evolution, April 2013

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Tomorrowland at Dusk What kind of sequencing capacity do they have in Tomorrowland? Photo by Big DumpTruck.

The April 2013 edition of the Carnival of Evolution is online over at Synthetic Daisies. This issue of the monthly collection of online writing about all things evolution-y is organized around the theme of the future of evolution—which looks to be full of exciting possibilities. There’s experimental phylogenetics and speculation about radio-sensing animals and species coming back from the dead, so maybe you should go peruse the whole thing.◼

Nothing in Biology Makes Sense: Making sense of pollinators’ role in creating new plant species

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Joshua tree flower closeup A Joshua tree flower. Photo by jby.

Over at Nothing in Biology Makes Sense! I’ve got a new post discussing freshly published results from my dissertation research on Joshua trees and their pollinators. I don’t have to tell you why Joshua trees are interesting, do I?

Joshua trees are pollinated by yucca moths, which are unusually focused, as pollinators go. Your average honeybee will blunder around in a flower, scooping up pollen and drinking nectar, and maybe accidentally pollinate the flower in the process. A yucca moth, on the other hand, gathers up a nice, tidy bundle of pollen in specialized mouthparts, carries it to another Joshua tree flower, and deliberately packs it into place. She does that because the fertilized flower provides more than a little nectar for her—she’s laid her eggs inside the fertilized flower, and when they hatch her offspring will eat some of the seeds developing inside it.

That’s pretty cool in its own right. But what’s especially interesting about Joshua trees, from an evolutionary perspective, is that they’re pollinated by two different moth species. And it turns out that the flowers of Joshua trees associated with the different moth species also look pretty different. The most dramatically different feature is in the length of the stylar canal in the pistil, the part of the flower that determines how the moths lay their eggs.

In the latest development, my collaborators and I tested for genetic evidence that Joshua trees pollinated by different moth species are isolated from each other. To learn what we found, go read the whole thing.◼

Science online, lupins for dinner edition

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Lupins Yum? Photo by Stephen Downes.

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Nothing in Biology Makes Sense: Making sense of the relationship between gut microbes and obesity

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Obese mouse, non-obese mouse. Photo via Nothing in Biology Makes Sense.

Over at Nothing in Biology Makes Sense, Sarah Hird discusses an attempt to suss out whether your gut microbes change when you’re overweight, or your gut microbes can make you overweight.

Historically, medical research has focused on pathogenic bacteria when trying to understand the relationship between human health and microorganisms. This makes intuitive sense – since pathogens make us sick – but our bodies host way more nonpathogenic bacteria than pathogens and they function in keeping us healthy. Our gastrointestinal tract has trillions of bacteria in it and much recent work has been trying to understand these complex communities. Mice are a common model for understanding human gut microbes and health. Enter Obie, the obese mouse (Figure 1, left) and Lenny, the lean mouse (right).

The new study demonstrates that bacteria cultured from the gut of an obese mouse cause normal-weight mice to gain weight when they’re fed a high-fat diet—and that the genetically similar mice without the bacteria can eat the same diet without becoming obese. You should definitely go read the whole thing.◼

Science online, selected swallows edition

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Cliff Swallow in flight Cliff swallow in flight. Photo by donjd2.
  • This week, at Nothing in Biology Makes Sense! Doing natural history like a Victorian—but with gigabytes of genetic data.
  • And, at the Molecular Ecologist: A tale of two Dryad submissions.
  • Speedy evolution in more ways than one. Cliff swallows living under highway bridges have evolved shorter wings—maybe because they help dodge oncoming cars.
  • Breaking! It’s possible to make science accessible without reinforcing sexist stereotypes.
  • Which, I would argue, is most of the time. When evolution and ecology happen at the same time.
  • Not the only way in which it’s fantastical. The paleofantasy of “alternative” medicine.
  • Step one: read good science writing. How to write good science.
  • Handy! Convert technical units of measurement into more comprehensible terms using Wolfram Alpha!
  • And why that makes the whole business suspect. Why proposals to resurrect extinct species are really all about Homo sapiens.
  • First, they came for the political scientists … The U.S. Senate decides it can ban the National Science Foundation from funding an entire field of research.
  • Related: who still does this? Why do we call it the “wild type,” anyway?

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