Category Archives: science

Science online, butterflies lost, found, and drawn edition

Posted on by
2008.11.28 - Heliconius melpomene Wallace didn’t collect this one. Photo by jby.
  • This week, at The Molecular Ecologist: In some viruses, mutation rates may be shaped by simple population dynamics.
  • And, at Nothing in Biology Makes Sense! Do African herbivores run for their dinner, or for their lives?
  • Bookmarked! A step-by-step guide for getting started with Github.
  • What is this, 1920? No, we humans haven’t freed ourselves from natural selection.
  • Because where else would it want them? Here is an insect with gears in its legs.
  • Good news: they’re nothing new. Bad news: they’re nothing new. A brief history of human fretting about pimples.
  • Found by a seventeen-year-old, too. Some butterflies collected by Alfred Russell Wallace, then apparently lost in a fire, have turned up in Oxford.
  • Yep, they have it. The latest approach for reconstructing past environmental condition involves whales’ earwax.
  • And how they link to animals’ physiology. A nice description of plant immune responses.
  • Eyeing the exits is never a good sign for the thing you’re exiting. No, PhDs looking at non-academic careers is not a sign that we should make more PhDs.
  • Vladimir Nabokov: He could write, he could catch butterflies, he could handle a colored pencil a little.
  • “She was a professor?” Yeah, but she was an adjunct.

◼

Nothing in Biology Makes Sense: Your dinner, or your life?

Posted on by
2010 076 Masai Mara b 24 Photo by ngari.norway.

Over at Nothing in Biology Makes Sense!, I’ve written about a new study that tries to disentangle conflicting sources of natural selection to determine whether big herbivores like antelope, zebras, and ostriches have evolved to run because they’re always running away from predators.

An antelope’s frame is under more demands than evading cheetahs—it also needs to travel long distances to follow food availability with the shifting rainy season. In fact, the North American fossil record suggests that big herbivores on that continent evolved long legs for distance running millions of years before there were predators able to chase after them. And then again, not all predators run their prey down; lions, for instance, prefer to pounce from ambush.

To find out whether gazelles are running for their lives, or running for dinner, go read the whole thing.◼

The Molecular Ecologist: Mutation rates shaped by population dynamics

Posted on by
Polio virus (picornavirus) Photo by Sanofi Pasteur.

Over at The Molecular Ecologist, I have a new post up discussing an interesting new modeling paper. It suggests that, for some viruses, variation in the rate of evolutionary change may be driven not by selection imposed by their hosts, but by the dynamics of the viral population within, and spreading among, host individuals.

Viruses based on RNA, as opposed to DNA, generally have very high mutation rates—in part because the process of replicating RNA is more error-prone than DNA replication. But there’s also tremendous variation in the substitution rate between different RNA viruses, even between populations of closely related viruses.

To find out how simple population dynamics could shape this wide variation in substitution rates, go read the whole thing.◼

Science online, home-brewed edition

Posted on by
Brewing Coffee with Light Photo by CoffeeGeek.
  • Queer in STEM update! A preliminary look at who participated in the online survey.
  • This week at the Molecular Ecologist: Auto-magically manage your analytic software with Homebrew.
  • And, at Nothing in Biology Makes Sense! You’re a scientific society with a financial surplus. How do you spend it?
  • In-depth, that is. How to go about reading a scientific paper.
  • Individuals aren’t averages. But … don’t averages have predictive power? Why psychological studies can’t tell you how to live.
  • Get your head out of the sand and invest in solar. We might beat climate change by innovating, but we won’t beat it by denial.
  • Attention spermologers. The emerging scientific value of Google’s Ngram viewer.
  • More than grants, more than grad students, more even than the sweet respite of tenure. What faculty want is time.
  • Also, less than English. Eek. Out of all the STEM fields, undergrad biology degrees earn the lowest starting salary.

And here’s some lovely video: footage of honeybee mating—taken in flight!


◼

Queer in STEM’s first results! Who participated?

Posted on by
Queer in STEM participants, sorted by gender identity and sexual orienation. Image via Queer in STEM.

I’m happy to announce that the two of us at the Queer in STEM study have finally found some time to put together our first report of results from the online survey. It’s a look at who participated—their identities, where they’re living, what kind of scientific work they’re doing.

When we closed sampling at the end of July, we had responses from 1,443 people. Those folks have given us a first look at a kind of diversity that isn’t well understood in scientific workplaces. Go have a look for yourself, and keep an eye on the study website for future updates, which will come out as often as we can pull them together.◼

Postdoc in genetics of complex traits

Posted on by
2012.10.22 - Medicago truncatula Your new favorite plant? Photo by jby.

Do you like evolution, genetics, and evolutionary genetics? Would you like to think of things to do with a whole lot of genetic data and a flagship model legume? Well, my boss, Peter Tiffin, is looking for another postdoc. Here’s the post description from EvolDir:

I have available a post-doctoral position to work on association and evolutionary genomics of the model legume Medicago truncatula. Collaborators and I have recently collected genome sequence for > 200 accessions and have used these data for GWAS and population genomic analyses. We are currently working to refine our understanding of genomic variation segregating within this species and are particularly interested in the evolutionary genetics of the symbiosis between Medicago and Sinorhizobia. The successful applicant will have considerable freedom to develop research in their area of interest.

The deadline for submissions is 15 September 2013, so get in touch with Peter pronto if you’re interested. (See the full ad for contact information and the application package requirements—it’s standard stuff.) Benefits of the position include working with population genomic data from the cutting edge of current technology in a collegial lab with some very smart people (and me) in the midst of a fantastic community of biologists at the University of Minnesota—as well as living in the Twin Cities, which are empirically awesome. Yes, even in winter.◼

Science online, cross-country flight of the honeybees edition

Posted on by
Honeybees with a nice juicy drone Photo by dni777.

◼

Nothing in Biology Makes Sense: For species delimitation, size matters

Posted on by
Shewanella Scanning electron micrograph of Shewanella putrefaciens. Photo by EMSL.

This week at Nothing in Biology Makes Sense!, Sarah Hird explains a new theoretical study proposing that species concepts are hard to define for microorganisms not because just because they reproduce asexually and trade genetic code like playing cards … but simply because they’re small and numerous.

Specifically, the product of mutation rate and carrying capacity (uK) needs to be below a certain threshold for species to form. This is because there needs to be a small amount of variation relative to the amount of niche space available or no clear “best” type will emerge that can outcompete all the other types quickly enough to become established. If mutation rate is high, there are too many available types. If carrying capacity is high, there is no way to limit who’s there at all. Many other things are happening with this paper, but their big conclusion, put plainly, is that if there is too much variation, differentiation cannot occur.

If that sounds as freaky to you as it does to me, you’ll want to go read the whole thing.◼

Science online, safety not defined edition

Posted on by
Tomatoes Are better mass-market tomatoes on the horizon? Photo by rachelandrew.
  • This week at the Molecular Ecologist: Introducing a new repository for useful snippets of code.
  • Yum. Modern genetic methods and old fashioned cross-breeding may yet make supermarket tomatoes tasty.
  • Selection is selection. An evaluation of genetically modified organisms, from an evolutionary biology perspective.
  • God only knows what’ll happen to NSF. The “sequestration” budget cuts are wreaking havoc at NIH.
  • Viral silliness. In which a marine biologist extensively objects to Buzzfeed.
  • With video! NASA’s plan to capture and sample an asteroid.

◼

The Molecular Ecologist: Got code? Share and enjoy!

Posted on by
Fall 2011 Student Hackathon Coding Coding is better when done together. Photo by hackNY.

Over at the Molecular Ecologist, Kim Gilbert announces a new initiative, the Molecular Ecologist code snippet repository. It’ll be a place to put bits of useful code that wouldn’t warrant their own publication as a package or program, but would still be helpful to other biologists:

Do you have a script you regularly run to convert between data formats? A quick and easy way to run a certain analysis? Making a common figure for a given type of data? If you’re willing to share your code, we’ll put it online for public access with credit to your name.

To find out how to submit your snippets, go read the whole thing.◼