Queer in STEM’s first results! Who participated?

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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

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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

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Honeybees with a nice juicy drone Photo by dni777.

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

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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

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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.

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The Molecular Ecologist: Got code? Share and enjoy!

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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.◼

Science online, heatmaps and actual heat edition

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[DSP] May 18: Heat Wave Photo by jo3design.

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The Molecular Ecologist: Making heatmaps in R

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Image by Arianne Albert via The Molecular Ecologist.

Over at the Molecular Ecologist, guest contributor Arianne Albert walks through how to make heatmap figures in R.

Heatmaps are incredibly useful for the visual display of microarray data or data from high-trhoughput sequencing studies such as microbiome analysis. Basically, they are false colour images where cells in the matrix with high relative values are coloured differently from those with low relative values. Heatmaps can range from very simple blocks of colour with lists along 2 sides, or they can include information about hierarchical clustering, and/or values of other covariates of interest. Fortunately, R provides lots of options for constructing and annotating heatmaps.

I’ve personally used heatmap graphics for visualizing population structure in a sample, or linkage disequilibrium along a stretch of genetic sequence, but I haven’t done anything very complex. Arianne’s examples use a data set that’s freely available on Dryad, and she includes a lot of step-by-step detail to build up complex figures—if you’re going to be visualizing some microarrary results or metagenomics data any time soon, you should read the whole thing, and probably bookmark it.◼

Science online, sugar-frosted peer review edition

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Cereal Photo by Shaun Bascara.

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