Tag Archives: Linkonomicon


Created by Josh Witten using Inspirograph (by Nathan Friend)

Created by Josh Witten using Inspirograph (by Nathan Friend)

For folks of a certain age (ie, approximately my age), set your “Nostalgia” dial to 11. Nathan Friend has created an addictive, online version of the spirograph called Inspirograph. Enjoy.

According to Friend, a mobile app is in the works.

HT: Brian Kelly and Sheila McNeill

Deep Pterosaur Breaths

I cannot begin tell you how excited my children will be to learn that scientists think* giant pterosaurs may have breathed in a similar way to crocodilians when they get home from school today. Read Brian Switek’s explanation of the newest research at National Geographic Phenomena.

*Geist, N. R., Hillenius, W. J., Frey, E., Jones, T. D. and Elgin, R. A. (2014), Breathing in a box: Constraints on lung ventilation in giant pterosaurs. Anat Rec, 297: 2233–2253. doi: 10.1002/ar.22839

“James Watson deserves to be shunned”

The phrase “must read” gets used too lightly. In this case, however, I must insist you read Adam Rutherford in The Guardian. Rutherford summarizes why we should respect the scientific discovery of James Watson, why we should shun the failed humanity of the man, and why this is far from a unique problem in the history of science.

Here’s our challenge: celebrate science when it is great, and scientists when they deserve it. And when they turn out to be awful bigots, let’s be honest about that too. It turns out that just like DNA, people are messy, complex and sometimes full of hideous errors. – Adam Rutherford

HT: Alok Jha


Rose Eveleth, editor at The Atlantic, spent the last few days targeted by threats and abuse for being the first to say the same thing we did, but being a woman while doing so.

Today, she came back with a ridiculously good article – “Why No One Can Design a Better Speculum” – on the racist/misogynist history of the despised speculum and why we’ve been unable to substantially improve on the basic design for 150 years:

One might expect our modern spirit of innovation and disruption to turn its eye on the speculum. Surely something invented so long ago, under such dubious circumstances, could use an update. And many have tried. In the past 10 years, new designs for the speculum have continuously cropped up, only to fade away again. But while medical manufacturers continue to improve the design in little ways, there has been no real contender to displace the duck-billed model. The speculum’s history is inextricably linked to extreme racism and misogyny. But for all that, it just may be the best design we’re ever likely to have.
Rose Eveleth, The Atlantic

The article does include images of specula and technical illustrations of female anatomy, which may not be considered “Safe for Work” in your workplace.

Would you outsource your gel to a gel-informatician?

Sean Eddy explains why sequencing is replacing many older assays, and why biologists need to learn to analyze their own data.

“High throughput sequencing for neuroscience”:

If we were talking about a well-defined resource like a genome sequence, where the problem is an engineering problem, I’m fine with outsourcing or building skilled teams of bioinformaticians. But if you’re a biologist pursuing a hypothesis-driven biological problem, and you’re using using a sequencing-based assay to ask part of your question, generically expecting a bioinformatician in your sequencing core to analyze your data is like handing all your gels over to some guy in the basement who uses a ruler and a lightbox really well.

Data analysis is not generic. To analyze data from a biological assay, you have to understand the question you’re asking, you have to understand the assay itself, and you have to have enough intuition to anticipate problems, recognize interesting anomalies, and design appropriate controls. If we were talking about gels, this would be obvious. You don’t analyze Northerns the same way you analyze Westerns, and you wouldn’t hand both your Westerns and your Northerns over to the generic gel-analyzing person with her ruler in the basement. But somehow this is what many people seem to want to do with bioinformaticians and sequence data.

It is true that sequencing generates a lot of data, and it is currently true that the skills needed to do sequencing data analysis are specialized and in short supply. What I want to tell you, though, is that those data analysis skills are easily acquired by biologists, that they must be acquired by biologists, and that that they will be. We need to rethink how we’re doing bioinformatics.

I would add this: it takes some time to learn, but in the end it’s not that hard, people. Students in chemistry and physics routinely learn the requisite skills. We need to educate biologists who expect to do programming, math, and statistics.