Just in time for Turkey Day – the lowdown on bird flu

With Thanksgiving coming this week, it seems like a good time to talk a little bit about the impending apocalypse, delivered unto us by poultry. In other words: avian influenza.


Avian influenza (AI) is a virus with two main biological components – the hemagglutinin (which binds the virus to a host cell ) and neuraminidase (which allows it to be released from a cell ). So when you hear H5N1 – the numbers refer to specific strains of hemagglutinin and neuraminidase that vary in their pathogenicity. Wild aquatic birds (ducks, geese, gulls and shorebirds) are the natural host of avian influenza. It is very common for these birds to have one (or more) strains of AI over the course of a year – they don’t die and barely even have symptoms. “Low pathogenicity” AI strains are no big deal to aquatic birds and when they can spread to poultry, the chickens and turkeys have mild symptoms. On the other hand, “high pathogenicity” AI strains can arise from low pathogenicity strains from within domesticated poultry and are highly lethal to chickens and turkeys. The strains most likely to do this are H5 and H7 – these are the strains you hear about in the news that result in massive poultry culls. These strains can spread back to wild aquatic birds, who – if you’re a hunter or birdwatcher know – migrate across entire continents in large flocks. These strains can also spread to humans who are in direct contact with sick, high pathogenicity poultry.

SO FAR, avian flu virus has rarely (but not never) been transmitted from human to human (i.e., airborne). This is good, because the death rate of one H7N9 AI strain in China in 2013 was around 33%. Slightly worryingly,  this strain still persists there – mutating all the while. The doomsday scenario that the WHO and CDC are worried about is a high pathogenicity strain mutating such that it becomes airborne – a scenario that could put tens of millions of people at risk. I suppose a secondary doomsday scenario would be high pathogenicity AI infected ducks dropping deadly high pathogenicity AI duck turds on our heads as they fly across the country. (Did I just come up with the plot for a horror/comedy movie? I await your call, Hollywood.) The USDA is monitoring cases of high pathogenicity AI in wild North American waterfowl and they’re specifically watching an H5 strain that showed up here last year.

The internet has tons more info if you want to read more or freak yourself out. I do kind of feel like a jerk for bringing this up as we’re all headed to airports and then to our families. At least there is some “good” news – no shortage of turkey! Happy Turkey Day! (gulp)


Being a good bioinformatician


Or more accurately,  how to avoid being a bad bioinformatician. Over at the blog opiniomics (which is my new favorite name for a blog beside Nothing in Biology), Mick Watson published a lovely post: 5 ways that you may be failing as a bioinformatician.

While the premise behind this post sounds fairly negative (why not 5 practices of productive bioinformaticians?) it is extremely informative. Especially for budding bioinformaticians such as myself.

Essentially it breaks down into:

  • Keep up with the literature
  • Use appropriate software
  • Document your procedures
  • Stop reinvent the wheel

I am definitely guilty of the last bullet, and my better bioinformatics peers get on me about it all the time (“You don’t need to write your own code to collapse a 2d array into a vector/write a sorting algorithm/pick a variable without replacement. Someone has already done that.”). Which ones are you guilty of?

Well worth a read, check it out here!

What do mummy seals tell us about climate change?

Antarctica has one of the worlds driest deserts, which it turns out is perfect for preserving seals. For thousands of years. For next summer this means a new mummy movie, Seal Mummies!

But seriously, Paleontologists Paul Koch and Emily Brault from UCSC are using these mummies for something besides next summer’s blockbuster. They are looking at the long term ecological impacts of the changing climate in Antartica. What’s more, there are a TON of seal mummies just lying around. Over 500 in fact, some of them hundreds or thousands of years old. What this can tell us about the changing ecosystem is invaluable. Read about it over at Forbes.

A seal mummy on the Taylor Glacier (Picture via brookpeterson on flickr.com CC BY-ND 2.0)

A living crabeater seal in Antarctica (Image via Liam Quinn on Wikimedia Commons CC-BY 2.0)

How the squashes hitched a ride with humans

Squashes are funny, as fruits go. Even after years of selection for human consumption they have thick, hard rinds, they’re not particularly sweet — in fact, they contain bitter compounds called cucurbitacins — and their seeds don’t separate from their flesh very easily. That all suggests that the wild ancestors of butternuts and pumpkins were dispersed by large mammals, but squashes are native to the Americas, and there haven’t been many large mammals of the sort that would eat them since humans showed up there, back at the end of the last ice age. Of course, those humans since domesticated squashes, which would obviate the need for seed dispersal — and a new genetic study of wild and domesticated squash species provides support for exactly that hypothesis.

Ed Yong has a nice write-up over at Phenomena:

[Squashes’] old dispersers were gone and the most likely substitutes were small rodents with diverse diets, who could have chiselled through the fruits and carried the seeds to pastures new. But Kistler found that these same animals are the most likely to be put off by the squashes’ bitter tastes. Compared to larger animals like elephants or rhinos, he found that smaller ones like mice and shrews have far more TAS2R genes, which allow them to taste bitter compounds.

Humans can’t stomach cucurbitacins either. People who’ve been unfortunate enough to swallow high levels of these chemicals have come down with a severe diarrhoeal illness called Toxic Squash Syndrome. But perhaps some ancient hunter-gatherers became skilled at finding individual squashes that produced low or tolerable levels. After eating such plants, they would have pooped the seeds out, inadvertently sowing the land with more palatable strains.

I am not personally a great fan of pumpkin pie, particularly since I tried sweet potato last Thanksgiving — but maybe this finding will make for some nice chatter over coffee after dinner. Unless you happen to have an uncle who’s into Pleistocene rewilding, anyway.


Kistler L., L.A. Newsom, T.M. Ryan, A.C. Clarke, B.D. Smith, & G.H. Perry. 2015. Gourds and squashes (Cucurbita spp.) adapted to megafaunal extinction and ecological anachronism through domestication
Proc. Nat. Acad. Sci.; published ahead of print November 16, 2015, doi: 10.1073/pnas.1516109112.

Having Dinner with Women in Science

Here at the University of Idaho (Go Vandals) we have some awesome resources in the biology department (IBEST, BCB program, BEACON to name a few).

But by far the most interesting an influential for me over the course of my graduate career has been the Randall Women in Science seminar.  It’s not that each seminar has deeply touched me because as a woman I am able to better connect with other women when they speak about any topic in science. Nor is it that each seminar happens to be exactly what I want to study/do when I grow up. But it has allowed me to talk to women have not only survived but thrived in science.

Jane Randall

Jan Randall and her gardening skills

But first, some history. The seminar series exists because of Dr. Jan Randall, who is on the faculty at San Fransisco State University. She is also an alumna of the University of Idaho’s Department of Biological Sciences (Go Vandals). She studied social structure in animals once thought to be asocial. Additionally she was (among many other things): a Fellow of the California Academy of Sciences, the Board of Directors of the Endangered Species Coalition, and Secretary of the Animal Behavior Society, and a Fellow of the Animal Behavior Society. Her website notes that she is enjoying gardening and traveling in her retirement.

In addition to all her accomplishments in science, she put an emphasis on promoting women in science. And one of her iniatives is the Randall Women in Science seminar. Since 2003, twice a year, women in science, often at the top of their respective fields, are brought to give a talk at the University of Idaho. It is an amazing opportunity as a department to bring excellent seminar speakers to the Palouse to talk about their work.

And yes, the free food and drink is wonderful.


But by far what’s more wonderful is the opportunity to sit and talk candidly with women in science who are on the other end of the career ladder. We are all just starting, working on PhDs and postdocs, while the seminar speakers are well established and completing their careers. So we have questions about how to do this science thing as a woman, some of which we make a point to ask every speaker. It occurred to me last night (at a wonderful Randall seminar dinner) that I’ll be leaving the Palouse soon, and perhaps it’s time to reflect on the answers to these questions we have asked so many influential women.


Question 1: When is a good time to have children?

This is usually the first question, as it is something all of us are thinking about. Science is EXTREMELY demanding early in your career. During your PhD we are flirting with the poverty line (dependent on your discipline/department), and having babies is expensive. Your postdoc is all about getting papers out and finding a job, which requires long hours and a fluid location, especially given it’s not likely that you’ll stay in the same town you postdoc in indefinitely. And then once you have a faculty position, the tenure clock is ticking and you have very little time to get funding and papers out the door. Financially and professionally, when in there is a good time to have a baby? What’s that you say? You can just wait till you have tenure? What about fertility?

One was a VERY successful scientist who waited till she was established (and was actually pregnant at the dinner).

Another told us how they decided to start having children during their postdoc. You’ll notice I say “they”, her husband was her co-PI and the shared child rearing 50-50.

Yet another one told us she didn’t think it was possible to have children and be successful. That she had had a number of VERY supportive partners, and made the decision to put her career first.

One other speaker told us how she had had her first child during her PhD and the department wrote her off, and didn’t think she would finish. But she (this is a theme among the success stories) decided that she had to be more efficient with her time. She could only work from 9-5 so she did nothing during those hours EXCEPT work. No reading the paper, no socializing, no talking. Like a Jedi master, she focused on the tasks at hand so she could do more with the hours she had available.

You must have the efficiency and mind control of a jedi

You must have the efficiency and mind control of a jedi.

What struck me the most is how each woman had a different strategy. There is not really good answer to this question. So the overall pattern was “This science thing is important to me. How can I make my life work within its confines?”.

Question 2: Have you felt discriminated against as a woman in science?

Surprisingly most people said no to this question. But there were some exceptions:

One scientist told us how she had tried to report a professor in her department for sexual harassment. He had propositioned his graduate student and threatened to kick her out of the program if his advances were rebuffed. The student went to our seminar speaker, who promptly approached the dean. The dean told her it wasn’t an issue, and she handed in her resignation the moment she found another job. This was the most extreme example, and we had a long discussion about how to avoid departments where the good old boys club still reigns supreme.

Another scientist told us she had only once felt discrimination. She had an established lab, a few successful graduates, a number of grants, and an impressive publication record. She is inarguably at the top of her field. But when she went for a job interview (a lateral move, she already had an established lab) she was told that she was too timid and the chair of the department doubted Women_in_Science3whether she would be able to run a research lab of her own. She laughed and left.

And another told us how she had been told that she couldn’t have an extra year on her tenure clock because she was having twins. So she jumped over the chair, the dean of science and the dean of the college and went to the president of the university and asked for the extra year so that she could spend time with her children. She was one of the first women granted this extension.

Question 3: How do you deal with the two body problem?

Most of our speakers have a spouse outside of science. But there were a few that faced the difficulty of balancing two careers.

One speaker gave us the whole love story of her marriage with her husband. They worked together, both with respect to their family and with their research. I have seen this work in a number of situations and find it admirable but difficult to achieve.

Another, both her and her husband were in the same field. They applied for the same jobs. He got a job, and she was a spousal hire. The department chair thanks her husband almost daily for bringing her to their department.


We all face these questions and concerns, especially early in our career. What has amazed me is how much variety there has been in answers. How differently each of these women have tackled these very fundament and challenging problems. It has been inspiring, not knowing that it will be easy, but knowing that we can figure it out, as many have before us. And that there are places/ways for us to succeed in this academic realm.


The War over Wood

The title of this post isn’t something clever I came up with, but rather what the locals have named the conflict over protecting trees and biodiversity in the Amazon rain forest.Self proclaimed “Guardians of the Forest” (local rubber tappers, read about them here) are defending the forest that gives them their livelihood. And they are defending it against not massive scale deforestation, but rather the selective logging of high value wood by what essentially are criminal entities.

In an excellent post over at NPR, Lourdes Garcia-Navarro describes a day on the front lines. What is remarkable is how insightful and dedicated these local people are to conserving their forest, rather than giving in to the desire to cash in on its value.
“Rubber tapper Helenílson Felix stands near the stump of a tree that was felled by illegal logging. The tappers explained that this is how deforestation begins: The forest is thinned of its biodiversity, picked apart tree by tree.”


And it appears that despite putting up a strong effort, they are losing the fight.

One of three illegal logging camps dismantled and set on fire by Elizeu Berçacola and his crew.


When and how to use comedy in your science presentations

Over at Science Careers a self proclaimed scientist/comedian Adam Ruben discusses why he used humor in science.

“Blah blah citric acid cycle blah blah succinic dehydrogenase blah blah DOONESBURY CARTOON blah blah pyruvate.”

More importantly, he discusses when he stopped.

“My adviser never outright said so, but I knew what he was thinking: You had time to make the goat picture, but you didn’t have time to improve the actual science? I wanted to explain that, in the same way that people who are full can still eat dessert and claim it’s destined for “a different stomach,” science-improving and goat-Photoshopping were not mutually exclusive activities, but I didn’t think it would bolster my cause.”

He also ends on a somewhat sobering note:

“Just don’t use humor in grant applications. There’s no need—scientific funding is already a joke.”

Worth thinking about for sure!

Read more of his column Experimental Errors!