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)


Stomach acid to pathogens: YOU SHALL NOT PASS

Did you know you’re walking around with a little vat of super acid in your belly? Human stomach acid registers 1.5 on the pH scale, making it more acidic than pure lemon juice. And we have to invest energy into not only making the powerful stuff, but then also into making sure we don’t accidentally kill ourselves with it. Why do we do that?

A recent paper by Beasley et al. (in open access PLOS ONE) hypothesizes stomach acid in vertebrates is used to protect our bodies from pathogens – and the more dangerous your diet, the more acidy your acid. “Obligate scavengers”, as defined in this paper, are animals that eat (and only eat) carrion – aka the decaying flesh of dead animals. Delicious? I guess they think so. But sanitary? Definitely not. These species should have the lowest stomach pHs because they need an acid “filter” to kill all the pathogens they’re ingesting with their diet. Herbivores, on the other hand, have plant-based diets with a much lower associated risk for pathogens. These species should have a higher stomach pH because they don’t need a “scorched earth” policy for their digestive tracts.

They further suspect that animals with a phylogenetically close diet might have a higher pathogen risk than animals that eat more phylogenetically distant organisms (and thus lower stomach pHs). The theory here is that eating something related to you means that their pathogens are potentially well-suited to also infect you.

Beasley et al. conducted a literature search and found pH data for 68 species of birds and mammals – which according to them was “far fewer than expected”, given its importance in digestion. They then categorized the species as “obligate scavenger”, “facultative scavenger”, “generalist carnivore”, “omnivore”, “specialist carnivore”, “hindgut herbivore” or “foregut herbivore”. The data show that obligate scavengers have the lowest pHs (average ~1.3) and foregut herbivores have the highest (average ~6.1, all seen in the very cool figure below from their paper). Omnivores and carnivores had the most variable stomach acid levels.

The authors conclude that these results are in line with their expectations – that organisms that eat “high risk” diets have lower stomach pHs. They leave room for the influence of other factors (like how much work it is to break down one’s diet once it’s been ingested) but note that all things being equal, a scavenger’s diet shouldn’t be more difficult to digest as a regular carnivore’s – the only difference being the – er – fact that it’s dead and rotting.

One note: humans have a stomach pH similar to carrion feeders, although we’re technically omnivores. Why would that be? Did we evolve eating a diet that contained more scavenging? (In practical terms, should the Paleo diet include roadkill?) Or does our relatively large number of “fecal-oral pathogens” favor a more acidic stomach? More data on other hominds would be illuminating here.

The paper finally discusses their expectation that when human stomach pH is raised more pathogens are able to become established. Elderly humans have a stomach pH of ~6.6 – a full 5 pH points higher than a healthy adult (wowza!); premature babies have a stomach acid of 4 or higher. Both of these groups suffer more bacterial infections than adults and children. Furthermore, gastric bypass patients have a stomach pH around 6 and may also suffer more bacterial infections. These facts seem to support their main hypothesis – that stomach acid acts as a barrier to pathogens as strong as the risk of infection – but statistical tests remain to be done.

It’s pretty interesting to me to contemplate why animals invest energy into the things that we do. But it seems at this point, stomach acid may be blocking the path of pathogens in the same way Gandalf stopped the Balrog: YOU SHALL NOT PASS. (And it occurs to me – if we stick with this analogy and the caves of Moria are a digestive tract – that would make the rest of the Fellowship that emerges from the caves…turds? Oh geez. I’m sorry, Tolkien…)

The Fellowship does not like being called turds.

Isn’t that just…sexism?

In case you missed it, there was a big-splash paper in PNAS recently entitled “National hiring experiments reveal 2:1 faculty preference for women on STEM tenure-track“. Williams & Ceci found one pretty huge result in their various experiments:

Given otherwise identical candidates, professors preferred female candidates over male candidates by 2:1.

When I first read that, I thought “Great!” But now, after thinking about it some more and reading the paper more carefully, I’m less enthused for two pretty gigantic reasons: methods and interpretation.

I see one major methodological flaw in the experimental design, which briefly is this: Williams & Ceci wrote narrative summaries describing two candidates. They then randomly used either female or male pronouns and asked real faculty members to rank the candidates as if they were potential hires for their department. In fairness, this seems like the most tractable way to hold all variables other than gender as “constant”. However, this design relies on the assumption that the sentences “We view her as a 9.5/10.” and “We view him as a 9.5/10.” are identical in the minds of the reader, which they absolutely are not. Randomizing male and female names on job applications for “lab manager” positions results in everyonScales_NIBe rating the male applicants as more competent, more hirable and deserving of higher salary and more mentorship. Another study put male and female names at the top of a woman’s CV and found the same thing – the male version of her CV was consistently ranked higher. It seems we all judge women more harshly than males. “He” and “she” are simply not equivalent and treating them as such greatly confounds the results presented in the paper. An alternate explanation for all the results in the study is that their methods are not comparing identical applicants at all and are instead showing underlying bias. I mean, riddle me this: if a woman has to be more competent to be viewed the same, given two identical candidates, isn’t the female one more competent?

Along that same vein, I don’t think the experiments were all that great in terms of controls. For example, they find that the single woman was preferred over the (“identical”) married man with children. This basically contradicts everything I’ve ever heard or read about the effects of gender and family on job prospects in Academia – which, summarized is this: Women are professionally penalized for being or wanting to be mothers. Women in general are thought of as ticking biological clocks and departments prefer candidates that will not stop the tenure clock, will not require any family leave and will devote 110% of their time to their labs. (There’s a good summary of the motherhood issue here and more info here or here, or there are some books available or you can go through the wonderful blog Tenure, She Wrote to get all sorts information). There are abundant stories about women being hassled regarding their family plans while on job interviews (it’s illegal to ask about for a reason – and people do it anyway, for a reason). It seems the “risk” of a woman eventually having a baby is something that strongly affects hiring decisions and candidate rankings in the real world. If we’re starting to intentionally overlook that, I think it’s great. But to just say flat-out that a single woman is preferred over a married man is so unbelievable to me that I think it indicates a flaw in this type of study: there is no cost to choosing the candidate you think you should pick vs. the one you might pick in real life. There’s no need to put your money where your mouth is. And again, I wonder if “identical” candidates are not “identical” in this experiment – maybe the hypothetical female candidate is imagined to be 28 years old and the married man with kids is 35 and the 7 year age difference dilutes the man’s accomplishments (or something like that). I just wonder if he’s ranked below her because people make unconscious assumptions about the person based on their lifestyle choices.

The final methods question I have involves a big “yippee” result from the paper – that people who chose to take a year off for family leave were not penalized for it, in fact they were preferred (again, against otherwise identical candidates). Here’s the problem with this one: if they’re identical except for the fact that one person skipped a whole year, who wouldn’t want the one who achieved the same amount of work in one year’s less time? Again, they’re not identical. I guess it’s good that prioritizing family in and of itself isn’t punished, but really, we’re saying “Do you want awesome candidate number one or do you want the equally awesome candidate two who also took a year off to do another awesome thing, stay home with their baby, who didn’t suffer any reduction in productivity?” The fact is, if you take time off, you get less (professional) work done. That’s what people hear when you talk about babies and maternity leave in the real world – you’re going to be a less (professionally) productive person and that might mean some of your work is going to be pushed on to a colleague. So I’m not all that excited or encouraged about this particular result.

Regarding their interpretation of their results – the authors believe what they have found means that women are now the preferred sex in hiring situations. If that’s true – if faculty really prefer females 2:1 over identical males, this has to be an intentional act for this to be good news. If the results indicate that faculty are aware of and would like to correct a dearth of female professors in their department, for instance – that’s great because if two candidates truly are identical, that’s the ideal situation to opt for the underrepresented group. Bravo. However, the authors specifically say their results do NOT represent faculty members actively choosing “socially desirable” outcomes (“i.e., endorsing gender diversity”) because one of their experiments evaluated a single candidate (instead of ranking three). According to them, this experimental design “avoids socially desirable reporting”. The single candidate experiment still showed a preference for females; the women were ranked an average of 10% higher than the identical male candidate. The authors say this “suggests that norms and values associated with gender diversity have become internalized in the population of US faculty.” Hm. I say again, favoring a female candidate because she’s female must be done intentionally. Otherwise, isn’t that just kind of maybe…sexism? (Cue me squeamishly opening a can of worms…) If we’re subconsciously awarding points for being female – that’s a problem. Identical candidates should be ranked identically, right? Correcting unbalanced diversity in departments needs to be done on purpose, not because we’ve “internalized” the message that women need extra help or are more deserving somehow. The authors briefly comment on this in the discussion:

Also, it is worth noting that female advantages come at a cost to men, who may be disadvantaged when competing against equally qualified women. Our society has emphasized increasing women’s representation in science, and many faculty members have internalized this goal. The moral implications of women’s hiring advantages are outside the scope of this article, but clearly deserve consideration.

Yikes! Everything about those sentences worries me. I guess the plus side of me having reservations about their methods means I’m not convinced that the survey respondents weren’t intentionally choosing females. Williams and Ceci did not inquire as to why the respondents were giving the rankings that they did and this would have been a really useful piece of the story. Perhaps the most useful piece because it distinguishes between a conscious “I’m aware of a diversity problem in our department and I think gender should be a factor in future hiring decisions, especially when all the candidates are truly outstanding with no difference in qualifications” and an unconscious “Women deserve points for being women.”

I hope the next gigantic study looks at non-identical candidates. I hope they ask people whether gender affected their decisions. I hope I’m not secretly sexist for thinking this study  – where identical candidates were not ranked identically – sounds sexist.

And finally, my most cynical thought about this whole thing: Do these results even matter? I mean, I guess it does because if they had found the opposite result, I would find that depressing. But I never really thought that this stage is the problem – that if I got the interview and nailed the interview, that I wouldn’t get a fair ranking. There are so many other factors that I think are bigger problems (e.g., implicit bias, stereotype threat, the baby penalty, lack of mentors) that this is almost irrelevant. Almost. It’s still pretty good news to know that there’s not some overarching bias against sex in ideal scenarios. But do I agree with the authors when they say it’s “a propitious time for women launching careers in academic science”? I’m not so sure we’re there yet (and this paper certainly hasn’t convinced me so).

Of dinosaurs and feathers

A 2014 study in Science – provocatively titled “A Jurassic ornithischian dinosaur from Siberia with both feathers and scales” – might just change how we think about all dinosaurs. Based on the age and identity of the specimen that the paper describes, the authors say perhaps all dinosaurs, not just the ones closely related to modern birds, had feathers! How cool is that?

“Probably that means the common ancestor of all dinosaurs had feathers,” says study lead author Pascal Godefroit of the Royal Belgian Institute of Natural Science in Brussels. “Feathers are not a characteristic [just] of birds but of all dinosaurs.”

National Geographic covered the story (about the little guy illustrated below) here.

This illustration of Kulindadromeus zabaikalicus, a newfound feathered dinosaur, shows it in its natural environment. Illustration by Andrey Atuchin; reposted from nationalgeographic.com

The secret ingedient is…crystals?

Chameleons are pretty special. With their independently moving Mad-Eye Moody eyeballs

and their “live long and prosper” hands,

Is Spock really a well disguised chameleon? That is not a very logical conclusion (despite their similar hand morphologies).

Probably has a killer Vulcan Death grip.

who isn’t intrigued by these goofy lizards?

Perhaps their most amazing feature is their ability to change color.

Recent research shows that the key to this process may be less biological and more CRYSTALS.

Studying male panther chameleons from Madagascar, a cross-disciplinary team of biologists and physicists from the University of Geneva found that the reptiles’ skin is covered by a thick layer of light-reflecting cells called iridophores, which are embedded with photonic crystals—a latticed organization of guanine nanocrystals. Depending on how closely those crystals are clustered, they reflect different wavelengths of light.

Read more in “The Secret to How Chameleons Change Color” over at wired.com or go straight to the (open!) source at Nature Communications – “Photonic crystals cause active colour change in chameleons“.

So – you want to be an academic?

Stumbled upon a great little slide show (by Josh Neufeld) with all the major pros (and some cons) of being an academic – from start to finish. There’s no script to go with the slides, but they’re put together in such a way that I think it’s pretty coherent as is. It also contains a lot of google-able resources for those knee deep in academia too. (Hat tip to @hollybik!)

National Darwin Day? (Yes, please.)

Charles Darwin is great, isn’t he? I mean – he discovered the theory of natural selection and by doing so, created an eloquently beautiful framework for studying and understanding the living world around us. He wrote On the Origin of Species (free text here!). He drew this:

“I think case must be that one generation should have as many living as now. To do this and to have as many species in same genus (as is) requires extinction . Thus between A + B the immense gap of relation. C + B the finest gradation. B+D rather greater distinction. Thus genera would be formed. Bearing relation” (next page begins) “to ancient types with several extinct forms”

Every year on February 12 (Darwin’s birthday), evolution enthusiasts celebrate Darwin Day with nerdy games, scientific seminars and frivolity. Mark your calendars! And this year, it may be even better, since bills (yes, plural!) have been introduced to the House of Representatives and to the Senate to officially name February 12, 2015 Darwin Day. Follow the links to read more. And from what I know about scientists, if we were to ever achieve a federal holiday for Darwin, I think we’d party harder than New Years, explode more things than Independence Day and drink more coffee than finals week. Dar-win! Dar-win! Dar-win!