Easter Break in the Alps

Coming from the U.S. and a non-religious family, I never thought about Easter all that much once I grew up and stopped having Easter egg hunts. But in Europe, the Easter weekend is a major holiday, a kind of spring break of sorts. Even in places that are no longer particularly religious (or, no longer very observantly religious), Good Friday and Easter Monday are often off from work, making a long weekend for family, friends, and maybe travel. Many people tack on a day or more on either side, or take the whole next week off.

If you follow any Scandinavian or Finns, you probably saw pictures of their Easter holidays spent skiing (cross-country, downhill, or touring), snowmobiling, ice fishing, and getting sunburnt up north. This always makes me jealous – the days are getting long up there, the sun is warm, and there’s still snow to play in. Exhibits A, B, and C.

This year we decided to go to the Valais, one fo the parts of Switzerland with the highest mountains, for our Easter weekend. We arrived Thursday night just in time to take in the views across the valley from our AirBnB. Clearly, this was going to be a nice time.

We were staying in Riederalp, a car-free village accessible by cablecar. The offseason had begun and many hotels and restaurants were closed. There were tourists, but only a few to add to the less than 500 people who live there (some of whom were certainly off on their own holidays in warmer places). Our rented apartment was between the two village centers, and so very quiet. This was exactly what I needed. Every morning we would wake up and have a coffee on the porch looking at this view and how the light changed on the mountains.

Riederalp is just below a ridge, and if you hike up there you are offered a view of the Aletsch glacier, the largest one in the Alps. It’s 23 kilometers long, surrounded by 4000-meter mountains, and by 2100 is predicted to lose 90% of its 27 billion metric tons of ice.

The “Aletsch Arena,” as the greater area has billed itself, is one of the big tourist draws. But we realized that it wasn’t the perfect time of year to have all kinds of adventures.

Riederalp is on the south side of the ridge and much of the snow had melted even at 1900 meters where we were staying. I thought maybe that meant we could make a trail running loop around the closest small mountain, but once we got going, reality set in. There was kind of a lot of snow.

This was one of those days where I made a plan and Steve was maybe not thrilled to be tagging along with my bad plan.

Still, part of the reason I had wanted to go to the mountains – other than the extreme happiness I get from just looking at them – was to do some running with vertical, as I’m training for a trail running race in the Alps in July. So I tried to make better plans. A few days, we ended up hiking/running on the “Winterwanderweg” winter hiking trails.

These were pretty high up, so the views were spectacular. They were also packed down – occasionally groomed, and then walked on by people in boots and sometimes snowshoes. Depending on whether the snow was still frozen or soft and slushy, this made it quite challenging running, either sliding around or constantly stretching your ankles in different directions as your feet landed in frozen ruts. It wasn’t the most fun running and by the end of the last day my ankle was sore, but at the same time it was the most fun running, because who can argue with this scenery!?

Two other days, I mapped out routes of about 20 km each that we hiked/ran. Both had a lot of vertical, and some snow patches despite my attempts to route down to lower elevations. The first was through villages and involved losing and then gaining about 1000 meters of elevation to get back to our porch, and it pretty much destroyed me.

The other was a new favorite loop following two local trails, the “Massaweg” and the “Hexeweg”, which curved over singletrack around the side of a mountain and then down a stream valley.

Anyway, we certainly got in some miles and some vertical.

But the nicest part of the holiday in many ways was just being quiet and not worrying too much about work. Sleeping late, sitting on the porch and looking at the mountains. We took some walks around the near-empty village and wondered what it would be like to have a place here. What it would be like to grow up here. What it was like to live here 200 years ago.

Spring is a great time to stop and take a breath. And this was a great place to take that breath.

“I Contain Multitudes”: Microbiomes, Ecology, a Book Review, and Speculation

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Perfect with a negroni.

What is the measure of a good science writer?

Both my boyfriend and I – one of us a scientist, the other not – adore reading Ed Yong’s columns in The Atlantic. That might be a pretty good measure, and it is one that Yong passes with flying colors: both the experts in fields he writes about, as well as nearly everyone else, are happy when he puts words on the internet.

(His Valentines tweets are no exception. I’m trying not to get sidetracked, but it’s hard, and that link is worth clicking, I promise.)

Nevertheless, when Yong’s first book, I Contain Multitudes, was released, I wasn’t that thrilled.

It’s about the microbiome, and I just wasn’t that excited to read about the microbiome. It seemed very of-the-moment, very bandwagon-y. As an ecologist I was kind of sick of hearing about the microbiome, and of people asking me whether my study organism’s microbiome might explain X or Y thing I had found about it.

Like, I’m studying all these complicated non-microbial things about my organism’s ecology, and I’m supposed to somehow have all the skills, techniques, and equipment to also understand its microbiome? Please go away. That’s so too much to ask.

Anyway, this month I finally read the book, and boy was I wrong.

The book was great.

And the microbiome is fascinating.

It was a delightful read, and among the reasons is that Yong describes perfectly some fundamental things about being an ecologist. Take this passage, for example:

“Here is a strange but critical sentiment to introduce in a book about the benefits of living with microbes: there is no such thing as a ‘good microbe’ or a ‘bad microbe’. These terms belong in children’s stories. They are ill-suited for describing the messy, fractious, contextual relationships of the natural world…. All of this means that labels like mutualist, commensal, pathogen, or parasite don’t quite work as badges of fixed identity. These terms are more like states of being, like hungry or awake or alive…”

For any scientist who has found a result, then explored seemingly the same situation over again and got a completely different result, this passage will spark a laugh or sigh of recognition.

It can seem like everything in ecology is context-dependent. Sometimes we can demonstrate what context matters and how the mechanism operates; other times it’s just a nice way of saying, we have no idea what’s going on.

Anyway, through Yong’s typically-excellent storytelling and the way I could identify with the scientists he profiled – men and women, young and old, at universities and zoos and NGO’s and research institutes around the world – I became immersed in tales about microbes.

As Yong points out, microbes were everywhere when multicellular life evolved. So we multicellular beings evolved with them. They made our lives easier, in some ways; and we helped them get ahead. Sometimes the relationship is good for everyone, sometimes not. But with microbes all around us for millions upon millions of years, the relationship is inevitable.

And so we have incredible interactions.

Of course, there are all the microbes in our guts: the gut microbiome, which is discussed all the time, it seems. Ours are worse than they used to be, worse than hunter-gatherer societies, worse if we eat more highly-processed food. This influences our health in so many ways.

But there are also more seemingly-fantastical things.

Microbes that help squids glow, canceling out the shadow that predators might see from below against the night sky, and thus protecting them from death! That makes a brilliantly intelligent cephalopod which just happens to be bioluminescent.

Mice that have gut microbes that help them eat creosote without any ill effects! Cute little fairy tail creatures that can eat a poison pill and just keep on going.

Another charming example? Having a pet, and a dog in particular, is one of the best ways to have a healthy, robust, microbiome. The pet brings microbes into the house from its travels outdoors, and those microbes become your microbes. I’m tallying up all the possible justifications for why we should get a dog, and this is a great one to add to the list! We need a dog because, science.

(Also on the list is that a dog can help you decide author order on papers. I mean, there are other ways, but let’s get a dog.)

Some stories are discouraging, like how a microbes help mountain pine beetles process and disarm the chemical defenses of trees, and thus to kill vast swathes of forest in North America. I thought I knew a fair bit about pine beetle devastation, but this was new to me.

Others stories are hopeful, however.

One of my favorites was a story about researchers trying to combat dengue fever. They raise mosquitos with a bacteria living inside them which makes them resistant to the dengue virus. And now they are letting those mosquitoes loose: they started in Australia, and went door to door to convince neighborhood residents to foster the new mosquitoes, even though most people would say “no way” if you asked whether you could drop some extra mosquito larvae next to their house. Bzzzzzz.

Just by carrying a bacteria, mosquitoes as a vector of this particular disease might be a thing of the past, at least in some places.

Yong also highlighted the work of Dr. Jessica Green, who was a new-ish professor in my department at University of Oregon back when I worked as a technician there.

Green studies the microbiome of buildings. It’s fascinating stuff, and even more interesting when you get to hospitals: leaving the window open to let natural microbes in might help fight off the bad microbes that give so many hospitalized people infections.

Thanks to microbes, there are simple interventions that might make a big difference in people’s lives. Our modern way of living and germ-phobic worldview has broken many of the relationships we used to have, but we are learning more and more about which ones we should preserve or restore. And it’s leading us to create new ones, too.

Along the way, I also began to think about a lot of things not covered in the book.

(I Contain Multitudeswas published in 2016, so a lot of science has happened since then in this rapidly-advancing field.)

For example, how might the microbiome alter human performance? The first thing that popped to mind was sleep. I have pretty much always been terrible at sleeping. I have a hard time falling asleep at night, and sometimes my sleep is restless.

In many aspects of life, sleep is vitally important. I think back to my time as an athlete: rest is one of the most important aspects of training, but if you aren’t sleeping well, you’re missing some of it. I definitely was.

Since 2016, some science has come out suggesting that lack of sleep alters your gut microbiome, and that the relationship also goes the other way, that your microbiome affects the process leading to sleep. But it’s hard to parse this research and assess its quality. I need someone like Yong to do that for me, and condense the reliable findings down into something digestible (see what I did there?).

In fact, I wondered about how the microbiome might affect athletes more generally. People doing a lot of training would benefit from all sorts of specific adaptations, including to diet and metabolism. Do microbes help in that? Does having the wrong microbiome hold you back?

Here, too, there has been a bit of research. For example, Outside wrote up a piece where they had seven elite athletes get their gut microbiomes sequenced. They found plenty of deviation from the average American, but as you can read in the piece, what did that actually mean? Hard to say. There is still so much we don’t know about microbes and which ones do what.

Another recent paper found that rugby players had increased prevalence of microbes that with functions that increased muscle turnover. This approach, looking at “metabolic phenotyping” and metabolomics rather than only the composition of the kinds of microbes, might be more informative. However, because the athletes in the study ate different diets than the non-athletes, it’s hard to totally understand the implications of such differences.

Still, I’m interested in work like this. What would it say about endurance athletes?

Something to remember, though, is that even if we figured out that the human gut microbiome could be used to get better athletic performances or to maintain a better training load, it might be hard to act on that information.

In humans, there are still few silver bullets for the microbiome. Knowing that a microbe is good isn’t enough. In many cases, a microbe can be helpful or protective in one context but harmful in another (for instance if it reaches too-high abundance).

And it’s also hard to deliver a microbe into the gut and have it take hold.

One of the first stories I heard about the microbiome was about fecal transplants, which were used with great success to reset some people’s guts and solve major, seemingly-unsolvable health problems. It was on a podcast, although I now can’t remember which one. It was a wild story.

Yong writes about this, too. But he points out something researchers have learned in the years since the first fantastic results using fecal transplants to cure people of aggressive diseases.

The reason that fecal transplants work so well with some diseases is that the native gut flora has been pretty much wiped out by the combination of the disease and the antibiotics used to treat it in its initial stages.

“This pharmacological carpet-bombing clears many of the native bacteria from their guts,” Yong writes of patients with Clostridium difficileinfections who receive fecal transplants. “When a donor’s microbes arrive in this wasteland, they find few competitors, and certainly few that are as well adapted to the gut as they are. They can easily colonise… ‘you can’t just infuse microbes into people and expect a transplant to happen’, says [gastroenterologist Alexander] Khoruts.”

So even if we knew of a silver-bullet microbe that would help you metabolize or do something else to perform better, could we get it to colonize an athlete’s gut? Unclear.

In the end, if you want a healthier microbiome, a lot of it probably just comes down to eating a healthy, diverse diet, and having healthy habits. And that’s what athletes should be doing anyway.

I wonder if the best way to have your microbiome help your athletic career is just to do a bunch of things that you already know you should do. Eat well. Sleep. Hug the people you care about.

Here’s my final take about the measure of a science writer. A good writer can make you understand things you’re already familiar with in a whole new light.

An entire research group in my department studies the aphid-Buchnerasystem.

Aphids are small insects that like to live on, for example, pea and bean plants. Buchnera are bacteria that live inside the aphids; they got there over 200 million years ago, and each strain of aphid has its own strain of Buchnera. The bacteria produce amino acids that they don’t get from their main food source, phloem. And there’s another microbe, Hamiltonella defense, that protects the aphids against parasitoid wasps, which lay their eggs in an aphid and whose larvae gradually consume them from the inside out, turning them into “mummies”. (Yeah, it’s gross.) Different Hamiltonella strains have different protective abilities and costs.

I can’t tell you how many research talks I have listened to about aphids. Usually, it has just seemed complicated and confusing – even when my friends and close colleagues are explaining it.

But when I read Yong’s description of the study system in his book, all of a sudden, the whole thing made sense to me. First of all what was going on, and secondly why it was fascinating. I will look at my colleagues’ projects differently, and with a lot more interest.

If that isn’t the measure of science writing success, I’m not sure what is.

You can purchase I Contain Multitudes at Powell’s or your favorite independent bookseller.

Women Get Cited Less. What Can We Do About It?

A few weeks ago, a paper came out about the fate of research papers in ecology and evolution (my field!) pre- and post-publication, comparing outcomes between male and female authors.

I want to focus on just one aspect of their nuanced analysis (you can read the whole paper here for free). In this section, the authors gathered citation data on over 100,000 papers published in 142 journals in our field.

They found a slight, but significant, difference in how often papers by men and by women got cited. On average, controlling for the impact factor (a proxy for quality[1]), papers by women accrued 2% less citations.

A hundred thousand papers! That’s a lot, and it’s why the authors could detect this small difference. The sample size allowed them to do a quite powerful analysis.

It also revealed some interesting interactions. For example, papers with female last authors (which often indicates seniority or leadership of the research group) were cited less than those with male last authors at high impact journals, but the effect was reversed at low-impact journals.

Because more people cite papers in high-impact journals, this meant that overall, women were cited less often. [2]

I guess this shouldn’t have been a surprise, but it’s not something I had seen data about before, and consequently something I hadn’t really thought about.

But it is something that matters. Like it or not, citations are a metric of success that is easy to measure, and therefore whether others cite your work is a good piece of evidence that you’re a valuable scientist when you’re up for a job position, tenure, or an award. It’s not great for women if there is bias preventing them from doing well on this metric. [3]

Sounds About Right

Like a lot of research and headlines about challenges facing women in science, this got me mad. I’m a feminist, and this stuff pisses me off.

I see the experiences of my female friends and colleagues, and see when they are treated differently than their male peers. Not always, of course, but enough to make a pattern of our own anecdotal experience.

Then there’s the fact that in my study topics, almost every giant in the field is a man. The ones that defined the discipline and published the equations in a top journal? Men. There are women there, doing great work, but they are less famous.

When data on various aspects of academic life backs up our experience it’s like, “yup, sounds about right.”

Academia is harsh on most people; it’s a place with a lot of rejection, high standards, low pay, job insecurity, and so many power dynamics. The fact that academic science is even harder on women is just not fair.

And that’s not getting into the more complex and devastating nature of the structural problems in academia, which are even worse for other minorities, especially minority women. This paper found that on average women are cited 2% less than men; how much less often are minority women cited?

Anyway, I read this paper, and I was mad.

What I Did Next

Being mad doesn’t accomplish all that much. I tried to think about what we, in our daily lives as scientists, could do to work against this problem.

As an individual early-career scientist, I can only do a very little bit about peer review outcomes or paper acceptances.

But citations? That’s different. I am always writing papers, and I am always citing others’ work. I realized that this was a small step I could take to try to contribute to supporting female scientists. It sounds trivial, but I can cite their work. Could we all do this?

I brought this idea to our lab group, and was curious what they would think.

Some colleagues immediately recognized that this was a problem, and something we don’t think about enough. There are a handful of big names in our subfield, and we mostly cite them over and over. But do we need to do that? Are their papers that we cite every time actually the most relevant? Maybe not. There is probably a lot of work being done around the world we could cite that instead, or at least in addition to the now-traditional canon.

Another common reaction was for someone to say that they don’t think about the gender of authors when they search for papers, read them, or cite them. Here it diverged: a few people said, “I don’t think about it and now I realize that I should.” Others said, “I don’t think about the gender of authors when I’m citing them, therefore I’m not part of this problem.”

I challenged this statement. Does that really mean you’re not part of the problem? Maybe not, I said – and if not, that’s great for you, good work! But instead of assuming that not consciously citing more papers by men means no harm is done, check your reference list on the paper you’re writing. What’s the author breakdown? Do you think this strategy is really working?

I don’t think I was popular for making this callout.

Rubber Meets the Road

As I mentioned in a tweet a few weeks ago, “caring means walking the walk.”

In my paper-reading project, I track the gender of the authors I read, and I found that I am reading fewer papers by women than by men. I was curious about what the ratio might be of the papers I end up citing.

I went through the references section of my current manuscript with a blue and a pink highlighter (I know, supporting stereotypes, etc., it was lazy). The results were not pretty.

I was frankly surprised at how few of the papers I had cited were by women. I knew it wouldn’t be 50/50 for a lot of reasons (discussed below), but I didn’t think it would be that bad.

I basically proved to myself that in order to cite women, you have to do it on purpose. Just not intentionally excluding them isn’t enough.

It’s like how colorblind policies don’t work. Not intentionally doing harm is not the same thing as not doing harm. As Evelyn Carter writes about claiming to be colorblind with respect to race, “if you ‘don’t see’ race, but you say you care about inclusion, how can you advance inclusion efforts that will effectively target communities of color?”

There is a lot of unconscious bias and systematic barriers that lead us to contribute to inequality. Working for equality and to recognize contributions made by women and minorities means actively working to overcome those unconscious biases and systematic barriers.

Shifting the Balance

After my discouraging experiment with the highlighters, I went through the paper and looked at the places I had cited different work. In some places, I was able to find a paper by a woman that I could cite instead – and often even one that supported my point even better than the paper I had cited originally.

That was the most delightful aspect of this task I had set out for myself: I discovered papers in my core area of study, that were by women and that I had never read. And they were really good and very interesting!

The point of reading and citing work by women isn’t just to check boxes and give women a fair shot at career metrics. The main reason is to do better science. Science is creative; it involves having ideas, being exposed to new things, thinking outside whatever box you’re in. Reading work by more different people will necessarily help that process.

I’m really glad that I found these new-to-me papers.

As I discussed with a different colleague later, a lot of this issue comes down in part to poor citation practice, which is endemic across academia. We cite something because everyone else cites it, even though maybe we haven’t read the whole paper. Or we cite something because it’s already in our reference library and we are in a hurry. I’m completely guilty of this, and I’m quite sure everyone else I work with is, too.

If we spent more time reading, and more time looking for and getting familiar with other work that’s related to what we’re doing, I think all of our papers would have much more diverse author lists – at least in terms of evenness and not being dominated by the famous people in our field.

Our papers might also just simply be better, because of all the ideas we would be having.

Don’t Worry, I’m Still Citing Men

After this citation overhaul, my reference list was still majority male first authors. You need to cite what is relevant, and in a lot of cases this work is by men. One reason is that over the history of ecology, there is a lot more work published by men than by women, especially the farther back you go. [4]

Plus, if you need to cite a classic paper, it doesn’t matter who it’s by. That’s the one you need to cite. That’s a second thing. [5]

And likewise, if you need to cite something about your specific study organism or system, there might be only a handful (or a few handfuls) of people in the world who publish on this very specialized niche. They are who they are. If you need to cite peer-reviewed literature, you may have limited choices, and you need to cite the best and/or most relevant work out of that array. [6]

So there are a lot of reasons you can’t just take your reference list and manipulate it towards 50/50 gender equality. I want to make it completely clear: I am not advocating for a departure from citing good and relevant science!

When I mentioned this idea to colleagues – that citing women was a seemingly small, basic thing that we could do in our everyday lives as scientists to make a difference in structural biases – some were deeply uncomfortable that if they sought out work by women, then they would have to leave out other papers.

Listen: there is so much research out there, it boggles the mind. It’s growing exponentially. It’s insane. And in no paper do we cite all the possibly important research on a topic. We’re going to leave things out anyway. It’s just that now, we seem to be structurally leaving out work by women. Again, to overcome this bias is going to require intentionality. This is not a problem that we can just hope will go away because we are good people and don’t mean to cause harm.

No matter what we do, we’re going to keep citing a lot of great research by men.

Tokenism?

Among women, there was another layer. Many of the women I talked to did not want to be cited just because they were women and someone needed to move their reference list towards gender parity. They wanted to be cited because someone genuinely thought their research was the best and most relevant.

And I get that. I was invited to give a talk once because the organizer was looking for a replacement female speaker after the originally-invited woman couldn’t participate. I was so excited for this opportunity, but at the same time it felt weird to get it explicitly because they were looking for a woman.

I’m not sure what to do with this concern, but I think it comes back to proper citation practice. Is your work relevant to the topic, and being cited correctly? Then you deserve to be cited. If papers by women are accepted less often and cited less often, then part of the reason you are not currently being cited might be simply because someone isn’t familiar with your work.

And The Inevitable Question, Does Quality Limit Equality

Finally, we had some conversations about whether this might be because women’s work just wasn’t as good as men’s.

It’s pretty hard to assess that (although the paper I started this blog post with tried to, by using journal impact factor as a covariate).

I have two thoughts. One is that I doubt it’s true. There was an interesting graphic and paper that went around Twitter – about economics, not ecology – showing that papers by women are better written than those by men, that women incorporate reviewer comments more often, and that they improve at presenting information over the course of their careers.

It’s provocative and I’m not sure if it’s also true in my field or not, but I believe it. I think we are culturally trained from a young age to try to please, and so we might be likely to try to pacify reviewers, and to make a revision extra perfect if it was rejected the first time around.

Also, in the sciences, women have to be better to be evaluated as being as qualified as men.

Second, about the content. If it is possible that the data and experiments presented by women are less strong, why might that be?

It is interesting to think about how structural problems would lead to this. Could it be because women get less funding to do their research, and thus might have less resources or support? Could it be that women are asked to do more departmental service and teaching, and have less time to do research?

If the research really is worse – which I’m not convinced it is, but there’s little way to objectively assess, at least not for a dataset of any size – this very well might be a result of the same structural issues that cause the citation patterns.

What Next

What do you think about this? Are there any other ways to work on this problem?

Notes

[1] Impact factor is not a perfect measure of journal quality. It is an estimate of how often work there gets cited, which is a traditional metric for how important it is. For any individual paper, the impact factor of the journal it is published in doesn’t say much about the quality of that paper. However, I think it was the best covariate the authors could find to control for the differences in quality between papers when comparing men’s and women’s outcomes. Also, for better or for worse scientists pay attention to impact factors, so it may affect citation practice even if it’s not an actual metric of “quality” per se.

[2] I have an interesting, harebrained idea about this: if papers by women are less likely to be accepted, do good papers with women as last authors end up in lower-impact journals? That could explain why the better-cited papers from those journals are by women. Totally spitballing here.

[3] Citations shouldn’t define one’s value as a scientist, colleague, or employee anyway, but… that’s a discussion for another day.

[4] Is it really though? Women probably contributed to many important ideas. They typed the manuscripts. Maybe they did some of the work. There are tons of cases in science where people had the same idea independently, and one person got famous, and the other didn’t. Sometimes both these people were white men. I’m guessing there’s a lot of times when some of these people were women, minorities, scientists from outside Europe and North America, and people who were/are otherwise excluded from the elite science community.

[5] Given what I just wrote, I think I – and we all – need to put more effort into finding papers that were written around the same time as the famous ones that “came up with” ideas, and represent contributions of the community-building of those ideas by other people.

[6] When you’re looking for very specific things, there might be a lot of important and relevant data in theses and lower-impact papers by students who did not continue in science. This is valuable literature to search for, and might expand what you think the contributions of women and minorities are, given that these people are less likely to continue in academic careers either by choice or by exclusion.