“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.

My #365papers Experiment in 2018

This year, based on initiatives by some other ecologists in the past, I embarked on the #365papers challenge. The idea of the challenge is that in academia, we end up skimming a lot of material in papers: we jump to the figures, or look for a specific part of the methods or one line of the results we need. Instead, this challenge urged people to read deeper. Every day, they should read a whole paper.

(Jacquelyn Gill and Meghan Duffy launched the initiative and wrote about their first years of it. But #365papers is now not just in ecology, but in other academic fields. Some of the past recaps I read were by Anne Jefferson, Joshua Drew, Elina Mäntylä, and Caitlin MacKenzie. Caitlin’s was probably the post that catalyzed m to do the challenge.)

I knew that 365 papers was too ambitious for me, and that I wouldn’t (and didn’t want to!) read on the weekends, for example. I decided to try nevertheless to read a paper every weekday in 2018, which would be 261 days total.

In the end, I clocked in at 217 papers (I read more than that, but see below for what I counted as a “paper” for this challenge) – not bad! I tweeted links to all the papers, so you can see my list via this Twitter search. I can confidently say that I have never read so many papers in a year.

In fact, I am guessing that this is more papers than I have read in their entirety (not skimming or extracting, as mentioned above), in my total career before 2018. That’s embarrassing to admit but I am guessing it’s not that unusual. (What do you think, if we’re all being honest here?)

This was a great exercise. I learned so much about writing, for one thing – there’s no better way to learn to write than to read a lot.

But the thing that was most exciting was that I read a lot more, and a lot of fun pieces. I had gotten to a place where there were so many papers that I felt I had to read for my own work, that I would just look at the pile, blanche, and put it off for later. Reading had become a chore, not something fun.

Titles_wordle

A Wordle of the paper titles. On my website it says I am a community and ecosystem ecologist, and I guess my reading choices reflect that! (I’d be interested to make a Wordle based on the abstracts, to see if there are more diverse words than the ones we choose for titles – but I didn’t make time to extract all the abstracts for that.)

That’s not a great way to do research, and luckily the challenge changed my reading status quo. If I was reading every day, I reasoned, then not every paper had to be directly related to my work as a community ecologist. There would be ample time for that, but I could also read things that simply looked interesting. And I did! I devoured Table of Contents emails from journals with glee and read about all sorts of things – evolution, the physical science of climate change, remote sensing.

These papers, despite seeming like frivolous choices, taught me a lot about science. Just because they were not about exactly what I was researching does not mean they did not inform how I think about things. This was incredibly valuable. We get stuck in our subfields, on our PhD projects, in our own little bubbles. Seeing things from a different angle is great and can catalyze new ideas or different framing of results. Things that didn’t make sense might make sense in a different light.

But I also did read lots of papers directly related to what I was working on. I think I could only do that because it no longer felt like a chore, like a big stack of paper sitting on the corner of my desk glaring at me. This challenge freed me, as strange as that sounds given the time commitment!

And finally, I tweeted each paper, and tagged the authors if possible. This helped me make some new connections and, often, learn about even more cool research. It helped me put faces to names at conferences and gave me the courage to strike up conversations. The social aspect of this challenge was fun and also probably pretty useful in the long run.

For all of the reasons I just mentioned, I would highly recommend this challenge to other academics. (It’s not just in ecology – if you look at the #365papers hashtag on Twitter, there are a lot of different people in different fields taking up the challenge.) Does 365 or 261 papers sound like too many? Set a different goal.  But make it ambitious enough that you are challenging yourself. For me, I found that making it a daily habit was key, because then it doesn’t feel like something you have to schedule (or something you can put off) – you just do it. Then sit down and read a whole paper, with focus and attention to detail. If you like it, why is that? Is the topic of interest to you? The writing good? The analyses particularly appropriate and well-explained? Is it that the visuals add a lot to the paper? Are the hypotheses (and alternative hypotheses) identified clearly, making it easier to follow? Or, if you don’t like it, why is that? Is it the science, or the presentation? What would you do differently?

One thing I didn’t nail down was how to keep notes. I read on paper, so I would highlight important or relevant bits or references to look up. But I don’t have a great system for how to transfer this to Evernote (where I keep papers’ abstracts linked to their online versions, each tagged in topic categories). In the beginning I was adding photos of each part of the paper I had highlighted to its note, but this was too time-consuming and I gave up. In the end it was like, if I had time, I would manually re-type my reading notes into Evernote, and if not, I wouldn’t. I do think the notes are valuable and important to have searchable, so this probably limits the utility of all that reading a little bit. It’s something I will think how to improve for next year. The biggest challenge is time.

In addition to reading a lot, I kept track of some minimal data about each paper I read. I’ll present that below, in a few sections:

  • Where (journals) and when the papers were published
  • Who wrote them – first authorship (gender, nationality, location)
  • A few thoughts about last authorship
  • Grades I assigned the papers when reading – potential biases (had I eaten lunch yet!?) and the three papers I thought were best at the time I read them

I plan to try this challenge again next year, and the data that I summarize will probably inform how I go about it. I’ll discuss that a little at the very end.

What Did I Count as One of My 365  261  217 Papers?

First, some methodological details. For this effort, I didn’t count drafts of papers that I was a co-author on, although that would have upped the number or papers quite a bit because I have been working on a lot of collaborative projects this year. I also didn’t count reading chapters of colleagues’ theses, or a chapter of a book draft. And I didn’t count book chapters, although I did read a few academic books, among them Dennis Chitty’s Do Lemmings Commit Suicide, Mathew Leibold & Jonathan Chase’s Metacommunity Ecology, Andy Friedland and Carol Folt’s Writing Successful Science Proposals, and a book about R Markdown. I started but haven’t finished Mark McPeek’s Evolutionary Community Ecology.

I did count manuscripts that I read for peer review.

Where The Papers Were Published

I didn’t go into this challenge with a specific idea of what I wanted to read. I find papers primarily through Table of Contents alerts, but also through Twitter, references in other papers, and searches for specific topics while I was working on my dissertation or on research proposals. This biases the papers I read to be more likely to be by people I’m already aware of or in journals I already read. Not entirely, but substantially.

We also have a “journal club” in our Altermatt group lab meeting which doesn’t function like a standard one, but instead each person is assigned one or two journals to “follow” and we rotate through each person summarizing the interesting papers in “their” journals once every few months (the cycle length depends on the number of people in the lab at a given time). That’s a good way to notice papers that might be good to read, and since we are a pretty diverse lab in terms of research topics, introduces some novelty. I think it’s a clever idea by my supervisor, Florian.

Given that I wasn’t seeking out papers in a very systematic way, I wasn’t really sure what the final balance between different journals and types of journals would be at the end of the year. The table below shows the number of papers for each of the 63 (!) journals that I read from. That’s more journals than I was expecting! (Alphabetical within each count category)

In addition, I read one preprint on BioRxiv.

I don’t necessarily think that Nature papers are the best ecology out there; that’s not why it tops the list. Seeing EcologyOikos, and Ecology Lettersas the next best-represented journals is probably a better representation of my interests.

But, I do think that Nature (and Science, which had just a few fewer papers) papers get a lot of attention and must have been chosen for a reason (am I naive there?). There are not so many of them in my field and I do try to read them to gauge what other people seem to see as the most important topics. I also read them because it exposes me to research tangential to my field or even entirely in other fields – which I wouldn’t find in ecology journals, but which are important to my overall understanding of my science.

I’m pleased that Ecology & Evolution is one of my top-read journals, because it indicates (along with the rest of the list) that I’m not only reading things for novelty/high-profile science, but also more mechanistic papers that are important to my work even if they aren’t so sexy per se. A lot of the journals pretty high up the list are just good ecology journals with a wide range of content.

There are a lot of aquatic-specific journals on the list, which reflects me trying to get background on my specific research. But there are also some plant journals on the list, either because I’m still interested in plant community ecology despite being in freshwater for the duration of my PhD, or because they are about community ecology topics that are useful to all ecology. It will be interesting to see if the aquatic journals stay well-represented when I shift to my next research project in a postdoc.

Society journals (from the Ecological Society of America, Nordic Society Oikos, British Ecological Society, and American Society of Naturalists, among others) are well represented. Thanks, scientific societies!

When The Papers Were Published

The vast, vast majority of papers I read were published very recently. Or, well, let’s be honest, because this is academic publishing: who knows when they were written? I didn’t systematically track this, but definitely noticed some were accepted months or maybe even a year before final paginated publication. And they were likely written long before that. But you get the point. As for the publication year, that’s below.

year_published

This data was not a surprise from me as a fair amount of my paper choices come from seeing journal table of contents alerts. I probably should read more older papers though.

Who Wrote the Papers: First Authors

Okay, on to the authors. Who were they? As I mentioned for journals, I didn’t systematically choose what I was reading, so I was curious what the gender and geographic breakdown of the authors would be. Since I didn’t very consciously try to read lots of papers authored by women, people of color, or people outside of North America and Europe, I guess I expected that the gender of first authors to be male-skewed, white, and from those continents. I wasn’t actively trying to counteract bias in this part of the process, so I expected to see evidence of it.

I did my best to find the gender of all first authors. Of those for which this was deducible based on homepages, Twitter profiles listing pronouns, in-person meetings at conferences, etc.,:

  • 59 first authors were women
  • 155 first authors were men
  • 2 papers had joint first authors
  • 1 paper I peer-reviewed was double-blind (authorship unknown to me)

I’m fairly troubled by this. I certainly wasn’t going out of my way to read papers by men, and I didn’t think it would be this skewed when I did a final tally. If I want to support women scientists by reading their work – and then citing it, sharing it with a colleague, contacting them about it, starting discussions, etc. – I am going to have to be a lot more deliberate. I want to learn about other women scientists’ ideas! They have a lot of great ones. I’m going to try harder in the future. Or, really, I’m going to try in the future – as mentioned, I was not intentionally reading or not reading women this past year.

I initially tried to track whether authors were people of color, but it’s just too fraught for me to infer from Googling. I don’t want to misrepresent people. But I can say that the number of authors who were POC was certainly quite low.

I did, however, take some geographic stats: where (to the best of my Googling abilities) authors originally came from, and where their primary affiliation listed on the paper was located.

For the authors for whom I could identify nationality based on websites, CVs, etc., 31 countries were represented.

FA nationality

The authors were numerically dominated by native English speakers, but those had relative geographic diversity, coming from the US, Canada, the UK, Ireland, Australia, and New Zealand (I’m not sure if English is the first language of the South African author). 15 different European nationalities were represented. There were a number of authors from Brazil, and one each from Chile, Colombia, and Ecuador, as well as Central America being represented by a Guatemalan. Maybe a surprise was that Chinese authors were underrepresented, either from Chinese institutions (see below) or those outside China; there were just five. There are many countries from which there are great scientists which are not represented in this dataset.

When it came to institutional country, the field narrowed to 24 countries plus the Isle of Man.

FA_inst

While there were 78 American first authors, 90 first authors came from American universities/institutions. In Europe, Denmark, Sweden and Switzerland gobbled up some of the institutional affiliations despite having low numbers of first authors originally from those countries (this is very consistent with my experience in those places).

(Note: it would have been really nice to make a riverplot showing how authors moved between countries, but I was too lazy to build a transition matrix. Sorry.)

This isn’t really surprising, the consolidation into fewer countries. It reflects that while small countries have great scientists, they often don’t have as many resources to have great research funding or many universities. Some places, even those with traditionally strong academic institutions, are simply going through austerity measures. I think of many Europeans I know who decided that leaving their countries – Portugal, Spain, the Baltics and Balkans, and other places – was their best bet to be able to do the research they wanted to do, and have a job. I think of others, notably a friend in Slovenia, who is staying there because he loves it, but whose opportunities are probably curtailed because of that.

I’d like to read more widely in terms of institutional location and author nationality, but it’s a bit overwhelming to make a solid plan. Reading more women is fairly straightforward. But when I think of all the places with good science but where I didn’t read a single paper, there are a lot of them. I can only read so many papers! So part of it will be recognizing that I can make an effort to read more diversely but I’m not going to solve bias in science just with my reading project. I need to make an effort that is meaningful, and then be okay with what it doesn’t accomplish.

Also, I don’t always know the gender, race, or nationality of an author before I Google them – this past year, I only did that after I read the papers. I might need to sometimes reverse that process, perhaps?

Do you have other ideas of how to tackle this? I’d love suggestions if anyone has them.

One thought is to more deliberately read from the non-North American, non-European authors in the journals I already read from. I already know I like the papers those editorial teams select. This would probably be the least amount of extra work required to diversify my reading, because I could stick to the same method of choosing papers (table of contents alerts), but execute differently on those tables of contents.

And a Bit About the Last Authors

I did not collect as detailed information about the last authors of each paper, but I did collect some. A big topic in academia is that women get fewer and fewer the higher you go in the academic hierarchy. I wondered if that was true in the papers I was reading.

There were fewer last authors because some papers were single-author. Of those that were multi-author, I filtered the dataset to look at only those where last-authorship seemed to denote seniority (based on author contribution statements, lab composition and relationships between authors, etc.) rather than being alphabetical or based on something else (on some papers with very many authors, all the senior authors were listed at the front of the author list). Of these,

  • 19 senior last authors were women
  • 105 senior last authors were men

Yikes!

That’s all one can say! Yikes!

Like the first authors, the last authors came from 31 different countries… but some different ones were represented (Venezuela, Serbia, India). They represented institutions in a few more places than the first authors, 28 different countries vs. 24 for first/single authors. I’m not sure what to make of that, especially since this is from a smaller subset of papers (since the single-author papers were removed), but obviously collaborative research and writing is alive and well.

Ratings and Favorite Papers

Right after I read each paper, I assigned it a letter grade. Looking back through my record keeping, I am less and less convinced that this is really meaningful. I think it had to do a lot with my mindset at the time, among other things. Did I just have a stressful meeting? Was I impatient to finish my reading and go home? Was I tired? Maybe I was less receptive to what I was reading. Or conversely, maybe if I was tired and a little distracted I was less likely to notice flaws in the paper. Who knows. Anyway, “B” was the grade I most frequently assigned.

grades

I didn’t keep detailed notes of why I felt different grades were merited, but I can make a few generalizations. Quite a number of the papers I gave poor grades were because I didn’t find methods to be well enough explained. I either couldn’t follow what the authors did, or maybe important statistical information wasn’t even included (or only in the supplementary information when I thought it was so essential to understanding the work that it really needed to be brought to the center). In particular this included some papers using fancy and cutting edge methods… just using those statistics or analysis techniques doesn’t make your paper magic. You still need to say what those analyses show and what they mean ecologically, and convince me that the fancy stats actually lead to a better understanding of what’s going on!

In some ways this is not authors’ faults – journals are often pressing for shorter word counts, and some don’t even publish methods in the main text, which is a total pain if you’re a reader. Also, it’s one of the biggest things I struggle with when writing – you know perfectly well what you did, and it can be hard to see that for an outsider your methods description seem incomplete. I get it! Reading papers where you don’t understand the methods is always a good cue to think about how you present your own work.

I assigned three papers grades of “A+”. Were they better than the ones I deemed “A”s? I’m not sure, but at the time, whether because of my general mood or their true brilliance, I sure thought they were great. They were:

I read a lot of other great papers too! But looking back, I can say that these were among my favorites, all for different reasons. I could go and add more papers to a “best-of” list but I’ll just leave it at that.

Recap!

Besides all the great reasons to do this challenge that I mentioned in the opening, this was pretty interesting data to delve into. I think I will try to keep doing the challenge in 2019, and I am currently thinking about how I choose which papers to read and if there are good strategies to read more diverse authors. I’m happy with the diversity of research that I read, but I would be happier if the voices describing that research were more diverse, to reflect the diversity of scientists in our world.

Do you have ideas about that? Comment below.

This was the final year of my PhD, and so in some ways a great time to do a reading challenge. It probably would have been more helpful if I had done this in the first year of my PhD, but hey, too late now. This year I wasn’t doing lab work, just writing and analyzing, so it was easy to fit in a lot of reading. It’s not good to stare at a screen writing all day, and I prefer to read on paper, so it was often a welcome break.

I don’t know what my work life will be like next year, so I will see how many papers I end up reading. It could be more, as I start a new project and need to get up to speed on a new subfield. Or it could be less as my working habits change. I’ll just do my best and adapt.

Finally, I’m thinking about whether there’s additional data I should track for next year’s challenge. Whether there is a difference between first and corresponding authors might be interesting. I’d welcome other suggestions too, but only if they don’t take much work to extract!

Understanding our values of nature

Above: a view from the Lägern forest outside of Baden, Switzerland, one of the research sites for Katie Horgan’s PhD work. I ran the Lägern ridge while I was training for a marathon this fall.

I’ve always been interested in conservation. Okay, maybe in the beginning it wasn’t a choice. My mother worked for (and now runs) a land conservation nonprofit, and I grew up kicking around the office and volunteering at events.

Some of my first research and jobs in ecology were about topics related to global change: invasive species, contamination, climate change. I was motivated to take these jobs because I cared about the issues and thought that doing research related to them would help.

But these projects were all very much ecology. The grants weren’t written and the studies weren’t designed with an outcome in mind that could be translated to stakeholders or implemented as policy. They were pure basic science: what is happening? Hey, that’s cool (or alarming, or boring, or …. ), and it’s good that we know it now!

Even though so many of our ecology results are framed in the context of global change, including sentences and maybe even paragraphs talking about implications for land management, I’ve never studied conservation biology. Neither have most of my collaborators.

Recently, I have begun to understand how my good intentions and environmentalism don’t help the environment that much. I’ve been doing ecology in a vacuum: I care about “issues”, but those issues are separate from my science (even if they are merged on my Twitter feed). I really like community ecology and understanding species interactions, and that’s what drives my research questions.

I’m not sure that in and of itself is problematic. But what is certainly problematic is the extent to which I didn’t realize what I was doing. It’s hard to expect your science to connect to and inform conservation and planning if you don’t really understand conservation and planning.

One of the things that made me more cognizant of this was the defense of a fellow University of Zurich PhD student, Katie Horgan, last week. Katie’s dissertation was highly interdisciplinary, and it exploded my conceptions of how we think about nature and ecosystems.

Embarrassingly, the big thing that I realized should be obvious: how we value nature depends more on us, than on nature.

(That might seem like a bit of a jump from my first few paragraphs, but I promise I will link it together at the end.)

When I write out my “big realization”, it looks stupid. I find myself thinking that I already knew that. I interact with people every day who think about the outdoors in a different way than I do.

My boyfriend illustrates this perfectly. When I go for a long run, I want to go somewhere new and see a new view. Steve? He would be happy running exactly the same loop around Uetliberg, the local ridge, that he ran the previous week.

“Why do you need to take the train for two hours?” he asks me. “It’s still just a forest.”

The value we place on seeing and experiencing ecosystems is completely different. Running around in the same forest, or similar forests, we pick up different things and take away different experiences.

How does that relate to ecology? In the past few decades, there has been a push to quantify the value of the natural world. We call them ecosystem services – things like clean water, clean air, the provision of fish to eat and wood to build with, nice places to go recreate in. All of these things can be assigned a dollar value and deemed “natural capital.”

This approach can then be used to make policies protecting natural areas. Asking people to identify what is valuable in their landscape helps set conservation priorities. This approach can also demonstrate that neglecting such protection would be economically costly. In some places the ecosystem services approach has worked great, and in others not so much.

Until last week, I have to admit that I kind of saw ecosystem services as black and white: this ecosystem either provides this service, or it doesn’t. This forest provides X and Y. That lake provides X and Z. I saw ecosystem services as something you could measure objectively.

Then I walked into Katie’s defense.

Katie’s research is fascinating. She worked at eight different research sites scattered around the world, from two right here in northeast Switzerland to those in Siberia and Borneo. At each site, she asked people who worked at the conservation areas a series of questions: did they think that ecosystem service X was being provided by this area? What about ecosystem service Y?

This is a seemingly simple dataset and study, but the work and the results are far from simple. Just getting the interview responses, despite cultural and language barriers and all the rest, was a huge feat.

The thing that struck me most from Katie’s talk was that even in ecosystems that seemed in some ways similar – and actually, even at the same ecosystem– the people Katie interviewed had different answers about whether an ecosystem service was provided or not.

In other words: assessing what ecosystem services are provided does depend on the ecosystem. It depends on how people see the ecosystem.

Katie also mined through the responses and deduced how people thought about the value of these conservation areas. Rather than thinking only about an ecosystem service, she classified the responses by what this service corresponded to.

Did people see the service provided as something more utilitarian (“instrumental”)?

Or did they value this service differently, in a more “intrinsic” way – is the service provided something more fundamental, like biodiversity, that just is?

The third type of value is the one that makes me go run in a new place whenever I can – “relational” value, defined by the way that we interact with nature.

Different ecosystem services, which are the metric by which we turn nature into “natural capital”, were valued in a wide range of ways. And importantly, nearly every ecosystem service that Katie asked about was valued in each of the three ways by at least one study participant. In fact, most participants places more than one value on a given service!

Katie’s big question was, what are the things that motivate people to take positive action about biodiversity?

I had been thinking, like a cold scientist, that the natural capital of an area or ecosystem was defined by the ecosystem itself: the biodiversity contained within, the black and white ecosystem services it provided. I thought we had to convince people of that value, and then they would be motivated to protect it.

What Katie illustrated so powerfully was that actually, the value of nature is defined by the people valuing that nature. If we don’t recognize that, then we won’t really succeed with protected areas and conservation policymaking.

And because of that, it’s a little bit stupid for someone like me who leaves human interaction completely out of my research to put in pompous statements about how that same research will inform conservation. The two parts of my brain that think about environmentalism and ecology had skipped a pretty fundamental dialogue that they could be having.

A few days later, I saw the following tweet from Andy Gonzalez, from a presentation by University of Vermont professor Taylor Ricketts at a science conference in Quebec. It distills this point in a different, perfect way.

 

I bet I’m not the only ecologist who needs to mull over that message.

We live and we learn, and I’m trying to become a better scientist and a better person all the time. Part of that is being humble and realizing when you’re being clumsy or just kind of an idiot.

Hearing from inspirational colleagues definitely helps in that process.

Before and After the Fall: A Meditation on Healthiness

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It was a busy summer. And so, I inevitably got sick.

After a rainy ridge run in the Jura mountains confirmed that me and my friend Steve were more or less compatible overdistance-run partners, we ran across Liechtenstein. I often do these sorts of point-to-point runs in the mountains in summer and fall, but a certain amount of caution is usually maintained in choosing routes when I’m alone. Having a buddy willing to go the crazy places I suggested opened up new route possibilities and with it, more wear and tear (and fitness!) for my body.

The summer was full of opportunity and I was giddy.

We ran a section of the Via Alpina, a 1500-mile trail which traverses the Alps from Monaco to Slovenia, crossing through six other countries on the way. While I’d love to trek the trail some day, these days section runs are the best I can do. We “only” went 25+ kilometers in Switzerland’s Kanton Glarus.

Another day we “ran”, or mostly walked, up an incredibly steep headwall on the far side of Walensee lake, climbing 1500 meters in just three kilometers. The run along a small shelf below the uppermost cliffs was gorgeous, as was the relatively gentle descent back to the other end of the lake. But after that one I told Steve he could pick the route because I had caused us a world of pain.

Later in the summer, I skiwalked up to a glacier with my friend Jonas. I don’t know if Jonas knew how steep it was going to be, but I certainly wasn’t mentally prepared. By the time we hit the ice my legs were rubber. We wisely decided across crossing the glacier.

View from the glacier down to Engelberg.

At some point, I started to feel fit like a warrior, even if each of these individual crazy adventures (and a few more long ones on my own) left me totally exhausted, achy and sore. Pain brings fitness, though. I was hardening up.

But then, when I thought I might be getting onto a bit of a roll, fieldwork started.

I was asked with another PhD student to organize a big joint project for our whole lab this summer. It was/is a really great project – lots of interesting angles, and a cool opportunity to be involved in something so big. I really love fieldwork, too. But organizing everything was incredibly stressful. And I had to be at work extra early to organize everything before the rest of the team showed up, then often stay late to process samples and equipment when the day was over.

I did not run those weeks. On the good days, I forced myself to ride my bike either to work (a measly 9 km) or back, but usually not both. By the end of the day of fieldwork I was so tired that riding home seemed impossible. It was mental exhaustion above all else: after a day of remembering details and always trying to plan two steps ahead, plus perhaps driving for three or four hours, any additional feat of willpower was doomed to fail.

But… I got to see many new corners of Eastern Switzerland. And I love fieldwork! Did I mention that I love fieldwork? Why would you ever work in an office if you could work outside?

Here’s what a block of summer fieldwork for an aquatic ecologist looks like. It looks, despite what I just wrote above, like happiness.

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I think that even those of us who love our jobs lie to ourselves a little bit and say that because the work is something we enjoy, it’s easier than it really is. This kind of research is what I dream of doing. I love the science and the questions we ask and (try to) answer; it’s outside; there’s always something new and it never gets dull. For better or for worse, there’s a new challenge every week, sometimes every day, and you end up using a crazy-diverse set of skills and developing new ones. I wouldn’t trade my job for anything (well….). But there’s no denying that it totally saps me to organize such ventures.

As soon as fieldwork was over – no, not really, just in the middle of the experiment when we let nature do its thing and tried not to stress out about what might be happening in our absence – I headed back to North America to visit friends and family, go to a few weddings of people near and dear to my heart, and give a talk at a big ecology conference.

The first night I was back on Eastern Standard Time, I slept for 14 1/2 hours.

It was so, so awesome to see so many people I love! But I was flying constantly across the country to get to one thing or another and I never really settled in. For the most part, it wasn’t a very relaxing vacation. I also had to put out some fires with the experiment from afar, not being able to see anything in person, which is always nerve-wracking.

With my cousins Jess and Emily at a family wedding in Houston.

Some of the most relaxing moments of my "vacation" were walks in the Lyme Town Forest with my mom and our dog during my six days at home.

A rainy-ish hike up Mount Moosilauke with Susan and Jenny was a great way to cap off my time in New Hampshire.

And so yes: I cannot even schedule my “vacation” to be recovery time. There’s so much exciting stuff to do! I’m like a squirrel chasing every fun thing that catches my attention.

As soon as I got back to Switzerland it was back to fieldwork as we took the experiment apart. Again with the organizing and the long days.

Because I had been in the south for a lot of my trip back to the States and I am legendarily bad at exercising in hot weather, I had lost a lot of my fitness – I just hadn’t been running a lot, much less biking or rollerskiing.

Nevertheless, on the yearly goals list I had made myself in the spring I had written “do a mountain running race.” This had been an idea of mine ever since moving to Switzerland: I couldn’t really live in the Alps without doing the mountain running thing, could I?

The previous summer I had chickened out. I was doing some other fieldwork, a bit more ski-specific training, and just generally didn’t feel great about my uphill running chops compared to people who grew up in the Alps. I was sure I would get demolished, which was one thing, but more scared that I just simply wouldn’t have fun.

But in September I thought, I’ve got to pull the trigger on this or else this goal will stay as an unchecked box on my list. If I waited much longer there would be snow in the mountains. So I impulsively signed up for a mountain half-marathon in Arosa and convinced Steve to join me. Then I’d at least have someone to commiserate with, I thought, and I was certainly right about that.

Pre-race in Arosa. This dude guided our way to one of the best hotel breakfasts I've ever had.

Earlier in the summer, I had done a not insignificant number of long trail runs – longer than a half marathon – with a lot of elevation. But that day, I just didn’t have it. I’m not sure if it was simply a bad day (those certainly happen) or whether the difference between self-pacing and trying to guess a sustainable race pace just wrecked me early, but it was a brutal slog. The course climbed 900 meters in about eight kilometers at the start, then dropped off a precipitous face where you felt more like you were free-falling than running. Then it was up a second peak and a long downhill run back to the finish.

Falling off the mountain.

By the time I was running the last few kilometers, I had totally bonked. I was a mess at the finish line: rubber legs, salt-crusted face, salt streaks covering my arms and legs, dehydrated, totally depleted but with no appetite. It took me hours to get back to anything resembling being alive. A crazy thunderstorm rolled into the mountains and we sat drinking a beer and watching the lightning, me just being thrilled that I didn’t have to so much as stand up.

My first mountain running race experience was tough, but I’d probably do it again, with a clearer understanding of how brutal the race was going to be. The event was great and there’s a nice camaraderie to this community. I felt at home. So next year’s goal list: “do a second mountain-running race”…. maybe I’ll be faster?

Work got crazy again as we decided to use a student project to do a pilot test of a new experimental setup. One day I ran home from the office and titled my Strava workout “Trying to avoid a nervous breakdown about the new experiment.” I was literally running away from my problems.

Planning new experiments is so exhilarating, but it’s also frustrating and stressful and involves revision after revision of plans and ideas.

Around that time, Steve and I ran from Zurich to Zug, a nearby city. It was a 34 k run with a surprising amount of elevation gain: more than 3,000 feet, not bad for living in Switzerland’s lowlands.

I didn’t realize it, but it was going to be my last good run for a while. At the end of the next week, I noted that my supposed-to-be-easy evening run “felt like garbage”. I was just tired, I figured.

The next day I got sick. Really sick: going through an entire box of kleenex a day, unable to do much of anything, debilitatingly exhausted. I first blamed allergies but then, after a day and a half of this misery, took some flu medicine. I immediately felt better. Not good, but better. Ah-ha! If medication made me feel better, that meant I was actually sick. Right.

I didn’t get better very quickly, and had to take some time off of work. I didn’t exercise for two weeks. When I did, I felt okay, so I got excited and a few days later did a 16 k point-to-point run with my boyfriend (who was visiting, and who I thus felt I needed to provide with some workout opportunities). Predictable result: setback, more kleenex boxes. After a few days of re-recovery, we tried a 26 k run/hike up to a mountain hut. It was beautiful.

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Because of the snow and ice, we didn’t push the pace that much. My main challenge was staying warm, but my immune system seemed to handle it okay. The 20 k point-to-point going south from Zurich two days later, though, was one push too far. It required another kleenex box, more medicine, a few more days off from running.

You’d think that at almost 30 years old, I would have learned how to take care of myself better than this. But when to go back to training can be a tricky question – and I’m not exactly training for anything. When I go out for a long run in the mountains, it’s because that’s what will make me happy on that particular day. The balance of long- versus short-term planning is quite a bit shifted from my “athlete” days, meaning that I can risk a little more do get out there sooner – but the potential consequence, lying in bed being miserable, isn’t so nice either.

At a certain point, it came down to this for me. After weeks of yo-yoing back and forth between really sick, sort of sick, and sort of healthy, I couldn’t tell what “really healthy” actually was supposed to feel like. Better than yesterday, better than yesterday, better than yesterday; that seems like a good trajectory. When is better good enough?

And how do you value the trade-offs in life when athletic pursuits are essential for your happiness, but “performance” isn’t your job? Doing two jobs (now three, but that’s another story) and trying to get in good blocks of exercise is certainly pushing the limits of what I can do, mentally and physically. Yet my jobs are stimulating and fulfilling; I want to do well at them. I couldn’t quit them. I also couldn’t quit running (or, in the winter, skiing). If I did that, I’d be less stressed and I might not get sick, but I would be unhappy and the lack of exercise would leave me unhealthy for an entirely different set of reasons. I think I’d be less efficient at my jobs. To non-athletes that sounds counterintuitive, but I suspect that any recreational sportsperson knows exactly what I mean.

I’m lucky that I have some role models in this department. Most of my peers don’t pursue sports – I suspect that if I was in a similar graduate program in the U.S. the number might be higher, but without organized college sports teams many in Europe drop out of organized sports when they start their bachelors, and by grad school are focused primarily on academics – but a few do. When we see each other it’s like a relief: yes, I’m not crazy, this is a real thing that people do! And I’m not the only one who feels like doing work and sport together makes me better at each.

But it undeniably comes with costs. And so, occasionally, you run yourself into the ground and you get sick. Then the longer you sit around waiting for your mythical health to arrive, the more you stew in your own unhappiness. But pushing the envelope also might mean longer sitting around, just drawing things out.

I seem to be healthy again, finally, and I’m going to push it – but not too far. Ski season is coming and somehow, I need to break this cycle.

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another paper.

In case you missed it – we had another paper published! I’m really happy that things seem to be getting out there, little by little. Of course, about the same day, I also got some comments from co-authors on another manuscript which left me with tears of frustration thinking of all the months I had spent on this darn paper, only to have to basically start all over again…. if only I had known what they thought earlier! well, such is life.

At least we have one more published to celebrate.

Here it is (open-access, free for anyone to download): ta-dah!!

Working on the Beach (updated).

My exit from Craftsbury was abrupt, much more abrupt than I meant it to be. After looking for jobs for the month-and-a-half after I decided to leave the Green Racing Project, with little success, I had decided to move back in with my parents for the spring while I continued to search for employment.

Then, my life took a U-turn. On a Friday, I applied for a research technician job with the University of Florida. I was interviewed over the phone the next day and by Monday had a job offer. I had less than a week to tie up loose ends in Craftsbury and move out, and then I drove down to Florida.

(And for the haters: the 1998 4-Runner got 22 miles per gallon, on average, over the course of the more than 1,400 miles I drove. Not so bad.)

So here I am, working on the beach in Navarre, Florida, studying the Santa Rosa beach mouse.

Every day we leave our cars at the Navarre Beach State Park and walk fifteen minutes along the beach until we come to our first field site. At 7:15, it’s a beautiful walk: it’s still cool and breezy, the sun is still rising, and the morning light is soft and pink. I drink my Earl Grey as we stroll but the surroundings are more than enough to jolt me awake.

Work so far is pretty much manual labor, but then again, fieldwork often is. Theoretically, we are looking at the foraging behavior of beach mice. Practically, we spend eight hours each day planting experimental plots of broom sedge in the sand.

My boss is awesome – she served in the Peace Corps after college and her last batch of fieldwork was in Bolivia. I am lucky to be working for someone who is happy to discuss the particulars of the study with me, and to explain how she selected an experimental design and all the nuances of what we are doing.

That interaction and education always makes it worthwhile to provide the legwork on a study like this. I’m not treated like a nobody; I’m treated like someone who also has a stake in whether the research works out. As such, I’m privy to a lot of the details.

Plus, we have to talk about something while we’re planting all that broom sedge.

Another fun part of the job is that our free housing is in a FEMA trailer in a trailer park. It still has its official U.S. Government plates on it, leading our neighbors to joke that we work for the CIA. Nope. We’re just beach mouse workers, hoping not to suffer from the formaldehyde that supposedly plagues these trailers. We spend a lot of time sitting at our picnic table outside.

So: it’s a pretty drastic change from New England. Exactly a week ago, I was skiing with Jennie Brentrup at Oak Hill. Now I’m watching people waterski as I work. Wow.