Should scientists write Wikipedia pages for their study species?

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I’ve been working on Penstemon digitalis for a long time now. I first met the plant as a starting PhD student looking for a new system to make my own. I wanted something local (to Ithaca, NY), a plant that was dependent on pollinators with pre-dispersal seed predators (those are insects that lay eggs in the fruit and the young larvae eat the seeds). I wanted to study conflicting selection on floral traits by mutualists and antagonists, not what my dissertation ended up being about but that is a story for another day. In my search for a species to work with, I also wanted something with larger seeds than Lobelia siphilitica that I had just spent my masters cursing over and to be taller than Collinsia parviflora that I broke my back over during my undergrad. Continue reading

On the ballooning of spiders and deep evolutionary branches

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To keep track of projects, I use a sophisticated app called Moleskine. But early on in grad school, when I had a new project, I created a disk for everything related to that project. Like this:

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One of these disks was labelled “Ballooning Spiders.” I had an idea for a side project that I humored for a few days.

I thought the ballooning behavior of spiders was pretty awesome. I still think the ballooning behavior of spiders is pretty awesome. I imagined it was quite likely that spiders could balloon across entire oceans. (Twenty years later, we know that’s true.) Continue reading

Natural history, synthesis papers and the academic caste system

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It’s been argued that in ecology, like politics, everything is local.

You can’t really understand ecological relationships in nature, unless you’re familiar with the organisms in their natural environment. Or maybe not. That’s probably not a constructive argument. My disposition is that good ecological questions are generated from being familiar with the life that organisms out of doors. But that’s not the only way to do ecology. Continue reading

What happens in the canopy stays in the canopy.

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For a few years, I’ve harbored a very cool (at least to me) natural history idea. But it’s a big technical challenge. The required fieldwork is never going to happen by me. So, I should write a blog post about it, right?

Bullet ants (Paraponera clavata) are one of the most charismatic creatures in Neotropical rainforests. My lab has done some work with them recently. These often-seen and well-known animals are still very mysterious. Continue reading

The field ecology of a gut microbe inside bullet ants

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The bullet ant Paraponera clavata. Image by Alex Wild.

The bullet ant Paraponera clavata. Image by Alex Wild.

This is the latest paper from my lab, which I’m really excited about. When we designed the project, several people told us that it would be useless. “It’s pointless to study the ecology of a symbiotic microbe in the wild when we have yet to specify its function inside the host.” It was only two days ago that Meg Duffy said that the microbiome is the most important recent conceptual advance in ecology, and I agree with her. That’s one of the reasons we did this project, to look at the ecology of gut microbe in the wild, which appears to be a true frontier.

There are plenty of advances that are yet to be made in the field biology of microbes, and these discoveries do not have an a priori requirement understanding of the comprehensive biology of an organism before understanding its ecology.

The microbial contents the guts of bullet ants are remarkably heterogeneous. In some colonies of bullet ants, we found oodles of a particular Bartonella microbe, closely related to those that facilitate N cycling in other animals. And most closely related (as far as we know) to other Bartonella inside ants on other distant continents. But, many bullet ant colonies lack this microbe. Perhaps not by accident, bullet ants have a remarkably varied diet, and some colonies eat more insects than anything else, and other colonies are functional herbivores. Perhaps the presence of this N-cycling microbe might be associated with – or even respond to – the trophic position of the ants?

Aren’t we getting ahead of ourselves by studying how diet affects microbes in the wild, when we don’t know what the microbes do? I say, phooey. Most of the ants that we study in tropical rainforest are just as mysterious as microbes. We don’t even know what most species of ants even eat! Nobody tells me I can’t study the ecology of ants without doing a comprehensive study of their diets and relationships to other organisms in the ecosystem. So, why do we need to know exactly what the role of microbe is in the gut of an animal before working to understand its distribution and ecology?

Working out the function of these microbes is mighty damn hard, if not impossible at the moment. But we can understand the distribution of these critters among colonies of ants an understand the environmental factors that shape its occurrence, as well as doing experiments to see how we can make incidence increase or decrease.

So, we ran an experiment that gave the ant colonies supplemental carbohydrates, or supplemental protein. (This was not easy at all, though you might think it would be. A post on this is forthcoming.) And we checked to see if how the microbes responded. It turns out that when you feed colonies sugar, this microbe becomes more prevalent. Moreover, the results from the manipulation recapitulate the ambient relationship between diet and microbial prevalence. Some colonies consistently collect more sugary nectar from the canopy than other colonies. (Learning this involved going out into the forest in the middle of the night, for an entire summer, to measure bullet ant colony diets.) The colonies that collect more nectar are more likely to have this microbe. So, we can clearly conclude that a sugary diet is predictive of the incidence of this particular Bartonella inside bullet ants.

And the stable isotopes tell an interesting story, too.

So what does this mean? While most ant species that forage in rainforest canopies are functionally herbivorous, bullet ants are true omnivores. They also don’t have the specialized obligate N-cycling microbes that the more herbivores canopy ants have. We found that the close bullet ant diets get to their competitors in the canopy, the more likely they have this facultative N-cycling microbe. If we’re trying to understand how the evolution of obligate sugar-feeding evolved among the dominant ants of rainforest canopies, then I suggest that understanding the ecology of the facultative bullet ant/Bartonella association is to get a window into the evolution this form of dietary specialization.

How this project happened inside a teaching institution

This was the Master’s thesis project of Hannah Larson. Hannah came to my lab with a specific interest in doing field ecology. Based on preliminary finds predating her arrival, Hannah and I developed this project in collaboration with Shana Goffredi, our microbial ecology collaborator. After taking courses for a semester, Hannah headed to the rainforest for eight months to conduct this project at La Selva Biological Station. Hannah found, marked and measured over a hundred bullet ant colonies (which became the start of a long-term monitoring project), and overcame a series of challenges in getting the molecular work done in a rainforest field station (with substantial help from our collaborating lab at the University of Costa Rica). Undergraduate Erica Parra is the one who (by her own choice I should point out) spent long nights in the pitch black of the rainforest at the base of actively foraging bullet ant colonies. The work was funded by an NSF-IRES grant OISE-1130156, though we scrambled for additional funds for reagents that were not in the project budget.

Reference:

Larson, H.K., S.K. Goffredi, E.L. Parra, O. Vargas, A. Pinto, T.P. McGlynn. 2014. Distribution and dietary regulation of an associated facultative Rhizobiales-related bacterium in the omnivorous Giant Tropical Ant, Paraponera clavata. Naturwissenschaften. DOI: 10.1007/s00114-014-1168-0

You can find a copy of this paper on my lab’s website.

Natural history is important, but not perceived as an academic job skill

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This post is a reflection on a thoughtful post by Jeremy Fox, over on Dynamic Ecology. It encouraged me (and a lot of others, as you see in the comments) to think critically about the laments about the supposed decline of natural history.

I aim to contextualize the core notion of that post. This isn’t a quote, but here in my own words is the gestalt lesson that I took away:

We don’t need to fuss about the decline of natural history, because maybe it’s not even on the decline. Maybe it’s not actually undervalued. Maybe it really is a big part of contemporary ecology after all.

Boy howdy, do I agree with that. And also disagree with that. It depends on what we mean by “value” and “big part.” I think the conversation gets a lot simpler once we agree about the fundamental relationship between natural history and ecology. As the operational definition of the relationship used in the Dynamic Ecology post isn’t workable, I’ll posit a different one.

As a disclaimer, let me explain that I’m not an expert natural historian. Anybody who has been in the field with me is woefully aware of this fact. I know my own critters, but I’m merely okay when it comes to flora and fauna overall. I have been called an entomologist, but if you show me a beetle, there’s a nonzero probability that I won’t be able to tell you its family. There are plenty of birds in my own backyard that I can’t name. Now, with that out of the way:

Let’s make no mistake: natural history is, truly, on the decline. The general public knows less, and cares less, about nature than a few decades ago. Kids are spending more time indoors and are less prone to watch, collect, handle, and learn about plants and creatures. Literacy about nature and biodiversity has declined in concert with a broader decline in scientific literacy in the United States. This is a complex phenomenon, but it’s clear that the youth of today’s America are less engaged in natural history than yesterday’s America.

On the other hand, people love and appreciate natural history as much as they always have. Kids go nuts for any kind of live insect put in front of them, especially when it was just found in their own play area. Adults devour crappy nature documentaries, too. There’s no doubt that people are interested in natural history. They’re just not engaged in it. Just because people like it doesn’t mean that they are doing it or are well informed. That’s enough about natural history and public engagement, now let’s focus on ecologists.

I honestly don’t know if interest in natural history has waned among ecologists. I don’t have enough information to speculate. But this point is moot, because the personal interests of ecologists don’t necessarily have a great bearing on what they publish, and how students are trained.

Natural history is the foundation of ecology. Natural history is the set of facts upon which ecology builds. Ecology is the search to find mechanisms driving the patterns that we observe with natural history. Without natural history, there is no such thing as ecology, just as there is no such thing as a spoken language without words. In the same vein, I once made the following analogy: natural history : ecology :: taxonomy : evolution. The study of evolution depends on a reliable understanding of what our species are on the planet, and how they are related to one another. You really can’t study the evolution of any real-world organism in earnest without having reliable alpha taxonomy. Natural history is important to ecologists in the same way that alpha taxonomy is for evolutionary biologists.

Just as research on evolution in real organisms requires a real understanding of their taxonomy and phylogeny, research in real-world ecology requires a real-world understanding of natural history. (Some taxonomists are often as dejected as advocates for natural history: Taxonomy is on the decline. There is so much unclassified and misclassified biodiversity, but there’s no little funding and even fewer jobs to do the required work. If we are going to make progress in the field of evolutionary biology, then we need to have detailed reconstructions of evolutionary history as a foundation.)

Of course natural history isn’t dead, because if it were, then ecology would not exist. We’d have no facts upon which to base any theories. Natural history isn’t in conflict with ecology, because natural history is the fundamental operational unit of ecology. Natural history comprises the individual bricks of LEGO pieces that ecologists use to build LEGO models.

The germane question is not to ask if natural history is alive or dead. The question is: Is natural history being used to its full potential? Is it valued not just as a product, but as an inherent part of the process of doing ecological research?

LEGO Master Builders know every single individual building element that the company makes. When they are charged with designing a new model, they understand the natural history of LEGO so well that their model is the best model it can be. Likewise, ecologists that know the most about nature are the ones that can build models that best describe how nature works. An ecologist that doesn’t know the pieces that make up nature will have a model that doesn’t look like what it is supposed to represent.

Yes, the best ecological model is the one that is the most parsimonious: an overly complex model is not generalizable. You don’t need to know the natural history of every organism to identify underlying patterns and mechanisms in nature. However, a familiarity with nature to know what can be generalized, and what cannot be generalized, is central to doing good ecology. And that ability is directly tied to knowing nature itself. You can’t think about how generalizable a model is without having an understanding of the organisms and system to which the model could potentially apply.

I made an observation a few months back, that graduate school is no longer designed to train excellent scientists, but instead is built to train students how to publish papers. That was a little simplistic, of course. Let me refine that a bit with this Venn diagram: 

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What’s driving the push to train grad students how to publish? It doesn’t take rocket science to look at the evolutionary arms race for the limited number of academic positions. A record of multiple fancy publications is typically required to get what most graduate advisors regard to be a “good” academic job. If you don’t have those pubs, and you want an academic job, it’s for naught. So graduate programs succeed when students emerge with as their own miniature publication factory.

In terms of career success, it doesn’t really matter what’s in the papers. What matters is the selectivity of the journal that publishes those papers, and how many of them exist. It’s telling that many job search committees ask for a CV, but not for reprints. What matters isn’t what you’ve published, but how much you have and where you’ve published.

So it only makes sense that natural history gets pushed to the side in graduate school. Developing natural history talent is time-intensive, involving long hours in the field, lots of reading in a broad variety of subjects. Foremost, becoming a talented natural historian requires a deliberate focus on information outside your study system. A natural historian knows a lot of stuff about a lot of things. I can tell you a lot about the natural history of litter-nesting ants in the rainforest, but that doesn’t qualify me as a natural historian. Becoming a natural historian requires a deliberate focus on learning about things that are, at first appearance, merely incidental to the topic of one’s dissertation.

Ecology graduate students have many skills to learn, and lots to get done very quickly, if they feel that they’ll be prepared to fend for themselves upon graduation. Who has time for natural history? It’s obvious that ecology grad students love natural history. It’s often the main motivator for going to grad school in the first place. And it’s also just as obvious that many grad students feel a deep need to finish their dissertations with ripe and juicy CVs, and feel that they can’t pause to learn natural history. This is only natural given the structure of the job environment.

Last month I had a bunch of interactions that helped me consider the role of natural history in the profession of ecology. These happened while I was fortunate enough to serve as guest faculty on a graduate field course in tropical biology. This “Fundamentals Course,” run by the Organization for Tropical Studies throughout many sites in in Costa Rica, has been considered to be a historic breeding ground for pioneering ecologists. Graduate students apply for slots in the course, which is a traveling road show throughout many biomes.

I was a grad student on the course, um, almost 20 years ago. I spent a lot of my time playing around with ants, but I also learned about all kinds of plant families, birds, herps, bats, non-ant insects, and a full mess of field methods. And soils, too. I was introduced to many classic coevolved systems, I learned how orchid bees respond to baits, how to mistnet, and I saw firsthand just how idiosyncratic leafcutter ants are in food selection. I came upon a sloth in the middle of its regular, but infrequent, pooping session at the base of a tree. I saw massive flocks of scarlet macaws, and how frog distress calls can bring in the predators of their predators. I also learned a ton about experimental design by running so many experiments with a bunch of brilliant colleagues and mentors, and a lot about communicating by presenting and writing. And I was introduced to new approaches to statistics. And that’s just the start of it the stuff I learned.

I essentially spent a whole summer of grad school on this course. Clearly, it was a transformative experience for me, because now I’m a tropical biologist and nearly all of my work happens at one of the sites that we visited on the course. Not everybody on the course became a tropical biologist, but it’s impossible to avoid learning a ton about nature if you take the course.

The course isn’t that different nowadays. One of the more noticeable things, however, is that fewer grad students are interested, or available, to take the course. I talked to a number of PhD students who wanted to take the course but their advisors steered them away from it because it would take valuable time away from the dissertation. I also talked to an equivalent number of PhD students who really wanted a broad introduction to tropical ecology but were too self-motivated to work on their thesis to make sure that they had a at least few papers out before graduating.

In the past, students would be encouraged to take the course as a part of their training to become an excellent ecologist. Now, students are being dissuaded because it would get in the way of their training to become a successful ecologist.

There was one clear change in the curriculum this year: natural history is no longer included. This wasn’t a surprise, because even though students love natural history, this is no longer an effective draw for the course. When I asked the coordinator why natural history was dropped from the Fundamentals Course, the answer I got had even less varnish than I expected: “Because natural history doesn’t help students get jobs.” And if it doesn’t help them get a job, then they can’t spend too much time doing it in grad school.

Of course we need to prepare grad students for the broad variety of paths they may choose. However, does this mean that something should be pulled from the curriculum because it doesn’t provide a specific transferable job skill? Is the entire purpose of earning a Ph.D. to arm our students for the job market. Is there any room for doing things that make better scientists that are not necessarily valued on the job market?

Are we creating doctors of philosophy, or are we creating highly specialized publication machines?

There are some of grad students (and graduate advisors) who are bucking the trend, and are not shying away from the kind of long-term field experiences that used to be the staple of ecological dissertations. One such person is Kelsey Reider, who among other things is working on frogs that develop in melting Andean glaciers. By no means is she tanking her career by spending years in the field doing research and learning about the natural history of her system. She will emerge from the experience as an even more talented natural historian who, I believe, will have better context and understanding for applying ecological theory to the natural world. Ecology is about patterns, processes and mechanisms in the natural world, right?

Considering that “natural history” is only used as an epithet during the manuscript review process, is natural history valued by the scientific community at all?  Most definitely it is! But keep in mind that this value doesn’t matter when it comes to academic employment, funding, high impact journals, career advancement, or graduate training.

People really like and appreciate experts in natural history. Unfortunately, that value isn’t in the currency that is important to the career of an ecologist. And it’d be silly to focus away from your career while you’re in grad school.

But, as Jeremy pointed out in his piece, many of the brilliant ecologists who he knows are also superb natural historians. I suggest that this is not mere coincidence. Perhaps graduate advisors can best serve their students by making sure that their graduate careers include the opportunity for serious training in natural history. It is unwise to focus exclusively on the production of a mountain of pubs that can be sold to high-impact journals.

We should focus on producing the most brilliant, innovative, and broad-minded ecologists, who also publish well. I humbly suggest that this entails a high degree of competency in natural history.

Changing families are behind the decline of field station culture

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The title of this post is more of a working hypothesis than an assertion. I put together a few observations I’ve made over the last month and this idea fell together.

Overall, there has been a steady decline in the pursuit of biological research involving long-term field research that relies upon a deep understanding of natural history. This is a well-recognized phenomenon among ecologists and evolutionary biologists. There are many potential causes, but here is one associated phenomenon:

A great variety of biological field stations throughout North and Central America have experienced a decline in research activity. At least, it seems to me, that many field stations have stagnated or shrunk, while the number of scientists has grown.

I’ve spent time in a variety of field stations, some with long histories that boast tremendous records of scientific productivity and discovery. The scientific progress at these sites was enabled by a culture of long-term scientists who have spent their careers working at particular locations in detail, and by bringing generations of students to work at these sites.

This doesn’t happen so much anymore. This was explained well by Chris Buddle of Arthropod Ecology.

What nearly all of these stations – with some notable exceptions – are missing is a set of senior researchers who are resident on site for long-term doing their field research. Nowadays, senior researchers don’t typically live at field stations for extended periods. Field stations are places where grad students, and maybe postdocs, work long-term. Undergraduates spend summers at field stations doing research and taking field courses, but at most field stations the faculty aren’t there for too long.

Without the consistent presence of senior researchers field stations do not serve as social and academic hubs like they have in the past. The emergent benefits from the field station as a thriving academic community, located in an active working site for field biologists, have diminished, if not fizzled.

Why has this happened? I think the answer is simple. Field biologists are no longer men whose spouses can stay at home with the kids all summer, or join them in the field to take care of the kids all summer. Decades ago, field stations that housed long-term senior researchers had trailing spouses who cared for all non-scientific matters, or had spouses who stayed at home and didn’t need to work for income.

All of us, regardless of gender, are now expected to support our families with a full combination of income, time, and direct parental care. I cannot be – nor do I want to be – the spouse that goes off to a field station while my spouse is required to tag along, or while my spouse stays at home. Either scenario requires me abdicating my responsibility as a parent. This summer, I’ve been away from my kid for almost a total of a month, over three trips, and that’s too much in my opinion. My situation isn’t different from many other biologists who are also parents, who have spouses who can’t drop everything during the field season.

I think my idea is reinforced, when considering the field stations that have maintained an active culture of long-term senior researchers. I haven’t worked there myself, but I’ve heard a lot about Rocky Mountain Biological Lab (RMBL), in southwestern Colorado. There is a large group of senior researchers who live on station full-time during the summer. Someone can correct me if I’m wrong, but I have the impression that nearly all of the senior researchers that work at RMBL have two parents that are both conducting research on site. So, there may be kids living on station, and these kids have two parents to juggle childcare together. Perhaps there are also senior researchers that have particularly flexible spouses or who are single. This seems to be a relatively unique scenario at RMBL, a special community that serves as home to two-career academic families over the summertime.

Another field station that has long-term senior researchers is Barro Colorado Island (BCI), part of the Smithsonian Tropical Research Institute in Panama. What makes BCI unique is that the Smithsonian employs many full-time research scientists whose job is to conduct research, often in BCI and the local environs. Other research stations don’t fully pay a big scientific staff to conduct research on site. However, it’s my understanding that the academic environment on BCI has atrophied a bit, with much of the community shifting to the little town of Gamboa, which hosts the launch site for the regular boat to BCI. Because working on BCI is pricier for long-term researchers, and Gamboa offers are more community for families, many researchers set up shop in town and may only occasionally visit BCI. Most of the senior researchers that live in Gamboa for longer periods are employed to work on site full-time. I suspect that senior researchers from universities abroad typically don’t work in Panama for longer periods, because of the same concerns about parenting.

If we want to promote long-term research in the field by senior scientists, then perhaps we could make sure that field biologists marry one another. Perhaps we could sterilize all field biologists.

I don’t have any practical recommendation about how to make sure that senior scientists spend more time in the field, which I do think would be good for science.

The field station where I work, La Selva Biological Station, constructed family housing more than 20 years ago, to accommodate scientists bringing their children. (I made use of this feature this summer for a couple weeks.) However, that can’t get me to live on station for the whole summer. While my kid could come along, my spouse isn’t going to drop her life to watch me at a field station all summer. I’m not going to take my kid away from my spouse for the whole summer and hire someone to care for him while I do science. The family housing can make me stay a little longer, but it can’t work for long periods.

The emergence of field stations in the United States happened during a time when most senior researchers were men who had spouses who handled the non-scientific aspects of their lives. Those times are gone. I don’t lament the change, but it does mean that field stations are less like to become long-term homes to senior scientists.

While I’d love to be at my field station all summer, I love my family infinitely more.

Am I less of a biologist by spending less than the whole summer in the field? Yes, I think that might be the case. However, my short visits to the field station make me more of a parent and more of a spouse. If there has to be a scientist/parent tradeoff, the parent side will always win out.

Note: I am writing this post while teaching a field course on Ants of the Southwest. Two of the course faculty are mothers, with their <2 year-old kids and non-ant spouses joining us on station. This bodes well.

Also, as an aside, here’s another prescription for helping improve the academic culture at field stations: shut off the damn internet between 8pm and 10pm. Lots of smart and interesting people hide with electronic devices when they could be interacting with one another.