Category Archives: Uncategorized

Tool use in ecology — conservatism & risk-taking

Why and when do ecologists adopt new tools — statistics, editors, workflows, systems, social networks? Obviously there is variation among ecologists — some adopt very early, others but those who adopt early are not only the first to reap the benefits; they also shape how their community uses and views these tools.

I’ve been thinking of this a lot lately, as I returned from the 2013 ESA. At the conference I was making new friends, meeting folks from Twitter, getting enthusiastic about nerdy things — all as per usual — and I tweeted about it:

And then there was controversy, and discussion, in the course of which I was branded <gasp!> a hipster (though not, it should be noted, for the first time:)

Caught Pabst-Handed

the author, at left, with a PBR at a local show. Brasstronaut in fact. You probably haven’t heard of them. Photo by Lewis Kelly

Markdown vs Word — a calmer, quieter Editor War?

Markdown itself has been defended already by better writers than I in these comments. There are lots of places to go to read about markdown. For example, Karthik Ram has several posts devoted to it — of which his “how to ditch Word” was most influential to me (e.g. I modelled my shell script on his).

You know what this reminds me of most? The great Editor War between emacs and Vi. Fellow ecologists — lets try to avoid starting our own, more underwhelming Editor war. Will we start referencing the “Holy Orthodoxy of Word”, or the “Zealous Cult of Markdown” or whatever? Face it, folks: the GNU/Linux community was there well ahead of us, and went way farther than we would.

The “You make me want to throw up” effect

Days after all this was happening, I found this excellent piece by Inger Mewburn. In it she describes the (sometimes scornful) reactions of her colleagues to her blogging. It struck me that a lot of content from that discussion could be copy-and-pasted into this one (maybe with a search&replace to change “blogging” -> “Markdown”):

This is quite true, but I still think the incentive structure is only part of the answer. Reluctance and determined avoidance may have multiple causes. The emotions that surround scholarly work are rarely attended to, but they are complex; ranging from curiosity and excitement to fear and envy and every stop in between. This volatile mix extends into online spaces.

Some of Dr. Mewburn’s colleagues really didn’t like that she was blogging. They thought it was frivolous, a waste of time, ‘unscholarly’. As she points out in the above quotation, the reasons people have for pushing back on a new tool can be really complicated. She compares the reactions she gets to her own feeling about the ‘cool kids’ in high school and, in my favourite quote, asks “have I become the cool kid? Am I witnessing a similar set of complex emotions, but from the other side?”

I was also reminded (HT Ethan White) of the classic TED talk featuring the first follower, that critical individual that turns a movement from an oddity to an event:

Whenever a new tool or technique comes along, we see some ecologists adopt it with zeal, some who eagerly follow the first, and others who hang back, saying “What’s in it for me”, “show me how this will improve my science first” etc. I think a study of how and why scientists adopt new techniques would be fascinating (as has been done already at CERN and I understand at NCEAS as well).

“Use what works for you” & the risks of novelty

One might argue that you can “Use what works for you” — select the tools that fit what your needs are right now. The alternative approach is to take the risk to invest time & effort in a new tool — and find your needs & mindset changing around it. Most of us are somewhere between these two extremes, though I think I’m more a proponent of taking a few risks and gaining the opportunity for serendipity.

You can’t really know, before you start learning a tool, how it is going to affect you, or your workflow. It is a risk, therefore, to adopting any new tool — the earlier, the riskier. You may waste a day, a week — or much more! — learning that technique, with no guarantee it will be useful once you do it. But you are risking something more important than your time: you’re risking your habits, your routine, even your worldview. Because you have no way of knowing, before you learn, how the New Thing is going to change your career.

For example, learning R didn’t just change the way I estimate parameters — it transformed how I collect, organize, and think about data. Learning git didn’t just help me version control my existing projects — it suggested a radical new way of organizing project directories. I’m sure that once I learn Python, Jekyll, SQL or whatever that my outlook will be changed again.

Early adopters determine the way a new tool is used by their community. Take github as an example. Look at Tim Poisot, who is soliciting comments on a preprint via his manuscript’s github issues page. Or look at Daniel Falster, writing an argument for opening up the massive TRY plant trait database and wants to know what you think about it. Is this the future of science? It might be! But if it becomes so it’ll be because these early adopters got up there and started dancing — not because they were using what had always worked for them in the past.

The graph and the serpent: a cautionary tale

The other day, my friends were walking out to the bar, which is right on the beach about 200m away (don’t be too charmed, its a sandy but really high-energy beach.  Not inviting at all.)  I really wanted to go too, but slightly stronger was my obsession with a figure that I almost had organized correctly.

Finally I got my figure! I had to learn some new stuff to do it.  A while ago I pledged I would only graph with ggplot2 until I understood it.  So that took a while.  I also read a wee bit about ordination techniques and spent some time selecting a pretty colour scheme.  The result!

The arrows show the before->after trajectory during the experiment, and the dots show the original, unmanipulated communities (more info on the experiment later!). Each panel is a block.  Yes, we named our experimental communities after Dr Who actors.

Lovely, isn’t it!? And a proper thing for an ecologist to be doing with his time in the field — already graphing and analyzing!  I felt pretty good about myself.

Then I caught up with my friends at the bar — and they showed me this photo:

I had missed seeing this awesome snake eating this lizard! They say that when then approached it dropped its prey and moved away, but when they saw it posed no threat it returned to swallowing the (very dead) animal. Photo Credit: Pedro Trasmonte (not me!)

So remember, ecologists — graphing is fine, and earning computer skills is awesome.  Just make sure you find time to look at awesome animals, too.

The happy doctoral student

I’m Andrew and I love being an academic ecologist.  I am happy, and doing ecology has always made me happy, and I intend to continue to be happy doing it until my brain goes back into the Nitrogen cycle.

Are you a new graduate student?  If so, you’ve been told you should quit.
You’ve been told you’ll be unhappy.  The narrative is told on all sides, with
ever wittier jokes and more devastating anecdotes.  I feel like as a good
blogger I should link to them, but I’m not going to.  They’ll find you.  Worse
than any blog are the examples of lives around us: quitting friends,
interminable PhDs, bitter postdocs, faculty who are in their 40s and still
eating dried soup because they have no time.

And yet here I am!  I’m in my 4th year of a PhD in ecology.  I’m taking down my last big field experiment tomorrow.  It is going to be five days of repetitive work which will do doubt yield a complicated, perhaps underwhelming answer to my question.

I love it!

Please understand: I am not a successful academic; I have published only one paper since starting my PhD — and that as a junior author.  Nor have I been groomed for this life from a young age: if I succeed, I will be the first PhD in my family, on either side, ever. Nor do I write you from some cushy position somewhere: I am in the field in rural Brazil — not the glories of the Amazon, but a prosaic hamlet in a National Park, cut off from my university community, my friends and my wife.

Nevertheless: here is a partial list of awesome things in my PhD:

  • Cultivating obsession with a single thing — I think about bromeliads (my favourite system) almost whenever I hear an ecological idea. The animals which live in bromeliads — the community that I have devoted my degree to studying — have become as familiar to me as my own cousins.

  • R — When I graduated from my undergrad, the best kind of statistics I could do was Excel regression lines.  Now I’m going on 6 years of R.  I love drawing graphs (I’ve recently fallen back in love with ggplot2).  I love when friends ask me to talk about stats with them, and I love improving those skills.

  • Foreign fieldwork — I’ve learned Portuguese and made lots of new friends and colleagues in Brazil. You can read all about that here.

Are there negatives?  Of course!  You want me to list them?  Well, I won’t because it’s the exact same list.  At least, it is for me.  Challenges are difficult! They ought to be.  The very things I love about grad school have caused me the most despair, doubt, and endless tortured nights.

Here is some quick advice, targeted at myself.  Perhaps it is also useful for you:

  • complain just the right amount — find some hardworking people that are about the same stage in their careers, and talk about how much the hard parts of academia can suck sometimes.  It’s normal to feel like this!  But remember to get excited about science with them, too.  Meanwhile avoid habitual complainers; they’re boring and they never learn or teach anything.

  • write down your victories — Write down the compliments that professors bestow on you.  Save grateful emails from friends and collaborators.  Every review submitted on time, every publication — remember them as successes.  BONUS I believe an edited version of such a list is called a “CV”.

  • work for free — A ridiculous thing to tell a grad student, perhaps.  But I mean it.  Every once in a while, drop what you are doing for an afternoon and obsess over a friend’s analysis, or his/her graph or design.  Nothing cures cynicism like sharing and supporting your colleagues.  BONUS: every time you get excited about science (yours or somebody else’s), you grow stronger against all the bitterness and doubt that erodes your ability to do your own work.

  • try to quit — In November 2011 I went to the grad secretary with the intention of asking how, exactly, you leave grad school.  I didn’t find out, because I decided I didn’t want to know.  If you try to quit, and you fail to do so, then you have another piece of evidence in your arsenal.  At least in my case, I found that one sincere, failed attempt to quit removed the desire more or less permanently.

  • read other narratives — There are happy successful academics in this world. They are on Twitter, they’re writing blogs and otherwise making things.  Go forth and find some! Some useful examples:
    and here

Finally I want to have a word with you, the older, wiser, but still-early-career ecologist who has read this with a mocking half-smile.  I acknowledge your suffering, and I honour you for your strength of character to have made it so far.  You are telling me that I have no idea of the trials I will face, that my puny resolve will be tested at dizzying heights of mental terror that you, alas!, know all too well.

Joking aside, I want to hear your advice and follow your example.  I know I’m at an earlier stage, and I need more experienced mentors and role models. But, it feels like the discussion around how we should feel about grad school has these miserable bitter people on one side, and super-positive cheerleaders on the other.

These grad students are not panicking about the misery of grad school.  Photo credit: Pedro Trasmonte
these grad students are not panickingg

Tips for a Successful Field Assistant — Researcher relationship

You can’t do a darn thing in the field without a good field assistant.  They can
make your field season wonderful, or they can be a permanent source of stress. A
field assistant is a weird confabulation of collaborator, employee and roommate
— and if you’re very, very lucky, a friend as well. I’ve had several wonderful
assistants throughout my grad school career, and this is a partial list of what
I’ve learned from them — written with lots of gratitude for all their patience
and hard work:

  1. Treat them like a junior collaborator, not a hired hand..  Lots of field
    assistants would be qualified for much more comfortable job than following you
    around with a field notebook — and yet they’re here, probably because they have
    the same kind of love for biology that you do, with less experience.  This is
    your chance to learn how to mentor a younger scientist — before you’re a
    supervisor.  Many assistants, in fact, end up in grad school themselves before
    long — you have a chance to help prepare them.

  2. Encourage feedback.  This is the other side of #1. Your assistant will
    save you lots of mistakes and missing data — but you’re going to have to take
    some criticism.  I think it’s the mark of an insecure scientist to shoot down an
    assistant’s suggestion, or to try to maintain some kind of ‘discipline’.
    Remember you’re out here to do science, not protect your ego.  If you’re doing
    it right, a passerby wouldn’t know which of you was ”in charge”.

  3. Let them indulge.  If your work is anything like my own, your fieldsite is
    rather far removed from a comfy office.  Your assistant is probably sacrificing
    lots for your project — such as Internet, machine laundry, skin free from
    mosquitoes, hot showers, etc.  So, if there are any creature comforts that
    they’re after — and if you can afford the time/cost — then do it. To
    paraphrase a similar post I once read ”if your assistant wants to spend 40
    minutes looking for fresh basil in rural Alberta, let them’.  Wise words.
    (another example: here in Brazil we make lots of brownies)

  4. Let them become an expert at one particular task.  I’ve learned to be
    comfortable letting a capable assistant carry out most of the work on one part
    of my project.  At first this kind of freaked me out, to be honest.  But it
    seems to me that when an assistant takes ownership of a component of a project,
    they work carefully and usually make many useful improvements on what you had
    first imagined.

  5. Let them use their strengths.  This comes back to ego.  Your field
    assistant will have different strengths from yourself; for example, all of mine
    have been excellent at organization and planning — much better than me (faint
    praise!).  Place a priority on the science, not on ”looking smart”, and let
    them lead parts of the work that are within their expertise.

All the science I’ve done has been better because of my excellent assistants.
What are your tips for field-assistant relationships?

Taxonomy tree!

Yesterday I wasted invested several hours in making this figure.  I used the amazing “Common Taxonomy Tree” through GenBank to type in the genus of each predator.  Then opened my new phylogeny in Mesquite (I have *never* used Mesquite before! or at least not since 3rd year) I popped in some extra polytomies for morphospecies of predators which are not identified to species (several are actually new to science!).  I felt pretty self-satisfied

Then I got to spend several hours trying to get the thing into R!  Turns out the trouble was branch lengths for my newly-added branches.  I eventually succeeded with this “arbitrarily ultrametric” tree.  It contains very little information — this is good, because we have very little information.  In this ‘tree’, the distances are only supposed to rank species by their relatedness.  So we see, for example, that Monopelopia and Bezzia are more closely related to each other than either is to Culex, which is satisfying.  It also shows the leeches (Hirudinidae) as being very far from everything else — though not so far as they actually are, since the division between these groups goes VERY far back.

This might not be quite the right way to include taxonomic information in an analysis.  But it IS approximately the one I was picturing in my head for weeks.



Yes! This week we welcomed two new researchers to our field lab.  They are my labmate Robin Lecraw and her assistant, Amelie Jauvin!  I am delighted to have more people around.  It makes the work more interesting, too, to have more people studying bromeliads at once. They are here to dismantle a large experiment which Robin set up last year.

I was going to put in a picture of them, but it came out very poorly focused so instead I have this symbolic picture of a rainbow:

an abstract for work in progress

I believe that many, if not most, field ecologists have, at some point, written an abstract for work which they are still doing, when the results are far from certain.

This is my vague conference abstract, and I would be delighted to hear what you think!

How do interactions between organisms shape their distributions?  How do these distributions compare with the range of environmental variables in which the organisms could survive?  The relationship between realized and fundamental niches is a central concept in ecology.  However, experimental tests of the relative importance of tolerance to environmental variables and different kinds of species interactions are still rare.

Tropical bromeliads (Bromeliaceae) collect water and detritus in their leaves, forming habitat for a diverse community of animals, with interactions including mutualism, competition and predation. Within a single species of bromeliad, these aquatic habitats can be small () or very large (), and may occur in a many different environments, from forest understory to arid, semiopen shrubland. This environmental variation, coupled with the species interactions, provides an interesting system in which to test species the effect of species interactions on environmental interactions.

We present preliminary results from a recent field season conducted in Southern Brazil.  Through a series of observations and experiments, we attempt to show how species interactions determine the distribution of species along environmental gradients in natural bromeliad ecosystems.

How the bromeliads got their spines

side A

There was once a certain wicked man, who hated all philosophers and scientists.  He hated them to such a degree that he sat, day after day, in the middle of the busiest part of town, armed with a sharp needle.  Whenever a philosopher passed by, he would stab the point of his weapon into their arms and legs until they ran away, bleeding slightly.

In delight the old sinner continued in this way for many years, until the scientists finally cried out in lamentation: “O deliver us from this persecution! We cannot work because our fingers are bleeding! We cannot research because of the wounds in our legs!”  Apollo hear their supplication and said to the wicked man “Behold, I have heard the cries of the thinkers you torment so much.  Because you have neglected to fill yourself with their wisdom, your mouth will be kept forever open, and will be filled with every rotting thing which falls into it, and this will be your only food forever”.  That instant the wicked man became a Quesnelia arvensis, and remained rooted to the spot.  To this day, scientists who get too close are stabbed.

side B
In a forest there grew a large patch of bromeliads.  They were happy and content, for the trees above them gave them shade, and dropped leaves which the bromeliads were glad to recieve.  Each bromeliad was also filled with a host of tiny helper insects, who broke down the leaves into delicious nutrients for their host.  The bromeliads grew and prospered in peace, until the Ecologists came.
The ecologists wanted the insects inside the bromeliads, but they did not care for the bromeliads themselves.  They stripped plants of their leaves, or plucked them from the earth and shook them upside down.  Sometimes they drained all the water, food and insects from a still-living bromeliad, and other times they tore the unhappy plants completely apart.
The bromeliads were helpless before this new threat, and loudly lamented their ill fortune: “O who shall defend us from these Ecologists?  When will we have our revenge on them?”.  Marsius the satyr overheard their wails, and turning to the bromeliads said “behold, you are not unavenged.  Do you not see how the spines on your leaves draw the blood from the ecologists?  Do you realize that the insects which live in your very leaves grow up to become the biting flies that torment them?  Therefore just as they drain you of your food, you drain their very lifeblood”  And thus the bromeliads were revenged on their tormentors.