Trial run, whooooo!

This week I did a full trial run of the field protocol, and it went GREAT! Super exciting!

Here is Marcia Macedo, being my field assistant for the day, even though she is a way better scientist than me and approximately one million times more experienced. Marcia rules! She was the official time keeper and data writer-downer. Plus she is my general advice-giver this week and always.

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Here is the set up of one of five chambers that we sampled every 20 minutes for an hour:

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Here is the picture of the lab where all the samples go afterwards and where the magic of soil processing happens:

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I spent much of last week scrubbing bat poo off the walls of this lab. So, needless to say, this lab and I are officially now old friends. Marcia noted that scrubbing bat poo off its walls is pretty much a mandatory rite of passage at this field site.

Samples!  (Yeah, those are empty bottles of air.  Experimental air!)

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One minor setback: when we were packing up the truck to head into the forest for the trial run, I picked up one of the gas sampling chambers and the o-ring around the edge had been all chewed up by some animal.

That was weather stripping from Home Depot, you bastards! It wasn’t meant to be delicious!!! Why would you eat that?????

Critters in the tropics will eat ANYTHING. Jerkfaces!

And the plot thickened! When I got back from dinner last night, what do I find? But a colony of ants eating more of my weather stripping!  Are you kidding me?

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So I dumped baby powder all over them, which seemed to scare them away. But not before one of the little guys made a beeline for me and bit me on the foot! Double jerkfaces!!! I guess I did screw up their dinner party… but, still.

Kate Brauman suggests smearing tiger balm all over things I want to render inedible.  Don’t think I won’t do it, my little ant friends.

In any case, now that the trial run went smashingly, all we do is sit back and wait for approval from the farm to conduct sampling on their fields as well as in the forest, all while having my fingers crossed that approval will, eventually, get the ok. If not, maybe this blog can become one of my dissertation chapters – eh, they’re pretty much the same thing, right?

The day that we flew a freaking DRONE

The most ridiculously amazing thing happened to me today. I stood next to a regular human being who flew a freaking drone over a portion of Amazon forest and mapped it. It took 20 minutes and it was the MOST. BADASS. THING. EVER!

Here are two pictures of Manuel Ferreira, a professor at Universidade Federal de Goiás (UFG), setting up the drone.


The thing, first off, is commercially available, which is insane. Sure, it costs $25,000, but in terms of scientific equipment that’s a vaguely accessible price. It’s made of some sort of fancy styrofoam and has embedded in it a little slot for a radio (to signal back to “home”, i.e. where you launched it so it knows where to land), a GPS (so it can fly a route that you pre-define using your friendly neighborhood GIS software), a camera (so it can take photos and map the place you want it to map) and two little rudders. Today the flight path we sent the drone on (!) flew over a riparian buffer zone of intact forest that my friend Marcia Macedo has studied.  “Urubu” (“vulture,” as we took to calling it) flew along the route at 300 m altitude (which is crazy high when you’re watching from the ground) and took photos at intervals along the way that were stitched together for one big photo of the forest at a 10 cm resolution. And then the drone flew itself back to us and landed calmly in a patch of soybean field without needing any extra instructions. An entire chunk of forest, photographed at 10 cm resolution, from a styrofoam airplane drone. That is nuts!


Manuel and his two colleagues (also from UFG) are here because they brought a group of 35 undergrads out to the field for a “short course,” a hands-on week long course that brings undergrads into field research environments (“prática integrada de campo II”, or the spring semester’s integrated field practicum). The students were great and I even gave a guest lecture about my nitrogen work in English while Marcia translated. My attempts at teaching in Portuguese were pretty hilarious.

Tomorrow we head back to town for the weekend, during which time I hope to post about my first chunk o’ data (rad!) and my adventures this week wearing lab gloves while scrubbing bat droppings. Research: very, very glamorous!

Getting my ducks in a row

What’s that phrase, a stitch in time saves nine? Field work kind of works that way, too. There’s a lot of time that you sort of feel like isn’t productive enough, but I have to remember to take the long view because if I don’t get your ducks in a row at the beginning it’s wayyyyy more difficult later to try and fix the problem/justify a decision I made. Inevitably I’ll screw a bunch of things up and not have taken care of them before the project started (first rule of field work: accept that for a bunch of the time it’ll be bananas), but the more things that I can guard against the better.

This week was (and next week will be) all about crossing those t’s and dotting those i’s. Luckily, I had a field veteran with me to rock some mentoring and make sure that I didn’t end the week curled up in the fetal position, weeping. This is Paul!

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Paul works as a researcher at WHRC and he is awesome. I adore him already. He’s been helping me put together the gas flux chambers and plan out a bunch of the organizational details that I had punted on until I got down here. (What time of day are we going to sample? How are we going to get everything done in the field with two people as efficiently as possible? What kinds of obstacles have other students run into that I should be thinking about? etc.) Paul is a complete treasure trove of wisdom about this sort of stuff. Plus he’s handy and rad and knows tons of science.

First thing we did was build a bunch of nitrogen gas flux chambers. Rod Venterea at UMN came up with this design for his lab and passed it on to me, but a lot of the assembly I waited to get in country to do since the materials packed up smaller as component parts:

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(More about Rod and his insanely great lab manager Mike Dolan in a future post I’m going to call “people who saved my butt when I was getting ready to leave for Brazil”… or something like that.)

We also had to go out into the forest and come up with a way to get the chamber bases (i.e. the bottom part of the chamber that we attach the top part to in order to capture the gas fluxes) into the ground as easily as possible. Baxi, one of the many amazing field workers at the ranch, carved this cool board to fit the bases perfectly so all I had to was jump on the thing a few times and, boom, I was ready to do science!


Finally, nitrogen gas fluxes are regulated in large part by temperature and soil water content, plus the amount of nitrogen floating around in the soil that’s available to bacteria. Soil water content we can’t really control, since rain drives it, but what temperature the soil is when sampling we can control – by sampling during the morning (cooler soil) or the afternoon (warmer soil). For this study, I don’t want to look at temperature changes, but I do want to make sure that I’m not sometimes sampling in the morning and sometimes sampling in the afternoon – i.e. I don’t want to introduce a confounding variable into the study. So, I need to have a sense of how much the soil temperature varies over the course of the day so that later I can justify that a sample at 10 am is within roughly the same temperature regime as a sample at 11:30 am.

So we did that! Paul and I (ok, Paul) set up two thermocouples to take the soil temperature every 15 minutes a few inches below the soil surface in a forest plot and in a soybean field. At the same time, I recorded what my analog soil thermometers reported the soil temperature as to make sure that the thermometers didn’t vary from each other and that they were aligned with the thermocouple data.

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Happy to report that there were no lemons out of my eight thermometers!


We’ll pick up the thermocouple equipment and download the data on Monday (it’s been running since Thursday) and I’ll get to take a look. Very excited to do so! Aside from letting me get some hands on some sweet data (data!!!!!!), I’ll get to head back into the forest. Yessssssssss!


Double take

Very busy and exciting week down in a floresta (the forest) – got a bunch of the equipment sorted out and built, tested out methods in the forest, and set some equipment up to get a few days worth of soil temperature data for use later. Awesome! And I’ll do a lengthier post about the details of all that at some point, hopefully tomorrow.

In the meantime, I wanted to give a sense of how extreme it feels to have large-scale, industrialized ag jutting up against Amazon forest. For a lot of the work I’ll be doing, I hop in a pickup truck and drive 20 or 45 minutes to a forest or cropland site that we’ll be sampling. Along the way, we’re routinely driving along roads with primary Amazon forest on one side and wide open soybean fields on the other side:

These are my friends Paul and Danúbia. We were heading to a northern part of the farm to check out how much harvesting had been done already. (Side note: they are rad!)

Sometimes the contrast is ridiculously striking, like when Paul took the scenic route north so that we could go check out this emergent tree (tree that is taller than the majority of the tropical forest canopy) that happens to have landed right next to the road.

huge emergent tree

Mato Grosso: formerly the wild frontier, now just a place where two completely different ecological worlds intersect.

Olá do Brasil!

Hey-ooooo! I’m in Brazil!

More precisely, I am in Canarana, Mato Grosso, an ag town on the border between the southeast Amazon forest and Brazil’s cerrado (tropical grassland system, pronounced say-ha-dough). Oooooh, embedded google maps! (This only worked on my browser after I refreshed, FYI.)

You can also see from the map that this is an area with tons of land-use/land-cover change. Lots o’ agriculture. Lots o’ opportunity to study its impacts on the Amazon!

All that being said, I’m primarily just thanking my lucky stars that I got here without losing either (a) any luggage or (b) my sense of what day of the week it is (though the second is debatable).

On Wednesday, Charlotte and Kristen, two amazing friends from my cohort at UMN, helped me pack up the ridiculous amount of science stuff that I carted down here into a few bags, with David tagging in for the last half of the packing and for the critical transfer of stuff from Living Room to Airport.

Charlotte and Kristen appropriately dubbed this Science Christmas:
Science Christmas!

After a crazy Thursday and Friday of getting all the last details in order (“Where is the Neosporin???”), I left Minneapolis at 4 pm on Friday, get routed through Atlanta and then down to Brasilia overnight. So far so good!


Next up: getting from Brasilia to Canarana, which involves getting through customs, finding a cab, getting to the bus station, waiting there for 10 hours, and then catching an overnight bus at 7 pm on Saturday so that I arrive into Canarana at 10 am on Sunday. All while hopefully making liberal use of the phrase “só falo um pouco de português” (I only speak a little Portuguese) and hoping that folks take pity on me. Since Brazilians are basically the nicest humans on earth, this strategy actually worked!

The Brasilia Terminal Rodoviária (bus depot), where I spent most of Saturday:
Brasilia Terminal Rodovaria

My five (!) epically huge bags, ready to get safely on the bus and trundle into the heart of Mato Grosso:
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And now I’m here! Good times! My friend Paul from Woods Hole is here too, to make sure that I get off to a good start and to help out with some other projects. Plus I’m excited to see the friends that I made this summer when I was visiting to plan things out. Things are officially happening!

When we’re in town (i.e. Canarana), I’ll be staying at a hotel that has internet and I’ll be relatively on the grid. This’ll be weekends, mostly. During the week I’ll be in the field, which often has internet too, though it’s a lot slower, so not skype-able. Though hopefully tomorrow I’ll pick up a local cell phone so I can text back and forth to the US!

We’re leaving for the field sometime tomorrow morning. This week is going to be all about setting up the equipment that I brought down, troubleshooting the things that I only sort of have a plan for, and testing out the methods. I’m also hoping to do a quick trial where I take soil temperature measurements every 90 minutes or so in the shaded forest and the open fields so that I have a good baseline idea of what time of day we should be sampling during to get the best temperature representation. Data! Plus that’s exciting since it involves actually writing stuff down and whatnot – a good way to test out the systems I’m going to put into place, like what notebook I bring with me, how I’m going to transfer the data and documentation to the laptop I brought in an organized fashion and where the different supplies that I’ll use most often are going to live. And I’ll get to make a pretty graph at the end!

I am zonked, so off to bed for me. Night!