Field work got messy last week (this is a warning for messy pictures below).

Most days of working in the field start out the same: Kezia and I wake up, drive through canyons with our radio receiver and telemetry equipment to listen for sheep and scan hillsides for visual cues of ewe groups. But on Sunday, we strayed from the normal routine of collecting observational data when our scopes hit something we’ve been both expecting and fearing: our first dead sheep.

Working amidst an outbreak, death is expected. Disease kills. We recognize this when we talk about disease imposing selection pressure, when we talk about host-pathogen evolution, or when we talk about virulence-transmission trade-offs. Death is different when it looks like a dead sheep on a hill side.

What do you do with a dead sheep? Kezia and I were told that we needed to recover the carcass and bring it to the vet lab where necropsy experts could determine the cause of death and microbiologists could test for the presumed causative agents of pneumonia. A carcass contains valuable data in an epidemic setting, especially in a system with a small population size, difficult terrain to navigate and rarely observed fresh carcasses (in remote areas, carcasses are sometimes not found for 5 to 10 days, if not months postmortem when body conditions are close to clean bones). We were told to find the carcass, hike it back to our truck and then deliver the whole body to the vet school in Pullman.

What do you do with a dead sheep when you can’t carry it back to your field truck? By the time we found additional hands to help carry the sheep, and managed to hike our way to where the ewe died, she had been dead for 40+ hours. Her carcass, sitting on a cliff in the middle of a hot Hells Canyon, was colonized by maggots. The skin sloughed off when we lifted the body. One-hundred-fifty pounds of dead weight needed to come down an incline that took both hands to boulder up. We could not carry the whole body out of the canyon, at least not in one piece.

Maggots break down tissues quickly postmortem. Forensic entomologists can use images like this one to gauge how long a carcass has been in an area and estimate time-since-death.

Option B was to do a necropsy in the field and bring back the essential parts which were more feasible to carry: the head and the pluck. For pneumonia, the most important samples come from the lungs, trachea and respiratory tissues.

I had never done a field necropsy. I had never touched a sheep. I was supposed to bring back the pluck. What was “the pluck”*?

Lucky for Kezia and me, one of the field biologists who tracks the bighorn population across the river from where we work had done a necropsy before and was willing to show us how it is done.

This is how you do a field necropsy:

Step one is to remove the head and try to take the pluck out intact. You do this with tools included in a “necropsy kit” — the kit includes a large knife, a saw, pliers, sampling bags, gloves, and a cutting scissor-like tool that reminded me of pruning sheers (you use those to crack ribs if the lungs don’t slide out).

Step two is to take out other organs which may not have come out with a first attempt to slide out the pluck. Bodies decay quickly in summer sun so we needed to remove additional parts of the lungs which were not removed with the trachea and upper respiratory tract (the lungs had nearly liquefied).

Step three is to take proxy measurements of the sheep’s health status. You do this by looking at the bottom of the hooves and checking the color of the bone marrow. With the hooves, you are checking to see if there are any abnormal growths, a common indicator of poor health in bighorns. The color of the bone marrow is used to gauge nutritional status. White bone marrow is healthy and rich in fats, indicating that the sheep had high enough body fat that it would not have died from starvation. Red marrow indicates that a sheep has used up all of it’s bodily fat reserves and has begun to use it’s last reserves — the fat reserves in the bone marrow. Our sheep had nice white marrow.

The inside of a femur bone gives us a glimpse of marrow, which here looks healthy as indicated by the white to pinkish color.

Step four is to bring back the samples to a lab where other scientists can test for pneumonia pathogens and give us a better idea of the cause of death. Even if the ewe did not die of pneumonia, testing the respiratory tissues for pneumonia agents will give us an idea of whether she had been infected in the past or was harboring low densities of pathogens that may not have made her sick but could have allowed her to spread the infection to sheep in her ewe group or to young lambs in the same group.

The data we obtain from carcasses will give us a better idea of the prevalence of infection in the population and the mortality rate associated with pneumonia. When we recover samples like we did on Sunday we hope that we are working toward a better understanding of how, when and why the outbreaks occur. The experience has left me so far with a deep appreciation of data from wildlife systems: often we look at a data set and see points on a graph. Out here, I am reminded of where mortality statistics come from and what disease as an evolutionary selection pressure looks like “on the ground.”

*the pluck is a term used to refer to internal organs

You find yourself standing in an empty lab thousands of miles from home and it is time to do something. When I thought about his moment previously it filled me with terror.  How do I start?  What does a PI do?  I have no formal training in this!  Strangely, I have now spent an entire fairly productive first day of work writing manuscripts and grants, email collaborators, looking into new lab members, and setting up the lab. So while, I still have a ton (A TON) to learn, I am happy to report that I have been 100% “Miyagied”.

For those of you unfamiliar with this term.  It is derived from the name of a character in the 1984 film, The Karate Kid.   Mr. Miyagi offers to train a punk kid named Daniel the ways of karate. Daniel is highly irritated to find that his training includes repetitive menial tasks such as painting Mr. Miyagi’s fence and waxing his car. However, when Daniel finally starts to learn how to fight he discovers that these tasks were training his muscles to make him a hard-core karate fighter (and go on to defeat the jerks of the Cobra Kai dojo, but that is another story).

So I don’t quite know how you did it, but thank you Drs. Harrington, Read, and Thomas!  And those that are soon to follow me: trust the process.

Wax on. Wax off.

Walking is pretty complicated.

Jessi very kindly sent me this article about how walking might help get the creative juices flowing and perhaps even improve memory. My daily commute is about 40 minutes each way, which sounds awful, but since I’m walking it’s actually very nice. I live along a well-serviced bus route, so if the weather gets bad I can always take a bus, but even though it only takes half as long, I end up staring blankly at my computer screen waiting for my brain to start up. A critical part of a successful walking commute is not getting too absorbed in a problem: a few weeks ago I was thinking about the issue of how to detect what malaria parasites invest into transmission to mosquitoes, and I stepped right in front of a car. It could have put a serious dent in my thesis, but fortunately I was downtown, where drivers expect that kind of behavior from pedestrians. I always figured that most people who wandered out in front of cars were drunk, but perhaps a few of them are just thinking too deeply about how best to use splines in their current scientific dilemma.

Skype. Adobe Connect. Gmail. Google Hangouts.

No one picks up the phone to call someone anymore, and rarely does a personal letter arrive by actual mail. We live and work connected to the computer, and increasingly, smart phones. This isn’t a surprise or really any great insight, but I’ve been thinking lately about how it has impacted scientific research.

We have a constantly moving culture where part of the definition of “scientist” seems to overlap with “nomad”. What this means is that while we are moving between universities and forging new collaborations at each one, that connections aren’t ever lost. (Shout outs to all of the Thomas/Read group nest-fledgers, most recently Lauren Cator – good luck and keep in touch!).

Even long after leaving an institution it is possible to publish in collaborations spanning several universities all across the world using these connectivity tools. As tricky as managing time zones and online meetings can be, I think that overall this type of connectivity has increased the quality of scientific research by allowing those with the experience that fits a given question best to come together online and come up with some cool ideas.

What’s your favorite technology?

Sunset in Hells Canyon — my new home for summer

I am on a wild sheep chase. Since Saturday, I have been mountain climbing, stream crossing, truck driving, tracking across Idaho, Washington and Oregon, and keenly watching through binoculars to find wild bighorn sheep. It is early May so the bighorns are lambing. Ewe groups start breaking apart as future mothers find quiet caves to give birth, rejoining groups when the lambs are old enough to walk.

Today the sheep look healthy. The fields are green from spring rain and the bright yellow asters dot the hill sides. Lots of food for sheep, no predators in sight, the sheep here should be thriving. But the populations have seen rapid declines since the 1990s from a different threat: spring pneumonia outbreaks.

Pneumonia has wreaked havoc on North American bighorns, wiping out a third to 90 percent of a herd when an infection outbreaks. There are many questions to ask in regard to why the outbreaks occur when they do, how they are spreading, what is spreading, and what we can do about it. There are lots of whys, hows and whats for ecologists to explore. So for the summer, I have moved west to ask a few questions of my own and to learn about the questions people here are already asking and learning much about.

I am working with Kezia Manlove from Pete Hudson’s lab and other members of the Bighorn Disease Research Consortium to better understand why these outbreaks are occurring, how to prevent future outbreaks and to assess management strategies that might help preserve the bighorns.

Each morning, we head out to the field, climbing and hiking through Hells Canyon to find radio-collared ewes which might have new lambs. We then perform behavioral assays to assess health and identify likely transmission behaviors. We monitor each sheep daily (provided we can find her in the miles and miles of canyon we cover) and track signs of disease.

When we set up our scopes on the sides of the road, people will stop to ask us what we are looking at. Maybe it’s a rare site to see two young women sitting on a hillside staring through scopes from sunrise to sunset. We get the opportunity to become community scientists when they do and explain to the public what we are looking for, why we are doing what we are doing and what we hope to learn. People are interested. People love the sheep and wonder the same thing we are: where have they all gone?

Our field truck. Four wheel drive is a must. Scopes at the ready.

The field is giving me a new perspective on being a disease ecologist. When I ask Kezia about how she started working on the sheep project and why she continues to, she says she remembers the first time she had to clean out a dead baby lamb from one of the hillsides and take its carcass back to the veterinarians in Lewiston. It’s different from working as an “indoor biologist.” When you study something in the field and you can figure out how it works, getting a positive result means that one day you don’t have to carry out anymore dead babies. Success means a lot out here, if tomorrow we are cleaning up dead carcasses and in a future year we see healthy growing lambs.

There is something about seeing and living among your study organism that gives me a new drive to keep doing what I’m doing.

For now there are no signs of pneumonia. If an outbreak hits, I’ll keep you all posted.

Can you find the bighorn in this picture? They are good at hiding.