From the Field to the Lab

Read about MA second-year Erin Eastwood’s genetic work with Fijian fishes!

Erin Eastwood

Over the last two months I have transformed from a perpetually damp, wetsuit-clad, village-hopping field scientist, into a (relatively) well-dressed, city-living, pipette-wielding lab scientist. Where I used to spend most of my time chasing fish around with my spear and catch bag, my life now largely consists of moving tiny amounts of liquid from one tube to another. And surprisingly enough….it’s pretty darn awesome.

IMG_7451 Step into my office.

Lab work is enjoyable to me for two main reasons – first, I am constantly in awe of the fact that we humans have even FIGURED OUT how to extract, amplify, and sequence DNA from living tissue. The decades of brainpower, creativity, and technological innovation required to make those little A’s, G’s, C’s, and T’s come up so nicely on our computer screens is boggling, and keeping that in mind brings a certain kind of appreciation to even the most tedious tasks at the bench. That’s not to say it’s always totally easy and…

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Oil Palm Development and Human-Wildlife Conflict in Cameroon

Greetings to my fellow Masters students working hard on summer research and also to all you kind readers interested in our adventures! I am writing from the town of Mundemba in Southwest Cameroon, where I have been based for just a little over a month now for my research on human-wildlife conflict. I had hoped to write earlier, but in just the first week my computer was tragically killed during one of the frequent power surges. Electricity is patchy and internet nearly non-existent. But, alas, I am writing now – here and well and better adjusted to the trials and tribulations of research in Cameroon!

For those of you not familiar, my research is centered on understanding human-wildlife conflict in the form of crop raiding within the context of existing and increasing oil palm development in Cameroon. Oil palm production has gained international attention in recent years due to the extensive deforestation and human displacement caused by plantation expansion in Indonesia. Now, many of the same Southeast Asian companies operating in Indonesia, in addition to new oil palm companies from the U.S. and Brazil, are looking to the forests of West and Central Africa as a new frontier for expansion. There are many reasons why large-scale oil palm production will differ between Indonesia and Africa, way too many to address here. Most significantly, the oil palm tree (Elais guineas) is native to Africa, so palm oil and its by-products hold significant cultural relevance bolstered by a long legacy of smallholder production. I chose to conduct my research in Cameroon, a country where many industrial oil palm concessions are in the works, because I believe the potential impact of these companies on human-wildlife conflict surrounding forested areas needs to be addressed in the African context.

My work here in Cameroon involves visiting four different villages at varying distances from two protected areas – Korup National Park and the Rumpi Hills Forest Reserve – and two oil palm production sites – one a long-standing government-owned oil palm plantation called PAMOL and the second a recent concession acquired by SGSOC (Sithe Global Sustainable Oils Cameroon). Within each village, I spend two weeks interviewing households chosen through systematic random sampling of homes. Each interview involves a set of around 40 questions regarding basic household information, diet (particularly bushmeat consumption), farming, and perspectives on land use change. The section on farming is the most substantial part of the interview. I ask about the different animals that visit the participant’s farm, how frequently, and the extent of damage for each animal. I then schedule a time to visit the farm and take a GPS point so that I can later uncover spatial predictors of crop raiding.

So far, I have completed a pilot study in the village of Meka Ngolo, two weeks in the village of Mundemba II, and am now wrapping up my first week in the village of Ikondo-kondo. Each village has proved to be an enriching experience for my perspective of conservation science in practice, as well as my personal development. I have been received with welcoming arms and in many cases, enthusiasm, because my research indirectly provides an outlet for them to express the daily grievances they face with the animals damaging their farms. As the majority of people in these villages identify as farmers, the damage caused by animals on farms often has significant consequences for household income and subsistence. Thus, it is not surprising that the direct, negative impact of animal raiding behavior on livelihoods often results in lethal action.

As I carry out my research, there have been some really interesting developments. I am not able to describe all of them just yet (without some preliminary analysis!), but one revelation concerns how deeply entrenched human-wildlife conflict is with broader elements of land use and tenure in this region. Both Meka Ngolo and Mundemba II share close boundaries with the Rumpi Hills Forest Reserve and the PAMOL plantation – two vastly different land use types with their own set of restrictions to farming. The village I am currently working in, Ikondo-kondo, was resettled out of Korup National Park fourteen years ago to a new area where crop-raiding by elephants is on the rise. And so, as goes the scientific process, I am working on adjusting my framework to incorporate the critical, changing dynamics of land use.

All in all, I am finding my time here to be incredibly rewarding. The work has certainly not been easy. Interviews often require tricky translation into Cameroonian Pidgin and local dialects. Visiting farms often involves trekking up hills that feel as if they are on a 90 degree incline, crossing wide streams and failing to keep my wellies dry, and trotting through thick farm bush that is known to hold Rhinoceros vipers and pythons. However, at the end of each day I remember that I am very privileged to be here – learning from the rich, bright culture of Cameroon while trying to make a dent in conservation practice through my work!

-Cynthia Malone

Careers and Communication: My top 5 takeaways from the ComSciCon Conference 2014

Out of the classroom and into the field! Summer is all about learning in unexpected settings and in new ways.

ComSciCon, at the Microsoft NERD center in Cambridge, Mass.

ComSciCon, a science communication conference at the Microsoft NERD center in Cambridge, Mass.

Hi! I’m Amy– a grad student in Dr. Josh Drew’s research group here in Columbia’s E3B Department. My research focuses on the diversity of coral reef fish in the Indo-Pacific Ocean. I’m interested in how these fishes have evolved, and how they have migrated over generations to populate the reefs they now call home.

Lately I’ve also been thinking a lot about science communication– how do we as a community share our research with a broader audience to increase enthusiasm (and funding) for science? And moreover, for the 9 out of 10 graduates who won’t find a tenure track job in academia, how do we parlay our salmagundi of skills into employment?

The majority of the year, I’m right here in New York, tackling the beast known as thesis research, quietly repressing thoughts of my next career move. But summer is a special time. It frees up a few weeks to mix up the normal routine, get out of town, and pursue new ideas in far-flung locales.

So, spicing up my summer work regimen, I headed to exotic Cambridge Massachusetts last week for ComSciCon 2014 –a conference all about communicating science! Over four full days, 50 graduate students met for a series of workshops on the effective communication of science to non-scientist audiences.

This conference is centered on a series of interactive panels, where policy makers, journalists, and academic research scientists discuss the state of science communication today. Central questions included: How is science portrayed differently to lawmakers on Capitol Hill, or to the general public, than it is to graduate students or research scientists? How do scientists perceive STEM, and are we effectively communicating our vision to broader audiences?

While we talked about communicating science, we also talked about working in science. And after each panel, I schmoozed; I dug; I generally begged for advice. Here is what I found– my top 5 insights from ComSciCon 2014:

 A graduate degree is not a silver bullet

Duh. These days credentials aren’t enough– your experience, skill set, and network matter tremendously too (more on this in a moment). But for students in the STEM fields, that realization comes as a particularly painful slap in the face. We used to have it good, man– a grad degree once translated to relative job security– but alas, no more. Now, at best, 1 in 10 PhDs will find a tenured professorship, and unfortunately, there isn’t a textbook on the way forward for everyone else.

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Outside of the ivory tower, career paths are numerous and decentralized. That well trodden pathway of PhD à post doc (or three) à assistant professor à tenure forever (!?) is actually quite unusual in it’s linear clarity.

A few universities are responding by creating graduate career counseling offices– previously unheard of in academia (Check out UC Berkeley’s Beyond Academia for one example). Resources for non-academic job placement are certainly growing as academic positions dwindle, but clearly outlined stepping stones to alternative careers are still a long way off.

 Networking is (almost) everything

So, there’s no silver bullet. Bummer.

But, after schmoozing ComSciCon panelists (ostensibly very successful people) around the hors d’oeuvres for four days straight, I did come away with one majorly helpful realization: the common denominator between all these employed people is a kickass network.

Panelists overwhelmingly cited networking and luck as the major factors that helped them get their start. And that makes sense doesn’t it? Graduate students are (for the most part) smart and driven. So what sets you apart in a sea of ambitious smarties, all looking for similar jobs? Leveraging a pre-established connection to someone on the inside, that’s what.

The beauty of a conference is the people you meet and the network you build.

That’s a great advantage of grad school too; the ability to attend conferences and workshops that would be unavailable to non-students allows us to build those critical connections now.

 Marketing Matters

IMG_0049Scientists need to stop hiding behind jargon, and learn to communicate science to non-scientists in interesting ways. That’s the whole message of ComSciCon! By and large the people attending this conference already know that.

But herein lies a dilemma. As journalist/ ComSciCon panelist Phil McKenna said, (and as panelist Dietram Scheufele subsequently tweeted), “If you lose the jargon, you lose precision; if you don’t, you lose the audience.”

Is that a real tradeoff? Do we have to sacrifice information quality to make science accessible? I don’t think so. Science communicators shouldn’t sacrifice intellect for buzz. So, especially when challenging technical content is involved, the way we sell science matters tremendously.

If we step out of our labs and communicate, but we do it on blogs that no one reads, or on esoteric sites only known to other scientists, we’re just preaching to the choir. To reach people who don’t traditionally seek out science news, we need to find a means of communicating that retains challenging technical concepts, but shares those ideas in engaging, accessible ways with many, many people.

Unfortunately, ComSciCon didn’t host a panel on the specifics of effective marketing. We established that broadly accessible science communication is important, but didn’t set out actionable next steps.

It’s a pitfall of conferences in general I’d say, that panels based on the exchange of good ideas don’t necessarily translate into actionable steps back home. Because speakers are addressing large and diverse audiences, they tend to focus on somewhat generalized ideas, rather than laying out a protocol to change the field (or the world).

As a biologist, I like protocols. That said, even the most distinguished conference speaker can’t tell you what to do, or how to live your life. So how do we make positive change then? We write. We communicate. We just start, and en masse, find our voices and share them. Lose the jargon (but don’t assume the reader is an idiot) and communicate your research wherever you can.

It’s a process.

Be prepared to struggle. Be prepared to fail. The development of a career is an organic process and takes a looooong time.

Panelists overwhelmingly cited grit, rather than credentials, as key to their success. The tenacity to keep working and failing had carried many through years of career flux and financial insecurity, while they built up the network and experience to land more stable, permanent positions.

UGH, right? The prospect of protracted struggle and failure isn’t pretty, and certainly won’t increase the appeal of STEM outside of academia.

In terms of reach though, it seems that science communicators themselves are accessing broader audiences than ever before. As more and more trained researchers leave the academy, a new crop of science communication outlets has emerged. From quarterly publications like Nautilus to weekly podcasts like Radiolab, science communicators have more fingers in the pie than ever before.

Hopefully this means that if we continue to work together on smaller projects in the short term, there will be more large-scale opportunities in the long term.

Invest in the hours of your life, not in the idea of what you want to become.

Don’t get me wrong– it’s important to have long-term goals. Treat them as the cardinal directions on which you set the compass of your life. But then, rather than asking, “What do I want to end up doing?” ask, “What do I want to try next?” and “How can I put myself in a position to do that?”

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All photos A. McDermott

If you invest in the moment and pursue the things you can’t help doing, you’re apt to take the inevitable challenges in stride, and to keep pushing through those early knee scrapes.

Not everyone has the privilege to do what he or she loves (financial security be damned), but if you are one of the lucky few with the opportunity to chase a not-so-lucrative passion, capitalize on that luck. Use it to build a more scientifically literate society. Use it to increase interest in science. Use it to build the foundations of a more diverse future in STEM!

–Amy McDermott

The Truth About Fieldwork

Fieldwork is about how well you can adapt. If you can’t adapt, can’t make plans on the fly, have no creativity and a quick temper you’ll never make it in fieldwork. And that is because fieldwork is never what you expect it to be. Even if you already know your field site well anything can happen out in the field and you always have to be on your toes. An example, you ask? Well the perfect one happened on base a mere few days ago.

            With some of the newly arrived volunteers gone for a day in town, Brie, a GVI staff member, and I were changing a gas bottle for the fridges. We requested some of the older volunteers to take the empty gas tank over to the garage and bring a new one over. A few minutes later we hear one of them shout “Yo…. Fire!” (to give him a little credit, he did have a slight panic in his voice). Looking over towards the generator we saw high flames pouring out of the window. Now, I also understand that people exaggerate. Especially people who want a good story. I definitely have been known to do this before. However, in this instance, no exaggeration is needed. Flames were pouring out the window. Now, unless you are a trained fire fighter, nothing really prepares you for that moment, aka, what the HELL are you going to do with high flames pouring out of the generator room, which is full of diesel and oil covering the floors? In an act of pure stupidity or bravery (I like to think the latter, but I know it was the former), I quickly grabbed the nearest fire extinguisher and ran straight into the generator room. Having spent hours of my childhood staring at fire extinguishers dreaming of yanking out the pin and spraying the extinguisher fumes everywhere just for the hell of it, I knew the general idea of what I needed to do, even if I never had needed to actually use one (I strongly urge for all of you to look at your own fire extinguisher and do the same, it does make a difference if you’re in an emergency). Keeping the volunteers at a safe distance away from the flames and building, we used 7 entire fire extinguishers to kill the fire. That’s right, 7. If you still thought I was exaggerating about how big the flames were, now you know. 

 

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So after that whole saga you would think that everyone would be done for the day. Or at least the vehicles and machinery would give us a break. Unfortunately, not to be out done by the generator, on of the bakkies on drive started smoking and burnt the battery wire. With minimal staff on base, and minimal functioning vehicles, Melanie and I delivered a new bakkie for Brie to continue on her drive while we waited with the broken/burnt bakkie for another vehicle to tow us back. By the time we have gotten the bakkie out of the dip and towing back to base the sun was setting. It’s frustrating when you get pushed back an entire day just because of things no one can control, however that sunset, like every sunset in Africa, just makes it completely worth it. And I think that is what I love most about fieldwork and being out in the bush. Every day is completely unexpected. You don’t know where the animals are going to move, you don’t know how they are going to react, you don’t know if your vehicle will get stuck or not… and you don’t know if your generator will explode randomly. But that’s good. It keeps you on your toes and forces you to constantly make plan A’s, B’s, C’s etc. A skillset that everyone should have.

And lets be honest, no one would love fieldwork if it was boring…

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(photos are of the presumed source of where the fire started, the seven fire extinguishers we used, and the aftermath of the generator room after being sprayed by fire retardant chemicals!)

—Kaggie Orrick, Masters candidiate, posted from South Africa

Did You Know?

Fun Facts about South African Animals by Kaggie Orrick

Did you know that porcupines can stay afloat in water because their quills keep them buoyant?

Did you know a rhinos horn is actually made of keratin, which also makes up your fingernails and hooves of cattle?

Did you know that a leopards tail is rounded while a cheetahs tail is flattened so it can act as a rudder and keep it balanced while is sprints?

Did you know elephants can communicate from kilometers away by feeling the vibrations through the ground? They can also hear each other from up to 8 kilometers away via trumpeting. 

Did you know that a type of amphibian called an African plantanna can tell you if your pregnant or not? (a dose of a pregnant womans pee will cause the female plantanna to lay eggs within 8 to 12 hours…)

Did you know you can tell the difference between a cat track and a dog track by counting the number of lobes on the back of the pad (dogs have two, cats have three: I would show you all a picture however my internet is too slow for photos at the moment!)

 

 

More fun facts and interesting information about my research to come!

Preparations of a Lab Rat

Welcome to the first text post of the summer! I’m Natalie Hofmeister, one of two Natalies in this group, and this summer I’ll be writing about my work in the Rubenstein lab here at Columbia. Given that most of us are in transit or getting settled at field sites, I’m starting us off with a run-down of what I’ve been doing to prepare for the summer. In a two-year Master’s program like Columbia’s, we complete the bulk of our thesis research during the summer in between academic years. However, there is a lot of preparation to be done before the summer begins: writing grants, planning methods, ordering equipment and supplies, and – of course – lots of reading. For me, preparation meant a semester of primer design and testing before I could get to data collection.

My thesis focuses on signatures of evolution in the glucocorticoid receptor, a gene that is critically important in the production of the stress response. To look at variation in this gene (NR3C1, which stands for nuclear receptor subfamily 3, group C, member 1*), the first step was designing primers for each of the eight exons. Beginning in January 2014, I spent many hours on the computer and in the laboratory, designing and optimizing primers. Luckily, I had a great teacher (Joe Solomon, thanks for your help!), and after a few months I now have primers for all eight exons and I’m ready to start collecting data.

*Finding that all of these strange combinations of letters and numbers in molecular biology actually mean something definitely made life a lot easier to understand.

Superb starlings, one of the species I study (Pedro Fernandes, Cornell Lab of Ornithology).

Superb starlings, one of the species I study (Pedro Fernandes, Cornell Lab of Ornithology).

So, what goes on behind-the-scenes? Many molecular projects go through the same steps I did this spring, so I’ll try to demystify what we do in the lab.

1. Half of my time this spring was spent designing primers and aligning NR3C1 sequences on Geneious. Obviously, I needed to begin my project by learning to use the software that could analyze all of my sequences. So, I started at the computer, trouble-shooting in Geneious. First, I aligned the superb starling transcriptome (constructed by Joe Solomon) to putative sequences of NR3C1 in the zebra finch and the chicken. Once I developed a hypothesis of the starling NR3C1, I designed primers for each exon using the built-in commands in Geneious. The image below shows an example of a primer with the selection criteria we use to judge which primer is best; generally speaking, you want a primer with about 45% GC content and low scores for dimer and hairpin formation.

An example of primer design in Geneious from the manual (v5.3.6).

An example of primer design in Geneious (Geneious Manual v5.3.6).

 

2. I spent the other half of my spring testing those primers. Usually, in testing primers you start with a temperature optimization to test the primers at many different annealing temperatures, and then proceed to magnesium optimizations to clean up the bands on a gel. Unfortunately, these optimizations don’t always get you pretty bands. Below, I show two unpretty gels and one lovely gel (with the bands boxed in red).

These are a few of the gels I ran to test primers this spring. The left-most gel was one of the worst (see the streaking), while the gel on the right shows clear and bright bands.

These are a few of the gels I ran to test primers this spring. The left-most gel was one of the worst (see the streaking), while the gel on the right shows clear and bright bands.

I used touchdown PCR to get the beautiful bands in the gel on the far right. I’d been working on a particularly troublesome exon for a few weeks when my PI suggested I try touchdown PCR (TD-PCR). This protocol gradually decreases the annealing temperature of a reaction, literally “touching down” by one degree in each subsequent cycle, which selectively amplifies the product that amplified at the highest annealing temperature. For more information on TD-PCR, see Korbie and Mattick 2008.

 

Next step: moving on to this guy! I'll be sequencing on a machine like this one (the ABI 3730) at AMNH this month.

Next step: moving on to this guy! I’ll be sequencing on a machine like this one (the ABI 3730) at AMNH this month.

 

Now that I’ve finished up this preliminary work, I’ll be shuttling back and forth between the Rubenstein lab and the Sackler lab at AMNH, where I’ll complete the actual sequencing of NR3C1 (using a machine like the one shown above). Stay tuned for some (hopefully forthcoming) results!