Tuesday, September 27, 2016

Undergraduate Field Research: Making it Happen

A group of female Himalayan Tahr looking at us!
It’s really amazing how far you can get when you aren’t afraid to “just go for it”, no matter what point you are in your career! My dream started sitting next to a colleague and best friend of mine at our graduation from the Panama Field Study Semester, an amazing program offered to undergraduates at McGill University. We turned to each other that day and made a promise that one day we would work together on a project. A few months later when I was back in school in my last year of my undergraduate degree in Biology, I got a phone call from this friend who was all the way in India with the exciting news that the local community he was working in, had approached him with a project. Our golden opportunity was here! As intimidating as starting this project from nothing was, we begun doing our research: what is a Himalayan Tahr and Himalayan Serow? Where is Uttarakhand, India? How do you write a project proposal? Which grants do we apply to? Slowly but surely, everything started coming together and I learnt many lessons along the way (and am still learning today!).

And so we were off to India! 
One of the most important lessons I learnt is: do not be afraid to contact people to ask for help! Though experts in their field such as professors may seem intimidating at first, they are just people! Every single professor we contacted was more than willing to help us out whether it was through providing specialist knowledge on a species, teaching us parasitology techniques, writing a letter of recommendation or being a constant support and helping us fund our project (thank you Andrew for being one of those!).  

In the end, through dedication, support from researchers and professors we had contacted worldwide, and above all a positive attitude, we received the necessary funding to go out and do our project. It is so that the Wild Ungulate Research and Conservation Initiative was born! (Check us out on Instagram: @wurc_itindia).

Our two study sites: Rudranath and Sohkark (near Tungnath)
Our project had two main goals: (1) To assess the health impact of livestock grazing on two ungulate species in the Kedarnath Wildlife Sanctuary, Uttarakhand, India, and (2) To conduct an ecological review on these two ungulate species as there has been little research done on them to date. The two species we were studying were Hemitragus jemlahicus (Himalayan tahr) and Capricornus tahr (Himalayan serow). To tackle the first aspect of our project, we collected tahr, serow and livestock faecal samples and used the FLOTAC method to analyze parasite eggs. For the ecological data, we took many focal and scan samples to record behaviour of individuals and the group. At each point of collection we also took a GPS point and will map their distribution, with special focus on the serow as their habitat preference remains unclear. We split our time between two research sites, the first being Rudranath: a site where tahr and serow are known to overlap with livestock herds, located between 3000-3800m along a pilgrimage trail to Rudranath Temple. The second site, Shokarkh, was expected to be devoid of livestock (but as so often happens in the field, this was not the case) and encompassed heights between 2700-4000m.

Me on the lookout for tahr - gotta get 
low to hide from their view 
Although the fieldwork is still in progress, we have some preliminary results. From scans, it was found that between both sites, Himalayan tahr spend the majority of their time foraging (58% and 65%). However, focal results indicated that adult females allocated more time in Rudranath to foraging and less time resting compared to in Sohkark. Even more interesting is that sub-adult and adult males showed seasonal differences in foraging activity. Furthermore, we observed curious subdivision of groups by age and sex in the Himalayan Tahr.

For prevalence and intensity of parasites, we found there were more parasites in both livestock and tahr in Sohkarkh than in Rudranath, however there was no significant change in intensity. This is interesting as livestock were in closer proximity to the tahr in Rudranath than in Sohkarkh so we had predicted the opposite to be true.

Our lab set up in the field
As you might have noticed, the Himalayan serow was mentioned a lot less in our findings. This is because we were not able to obtain any direct observations as we have yet to spot an individual. Nevertheless, we were able to infer some information from indirect observations and informal interviews. The most alarming finding was that Himalayan Serow populations are suffering big losses this year as they are being affected by sarcoptic mange disease, a skin disease caused by a mite (species unknown). Affected serow have been found on both sides of the Mandal valley. This was further reinforced when we found a diseased and deceased serow near Mandal village (base for trek to Rudranath), as well as by the lack of serow spotted this year which according to our local guide, is very unusual. This is super interesting and a huge red flag, so we are hoping to really keep exploring this issue and learning more about the species.

Deceased Himalayan Serow found near Mandal village

As fascinating as all the research was, what I will really take away from this time in the field was all the lessons learnt. And by this I mean more than just learning how to improve our record keeping sills and how to adapt our schedule to maximize and improve data collection. This project was deeply satisfying in two main ways. The first was through the confirmation of my love for field biology and research, which has given me the drive and assurance that this is what I want to be doing for the next few years of my life. The second was through shaping my personal growth, mainly through showing me that I am capable of more than I give myself credit for. A lot of the field work was very physically demanding as it required us to trek for long hours at high altitudes every day, and I came to appreciate my mental strength proving to myself how many barriers you can overcome through being mentally strong. Furthermore, the fact that this project went from a dream to a reality was proof enough of itself that if you work hard enough and put heart into something you want, results will show!

A great field example of the lesson we have all heard before that goes something like “don’t give up hope when things don’t seem to be going your way” was our situation with finding male tahr. For days we had been searching for a herd of male tahr without fruition. Some team members even embarked on a gruesome hike up to 5000m in altitude in attempt to go find them. Then suddenly, we got notice that they were a 15min hike from our camp! And one night when we had set out to go have tea with a local shepherd in the area, without the intention of collecting any data at all, we spotted the group of male tahr!
The group of subadult and adult males tahr found in Rudranath

Perhaps what I developed the most appreciation for this summer is something that too often goes unmentioned: the essentiality of local team members. Our local field guide was invaluable when it came to finding our way around the mountains, recognizing animal signs, establishing crucial local contacts and even in what would appear to be simple tasks as shopping for food supplies. Our field cook was another invaluable and not-frequently-enough-mentioned part of our team as by him taking on the cooking duties, we were able to go out into the field for longer periods of time and really dedicate our efforts on doing the research.  Our project would have never gotten as far without their collaboration, and the value of local knowledge is something I will always treasure.

Harsh Maithani, our local field guide,
posing for his picture
On a similar note, what was amazing to see is the amount a project like ours can do for a community. 
In addition to learning more about the species they treasure, it created well-paid jobs (alas temporary for now) for locals in a field they are passionate about and gave them the opportunity to work doing something they love. As an example, Prabhat is a boy of 18 who worked as a field assistant and relief cook with us this summer during his summer vacation. Instead of hanging around the village with his friends, he was ecstatic about the opportunity to learn what it is like to be a field guide and discovered that it is possible to have a career that matches his love for the mountains.                                                                                     

All the girls at camp and Prabhat
posing in front of the beautiful
I could not be more grateful to have had this incredible experience. We are now working on finding additional funding to continue this project next year and hopefully expand our research initiative. It is astounding what can happen if you really put your mind and heart towards something and give it your best effort. If there is something you have always wanted to do, but have always thought is not quite feasible or is too much work, I encourage you to give it a try. You never know what will come of it!

Our field team for Sohkark, site 2!

Friday, September 16, 2016

No prize for finishing (or starting) your PhD first

The first time I came to Montréal was a couple of years ago. I was just finishing up my undergraduate degree at the University of Notre Dame and had the opportunity to attend the Genomes to/aux Biomes conference where I presented some research I was doing on speciation genomics of apple maggot flies out of Jeffrey Feder’s lab.

discovering the culinary delicacies of the north

It was a pleasant and sunny few days packed with science and poutine. For me, it was also a chance to explore the city and McGill University where I was to begin my Ph.D. in the fall and meet up with Rowan Barrett, my supervisor. I knew Rowan from years back when we were both working in Hopi Hoekstra’s lab and I had already gone out to the sandhills of Nebraska with him a few times to catch mice for the project that I would work on in my Ph.D. I had already been accepted to McGill and the funding was in place. The situation was ideal and everything was going according to plan. But sometimes life has other things in store.

corn thuggin with Rowan

Besides this Ph.D., the one thing I applied for was the MEME Erasmus Mundus Master Programme in Evolutionary Biology. It’s a joint 2-year master programme between four European universities (University of Groningen, Ludwig Maximilians University of Munich, Uppsala University, and University of Montpellier) and had been somewhat of a dream of mine ever since I found out about it in my freshman year.

our logo is pretty lit

The programme is set up such that students choose to take courses in either Groningen, Netherlands or Uppsala, Sweden in the first semester. Students then go to either Munich, Germany or Montpellier, France for more courses and a half-semester research project. In the final year, students conduct two separate thesis projects in any of the four universities, Harvard University (a partner of the programme), or basically any university or research institution in the world so long as a professor from one of the four universities is willing to supervise the project. In the end, students earn double or even triple M.Sc. degrees and often come out with multiple publications. Having never been to Europe before in my life and having been awarded a full scholarship, MEME was a once-in-a-lifetime opportunity I could not refuse. So I decided to take a detour to my Ph.D. I figured, if it was meant to be, I would find my way back eventually. Thankfully, Rowan agreed. :)

What I can say is it was simply the best time of my life. We were 22 representing 17 countries, each bringing something different to the table from our diverse cultural and educational backgrounds. Our discussions ranged from Dawkins and The Selfish Gene to the insanity of dealing with French banks to which new country was going to be our next adventure. And I won’t lie, it was fun to see a Syrian doctor interested in evolutionary medicine and bacteriophages struggle on the mudflats of the northern Dutch island of Schiermonnikoog doing field work, wondering out loud why the entire field of evolutionary ecology exists in the first place.

flatness can be beautiful too

Travel became life and life fit in a backpack. MEME took me from the Netherlands to France to California to Sweden to China, all within a span of 24 months. Each new country came with its own set of challenges and trying to open and close entire chapters of your life within months wasn't easy. A Malaysian classmate of mine put it best as going through breakup after breakup, but with each new relationship, you learn and become more experienced. The projects I worked on were equally diverse from the genetics of starvation tolerance in European seabass with Bruno Guinand to genetic mark-recapture of giant pandas with Per Palsbøll, Matt Durnin, Katja Guschanski and Jacob Höglund and taxonomic assignment of metabarcoding data with Douglas Yu. It was an intense, crazy, unforgettable experience. A rollercoaster or a whirlwind... or a rollercoaster caught in a whirlwind. And don’t get me started on the parties. Oh the parties…

MEME graduation 2016 - Erken, Sweden

So a full 2 years later, I now have 3 M.Sc. degrees in evolutionary biology from 3 countries, 1 paper accepted, 1 submitted and more to come. I have a deeper understanding of what it really means to be a global citizen and greater personal and scientific maturity to start my new life and Ph.D. at McGill. So if you’re reading this and this all sounds pretty cool to you, the next application cycle opens soon on October 15, 2016. My advice to any undergrads out there is to take your time. In fact, I almost wish I had taken more. The academic road is a long one and there is no prize for who gets their Ph.D. first. Of course, its best to be productive by becoming a research assistant or doing a masters, especially if you want a career within academia, but if you're not sure about your next step, it wouldn't be the wisest idea to jump straight into a Ph.D. Or perhaps this is just the European culture rubbing off on me (which isn't so bad!). In part because I decided to do MEME before starting my Ph.D. at McGill, I successfully applied for the Vanier Canada Graduate Scholarship so it seems like I made the right decision after all. The next big challenge for me will be to settle myself in at McGill, get used to living in one place for more than 5 months, and sink my teeth into some long term projects, which I now gladly accept.

Tuesday, September 13, 2016

Is Prediction an Exquisite Fiction?

As I described in a previous post, a long-standing topic of discussion is the usefulness of a given scientific endeavor or study. Along these lines, science is often divided into BASIC and APPLIED. Applied science is – by definition – useful. It cures some disease. It improves crop levels. It saves some endangered species. Basic science is – at least classically – not obviously or immediately useful. Instead, it addresses a (hopefully) interesting question – interesting at least to the researcher. Sometimes called “curiosity-driven” science, basic research might one day have great utility but, at the time it is conducted, its uses aren’t obvious.

The motivation for my earlier post on basic vs. applied science.
Basic science was once considered an admirable pursuit – perhaps even preferable as an intellectual, university-based enterprise. More recently, however, universities and funding agencies want to hear how your research – whether basic or applied – will have “broader impacts” or “direct benefit to the people of ...” No longer is it enough for the science itself to be interesting and clever and well designed; it also has to have a clear utility. When justifying a research project, these pay-offs are expected to be clearly and forcefully presented, usually at the outset of a proposal and in an explicit section at the end.

For basic scientists in ecology and evolution, these applied justifications tend to involve conservation (e.g., saving some endangered species or place), management (e.g., of natural resources), discovery (e.g., new drugs), or ecosystem services (e.g., greater biodiversity generates greater productivity or resilience or whatever). In many cases, the specific link between the science and the proffered application is PREDICTION. For example, “we need to be able to predict what is going to happen, in the face of environmental change or management actions, if we are going to design effective strategies for conservation or management.” This sort of justification is a natural and easy one because we can always say “If we don’t understand the system well, we can’t predict it. My research will help us to understand the system better, which will improve prediction, which will be useful, right?”

Just last week I – along with 21 other scientists – published an opinion/review paper in Science amplifying this last point. Specifically, we need to predict what will happen with climate change and – to do so accurately – we need much more information about organisms, communities, and ecosystems than we currently have. In this post, I would like to play Devil’s Advocate to my own paper by arguing that prediction is often hopeless.

From our Science paper.
A first important distinction is whether we wish to make a prediction or whether we wish to make an ACCURATE prediction. It might seem obvious that we want the latter but even the former is sometimes hard. That is, we might not have enough information about a given system to even speculate effectively as to whether or not some action (e.g., climate change) will have a particular effect on a particular species. Most of the time, however, we are able to make some sort of prediction based on intuition or similar systems or mathematical models or experiments or whatever. So the real concern becomes “how correct (accurate/precise) will be our predictions?”

The accuracy of prediction will depend on the type and precision of prediction. For instance, we might first want to predict simply WHETHER a given environmental change or management action will have an effect at all. Here we might be safe in many instances. Will climate change influence biological diversity? Yes! If the environmental change is large, something will respond to it. However, this isn’t the sort of prediction that we – or the public or managers or governments – care about.

We might next want to predict the DIRECTION of an effect. In some cases, this will work fairly well. For instance, we can safely say – based on many examples from nature – that climate warming will advance the timing of reproduction of many plants and animals and that commercial fisheries will lead to smaller body size in harvested populations. A few exceptions will certainly occur but these will tend to be of the type that “prove the rule.” In many other cases, however, predictions as to the direction of an effect will be incorrect. Will climate warming increase or decrease local biodiversity? Hard to say. Will fish harvesting increase or decrease productivity? It depends. In such cases, increased information – including from “basic science” – might improve predictions. 

Experience teaches, however, that expectations developed from theory, from related systems, and from detailed information are – not infrequently – incorrect.
At the most precise level, we might want to predict an effects size, such as a particular rate or endpoint state. How fast will species be lost with climate warming? How many species will be present 25 years from now – and where will they be? How small will harvested fish become and how quickly will they recover when fishing ceases? I suggest that – in many cases – predictions of this sort will be hopelessly inaccurate, except perhaps by blind luck. Each system (and year) has so much contingency that prior information will not be sufficient. Of course, this is precisely the logic that we invoke when seeking funding: “We can’t make accurate predictions unless we get more information, so give me some money to get it.” It is certainly true that if one had complete information on the driving forces in any given system and complete information about how those driving forces will change in the future, then accurate predictions of endpoints and rates might be possible. But this “complete” information is generally unattainable.

Another opinion in Science about prediction
In short, many of the arguments one reads in proposals that the particular basic science being proposed is critical for better prediction are really just smoke-and-mirrors or, perhaps more accurately, a bait-and-switch. Five years later: “Although I didn’t make better predictions, I did do some cool stuff anyway, no?” Of course, these studies can also weasel out of accountability by saying “Here is some new information that other people might find useful in making better predictions” or they might say “Here are some new predictions.” – with the last being particularly disingenuous because the accuracy of those predictions won’t be known for sometimes decades.

My point in this post isn’t that basic science should be abandoned in favor of applied science. My point instead is that it would be nice if we could all just drop the applied BS at the start and end of our proposals. That isn’t why we are doing the study – it is just what we think the reviewers want to hear. The reality is that science has made incredible strides in the past few centuries – and most of those advances, I will speculate, were made by basic rather than applied science. Think of all of the ramifications Darwin’s theory or natural selection, and – coincidentally – all of the incredible and amazing applications. At the time, however, Darwin – and the people who read his book – didn’t focus on its potential applications but rather its potential to explain how the world around us came to be.

I had better circle back to that Science paper for which I am here playing Devil’s Advocate. It is certainly true that we don’t have enough information to make good predictions of how biodiversity and species ranges will change with climate change. It is also true that getting more information about those species and environments has the potential to improve predictions – although we won’t know if we are correct for decades. Thus, I am not disputing the main arguments we made in the paper. Instead, I am using it as a jumping-off point to argue that additional information is probably even more useful simply in improving our understanding of the world around us, whether or not we attempt predictions. Sometimes this improved basic understanding will eventually have massive benefits for biodiversity and the humans that depend on it.

I think it cheapens, and potentially slows, progress in science to require it (or encourage it) to have obvious immediate applications. The best route to the best possible future applications is to simply turn researchers loose to study what they feel is most interesting, whether applied or basic. Basic research isn’t flawed and in need of an applied crutch to hold it up.


After I posted this, I was told about a similar post on Dynamic Ecology:

A 25-year quest for the Holy Grail of evolutionary biology

When I started my postdoc in 1998, I think it is safe to say that the Holy Grail (or maybe Rosetta Stone) for many evolutionary biologists w...