Arrival and the first weekend

A significant amount of time has passed between my first post and now. This very much goes against what I was originally hoping to capture, a real time collection of my thoughts, but I hope the substance of what I am writing will be as interesting. I very simply underestimated the time commitment (at least slightly) of the work we are doing here, as we often work 6 days in a row for as long as 16 hours a day in some cases (especially early on in the trip). Since it has now been a couple of weeks since I arrived in Africa, my delivery will likely be more reflective than reactive. Hopefully blog posts will be coming in more steadily now - as I feel slightly more of a veteran to our daily process and many of the tasks are being completed significantly faster than a few weeks ago.

I hope to now draw on the memories of arriving in South Africa, the journey to Kruger Nation Park, and what we were doing the first few days in country. Since that time, I have learned so much about the people, places, wildlife, an ecology of this pristine savanna system. It is actually unbelievable to me that it has only been a couple of weeks, as it feels like it was a lifetime ago that we started. I don't think this feeling of prolonging has anything to do with a negative association to this place, but rather that every single day is stunning, new, and generally completely tangential to what I am used to back in the United States. There is certainly something about being exposed to new things that seems to freeze time, and this place is so incredible distinct from my typical day-to-day life that I can't help but feel like a significant development has occurred. This sensation is not unlike the feeling I have gotten after major life events such as graduations, funerals, and life accomplishments. Similar to what many astronauts say when they return to Earth for the first time (which I am certainly not comparing myself to, what they get to do is on a whole different level of bad ass), I feel that I have lost hold of the context for the problems I tend to think are large. Here it seems incredibly obvious what the true natural state of the Earth and the legacy of life is - as well as how far we have drifted from it. I can not help but feel that the problems I tend to worry about are so very small compared to this drift quite apparently caused by the evolution of modern humans. Nor can I leave this place without feeling more empowered to dedicate my life towards conservation and ecology. Ultimately, I hope that I can transfer some of these feelings to you, the readers. Or, better yet, I hope I can convince you to dedicate time to see a place like Kruger for yourself. After all, the savannas of Africa are quite literally your ancestral home before many generations of dispersal across the planet. What better a place to realize that we are an evolutionary product of biology capable, and even responsible, for understanding biology itself?

Travel

On January 9th, our lab's lab coordinator (super hero) and myself  drove to Boston Logan far too early on a far too cold morning with far too much equipment. We arrived at the airport very early, which I am now extraordinarily grateful for, as I was still almost late to my flight. As it turns out, when you check massive amounts of expensive scientific equipment, it is best to have an export license (called a carnet) so that you are not hit with enormous taxes traveling to and from an international destination (we knew this). As it also turns out, the 24 hour customs desk that can stamp the license is checked by an officer only once every few hours (we did not know this). A couple of very stressful and sweaty hours later, we had the stamp, I said goodbye to our coordinator and boarded a plane headed towards London Heathrow. Unfortunately, there are no direct flights to South Africa from Boston, and the flights that do head direct from the US are on the unnecessarily expensive Delta Airlines, so a stop in Europe was not optional for me. Having only been to Europe once before, it is funny how short the flight feels when you know it is the shorter leg to the overall destination.

I actually really enjoyed my short layover abroad. I am not exactly sure why, but the world felt very interconnected when I was passing over the London greater area, a place entirely foreign to me. This feeling was extended as I passed through the terminal, grabbed a quick bite to eat, and people watched individuals from all over the world waiting for the gate listing for their international destination. Maybe it is my perspective as an American (we are notoriously isolated in some sort of cultural bubble with little concern for international travel), but the rest of the world seems to circulate far more outside of North America. It felt as if every possible language and accent was being spoken around me with a distinct lack of the American dialects I am most familiar. Personally, I find the detachment refreshing. Not long after I found a place to sit in the mall like terminal, it was time to board the 11 hour long haul to Johannesburg.

My ride to Johannesburg: Boeing 787

Arrival

I landed in Johannesburg very confused as to what day it was, but surprisingly not at all jet lagged (perhaps it was the excitement).  The airport experience was one that would be familiar with anyone traveling internationally anywhere. If anything, getting through the airport was more efficient than what you would expect in the global North with very obvious solutions in place to simplify headaches that one would experience in America or Europe. This will become somewhat of a theme, South Africa is really quite efficient where it counts. Most surprising, as I have never had anything like this before, a special baggage carousel for fragile luggage was very close to the main carousel for my flight. All 5 checked pieces of equipment came out of the fragile compartment and placed gently in front of me. How exactly they knew that these things were more fragile then my luggage, I am not sure, but it was a nice change. Leaving the airport, I once again had to get my equipment documentation checked and signed. Instead of an absent customs agent, I was immediately helped, asked a few questions, received a stamp, and was on my way. This was probably one of the easiest airport experiences I had ever had.

Outside the arrival area I met with the rest of our team who had all arrived relatively close together. We packed our stuff into what might be the world's worst field vehicle (more stories about that later) and began the drive to Kruger. Johannesburg, the largest city in South Africa, is about a 6 hour drive away from Kruger National Park, which is located on the eastern boundary of the country touching Mozambique, Swaziland, and Zimbabwe. It is technically possible to fly on a commercial flight directly to Kruger, but I am very glad we did the drive. Besides being very disoriented by the left side driving, which I admittedly still haven't gotten used to, the drive was beautiful. We drove across the rolling stretches of the highveld region of the country, down through deep canyons with jungle vegetation, and into the lowveld region which contains the savannas that make up Kruger. The drive was very beautiful and somewhat reminiscent of the long cross country drives I had previously taken through some of the more beautiful stretches of North America. Of course, North America lacks roadsides that warn drivers of hippos, but this is a minor detail. By this point, we had not seen any noticeable wildlife.

A transitional zone between forest and lowveld savanna on the way to Kruger

We got to Kruger literally minutes before the gates closed. The guard checked out research permit and allowed us to enter the park. Within literal seconds, my expectations for the park were shattered in the best possible way. I knew that I would see many kinds of wildlife on this trip, but I had no idea for the remarkable pace at which I would be exposed to wildlife. Perhaps 30 seconds after entering the park, we made our first sighting. A pair of spotted hyena (Crocuta crocuta) walked behind some tall bushes not far from our car. I tried to take in the moment as if it would be the last time I would experience this animal. Fortunately, I was extraordinarily mistaken. Moments later, a semi-distant herd of elephants( Loxodonta africana) were visible with two relatively young individuals play fighting. This herd was small in terms of size, but also individuals. It did not contain some of the massive bull elephants I would become accustom to in later days, and all the cows were relatively young. Shortly after, a small group of impala (Aepyceros melampus) were sighted. We stopped to see this small of animals, a clear sign that we have just arrived. While we have stopped for largely groups of impala during later days in the trip, it is a rare occurrence. You simply become immune to the literal thousands you see throughout the park. What is important to understand here is that within 5 minutes 3 large species of mammal were observed. This is simply how things are in Kruger especially the southern section where we were. The park is absolutely enormous, running about 350km long, and yet wildlife sightings are sometimes near constant. The abundance of wildlife is not possible to overstate. It makes one wonder the rest of that 6 hour drive would have been like should it lack the human settlements like the park lacks. Or, more personally, what would similar systems in North America look like without human influence?

We got to the place we stayed the first few nights right before sundown - an educational compound in the village/camp of Skakuza. Skakuza is the most popular of the camps and certainly the most developed. Despite this, as a tourist especially, you would never know that this is also the headquarters of the park which contains offices, a staff village, research camps, and an airport. It still looks remarkably wild - which it mostly still is. The compound is fenced, like almost all of the camps here, which brings a sense of security from the very intense wildlife outside. I rested my head in a giant savanna tent, as I would for the next several days, which is perhaps still my favorite place I have slept here. It is almost completely open to nature, and since we were getting up before the sunrise, I would open the window (with a bug net to protect me as I am not crazy) and effectively sleep under the stars. Throughout my first night I remember falling asleep to the incredible array of sounds that are produced here. An orchestra of noises from animals I did not yet know to identify. Eventually I would learn the unmistakable sounds of bush babies, hyenas, lions, birds, and assortment of insects. This, of course, would take some time. Despite the relatively loud and certainly constant assortment of noises, I slept remarkably well in that tent. As I would continue to for days to come.

The first weekend of work: Flight Tests

Early the next day we headed to the Skakuza airport. Late the night we arrived, the head of the South Africa National Parks (SANParks) airwing met with us to discuss our operations. Being that I am familiar with flying drone in the US, I was expecting some level of hesitation to our activities in the park, especially considering he is a helicopter pilot with important anti-poaching activities to take care of. Instead, we were met with complete enthusiasm and unrelenting support. To him, we were a case of people who know what they are doing and went through the proper channels to fly legally in the Kruger. In many ways, we are the test case for drone operations in Kruger and opening the door to other people to follow our footsteps via our protocol to operate in the park - but of course only if things go well. The air wing opened the doors to their hangers for us, along with any tools and resources we would need. An incredibly kind offer of much needed space. But why did we need space like this in the first place?

Being that South Africa's drone laws are very complex, it was unrealistic that we would fly our own drone in the country this year. Instead, we contracted out a company, Integrated Aerial Systems (IAS) out of Cape Town to do the flying for us. We needed space to integrate our sensor package to IASs drone and to test fly the drone with our payload to make sure everything works together. From there, we could then test the sensor in real savanna landscapes out in the field. This brings up two important questions: 1) what is our payload? 2) Why do we need to test it in the field?

The first can be answered largely with a description. Our payload is a combination of three different types of sensor integrated into one package via a navigation box. The first sensor is something that makes sense to a lot of people, a modified over the counter mirrorless camera. If you haven't heard the term mirrorless camera, you have certainly seen one. Essentially, any camera you could purchase at BestBuy or Amazon that has been designed in the last few years is a mirrorless camera. They will replace DSLR cameras that have been around for sometime. mirorless cameras are particularly well suited to drones because they have a much quicker shutter speed and are less prone to distortion due to a very simple imaging system. Since drones fly low and cover ground quickly, this is particularly important. This camera takes aerial pictures so that we can identify objects via color and, with some advanced processing steps, can make maps of large areas in two dimensions.

Our second sensor on the payload is a thermal sensor. This is a camera that measures emissivity of long-wave infrared radiation. This sounds quite fancy, and in some technical ways it sort of is, but long-wave infrared radiation is what is given off by Earthly objects and sensationalized as heat. Essentially, this camera can measure a proxy for temperature across the ground. This could become a very useful tool to measure various ecologically interesting variables. Some are obvious, such as the ability to find animals that would be hard to see with a normal camera or at night by seeing body heat. Others are more complex, such as measuring the thermal gradient across a landscape due to shade which has implications for how animals would use a given plot of land.

Our last sensor, the largest sensor and really the main sensor, is our LiDAR. In the next picture you can see the payload as a whole, and the LiDAR makes up almost the entire thing. At its core, LiDAR is a very simple technology. Many of you have actually experienced the value of LiDAR technology before if you have a car with collision avoidance, self-regulating cruise control, or have been pulled over by a police officer with modern speed measuring equipment. LiDAR stands for light detection and ranging and works very similar to radar. Basically, LiDAR uses a laser beam like a really long ruler. All LiDAR devices fire a laser at an object, the laser then reflects back off the object, and a receiver on the LiDAR receives the laser. Because the speed of light is constant, the time it takes to reach an object, bounce off said object, and returns to the sensor should be entirely dependent on the distance away from said object. So, if you divide the time it takes for the laser beam to return to the sensor since it was released by 2 (divided by 2 so you only worry about the time it takes to get to the object) and multiply that value by the speed of light, you get the distance between the sensor and the object being measured. Simple LiDARs can do this very cheaply, such as the ones in a car which just measure if you are getting closer to the car in front of you. However, imaging LiDARs like ours are very complex. If you want to map massive areas of vegetation like we do, you need to fire LOTS of laser beams VERY quickly. You also need to do so with the proper settings so that the beam is an ideal size when it reaches the object or that subsequent beams are spaced properly. In addition, there is a problem (and really cool opportunity) in that LiDAR beams can bounce off things and hit other things before returning to the sensor. This is actually a really great aspect of LiDAR since it means you can measure features under vegetation, such as the ground, by receiving beams that have bounced a few times. This is very complicated for the sensor to understand however, and requires not only a powerful laser to produce the most bounces (returns) but also process that information meaningfully. Our sensor handles these problems by firing a massive amount of laser pulses. In fact, it can fire as many as 820,000 pulses a second, each of which can bounce as many as 8 times before returning to the sensor. Each of those bounces from each of those pulses is a new measurement of the environment. The laser emitter is within a spinning disk which spins as fast as 120 times a second creating streaks of laser beams similar to how a laser printer prints across a page. The result is a 3D model of the entire environment you are scanning. There are many many other technical things to consider when thinking about airborne LiDAR, but there is no sense in writing about it hear. If anyone is interested, feel free to reach out. Examples of LiDAR data will be shared in future posts.

The last component is the navigation box. This box combines and sends information to each of the sensors independently, and is essentially the brains of our payload observatory. It also interacts with the drone power system and our sensor's GPS unit that we mounted to the drone. It sends out information to a computer we have on the ground and receives my instructions that I send back to the sensor during flight. This piece of hardware is what really sets our observatory apart from the rest in the industry.

The second question, why do we need to test things, has a much shorter answer. The answer as to why we need to do flight tests is because nobody has done this type of data collection before. Nobody has flown drone based LiDAR in savannas at all, let alone to study ecology and even more so animal ecology. This includes LiDAR of all types, and being that we believe our LiDAR will be more capable than essentially any other option, we have much to prove. We do not understand what we will see for certain, nor do we understand what the quality of our measurements will be, or the best way to fly the sensor. Indeed, this entire trip is basically a big test where we are hoping good science will come out of. Because of some of the sites we are targeting, I am sure interesting results will come from this work. Being that this post is about events that have happened a few weeks ago, I do already have exciting things to share with you all but they will have to wait for now.

The final stages of systems integration on the logo of SANParks

Integration came with it's struggles. First it was issues with wiring systems together, then power system issues, then software issues, then parts issues, etc, etc. Eventually however, we prevailed with a successfully data collecting flight test on the airport runway. Just the fact we were operating in such a place with such strict and conservative aviation regulation was a sign of just how much faith was being put in us to do good work here - as well as how large the stakes and rigorous the test. During our time in the hangers we saw the helicopter pilots leave on anti-poaching missions. Rhino poaching is an enormous problem in the park with a rhino killed every day, three killed a day a few years ago. This topic is massive and warents its own post in the future, but it did provide some context for this place. Remarkably beautiful and wild (as I hope to show you more through pictures), there are people here fighting a fight constantly to give these animals a chance. It also gave some context to our work, as we plan to put out papers as our data could become important for determining the well being of animals like rhino.

Our drone and sensor combination during the first flight test w/ sensor package down below

SANPark helicopter on way to anti-poaching mission

This integration process took 2 days, the length of the first weekend. Each day traveling to and from the airport we saw wildlife. Warthogs, hippo (from a distance), kudu, bushbuck, waterbuck, and an absolutely massive snail were seen for the first time by our team among other things. It became incredibly exciting and nerve wracking to know that we were bringing this equipment out into the bush with all these animals in short time. In the meantime, I enjoyed the animals we saw on our short drives to the airport and heard from my tent each night. Things were just beginning.

ANIMAL OF THE POST

I am going to feature a specific animal in each post, most likely one that was mentioned but not previously shared with a photo, and always one that I have photographed. This time around we are featuring the waterbuck (Kobus ellipsiprymnus). Besides being extremely cute and very very fluffy for a savanna antelope, the waterbuck is a very fascinating creature behaviorally. Waterbuck live in herds typically consistent of a single male and several females in which that male is mating. The female waterbuck do not have any horns. Perhaps the most striking physical feature of the species is the white ring around it's butt that looks like it sat on a freshly painted toilet seat. This is a unique feature among African antelope and it serves a very interesting purpose. The waterbuck typically lives near rivers because rivers are an important escape avenue for these animals. It turns out, waterbuck are fantastic swimmers. When threatened by a predator, waterbuck will scramble to reach water so that they can safely escape predation. Being that vegetation can often be quite thick near the rivers in savanna systems, it can be difficult for waterbuck to effectively navigate towards water. The white marks around their butt act as a navigational aid, allowing the lead waterbuck in the group to be easily followable by subsequent animals. The individual pictured below is a female I observed in the Satara area of Kruger very close to a major river area.

Waterbuck in the Satara section of KNP

1/7/2020: An Introduction - The Blog, The Science, and The Field Season

A while ago, I decided I wanted to record my experiences from my upcoming field season in a high degree of detail. Not exactly in a technical way - the bundle of field notebooks, holster of SD cards, and mobile solid state drives that I have packed are better suited for that. Instead, I wanted to record the bigger picture - thoughts with more nuance, the beginnings of hypotheses, and perhaps in some cases bits of subjectivity. The reasons are largely personal. Perhaps a journal like archive of this time may help me become a better ecologist by sparking a new idea. This may come when a future Evan looks back on this blog better informed, better educated, and better equipped to spot interesting questions. Maybe I will later look back onto the posts to follow as humorous (if not embarrassing) first attempts at synthesizing something out of the vast complexities of a ecosystem currently unfamiliar to me in every way besides what can be read in the literature or seen in videos. Or, hopefully, this blog will be a positive relic to a time where everything is fresh and new. In this final case, I can look back on this blog to inspire a likely more jaded future version of myself to remember why I am a scientist in the first place. Whatever the effect will be, I have known for a while that the selfish purpose of this media is to be a bridge between the inquiring and creative sides of my brain.

However, it was not until maybe a month ago that I decided to vent these ideas in the form of a blog instead of a private journal. While the choice may seem like an attempt to bolster my position, it is truly not the intent (in fact, I am quite nervous about sharing my thoughts in such a public place). Instead, I found it to be unique opportunity to platform scientifically supported concepts found in nature that I believe are important for everyone to understand. Obviously, I am deeply biased on this point because of course I believe my field is important - so hopefully I can convince you that this is the case. But why now? Why create a blog on my science at this stage? Well, first of all, it is certainly timely. As of today, over half a billion animals are estimated to be dead in Australia from fires that have been raging for several weeks on a continent engulfed in flames. Ecologically, what is important to ask about these fires is Why there, why this devastating,  and why now? Are fires of the scale currently burning in Australia natural occurrences or unique to the age of humans? If these systems were modulated by unrestricted wildlife, would they burn nearly as hot, as large, in the same places, or for as long? If the Australian government better conserved habitat, and perhaps more importantly, better conserved the processes that would naturally take place in those habitats, would the result have been so drastic? Could a healthy ecosystem, modulated by the vastly complex interactions of predators, herbivores, decomposers, and producers, have prevented the fires of this enormous proportion from happening in the first place? Should civilization be looking towards ecology, and in some cases specifically animals, to take on our environmental challenges? Each of these questions could possible be answered through knowledge of how animals interact with landscapes, the topic I am studying for my PhD.

My hope through this blog is to get each reader to the place where they think about questions similar to the ones above whenever an environmental topic is discussed, whenever the value of conservation is questioned, and whenever the resources society takes for granted are exploited for corporate gain. My job is to convince you that humanity is as dependent on the ecosystems of the Earth as any other living thing and that our actions have ecological consequences that will not only perturb the well being of natural systems, but human systems as well. This, I believe, will be a monumental task. I could perhaps do so easiest by sharing some recent discoveries such as how forest elephants create fire breaks on the edges of tropical rainforests that prevent parts of Central Africa from burning, how wildebeest cycle so much carbon in their massive herds that they negate Eastern Africa's fossil fuel usage, or how the loss of wolves have completely restructured North America's forests and vastly decreased carbon storage capacity across a continent (weakening an important barrier against climate change, among other problems). Maybe I will point out some of these topics from time to time, but I do not want this to feel like cherry picking. Instead, I plan to point out just how clear and common large scale animal driven ecological effects are across a single system. The point of doing so is to show how vastly complex landscapes and their ecosystems are and how that complexity, as driven by wildlife in many cases, is why landscapes are the way they are in the first place.

Perhaps the most ambitious part of my goal is that I will attempt to convey the aforementioned points through the perspective of an active scientific data collection campaign. From January 9th to February 11th, and again from February 28th to March 20th, I will be collecting data with my lab in South African landscapes with a method that has never been done before. Because of the novelty of our method we truly do not know for sure what we will be able to measure - thus readers will be learning with us. The goal is to demonstrate the often unexpected high-tech nature of ecological research and the implications of remote sensing and spatial technologies in the field. Hopefully the combination of new science, neat pictures of landscapes and wildlife we are studying, and thoughts and stories regarding the importance of wildlife in these systems will be an interesting and worth while read.

The Sites

The second reason I am choosing to make this blog at this time is because this field season is taking place in areas that may be more ideal than anywhere else to discuss how animals drive changes in landscapes. The first trip is taking place in Kruger National Park on the eastern border of South Africa. Kruger, a national park the size of Israel has been managed (under a few different forms and a couple different names) for about 100 years and is as close to pristine as one can find almost anywhere. The park, with nearby lands only being settled by Westerners in the last century and sustainably settled by indigenous people before that, has been spared of major urban development in the region. That is not to say it has not degraded, as many of the largest megafauna have only recently been re-added to the park after local extinctions were numerous due to non-sustainable game hunting methods. What is fortunate is that the park has since recovered from these poor management practices, maintaining active populations of elephants, black and white rhino, lions, and many of the other charismatic animals one associates with savannas that are now extinct throughout most of the rest of the continent. Kruger management does this by embracing the fact that landscapes should be dynamic changing systems, composed of many different habitats through natural fire, actions of animals, the differences in rain, seasonal droughts, and other natural fluctuations. By managing the processes that create variation, or heterogeneity (a post on this topic later), Kruger is a truly successfully place of conservation and a critically important scientific test bed of what a 'natural' system even is. In a few days I will post about what I will actually be doing in Kruger, as well as more specifics about the park in general.

Map of South Africa and Kruger National Park. From Adams & Snode, 2015. DOI: 10.1186/s40555-014-0087-2

The second site we will be working in is the Great Fish River Nature Reserve in the Eastern Cape of South Africa. This site, while being notoriously rugged and less visited by tourists, has still not escaped the impacts of humans. While the very thick brush of this topographically intense landscape has the most dense population of black rhino left in Africa, it is also completely cleared of its elephant population. Fortunately, that will soon be changing as there is an effort to reintroduce elephant to the park later this year. We will be surveying the park before the elephants arrive so that we can measure the short term impact of elephants in the region by comparing data from the March trip to a yet to be determined field campaign after the elephants are in place. This trip is not until March, so we will return to discuss GFRNR later.

Next Post

Later this week, likely during my travels to South Africa in a couple days, I will post about the actual data collection campaign in Kruger that will be undertaken over the course of the next month. I hope to explain why the title is called "digitizing the Savanna" and the implications of this language. In addition, I will discuss in more detail, the interesting structure of the park and the fascinating things I hope to see during my visit. I hope that this blog will continue to be a project I am excited about and something you enjoy to read.