s463p656's blog

Friday, June 15, 2012

Good Company


As the centennial KU Philippine expedition continues, we are all continually impressed by the abilities, incredible hospitality, and hard work ethic of our collaborators and local field counterparts.

Our primary collaborator, Dr. Marites (“Tess”) Bonachita Sanguila, an instructor at the nearby Father Saturnino Urios University in Butuan City, has taken charge of all logistical details for supporting the field crew.  This amounts to numerous massive shopping trips per week, responding to all the miscellaneous requests from the field team, and coordinating our activities with the village head, tribal chieftain, municipal authorities, provincial administrators, police, military, and nearby townspeople.  It's important that everyone knows we’re here, are aware of what we’re doing, and gets an opportunity to voice any concerns they might have about a bunch of foreigners coming to their home town.


Tess has an admirable way of making everyone feel at ease, even during difficult negotiations and discussions of delicate topics like local politics, jurisdiction and land access, permitting, and security in the area.   Even the village dogs have taken a shining to her (no small feat: dogs in rural areas here are more “scavenger” than they are “pet”).

Randy, the son of the Datu (the head of the indigenous peoples’ group with tribal jurisdiction over our study area) is a strong personality with a confident, direct, and strikingly vociferous demeanor. 
He has taken charge of organizing the porters (it takes 20-30 people to move our gear up and down the slopes of the mountain) and local guides.  He definitely has their well being in mind and he is not afraid to tell us when their needs are not yet quite met.  Making sure everyone is happy and well fed is priority number one! —Rafe

Thursday, June 21, 2012

The oldest Batesian trick in the book

I’m proud to say, a few days ago at Camp Putik, I fell for the oldest trick I the book.  Million of years of evolution and selection pressures exerted by predators have produced many flavors of harmless animals which avoid predation by “mimicking” noxious, toxic, foul-tasting, or venomous co-distributed species.

Thus, back in Kansas, the harmless Regal Frittillary Butterfly (Speyeria idalia) are the same brilliant shades of red and brown as the toxic Monarch Butterfly (Danaus plexippus) and birds apparently cannot tell the difference and avoid eating them both.  The “mimic” benefits from the predator education on the part of the “model.”

Of course individuals of the mimic species (the harmless beneficiary of this trick) and the model (the species that packs the dangerous punch) are not actually engaged in conscious or active mimicry strategies.  Rather, it’s the predators who are born with innate, evolved, “instincts” to avoid brightly colored “warning” patterns that exert selection pressures by eating the harmless, drab colored individuals and avoiding the brightly colored ones.   Thus, the brightly colored variants disproportionately pass on a greater proportion of their genes to the next generation and, through time, the population as a whole becomes more brightly colored—and “mimics” the venomous model.  This all according to the famous Batesian Mimicry hypothesis of evolution of aposematic coloration.

In any case, last week as we enjoyed a few sips of rum late at night in camp, a brightly colored, banded snake crawled past our feet through the mud.  At a glance, I identified it as a Philippine coral snake (Calliophis intestinalis).  We very carefully captured it with sticks and gloves and only after it was in the bag did we realize we had before us the harmless example of Boie’s Dwarf Snake Calamaria lumbricoides.

I don't mess around with venomous reptiles.  In contrast to what you see on TV, most herpetologists who study venomous reptiles avoid touching subjects, never pin snakes behind the head and hold them in their hands, and in general, don't take chances.  In my book, every snake-wrangling cowboy made famous on the Discover Channel is living on borrowed time; eventually the odds will catch up with all of them. Given that handling venomous reptiles is part of my job description, I’m determined not to be a snakebite statistic…I lost a friend ten years ago to a krait bite in Burma, and I’d rather be safe than sorry.  Meanwhile, I have to admire the exquisitely precise coral snake mimicry achieved by Boie’s Dwarf Snake. —Rafe

Saturday, June 9, 2012

A Fungus Among us at Camp Putik on Mt. Hilong-hilong


From the coast of Agusan Del Norte, Mt Hilong-hilong looks pretty tame.  “Hilong” means “nose” in the local dialect….I guess if you squint, the peak looks a bit like a face in silhouette with a prominent nose.  

Down at low elevation it is hot, arid, and dry near the north coast of Mindanao Island.  The skies are clear, the sun is out; definitely good conditions for trecking up this mountain.


Up on Mt. Hilong-hilong, a different story is unfolding.  Below the forest canopy, only a little sunlight reaches the ground.  The forest floor is saturated and in just a few days’ time the comings and goings of 20 field biologists have turned our kitchen (and the rest of the camp) into a frothy soup of brick-colored mud. Eventually our guides attempted to put down a floor of saplings, but I can soon see the poles slipping under the mud….

It’s a good thing that everyone has rubber boots.  “putik” translates to “mud” in Tagalog, so Camp Putik was quickly coined and universally adopted by our field team. 

A few days later my right ear and side of my head has begun to sting and itch incessantly.  Some scaly, itchy thing is spreading around on my neck as well.  As it turns out, I have been infected with some sort of tropical fungus; it’s now responding well to fungicide and showing signs of retreating—but how gross is that?  Can you imagine having Athletes’ Foot on your ear? -Rafe

Five days later, the team departs Camp Putik (with an amazing collection of specimens, several species new to science, and fantastic new data on the startling high resident biodiversity) and heads for the blissfully hot and dry lowlands.  First order of business: wash the mold off everything, do laundry and dry out tents, get as much mud out of our gear as possible, and visit the local university clinic for an infusion of fungicide.  It turns out three more people have broken out in strange rashes and can’t stop scratching.

Monday, June 4, 2012

Tadpole Conundrum, the Philippines

It’s always interesting to see how people adjust to life in camp when first arriving in the field.  I am particularly intrigued by what appeals to new students—what interests them, which animals they like, what questions develop.  It’s a finer point, but these initial impressions can have a profound impact on someone’s life.  It is that passion for the organism that not only has the potential to inspire someone to take up a career in biology, but which may also sustain them for five or six years of graduate school or whatever higher training they may undertake.


This year, as we embark on the 100th year anniversary of herpetological collaboration between the University of Kansas and the National Museum of the Philippines (actually titled the Philippine Bureau of Science when Dr. E. H. Taylor first travelled to the archipelago in 1912), I am accompanied by a new student, Kerry Cobb, who has just earned his bachelor’s degree from KU and has been excitedly looking forward to this trip (his first time out of the States) for the last several months. 

Kerry is already an accomplished field biologist who has done very hard-core, months-long, back-country fieldwork on salmon ecology in major parks in the western U.S.  He wasted no time fitting right in to the group social dynamic of our all-Filipino field team, going out every night to catch amphibians and reptiles with the herpers, cracking jokes with the mammalogists, poking fun at the parasitologists for their study of very gross things, and in general staying amused and in good spirits.  On our second day he discovered that the nearby river was full of tadpoles and went back to his tent with a purpose, produced a pair of swimming goggles, and spent the next couple of hours swimming back and forth across one of the larger pools.  He then triumphantly came back to camp with several goldfish bags of tadpoles and spent another hour or two sorting the larvae into batches corresponding to species.  A day later, after he had time to think about it a bit, he did the math and perceptively pointed out that although we had encountered six or seven species of frogs in the area, there were nine species of tadpoles present in the site.  What could be going on here?
As it turns out, the idiosyncratic reproductive cycles of the various frog species present at any given site and time is always in flux.  Clearly there were two or three additional species breeding here a month ago, and while we have not yet encountered the adults, we know they were here because of the presence of their larvae in the river.  Perhaps the adults have dispersed back into the forest at this point, may have gone under ground or up into the tree canopy…we just don’t know.  “Well, how do we identify them?” Kerry asked, “And are there any published papers that we can use to key out the tads?”  Unfortunately, the state of knowledge of vertebrate biodiversity is so underdeveloped in this part of the country that those kinds of resources do not yet exist.  The best we can do is sort the tadpoles to apparent species, preserve a few of each kind for future studies back in the museum, and take tissue samples for subsequent DNA identification.  When we get back to the lab in several months, we can sequence the DNA of all the adults and tadpoles for a common gene fragment.  Then we can match them up and identify the tadpole of each resident species….but the mystery tads will remain a mystery until an adult (possibly from another part of the island, or the next island over) can be sequenced and matched to their genotype.  Doing this systematically for the country, trying to match all the larvae with all the adults (there are more than 110 frog species in the Philippines), would be a great first step for a graduate project and constitute a major contribution to Philippine herpetology. Hopefully a bright student with a passion for tadpoles will emerge.  I can see the first kernel of curiosity in Kerry; hopefully someone like him will be inspired to take on the Philippine tadpole challenge. —Rafe

Wednesday, May 30, 2012

Setting Sail — 100 Years Later for Herpetology Research

As I pack for our trip (tomorrow) to the Philippines, something very interesting occurred to me: right now is the one century anniversary of KU herpetological expeditions to the Philippines.  KU professor Dr. Edward Taylor first arrived in Manila in April-May 1912, exactly 100 years ago.  It's very interesting to reflect on how much has changed over the past 100 years…personally, my experience is obviously quite different from Ed's.  He spent months on a schooner, on his way to Manila (through Singapore), and my trip will take 30 hrs (through Japan).  His supplies were packed in a wooden crate; mine in a cordura duffel bag.  He collected herps alone with the use of a lantern, I collect specimens in groups of hunters, equipped with halogen headlamps.  More importantly, our collaboration has advanced conceptually so far, surpassing I suspect, Taylor's wildest imagination of the future before him.

Another interesting fact: on this trip, we will target Mt. Hilong-hilong in northeast Mindanao, an historically significant site that was first surveyed by Angel Alcala and Walter Brown in the early 1960s.  Our data and observations will constitute poignant comparisons to their formative earlier work, enabling direct quantitative analysis of temporal variation across sampling efforts (most notably, with an eye for impacts of land use and climate change).  The results are sure to be astounding!  All data we gather will be turned over to Dr. Alcala for comparative purposes with his many earlier surveys in the late 1950s, 1960s, and 1970s.

Anyone inherently interested: I'd recommend the California Academy of Sciences "Digitization and Rectification of the Brown and Alcala Philippine Collection" webpage. —Rafe

Tuesday, January 18, 2011

Grant to Support 2011 Peru Expedition

Graduate student Peter Hosner and collection manager Mark Robbins received notification this week that they have been awarded a National Geographic Society Research and Exploration Grant to continue Ornithology's work in the Andes of central Peru. The grant will fund a field expedition to survey and elevational transect through high elevation grasslands, elfin forests, cloud forests, and rainforests in the vicinity of Rumichaca, Ayacucho. Ayacucho is biologically one of the most poorly known departments in Peru. The Andes hold tremendous avian diversity, including birds with exotic names such as Mountain-Toucans, Flower-piercers, Thistle-tails, and Sun-angels. Steep forests of the Andes are often dark, wet, and cloaked with clouds.

Wednesday, September 4, 2013

Inside a Scientific SWAT Team: On the Front Lines of Biodiversity Discovery & Conservation

We signaled to the pilots it was a go. The helicopter descended into a small mountaintop clearing no bigger than a backyard swimming pool. The four of us strapped on our machetes, grabbed our duffel bags and hopped out of the chopper. One of the pilots gave me a stern look and held up four fingers–we had four hours.

With a turbulent swirl of leaves and branches, they were gone, and we were left standing in the middle of one of the world’s largest unspoiled jungles. On our right, the unbroken Surinamese forest undulated over low mountain ridges as far as we could see. On our left, over a deep valley, lay the same view, but those mountains belonged to Brazil- our position was literally on the frontier between the two countries.

We were on a recon mission for Conservational International’s Rapid Assessment Program (RAP), which inserts teams of scientists into some of the world’s most remote and unspoiled places. These teams, typically composed of field and conservation biologists as well as local collaborators, are tasked with providing a snapshot in time of the biological diversity and integrity of these amazing sites.

That particular day last March, we were standing atop a peak in the Grensgebergte, a mountain range so remote and rugged that it had never before been entered by explorers or scientists. Gathering the most basic data on the biodiversity and ecosystem services here allows us to contextualize the importance of these areas as well as detect potential threats.

Sometimes the results are alarming: despite this area’s remoteness, some water samples contained unsafe levels of mercury–possibly the result of air deposition from mining in neighboring regions.

With our short time ticking down, we got to the task at hand: could we establish a basecamp on the summit, and if so, where and how? And just in case we couldn’t make it back, we had to collect as much data on plants and animals surrounding us as we could.

The narrow, kilometer-long mountain ridge had nearly vertical granite walls, with clumps of forest sprouting from both ends. Ornithologist Brian O’Shea and I headed east, while botanist Olaf Banke and Johan, leader of a group of Wayana Amerindians that were assisting our expedition disappeared into the forest on the western flank.

A couple hours later we reconvened: we would establish a camp near the helicopter clearing in a stand of trees. Water was going to be a problem, we would have to plan on lifting it in via helicopter unless in rained.

After grabbing some plant and insect samples and deciphering some birdcalls, the helicopter returned and plucked us off the summit. We returned to a freshly-cut jungle helipad near our RAP team’s basecamp about 30 kilometers away and reported back to the dozen other scientists—with specialties ranging from mammals, ants, fishes, to primates and snakes—  who were waiting for word of what we found.

The Amerindians huddled around my laptop to watch the video clips of an area even they had never seen. For the next week, we flew daily helicopter flights to our mountaintop camp where we found species no one had ever seen.

These RAP trips are special in that they bring authorities from so many different taxonomic groups together on one expedition. Field biologists are frequently only in the field with others in our respective disciplines—herpetologists with other herpetologists and botanists with other botanists for example.

On any one RAP, there might be specialists from a dozen different groups. No matter what you find in the forest, someone will be able to tell you about it. Our “science tent” (the tarp under which we sort and process our samples) is a constant hum of activity from 4am when the ornithologists rise to record birdcalls, to 1am when the mammologists close their bat nets.

And therein lies the power of a RAP: the biological snapshot we take is not just of this group of beetles or that group of fish, but captures a broad spectrum data that tells a much richer, holistic story about the diversity and health of the area.

This week, our team’s report on this first ever expedition to this region of Suriname was released by Conservation International. It was more than a year in the making (it takes a lot more time to prepare and identify specimens than it does to collect them!), and our team was able to document more than 1300 species in less than three weeks.

Dozens of those species are new to science—among them a new snake, 11 new fish, 6 frogs, and dozens of bizarre new insects. It’s trip like these that make one realize just how little we really know about the life around us.

Monday, June 6, 2011

The Monkey Puzzle

We were standing at the top of what looked like a pyramid made of mud blocks, about thirty meters tall, which had a broad, dusty plateau at the top. The half pyramid was located rather incongruously in a wealthy residential district, rather like a dung beetle caught napping in a lingerie drawer. Our tour guide had told us that at the turn of the century, there had been more than two hundred such mounds in Lima, and now fewer than one hundred remained. They had been used as a means of communication with other pyramids – which loomed over the desert landscape -- and religious worship. From our vantage point, we could see sky scrapers, banks, private condos, and (another incongruity) lines of drying laundry. I pointed out a strange looking tree, asking no one in particular what it was. The guide answered that it was a monkey puzzle tree. I thought it was an apt name: the branches were arranged like spokes around a central axis, each frond positioned for optimal sunlight. As I stood looking at the trees, I thought about how odd they looked, and I reached for my sketchbook to whip out a quick drawing before we had to leave. Then one of the biology people on the trip asked the scientific questions: what climate did the tree flourish in? What organisms relied on it? Was it a native plant? At that point, I had a miniature epiphany.

Even though the other student and I were looking at the same object, our different disciplines and interests lead us to have very different experiences with the same tree. We occupied the same world, but that world had a doubleness to it -- they would see the tree as an organism, as part of the complex web of life, as a thing that functions in a certain way to achieve a certain end. On the other hand, as the self-described “art person,” I saw the tree for its appearance – for the shapes and colors and how it was set against the white background of the buildings. As a “literature person,” I saw the tree for what it represented: a symbol of the life that thrives despite pollution, despite being choked by cramped alley ways and concrete and refuse. A thing of beauty tucked into an ugly world, subject to the same hardships as the inhabitants of Lima.

I began thinking about how the scientific mind observes the world in contrast with the humanistic mind. If one sees the world in terms of function and metrics and the physical, and the other sees the world as a complex arrangement symbols and truths that humans create, then what can form a bridge between the two?

The study abroad trip itself provided the answer: communication is the bridge. Though we see the world with two different lenses, we experience the same world. We´re able to touch the leaves and examine the trunk and take photos. We talk about what we see and feel and reaffirm the oneness of physical place.

This may seem like an incredibly obvious point to some of the readers, but others may understand the difficulty I´ve faced in trying to reconcile the aims of science and art. Like many others across the countryside, our university is reassessing how and where it allocates funds. Each discipline feels it must defend itself against budget cuts; unfortunately, the result is often that one discipline tries to downplay the usefulness of the “other” to emphasize its own value.

This is lamentable, in my opinion. We need a variety of voices and perspectives to tackle our problems. As one of the faculty members on this trip said to us many weeks ago (I remember it because I thought it was such an insightful phrasing of the issue), “Science and art are complimentary and equally valid ways of investigating our world.” The monkey puzzle tree is a sadly one-dimensional creature when I look at it from a single perspective – artistic or otherwise.

Sunday, June 5, 2011

Form and Function

Lima museum

Lima pyramid

Our trip to Lima went swimmingly, and we arrived at our hostel around midnight last night. We awoke this morning to the call of an unfamiliar bird, chirping and whooping despite bus and car traffic, singing as we ate breakfast in our hostel’s courtyard.

The group’s first visit was to one of over 200 of Lima’s earthen mounds from the 5th or 6th century, most of which have since been destroyed. It was an island of history among the bustle of the city – an appropriate segue from pastoral Kansas.

Our guide’s name is Luis Villacorta, a savvy man with a ready smile. “People have always used mountains to meet God,” he said, pushing his palms together as we stood at the top of the dusty mound, surrounded by skyrise, all of which were taller than the mound. He was talking about the significance of the mound, which had muddily eroded away over time, though only slightly because of Lima’s arid climate. The Andes create a rain shadow over Lima. It almost never rains here.


Luis then took us to the National Museum of Archaeology and Anthropology, in which we received a crash course in Peruvian prehistory. But our next stop, Museo Larco, stole today’s show.

Vines and flowers covered the museum’s bright white walls, creating an idyllic environment. It had an extensive garden within. The museum’s collections were strong in pottery and metalworking, and much of the jewelry and figurines within were stunning. “When people died, they wanted to become animals,” said Luis, explaining the designs on gold and silver necklaces made by the Incas. They had images of jaguars, alligators, and countless other animals. “Only after the Spanish arrived did the art show humans dominating animals,” he continued, and my mind immediately went to one of the chief purposes of our trip – to collect and document insects for the purposes of research. We’ll be leaving for the field station on the 7th.


Our research will help document an ecosystem that may not last much longer. Peru plans to build (and has already started building) the Trans-Oceanic Highway through the rainforest, imperiling biodiversity like nothing before. A paradox that describes our world: researchers racing to document biodiversity that may soon disappear because of the intractable advance of industry, and yes, science.

An item in the Museo Larco sparked a small conversation about the relationship of art and science, a relationship that this interdisciplinary team has been challenged to confront. The item was a quipu, a kind of abacus made of threads and knots used by the Incas. When laid out, they are beautiful, and not completely unlike a phylogenetic tree. It is interesting how beautiful forms can spring, unintended, from systems designed primarily for function. And the other way around.

Friday, June 3, 2011

Super Popped

Field stationAt the field station

Looking at the collectionSurveying KU’s Entomology (insect) collection

Spencer print roomIn the Spencer print room

We sat in a classroom that smelled of mothballs. Drawers upon drawers of dead bugs lined the room, their bodies pinned to foam boards. It seemed the farthest place that one could possibly be from a jungle. The giant insects taunted us as we looked at them, mandibles frozen wide, and it seemed that we would never see them move.

It is now about 12 hours until we leave Lawrence, and the truth is hitting home. We’re about to see these giant insects, alive and gnashing, right in front of us in the Peruvian jungle. The Amazon.

The bags are packed, the plane tickets bought, the boots broken in, the checklist checked. We’ve had a whirlwind of preparation pre-departure, and it was a lot of fun. In that stuffy classroom, Dr. Chaboo talked about how insects fit into the tree of life, how they function, how they’re different from spiders, crabs, and worms, and about the group of insects that she studies, Chrysomelid beetles.

“We are descended, if you go back far enough, from the same ancestors that gave rise to insects. Your diaphragm is leftover segmentation,” she said, and I conjured an image of a human skeleton with its segment-like ribs and vertebrae. I certainly felt different from the shiny critters impaled on stainless steel spikes in front of me. But we’re related.

Relatedness is perhaps what our team is after. Half of us are trained in the arts and half are science-oriented, though we’ve all dabbled in both. If you’re interested in the training of the team, check out the Meet the Team post I did previously.

Our training has taken us to the Spencer Art Museum, the KU Natural History Museum, and KU’s field station just north of Lawrence. We looked at prints, drawings and paintings in the Spencer’s printroom, visited the Natural History Museum’s BugTown exhibit, and practiced collecting insects at the field station.

We will all assist Dr. Chaboo’ work on Chrysomelid beetles, but each student will also work on a project of their own. Art and writing students will craft creative works and biology students will conduct field research. But the idea is that we will be informed by the work done on both sides of the art/science divide. I hope to encourage these crossovers, catching them if they arise, and relate their ramifications on this blog in the days forthcoming.

Insects also take center stage in this endeavor, and I believe that it is important to convey their world, if possible. To bring them to the fore, I will strive to present them to the reader visually. Check out some close-ups of insects at the KU field station:

“It’s going to be a very physical experience,” Dr. Chaboo said, “The rain forest is not sexy because you will be covered in DEET!”

Preparation would be intimidating if she did not approach the study of insects with the energy and enthusiasm of an on-stage pop star.

“I’m super pumped!” said someone.

“Super popped?” asked Dr. Chaboo. Thus our pre-departure catch-phrase was born.