Thomas Hardy

Wednesday, September 22, 2010

Roads and Research

Last week's NYTimes article about roadkill ( got us thinking about how roads change the way scientists do research.  Roads are in part a great research tool because they provide easy access to every region of the country but, as well as creating other issues, they can also skew data.

Craig Freeman, a botanist at the Biodiversity Institute, studies the flora of the Great Plains.  His research often requires him to drive a lot:

"Not surprisingly, when we plot the collect locations of our specimens on a map showing the network of highways in the state, many occur at sites along or near roads, urban areas, and public lands," Freeman said. "Why? Botanists are more likely to see plants (or habitats) of interest from the roads that they travel and in areas where access is not limited. Consequently, there is a collection bias in our data."

This is particularly evident in the western quarter of Kansas, where there is very little public land and few urban areas. Many records documenting the flora of western Kansas come from roadside or near-roadside habitats. So, Freeman said, it's necessary to access lands away from roads to get a more accurate estimate of the diversity and abundance of plants.

Not only do roads change how we investigate the environment, but they also provide habitats for plants that wouldn't normally grow in the plains.  Freeman continues:

"The use of salt to melt snow and ice on paved roads in eastern Kansas has permitted both alkali sacaton and saltmarsh aster to spread eastward in Kansas, taking advantage of shoulders of highways where regular mowing elevated salinity limits competition from most other species. Alkali sacaton and saltmarsh aster can be found along I-70, KS Hwy 10, and other major highways through eastern Kansas into the Kansas City metropolitan area, places where they did not occur as recently as 40 years ago."

Next time you're driving to KC via I-70, keep an eye out for the salty intruders.

Wednesday, August 11, 2010

The Known and the Obscure

water buffalo

Last week, The New York Times put out an article (  on animal ugliness — how it affects which animals we like, which we have as pets, and ultimately which animals we spend most of our time studying.

Though the article does a good job of pointing out that cute animals get more than their fair share of study, the article itself only mentions conspicuous organisms.  As Biodiversity Institute research assistant Kendra Koch points out:

"From my point of view the inconspicuous and less 'palatable' organisms are often simply ignored or at least shied away from. Parasites of course seem to have a special cringe factor. Even this article on ugly creatures focuses on mammals and vertebrates with no mention of the bulk of animal diversity, let alone any of the other kingdoms."

Animals are far outnumbered by other kingdoms in regard to number of individuals, and if the under-studied insects weren't included (insects are animals!), they would be dwarfed in species count, as well.  An in-the-flesh example of this diversity is shown in our museum's BugTown exhibit. 


Koch is a Research Assistant for Parasitology, a field of study still making sense of a huge diversity, the extent to which is unknown.  New parasites are found every year, and it is estimated that there may be twice as many undiscovered species as known species. 

"Nearly every time I explain what I do to someone who asks, the response is similar," says Koch. "A surprised and sometimes disgusted look accompanied by the question, 'why does studying elasmobranch tapeworms matter?' All living things (even parasites) are part of a greater system that has evolved toward some balance and ideally have an equal right to be conserved."

The natural world is always more complex than we think.  Ugly critters have something going for them, as well — they're ugly.  While we're worrying about the cute ones, or even the ugly ones, the worst off are the unnoticed.

Wednesday, March 30, 2011

Biodiversity Observing Network

Daphne Fautin, Curator of Invertebrate Zoology, recently helped generate a paper that plans a Biodiversity Observing Network or BON — a system that may be a key factor in encouraging sustained marine ecosystem health. The effort would create a standardized, coordinated system for measuring marine biodiversity.

"I think a major message is that we don't know what we don't know," she said. "Not only do we not know what we might be losing, we do not know the roles even known organisms play in the ecosystem.  Thus the BON.  An Ocean Observing System is being developed to monitor the state of the oceans — to detect rises in temperature and drops in pH, for example.  But why should those parameters interest us?  One reason only — because they affect the ability of the ocean to sustain life, and we depend, indirectly and directly, on life in the ocean."

Serving on a steering committee, Fautin helped identify key methods for observing biodiversity. The paper listed many recommendations, including:

1. Coordinate biodiversity sampling across taxa, habitats, hierarchical levels, and methods from microbes to mammals;
2. Maximize compatibility of BON with legacy data;
3. Establish one or more Biodiversity Observation Center(s) to coordinate sample processing, including taxonomic identifications, data management, and training and invest in the computational expertise to handle large datasets in an open access environment;
4. Synthesize and make accessible marine taxonomic resources;
5. Invest in developing new approaches for automated sample processing;
6. Modernize and enhance the nation’s physical infrastructure for marine exploration; and
7. Initiate an integrated marine BON demonstration project soon.

Friday, November 19, 2010

Limbless Lizards

Usually, your close relatives resemble you.  Or at least they have the same number of limbs.

Cameron Siler

Not true, however, for Brachymeles lukbani, a species recently discovered by Cameron Siler, one of the museum's graduate students in herpetology.  This critter (which has lost its limbs through evolution) looks like a snake but is actually a skink — a type of lizard.  The genus Brachymeles has a diverse membership. 

"They have the full suite from limbed to limbless, from working limbs with five fingers to no limbs at all," says Siler. 

But this makes the lizards an excellent group for studying how and why limb loss occurs.  Brachymeles lukbani "swims" through rotten logs and undergrowth, looking for food.  In that situation, possessing limbs might not be very useful, or even counter-productive. 

Siler's research has increased the museum's holdings of skinks, making it a leader in skink research

Tuesday, August 10, 2010

Cleared and Stained

cleared and stined

Caiman latirostris — a crocodile

Some of our specimens, recently discussed in our post about specimens as snapshots in time, take on a unique role after entering the museum's collections. Certain reptiles, amphibians and fishes undergo a process called clearing and staining, which helps scientists look into the critters.

After being turned translucent by a digestive enzyme called Trypsin (found in the bellies of many vertebrates including us), dyes are added.  Bones and hard tissue are stained red with a chemical called Alizarin, and soft tissues are highlighted by adding Alcian blue. 

The contrasting colors help scientists study the morphology - the skeletal and skin structures - of an animal.  As an example, they prove especially useful for studying frog skulls, which undergo a peculiar dance of morphological change as frogs mature. 

Tuesday, July 27, 2010

From the Field to the Lab


Fieldwork and lab work are at the heart of what we do at the Biodiversity Institute. 

Mark Robbins, ornithology collection manager, bridges fieldwork (collecting specimens, recording data, investigating habitats) and lab work (DNA analysis, taxonomic classification, morphological comparisons).  All specimens caught in the field spend time in the lab; all of the analyses and data obtained in the lab help to answer research questions about the life in the field.

Robbins' research questions pertain to the migration patterns of small birds called marsh and sedge wrens.  To do his work, he collects specimens from the field in Northwestern Missouri and elsewhere.  He is one of many Biodiversity Institute scientists who spend time in both the field and the lab - collecting and then analyzing data.  To learn more about Robbins' work, investigate the gallery below or learn about his research methods.

Wednesday, June 2, 2010

On Cleaning an Ancient Fish

The word “fossil” often conjures images of Tyrannosaurus rex skulls, mammoth femurs, or other large bones. But those aren’t the only ones that survive through the millennia, and certainly aren’t the only ones that have importance.

KU Biodiversity Institute graduate students Sarah Spears and Kathryn Mickle study prehistoric fishes. Their fossils are so small that, in order to get them ready for study, Sarah and Kathryn have to use tiny tools to remove excess rock. Sometimes, even metal tools are too rough and inexact, so they switch over to porcupine quills — just sharp and flexible enough to clean tiny fish bones.

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.