s463p656's blog

Saturday, February 12, 2011

Fiji Expedition Broadens Genetic Research

In December 2010, KU Biodiversity Institute graduate student Mike Andersen, and curator of birds, Rob Moyle, completed a three-week expedition to Fiji. This effort marked Ornithology’s third expedition to Fiji, work that began in November 2009.

They collected specimens of 23 species from two locations: the isolated Nakauvadra Range in the extreme northeastern part of Fiji’s largest island, Viti Levu; and the southern island of Kadavu. The Kadavu specimens were the world’s first from this island with associated genetic tissue samples, and the collection included three endemic bird species: Whistling Dove (Ptilinopus layardi), Kadavu Honeyeater (Xanthotis provocator), and Kadavu Fantail (Rhipidura personata), plus numerous morphologically unique island forms such as Golden Whistler (Pachycephala pectoralis) and Collared Kingfisher (Todiramphus chloris).

The Nakauvadra Range is the third locality on Viti Levu where Biodiversity Institute researchers have worked, making it possible to analyze genetic differentiation among avian populations across this oceanic island. Andersen and Moyle are developing the Fiji project in close collaboration with students and researchers in the Institute of Applied Science at the University of the South Pacific. The collections-based research effort forms the foundation for Andersen’s dissertation research on the origins and diversification of the Fijian avifauna, as well as future dissertation projects by Fijian students at the University of the South Pacific. 

—Town Peterson

 

Tuesday, January 3, 2012

Knowledge Punched by Pundits in 2011

2011 featured pernicious political posturing over what we know and how we discover it. Florida Gov. Rick Scott told the state’s universities that they should be educating students in areas “where people can get a job in this state.” Accordingly, he intends to invest higher education dollars in physical science, math, engineering and technology departments, and let the humanities, arts and social sciences go fallow. Scott singled out anthropology as an example of a job-less education, saying, “Is it a vital interest of the state to have more anthropologists? I don’t think so.”

Well, think again. Anthropology sits at the busy intersection of nature and culture, one that has seen explosive accelerations, enormous traffic jams and massive pile-ups in the human condition for at least the past 2 million years. Its lessons are instructive for Florida, the nation and global communities: how peoples have exploited their environments for food, fiber, fuel and pharmaceuticals, how they fashioned their cultures, economies, industries, technologies and jobs, and why they went boom and bust.

According to the National Association of Colleges and Employers, graduates in career-oriented majors, such as science, math and technology, do indeed have a higher probability of landing a job — at least initially. But, a few years down the career path, liberal arts graduates “frequently catch or surpass graduates with career-oriented majors in both job quality and compensation.” Why? Because of their knowledge of ethics, communication and social dynamics, which is adaptive to rapidly changing global economic, political and cultural environments.

Scott might be interested in the career paths of people who majored in job-less disciplines: Carly Fiorina, former CEO of Hewlett-Packard, medieval history and philosophy; George W. Bush, 43rd U.S. president, history; Dick Cheney, former U.S. vice president, political science; Clarence Thomas, U.S. Supreme Court justice, English; Michael Crichton and Ursula K. LeGuin, best-selling authors, anthropology; Sally Ride, astronaut and first woman in space, English; Ronald Reagan, 40th U.S. president, 33rd governor of California, economics and sociology.

Earlier in the year, three Republican presidential candidates went AWOL from modern science. Former U.S. Sen. Rick Santorum, U.S. Rep. Michele Bachmann, and Texas Gov. Rick Perry opined on talk shows and stump speeches that 20 years of research on climate change involving thousands of investigators was “junk science.”

Apparently, they choose to be deaf/dumb/blind to evidence. They didn’t issue a retraction when a leading skeptic of global warming, physicist Richard Muller and his Berkeley Earth group, confirmed the findings of the “junk” scientists: Global temperatures have risen sharply since the mid-1800s because of a jump in greenhouse gases, notably CO2. “Our biggest surprise was that the new results agreed so closely with the warming values published previously by other [scientific] teams,” said Muller’s Berkeley Earth study, which has solid conservative credentials: It was funded by the U.S. Department of Energy and foundations established by Bill Gates and the Koch brothers.

While on the stump, Bachmann and Santorum proudly flashed their pre-Enlightenment credentials, espousing their belief in intelligent design as the best biology curriculum for the nation’s students. One can’t be polite about this. What’s next? Scrap Pasteur and teach the Bad Air Theory of disease in medical school? Dump Aristotle for the Flat Earth Theory in geography class? Bachmann and Santorum are entitled to their private discomfort with the established knowledge of Darwinian evolution. But, hubris aside, their personal discomfort is not a rationale for national policy on science education.

The prize for sanctimonious social science goes to Cal Thomas’ editorial piece on the Sandusky-Penn State affair (Journal-World, Nov. 15, “Penn State’s shame — and America’s too”). The blame, he writes, extends beyond the individuals involved to all society, to the “free-loving ’60s, (when) we seem to have taken a wrecking ball to social mores.” Really? No song at Woodstock advocated rape or pedophilia.

Thomas also blames human nature, “but society — buttressed by religion — once did a better job of keeping human nature in check,“ specifically, keeping “lesbian, gay, and bisexual orientations” in check as “sinful.” Hmmm. You’d think being buttressed by religion against sin would naturally have kept the Catholic clergy in check. Yet, as we now know, its systematic sexual abuse and pedophilia were rampant, with the crimes abetted and covered up by repeatedly moving the abusers from diocese to diocese. It started long before the free-loving ’60s,” and went beyond one locker room at Penn State to parishes worldwide. Its innocent victims are countless.

The complex challenges of the world in 2012 and beyond demand more from our self-declared leaders and sages than wishful, simplistic nostrums as our default solutions or salvation.

Originally published in the Lawrence Journal-World on January 2, 2012.

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

specimens

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.

Friday, June 1, 2012

Fun Facts About our Ethanol Collections

jars of specimens

Inside the herpetology collection

Specimens

A jar of snake specimens

Most of the museum's reptile, amphibian and fish specimens are kept in jars, along with ethanol to preserve them. These collections contain nearly one million specimens that provide vital information to biologists doing research in areas ranging from evolutionary patterns to locomotion to conservation. Here are some interesting facts about our collections:

1.We try to keep the fluid collections in relative stasis in regard to temperature and humidity. The goal is 65 degrees F and 50% relative humidity. In practice, however, the temperature is fairly steady but the relative humidity varies quite a bit.

2.The oldest specimen in the herpetology collection is Ceratophrys aurita, KU 98129, collected in Brazil in 1863. It, however, is an exchange specimen. The oldest specimen collected by a museum affiliate is a Thamnophis elegans from New Mexico, KU 2408, collected in 1880. The oldest specimens collected in Kansas are two copperheads and a massasauga from Franklin county in 1888. The history of specimen collecting for these collections has been steady ever since. There are 60 specimens collected prior to 1900.

3.The specimen with catalogue number 'KU 001' is Alligator mississippiensis.  The specimen is on display in the panorama at present for the Adopt-A-Specimen exhibit.

4.The sheer volume of ethanol used in the collection is impressive. We have a 1795 gallons for amphibians, and about 1875 gallons in large specimen tanks. The reptiles utilize about 1500 gallons. That's a 5,170 gallon capacity for reptiles and amphibians. Double that in fishes, and add a touch for the others. For everything together, 12,000 gallons total is a reasonable estimate. Of that, a substantial amount of space in the jars is taken by specimens and air, so we would actually have about 8,000 gallons of 70% EtOH (ethanol) in the wing. That's about 5,600 gallons of Ethanol (about 102 drums), significantly less than a typical residential swimming pool.

Monday, October 10, 2011

Specify Software Sustains 20% Growth

Specify logo

Specify is now the database management of choice for over 375 biological collections worldwide. The Project is sustaining a 20% annual growth in the number of supported biological collections. In addition to offering research community software helpdesk support, the Project has produced 11 software updates in 2011, many of them extending and enhancing features researchers have requested for more effective management and analysis of specimen information.  Recent research funding awards by the U.S. National Science Foundation's 'ADBC' initiative for accelerating the computerization of information associated with biodiversity specimens have stimulated additional research repository adoption of Specify for their project data management.

The Specify Project has a number of new capabilities and releases planned for 2011 and 2012 including: (1) a Specify web client for remote access (editing, querying, reporting, etc.) over the internet to remote Specify databases (being developed in collaboration with the Swedish Natural History Museum), (2) release of the new Scatter-Gather-Reconcile or "SGR" capabilities which allow researchers to look for specimens which are related or duplicative to their own (in collaboration with the University Autonoma de Barcelona), and (3) innovative data entry software for acquiring specimen images for digital archives and specimen label data computerization.

The ultimate goal of mobilizing the locality, species identity, and collection date information associated with biological specimens into databases and onto the web is to provide easy open access to the information for biodiversity documentation and analysis, and for forecasting the impacts of climate change on species ranges.

Wednesday, December 22, 2010

A Symposium and an Ancient Seaway

This past month I co-chaired a technical session at the national Geological Society of America conference in Denver. The session was entitled "Paleontology, Paleobiogeography, and Stratigraphy of the Late Cretaceous North America Seas: A Tribute to Bill Cobban." Dr. Cobban is a scientist at the US Geological Survey who has over 60 years of experience working on the statigraphy and paleontology of the Late Cretaceous Western Interior Seaway. The Western Interior Seaway (WIS) ran through the middle of the U.S. during the Cretaceous (about 65-100 million years ago) and was home to some amazing seafaring creatures, including the mosasaur that hangs over the doorway to the KU Natural History Museum.

I gave a talk entitled "Using GIS to investigate bias in the fossil record: a case study of the Late Cretaceous Western Interior Seaway of North America." In that talk I presented some tests that I performed to assess how good the fossil record in the WIS is. I was curious if the fossil record is biased in any way that would prevent us from mapping out the ranges of prehistoric species. The factors that I'm particularly interested in are competition, environmental change, and whether biological interactions between species are more or less important than environmental changes in determining which species go extinct and which do not.

I relate my research to the current biodiversity crisis: when you are trying to understand how invasive species, habitat fragmentation, and climate change are going to affect species in the future, there is a WEALTH of information (~544 million years in fact) in the fossil record that provides exactly that. The fossil record tells stories of how critters responded to species invasions and habitat loss and it teaches us about the effects of climate change and sea level fluctuations. These are the very factors that conservationists consider when attempting to save habitats and species.

One of the symposium's invited talks was by Neil Landman, a renowned cephalopod paleontologist from the American Museum of Natural History. He spoke eloquently on the life history of scaphite ammonites. Scaphites are shelled cephalopods (similar looking to modern Nautilus, also related to squid and octopi), but instead of having a properly coiled shell (like the Nautilus, their shell straightens out a bit at the end. Neil is probably one of the world's expert on scaphites. His talk described his latest interpretation of how these animals caught prey, what kind of prey, how they swam, at what orientation they held their body in the water column, how they reproduced, etc. Late Cretaceous cephalopds got SUPER weird, so this sort of talk is *really* exciting for folks like me who are into cephalopods and life in general in the WIS.

Overall, we had a very nice day talking about the current status of Late Cretaceous WIS research from a variety of geologically related fields: geochronology (age-dating the rocks), biology (mostly cephalopods, but also foraminifera, mosasaurs, sharks, etc.), biogeography, mapping, stratigraphy, and biostratigraphy. We are still working to better understand a number of the animal groups and how they might be used to date rocks. The great news is that it looks like the fossil and rock records are good enough to test many of our questions!

Tuesday, November 30, 2010

Winter Orchids

winter orchid

When the cold winds of November tug the last leaves from the maples, basswoods, and elms, orchids probably are the farthest thing from most Kansans’ minds.  However, fall, winter, and early spring are the best seasons to search for one of the state’s more secretive plants – the puttyroot orchid or Adam-and-Eve [Aplectrum hyemale (Muhl. ex Willd.) Nutt.].  The plant’s specific epithet “hyemale”, referring to winter, alludes to the plant’s habit of producing a winter leaf.  The name puttyroot is a reference to sticky substance released from the crushed tubers, which usually occur in pairs (hence the name Adam-and-Eve).

Puttyroot has evolved a fascinating strategy to survive in the low-light environments of rich, deciduous forests.  As forest canopies develop in the spring, light limits the ability of understory plants to photosynthesize.  Consequently, many herbaceous species flower and fruit in the spring, before the canopy fills in, or in the fall, when the canopy begins to thin.  Puttyroot takes this strategy to an extreme.  Each plant produces a single, elliptic, dark green, pleated, 3-6 inch-long leaf in the fall.  The ground-hugging leaf remains green and photosythetic from fall through winter and into spring, producing sugars needed by the plant to grow.  From late May into mid June, some plants will produce a single, 10-20 inch-tall flowering, each bearing a dozen whitish purple or brownish white flowers near the tip.  Ribbed, pendent fruits – each about 1 inch long – mature through the summer and persist into the fall, leaving another clue to the plant’s presence.  

Populations of puttyroot are documented in 10 eastern Kansas counties (Anderson, Coffey, Crawford, Douglas, Franklin, Johnson, Leavenworth, Linn, Miami, and Wyandotte).  Most occur in moist, maple-basswood forests or cottonwood-dominated floodplain forests along rivers and streams.  Populations generally comprise a few, closely-spaced individuals, but large populations can contain several hundred plants.

The next time you head out to your favorite forest trail for a fall or winter walk, keep an eye to the ground.  If you are lucky, you may spy the distinctive leaves of this forest gem.  If you do find this rare Kansas orchid, plan a return visit to marvel at its amazing flowers and fruits in the dim light of the forest floor.