Blogs

Wednesday, September 7, 2011

Waste Not, Want Not

fish

Like any good ichthyologist, I keep saltwater fish.  When I lost a Banggai cardinalfish recently, how did I deal with this tragedy? Not by flushing it or starting a pet cemetery, but by turning that loss into a gain for the Biodiversity Institute's Ichthyology collection. 

It is true that aquarium fish make less than ideal specimens.  It is impossible to get accurate, reliable information on the natural habitat, behavior, distribution, and population structure of such a specimen.  However, for large-scale genetic studies, a specimen without such data can still provide valuable insight into the evolutionary relationships among fish species.  Likewise, we can gain important morphological information to further inform our ideas on the evolution of structures like jaws and tails.

So how does a fish reach scientific immortality after passing on to the great aquarium in the sky?  First, and not surprisingly, it's important to get the fish into the freezer as soon as possible to keep it from decomposing (genetic material starts to break down quickly as the fish decomposes).  When we are ready to process the fish, we first take photos of it, since preservation often causes bright colors and patterns to fade. Then a small piece of muscle is taken from one side and added to our tissue collection--this leaves the other side of the fish intact for morphological studies.  We then inject the fish with formalin and store it in alcohol, or clear and stain it.

While at first blush this may seem perverse, my cardinalfish now lives on as frozen tissue and fluid specimens, where it will provide valuable genetic and morphological information for researchers and students.  I know I would much prefer that to being flushed.

Tuesday, August 2, 2011

Recent Discovery in China Relates to KU Research

fossil

While a recent discovery may change textbooks and the way that many scientists think about bird and dinosaur evolution, it comes as no surprise us.

This week, Xing Xu, H. You, K. Du and F. Han published in the journal Nature a reanalysis of early bird evolution. The analysis knocks Archaeopteryx off its perch as a grandfather to later birds. 

KU has been the central hub for the discovery of the fossil bird beds in the Early Cretaceous of China with the description of the primitive bird, Confuciusornis, and has continued to be involved with all the new discoveries coming out of this region in part through an alumnus of the KU vertebrate paleontology program.

The alumnus, Zhonghe Zhou, presently leads Chinese studies in that region and was recently elected to the prestigious National Academy of Sciences.  Zhou and one of the paper’s authors, Xing Xu, had already precipitated a revolution in our understanding of bird evolution with the discovery of the four-winged gliding bird/dinosaur, Microraptor. With Microraptor, they showed that bird flight began with gliding. 

Zhou has a long-term collaboration with KU vertebrate paleontology researchers at the Biodiversity Institute. Preparator David Burnham, collection manager Desui Miao and I regularly visit China to work on early birds. Our research also has suggested that Archaeopteryx along with other archaic birds represents a side branch that split off much earlier than the new bird, Xiaotingia, and its sister Anchiornis, another four-winged gliding animal. 

While the recent paper in Nature calls these animals “feathered dinosaurs,” we think that they and their common ancestor with modern birds can be best considered true birds. Rather than removing Archaeopteryx from Aves because its avian features were shared with birdlike dinosaurs, we place a stronger emphasis on these features thereby pulling the dinosaur-like birds into Aves. This limits these flying, feathered animals to the Class Aves and pushes the origin of birds into the Early Jurassic or Late Triassic at about the same time as the dinosaurs themselves.

Friday, February 4, 2011

Lifemapper + VisTrails = Better Science

Lifemapper logo

We have combined Lifemapper and VisTrails software to create an intuitive and powerful new way to analyze species distributions. Lifemapper is our NSF funded species distribution mapping and modeling initiative. VisTrails is a scientific workflow management system developed by the Scientific Computing and Imaging Institute at the University of Utah.

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Workflow systems allow scientists to assemble complex computational pipelines consisting of sequential tasks which are stitched together using a single desktop software program. Typically an automated research workflow will start by inputting data from an external source, then dragging that data through one or more computational or modeling tasks, and then outputting the results in formats which can then be analyzed. LM3 LogoData output formats might include geographical maps, numeric data sets or statistically summarized results. Workflow management software is integrative by design and it is an excellent tool to connect internet data and computer processing services together across institutional and  discipline boundaries. VisTrails is particularly suited for our Lifemapper Project because of its capabilities for integration with internet-accessible data and services and because of its strength with capturing the metadata or 'provenance' information associated with research workflows.

We have developed software extensions that computationally integrate VisTrails' functions with our Lifemapper Project's web services for species distribution modeling. Technically, this integration includes interfaces to post and retrieve species occurrence sets from our installation of theVT Logo Global Biodiversity Information Facility's global database of museum specimen data points. This software integration allows biodiversity researchers to quickly compose and execute species niche modeling experiments, using VisTrails' drag-and-drop workflow creation software.  Our latest Lifemapper VisTrails software (version 1.1.0) introduces the following features:

Lifemapper Ecological Markup Language (EML) Reader Software

EML is a standard, XML-based language for describing and archiving all of the background information  or 'metadata' associated with research data sets in environmental biology.  The Lifemapper EML Reader software enables researchers who map and model species distributions to automatically store the metadata associated with a Lifemapper/VisTrails workflow (modeling experiment) in an EML archive file.  An EML file would include metadata on such things as sources and formats of input data, any pre-processing steps or data filters that might be used, parameters for the modeling algorithms, as well as information about the resulting output files. This new capability makes complex modeling experiments easier to manage, archive and reference.  Best of all, storing Lifemapper/VisTrails metadata in EML files, enables the species range modeling experiment to be easily re-executed by the same or other researchers.  Being able to fully reference, re-use, and repeat a complex computational niche modeling process directly results in more transparent and verifiable science.

Enabling VisTrails for OpenLayers Display 

OpenLayers is open source software product which enables the creation of sophisticated map displays with point and click manipulation functions such as panning and zooming.  With our latest LM / VT client release we have enabled VisTrails' output screens to provide these mapping functions.  These new capabilities in VisTrails greatly facilitate the research exploration of species distribution maps and model outputs produced by running VisTrails / Lifemapper workflows.

Simplified Algorithm Inputs 

In previous versions of our Lifemapper / VisTrails this integration, species model algorithm parameters had to be specified, even if using default values. While it is still possible to change model parameters, default settings are now automatically applied.

Simplified Inputs and Outputs 

VisTrails works with software modules that are selected from a screen listing and dragged and dropped into a workflow workspace.  Modules have data Inputs and outputs as data are brought into a workflow, streamed through various processing steps and then output for analysis.  In our latest software we have simplified input and output links for Lifemapper's species niche modeling components, which makes the creation of new workflows faster and easier.

Our Lifemapper / VisTrails client allows one to wield the power of the Lifemapper web services inside a desktop application.  Researchers can quickly connect elements together without worrying about the work behind the scenes.  No studying APIs.  No constructing HTTP requests.  Just click, connect, and go!  The Lifemapper / VisTrails client software can be downloaded from the Lifemapper Project web site at: http://lifemapper.org

For assistance with installing or using Lifemapper / Vistrails software for research, send e-mail to: lifemapper@ku.edu or call the helpdesk at 785.864.4400.

Saturday, January 28, 2012

Venezuela 2012, part 1

Greetings from San Carlos del Zulia, Venezuela. I'm a bit over a week into my first expedition of the year — this one to continue our aquatic insect survey efforts in Venezuela. We've spent he last 8 days driving around the country and splashing around in various rivers and lagoons. It is hard for me to believe, but this is my 10th trip to Venezuela since my first in 2006. And, in terms of general volume of material and 'good stuff', this might be the best. We hit the dry season perfectly — when it is well underway and rivers and low and lagoons are reduced, but before things really get dry. A number of great sites on this trip, and it will take months get through these dense samples when I return. One highlight was getting up high in the Andes and collected at some lagoons over 12,000 feet — the highest we've gotten samples to date. More soon.

Tuesday, December 30, 2008

And so it begins

It has been a long but nearly flawless 15 hours of traveling today, beginning with the 3:30 a.m. shuttle pick-up in Lawrence to clearing customs in Maracaibo, Venezuela, at 8:30 p.m. (quick fact: Venezuela has its own time zone, which is 30 minutes ahead of Eastern Standard Time). My colleagues from the Universidad del Zulia, Mauricio Garcia and Jesus Camacho, greeted me at the airport. We retired to Mauricio’s house to unwind and catch up for a couple of hours.

The immediate issue upon arrival that always splashes me in the face like a bucket of cold water is switching over exclusively to Spanish. Usually it takes me a week to get back up to a functional level. Having only been gone for 5 months, it shouldn’t take very long. On the plane there was some confusion over seat assignments, and I got some very strange looks when I was trying to sort it out. Later I realized that I had confused the words “sentarse” (to sit) and “sentirse” (to feel), and had essentially been saying something like “I think I’m supposed to feel there” and “I can feel where you were feeling.” The next few days of the trip will be devoted to some of the more mundane housekeeping and logistical issues, such as making and confirmation reservations, scouting a few local field sites before the full field crew assembles, and getting all our gear in order and packed in a semi-efficient manner. Of course, celebrating the New Year will be thrown in there as well. The main expedition does not start until next week, after my other US collaborators arrive.

Tuesday, December 30, 2008

Clean water

Curious children often observe scientists such as my collaborator, Mauricio Garcia, whenever we're collecting insects

Mauricio, Jesus and I scouted a few new field sites today in the Serrania de Perija- the mountainous border region that forms the western boarder with Colombia. Just a few hours from the relatively affluent oil city that is Maracaibo, the roads gradually narrow into small dirt paths winding around large rural haciendas (ranches) and indigenous communities. Cars give way to burrows and horses as the primary (and functional) means of transport.

Sunday, August 2, 2009

Endgame: Caracas for a course on biodiversity

The last week has been a bit hairier than normal. Joined by another Colombian water beetle student, we flew down to Puerto Ayacucho in southern Venezuela to scope out some new sites. No need for details at this point but things did not go quite as planned. The fact that an American and a Colombian were traveling together along the boarder with Colombia the day after Venezuela shut down all relations with Colombia because of perceived US military aggression (likely) played a role, if you are curious. But, enjoy the two landscape photos of this area below that make it one of my favorite places in the world. After a very (very) long, 13 hour bus ride, I'm now in Caracas to participate in a Neotropical Biodiversity course put on by IVIC (the national Venezuelan Institute of Scientific Investigation). My 30 minute talk tomorrow will be the first full-length presentation I attempt to give entirely in Spanish...we shall see how that goes. This marks the final phase of the trip...I return to Kansas on 6 August.

Wednesday, July 15, 2009

Dunes and Lagoons

From San Cristobal: The last week has been a whirlwind of different habitat types (as normal). We zipped across from Maracaibo to Coro in Falcon state where we stayed for a few days to work the region. This part of Venezuela is mostly dry semi-desert. Lots of cactus. Among the more striking feature is a dune region which is large enough to make you think you were in lost somewhere in the Sahara. Of course, there are oases of sorts that were full of beetles. We crossed the Sierra San Luis and headed south to Barquisimeto and made our first foray into the Andes nearby, climbing up to just over 6000 feet. Heading down the Andes a bit to Biscucuy and Bocono we stopped at a number of rivers and lagoons with mixed success. We dropped out of the Andes yesterday near Guanare, went south to hit the exiting streams, and today eventually climbed back up into them in the state of Tachira. We will collect here tomorrow before heading up the main Andean chain to Merida and Trujillo later in the week. There has been regular rain but usually only part of a day or at night, and it has had minimal impact on our actual collecting...although it has made some rivers either a bit too swift for our taste or pretty gauged out and not much to collect.

Tuesday, July 7, 2009

Species of the Month: July

beetleThe Gyrinidae are a family of charismatic aquatic Coleoptera commonly known as whirligig beetles, for their gyrating swimming style. Gyrinids are peculiar for having completely divided eyes giving them the appearance of having four eyes: two that peer above the water and two that peer below the water. They swim about on the surface tension of the water kicking with two pairs of paddle-like legs. The species selected for this month is a whirligig beetle in the genus Gyretes. Gyretes can be characterized by a furry pubescence that usually outlines most of the beetle´s body. However, the Gyretes selected here is nearly completely covered in this hairy pubescence. It also happens to be one of the largest known Gyretes. It is found here in Venezuela and I (Grey) am hoping that I will have the opportunity to collect this charismatic gyrinid on this trip.