Tuesday, May 20, 2014

Datasphere at the Biosphere

Julie Allen

Estimates suggested that less than 8% of non-genetic data in ecology is available for reuse from NSF funded projects, meaning that the vast majority of ecological data cannot be incorporated into big picture ideas. This “long-tail problem” is largely because a few large labs do the majority of data sharing now while smaller labs have more difficulty sharing data. To address this issue, I recently attended a two-day meeting at the Biosphere in Tucson Arizona (May 5-6, 2014). The meeting was called Datasphere at the Biosphere and centered on creating a software institute for biodiversity and environmental science. This effort would use cloud computing with the idea of Software as a Service (SaaS) to create tools that will benefit biologists by both helping with data management and also enabling more data sharing. These new tools were also discussed in the context of new educational efforts like AIM-UP! (aim-up.org). Allowing students access to data to ask their own questions and do analyses would increase critical thinking and the authenticity of research projects in the classroom.

Outside view of the Biosphere.

Because the meeting consisted primarily of biologists representing field stations, including directors and managers, we discussed how to coordinate efforts related to ecological data, and discuss specifically what field stations need. We had a number of discussion groups to provide ideas for tools that could be built that would enable field stations and small labs to share data. These included new templates for data management all the way through having pipelines and people available to do analysis. We also discussed tools that could be created that would promote the use of these data, with much of the discussion centered on motivations for biologists and field station managers to put data online.

Inside the biosphere. This area was formerly the farm for the 
Biospherians is now being used in soil respiration studies.

We discussed big ideas that could be answered with online, shared data, including things like How will ecosystems respond to climate change, and What is the tipping point for a species to go extinct from an area? We also discussed different kinds of data that would be needed to answer these big picture questions.

Finally, we toured the Biosphere which is a very interesting place, currently under the University of Arizona management.  A series of science projects are underway in the Biosphere and it serves as public outreach.  People can come and learn how the ‘Biospherians’ lived for 2 years without any outside resources. Enjoy the pics!

Inside the ‘lung’ of the biosphere. This area regulates the air circulation. 


Rainforest habitat inside the biosphere.





Wednesday, May 7, 2014

Education is Key: Further Combating Misconceptions about Collections
Kayce Bell

Natural history museums are a hot topic in popular and scientific online discussions right now due to a controversial opinion article published in the 18 April edition of Science that questioned the value, or necessity, of collecting voucher specimens. The value of these specimens to research has been explained in other places (here, here, here, and herebut there has been little discussion on the value of specimens to education.

This contribution of natural history collections is too often underappreciated. AIM-UP! (http://www.aim-up.org/; Advancing Integration of Museums into Undergraduate Programs) has been working to identify what educators and students know (or think they know) about natural history collections and how to increase awareness of their existence and value. Opinions such as the one discussed in the Science article are an example of the profound misunderstanding of the value and potential of natural history collections. Increasing the use of specimens and their associated data in undergraduate education will go a long way toward combatting these misconceptions.

There is an urgent need to continue to collect and to grow natural history collections, not just for science and research, but also to benefit society (some examples here). One of those benefits is providing hands-on experience with specimens and their data.  Recent development of tools provides access to digital information about natural history collections. These novel resources allow teachers to guide students as they develop and answer their own research questions, providing powerful alternatives to “canned” activities with a pre-determined outcome. Learning from these inquiry-driven activities is the type of reform that has been called for in undergraduate biology education (see Brewer, et al. 2010).


Incorporating natural history collections into new initiatives in undergraduate education will help students understand real-world threats and impacts from human activity. For example, misunderstanding of the causes and consequences of global change, such as climate and landscape modification, is common in the United States. Natural history collections and associated data allow students to explore and test their own hypotheses about the impact of environmental change on biotic diversity. The Grinnell Resurvey project uses historic museum specimens and contemporary collections to look at species distributional shifts along elevational transects in the Sierra Mountains since the early 1900s. This project has documented changes in small mammal distributions that relate to climatic changes, such as temperature increases, over the last 100 years.  There are many fantastic examples of such resurvey projects ranging from tracking plant flowering times at Thoreau’s Walden Pond, to grasshopper emergence in the Rockies, to large-scale marine censuses.

 Although students and educators cannot all participate in these resurvey projects on the ground, there are many opportunities to utilize resurvey data to visualize changes through time. AIM-UP! participants are developing educational modules that serve as examples of how educators and students can use these on-line databases so they can formulate and pursue their own questions about biological responses in a human dominated age. 

Creating and maintaining biocollections and associated data is a vibrant and growing enterprise, and one that has remarkable potential to engage students, both for its tangible aspects and for its value in documenting the biosphere (past and present). AIM-UP! will continue to serve as a catalyst for informing science educators about the  multifaceted opportunities emerging from natural history collections and also to establish connections among instructors and museum staff from diverse institutions. 


Thursday, September 29, 2011

An Introduction to Aim-UP!

RCN-UBE: Advancing Integration of Museums into Undergraduate Programs (AIM-UP!)

AIM-UP! is a NSF sponsored Research Coordination Network in Undergraduate Biological Education that is exploring the tremendous potential of our vast natural history collections, associated databases, and data linkages to contribute to traditional classroom and laboratory teaching and non-traditional research experiences in biology. This network of museum scientists, collection specialists, undergraduate educators and artists intends to produce new ways of incorporating the extensive archives and cyberinfrastructure of natural history museums into undergraduate education under 5 primary themes: 1) Integrative Inventories: Exploring Complex Biotic Associations Across Space and Time, 2) Decoding Diversity: Making Sense of Geographic Variation, 3) Generating Genotypes: Evolutionary Dynamics of Genomes, 4) Fast Forward: Biotic Response to Climate Change, 5) Coevolving Communities: Pathogens, Hosts, and Emerging Diseases.

We anticipate developing additional subthemes through our meetings, on-line discussions and workshops at scientific meetings including an exploration of the use of natural history collections and associated databases to facilitate teaching in other subdisciplines in Biology (e.g., developmental biology, behavior, physiology, and cellular biology) and in other fields (e.g., geography). Already we developed a series of 2 day workshops and a cross-listed course with the Art and Ecology Program at the University of New Mexico. AIM-UP! will refine existing efforts and develop new integrated approaches to collections-based training in large-scale questions using the combined and broadly-based expertise of educators, curators, collection managers, database managers, and scientists whose teaching and investigations span across various disciplines and relate to topics covering a wide spectrum of time and space. We anticipate that, by integrating our expertise and experiences across university-based museums, we can greatly advance traditional and emerging fields that could use museum collections. Inclusion of participants from federal agencies, large free-standing museums, and leading educators from Latin America are ensuring wider dissemination of our educational products. Our plan is to 1) discuss and develop much needed teaching and analytic tools and methodologies for using museum specimens in training students in the emerging fields such as climate change, evolutionary genomics and molecular ecology, 2) develop instructional tools for museum databases (e.g., ARCTOS ) that will be freely available to both the public and to other teachers and scientists, 3) develop an integrated network of educators working on specimen-based questions on different taxa and disciplines, 4) include diverse collaborators, including minority and female scientists, federal agency biologists, academics, international participants, and museums with large public audiences, 5) train and mentor undergraduate students in museum-based field and laboratory research, and 6) outreach especially to underrepresented students with an emphasis on issues relevant to their communities (e.g., Native communities in New Mexico or bush Alaska).