Newsletter Vol. 3 No. 1 February, 2009

 

In this issue:

Science and Synthesis

Craig McClain, NESCent's new Assistant Director of Science

Recent publications and databases from NESCent working groups

Informatics

Events

Training Opportunities

Summer Internships

Other IT news

Education and Outreach

Celebrating Darwin's Bicentennial

Darwin Day 2009

Evolution Speakers Series

Illuminating Biology: an Evolutionary Perspective - videos available

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Science and Synthesis

Craig McClainCraig McClain, Assistant Director of Science

NESCent welcomes Craig McClain as the Assistant Director of Science. Craig received a Ph.D. in environmental biology on deep-sea biology from UMASS Boston, was a postdoctoral fellow at the University of New Mexico and the Monterey Bay Aquarium Research Institute.  His  research focuses on untangling the complexity of processes that underlies the structure and dynamics of marine invertebrate biodiversity and body size range.  This often encompasses examining the interconnections of ephemeral processes occurring within local ecological communities and long-term macroecological and macroevolutionary drivers occurring at regional/global levels. His current research focuses on how marine invertebrate communities are coupled to temporal and spatial variation in primary production.  As a model system, he focuses regularly on deep-sea systems, which proves a fertile ground to develop and test models under the bottom-up dynamics of food limitation.  During his research career, Craig has been to Antarctica, participated in several research expeditions to the Pacific and Atlantic, played with ROV’s and submersibles, and lost some hair.  In his free time he enjoys, rather unsurprisingly for a Marine Biologist, scuba diving.  Craig says he was drawn to the energy surrounding NESCent and the spirit of collaborative and synthetic research and that he is looking forward to tackling the challenge of serving as a more administrative director.  He will continue to serve as the Marine and Aquatic Science Section Editor for PLoS One. 

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Recent publications and databases from NESCent working groups

Many NESCent working groups generate publications to share their results, or information about community resources they have developed.  Here we highlight two recent publications from working groups.size logo

In 3.5 billion years, the maximum size of living organisms on Earth went from a single cell invisible to the naked eye, to giant sequoias over 300 feet tall (91.4 m) and blue whales over 110 feet in length (33.6 m). This tremendous range in size has puzzled biologists and paleontologists for centuries. The Phanerozoic Body Size Trends in Time and Space: Macroevolution and Macroecology working group, lead by Jonathan Payne, Jennifer Stempien and Michal Kowaleski, has published a paper in PNAS that recieved a great deal of attention from both the scientific and public press.  Their publication presents the results of their analysis of the database generated during the course of the working group. The newly released Maximum Bodysize Database contains body size information (length, width and body volume) for the largest known species in each of the major biological lineages over the history of life. The data are tied to published scientific sources, and are searchable by geologic time period, organism type, and environment.

Payne,J.L., Boyer, A.G., Brown, J.H., Finnegan, S., Kowaleski, M., Krause, R.A., Lyons, S.k., McClain, C.R., McShea, D.W., Novack-Gottshall, P.M., Smith, F.A., Stempien, J.A., Wang, S.C. 2009. Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity. PNAS Vol106(1):24-27.doi/10.1073/pnas.0806314106

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northern hemi

               

Michael Donoghue, one of the PIs for the Phytogeography of the Northern Hemisphere working group published a Colloquium paper in PNAS discussing ideas from this group's work.  The NESCent working group focused on the history of plant movements and diversification around the Northern Hemisphere, and the assembly of modern plant communities. The group consisted of paleobotanists, plant phylogeneticists, and theoreticians who worked together to generate a comprehensive database for Northern Hemisphere plant lineages, including relevant phylogenetic, fossil, character, and distribution data.

In his paper, Donoghue discusses the importance of understanding the evolutionary history of ecological plant communities both for ecological studies and conservation efforts.  He suggests that phylogenetic studies provide valuable information about the assembly of ecological communities, and the conservation of ecological niches across time.

Donoghue, M.J. 2008. A phylogenetic perspective on the distribution of plant diversity. PNAS Vol 105(supplement 1):11549-11555 doi: 10.1073/pnas.0801962105

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Informatics

Events

Evolutionary Database Interoperability Hackathon
NESCent is excited to be sponsoring an Evolutionary Database Interoperability Hackathon from March 9-13 in Durham, North Carolina. The focus of the hackathon will be the implementation of emerging standards for evolutionary data exchange, data/metadata semantics, and web services. It is being co-organized by leaders of the Evolutionary Informatics working group. While applications for on-site participation are now closed, the organizers continue to welcome input from the community at large. For more info, please see the hackathon wiki at: http://evoinfo.nescent.org/Database_Interop_Hackathon.

ich and herp

Evolution and Ontologies workshop at Ichs and Herps
It is difficult to describe a phenotype to a computer, and even harder for two computers to describe phenotypes to each other. In order to enable computational technologies that can reason over phenotypic data, we need to be able to describe those phenotypes using ontologies, and we need biologists who know how to use ontologies. Under the auspices of the Phenoscape project, NESCent will be sponsoring the third in a series of open workshops on Evolution and Ontologies at the Joint Meeting of Ichthyologists and Herpetologists , July 22-27, 2009 in Portland, Oregon. The workshop is aimed at biologists interested in learning what ontologies are and seeing demonstrations of early applications of ontologies to phenotypic data, particularly in nonmammalian vertebrates. Stay tuned to http://phenoscape.org for more information.

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Training Opportunities

Meta-analysis in ecology and evolution
NESCent is pleased to offer for the first time a summer course on meta-analysis in ecology and evolution. The course, organized by Dr. Jessica Gurevitch of Stony Brook University, will be offered July 6-10th, 2009 in Durham, North Carolina. Students will become familiar with what meta-analysis is, where it comes from, examples of how it has been used in ecology and evolutionary biology, and its major strengths, weaknesses, advantages and limitations as a tool for the quantitative summary of research results. They will be introduced to issues and methods for gathering data from the scientific literature, will conduct a preliminary meta-analysis and will learn how to evaluate and critique the results. Application information will be announced shortly.

gmod

GMOD Summer School spans the Atlantic
The GMOD Summer School returns to NESCent this year and - due to popular demand - also goes to Europe! This course, which gets new users up and running with popular model organism database tools such as GBrowse, Chado. Apollo and BioMart, will be held once in the U.S. (in Durham, North Carolina from July 16-19th) and once in England (at Oxford from August 3-7th. 2009). As before, it will focus on installation, configuration, and tool integration, and require some level of comfort with Linux systems administration. The Oxford course is being generously hosted by the Computational Biology Research Group at Oxford University. Keep your eyes on the GMOD web site for forthcoming application information.

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Summer Internships for Graduate Students and Postdocs

Phenoscape
We are pleased to announce summer traineeships for graduate students and postdocs interested in gaining expertise in informatics and the application of ontologies to evolutionary, anatomical, developmental, and genetic data. Students may be in residence either at NESCent or at the University of South Dakota, and may undertake a project in open source software/database development or data curation at either location. These internships are being offered under the auspices of the Phenoscape project. Applications from women and underrepresented minorities are specifically encouraged. For more information and application instructions, please see the Phenoscape Summer Training site. 

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Other informatics news

dryad

 

Do you have published datasets that you would like to archive?
Dryad is an open data repository designed to provide a home for the data that underlie publications in evolution, ecology and related fields. Dryad is now open for data submissions, and can provide permanent data identifiers for you to include in the published version of your manuscript or on your webpage. Submissions are being accepted by email, and a web submission system is under development. Note that articles must be accepted or published at the time of submission.

 

NESCent joins Virtual Data Center initiative
NESCent has partnered with a coalition of organizations to design a "virtual data center" for integrated access to biodiversity, ecology and environmental data, with the aim of making Dryad one of the member nodes of the network. The coalition is supported by a recent award from the National Science Foundation INTEROP program.

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Education and Outreach

birthday

Celebrating Darwin's Bicentennial

2009 marks the 200th anniversary of Darwin’s birth and the 150th anniversary of the publication of the Origin of Species.  NESCent is celebrating these anniversaries with several events.  For the entire month of February, posters wishing Darwin a happy birthday can be found on the buses in Chapel Hill and on the Duke campus.  Follow the poster link from NESCent’s front page to learn more about how the anniversaries are being celebrated across the world and in your backyard. 

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symposium poster

 

 

 

Darwin Day 2009

The third annual NESCent Darwin Day Symposium, entitled “Darwin’s Legacy: Evolutionary Approaches to World Challenges,” focuses on the societal benefits that result from applying evolutionary theory to problems such as agriculture, public health, conservation, and improving industrial enzymes.  The symposium will be held February 21, 2009 and features presentations by Barbara Schaal, Katia Koelle , Dan Faith, Steve Benner, and Fred Gould.  The event is free and open to the public, however registration is required (click here to register).

 

Zimmer

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Evolution Speaker Series

NESCent is collaborating with the North Carolina Museum of Natural Science, and NCSU’s Keck Center for Behavioral Biology to celebrate all year with a series of distinguished speakers.  We kick of the series Feb. 12 – Darwin’s 200th birthday – with Carl Zimmer.  Mr. Zimmer is a well known science writer who has written widely on evolution.  Rob Dunn, assistant professor of zoology at NCSU and author of Every Living Thing, will follow later this Spring and Anne Yoder, Director of the Duke Lemur Center and professor of Biology at Duke, will present in the Summer.  These events are free and open to the public but registration is requested.  Please send email to museum.reservations@ncmail.net to register .  Speaker presentations will also be posted on the web for those who cannot attend and for educational use. 

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2008CD

 

 

Illuminating Biology: an Evolutionary Perspective - videos available

The presentations from the 2008 Evolution Symposium at the National Association of Biology Teachers (NABT) Annual Conference are now posted.  Check the online version of the CD for supporting educational resources for each speaker.  Additional resources are listed on the Symposium site. 

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Image Credits:

Northern Hemisphere - NASA

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