Welcome to the web home of the Stoltzfus research group at The Institute Formerly Known as CARB.

Exploring the Curious Disconnect in evolutionary theory

Posted Tue, 03/23/2010 - 11:01 by arlin

In "The Curious Disconnect", a blog launched in mid-March, 2010, Arlin Stoltzfus argues that there is a major "disconnect" between how we think about evolution, and how we we would think about it if we were freed from the historical baggage of Darwin's view and the subsequent "Modern Synthesis" (sometimes called "neo-Darwinism").  Installments of The Curious Disconnect will appear here and at at Larry Moran's Sandwalk site.  

Computational and Analytical Molecular Evolution Lab at IBBR

Posted Fri, 11/20/2009 - 16:08 by arlin

This is the home page of the Stoltzfus research group at IBBR (Institute for Bioscience and Biotechnology Research), a partnership of UMD, UMB and NIST.  

We rely on computer-based approaches to address challenges in the areas of molecular evolution, evolutionary theory, and bioinformatics.  Some currently active projects include: 

  • New methods for calibrating phylogenetic trees using fossil data (Ryan Norris)
  • The evolution of ORFans in E. coli (Guoqin Yu)
  • The significance of origin-fixation models in evolutionary genetics (with David McCandless of Duke U)
  • Improving interoperability of software and data resources  in evolutionary research (see the HIP working group for more details)

Phyloinformatics VoCamp in Montpellier, France

Posted Tue, 10/13/2009 - 14:02 by arlin

A phyloinformatics "VoCamp" is taking place in coordination with the Biodiversity Information Standards (TDWG) meeting in Montpellier, France. The VoCamp takes place over 4 days from November 7 to 11. The plan for the meeting emerged from a group of individuals (Cellinese, Cranston, Lapp, MacKay, Pontelli, Stoltzfus) involved in previous phyloinformatics activities at the US National Evolutionary Synthesis Center, NESCent.

Mutation and evolutionary genetics

Posted Fri, 08/14/2009 - 13:27 by arlin

In this year of over-the-top homages to Darwin, one wonders why evolutionary biologists even bother coming to work every day, knowing that the last great insight into evolution happened 150 years ago. Actually, evolutionary thinking is undergoing a slow and uncertain revolution (if you can call it that) from Darwin's view of evolution as a process of shifting available variation to match an optimum, to a more open-ended process of mutational exploration of fitness landscapes. "Darwinists" of the past were so confident in the first view that they ridiculed the second one ("mutationism"). The first view takes abundant variation as a given and assumes that the character of variation does not influence the course of evolution (except by its complete absence). In the second view, mutation supplies initiative and direction.

CDAO Developers meet in New Mexico

Posted Fri, 08/14/2009 - 13:17 by arlin

The Comparative Data Analysis Ontology (CDAO), is an OWL ontology representing knowledge in the area of comparative evolutionary analysis. It focuses on phylogenetic trees, OTUs, character data, and evolutionary transitions. CDAO developers recently met to develop the ontology further.

Climbing Mount Probable: Mutation as a cause of non-randomness in evolution

Posted Fri, 08/14/2009 - 13:01 by arlin

Climbing Mount Probable: After what seems like years (2 years, to be exact-- but who's counting?), Climbing Mount Probable: Mutation as a cause of non-randomness in evolution is accepted for publication (in J. Heredity). Look here for a video link to appear soon.

CDAO published in Evolutionary Bioinformatics

Posted Fri, 08/14/2009 - 13:00 by arlin

CDAO: The Comparative Data Analysis Ontology (CDAO) project has been going on for about 18 months. Collaborators including Enrico Pontelli and Brandon Chisham of NMSU, and Julie Thompson and Francisco Prosdocimi of U. Strasbourg (France). The initial published description of CDAO has been accepted for publication in Evolutionary Bioinformatics.

Data Interop Hackathon held at NESCent

Posted Fri, 08/14/2009 - 12:58 by arlin

Evolutionary Data Hackathon: This spring NESCent organized an event that challenged a select group of programmers to improve interoperability of resources used in phylogenetics and evolutionary studies.

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