The Tree of Life: Challenges for Discrete Mathematics and Theoretical Computer Science. Fred S. Roberts DIMACS Rutgers University. The tree of life problem raises new challenges for mathematics and computer science just as it does for biological science.
Fred S. Roberts
The tree of life problem raises new challenges for mathematics and computer science just as it does for biological science.
These are some of the motivations for this meeting.
I will lay out some of the challenges for math and CS, with emphasis on discrete math and theoretical CS.
What are DM and TCS?
DM deals with:
TCS deals with the theory of computer algorithms.
During the first 30-40 years of the computer age, TCS, aided by powerful mathematical methods, had a direct impact on technology, by developing models, data structures, algorithms, and lower bounds that are now at the core of computing.
DM and TCS have found extensive use in many areas of science and public policy, for example in Molecular Biology.
These tools seem especially relevant to problems of the tree of life
DM and TCS Continued
These tools are made especially relevant to the tree of life problem because of:
Geographic Information Systems
DM and TCS Continued
Availability of large and disparate computerized databases on subjects relating to species and the relevance of modern methods of data mining.
Phylogenetic Tree Reconstruction
New methods of phylogenetic tree reconstruction owe a significant amount to modern methods of DM/TCS.
Trees, supertrees, consensus trees will all be discussed at length in this meeting
I will only make a few brief remarks about them.
Phylogenetic Challenges for DM/TCS
Tailoring phylogenetic methods to describe the idiosyncracies of viral evolution -- going beyond a binary tree with a small number of contemporaneous species appearing as leaves.
Dealing with trees of thousands of vertices, many of high degree.
Making use of data about species at internal vertices (e.g., when data comes from serial sampling of patients).
Phylogenetic Challenges for DM/TCS: Continued
Network representations of evolutionary history - if recombination has taken place.
Modeling viral evolution by a collection of trees -- to recognize the “quasispecies” nature of viruses.
Devising fast methods to average the quantities of interest over all likely trees.
Thanks to Eddie Holmes and Mike Steel for ideas.
DIMACS Working Group on Phylogenetic Trees and Rapidly Evolving Diseases, Sept. 3-6, 2003
Thanks to the Global Biodiversity Information Facility (GBIF) for many of the following ideas.
(See: DIMACS project on Monitoring Message Streams)
(Thanks to Diana Lipscomb for this example.)