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Distinguished Speaker Seminar – TT2017

09 Jun 17

Speaker: David Swafford, Senior Research Scientist, Biological Sciences, Duke University

Title: Generality and Robustness of the SVDQuartets Method for Phylogenetic Species Tree Estimation

Abstract: Methods for inferring evolutionary trees based on phylogenetic invariants were first proposed nearly three decades ago, but have been virtually ignored by biologists. A new invariants-based method for estimating species trees under the multispecies coalescent model was recently developed by Julia Chifman and Laura Kubatko, building on earlier work by Elizabeth Allman, John Rhodes, and Nicholas Eriksson. This method comes from algebraic statistics and uses singular value decomposition to estimate the rank of matrices of site pattern frequencies. Although the approach shows great promise, its performance on empirical and simulated data sets has not been adequately evaluated.

I will give a general introduction to the SVDQuartets method and present some results from a simulation study currently in progress (collaboration with Laura Kubatko and Colby Long) that demonstrate that SVDQuartets is potentially highly robust to deviations from the standard evolutionary models assumed by other species-tree estimation methods.

 

Speaker: Wim Hordijk, The KLI Institute, Klosterneuburg, Austria

Title: Autocatalytic Sets and the Origin of Life

Abstract: The main paradigm in origin of life research is that of an RNA world, where the idea is that life started with one or a few self-replicating RNA molecules. However, so far nobody has been able to show that RNA can catalyze its own template-directed replication. What has been shown experimentally, though, is that certain sets of RNA molecules can mutually catalyze each other’s formation from shorter RNA fragments. In other words, rather than having each RNA molecule replicate itself, they all help each other’s formation from basic building blocks, in a self-sustaining network of molecular cooperation.

Such a cooperative molecular network is an instance of an autocatalytic set, a concept that was formalized and studied mathematically and computationally as RAF theory.This theory has shown that autocatalytic sets are highly likely to exist in simple polymer models of chemical reaction networks, and that such sets can, in principle, be evolvable due to their hierarchical structure of many autocatalytic subsets. Furthermore, the framework has been applied succesfully to study real chemical and biological examples of autocatalytic sets.

In this talk I will give a general (and gentle) introduction to RAF theory, present its main results and how they could be relevant to the origin of life, and argue that the framework could possibly also be useful beyond chemistry, such as in analyzing ecosystems or even economic systems.