Electrical Engineering
      and Computer Sciences

Electrical Engineering and Computer Sciences


UC Berkeley


2008 Research Summary

The Path of the Blind Watchmaker: A Large-Scale, Interspecies Markov Model of Evolution (LIMME)

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Andrew Anthony Poggio, David A. Patterson, Christos Papadimitriou, Adam Arkin1 and Brent Mishler2

Evolution from a very primitive organism to Homo sapiens has been a significant biological process and thorough knowledge of it is vital to understanding all aspects of biology including disease treatment. This project attempts to take a large scale approach to evolution. To do so, we will reconstruct the genome of a small number of reference species and create an overall model comprised of a unique Markov model between each adjacent reference species pair that represents the specific mutations and probabilities of the potential evolutionary paths between the two species. The model will include an analysis of genome alignments, mutation mechanisms, population models, and other relevant factors. The result will allow us to describe the likely path that was taken by evolution between sample species and to calculate the duration of that process. This model will provide an ongoing, computational test bed for evolutionary biology theory, results from which can often be directly compared to fossil and experimental data.

Figure 1
Figure 1: LIMME path overlaid on tree of life image

2Integrative Biology