DIMACS Computational and Mathematical Epidemiology Seminar Series

Title: The Simpson-Elsasser-Wolfram (SEW) Framework for Modeling the Living Cell

Speaker: Sung Ji, Rutgers University

Date: April 17, 2006 12:00 - 1:30 pm

Location: DIMACS Center, CoRE Bldg, Room 431, Rutgers University, Busch Campus, Piscataway, NJ

Abstract:

Physicists successfully modeled the atom in the early decades of the 20th century. I predict that biologists will succeed in constructing computational models of the living cell in the early decades of the 21st century. The method employed by physicists in modeling the atom was essentially based on mathematics without relying on the computer, but the method that biologists will need to model the cell may turn out to be, not mathematics (alone), but mainly logic- and computer-based. My thinking along this line has been greatly influenced by the ideas and theories advanced by the following three scientists -- the American paleontoligist G. Simpson (1902-1984), the German-American physicist-turned biologist W. Elsasser (1904-1991), and the British-American physicist-turned computer scientist S. Wolfram (1959- ). Their ideas are briefly summarized below:

1. G. Simpson: Physicists study the principles that apply to all phenomena; Biologists study phenomena to which all principles apply ["This View of Life: the World of an Evolutionist", Harcourt, Brace & World, Inc., New York, 1963, p. 107].
2. W. Elsasser: Physicists study objects that belong to pure classes to which (continuous) mathematical methods can be applied; biologists study objects that belong to heterogeneous classeses to which logic (including discrete mathematics), but not (continuous) mathematics, can be applied ["Refelctions on a Theory of Organisms: Holism in Biology", the Johns Hopkins University Press, Baltimore, pp. 145-149].
3. S. Wolfram: All structures and phenomena, whether internal (to human mind) or external, can be modeled on the computer as simple programs, some of which lead to fractals, the structures and patterns that emerge as the consequences of iterating the application of sets of simple rules n times, where n can be a large number (10^2~10^6) [see the principle of computational equivalence on p. 715 in "A New Kind of Science", Wolfram Media, Champaign, Il, 2002].

The Simpson-Elsasser-Wolfram (SEW)framework for modeling the cell maintains that, to successfully model the living cell, it is necessary (and sufficient?) to implement the above three assertions as applied to the cell.

The conceptual model of the living cell known as the Bhopalator formulated in 1985 (see p. 50 in "Semiotics of Life: A Unified Theory of Molecular Machines, Cells, the Mind, Peircean Signs and the Universe based on the Principle of Information-Energy Complementarity", available at http://www.grlmc.com, under Publications) will be described and shown to be consistent with the SEW framework. This model will be utilized in analyzing the time-series data on the genome-wide transcript levels and transcription rates measuremed with DNA arrays from budding yeast undergoing glucose-galactose shift [Gacia-Martrinez et al, Mol. Cell 15:303-313 (2004)].

see: DIMACS Computational and Mathematical Epidemiology Seminar Series 2005 - 2006