InterJournal Genetics, 413 Status: Submitted Manuscript Number:  Submission Date: 609 Teaching the modeling of biological systems
Author(s): Claire EDELIST

Subject(s): BG.14, BG.24, CX.19, CX.17

Category: Brief Article

Abstract:

Teaching the modeling of biological systems (using mathematical and computer sciences) C. Edelist, Bio-informatique, Bureau 250, Bâtiment 332, Université Paris-Sud, 91405 ORSAY-Cedex, FRANCE and Génétique des virus, CNRS, 91198 Gif/Yvette - Cedex, FRANCE For several years, I have been in charge of a course called "Mathématiques appliquées ŕ la biologie" for biology's students in university third or fourth year. This teaching is given partially by mathematicians, partially by myself, a biologist. This course is an elective, therefore most of the students enrolled are very interested in the subjects. My first subject is to teach Turbo Pascal at a level sufficient that enables students to write computer programs for modeling of biological systems (related to ecology, biochemistry, genetics, populations dynamics etc., depending on their preferences). The use of a computer forces them to be very rigorous; they have to put forward, before writing the program, all their hypotheses and what data must be fed into the computer. Then, they have to analyze the results (output) obtained through the computer and to discuss them from a biological point of view, taking into account their starting hypotheses. The second part of my teaching is kinetic logic, a qualitative and useful description of systems with feedback loops (= closed oriented circuits), conceived by R. Thomas (1973, 1978), Thomas and d'Ari 1990. The unique hypothesis underlying kinetic logic is the existence of threshold(s) of activity for each variable, which is often the case in biological systems. As an intermediate between purely verbal and differential description, it allows to represent in relatively simple terms complex systems, which are difficult to grasp in purely verbal terms. It takes time into account through various on and off delays and sometimes it will suggest new experiments. Most of the non-linear ordinary differential equations cannot be solved analytically, and therefore, involve hidden simplifications. On the contrary, the equations used in kinetic logic are always solved without mathematical simplification. The fields of applications are wide: molecular biology, genetics, virology, ecology, cellular biology etc. This allows the students to grasp the difficulties first of writing clearly the hypotheses, second of transforming propositions in natural language into logical equations. Thus, I think these easy mathematical and computer sciences lead students in biology to represent relatively complex biological systems and to understand the interest of modeling. Thomas, R. (1973). Boolean formalization of genetic control circuits. Journal of theoretical Biology 42: 563-585. Thomas, R. (1978). Logical analysis of system comprising feedback loops Journal of theoretical Biology 73: 631-656. Thomas, R. and R. d'Ari (1990). Biological Feedback. Boca Raton, Ann Arbor, Boston, CRC Press.

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