Syllabus Number 26
Course
Name
Mathematics and physics of metabolic organization
Semester, Year
First Semester, 2017
Course level
3000
Instructor(s)
(Institution)
Jusup Marko (電子科学研究所 附属社会創造数学研究センター)
Number of Credits
2 credits
Course Number
027027
Course
Objectives
We will review the most comprehensive metabolic theory of life existing to date. A special focus will be given to the
thermodynamic roots of this theory and to implications that the laws of physics?such as the conservation of mass
and energy?have on all life. Specific examples will be used to illustrate a range of possible applications of the
theory.
Course Goals
(i) Learn about the role of mathematics and physics in the study of life
(ii) Study how a consistent biophysical theory of life is built using epistemiological and evolutionary principles
(iii) Use examples from biology to motivate the introduction of new concepts and to justify the theoretical
assumptions
(iv) Show how careful formalism captures important life history features of all living species
Course
Schedule
1. Introduction
2. Occam's razor: a basis for building a biophysical theory
2.1. Scientific reasons for simplicity
2.2. Evolutionary reasons for simplicity
3. Introduction to metabolic processes
4. Thermodynamics of life
4.1. Conservation of mass
4.2. Conservation of energy
4.3. Entropy production
5. From theory to applications: building a basic mathematical model
5.1. Eating: food assimilation
5.2. Staying alive: maintenance
5.3. Maturing: life stages and reproduction
5.4. Equations of life
6. Applications
6.1. Ecology
6.2. Toxicology
6.3. Evolution
Homework
Weekly reading and reporting assignments that complement the main contents of the course
Grading
System
1. Attendance 20%
2. Homework 30%
3. Multiple choice quiz 50%
Textbooks /
Reading List
Websites
Website of
Laboratory
Additional
Information
数理生物学入門:生物社会のダイナミックスを探る 巌佐庸 共立出版 1998
Dynamic Energy Budget theory for metabolic organisation S.A.L.M. Kooijman Cambridge University Press 2010
https://en.wikipedia.org/wiki/Mathematical_and_theoretical_biology
http://www.math.rutgers.edu/~sontag/math-bio-interface/Contents.html
http://papa.indstate.edu/amcbt/volume_23/v23-1p11-36.pdf