Thermodynamics for Systems Biology

This paper aims to provide a comprehensive introduction to thermodynamics designed specifically for the needs of the systems biologist. It departs from modern treatments in paying attention to the macroscopic aspects of the subjects rather than focusing purely on the statistical character of the facts. It also makes a real effort to communicate certain lesser known aspects of the subject that have to do with modeling, i.e. to communicate thermodynamics as a body of worldviews, methods and interpretations. Here macroscopic thermodynamics is an example of systems thinking, and a body of thought which is methodologically and conceptually different from mechanics. To focus on this aspect of the subject, we follow its historical development.