Modeling scientific argumentation in full-text biochemistry research articles

This article addresses the theme of “domains of natural argument,” in particular, argumentation in several full-text biochemistry research articles on protein structure and signal transduction pathways. It explores how domain-specific patterns of argument in these biochemistry articles relate to general models of natural argument. The main contribution of this work is an in-depth analysis of some characteristics of arguments in the articles, including how the argumentation relates to experimental goals and research methods (the hypothetico-deductive and abductive approaches); how premises of arguments may be based upon experimental results presented in the article via text and/or figures, as well as citations of previous research, general background knowledge, or conclusions of previous arguments in the article; what general principles license claims of arguments, that is, argumentation schemes, Mill's “methods” of scientific reasoning about causation, defeasible rules of logical inference (disjunctive syllogism and modus ponens) and rules of arithmetic; how defeasible, domain-specific rules instantiating the above principles can be encoded for practical, computational uses; and how the progression of interrelated premises and conclusions in an article can be presented in graphical form.