Laura Perini

Analysis of two key ways of characterizing genes—as causes of phenotypic effects and as genomic DNA sequences—has yielded widespread pessimism that they can be united in a coherent gene concept. This raises important questions about the epistemology of genomic research: If analysis of a genome sequence cannot yield information about genes defined both in terms of their products and their DNA sequence, then what could we learn from it? I investigate basic tools of genomic analysis, argue that they do not reflect the application of either gene concept, and clarify how we learn from genomic research.

Molecular biologists and biochemists often use diagrams to present hypotheses. Analysis of diagrams shows that their content can be expressed with linguistic representations. Why do biologists use visual representations instead? One reason is simple comprehensibility: some diagrams present information which is readily understood from the diagram format, but which would not be comprehensible if the same information was expressed linguistically. But often diagrams are used even when concise, comprehensible linguistic alternatives are available. I explain this phenomenon by showing why diagrammatic representation is especially well suited for a particular kind of explanation common in molecular biology and biochemistry: namely, functional analysis, in which a capacity of the system is explained in terms of capacities of its component parts.

Scientists typically use a variety of representations, including different kinds of figures, to present and defend hypotheses. In order to understand the justification of scientific hypotheses, it is essential to understand how visual representations contribute to scientific arguments. Since the logical understanding of arguments involves the truth or falsity of the representations involved, visual representations must have the capacity to bear truth in order to be genuine components of arguments. By drawing on Goodman's analysis of symbol systems, and on Tarski's work on truth, I show that the figures used in science meet this criterion.

One way visual representations might function in scientific reasoning is to convey content that is true or false, analogous to making a claim. An alternative way that visual representations might function is as an object that may make statements true or false, but is not itself true or false, analogous to a scientific model. In this paper I evaluate the most recent and extended defense of this latter position and show that the case study involved does not in fact support the view that the diagrams discussed function as truth-makers rather than truth bearers

Publications in contemporary science journals often include figures like graphs, diagrams, photographs, and MRIs, which are presented as support for the hypothesis the author is defending. As a first step to explaining how figures contribute to confirmation, I present an account of visual representation and use examples to show how the visual format is involved in the support those figures provide the authors’ conclusions. I then show that attempts to explain what figures contribute to scientific arguments without analyzing them as visual representations will not succeed.

There is currently a gap in our understanding of how figures produced by mechanical imaging techniques play evidential roles: several studies based on close examination of scientific practice show that imaging techniques do not yield data whose significance can simply be read off the image. If image-making technology is not a simple matter of nature re-presenting itself to us in a legible way, just how do the images produced provide support for scientific claims? In this article I will first show that there is a distinct question about the semiotics of mechanically produced images that has not yet been answered. I show that my account of visual representations can do so, and I argue that the role of convention involved in my account is compatible with the view that visual representations produced through mechanized imaging techniques can play genuine evidential roles in scientific reasoning

Biologists depend on visual representations, and their use of diagrams has drawn the attention of philosophers, historians, and sociologists interested in understanding how these images are involved in biological reasoning. These studies, however, proceed from identification of diagrams on the basis of their spare visual appearance, and do not draw on a foundational theory of the nature of diagrams as representations. This approach has limited the extent to which we under- stand how these diagrams are involved in biological reasoning. In this paper, I characterize three different kinds of figures among those previously identified as diagrams. The features that make these figures distinctive as representational types, furthermore, illuminate the ways in which they are involved in biological reasoning.