Diagrams in Scientific Reasoning
Cognitive Science 200
Fall, 2012

Meeting for Enrolled Students: Fridays, 2:00-2:55

Lecture to which UCSD community is invited: 3:00 to 4:30

Both in Cognitive Science Building, Room 003

Professor: William Bechtel Office Hours: Wed., 5:00-6:00 and by appointment
Office: HSS 8076 Email: cs200@mechanism.ucsd.edu
Telephone: 822-4461 Wiki: mechanism.ucsd.edu:8080/CS200


Scientific talks and papers are filled with diagrams: characterizations of a target phenomenon or hypothesis, sketches of an apparatus or experimental set-up, flow charts of steps in the procedure, graphs displaying data, "cartoons" of the mechanism proposed to explain the data, and so forth. One efficient way of reading a journal article is to read the abstract and then study each diagram in turn, only skimming the text or consulting it as needed to understand the diagrams. Diagrams play crucial roles not only in communicating to readers what already has been done, but in supporting the cognitive activities of scientists as they investigate phenomena, advance and evaluate explanations, and so forth.

This seminar will focus on the roles played by diagrams in science and especially in the cognitive activities of scientists. We are interested in how, why, and when scientists develop new diagrams or use existing ones. Thus, we will address such questions as: In what ways do diagrams convey scientific content? Do they convey different information, or do so differently, than propositional representations? How do diagrams figure in the reasoning activities of scientists as producers of their own research and as consumers of others' research. What considerations determine how researchers modify diagrams over time?

The speakers come from several cognitive science disciplines: psychology, computer science, and philosophy. Each has done extensive work on particular roles diagrams play in science.

Overview of Schedule



Title of Talk


September 28

William Bechtel, UCSD

Studying the Use of Diagrams in Science

1. Larkin, J. H., & Simon, H. A. (1987). Why a diagram is (sometimes) worth ten thousand words. Cognitive Science, 11, 65-99.
2. Gooding, D. C. (2010). Visualizing Scientific Inference. Topics in Cognitive Science, 2, 15-35.

October 5

Barbara Tversky, Stanford

Visualizing Thought

1. Tversky, B. (2011). Visualizing Thought. Topics in Cognitive Science, 3, 499-535.

October 12

Laura Perini, Pomona

Why Less is More: Reasoning with Diagrams in the Life Sciences

1. Perini, L. (2012). Form and function: A semiotic analysi of figures in biology textbooks. In N. Anderson & M. R. Dietrich (Eds.), Form and function: A semiotic analysis of figures in biology textbooks (pp. 235-254). Dartmouth, NH: Dartmouth College Press.
2. Perini, L. (2005). Explanation in two dimensions: Diagrams and biological explanation. Biology and Philosophy, 20, 257-269.

October 19

Mary Hegarty, UCSB

Broadening the Study of Spatial Intelligence

1. Hegarty, M. (2004). Mechanical reasoning by mental simulation. Trends in Cognitive Science, 8, 280-285.
2. Hegarty, M. (2011). The Cognitive Science of Visual-Spatial Displays: Implications for Design. Topics in Cognitive Science, 3, 446-474.

October 26

Morana Alač, UCSD

fMRI Brain Visuals as Diagrams

1. Alač, M. (2011). Chapter 2: fMRI brain visuals as fields for interaction. Handling digital brains: A laboratory study of multimodal semiotic interaction in the age of computers. Cambridge, MA: MIT Press
2. Alač, M. (2008). Working with brain scans: Digital images and gestural interaction in fMRI laboratory. Social Studies of Science, 38, 483-508.

November 2

David Kirsh, UCSD

Thinking with Illustrations

1. Kirsh, D. (2010). Thinking with external representations. AI and Soc, 25, 441-454.

November 9

Peter Cheng, Sussex

Cognitive and conceptual benefits of re-codifying knowledge: Towards a representational epistemic science

1. Cheng, P. C. H. (2011). Probably good diagrams for learning: Representational epistemic recodification of probability theory. Topics in Cognitive Science, 3, 475-498.
2. Cheng, P. C. H. (2002). Electrifying diagrams for learning: principles for complex representational systems. Cognitive Science, 26, 685-736.

November 16

Nancy Nersessian, Georgia Tech

Diagrams in Creative Reasoning

1. Nersessian, N. (2002). The cognitive basis of model-based reasoning in science. In P. Carruthers, S. Stich & M. Siegal (Eds.), The cognitive basis of science (pp. 133-153). Cambridge: Cambridge University Press.
2. Dogan, F., & Nersessian, N. J. (2006). Design problem solving with conceptual diagrams. Proceedings of the 28th Annual Conference of Cognitive Science Society (pp. 600-6005). Austin, TX: Cognitive Science Society.

November 23

No Class: Thanksgiving



November 30

Jim Griesemer, UCDavis

A Theoretical Role of Visual Representation in the Formation of Biological Theories

1. Griesemer, J. R. (2007). Tracking organic processes: Representations and research styles in cloassical embryology and genetics. In M. D. Laubichler & J. Maienschein (Eds.), From embryology to evo-devo: A history of developmental evolution (pp. 375-433). Cambridge, MA: MIT.

December 7

Benjamin Sheredos, Dan Burnston, and William Bechtel, UCSD

Diagrams for Reasoning about Mechanisms in Chronobiology

1. Sheredos, B., Burnston, D. C, Abrahamsen, A., Bechtel, W. (forthcoming). Why do biologists use so many diagrams? Philosophy of Science.
2. Jones, N., & Wolkenhauer, O. (in press). Diagrams as locality aids for explanation and model construction in cell biology. Biology and Philosophy.

Course Discussion Website

A discussion site has been established for this course: mechanism.ucsd.edu:8080/CS200/. The pages are viewable by everyone. To edit or comment on these pages, you must get an account. Email me at cs200@mechanism.ucsd.edu to request an account.

Course Requirements and Evaluation

Students are required to:

  1. Attend all class sessions, both the class-only meeting from 2:00 to 2:55 and the lecture from 3:00 to 4:30 and complete the readings assigned before each meeting. During each session I will call on registered students both at the beginning to address "What are the main points of the paper?" and later in the class to discuss these points.
  2. For each week after the first session, selected students will be assigned to add a diagram encountered outside this course (preferably in their primary field of study) to the discussion site and comment briefly on how it relates to issues discussed in the readings. This must be done by Noon on Wednesday. All other students are required to add a comment about one of the entries for the week. As well, you are invited to submit diagrams you find to be interesting and relevant to this course at any time by creating a new page on the discussion site.
  3. Write one paper, 5-7 pages in length, that advances a systematic analysis of a set of related diagrams that draws upon the content of the course. This paper is due by December 10.

This course should be taken for S/U grade only. If your department requires a letter grade, or you have some other reason why you need a letter grade, please let me know.