Information science for biology

Cold War Kuhn and industrial science

I read Kuhn early on in my PhD work, and was much impressed, as many before me, by Kuhn’s portrayl of a science governed by paradigms and puzzle-solving. His writings have served a useful purpose thus far in my thinking, which is to undermine any traditional and mythological preconceptions I may still hold about science.

What I have taken from Kuhn, and to a lesser extent from Merton and Polanyi, is that there are other important elements in the story which is the way science is done, and many of these elements are quite unscientific.

However, I feel my philosophical preferences fall firmly on the side contra-sociological models for science and I believe rationality, realism and critical argument do play a part in what science *is*. Scientific knowledge is special and different from lay-knowledge – we can test theories, we can challenge our models of the world and thus aspire to a bit more truth tomorrow to the truth we have today.

Fuller’s book casts Kuhn in a Cold War context, and convinces me at least that a lot of what Kuhn was describing in his historicist re-envisioning of scientific enterprise was coloured by his pre-dilections for country and conservatism. No liberal was Kuhn, and in the Cold War climate his painting of science as ruled by paradigm and a theoretical conservatism fitted with an American way of thinking about the world, with loyalty to codes and just causes.

The Popper bits are a bit superfluous. In a simple way though, Popper’s critical liberalism does contrast with Kuhn’s conservatism.

And it is interesting to think that Kuhn’s view on science, and the popularity of social studies of science today, stifle criticism in science and serve to propagate an industrialised science.

Fuller, S., Kuhn vs. Popper : the struggle for the soul of science. (Columbia University Press, New York, 2004).

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For and against methods in ontologies

My interest in ontologies and specifically in ontologies for biology have compelled me to extend my reading into the philosophy of science. If an ontology is a representation of some knowledge and how the named elements in this knowledge relate to one another, then what are the criteria for admitting new knowledge into this structure?

This is an old problem in the philosphy of science and can be variously phrased as the demarcation problem, the way to separate science from pseudoscience, or put simply – how scientists choose between good theories and bad theories?

Science clearly changes over time, and old theories morph or become substitued by new and, in some sense, better theories. Lakatos’s series of lectures published in the book ‘For and against method’ (reference below) are a superb introduction to this fascinating area, and his style is frequently hilarious:

In 1492, however, Columbus had discovered America, and that led to some trouble because in 1949 an American named Alonzo Church reviewed Ayer’s book in the Journal of Symbolic Logic. The review is actually twelve lines long.

It really makes me wish I’d been born a few decades earlier so I could have listened to lectures at the LSE with people like Popper and Lakatos. The problems which preoccupied these men have seemingly been sidelined to the sociological strands in the study of science.

However I believe the development and application of ontologies in the sciences force us to confront old questions of the kind that interested people like Lakatos. How or who gets to decide what goes into an ontology?

What is the method for deciding how an ontology changes?

Lakatos, I., Feyerabend, P., & Motterlini, M., For and against method : including Lakatos’s lectures on scientific method and the Lakatos-Feyerabend correspondence. (University of Chicago Press, Chicago, 1999).

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