The nature of science and its claims for rationality have led to thousands of books on the history and philosophy of science over the past century. In addition to traditional philosophy of science (represented by Popper below) which largely deals with the logical claims of science as a way to find truth, the newer philosophy of science is implicitly (Kuhn) or explicitly (Feyerabend) critical of claims that science has any inside track on truth or even rationality. A complete account would also include some work on the sociology of science, the study of how social and political factors affect what scientists do and their value system.
Cromer, Allan. Uncommon Sense: The Heretical Nature of Science. Oxford University Press, 1993. A recent defense of the idea that science is an advanced mode of thought that supersedes superstition. Comer further defends the proposition that science is the highest form of Western thought and could have only developed within the Western tradition begun by the ancient Greeks. In short this is a politically incorrect argument, but one that has considerable force.
Feyerabend, Paul. Farewell to Reason. (*) Verso, 1987. A philosopher offers a radical attack on the claims of rationality that underlie modern science. As the argument develops it becomes clear that science must be interpreted as a part of its cultural context, that different cultures and historical epochs offer different solutions to life's mysteries, and that science is only one and perhaps not even the most privileged method of getting at "truth" which is, in any case, seen as relative to time and place. His earlier, Against Method (Verso, 1975) has probably been the more influential, but the former book presents a more elaborated argument.
Gardner, Martin. Fads and Fallacies in the Name of Science. (*) Dover Books, 1952. The classic treatment of crank science and the cults that often surround pseudoscience.
Gross, Paul R. & Levitt, Norman. Higher Superstition: The Academic Left and Its Quarrels with Science. The Johns Hopkins Press, 1994. A defense of science from the claims of certain members of the academic world that science is inherently biased and privileges some forms of thinking over others. This book takes no prisoners, and those who are attacked argue that their criticisms of science have been misunderstood.
Huizenga, John R. Cold Fusion: The Scientific Fiasco of the Century. (*) University of Rochester Press, 1992. A shorter, but more technical and less readable version than Taubes below. The book is mostly valuable in showing how the cold fusion controversy echoes previous examples of bad science.
Kuhn, Thomas S. The Structure of Scientific Revolutions. 2nd edition. The University of Chicago Press, 1962, 1970. One of the most influential books of this century. Kuhn argues that paradigms in science control the ways scientists think and do their research. Paradigms do not change gradually but fairly radically over fairly short periods of time. Since these paradigms are, in part, creations of cultural forces, it follows that the foundations of science are partially cultural creations. Thus the tenor of the argument is against traditional views of science that focus on how geniuses create masterful theories built on empirical data that map external realities. This is a quite readable book although it helps to have some basic knowledge about the history of science.
Popper, Karl R. The Logic of Scientific Discovery. (*). various editions, 1959. A classic treatment of philosophy of science that emphasizes the idea that theories and hypotheses must be falsifiable, capable of being proven wrong. This is a fairly technical book, but it has been an important classic treatment of the logic of science. It is an obvious companion to Popper's Open Society and Its Enemies (listed under ideology) in which he alerts us to the dangers of claims of absolute knowledge in the social realm, claims that are usually not falsifiable.
Soyfer, Valery. Lysenko and the Tragedy of Soviet Science. Rutgers University Press, 1994. Lysenko was a communist party agronomist who essentially led Soviet agricultural and biological research during the Stalin era. He became the most decorated Soviet scientist on the basis of his claims that genes do not exist and that acquired characteristics could be inherited, claims that fit communist ideology about the importance of the environment quite well. In the process he completely ruined Soviet biology from the 1930s to the present. A morality play about what happens when religion and politics run science.
Taubes, Gary. Bad Science: The Short Life and Weird Times of Cold Fusion. Random House, 1993. The most complete account of the cold fusion controversy. Although readable generally, this book does not avoid scientific details (which can be skipped over only partially). It is strong especially on the interpersonal relationships and politics of the situation.
Traweek, Sharon. Beamtimes and Lifetimes: The World of High Energy Physics. Harvard University Press, 1988. A former Rice anthropologist uses cultural analysis to study the highly competitive, prestigious, and male-dominated word of high energy physics with some lessons about how the views of scientists re affected by the way science is organized