A striking fact about the making of science is that in any field of research, there are considerable disagreements between scientists. This is an interesting observation, because it contradicts the naive view of science as a progressive accumulation of knowledge. Indeed, if science worked in this way, then any disagreement should concern empirical data only (e.g. whether the measurements are correct). On the contrary, disagreements often concern the interpretation of data rather than the data themselves. The interpretative framework is provided by a scientific theory, and there are often several of them in any field of research. Another type of disagreement concerns the judgment of how convincingly some specific piece of data demonstrates a particular claim.
There are two possibilities: either a large proportion of scientists are bad scientists, who do not correctly apply sound scientific methodology, or the adhesion to a theory and the judgment of particular claims are not entirely based on scientific principles. The difficulty with the first claim, of course, is that there is no systematic and objective criterion to judge what “good science” is and what “bad science” is. In fact, the very nature of this question is epistemological: how is knowledge acquired and how do we distinguish between different scientific theories? Thus, part of the disagreement between scientists is not scientific but epistemological. Epistemological questions are in fact at the core of scientific activity, and failure to recognize this point leads to the belief that there is a single way to do science, and therefore to dogmatism.
So why do scientists favor one theory rather than the other, given the same body of empirical data? Since the choice is not purely empirical, it must rely on other factors that are not entirely scientific. I would argue that a major determinant of the adhesion to a particular theory, at least in neuroscience, is the consonance with philosophical conceptions that the scientist holds. These conceptions may not be recognized as such, because many scientists have limited knowledge or interest in philosophy. One such conception would be, for example, that the objects of perception exist independently of the organism and that the function of a perceptual system is to represent them. Such a conception provides a framework in which empirical data are collected and interpreted, and therefore it is not generally part of the theoretical claims that are questioned by data. It is a point of view rather than a scientific statement, but it guides our scientific enquiry. Once we realize that we are in fact guided by philosophical conceptions, we can then start questioning these conceptions. For example, why would the organism need to represent the external world if the world is already there to be seen? Shouldn’t a perceptual system rather provide ways to act in the world rather than represent it? Who reads the “representation” of the world? Given that the world can only be accessed through the senses, how can this representation be interpreted in terms of the external world?
Many scientists deny that philosophy is relevant for their work, because they consider that only science can answer scientific questions. However, given that the adhesion of a scientist to a particular scientific theory (and therefore also the making of a scientific theory) is in fact guided by philosophical preconceptions, rejecting philosophy only has the result that the scientist may be guided by naive philosophical conceptions.
Finally, another determinant of the adhesion to a particular scientific theory is psychological and linked to the personal history of the scientist. The theory of cognitive dissonance, perhaps the most influential theory in psychology, claims that human psychology is determined by the drive to minimize the dissonance between different cognitive elements. For example, when a piece of evidence is presented that contradicts the beliefs of the scientist, this produces cognitive dissonance and a drive to reduce it. There are different ways to reduce it. One is that the scientist changes her mind and adopts another theory that is consistent with the new piece of data. Another one is that the piece of data is rejected or interpreted in a way that is consonant with the beliefs of the scientist, possibly by adding an ad hoc hypothesis. Another one is to add consonant elements, e.g. by providing new pieces of evidence that support the beliefs of the scientist. Another one is to seek consonant information and to avoid dissonant information (e.g. only read those papers that are most likely to support the beliefs of the scientist). The theory of cognitive dissonance predicts that the first way rarely occurs. Indeed, as the scientist develops his carrier within a given scientific theory, she develops more and more ways to discard dissonant pieces of information, seeks information that is consonant with the theory and by taking all these decisions, many of them public, increases the dissonance between her behavior and contradictory elements. An important and counter-intuitive prediction of the theory of cognitive dissonance is that contradictory evidence generally reinforces the beliefs of the scientist that is deeply committed to a particular theory.
In summary, a large part of scientific activity, including the making of and the adhesion to a scientific theory, relies on epistemological, philosophical and psychological elements.