Preliminary statements: Although the idea of "science" undergoing a change in theory (as though it were a person going through stages of physical development) may strike some as strange, it is not inappropriate. Science, taken as a cultural entity or an intellectual project, can be seen as something unified. As trends come and go within the scientific community, the face of science itself changes. Consider the way in which we view science today, compared with the way science was received in the time of Galileo, and you may be able to see what I mean. In this sense, then, we can look at how science undergoes changes of theory (which in turn changes the perceived nature of science, notwithstanding its basic propositions of discovery and truth-finding).
The basis for a change of theory in science seems to lie in the appearance of sufficient anomalous information to make a theory seem plausible. The standard view of science says that scientific theories are arrived at by making observations of natural phenomena, figuring out what "facts" those phenomena represent, and then developing hypotheses based on those "facts". Depending on what school of thought you identify with, your scientific project then proceeds based on the confirmation or falsification of your theory (which seems to me to be essentially the same thing; if your theory is not meeting up with supporting evidence, it is probably either stagnating or being proven wrong, no matter what name you put on your method of doing science). Carl Hempel, for example, adheres to the received view of science as a progressive endeavor in which one observes phenomena, derives universal rules out of those observations and then looks for observable, testable facts. As a positivist, Hempel emphasizes the importance of scientific method; it will always be logical and will always follow one of two routes. These two routes are the deductive method, which starts investigations from a universal rule, and the inductive method, which starts with observations. The problem with induction is that it is hard to move from your observations to solid universal rules, because there are so many other "facts" running on a tangent with your "facts" that it is impossible to properly observe everything that could be of significance to what you are trying to do or figure out. Deciding on what is relevant is also a problem, because there are myriad reasons why this fact or that fact might be important; here we can see that objectivity in science becomes slightly doubtful, because there must be a choice made when deciding to pay attention to certain facts. It is fair to assume that the decision is not always made by flipping a coin.
Again, in this model, either confirmation or falsification is trump (depending on which way you look at it). Confirmation depends on the quantity of tests you run your theory through, the variety of tests you use, and whether or not your theory agrees with accepted doctrine. This does not entirely make sense, because if one of the requirements of confirmation is that your theory agrees with accepted theories, then it follows that scientists may only adopt theories that already agree with mainstream science just so they can proceed! When a theory does not meet these criteria, it is viewed as fruitless, and is then discarded. This also presents a problem, because if you are only looking for proof that your theory fits what has already a part of the scientific canon, then you would have a hard time actually finding out anything new. Instead, you would just be trying to support what everyone already thinks anyway! It appears that in the positivist perspective, theories do not change; they are only supported by accepted theories because they support accepted theories (or else they do not do the former, which means the latter is not even a possibility).
The falsificationist method is more progressive and logical. Instead of looking for support, the researcher attempts to disprove his or her theory. Anomalies are reason to call your project into doubt, and when enough anomalous information pops up, you theory has to be seriously reworked or thrown out. This brings to mind a sort of Hegelian dialectic (as it has been formulated - he did not actually use these terms) in which the thesis (proposed hypothesis) meets antitheses (anomalies) and out of that meeting a new thesis arises, and progress takes place. A change in theory as per this method occurs in cases of falsifying evidence presenting itself, which causes scientists to rethink their course of action. Sir Karl Popper, a proponent of falsificationism, says that this methodology is preferable to that of confirmation because you can "confirm" anything if you are performing poor science. W.O. Quine agrees, saying that any body of evidence can be used to support an innumerable amount of other theories. Falsification requires that a theory must meet a standard of reliability ; this is the improvement upon the confirmation methodology.
The problem with falsficationism is that what could be a productive theory (given time) is often unduly buried because of anomalies that could be put aside and worked out later on. Increased accuracy could lead to new discoveries in areas that would otherwise be brushed off and forgotten. For this reason, the falsificationist model is also not entirely useful.
Thomas Kuhn comes in here and looks at scientific method differently; changes in theory can and do occur because of reasons external to pure evidence and method. The way in which scientists were trained, their system of beliefs, and even their personal preferences all contribute to what gets supported and what gets dismissed. A scientist trained in a certain way is prone to put an emphasis on certain things and not notice other things. These modes of indoctrination are prevalent in periods of "normal science"; in such periods, says Kuhn, progress does not really take place. Instead, scientists engage in research focused on their on fields, problem solving and brushing up on existing theories.
Real change occurs when a when a new theory comes along that shakes up all the "normal" science. These are times of crisis in which progression finally occurs. First, numerous anomalies show up, which causes a crisis, and then a new perspective arises- this is a scientific revolution.
Shifts of theory in science always seem to be rooted in anomaly and uncertainty. The discovery of crisis-inducing evidence is what opens the opportunity for a new way of looking at things; it is through the difficulties of readjusting and rethinking scientific research that theories evolve and move in different directions.