It is clear that most people do not have a good grasp of the fundamental nature of science. I think the fact that a large number of Americans believe that things like creationism/intelligent design should be taught in high school biology classes is evidence of this conclusion. Ths si why, as a science educator, I am always on the lookout for examples that give a clear snapshot of how science works. A recent example is the case of the pentaquark. A nice, understandable article regarding the pentaquark can be found in Symmetry Magazine, a joint publication from the Stanford Linear Accelerator (SLAC) and the Fermi National Accelerator Laboratory (FNAL, or simply Fermilab).
In a nutshell, quantum chromodynamics (QCD), which is the current quantum field theory that describes the strong nuclear force (responsible for binding quarks into observed particles, as well as holding the nuclei of atoms together), allows for particles that are combinations of five quarks, hence the name pentaquarks. This is very different than the particles that we observe normally, which are baryons (3-quark combos, such as protons and neutrons) and mesons (2-quark combos). When the possibility of pentaquarks was first theoretically predicted in 1997, experimentalists at a variety of labs around the world began looking for evidence of this potentially strange breed of particle. In 2003, the first announcement that there was some evidence for pentaquarks was made.
This doesn't seem like much right now. A well-established theory predicts something, and when it is looked for it is found. However, that is just the beginning in science. What many people don't understand about the nature and process of science is that just because one person or one group say they found evidence for something, that doesn't mean we should believe it. Rather, the opposite is true. When new discoveries are announced, the scientific community takes on the role of skeptic. The articles announcing the discovery are looked at with a fine-tooth comb, at least this is how it is supposed to work. Other scientists in that particular field think about the analysis and methodolgies used in the research. Statistical standards must be met within the field in order to announce discovery. The article was peer-reviewed before even being published. The whole community is supposed to try and find flaws in the work. In the case of the pentaquark, the concept of reproducibility took place, where independent groups at different labs try and reproduce the results.
As other groups designed and ran experiments specifically to look for pentaquark signatures and collected greater volumes of data, better statistical results were determined, and the new conclusion from several independent groups was that there was actually no reliable evidence for pentaquarks. The original studies suggesting there could be this new type of particle were isputed by better experiments and data sets. Does this mean the original experimentalists fabricated their data or did not know what they were doing? Not at all. There could have been a variety of reasons why they reached their conclusions, such as statistical fluctuations in the data, high background rates, detector issues, low statistics, unknown systematic errors, and so on.
The point is, science is always evolving. As technology improves, as new knowledge is developed, and as old, accepted ideas are re-examined under new points of view and studies, if there is evidence that suggests old, accepted theories or ideas are incorrect and need to be modified, then the appropriate changes based on the best new information are made. Perhaps the most impressive example is when young Albert Einstein, with a new, fresh point of view, came out and said that the bedrock foundation of physics, Newton's laws, were fundamentally flawed and simply did not work when objects moved at a substantial fraction of the speed of light. He presented a new theory, the special theory of relativity, which did a better job of describing Nature.
Science is self-correcting. It is skeptical. It challenges us to not accept something the way it may appear at first glance, but rather what it is after exhaustive study. Science bases its conclusions on observation, reality and evidence, rather than on common sense and logic. If at all possible, scientific conclusions and discoveries should be re-tested independently and either confirmed or disputed. It can be a slow process at times, but this is simply the nature of this realm of human thought and productivity.
Philosophy differs from science in that logic dominates the process. This does not necessarily allow us to accurately describe the world, though, as we found out when heavy objects don't fall faster than lighter objects, as Aristotle argued based on logic/common sense, but rather at the same rate. We also see a complete loss of comon sense and logic in something like quantum mechanics...but all physical tests of the many bizarre predictions of the theory have confirmed the theory. Religion also differs in its process of understanding the world around us, as religious texts lay down down exactly what should be believed. There is little to no room for skepticism in religion, for one either accepts the word of the Creator or not, and typically it is left at that. And religion lacks physical tests or evidence to prove a Creator exists; rather one's faith in the Creator is necessary for one's religious development.
Do pentaquarks exist? The best evidence suggests we have not found them. Does this mean we accept this and never look again? Definitely not. Perhaps in a future experiment there will be some strange signal that appears and we get one of the 'accidental' discoveries that are comon in science (such as penicillin or X-rays). Perhaps the calculations that led to the prediction were not done accurately and pentaquarks are in reality heavier than first thought, and it will take a new facility to produce them. Who knows? But this is what continues to drive science forward as it tries to figure out how the physical world around us works. And it is a very different approach than what is done in philosophy and religion.