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- Once upon a time, there was a man who was convinced that he possessed a Great Idea. Indeed, as the man thought upon the Great Idea more and more, he realized that it was not just a great idea, but the most wonderful idea ever. The Great Idea would unravel the mysteries of the universe, supersede the authority of the corrupt and error-ridden Establishment, confer nigh-magical powers upon its wielders, feed the hungry, heal the sick, make the whole world a better place, etc. etc. etc.
- The man was Francis Bacon, his Great Idea was the scientific method, and he was the only crackpot in all history to claim that level of benefit to humanity and turn out to be completely right. 
The scientific method is the single most successful epistemological system for deriving knowledge that the human mind has created. At its core is is the idea that the truth value of a hypothesis, theory, or concept is best determined by its ability to make falsifiable predictions that can be tested against an empirical reality. This means higher powers cannot be included in a hypothesis (you can't put a sample of God in a test-tube).
The following five steps make up the scientific method:
2) Come up with an explanation — the hypothesis.
3) Compare the hypothesis with empirical evidence, (usually experimental evidence often supported by mathematics) — this step is the reason why a hypothesis or theory has to be falsifiable). Have the experiment reproduced by third parties.
4) If the hypothesis is in agreement with the evidence it becomes a theory; if it doesn't, return to step 2.
5) Use the theory to make predictions.
A prediction forms a new hypothesis, making the cycle repeat. Additionally, confirmation of these predictions strengthens the original theory.
Steps 3 to 5 are omitted from the process in pseudosciences such as Intelligent Design (where step 3 would be impossible) and homeopathy. However, because steps 1 and 2 are still there, to some laymen, pseudosciences may mistakenly appear to have scientific authority.
The scientific method was not always accepted during its period of development. The work of Ignaz Semmelweis provides a telling example of what happens when the method, or the conclusions arrived at by its use, are ignored.
There are other schools of "scientific criticism" that look at science critically from an economic perspective, or that focus on discourse, but these are more academic and less practical critiques.
Popper described the modern formulation of falsifiability, that is, the concept that for an idea to be "scientific" it must be possible to devise an experiment (even a thought experiment) that might render it false.
Kuhn described the dynamics of scientific change, coining the terms scientific revolution and paradigm shift to help described what he saw as the way a fundamentally conservative set of ideas could be overturned and become a new, different set of conservative ideas. Summary: humans remain humans and don't naturally think in a scientific manner, but have to learn it, and easily backslide.
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