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The scientific method is a collection of techniques used to explain a phenomena. Most of us have already read through this in high school science classes, so I'll just make it short. The steps are:
1. Ask a question
2. Gather data
3. Form hypothesis
4. Conduct experiments to prove the hypothesis
5. Assuming all goes well, publish your results as a theory and submit for peer review
Through this process, we must consider that observations should not be assumed to be true because of observer bias. Hearsay is even less reliable, and unexplained phenomena cannot be used as evidence. Opinions of professionals and authorities may also be biased or incorrect. However, you should exercise some level of reason, common sense, reality check, whatever -- if your doctor tells you to get an X-ray, it's possible that his assumptions are wrong, but it'd be stupid to disregard it because it might be fatal to you.
When forming hypothesis, it's generally recommended to form as many as you can, like brainstorming. If you find yourself attached to any particular hypothesis, then you're biased. Scientists are all biased in some way or other. Personally, as an analyst, I'm biased toward statistical probabilities, which I'll explain later.
Because of bias and uncertainty, the most critical part is to conduct experiment and test your hypothesis. The experiment must also be repeated multiple times to ensure that it wasn't a lucky event. The experiment must accurately record or reflect external conditions. Sometimes you cannot conduct the test in real life due to restrictions, such as nuclear detonation testing. So you have to rely on computer model simulation, which is far less reliable than actually dropping a few bombs on Bikini Atoll.
After you've verified your test results, you can write your scientific theory and submit it for peer review. You must include all relevant data so that other scientists could replicate your testing. Until other scientists successfully verify your claims, your theory would not be accepted. This is important because you cannot cherry-pick only those who support your position. Investigative reporters do that, Scientists don't.
When dealing with elaborate plots/conspiracies and hoaxes, the Scientific method process itself is biased against them due to Occam's Razor, Chain of Argument rules, etc. Occam's Razor rule is biased toward the most simple and direct route, which cuts right through complicated plots. The Chain of Argument rule says that when you "connect the dots", each dot must be proven to be true before you can connect them (something that is unexplained is not proven). This is because the more assumptions you make, the higher the probability of failure. Consider:
The chance of rolling a 6 on a 6-sided dice (1d6) is 1 in 6.
The chance of getting 18 from 3d6 (rolling 3 x 6 sided dice at same time) is 0.46%, or roughly 1 in 216.
From anothert perspective, the more complex the plot and the more people you involve, the higher the chance of failure, or that someone will squeal (see: Iran-Contra).
Thus, to actually believe in an elaborate conspiracies where individual "dots" cannot be proven with the Scientific Method, one must make a "leap of faith".
Statistically speaking, people who believe in one conspiracy has a higher tendency to believe in another. This is a psychological trait and those who weave hoaxes know how to exploit. They go after people who think they're smarter than others, that the majority are ignorant, that they're unjustly discriminated against, that others (the establishment) is plotting against him, etc. and lead them by the nose.
Secret societies and conspiracies DO EXIST in present and past. However, people tend to give them too much credit, from their own imaginations. Like, imagine if everything that your perceive is wrong is the world was actually an elaborate plot from an evil group of masterminds! Instead of fixing your own problems, you could just point fingers at others and say "they did it". The most recent Housing market is an excellent example. Yes the bankers had a hand in being greedy and loosening the mortgage rules ("you are alive? OK we give you $500,000..."), but it takes 2 to tango. It took the combined forces of millions of greedy home owners using their home equity like an ATM to create the bubble that popped in 2006.