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What is a hypothesis?
A hypothesis is a statement that contains an expectation about a difference between groups or an effect between factors. Through scientific research, scientists test whether a hypothesis can be accepted or rejected. A hypothesis (and so the expectation) is formed on the basis of a question that scientists want answered. Behind the question is a theory that is supported by biological mechanisms and scientific research.
This is a follow-up to 'What is the Pyramid of Evidence Strength? (part 2)

It all starts with a question, a question about reality that scientists want to answer.
Question: 'Does our immune system get stronger when we get more vitamin C?'
Questions follow from current theories about reality. These theories are often based on assumptions, biological mechanisms and other scientific research.
Theory: ‘Vitamin C stimulates the formation of white blood cells. White blood cells are an important part of our immune system.’
To answer the questions, and so to test whether the theories are correct, scientists formulate a statement that creates an expectation about the answer.
Hypothesis: ‘People who take a vitamin C pill catch colds less often than people who do not.’
The hypothesis is then tested through scientific research, so that the theory can then be sharpened or changed. In this way scientists get closer and closer to the truth about reality. Scientific research is therefore not the same as that truth. Scientific research is the process between asking a question and giving an answer to that question, so that theories about reality come closer and closer to reality.
The scientific method
This is the scientific method: answering a research question in a way that is as organised, structured and objective as possible, through hypothesis testing. This makes science reproducible and transparent. This is important, because one result can be chance. By being transparent about the method and by repeating the research, a theory becomes better and better supported. We test the hypothesis with statistics; I will come back to this in an article.
A court case: two kinds of hypotheses
There are two kinds of hypotheses that cannot exist without each other: the null hypothesis and the alternative hypothesis. The null hypothesis always assumes that there is no difference or effect. The alternative hypothesis creates the expectation that there is a difference or effect.
Null hypothesis: People who take a vitamin C pill catch colds just as often as people who do not.
Alternative hypothesis: People who take a vitamin C pill catch colds less often than people who do not.
You can see science as a court case. The prosecutor (scientists) has a theory about the truth and presents a case (scientific research) to prove that the defendants are guilty (reject the null hypothesis and accept the alternative hypothesis). When the prosecutor does not manage to present enough (strong) evidence, the defendant is not declared innocent, but not guilty (do not reject the null hypothesis, but do not accept it either). So the null hypothesis is (just like in a court case) NEVER accepted, because scientific research always looks at the plausibility of the alternative hypothesis and never at the plausibility of the null hypothesis. The burden of proof always lies with the prosecutor to prove guilt.
In nutrition science it works in exactly the same way. It is important to stress once more that the scientific method is a system for forming theories about reality and constantly refining these theories. Science is not reality itself. Scientists formulate theories about reality, from which new questions and hypotheses to test then follow. Investigating the new hypotheses then leads again to an adjustment of the theory. We test the hypothesis by means of statistics and by finding significant results.
In the next part I will go into ‘What is significance?’
