Scientific theory is based on the fundamental concept that as our knowledge of planet Earth increases, so must our theory. It is the developed human brain's ability to observe, question analyze and interpret how everything works that has allowed the human race to evolve away from our closet ancestors into our own unique phyla to the point of manipulating our physical habitat to populate and dominate the planet.
The scientific process is made up of three fundamental stages - hypothesis, experimentation and analysis. In fact a scientific journal article always follows the strict structure of an abstract, introduction, methodology, discussion, conclusion and reference list to ensure that once a hypothesis is tested the documented procedure can be replicated exactly, questioned and peer reviewed. Why? Because science never says that any current human understanding is foolproof. There is always human error and that is why there are no "facts" in science only "theories" because unlike a fact, a theory can always be updated and changed when new knowledge is gained.
So how does a hypothesis form? A hypothesis by definition is 'a supposition made on the basis of limited evidence as a starting point for further investigation (Oxford Dictionary)' meaning that a hypothesis is a proposition made as a basis for reasoning. It is formed from the aim of an experiment - what an individual is trying to provide support for or against (essentially taking either a side of an argument based on previous research). For every hypothesis there is always the null hypothesis which is the opposite outcome of the aim and in statistical testing is the theory that any observed differences between two groups are due to sampling or experimental error. When a hypothesis is presented in scientific reporting, it is always proposed in the form of an introduction taking previous research in that is associated with the experimental aim and supports the hypothesis to be tested. It is used as a guide, support and indicator for the experimental results given that the hypothesis and previous research is correct.
This is then followed by the method or phase of experimentation. Firstly every experiment has a control test group. A control is a defined known marker which is used to compare the experimental groups against. If there is something wrong with the control then that same problem is present in the entire experiment and the procedure can be countered to include that error or act as an indicator to redo an experiment over. A common control is distilled water another is having a number of replicated experiments and another is physical controls such as time, atmospheric pressure, heat and light. What is important in the experimental process is the ability to repeat a method exactly the same way independent of who the individual conducting the test is, where they are or when they do it if it is clearly defined that experiment can be done exactly the way it was done the first time with the exact same results.
The third stage is observation and analysis - taking what the individual has witnessed occur and questioning why they got the results they did. It involves statistical analysis, comparisons between the control and test groups, comparisons with other research and then putting forward the most logical reason based on the information of why the results are what they are. It also involves suggestions of how improvements to the procedure can be made and potential hypotheses for further research and concluding whether the results support the hypothesis or the null hypothesis. This section is also known as the discussion where the analyst discusses their research and findings with reference to others and their own results.
So that is an introduction to the basic analytical process of scientific thinking. It is the ability to question without bias and to increase collective human understanding and improvement. Through the ability to question, experiment and reason the human species has evolved rapidly and beyond any other group on Earth to the point that we manipulate our habitat instead of living within. It is the human brain's ability to learn that has been our greatest evolutionary feature.