Following is an extract from an article -
In the age of science people have come to believe that because of the amazing discoveries of science and the dramatic impact of technology based on scientific research and discovery through experimentation, scientists using the scientific method hold the superior knowledge. This however, is a shallow error committed by the one who does not know the reality of the scientific method and the principles on which it is built. Firstly, we should distinguish between scientific theory and scientific fact. Scientific theory is a speculative idea that may be logical but not necessarily based on reality and could be based on imagination. The scientist then searches for evidence or what he erroneously perceives to be evidence. The evidence is often incomplete and does not take into consideration other possible factors an example of scientific theory is the theory of evolution. Although people may think it a fact, scientists must submit to the reality that it lacks evidence and is unproven, on further investigation the theory is full of inconsistencies and much contradictory evidence exists, more importantly however the theory is fundamentally refuted by rational principles and things already established as fact about the reality of living organisms.
Scientific fact on the other hand, is sound because it is not speculative but is only based on observation of natural phenomena or experiments, all factors are considered and the conclusions are only based on the reality and do not go on to project beyond the evidence.
Sound scientific method however, although necessary for discovery and progression is not the superior form of thought. The superior thought is rational thought and this what sound scientific method depends upon. Science is not a comprehensive thought upon which life can be based, it is only of use in observing present things. Things not present, and intangible concepts are beyond its scope. It does not produce answers to the three fundamental questions about life on which true progress is based. Science therefore can not produce the foundation of a system of life or the foundation of a comprehensive viewpoint about life. Science often bases its conclusions on that which is outside its natural conditions, experiments are error prone and often open to different interpretations and results often not decisive enough to outweigh the possibility of external factors or minor errors. Science studies a specific object or group and then applies the conclusion to all similar species generally. Thus science makes a jump of faith to the general from the specific.
Rational thought looks at the whole of perceived reality and applies the judgement to the specific element of reality. The reality is all that the human being can base his conclusions on and he can then progress when he combines this with previous information about the reality. When a scientist sees change in experiments after making an alteration to the subject matter, he concludes that his interference brought about the change in the results, this is because he believes in cause and effect and he knows that the change did not just happen by itself. This is not because cause and effect was proven through scientific experimentation but it was always assumed because it is intrinsic to the reality and is constantly perceived in the reality. Without cause and effect all scientific experimentation would be pointless because the results may have been caused by the experiment or may have just occurred by themselves and there would be no way of knowing. Additionally, science can not judge cause and effect through experimentation because the analysis of the results of the experiment itself are based on cause and effect and an independent test can not be dependent upon the principle which it is supposed to be testing. To conclude cause and effect is based on ration and is external and prior to scientific method, scientific experimentation is dependent upon the belief in cause and effect which itself emanates from rational thought.
You have to differentiate between scientific theory (better word would be scientific fantasy) - such as evolution etc. and sound scientific fact - which most scientific theories of today are void of.