Intuition - its role in scientific discoveries
Due to the great success of the scientific method since Newton to the nineteenth century, scientists tended to believe that all scientific theories and discoveries are a matter of empirical development. They held the view that sufficient efforts invested in experiments and calculations will lead to understanding of the whole universe. In other words they believed in rational explanation of the nature & universe. They had a firm explanation for this view :

Newton's success to explain as "small" thing as falling of a stone to the ground or the movement of a body under forces exerted onto it, or as "big" things as circulation of celestial bodies one around another like the moon around the earth or the earth around the sun, all based upon simple laws (known as the Three Law's of Mechanics by Newton). 

Furthermore, in 1864 electromagnetism laws were formulated by James Clark Maxwell. He expressed these laws in four simple mathematical equations known as the Maxwell Equations. This development together with Newton's Laws of Mechanics, made the scientists believe that final exploration of the nature is only a matter of time and efforts invested in empirical means dedicated to the exploration. 

Towards the end of the nineteenth century the majority of them believed that all the secrets of universe are revealed and the theoretical physics has came to an end. 

Saying so two things were ignored : 
1. Some electromagnetic phenomena that arose from Maxwell's Equations like the velocity of light measured from two relatively moving frames. Later it was found that this "little" discrepancy conceals within it a whole world of new theoretical physics.

2. The fact that there was not any known record of ideas before Newton about gravitation or any formulation of rules that could explain movement of materialistic bodies under forces. After all, the apple which Newton saw and was the reason (at least by the popular version) that triggered him to formulate the Three Laws of Mechanics, was not the first thing falling down that was seen by a human being throughout mankind's history. The simple questions which should had been asked by those scientists are "why among so many countless people who saw everyday things falling down, only Newton thought that there must be certain rules dominating this and other phenomena?".  How did only he come to the conclusion that this "local" phenomena of "falling down" and a celestial phenomena like the planets circling one another, are ruled by the same simple laws ?

Ignoring this simple fact was a fundamental mistake which led to exclusion of intuition which could be necessary to make significant breakthroughs in science. 

However, one fact should be considered. The Laws of Mechanics formulated by Newton seem to be very logical. They are simple and do not contradict any of our daily experience. Now, it seems being such logical and simple, the scientists were tempted to assume that unexploration of these laws before Newton was due to lacking of sufficient rationality or just a mere coincidence. Intuition did not seem to be necessary in order to explore these laws. 

Newton himself held the same view that notions and laws about nature can be derived from empirical experience. 

In 1887 an experiment was carried out in order to find an universal fixed frame denoted "Ether". The experiment is known as the Michelson and Morely Experiment. The aim of this experiment was to provide a mechanical basis for the electromagnetic waves. 

It was assumed for many years that as sound waves require a materialistic medium to travel from one point to another, thus the electromagnetic waves (light) require some kind of materialistic medium to travel. The medium which was assumed to exist for this all over the space was called "Ether". The electromagnetic waves were supposed to propagate through Ether as the sound waves propagate through air. This was an attempt to bend the electromagnetic reality as formulated by Maxwell Equations towards the mechanistic reality as formulated by Newton Laws. 

The reason for this was clear. The mechanistic reality can be seen with eyes and also experienced easily with other senses, while the electromagnetic reality is somewhat vague and do not always appeal to the common sense. So intuitively scientists tried to apply the mechanistic logic to the electromagnetic phenomena. Only that this time it was a wrong intuition. 

After Michelson and Morely carried out their experiment, it became evident that either there is no ether - meaning Newton's laws shoul be modified, or another explanation should be given which will enable to keep the Newton's laws as they are while Maxwell's equations should be modified. 

Many attempts were made by several scientists to explain these results. Different theories were conceived with many experiments to prove the existence of Ether. But the results were the same. No evidence for Ether was found and none of these experiments could approve the different theories completely. 

In 1905, Albert Einstein published an article under the title "On the Electrodynamics of Moving Bodies". This was the first publication of what became later known as The Theory of Special Relativity. In this theory Einstein chose to change the point of view totally. He took for granted the Maxwell Equations of electromagnetism and claimed that Newton's Laws should be modified.

This choice is a consequence of an intuitive understanding that the Maxwell Equations are more fundamental than Newton's Laws. Unlike his colleagues, Einstein preferred to bend the Laws of Mechanics towards the electromagnetic equations. Again, like in the case of Newton who was not the first person to see something falling down, Einstein was not the first who saw the problems arising from the incorporation of the mechanical and electromagnetic phenomena. But only he like Newton (in mechanics), conceived the right solution. It seems they both possessed something (intuition) which made it possible only for them among so many others who were witnessing exactly the same phenomena, to reach the correct answers.

This is well illustrated in the following quotation from the book "Introduction to Special Relativity" by Robert Resnik. "For examle, Lorentz, who never really accepted Einstein's relativity, used a great many ad hoc hypothesis to arrive the same transformations in 1904 as Einstein did in 1905 (and as Voigt did in 1887); furthermore Lorentz had assumed these equations a priori to obtain the invariance of Maxwell's equations in free space. Einstein on the other hand derived them from the simplest and most general postulates - the two fundamental principals of special relativity. And he was guided by his solution to the problem that has occupied his thinking since he was 16 years: the nature of time. Lorentz and Poincare had accepted Newton's universal time (t=t' ), whereas Einstein abandoned the notion." 

Einstein's the free, independent and intuitive nature is illustrated in a quotation from the same book. "Einstein simply could not accept conformity required of him, whether in educational, religious, military or governmental institutions. He was an avid reader who pursued his own interests, had a great curiosity about nature and was a genuine "free-thinker" and independent spirit."  Einstein himself believed that significant scientific breakthroughs occur not through empirical or rational means but as said by Einstein himself: "free explorations of the human spirit." 

It seems that hints about the nature and its rules are planted all over the universe and also in the results of the countless experiments carried out by the human being. The role of intuition is to find out the hints, make the right connections between the different hints, ask the right questions and finally coming to the right conclusions. These conclusions may be sometimes a significant breakthrough in science. It seems that the way for coming to the right conclusions is not always rational. In many cases, the right conclusions are reached intuitively and later explained rationally.
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