Science and direct perception: Science is the logical analysis of the universe. It relies primarily on one authority (valid means of knowledge) namely direct perception (pratyaksa pramanam). Direct perception includes perception with any of the five senses. Scientists assume that spirituality is averse to a rational analysis and that the spiritual goal and means are not available to direct perception. This is a misconception. Our ancient knowledge of the scriptures recognizes different valid means of knowledge or pramanas (authorities). However they are all based on perception alone. For example, inference is a pramana. You see smoke on the mountain and you infer that there must be fire. Although at that moment you are not able to see fire, you can infer its presence based on past observations that smoke is always accompanied by fire.
Thus prior to making an inference you need direct perception of both fire and smoke and the recognition of an invariable relation between them. Inference is called the anumana pramana. Another pramana or valid means of knowledge is the sabda pramana or the word 'pramana'. Suppose you do not know that smoke is always accompanied by fire. However a very knowledgeable and reliable person says that so, then you can take the relation between fire and smoke for granted. Again this pramana is also based on direct perception since that person has seen smoke to be always accompanied by fire. Not only is the sabda pramana or the word 'pramana' based on direct perception but it is subject to verification by direct perception. If you observe a contradiction between the sabda pramana and your own perception, you are sure to take your perception to be true. However since it is not necessary and practical to verify each and every told word, we take some reliable information obtained from another to be true. There is always the possibility of verifying it at appropriate junctures. Therefore taking the relation between smoke and fire for granted, you can use another pramana such as inference to infer the presence of fire from a visual perception of smoke. Thus in daily life, we use several combinations of pramanas but perception is always an essential basis of it. Direct perception is the basis of all knowledge.
The scriptures of different religions contain the knowledge of spirituality. They are in the form of words and are the trusted and reliable authority in spirituality. They are the sabda pramama. They are reliable as they do not contradict experience or perception.
The Vedas (scriptures) classify the pramanas for spiritual knowledge, into four categories.
Sruti: the original scriptures.
Smrti: the commentaries of scholars on the original scriptures. These may be regarded as secondary scriptures.
Yukti: the rational or logical analysis based on inference, comparison, deduction, comparison, and negation.
Anubhava: the experience based on the perception of the items in this world, which may be direct or indirect.
Out of these four ways, the fourth way is the final and most powerful. If anything contradicts experience, it is either invalid or it may the result of a misinterpretation of the Sruti, Smati or a flawed yukti (reasoning). Thus the ways of science and spirituality are not separate. The scientific method is the very foundation and framework of the spiritual knowledge of all the scriptures.
A true scientist should always rely on perception as the final means of knowledge. He should not deny experience derived by perception. If he denies, he is not a scientist. The topmost scientists in the world were philosophers and spiritual people. Those scientists traveled along the river of science and reached its end, which is the ocean of spiritual knowledge. This spiritual knowledge is called philosophy and it pervades all branches of science. Every branch of science gives a PhD as the final degree. A doctor of philosophy would not be given if science and philosophy were basically different.
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