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In terms of Ayurveda, every organism is made up of five layers (पञ्चकोशीय). One of them is प्राणमय कोष – A body layer of प्राण. I have my प्राणमय कोष, you have your own. Our food too have residual प्राण. So our food is mix of cooked and raw food.

Raw food is full of natural prana instilled by parent organism, ultimately by universal source i.e The Sun (Plants/Trees/Animals).

Cooked food is impregnated by prana of fire by which it is cooked. Now this prana’s quality depends upon the quality of combustion and substance used. If cooked on Cow dung cakes or Biogas or wood , it is full of good innocent prana. LPG – not so good prana as it is processed fuel. Microwave – nil as heat is generated by vibration of food molecules and watery content of the food, which actually dissipates whatever remaining prana food had.

Besides cooking method and material, best source of prana Shakti are fresh air and sun rays. अमूर्या उप सूर्ये याभिर्वा सूर्यः सह | ता नो हिन्वन्त्वध्वरम || – अथर्ववेद

Meaning: When सूर्यः (Sun Rays, Wind- Fresh Air in day light) touches water, it becomes nectar/Amrit. When both are missing, water is poison, slow poison.

Cooking in pressure cooker and microwave restricts exposure to Sun rays. Again devoid of prana. Cooking in a kitchen where sun rays cannot reach or water stored in closed containers, not exposed to sun, is not preferable place to cook.

In short, cooking is required to instill additional prana to the dead parts of organisms which we do not eat Raw (Grains mostly). Keep in mind, prana is not Oxygen. Prana is not energy.

Field of Ayurveda is not explored much for finding rational proofs yet. What I shared here is my interpretation. You may not agree. However, you should study facts of modern science studies about microwave cooking.
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Modern science perspective
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In terms of modern physics, our body is electrochemical in nature. Any force that disrupts or changes human electrochemical phenomena will affect the physiology of the body. So our cell phone, our wifi, our microwave – all affect electrochemical imprints of our bodies. Microwave is not an ideal method. It alters DNA. It kills microbial flora of the food.

 

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Side note

Why Did the Russians Ban an Appliance Found in 90% of American Homes?

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http://articles.mercola.com/sites/articles/archive/2010/05/18/microwave-hazards.aspx