How many wrong dogma's does it take to make a right

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I've been wondering what to write about next for my podcast series. One of the things I'm pondering on is basically if they have germ theory wrong what else do they have wrong. I started compiling a list of the things we have all been taught for a long time which are only now being questioned. Obviously the 'immune system' is number one because it springs directly from germ theory (or does it). Did germ theory just absorb another hypothesis and turn it into something it could use? Do we build up a 'tolerance' to poisons or is the body overwhelmed and giving up? What causes the body to over-react as in the case of anaphylaxis and allergies. Where/what is the tipping point? Why does the body switch from tolerance to hypersensitivity as in 'cytokine storms' and 'anaphylaxis'? These are questions I want to dive into.
Next on my list is digestion, the whole stomach making battery acid thing has never sat well. Now Robert O'Young has turned that on it's head and given us his 'alkalizing chamber' theory which makes more sense. Why (or even how) would the body make an acid so strong it can eat itself? If mucus is supposed to protect the stomach from being burned by this acid why doesn't the mucus itself get burned away?
This leads me to energy/calories and fat. WTF are calories and how do they measure them? How do we 'burn' them? Is that really where we get energy from food or is it a frequency/life force exchange? We know that 'living food' is what makes us healthy. Is it an absorption of chi? Do we even need food? (breatharians). What is fat? Is it really an energy storage or is it a toxic waste management system? (Dead processed 'food' seems to cause the fat build-up. Diets to 'lose weight' are basically detox diets).
Teeth. We were always told they cannot be repaired but now they are having to admit that is a lie. Enamyl can be rebuilt, teeth can be repaired by the body. Look at scurvy which manifests as rotten teeth and gums so a lack of fruit seems to cause tooth decay yet dentists still insist that the 'acid' in fruits eats our teeth away. Damned lies.
The heart.
Is it a pump? How big a force would be needed to pump your blood around such a huge system of pipes? Not something as small as the heart for sure and how does a pump manage to reverse the direction of blood in the capillaries to turn 180 degrees and come back on itself. Impossible. Tom Cowan has a new view that the heart creates a vortex and that the blood itself is involved in it's own movement.
I'd love some input from my brainiac friends. What have you found out? Where are good places to look for answers? I'll be making a detailed talk out of this if I can make sense of what I find and make it easily understandable.

The pioneer scientist must have "a vivid intuitive imagination, for new ideas are not generated by deduction, but by artistically creative imagination."
Max Planck

Some sources;
http://alkalineworld.com.au/blog/the-stomach-does-not-digest-food-chew-on-that/
https://www.faim.org/sites/default/files/documents/What-Causes-Heart-Attacks-Cowan-reprint.pdf
https://www.nobelprize.org/prizes/medicine/1913/richet/lecture/
http://www.columbia.edu/itc/hs/medical/pathophys/immunology/2005/IMM20-SlidesBW.pdf
(will add more when I find them)