Bad science?

I don't understand the whole concept that cooking food destroys proteins. Certainly it denatures (meaning they lose their "shape") them and alters their chemical and biochemical properties.. But essentially proteins are long chains of different amino acids, and cooking the food will not alter the amino acids. Our bodies break down proteins into amino acids so that we can make our own proteins. We don't simply absorb proteins from raw food and use as is. the acid environment in our stomach denatures proteins, and the enzymes in our disgestive track further break down proteins so that our cells can absorb smaller amino acid fragments. I understand that the enzymes that breakdown our food will recognize proteins from raw and cooked food differently ( because of the shape)so is that the argument? That our bodies recognize raw food proteins better? I always hear this argument about protein being destroyed by cooking but it makes no sense to me, because the amino acids are still there, they are chemically intact.They never explain in what way the proteins are destroyed, I am not convinced that the man who made this claim in the movie remembers anything from high school biology.... i can appreciate that nutrient deficient soil will result in less nutritious produces. I believe that cooking removes some of the nutrients ( water soluble vitamins) and minerals, but beyond that I don't see a difference, and a lot of the arguments seem like pseudo science to me :S

If anybody can explain the protein thing to me, please do try.