When you cook food you break down the molecules that the food is made of. This is also what the digestion system is doing with enzymes and acids. For example starch can not be absorbed into the blood stream by our intestines but we produce an enzyme that breaks down starch into sugar. However you can heat starch to make it break down into sugar. This is what you do when you boil potato, you can actually taste the difference in sweetness between a raw potato and a boiled potato, and you can even try chewing a raw potato for a while until it becomes sweet.
Overcooking however makes the molecules brake down too much. If you heat a potato a bit you convert the starch to sugar but if you heat it too much you convert the sugar into sot and charcoal. This have no nutritional value to us. So you need to find the happy medium between cooking it so much that you break down the starch into sugar and breaking down the sugar into less nutritional molecules. And of course you have different types of molecules like proteins and fat clusters. And you have membranes, both around cells and around organs, that will get broken down by heat giving access to the nutrition inside.
If you compare the human digestion system to that of other apes and indeed that of other animals our digestion system is quite simple. It even starts with our teeth being smaller because we do not have to spend a lot of time chewing food. We are one of the few animals with only one appendix for example and even our appendix is small compared to those in other animals. The ability to heat our food have changed how our digestion system have evolved.
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