This post is not comprehensive, but you're welcome to add to it, if you can.
Toxins and issues that appear via cooking include such as these:
• Hydrogenated oils
• Partially hydrogenated oils
• Polycyclic aromatic hydrocarbons
• Nitrites (if one considers them toxins)
• If you're cooking tomatoes in a copper pot, you might get lethal amounts of copper in your sauce.
• Burned Teflon isn't exactly nutritious.
• I've read somewhere that the oxalic acid in cooked rhubarb is less healthy than in raw rhubarb. I need to find a source on that to verify it.
• Certain vitamins might be destroyed when cooked. (I'm actually a bit skeptical about this, because when I looked into it, most people were just talking about nutrients leaching out into boiling water, rather than being destroyed, and I didn't find any explanation as to how cooking destroyed the remaining few vitamins, or what they turned into).
• Cooking may destroy some beneficial enzymes.
• Cooking may destroy some beneficial microbes.
• The metal in a pan (if the pan is metal) may interact with the acids in the food.
Benefits of cooking:
• Acylamide in proper amounts can taste good.
• Lycopene is said to be more beneficial from cooked red tomatoes, as opposed to raw red tomatoes.
• Cooking kills many pathogens and harmful microbes (and many pathogens produce toxins).
• Cooking can denature some toxins, and probably some harmful enzymes.
• Cooking may remove some harmful chemicals (such as chlorine or hydrogen sulfide), and degrade some contaminants, according to what John Boyce, the president of Water Softening Systems said on Quora on 20 Feb 2018. Degraded chemicals may or may not degrade into something else harmful, potentially, though, I might add.
Also consider that sometimes toxins and pathogens (which can produce toxins) are removed in cooking; potentially, harmful enzymes might be removed, too.
Location: SW Idaho, USA
USDA hardiness zone: 6
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