We have a tendency to condense The Past into a single time in order to contrast it with the present, in things like how children were brought up or what we ate for diet. For thousands of years, children were instructed...or Our ancestors didn't have all the ultra-prepared foods...
But they don't actually condense well. The vague term hunter-gatherer neglects that they hunted and gathered very different things, place to place and even century to century. If you are eating paleo, you eat meat, but which meat? And vegetables, but those vary enormously. No processed oils? I dunno, heating olive oil before packing it into a ceramic jug to be sent hundreds of miles by boat, a practice that is millennia old, sounds like processing to me. We are doing new things with food, and such things as repeated reheatings of oil in the various steps of assembling a packaged cake is something unknown to our ancestors, sure. But your million ancestors from around 1400 ate things quite different from each other, even in the case of someone like me, where the whole group were within a few miles of the North Sea.
So our guts didn't evolve thousands of years ago to digest in a certain way, except that they perhaps evolved to run on lots of different types of fuel. Our guts have in fact taken repeated shocks over the centuries in terms of what is available and what they have to accomplish, and those guts that could should a few percent advantage moved on to the next generation more regularly. Culture always runs up against biology.
The "good old days" were when I could eat paleo or keto or carbo without worrying about how much of what.
I don't see the keto connection in your post. They aren't claiming to eat like their ancestors, at least, not for evolutionary reasons.
There are a lot of new things we put into our bodies today, like vaccines, antibiotics, high fructose corn syrup, etc. It would surprise me if some of them didn't have side effects on our digestive system, appetite, metabolism, etc.
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