It's all sorts of stuff, but avoiding "processing" will lead you to make the best choices in practice.

Food processing is complex, dynamic, and adversarial (see my comment above)

As Hall points out, there is more research possible to find the underlying mechanisms. However even those mechanisms are proximate causes, not the ultimate cause.

We already know a lot -- it basically boils down to economics:

(1) Processing uses ingredients you can't find in your kitchen which may be bad for you. For example, emulsifiers -- did your grandma cook with xanthan gum, etc.? Because these things make it easy to process food at scale.

A mechanism that has been suggested by Lustig is that the emulsifiers still emulsify in your stomach, and give you leaky gut syndrome

This is just one example; there are hundreds of food additives that basically exist to support SCALE of manufacturing and sale, including increased shelf life

(2) Predictable inputs to assembly lines support food processing, including both plants and animals

In plants, this is a monoculture of single breeds of wheat, corn, and rice. (Pollan talks about how everything in the middle supermarket shelves is like this. It has a very wide range of labeling, colors, packaging, etc. but most of it is the SAME commodities processed in various ways, and lacking in nutrition. Picture: think about that commodity wheat that was stuck on a boat in Ukraine.)

And a lack of things like fermentation, which is hard to control industrially.

In animals, it's factory farming, which optimizes the mass of the animal against all else (including nutrition). These homogeneous animals have a very homogeneous set of diseases treated with antibiotics and so forth

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In addition to dozens of other books, the recent book "What Your Food Ate" by U of W scientists talks how this optimizes for CALORIES and deoptimizes for NUTRITION.

e.g. Think bland, tasteless supermarket carrots and tomatoes -- those didn't exist 80 years ago! McDonald's has to put mayo and sauce on them to make them palatable, but a real carrot or tomato tastes amazing

If you believe in capitalism, and believe that it's possible for say a carrot of great mass/calories to have less nutrition, you would have to explain how this would NOT happen (e.g. regulation, which doesn't do it).

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Basically people have to eat more to get the same amount of nutrition, making them fatter.

I think this gets at the core of it more than say "emulsifiers" or "trans fat". Your body is extremely resilient -- it can metabolize small amounts of almost any chemical.

But it CANNOT metabolize this steady and large volume of processed food -- say 50% more daily calories than what people ate in 1940, with fewer nutrients. This is what gets you chronic diseases, i.e. "Western diet disease"

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Although I think Pollan's books have the most explanatory power -- they talk about how this system arose. (including advertising toward women, e.g. freeing the women of the burden of booking)

"Food Rules" has aphorisms that get at the cause:

https://www.amazon.com/Food-Rules-Eaters-Michael-Pollan/dp/0...

Like "don't eat what doesn't spoil". Processed food is made NOT to spoil. That's what makes it profitable.

One way to make it not spoil is to take out things that microorganisms want to eat. But if a bacteria doesn't want to eat it, then YOU probably don't want to eat it either! It's probably just empty calories and processed wheat/corn, with little nutrition

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tl;dr processing, scale, and profits are the fundamental causes. You can find more specific mechanisms and specific chemicals, but just avoiding processed foods is the most actionable advice. There have been dozens of vilified nutrients and foods in the past, so if you focus on that now, the food industry will "work around" it tomorrow