Studies re: antioxidants show that large doses of isolated compounds are not so good for you. The famous vitamin E study is an example of this. Scientists decided to study vitamin E, though, because people whose diets were high in naturally-occurring vitamin E had improved mortality -- in particular, these diets were cardioprotective. A similar paradox is being seen, to a lesser degree, in comparing diets high in fish and diets that include fish oil supplements or omega-3 supplements.

The combination of studies shows not that "antioxidants are bad" but that we don't understand how to isolate their benefits. Diets high in antioxidants from whole foods (dead plants and animals), rather than nutraceuticals or supplements, are consistently linked with health. Apparently it's not so simple as isolating one compound -- we need a balance of chemical compounds coming in, working in concert.

(It's like we evolved to thrive on real food instead of pills! Weird!)

You're going a little bit strawman by the end there. There are many types of diets that qualify as 'balanced real food', and the questions are in why they have different health benefits and trying to find the bottleneck compounds so that you can have more benefits at once. So you would still eat real food, but for chemicals whose ideal quantities require extremely biased diets you would put some in a pill and focus your diet on filling in the rest of the concert evenly.

I don't think there are many chemicals that work that way, though. Is there any one chemical that is so great for us that only a very biased diet would give it?

Different soil conditions could lead to deficiencies -- if you only "eat local" you might have to pay attention to selenium or magnesium (http://tin.er.usgs.gov/geochem/doc/averages/se/usa.html) due to geography or geology. But setting aside deficiency, what chemical would we want to load up on in isolation?

(ok, caffeine comes to mind. but that's not really for health, and I get it pretty well from ground plant products.)

You'd conclude everything is unhealthy if you lived your life the way studies told you to. Problem is most studies you see these days are backed/funded by an agenda to be basically their marketing.

I'd like to see a study that dismisses labels like "organic"/not and look for the nutritional content AND poisonous content.

That way, we'd find the best current/future farming methods available instead of this inane religious branding war between marketing giants.

That leads to the obvious conclusion that we should skip the foods and eat the pesticides directly!

The studies that have shown antioxidants are unhealthy use mega doses. Getting enoug vitamin E is healthy; getting 100 times the needed amount isn't.