Hi,
At harvest, peas — usually flavorful red or cream-colored varieties — were eaten green and fresh, in a dish called “reezy peezy” (a name that shows the influence of the 17th-century Italian engineers who advised local rice planters: “risi e bisi” is a spring specialty in the Veneto). In winter, the dried peas (what Northerners call beans) were the standard for hoppin’ John.
Later, when mechanized farming took hold, black-eyed peas (which Mr. Roberts described as “burpy” and starchy) become dominant because they were easy to grow, with high yields. And machine-milled rice, sprayed with vitamins and pesticides, became the standard. “Machining takes the flavor nuances out,” Mr. Roberts said.
(Southern Farmers Vanquish the Clichés; The NY Times)
Is "take out" used figuratively (to remove) in the above?
Being sprayed with vitamins and pesticides would cover up, alter, change the flavor.
In cooking we do use the term "take out" flavor, but it really means to change it, usually by a cooking process.
This is talking about losing the potential for a special flavor because of a process done even before it gets to the cook.
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Yes. The claim is that machine harvesting affects the flavor.