These cookies are the size of your palm, with thick, chewy edges, soft centers–and big chocolate chunks. It's surprising just how delicious the whole-wheat version of an old classic is. Unlike many of the recipes in Good to the Grain, this cookie is made with 100 percent whole-wheat flour, which gives it a distinctive, nutty taste. Use a good bittersweet chocolate for these cookies, as the flavor of high-quality chocolate pairs best with whole-wheat flour. —Kim Boyce
Place two racks in the upper and lower thirds of the oven and preheat to 350°F. Line two baking sheets with parchment. Although you can butter the sheets instead, parchment is useful for these cookies because the large chunks of chocolate can stick to the pan.
Sift the dry ingredients into a large bowl, pouring back into the bowl any bits of grain or other ingredients that may remain in the sifter.
Add the butter and the sugars to the bowl of a standing mixer fitted with a paddle attachment. With the mixer on low speed, mix just until the butter and sugars are blended, about 2 minutes. Use a spatula to scrape down the sides of the bowl. Add the eggs one at a time, mixing until each is combined. Mix in the vanilla. Add the flour mixture to the bowl and blend on low speed until the flour is barely combined, about 30 seconds. Scrape down the sides and bottom of the bowl.
Add the chocolate all at once to the batter. Mix on low speed until the chocolate is evenly combined. Use a spatula to scrape down the sides and bottom of the bowl, then scrape the batter out onto a work surface, and use your hands to fully incorporate all the ingredients.
Scoop mounds of dough about 3 tablespoons in size onto the baking sheet, leaving 3 inches between them, or about 6 to a sheet.
Bake the cookies for 16 to 20 minutes, rotating the sheets halfway through, until the cookies are evenly dark brown. Transfer the cookies, still on the parchment, to the counter to cool, and repeat with the remaining dough. These cookies are best eaten warm from the oven or later that same day. They'll keep in an airtight container for up to 3 days.