Preheat oven to 350°F. Whisk together flour, baking soda, baking powder and salt in a mixing bowl, set aside.
Cut the stick of butter in half or into cubes and place them in a small saucepan. Melt the butter over medium heat, stirring the butter around as it melts. After 5 minutes, the butter will develop an amber color with butter with brown specks. For dark brown butter, you can go as long as 8 minutes. Turn the flame off and let the butter cool down.
While the butter cools, whisk together both sugars, egg, and vanilla extract in a clean mixing bowl. Whisk quickly as you pour in the melted brown butter. The sugar mixture should be wet and smooth.
Add flour mixture to the bowl with the wet mixture and combine with a rubber spatula to form the cookie dough. You'll know the dough is fully combined once there are no visible streaks of flour.
Add the chocolate chops and pecans to the bowl with the cookie dough and use your spatula to combine them with the dough. The chocolate chips and pecans should be evenly disbursed.
Line 2 baking sheets with parchment paper and scoop the dough into 1.5 tablespoon-sized balls. Place 12 scoops on each baking sheet, leaving 2 inches of space between them. Top each ball of dough with a light sprinkle of coarse sea salt if desired.
Bake the cookies for 14 minutes. Remove them from the oven and let cool on the baking sheet for 5 minutes, then transfer them to a metal cooling rack. The cookies will become firm as they cool.