It's all about the chemistry.

"Don't let that apron deceive you. Bakers are mad scientists," the narrator of the animation says. "When you put the raw cookie dough into the oven, you're setting off a series of chemical reactions."

By playing around with the ingredients in your favorite recipe, you can tweak these reactions and engineer your ideal cookie. For instance, you can make it chewier, fluffy or thinner.

We'll get to that part in a moment, but first, let's take a look at the three major steps of the cookie-baking process:

The spread: As the cookie dough starts to heat up, the butter inside it melts. The ball of dough loses its structural integrity and spreads out. The diameter of the cookie is set by how long the cookie expands.
The rise: At about 212 degrees Fahrenheit, the water in the dough turns into steam. The cookie starts to rise as the vapors push through the dough. Eventually, the baking soda or powder starts to break down into carbon dioxide gas, which raise up the cookie farther. All these gases leave little holes in the maturing cookie, which makes it light and flaky.
Color and flavor injection: Now the magic really starts to happen. Just as the cookie is almost finished baking, two chemical reactions fill it with hundreds of flavors and infuse it with its characteristic brown hue. First off, there's caramelization: As sugars in the dough break down, they transform from clear, odorless crystals into a brown, fragrant liquid that's overflowing with aromas and tastes — think butterscotch, sweet rum and popcorn. The second yummy process, called the Maillard reaction, packs the cookie with even richer tastes. The reaction involves not only the sugars in the dough but the proteins from the egg and flour as well. So it churns out toasty, nutty and even savory flavors. The Maillard reaction also helps to darken the cookie's surface.

Why Does The Cookie Stop Spreading?

Of course, a cookie can't expand forever. So what makes it stop? That's the job of the egg.

Proteins inside the egg are sensitive to temperature. As they heat up, they get all tangled up with each other and form a firm, solid structure. These protein networks are like the backbone or skeleton of the cookie. They give it strength and keep it from deflating in the oven.

Engineering the perfect cookie: You can control the diameter and thickness of your favorite chocolate chip cookies by changing the temperature of the butter and the amount of flour in the dough. Photo: Morgan Walker/NPR

All this baking chemistry provides the building blocks for refining the cookie's architecture, says molecular biologist Liz Roth-Johnson, who runs the Science and Food blog at the University of California, Los Angeles.

"Say I have a cookie recipe, and it's not quite what I want," she says. "You can take these basic concepts and use them to engineer the perfect cookie."

Take, for instance, the cookie's diameter. Its size depends on how quickly the dough spreads out as the butter melts in the oven.

"If you start off with melted butter in the raw dough — instead of cold butter chunks — the dough is immediately wetter and will spread out faster," Roth-Johnson tells The Salt. The result is a flatter, wider cookie.

But the butter's temperature will also affect the cookie's texture. It changes the air pockets left behind as the water in the butter converts into gas, Roth-Johnson explains.

Melted butter creates smaller and more holes. That makes for a chewier cookie.

"On the other hand, if you incorporate chunks of cold butter into the dough, you get larger pockets of air and a fluffier, cakier cookie," she explains.

You can also switch out the baking soda for baking powder for a fluffier treat. "The powder gives the cookie an extra kick of leavening," she says, "because it produces carbon dioxide gas both when it's mixed in the dough and when it heats up."

To make a thicker cookie, Roth-Johnson says, try using more flour.

Finally, you can pump up the cookie's flavor and aromas by spiking the dough with dark sugars. White granulated sugar doesn't participate very well in the Maillard reaction because it contains mostly sucrose. Darker sugars — like molasses, honey and brown sugar — are packed with glucose and fructose, which are happy to churn out rich, complex tastes from the Maillard reaction.

Copyright 2013 NPR.

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