My family was big on Sunday morning breakfasts growing up, and pancakes made a frequent appearance. When I was old enough to learn how to make them, my father shared one common piece of advice: wait to flip the pancakes until bubbles start to burst on the top of the batter and hold their shape.
I always thought the most interesting part of this instruction was waiting for the shape to hold. That precise moment indicates the pancake is in the state of changing from a liquid to a gel, and bubbles are the best way to tell.
Pancakes are fairly easy to make. They can include flour, sugar, butter, an egg, salt, milk, and some combination of baking soda and an acid. Sometimes the acid comes in the form of buttermilk, or regular milk and baking powder (baking powder contains baking soda and some acid). The interaction between the baking soda and the acid in the batter creates carbon dioxide. This puts the bubbles in the batter in the first place. This is also why you shouldn't make your pancake batter too far ahead of time if your goal is fluffy pancakes - too much time means too much carbon dioxide will escape, and your pancakes will fall flat.
Once the pancake batter is poured on whatever flat heating mechanism you're using, the waiting begins. Because carbon dioxide is less dense than the batter, the bubbles float to the top of the pancake as it begins to cook. According to Dr. Mike Mangino, Professor Emeritus at The Ohio Sate University, "The structure of the pancake comes from the starch. It has to be heated to a high enough temperature to gelatinize." Heat is important in this equation, too. If the pan isn't hot enough, it won't allow the pancake to turn to gel fast enough, and if it's too hot, the outside will burn before the batter has set.
As the pancakes heat, the starch molecules in the batter swell, break down, and the water in the batter becomes absorbed. Imagine when you cook dry pasta - you start with a small, breakable noodle, add hot water, and then you end up with a larger, more flexible food. When you cool cooked pasta it doesn't revert back to its original state because the water is locked in to the starch molecules in the pasta. The same is true of your pancake batter. Once it's cooked, the pancake will keep its gel-like structure. The new molecular structure inside the pancake is perfect for trapping carbon dioxide bubbles.
If you wait until the bubbles in the pancake start popping and just start to hold their shape, you're allowing just the right amount of gelatinization to happen. If you wait too long to flip the pancakes, the pancake becomes too firm and all the carbon dioxide escapes from the pancake, making it very dense (also, the bottom of your pancake will probably burn). If you don't cook the pancakes long enough, the starch doesn't have time to gelatinize, and you'll end up with unevenly cooked pancakes. The bubbles are a visual cue that you have the perfect pancake structure: the right amount of heat, a batter that's just gel-like enough to trap carbon dioxide, and a fluffy pancake.