Starch starts to thicken before boiling, but it cannot finish its job until the mixture boils. The granules absorb water and swell, thickening the mixture; the full network forms only after it starts bubbling. A dessert taken off the heat too early can taste of raw flour and become watery as it cools. In recipes with egg yolks, a brief boil is also necessary because an enzyme in the yolks breaks down starch and is not inactivated until heated.
A starch granule remains intact in liquid at first. As the mixture heats, the granule begins absorbing water, swells, and eventually opens up. Chains released from the opened granule tangle together and form a network that holds water. This network is what thickens the mixture. Swelling begins before boiling, so the mixture may look thick even before it bubbles; at that stage, however, the network is not fully formed and the thickening is temporary. Dissolving the starch in cold liquid before adding it helps the granules disperse separately from the start, preventing lumps.
In a mixture brought to a boil and held there briefly, the granules open completely. This difference is also noticeable in the taste. An undercooked starch mixture leaves a floury taste in the mouth that sugar or vanilla cannot cover afterward. In most recipes, cooking for another 1 to 2 minutes while stirring after boiling begins helps the flavor and consistency come together. The type of starch also affects the time: rice flour and wheat starch need a little longer than cornstarch.
In recipes that include egg yolks, there is a second, less familiar reason to boil the mixture. Egg yolks contain an enzyme that breaks down starch; if the mixture is not heated enough, this enzyme remains active and breaks down the network over the course of several hours. The result is a custard that thins while it sits in the refrigerator. Heat inactivates the enzyme, so mixtures with egg yolks are brought to a boil and held at a boil briefly. For this reason, yolk-heavy recipes such as pastry cream are never left merely warmed through.
Stopping the stirring during boiling creates another problem. A thickening mixture does not transfer heat upward, so the portion at the bottom burns and its flavor spreads through the whole batch. Keep a whisk or wooden spoon moving across the bottom and corners of the pot. Choose a heavy-bottomed pot. When the mixture starts splattering, lower the heat but do not turn it off completely; the boil should remain visible. A silicone-tipped spatula reaches the corners better than a whisk and leaves no untouched spots at the bottom.
It is also possible to go too far, with its own consequences. If a starch mixture boils for too long, its network starts to break down and the mixture thins again; too much water also evaporates, making the dessert heavy. The right point is when the mixture coats the back of a spoon and a line drawn through it with a finger does not close. Turn off the heat then and transfer the dessert immediately to molds. Prepare the molds beforehand, because a mixture that has started to cool can form a skin on the surface while being poured.