YOUR BRAIN IS A TIME MACHINE
When your brain picks up a signal from its surroundings, such as a whiff of French fries the Supplementary Motor Area (SMA) acts as a timer: Its activity increases the longer a stimulus lasts. As long as the external signal remains, neurons within the SMA fire, retaining information for other areas of the brain.
You can't estimate time without a short-term memory, which lives in the Right Inferior Frontal Cortex, just behind your forehead. For example, to count the length of a baby's cry, this area tracks when the sound starts and ends. Without memory, the wail's beginning would disappear from the brain after only a few seconds.
To be productive, humans must be able to recognize the order of a series. The syllables in a word, the steps of a line dance, and the process of getting dressed in the morning all occur in set sequences. In MRI studies, the brain's Hippocampus lights up, which is a signal of activity, when we're sorting this stuff out.
The cerebellum coordinates your muscles' movements, so it's involved in all sorts of timing tasks especially holding a beat. On research subjects, this area lights up like a disco ball during predictive timing tasks, such as tapping a rhythm: It helps you decided how long you should wait between taps.
If you love chocolate, you will probably wait a while if you know it's coming. For that, you can thank a strangely shaped conglomerate of neuron clusters, or nuclei, known as Basal Ganglia. It heads up a process dubbed delayed discounting, which tells you how long you should wait or not depending on the payoff.