Question

How does a biological clock stay in time with an organism's environment?

Answer 1

The biological clocks are the internal rythms.

Explanation:

Many organisms maintain these internal rythms or clock.These rythms are cyclical in nature. These rythms are present in the Genes of organism. That's why these rythms detect the start of periodic changes. Thus the organism prepare himself for the change.
In other words, we can also say that the combination of rythmical internal processes and timed events of the environment produces timing of behaviour of organism.