Re: how do male birds know when to wake up and sing in the morning?

Most behaviors and physiological processes that occur on a periodic basis
(such as singing in the morning or sleeping and waking) and appear to have
some connection to light/dark cycles are called circadian rhythms. Usually
the connection between light/dark cycles and the behavior/process is fairly
loose but alteration of the light/dark cycle will result in a significant
change in the periodicity of the behavior/process. These cycles are
governed by a set of genes which have a periodic pattern to their
expression. Usually, the presence of light will turn on one gene, which in
turn activates several other genes (this type of regulation is known as
downstream activation). For the gene activity to be periodic one of the
downstream genes must stop the inital, upstream gene from being expressed.
In the case of the genes that govern circadian rhythms in flies (and
probably mammals and birds) the gene that starts the cycle encodes a
transcription factor (a protein that binds to DNA and allows transcription
to begin). This transcription factor can only bind DNA if it is complexed
with its specific partner, forming a dimer (when the two parts are
different proteins they form a heterodimer and when the parts are the same
protein a homodimer is formed). To block transcription of the initial gene
the downstream gene encodes a protein that binds the initial transcription
factor instead of the normal dimerization partner. This stops the initial
transcription factor from binding DNA and the downstream cascade of gene
expression is stopped. As this also means the transcription of the
competing protein is stopped then, once the population of the competing
protein falls below a certain concentration, expression of the initial
transcription factor can begin again. It is the cyclic nature of the
expression of these genes that is the root cause of most periodic
behaviors, which would include singing in the morning. So the male bird
"knows" when to start singing because his genes have told him it's time to
sing.