We investigate the hypothesis that Ly alpha absorption lines arise in
two populations of halos-minihalos of small circular velocity (V-c les
s than or similar to 55 km s(-1)), in which star formation and metal p
roduction are inhibited by photoionization of the UV background radiat
ion, and large galactic halos (55 less than or similar to V-c less tha
n or similar to 250 km s(-1)) that contain stars and metals. Based on
the model of Ly alpha-absorbing gas confined in both populations of ha
los, we attempt to explain the recent observations of(1) associations
of visible galaxies with Ly alpha lines at low redshifts z less than o
r similar to 1 and (2) metal lines associated with a nonnegligible fra
ction of low H I column density Ly alpha lines at z similar to 3. For
galactic halos, we find that photoionized gas clouds confined in the p
ressure of ambient hot gas can produce Ly alpha absorption for H I col
umn densities as low as 10(14) cm(-2) and that the impact parameter of
a sight line for such absorptions matches well with the observed radi
us of the gaseous envelope of a typical luminous galaxy. Using the Pre
ss-Schechter prescription for the mass function of halos, we also show
that the fraction of Ly alpha lines with associated metal lines can b
e understood in terms of the fraction of Ly alpha absorbers associated
with galactic halos. In particular, the reported fraction of similar
to 0.5-0.75 at z similar to 3 is reproduced when the boundary value of
V-c, to separate minihalos or galactic halos is 40-60 km s(-1), which
is consistent with the theoretical prediction of galaxy formation und
er photoionization. The average metallicity of both Ly alpha forest an
d damped Ly alpha systems at z similar to 3 is explained in terms of t
he model of halo-formation history combined with the age-metallicity r
elationship of Galactic halo stars. Possible methods to test this hypo
thesis and alternative scenarios are also discussed.