The oxidizing atmosphere of the Earth is not in chemical equilibrium with the crust and mantle. Rather, the abundances of carbon dioxide, water, and the products of photosysnthesis, reduced carbon and free oxygen, are dynamically maintained in the Earth's oceans and atmospheres. Over short periods of time, the cycles of evaporation-precipitation and organic productivity-metabolism are quite vigorous. The amounts of reduced carbon and carbon dioxide in the atmosphere, the ocean, and living organisms, however, are much smaller than those within sedimentary rocks. Thus over geologic time, slow processes, such as removal of carbon dioxide from the atmosphere by weathering reactions and burial of carbonate and reduced carbon in sedimentary rocks, have large net effects.
For example, consider free oxygen in the Earth's atmosphere and oceans. As an early atmosphere in equilibrium with rocks would be too reducing for free oxygen, it is reasonable to expect that atmospheric free oxygen has increased with time. Two necessary conditions need to be satisfied for this build-up to occur: (1) Free oxygen and reduced carbon from photosynthesis need to be separated by burial of the reduced carbon in sediments so that reaction does not occur. (2) Free oxygen needs to be produced in sufficient quantities that it is not used up in weathering ferrous iron in rocks or by reactions associated with hydrothermal circulation at mid-oceanic ridges. (Note that free oxygen also reacts with sulfide in rocks to form sulfate, which may be buried in evaporite deposits. The total moles of sulfate buried in sedimentary rock and sulfate in dissolved in the ocean exceed the moles of oxygen in the atmosphere. Sulfate is an available oxident for many microorganisms.)
Factors affecting the oxidation state of the atmosphere of the early Earth over the time where life and photosynthesis originated have been discussed theoretically. For example, volcanic gases were highly reduced until reduction of water and escape of hydrogen from the atmosphere caused significant ferric iron to accumulate in the mantle [ Kasting et al., 1993]. The impact of asteroids and comets may have added enough metallic iron and reduced carbon to shallow reservoirs to have at least transiently created a very reduced atmosphere with methane and ammonia [ Kasting, 1990, 1993]. In addition, ejecta from impacts was the dominant source of sediments in the deep oceans and probably many land areas. Weathering of ejecta was a major sink which may have kept atmospheric carbon dioxide at low levels and the atmosphere cool [ Koster van Groos, 1988].
The geological record in Proterozoic and Phanerozoic times is
good enough to provide direct constraints.
The buried reduced carbon reservoir is more easily monitored
than the complimentary free oxygen and sulfate
reservoirs. Basically carbon has two stable isotopes 
C and
C. The ratio of the isotopes is conventionally represented by
where 
is a reference ratio.
The global average carbonate carbon isotope ratio
is determined from marine carbonates
that have not been significantly altered since their time of deposition
because the ocean is well mixed. However, reduced carbon isotopic ratios
vary locally depending on the source of the organic matter.
The global average reduce carbon isotope ratio
is obtained with
uncertainty by averaging measurements from many deposits of an age range.
The relative fraction of carbonate and reduced reservoirs is obtained
from the measured carbonate ratios by assuming that the average ratio is
the bulk-earth ratio 
obtained from igneous rocks and meteorites
where M are the relative mass fractions.
Rapid changes in 
of carbonates and organic sediments
indicate the mass of reduced
carbon and hence the amount of atmospheric oxygen increased
rapidly at times during the Proterozoic Era [ DesMarais et al., 1992].
The episodes of rapid increase correlate with times of widespread continental
fragmentation.
For example, the episode at the end of the Proterozoic Era involved the
break-up of Laurentia and the reassembly of several of the
fragments to form Gondwanaland [ Hoffman, 1991].
Restricted marine circulation within new ocean basins caused the water to
become anoxic and allowed thick deposits of organic sediments to accumulate.
That is, global tectonics is considered to have bought about biological
innovations associated with an oxidizing atmosphere, rather than the
other way around [ Veizer, 1992].