Many chemical proxies of environmental change act like isotopic ratios in the measurement of availability of a species. For example, if decreased rainfall increases the concentration of magnesium or strontium ions in lake water, they will become more common in calcium-carbonate shells that grow in that water. However, warming can also allow increased incorporation of substitute ions in shells. Such nonuniqueness can usually be resolved through use of multiple indicators. Other chemical indicators are allied to biological processes. For example, some species of marine diatoms incorporate stiffer molecules in their cell walls to offset the softening effects of higher temperature, and these molecules are resistant to changes after the diatoms die. The fraction of stiffer molecules in sediments yields an estimate of past temperatures. This analytic technique, known as alkenone paleothermometry, is increasingly used to learn about paleotemperatures in the marine environment.

Biological indicators of environmental conditions typically involve the presence or absence of indicator species or assemblages of species. For example, the existence of an old rooted tree stump shows that the climate was warm and wet enough for trees, and the type of wood indicates how warm and wet the climate was; if that tree stump is in a region where trees do not grow today, the climate change is clear. In ocean and lake sediments, the microfossil species present can indicate the temperature, salinity, and nutrient concentration of the water column when they were deposited. Pollen and macrofossils preserved in sediments are important records of variability in the terrestrial environment (see Plate 3). The presence of specific organic compounds called biomarkers in sediments can reveal what species were present, how abundant they were, and other information.

The complicated nature of paleoclimatic interpretation can be seen when proxies are viewed in a practical example. During ice ages, the oceans were colder, but the water in them was also isotopically heavier because light water was removed and used in growing ice sheets. Shells that grew in water during ice age intervals contain heavier isotopes owing to cooling and changes in the isotopic composition of ocean waters. The change in ocean isotopic composition can be estimated independently from the composition of pore waters in sediments, whereas the change in temperature can be estimated from both the abundance of cold- or warm-loving shells in sediment and the abundance of stiff diatom cell-wall molecules in sediments. Concentrations of non-carbonate ions substituted into calcium carbonate shells provide further information. Because there is redundancy in the available data, reliable results can be obtained.

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