It is the chemical composition of the groundwater that determines what the composition of the fossil will be. A common type of replacement is silification. Silification is the process by which silica minerals such as quartz, chalcedony, and opal fill pores or replace existing minerals, rock, or wood.
Silicification occurs in the earth’s interior through the action of hydrothermal and cold water saturated with silica. As aluminosilicate rock is weathered, a great deal of silica is freed and dissolves. Much of the dissolved silica is carried to the sea, but in places, it moves downward and replaces various rock.
Hydrothermally silicified carbonate rock is frequently associated with ores of mercury, antimony, and other nonferrous metals. At ordinary temperatures, loose rock on the bottom of lakes and seas is subject to silicification, as is solid rock; this occurs most frequently with limestones and dolomites, more rarely with clays and phosphorites.
Accumulations of fine-grained quartz form when carbonate rocks are replaced and aggregates of quartz and chalcedony develop when clayey rock is replaced. The presence of fine-grained quartz and quartz and chalcedony aggregates in ultrabasic rock indicates that deposits of silicate ores of nickel and cobalt may be found. Excellent examples of silification are fossil molluscs and petrified forests.