Polished pebble of a fossil fern stem, close-up. The petrification (fossilisation) process begins when a plant falls into water or mud. The minerals in the stem are gradually replaced by minerals from the water or mud, which solidify into stone. In this case the mineral is chalcedony, an amorphous, or non-crystalline, form of silica (SiO2). This process means that dead animals and plants can be preserved for millions of years.