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A fossil is preserved evidence of past life in a geological context. A body fossil retains evidence of an organism's body, such as a tooth, bone or leaf; a trace fossil, such as a footprint or burrow, records activity. Complete replacement by minerals is not required for something to be a fossil.^[ref]

Fossilization can preserve different kinds of information. Permineralization fills spaces in biological material with minerals, while an impression may retain only external shape. These pathways help explain why the fossil record samples some anatomy characters much better than others, and why a transitional fossil is assessed through a combination of characters rather than overall resemblance.

Permineralization preserves biological material when minerals precipitate in its pores or internal spaces. Filling spaces in wood or bone can support and retain details of the original cellular architecture. This differs from replacing the original substance with a new mineral, although both processes can occur in one fossil.

Experiments placing wood in silica-bearing hot-spring water documented deposition of silica within the spaces of the tissue. Such observations connect a recognizable fossilization mechanism to mineral-bearing water entering a porous biological structure.^[ref] The speed observed in one chemical environment is not a universal clock for permineralization; composition, fluid access and subsequent alteration differ among deposits.

Petrification is preservation of biological material in a stone-like form through mineral deposition and/or replacement. In permineralization, dissolved material precipitates within pores and spaces; replacement instead substitutes mineral material for some original substance. The processes can occur together, so a detailed fossil can retain structural information even when much of its chemistry has changed.

Silicified wood supplies a motivating experiment. Hisatada Akahane and colleagues studied wood in silica-rich hot-spring water, where silica spheres accumulated on split surfaces and cell walls. The observed textures resembled some naturally silicified wood in the fossil record.^[ref]

The result shows that appreciable mineral deposition can proceed rapidly under suitable chemical conditions. It does not assign one universal duration to petrification, prove complete replacement of all organic matter, or determine the age of the surrounding rock.