Are these words synonymous?
The editor of the French Journal de physique, de chimie et d'histoire naturelle, Henri Marie Ducrotay de Blainville, invents the word "paleontologie" in 1822, for the study of ancient living organisms through fossils. But “fossil” is an older word. The first use of “fossil” is uncertain (1555-1665): Latin fossilis dug up (to dig), replacing earlier fossile French word. It seems that the restricted sense "geological remains of a plant or animal" is from 1736.
Taphonomy is a recent word, defined in 1940 by Efremov as “the laws of embedding”. It was a part of paleontology: “The passage from the biosphere into the lithosphere occurs as a result of many interlaced geological and biological phenomena. That is why, when this process is analyzed, the geological phenomena must be studied in the same measure as the biological ones.”
The word "diagenesis" was used by Von Gumbel (1868), for a post-sedimentary, non-metamorphic transformation. Diagenesis is the modification of sediments or sedimentary rocks into a different sedimentary rock during and after rock formation (lithification), at low temperatures and pressures.
These words were created because they refer to different events. Nevertheless, they have a common the modification of an object through its geological history. Diagenesis is used for fossils, but fossilisation is not used for sediments. Taphonomy is now used for tools and artefacts. They are now more or less synonymous in most papers.
See also: /http://lampea.cnrs.fr/spip.php?article3149&lang=fr
De Blainville H.M. (1822) Analyse des principaux travaux dans les sciences physiques, publiés dans l’année 1821. Journal de physique, de chimie et d'histoire naturelle, t. XCIV.
Efremov I. A. (1940) Taphonomy: a new branch of paleontology. Pan-American Geology 74, 81-93.
Von Gumbel C. W. (1868) Geognostische Besckreibung des ostbayerischen Grenzgebirges oder des bayerischen und oberpfalzer Waldgebirges. Perthes, Gotha, 968 pp.