Editing Diagenesis (section)

== Role in anthropology and paleontology ==
[[File:Crinoid stem replaced with marcasite.JPG|thumb|Originally [[calcite|calcitic]] [[crinoid]] stem (in cross-section) diagenetically replaced by [[marcasite]] in a [[siderite]] concretion; [[Lower Carboniferous]].]]
The term diagenesis, literally meaning "across generation",<ref name="O.E.D.">Oxford English Dictionary.</ref> is extensively used in [[geology]]. However, this term has filtered into the field of [[anthropology]], [[archaeology]] and [[paleontology]] to describe the changes and alterations that take place on skeletal (biological) material. Specifically, diagenesis "is the cumulative physical, chemical, and biological environment; these processes will modify an organic object's original chemical and/or structural properties and will govern its ultimate fate, in terms of preservation or destruction".<ref name = "Wilson">{{cite journal|doi=10.1021/ar000203s|pmid=12186569|s2cid=20545137|title=Here Today, Gone Tomorrow? Integrated Experimentation and Geochemical Modeling in Studies of Archaeological Diagenetic Change|year=2002|last1=Wilson|first1=Lyn|last2=Pollard|first2=A. Mark|journal=Accounts of Chemical Research|volume=35|issue=8|pages=644–651}}</ref><ref name = "Zapata">{{cite journal | vauthors = Zapata J, Pérez-Sirvent C, Martínez-Sánchez MJ, Tovar P | title = Diagenesis, not biogenesis: Two late Roman skeletal examples | journal = The Science of the Total Environment | volume = 369 | issue = 1–3 | pages = 357–68 | date = October 2006 | pmid = 16828844 | doi = 10.1016/j.scitotenv.2006.05.021 | bibcode = 2006ScTEn.369..357Z }}</ref> In order to assess the potential impact of diagenesis on archaeological or [[fossil]] [[bone]]s, many factors need to be assessed, beginning with elemental and mineralogical composition of bone and enveloping soil, as well as the local burial environment (geology, [[climatology]], [[groundwater]]).<ref name = "Zapata"/>

The composite nature of bone, comprising one-third organic (mainly [[protein]] [[collagen]]) and two thirds mineral ([[calcium phosphate]] mostly in the form of [[hydroxyapatite]]) renders its diagenesis more complex.<ref name="Nicholson">{{cite journal | vauthors = Nicholson RA | year = 1996 | title = Bone Degradation, Burial Medium and Species Representation: Debunking the Myths, and Experiment-based Approach | journal = [[Journal of Archaeological Science]] | volume = 23 | issue = 4| pages = 513–533 | doi=10.1006/jasc.1996.0049}}</ref> Alteration occurs at all scales from molecular loss and substitution, through crystallite reorganization, porosity, and microstructural changes, and in many cases, to the disintegration of the complete unit.<ref name = "Neilsen-Marsh">{{cite journal | vauthors = Nielsen-Marsh CM | title = Patterns of Diagenesis in Bone I: The Effects of Site Environments | doi = 10.1006/jasc.1999.0537| journal = Journal of Archaeological Science | year = 2000 | volume = 27| issue = 12 | pages = 1139–1150 }}</ref> Three general pathways of the diagenesis of bone have been identified:

# Chemical deterioration of the organic phase.
# Chemical deterioration of the mineral phase.
# (Micro) biological attack of the composite.<ref name = "Collins">{{cite journal | vauthors = Collins MJ, Nielsen, Marsh CM, Hiller J, Smith CI, Roberts JP, Prigodich RV, Wess TJ, Csapo J, Millard AR | display-authors = 6 | year = 2002 | title = The Survival of Organic Matter in Bone: A Review | journal = Archaeometry | volume = 44 | issue = 3| pages = 383–394 | doi=10.1111/1475-4754.t01-1-00071| doi-access = free }}</ref>

They are as follows:
# The [[Dissolution (chemistry)|dissolution]] of collagen depends on time, temperature, and environmental [[pH]].<ref name = "Collins"/> At high temperatures, the rate of [[collagen loss]] will be accelerated, and extreme pH can cause collagen swelling and accelerated [[hydrolysis]].<ref name = "Collins"/> Due to the increase in porosity of bones through collagen loss, the bone becomes susceptible to hydrolytic [[infiltration (hydrology)|infiltration]] where the hydroxyapatite, with its affinity for [[amino acids]], permits charged species of [[endogenous]] and [[exogenous]] origin to take up residence.<ref name = "Hedges"/>
# The hydrolytic activity plays a key role in the mineral phase transformations that expose the collagen to accelerated chemical- and bio-degradation.<ref name = "Collins"/> Chemical changes affect [[crystallinity]].<ref name = "Hedges"/><ref name=":0">{{cite journal | vauthors = de Sousa DV, Eltink E, Oliveira RA, Félix JF, Guimarães LM | title = Diagenetic processes in Quaternary fossil bones from tropical limestone caves | journal = Scientific Reports | volume = 10 | issue = 1 | pages = 21425 | date = December 2020 | pmid = 33293631 | pmc = 7722736 | doi = 10.1038/s41598-020-78482-0 | bibcode = 2020NatSR..1021425D | url = }}</ref> Mechanisms of chemical change, such as the uptake of F<sup>−</sup> or {{chem|CO|3|2-}} may cause [[recrystallization (chemistry)|recrystallization]] where hydroxyapatite is dissolved and re-[[precipitated]] allowing for the incorporation or substitution of exogenous material.<ref name = "Hedges"/><ref name=":0" />
# Once an individual has been [[interred]], microbial attack, the most common mechanism of bone deterioration, occurs rapidly.<ref name = "Collins"/> During this phase, most bone collagen is lost and porosity is increased.<ref name = "Hedges"/> The dissolution of the mineral phase caused by low pH permits access to the collagen by extracellular microbial enzymes thus microbial attack.<ref name = "Collins"/>