Editing Fossil (section)

== Fossilization processes ==
=== Recrystallization ===
A fossil is said to be ''recrystallized'' when the original skeletal compounds are still present but in a different crystal form, such as from [[aragonite]] to [[calcite]].{{sfn|Prothero|2013|pp=8-9}}
<gallery widths="150" heights="200">
File:Calcite-60801.jpg|[[Calcite]]-recrystallized fossil shell of ''[[Mercenaria permagna]]'' from [[Fort Drum, Florida]]
File:Geodized fossil Busycon snail with yellowish calcite crystals (Anastasia Formation, Upper Pleistocene to lower Holocene, 126 to 8 ka; Indrio Pit, northern side of the town of Fort Pierce, southeastern Florida, USA) (15227151971).jpg|Calcite-recrystallized fossil shell of ''[[Busycon]]'' sp. from Indrio Pit
File:MatmorScleractinian.JPG|Recrystallized [[scleractinia]]n coral (aragonite to calcite) from the [[Jurassic]] of southern [[Israel]]
File:Geodized pentamerid brachiopods (Silurian; Swayzee, Indiana, USA) 1.jpg|Calcite-recrystallized fossil shell of [[pentamerid]] [[brachiopods]] from [[Indiana]]
File:GeopetalCarboniferousNV.jpg|Recrystallized bivalve shell with sparry calcite from [[Bird Spring Formation]]
</gallery>

=== Replacement ===
[[File:Permineralized bryozoan.jpg|thumb|Permineralized [[bryozoan]] from the [[Devonian]] of Wisconsin]]
Replacement occurs when the shell, bone, or other tissue is replaced with another mineral. In some cases mineral replacement of the original shell occurs so gradually and at such fine scales that microstructural features are preserved despite the total loss of original material. Scientists can use such fossils when researching the anatomical structure of ancient species.<ref>{{Cite web|title=Molecular Expressions Microscopy Primer: Specialized Microscopy Techniques - Phase Contrast Photomicrography Gallery - Agatized Dinosaur Bone|url=https://micro.magnet.fsu.edu/primer/techniques/phasegallery/agatizeddinobone.html|access-date=2021-02-12|website=micro.magnet.fsu.edu}}</ref> Several species of saurids have been identified from mineralized dinosaur fossils.<ref name=natgeo>{{Cite web|date=2018-12-04|title=Exclusive: Sparkly, opal-filled fossils reveal new dinosaur species|url=https://www.nationalgeographic.com/science/2018/12/exclusive-sparkly-opal-filled-fossils-reveal-new-dinosaur-species-paleontology/|archive-url=https://web.archive.org/web/20181204142402/https://www.nationalgeographic.com/science/2018/12/exclusive-sparkly-opal-filled-fossils-reveal-new-dinosaur-species-paleontology/|url-status=dead|archive-date=December 4, 2018|access-date=2021-02-12|website=Science|language=en}}</ref><ref>{{Cite web|date=2019-06-03|title=Gem-like fossils reveal stunning new dinosaur species|url=https://www.nationalgeographic.com/science/2019/06/opal-fossils-reveal-new-species-dinosaur-australia-fostoria/|archive-url=https://web.archive.org/web/20190604033106/https://www.nationalgeographic.com/science/2019/06/opal-fossils-reveal-new-species-dinosaur-australia-fostoria/|url-status=dead|archive-date=June 4, 2019|access-date=2021-02-12|website=Science|language=en}}</ref>

==== Permineralization ====
[[Permineralization]] is a process of fossilization that occurs when an organism is buried. The empty spaces within an organism (spaces filled with liquid or gas during life) become filled with mineral-rich [[groundwater]]. Minerals precipitate from the groundwater, occupying the empty spaces. This process can occur in very small spaces, such as within the [[cell wall]] of a [[plant cell]], and can produce very detailed fossils at small scales.<ref>{{cite book |last1=Prothero |first1=Donald R. |title=Bringing fossils to life : an introduction to paleobiology |date=2013 |publisher=Columbia University Press |location=New York |isbn=978-0-231-15893-0 |page=8 |edition=Third}}</ref> For permineralization to occur, the organism must become covered by sediment soon after death, otherwise the remains are destroyed by scavengers or decomposition.{{sfn|Prothero|2013|pp=12-13}} The degree to which the remains are decayed when covered determines the later details of the fossil. Some fossils consist only of skeletal remains or teeth; other fossils contain traces of [[skin]], [[feather]]s or even soft tissues.{{sfn|Prothero|2013|p=16}} This is a form of [[diagenesis]].

====Phosphatization====
Phosphatization refers to a process of fossilization where organic matter is replaced by abundant [[calcium]]-[[phosphate]] [[mineral]]s. The produced fossils tend to be particularly dense and have a dark coloration that ranges from dark orange to black.<ref>{{Cite journal | doi = 10.1016/S0016-6995(97)80056-3 | last1 = Wilby | first1 = P. | last2 = Briggs | first2 = D. | title = Taxonomic trends in the resolution of detail preserved in fossil phosphatized soft tissues | journal = Geobios | volume = 30 | pages = 493–502 | year = 1997| bibcode = 1997Geobi..30..493W }}</ref>

====Pyritization====
This fossil preservation involves the elements [[sulfur]] and [[iron]]. Organisms may become pyritized when they are in marine sediments saturated with iron sulfides. As organic matter decays, it releases sulfide which reacts with dissolved iron in the surrounding waters, forming [[pyrite]]. Pyrite replaces carbonate shell material due to an undersaturation of carbonate in the surrounding waters.  Some plants become pyritized when they are in a clay terrain, but to a lesser extent than in a marine environment. Some pyritized fossils include [[Precambrian]] microfossils, marine [[arthropods]], and plants.<ref>Wacey, D. et al (2013) Nanoscale analysis of pyritized microfossils reveals differential heterotrophic consumption in the ~1.9-Ga Gunflint chert ''PNAS'' 110 (20) 8020-8024 {{doi| 10.1073/pnas.1221965110}}
</ref><ref>Raiswell, R. (1997). A geochemical framework for the application of stable sulfur isotopes to fossil pyritization. ''Journal of the Geological Society'' 154, 343–356.
</ref>
<gallery widths="150" heights="200">
File:Pleuroceras solare, Little Switzerland, Bavaria, Germany.jpg|Pyritized ammonoid ''[[Pleuroceras solare]]'' fossil specimen
File:Paraspirifer bownockeri.fond.jpg|Pyritized specimen of the brachiopod ''[[Paraspirifer bownockeri]]''
File:Triarthrus eatoni (pyritized fossil trilobite with appendages) (Whetstone Gulf Formation, Upper Ordovician; Lewis County, New York State, USA) 3.jpg|Pyritized ''[[Triarthrus eatoni]]'' from [[Whetstone Gulf Formation]]
File:Furcaster paleozoicus fossil brittle star (Kaub Formation, Hunsrück Slate Group, Lower Devonian; Budenbach area, western Germany) 4 (15302668235).jpg|Pyritized ''[[Furcaster paleozoicus]]'' from [[Hunsrück Slate]]
File:Tornoceras uniangulare aldenense fossil goniatite (Alden Pyrite Bed, Ludlowville Formation, Middle Devonian; western New York State, USA) 1 (15359943429).jpg|Pyritized ''[[Tornoceras uniangulare]]'' from [[Ludlowville Formation]]
</gallery>

====Silicification====
In [[silicification]], the precipitation of [[silica]] from saturated water bodies is responsible for the fossil's formation and preservation. The mineral-laden water permeates the pores and cells of some dead organism, where it becomes a [[gel]].  Over time, the gel will [[drying| dehydrate]], forming a [[silica]]-rich crystal structure, which can be expressed in the form of [[quartz]], [[chalcedony]], [[agate]], [[opal]], among others, with the shape of the original remain.<ref>Oehler, John H., & Schopf, J. William (1971). Artificial microfossils: Experimental studies of permineralization of blue-green algae in silica. ''Science''. 174, 1229–1231.</ref><ref>{{Cite journal |last1=Götz |first1=Annette E. |last2=Montenari |first2=Michael |last3=Costin |first3=Gelu |date=2017 |title=Silicification and organic matter preservation in the Anisian Muschelkalk: Implications for the basin dynamics of the central European Muschelkalk Sea |journal=Central European Geology |volume=60 |issue=1 |pages=35–52 |doi=10.1556/24.60.2017.002 |bibcode=2017CEJGl..60...35G |issn=1788-2281 |doi-access=free}}</ref>
<gallery widths="150" heights="200">
File:2017-07-15 22-10-35 (C) DxO.jpg|Chalcedony replaced fossil shells of ''[[Elimia tenera]]'' with inclusions of [[ostracods]]
File:Chalcedonized fossil gastropods (Cretaceous; possibly from Dakhla, southern Morocco) (15230327942).jpg|Chalcedonized [[gastropods]] internal molds
File:Schnecken auflicht small.jpg|Agatized internal molds of gastropods from [[Deccan Traps]]
File:Agate Chalcedony GE9323 540424.jpg|Agatized fossil coral from [[Florida]]
File:Opaleautralie.jpg|Fossil bivalves replaced by [[opal]], from [[Queensland]]
File:Addyman 3.JPG|Rear view of an opalized Addyman [[Plesiosauria|Plesiosaur]] fossil at the [[South Australian Museum]]
</gallery>

=== Casts and molds ===
{{anchor|Cast}} <!--[[Cast (geology)]] and [[Casting (geology)]] redirect here-->
In some cases, the original remains of the organism completely dissolve or are otherwise destroyed. The remaining organism-shaped hole in the rock is called an ''external mold''. If this void is later filled with sediment, the resulting ''cast'' resembles what the organism looked like. An [[endocast]], or ''internal mold'', is the result of sediments filling an organism's interior, such as the inside of a [[bivalve]] or [[snail]] or the hollow of a [[skull]].{{sfn|Prothero|2013|pp=9-10}} Endocasts are sometimes termed {{lang|de|Steinkerns}}, especially when bivalves are preserved this way.<ref>{{cite web |url=https://www.merriam-webster.com/dictionary/steinkern |title=Definition of Steinkern |website=Merriam-Webster |access-date=13 May 2021 |quote=a fossil consisting of a stony mass that entered a hollow natural object (such as a bivalve shell) in the form of mud or sediment, was consolidated, and remained as a cast after dissolution of the mold |archive-date=13 May 2021 |archive-url=https://web.archive.org/web/20210513191727/https://www.merriam-webster.com/dictionary/steinkern |url-status=live }}</ref>
<gallery widths="150" heights="200">
File:Internal mold, Hormotoma, Mollusca, Gastropoda, Murchisonioidea - Iowa, USA.jpg|Internal mold (steinkern) of ''[[Hormotoma]]'' sp. from [[Galena Formation]]
File:Small-gasteropod-bariloche.jpg|Gastropod internal mold (steinkern) from [[Ventana Formation]]
File:Anomalodonta gigantea Waynesville Franklin Co IN.JPG|Shell external mold of ''[[Anomalodonta gigantea]]'' from [[Waynesville Formation]]
File:Glycymeris alpinus 01.jpg|Internal mold (steinkern) of ''[[Glycymeris alpinus]]'', [[Austria]]
File:Aviculopecten subcardiformis01.JPG|External mold of ''[[Aviculopecten subcardiformis]]'' from the [[Logan Formation]], Lower [[Carboniferous]], Ohio
</gallery>

==== Authigenic mineralization ====
This is a special form of cast and mold formation. If the chemistry is right, the organism (or fragment of organism) can act as a nucleus for the precipitation of minerals such as [[siderite]], resulting in a nodule forming around it. If this happens rapidly before significant decay to the organic tissue, very fine three-dimensional morphological detail can be preserved. Nodules from the Carboniferous [[Mazon Creek fossil beds]] of Illinois, US, are among the best documented examples of such mineralization.{{sfn|Prothero|2013|p=579}}

=== Adpression (compression-impression) ===
[[Compression fossil]]s, such as those of fossil ferns, are the result of chemical reduction of the complex organic molecules composing the organism's tissues. In this case, the fossil consists of original material, albeit in a geochemically altered state. This chemical change is an example of [[diagenesis]]. What remains is often a [[carbonaceous film]] known as a phytoleim, in which case the fossil is known as a compression. Often, however, the phytoleim is lost and all that remains is an impression of the organism in the rock—an impression fossil. In many cases, however, compressions and impressions occur together. For instance, when the rock is broken open, the phytoleim will often be attached to one part (compression), whereas the counterpart will just be an impression. For this reason, one term covers the two modes of preservation: ''adpression''.<ref name="ShuteCleal 1986">{{cite journal|last1=Shute |first1=C. H. |last2=Cleal |first2=C. J. |year=1986 |journal=Geological Curator |volume=4 |title=Palaeobotany in museums |issue=9 |pages=553–559|doi=10.55468/GC865 |s2cid=251638416 |doi-access=free }}</ref>

==== Carbonization and coalification ====
Fossils that are carbonized or coalified consist of the organic remains which have been reduced primarily to the chemical element carbon. Carbonized fossils consist of a thin film which forms a silhouette of the original organism, and the original organic remains were typically soft tissues. Coalified fossils consist primarily of coal, and the original organic remains were typically woody in composition.

<gallery widths="150" heights="200">
File:Probable leech from the Waukesha Biota.jpg|Carbonized fossil of a [[cycloneuralia]]n worm that was once misidentified as a [[leech]]<ref>{{Cite journal |last1=Braddy |first1=Simon J. |last2=Gass |first2=Kenneth C. |last3=Tessler |first3=Michael |date=2023-09-04 |title=Not the first leech: An unusual worm from the early Silurian of Wisconsin |url=https://www.cambridge.org/core/journals/journal-of-paleontology/article/not-the-first-leech-an-unusual-worm-from-the-early-silurian-of-wisconsin/2AB9EDAF214C38A8EE93C260BAC9878D |journal=Journal of Paleontology |volume=97 |issue=4 |language=en |pages=799–804 |doi=10.1017/jpa.2023.47 |bibcode=2023JPal...97..799B |s2cid=261535626 |issn=0022-3360}}</ref> from the Silurian [[Waukesha Biota]] of Wisconsin.
File:Lycopod axis.jpg|Partially coalified axis (branch) of a [[lycopod]] from the Devonian of [[Wisconsin]].
</gallery>

=== Soft tissue, cell and molecular preservation ===
Because of their antiquity, an unexpected exception to the alteration of an organism's tissues by chemical reduction of the complex organic molecules during fossilization has been the discovery of soft tissue in dinosaur fossils, including blood vessels, and the isolation of proteins and evidence for DNA fragments.<ref name=Smith>{{cite journal |url= http://www.smithsonianmag.com/science-nature/dinosaur-shocker-115306469/?no-ist |author=Fields H |title=Dinosaur Shocker – Probing a 68-million-year-old T. rex, Mary Schweitzer stumbled upon astonishing signs of life that may radically change our view of the ancient beasts |journal=Smithsonian Magazine |date= May 2006 |archive-url= https://web.archive.org/web/20150118153415/http://www.smithsonianmag.com/science-nature/dinosaur-shocker-115306469/?no-ist |url-status=live |archive-date= 18 January 2015}}</ref><ref name=MHS1>{{cite journal |vauthors=Schweitzer MH, Wittmeyer JL, Horner JR, Toporski JK |title= Soft-tissue vessels and cellular preservation in Tyrannosaurus rex |journal= Science |volume=307 |issue=5717 |pages=1952–5 |date= 25 March 2005 |pmid=15790853 |doi= 10.1126/science.1108397 |bibcode=2005Sci...307.1952S |s2cid= 30456613 }}</ref><ref name=MHS2>{{cite journal |vauthors=Schweitzer MH, Zheng W, Cleland TP, Bern M |title=Molecular analyses of dinosaur osteocytes support the presence of endogenous molecules |journal=Bone |volume=52 |issue=1 |pages=414–23 |date=January 2013 |pmid=23085295 |doi= 10.1016/j.bone.2012.10.010}}</ref><ref name=Emb>{{cite journal | url= https://www.researchgate.net/publication/10586201 |vauthors=Embery G, Milner AC, Waddington RJ, Hall RC, Langley ML, Milan AM |title=Identification of Proteinaceous Material in the Bone of the Dinosaur Iguanodon |journal=Connective Tissue Research |volume=44 |pages=41–6 |date=2003 |pmid=12952172 | doi= 10.1080/03008200390152070 |issue=Suppl 1|s2cid=2249126 }}</ref> In 2014, [[Mary Higby Schweitzer|Mary Schweitzer]] and her colleagues reported the presence of iron particles ([[goethite]]-aFeO(OH)) associated with soft tissues recovered from dinosaur fossils. Based on various experiments that studied the interaction of iron in [[haemoglobin]] with blood vessel tissue they proposed that solution hypoxia coupled with iron [[chelation]] enhances the stability and preservation of soft tissue and provides the basis for an explanation for the unforeseen preservation of fossil soft tissues.<ref name= SchweitzerOthers2014a>{{cite journal |vauthors=Schweitzer MH, Zheng W, Cleland TP, Goodwin MB, Boatman E, Theil E, Marcus MA, Fakra SC | title= A role for iron and oxygen chemistry in preserving soft tissues, cells and molecules from deep time |journal= Proceedings of the Royal Society | volume= 281 |issue= 1774 |date= Nov 2013 |pmid= 24285202 |pmc= 3866414 | doi= 10.1098/rspb.2013.2741 | page=20132741}}</ref> However, a slightly older study based on eight [[taxa]] ranging in time from the [[Devonian]] to the [[Jurassic]] found that reasonably well-preserved fibrils that probably represent [[collagen]] were preserved in all these fossils and that the quality of preservation depended mostly on the arrangement of the collagen fibers, with tight packing favoring good preservation.<ref name=ZL11>{{cite journal| last1=Zylberberg |first1=L. | last2=Laurin|first2=M.|year=2011 |title=Analysis of fossil bone organic matrix by transmission electron microscopy |journal=Comptes Rendus Palevol |volume=11 |issue=5–6 |pages=357–366 | doi = 10.1016/j.crpv.2011.04.004}}</ref> There seemed to be no correlation between geological age and quality of preservation, within that timeframe.

=== Bioimmuration ===
[[File:Catellocaula.jpg|thumb|The star-shaped holes (''Catellocaula vallata'') in this Upper Ordovician bryozoan represent a soft-bodied organism preserved by bioimmuration in the bryozoan skeleton.<ref>{{cite journal | last1 = Palmer | first1 = T. J. | last2 = Wilson | first2 = MA | year = 1988 | title = Parasitism of Ordovician bryozoans and the origin of pseudoborings | journal = Palaeontology | volume = 31 | pages = 939–949 }}</ref>]]

Bioimmuration occurs when a skeletal organism overgrows or otherwise subsumes another organism, preserving the latter, or an impression of it, within the skeleton.<ref name="Taylor, PD. 1990">{{cite journal | last1 = Taylor | first1 = P. D. | year = 1990 | title = Preservation of soft-bodied and other organisms by bioimmuration: A review | journal = Palaeontology | volume = 33 | pages = 1–17 }}</ref> Usually it is a [[Sessility (zoology)|sessile]] skeletal organism, such as a [[bryozoan]] or an [[oyster]], which grows along a [[Substrate (biology)|substrate]], covering other sessile [[sclerobiont]]s. Sometimes the bioimmured organism is soft-bodied and is then preserved in negative relief as a kind of external mold. There are also cases where an organism settles on top of a living skeletal organism that grows upwards, preserving the settler in its skeleton. Bioimmuration is known in the fossil record from the [[Ordovician]]<ref>{{cite journal | last1 = Wilson | first1 = MA | last2 = Palmer | first2 = T. J. | last3 = Taylor | first3 = P. D. | year = 1994 | title = Earliest preservation of soft-bodied fossils by epibiont bioimmuration: Upper Ordovician of Kentucky | journal = Lethaia | volume = 27 | issue = 3| pages = 269–270 | doi=10.1111/j.1502-3931.1994.tb01420.x| bibcode = 1994Letha..27..269W }}</ref> to the Recent.<ref name="Taylor, PD. 1990" />