Diagenesis

Diagenesis

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In geology
Geology
Geology is the science comprising the study of solid Earth, the rocks of which it is composed, and the processes by which it evolves. Geology gives insight into the history of the Earth, as it provides the primary evidence for plate tectonics, the evolutionary history of life, and past climates...

 and oceanography
Oceanography
Oceanography , also called oceanology or marine science, is the branch of Earth science that studies the ocean...

, diagenesis is any chemical, physical, or biological change undergone by a sediment
Sediment
Sediment is naturally occurring material that is broken down by processes of weathering and erosion, and is subsequently transported by the action of fluids such as wind, water, or ice, and/or by the force of gravity acting on the particle itself....

 after its initial deposition and during and after its lithification, exclusive of surface alteration (weathering
Weathering
Weathering is the breaking down of rocks, soils and minerals as well as artificial materials through contact with the Earth's atmosphere, biota and waters...

) and metamorphism
Metamorphism
Metamorphism is the solid-state recrystallization of pre-existing rocks due to changes in physical and chemical conditions, primarily heat, pressure, and the introduction of chemically active fluids. Mineralogical, chemical and crystallographic changes can occur during this process...

. These changes happen at relatively low temperatures and pressures and result in changes to the rock's original mineral
Mineral
A mineral is a naturally occurring solid chemical substance formed through biogeochemical processes, having characteristic chemical composition, highly ordered atomic structure, and specific physical properties. By comparison, a rock is an aggregate of minerals and/or mineraloids and does not...

ogy and texture. There is no sharp boundary between diagenesis and metamorphism, but the latter occurs at higher temperature
Temperature
Temperature is a physical property of matter that quantitatively expresses the common notions of hot and cold. Objects of low temperature are cold, while various degrees of higher temperatures are referred to as warm or hot...

 and pressure
Pressure
Pressure is the force per unit area applied in a direction perpendicular to the surface of an object. Gauge pressure is the pressure relative to the local atmospheric or ambient pressure.- Definition :...

 than the former.

After deposition, sediments are compacted as they are buried beneath successive layers of sediment and cemented by minerals that precipitate from solution
Solution
In chemistry, a solution is a homogeneous mixture composed of only one phase. In such a mixture, a solute is dissolved in another substance, known as a solvent. The solvent does the dissolving.- Types of solutions :...

. Grains of sediment, rock
Rock (geology)
In geology, rock or stone is a naturally occurring solid aggregate of minerals and/or mineraloids.The Earth's outer solid layer, the lithosphere, is made of rock. In general rocks are of three types, namely, igneous, sedimentary, and metamorphic...

 fragments and fossil
Fossil
Fossils are the preserved remains or traces of animals , plants, and other organisms from the remote past...

s can be replaced by other minerals during diagenesis. Porosity
Porosity
Porosity or void fraction is a measure of the void spaces in a material, and is a fraction of the volume of voids over the total volume, between 0–1, or as a percentage between 0–100%...

 usually decreases during diagenesis, except in rare cases such as dissolution
Solvation
Solvation, also sometimes called dissolution, is the process of attraction and association of molecules of a solvent with molecules or ions of a solute...

 of minerals and dolomitization
Dolomitization
Dolomitization is a process by which dolomite is formed when magnesium ions replace calcium ions in calcite. It is common for this alteration into dolomite to take place due to evaporation of water in the sabkha area. Dolomitization involves substantial amount of recrystallization...

.

The study of diagenesis in rocks is used to understand the tectonic history they have undergone; the nature and type of fluids that have circulated through them. From a commercial standpoint, such studies aid in assessing the likelihood of finding various economically viable mineral and hydrocarbon
Hydrocarbon
In organic chemistry, a hydrocarbon is an organic compound consisting entirely of hydrogen and carbon. Hydrocarbons from which one hydrogen atom has been removed are functional groups, called hydrocarbyls....

 deposits.

Lithification


Lithification (from the Greek
Greek language
Greek is an independent branch of the Indo-European family of languages. Native to the southern Balkans, it has the longest documented history of any Indo-European language, spanning 34 centuries of written records. Its writing system has been the Greek alphabet for the majority of its history;...

 word lithos meaning 'rock' and the Latin
Latin
Latin is an Italic language originally spoken in Latium and Ancient Rome. It, along with most European languages, is a descendant of the ancient Proto-Indo-European language. Although it is considered a dead language, a number of scholars and members of the Christian clergy speak it fluently, and...

-derived suffix -ific) is the process in which sediment
Sediment
Sediment is naturally occurring material that is broken down by processes of weathering and erosion, and is subsequently transported by the action of fluids such as wind, water, or ice, and/or by the force of gravity acting on the particle itself....

s compact under pressure
Pressure
Pressure is the force per unit area applied in a direction perpendicular to the surface of an object. Gauge pressure is the pressure relative to the local atmospheric or ambient pressure.- Definition :...

, expel connate fluids
Connate fluids
The term connate fluids in the context of geology, and of sedimentology in particular, refers to the liquids that were trapped in the pores of sedimentary rocks as they were deposited. These liquids are largely composed of water, but also contain many mineral components as ions in solution.As...

, and gradually become solid rock. Essentially, lithification is a process of porosity
Porosity
Porosity or void fraction is a measure of the void spaces in a material, and is a fraction of the volume of voids over the total volume, between 0–1, or as a percentage between 0–100%...

 destruction through compaction
Compaction (geology)
Compaction refers to the process by which a sediment progressively loses its porosity due to the effects of loading. This forms part of the process of lithification. When a layer of sediment is originally deposited, it contains an open framework of particles with the pore space being usually...

 and cementation
Cementation (geology)
Cementation involves ions carried in groundwater chemically precipitating to form new crystalline material within sediment pores; this is how "sediment" becomes "rock". The new pore-filling minerals form "bridges" between original sediment grains, thereby binding them together. So sand becomes...

. Lithification includes all the processes which convert unconsolidated sediments into sedimentary rock
Sedimentary rock
Sedimentary rock are types of rock that are formed by the deposition of material at the Earth's surface and within bodies of water. Sedimentation is the collective name for processes that cause mineral and/or organic particles to settle and accumulate or minerals to precipitate from a solution....

s. Petrification, though often used as a synonym, is more specifically used to describe the replacement of organic
Organic compound
An organic compound is any member of a large class of gaseous, liquid, or solid chemical compounds whose molecules contain carbon. For historical reasons discussed below, a few types of carbon-containing compounds such as carbides, carbonates, simple oxides of carbon, and cyanides, as well as the...

 material by silica in the formation of fossil
Fossil
Fossils are the preserved remains or traces of animals , plants, and other organisms from the remote past...

s. In geology consolidation is a synonym for lithification.

The role of diagenesis in anthropology and paleontology


The term diagenesis is extensively used in geology
Geology
Geology is the science comprising the study of solid Earth, the rocks of which it is composed, and the processes by which it evolves. Geology gives insight into the history of the Earth, as it provides the primary evidence for plate tectonics, the evolutionary history of life, and past climates...

. However, this term has filtered into the field of anthropology
Anthropology
Anthropology is the study of humanity. It has origins in the humanities, the natural sciences, and the social sciences. The term "anthropology" is from the Greek anthrōpos , "man", understood to mean mankind or humanity, and -logia , "discourse" or "study", and was first used in 1501 by German...

 and paleontology
Paleontology
Paleontology "old, ancient", ὄν, ὀντ- "being, creature", and λόγος "speech, thought") is the study of prehistoric life. It includes the study of fossils to determine organisms' evolution and interactions with each other and their environments...

 to describe the changes and alterations that take place on skeletal (biological) material in a burial context. 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”. In order to assess the potential impact of diagenesis on archaeological or fossil
Fossil
Fossils are the preserved remains or traces of animals , plants, and other organisms from the remote past...

 bone
Bone
Bones are rigid organs that constitute part of the endoskeleton of vertebrates. They support, and protect the various organs of the body, produce red and white blood cells and store minerals. Bone tissue is a type of dense connective tissue...

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
Climatology
Climatology is the study of climate, scientifically defined as weather conditions averaged over a period of time, and is a branch of the atmospheric sciences...

, groundwater
Groundwater
Groundwater is water located beneath the ground surface in soil pore spaces and in the fractures of rock formations. A unit of rock or an unconsolidated deposit is called an aquifer when it can yield a usable quantity of water. The depth at which soil pore spaces or fractures and voids in rock...

).

The composite nature of bone, comprising one third organic (mainly protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

 collagen
Collagen
Collagen is a group of naturally occurring proteins found in animals, especially in the flesh and connective tissues of mammals. It is the main component of connective tissue, and is the most abundant protein in mammals, making up about 25% to 35% of the whole-body protein content...

) and two thirds mineral (calcium phosphate
Calcium phosphate
Calcium phosphate is the name given to a family of minerals containing calcium ions together with orthophosphates , metaphosphates or pyrophosphates and occasionally hydrogen or hydroxide ions ....

 mostly in the form of hydroxyapatite) renders its diagenesis more complex. Alteration occurs at all scales from molecular loss and substitution, through crystallite reorganization, porosity and microstructural changes, and in many cases, to disintegration of the complete unit. Three general pathways of the diagenesis of bone have been identified:
  1. chemical deterioration of the organic phase.
  2. chemical deterioration of the mineral phase.
  3. (micro) biological attack of the composite.


They are as follows:
  1. The dissolution of collagen depends on time, temperature and environmental pH. At high temperatures, the rate of collagen loss will be accelerated and extreme pH
    PH
    In chemistry, pH is a measure of the acidity or basicity of an aqueous solution. Pure water is said to be neutral, with a pH close to 7.0 at . Solutions with a pH less than 7 are said to be acidic and solutions with a pH greater than 7 are basic or alkaline...

     can cause collagen swelling and accelerated hydrolysis
    Hydrolysis
    Hydrolysis is a chemical reaction during which molecules of water are split into hydrogen cations and hydroxide anions in the process of a chemical mechanism. It is the type of reaction that is used to break down certain polymers, especially those made by condensation polymerization...

    . Due to the increase in porosity of bones through collagen loss, the bone becomes susceptible to hydrolytic infiltration where the hydroxyapatite, with its affinity for amino acids, permits charged species of endogenous and exogenous origin to take up residence.
  2. The hydrolytic activity plays a key role in the mineral phase transformations that exposes the collagen to accelerated chemical- and bio-degradation. Chemical changes affect crystallinity. Mechanisms of chemical change, such as the uptake of F- or CO3- may cause recrystallization where hydroxyapatite is dissolved and re-precipitated allowing for the incorporation of substitution of exogenous material.
  3. Once an individual has been interred, microbial attack, the most common mechanism of bone deterioration, occurs rapidly. During this phase, most bone collagen is lost and porosity is increased. The dissolution of the mineral phase caused by low pH permits access to the collagen by extracellular microbial enzymes thus microbial attack.

The role of diagenesis in hydrocarbon generation


When animal or plant matter is buried during sedimentation, the constituent organic molecule
Molecule
A molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...

s (lipid
Lipid
Lipids constitute a broad group of naturally occurring molecules that include fats, waxes, sterols, fat-soluble vitamins , monoglycerides, diglycerides, triglycerides, phospholipids, and others...

s, protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

s, carbohydrate
Carbohydrate
A carbohydrate is an organic compound with the empirical formula ; that is, consists only of carbon, hydrogen, and oxygen, with a hydrogen:oxygen atom ratio of 2:1 . However, there are exceptions to this. One common example would be deoxyribose, a component of DNA, which has the empirical...

s and lignin
Lignin
Lignin or lignen is a complex chemical compound most commonly derived from wood, and an integral part of the secondary cell walls of plants and some algae. The term was introduced in 1819 by de Candolle and is derived from the Latin word lignum, meaning wood...

-humic compounds) break down due to the increase in temperature
Temperature
Temperature is a physical property of matter that quantitatively expresses the common notions of hot and cold. Objects of low temperature are cold, while various degrees of higher temperatures are referred to as warm or hot...

 and pressure
Pressure
Pressure is the force per unit area applied in a direction perpendicular to the surface of an object. Gauge pressure is the pressure relative to the local atmospheric or ambient pressure.- Definition :...

. This transformation occurs in the first few hundred meters of burial and results in the creation of two primary products: kerogen
Kerogen
Kerogen is a mixture of organic chemical compounds that make up a portion of the organic matter in sedimentary rocks. It is insoluble in normal organic solvents because of the huge molecular weight of its component compounds. The soluble portion is known as bitumen. When heated to the right...

s and bitumens.

It is generally accepted that hydrocarbons are formed by the thermal alteration of these kerogens (the biogenic theory). In this way, given certain conditions (which are largely temperature-dependent) kerogens will break down to form hydrocarbons through a chemical process known as cracking
Cracking (chemistry)
In petroleum geology and chemistry, cracking is the process whereby complex organic molecules such as kerogens or heavy hydrocarbons are broken down into simpler molecules such as light hydrocarbons, by the breaking of carbon-carbon bonds in the precursors. The rate of cracking and the end products...

, or catagenesis
Catagenesis (geology)
Catagenesis is a term used in petroleum geology to describe the cracking process which results in the conversion of organic kerogens into hydrocarbons.-Theoretical reaction:...

.

A kinetic model based on experimental data can capture most of the essential transformation in diagenesis, and a mathematical model in a compacting porous medium to model the dissolution-precipitation mechanism. These models have been intensively studied and applied in real geological applications.