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Echoes of Life Through Time:
Human’s Evolving Views of Fossils and the
Patterns They Reveal

The Nature of Fossils: A Historical Perspective
Fossils are an integral part of our culture. We encounter them in museums, schools, television, and movies. We know so much about fossils; it is difficult to believe our ancestors were so unsure about their nature.

Throughout recorded history there have been both naturalistic and super-naturalistic explanations for fossils. The Greeks believed mammoth fossils were the bones of human giants. Xenophanes (ca. 570-500 BCE), a Greek philosopher, hypothesized that there existed a cycle in which moisture eroded land into mud followed by another beginning. Xenophanes cited marine fossils found on land as evidence to support his ideas (Kirk, Raven, and Schofield 1983, p. 177). Aristotle (384-322 BCE) speculated that ancient fish swam into cracks in the rock and got stuck. Popular conceptions included the ideas that crinoids with star-shaped centers were formed by falling stars and that ammonites were decapitated snakes. The word fossil is Latin for “dug up” and was coined during the Renaissance. People wondered whether fossils are pranks of nature, works of the Devil, or supernatural representations of ideal life forms. Many believed that fossils formed during Noah’s flood. Leonardo da Vinci (1452-1519) recognized that fossil shells in the Apennine Mountains of Italy were the remains of ancient sea life and argued they could not have formed during Noah’s flood. He recognized that different specimens had been formed at different times (Prothero, 2004, pp. 5 & 6).

Many people in Western cultures were taught to believe in a literal interpretation of the Bible. It was natural to believe every species in existence was made in a single creation event. This idea also extended to rocks, believed to have been formed as we see them during the first days of creation. Thus in the absence of two key concepts, extinction and sedimentary rock formation, a more accurate understanding of fossils was not possible. Robert Hooke (1635-1703) and Niels Stensen (1638-1686) would put science on a more productive path to understanding the origins of fossils and the formation of sedimentary rocks.

Niels Stensen (Latinized to Nicholaus Steno) was an anatomist and naturalist. A chance encounter between determined fishermen and a great white shark off the Tuscan coast in 1666 sparked a chain of events that would help change our views of fossils and of Earth’s geologic past (Cutler 2003, pp. 5-8). Steno dissected the head of this shark and realized that fossil tongue stones previously believed to be petrified snake or dragon tongues were actually fossil shark teeth (Prothero 1998, p. 3). One problem still existed: how do fossils become embedded in solid rock? Steno recognized that fossils represent organisms that became buried in sediment, which later turned into rock. The realization that sediments turn into rock was counter to the view that all rocks on Earth formed in a single creation event. Once Steno recognized that the fossils he was contemplating (sharks teeth and sea shells) were formed in the sediments of oceans he was able to work out the basic rules that would eventually be the foundations of a new branch of geology called stratigraphy. Steno formalized the laws of superposition, original horizontality, and original continuity in his 1669 publication titled De solido intra solidum naturaliter contento dissertationis prodromus (Prothero 2004, p. 6).

The law of superposition is the foundation of Steno’s work on stratigraphy. The principle of superposition states that in an undisturbed sequence of strata each layer is older than the one above and younger than the one below. The law of original horizontality states that sedimentary strata are deposited in horizontal sheets. If these layers are not horizontal, subsequent movements have occurred. The law of lateral continuity states that strata extend laterally in all directions and pinch out at the edge of their deposition. Modern forms of these laws include lava flows. Steno’s description of how fossils become embedded in water born sediments that later harden into rock also hints at the principle of inclusion. Later, James Hutton, William Smith, Georges Cuvier, and Alexandre Brongniart would add to these basic rules making stratigraphy an effective way to study the distribution, deposition, relative age, and fossil life of rock strata.

Robert Hooke, an English scientist and inventor, made some of the first accurate illustrations of fossils. He suggested that species may have a fixed “life span” and might be used to order rocks chronologically (Prothero, 2004, p. 7). Hooke argued that there was evidence for three stages in fossil formation. The first stage could be seen in the organic bones, shells and plant matter found in mud, peat and moss. Plant and animal parts that were modified in layers of lignites and brown coal represented the second stage. The third stage could be witnessed by examining plant parts and shells that had turned to coal embedded within layers of coal. The fossils had changed to rock just as the peat had changed to lignite and the lignite into coal (Winchester, 2001, p. 38). Not long after Hooke’s discovery of plant cells he was asked at a meeting of the Royal Society to examine petrified wood under his microscope. Hooke discovered the fossil wood had the same structure as living wood. At the time petrified wood was thought to form as stone in rock layers and then into clay that eventually turned to wood. This idea was seemingly supported by a clay deposit in Italy that contained fossil wood in various stages of petrifaction. After examining the fossil wood Hooke came to the conclusion that the wood had soaked in mineral solutions that filled the pores and turned to stone (Cutler, 2003, p. 131). Thus, rock layers did not generate petrified wood that transformed into wood; rather, once living wood buried in sediments turned to stone as minerals replaced the once living material of the tree.

Hooke, like Steno, championed the idea that fossils represented ancient plant and animal life. Hooke and Steno helped to jump-start the science of stratigraphy, making it possible to answer the question, “what came first?” Steno recognized that his principles could be used to reconstruct the geologic past (Cutler, 2003, p. 114). The ideas of Hooke and Steno would not be widely accepted for another century; although, Carolus Linnaeus (1707-1778) treated fossil organisms as if they were living organisms in his 1735 publication Systema Naturae, which was an attempt to classify life on Earth (Prothero, 2004, p. 7).

Deep Time & Extinction
Steno and Hooke argued for a naturalistic interpretation of fossils. Perplexing questions remained, such as the age of rock layers and the proper interpretation of the unfamiliar organisms that appear in the fossil record.

James Hutton (1726-1797), often considered the father of geology, developed the theory of uniformitarianism, which states that geologic events are caused by natural processes, many of which are operating in our own time. Put another way, the natural laws that we know about in the present have been constant over the geologic past. Hutton argued that many of Earth’s surface features were formed through a slow cycle of land erosion, seabed deposition, and uplift. Hutton’s theory of uniformitarianism and the principles of stratigraphy would be fully developed and made popular by another Scottish geologist Charles Lyell (1797-1875) with his classic three volume work, first published from 1830 to 1833, entitled Principles of Geology: being an attempt to explain the former changes of the Earth’s surface by reference to causes now in operation (Levin, 1999, p. 9).

Hutton formulated three principles used in the science of stratigraphy that must be considered when seeking relative dates for rock layers. The principle of inclusion states that any inclusion is older than the rock that contains it. An inclusion may be a fossil or rock fragment contained in another rock. Care must be taken with this law as crystals and concretions may be deposited by groundwater within already formed rock. The principle of cross-cutting states that any feature that cuts across a rock or sediment must be younger than the rock or sediment through which it cuts. Examples include fractures, faults, and igneous intrusions. Igneous intrusions are sometimes referred to as a separate principle, the principle of intrusive relationships. Unconformities represent gaps in geologic time when layers were not deposited or when erosion removed layers. This principle includes three types of unconformities. A disconformity is an unconformity between parallel layers. An angular unconformity exists when younger more parallel strata overlie tilted strata. A nonconformity is formed when sedimentary layers are deposited on igneous or metamorphic rock.

The concept of geologic time or deep time was a logical consequence of Hutton’s theory. In 1788 John Playfair (1748-1819), a Scottish geologist and mathematician, came to see Hutton’s Unconformity in Inchbonny. The angular unconformity at Siccar Point in Eastern Scotland consists of many vertical tilted layers of grey shale overlaid by many layers of horizontal red sandstone. Playfair later commented that, "the mind seemed to grow giddy by looking so far into the abyss of time." McPhee (1998) points out that Hutton removed humans from a specious place in time just as Copernicus had removed humans from a specious position in the universe (p. 74).

Today, extinction, the permanent disappearance of a species, is an all too familiar concept. In recent history we have witnessed the extinction of many species due to human activities of hunting and habitat destruction. As little as 200 years ago many people thought extinction was impossible. Theology fueled opposition to the idea of extinction. People believed that the biosphere constituted a perfect creation. The concept of extinction was contrary to several deeply held Christian beliefs. First, was the concept of divine providence. An all-powerful and all-loving God would never allow any creature to become extinct. This is illustrated in the story of Noah’s ark. God would not suffer any species to become extinct and thus ordered Noah to populate the ark with two of each creature. Second, was the idea of the plenitude or fullness of nature. God’s creation was perfect and an organism’s extinction would render it incomplete. Finally, was the concept of a “Great Chain of Being.” This chain linked animals to humans to angels to God. Extinction would take away links in the chain leading to its destruction (Prothero, 2004, p. 8).

Thomas Jefferson (1743-1826) initially resisted the idea of the extinction of species. In his “Notes on the State of Virginia,” published in 1789, he denied that the Mammoth is extinct on the grounds that the economy of nature would not allow any break in nature’s “great work” to be broken (Peterson 1975, p. 86). Jefferson and many others argued that the strange organisms found in the fossil record must still exist in unexplored parts of the world. A large fossil claw prompted Jefferson to ask Lewis and Clarke to look for a giant prairie lion on their expedition. This claw was later found to be a part of the extinct giant ground sloth. By the end of his life, however, Jefferson had apparently become convinced of the fact of extinction, for in an 1823 letter to John Adams, he clearly accepts the idea that “certain races of animals go extinct” (Adams 1983, p. 411).

The great French anatomist Georges Cuvier (1769-1832) established extinction as a fact in a historic lecture given to the French Institute in 1796. Cuvier talked about mammoths, woolly rhinos, giant cave bears, and the sea reptile mosasaur in his lecture. In his paleontological studies Cuvier came to recognize what we now call mass extinctions at the end of the Permian and Cretaceous periods. Cuvier developed the Theory of Catastrophism. Cuvier believed supernatural cataclysms occurred before Noah's flood (antideluvial) and were regional not global (Prothero, 2004, p. 82).

Stephen J. Gould (1941-2002), American paleontologist and writer, believed that extinction is needed to tell time and is the motor of evolution. If all the species stayed the same there would be no way to tell geologic time. Furthermore, if species didn’t disappear there would be no room for new ones to evolve. For example, during the reign of the dinosaurs, mammals never got bigger than an ordinary house cat. If the dinosaurs had not died out there is no reason to believe that mammals would have increased in size and, in that case, we would not be here (Infinite Voyage, 1988).

It is ironic, that in the last two hundred years scientist have gone from believing that extinction was impossible to establishing that 99.9% of all plant and animal species that have ever existed on Earth are now extinct.

The Fossil Record & A History of Life on Earth
As already noted, Cuvier established the revolutionary idea of extinction. It is said that Cuvier could identify the remains of an organism from just a few bones. Several people were key to ordering fossils chronologically and thus building a history of life on Earth.

The Industrial Revolution helped to enlarge our understanding of fossils and the history of life on Earth. Large machines used for digging coal, making railroad beds and canals removed great volumes of earth exposing many rock layers and their fossils. William Smith (1769-1839), a British engineer, was in charge of building the Somerset Canal. Smith realized that fossils exhibited a regular pattern in different strata. Thus Smith could recognize a particular rock layer from the combination of fossils present. This observation allowed Smith to predict the locations of different rock layers making him more efficient and successful when surveying for canal construction. Smith was able to map out the succession of fossils found in different rock formations. His geologic maps showed that life forms appear and disappear through time (Winchester, 2002, pp. 117-119).

At about the same time, Cuvier and Alexandre Brongniart (1770-1847), a French naturalist and geologist, were mapping the Paris Basin. In reconstructing the changing sea levels of the Atlantic Ocean, Brongnairt and Cuvier showed that fossils had been laid down during alternating fresh and salt-water conditions thus establishing the fact that there existed a succession of fossils in different formations representing different environments. Thus, Smith, Cuvier, and Brongniart added another basic principle to the growing science of stratigraphy. This is the principle of faunal succession which states that fossil organisms succeed one another in a definite, irreversible, and determinable order (Prothero, 2004, p. 8). Embedded within the principle of faunal succession is the concept of an index fossil. Good index fossils possess several characteristics that make them excellent tools for determining the age of the rock layer in which they are found. Index fossils are abundant and have a wide geographic distribution, that is, they are found in many locations. Index fossils are easy to identify even when the specimens are incomplete. Finally, index fossils existed for only a short geologic time. Thus, index fossils help to pinpoint the age of a geologic formation with precision. Index fossils are often used to correlate the age of related formations.

Cuvier noticed that the more ancient a fossil the less it resembled present day organisms. In ordering fossils chronologically Cuvier, like Smith, was constructing a history of life on Earth using geologic strata. Thus began the science of biostratigraphy. Smith did not know why each unit of rock had a particular fauna. Cuvier was opposed to early theories of evolution and viewed faunal succession as evidence for a cycle of creation and extinction known as the Theory of Catastrophism. Cuvier's contributions to our understanding of geologic time, extinction, and fossil vertebrates were essential in developing the concepts of deep time and evolution. And yet, as Michael Benton (2001), an English paleontologist, points out Cuvier himself was unable to ". . . make two vital connections: between extinction and evolution, and between geological change and time (p. 99)." Later, the work of Charles Darwin (1809-1882), the great English naturalist and geologist, would make it possible to see that rock units of different ages contain different assemblages of fossils because life has evolved continuously.

One of the chief legacies of these 19th century efforts is the geological time scale. The present day scale or column divides geologic time into intervals separated from each other by changes in rock type and abrupt changes in fossil groups. Gould believed the geologic time table to be one of the greatest contributions to human understanding. According to Gould:

The establishment of a time scale, and the working out of a consistent and worldwide sequence of changes in fossils through the stratigraphic record, represents the major triumph of the developing science of geology during the first half of the nineteenth century....By 1850, geology had developed a coherent global chronology based on life's history. This discovery and construction of history itself must rank as the greatest contribution ever made--indeed, I would argue, ever makeable--by geology to human understanding (Gould 2001, p.15).

The science of stratigraphy allowed geologists to work out the spatial and temporal relationships of rock layers making possible a relative time scale. The biogeographical distribution of species through time and space revealed by this work would be a critical influence on Charles Darwin’s Theory of Evolution by Natural Selection published in 1859 (Darwin, 1859/2009, pp. 223-225). In the 20th century scientists would develop and apply radiometric dating which places absolute dates on the relative time scale. Whereas relative dating only specifies the chronological sequence of events absolute time is measured in units such as years. Radiometric dating confirmed and reinforced the consistency between deep time, relative time and Darwinism (Miller, 1999, pp. 68 & 69).

The science of stratigraphy changed our view of the world. Where before the world was viewed as static, now it is seen as dynamic and changing. Fossil deposits of different ages reveal that different organisms have lived at different times. The rock in which these fossils are embedded is geologic truth, speaking to the fact that environments change. The fossil record affords only pieces of the past. Science has learned to use these pieces to work out the evolution of life on Earth using a system of independent empirical verification. Together, impressions of the past explored by this most important human epistemology work out to be a way for nature to remember itself.

Mass Extinction
Cuvier not only established extinction as fact, he was also the first to recognize that mass extinctions have occurred at the end of what we now call the Paleozoic and Mesozoic eras (Stanley, 1987, p. 2). Extinction is the total disappearance of a species and is represented by the contraction of the geographical range of the species and the reduction of the population to the number zero. This contraction and reduction is governed by limiting factors. Limiting factors include the physical environment, competition, predation, and chance factors. Climate is one of the most important environmental factors (Stanley, 1987, p. 10).

In 1973, Leigh Van Valen (1935-2010), an American evolutionary biologist, published a study that compared the duration of certain groups of organisms against the number that survived. He found that species do not become better at avoiding extinction as they persist through time; old species have the same probability of becoming extinct as young ones. He inferred from this data that organisms can never be perfectly adapted as environments are not static. Thus, natural selection enables organisms to maintain not improve adaptation. Van Valen called this the Red Queen Hypothesis. The Red Queen in Lewis Carrol’s Alice Through the Looking Glass told Alice that she must keep running to stay in the same place. Thus, species must constantly evolve to avoid extinction (Milner, 1990, p. 387; Prothero, 2004, p. 86).

In 1982 David Raup (1933-2015) and John Sepkoski (1948-1999), American paleontologists, plotted the number of extinctions in marine invertebrate and vertebrate families during the last 560 million years. They discovered a steady background rate of 2 to 4 family extinctions per million years. However, five intervals stood out in which 10 to 20 families became extinct per million years. They also identified 10 mass extinctions of the second order over the last 600 million years (Stanley, 1987, p. 13).

What is the nature of these five extinctions and how do they differ from background extinctions? In 1986 David Jablonski (1953-), an American geophysical scientist, published a study comparing the extinction of Cretaceous aged molluscan species with different larval developments. In one type of development larvae feed while floating on the ocean for weeks, thus attaining a wide geographic distribution. In the second type of development larvae do not feed and float for hours, days or not at all. During background extinctions the mollusks with a wider geographic range were more extinction resistant. However, both groups suffered equally during the terminal Cretaceous extinction (Stanley, 1987, p. 17). Jablonski’s study suggests that during mass extinctions organisms with extinction-resistance qualities, such as wide geographic distributions, are just as likely to become extinct as those without these properties. Thus, mass extinctions seem to be fundamentally different from normal background extinction.

Looking for the causes of mass extinction has fired the imagination of the public and scientists from various backgrounds. Steven Stanley (1941-), an American paleontologist and evolutionary biologist, in his book Extinction identifies five themes in mass extinction (1987, pp. 17 & 18).

  • Extinction occurs on land and sea.

  • On the land, animals suffer extinctions repeatedly while plants seem to be more extinction resistant.

  • There is preferential disappearance of tropical life forms in mass extinction.

  • Some groups experience extinction repeatedly (trilobites &

The themes identified by Stanley may imply a common agent or agents of destruction.

Theories of Extinction & Seeking Patterns
A multitude of factors that are associated with or might contribute to mass extinction have been put forward. A brief overview of proposed agents of biological catastrophe is in order.

Glaciation occurs as a result of global cooling. Much of the Earth’s water can be locked up in ice sheets that expand over oceans and land. Evidence for glaciation comes from deposits containing glacial sediments and the disappearance of warmer climate species from the fossil record. Global cooling and the drop in sea levels obviously disrupt many ecological niches. Ocean salinity and oxygen content may also change during periods of glaciation. A quick cooling event may also result in an overturn of ocean water. Cold, nutrient rich, but oxygen poor water may be brought to the surface. This water may be toxic to benthic life in shallow warmer waters. It is clear that glaciation is associated with climate change.

Extraterrestrial Impacts
In 1980 Luis Alvarez (1911-1988), an American physicist, hypothesized that a large extra terrestrial impact had caused the great Cretaceous extinction. A large asteroid could trigger global fires, earthquakes, tidal waves, atmospheric dust, acid rain, and global warming. Atmospheric dust could cause a nuclear winter in which the Sun’s light is blocked out to such an extent that plants have problems photosynthesizing. Evidence for the Late Cretaceous impact comes from the presence of a rare element called Iridium found in a layer at the K-T boundary (Cretaceous-Tertiary boundary). Iridium is rare in Earth’s crust, but can be common in asteroids and volcanoes fed by the Earth’s mantle. Shock quartz or quartz grains that are formed from high pressures are also found in these layers as well as a form of carbon formed under intense heat and pressure. Finally, in 1981 a large crater 65 million years old and of the correct size to fit Alvarez’s theory was found in the Yucatan Peninsula of Mexico. The name of this crater is Chicxulub. Some have suggested that asteroids could cause a large distribution of the element nickel which can prevent plants from photosynthesizing.

Marine Regression
Sea level changes known as marine regressions can cause major disruptions in ecological niches. Sea level changes can be caused by the movement of the Earth’s crustal plates. As two plates come together seaways can slowly drain away. Sea levels drop and rise as glacial periods come and go. Sea level changes can also affect the salinity and gas content of the water.

Volcanic Activity
Volcanic activity can fill the air with large volumes of dust and gases causing climate change. Carbon dioxide and sulfur dioxide emissions from volcanic activity act as greenhouse gases. However, sulfur dioxide quicky reacts with moisture in the air forming sulfate aerosols that absorb and scatter sunlight, which can cause global cooling (Wignall, 2001, p. 2). As with asteroids, volcanic activity can produce iridium. In the geologic past there have been extremely large accumulations of intrusive or extrusive igneous rocks within a short geologic time, a few million years or less. These large eruptions of mostly basaltic (mafic) magmas are known as Large Igneous Provinces (LIP) and are unrelated to normal sea-floor spreading and subduction. LIP's occur as continental flood basalts, oceanic flood basalts, ocean ocean plateaus, and volcanic rifted margins (Ernst, 2014).

Methane Clathrates
Methane clathrate is a solid similar to ice in which large amounts of methane are trapped within the crystaline structure of water. Deposits of methane clathrates are found in sedimentary structures at shallow depths under cold or deep oceans and in continental polar permafrost regions. During global warming episodes the release of methane from these repositories could significantly contribute to the warming trend (Wignall, 2001, p. 14).

Cosmic Radiation
Cosmic radiation could increase to dangerous levels from a nearby supernova. This cosmic radiation could cause mutation and increased cancer rates among organisms.

The idea that mass extinction occurs at regular intervals is heavily debated. There have been many attempts to explain the proposed periodicity of mass extinctions, these include: comet showers, the existence of a planet X, the existence of a companion star to our Sun called Nemesis, sudden overturns of the Earth’s mantle causing pulses of volcanism, Earth’s oscillation through the Milky Way galactic plane, meteor impacts, basalt floods, climatic cooling, marine regressions and species-species interactions (Interactions between species may occasionally lead to an instability that cascades through an ecosystem). Some believe that these periods between extinctions just represent the time it takes for extinction sensitive species to evolve (Stanley, 1987, p. 215). Some of these ideas, such as planet X, a companion to our Sun, and sudden overturns of the Earth’s mantle have been discredited (Prothero, 2004, pp. 93 & 94). However, as we look at the “Big Five” we will see evidence pointing to some of these proposed causes.


The Five Major Mass Extinctions
Stanley defines mass extinction as “the extinction of many taxa on a global scale during a brief interval of geologic time” (Stanley 1987, p. 238). Five intervals of extinction stand out as the most devastating. Scientists look for common patterns within these events in the hope of developing a general theory of extinction. We will give a brief overview of the effects and possible causes for the “Big Five.”


The marine ecosystems experienced extinction on a global scale towards the end of the Ordovician period. The Ordovician extinction may be second only to the mass extinction that would end the Paleozoic Era. Heavy extinction occurred in the reef communities. Graptolites, bryozoans, brachiopods, nautiloids, and trilobites were especially hard hit. Nearly 25 percent of all animal families were wiped out (Selden & Nudds, 2004, p.36). Over fifty percent of trilobite families went extinct (Nudds & Selden, 2008, p. 69). There is evidence of glaciation and with this a lowering of sea level, and the expansion of cold water adapted species to lower latitudes as the Ordovician extinction event unfolded (Stanley, 1987, pp 71-75). An ocean turn over may have accompanied the cooling event bringing deep ocean water to the surface, which would have been toxic to the sensitive shallow marine benthic community. The Ordovician event took place over a span of 2 million years (Prothero, 2004, p. 90).

The mass extinction that occurred in the Late Devonian affected mainly the marine environment with terrestrial plants escaping the crises. It is estimated that up to 75% of marine species and 50% of marine genera were lost (Prothero, 2004, p. 90). Brachiopods, trilobites, conodonts, ammonoid, corals, and stromatoporoids were hit hard. Reef building communities were decimated. Tabulate corals and stromatoporoids would never again be major reef builders after the Devonian crises. The rest of the Paleozoic would see very little reef building. Reef building would recover in the Mesozoic with the appearance of modern corals (Stanley, 1987, pp. 78-79). The Devonian crisis seems to be correlated with cooling. Coral reefs were in decline as cold water glass sponges expanded. Shallow, warm water marine species declined. Freshwater fish that were adapted to seasonal environments survived, while warm water marine fish experienced heavy extinction. As these shallow warm water species declined the stromatolites had a small resurgence in reef building. There is evidence of glaciation and lower sea levels. Both the Ordovician and Devonian cooling events may be tied to the movement of Gondwanaland over the South Pole (Stanley, 1987, pp. 86-89). The cooling event may also explain Late Devonian carbon and oxygen isotope anomalies. A severe cooling would trigger a massive overturn within the ocean. This overturn would bring deep ocean water to the surface. The deep ocean water is nutrient rich, but cold and oxygen poor. The Devonian crises lasted for 4 million years (Prothero, 2004, p. 90).

The Permian period ended with the largest recorded mass extinction that hit both aquatic and terrestrial environments. It is estimated that 75 to 90 percent of all living species became extinct over a period of 10 million years (Stanley, 1987, pp. 96-97). Sixty percent of marine families became extinct (Palmer, 1999, p. 90). In the marine realm crinoids, brachiopods, bryozoans, and ammonoids were hit hard. Fusulinids, trilobites, graptolites, blastoids, rugose corals, tabulate corals, and eurypterids met with extinction. Among the fish Acanthodians and Placoderms became extinct. Rhipidistians, lobe-finned fish (Osteichthyes) that are the ancestors of land vertebrates also went extinct. Extinction in the marine realm marked a change from a Paleozoic dominated fauna composed of crinoid, coral, bryozoan, and brachiopods to a modern fauna dominated by bivalves, gastropods, and echinoids (Prothero, 2004, p. 86).

Two-thirds of the amphibian and reptile families met with extinction. The larger terrestrial vertebrates did not fare as well. Thirty-three percent of amphibian families went extinct at the end of the Permian (Palmer, 1999, p. 90). Among the amphibians some labyrinthodonts would survive into the Triassic. Lepospondyls (Lepospondyli) amphibians went extinct by the end of the Permian. All but one group of anapsid type reptiles died out. The fossil evidence for diapsid reptiles is sparse during the mid Permian, although many new groups make their first appearance during the late Permian. The most primitive groups of diapsids went extinct at the end of the Permian (Dixon, 1988, p. 84). The first synapsids were the pelycosaurs, which made up 70% of the vertebrate terrestrial fauna in the early Permian. During the middle Permian another group of synapsids, the therapsid, would evolve and displace the pelycosaurs. Pelycosaurs died out in the middle Permian. Therapsids would loose 21 families at the end of the Permian (Palmer, 1999, p. 90).

For the first time insects suffered a mass extinction. Many of the primitive orders of insects went extinct during the Permian event. Among the fixed-winged insects (Paleoptera) the following orders went extinct: Palaeodictyoptera, Megasecoptera, Diaphanopterodea, and Protodonata. Among the folded-winded insects with incomplete metamorphosis (exopterygota Neoptera) the following orders went extinct: Protorthoptera, Caloneurodea, Protelytroptera, and Miomoptera) (Carpenter & Burnham, 1985, p. 302). Insect fossils found after the Permian belong mostly to modern insect groups.

Globally, plants experienced their greatest losses during the Permian extinction. Only 9 out of 22 known families survived into the Triassic (Cleal & Thomas, 2009, p. 209). As noted earlier, the swamp forests of the Carboniferous contracted during the Permian. As the clubmosses waned, ferns and primitive conifers expanded to take their place. The change from Paleophytic to Mesophytic flora occurred over a period of 25 million years. Tropical plant ecosystems suffered major disruptions with some extinction at the end of the Permian period. Cordaites went extinct as well as the seed fern Glossopteris. The dominant conifer families (Walchiaceae, Ullmanniaceae, and Majonicaceae) of the time went extinct. For a geologically short time, woody coniferous forests were replaced by herbaceous species of clubmosses and quillworts (4-5 million years). In the Triassic, woody coniferous forests of a different type would be reestablished (Kenrick & Davis, 2004, p. 154).

Uranium-lead zircon geochronology has been used to date ash layers, associated with the Siberian Traps, at the Permian-Triassic boundary in Southern China. The results establish a date of 251 Ma (Wignall, 2001, p. 8). The extinction interval is thought to be very short on the order of 165,000 years or less (Prothero, 2004, p. 87). What caused the "mother of all extinctions?"

An increase in dune deposits, evaporite salts, and a lack of coal forming swamps may indicate arid conditions in some terrestrial environments. There is evidence of a marine regression, which would reduce habitat in shallow marine environments. A rapid warming trend occurred at the end of the Permian. A shift in oxygen isotopes may record this event. An increase in O-16 over O-18 in the calcite skeletons of marine organisms indicates global temperatures may have increased by as much as 6 degrees Celsius. An increase in C-12 found in terrestrial and marine sections could be an indication of increased volcanic activity and massive death in the marine and terrestrial realms (Benton, 2003, p. 38). Like the Ordovician and Devonian events a reduction in the formation of marine limestone and reef building occurred after the Permian extinction. Layers containing abundant pyrite above the limestone layers indicate a low oxygen environment.

Onset of flood basalts making up the Siberian Traps occur at the Permian-Triassic boundary. This LIP formed in northern Asia and may have been the source of carbon dioxide that started a global warming event. As the climate warmed methane may have been released from methane clathrates accelerating the warming event. The release of these gasses into the atmosphere is called the "big belch" and may have increased temperatures and lowered oxygen levels (Cleal & Thomas, 2009, p. 209). Climate change may have also altered oceanic circulation in such a way as to bring stagnant deep water rich in carbon dioxide and hydrogen sulfide to the surface. The Permian crises would usher in a new era represented by different flora and fauna evolved from the small percentage of survivors who were, at first, cosmopolitan in their distribution.

The Triassic ended with mass extinctions in marine and terrestrial environments. The terrestrial extinctions took place millions of years before the marine crises. The Triassic crisis is actually several extinctions that took place over a 17 million year time span (Prothero, 2004, p. 91). Labyrinthodont amphibians and dicynodonts (a group of mammal-like reptiles) went extinct. Land plants were hit hard, especially the gymnosperms with 23 of their 48 known families going extinct during the last third of the Triassic (Cleal & Thomas, 2009, p. 211). In the marine realm placodonts, nothosaurs, and conodonts went extinct. Ammonoids, brachiopods, gastropods, and bivalves took heavy losses. It is estimated that 20% of marine families went extinct during the Triassic crises. Reef growth was greatly reduced as well as marine limestone and dolomite deposition.

What caused the end-Triassic extinction (ETE) 201 million years ago? There is some evidence for sea level changes and some cooling. An abundance of black shales and geochemical anomalies indicate massive oceanic changes. Some believe the rifting of the North Atlantic may have released large volumes of volcanic gasses contributing to global climate change (Prothero, 2004, p. 91). The Central Atlantic Magmatic Province (CAMP) is a LIP that formed from the rifting of Pangea and spans the Triassic-Jurassic boundary. CAMP is associated with the breakup of the supercontinent Pangea and the formation of the Atlantic ocean basin. At an estimated 11 million square kilometers CAMP covers the largest area of any known LIP. It is also one of the most voluminous at an estimated 2 to 3 million cubic kilometers.

Remnants of CAMP are found on four continents including North America, South America, Europe, and Africa. Using samples from these remnants Blackburn et al. (2013) demonstrated that zircon uranium-lead geochronology provides a temporal link between the ETE and CAMP. The release of magma and associated atmospheric flux occurred in four pulses over 600,000 years. The earliest known eruptions took place at the same time as the extinction events. Further pulses of CAMP occurred as life was recovering from the extinction event. Although a temporal link between early pulses of CAMP and ETE has been established, we still do not understand the details of how these massive eruptions induced a global biological crises (Blackburn, 2013, p. 943). As a group, dinosaurs benefited from this extinction event, as they would undergo a great adaptive radiation during the Jurassic period.

At the end of the Cretaceous, 65 million years ago, 85% of all species would go extinct, making this event second only to the Permian mass extinction (Hooper Museum, 1996). Sixteen percent of marine families went extinct. Ammonoids, belemnoids, rudist bivalves, inoceramid bivalves and many brachiopod groups went extinct. Most of the large marine reptiles (ichthyosaurs, plesiosaurs, and mosasaurs) were lost. Some families of sharks and teleost fishes went extinct. Eighteen percent of terrestrial vertebrate families would go extinct (Siegel, 2000). Dinosaurs, pterosaurs, many lineages of early birds, and some mammals went extinct. In fact most terrestrial animals more than 1 meter in length would go extinct (Nudds & Selden, 2008 p. 169). One third of higher level plant taxa went extinct and for a short time ferns became dominant over the angiosperms and conifers in North America (Stanley, 1987, p. 157). Some of these organisms mentioned went extinct before the K-T (Cretaceous-Tertiary) boundary, while others were on the decline. Some groups disappeared catastrophically right at the KT boundary. Some interesting ecological patterns can be observed.

The hardest hit marine organisms were free-swimming or surface forms (plankton, ammonites and belemintes). On the sea floor filter feeders (corals, bryozoans, and crinoids) were hit hard while organisms that fed on detritus were little affected. Open water fish fared well. Mollusks with wide geographic ranges had a higher survival rate than those with a small geographic distribution. Tropical species were affected more than those who were cold tolerant. In the terrestrial realm, as we have already mentioned, being large was a disadvantage. The only large land animals to survive were crocodilians (Benton, 2005, pp. 248-251). Amphibians seem not to have been affected by the extinction event. At the family level, 70 to 75% of taxa surived the event (Benton, 2005, p. 255). What contributed to this mass extinction?

Scientists at the University of California at Berkeley including Luis and Walter Alvarez, Frank Asaro, and Helen Michel discovered an iridium anomaly in a fine-grained clay layer in several K-T (Cretaceous/Tertiary) boundary sites around the world (now the Cretacous/Paleogene boundary or K-Pg). These K-T boundaries are found in both marine and terrestrial deposits and show the same succession, an ejecta layer followed by the clay enriched iridium layer (Benton, 2005, p. 250). The group recognized that iridium is abundant in stony meteorites and proposed that the fallout from a meteorite on the order of 10 kilometers could explain the anomaly and possibly the extinction event. Subsequently, a crater was found beneath the Gulf of Mexico off the Yucatan Peninsula during exploration for oil. The Chicxulub crater is of the right size and age. Volcanic activity may also act as a source of iridium. The Deccan Traps in India represent a large terrestrial flood basalt. Ironically, the Deccan Traps would have been positioned on the opposite side of the Earth at the time of the Chicxulub impact.

There is also evidence for climatic changes as well as floral and fauna changes leading up to these events. Many organisms were already on the decline during the Late Cretaceous. Planktonic foraminiferans experienced major losses before the end of the Cretaceous. Calcareous nonoplankton were also on the decline. Ammonoids, inoceramid bivalves, and the reef building rudists experienced attrition. Multiple lines of evidence, including preferential survival of cold water tolerant organisms and isotopic ratios, suggest the climate was cooling. There is also evidence to support a decline in abundance and diversity of dinosaurs (Stanley, 1987, pp. 133-171).

However, the iridium anomaly, which in some areas is also associated with shocked quartz grains (quartz grains that bear criss-crossing lines produced by meteorite impacts), glassy spherules close to the impact site (produced from melted material under the crater and then ejected into the air), carbon particles associated with massive fires, the spike in ferns (associated with ash falls), and the Chicxulub crater support that a meteor impact may have caused a final pulse of extinction that occurred on a global scale. Whether this mass extinction was the result of multiple factors or primarily one, its effects on the evolution of life had great consequences.

The largest mass extinction at the end of the Permian period provided reptiles with the opportunity to become the dominant vertebrate life forms on Earth. Roughly, one hundred and eighty-six million years later the second largest mass extinction would take away Mesozoic reptilian dominance and usher in the Cenozoic, an age for mammals. Mass extinctions of the past have severely reduced biodiversity, but ironically have also provided opportunities for survivors to evolve and diversify.

Pulses of extinctions can be seen within each mass extinction event. The timing and duration of these pulses appears to be different for each of the “Big Five.” This may indicate that there is not a common cause for mass extinction (Prothero, 2004, p. 93). It is clear that climatic cooling, marine regressions, large igneous provinces, and at least one of the many meteor impacts recorded in the geologic record can be implicated in mass extinction events. The study of extinction is in its infancy, but has major implications for our own time.

A Sixth Mass Extinction?
The study of mass extinctions and their causes is important because it allows humans to look to the past to anticipate future possibilities. Programs designed to monitor extraterrestrial objects that may impact Earth, such as NASA’s Near Earth Object Program are steps to possibly diverting such objects (NASA, 2013). USGS monitors volcanic activity around the world (USGS, 2008). At this point the monitoring of volcanic activity can save lives in local areas. The monitoring of both local and global threats is in its infancy; however, these efforts are informed by knowledge of past events deciphered from the geologic record.

Many scientists argue that we are in the midst of a sixth mass extinction as revealed by contemporary extinction rates that are on the order of 100 to 10,000 times greater than background rates calculated from the fossil record (Holsinger, 2011, p. 8; Center for Biological Diversity, 2013). The sixth mass extinction event may have started in the Pleistocene and continued in the Holocene with the loss of mammals known as megafauna roughly 50,000 to 10,000 years ago. Both climate change and the proliferation of humans are thought to be factors in the extinction of megafauna.

Today, the Holocene extinction event continues with humans playing an ever larger role. The global human population is now at 7 billion (Worldometers, 2013). Humans need resources and space for their growing populations. The quest for these needed resources and space play a role in this possible sixth mass extinction. Habitat destruction, invasive species, pollution, burning fossil fuels, and commercial hunting place incredible stress on ecosystems worldwide.

Alterations to the environment in North America since 1600 illustrate how humans can affect entire ecosystems. In the lower 48 states since the year 1600 over 90% of old growth forests have been cut down, over 50% of wetlands have been drained, and over 98% of grasslands have been plowed under (EPA: Wetlands, 2013; EPA-Smart Growth, 2013; Global Deforestation, 2010; Pieper, R.D. (2005). Similar patterns of habitat destruction can be found worldwide (Holsinger, 2011, p. 5).

As humans have spread over the globe a massive biotic exchange has taken place. Humans have directly and indirectly introduced non-native species to many ecosystems. Non-indigenous species that have an adverse affect on the ecosystem to which they are introduced are referred to as invasive species. The introduction of invasive plants, animals and disease has had devastating effects on both human and non-human populations across the globe (Crosby, 2003; National Invasive Species Information Center, 2013; Natural History Museum 2013).

Human use of fossil fuels is having a global impact on the atmosphere and climate. The burning of fossil fuels has released large amounts of carbon dioxide thereby increasing the amount of greenhouse gases in the atmosphere. The rise in greenhouse gasses can be correlated with an increase in Earth’s surface temperature (EPA-Causes of Climate Change, 2013). Coal burning power plants and the combustion of gasoline in cars contribute to the formation of acid rain. Our massive use of fossil fuels leads to other kinds of pollution, such as oil spills.

In fact, the industrial revolution has created human societies that consume Earth’s resources at increasingly alarming rates. Waste products resulting from this massive consumption often pollute the environment. Humans create government agencies in an attempt to manage the production and disposal of waste products that pollute the environment (EPA, Home 2013).

Oceans cover 71% of the Earth’s surface and are not immune to the effects of human activity. Many marine ecologists rank commercial overfishing as the greatest threat to our oceans (DUJS, 2012). Humans even try to keep track of the threats posed to Earth’s biological diversity and attempt to organize solutions with governments worldwide (IUCN, 2009). In this fact, there is hope.

A naturalistic interpretation of rock and fossil genesis allowed us to decode principles that govern the formation of the geologic record. Applying these principles through a system of independent empirical verification has afforded us a glimpse of the 3.8 billion year history of life on Earth, a history that includes our own origins.

Modern humans (Homo sapiens) range from 160,000 years ago to the present (Benton, 2005, p. 385). The Cro-Magnon people of Europe (40,000-30,000 years ago) are associated with Upper Paleolithic tools, carved art objects, and the cave paintings of France. Archaic H. sapiens increasingly used bone, ivory, and wood to make more sophisticated tools. Benton (2005, p 387) recognizes major benchmarks in human evolution:

  • Bipedalism (10-5 Ma)

  • Enlarged Brain (3-2 Ma)

  • Stone Tools (2.6 Ma)

  • Wide Geographic Distribution (2-1.5 Ma)

  • Use of Fire (1.5 Ma)

  • Art (35,000 years ago)

  • Agriculture (10,000 years ago)

We can include two more benchmarks, the awareness of the evolutionary history of life on Earth as revealed by the geologic record (200 years ago) and the awareness of our own species role in a mass extinction event (50 years ago).

Scientists and philosophers debate whether or not evolution is progressive. Is there a trend in efficiency, complexity, and intelligence? When examined in detail the fossil record of each group of organisms, even humans, exhibits an evolutionary pattern that is very bushy. The branch that ends with humans is only one of thousands of mammalian evolutionary lines; however, it is special in that it represents a way for the universe to know itself. Modern humans are the first organisms to comprehend and appreciate the history of life on Earth.


The word fossil is derived from the Latin fossilis, which means "dug up". Initially, the term fossil applied to any strange or interesting material found within rock whether or not it was of organic origin (Prothero, 2004, p. 5). Most modern definitions include the concept that fossils are evidence of ancient organisms, which have become a part of the Earth’s crust. The word ancient is arbitrary. To some ancient applies only to extinct organisms while to others it implies time limits. Grimaldi and Engel (2005) point out that many would like to restrict the term fossil to species that have become naturally extinct. They argue that having this knowledge is problematic. Grimaldi and Engel suggest the following practical definition, "...a fossil is the remains or workings of any species, living or extinct, that have been naturally preserved for several thousand years or more (p. 62). A more common time limit defines fossils as being prehistoric thus; fossils preserve remains or activities of ancient organisms older than 10,000 years (Garcia & Miller, 1998, p. 14; Schopf, 1975, p. 27).

The majority of fossils are found in sedimentary rocks. Organisms become trapped within sediment layers due to the action of water, wind or gravity. Fossils can sometimes be found in metamorphic rocks formed from fossiliferous sedimentary rocks altered by heat and pressure. Fossils can even be found in igneous rock created from lahars or pyroclastic flows that entomb trees or other organisms.

Two major types of fossils are recognized. Body fossils reveal the structure of an organism, while trace fossils reveal the activities of organisms. There are many reasons to study fossils. The fossil record indicates that different life forms have existed at different times revealing the evolution of life on Earth. Fossils and rock types serve as clues to determining ancient environments. Finally, fossils are the most practical way of telling time in geology (Prothero, 2004, p. vii). How do fossils form and how are they classified into different preservation types?

Taphonomy or How Fossils Form

A Fossil represents evidence of past life that is found in the Earth’s crust. Taphonomy ("laws of burial") is the term used to describe the process that results in the formation of a fossil. Taphonomy or the transition of an organism or part of an organism from the biosphere to the lithosphere is accomplished in basically two steps. The process of burial or entombment is referred to as biostratinomy. After burial or entombment, diagenesis begins; the conversion of sediments or other deposits to rock. Biostratinomic and diagenetic processes destroy most traces of organisms. The extent of preservation depends upon what happens during biostratinomy and diagensis. The biostratinomy and diagensis associated with a fossil can reveal much about the environment in which the organism lived. In other words, how fossils form can often provide clues to past environments.


Fossilization often occurs as a result of rapid burial, usually by water-borne sediment, followed by chemical alteration. Rapid burial and specific chemical environments help to reduce decomposition from bacteria and fungi. Decomposition, erosion, deposition and rock formation are processes that often destroy soft tissue, so it is the hard parts of organisms such as shells, bones and teeth, which are most often preserved. Occasionally conditions exist that allow for preservation of organisms in environments that rarely produce fossils. Exceptional conditions may also help to preserve soft tissue or impression of soft body parts.

Fossil deposits with soft-bodied organisms well preserved or with terrestrial animals, such as dinosaurs in the Morrison formation are termed Lagerstätten. Lagerstätten is a German word used in mining that denotes a particularly rich seam and has been adopted by paleontologist to signify these rare fossil deposits because they give us a window into past environments seldom preserved in the fossil record (Selden & Nudds, 2004, p. 7). Two types of fossil lagerstätten are recognized. Deposits that contain vast numbers of fossils represent Concentration Lagerstätten. The preservation may not be exceptional, but the great numbers can be very informative. Conservation Lagerstätten contain fossils with soft body preservation, impressions of soft tissue or fossils of well-articulated skeletons without soft tissue preservation. Conservation Lagerstätten are particularly important because they provide knowledge of soft-bodied organisms, allowing paleontologists to reconstruct paleoecosystems, and give insights into the morphology and phylogentic relationships of organisms (Nudds & Selden, 2008, pp. 8-9).

Preservation Types

The science of taphonomy explores the environmental conditions that promote fossilization. Both body and trace fossils can form under a variety of circumstances representing multiple modes of preservation. Compare several books on fossils off any library or bookstore shelf and you will soon realize there is no standard for categorizing types of fossil preservation. Click on the pictures below to explore modes of preservation that one is likely to find in both scientific papers and popular books.

Molds & Casts

Organisms buried in sediment may decay or dissolve away leaving a cavity or mold. If the space is subsequently filled with sediment, an external cast can be made. Molds and casts are three dimensional and preserve the surface contours of the organism. A mold preserves a negative imprint of the surface, while a cast preserves the external form of the organism (Taylor, Taylor & Krings, 2009, p. 22).

Sometimes a shell can be filled with minerals and then dissolve away. The internal cast that remains is termed a steinkern, which in German means "stone cast" (Pothero, 1998, p. 7). Steinkerns are most often represented by the internal molds of mollusks. The pith cast of Calamites is the most common plant steinkern. As a Calamites tree matured the center of the stem (pith) became hollow, developing into a tube-shaped air cavity. The pith cast preserves an impression of the pith cavities outside surface, which represents the inside vascular and cortex tissue (Taylor, Taylor & Kring, 2009, p. 23).

Most molds and casts do not contain the actual remains of an organism. Shells, bone, and wood often form as molds or casts. Some trace fossils (ichnofossils), such as tracks and burrows can form as casts or molds. Tracks and burrows can provide clues to the behavior and biomechanics of an organism while it was alive.

Concretions often encapsulate a fossil mold and cast. The siderite (iron carbonate) nodules of Mazon Creek, Illinois preserve Carboniferous aged animals and plants as molds and casts (Nudds & Selden, 2008, p. 120). It should be noted that some authors classify the fossils in Mazon Creek nodules as impressions (Janssen, 1979, p. 24; Rich, Rich, Fenton & Fenton, 1996 pp. 4-6). Limestone concretions in Ft. Collins, Colorado contain the molds and casts of Cretaceous aged mollusks. As kids, my friends and I collected multiple Inoceramus clams from a 3-foot diameter concretion. These fossils are found as molds and casts with the cast filling the mold.

It is important to realize that many fossil specimens represent more than one mode of preservation. For example, the cast in a Mazon Creek nodule also represents fossilization by authigenic mineralization, a type of replacement. Subtle pH changes created by the decaying body of the buried organism caused available iron carbonate to precipitate. Thus, the organism became its own nucleation site for the formation of a siderite nodule. Some of the shells found in the limestone nodules of Ft. Collins retain altered shell material, which represents recrystallization. Aragonite (calcium carbonate) in the shell recrystallized to calcite, a more stable form of calcium carbonate.

We usually think of casts and molds as exhibiting obvious three-dimensional character. The thin leaves of plants or the wings of insects can produce shallow casts and molds. Shallow casts and molds may take the form of imprints, or impressions, preserving the three dimensional character of an organism. Impressions of wings are a common insect fossil. Even some of the relief, like pleating on the wings can be preserved. This is important because the veins on a wing can be used to key an insect to the family level (Grimaldi, D. & Engel, M.S., 2005, pp 42-45).

Imprints, impressions and many trace fossils, such as, burrows, insect galleries, and tracks, may represent types of molds or casts if they retain their three-dimensional character. Molds and casts are important because they can faithfully replicate the external form of an organism in a three-dimensional fashion, giving the paleontologist information about surface anatomy.

Imprints & Impressions

Imprints are really shallow external molds or voids left by animal or plant tissue. When the siltstone pictured above was split into two slabs the organic matter adhered to one side. The top picture represents an imprint in which bones and scales left a shallow external mold. The lower picture is a compression because it possess organic residue left from scales, original bone, and bone reinforced with calcite. Compressions retain original or chemically altered organic material while imprints do not. Fish and leaves are often found as imprints and compressions.

Fossil leaves discovered by splitting bedding planes may reveal two fossils from a single specimen. The side with more organic material is called a compression. The thin carbon layer on a plant compression is known as a phytoleim (Cleal & Thomas, 2009, p. 4). The phytoleim may retain original cuticle, which resists decay. The cuticle is the protective noncellular waxy covering of the epidermis. When removed and studied the cuticle may reveal the arrangement of epidermal cells and stomata, which can sometimes aid in species identification (Tidwell, 1998, p. 27). The side with little or no organic material is called an impression (Tidwell, 1998, p. 27; Taylor, Taylor & Krings, 2009, p. 21; Schopf, 1975, p. 37). Sometimes parts of a specimen are preserved as a compression while other parts are an impression. In this case the term adpression may be used. Adpressions form when the matrix of a fossil is soft and the phytoleim has fallen off in some places (Cleal & Thomas, 2009, p. 4).

Paleobotanists refer to the compression as the part (positive side) and the impression as the counterpart (negative side). The impression in this case shows all the surface details of the compression and represents a leaf imprint (Taylor, Taylor & Krings, 2009, p. 21). The counterparts of Green River fish that represent imprints can be used to make positive laytex casts for further study (Grande, 1984, pp. 119 & 120). If the layer of carbon is lost on the compression through weatherning or further diagenesis then it is also known as an impression (Cleal & Thomas, 2009, p. 4). Many Mazon Creek nodules do not retain organic material and so both the part and counterpart are referred to as impressions (Janssen, 1979, p. 24; Rich, Rich, Fenton & Fenton, 1996 pp. 4-6). For more information on Mazon Creek fossils read our article on Replacement.

Compressions and impressions are the most common insect fossil. Insects with organic matter are called compressions, while those with no organic matter are referred to as impressions. For the paleontologist that studies insects, impressions are like casts and molds, which may preserve some relief like pleating on wings (Grimaldi & Engel, 2005, p. 43). This is important because wing venation can be used to identify an insect.

Lake deposits are the most common environment in which leaf and insect fossils form. Insects and leaves become trapped in sediments. As the sediments accumulate the insects and leaves may decompose leaving behind imprints. As the sediments compact and hardened into rock the imprints become impression fossils. If organic matter remains then a compression fossil has formed. Even a single specimen can represent both a compression and impression. Many insects found at Florissant, Colorado are found with their bodies fossilized as compressions and their wings as impressions. The body still retains the altered cuticle, while the wings do not have any organic matter remaining.


Permineralized fossils form when solutions rich in minerals permeate porous tissue, such as bone or wood. Minerals precipitate out of solution and fill the pores and empty spaces. Some of the original organic material remains, but is now embedded in a mineral matrix (Schopf, 1975). Bone and wood tissues act as excellent frameworks to preserve cell structure. Silicates, iron oxides, metal sulfides, native elements, carbonates, and sulfates can be involved in permineralization. Permineralization is one of the most faithful modes of fossil preservation. In fact, scientists have tried to replicate the process in the laboratory, but no artificial permineralization is equal to the best natural preservation by cryptocrystalline silica or calcium carbonate (Schopf, 1975).

Formation of the finest petrified wood involves permineralization with silica, usually from a volcanic source, along with replacement and recrystallization. During the initial stages of permineralization amorphous silica infills pits connecting cells and pricipitates on cell walls. At this early stage no replacement has occurred. Replacement of cellulose in cell walls may occur as permineralization continues. Cellulose that degrades leaves room for the emplacement of silica between and within cells walls. The more decay resistant lignin that remains in the cell walls continues to act as a guiding framework to preserve structure. Later, silica is deposited in cell lumina, the cavity enclosed by the cell walls, and voids created by wood degradation.

Silica that initially permeates the porous tissue and that which replaces cell wall material is amorphous. This amorphous silica is unstable and slowly crystallizes to more stable forms over millions of years. The transition to more stable forms of silica involves continued polymerization and water loss. Higher ordered forms of opal are created through this process and eventually lead to the thermodynamically more stable silica quartz (Stein, 1982). The quality of preservation usually, but not always, declines during successive stages of silicification (Mustoe, 2003). In some instances higher ordered opal and chalcedony may act as the initial replicating minerals (Mustoe, 2008).

Petrified forests, representing small to large deposits of permineralized wood, capture people’s imagination. What processes allow wood structure to be preserved in stone? How long does it take to form petrified wood? Explore these questions in depth as you read our article on Permineralization further down this page or click on the word Permineralization to obtain a printable version of our article. Our article on permineralization was updated on April 29, 2014.

Petrified wood and petrified dinosaur bone are probably the best known permineralized fossils among the general public. Although not as well known, the coal ball represents a very informative permineralized fossil. A special type of fossil, the coal ball, can be found in the coal deposits of the Pennsylvanian and Permian periods. Coal balls contain swamp vegetation, which has been permineralized with calcium carbonate, preserving 3-D cellular structure. Coal balls are studied in serial section using the cellulose acetate peel method to reveal microscopic structure. Serial sections can be used to reconstruct organs and entire plants. The five major groups of plants found in coal balls include: Lycophytes, sphenopsids, ferns, seed ferns, and cordaiteans (Rothwell, 2002). The in situ preservation of plant materials in coal balls allows paleontologist to study plant associations that tell us something about the palaeoecology of the coal swamps. Coal balls reveal that the arborous fern Psaronius became the dominant canopy tree after the extinction of Lepidondendrales near the Middle Pennsylvanian. Certain species of small ferns and horsetails have been found, which grew in association with the roots of Psaronius (Rothwell, 2002).

Petrified Wood: The Silicification of Wood by Permineralization


Organisms entombed in sediment, such as volcanic ash, which becomes saturated with water, may petrify or permineralize under the right pH and temperature conditions. Traditionally, petrification or petrifaction refers to animal or plant tissue that has turned to stone. Petrified wood and dinosaur bone are familiar examples; however, these fossils actually form through permineralization and often contain original organic material. In this article we will use petrifaction and permineralization synonymously.

Permineralized fossils form when solutions rich in minerals permeate porous tissue, such as bone or wood. Minerals precipitate out of solution and fill the pores and empty spaces. In the case of wood, petrifaction occurs when cellulose, hemicellulose, and lignin within the cell walls of the woody tissue act as a framework to preserve cell structure. Silicates, iron oxides, metal sulfides, native elements, carbonates, and sulfates can be involved in permineralization. Silicified wood is the most common and provides the most detailed preservation of cell structure.

The specimen pictured at the top of this page is a cross-section of a limb permineralized with silica. Volcanic material often serves as a source of silica for wood and bone. Volcanic activity resulting in pyroclastic flows, lahars, and ash falls can bury portions of forests that later become permineralized. Many permineralized specimens retain patterns of cell structure. Both cell structure and insect damage, in the form of galleries, have been preserved in the above specimen.

Silicified Fossil Wood Composition

When one holds a specimen of silicified wood it certainly appears to be made entirely of mineral matter with no original cellular material remaining. However, when examined under magnification many specimens reveal microscopic cellular structure leaving one to wonder if some of the original organic matter is still present. It is informative to make some basic comparisons between fresh wood and silicified fossil wood.

Cellulose, hemicellulose and lignin account for over 95% of the dry weight of wood (Leo & Barghoorn, 1976). The average density of 43 species of softwoods and 96 species of hardwoods examined by Hoadley is 0.53 g/cm3 (Hoadley, 1990). The average density of the softwoods alone was 0.43 g/cm3, while for the hardwoods it was 0.57 g/cm3. Silicified wood generally contains more than 90%, by weight, of silica (Leo & Barghoorn, 1976; Sigleo, 1978; Furuno et al., 1986 II; Mustoe, 2008). Woods mineralized with opal have densities of 2.04 g/cm3 or less. Woods permineralized with quartz have densities of 2.34 g/cm3 or greater (Mustoe, 2008). Leo and Barghoorn (1976) note that many mineralized woods preferentially fracture toward a radially longitudinal plane as do non-mineralized woods. They hypothesized that this is due to retention of wood in the permineralized specimen or to discontinuities in silica deposition predetermined by the orgininal wood structure at the time of petrifaction.

How much of the original wood is present? The first well documented attempt to answer this question was carried out by St. John (1927). St. John examined 25 prepared sections of various silicified wood specimens for cell structure under a light microscope. The sections were treated with a solution of one third hydrofluoric acid and two thirds alcohol to remove silica and then reexamined under the microscope. Some specimens retained most or some of the structure indicating the presence of organic matter. Other specimens lost all of their structure with no trace of organic matter.

Mustoe (2008 and written personal communication, 2011) employed a more quantitative method to determine the presence of organic matter utilizing heat to destroy residual organic matter and measuring loss in mass. Mustoe concluded that most of the plant tissue is destroyed during silicification. Sigleo (1978) isolated lignin derivatives from 200 Ma Araucarioxylon arizonicum specimens deomonstrating that small traces of relic organic matter can persist after many millions of years. Overall, evidence suggests that very little of the original organic matter remains in silicified wood.

How do we account for the visual appearance of cellular detail in silicified specimens that have little to no organic material? Leo and Barghoorn (1976) outline five ways in which cellular detail may be retained in silicified specimens:

1. The actual wood may remain intact after permineralization.
2. Products from the breakdown of cell walls may be immobilized in silica close to their site of origin.
3. Variations in the mineralogy of successive silica generations, including color, texture, and impurities.
4. Infiltration of foreign tar-like organic matter into the specimen.
5. Patterns of entrapped air, which darken silica.

Specimens from the same wood deposit can vary in how much structure is retained. Even single specimens may exhibit variation in the retention of wood structure. The idea that variations in mineralogy lead to differences in texture accords with my own experience. I have specimens from Sweet Home Oregon that exhibit beautiful annual rings. Upon closer inspection with a 10x loupe, variations in cellular detail are immediately apparent. In some areas that have a grainy texture, described by collectors as “sugary”, no cellular detail is revealed. In other areas, on the same specimen, the grain size of silica is so fine that wood histology can be studied with much satisfaction. Do these differences in how cell structure is preserved represent different taphonomic pathways or different stages within the same pathway? What are the conditions and processes that lead to the formation of siliceous petrifactions?

Geochemical Conditions for Silicification

Silicified wood forms in principally two geologic environments. Trees transported by streams and rivers can become buried in the fine-grained fluvial sediments of deltas and floodplains or volcanic ash can bury trees while still upright (Mustoe, 2003, p. 34). Fresh wood entombed in soft mud beneath water carrying large amounts of sediment may set up conditions necessary for fossilization. Rapid burial in volcanic ash is the initial stage for many fossil woods preserved with silica (Leo & Barghoorn, 1976, p. 5). Volcanic ash acts as an abundant source of silica for groundwater. The presence of water is important for several reasons: it reduces oxygen thereby inhibiting tissue deterioration from aerobic fungi, acts as an agent for the alteration of ash, maintains wood shape for maximum permeability, and creates a medium for the transport and deposition of silica.

The conditions of temperature and pressure during fossil wood formation are equivalent to those found in sedimentary environments of shallow depth. Excessive pressures would deform wood shape and tissues. Excessive temperatures (above 100 degrees Celsius) break down wood substances. The pH of the sediment-laden water within the wood is probably neutral to slightly acidic. Wood chemically breaks down at pH values below 4.5 and above 7. Silica is highly soluble at a pH of above 9 making precipitation less likely. The weathering of volcanic ash may produce a pH that is quite high (alkaline), which would release silica into solution making it available for emplacement in wood as the pH is lowered (Leo & Barghoorn, 1976). These physical and chemical parameters help to define the environmental conditions in which wood can act as a template for silica deposition.

A study of silicified wood from the Triassic-aged Chinle Formation of Arizona supports the parameters above. Sigleo (1979) compared the geochemistry of silicified wood and its associated sediments (sandstone with some siltstone and clay) to determine the environmental conditions for the process of wood mineralization. Fossil wood that has stayed in place since deposition and mineralization was carefully chosen for the study. The abundance of minerals and trace elements were measured from the core of the fossil wood to its periphery. Abundance of the same minerals and trace elements were measured in associated sediments and clays from the periphery of the spcimen up to 3 meters away. The clay consisted of 80-90% montmorillonite, which formed from volcanic ash. Identical aluminum concentrations in the clay at the boundary of the fossil and within the periphery of the fossil wood suggest that montmorillonite co-precipitated with silica. The abundance of most trace elements increased from the core of the fossil to its periphery with some notable exceptions.

Antimony (Sb) was found to be much more abundant within the fossil wood than in surrounding sediments with its highest concentrations at the core where carbon was also the most abundant. The abundance of uranium was highest in the carbonaceous core and decreased to the periphery of the fossil wood. Uranium and antimony are more mobile when in an oxidized state, but precipitate when reduced. In contrast, the abundance of manganese, which is more soluble in a reduced state, was low within the fossil specimen and had its highest concentration with in the sediments adhering to the branch. Clays in the associated sediments were depleted of rare earth elements (REE) relative to the total sediments. REE can be leached from clays in soils with a pH of 4-5.

Sigleo (1979) concluded that the geochemistry of the fossil wood and associated sediments supports a fossil-forming environment that was anoxic and slightly acidic. The silicification process occurred at surface temperatures and pressures associated with typical surface and groundwater conditions. There was no evidence of alkaline conditions or exceptionally high silica concentrations in solution. A continuous supply of silica in solution was provided by the hydrolysis of volcanic ash. Later we will see evidence for secondary stages of silicification associated with hydrothermal events in Chemnitz fossil wood.

The Process of Wood Silicification

Leo and Barghoorn (1976) developed a hypothetical model for wood silicification based upon wood anatomy, a low temperature laboratory process for incipient silicification, and inferred geochemical parameters found in natural settings. Leo and Barghoorn hypothesized that there is a chemical affinity between wood and silica through hydrogen bonding. Several observations support the idea that relative unaltered wood may actually serve as a silica sink through hydrogen bonding. Coalified wood does not silicify well as it has lost functional groups capable of hydrogen bonding. Carbonate, sulfide, and fluoride petrifactions are less common and of lower quality possibly because these ions do not establish hydrogen bonds as well as silica. Silicified woods are often encased within a matrix that is not cemented with silica, suggesting a differential affinity for silica between the wood and the surrounding sediment.

Leo and Barghoorn’s experiments with artificial silicification of wood, described later, also support the idea that wood has an affinity for silica. According to their hypothesis, when wood is permeated by silica solution, hydrogen bonding links silicic acid to hydroxyl groups on cellulose making up the inner cell walls. As water is lost silicic acid is polymerized into opal. Layers of silica are deposited with the wood acting as a template (pp. 22-25). Initially, silica is fixed to the inner cell walls and along the perimeter of the tracheid lumen and infill pits connecting adjacent tracheids. During initial stages of permineralization silica deposition fills voids, especially the lumina.

Cell walls may be replaced with silica in later stages of silicification. To replicate cell structure with high fidelity a balance between wood degradation and mineral deposition must be achieved. The amorphous silica that initially permeates wood is highly hygroscopic (attracts water) and highly permeable to fluid flow (Leo & Barghoorn, 1976). The rate at which this silica crystallizes to more impervious forms is extremely slow in geologic terms. Thus, long after silicification begins the influx of silica and the migration of degraded organic matter can continue through this porous medium.

As silicification proceeds to more advanced stages cellulose degrades leaving more room for the emplacement of silica between cells and within cell wall layers. Lignin, under anaerobic conditions, is the most decay resistant compound in wood and continues to act as a template for structural detail. In fact, fossil woods show an increase in the ratio of lignin to holocellulose (cellulose & hemicellulose) when compared with contemporary counterparts. Specimens aged Eocene or older are devoid of holocellulose. Thus, lignin is the last organic matter to be replaced. The balance between removing organic matter and the deposition of minerals is often not complete so, some organic matter remains in many petrifactions. As the process continues silica deposits in intercellular spaces and voids created by shrinkage and wood degradation.

Silica that initially fixes to the wood structure is amorphous. This amorphous silica is unstable and slowly crystallizes to more stable forms. The transition to more stable forms of silica involves continued polymerization and water loss. Higher ordered forms of opal are created through this process and eventually lead to the thermodynamically more stable silica quartz (Stein, 1982). Multiple studies have examined natural wood petrifactions representing different fossil deposits providing insights into the physical and chemical processes involved in wood silicification. Many of these studies lend evidence in support of Leo and Barghoorn's model of silicification.

Buurman (1972) examined fossil wood specimens preserved with a variety of minerals using X-ray diffraction, optical and scanning electron microscopy. We will summarize his findings relating to silicification. In one group of silicified woods Buurman found evidence suggesting that wood preservation is best when disordered tridymite (opal-CT) replaces cell walls or when this opal is subsequently transformed to chalcedony through recrystallization. In both instances, Buurman suggests the fossil wood has formed by replacement rather than filling. A second group of silicified woods preserved with chalcedony and quartz retained some woody tissue. Buurman suggested that these specimens had formed through permineralization (filling). Buurman concluded that replacement and permineralization are distinct processes.

In a more detailed study, Scurfield and Segnit (1984) examined 75 fossil wood specimens from Australia using X-ray diffraction, differential thermal analysis, electron probe techniques, optical and scanning electron microscopy. Their study found that replacement of the cell walls of tracheids and vessels occurred in addition to permineralization. They conclude that petrifaction of wood occurs in five stages, summarized as follows:

1. Wood is permeated by silica solution or colloid.
2. The pores of cell walls are penetrated.
3. Progressive dissolution of cell walls occurs as a mineral framework builds to maintain wood structure.
4. Silica deposits in voids, intercellular spaces, and finally cell lumina.
5. Lithification occurs, as water is lost. Silica may transform from one form to another by pseudomorphic replacement and/or repeated solution and recrystallization.

Scurfield and Segnit found evidence, in the specimens they studied, for transformation from opal-CT to chalcedony and chalcedony to quartz. Evidence for the conversion of opal-A to opal-CT was not strong. They also hypothesized that the rate of cell wall breakdown may determine whether opal-CT or chalcedony is the initial replicating substance.

Furuno et al. (1986 I & II) used light microscopy, SEM, electron probe X-ray microanalysis (EPMA), polarizing microscopy, and X-ray diffraction to study the anatomy and mineralization of Pliocene and Miocene silicified woods collected in Japan. Chemical and physical parameters such as color, reaction to hydrofluoric acid on fractured surfaces, and loss on ignition were also examined. Three samples representing the Pliocene were collected from the Mukaiyama Foramation. Three samples representing the Miocene were collected from the Hata, Fujina, and Kori Formations.

Two Sequoia petrifactions of Pliocene age are black in color. When fractured radially and treated with hydrofluoric acid these specimens produced silica casts of tracheid lumens. The cell walls of these specimens are not silicified and retain substantial organic matter. Cell lumens and pit chambers are permineralized with opal-CT and some quartz, with one specimen showing more quartz than the other. By weight one specimen is 22.89% organic matter and 77.11% silica, while the other is 20.56% organic matter and 79.44% silica. A third Tsuga petrifaction of Pliocene age is white to light brown in color. When fractured radially and treated with hydrofluoric acid isolated silicified tracheids were produced. The cell walls of this specimen are preserved in silica. The lumens and cell walls are preserved in opal-CT and some quartz. By weight the specimen is 2.42% organic matter and 97.68% silica.

One Podocarpus petrifaction of Miocene age is black in color. Cell lumens and cell walls are preserved in mostly quartz. The Podocarpus specimen contains some carbon in the cell walls and in resin cells. The authors hypothesize that resin within the resin cells may have fossilized into amber. By weight the Podocarpus specimen is 5.93% organic matter and 94.08% silica. A second Miocene aged Tsuga specimen is light grey in color. The Miocene-aged Tsuga has cell lumens and walls preserved in quartz. By weight this specimen is 0.09% organic matter and 99.91% silica. One Celtis petrifaction of Miocene age is the only angiosperm dicot in the study and is light grey to brown in color. The Celtis specimen has cell lumens and cell walls preserved in quartz. By weight the Celtis specimen is 0.90% organic matter and 99.10% silica. Hydrofluoric acid applied to radially fractured surfaces on Miocene samples did not produce lithomorphs as easily as the Pliocene samples.

The samples in this study show a correlation between specimen color and carbon content. The study also shows a correlation between the extent of silicification and time. Specimens in this study exhibit a pattern of increasing quartz content over time. Furuno et al. (1986 I & II) proposed the following phases for the silica mineralization of wood.

1. Deposition of silica filling voids like cell lumens and pit chambers, but no penetration of silica into the walls, which remain.
2. Formation of casts of lumens by deposition of silica followed by loss of wall substance.
3. Deposition of silica in the voids and penetration of silica into the wall, some of which are replaced by silica.
4. Deposition of silica in the voids and penetration of silica into the walls, most or all of which are completely replaced, and in some cases loss of intercellular substance.

The authors note that phase 2 was not observed in the specimens of their study. Furuno et al. (1986 II) present the following senario for wood silicification. First opal-A dissolved in an alkaline solution that permeated the wood. Silica precipitated within the acidic wood. Opal-CT was formed. The mineral was kept in a solid state and over tens of millions of years the opal-CT was crystallized to quartz. In the course of time all of the silica minerals were transformed to quartz.

Jefferson (1987) studied the preservation of Cretaceous-aged, silicified conifer wood from Alexander Island, Antarctica. Microscopic examination was made of acetate peels and thin sections made in the transverse, tangential longitudinal, and radial longitudinal planes. Fractured surfaces, which broke preferentially in the radial plane, were examined using SEM. EDAX was utilized to identify the amount of silica and organic materials present in the cell walls as well as the distribution of minerals filling cell lumina.

Alexander wood in which silica infiltrated lumina without penetrating cell walls is poorly preserved. Cell walls in these specimens are reduced to thin lines of carbon inclusions embedded in silica. Well-preserved Alexander wood resulted from a process in which silica infiltrated cell lumina and impregnated cell walls. Cell walls in well-preserved specimens contain between 82 and 87% silica with only scattered carbonized residue remaining. Jefferson surveys how the preservation and form of bordered pits along fractured longitudinal surfaces can be used to determine the extent to which silica infiltrated pit chambers. For example, silica infilling creates casts of pit chambers.

Silicified microfibrills making up the cell walls of Alexander wood are 20 to 150 times larger in diameter than extant conifers. Tracheids of Alexander wood often contain preserved fungi hyphae and lensoid-ovoid organic bodies interpreted as fungal spores. The author suggests that cell walls of Alexander wood were delignified by fungal activity seperating microfibrils, making them available for silica coating. Growth of silica on fibrillar bundles exposed by fungal activity allowed cell wall structures to be preserved. Thus, cell walls were not replaced; rather, they were preserved through a process of silica infiltration and impregnation enhanced by biogenic degradation.

Euhedral, cubic iron sulfied crystals enclosed in silica are found within the lumina of some tracheids. The growth of pyrite crystals indicates an initial reducing environment. Quartz crystals within cell lumina most often grow inward without penetrating cell walls. In some lumina apatite and collophane fill up the remaining space not occupied by quartz. Thus, it appears that the cell walls were already silicified when cell lumina were mineralized. Furthermore, the presence of apatite and collophane probably represent a major change in the composition of the permineralizing solution. Jefferson proposed a two-phase silicification process for Alexander petrifactions.

1. Silica impregnated cell walls. Biogenic delignification and decay of the cell wall opened up spaces and isolated microfibrils creating interfibrillar porosity. Silicic acid precipitated and polymerized onto the microfibrils and filled the interfibrillar porosity. The amorphous silica coating microfibrils crystallized into chalcedony and microcrystalline quartz. The author references work that states the subsequent transformation and ordering of silica would be expected to take millions of years.
2. Cell lumina were infilled by chalcedony and euhedral-subhedral quartz crystals and or apatite and cellophane.

Jefferson concluded that Alexander wood supports the two-stage theory of wood silicification proposed by Leo and Barghoorn (1976). However, results from the study of Alexander wood suggest that the impregnation of cell walls can be promoted by biogenic degradation.

The progressive transformation of opal-A to opal-CT to chalcedony and finally quartz is an important aspect of the accepted model for wood silicification. Recent work by Mustoe (2008) reveals that the silica transformation aspect of this model is inconsistent with the mineralogy of fossil wood in the Florissant Formation. Mustoe examined 15 specimens representing six silicified stumps. The samples were analyzed using X-ray diffraction, X-ray fluorescence, scanning electron microscopy/energy-dispersive X-ray spectrometry (SEM/EDX), and optical microscopy. Basic physical properties including density, color, and loss on ignition were also determined.

Some of the specimens were permineralized with only opal-CT, others were a combination of opal-CT and chalcedony, and still others were quartz. In specimens permineralized with both opal-CT and chalcedony the two silica phases appeared to coexist as primary minerals. Thus, evidence for the transformation of opal-CT to chalcedony was missing. Evidence gathered by this study suggests that the Florissant specimens were directly mineralized with chalcedony. The precipitation of opal, chalcedony, and quartz are influenced by concentrations of dissolved silica. Opal is precipitated with high concentrations of dissolved silica while chalcedony is precipitated with low concentrations and quartz still lower. Mustoe speculates that these geochemical characteristics may explain the patterns of mineralization found at Florissant. Mustoe concluded that petrification at Florissant occurred in several stages.

1. First, amorphous silica precipitated on cell wall surfaces.
2. Second, opal-CT and chalcedony filled cell lumina.
3. Finally, chalcedony filled fractures that crosscut permineralized tissues in some specimens.

Spaces between adjacent tracheids were often unmineralized, making the fossil wood permeable to water and susceptible to cleaving radially, tangentially and transversely from freeze-thaw weathering. This finding has important implications to the preservation of specimens at Florissant Fossil Beds National Monument. Mustoe’s findings are important because they suggest that petrifaction may occur through multiple processes or pathways.

Witke et al. (2001) used Raman and cathodoluminescence spectroscopy to study the chemical composition and structural order of silicified plants from the 290 million year old Chemnitz Petrified Forest. Samples of the seed fern Medullosa, gymnosperm Dadoxylon, sphenopsid Calamodendron striatum, and tree fern Psaronius were used in the study. Tracheid and sclerenchyma cells making up vascular tissues are preferentially preserved in Chemnitz fossil plants. Cell walls are preserved primarily in microcystalline alpha quartz. In areas where tissue is not preserved as as in the pith of Medullosa one finds banded agate structures composed of phanerocystalline and microcrystalline alpha quartz along with moganite. A very low percentage of original organic material remains in the Chemnitz silicified plants. Raman spectra of carbonized material dispersed within Chemnitz petrifcations reveals a rank equal to bituminous and anthracite coals. Witke et al. (2001) proposed the following steps for the mineralizations of Chemnitz petrifcations.

1. First, plants were mineralized with quartz and fluorite.
2. Second, a hydrothermal alteration transformed the silica. Iron oxides were associated with this process. Minor residues of carbonaceous material of anthracite rank found in Chemnitz specimens seem to be consistent with a hydrothermal event.
3. The third step consisted of secondary mineralizations with calcite and barite in cracks of the former wood.

Dietrich et al. (2013) used backscatter electron imaging (BSE) and electron backscatter diffraction (EBSD) in a scanning electron microscope to study the ordering of silica preserving xylem tissue in three different fossil tree forms found in Chemnitz Petrified Forest.

The study of Chemnitz petrifactions included the root mantle of the tree fern Psaronius, vascular segments in the pith of the seed fern Medullosa stellata, and the secondary xylem of the gymnosperm Dadoxylon. Former open spaces and specific tissue structures were found to be correlated with different silica ordering.

Tracheid cell walls inthe aerial roots of Psaronius are largely preserved by well-ordered microcrystalline quartz grains. The thickened cell walls of the sclerenchyma fibers, making up the outer boundary of the aerial root, are preserved with extremely fine-grained but well-ordered quartz. Cell lumina are filled with cryptogrystalline quartz. Tracheid cell walls in M. stellata exhibited multiple microcrystalline layers outlining the former cell wall layers. In fact, crystal growth directions within these layers seem to mirror former cellulose fibril orientations. As in Psaonius, cell lumina were largely filled with cryptocrystalline quartz. Tracheid cell walls in the secondary xylem of Dadoxylon are preserved with microcrystalline quartz. Cell lumina are filled mostly with cryptocrystalline quartz or more infrequently with microcrystalline quartz or large fluorspar crystals.

In general the cell lumina of all three specimens are filled with cryptocrystalline quartz, while the cell walls were preserved with microcrystalline quartz. Microcrystalline quartz grain size decreased with tracheid cell diameter. Psaronius tracheid cell walls are preserved with the largest grain size, while the cell walls of Psaronius sclerenchyma, M. stellata tracheids, and Dadoxylon tracheids are preserved with a finer grain size. The tissues of these plants vary in their proportions of cellulose, hemicellulose, and lignin. The results of this study suggest that tissue composition affects silicification ordering in petrifactions. Dietrich et al. (2013) proposed the following stages of petrifaction to explain the patterns of silica ordering observed in the tissues of Chemnitz specimens.

1. Silica solution permeates the porous xylem tissue and forms a silica gel inside the tracheid lumina starting at the inner cell walls.
2. Thus, cell lumina are quickly preserved in silica, which may be transformed later to cryptocrystalline silica or to alpha quartz.
3. The gel cast of the lumina is initially porous and allows a continued influx of silica solution (presumably in a hydrothermal process), which over longer periods of time permeates into the ligno-cellulose making up the former cell walls and intercalates the cellulose fibrils.
4. Cellulose fibrils act as templates for microcrystalline growth of silica. Thus, the preserved cell walls can be distinguished from the cell lumina by different crystal growth.
5. In a third stage, agate and/or larger grains of microcrystalline quartz form in areas with fewer precipitation sites such as cell corners, central piths and fissures resulting from cracking, drying, and tissue degradation.

Is there a place we can go to examine the silicification of wood occurring in more recent times? Karowe and Jefferson (1987) investigated the initial stages of silicification by examining trees buried by Mount St. Helens lahars or mudflows dated at 1980, 1885, A.D. 1450-1550, and 36,000 years B.P. Wood samples were examined using scanning electron microscopy and energy dispersive X-ray analyses. Wood buried in 1980 showed no significant mineral deposition. Wood buried in 1880 and A.D. 1450-1550 exhibited traces of silica on cell walls as well as cell wall decay. Wood buried 36,000 years B.P. showed silica impregnation of cell walls. Decay in these older specimens affecgted the secondary wall and removed the middle lamella. Karowe and Jefferson concluded that the increase in silica deposition as well as decay associated with the age of these trees supported the model of silicification proposed by Leo and Barghoorn in 1976.

The apprent increase in silica deposition was an exciting find. However, researchers at the University of Bonn were unable to reproduce the results of Karowe and Jefferson even when using specimens prepared from the same trees (Hellawell et al., 2011). Perhaps Karowe and Jefferson were looking at an instrumental artifact. Scientists at the University of Bonn are currently working on a paper that will explore the results of their study in more depth. It is clear that many petrified wood deposits, such as those found at Yellowstone, are associated with volcanic mudflows. George Mustoe has examined many Holocene wood specimens from mudflows and has found no evidence of silicification (Mustoe, written personal communication, 2012).

Time and Silicified Wood

Fossil plant deposits including petrified forests from around the world allow paleontologists to trace the evolutionary history of vascular plants from 420 Ma ago (Silurian) to the present (Kerp, 2002). Petrified forests throughout the world capture the public’s imagination (Ransom, 1955; Dernbach, 1996; Dernbach and Tidwell, 2002; Daniels and Dayvault, 2006). Many want to know how long it takes to form natural petrified wood. Some Pleistocene deposits contain peat and wood fragments that can be carbon dated. Ice Age gravels deposited 12,000 years ago contain fresh looking wood pieces. Wood dated at 15 million years weathering out of the Wilkes Formation in Washington can be carved with a pocketknife and ignited with a match (Mustoe, 2001). It is clear that wood can be preserved for long periods of time under the right conditions.

It is equally clear that wood can be quickly mineralized under the right conditions. Timbers in copper mines from Cyprus and Arizona have been found that contain copper (Daniels & Dayvault, 2006). It would be interesting to study the amount of original wood, extent of permineralization and lithification in these specimens and compare them with silicified woods. Wood buried in ash produced from the 1886 eruption of Mt. Tarawera in New Zealand is mineralized with silica. Wood specimens recently exposed to hot springs in Yellowstone exhibit the beginning stages of silicification; however, geologic evidence suggests siliceous thermal springs have not been major sites of wood petrifaction (Leo & Barghoorn, 1976). Silicified wood from Wyoming contained enough organic material to be carbon dated at less than 3,000 B.P. X-ray diffraction reveals that these recently silicified woods are impregnated with amorphous opal (Leo & Barghoorn, 1976; Stein, 1982).

The question of how long it takes to form petrified wood also depends on the physical qualities of the fossil wood we have in mind. Are we looking at wood that is mostly intact and has cell lumina and intercellular spaces impregnated with minerals or fossil wood that has little to no wood remaining and has cellular detail replicated in opal-CT, chalcedony, and microgranular quartz? If we have in mind the latter then these recent petrifactions are not what collectors think of as gem quality petrified wood, which can be cut and polished at the lapidary.

The initial emplacement of silica as a film may occur rapidly. Artificial silicification of wood in the lab and studies of natural silicified wood demonstrate that the physical state of silica in newly formed petrifactions is amorphous (Leo & Barghoorn, 1976). Conversion of this silica to increasingly stable forms of opal-A (amorphous), to opal-CT (cristobaite & tridymite), to chalcedony (cryptocrystalline quartz), and finally to microgranular quartz requires millions of years (Leo & Barghoorn, 1976; Stein, 1982; Kuczumow et al., 1999). Under normal conditions conversion of opal to quartz requires tens of millions of years; however, under geothermal conditions the same process may occur in 50,000 years or less (Mustoe, 2003).

X-ray diffraction patterns for different aged silicified specimens examined by Stein support the well established transformational sequence of opal-A to opal-CT, to quartz. A Yellowstone Wyoming sample carbon dated at 2,430 years was composed of opal-A. A Pliocene-aged sample from the Sante Fe Formation of New Mexico was composed of opal-CT. A Miocene-aged sample from the Bozeman Lake Beds was composed of opal-CT and some quartz. A Late Eocene sample from Florissant, Colorado was composed of quartz. However, Mustoe (2008) has determined that some Florissant wood is also permineralized with opal-CT and chalcedony. Still, chalcedony and microgranular quartz are the most common forms of silica found in fossil woods that are Eocene or older. X-ray diffraction studies, specific gravity measurements and indices of refraction all support an increase in silica ordering with increase in age (Stein, 1982).

Instant Petrified Wood?

Fascination with natural permineralized specimens has sprurred interest in creating methods for artificial petrifaction. Artificial petrifaction reflects both scientific and commercial interests. Methods for artificial petrifaction have been devised as ways to study wood structure and model the initial stages of natural silicification. Artificial petrifaction is also used to develop wood composites and ceramics. Leo and Barghoorn (1976) document early attempts at creating artificial silicified wood in the 1500's by Basil Valentine and Johannes Kentmann.Experimental replication of these early recipes has not been successful. More recent attempts have produced some positive results.

Ryan W. Drum from the University of Massachusetts, Amherst, describes his attempt at the laboraty silicification of twigs in a 1968 article that appeared in the journal Science. Twigs were soaked in solutions of sodium metasilicate, washed, and then treated with chromic acid to remove organic remains. Entire twigs did not remain intact; however, single cells and small aggregates of cells were replicated in silica. Drum described these replicas as very fragile and included electron micrographs of his results. Drum goes on to say that his in vitro silicification process might provide a method to study cellular spaces in 3-D, intercellular connections, and the morphology of woody cells.

Leo and Barghoorn (1976) improved upon Drum's experiments. Their procedure included boiling wood to degas and waterlog specimens. The wood was alternately soaked in solutions of water and ethyl silicate at neutral pH and 70 degrees Celsius. Ethyl silicate decomposes to monomolecular silicic acid, which is thought to be the silicifying agent in natural processes. Nitric acid and potassium chlorate were used to remove organic matter. The silica lithomorphs that remained replicated cell structure and were more substantial than those produced from Drum's procedure. The silica lithomorphs were fragile and composed of amorphous silica. These silica lithomorphs resemble the first stages of permineralization observed in recent silicified specimens.

Persson et al. (2004) evaluated the use of sol-gel mineralization to study the wood morphology of spruce and birtch xylem. Wood chips of birch, Betula verrucosa, and spruce, Picea abies, along with the pulp of spruce were used in the study. Spruce pulp was prepared using the Kraft process. The Kraft process uses a mixture of sodium hydroxide and sodium sulfide along with cooking at high tempertures (170 degrees Celsius) to degrade lignin and hemicellulose, converting the wood to a pulp consisting of almost pure cellulose fibers.

Wood chip samples and the pulp were soaked in ethanol and vacuum dried two times to facilitate impregnation. The prepared wood and pulp samples were immersed in a sol-gel mixture (polysilicic acid) for three days at 60 degrees Celsius. Silica casts of the wood and pulp were recovered by removing all organic material by heating to 575 degrees Celsius for 6 hours. The brittle silica casts replicas were studied using environmental scanning electron microscopy (ESEM) and transmission electron microscopy (TEM). Persson et al. (2004) found that their sol-gel casting medium penetrated and condensed on the ultrastructure of cell walls. The high-resolution silica casts were used to observe the three dimensional structure of xylem and pit structures connecting wood cells.

Experiments in artificial silicification described above have been used as methods to replicate the process of natural incipient silicification and to study the ultrastructure of wood. These experiments suggest that the organic cell structure of wood acts as a template for initial silica deposition. The fact that wood is removed in making silica-cast replicas limits the use of these procedures for studying advanced stages of natural silicification.

More recently, Ballhaus et al. (2012) designed closed-system experiments at 100 degrees Celsius to simulate the silicification of trees buried by volcanic pyroclastics. Silica rich solutions were prepared by reacting powdered obsidian with water at 100 degrees Celsius for several days. Under these conditions it was found that silica and alkali oxides readily go into solution while aluminum oxide remains in the residue. The pH of the solution increases to values of 9.4-10.5. Wooden cubes made of Douglas-fir (Pseudotsuga menziesii) were reacted with the silica solution in an autoclave for up to 300 hours. In the presence of the wood the pH and silica concentrations decreased, while alkalis remained in solution.

Silica rich solutions were again prepared by reacting powdered obsidian with water at 100 degrees Celsius for several days. The solution was doped with NaOH to increase the pH values to 12.5 and 13.2 in order to increase the solutions silica concentration. Douglas-fir wood cubes were reacted with the solutions in autoclaves for 112 days. Periodically, slices of wood were prepared and analyzed for precipitates. After several days many of the cell lumina were infilled with silica. Most precipitates were found on wood that exhibited final pH values near neutral. Under SEM the silica precipitates appeared as microspheres of opal.

These experiments simulate and provide evidence in support of processes thought to be involved in the incipient permineralization of wood. Volcanic material rich in siliceous glass can be quite alkaline. When these solutions come into contact with wood the pH is lowered and silica becomes less soluble, precipitating onto wood surfaces. This pH gradient between the silica rich alkaline water and the acidic environment of the wood tissue acts as force to precipitate opal onto wood surfaces. A second force driving permineralization is the ability of wood tissue to extract silica out of solution. The decrease in the silica concentration in the presence of Douglas-fir wood cubes is indirect evidence that is consistent with Leo and Barghoorn’s (1976) hypothesis that silica species chemically bond with hydroxyl groups on wood surfaces.

Ballhaus et al., (2012) used simple diffusion and advection models to estimate how long it would take to permineralize a tree with opal. Using Frick’s Law a theoretical conifer tree trunk with a diameter of 100 cm and a length of 100 cm buried horizontally in a pyroclastic deposit would be permineralized through diffusion within an estimated time of 47,000 years. Using an advection model the same tree buried upright (in situ) would require approximately 3,600 years for cell lumina and intercellular spaces to become impregnated with opal. This estimate assumes wood structure remains intact. The results of this study are consistent with other findings and indicate that the incipient permineralization of large trees with opal is on a time scale of thousands of years.

The process of natural permineralization has also inspired the pursuit of artificial wood composites. These wood composites use fresh wood as a framework for creating either a wood composite or a ceramic. An October 1992 Popular Science news article read ‘Instant petrified wood?’ In reality researchers at the Advanced Ceramic Materials Lab at the University of Washington in Seattle were making wood ceramic composites. Wood is soaked in solutions of silica and aluminum and then oven-cured to create the composites. The solution penetrates the wood to a depth of up to 0.2 inches. The wood is abrasive, but can be worked with carbide tools. The authors speculate that these composites could be made with the same rock-hardness of petrified wood. The composite is wood impregnated with silica and aluminum up to a depth of 0.2 inches.

Yongsoon Shin and colleagues at the Pacific Northwest National Laboratory (PNNL) developed a method for creating a silica-based ceramic that mimics wood structure. The process uses surfactants and silicate solutions to mineralize wood that has been soaked in an acid solution. After the silicate solution penetrates cell wall structures it is heated to high temperatures in air to oxidize the silicate and remove organic residue. This method creates a ceramic, which faithfully reproduces cellular structures in great detail as confirmed by SEM images (Shin et al. 2001). Shin et al (2001) points out that, “Another important phenomenon related to the current study is natural petrification, which takes place over a very long period of time. In some cases the cellular tissue is completely replaced by silicate and other minerals. Our study not only points to a more rapid approach to transforming organic tissues into ceramic materials, it may also shed some light on how natural petrification takes place.”

An article on entitled ‘Petrified wood yields super ceramics’ describes a process developed at PNNL for using wood to form the ceramics silicon carbide (SiC) and titanium carbide (TiC). The process involves soaking the wood in acid, infusing it with titanium or silicon, and baking it in an argon-filled furnace at 1,400 degrees Celsius. This process is the same as Shin's 2001 study except for heating in an argon atmosphere instead of air. The 2001 and 2005 experiments used small blocks of pine and poplar wood. Both the macro and microstructure of the wood is preserved in this ceramic. The material has the strength of steel, and can resist temperatures of up to 1,400 degrees Celsius. PNNL scientist Yongsoon Shin is quoted as saying that one-gram of this material flattened has enough porosity to cover an entire football field. SEM and TEM images were used to study the microscopic structure of these ceramics (Shin et al. 2005). The SiC ceramics could be used for making filters, catalysts, cutting tools, abrasives, and coatings. The purpose of Shin’s research is to develop methods for using natural biological materials as templates to construct inorganic materials.

Hamilton Hicks was issued US patent 4612050 on September 16, 1986 for a mineralized sodium silicate solution used to create wood with the “non-burning characteristics of petrified wood” (Patent Storm). In one experiment a horse stall was set on fire with combustible materials. The treated wood showed signs of charring, but did not burn. The patent indicates that the treated wood is non-toxic and has an inherently bad taste. This bad taste prevents horses from “chewing or nibbling the wood to shreds”. The inventor speculates, “petrifaction of the treated wood is achieved when minerals in his solution “replace the cells” and the solution hardens the wood. It would be interesting to compare the amount of wood still present as well as the nature and extent of silicification in this product with that found in naturally silicified wood.

Products referred to as "instant petrified wood" may provide insights in the initial stages of permineralization. However, many of the materials and procedures used to make these products are not found in nature. Furthermore, procedures to make silica-cast replicas and ceramics remove wood after the initial permeation with artificial mediums. Products made from the initial emplacement of silica, represented by both artificial and recent natural petrifactions do not resemble what a collector regards as gem quality petrified wood. Multiple lines of evidence suggest that natural fossil wood silicified with opal-CT, chalcedony, and microgranular quartz requires millions of years to form.


Evidence for pathways that lead to the formation of silicified wood comes from studies of fossil wood representing different aged deposits, laboratory procedures for artificial petrifaction, and examination of trees buried recently by volcanic deposits. The formation of silicified wood includes permineralization, replacement, and recrystallization. A summary of an accepted model for natural silicification is as follows.

When wood is permeated by silica solution, hydrogen bonding links silicic acid to cellulose making up the inner cell walls. Silicic acid is polymerized into opal through water loss. Silica that initially fixes to wood structure is amorphous and can recrystallize to a more stable form. Layers of silica are deposited with the wood acting as a template. Initially, silica is fixed to the inner cell walls and infills the lumina of tracheary elements (vessel elements and or tracheids) and the pits connecting adjacent tracheary elements. Cell walls may be replaced with silica as permineralization continues. To replicate cell structure with high fidelity a balance between the chemical and biological decomposition of wood and the precipitation of silica must be achieved. As silicificaiton proceeds to more advanced stages cellulose degrades leaving more room for the emplacement of silica between cells and within cell wall layers. This replacement is not molecule-by-molecule. Lignin is the most decay resistant compound in wood and continues to act as a template for structural detail. Later, cracks and fractures are preserved with silica. A traditional model of silicification includes a transformation of the initial silica to increasingly more stable forms from opal-A to opal-CT to chalcedony and finally to quartz. However, evidence for silica recrystallization is lacking in some specimens suggesting more than one pathway for silicified wood formation (Mustoe, 2008).

Studies of silicified wood from Florissant and Chemnitz demonstrate that cell walls and lumina can be preserved in different forms of silica. Thus, forms of silica that serve as the initial replicating material for cell walls and open spaces may be different from what initially permineralized the wood. Factors that affect what form of silica serves as the initial replicating material will lead to a better understanding of natural silicification pathways. One of these factors may include the plant tissues themselves. Examination of microstructure in petrifactions of Chemnitz encourages further investigations into how tissue composition affects what form of silica may act as a replicating material (Dietrich et al. 2013).


I would like to thank George Mustoe, Dagmar Dietrich, Yongsoon Shin, and Jim Mills for their expertise and encouragement.


Post Script

Our readers might find the following recent articles helpful in exploring the silicification of wood.

Petrifactions and Wood-Templated Ceramics: Comparisons Between Natural and Artificial Silicification

Late Tertiary Petrified Wood from Nevada USA: Evidence of Multiple Silicification Pathways

Opalized Wood from Clover Creek, Gooding County, Idaho

Multi-Stage Silicification of Pliocene Wood: Re-Examination of an 1895 Discovery from Idaho, USA.

Mineralogy of Paleocene Petrified Wood from Cherokee Ranch Fossil Forest, Central Colorado, USA.

The Bruneau Woodpile: A Miocene Phosphatized Fossil Wood Locality in Southwestern Idaho, USA

Wood Petrifaction: A New View of Permineralization and Replacement

Mineralogy of Non-Silicified Wood

Mineralogy of Eocene Fossil Wood from the "Blue Forest" Locality, Southwestern Wyoming, United States

A Silicified Carboniferous Lycopsid Forest in the Colorado Rocky Mountains, USA

The Blue Forest of Ancient Lake Gosiute: Sweetwater County, Wyoming