Glossary of
Scientific Terminology Related to Paleontology, Evolution and Fossils

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abyssal plain: Large area of extremely flat ocean floor lying near a continent and generally over 4 km in depth.

acanthodians: Now extinct, earliest group of fish with jaws, ranging from the Silurian to the Permian.

acritarchs: Organic-walled microfossils common throughout the Proterozoic and early Paleozoic

adaptation: Any heritable characteristic of an organism that improves its ability to survive and reproduce in its environment. Also used to describe the process of genetic change within a population, as influenced by natural selection. Alternatively, some heritable feature of an individual's phenotype that improves its chances of survival and reproduction in the existing environment.

adaptive radiation (also "radiation", for short): The diversification, over evolutionary time, of a species or group of species into several different species or subspecies that are typically adapted to different ecological niches (for example, Darwin's finches). The term can also be applied to larger groups of organisms, as in "the adaptive radiation of mammals." For example, trilobites underwent a massive radiation during the Cambrian, and insects during the Cretaceous.

Adenosine triphosphate: Adenosine-5'-triphosphate (ATP) transports chemical energy within cells for metabolism. It is produced by photophosphorylation and cellular respiration and used by enzymes and structural proteins in many cellular processes.

Agnathans: A jawless, heavily armored fish that appeared in the Devonian.

algae: Photosynthetic, almost exclusively aquatic, nonvascular plants that appeared in the Precambrian and that range in size from simple unicellular forms to giant kelps.

allele: One of the alternative forms of a gene. For example, if a gene determines the color of eyes, one allele of that gene may produce brown eyes and another allele produce blue eyes. In a diploid cell there are usually two alleles of any one gene (one from each parent). Within a population there may be many different alleles of a gene; each has a unique nucleotide sequence.

allopatric speciation: Speciation that occurs when two or more populations of a species are geographically isolated from one another sufficiently that they do not interbreed.

allopatry: Living in separate places. Compare with sympatry.

allotype: specimen designated from the type series that is the opposite sex of the holotype.

amino acid: The unit molecular building block of proteins, which are chains of amino acids in a certain sequence. There are 20 main amino acids in the proteins of living things, and the properties of a protein are determined by its particular amino acid sequence.

amino acid sequence: A series of amino acids, the building blocks of proteins, usually coded for by DNA. Exceptions are those coded for by the RNA of certain viruses, such as HIV.

ammonoids: Cephlapods that evolved from nautiloids and are generally spiral-shaped shell with numerous chambers.

amphibians: A transitional group of vertebrates between fish and reptiles, capable of living on land, but returning to the water to reproduce. ( Devonian to Holocene)

anoxic: Generally, a lack of oxygen, usually in refernce to a marine environment. Anoxic sea water refers to water depleted of oxygen that can occur with restricted water exchange. In most cases, oxygen is prevented from reaching the deeper parts of the sea area by a physical barrier (sill) as well as a pronounced density stratification. Anoxic conditions will occur if the rate of oxidation of organic matter by bacteria is greater than the supply of oxygen. When oxygen is depleted, bacteria first turn to the second-best electron acceptor, which in sea water is nitrate. Denitrification occurs, and the nitrate will be consumed rather rapidly. After reducing some other minor elements, the bacteria will turn to reducing sulphate. If anoxic sea water becomes reoxygenized, sulphides will be oxidized to sulphate according to: HS + 2O2 > HSO4.

archaeocyaths: conical, calcareous, Cambrian fossils with a long history of phylogenetic uncertainty and changing interpretations. There is now a strong consensus that archaeocyaths are sponges.

Autotrophs: can use carbon dioxide (CO2) and water to form oxygen and complex organic compounds, mainly through the process of photosynthesis.

bedding plane: A surface separating layers of sedimentary rocks and deposits. A bedding plane marks termination of one deposit and beginning of another of different character, such as a surface separating a sandstone bed from an overlying mudstone bed. Rocks tend to breaks or separate along bedding planes.

benthic: term used to designate aquatic organisms that are bottom dwelling.

bilateral symmetry: The condition, found in many organisms, where one half of the body or structure is the mirror image of the other.

bilaterians: A clade of animals whode members share: bilateral symmetry, are triploblastic (three tissue layers: ectoderm, mesoderm, endoderm), and with HOX genes in one or more clusters with the genes within a cluster arranged in the same order as the body parts they affect.

biological species concept: The concept of species, according to which a species is a set of organisms that can interbreed among each other. Compare with cladistic species concept, ecological species concept, phenetic species concept, and recognition species concept.

biomineralization: The formation of minerals by organisms. Biominerlization is a widespread phenomenon within nature whereby organisms form complex and genetically determined mineral structures for a myriad of reasons such as stiffening of soft tissues as in insect exoskeletons, mammal endoskeletons, and the formation of animal teeth for chewing food. In the process, minerals nucleate and grow on purely organic templates.

biostatigraphy: The branch of geology concerned with the separation and differentiation of rock units by means of the study of the fossils they contain.

bivalve: A mollusk having two shells hinged together, as the oyster, clam, or mussel; or any animal with two halves to its shell such as an ostracode or brachiopod.

bolide: very generally, an extraterrestrial body of indeterminant composition, in the 1-10-km size range, that impacts the earth at velocities faster than a bullet (20-70 km/sec = Mach 75), explodes upon impact, and creates a large crater.

bony fishes: Fish of the class Osteichthyes, characterized by a skeleton composed of bone in addition to cartilage, gill covers, and an air bladder.

Bryophyta: Bryophytes comprise the mosses (Class Musci), as well as liverworts (Class Hepaticae) and hornworts (Class Anthocerotae). They are believed to have been the first true plants, evolving from charophytes almost 500 million years ago. Unlike other plants, bryophytes do not have true organs, such as leaves, stems, or roots. In place of roots, most bryophytes have thin, hairy tubes called rhizoids that provide anchorage and nutrient uptake from the soil. The bryophyte life cycle is unique in having a dominant gametophyte generation. The actual green plant in mosses and worts is the gametophyte plant, while the sporophyte consists of simply an enclosed sporangium, typically atop a stalk.

calcareous: Of, containing, or like calcite (calcium carbonate).

calcite: A common compound (CaCO3) in rock formation and the main component of limestone. Calcite can be many colors and effervesces (bubbles) in hydrochloric acid

carbonate rock: A rock consisting primarily of a carbonate mineral such as calcite or dolomite, the chief minerals in limestone and dolostone, respectively.

carpoids (formally Homalozoa): Extinct subphylum (Phylum Enchinodermata) whose members have no trace of radial symmetry. The theca is depressed and asymmetrical. Homalozoa are known from Middle Cambrian to Middle Devonian rocks.

catabolism: the destructive metabolism of larger organic molecules into smaller constituents, usually with the release of energy (usually as ATP).

chalk: A variety of limestone made up in part of biochemically derived calcite, in form of skeletons or skeletal fragments of microscopic oceanic plants and animals mixed with fine-grained calcite deposits of biochemical or inorganic-chemical origin.

chert: A cryptocrystalline form of quartz, microscopically granular. Occurs as nodules and as thin, continuous layers. Duller, less waxy luster than chalcedony. Occurs in limestone, dolostone, and mudstones.

choanoflagellates: A group of sigle-celled and colonial flagellate eukaryotes, generally accepted as the closest living relatives of the animals (metazoa).

chordate: animal with a notochord, a cartilaginous rod extending the length of its body, dorsal hollow nerve cord (a fluid-filled tube running the length of the body), gill slits or pouches, and a tail at some stage during its life cycle.

chromosome: A structure in the cell nucleus that carries DNA. At certain times in the cell cycle, chromosomes are visible as string-like entities. Chromosomes consist of the DNA with various proteins, particularly histones, bound to it.

clade: A set of species descended from a common ancestral species. Synonym of monophyletic group.

cladism: Phylogenetic classification. The members of a group in a cladistic classification share a more recent common ancestor with one another than with the members of any other group. A group at any level in the classificatory hierarchy, such as a family, is formed by combining a subgroup at the next lowest level (the genus, in this case) with the subgroup or subgroups with which it shares its most recent common ancestor. Compare with evolutionary classification and phenetic classification.

cladistic species concept: The concept of species, according to which a species is a lineage of populations between two phylogenetic branch points (or speciation events). Compare with biological species concept, ecological species concept, phenetic species concept, and recognition species concept.

cladogram: A branching diagram that illustrates hypotheses about the evolutionary relationships among groups of organisms. Cladograms can be considered as a special type of phylogenetic tree that concentrates on the order in which different groups branched off from their common ancestors. A cladogram branches like a family tree, with the most closely related species on adjacent branches.

clastic: Refers to rock or sediments made up primarily of broken fragments of pre-existing rocks or minerals.

coccoliths: Microscopic structures of varying shape and size that are made of calcite, are secreted by calcareous nannoplankton, and are found in marine deposits from the Triassic period to the Recent. Coccoliths range in size from one to thirty-five microns.

codon: A triplet of bases (or nucleotides) in the DNA coding for one amino acid. The relation between codons and amino acids is given by the genetic code. The triplet of bases that is complementary to a condon is called an anticodon; conventionally, the triplet in the mRNA is called the codon and the triplet in the tRNA is called the anticodon.

coelom: body cavity within which internal organs can develop, which is completely lined with tissue of mesodermal origin.

concretion: A compact mass of mineral matter, usually spherical or disk-like in shape and embedded in a host rock of different composition. They form by precipitation of mineral matter about a nucleus such as a leaf, trilobite exoskelton or a piece of shell of bone.

continental crust: Solid, outer layers of the earth, including the rocks of the continents. The part of the crust that directly underlies the continents and continental shelves. Averages about 35 km in thickness, but may be over 70 km thick under largest mountain ranges.

continental drift: The theory that horizontal movement of the earth's surface causes slow, relative movements of the continents toward or away from one another.

continental shelf: That portion of the continental margin that extends as a gently sloping surface from the shoreline seaward to a marked change in slope at the top of the continental slope . Seaward depth averages about 130 m.

continental slope: That portion of the continental margin that lies between the continental shelf and the continental rise. It is relatively steep, i.e., 3o - 6o degrees. The continental slope is underlain by crustal rocks of the continent.

continental rise: That portion of the continental margin that lies between the abyssal plain and the continental slope. The continental rise is underlain by crustal rocks of the ocean basin.

coprolite: The fossilized waste (dung; fecies; poop) matter of animals.

craton: A part of the earth's crust that has attained stability and has been little deformed for a prolonged period.

crown group: A designation in phylogenetics denoting a agreggation of species comprising all living representatives, if any are extant, plus all their ancestors back to their most recent common ancestor, as well as all of that ancestor's descendants. In simpler terms, it is a clade comprising a species together with all its descendants. Related stem group members are excluded from the crown group.

cytoplasm: The region of a eukaryotic cell outside the nucleus.

Darwinian evolution: Evolution by the process of natural selection acting on random variation.

deuterostome: Clade of Bilateran animals that share multiple HOX genes for the posterior. Means "second mouth", so called because the mouth develops from the second opening into the embryonic gut. The first opening (the blastopore) forms the future anus only, and the mouth forms later. The body cavity (coelom) develops from buds off the gut. Deuterostomes belong to a larger group within the Animalia called the Bilateria, because they are bilaterally symmetrical with a left and a right side to their bodies. Some d euterostomes such as echinoderms like starfish exhibit radially symmetry. They are nonetheless in the group because during embryonic starfish develop, they begin bilaterally, but switch to radial symmetry during development.

diagenesis: The physical, chemical or biological alteration of sediments into sedimentary rock at relatively low temperatures and pressures that can result in changes to the rock's original mineralogy and texture. After deposition, sediments are compacted as they are buried beneath successive layers of sediment and cemented by minerals that precipitate from solution. Grains of sediment, rock fragments and fossils can be replaced by other minerals during diagenesis. Porosity usually decreases during diagenesis, except in rare cases such as dissolution of minerals and dolomitization.

diploid: Having two sets of genes and two sets of chromosomes (one from the mother, one from the father). Many common species, including humans, are diploid. Compare with haploid and polyploid.

diversity (or genetic diversity): A measure of the possible choices of different information at a gene. For example, whether it codes for brown or blue eyes.

Deoxyribonucleic acid (DNA): A nucleic acid that constitutes the genetic material of all cellular organisms and the DNA viruses; DNA replicates and controls through messenger RNA the inheritable characteristics of all organisms. A molecule of DNA is made up of two parallel twisted chains of alternating units of phosphoric acid and deoxyribose, linked by crosspieces of the purine bases and the pyrimidine bases, resulting in a right-handed helical structure, that carries genetic information encoded in the sequence of the bases.

DNA base sequence: A chain of repeating units of deoxyribonucleotides (adenine, guanine, cytosice, thymine) arranged in a particular pattern.

dominance (genetic): An allele (A) is dominant if the phenotype of the heterozygote (Aa) is the same as the homozygote (AA). The allele (a) does not influence the heterozygote's phenotype and is called recessive. An allele may be partly, rather than fully, dominant; in that case, the heterozygous phenotype is nearer to, rather than identical with, the homozygote of the dominant allele.

ecological species concept: A concept of species, according to which a species is a set of organisms adapted to a particular, discrete set of resources (or "niche") in the environment. Compare with biological species concept, cladistic species concept, phenetic species concept, and recognition species concept.

endosymbiosis: The relationship between organisms which live one within another (symbiont within host) in a mutually beneficial relationship. This process is believed to have accurred in the the evolution of eukaryotes from prokaryotes involved the symbiotic union of several previously independent ancestors. According to the theory, these ancestors included a host cell, an ancestor of mitochondria, an ancestor of chloroplasts, and, more controversially, a prokaryote that brought with it the structures that today provide cellular motion.

ecdysozoans: Clade of animals that: grow by periodically moulting - shedding their skin or exoskeleton (timed by steroid hormone signals); share a unique pattern of HOX genes, lack cilia; have separate sexes that copulate to achieve egg fertilization.

environmental variance: Within a population, the measure of how much of the variation of a particular phenotype is due to environmental factors (as opposed to variations in genotype - see genetic variance). An example might be the height of a plant as determined by such factors as nutrition or damage during development.

eukaryote: Any organism made up of eukaryotic cells. Eukaryotes are generally larger and have more DNA than prokaryotes (whose cells do not have a nucleus to contain their DNA). Almost all multicellular organisms are eukaryotes.

eumetazoa: The primary clade of Kindom Animalia that can be considered a subkingdom. The cells of Eumetazoans truly co-operate to form unmistakable tissues and organs. Nutrients and signals (e.g., hormones) flow efficiently betwwen cells, such that only specialized cells are involved in the acquisition of food.

exon: The nucleotide sequences of some genes consist of parts that code for amino acids, with other parts that do not code for amino acids interspersed among them. The coding parts, which are translated, are called exons; the interspersed non-coding parts are called introns.

exoskeleton, in contrast to an endoskeleton, is an external anatomical feature that supports and protects an animal's body. Many invertebrate animals such as insects, spiders, crustaceans and shellfish have exoskeletons. Lobsters, for example, have tough outer shell systems which provide rigidity and shape to their bodies. An exoskeleton may interfere with an animal's growth. To overcome this, arthropods go through a process called moulting in which they shed their exoskeleton and replace it with a new, larger one.

facies, metamorphic: A set of metamorphic mineral assemblages, repeatedly associated in space and time, such that there is a constant and therefore predictable relationship between mineral composition and chemical composition. That relationship is a consequence of conditions of temperature and pressure under which the assemblages are stable.

family: The category of taxonomic classification between order and genus (see taxon). Organisms within a family share a close similarity; for example, the cat family, Felidae, which includes lions and domestic cats.

fitness: The success of an individual (or allele or genotype in a population) in surviving and reproducing, measured by that individual's (or allele's or genotype's) genetic contribution to the next generation and subsequent generations.

fungi: A group of organisms comprising the kingdom Fungi, which includes molds and mushrooms. They can exist either as single cells or make up a multicellular body called a mycelium. Fungi lack chlorophyll and secrete digestive enzymes that decompose other biological tissues.

gamete: Haploid reproductive cells that combine at fertilization to form the zygote, called sperm (or pollen) in males and eggs in females.

gene: A sequence of nucleotides coding for a protein (or, in some cases, part of a protein); a unit of heredity.

gene expression: The degree to which a gene is active in a certain tissue of the body, measured by the amount of mRNA in the tissue.

genetic: Related to genes. A gene is a sequence of nucleotides coding for a protein (or, in some cases, part of a protein); a unit of heredity.

genetics: The study of genes and their relationship to characteristics of organisms.

genetic code: The code relating nucleotide triplets in the mRNA (or DNA) to amino acids in the proteins.

genetic drift: Changes in the frequencies of alleles in a population that occur by chance, rather than because of natural selection.

genetic variance: Within a population, the measure of how much of the variation of a particular phenotype is due to genotypic variation (as opposed to environmental factors - see environmental variance). An example might be the height of a tree as determined by genes inherited from the parents.

genome: The full set of DNA in a cell or organism.

genomics: The science dealing with analysis of the full range of genes in an organism.

genotype: The set of two genes possessed by an individual at a given locus. More generally, the genetic profile of an individual.

genus (plural genera): The second-to-lowest category in taxonomic classification. The phrase "species name" generally refers to the genus and species together, as in the Latin name for humans, Homo sapiens. See taxon.

glaciation: The formation of large sheets of ice across land. Glaciation of the continents marks the beginning of ice ages, when the makeup of Earth and organisms on it changes dramatically.

Gondwana: The southern portion of the late Paleozoic supercontinent known as Pangea. It means, literally "Land of the Gonds" (a people of the Indian subcontinent).

haploid: The condition of having only one set of genes or chromosomes. In normally diploid organisms such as humans, only the gametes are haploid.

hardness: The resistance of a mineral to scratching.

heterotrophic: Comprise organisms that are not self-sustaining; that is, they derive energy from the oxidation of organic compounds either by consumption or absorption of other organisms.

heterozygote: An individual having two different alleles at a genetic locus. Compare with homozygote.

holotype: specimen that serves as the standard bearer of a species or subspecies name.

Homalozoa (informally carpoids): Extinct subphylum (Phylum Enchinodermata) whose members have no trace of radial symmetry. The theca is depressed and asymmetrical. Homalozoa are known from Middle Cambrian to Middle Devonian rocks.

HOX genes (Hox cluster): Genes (transcription factors) paramount in development and found to be highly conserved in evolution. Occuring in clusters they act as master switches for other genes in that express and time developmental processes. The genomes of all animals that have been sequenced have at least one Hox cluster that show strong homology to the genes in Drosophila (the friut fly). For example, mice and humans have 4 Hox clusters (a total of 39 genes in humans) located on four different chromosomes.

Incertae sedis, meaning "of uncertain position (seat)", is a term used to define a taxonomic group where its broader (phylogenetic) relationships are unknown or undefined

ichnofossils: trace fossils that are seen as preserved tracks or other signs of the behaviors of animals in the substrate. Ichnofossils can provide insights on the behavior of an extinct animal. Very rarely is the animal itself found in direct association with the ichnofossil it created.

intron: The nucleotide sequences of some genes consist of parts that code for amino acids, and other parts that do not code for amino acids interspersed among them. The interspersed non-coding parts, which are not translated, are called introns; the coding parts are called exons.

Kingdom Animalia: Comprises the animals. These are multicellular organisms with cells that lack a cell wall. Many are capable of movement, or movement of some of their body parts, at some time of their life. Animals are heterotrophic, that is, they cannot obtain energy from non-living forms and must eat other organisms, or their products, to obtain energy.

Kingdom Fungii: Comprise mushrooms, yeasts, and other fungi. These are eukaryotic multicellular organisms that are typically non-moving, have a cell surrounded by a cell wall, and are heterotrophic, that is, they cannot use energy from non-living forms and must consume other organisms, or their products, to obtain energy. Many are decomposers, that is, they obtain energy by breaking down molecules in dead, decaying organisms.

Kingdom Monera: Comprise bacteria and cyanobacteria. These are unicellular organisms that are prokaryotic, that is, do not have a nucleus surrounded by a nuclear membrane. The bacteria are mostly heterotrophic, that is, they cannot obtain energy from non-living forms and must eat other organisms, or their products, to obtain energy. The cyanobacteria are autotrophic, that is, they can convert energy from non-living forms into biologically useful energy (stored in the chemical bonds of biological molecules); cyanobacteria, like plants, accomplish this through the process of photosynthesis.

Kingdom Plantae: Comprise the plants. These are eukaryotic multicellular organisms with cells surrounded by a cell wall made of the carbohydrate cellulose. Plants are typically non-mobile. They are autotrophic, that is, they can convert energy from non-living forms into biologically useful energy (stored in the chemical bonds of biological molecules); plants accomplish this through the process of photosynthesis, synthesis of energy-containing biological compounds by trapping light energy.

Kingdom Protista: Comprise unicellular organisms that are eukaryotic, that is, have a nucleus separated from the cytoplasm of the cell by a nuclear membrane. Some are plant-like in that they are autotrophic, while others are animal-like in that they are heterotrophic.

Laurasia: The northern portion of the late Paleozoic supercontinent called Pangea.

limestone, is a sedimentary rock composed largely of the mineral calcite (calcium carbonate: CaCO3). Limestones often contain varying amounts of silica in the form of chert or flint, as well as varying amounts of clay, silt and sand as disseminations, nodules, or layers within the rock. The primary source of the calcite in limestone is most commonly marine organisms.

lithification (from the Greek word lithos meaning 'rock' and the Latin-derived suffix -ific) is the process whereby sediments compact under pressure, expel connate fluids, and gradually become solid rock. Essentially, lithification is a process of porosity destruction through compaction and cementation. Lithification includes all the processes which convert unconsolidated sediments into sedimentary rocks. Petrification, though often used as a synonym, is more specifically used to describe the replacement of organic material by minerals in the formation of fossils.

lithosphere: the outer skin of the earth, composed of the crust and the uppermost mantle.

lophotrochozoans: A clade of animals that share a cluster of HOX genes quite different from those found in the ecdysozoans (and deuterostomes). They share similar sequences in their 18S rRNA genes. The phylogeny of this clade that includes brachiopods, mulluscs, bryozoa, and many other groups is the subject of many competing hypothses.

mantle: The zone of the earth below the crust and above the core.

marl: marine sediment made of sand, clay, and glauconite in different ratios.

matrix: The solid matter in which a fossil or crystal is embedded. Also, a binding substance (e.g., cement in concrete).

messenger RNA (mRNA): The molecule transcribed by DNA that then carries genetic information from a gene to the site in the cell where the information determines the order of amino acids in the synthesis of a protein.

metazoa: all the multicellular, eukaryotic organisms comrising Kingdom Animalia (the animals).

monophyletic: A group composed of a collection of organisms, including the most recent common ancestor of all those organisms and all the descendants of that most recent common ancestor. A monophyletic taxon is also called a clade.

natural selection: The differential survival and reproduction of classes of organisms that differ from one another in on or more usually heritable characteristics. Through this process, the forms of organisms in a population that are best adapted to their local environment increase in frequency relative to less well-adapted forms over a number of generations. This difference in survival and reproduction is not due to chance.

ontogeny (also ontogenesis or morphogenesis): describes the origin and the development of an organism from the fertilized egg to its mature form. Ontogeny is studied in developmental biology.

opisthokonts: a large and believed monophyletic group of eukaryotes, including both the animals and fungi, and some protists that have the common characteristic of flagellate cells to propel themselves.

organism: Any individual living thing.

ostraderms: Primitive jawless fishes, covered by bony armor, that lived in the Cambrian through Devonian periods.

oxidation: The act of oxidizing or state of being oxidized. Chemically it consists in the increase of positive charges on an atom or the loss of negative charges. Most biological oxidations are accomplished by the removal of a pair of hydrogen atoms (dehydrogenation) from a molecule. Such oxidations must be accompanied by reduction of an acceptor molecule.

pelagic: living in the open ocean.

paleobiology: The biological study of fossils.

paleomagnetism: Study of the Earth's past magnetism as it is recorded in the rocks.

paleontologist: A scientist who studies fossils to better understand life in prehistoric times.

paleontology: The scientific study of fossils.

Pangea: A supercontinent that existed from about 300 to 200 million years ago, and included most of the continental crust of the Earth.

parapatric speciation: Speciation in which the new species forms from a population contiguous with the ancestral species' geographic range.

paraphyletic group: A set of species containing an ancestral species together with some, but not all, of its descendants. The species included in the group are those that have continued to resemble the ancestor; the excluded species have evolved rapidly and no longer resemble their ancestor.

paratype: All of the specimens in the type series of a species or subspecies other than the holotype.

peripatric speciation: A synonym of peripheral isolate speciation.

peripheral isolate speciation: A form of allopatric speciation in which the new species is formed from a small population isolated at the edge of the ancestral population's geographic range. Also called peripatric speciation.

petrifaction: Petrifaction or petrification is the process by which organic material is converted into stone or a similar substance. It is approximately synonymous with fossilization. Petrified wood is the most well known result of this process.

Pharmacogenomics: The application of genomic information to clinical trials to determine which patients, based on their genetic make-up, are most likely to benefit from a certain drug or which are likely to suffer adverse effects.

photosynthesis: The fundamental biological process by which green plants make organic compounds such as carbohydrates from atmospheric carbon dioxide and water using light energy from the Sun. The process has two main phases: the light-dependent light reaction responsible for the initial capture of energy, and the light-independent dark reaction in which this energy is stored in the chemical bonds of organic molecules. Since virtually all other forms of life are directly or indirectly dependent on green plants for food, photosynthesis is the basis for almost all life on earth.

phenetic species concept: A concept of species according to which a species is a set of organisms that are phenotypically similar to one another. Compare with biological species concept, cladistic species concept, ecological species concept, and recognition species concept.

phenotype: The physical or functional characteristics of an organism, produced by the interaction of genotype and environment during growth and development.

Phenotypic variance: Variance of the phenotype due to genotypic and environmental factors combined. Phenotypic variance = genetic variance + environmental variance.

phylogeny: The study of ancestral relations among species, often illustrated with a "tree of life" branching diagram, which is also known as a phylogenetic tree. Phylogenetics is the study of evolutionary relationships and relatedness among various groups of organisms as applied to the level of domains, phyla, orders, etc. Phylogeny (or phylogenesis) traces the origin and evolution of a set of organisms, usually a set of species. A major task of systematics is to determine the ancestral relationships among both extant and extinct known species.

phylum (plural phyla): One of the highest levels of taxonomic classification. See taxon. More

physiological Pathway: The sequence of biochemical interactions among proteins that regulates the function of living cells.

phytoplankton: Microscopic aquatic organisms that, like plants, use photosynthesis to capture and harness solar energy.

polygenetic: Originating in various ways or from various sources.

plate tectonics: The theory that the surface of the earth is made of a number of plates, which have moved throughout geological time resulting in the present-day positions of the continents. Plate tectonics explains the locations of mountain building as well as earthquakes and volcanoes. The rigid plates consist of continental and oceanic crust together with the upper mantle, which "float" on the semi-molten layer of the mantle beneath them, and move relative to each other across the earth. Six major plates (Eurasian, American, African, Pacific, Indian, and Antarctic) are recognized, together with a number of smaller ones. The plate margins coincide with zones of seismic and volcanic activity.

polymorphism: A condition in which a population possesses more than one allele at a locus. Sometimes it is defined as the condition of having more than one allele with a frequency of more than five percent in the population.

polyphyletic group: A set of species descended from more than one common ancestor. The ultimate common ancestor of all species in the group is not a member of the polyphyletic group, usually because the common ancestor lacks the characteristics of the group.

polyploid: An individual containing more than two sets of genes and chromosomes.

population: A group of organisms, usually a group of sexual organisms that interbreed and share a gene pool, and are normally relatively isolated from other groups of the same species.

postzygotic isolation: A form of reproductive isolation in which a zygote is successfully formed but then either fails to develop or develops into a sterile adult. Donkeys and horses are postzygotically isolated from one another; a male donkey and a female horse can mate to produce a mule, but the mule is sterile.

prezygotic isolation: A form of reproductive isolation in which the two species never reach the stage of successful mating, and thus no zygote is formed. Examples would be species that have different breeding seasons or courtship displays, and which therefore never recognize one another as potential mates.

probe array: Used in microarray technology - a silicon or glass chip to which small pieces of DNA, or probes, have been attached, with each probe representing a sequence of bases unique to a known gene or gene fragment. Also known as a microarray or DNA chip.

prokaryote: A cell without a distinct nucleus. Bacteria and some other simple organisms are prokaryotic. Compare with eukaryote. All prokaryotes form a paraphyletic grouping.

protaspis: The earliest stage recognized in larval trilobite (Trilobita) development. The larva is small, often spiny, and grows through successive moult stages. Initially it is a small disc but size and segmentation increase with each successive moult.

protein: A molecule made up of a sequence of amino acids (there are 23 different amino acids). Many of the important molecules in a living thing -- for example, all enzymes -- are proteins.

protist: An organism that belongs to the kingdom Protista, which includes forms with both plant and animal affinities, i.e., protozoans, bacteria, and some algae, fungi, and viruses.

radial symmetry: The arrangement of parts in an organ or organism such that cutting through the centre of the structure in any direction produces two halves that are mirror images of each other. The stems and roots of plants usually show radial symmetry, while all animals belonging to the Cnidaria (e.g. jellyfish) and Echinodermata (e.g. starfish) are radially symmetrical - and typically sessile - in their adult form. The term actinomorphy is used to describe radial symmetry in flowers.

receptors: Proteins that can bind to other specific molecules. Usually on the surface of a cell, receptors often bind to antibodies or hormones.

recessive: An allele (A) is recessive if the phenotype of the heterozygote (Aa) is the same as the homozygote (aa) for the alternative allele (a) and different from the homozygote for the recessive (AA). The allele (a) controls the heterozygote's phenotype and is called dominant. An allele may be partly, rather than fully, recessive; in that case, the heterozygous phenotype is nearer to, rather than identical with, the homozygote for the dominant allele.

recognition species concept: A concept of species according to which a species is a set of organisms that recognize one another as potential mates; they have a shared mate recognition system. Compare with biological species concept, cladistic species concept, ecological species concept, and phenetic species concept.

recurrent fauna: A group of animal species that is found in a particular environment. As the environment recurs, so does the fauna.

reproductive isolation: Two populations or individuals of opposite sex are considered reproductively isolated from one another if they cannot together produce fertile offspring. See prezygotic isolation and postzygotic isolation.

ridge, oceanic: A major submarine mountain range.

rift system: The oceanic ridges formed where tectonic plates are separating and a new crust is being created; also, their on-land counterparts such as the East African Rift.

rift zone: A zone of volcanic features associated with underlying dikes. The location of the rift is marked by cracks, faults, and vents.

Ring-of-Fire: The regions of mountain-building earthquakes and volcanoes which surround the Pacific Ocean.

RNA: a linear, usually single-stranded polymer of ribonucleotides, each containing the sugar ribose in association with a phosphate group and one of four nitrogenous bases: adenine, guanine, cytosine, or uracil. RNA is found in all living cells; in prokaryotic and eukaryotic cells, it encodes the information needed to synthesize proteins (i.e., it copies “instructions” that it receives from DNA); in certain viruses, it serves as the genome. (An abbreviation for ribonucleic acid.)

sandstone: A clastic sedimentary rock in which the particles are dominantly of sand size, from 0.062 mm to 2 mm in diameter.

sessile: attached or stationary, as opposed to free-living or motile.

seafloor spreading: The mechanism by which new seafloor crust is created at oceanic ridges and slowly spreads away as plates are separating.

seamount: A submarine volcano.

sedimentary facies: An accumulation of deposits that exhibits specific characteristics and grades laterally into other sedimentary accumulations that were formed at the same time but exhibit different characteristics.

sedimentary rock: Rock formed from the accumulation of sediment, which may consist of fragments and mineral grains of varying sizes from pre-existing rocks, remains or products of animals and plants, the products of chemical action, or mixtures of these.

sequence: The order of the chemical bases -adenine (A), thymine (T), cytosine (C), and guanine (G)-in a gene. The base sequence determines the order of amino acids making up the protein encoded by the gene.

shale: Shale is a fine-grained sedimentary rock whose original constituents were clays or muds. It is characterized by thin laminae breaking with an irregular curving fracture parallel to in situ bedding planes.

silica: A chemical combination of silicon and oxygen.

Single nucleotide polymorphism (SNP): A site on the DNA at which the base sequence differs among individuals. (The abbreviation is pronounced "snip.")

Sirenia: mammal herbivors adapted to aquatic coastal environments such that arms are modified into paddles, have no legs, are fat, and have highly modified skulls with greatly reduced dentition. Their nipples are under their arms (e.g. the extant manatees).

speciation: Changes in related organisms to the point where they are different enough to be considered separate species. This occurs when populations of one species are separated and adapt to their new environment or conditions (physiological, geographic, or behavioral).

species: An important classificatory category, which can be variously defined by the biological species concept, cladistic species concept, ecological species concept, phenetic species concept, and recognition species concept. The biological species concept, according to which a species is a set of interbreeding organisms, is the most widely used definition, at least by biologists who study vertebrates. A particular species is referred to by a Linnaean binomial, such as Homo sapiens for human beings.

specific gravity: The ratio of the density of a material to the density of water.

stem group: a paraphyletic grouping of organisms comprising the total group (pan-group) less members of the crown group, and consequently excluding all extant members of the pan-group. By this definition, a stem group contains only the primitive relatives of members of the crown groups, all the way back to and excluding the crown group’s last common ancestor as well as the crown groups nearest extant relatives. By definition then, all members of a stem group are, in fact, extinct.

stratigraphic: The study of rock strata, especially of their distribution, deposition, and age.

stratigraphy: The succession and age relation of layered rocks.

stromatolites: Morphologically circumscribed accretionary growth structures with primary lamination that is, or may be, biogenic.

subsidence: In geology, engineering, and surveying, subsidence describes the motion of a surface (usually, the Earth's surface) as it shifts downward relative to a reference point such as sea-level. The opposite of subsidence is uplift, which results in an increase in elevation.

taxon (plural taxa): Any named taxonomic group, such as the family Felidae, or the genus Homo, or the species Homo sapiens. Also, a formally recognized group, as distinct from any other group (such as the group of herbivores, or the group of tree-climbers).

taxonomy: The theory and practice of biological classification.

trait: An attribute or character of an individual within a species for which heritable differences can be defined.

transcription: The process by which messenger RNA is read from the DNA forming a gene.

transcriptome: set of activated genes associated with specific tissue, which will vary over time.

transfer RNA (tRNA): A type of RNA that brings the amino acids to the ribosomes to make proteins. There are 20 kinds of transfer RNA molecules, one for each of the 20 main amino acids. A transfer RNA molecule has an amino acid attached to it, and contains the anticodon corresponding to that amino acid in another part of its structure. In protein synthesis, each codon in the messenger RNA combines with the appropriate tRNA's anticodon, and the amino acids are arranged in order to make the protein.

vertebrates: The group (specifically, a subphylum) of animals, descended from a common ancestor, that share the derived character of an internal skeleton made of bone or cartilage.

viscosity: A measure of resistance to flow in a liquid (water has low viscosity while honey has a higher viscosity.)

zygote: The cell formed by the fertilization of male and female gametes.

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