adaptation: a feature of an organism that enables it to survive and reproduce in a specific environment.

adenine: one of the four bases in the nucleotides of DNA, commonly denoted by the letter “A.”

adulthood: the mature stage of an organism in its life cycle, usually meaning that it is able to reproduce.

allele: alternative form of the same gene locus; one of a pair of genes that occupy corresponding positions on homologous chromosomes and determine alternative expressions of a single trait.

allele frequency: the proportion of a particular allele in a population as a percentage of the total alleles at that locus; also called gene frequency.

allopatric speciation: the process by which, in theory, a new species originates when a population that is geographically separated from the rest of the species becomes unable to reproduce with the original population.

amino acid: an organic compound that contains one or more amino groups and one or more acidic carboxyl groups; amino acids can be combined in chains (polymerized) to form peptides and proteins.

Amphibia: a class of cold-blooded, smooth-skinned vertebrates with legs; offspring usually hatch as aquatic larva with gills, which in most cases metamorphose into adults with air-breathing lungs; includes frogs and salamanders.

analogous structure: a body part in two or more species that performs a similar function but has a different structure; for example, the wings of bats and butterflies.

Animalia: in biological classification, the kingdom comprising all multicellular animals.

angiosperm: a flowering plant that forms its seeds in a protected ovary.

Annelida: a phylum of animals that have segmented bodies with a one-way digestive tract, a circulatory system and a nervous system; includes earthworms.

antibiotic: a chemical produced by one microorganism that can kill or inhibit the growth of other microorganisms; for example, penicillin and streptomycin.

antibiotic resistance: the ability of a microorganism to avoid the harmful effects of an antibiotic by destroying it, transporting it out of the cell, or undergoing changes that block its effects.

Archaea: one of the three domains of life; consists of single-celled organisms without a nucleus (prokaryotes) that differ from Eubacteria in their cell membranes, ribosomes and RNA; includes organisms that thrive in extreme environments such as high salt or heat.

Archaeopteryx: An extinct toothed bird that had a bony, feathered tail and claws.

Arthropoda: a phylum of animals that have a chitinous exoskeleton and a segmented body with paired, jointed appendages; includes insects, crustaceans, arachnids, centipedes and millipedes.

artifact hypothesis: the idea that the Cambrian animal phyla had ancestors, but those ancestors either left no fossil record or have not been found.

artificial selection: the process by which humans deliberately choose to breed only those organisms in a population that have desirable traits.

Aves: a class of warm-blooded feathered vertebrates that have wings for forelimbs; includes both flying and flightless birds.

base pair: two nucleotides on opposite but complementary strands in a DNA molecule; because of their shapes, adenine (A) forms a base pair with thymine (T) and guanine (G) forms a base pair with cytosine (C).

biogeography: the study of the geographical distribution of species.

body plan: the basic symmetry and architecture of an organism; the distinctive anatomical arrangement of fundamental structural elements such as the skeleton or shell; circulatory, respiratory and nervous systems; digestive tract; and appendages.

Burgess Shale: a Middle Cambrian (about 515 million years ago) deposit in British Columbia that contains exquisitely preserved fossils, including many soft-bodied organisms.

bushing: A cylindrical lining used to reduce friction or guide motion.

Cambrian: the first geological period of the Paleozoic Era, lasting from about 540 to 488 million years ago; named after Cambria, Wales.

Cambrian Explosion: an event at the beginning of the Cambrian, lasting less than 10 million years, during which most of the major animal phyla first appear in the fossil record.

Cesarean section: a surgically-assisted birth in which an incision is made in the walls of the mother’s abdomen and uterus and the baby is removed without passing through the birth canal; also called C-section.

cassette mutagenesis: a procedure that systematically alters individual DNA codons to determine the effects of those alterations on protein folding or function.

Carnivora: an order of mammals that have large, sharp teeth and powerful jaws and prey on other animals; includes cats, dogs, bears, and weasels.

catalyst: a chemical that increases the rate of a chemical reaction but is not permanently changed by it.

Cephalopod: a class of marine mollusks that have tentacles, horny jaws and well-developed eyes and nervous systems; includes octopuses, squids, and Nautilus.

Cetacea: an order of marine mammals; includes whales, dolphins and porpoises.

chance: the characteristic of lacking any discernible pattern or direction, with more than one outcome being possible in a given set of circumstances.

cell: the basic structural and functional unit of all living organisms, enclosed by a semipermeable plasma membrane.

Chengjiang biota (or fauna): a suite of fossils from the lower Cambrian Maotianshan shale in China, characterized by exquisite soft-body preservation.

Chiroptera: an order of flying mammals; includes bats.

Chordata: a phylum of animals that have a dorsal nerve cord and a notochord during development; includes the vertebrates (animals with backbones).

chromosome: a thread-like structure in the nucleus of a eukaryotic cell; consists of a single compacted molecule of DNA and some proteins.

cilia: short, cylindrical projections on living cells that typically function in locomotion.

circular definition: a logical fallacy in which the term being defined is used as part of the definition.

cladogram: a branching diagram that arranges organisms according to their shared and unshared characteristics; often used to construct hypotheses about the ancestor-descendant relationships of those organisms.

class: the level of biological classification above an order and below a phylum.

codon: The basic unit of the genetic code; a sequence of three adjacent nucleotides in DNA or mRNA that specifies one amino acid.

collagen: a long fibrous protein that is the main constituent of connective tissues and the most abundant protein in animals.

compensatory mutation: a secondary mutation in a bacterium that helps to restore the original function lost due to a prior mutation that rendered the bacterium resistant to an antibiotic.

competitive advantage: the increased ability of an organism to survive and reproduce in comparison with other organisms competing for limited resources.

complexity: the improbability of assembling a structure, system, or molecule.

contingency: characteristic of an event that is only one of several logically or physically possible outcomes.

convergent evolution: the appearance of similar characteristics in two or more taxa by independent lines of descent.

co-option: the use of an existing biological structure or feature for a new function; also called exaptation.

Cretaceous: a geological period lasting from about 145 to 65 million years ago, at the end of which dinosaurs became extinct.

cytochrome c: an iron-bearing molecule utilized in the electron transport chains of mitochondria and chloroplasts.

cytosine: one of the four bases in the nucleotides of DNA, commonly denoted by the letter “C.”

cytoskeleton: a network of microscopic fibers that stabilize the shape of a eukaryotic cell and function in intracellular transport.

cytoplasm: all the contents of a cell inside the plasma membrane (but, in eukaryotes, outside the nucleus).

Darwinism: the theory that all living things are descended from a common ancestor and modified by unguided natural processes such as natural selection and random variation.

developmental pathway: the route or process by which a structure or organ forms in the embryo of an organism.

diaphragm: a large, thin sheet of muscle that seals the airtight sac or chamber containing the lungs, and completely separates the chest cavity from the abdomen.

differential reproduction: variation in the rate of producing offspring between organisms that are better adapted to their environment and those that are less well adapted.

disparity: major variations in morphology or body plan.

diversity: minor variations within a basic body plan or biological form; for example, variations among dogs such as a golden retriever and St. Bernard.

DNA: deoxyribonucleic acid; a molecule consisting of two long, intertwined chains of nucleotides that carry the information to specify the sequence of amino acids in proteins.

domains: taxonomic categories higher than kingdom, defined by the gene sequences and basic mechanisms used to perform fundamental cellular functions; the three domains are the Archaea, Eubacteria, and Eukaryota.

duplication mutation: the production of a copy of some segment of DNA during meiosis.

Echinodermata: a phylum of marine animals that are radially symmetrical as adults and have a calcareous endoskeleton, tube feet and water vascular system; includes starfishes and sea urchins.

Ediacaran fauna: a group of Precambrian (Vendian) multicellular organisms, named after the Ediacaran Hills in Australia.

embryo: an early developmental stage of a multicellular organism.

enzyme: a protein that functions as a catalyst in biochemical reactions.

Eocene: a geological period lasting from about 56 to 34 million years ago, marked by the diversification of mammals.

Eubacteria: one of the three domains of life; consists of single-celled organisms without a nucleus (prokaryotes) that differ from Archaea in their cell membranes, ribosomes and RNA; includes gram-negative bacteria such as E. coli and gram-positive bacteria such as Staphylococcus and Streptococcus.

eukaryote: a cell containing membrane-bound organelles, including (most importantly) a nucleus.

Eukaryota (also known as Eukarya): one of the three domains of life; includes all organisms composed of one or more cells that contain a distinct membrane-bound nucleus.

evolution: of the many meanings of this word, three are used here: (1) change over time; the fact that most of the organisms alive today are different from organisms that existed in the past; (2) universal common descent; the hypothesis that all organisms are modified descendants of a single common ancestor in the distant past; (3) the mechanisms of biological change; the hypothesis that natural selection acting on random variations has been the principal cause of modification.

exaptation: the use of an existing biological structure or feature for a new function; co-option.

exoskeleton: a stiff external covering that contains, supports, and protects an animal’s body.

extrapolation: a conjecture based on the assumption that a phenomenon or trend observed in the present can be extended into the past or future.

family: the level of biological classification above a genus and below an order.

fitness: the ability of an organism to survive and produce viable offspring in a given environment.

fitness cost: the decrease in an organism’s ability to survive and reproduce in other environments following a mutation that confers a selective advantage in one environment.

flagellum: a long whiplike appendage that provides some function (usually locomotion) in microorganisms.

fossil: the mineralized remains, impression, or trace of a once-living organism.

fossil succession: the specific order of fossils, from lower to higher, within geological strata.

function: the role that a biological structure or feature plays in survival, reproduction or other activities of an organism.

functional information: nucleotide sequences of DNA and RNA that code for proteins with biological functions.

Galápagos Archipelago: a group of volcanic islands about 600 miles off the west coast of Ecuador, South America.

gene: a unit of heredity on a chromosome, usually understood as a DNA sequence that specifies a particular protein.

gene pool: the total genetic material in a population at a given time.

genetic information: the sequences of nucleotides in DNA and RNA that specify the sequences of amino acids in proteins.

genome: the total DNA of an organism.

genotype: the combination of alleles inherited for a particular trait.

genus: the level of biological classification above a species and below a family.

geographic barrier: any physical feature of the earth that separates two populations and prevents interbreeding between them.

Gondwanaland: A prehistoric supercontinent in the southern hemisphere that was broken up by the action of plate tectonics to form the modern continents.

gradualism: the Darwinian view that since all species have descended from other species by the ordinary process of reproduction, evolution has occured in steps no larger than those that now distinguish parents and offspring.

guanine: one of the four bases in the nucleotides of DNA, commonly denoted by the letter “G.”

halteres: tiny structures behind the wings in some insects (such as fruit flies), which help to stabilize the animal in flight; also called balancers.

hemoglobin: an iron-containing protein that carries oxygen in the blood.

heredity: the transmission of traits from parents to offspring.

heritability: the proportion of phenotypic variation in a population that is attributable to differences in genotype.

hexokinase: an enzyme that catalyzes the addition of a phosphate group (“phosphorylation”) to a six-carbon sugar (“hexose”), a vital step in metabolism.

historical science: an enterprise that observes and studies clues left by past events and uses what is known about present cause-and-effect relationships to reconstruct the history of those events; examples include geology, paleontology, archaeology and forensics.

homeotic gene: a DNA sequence that affects embryo development by specifying the character of a body segment; for example, Antennapedia, in which a mutated gene can cause a fly to grow a leg from its head instead of an antenna.

homologous structure: a body part that is similar in structure and position in two or more species but has a different function in each; for example, the forelimbs of bats, porpoises and humans.

homoplasy: structural similarity not thought to be due to inheritance from a common ancestor; see convergent evolution.

hopeful monster: a hypothetical organism that supposedly originates in a single generation from a “macromutation” with large-scale effects on anatomy.

Hox gene: one of a cluster of homeotic genes; the Hox genes of many animals (such as insects and mammals) are remarkably similar.

humerus: in humans, a long bone in the upper arm that extends from the shoulder to the elbow; also, the corresponding bone in other animals.

Hymenoptera: an order of insects that includes bees, wasps and ants.

hypothesis: (1) an educated guess; (2) a tentative explanation; (3) a proposition to be tested by comparing it to evidence.

inference to the best explanation: a method of scientific reasoning that favors the hypothesis that would, if true, best explain the relevant evidence; hypotheses that qualify as “best” typically provide coherent and causally adequate explanations of the evidence or phenomenon in question.

Insecta: a class of arthropods characterized by a body divided into three parts (head, thorax, and abdomen); the head has compound eyes and the thorax has three pairs of legs.

irreducible complexity: the characteristic of a system of well-matched, mutually interacting parts performing a specific function, in which the removal of any one of the parts causes the system to cease functioning.

kingdom: the highest level of biological classification below a domain; the domain Eukaryota includes the kingdoms Protista, Fungi, Plantae and Animalia.

LUCA: Last Universal Common Ancestor; the most recent organism from which, in theory, all subsequent organisms have descended.

macroevolution: the origin of new large-scale features such as organs or body plans.

maladapted: poorly suited to survive and reproduce in a given environment.

Mammalia: A class of warm-blooded, fur-bearing vertebrates characterized by mammary glands, with which females produce milk to feed the young.

mammal-like reptiles: an extinct group of reptiles that first appeared during the Permian period.

manus: the most distal part of the forelimb of a vertebrate; in humans, this includes the wrist and hand.

marsupial: an animal (usually a mammal) in which embryos complete their development in a maternal pouch called a “marsupium.”

mechanism: the process by which something occurs.

microevolution: small-scale changes within existing species.

minimal complexity: the simplest state, either genetic or metabolic, that is consistent with the viability of an organism.

mitochondria: organelles in eukaryotic cells that convert food into a form of energy usable by the cell.

molecular homology: similarity of the nucleotide sequences of DNA or RNA molecules, or the amino acid sequences of proteins.

molecular machines: microscopic assemblages of biological molecules (such as proteins) that move and perform key cellular functions.

Mollusca: a phylum of animals that are unsegmented and soft-bodied, and have a muscular foot and often one or more hard shells; includes clams, snails and octopuses.

monophyletic: descended from a single common ancestor.

morphology: the form or structure of an organism; anatomy.

mRNA: messenger RNA; the sequence of mRNA contains the same information as the DNA sequence in a “gene” and specifies the order of amino acids in a protein.

mutant: an organism with a new trait resulting from a mutation.

mutation: alteration of an organism’s DNA due to mistakes during replication or damage from external agents such as chemicals or radiation.

natural selection: the process in which organisms better adapted to their environment survive and reproduce at a higher rate than those less adapted, with the result that the survivors’ characteristics are more prevalent in subsequent generations.

Nautilus: a cephalopod with an external spiral shell.

necessity: characteristic of an event in which there were no other logically or physically possible outcomes.

Nematoda: a phylum of animals that have cylindrical, bilaterally symmetrical bodies; includes roundworms and hookworms.

neo-Darwinism: the modern version of Darwinian evolutionary theory, according to which new variations originate in DNA mutations that provide the raw materials upon which natural selection may act to produce evolutionary change.

notochord: a flexible column located between the gut and nerve cord in the embryos of all chordates, a group of animals that includes the vertebrates (animals with backbones).

nucleic acid: a molecule consisting of joined nucleotides that can carry biological information; for example, DNA and RNA.

nucleotide: the fundamental structural unit of a nucleic acid (DNA or RNA); consists of a nitrogen-carrying base (purine or pyrimidine), a sugar molecule, and a phosphate group.

ontogeny: the development of an organism over its lifetime, from conception to death.

order: the level of biological classification above a family and below a class.

ORFan genes: DNA sequences that resemble no other known genes in biology and are thus evolutionarily untraceable.

organ: a group of tissues that form a distinct structure and perform a specific function, such as a heart or lung.

paleontology: the scientific study of fossils and their use to reconstruct the history of life.

parabronchi: tiny air vesicles in a bird’s lung where gas exchange occurs.

penicillin: an antibiotic naturally produced by some molds of the genus Penicillium that interferes with the construction of new bacterial cell walls.

penicillinase: a complex enzyme found in some bacteria, which destroys penicillin and confers resistance to it.

peppered moths: Biston betularia, a species of night-flying moth sometimes cited in textbooks as an example of evolutionary change produced by natural selection.

pharyngula: a developmental stage in vertebrate embryos, after fertilization, cleavage and gastrulation, in which the embryos are characterized by a notochord, a post-anal tail, and a series of paired folds in the neck region.

phenotype: the observable physical characteristics of an organism or the physical manifestation of some trait, such as blood type, protein structure or body plan.

phylogeny: the evolutionary history of a group of organisms.

phylum: the highest level of biological classification within a kingdom.

point mutation: the substitution of one nucleotide for another in DNA or RNA.

polypeptide: a molecule consisting of many amino acids joined by chemical bonds between their amino and carboxyl groups; not necessarily biologically active.

polyphyletic: descended from different ancestors.

population: a group of individuals of one species in the same geographical area.

prebiotic: before the existence of biological life.

Precambrian: the geological time in Earth’s history before the beginning of the Cambrian period (about 540 million years ago).

primates: an order of mammals with binocular vision, specialized appendages for grasping and enlarged brains; includes lemurs, monkeys, apes and humans.

protein: a large polypeptide that performs a biological function.

protoplasm: the substance inside a living cell, once thought to be simple, but now known to be a complex network of biomolecules, microscopic structures and molecular machines; includes the cytoplasm and (in eukaryotes) the nucleus.

punctuated equilibrium: a characteristic of the fossil record in which new species appear suddenly (punctuation), then persist unchanged (stasis) until they disappear (extinction); named by Stephen Jay Gould and Niles Eldredge and attributed by them to allopatric speciation.

random variation: minor differences among the individual organisms in a population.

radius: in humans, a bone in the forearm that extends from the inside of the elbow to the thumb side of the wrist; also, the corresponding bone in other animals.

respiratory system: the organs in animals used for gas exchange.

reproductive success: the ability of an organism to reproduce and pass on its genes to offspring.

ribosome: an organelle composed of protein and RNA that uses the information in mRNAs to synthesize proteins inside a cell.

RNA: ribonucleic acid; a molecule consisting of the nucleotides adenine, guanine, cytosine and uracil (instead of thymine); involved in converting DNA sequences into amino acid sequences during protein synthesis in living cells.

scute: a protective horny plate on the exterior of a reptile.

selective advantage: the characteristic of an organism that enables it to survive and reproduce better than other organisms in a population in a given environment.

selective predation: a behavior in which a predator attacks only certain types of individuals in a population of potential prey.

speciation: the origin of a new species from an existing one.

species: the taxonomic rank below genus; there are many definitions of this word, all of which are controversial to some extent, but the most common definition used for sexually reproducing organisms is “a group of interbreeding organisms that is reproductively isolated from other such groups.”

stasis: the persistence of a particular species without discernible change through geological strata.

stator: a stationary part of a machine that remains fixed while other parts rotate around it.

sternum: the breastbone in vertebrates; a long, flat bone located in the middle of the chest.

strata: layers of rock, typically horizontal.

sympatric speciation: the process by which, in theory, a new species originates from another without being geographically separated from it.

taxon: a group or category of biological classification at any level (plural: taxa).

tetrapod: a vertebrate animal with four legs or leg-like appendages.

theropod: a group of terrestrial, bipedal dinosaurs that were primarily carnivorous; one example was Tyrannosaurus rex.

thymine: one of the four bases in the nucleotides of DNA, commonly denoted by the letter “T.”

tissue: a group of interconnected cells forming a structure or performing a particular function in a multicellular organism.

transcription: the process by which mRNA is synthesized using DNA as a template.

transitional form: an organism that is intermediate between an ancestor and a descendant in a evolutionary sequence.

translation: the process by which protein is synthesized by a ribosome using mRNA as a template.

trait: any characteristic of an organism, whether genetic or structural.

Tree of Life: Darwin’s metaphor for the history of life, which portrays all living things (the tips of the branches) as modified descendants of a single common ancestor (the root or trunk).

trunk: the body of a vertebrate animal excluding the head, limbs and tail.

type III secretory system: a microscopic needle-like structure that some bacteria use to inject toxins into other cells; abbreviated TTSS.

ulna: in humans, a bone in the forearm that extends from the outside of the elbow to the side of the wrist opposite the thumb; also, the corresponding bone in other animals.

universal common ancestry: the hypothesis that all species are biological descendants of a single common ancestor, and that all life can be portrayed as a tree with a single trunk or root.

variation: one or more differences among individual organisms in the same species.

Vendian: the geological period just before the Cambrian, lasting from about 650 to 540 million years ago; contains fossils of the Ediacaran fauna.

vertebrates: chordates with a backbone; these include fish, amphibians, reptiles, birds, and mammals.

viability: the ability of an organism to survive.

For Discussion on the Debate