abiogenesis — scientific term for the generation of life from inorganic matter, as distinguished from “spontaneous generation” (e.g. maggots arising spontaneously from rotting meat), which was disproven by Louis Pasteur; today refers to hypotheses about the chemical origin of life, as from a primordial sea, via self-replicating molecules

abduction — “an inspired inference,” term coined by philosophers of science William Whewell (1794-1866) and Charles Sanders Peirce (1839-1914) as another way of “thinking backward” through imagining an hypothesis which, if true, would help to explain the data. Peirce believed in an “experimental logic” that codifies how we think when we are most innovative, the art of guessing right. So Peirce’s method had three steps: abduction, through which a new hypothesis was postulated; deduction of the consequences from that hypothesis, and induction or testing of the hypothesis (through reasoning from particular instances to arrive at a general rule).

Abduction has also been defined as a heuristic procedure that reasons inductively from available empirical evidence to the discovery of the probable hypotheses that would best explain its occurrence. Both Peirce and Reichenbach developed detailed theories about the invention of such hypotheses in what is sometimes called "the logic of discovery." The success of this enterprise may founder on the under-determination of incompatible hypotheses. See Abduction and Induction: Essays on Their Relation and Integration, ed. by Peter A. Flach and Antonis C. Kakas (Kluwer, 2000)

In fault diagnosis and machine learning, the technique of using certain plausible (but non-logical) inferences, e.g. to generate explanations from observations and logical sentences. Abduction is used here to characterize that third way of thinking, which is neither induction nor deduction, but the imaginative leap to generate a new idea.

acceptor strand — a strand of nucleic acid into which a piece of foreign genetic material can be placed

accident — Accident as a formal category first appeared in Aristotle’s Categories. For some interpreters accident is an entity, for others a predicate (i.e. action) or qualifier of something else (i.e. distinguishing between a thing and its properties). The term here is used to refer to entities and is fully defined in the context of the argument.

achiral — lacking chirality (screw-like morphology)

adaptability, somatic — organism response to environmental change, either to offset adverse effects of the environment or to increase the organism’s performance

adaptation, evolutionary  — heritable change in the phenotype of an organism selected for increased reproductive fitness in a given environment

adaptive cell behavior — cell response to local environments and cell-cell signals, which can change in combinations and amounts to generate the observable phenotype

adenine (A) — one of the bases of the nucleic acids (see base)

adenosine triphosphate (ATP) — a nucleoside triphosphate consisting of adenine, ribose, and three phosphate groups; a high energy compound that releases a large amount of energy when it transfers a phosphate to an acceptor; an energy-rich phosphate ester, used as a molecular energy store in the cell. Splitting one of the bonds linking the phosphate groups releases the energy and makes it available for biochemical reactions.

adsorption — adhesion of a thin layer of molecules to the surface of solids or liquids

aerobic — organisms (aerobes) that require atmospheric oxygen for their metabolic processes

alanine — one of the twenty common naturally occurring amino acids, a basic building block of proteins

alpha-helix — one of the structures adopted by polypeptide chains of proteins; a helical (spiral-staircase) structure stabilized by hydrogen bonds between each CO group and the fourth nearest NH group

algorithm — a step-by-step problem-solving procedure, often recursive

allopatric speciation — evolution of new species through divergence of species that are geogrpahically separated

allosteric regulation — regulation of an enzyme or protein by binding an effector molecule at the protein’s allosteric site (a site other than the protein's active site)

allostery — proteins with two kinds of surface sites, one at which a function occurs, the other at which regulation of that function occurs

ambiguity — an attribute of the object we are trying to know, while uncertainty pertains to our capacity to know

amino acids — compound containing both an acidic carboxyl group (COOH) and a basic amino group (NH2); twenty commonly occurring amino acids are the building blocks of proteins. They are all L-stereo-isomers (left-handed) and all have the same basic structure, differing only in their single, functional side chain. Using amino acids as its building blocks, each protein is composed of particular amino acids joined by peptide bonds in a particular order.

amphiphiles — molecules that have one end that is hydrophobic with the other end being hydrophilic; see micelles

amplification — selective increase in the number of copies of one region of DNA

anaerobic — organisms (anaerobes) that live in the absence of atmospheric oxygen with metabolic processes that do not require oxygen

Angstrom unit — measure of length used to specify sizes on the atomic scale; one Angstrom unit equals one ten thousand millionth of a meter (10–10m)

antibody — protein molecule produced in vertebrates by the immune system in defense against foreign substances (antigens)

anticodon — sequence of three nucleotides (bases) in tRNA. Dring the translation process the anticodon interacts with the codon (which also consists of three nucleotides) and is thus selects the correct amino acid to incorporate into the growing protein chain

antigen — a protein on the surface of a virus, bacteria or cell that can stimulate the immune system to produce antibodies as a defense mechanism

A-PR Hypothesis — hypothesis that Autonomy and Pattern Recognition define A-PR cycles and that initiation of the first A-PR cycle defined the threshold when non-life came to life; A-PR cycles are also posited to explain how evolution advances toward increased functional effectiveness (work of Zann Gill)

apoptosis — programmed cell death to benefit the living organism (in contrast to necrosis, which is cell death from injury)

a priori — A priori knowledge is known generally independent of experience, except to the extent that its concepts are informed by experience, and so must be justified in some other way, whereas a posteriori knowledge designates what is known “after the fact” of experience.

archaea — one of three domains: bacteria, eukarya, and archaea (discovered by Carl Woese)

aristogenesis — an rejected theory holding that evolution proceeds along a determined path in contrast to the ultra-Darwinian view is that natural selection does not direct evolution towards any particular kind of organism or physiological attribute, nor is there any inner guiding force.

association — a relation between two or more ideas such that the appearance of one of them in the mind naturally leads to other(s)

antigen — usually a macromolecular protein or carbohydrate substance (as a toxin or enzyme) that triggers the production of antibodies when introduced into an organism

assimilation — heritable stabilization of somatic adaptation by genetic change

ATP — see adenosine triphosphate

attribute — used synonymously with “quality”, a characteristic of an object, seen by some as universals, by others as particulars; exemplified by properties. Attributes can be further qualified as relational, categorical, hypothetical etc.

AUs (astronomical units) — each AU being the distance between the Earth and the sun, 93 million miles

autocatalysis — occurs when the product of a reaction is also a catalyst for he same reaction

autocatalytic set — coherent, self-reinforcing webs of chemical reactions through which a new set is produced entirely from reactions within the original set

autonomy — capacity to make independent choices, self-governing

autopoiesis — autonomous, self-producing, self-maintaining, self-directed (Maturana, Varela)

autotrophy — self-nourishment

axiom — self-evident principle that does not require proof and that cannot be justified or further reduced logically

bacteriophage — viruses that attacks (multiplies in) bacteria; parasite which has lost its metabolic function and retains only the ability to replicate

Baldwin effect — effect seen when environmental induction of physiological or behavioral adaptation allows a population to survive long enough for the acculmulation byt selection of similar constitutive hereditaty changes

basal body — cytoplasmic organelle made up of microtubules which is found at the base of eukaryotic cilia and flagella

base — the symbols for genetic information in biochemistry, the basic components of the nucleic acids, which include: adenine (A), cytosine (C), guanine (G), and thymine (T) in DNA, with its close relation uracil (U) substituting for T in RNA.

base pairing — a specific interaction between bases, which occurs between guanine and cytosine and between adenine and thymine/ uracil

bias — predisposition or inclination influencing an outcome

biophores — August Weismann's term for the fundamental hereditary units of living matter

black smokers — the hottest vents, spewing out iron and sulfide

blastula — stage in the development od animals n which the embryo consists of an outer layer of cells, the trophectoderm, and an inner cell mass from which the embryo is formed

bootstrapping — after legend of Baron Münchhausen, who lifted himself out of a swamp by his own boot straps, self-starting

bottleneck — a stage of the process impeded by a required, but unlikely, contingency, a link that might break the chain of events required to complete the process. The challenge is to identify alternative pathways, scenarios, and events that could bypass the bottleneck. See choke point.

boundary element — A DNA sequence that isolates one domain of DNA from the regulatory influences of a neighboring domain

bounded variance — local variance needed to maintain global order under changing conditions

canalization — adjustment of developmental pathways by natural selection to produce a uniform result despite genetic and environmental variations

canalizing selection — selection for a well-buffered developmental pathway that ensures the production of a standard phenotype in spite of genetic and environmental variations

carbonaceous chrondrites — class of meteorites, which contain oil-like hydrocarbons

catalysis — the acceleration of a chemical reaction

catalyst — agent that accelerates a chemical reaction, an itself emerges unchanged at the end of the reaction; this agent can be a molecule, a clay surface area (as in the montmorillonite clay hypothesis); catalysts are most frequently proteins called enzymes, but they may be either inorganic or organic molecules

cation — positively charged ion

cell memory — the retention of functional or structural states in cell lineages

cellular inheritance — transmission of functional or structural states in cell lineages

central dogma — view that the flow of hereditary information is uni-directional from nucleic acids to proteins but never in the reverse direction

chemoautotroph — organism whose nutrition and metabolism is based upon obtaining energy from the oxidation of inorganic substances such as sulfur, nitrogen, iron and cell carbon from CO2 (carbon dioxide)

chert — chemical precipitate from groundwater creating sedimentary rock, often containing small fossils, often fine-grained and  silica-rich

chert dikes — vertical rock intrusions

chirality — the “handedness” of a screw or helix (right- or left-handed); a molecule exhibiting chirality is termed “chiral”

chloroplast — particles responsible for photosynthesis, which are green due to their constituent chlorophyll

choke point — low probability prerequisites; event in a hypothetical scenario with lowest probability of occurence. See bottleneck.

chondrite — a meteorite containing chondrules (from Greek chondros, grain), which are small, spherical silicate objects on the order of a millimeter in size that formed in the solar nebula before the asteroids were formed. Chondrites consist up to 80% of chondrules, embedded in a fine grained matrix.

chromosome — unit of heredity containing many genes; a linear structure containing hereditary information

classification — scheme for, or process of establishing, defining, and ranking taxa within hierarchical series of groups, either artificial or natural

coacervates — mixture of colloid particles that separates itself from colloidal solutions of opposite charge; colloidal droplets held together by electrostatic attractive forces; structures that segregate themselves from a water solution to form tiny droplets; these microscopic gel-like structures may be produced by lipids or other compounds, e.g. as when polymeric substances like gum arabic and gelatin are mixed with other compounds

codon — sequence of three consecutive nucleotides that code for an amino acid or for the signals “start” or “stop”

coenzymes — small, non-protein molecules required by many enzymes before they can act as catalysts, which may be bound to the enzyme and, unlike enzymes, can participate in many different reactions, e.g. ATP

cognition — the processes of consciousness through which knowledge is acquired, which include perceiving, recognizing, conceiving, reasoning, and judgment

coherence-seeking behavior — contrasted with goal-directed behavior. Non-living systems do both. Robots can be pre-programmed with goals; there are many examples of coherence-seeking behavior in inanimate systems; sand on a vibrating plate will arrange itself into coherent patterns.

collaboration — particular form of cooperation in which a system of diverse entities with unique attributes and identities, is able together to accomplish a task more complex than what any entity could have accomplished alone; collaboration does not imply consciousness or anthropocentricity (e.g. the elements of an ecosystem collaborate to create that ecosystem).

collaborative autonomy — principle underpinning collaboration, which does not require shared ownership or consensus; each player has autonomy and ownership of his piece of the big picture. Collaborative autonomy is proposed as a basic principle, both in the origin of life and, more generally, in evolution and the origination of novelty.

colloid — substance containing particles in a continuous medium (solvent); stable colloidal particles are organized such that the cohesive forces are directed inwards, while the particle’s surface has an affinity for the continuous medium

complementary, complementarity — a) in physics, the characterization of a system in different, independent ways that complement each other b) in biochemistry the capacity of nucleic acids to undergo specific base-pairing interactions (G-C, A-T/U)

complexity — in science the study of self-organization from simpler to more complex

complex adaptive systems — systems which are complex in that they contain diverse, multiply interconnected elements and adaptive in that they can change and learn from experience

constraint — a limitation, restriction or guiding force; in genetics used to indicate that an organism cannot possess a particular kid of heritable phenotypic variation because it is lethal

convergence — traditionally in biology used to describe two organisms with similar structures performing similar functions that evolved independently; here used as applied to collaborative problem-solving to describe the gradual accommodation of different lines of development toward synergetic outcomes (where the behavior of the whole is not predicted by the behaviors of its component parts)

cooperation — cooperating entities, alike or diverse, benefit from association; cooperation does not imply consciousness or anthropocentricity, a mechanistic term and complement to the concept of competition in evolution; collaboration is one type of cooperation

correlated fitness landscape — a fitness landscape where the fitness values at one point are similar to the fitness values at neighboring points; landscapes whose slope changes gradually like landscapes in the real world

covalent bonds — also known as a polar bonds; covalent bonds are formed as a result of the sharing of one or more pairs of bonding electrons. Each atom donates half of the electrons to be shared. This sharing of electrons is as a result of the electro-negativity (electron attracting ability) of the two bonded atoms

cyanelles — chloroplast-like cyanobacterial endosymbionts

cyanobacteria — also known as blue-green algae (a misnomer because they are bacteria), a very early product of evolution; micro-organism that has the prokaryotic cell structure of bacteria and is able to carry out photosynthesis highly efficiently, liberating oxygen, in the manner of chloroplasts and (eukaryotic) plants

cytoplasm — region of the cell outside the nuclear membrane; the contents of the cell minus the nucleus; the cell contents without the organelles and cell skeleton

cytosine — one of the bases of the nucleic acids; see base

cytoskeleton — internal framework of a cell, composed largely of actin filaments and microtubules

cytotaxis — a term coined by Sonneborn to describe the processes whereby new cell structures are ordered and arranged under the influence of existing cell structures

Darwinian evolution — theory of Charles Darwin in Origin of Species (published 1859) that diverse life originated on Earth through descent with modification from ancestors. According to this view populations vary genetically, compete under pressures of the environment, and the fittest are selected by the environment to survive, reproduce and transmit their genetic inheritance, gradually strengthening the population through random variation and environmental selection of heritable variations.

Darwinism — as above, Darwinian theory that species originate by descent, with variation, from parent forms, through the natural selection of those individuals best adapted for the reproductive success of their kind.

decanoic acid — a ten-carbon chain producing a carboxylic acid, CH3(CH2)8COOH, also known as capric acid. used in organic synthesis and industrially in the manufacture of perfumes, lubricants, greases, rubber, dyes, plastics, food additives and pharmaceuticals

deconstraint — reduction of constraint

deoxyribose — sugar component of the nucleotides from which deoxyribonucleic acid (DNA) is assembled; related to ribose by removal of one oxygen atom

design — the process of producing an outcome that responds to identified needs, leaving open the possibility that the method of arriving at that response may be evolutionary or interventionist. Both evolutionary design, a process of change via local adjustment, and human design can be characterized as searches for the optimal response to a given need.

determinant — August Weismann's term for a compoent of an id (complete set of hereditary information) responsible for the properties of a particular cell type

determination — the process through which a cell commits to a particular developmental pathway

developmental placticity — responsiveness of the phenotype to new inputs from both the internal and external environment; phenotypic change without genetic change including modularity of structure

differentiation — the process of change in cell shape and physiology leading to production of a specialized cell type

diffusion — transport by thermo-molecular movement; mechanism for transport of molecules and atoms from regions of high concentration to regions of lower concentration

divergence — departure of lines of development caused either by an accumulation of mutations or through the accumulation and integration of new genetic material

DNA — deoxyribonucleic acid; the molecular carrier of hereditary information; usually occurs as a double-stranded, double helical structure comprised of the four bases adenine thymine, guanine, and cytosine; DNA organization is similar to that of a language document, divided into words (codons), sentences (genes), paragraphs (operons), volume (chromosomes).

DNA polymerase — polymerase that catalyzes stepwise synthesis (polymerization) of DNA strands in the complementary copying of DNA

donor strand — strand of DNA from which a gene sequence is removed and transferred to an acceptor strand

Drake equation — an equation formulated by Frank Drake and Carl Sagan that starts with the number of stars in our Milky Way galaxy (several hundred billion), multiplied by the fraction of stars that are “plausible” (single G and K stars), multiplied by the fraction with planets with active biospheres, multiplied by the fraction of biospheres that might be “mature” enough to harbor life.

drift, genetic — progressive change in a gene due to neutral mutations, i.e. mutations that are neither advantageous nor disadvantageous in natural selection

effect hypothesis — model proposed in 1980 by palaeontologist Elisabeth Vrba that a species, occupying a restricted ecological niche, would continually give rise to daughter species by punctuated equilibrium. These new species would have a variety of characteristics; but because of the features of the particular ecological niche, only species that possessed a particular suite of characters would survive; the surviving species would speciate in their turn, with the same result, and at each level the lineage appears to be ‘pushed’ further and further in a given direction, showing how ecological niches account for evolutionary trends.

enantiomer — isomers whose only difference is that they are of opposite chirality (left- or right-handed)

endosymbiont — symbiont living inside its host

Endosymbiotic Theory — now widely accepted theory of microbiologist Lynn Margulis that eukaryotic cells first appeared when a prokaryotic cell was absorbed into another cell without being digested. This theory also postulates that mitochondria evolved from aerobic bacteria and that the chloroplast evolved from cyanobacteria.

entelechy — from the Greek entelekheia, ‘become perfect,’ entelechy is that which is already present within. According to Aristotle, the potential form (entelechy) is gradually realized as the potential of the organism, its telos. This rejected theory holds that evolution proceeds along a determined path, which contrasts with the ultra-Darwinian view that natural selection does not direct evolution towards any particular kind of organism or physiological attribute, nor is there any inner guiding force. Theory holding that evolution proceeds by the realization of that which was always potential.

entropy — used to describe a macroscopic dynamics (classical thermodynamics), microscopic dynamics (statistical thermodynamics), and information dynamics (information theory). Entropy is
a) a measure of the amount of energy (potential for organization) versus degree of disorganization in a system; b) thermal motion expressed in temperature; c) in information theory the concept of “negative entropy” is used to measure the amount of information needed, i.e. the number of binary bits (yes/ no decisions) required to describe a message of a given length; d) an increase in entropy is a decrease in order; the system can only become more organized through a supply of free energy (capable of doing work).

enzyme — biological catalyst, usually a protein, which has a particular affinity for the molecule that is to be chemically transformed

error threshold — critical value of the mutation rate above which errors accumulate leading to loss of information (the error catastrophe); stable selection requires that the error rate be below the error threshold

eukaryotes — single-celled organisms with a membrane boundary, internal membrane-boundedd organelles, including a nucleus, secretory vesicles, mitochondria (or remnants) and (in plants) chloroplasts, which reproduce through mitosis (dividing); the basic cell type for complex organisms

Europa — one of the moons of Jupiter; its frozen ocean is of interest to origin of life researchers who speculate that below its frozen crust there might be an ocean habitat able to harbor life

evolvability  — the creative capacity of organisms to evolve as in the capacity to evolve faster or more effectively using mechanisms such as facilitated variation

exon — (abbreviation for “expressed region”) information-carrying, coded sequence of a eukaryotic gene, whose transcript appears in the completed mRNA that is expressed as a protein; frequently correlated with structural domains in the protein molecule

facilitated genotypic variation — theory (for which evidence is lacking) that an organism can respond to stressful environmental conditions by making directed changes in DNA sequences that result in phenotypic changes of benefit to its survival under stress

facilitated variation — theory proposed by Marc Kirschner and John Gerhart. Facilitated variation is variation that is biased to be viable, biased to give functional outcomes, and biased to be relevant to environmental conditions. It is variation that an organism uses to generate complex phenotypic change from a small number of random changes of the genotype. Conserved core processes greatly facilitate evolutionary change by reducing the amount of genetic change required to generate phenotypic novelty, and enabling reuse in new combinations and in different parts of their adaptive ranges of performance.

fatty acids — a carboxylic acid often with a long unbranched aliphatic tail (chain), which is either saturated or unsaturated, e. g. carboxylic acids

fitness — in ecology the extent to which an organism is adapted to its environment; one measure of the fitness of an individual is its ability, relative to others, to leave viable offspring

fitness landscape — a three-dimensional landscape-like graph on which fitness is plotted; higher fitness is represented by higher elevation (peaks); a metaphor used to represent how evolutionary fitness might evolve

fluctuation — in molecular physics, a small variation, the occurrence of which cannot be predicted except through stochastic (statistical) methods

G stars — yellow stars with a surface temperature of 4300 to 5500 K. in the case of giants and 5000 to 6000 K. in the case of dwarfs. Our sun and Capella are best known examples.

gene — unit of heredity in the DNA double strand of the chromosome which contains the information needed to synthesize a protein

genetic code — assignment of groups of three nucleotides (triplets) to the amino acids that occur in proteins; the sequence of amino acids in each protein in the cell depends upon the sequence of nucleotides in the portion of DNA in the nucleus of that cell; transcription of the genetic code is mediated by RNA molecules

genetic drift — a mechanism for evolutionary change resulting from the random fluctuations of gene frequencies (e.g. from one generation to the next). Unlike natural selection, whereby gene variants become more or less common based upon reproductive success, changes due to genetic drift are not driven by environmental or adaptive pressures, and may be beneficial, neutral, or detrimental to reproductive success.

genetic takeover — theory introduced by Graham Cairns-Smith to describe instances when earlier materials and mechanisms could have been entirely superseded by later materials and mechanisms with superior capacity to perform the original function

genetic variation — change in the sequence of DNA due to mutation, recombination, assortment of different chromosomes, and insertion of DNA from viruses and other organisms; specific variation is unlinked to the environment and independent of selection

genome — the entire DNA sequence of an organism (ordering of the four elements ATGC), also called the genotype) collective term for all the genes in a cell

genotype — genome; sum of all the genetic information present in an organism

germ line — special group of cells in a multicellular organism that produce eggs or sperm in contrast to somatic (body) cells, which are not capable of inheritance

glycine — one of twenty commonly occurring amino acids, a basic building block of proteins

goal — result or conclusion toward which an effort is directed and by which it is directed, an objective

guanine (G) — one of the bases of the nucleic acids; see base

heterogenesis — generation of life from inorganic matter

heterotroph — organism that feeds on other organisms

holism — the whole not reducible to its parts, such that the interaction among parts produces new properties (emergence) and the parts cannot be understood independent of the whole to which they belong

homeostasis — ability of a system to self-regulate and maintain a particular state; the process of keeping the internal environment of the body stable while the outside world changes

homochirality — all the vital biomolecules of life having the same handedness or chirality, e.g. proteins comprise almost entirely ‘left-handed’ amino acids, while nucleic acids, starch, glycogen etc. contain sugars that are all ‘right handed.’ Homochirality is a prerequisite to produce the shapes of enzymes and the DNA double helix. Since chemistry always produces a 50/50 or racemic mixture of left and right-handed forms (enantiomers), a key question for origin of life and evolutionary theorists is why this preference for right or left-handed forms arose.

horizontal inheritance — spread of genetic material by genetic recombination 

hydrogen bond —  weak chemical bond between an electro-negative atom (e.g. oxygen, nitrogen) and electro-positive hydrogen which is bound to a second electro-negative atom

hydrolysis — chemical decomposition that splits bonds, adding molecules of water; hence breaking of a chemical compound by water; the elements of water are added to the “free ends” created by each broken chemical bond

hypercycle — term introduced by Manfred Eigen and Peter Schuster to denote a cyclic coupling pattern relating to individual reproduction; a principle of self-organization allowing integration and coherent evolution of a set of functionally coupled self-replicative entities, a precursor for genetic evolution

hypertonic cell — Having an osmotic pressure higher than that of the environment; a hypertonic cell  has a higher concentration of solute inside the cell than in the environment, making the net flow of water out of the cell.

hypotonic cell — Having an osmotic pressure less than that of the environment; a hypotonic cell a lower concentration of solute inside the cell than in the environment, making the net flow of water into the cell.

intron — (abbreviation for “intervening region”) non-coding intervening sequence on a mosaic gene; in contrast to an exon it carries no genetic information; its genetic function is at present unknown

isomers — chemical compounds with the same number of atoms distributed differently in space with respect to one another

isotonic cell — relaxed, having the same concentration of solutes inside and outside

isotopes — atoms of the same element that differ in the number of neutrons in their nuclei, which have the same atomic number but different atomic weights

Isotropic variation — heritable phenotypic variation not directed toward adaptive needs of the organism. If all variation is isotropic, selection would be the creative force in evolution.

ligation — joining linear DNA fragments together with covalent bonds

lipids — along with proteins, principle structural components of living cells, which include fats and other compounds, generally insoluble in water, which have a tendency to pack side by side in sheets, as in cell membrane

liposomes — spherical synthetic layers of lipids, which form vesicles that enclose water, organics and other matter

LUCA — our Last Universal Common Ancestor

macromolecule — giant molecule; a polymer such as proteins, nucleic acids, and sugars

messenger RNA (mRNA) — RNA that serves as a template for the synthesis of proteins

metabolism — the production of chemical energy (ATP) and biological useful chemicals in the cell

micelles — a class of aggregate formed by lipids or other amphiphilic molecules (most frequently, though not exclusively) in an aqueous environment. See amphiphiles.

microbe — also microorganism or germ, an organism of microscopic or ultra-microscopic size

microsphere — a primitive compartment easily formed by protein and postulated by Sidney Fox to have been the precursor of the living cell

mitochondria — organelles in the cytoplasm of all aerobic eukaryotic cells that house the enzymes of the respiratory chain and are the site of ATP production

mitochondrial Eve — the most recent common ancestor for all living humans

monomer — repeating molecular subunit of a polymer through which, by a repeated chemical reaction, the polymer is assembled

mutation — an heritable change in a chromosome

naked gene — proposed by H. J. Muller, later Carl Sagan and others, a “stripped down” definition of the minimum living entity that has the potential to evolve through natural selection, a proto-DNA molecule central to many information replicator origin theories. The “naked gene” implied that a self-replicating polymer could have arisen from the random association of its building blocks

nanobacteria — also nanobes; cell walled micro-organisms with a diameter well below the generally accepted lower limit (about 200 nanometers) for bacteria.

negentropy — the opposite of entropy, often cited as a unique attribute of living systems

neo-Darwinism — also known as the Modern Synthesis; a revision (1940s) of Darwin’s theory that random mutation and environmental selection are together a sufficient and complete explanation of evolutionary change to account for modern genetics, fusing genetics with Darwin’s “descent with modification” and emphasizing natural selection as the source of evolutionary change; a gradualist view incorporating Mendelian inheritance and population genetics

nomogenesis —  evolutionary model holding that the direction of evolution operates to some degree by rules or laws that operate independently of natural selection. Once regarded as an outmoded hypothesis, more recently observed to correspond with observations of evolution in the fossil record, and that such mechanisms as heterochrony and molecular drive would produce nomogenetic effects.

nonanoic acid — a nine-carbon chain producing a carboxylic acid, also called pelargonic acid, an organic compound used in plasticizers and lacquers and as flavorings

nucleic acids — polymers comprised of nucleotides found in all living cells, which occur primarily in the form of DNA and RNA

nucleobase — the parts of RNA and DNA that may be involved in pairing up (see also base pairs). These include cytosine, guanine, adenine, thymine (DNA) and uracil (RNA). These are abbreviated as C, G, A, T, and U, respectively; also called bases in genetics

nucleoprotein — any of several substances found in the nuclei of all living cells, consisting of a protein bound to a nucleic acid, the principal constituent of the hereditary material in chromosomes required for cell division and reproduction

nucleosides — created by adding a sugar to a base; nucleic acid condensed with a molecule of sugar ribose or deoxyribose; compounds, such as guanosine or adenosine, that consist of a purine or pyramidine base combined with deoxyribose or ribose, found especially in DNA or RNA. Any of various compounds consisting of a sugar, usually ribose or deoxyribose, and a purine or pyrimidine base, especially a compound obtained by hydrolysis of a nucleic acid, such as adenosine or guanine.

nucleotide — created by adding an inorganic phosphate to the sugar phosphate backbone of the nucleoside (nucleoside condensed with a single phosphate group), you have a nucleotide; a molecule consisting of three parts: an organic base plus a sugar plus a phosphate ion; when nucleotides are strung together, they produce RNA or DNA polymers; the nucleotide (a monomer) is the repeating unit of nucleic acids

operon — group of genes regulated together as a single unit

opportunity window — co-defined by all tolerance windows when overlaid

organelle — precursor of an organ, a differentiated structure within a cell, such as a mitochondrion, vacuole, or chloroplast, that performs a specific function.

orthogenesis — Evolutionary trends that remain fairly constant over long periods of time and so appear to lead directly from ancestor organisms to their descendants; once defined as an internal directing force or ‘need’ within the organisms themselves; more recently defined by the concepts of ortho-selection and species selection.

orthoselection — primary selective pressure of a directional kind, which results in a self-perpetuating evolutionary trend. Species selection, via the effect hypothesis, has been advanced as an alternative explanation for such trends, also Dollo's Law. This core Darwinian view was restored by Ronald Fisher, JBS Haldane, and Sewall Wright.

oxidation — combination of a substance with oxygen. A reaction in which the atoms in an element lose electrons and the valence of the element is correspondingly increased. a) chemistry: originally the addition of oxygen and removal of hydrogen; now more broadly the loss of electrons through the gain of oxygen b) biology: production of useful energy by the stepwise oxidation of energy-rich matter

pangenesis — Darwin’s theory (later refuted) of the inheritance of acquired characteristics (see Lamarkism). He proposed that cells in the body produce informational particles in amounts related to their physiological use. theory Charles Darwin sought to explain the use and disuse of organs through gemmules containing hereditary information from every part of the body that coalesce in the gonads and are incorporated into the reproductive cells.

panspermia — notion that living microbes pervade the universe and that life was seeded on Earth rather than starting here

paradox —an acceptable premise or line of argument that leads (circularly) to an impossible conclusion, which expresses a fundamental contradiction; exemplified in Bertrand Russell’s Theory of Types as the “vicious circle principle”; i.e. no collection of objects can be a member of itself, as in the barber who shaved all men in the town who did not shave themselves

peptides — compound formed of two or more amino acids linked by peptide bonds; short protein chains; linear molecule formed by the condensation of two or more amino acids with the expulsion of water; any of various natural or synthetic compounds containing two or more amino acids linked by the carboxyl group of one amino acid to the amino group of another.

persistence — continuing existence of an effect even after its cause is removed

phenotype — expression of genes in an organism; the organism itself

phenotypic placticity — responsiveness of the phenotype to new inputs from the external environment; phenotypic change without genetic change; one component of developmental placticity, which includes also responses to the internal environment

photoautotroph — organism capable of using light for its nutrition by converting light into energy to synthesize cell material from inorganic compounds (carbon dioxide, nitrogen salts)

photolysis — chemical decomposition by the action of radiant energy

plasmid — independent unit of hereditary material that lives in symbiosis with a cell; some plasmids are replicated with the cell’s nucleus; others proliferate independently

plasticity — capacity of organisms with the same genotype to vary phenotype in response to varying environmental conditions; or capacity to alter neural circuits and synapses of the nervous system in response to experience or injury

Poisson distribution — limiting case of the binomial distribution in which the probability of a particular event is very small but the number of chances of its occurrence is high; the Poisson distribution is used to calculate the number of chances that a particular mutation will occur, given the number of errors and error frequency.

polar bonds — also known as a covalent bonds; covalent bonds are formed as a result of the sharing of one or more pairs of bonding electrons. Each atom donates half of the electrons to be shared. This sharing of electrons is as a result of the electro-negativity (electron attracting ability) of the two bonded atoms

polymer — macromolecule (giant molecule) composed of monomers; four types of polymers make up the living cell: nucleic acids, proteins, sugars, and lipids, a regular, ordered chain

polymerization — the process through which simple molecules join to form complex molecules that contain repeating structural units of the original molecules, preserving their functional integrity; formation of a polymer by a succession of similar linkages between monomers; polymerization may occur either through addition in which the whole monomer is incorporated into the polymer, or by condensation, in which the linkage is formed through elimination of a small molecule (e.g. H2O in the case of the peptide linkage)

polymerase — group of enzymes that catalyze the synthesis of polynucleotides from energy-rich monomeric nucleoside triphosphates

polypeptide — combination of peptides

prebiotic synthesis — synthesis of basic biochemical monomers, such as amino acids or nucleotides under conditions assumed to correspond to those that existed on early Earth, e.g. the Miller-Urey experiment.

prokaryotes — the smallest free-living organisms, the eubacteria and archaebacteria (or archaea); primitive one-celled organisms that preceded the eukaryotes; prokaryotes have a genome of circular DNA contained in the cytoplasm, but lack a membrane boundary or nucleus, e.g. bacteria. They divide asexually, some rapidly.

proteinoids — high molecular weight polymers; synthesized proto-proteins important in the origin of life theory of Sidney Fox , which he formed by heating mixtures of amino acids containing high proportions of aspartic and glutamic acids

protein sequence — sequence of covalently linked amino-acid monomers in a protein (also called the primary structure of a protein)

protist — eukaryotic single-celled organism, such as an amoeba or paramecium; the first protests probably arose 2 billion years ago

protobionts — transitional creatures that preceded living cells in the origin of life, the first self-replicating entities

purine — class of nucleic acid bases whose members are adenine and guanine

pyramidine — class of nucleic acid bases whose members are cytosine, thymine and uracil

quasi-species — defined by Manfred Eigen as a weighted distribution of mutants centered around one or several master sequences; the target of selection in a system of replicating individuals that replicate without cooperating with one another (RNA molecules, viruses, bacteria); in evolution theory it replaces the “wild type”,, which was regarded as the target of selection in he classical analyses of selection; group of species with a defined probability distribution that emerges via selection.

racemic — system containing equal proportions of left- and right-handed derivatives (enantiomers) of the same compound

Red Queen hypothesis — Originally proposed by Leigh Van Valen (1973), the metaphor of an evolutionary arms race refers to the Red Queen's race in Lewis Carroll's Through the Looking-Glass. The Red Queen said, "It takes all the running you can do to keep in the same place" i.e. continual adaptation is required in order for a species to maintain its relative fitness in the ecosystem in which the species co-evolved with other species and systems. 

redox — shorthand for reduction-oxidation reactions; all chemical reactions in which atoms have their oxidation number (oxidation state) changed. This can be either a simple redox process, such as the oxidation of carbon to yield carbon dioxide (CO2) or the reduction of carbon by hydrogen to yield methane (CH4), or a complex process such as the oxidation of sugar (C6H12O6) in the human body through a series of complex electron transfer processes.

• Oxidation is the loss of electrons or an increase in oxidation state by a molecule, atom, or ion.
• Reduction is the gain of electrons or a decrease in oxidation state by a molecule, atom, or ion.

reduction — the gain of electrons or a decrease in oxidation state by a molecule, atom, or ion.

replication — doubling the nucleic acid molecule to give two identical products, normally with the help of a catalyst (enzyme)

replicator — any individual that is self-reproducing by whatever means (DNA molecule, virus, clay etc.)

ribonucleic acid — RNA; differs from DNA in  its use of the sugar ribose (instead of deoxyribose) and the base U (instead of T) and usually occurs in a single-stranded, rather than double-stranded structure; plays structural, functional, and information transmission roles

ribosome — readout device, not unlike a tape player, that translates the mRNA message by converting the purine/ pyrimidine language into an amino acid

ribozyme — enzyme composed of RNA that catalyzes template-directed assembly of complex RNA molecules from simpler molecules (the process called polymerization)

ribose — the sugar component of the nucleotides from which ribonucleic acid (RNA) is assembled; simple sugar molecule comprised of five carbon atoms

RNA World — The discovery that RNA could both catalyze and replicate led Walter Gilbert in 1986 to coin the expression “RNA World” to designate this hypothetical stage when RNA was a precursor for the evolution of life. The “RNA World” hypothesis posits that before the evolution of proteins, RNA enzymes catalyzed the chemical reactions necessary for life, including the replication of DNA.

rRNA — RNA component of the ribosome

rules  of inference — rules by which reasoning from an initial state toward a goal occurs

scientific method — accepted method for discovering knowledge. The scientific method has been defined in different ways by a range of thinkers since Plato. It has been represented both as rationalist and theoretical (following from Rene Descartes) and as materialist and empiricist/ experimental (following from Francis Bacon). From the time of the Renaissance this expression has generally referred to a method characterized by starting from basic premises assumed to be true, stating an hypothesis and proceeding either through argument or experiment to reach the conclusion of proving or disproving the hypothesis.

self organization — in nature illustrated by systems that start disordered and featureless, but then spontaneously organize themselves to produce definite structures

self-organized criticality — in physics, a critical point at which a system radically changes its behavior or structure, e.g., from solid to liquid

signal transduction — the process through which a cell receives a signal at its surface and relays it through the cytoplasm through controlled internal chemical changes. See transduction (signal)

signaling (permissive and instructive) — Permissive signaling denotes a complete response built into the receiver, then internally repressed. When the signal relieves the repression, the receiver unleashes its ready-made response. In instructive signaling, the response is not built in ahead of time; the signal must provide information for generating the response.

simulation — the imitation of the behavior of some situation or process by means of a suitably analogous situation or process, especially for the purpose of research and development or training. The process of executing operations in a model resembling a real system rather than in the system itself. The goal is to predict aspects of the behavior of the real system based on results obtained from the model.

somatic — of or pertaining to the body

specified complexity — term coined by Intelligent Design theorist William Dembski, who argues that one can rigorously show by applying so-called no free lunch theorems the inability of evolutionary algorithms to select or generate configurations of high specified complexity, though his arguments have generally been rejected by the scientific community

species — category in a classification system, a type or class. “Species” refers to the lowest level category in a classification system for living organisms; it was originally defined as comprising a breeding population of organisms able to produce offspring also capable of reproduction. But recently this definition has been questioned as it has been shown not to apply to plants and to have exceptions in animals. Species is the basic unit of biological classification the category below genus.

state cycle — term used by Stuart Kauffman to describe an attractor or cell type in his Random Boolean Network model for gene regulatory networks.

stigmergic — lacking direct inter-agent communication or a preprogrammed global blueprint of the final design; each agent’s behavior is controlled by stimuli provided by the common environment, a form of indirect communication

stigmergy — indirect communication among agents via the environment without targeting any specific recipient. In stigmergy communication is achieved by modifying the environment, as in ant pheromone trails.

stochastic — random behavior of individual participants in a dynamic (time-dependent) process characterized by statistical methods

strand displacement — the ability to displace downstream DNA encountered during synthesis. Protocols such as the isothermal amplification method Strand Displacement Amplification (SDA) exploit this activity. SDA is an isothermal nucleic acid amplification method.

subjectivity — entities that could not exist except through knowing, perceiving, believing and other mental acts

symbiosis — a long term association between species; partner sharing in symbiosis may be behavioral, metabolic, and genetic

symbiogenesis — the formation of a new organ, or a whole new organism, through mutual selection

synergetic evolution — evolution comprised not only of random variation (or mutation) and environmental selection, the Darwinist view, but also complemented by other theories, such as the Theory of Facilitated Variation of Marc Kirschner and John Gerhart whereby the effectiveness of behavioral choices plays a role in evolutionary direction as the target of selection improves its performance.

synergy — when the behavior of the wholesystem is unpredicted by the behavior of system components

taphonomy — field that studies how the fossil record is produced, and factors that may bias its interpretation

template —  a) biology: a molecule or molecular pattern that determines how other molecules are assembled into a macromolecule, e.g. DNA and RNA molecules that contain information in a particular nucleotide sequence used to synthesize other like molecules; b) mechanics: a mould or model against which to design or compare something being fabricated; c) cognition: a pattern against which to compare and match something to be identified and recognized.

tensegrity — “discontinuous compression structures” where compression forces (the rods pushing out) are not connected, while tension forces (the cables or wires pulling in) make a continuous structural web. No rod touches any other; the rods appear to be floating in space, held in place only by the web of cables at their endpoints.

theory — an integrated mental abstraction offered to make sense of more complex data and information in a given domain

thioesters — compounds resulting from the bonding of sulfur with an acyl group (an alkyl group attached to a carbon-oxygen double bond), with the general formula R-S-CO-R and also esters in which the ester carbonyl oxygen has been replaced with a sulfur with the general formula R-O-CS-R. Nobel laureate Christian de Duve believes that the thioester bond was critical for the origin of life and proosed that a "Thioester World" which preceded and developed into an "RNA World.”

threshold — critical value for a system at which a major change in systemic behavior will occur (e.g. error threshold)

tolerance — in engineering, the specification of a machine part to a certain standard of accuracy to allow for a standard level of deviation, and the permitted variation parameter for a product. The term is here used to refer to the permitted level of variation or deviation from a given norm.

tolerance windows — ranges of acceptability for variables; all tolerance windows when overlaid, co-define an opportunity window

transcription — rewriting of a genetic message of DNA into RNA, resulting in a transcript of the information in the DNA; the process by which messenger RNA is synthesized from a DNA template resulting in the transfer of genetic information from the DNA molecule to the messenger RNA

transduction (energy) — transfer of molecules across membranes against a concentration gradient - from low to high chemical potential

transduction (genetic) — transfer of genetic material from one microorganism to another by means of a viral agent (bacteriophage); introduction of viral gene carriers into cells for the purpose of gene transfer
energy transduction

transduction (signal) — transfer of signals so cells can respond to their environment, degrade, differentiate, divide, grow, cease growth, secrete, synthesize, and even die when the appropriate signal is given. This signal invariably is a molecule, which binds to a receptor, typically on the cell surface.

transfer RNA (tRNA) — smallish RNA molecules (c. 70 to 90 nucleotides); each binds a particular amino acid and, by means of interaction between its anticodon and the genetic message, determines the incorporation of the amino acid at the correct point in the growing protein.

translation — translation of a message from messenger RNA into the corresponding amino acid sequence of a protein

transposition — transfer of a piece of DNA from one place within the genome to another, which occurs relatively frequently in some DNA regions, which cannot be associated with a particular location

transposons — sequences of DNA that can move to different places in the cell genome, duplicate and excise themselves, and so are a source of mutation. First discovered by Barbara McClintock in her work on maize (1948, Nobel Prize 1983), transposons are similar in some ways to viruses and may share a common ancestor.

trigger — immediate cause of another event or chain reaction

uncertainty — Uncertainty has two connotations. In a world that we attempt to make objective, uncertainty connotes “indeterminacy” relative to quantitative domains where objective measurement is frustrated (e.g. quantum theory, Heisenberg’s Uncertainty Principle). Heisenberg used the word “uncertainty” to connote a definite quality whose actual value is not accurately known. In other words, if the clock is broken, it does not mean that time itself is uncertain. Heisenberg distinguished between uncertainty (that which we do not know accurately) and ambiguity (that which we cannot know accurately). The second connotation of uncertainty connotes more broadly the limitations of subjective perception and “doubt,” our recognition of what we cannot know. Uncertainty pertains to our capacity to know, while ambiguity is an attribute of the object that we are trying to know.

utility function — an agent’s criterion for decision-making, for deciding how to behave

uracil (U) — one of the bases of the nucleic acids; see base.

variation — how one quality is dependent in its change upon another (e.g. the circumference of a circle varies with its diameter), and how output varies with input

vertical inheritance — inheritance of genetic material by direct descent “down” a cell line, so only direct descendants can inherit genetic material

vesicle — small vessel or pouch surrounded by a membrane, usually filled with fluid, such as water