Glossary a posteriori a priori adaptation, ahistorical defi nition of adaptation, historical defi nition of adaptation, process defi nition of

Transcription

1 a posteriori A concept, idea, judgment, or knowledge obtained only after empirical investigation. a priori A concept, idea, judgment, or knowledge held before empirical investigation. adaptation, ahistorical definition of A biological trait that confers an advantage to its possessors which consequently survive and reproduce better than others in a particular environment. adaptation, historical definition of A biological trait which plays a role in the ecology of an organism lineage as a result of a history of selection for this trait because it has played the particular role. adaptation, process definition of The evolutionary process by which populations become adapted to their environment. adaptationism A family of views about the power, prevalence, and importance of natural selection. Particular adaptationist views involve different empirical, methodological, or philosophical commitments. adaptationism, empirical The view that most biological traits are adaptations. This is a claim about the world that is testable. adaptationism, explanatory The view that evolution by natural selection occupies a special place in our scientific world view and changes our image of humanity and human nature. This philosophical view may or may not have consequences for scientific practice. adaptationism, methodological The view that looking for adaptations first is a good investigative strategy for evolutionary biology. This is a claim about how best to do evolutionary science. adaptedness An assessment of fit between some biological trait of an organism and the current environment that this organism inhabits. Degrees of adaptedness often translate into a measure of evolutionary fitness. analogy A relation of similarity between traits in two or more organisms with different body-plans. A pre-darwinian concept and term. K. Kampourakis (ed.), The Philosophy of Biology: A Companion for Educators, History, Philosophy and Theory of the Life Sciences 1, DOI / , Springer Science+Business Media Dordrecht

2 746 ancestry informative marker (AIM) DNA variants (usually single nucleotide polymorphisms) whose frequencies vary sufficiently between populations so that they can be predictive of membership in those populations. animism The perception of non-living objects as alive. anomaly A phenomenon that is not readily explainable by established theories. apomorphy A trait in a set of homologous traits which is derived (apomorphic), i.e. in an innovative condition with respect to the condition in a reference ancestor. argument from design Traditional argument purporting that organisms are outcomes of intentional design and therefore evince the existence of God as the source of the design. artifact Any object intentionally created by humans which exhibits properties designed to serve a particular purpose. artificial kind A category of entities that exist as a result of human actions or interests, or conventions. astrobiology A field of science concerned with life other than familiar life, especially on planets or moons other than Earth. behavioral genetics The study of how genetic factors influence behavioral characteristics. In contrast to molecular behavioral geneticists, who use the tools of molecular biology to study how specific DNA segments influence behavior, quantitative behavioral geneticists use the tools of population genetics to study how behavioral and genomic variation are related. belief Although there are many theories as to the precise nature of belief, it is commonly held that belief is a mental state in which one accepts a particular proposition to be true. biocentric ethics Ethical theories that hold that all individual living beings are part of the moral community. bioethics The study of ethical questions in medicine and in biomedical research. biogeographical ancestry (BGA) Representation of population structure at various hierarchical levels that assigns individuals proportionate ancestry in one or more populations based on their genomic makeup. bioinformatics The science concerned with collecting, categorizing, managing, storing, processing, retrieving, disseminating, mining, and querying biomedical data and information appropriately and efficiently by computational means. bioinformation (biological information) Information in the biological realm. Information implies a relationship between: (1) a message which may be any event, linguistic, or otherwise; (2) a system of reference which the message informs the receiver about; and (3) a receiver. Bioinformation occurs when there are biological entities nucleic acids, cell cytoplasm, proteins, antibodies, neurons, sensory organs, organisms, or even ecosystems involved as such in the informational relationship. biological advantage An ability that increases an organism s potential to stay alive, including its chances to survive and reproduce. Such abilities are involved in the performance of a biological role, and they are advantageous precisely because they enable the organism to perform this role better than certain alternatives.

3 747 Biometricians A group of late-nineteenth/early-twentieth century biologists who were united by their belief that the understanding of inheritance depended on statistical analysis of the full range of biological data in randomly combining populations. This belief entailed a commitment to continuous variation as the material for natural selection, and blending inheritance. The biometrical research programme was based largely on observations of natural populations in the field (including analysis of human traits). The most prominent promoters of biometry were Francis Galton, Karl Pearson and W.F.R. Weldon. blastocyst An early embryo of approximately 150 cells produced by cell divisions following fertilization. The blastocyst is a spherical cell mass consisting of an outer layer of cells (the trophoblast) and a cluster of cells in the interior (the inner cell mass). causal account of explanation Any account of explanation according to which an explanation of a phenomenon is a description of the state of affairs of which the phenomenon is an effect. Many causal accounts involve identification of that which is necessary and sufficient for an effect s occurrence. cell line Cells that are grown and maintained in culture for research or therapy. ceteris paribus clauses Provisos meaning All other things being equal that are attached to certain claims. chimera An entity that is comprised of whole cells originating from different organisms. chromosomal theory of the gene This theory was fairly well established with the publication of The Mechanism of Mendelian Heredity by T. H. Morgan and his coworkers in According to this theory, the term gene referred to a segment of a chromosome which, when activated or deactivated, performed a certain function or had a characteristic effect. circadian rhythms Endogenously controlled oscillations of approximately 24 h in many physiological processes (e.g., basic metabolism and body temperature) and behaviors (e.g., locomotion and cognitive performance). cladistics (phylogenetic systematics) The classification of organisms according to their evolutionary history as reconstructed by their shared traits. clinical research Research conducted in a clinical setting e.g., on the effectiveness of some drug, screening or treatment regimen. community A set of populations of different species that interact in some way and to some degree. Other features biological communities are often claimed to possess are clear spatial boundaries, internal regulation, and a determinate successional trajectory following perturbation. Communities, unlike ecosystems, do not encompass the abiotic environment. complementarity model The idea that science and religion provide complementary narratives about the same reality. condition, necessary A property, characteristic or feature that an entity must have in order to be a member of a given category. condition, sufficient A property, characteristic or feature that is enough to guarantee that an entity is a member of a given category.

4 748 conflict model The idea that science and religion are intrinsically in conflict and always have been. constraints Any properties or processes that limit or facilitate evolutionary change by biasing what is or is not possible. They can be interpreted in terms of adaptation (e.g., constraints prevent optimal phenotypes from evolving) or development (e.g., constraints facilitate specific types of variation for natural selection to act upon). context of discovery The invention of theories; because of the role played by psychological, social, and historical factors, not considered of interest to philosophers. context of justification The process by which hypotheses and theories are accepted. According to this, logic and empirical data alone serve to justify the hypotheses and theories proposed. corroboration Corroboration refers to a body of evidence providing further support for a proposition or hypothesis that has been supported by some earlier evidence. For example, if an hypothesis is supported by some evidence and then additional evidence in support of the hypothesis is discovered, this new evidence is said to corroborate the hypothesis. counterfactual conditionals If-then statements concerning what would have happened under certain hypothetical circumstances that did not actually take place. creation The ontological belief that everything that exists does so due ultimately to God as the ground of all being and existence. creationism The belief that God creates by a series of miracles to bring about the universe in general and this planet and humankind in particular. Young Earth creationism perceives the world to have been created in six literal days of 24 h sometime within the last 10,000 years. Old Earth creationism accepts the scientific account of the age of the Earth but believes that the creation of life and of living creatures occurred by a series of miraculous interventions. deduction One of two fundamental types of reasoning (the other being induction). Particularly used in logic and mathematics, though useful in science as well. Deductive reasoning begins with one or more premises which if true and properly logically linked to each other yield a conclusion that must also be true. For instance, IF all men are mortal; and IF Socrates is a man; THEN it follows that Socrates is mortal. Deductive-Nomological (D-N) account of explanation The D-N account of explanation requires that in an explanation, whatever is doing the explaining (explanans) logically implies the phenomenon to be explained (explanandum) that is, the explanandum results from the explanans via a sound deductive argument. Further, at least one premise of the argument must be a natural law. deism the idea that God creates the physical laws needed for the universe to exist and function, but otherwise does not interact with the universe. design teleology A mode of teleological explanation which suggests that a feature exists for some purpose because it is intentionally designed to fulfill it.

5 749 Teleological explanations based on design are appropriate for artifacts but not for organisms or non-living natural objects (e.g. stones, clouds). design, intentional Blueprint, as in the attribution of the adaptations of organisms to the Creator. design, natural Pattern or arrangement arising by natural processes, as in the adaptations of organisms by natural selection. development The processes of growth, change, and transformation that organisms undergo in their life cycle, such as from a fertilized egg to a sexually mature adult. It is also called ontogeny (adjective: ontogenetic). Development includes changes that entail increasing order, via the differentiation and integration of specialized parts. developmental plasticity Modifiability of the phenotype during development. Developmental plasticity is typically considered synonymous with phenotypic plasticity. DNA information Since the middle of last century, DNA has been often identified as the informational molecule par excellence. It has become commonplace to say that DNA encodes, contains, or stores information; even that it transmits or conveys hereditary information from one generation to another. What these expressions really mean is that DNA plays an important role in certain bioinformational relationships, by usually playing the role of a message, i.e. as a small factor of great specificity in relation to a given function and displaying a high potential for variability. DNA possesses precisely these characteristics in relation to reproduction and metabolism. However, this does not force us to identify bioinformation simply with a property of DNA but, instead, as a complex relation in which DNA has an important role. domains Superkingdoms of life the most fundamental division of living entities into the three groups of Archaea, Bacteria and Eukarya. dominance In classical genetics, a quality inherent in one of a pair of alleles in a diploid organism, the phenotype of which is manifest in the heterozygote. drift An indiscriminate sampling process that typically produces a pattern of random variability. ecocentrist ethics Ethical theories (particularly that of Aldo Leopold, or inspired by Aldo Leopold) that hold that ecosystems, considered holistically, are part of the moral community. ecological stability The tendency of an ecological system to remain the same. The tendency takes three characteristic forms. With respect to biological communities, more stable communities are less changed by perturbations, more rapidly return to a reference state or dynamic following perturbation, and are able to sustain stronger perturbations than less stable ones. These different mechanisms by which systems tend to remain the same capture the sense in which there may be a balance of nature. embryo In humans, the organism that develops from the time of fertilization until the end of the eighth week of gestation, at which point it is called a fetus. environmental ethics An area of philosophy concerned with the systematic study of right and wrong behavior toward non-human entities as well as humans.

6 750 Among other things, environmental ethics pays particular attention to the composition of the moral community. epigenetics This term captures all processes of phenotype organisation above the level of DNA sequence. Epigenetics is now often more narrowly defined as the set of (molecular) mechanisms involved in regulating gene activity (often specifically during development rather than in adulthood). epistemology Epistemology is the branch of philosophy that addresses questions having to do with the nature of knowledge and rational belief. essence The necessary properties of a thing that make it the kind of thing it is. In logic, essence is the set of necessary criteria of a general notion or term. Essence is often contrasted to accidental or contingent properties. essentialism The idea that classes or kinds must have jointly necessary and severally sufficient conditions. That is, a general term like animal must be definable in terms of properties that only animals jointly have. essentialism, biological (taxic) The claim that biological kinds or taxa must have necessary shared properties or traits that no other kind or taxon does. essentialism, scientific The claim that natural kinds must have modally necessary shared properties that nothing else does. ethical theory A systematic and overarching account of right and wrong behavior. Examples include Kantian ethics, utilitarian ethics, ecocentrism, and biocentrism. ethics An area of philosophy concerned with the systematic study of right and wrong behavior. eugenics The scientific improvement of the human species by encouraging reproduction of individuals or groups with desirable characteristics and discouraging that of individuals or groups considered unfit. eukaryote A macro- or microorganism that is not in Archaea or Bacteria, possessing well defined cellular compartments, such as the nucleus. evidence The word evidence has many different meanings in ordinary language. However, when philosophers and scientists speak of evidence they generally have in mind the sort of thing that can make a belief rational. This can be things such as experimental data, mathematical proofs, perceptual experiences, memory, and so on. evil, problem of How to account for the existence of physical and moral evil in the world if the world s features are the outcome of God s direct creation ; also known as the theodicy problem. evo-devo A constellation of biological disciplines that investigate the evolution of development (how patterns and processes of ontogeny vary and change over time) and the developmental basis of evolution (how ontogenetic processes causally impact the evolution of organismal traits). evolution In biology, the process of change that over eons of time accounts for the origin and diversity of species and for the adaptations of organisms. evolutionary game theory Imported and modified from the field of economics, evolutionary game theory studies the behavior of populations of agents who repeatedly engage in strategic interactions. Changes in the populations are

7 751 typically understood as resulting from differences in birth and death rates (differential fitness) resulting from different strategies. evolutionary morality The idea that morality evolves as an adaptation and/or that evolution indicates what moral code humans should adopt. evolvability The capacity or disposition to evolve, usually ascribed to a group of organisms (e.g., a population or lineage). Evolvability is often described as depending on other properties, such as modularity (e.g., increased modularity leads to increased evolvability). exaptation An adaptive trait which originally evolved for reasons unrelated to its current biological role. experimental sciences Sciences marked by the lack (or relatively lower importance) of historical components affecting the phenomena under study. In physics and chemistry, for instance, researchers can experiment on particles or molecules without having to be concerned about the past history of such objects, since they behave the same regardless of such history. explanandum In an explanation, that which is to be explained. Usually, the target of explanation is some specific phenomenon, a group of seemingly related phenomena, or a law-like regularity. explanans In an explanation, that which explains a phenomenon (the explanandum). explanation In common use, an explanation is a set of statements or an account that makes something clear. There are competing notions of explanation in philosophy of science, but they all assume that there is something that distinguishes scientific explanation from mere description. For example, scientific explanations provide us with an understanding of why particular events or types of events occur. Paradigm explanations in science are why explanations, e.g.: the reason why dinosaurs went extinct is because a large asteroid impacted the Earth at the end of the cretaceous period. explanatory pluralism The view that there is no objectively privileged level of explanation. Rather, higher-level explanations (e.g. as formulated in biology or psychology) are expected to remain valuable, even if we possess complete lowerlevel explanations (e.g. in physics or chemistry). falsification A theory is falsifiable if and only if an observational consequence can be derived from the theory. The idea is that if such a consequence can be derived, then an observation designed to determine whether the consequence obtains provides a genuine test of the theory, and if the test fails then the theory must be false. fetus In humans, the developing organism from about eight weeks after fertilization until birth. fitness A measure of evolutionary success, often broken down into two components: viability (survival) and fecundity (reproduction). function A role in an organization. The role of a component in the organization of a system whose very existence is an organizational problem might be called an essential function. The functions of the parts and activities of artifacts in the organization of their ability to meet our expectations (such as the keyboard s function to enter text) are artifact functions. The functions of the parts and activities

8 752 of organisms in enabling their continued existence are biological functions or biological roles. functional explanations In biology, functional explanations answer the question why certain organisms have a certain trait rather than some specific alternatives. Such explanations point out that the trait to be explained is advantageous to those organisms because some of their other traits are functionally dependent on that trait, and so it is these traits that explain its presence. Functionally dependent means that the ability to maintain the living state of an organism with the traits doing the explaining would diminish if the trait to be explained were replaced by an alternative, whereas replacing the trait to be explained would not make much difference or have a negative effect if the organism lacked the traits doing the explaining. fusion model The attempt to fuse scientific and religious ideas into a single discourse. gene composition and localization Refers to what genes are made of (e.g. DNA) and where they are located within the cell (e.g. nucleus). gene concepts, definite These are specific concepts of the gene, which are committal, at least to some degree, about the structure or location of genes. What is typically required is a mixed mode of identification in terms of both structure and function. Thus, one must specify the substrates out of which genes are built and the structures that deserve to be identified as genes in order to individuate genes among the factors contributing to the relevant functional state. For this class of gene concepts, the choice of a phenotype is crucial in determining what counts as a gene; when the phenotype is an amino acid sequence, genes will be individuated differently than when the phenotype is something like the suppression of the expression of certain other genes. gene concepts, referentially indefinite causal (or functional) These gene concepts are based on very open-ended indefinite, functional descriptions consisting of two parts. The first part specifies a difference in the phenotype of the organism bearing a gene or gene variant (i.e., allele) e.g., tall vs. short whereas the second requires a pattern of transmission of the factor(s) responsible for the change. A schematic formulation of a referentially indefinite functional gene concept is the following: a gene for trait x is any stably inherited factor that causes an organism (or certain cells of the organism), given the rest of what it has in common with conspecifics, to have the potential for manifesting x, where x will (or can be made to) appear under the appropriate developmental plus environmental circumstances. gene function Refers to the contributions/consequences of genes to traits affected by them (e.g. be implicated in the synthesis of a particular peptide). gene networks Gene regulatory networks represent all the regulatory interactions existing between a number (which can be a large one) of genes. In such models, genes are represented as nodes and regulatory interactions as links between the nodes. Various mathematical and computational methods are used to model the dynamics of these networks. gene structure Refers to which features of genes (e.g. base sequence) correlate with the phenotypes they produced (e.g. a particular kind of protein), or how they store and transmit some kind of information.

9 753 gene-centric perspective, on evolution The notion that evolutionary insights can emerge from viewing genes (particular DNA sequences) as units of selection by virtue of their different rates of proliferation within and among organismal genomes. genetic accommodation Gene frequency change due to selection on variation in the regulation, form, or side effect of novel traits in the subpopulation of individuals that express the trait. genetic annotation Reading annotation here as commentary or explanation, the methods and technologies used to identify the locations of genes (as well as the coding regions in a genome) and determine specifically what those genes do. genetic code Nucleotides are composed of a sugar (deoxyribose in DNA, ribose in RNA), a phosphate group, and one of four different nitrogen- containing bases, namely, adenine, guanine, cytosine, and thymine in DNA (uracil replaces thymine in RNA). These four bases are like a four-letter alphabet, and triplets of bases form three-letter words or codons that comprise the information which identifies an amino acid or signals a function. The specific correspondence between codons and amino-acids is the genetic code. genetic material Any nucleic acid with the propensity to be inherited and to interact with other cellular components as a source of sequence information, eventually affecting or being implicated in cellular processes with local or extended impact. genetic sequencing The methods and technologies used to determine the specific order of the bases in a molecule of RNA (adenine, guanine, cytosine, and uracil) or DNA (adenine, guanine, cytosine, and thymine). genomics Biological research that focuses on whole genomes, i.e. the base sequence of the genetic material of organisms. heredity The transmission of material from ancestors to descendants. heritability (in the broad sense) A statistic that specifies the proportion of variation in a characteristic across a population, which can be accounted for by variation in that population s genes. (Note: Although the words sound similar, heritability need not accurately reflect how inheritable a characteristic is). heterochrony The different times or different speeds with which the different parts of the body are formed during the development of the two organisms under comparison. historical sciences Sciences marked by a significant historical component affecting the phenomena they study, meaning that the characteristics of an object of study (e.g., a living organism) depend on the past history of similar types of objects (e.g., their line of descent). The emphasis is on observation- based, rather than experiment-based hypothesis testing. They include evolutionary biology, geology and astronomy, among others. homology A relation of sameness between two or more traits in two or more organisms, or within the same organism, usually evaluated in an evolutionary context. A complex concept, so that the precise meaning is often given through specific adjectivation (e.g., serial homology). For the historical concept of homology, homologous traits in a set of organisms are those that derive from the same trait in the most recent common ancestor of those organisms.

10 754 homoplasy A relation of similarity between two traits in two or more organisms that do not derive from the same trait in the most recent common ancestor of those organisms, but due to independent evolution (e.g. convergence). human embryonic stem cells Undifferentiated human cells that are derived from the inner cell mass of developing blastocysts and that are (a) self- renewing, (b) pluripotent, and (c) capable of indefinitely dividing without differentiating in culture. human pluripotent stem cells Human cells that have the capacity to differentiate into all tissues of an organism, but are not able to form embryonic components of the trophoblast and placenta and so are not alone capable of sustaining the full development of an organism. in utero In the uterus. in vitro Literally, in glass ; in a test tube, culture dish, or other artificial environment. in vivo Within a living organism. induced pluripotent stem cells Stem cells created by converting adult human skin cells into cells that are pluripotent and self-renewing. induction One of two fundamental types of reasoning (the other being deduction). Particularly used in science, though also at the basis of much commonsense inferences. Philosophers recognize various types of induction, but essentially the approach consists in making generalizations from particular instances. For example, from the observation that all known living organisms are characterized by some type of information-carrying molecule (DNA or RNA), one can induce that all terrestrial (and perhaps extraterrestrial) organisms do too. information entropy (Shannon entropy) A measure of uncertainty, usually expressed in bits, whose mathematical formula is H(S) = K i P(s i ) logp (s i ), where H is the entropy of a source, S is a source (that is, a discrete random variable), s i is one of the possible values of S, P(s i ) is the probability of s i, and K is a positive constant. In more intuitive terms, information entropy enables us to estimate the amount of uncertainty reduced on average by each symbol produced by a given source. informational molecule Any molecule capable of participating in a bioinformational relationship, either as a message, receiver, or a reference system such as a fragment of DNA, a neurotransmitter, an antigen, and a protein. When speaking specifically about genetic or hereditary information, it is very usual to ascribe the role of message to DNA or RNA, the role of reference to the proteins, and the role of receiver to the molecules of the cytoplasm, such as those that make part of a ribosome. This ascription is not arbitrary, but it is worth noting that the same molecule may be involved in different informational relationships with different roles. For instance, an mrna molecule may be seen as the reference of a DNA fragment, but it can be also seen as a message regarding a protein. inheritance The reception by offspring of material from parents. Inheritance was traditionally understood to involve property, but was later invoked to also explain how offspring have characteristics like their parents characteristics. Many theorists today recognize that characteristics cannot be inherited; instead, they are

11 755 built by offspring during development, using genetic and non-genetic materials inherited from parents. inner cell mass A cluster of cells attached to the inner wall of the blastocyst. Embryonic stem cells are isolated and cultured from cells that form the inner cell mass. In development, the inner cell mass gives rise to the organs and tissues of the organism. intelligent design The idea that some intelligent, supernatural agent has influenced the history of organismal life on Earth. Intelligent design proponents claim that it is possible to infer the past action of an intelligent designer from some features of extant organisms (e.g., cellular structures, genetic information). The label intelligent design was created and promoted by American creationists to hide the religious aspects of creationism. It was developed as part of the attempt to integrate anti-evolution views into US public high schools, where, due to the constitutional separation of state and church, no religious views may be taught. There is no intelligent design theory that would predict and explain a variety of biological phenomena. Instead, intelligent design textbooks contain (unsound) arguments against evolutionary theory. interdisciplinarity It involves efforts to combine different fields or disciplines in order to address a problem or a family of problems. Interdisciplinarity arises from the recognition that a particular discipline is not able to analyze and explore important aspects of a problem. irreducible complexity A subsystem of an organism (e.g., a molecular mechanism) consisting of parts that interact so as to fulfill a function, is irreducibly complex when the removal of any part leads to the system no longer performing the function. Intelligent Design proponents consider e.g. the vertebrate eye or the bacterial flagellum as irreducibly complex systems which cannot have evolved by gradual evolution based on natural selection; they consider such systems as evidence for intelligent design since they believe they could only have been crafted ex nihilo for their current roles by an intelligent agent or Creator God. Kantian ethics Ethical theories inspired by the work of Immanuel Kant, emphasizing (particularly in environmental contexts) that members of the moral community ought to be treated as ends in themselves rather than mere things, tools, or instruments. knowledge One knows a proposition when: (1) the proposition is true, (2) one believes the proposition, (3) one s belief in the proposition is based on sufficiently strong evidence, and (4) one satisfies whatever condition is required to handle the Gettier problem. laws Facts (such as Newton s laws of motion and gravitation, according to classical physics) that play certain special roles in connection with scientific explanations, natural necessity, counterfactual conditionals, and inductive reasoning. levels of selection Different levels (such as genes, cells, individuals, or kinship groups) at which natural selection can operate in a biological hierarchy. life That which distinguishes animate objects from inanimate objects. A precise characterization is not available.

12 756 logical necessity The sense in which truths that hold as a matter of logic alone could not have been false. Truths that lack logical necessity are contingent. macrobe A non-microscopic organism. mechanism A structure performing a function in virtue of its component parts, component operations, and their organization. The orchestrated functioning of the mechanism is responsible for one or more phenomena. mechanism decomposition Identifying the parts that constitute a mechanism and the activities or operations these perform. mechanism recomposition Determining how the parts are organized and their operations orchestrated in the generation of the phenomenon. mechanistic account of explanation Especially relevant in the biological sciences, this account views explanations as representations of causal mechanisms, viz., physical structures that perform some function in virtue of their constitutive parts, organization, and operation. A mechanistic explanation is the explanation of a phenomenon by identifying the working parts of the responsible mechanism, i.e. the parts that perform the various operations that go into producing the phenomenon. Mendelians A group often seen in opposition to the biometricians espousing and promoting the work of Gregor Mendel as the best way to elucidate inheritance. The Mendelians believed in particulate inheritance as exemplified by Mendel s results. Contra the biometricians, the Mendelian research programme centered on selective breeding of experimental subjects in the laboratory. William Bateson is generally considered to be the leading Mendelian in Britain in the early twentieth century. Mendelism The study of inheritance based on the premise of discrete, heritable particles, as suggested by Mendel s re-discovered results in microbe A microscopic organism or virus. missing links Taxa intermediate between major groups of organisms which have not yet been discovered. model-based science An approach to understanding complex real-world systems through the use of simpler hypothetical systems that resemble their target realworld systems in some relevant respects. modularity The property of being a module or distinguishable unit (e.g., a segment), behaving in a quasi-autonomous fashion. Modularity allows for evolutionary change to occur in one trait without detrimentally affecting another trait or the entire organism. molecular clock The hypothesis that the rate of molecular evolution is approximately constant for each different type of molecule. molecular evolution The study of the evolutionary patterns and processes of biological macromolecules. molecular systematics The use of molecular data to infer evolutionary relationships. moral community The entities that are deserving of moral consideration; the entities to which an ethical theory applies. Different ethical theories offer different criteria for inclusion in the moral community, resulting in different candidates for the correct moral community.

13 757 natural kind A class of entities in nature that exist independently of human cognition or ideas, actions or interests. Natural kinds are usually held to require essences. natural selection An evolutionary process that occurs when heritable variation in features or traits of organisms in a population produces difference in reproductive success. The result is the differential reproduction of organisms with different traits. natural selection, creative view of Natural selection, properly conceived, evolves genuinely functional goal-directed adaptive traits only by working over much time and many generations on small variants in traits that first arise independently of the utility they subsequently acquire as they move toward fixation. This was Charles Darwin s view. natural selection, eliminative view of In this view, natural selection is either favoring or eliminating organisms whose traits are or are not adapted from the outset. Selection is thus conceived as an eliminative force that discriminates among whole organisms rather than the slightly variant traits they bear and that adaptations are nothing but retained accidents. This is the view of natural selection summarized in the phrase survival of the fittest, a phrase coined by Herbert Spencer and adopted by Charles Darwin. natural theology Systematic arguments purporting to demonstrate the existence and attributes of God based on the features of the natural world. naturalism, metaphysical Asserts that the material phenomena studied by science are all that exist. This includes the agency of persons and social phenomena, based on the idea that the reasoning and actions of humans are material (as opposed to immaterial or supernatural) phenomena, studied and explained by the cognitive and social sciences. Creationists and intelligent design proponents have claimed that a commitment to methodological naturalism entails metaphysical naturalism. This is false, for while endorsing methodological naturalism, scientists with religious beliefs reject metaphysical naturalism insofar as they believe in the presence of a non-material deity. naturalism, methodological A claim about the aims and methods of science which asserts that science studies natural (as opposed to supernatural) phenomena only, supports its claims with empirically accessible evidence and explains by appeal to material causes. Methodological naturalism does not maintain that there are no supernatural phenomena (such as the presence of a deity), it merely asserts that science does not and cannot study the supernatural. For this reason, methodological naturalism has to be distinguished from metaphysical naturalism. Creationists and intelligent design proponents reject methodological naturalism (and thus the scientific approach), as they intend to infer the supernatural from empirical observations. nature and nurture Traditionally seen as independent factors that contribute to the development of biological and psychological characteristics. Now understood to be two poorly defined but mutually interdependent factors that contribute to development. neutral theory of molecular evolution A theory of molecular evolution that claims that the majority of observed changes in biological macromolecules

14 758 (DNA, RNA, and proteins) are neutral or nearly neutral. That is the behavior of these observed changes is dictated by random drift, rather than selection. The neutral theory combines both drift and selection, since selection is presumed to operate on a number of molecular changes. niche There are two senses of the niche concept. One focuses on the causal role a species plays in the overall community dynamics, a species way of making a living. The other focuses on distinct portions of the abiotic environment in which species persist and reproduce. The latter makes sense of the idea there are vacant niches into which species can successfully colonize or invade. NOMA model Stands for Non-Overlapping Magisteria, a phrase popularised by the late Stephen Jay Gould to suggest that science and religion address different questions and are therefore located in quite separate compartments. nominalism The view that only individual things exist, and no universal kinds do. The name is from the Latin for name, as nominalists hold that general classes of things are just names, usually used for convenience. Methodological nominalism aims at describing how a thing behaves, and especially, whether there are any regularities in its behavior. nomological principles See laws. non-genetic (epigenetic) inheritance Refers to the many different mechanisms in addition to the transfer of DNA by which the parental phenotypes (or more remote ancestors) affect the development of their offspring. This definition is the same as a recent definition of parental effect. Non-genetic inheritance includes cellular epigenetic inheritance, which is the transmission from mother to daughter cell of variation in the molecular epigenetic regulation of gene expression, but can also involve other mechanisms, including behavioral interactions between parents and offspring. non-living natural object Any natural object other than organisms (e.g. clouds, rocks). novelty (evolutionary) A trait which has no obvious homology with any other trait in another organism or the same organism, and whose origin cannot be easily traced back to a modification of a body structure already existing in the ancestral lineage leading to that organism. In other words, an evolutionarily new trait that is a qualitative departure from the ancestral condition (e.g., avian feathers), which is sometimes defined as neither homologous to a trait in an ancestral taxon nor serially homologous to any trait of the species. Often invoked in evo-devo to focus investigation on the developmental origin of variation rather than adaptation by natural selection. organization A system is organized for a certain property or ability if the latter is critically dependent not only on the system s material composition, but also on the arrangement of its components and on the order and timing of their activity. The notion of organization can be oblivious to both the way in which the organization came into being and the way in which it is maintained (if it is at all maintained), and so does not assume the existence of an organizer in any sense of that term.

15 759 origin of life The transition from a nonliving suite of chemicals to a living system that occurred on Earth approximately 4 billion years ago and gave rise to all known life. orthology A relation between homologous genes that are present in different organisms and have evolved from a common ancestral gene by means of speciation events. overdetermination In philosophy of science, a term applied to situations in which a subset of information is sufficient to predict or explain a particular outcome. For instance, a relatively small number of geological clues have been enough to establish that a large asteroid hit the Earth 65 million years ago, probably contributing to the extinction of dinosaurs and other species. It is the same phenomenon that makes it possible to identify the culprit of a crime even though there are no eyewitnesses or actual footage of the crime itself. paralogy A relation between homologous genes that are present in the same organism or in different organisms and have evolved from a common ancestral gene by gene duplication. phenetics Also called numerical taxonomy. The classification of organisms by the closeness or not of their similarities, arbitrarily selected. phenotypic accommodation Refers to the capacity of organisms for mutual adjustment of different parts during development to produce a functional phenotype even when perturbed by genetic or environmental input. philosophy The word philosophy comes from two Greek words: philos deriving from philein love, and sophos meaning wisdom. Love here means something like an intense desire for something, while wisdom is arguably a kind of knowledge gained from experience, whether this is practical experience (gained from living life with all of its ups and downs) or theoretical experience (gained from understanding, evaluating, critiquing, and synthesizing ideas, positions, and concepts). Ever the theoretician, the philosopher has always been the person who not only desires to look deeper into some claim, idea, argument, event, or state of affairs by questioning assumptions and challenging status quo thinking, but also attempts to explain and systematize aspects of reality as it is perceived. philosophy of biology A sub-discipline of philosophy, the concern of which is the meta-leveled attempt on the part of philosophers, biologists, and other thinkers to understand, evaluate, and critique the methods, foundations, history, and logical structure of biology in relation to other sciences, disciplines, and life endeavors so as to better clarify the nature and purpose of biological science and its practices. plasticity The property of being flexible during development as a function of internal or external perturbations during the life cycle of an organism, such as the ability to produce different traits (behavioral or morphological) depending on environmental cues (e.g., diet or population density). Plasticity refers to the variety of developmental processes or traits that can be generated viably from a single genotype or genome. pleiotropy The phenomenon whereby one gene has a causal impact on multiple phenotypic traits. Pleiotropy can affect evolutionary change by constraining

16 760 what genetic changes are possible or encouraging properties such as modularity (e.g., modules as discrete sets of pleiotropic interactions). plesiomorphy A trait in a set of homologous traits which is primitive (plesiomorphic), i.e. in the same condition with respect to the condition in a reference ancestor. prokaryote A microorganism that belongs to Archaea or Bacteria; possessing cellular structures that are less obviously compartmentalized than in cells of non-prokaryotes. proximate causes Proximate causes are immediate, mechanical influences on the phenotype that explain how internal (e.g. hormonal) and external (e.g. temperature, day length) factors combine to elicit or generate a specific character. rate constancy in evolution The idea that the rate of observed substitutions in a protein or nucleotide sequence is approximately constant with regard to time. Rate constancy is usually explained as the result of the action of random drift on neutral or nearly neutral sites. rate variability in evolution The idea that the rate of observed substitutions in a protein or nucleotide sequence varies over time. Rate variability is expected if the sequence is selected since the variability will reflect variations in the environment. recessiveness In classical genetics, a quality inherent in one of a pair of alleles in a diploid organism, the phenotype of which is not manifest in the heterozygote. reductionism Reductionism can mean many different things, depending whether one talks about ontology, scientific theories or methodology and explanatory strategies. In science it often implies that higher-level phenomena (e.g., as studied in biology or psychology) must be explained by more fundamental, lower-level laws or processes (e.g., in molecular biology, or even fundamental physics). reductionism methodological The approach used in science to take something to pieces in order to understand its components and determine how they function. reductionism ontological The idea that a system is nothing but its components and that there is no more to say once the components have been analysed and described. research ethics Ethical standards for the responsible conduct of research. resilience The rate a system returns to a reference state or dynamic following a perturbation. Lake communities that return to a reference state or dynamic quickly after an incident of thermal pollution, for instance, are more resilient than those with slower return rates following similar incidents. resistance Inverse of the magnitude a system changes relative to a reference state or dynamic following a perturbation. Resistance is often characterized as the tendency of a system to remain the same when perturbed. A biological community that can withstand severe drought with little change, for instance, is more resistant than one modified dramatically. saltative evolution Evolution by sudden or abrupt and discontinuous changes ( leap = saltus in Latin). selection teleology A mode of teleological explanation which suggests that a feature exists in a population because it is being selected for its beneficial

17 761 consequences to its bearers. Teleological explanations based on natural selection are appropriate for organisms but not for artifacts or for non-living natural objects (e.g. stones, clouds). selfish gene Any stretch of DNA sequence that displays self-perpetuating evolutionary behavior without apparent benefit to the organism. sexual genome The full suite of genetic material within each cell of a sexual species. small probability arguments A common type of argument raised by creationists against evolution which asserts that the origination of complex biological features (e.g., anatomical structures, cells, or genetic information) by means of Darwinian evolution is too unlikely to be credible. All such small probability arguments against evolution are fallacious, as it is easy to generate events with a probability smaller than any bound (e.g., the outcome of repeated tosses of a coin). Therefore, an event (e.g., the origin of complex biological structures) having a small probability does not imply the improbability of the theory assigning this probability (e.g., Darwinian evolution). symbiosis A broad term that covers parasitic, mutualist and commensal interactions between biological entities; interactions may be obligatory or facultative; endosymbiosis refers to symbioses that take place within cells (as opposed to between cells or organisms). symplesiomorphy A plesiomorphy shared by members of a taxon. synapomorphy An apomorphy shared by members of a taxon. synthesis, Modern The standard theoretical framework in evolutionary biology, a synthesis of the original Darwinism and of Mendelism, based on the modern theory of population genetics. Achieved from the 1920s through the 1940s. synthesis, Extended A proposed extension of the Modern Synthesis to take into account a broader range of biological phenomena (e.g., phenotypic plasticity), to incorporate new disciplines (e.g., evo-devo, genomics), and to factor in new concepts (e.g., evolvability). systematics The scientific practice of classifying objects, usually biological organisms, by the relations between them. It is similar to but not identical with taxonomy. systemic approach (or systems thinking) A general methodology holding that a system cannot be explained by decomposing it in its parts and then looking at their properties in isolation. Components must be understood in the context of the whole system. Systemic approaches focus on circular rather than linear causality. systems biology A group of experimental, analytical and modeling approaches, developed to explain how biological properties emerge through complex interactions. Largely based on integration of data from functional genomics methods, systems biology focuses on dynamical modeling and analysis of large networks (e.g. gene regulatory networks or metabolic networks). taxon A natural (usually biological) group. taxonomy In biology the discipline of identifying and describing species and subspecific kinds. It is the basis on which systematics is undertaken.