Multiple sequence alignment
(in this case DNA sequences) and illustrations of the use of
substitution models to make evolutionary inferences. The data in this
alignment (in this case a toy example with 18 sites) is converted to a
set of site patterns. The site patterns are shown along with the number
of times they occur in alignment. These site patterns are used to
calculate the likelihood given the substitution model and a phylogenetic tree
(in this case an unrooted four-taxon tree). It is also necessary to
assume a substitution model to estimate evolutionary distances for pairs
of sequences (distances are the number of substitutions that have
occurred since sequences had a common ancestor). The evolutionary
distance equation (d12) is based on the simple model proposed by Jukes and Cantor in 1969. The equation transforms the proportion of nucleotide differences between taxa 1 and 2 (p12
= 4/18; the four site patterns that differ between taxa 1 and 2 are
indicated with asterisks) into an evolutionary distance (in this case d12=0.2635 substitutions per site).
Some phylogenetic methods account for variation among sites and among tree branches. Different genes, e.g. hemoglobin vs. cytochrome c, generally evolve at different rates. These rates are relatively constant over time (e.g., hemoglobin does
not evolve at the same rate as cytochrome c, but hemoglobins from
humans, mice, etc. do have comparable rates of evolution), although
rapid evolution along one branch can indicate increased directional selection on that branch. Purifying selection causes functionally important regions to evolve more slowly, and amino acid substitutions involving similar amino acids occurs more often than dissimilar substitutions.
Gene phylogeny as lines within grey species phylogeny. Top: An ancestral gene duplication produces two paralogs (histone H1.1 and 1.2). A speciation event produces orthologs in the two daughter species (human and chimpanzee). Bottom: in a separate species (E. coli), a gene has a similar function (histone-like nucleoid-structuring protein) but has a separate evolutionary origin and so is an analog.
Gene duplication can produce multiple homologous proteins (paralogs) within the same species. Phylogenetic analysis of proteins has revealed how proteins evolve and change their structure and function over time.
For example, ribonucleotide reductase (RNR) has evolved a multitude of structural and functional variants. Class I RNRs use a ferritin subunit and differ by the metal they use as cofactors. In class II RNRs, the thiyl radical is generated using an adenosylcobalamin cofactor and these enzymes do not require additional subunits (as opposed to class I which do). In class III RNRs, the thiyl radical is generated using S-adenosylmethionine bound to a [4Fe-4S] cluster. That is, within a single family of proteins numerous structural and functional mechanisms can evolve.
In a proof-of-concept study, Bhattacharya and colleagues converted myoglobin, a non-enzymatic oxygen storage protein, into a highly efficient Kemp eliminase using only three mutations. This demonstrates that only few mutations are needed to radically change the function of a protein. Directed evolution is the attempt to engineer proteins using methods inspired by molecular evolution.
This hedgehog has no pigmentation due to a mutation.
Mutations are permanent, transmissible changes to the genetic material (DNA or RNA) of a cell or virus. Mutations result from errors in DNA replication during cell division and by exposure to radiation, chemicals, other environmental stressors, viruses, or transposable elements. When point mutations to just one base-pair of the DNA fall within a region coding for a protein, they are characterized by whether they are synonymous
(do not change the amino acid sequence) or non-synonymous. Other types
of mutations modify larger segments of DNA and can cause duplications,
insertions, deletions, inversions, and translocations.
The distribution of rates for diverse kinds of mutations is called the "mutation spectrum" (see App. B of [14]). Mutations of different types occur at widely varying rates. Point mutation rates for most organisms are very low, roughly 10−9 to 10−8 per site per generation, though some viruses have higher mutation rates on the order of 10−6 per site per generation. Transitions (A ↔ G or C ↔ T) are more common than transversions (purine (adenine or guanine)) ↔ pyrimidine (cytosine or thymine, or in RNA, uracil)). Perhaps the most common type of mutation in humans is a change in the length of a short tandem repeat
(e.g., the CAG repeats underlying various disease-associated
mutations). Such STR mutations may occur at rates on the order of 10−3 per generation.
Different frequencies of different types of mutations can play an important role in evolution via bias in the introduction of variation (arrival bias), contributing to parallelism, trends, and differences in the navigability of adaptive landscapes. Mutation bias makes systematic or predictable contributions to parallel evolution. Since the 1960s, genomic GC content has been thought to reflect mutational tendencies. Mutational biases also contribute to codon usage bias. Although such hypotheses are often associated with neutrality, recent
theoretical and empirical results have established that mutational
tendencies can influence both neutral and adaptive evolution via bias in the introduction of variation (arrival bias).
Selection can occur when an allele confers greater fitness, i.e. greater ability to survive or reproduce, on the average individual than carries it. A selectionist approach emphasizes e.g. that biases in codon usage are due at least in part to the ability of even weak selection to shape molecular evolution.
Genetic drift is the change of allele frequencies from one generation to the next due to stochastic effects of random sampling in finite populations. These effects can accumulate until a mutation becomes fixed in a population.
For neutral mutations, the rate of fixation per generation is equal to
the mutation rate per replication. A relatively constant mutation rate
thus produces a constant rate of change per generation (molecular
clock).
Slightly deleterious mutations with a selection coefficient less than a threshold value of 1 / the effective population size
can also fix. Many genomic features have been ascribed to accumulation
of nearly neutral detrimental mutations as a result of small effective
population sizes. With a smaller effective population size, a larger variety of mutations
will behave as if they are neutral due to inefficiency of selection.
Gene conversion occurs during recombination, when nucleotide damage is repaired
using an homologous genomic region as a template. It can be a biased
process, i.e. one allele may have a higher probability of being the
donor than the other in a gene conversion event. In particular,
GC-biased gene conversion tends to increase the GC-content of genomes, particularly in regions with higher recombination rates. There is also evidence for GC bias in the mismatch repair process. It is thought that this may be an adaptation to the high rate of
methyl-cytosine deamination which can lead to C→T transitions.
The dynamics of biased gene conversion resemble those of natural selection, in that a favored allele will tend to increase exponentially in frequency when rare.
Genome size is influenced by the amount of repetitive DNA as well as
number of genes in an organism. Some organisms, such as most bacteria, Drosophila, and Arabidopsis
have particularly compact genomes with little repetitive content or
non-coding DNA. Other organisms, like mammals or maize, have large
amounts of repetitive DNA, long introns, and substantial spacing between genes. The C-value paradox
refers to the lack of correlation between organism 'complexity' and
genome size. Explanations for the so-called paradox are two-fold.
First, repetitive genetic elements can comprise large portions of the
genome for many organisms, thereby inflating DNA content of the haploid
genome. Repetitive genetic elements are often descended from transposable elements.
Secondly, the number of genes is not necessarily indicative of
the number of developmental stages or tissue types in an organism. An
organism with few developmental stages or tissue types may have large
numbers of genes that influence non-developmental phenotypes, inflating
gene content relative to developmental gene families.
Neutral explanations for genome size suggest that when population
sizes are small, many mutations become nearly neutral. Hence, in small
populations repetitive content and other 'junk' DNA
can accumulate without placing the organism at a competitive
disadvantage. There is little evidence to suggest that genome size is
under strong widespread selection in multicellular eukaryotes. Genome
size, independent of gene content, correlates poorly with most
physiological traits and many eukaryotes, including mammals, harbor very
large amounts of repetitive DNA.
However, birds
likely have experienced strong selection for reduced genome size, in
response to changing energetic needs for flight. Birds, unlike humans,
produce nucleated red blood cells, and larger nuclei lead to lower
levels of oxygen transport. Bird metabolism is far higher than that of
mammals, due largely to flight, and oxygen needs are high. Hence, most
birds have small, compact genomes with few repetitive elements.
Indirect evidence suggests that non-avian theropod dinosaur ancestors of
modern birds also had reduced genome sizes, consistent with endothermy and high
energetic needs for running speed. Many bacteria have also experienced
selection for small genome size, as time of replication and energy
consumption are so tightly correlated with fitness.
Chromosome number and organization
The ant Myrmecia pilosula has only a single pair of chromosomes whereas the Adders-tongue fern Ophioglossum reticulatum has up to 1260 chromosomes. The number of chromosomes in an organism's genome does not necessarily correlate with the amount of DNA in its genome. The genome-wide amount of recombination is directly controlled by the number of chromosomes, with one crossover per chromosome or per chromosome arm, depending on the species.
Changes in chromosome number can play a key role in speciation, as differing chromosome numbers can serve as a barrier to reproduction in hybrids. Human chromosome 2 was created from a fusion of two chimpanzee chromosomes and still contains central telomeres as well as a vestigial second centromere. Polyploidy,
especially allopolyploidy, which occurs often in plants, can also
result in reproductive incompatibilities with parental species. Agrodiatus
blue butterflies have diverse chromosome numbers ranging from n=10 to
n=134 and additionally have one of the highest rates of speciation
identified to date.
Cilliate genomes house each gene in individual chromosomes.
In addition to the nuclear genome, endosymbiont organelles contain their own genetic material. Mitochondrial and chloroplast DNA varies across taxa, but membrane-bound proteins, especially electron transport chain constituents are most often encoded in the organelle. Chloroplasts and mitochondria are maternally inherited in most species, as the organelles must pass through the egg. In a rare departure, some species of mussels are known to inherit mitochondria from father to son.
Gene duplication initially leads to redundancy. However, duplicated gene sequences can mutate to develop new functions or specialize so that the new gene performs a subset of the original ancestral functions. Retrotransposition duplicates genes by copying mRNA to DNA and inserting it into the genome. Retrogenes generally insert into new genomic locations, lack introns, and sometimes develop new expression patterns and functions.
Chimeric genes
form when duplication, deletion, or incomplete retrotransposition
combines portions of two different coding sequences to produce a novel
gene sequence. Chimeras often cause regulatory changes and can shuffle
protein domains to produce novel adaptive functions.
De novo gene birth can give rise to protein-coding genes and non-coding genes from previously non-functional DNA. For instance, Levine and colleagues reported the origin of five new genes in the D. melanogaster genome. Similar de novo origin of genes has also been shown in other organisms such as yeast, rice and humans. De novo genes may evolve from spurious transcripts that are already expressed at low levels.
Constructive neutral evolution
(CNE) explains that complex systems can emerge and spread into a
population through neutral transitions with the principles of excess
capacity, presuppression, and ratcheting, and it has been applied in areas ranging from the origins of the spliceosome to the complex interdependence of microbial communities.
Journals and societies
The
Society for Molecular Biology and Evolution publishes the journals
"Molecular Biology and Evolution" and "Genome Biology and Evolution" and
holds an annual international meeting. Other journals dedicated to
molecular evolution include Journal of Molecular Evolution and Molecular Phylogenetics and Evolution. Research in molecular evolution is also published in journals of genetics, molecular biology, genomics, systematics, and evolutionary biology.
Ontology is the philosophical study of being. It is traditionally understood as the subdiscipline of metaphysics focused on the most general features of reality. As one of the most fundamental concepts, being encompasses all of reality and every entity
within it. To articulate the basic structure of being, ontology
examines the commonalities among all things and investigates their
classification into basic types, such as the categories of particulars and universals. Particulars are unique, non-repeatable entities, such as the person Socrates, whereas universals are general, repeatable entities, like the color green. Another distinction exists between concrete objects existing in space and time,
such as a tree, and abstract objects existing outside space and time,
like the number 7. Systems of categories aim to provide a comprehensive
inventory of reality by employing categories such as substance, property, relation, state of affairs, and event.
Ontologists disagree regarding which entities exist at the most basic level. Platonic realism asserts that universals have objective existence, while conceptualism maintains that universals exist only in the mind, and nominalism denies their existence altogether. Similar disputes pertain to mathematical objects, unobservable objects assumed by scientific theories, and moral facts. Materialism posits that fundamentally only matter exists, whereas dualism asserts that mind
and matter are independent principles. According to some ontologists,
objective answers to ontological questions do not exist, with
perspectives shaped by differing linguistic practices.
The origins of ontology lie in the ancient period with speculations about the nature of being and the source of the universe, including ancient Indian, Chinese, and Greek philosophy. In the modern period, philosophers conceived ontology as a distinct academic discipline and coined its name.
Definition
Ontology is the study of being. It is the branch of philosophy that investigates the nature of existence, the features all entities have in common, and how they are divided into basic categories of being. It aims to discover the foundational building blocks of the world and characterize reality as a whole in its most general aspects. In this regard, ontology contrasts with individual sciences like biology and astronomy, which restrict themselves to a limited domain of entities, such as living entities and celestial phenomena. In some contexts, the term ontology
refers not to the general study of being but to a specific ontological
theory within this discipline. It can also mean an inventory or a conceptual scheme of a particular domain, such as the ontology of genes. In this context, an inventory is a comprehensive list of elements. A conceptual scheme is a framework of the key concepts and their relationships.
Ontology is closely related to metaphysics
but the exact relation of these two disciplines is disputed. A
traditionally influential characterization asserts that ontology is a
subdiscipline of metaphysics. According to this view, metaphysics is the
study of various aspects of fundamental reality, whereas ontology
restricts itself to the most general features of reality. This view sees ontology as general metaphysics, which is to be
distinguished from special metaphysics focused on more specific subject
matters, like God, mind, and value. A different conception understands ontology as a preliminary discipline
that provides a complete inventory of reality while metaphysics
examines the features and structure of the entities in this inventory. Another conception says that metaphysics is about real being while ontology examines possible being or the concept of being. It is not universally accepted that there is a clear boundary between
metaphysics and ontology. Some philosophers use both terms as synonyms.
The etymology of the word ontology traces back to the ancient Greek terms ὄντως (ontos, meaning 'being') and λογία (logia, meaning 'study of'), literally, 'the study of being'. The ancient Greeks did not use the term ontology, which was coined by philosophers in the 17th century.
Basic concepts
Being
The
scope of ontology covers diverse entities, including everyday objects,
living beings, celestial bodies, ideas, numbers, and fictional
creatures.
Being, or existence, is the main topic of ontology. It is one of the most general and fundamental concepts, encompassing all of reality and every entity within it. In its broadest sense, being only contrasts with non-being or nothingness. It is controversial whether a more substantial analysis of the concept or meaning of being is possible. One proposal understands being as a property possessed by every entity. Critics argue that a thing without being cannot have properties. This
means that properties presuppose being and cannot explain it. Another suggestion is that all beings share a set of essential features. According to the Eleatic principle, "power is the mark of being", meaning that only entities with causal influence truly exist. A controversial proposal by philosopher George Berkeley suggests that all existence is mental. He expressed this immaterialism in his slogan "to be is to be perceived".
Depending on the context, the term being is sometimes used
with a more limited meaning to refer only to certain aspects of
reality. In one sense, being is unchanging and permanent, in contrast to
becoming, which implies change. Another contrast is between being, as what truly exists, and phenomena, as what appears to exist. In some contexts, being expresses the fact that something is while essence expresses its qualities or what it is like.
Ontologists often divide being into fundamental classes or highest kinds, called categories of being. Proposed categories include substance, property, relation, state of affairs, and event. They can be used to provide systems of categories, which offer a
comprehensive inventory of reality in which every entity belongs to
exactly one category. Some philosophers, like Aristotle, say that entities belonging to different categories exist in distinct ways. Others, like John Duns Scotus, insist that there are no differences in the mode of being, meaning that everything exists in the same way. A related dispute is whether some entities have a higher degree of being than others, an idea already found in Plato's
work. The more common view in contemporary philosophy is that a thing
either exists or not with no intermediary states or degrees.
The Taj Mahal is a particular entity while the color green is a universal entity.
A central distinction in ontology is between particular and universal entities. Particulars, also called individuals, are unique, non-repeatable entities, like Socrates, the Taj Mahal, and Mars. Universals are general, repeatable entities, like the color green, the form circularity, and the virtue courage. Universals express aspects or features shared by particulars. For example, Mount Everest and Mount Fuji are particulars characterized by the universal mountain.
Universals can take the form of properties or relations. Properties describe the characteristics of things. They are features or qualities possessed by an entity. Properties are often divided into essential and accidental properties. A property is essential if an entity must have it; it is accidental if the entity can exist without it. For instance, having three sides is an essential property of a triangle, whereas being red is an accidental property. Relations are ways how two or more entities stand to one another.
Unlike properties, they apply to several entities and characterize them
as a group. For example, being a city is a property while being east of is a relation, as in "Kathmandu is a city" and "Kathmandu is east of New Delhi". Relations are often divided into internal and external relations. Internal relations depend only on the properties of the objects they connect, like the relation of resemblance. External relations express characteristics that go beyond what the connected objects are like, such as spatial relations.
Substances play an important role in the history of ontology
as the particular entities that underlie and support properties and
relations. They are often considered the fundamental building blocks of
reality that can exist on their own, while entities like properties and
relations cannot exist without substances. Substances persist through
changes as they acquire or lose properties. For example, when a tomato
ripens, it loses the property green and acquires the property red.
States of affairs are complex particular entities that have
several other entities as their components. The state of affairs
"Socrates is wise" has two components: the individual Socrates and the property wise. States of affairs that correspond to reality are called facts. Facts are truthmakers of statements, meaning that whether a statement is true or false depends on the underlying facts.
Events are particular entities that occur in time, like the fall of the Berlin Wall and the first moon landing.
They usually involve some kind of change, like the lawn becoming dry.
In some cases, no change occurs, like the lawn staying wet. Complex events, also called processes, are composed of a sequence of events.
Concrete objects are entities that exist in space and time, such as a
tree, a car, and a planet. They have causal powers and can affect each
other, like when a car hits a tree and both are deformed in the process.
Abstract objects, by contrast, are outside space and time, such as the
number 7 and the set of integers. They lack causal powers and do not undergo changes. The existence and nature of abstract objects remain subjects of philosophical debate.
Concrete objects encountered in everyday life are complex
entities composed of various parts. For example, a book is made up of
two covers and the pages between them. Each of these components is
itself constituted of smaller parts, like molecules, atoms, and elementary particles. Mereology
studies the relation between parts and wholes. One position in
mereology says that every collection of entities forms a whole.
According to another view, this is only the case for collections that
fulfill certain requirements, for instance, that the entities in the
collection touch one another. The problem of material constitution asks whether or in what sense a
whole should be considered a new object in addition to the collection of
parts composing it.
Abstract objects are closely related to fictional and intentional objects. Fictional objects are entities invented in works of fiction. They can be things, like the One Ring in J. R. R. Tolkien's book series The Lord of the Rings, and people, like the Monkey King in the novel Journey to the West. Some philosophers say that fictional objects are abstract objects and
exist outside space and time. Others understand them as artifacts that
are created as the works of fiction are written. Intentional objects are entities that exist within mental states, like perceptions, beliefs, and desires. For example, if a person thinks about the Loch Ness Monster then the Loch Ness Monster is the intentional object of this thought. People can think about existing and non-existing objects. This makes it difficult to assess the ontological status of intentional objects.
Other concepts
Ontological
dependence is a relation between entities. An entity depends
ontologically on another entity if the first entity cannot exist without
the second entity. For instance, the surface of an apple cannot exist without the apple. An entity is ontologically independent if it does not depend on
anything else, meaning that it is fundamental and can exist on its own.
Ontological dependence plays a central role in ontology and its attempt
to describe reality on its most fundamental level. It is closely related to metaphysical grounding, which is the relation between a ground and the facts it explains.
An ontological commitment of a person or a theory is an entity that exists according to them. For instance, a person who believes in God has an ontological commitment to God. Ontological commitments can be used to analyze which ontologies people
explicitly defend or implicitly assume. They play a central role in
contemporary metaphysics when trying to decide between competing
theories. For example, the Quine–Putnam indispensability argument defends mathematical Platonism, asserting that numbers exist because the best scientific theories are ontologically committed to numbers.
Possibility and necessity are further topics in ontology.
Possibility describes what can be the case, as in "it is possible that extraterrestrial life
exists". Necessity describes what must be the case, as in "it is
necessary that three plus two equals five". Possibility and necessity
contrast with actuality, which describes what is the case, as in "Doha is the capital of Qatar". Ontologists often use the concept of possible worlds to analyze possibility and necessity. A possible world is a complete and consistent way how things could have been. For example, Haruki Murakami was born in 1949 in the actual world but there are possible worlds in which he was born at a different date. Using this idea, possible world semantics
says that a sentence is possibly true if it is true in at least one
possible world. A sentence is necessarily true if it is true in all
possible worlds. The field of modal logic provides a precise formalization of the concepts of possibility and necessity.
In ontology, identity
means that two things are the same. Philosophers distinguish between
qualitative and numerical identity. Two entities are qualitatively
identical if they have exactly the same features, such as perfect
identical twins. This is also called exact similarity and indiscernibility.
Numerical identity, by contrast, means that there is only a single
entity. For example, if Fatima is the mother of Leila and Hugo then
Leila's mother is numerically identical to Hugo's mother. Another distinction is between synchronic and diachronic identity.
Synchronic identity an entity to itself at the same time.
Diachronic identity relates an entity to itself at different times, as
in "the woman who bore Leila three years ago is the same woman who bore
Hugo this year". The notion of identity also has a number of philosophical implications
in terms of how it interacts with the aforementioned necessity and
possibility. Most famously, Saul Kripke contended that discovered identities such as "Water is H2O" are necessarily true because "H2O" is what's known as a rigid designator.
Branches
There
are different and sometimes overlapping ways to divide ontology into
branches. Pure ontology focuses on the most abstract topics associated
with the concept and nature of being. It is not restricted to a specific
domain of entities and studies existence and the structure of reality
as a whole. Pure ontology contrasts with applied ontology,
also called domain ontology. Applied ontology examines the application
of ontological theories and principles to specific disciplines and
domains, often in the field of science. It considers ontological problems in regard to specific entities such as matter, mind, numbers, God, and cultural artifacts.
Social ontology, a major subfield of applied ontology, studies social kinds, like money, gender, society, and language. It aims to determine the nature and essential features of these concepts while also examining their mode of existence. According to a common view, social kinds are useful constructions to
describe the complexities of social life. This means that they are not
pure fictions but, at the same time, lack the objective or
mind-independent reality of natural phenomena like elementary particles,
lions, and stars. In the fields of computer science, information science, and knowledge representation,
applied ontology is interested in the development of formal frameworks
to encode and store information about a limited domain of entities in a
structured way. A related application in genetics is Gene Ontology,
which is a comprehensive framework for the standardized representation
of gene-related information across species and databases.
Formal ontology
is the study of objects in general while focusing on their abstract
structures and features. It divides objects into different categories
based on the forms they exemplify. Formal ontologists often rely on the
tools of formal logic to express their findings in an abstract and general manner. Formal ontology contrasts with material ontology, which distinguishes
between different areas of objects and examines the features
characteristic of a specific area. Examples are ideal spatial beings in the area of geometry and living beings in the area of biology.
Descriptive ontology aims to articulate the conceptual scheme
underlying how people ordinarily think about the world. Prescriptive
ontology departs from common conceptions of the structure of reality and
seeks to formulate a new and better conceptualization.[82]
Another contrast is between analytic and speculative ontology.
Analytic ontology examines the types and categories of being to
determine what kinds of things could exist and what features they would
have. Speculative ontology aims to determine which entities actually
exist, for example, whether there are numbers or whether time is an
illusion.
Martin Heidegger proposed fundamental ontology to study the meaning of being.
Metaontology
studies the underlying concepts, assumptions, and methods of ontology.
Unlike other forms of ontology, it does not ask "what exists" but "what
does it mean for something to exist" and "how can people determine what
exists". It is closely related to fundamental ontology, an approach developed by philosopher Martin Heidegger that seeks to uncover the meaning of being.
The term realism is used for various theories that affirm that some kind of phenomenon is real or has
mind-independent existence. Ontological realism is the view that there
are objective
facts about what exists and what the nature and categories of being
are. Ontological realists do not make claims about what those facts are,
for example, whether elementary particles exist. They merely state that
there are mind-independent facts that determine which ontological
theories are true. This idea is denied by ontological anti-realists, also called
ontological deflationists, who say that there are no substantive facts
one way or the other. According to philosopher Rudolf Carnap,
for example, ontological statements are relative to language and depend
on the ontological framework of the speaker. This means that there are
no framework-independent ontological facts since different frameworks
provide different views while there is no objectively right or wrong
framework.
Plato (left) and Aristotle (right) disagreed on whether universals can exist without matter.
In a more narrow sense, realism refers to the existence of certain types of entities. Realists about universals say that universals have mind-independent existence. According to Platonic realists,
universals exist not only independent of the mind but also independent
of particular objects that exemplify them. This means that the universal
red could exist by itself even if there were no red objects in the world. Aristotelian realism, also called moderate realism, rejects this idea and says that universals only exist as long as there are objects that exemplify them. Conceptualism,
by contrast, is a form of anti-realism, stating that universals only
exist in the mind as concepts that people use to understand and
categorize the world. Nominalists
defend a strong form of anti-realism by saying that universals have no
existence. This means that the world is entirely composed of particular
objects.
Mathematical realism, a closely related view in the philosophy of mathematics,
says that mathematical facts exist independently of human language,
thought, and practices and are discovered rather than invented.
According to mathematical Platonism, this is the case because of the
existence of mathematical objects,
like numbers and sets. Mathematical Platonists say that mathematical
objects are as real as physical objects, like atoms and stars, even
though they are not accessible to empirical observation. Influential forms of mathematical anti-realism include conventionalism,
which says that mathematical theories are trivially true simply by how
mathematical terms are defined, and game formalism, which understands mathematics not as a theory of reality but as a game governed by rules of string manipulation.
Modal realism is the theory that in addition to the actual world, there are countless possible worlds
as real and concrete as the actual world. The primary difference is
that the actual world is inhabited by us while other possible worlds are
inhabited by our counterparts.
Modal anti-realists reject this view and argue that possible worlds do
not have concrete reality but exist in a different sense, for example,
as abstract or fictional objects.
Scientific realists say that the scientific description of the world is an accurate representation of reality.[k] It is of particular relevance in regard to things that cannot be directly observed by humans but are assumed to exist by scientific theories, like electrons, forces, and laws of nature. Scientific anti-realism says that scientific theories are not descriptions of reality but instruments to predict observations and the outcomes of experiments.
Moral realists
claim that there exist mind-independent moral facts. According to them,
there are objective principles that determine which behavior is morally
right. Moral anti-realists either claim that moral principles are subjective and differ between persons and cultures, a position known as moral relativism, or outright deny the existence of moral facts, a view referred to as moral nihilism.
By number of categories
Monocategorical
theories say that there is only one fundamental category, meaning that
every single entity belongs to the same universal class. For example, some forms of nominalism state that only concrete particulars exist while some forms of bundle theory state that only properties exist. Polycategorical theories, by contrast, hold that there is more than one
basic category, meaning that entities are divided into two or more
fundamental classes. They take the form of systems of categories, which
list the highest genera of being to provide a comprehensive inventory of
everything.
The closely related discussion between monism and dualism
is about the most fundamental types that make up reality. According to
monism, there is only one kind of thing or substance on the most basic
level. Materialism
is an influential monist view; it says that everything is material.
This means that mental phenomena, such as beliefs, emotions, and
consciousness, either do not exist or exist as aspects of matter, like
brain states. Idealists
take the converse perspective, arguing that everything is mental. They
may understand physical phenomena, like rocks, trees, and planets, as
ideas or perceptions of conscious minds. Neutral monism occupies a middle ground by saying that both mind and matter are derivative phenomena. Dualists state that mind and matter exist as independent principles, either as distinct substances or different types of properties. In a slightly different sense, monism contrasts with pluralism
as a view not about the number of basic types but the number of
entities. In this sense, monism is the controversial position that only a
single all-encompassing entity exists in all of reality. Pluralism is more commonly accepted and says that several distinct entities exist.
By fundamental categories
The historically influential substance-attribute ontology
is a polycategorical theory. It says that reality is at its most
fundamental level made up of unanalyzable substances that are
characterized by universals, such as the properties an individual
substance has or relations that exist between substances. The closely related substratum theory says that each concrete object is
made up of properties and a substratum. The difference is that the
substratum is not characterized by properties: it is a featureless or bare particular that merely supports the properties.
Various alternative ontological theories have been proposed that
deny the role of substances as the foundational building blocks of
reality. Stuff ontologies say that the world is not populated by distinct
entities but by continuous stuff that fills space. This stuff may take
various forms and is often conceived as infinitely divisible. According to process ontology,
processes or events are the fundamental entities. This view usually
emphasizes that nothing in reality is static, meaning that being is
dynamic and characterized by constant change. Bundle theories state that there are no regular objects but only
bundles of co-present properties. For example, a lemon may be understood
as a bundle that includes the properties yellow, sour, and round.
According to traditional bundle theory, the bundled properties are
universals, meaning that the same property may belong to several
different bundles. According to trope bundle theory, properties are particular entities that belong to a single bundle.
Some ontologies focus not on distinct objects but on
interrelatedness. According to relationalism, all of reality is
relational at its most fundamental level. Ontic structural realism
agrees with this basic idea and focuses on how these relations form
complex structures. Some structural realists state that there is nothing
but relations, meaning that individual objects do not exist. Others say
that individual objects exist but depend on the structures in which
they participate. Fact ontologies present a different approach by focusing on how
entities belonging to different categories come together to constitute
the world. Facts, also known as states of affairs, are complex entities;
for example, the fact that the Earth is a planet consists of the particular object the Earth and the property being a planet.
Fact ontologies state that facts are the fundamental constituents of
reality, meaning that objects, properties, and relations cannot exist on
their own and only form part of reality to the extent that they
participate in facts.
In the history of philosophy,
various ontological theories based on several fundamental categories
have been proposed. One of the first theories of categories was
suggested by Aristotle, whose system includes ten categories: substance, quantity, quality, relation, place, date, posture, state, action, and passion. An early influential system of categories in Indian philosophy, first proposed in the Vaisheshika school, distinguishes between six categories: substance, quality, motion, universal, individuator, and inherence. Immanuel Kant's transcendental idealism
includes a system of twelve categories, which Kant saw as pure concepts
of understanding. They are subdivided into four classes: quantity,
quality, relation, and modality. In more recent philosophy, theories of categories were developed by C. S. Peirce, Edmund Husserl, Samuel Alexander, Roderick Chisholm, and E. J. Lowe.
Others
The dispute between constituent and relational ontologies concerns the internal structure of concrete particular objects.
Constituent ontologies say that objects have an internal structure with
properties as their component parts. Bundle theories are an example of
this position: they state that objects are bundles of properties. This
view is rejected by relational ontologies, which say that objects have
no internal structure, meaning that properties do not inhere in them but
are externally related to them. According to one analogy, objects are
like pin-cushions and properties are pins that can be stuck to objects
and removed again without becoming a real part of objects. Relational
ontologies are common in certain forms of nominalism that reject the
existence of universal properties.
Hierarchical ontologies state that the world is organized into
levels. Entities on all levels are real but low-level entities are more
fundamental than high-level entities. This means that they can exist
without high-level entities while high-level entities cannot exist
without low-level entities. One hierarchical ontology says that elementary particles are more
fundamental than the macroscopic objects they compose, like chairs and
tables. Other hierarchical theories assert that substances are more
fundamental than their properties and that nature is more fundamental
than culture. Flat ontologies, by contrast, deny that any entity has a privileged
status, meaning that all entities exist on the same level. For them, the
main question is only whether something exists rather than identifying
the level at which it exists.
The ontological theories of endurantism and perdurantism
aim to explain how material objects persist through time. Endurantism
is the view that material objects are three-dimensional entities that
travel through time while being fully present in each moment. They
remain the same even when they gain or lose properties as they change.
Perdurantism is the view that material objects are four-dimensional
entities that extend not just through space but also through time. This
means that they are composed of temporal parts
and, at any moment, only one part of them is present but not the
others. According to perdurantists, change means that an earlier part
exhibits different qualities than a later part. When a tree loses its
leaves, for instance, there is an earlier temporal part with leaves and a
later temporal part without leaves.
Differential ontology is a poststructuralist approach interested in the relation between the concepts of identity and difference.
It says that traditional ontology sees identity as the more basic term
by first characterizing things in terms of their essential features and
then elaborating differences based on this conception. Differential
ontologists, by contrast, privilege difference and say that the identity
of a thing is a secondary determination that depends on how this thing
differs from other things.
Object-oriented ontology belongs to the school of speculative realism
and examines the nature and role of objects. It sees objects as the
fundamental building blocks of reality. As a flat ontology, it denies
that some entities have a more fundamental form of existence than
others. It uses this idea to argue that objects exist independently of
human thought and perception.
Methods
Methods
of ontology are ways of conducting ontological inquiry and deciding
between competing theories. There is no single standard method; the
diverse approaches are studied by metaontology.
Conceptual analysis is a method to understand ontological concepts and clarify their meaning. It proceeds by analyzing their component parts and the necessary and sufficient conditions under which a concept applies to an entity. This information can help ontologists decide whether a certain type of entity, such as numbers, exists. Eidetic variation is a related method in phenomenological
ontology that aims to identify the essential features of different
types of objects. Phenomenologists start by imagining an example of the
investigated type. They proceed by varying the imagined features to
determine which ones cannot be changed, meaning they are essential. The transcendental
method begins with a simple observation that a certain entity exists.
In the following step, it studies the ontological repercussions of this
observation by examining how it is possible or which conditions are required for this entity to exist.
Another approach is based on intuitions in the form of non-inferential impressions about the correctness of general principles. These principles can be used as the foundation on which an ontological system is built and expanded using deductive reasoning. A further intuition-based method relies on thought experiments to evoke new intuitions. This happens by imagining a situation relevant to an ontological issue and then employing counterfactual thinking to assess the consequences of this situation. For example, some ontologists examine the relation between mind and matter by imagining creatures identical to humans but without consciousness.
Naturalistic methods rely on the insights of the natural sciences to determine what exists. According to an influential approach by Willard Van Orman Quine, ontology can be conducted by analyzing the ontological commitments of scientific theories. This method is
based on the idea that scientific theories provide the most reliable
description of reality and that their power can be harnessed by
investigating the ontological assumptions underlying them.
Principles of theory choice offer guidelines for assessing the
advantages and disadvantages of ontological theories rather than guiding
their construction. The principle of Ockham's Razor says that simple theories are preferable. A theory can be simple in different respects, for example, by using
very few basic types or by describing the world with a small number of
fundamental entities. Ontologists are also interested in the explanatory power of theories
and give preference to theories that can explain many observations. A further factor is how close a theory is to common sense.
Some ontologists use this principle as an argument against theories
that are very different from how ordinary people think about the issue.
In applied ontology, ontological engineering is the process of creating and refining conceptual models of specific domains.[151]
Developing a new ontology from scratch involves various preparatory
steps, such as delineating the scope of the domain one intends to model
and specifying the purpose and use cases of the ontology. Once the
foundational concepts within the area have been identified, ontology
engineers proceed by defining them and characterizing the relations
between them. This is usually done in a formal language to ensure precision and, in some cases, automatic computability. In the following review phase, the validity of the ontology is assessed using test data. Various more specific instructions for how to carry out the different steps have been suggested. They include the Cyc method, Grüninger and Fox's methodology, and so-called METHONTOLOGY. In some cases, it is feasible to adapt a pre-existing ontology to fit a
specific domain and purpose rather than creating a new one from
scratch.
Related fields
Ontology overlaps with many disciplines, including logic, the study of correct reasoning. Ontologists often employ logical systems to express their insights, specifically in the field of formal ontology. Of particular interest to them is the existential quantifier (), which is used to express what exists. In first-order logic, for example, the formula states that dogs exist. Some philosophers study ontology by examining the structure of thought
and language, saying that they reflect the structure of being. Doubts about the accuracy of natural language have led some ontologists to seek a new formal language, termed ontologese, for a better representation of the fundamental structure of reality.
Ontologies are often used in information science to provide a
conceptual scheme or inventory of a specific domain, making it possible
to classify objects and formally represent information about them. This
is of specific interest to computer science, which builds databases to store this information and defines computational processes to automatically transform and use it. For instance, to encode and store information about clients and
employees in a database, an organization may use an ontology with
categories such as person, company, address, and name. In some cases, it is necessary to exchange information belonging to
different domains or to integrate databases using distinct ontologies.
This can be achieved with the help of upper ontologies, which are not limited to one specific domain. They use general categories that apply to most or all domains, like Suggested Upper Merged Ontology and Basic Formal Ontology.
Similar applications of ontology are found in various fields
seeking to manage extensive information within a structured framework. Protein Ontology is a formal framework for the standardized representation of protein-related entities and their relationships. Gene Ontology and Sequence Ontology serve a similar purpose in the field of genetics. Environment Ontology is a knowledge representation focused on ecosystems and environmental processes. Friend of a Friend provides a conceptual framework to represent relations between people and their interests and activities.
The topic of ontology has received increased attention in anthropology since the 1990s, sometimes termed the "ontological turn". This type of inquiry is focused on how people from different cultures
experience and understand the nature of being. Specific interest has
been given to the ontological outlook of Indigenous people and how it differs from a Western perspective. As an example of this contrast, it has been argued that various indigenous communities ascribe intentionality to non-human entities, like plants, forests, or rivers. This outlook is known as animism and is also found in Native American
ontologies, which emphasize the interconnectedness of all living
entities and the importance of balance and harmony with nature.[170]
Ontology is closely related to theology and its interest in the existence of God as an ultimate entity. The ontological argument, first proposed by Anselm of Canterbury, attempts to prove the existence of the divine. It defines God
as the greatest conceivable being. From this definition it concludes
that God must exist since God would not be the greatest conceivable
being if God lacked existence. Another overlap in the two disciplines is found in ontological theories
that use God or an ultimate being as the foundational principle of
reality. Heidegger criticized this approach, terming it ontotheology.
Kapila was one of the founding fathers of the dualist school of Samkhya.
The roots of ontology in ancient philosophy
are speculations about the nature of being and the source of the
universe. Discussions of the essence of reality are found in the Upanishads,
ancient Indian scriptures dating from as early as 700 BCE. They say
that the universe has a divine foundation and discuss in what sense ultimate reality is one or many. Samkhya, the first orthodox school of Indian philosophy, formulated an atheist dualist ontology based on the Upanishads, identifying pure consciousness and matter as its two foundational principles. The later Vaisheshika school proposed a comprehensive system of categories. In ancient China, Laozi's (6th century BCE) Taoism examines the underlying order of the universe, known as Tao, and how this order is shaped by the interaction of two basic forces, yin and yang. The philosophical movement of Xuanxue emerged in the 3rd century CE and explored the relation between being and non-being.
Starting in the 6th century BCE, Presocratic philosophers in ancient Greece
aimed to provide rational explanations of the universe. They suggested
that a first principle, such as water or fire, is the primal source of
all things.[182]Parmenides
(c. 515–450 BCE) is sometimes considered the founder of ontology
because of his explicit discussion of the concepts of being and
non-being.[183] Inspired by Presocratic philosophy, Plato (427–347 BCE) developed his theory of forms. It distinguishes between unchangeable perfect forms and matter, which has a lower degree of existence and imitates the forms.[184]Aristotle
(384–322 BCE) suggested an elaborate system of categories that
introduced the concept of substance as the primary kind of being.[185] The school of Neoplatonism arose in the 3rd century CE and proposed an ineffable source of everything, called the One, which is more basic than being itself.[186]
The problem of universals was an influential topic in medieval ontology. Boethius (477–524 CE) suggested that universals can exist not only in matter but also in the mind. This view inspired Peter Abelard (1079–1142 CE), who proposed that universals exist only in the mind. Thomas Aquinas (1224–1274 CE) developed and refined fundamental ontological distinctions, such as the contrast between existence and essence, between substance and accidents, and between matter and form. He also discussed the transcendentals, which are the most general properties or modes of being. John Duns Scotus (1266–1308) argued that all entities, including God, exist in the same way and that each entity has a unique essence, called haecceity. William of Ockham
(c. 1287–1347 CE) proposed that one can decide between competing
ontological theories by assessing which one uses the smallest number of
elements, a principle known as Ockham's razor.
The Neo-Confucian philosopher Zhu Xi conceived the concept of li as the organizing principle of the universe.
In Arabic-Persian philosophy, Avicenna (980–1037 CE) combined ontology with theology. He identified God as a necessary being that is the source of everything else, which only has contingent existence. In 8th-century Indian philosophy, the school of Advaita Vedanta
emerged. It says that only a single all-encompassing entity exists,
stating that the impression of a plurality of distinct entities is an illusion. Starting in the 13th century CE, the Navya-Nyāya school built on Vaisheshika ontology with a particular focus on the problem of non-existence and negation. 9th-century China saw the emergence of Neo-Confucianism, which developed the idea that a rational principle, known as li, is the ground of being and order of the cosmos.
René Descartes
(1596–1650) formulated a dualist ontology at the beginning of the
modern period. It distinguishes between mind and matter as distinct
substances that causally interact. Rejecting Descartes's dualism, Baruch Spinoza (1632–1677) proposed a monist ontology according to which there is only a single entity that is identical to God and nature. Gottfried Wilhelm Leibniz
(1646–1716), by contrast, said that the universe is made up of many
simple substances, which are synchronized but do not interact with one
another. John Locke
(1632–1704) proposed his substratum theory, which says that each object
has a featureless substratum that supports the object's properties. Christian Wolff
(1679–1754) was influential in establishing ontology as a distinct
discipline, delimiting its scope from other forms of metaphysical
inquiry. George Berkeley (1685–1753) developed an idealist ontology according to which material objects are ideas perceived by minds.
Immanuel Kant
(1724–1804) rejected the idea that humans can have direct knowledge of
independently existing things and their nature, limiting knowledge to
the field of appearances. For Kant, ontology does not study external
things but provides a system of pure concepts of understanding. Influenced by Kant's philosophy, Georg Wilhelm Friedrich Hegel (1770–1831) linked ontology and logic. He said that being and thought are identical and examined their foundational structures. Arthur Schopenhauer (1788–1860) rejected Hegel's philosophy and proposed that the world is an expression of a blind and irrational will. Francis Herbert Bradley (1846–1924) saw absolute spirit as the ultimate and all-encompassing reality while denying that there are any external relations. In Indian philosophy, Swami Vivekananda (1863–1902) expanded on Advaita Vedanta, emphasizing the unity of all existence. Sri Aurobindo (1872–1950) sought to understand the world as an evolutionary manifestation of a divine consciousness.
At the beginning of the 20th century, Edmund Husserl (1859–1938) developed phenomenology and employed its method, the description of experience, to address ontological problems. This idea inspired his student Martin Heidegger (1889–1976) to clarify the meaning of being by exploring the mode of human existence. Jean-Paul Sartre responded to Heidegger's philosophy by examining the relation between being and nothingness from the perspective of human existence, freedom, and consciousness. Based on the phenomenological method, Nicolai Hartmann
(1882–1950) developed a complex hierarchical ontology that divides
reality into four levels: inanimate, biological, psychological, and
spiritual.
Alexius Meinong (1853–1920) articulated a controversial ontological theory that includes nonexistent objects as part of being. Arguing against this theory, Bertrand Russell (1872–1970) formulated a fact ontology known as logical atomism. This idea was further refined by the early Ludwig Wittgenstein (1889–1951) and inspired D. M. Armstrong's (1926–2014) ontology. Alfred North Whitehead (1861–1947), by contrast, developed a process ontology. Rudolf Carnap
(1891–1970) questioned the objectivity of ontological theories by
claiming that what exists depends on one's linguistic framework. He had a strong influence on Willard Van Orman Quine (1908–2000), who analyzed the ontological commitments of scientific theories to solve ontological problems. Quine's student David Lewis
(1941–2001) formulated the position of modal realism, which says that
possible worlds are as real and concrete as the actual world. Since the end of the 20th century, interest in applied ontology has
risen in computer and information science with the development of
conceptual frameworks for specific domains.
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