Heteroplasmy

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https://en.wikipedia.org/wiki/Heteroplasmy

Heteroplasmy is the presence of more than one type of organellar genome (mitochondrial DNA or plastid DNA) within a cell or individual. It is an important factor in considering the severity of mitochondrial diseases. Because most eukaryotic cells contain many hundreds of mitochondria with hundreds of copies of mitochondrial DNA, it is common for mutations to affect only some mitochondria, leaving most unaffected.

Although detrimental scenarios are well-studied, heteroplasmy can also be beneficial. For example, centenarians show a higher than average degree of heteroplasmy.

Microheteroplasmy is present in most individuals. This refers to hundreds of independent mutations in one organism, with each mutation found in about 1–2% of all mitochondrial genomes.

 

 

Types of heteroplasmy

In order for heteroplasmy to occur, organelles must contain a genome and, in turn, a genotype. In animals, mitochondria are the only organelles that contain their own genomes, so these organisms will only have mitochondrial heteroplasmy. In contrast, photosynthetic plants contain mitochondria and chloroplasts, each of which contains plastid genomes. Therefore, plant heteroplasmy occurs in two dimensions.

Organelle inheritance patterns

In 1909, while studying chloroplast genomes, Erwin Baur made the first observations about organelle inheritance patterns. Organelle genome inheritance differs from nuclear genome, and this is illustrated by four violations of Mendel's laws.

1. During asexual reproduction, nuclear genes never segregate during cellular divisions. This is to ensure that each daughter cell gets a copy of every gene. However, organelle genes in heteroplasmic cells can segregate because they each have several copies of their genome. This may result in daughter cells with differential proportions of organelle genotypes.
2. Mendel states that nuclear alleles always segregate during meiosis. However, organelle alleles may or may not do this.
3. Nuclear genes are inherited from a combination of alleles from both parents, making inheritance biparental. Conversely, organelle inheritance is uniparental, meaning the genes are all inherited from one parent.
4. It is also unlikely for organelle alleles to segregate independently, like nuclear alleles do, because plastid genes are usually on a single chromosome and recombination is limited by uniparental inheritance.

There is a wide variety of mitochondrial DNA genotypes in the maternal pool, which is represented by the bottle. The two genotypes in this maternal pool are represented by blue and yellow. When generated, each oocyte receives a small subsampling of mitochondrial DNA molecules in differing proportions. This is represented by the conveyor belt with oocytes, each one unique, as they are produced.

 

Vegetative segregation

Vegetative segregation, the random partitioning of cytoplasm, is a distinguishable characteristic of organelle heredity. During cell division, the organelles are divided equally, providing each daughter cell with a random selection of plasmid genotypes.

Uniparental inheritance

Uniparental inheritance refers to the fact that, in most organisms, many offspring inherit organelle genes from only one parent. However, this is not a general law. Many organisms that have the ability to differentiate maternal and paternal sexes will produce offspring with a mixture of maternal, paternal, and biparental mitochondrial DNA.

Mitochondrial bottleneck

Entities undergoing uniparental inheritance and with little to no recombination may be expected to be subject to Muller's ratchet, the inexorable accumulation of deleterious mutations until functionality is lost. Animal populations of mitochondria avoid this buildup through a developmental process known as the mtDNA bottleneck. The bottleneck exploits stochastic processes in the cell to increase in the cell-to-cell variability in mutant load as an organism develops: a single egg cell with some proportion of mutant mtDNA thus produces an embryo where different cells have different mutant loads. Cell-level selection may then act to remove those cells with more mutant mtDNA, leading to a stabilisation or reduction in mutant load between generations. The mechanism underlying the bottleneck is debated, with a recent mathematical and experimental metastudy providing evidence for a combination of random partitioning of mtDNAs at cell divisions and random turnover of mtDNA molecules within the cell.

The mitochondrial bottleneck concept refers to the classic evolutionary term, which is used to explain an event that reduces and specifies a population. It was developed to describe why mitochondrial DNA in an embryo might be drastically different from that of its mother. When a large population of DNA is subsampled, each sample population will receive a slightly different proportion of mitochondrial genotypes. Consequently, when paired with a high degree of replication, a rare or mutated allele can begin to proportionally dominate. In theory, this makes possible a single-generation shift of overall mitochondrial genotype.

Selection

Although it is not well characterized, selection can occur for organelle genomes in heteroplasmic cells. Intracellular ("within cells") selection occurs within individual cells. It refers to the selective segregation of certain genotypes in mitochondrial DNA that allows the favoured genotype to thrive. Intercellular ("between cells") selection occurs on a larger scale, and refers to the preferential growth of cells that have greater numbers of a certain mitochondrial genotype. Selective differences can occur between naturally occurring, non-pathological mtDNA types when mixed in cells, and may depend on tissue type, age, and genetic distance. Selective differences between naturally occurring mtDNA types may pose challenges for gene therapies.

In mitochondrial DNA, there is evidence for potent germline purifying selection, as well as purifying selection during embryogenesis. Additionally, there is a dose-dependent decrease in reproduction ability for females that have mutations in mitochondrial DNA. This demonstrates another selection mechanism to prevent the evolutionary preservation of harmful mutations.

Reduced recombination

It is very rare for organelle genes from different lineages to recombine. These genomes are usually inherited uniparentally, which does not provide a recombination opportunity. If they are inherited biparentally, it is unlikely that the organelles from the parents will fuse, meaning they will not share genomes. 

However, it is possible for organelle genes from the same lineage to recombine. Intramolecular and intermolecular recombination can cause inversions and repeats in chloroplast DNA, and can produce subgenomic circles in mitochondrial DNA.

Mitochondrial mutations in disease

Mutations in mitochondrial DNA are usually single nucleotide substitutions, single base insertions, or deletions.

Because each cell contains thousands of mitochondria, nearly all organisms house low levels of mitochondrial variants, conferring some degree of heteroplasmy. Although a single mutational event might be rare in its generation, repeated mitotic segregation and clonal expansion can enable it to dominate the mitochondrial DNA pool over time. When this occurs, it is known as reaching threshold, and it usually results in physiological consequences.

Severity and time to presentation

Symptoms of severe heteroplasmic mitochondrial disorders do not usually appear until adulthood. Many cell divisions and a great deal of time are required for a cell to accumulate enough mutant mitochondria to cause symptoms. An example of this phenomenon is Leber optic atrophy. Generally, individuals with this condition do not experience vision difficulties until they have reached adulthood. Another example is MERRF syndrome (or Myoclonic Epilepsy with Ragged Red Fibers). In MELAS, heteroplasmy explains the variation in severity of the disease among siblings. 

Screening

Preimplantation genetic screening (PGS) can be used to quantitate the risk of a child of being affected by a mitochondrial disease. In most cases, a muscle mutation level of approximately 18% or less confers a 95% risk reduction.

Sequence illustrating heteroplasmy genotype of 16169 C/T in Nicholas II of Russia.

 

Notable cases

One notable example of an otherwise healthy individual whose heteroplasmy was discovered incidentally is Nicholas II of Russia, whose heteroplasmy (and that of his brother) served to convince Russian authorities of the authenticity of his remains.

Vestigiality

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Vestigiality

 

In humans the vermiform appendix is a vestigial structure; it has lost much of its ancestral function.

Vestigiality is the retention during the process of sexual reproduction of genetically determined structures or attributes that have lost some or all of their ancestral function in a given species. Assessment of the vestigiality must generally rely on comparison with homologous features in related species. The emergence of vestigiality occurs by normal evolutionary processes, typically by loss of function of a feature that is no longer subject to positive selection pressures when it loses its value in a changing environment. The feature may be selected against more urgently when its function becomes definitively harmful, but if the lack of the feature provides no advantage, and its presence provides no disadvantage, the feature may not be phased out by natural selection and persist across species. 

Examples of vestigial structures are the loss of functional wings in island-dwelling birds; the human appendix and vomeronasal organ; and the hindlimbs of the snake and whale.

Overview

The Darwin-tubercle (left) is a vestigial form of the ear tip (right) in the mammalian ancestors of humans—here shown in a crab-eating macaque.

Vestigial features may take various forms; for example, they may be patterns of behavior, anatomical structures, or biochemical processes. Like most other physical features, however functional, vestigial features in a given species may successively appear, develop, and persist or disappear at various stages within the life cycle of the organism, ranging from early embryonic development to late adulthood. 

Vestigial hindlegs (spurs) in a boa constrictor

 

Vestigiality, biologically speaking, refers to organisms retaining organs that have seemingly lost their original function. The issue is controversial and not without dispute; nonetheless, vestigial organs are common evolutionary knowledge. In addition, the term vestigiality is useful in referring to many genetically determined features, either morphological, behavioral, or physiological; in any such context, however, it need not follow that a vestigial feature must be completely useless. A classic example at the level of gross anatomy is the human vermiform appendix—though vestigial in the sense of retaining no significant digestive function, the appendix still has immunological roles and is useful in maintaining gut flora.

Similar concepts apply at the molecular level—some nucleic acid sequences in eukaryotic genomes have no known biological function; some of them may be "junk DNA", but it is a difficult matter to demonstrate that a particular sequence in a particular region of a given genome is truly nonfunctional. The simple fact that it is noncoding DNA does not establish that it is functionless. Furthermore, even if an extant DNA sequence is functionless, it does not follow that it has descended from an ancestral sequence of functional DNA. Logically such DNA would not be vestigial in the sense of being the vestige of a functional structure. In contrast pseudogenes have lost their protein-coding ability or are otherwise no longer expressed in the cell. Whether they have any extant function or not, they have lost their former function and in that sense, they do fit the definition of vestigiality.

Vestigial structures are often called vestigial organs, although many of them are not actually organs. Such vestigial structures typically are degenerate, atrophied, or rudimentary,^[3] and tend to be much more variable than homologous non-vestigial parts. Although structures commonly regarded "vestigial" may have lost some or all of the functional roles that they had played in ancestral organisms, such structures may retain lesser functions or may have become adapted to new roles in extant populations.

It is important to avoid confusion of the concept of vestigiality with that of exaptation. Both may occur together in the same example, depending on the relevant point of view. In exaptation, a structure originally used for one purpose is modified for a new one. For example, the wings of penguins would be exaptational in the sense of serving a substantial new purpose (underwater locomotion), but might still be regarded as vestigial in the sense of having lost the function of flight. In contrast Darwin argued that the wings of emus would be definitely vestigial, as they appear to have no major extant function; however, function is a matter of degree, so judgments on what is a "major" function are arbitrary; the emu does seem to use its wings as organs of balance in running. Similarly, the ostrich uses its wings in displays and temperature control, though they are undoubtedly vestigial as structures for flight.

Vestigial characters range from detrimental through neutral to favorable in terms of selection. Some may be of some limited utility to an organism but still degenerate over time if they do not confer a significant enough advantage in terms of fitness to avoid the effects of genetic drift or competing selective pressures. Vestigiality in its various forms presents many examples of evidence for biological evolution.

History

The blind mole rat (Spalax typhlus) has tiny eyes completely covered by a layer of skin.

Vestigial structures have been noticed since ancient times, and the reason for their existence was long speculated upon before Darwinian evolution provided a widely accepted explanation. In the 4th century BC, Aristotle was one of the earliest writers to comment, in his History of Animals, on the vestigial eyes of moles, calling them "stunted in development" due to the fact that moles can scarcely see. However, only in recent centuries have anatomical vestiges become a subject of serious study. In 1798, Étienne Geoffroy Saint-Hilaire noted on vestigial structures:

“

Whereas useless in this circumstance, these rudiments... have not been eliminated, because Nature never works by rapid jumps, and She always leaves vestiges of an organ, even though it is completely superfluous, if that organ plays an important role in the other species of the same family.

”

His colleague, Jean-Baptiste Lamarck, named a number of vestigial structures in his 1809 book Philosophie Zoologique. Lamarck noted "Olivier's Spalax, which lives underground like the mole, and is apparently exposed to daylight even less than the mole, has altogether lost the use of sight: so that it shows nothing more than vestiges of this organ."

Charles Darwin was familiar with the concept of vestigial structures, though the term for them did not yet exist. He listed a number of them in The Descent of Man, including the muscles of the ear, wisdom teeth, the appendix, the tail bone, body hair, and the semilunar fold in the corner of the eye. Darwin also noted, in On the Origin of Species, that a vestigial structure could be useless for its primary function, but still retain secondary anatomical roles: "An organ serving for two purposes, may become rudimentary or utterly aborted for one, even the more important purpose, and remain perfectly efficient for the other.... [A]n organ may become rudimentary for its proper purpose, and be used for a distinct object."

In the first edition of On the Origin of Species, Darwin briefly mentioned inheritance of acquired characters under the heading "Effects of Use and Disuse", expressing little doubt that use "strengthens and enlarges certain parts, and disuse diminishes them; and that such modifications are inherited". In later editions he expanded his thoughts on this, and in the final chapter of the 6th edition concluded that species have been modified "chiefly through the natural selection of numerous successive, slight, favorable variations; aided in an important manner by the inherited effects of the use and disuse of parts".

In 1893, Robert Wiedersheim published The Structure of Man, a book on human anatomy and its relevance to man's evolutionary history. The Structure of Man contained a list of 86 human organs that Wiedersheim described as, "Organs having become wholly or in part functionless, some appearing in the Embryo alone, others present during Life constantly or inconstantly. For the greater part Organs which may be rightly termed Vestigial." Since his time, the function of some of these structures have been discovered, while other anatomical vestiges have been unearthed, making the list primarily of interest as a record of the knowledge of human anatomy at the time. Later versions of Wiedersheim's list were expanded to as many as 180 human "vestigial organs". This is why the zoologist Horatio Newman said in a written statement read into evidence in the Scopes Trial that "There are, according to Wiedersheim, no less than 180 vestigial structures in the human body, sufficient to make of a man a veritable walking museum of antiquities."

Common descent and evolutionary theory

Vestigial structures are often homologous to structures that are functioning normally in other species. Therefore, vestigial structures can be considered the evidence for evolution, the process by which beneficial heritable traits arise in populations over an extended period of time. The existence of vestigial traits can be attributed to changes in the environment and behavior patterns of the organism in question. Through an examination of these various traits, it is clear that evolution had a hard role in the development of organisms. Every anatomical structure or behavior response has origins in which they were, at one time, useful. As time progressed, the ancient common ancestor organisms did as well. Evolving with time, natural selection played a huge role. More advantageous structures were selected, while others were not. With this expansion, some traits were left to the wayside. As the function of the trait is no longer beneficial for survival, the likelihood that future offspring will inherit the "normal" form of it decreases. In some cases, the structure becomes detrimental to the organism (for example the eyes of a mole can become infected). In many cases the structure is of no direct harm, yet all structures require extra energy in terms of development, maintenance, and weight, and are also a risk in terms of disease (e.g., infection, cancer), providing some selective pressure for the removal of parts that do not contribute to an organism's fitness. A structure that is not harmful will take longer to be 'phased out' than one that is. However, some vestigial structures may persist due to limitations in development, such that complete loss of the structure could not occur without major alterations of the organism's developmental pattern, and such alterations would likely produce numerous negative side-effects. The toes of many animals such as horses, which stand on a single toe, are still evident in a vestigial form and may become evident, although rarely, from time to time in individuals. 

The vestigial versions of the structure can be compared to the original version of the structure in other species in order to determine the homology of a vestigial structure. Homologous structures indicate common ancestry with those organisms that have a functional version of the structure. Douglas Futuyma has stated that vestigial structures make no sense without evolution, just as spelling and usage of many modern English words can only be explained by their Latin or Old Norse antecedents.

Vestigial traits can still be considered adaptations. This is because an adaptation is often defined as a trait that has been favored by natural selection. Adaptations, therefore, need not be adaptive, as long as they were at some point.

Examples

Non-human animals

Letter c in the picture indicates the undeveloped hind legs of a baleen whale.

 

Vestigial characters are present throughout the animal kingdom, and an almost endless list could be given. Darwin said that "it would be impossible to name one of the higher animals in which some part or other is not in a rudimentary condition."

The wings of ostriches, emus, and other flightless birds are vestigial; they are remnants of their flying ancestors' wings. The eyes of certain cavefish and salamanders are vestigial, as they no longer allow the organism to see, and are remnants of their ancestors' functional eyes. Animals that reproduce without sex (via asexual reproduction) generally lose their sexual traits, such as the ability to locate/recognize the opposite sex and copulation behavior.

Boas and pythons have vestigial pelvis remnants, which are externally visible as two small pelvic spurs on each side of the cloaca. These spurs are sometimes used in copulation, but are not essential, as no colubrid snake (the vast majority of species) possesses these remnants. Furthermore, in most snakes, the left lung is greatly reduced or absent. Amphisbaenians, which independently evolved limblessness, also retain vestiges of the pelvis as well as the pectoral girdle, and have lost their right lung.

Vestigial attachement clamps in various genera of protomicrocotylids. Accessory sclerites (black) are present in normal clamps but absent in simplified clamps. Lethacotyle (right) has no clamp at all.

 

A case of vestigial organs was described in polyopisthocotylean Monogeneans (parasitic flatworms). These parasites usually have a posterior attachment organ with several clamps, which are sclerotised organs attaching the worm to the gill of the host fish. These clamps are extremely important for the survival of the parasite. In the family Protomicrocotylidae, species have either normal clamps, simplified clamps, or no clamps at all (in the genus Lethacotyle). After a comparative study of the relative surface of clamps in more than 100 Monogeneans, this has been interpreted as an evolutionary sequence leading to the loss of clamps. Coincidentally, other attachment structures (lateral flaps, transverse striations) have evolved in protomicrocotylids. Therefore, clamps in protomicrocotylids were considered vestigial organs.

In the foregoing examples the vestigiality is generally the (sometimes incidental) result of adaptive evolution. However, there are many examples of vestigiality as the product of drastic mutation, and such vestigiality is usually harmful or counter-adaptive. One of the earliest documented examples was that of vestigial wings in Drosophila. Many examples in many other contexts have emerged since.

Humans

The muscles connected to the ears of a human do not develop enough to have the same mobility allowed to many animals.

Human vestigiality is related to human evolution, and includes a variety of characters occurring in the human species. Many examples of these are vestigial in other primates and related animals, whereas other examples are still highly developed. The human caecum is vestigial, as often is the case in omnivores, being reduced to a single chamber receiving the content of the ileum into the colon. The ancestral caecum would have been a large, blind diverticulum in which resistant plant material such as cellulose would have been fermented in preparation for absorption in the colon. Analogous organs in other animals similar to humans continue to perform similar functions. An alternative explanation would be the possibility that natural selection selects for larger appendices because smaller and thinner appendices would be more susceptible to inflammation and disease. The coccyx, or tailbone, though a vestige of the tail of some primate ancestors, is functional as an anchor for certain pelvic muscles including: the levator ani muscle and the largest gluteal muscle, the gluteus maximus.

Other structures that are vestigial include the plica semilunaris on the inside corner of the eye (a remnant of the nictitating membrane); and, as pictured, muscles in the ear and other parts of the body. Other organic structures (such as the occipitofrontalis muscle) have lost their original functions (keep the head from falling) but are still useful for other purposes (facial expression).

Humans also bear some vestigial behaviors and reflexes. The formation of goose bumps in humans under stress is a vestigial reflex; its function in human ancestors was to raise the body's hair, making the ancestor appear larger and scaring off predators. The arrector pili muscle, which is a band of smooth muscle that connects the hair follicle to connective tissue, contracts and creates the goosebumps on skin.

There are also vestigial molecular structures in humans, which are no longer in use but may indicate common ancestry with other species. One example of this is a gene that is functional in most other mammals and which produces L-gulonolactone oxidase, an enzyme that can make vitamin C. A documented mutation deactivated the gene in an ancestor of the modern infraorder of monkeys, and apes, and it now remains in their genomes, including the human genome, as a vestigial sequence called a pseudogene.

The shift in human diet towards soft and processed food over time caused a reduction in the number of powerful grinding teeth, especially the third molars or wisdom teeth, which were highly prone to impaction.

Plants and fungi

Plants also have vestigial parts, including functionless stipules and carpels, leaf reduction of Equisetum, paraphyses of Fungi. Well known examples are the reductions in floral display, leading to smaller and/or paler flowers, in plants that reproduce without outcrossing, for example via selfing or obligate clonal reproduction.

Atavism

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https://en.wikipedia.org/wiki/Atavism

 

Early embryos of various species display some ancestral features, like the tail on this human embryo. These features normally disappear in later development, but it may not happen if the animal has an atavism.

 

In biology, an atavism is a modification of a biological structure whereby an ancestral trait reappears after having been lost through evolutionary change in previous generations. Atavisms can occur in several ways; one of which is when genes for previously existing phenotypic features are preserved in DNA, and these become expressed through a mutation that either knocks out the overriding genes for the new traits or makes the old traits override the new one. A number of traits can vary as a result of shortening of the fetal development of a trait (neoteny) or by prolongation of the same. In such a case, a shift in the time a trait is allowed to develop before it is fixed can bring forth an ancestral phenotype. Atavisms are often seen as evidence of evolution.

In social sciences, atavism is the tendency of reversion. For example, people in the modern era reverting to the ways of thinking and acting of a former time. The word atavism is derived from the Latin atavus—a great-great-great-grandfather or, more generally, an ancestor. 

Biology

Evolutionarily traits that have disappeared phenotypically do not necessarily disappear from an organism's DNA. The gene sequence often remains, but is inactive. Such an unused gene may remain in the genome for many generations. As long as the gene remains intact, a fault in the genetic control suppressing the gene can lead to it being expressed again. Sometimes, the expression of dormant genes can be induced by artificial stimulation.

Atavisms have been observed in humans, such as with infants born with vestigial tails (called a "coccygeal process", "coccygeal projection", or "caudal appendage"). Atavism can also be seen in humans who possess large teeth, like those of other primates. In addition, a case of "snake heart", the presence of "coronary circulation and myocardial architecture [which resemble] those of the reptilian heart", has also been reported in medical literature. Atavism has also recently been induced in modern avian dinosaur (bird) foetuses to express dormant ancestral non-avian dinosaur features, including teeth.

Other examples of observed atavisms include:

• Hind limbs in cetaceans.
• Extra toes of the modern horse.
• Reappearance of limbs in limbless vertebrates.
• Re-evolution of sexuality from parthenogenesis in orbitid mites.
• Teeth in chickens.
• Dewclaws in dogs.
• Reappearance of prothoracic wings in insects.
• Reappearance of wings on wingless stick insects and earwigs.
• Atavistic muscles in several birds and mammals such as the beagle and the jerboa.
• Extra toes in guinea pigs.
• Reemergence of sexual reproduction in the flowering plant Hieracium pilosella and the Crotoniidae family of mites.
• Webbed feet in adult axolotls.
• Human tails (not pseudo-tails) and supernumerary nipples in humans (and other primates).
• Color blindness in humans.

Culture

Atavism is a term in Joseph Schumpeter's explanation of World War I in twentieth-century liberal Europe. He defends the liberal international relations theory that an international society built on commerce will avoid war because of war's destructiveness and comparative cost. His reason for World War I is termed "atavism", in which he asserts that senescent governments in Europe (those of the German Empire, Russian Empire, Ottoman Empire, and Austro-Hungarian Empire) pulled the liberal Europe into war, and that the liberal regimes of the other continental powers did not cause it. He used this idea to say that liberalism and commerce would continue to have a soothing effect in international relations, and that war would not arise between nations which are connected by commercial ties.

University of London professor Guy Standing has identified three distinct sub-groups of the precariat, one of which he refers to as "atavists", who long for what they see as a lost past.

Social Darwinism

During the interval between the acceptance of evolution in the mid-1800s and the rise of the modern understanding of genetics in the early 1900s, atavism was used to account for the reappearance in an individual of a trait after several generations of absence—often called a "throw-back". The idea that atavisms could be made to accumulate by selective breeding, or breeding back, led to breeds such as the Heck cattle. This had been bred from ancient landraces with selected primitive traits, in an attempt of "reviving" the aurochs, an extinct species of wild cattle. The same notions of atavisms were used by social Darwinists, who claimed that inferior races displayed atavistic traits, and represented more primitive traits than other races. Both atavisms and Ernst Haeckel's recapitulation theory are related evolutionary progress, as development towards greater complexity and superior ability.

In addition, the concept of atavism as part of an individualistic explanation of the causes of criminal deviance was popularised by the Italian criminologist Cesare Lombroso in the 1870s. He attempted to identify physical characteristics common to criminals and labeled those he found as atavistic, 'throw-back' traits that determined 'primitive' criminal behavior. His statistical evidence and the closely related idea of eugenics have long since been abandoned by the scientific community, but the concept that physical traits may affect the likelihood of criminal or unethical behavior in a person still has some scientific support.

Spandrel (biology)

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https://en.wikipedia.org/wiki/Spandrel_(biology)

 

Stephen Jay Gould and Richard Lewontin used the architectural term spandrel (the triangular gap at the corner of an arch) to describe a byproduct of evolution. Basilica di San Marco, Venice

In evolutionary biology, a spandrel is a phenotypic characteristic that is a byproduct of the evolution of some other characteristic, rather than a direct product of adaptive selection. That is, it is a trait that is not particularly advantageous to have, though it is retained because it is not particularly harmful to have.

The term "spandrel" originated as an architectural word for the roughly triangular space between the tops of two adjacent arches and the ceiling. These spaces were not actually utilized until later on, when artists realized they could make designs and paint in these small areas, enhancing the overall design of the building. 

Stephen Jay Gould and Richard Lewontin brought the term into biology in their 1979 paper "The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme". This defined the biological concept and argued the case for a structuralist view of evolution.

Origin of the term

The term was coined by Harvard paleontologist Stephen Jay Gould and population geneticist Richard Lewontin in their paper "The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme" (1979). Evolutionary biologist Günter P. Wagner called the paper "the most influential structuralist manifesto".

In their paper, Gould and Lewontin employed the analogy of spandrels in Renaissance architecture: curved areas of masonry between arches supporting a dome that arise as a consequence of decisions about the shape of the arches and the base of the dome, rather than being designed for the artistic purposes for which they were often employed. The authors singled out properties like the necessary number of four spandrels and their specific three-dimensional shape. At the time, it was thought in the scientific community that everything an animal has developed that has a positive effect on that animal's fitness was due to natural selection or some adaptation. Gould and Lewontin proposed an alternative hypothesis: that due to adaptation and natural selection, byproducts are also formed. These byproducts of adaptations that had no real relative advantage to survival, they termed spandrels. In the biological sense, a "spandrel" might result from an architectural requirement inherent in the Bauplan of an organism, or from some other constraint on adaptive evolution.

Evolutionary biology uses the term spandrel for features of an organism arising as byproducts, rather than adaptations, that have no clear benefit for the organism's fitness and survival. In response to the position that spandrels are just small, unimportant byproducts, Gould and Lewontin argue that "we must not recognize that small means unimportant. Spandrels can be as prominent as primary adaptations". A main example used by Gould and Lewontin is the human brain. Many secondary processes and actions come in addition to the main functions of the human brain. These secondary processes and thoughts can eventually turn into an adaptation or provide a fitness advantage to humans. Just because something is a secondary trait or byproduct of an adaptation does not mean it has no use.

In 1982, Gould and Vrba introduced the term "exaptation" for characteristics that enhance fitness in their present role but were not built for that role by natural selection. Exaptations may be divided into two subcategories: pre-adaptations and spandrels. Spandrels are characteristics that did not originate by the direct action of natural selection and that were later co-opted for a current use. Gould saw the term to be optimally suited for evolutionary biology for "the concept of a nonadaptive architectural by-product of definite and necessary form – a structure of particular size and shape that then becomes available for later and secondary utility".

Criticism of the term

Gould and Lewontin's proposal generated a large literature of critique, which Gould characterised as being grounded in two ways. First, a terminological claim was offered that the "spandrels" of Basilica di San Marco were not spandrels at all, but rather were pendentives. Gould responded, "The term spandrel may be extended from its particular architectural use for two-dimensional byproducts to the generality of 'spaces left over', a definition that properly includes the San Marco pendentives."

Other critics, such as Daniel Dennett, further claimed (in Darwin's Dangerous Idea and elsewhere) that these pendentives are not merely architectural by-products as Gould and Lewontin supposed. Dennett argues that alternatives to pendentives, such as corbels or squinches, would have served equally well from an architectural standpoint, but pendentives were deliberately selected due to their aesthetic value. Critics such as H. Allen Orr argued that Lewontin and Gould's oversight in this regard illustrates their underestimation of the pervasiveness of adaptations found in nature.

Ian Kluge criticizes the whole subject of spandrels to be bogged down in a definitional debate. He argues it is not entirely clear what is and is not a spandrel. He also argues all examples of spandrels, pendentives, corbels and squinches do actually serve a function; they are necessary to achieve something, but that necessity is exactly what epiphenomenalism denies.

Response to criticism

Gould responded that critics ignore that later selective value is a separate issue from origination as necessary consequences of structure; he summarised his use of the term 'spandrel' in 1997: "Evolutionary biology needs such an explicit term for features arising as byproducts, rather than adaptations, whatever their subsequent exaptive utility... Causes of historical origin must always be separated from current utilities; their conflation has seriously hampered the evolutionary analysis of form in the history of life." Gould cites the masculinized genitalia of female hyenas and the brooding chamber of some snails as examples of evolutionary spandrels.

Gould (1991) outlines some considerations for grounds for assigning or denying a structure the status of spandrel, pointing first to the fact that a structure originating as a spandrel through primary exaptation may have been further crafted for its current utility by a suite of secondary adaptations, thus the grounds of how well crafted a structure is for a function cannot be used as grounds for assigning or denying spandrel status. The nature of the current utility of a structure also does not provide a basis for assigning or denying spandrel status, nor does he see the origin of a structure as having any relationship to the extent or vitality of a later co-opted role, but places importance on the later evolutionary meaning of a structure. This seems to imply that the design and secondary utilization of spandrels may feed back into the evolutionary process and thus determine major features of the entire structure. The grounds Gould does accept to have validity in assigning or denying a structure the status of spandrel are historical order and comparative anatomy. Historical order involves the use of historical evidence to determine which feature arose as a primary adaptation and which one appeared subsequently as a co-opted by-product. In the absence of historical evidence, inferences are drawn about the evolution of a structure through comparative anatomy. Evidence is obtained by comparing current examples of the structure in a cladistic context and by subsequently trying to determine a historical order from the distribution yielded by tabulation.

Language and music as spandrels

Linguist Noam Chomsky has argued that the "language faculty", and the property of discrete infinity or recursion that plays a central role in his theory of universal grammar (UG), may have evolved as a spandrel. In this view, Chomsky initially pointed to language being a result of increased brain size and increasing complexity, though he provides no definitive answers as to what factors led to the brain attaining the size and complexity of which discrete infinity is a consequence. Steven Pinker and Ray Jackendoff say Chomsky's case is "unconvincing" and that "language maps among recursive systems rather than being a straightforward externalization of a single recursive system", and as an example, numerical recursion "is parasitic on language (rather than vice versa)" among other arguments. Pinker contends that the language faculty is not a spandrel, but rather a result of natural selection. Newmeyer (1998) instead views the lack of symmetry, irregularity and idiosyncrasy that universal grammar tolerates and the widely different principles of organization of its various sub-components and consequent wide variety of linking rules relating them as evidence that such design features do not qualify as an exaptation. He suggests that universal grammar cannot be derivative and autonomous at the same time, and that Chomsky wants language to be an epiphenomenon and an "organ" simultaneously, where an organ is defined as a product of a dedicated genetic blueprint. Rudolph Botha counters that Chomsky has offered his conception of the feature of recursion but not a theory of the evolution of the language faculty as a whole.

Pinker has written that "As far as biological cause and effect are concerned, music is useless. It shows no signs of design for attaining a goal such as long life, grandchildren, or accurate perception and prediction of the world", and "I suspect that music is auditory cheesecake, an exquisite confection crafted to tickle the sensitive spots of at least six of our mental faculties." Dunbar found this conclusion odd, and stated that "it falls foul of what we might refer to as the Spandrel Fallacy: 'I haven't really had time to determine empirically whether or not something has a function, so I'll conclude that it can't possibly have one.'" Dunbar states that there are at least two potential roles of music in evolution: "One is its role in mating and mate choice, the other is its role in social bonding."

Agent detection

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Agent_detection

Agent detection is the inclination for animals, including humans, to presume the purposeful intervention of a sentient or intelligent agent in situations that may or may not involve one.

Evolutionary origins

It is believed that humans evolved agent detection as a survival strategy. In situations where one is unsure of the presence of an intelligent agent (such as an enemy or a predator), there is survival value in assuming its presence so that precautions can be taken. For example, if a human came across an indentation in the ground that might be a lion's footprint, it is advantageous to err on the side of caution and assume that the lion is present.

Psychologists Kurt Gray and Daniel Wegner wrote:

“

The high cost of failing to detect agents and the low cost of wrongly detecting them has led researchers to suggest that people possess a Hyperactive Agent Detection Device, a cognitive module that readily ascribes events in the environment to the behavior of agents.

”

Time-consuming steps, fast escapes and criticism

Since it takes time to think of why a stimulus is present while simply reacting to it goes much faster, some evolutionary biologists criticize the assumption that agent detection would enhance the ability to escape predators as making a fast escape is of high importance to survive. These biologists state that simple reactions to stimuli that do not take a by-route over speculation about causes, such as running from the shape of certain footprints or a pair of eyes by simple reflex without even making a time-consuming association to a predator, would be selected instead by saving one step and therefore time. As a result, these biologists conclude that there are no specialized brain mechanisms for agent detection.

Role in religion

Some scientists believe that the belief in creator gods is an evolutionary by-product of agent detection. A spandrel is a non-adaptive trait formed as a side effect of an adaptive trait. The psychological trait in question is "if you hear a twig snap in the forest, some sentient force is probably behind it". This trait helps to prevent the primate from being murdered or eaten as food. However this hypothetical trait could remain in modern humans: thus some evolutionary psychologists theorize that "even if the snapping was caused by the wind, modern humans are still inclined to attribute the sound to a sentient agent; they call this person a god".

Gray and Wegner also said that agent detection is likely to be a "foundation for human belief in God" but "simple overattribution of agency cannot entirely account for the belief in God..." because the human ability to form a theory of mind and what they refer to as "existential theory of mind" are also required to "give us the basic cognitive capacity to conceive of God."

According to Justin L. Barrett, having a scientific explanation for mental phenomena does not mean we should stop believing in them. "Suppose science produces a convincing account for why I think my wife loves me — should I then stop believing that she does?"

Religion Explained

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Religion_Explained

 

Religion Explained: The Evolutionary Origins of Religious Thought

Cover
Author	Pascal Boyer
Language	English
Subjects	Evolutionary psychology of religion Evolutionary origin of religions
Publisher	Basic Books
Publication date	2001
Media type	Print
Pages	384
ISBN	0-465-00696-5
OCLC	50628396

Religion Explained: The Evolutionary Origins of Religious Thought is a 2001 book by cognitive anthropologist Pascal Boyer, in which the author discusses the evolutionary psychology of religion and evolutionary origin of religions.

Summary

Boyer describes the genesis of religious concepts as a phenomenon of the mind's cognitive inference systems, comparable to pareidolia and perceptions of religious imagery in natural phenomena resulting from face perception processes within the human brain. Boyer supports this naturalistic origin of religion with evidence from many specialized disciplines including biological anthropology, cultural anthropology, cognitive science, linguistics, evolutionary biology, cognitive psychology, evolutionary psychology, neuroscience, and information processing.

Religion Explained frames religious practices and beliefs in terms of recent cognitive neuroscience research in the modularity of mind. This theory involves cognitive "modules" ("devices" or "subroutines") underlying inference systems and intuitions. For instance, Boyer suggests culturally-widespread beliefs in "supernatural agents" (e.g., gods, ancestors, spirits, and witches) result from agent detection: the intuitive modular process of assuming intervention by conscious agents, regardless of whether they are present. "When we see branches moving in a tree or when we hear an unexpected sound behind us, we immediately infer that some agent is the cause of this salient event. We can do that without any specific description of what the agent actually is." Boyer cites the anthropologist E. E. Evans-Pritchard's classic Zande story about a termite-infested roof collapsing.

For the anthropologist, the house caved in because of the termites. For the Zande, it was quite clear that witchcraft was involved. However, the Zande were also aware that the termites were the proximate cause of the incident. But what they wanted to know was why it happened at that particular time, when particular people were gathered in the house.

Within Boyer's hypothesis, religion is a "parasite" (or "spandrel") offshoot from cognitive modules, comparable to the way the reading process is parasitic upon language modules.

As I have pointed out repeatedly the building of religious concepts requires mental systems and capacities that are there anyway, religious concepts or not. Religious morality uses moral intuitions, religious notions of supernatural agents recruit our intuitions about agency in general, and so on. This is why I said that religious concepts are parasitic upon other mental capacities. Our capacities to play music, paint pictures or even make sense of printed ink-patterns on a page are also parasitic in this sense. This means that we can explain how people play music, paint pictures and learn to read by examining how mental capacities are recruited by these activities. The same goes for religion. Because the concepts require all sorts of specific human capacities (an intuitive psychology, a tendency to attend to some counterintuitive concepts, as well as various social mind adaptations), we can explain religion by describing how these various capacities get recruited, how they contribute to the features of religion that we find in so many different cultures. We do not need to assume that there is a special way of functioning that occurs only when processing religious thoughts.

Boyer admits his explanation of religion

is not a quick, shoot-from-the-hip solution of the kind that many people, either religious or not, seem to favor. There cannot be a magic bullet to explain the existence and common features of religion, as the phenomenon is the result of aggregate relevance – that is, of successful activation of a whole variety of mental systems.

Reception

Critical reception of Religion Explained has been mixed. 

The psychologist Benjamin Beit-Hallahmi called the book "a milestone on the road to a new behavioral understanding of religion, basing itself on what has come to be known as cognitive anthropology, and pointedly ignoring much work done over the past one hundred years in the behavioral study of religion and in the psychological anthropology of religion." He continues:

The clearest virtue of this book is that of dealing with the real thing. Even today, most scholarly work on religion consists of apologetics in one form or another, and we are deluged by offers of grants to study "spirituality" or teach "religion and science". This all serves to make us forget that religion is a collection of fantasies about spirits, and Boyer indeed aims to teach us about the world of the spirits in the grand tradition of the Enlightenment. Any general introduction to the world of the spirits must be ambitious because it hasn't been done and also because it has been done intuitively by all of us.

The journalist David Klinghoffer wrote in National Review that "Boyer's talk of 'religion is suspiciously generic" and describes his work as "professorial noodlings" that attempt to raise the question whether "all religions are somehow the same". He further claims that "debunkers like Boyer ... have their own unconscious motivations (to undermine religious faith, after all, is to set oneself free of its many inconvenient strictures)."

Michael Shermer, founder of The Skeptics Society, described Boyer's book as:

a penetratingly insightful scientific analysis of religion because as an anthropologist he understands that any explanation must take into account the rich diversity of religious practices and beliefs around the world, and as a scientist he knows that any explanatory model must account for this diversity. Boyer is at his ethnographic best in describing the countless peculiar religious rituals he and his anthropological brethren have recorded, and especially in identifying the shortcomings of virtually every explanation for religion ever offered. … As a consequence, however, Boyer himself fails to provide a satisfactory explanation because he knows that religion is not a single entity resulting from a single cause.

Brigitte Schön, a theology professor at the University of Bonn, wrote,

Apart from being fascinating to read and containing many more highly original ideas than could be mentioned here, Religion explained is an important book for a number of reasons. First of all, Boyer is able to present a very dense network of theories which not only explains many religious phenomena but also sets them in relation to each other. The integration of cognitive science research leads to a very realistic model of how religious concepts are processed and communicated, something which has been conspicuously absent from most theories of religion so far. Boyer's account of the natural basis of religion explains very well the persistence and re-emergence of religion even in a secularized environment, as well as the tensions between official and folk religion.

Garry Runciman, sociologist at Trinity College, Cambridge, asked "Are we hardwired for God?"

The diverse beliefs which Boyer cites extend from Apollo and Athena, to shamanism among the Panamanian Cuna, to aliens from remote galaxies allegedly landing in New Mexico. But his central agenda is the particular set of unobservable causal agencies cited in his subtitle, and his primary concern is with the question of how we are to account for beliefs that involve the attribution of conscious agency to beings other than humans and animals of the normal and familiar kind. Such beliefs are, as Boyer says, remarkably widespread, and for all their variant forms the variation is neither limitless nor random. His answer falls into two parts: first, these beliefs have in common a counterintuitive attribution of a certain range of properties to certain kinds of quasihuman being; second, the explanation of their diffusion and persistence is to be sought not in the extensive anthropological literature about the origins and functions of religion, but in recent advances in developmental, cognitive and evolutionary psychology.

Author and economist Zachary Karabell found stylistic faults. "Boyer's use of cognitive psychology, anthropology and other disciplines does generate a new template for examining old questions. But his method, however compelling, does not save the book from its considerable flaws. To begin with, the writing is frequently impenetrable." He concludes, "Of course, Boyer may be right. Human existence may simply be a story of living, breathing, eating and dying. But by not grappling with the possibility that a nonmaterial realm exists, Boyer has written a book about religion that is occasionally illuminating and utterly unconvincing."

The comparative religion author Karen Armstrong reviewed Boyer's thesis.

Religion, he argues, is nothing more or less than a by-product of the human mind. It is a side effect of having a particular kind of brain. By far the most fascinating part of this highly accessible and informative book is Boyer's description of the way our minds work. We have an inbuilt set of ontological expectations and a tendency to dwell on intuitions which violate these, such as mountains that float or companions whom we do not see. From the dawn of modern consciousness, men and women have focused on certain imaginary personalities that transcend the norm, convinced that they can help them in strategic ways. These supernatural agents link with other mental systems, such as our moral intuitions and social categories, for which we can find no conceptual justification.

John Habgood, formerly Archbishop of York, wrote.

This is a bold and far-reaching book. What its author lacks in modesty, he makes up for in cogency of argument and elegance of style. His "explanation" of religion is lucid, entertaining, full of valuable insights and almost, but not quite, convincing. The usual explanations of religion—as an attempt to explain what is otherwise puzzling, as a provider of comfort, as a good thing for society or as an escape from reason—are quickly dismissed. Pascal Boyer seeks to demonstrate that its origins and motivations are more deep seated in our mental structures than any of these, which is why religion is so universal, so powerful and so unlikely to disappear even though, as he also claims, it is in the end only a mental phenomenon. Recent experience of the dreadful consequences of religious fanaticism gives his analysis a frightening contemporary relevance, not least because of the minor role within religion that he assigns to rationality.

Editions and translations

Boyer's book is available in several English versions, as well as Finnish, French, German, Greek, Italian and Polish translations. Publishers have variously altered the Religion Explained title.

The American edition was published as:

• Religion Explained: The Human Instincts That Fashion Gods, Spirits and Ancestors, hardcover, Basic Books, 2001, ISBN 0-465-00695-7.
• Religion Explained: The Human Instincts That Fashion Gods, Spirits and Ancestors, paperback, Vintage, 2002, ISBN 0-09-928276-3.
• Religion Explained, paperback, Basic Books, 2002, ISBN 0-465-00696-5.

The British edition, which changed the subtitle from "The Evolutionary Origins of Religious Thought" to "The Human Instincts That Fashion Gods, Spirits and Ancestors", was published as:

• Religion Explained: The Human Instincts That Fashion Gods, Spirits and Ancestors, hardcover, William Heinemann Ltd, 2001, ISBN 0-465-00695-7.
• Religion Explained: The Human Instincts That Fashion Gods, Spirits and Ancestors, paperback, Vintage, 2002, ISBN 0-09-928276-3.

Translated editions of Religion Explained are available in several European languages:

• Finnish translation by Tiina Arppe as Ja ihminen loi jumalat: kuinka uskonto selitetään [And Man Created the Gods: How to Explain Religion], WSOY 2007, ISBN 978-951-0-31815-7.
• French translation by Claude-Christine Farny as Et l'homme créa les dieux: Comment expliquer la religion [And Man Created the Gods: How to Explain Religion], Paris: Robert Laffont, 2001, ISBN 978-2-221-09046-6.
• German translation by Ulrich Enderwitz, Monika Noll, and Rolf Schubert as Und Mensch schuf Gott [And Man Created God], Klett-Cotta, 2004, ISBN 978-3-608-94032-9.
• Greek translation by Dimitris Xygalatas and Nikolas Roubekas as Και ο Άνθρωπος Έπλασε τους Θεούς [And Man Created the Gods], Thessaloniki: Vanias, 2008. ISBN 978-960-288-225-2.
• Italian translation by Donatella Sutera Sardo as "E l'uomo creò gli dei. Come spiegare la religione" [And man created the Gods. How to Explain Religion], Bologna, Odoya, 2010 ISBN 978-88-6288-073-2.
• Polish translation by Krystyna Szeżyńska-Maćkowiak as I człowiek stworzył bogów... [And man created the gods...], Warsaw, 2005, ISBN 83-7337-985-1.
• Dutch translation by Leo Gillet as "Godsdienst verklaard", Amsterdam: De Bezige Bij, 2002 ISBN 90-234-7083-4 .
• Russian translation by Mariya Desyatova as "Объясняя религию. Природа религиозного мышления" [Religion Explained. Nature of religious thinking], Moscow: Alpina nonfiction, 2016 ISBN 978-5-91671-632-0 .