Chromosome

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Chromosome

Chromosome (107 - 1010 bp) DNA Gene (103 - 106 bp ) Function A chromosome and its packaged long strand of DNA unraveled. The DNA's base pairs encode genes, which provide functions. A human DNA can have up to 500 million base pairs with thousands of genes.

Condensed chromosome (purple rod) inside a bone marrow erythrokaryocyte undergoing mitosis

Diagram of a replicated and condensed metaphase eukaryotic chromosome:

1. Chromatid
2. Centromere
3. Short arm
4. Long arm

A chromosome is a package of DNA containing part or all of the genetic material of an organism. In most chromosomes, the very long thin DNA fibers are coated with nucleosome-forming packaging proteins; in eukaryotic cells, the most important of these proteins are the histones. Aided by chaperone proteins, the histones bind to and condense the DNA molecule to maintain its integrity. These eukaryotic chromosomes display a complex three-dimensional structure that has a significant role in transcriptional regulation.

Normally, chromosomes are visible under a light microscope only during the metaphase of cell division, where all chromosomes are aligned in the center of the cell in their condensed form. Before this stage occurs, each chromosome is duplicated (S phase), and the two copies are joined by a centromere—resulting in either an X-shaped structure if the centromere is located equatorially, or a two-armed structure if the centromere is located distally; the joined copies are called 'sister chromatids'. During metaphase, the duplicated structure (called a 'metaphase chromosome') is highly condensed and thus easiest to distinguish and study. In animal cells, chromosomes reach their highest compaction level in anaphase during chromosome segregation.

Chromosomal recombination during meiosis and subsequent sexual reproduction plays a crucial role in genetic diversity. If these structures are manipulated incorrectly, through processes known as chromosomal instability and translocation, the cell may undergo mitotic catastrophe. This will usually cause the cell to initiate apoptosis, leading to its own death, but the process is occasionally hampered by cell mutations that result in the progression of cancer.

The term 'chromosome' is sometimes used in a wider sense to refer to the individualized portions of chromatin in cells, which may or may not be visible under light microscopy. In a narrower sense, 'chromosome' can be used to refer to the individualized portions of chromatin during cell division, which are visible under light microscopy due to high condensation.

Etymology

The word chromosome (/ˈkroʊməˌsoʊm, -ˌzoʊm/) comes from the Greek words χρῶμα (chroma, "colour") and σῶμα (soma, "body"), describing the strong staining produced by particular dyes. The term was coined by the German anatomist Heinrich Wilhelm Waldeyer, referring to the term 'chromatin', which was introduced by Walther Flemming.

Some of the early karyological terms have become outdated. For example, 'chromatin' (Flemming 1880) and 'chromosom' (Waldeyer 1888) both ascribe color to a non-colored state.

History of discovery

Walter Sutton (top) and Theodor Boveri (bottom) independently developed the chromosome theory of inheritance in 1902.

Otto Bütschli was the first scientist to recognize the structures now known as chromosomes.

In a series of experiments beginning in the mid-1880s, Theodor Boveri gave definitive contributions to elucidating that chromosomes are the vectors of heredity, with two notions that became known as 'chromosome continuity' and 'chromosome individuality'.

Wilhelm Roux suggested that every chromosome carries a different genetic configuration, and Boveri was able to test and confirm this hypothesis. Aided by the rediscovery at the start of the 1900s of Gregor Mendel's earlier experimental work, Boveri identified the connection between the rules of inheritance and the behaviour of the chromosomes. Two generations of American cytologists were influenced by Boveri: Edmund Beecher Wilson, Nettie Stevens, Walter Sutton and Theophilus Painter (Wilson, Stevens, and Painter actually worked with him).

In his famous textbook, The Cell in Development and Heredity, Wilson linked together the independent work of Boveri and Sutton (both around 1902) by naming the chromosome theory of inheritance the 'Boveri–Sutton chromosome theory' (sometimes known as the 'Sutton–Boveri chromosome theory'). Ernst Mayr remarks that the theory was hotly contested by some famous geneticists, including William Bateson, Wilhelm Johannsen, Richard Goldschmidt and T.H. Morgan, all of a rather dogmatic mindset. Eventually, absolute proof came from chromosome maps in Morgan's own laboratory.

The number of human chromosomes was published by Painter in 1923. By inspection through a microscope, he counted 24 pairs of chromosomes, giving 48 in total. His error was copied by others, and it was not until 1956 that the true number (46) was determined by Indonesian-born cytogeneticist Joe Hin Tjio.

Prokaryotes

Main article: Nucleoid

The prokaryotes – bacteria and archaea – typically have a single circular chromosome. The chromosomes of most bacteria (also called genophores), can range in size from only 130,000 base pairs in the endosymbiotic bacteria Candidatus Hodgkinia cicadicola and Candidatus Tremblaya princeps, to more than 14,000,000 base pairs in the soil-dwelling bacterium Sorangium cellulosum.

Some bacteria have more than one chromosome. For instance, Spirochaetes such as Borrelia burgdorferi (causing Lyme disease), contain a single linear chromosome. Vibrios typically carry two chromosomes of very different size. Genomes of the genus Burkholderia carry one, two, or three chromosomes.

Structure in sequences

Prokaryotic chromosomes have less sequence-based structure than eukaryotes. Bacteria typically have a one-point (the origin of replication) from which replication starts, whereas some archaea contain multiple replication origins. The genes in prokaryotes are often organized in operons and do not usually contain introns, unlike eukaryotes.

DNA packaging

Prokaryotes do not possess nuclei. Instead, their DNA is organized into a structure called the nucleoid. The nucleoid is a distinct structure and occupies a defined region of the bacterial cell. This structure is, however, dynamic and is maintained and remodeled by the actions of a range of histone-like proteins, which associate with the bacterial chromosome. In archaea, the DNA in chromosomes is even more organized, with the DNA packaged within structures similar to eukaryotic nucleosomes.

Certain bacteria also contain plasmids or other extrachromosomal DNA. These are circular structures in the cytoplasm that contain cellular DNA and play a role in horizontal gene transfer. In prokaryotes and viruses, the DNA is often densely packed and organized; in the case of archaea, by homology to eukaryotic histones, and in the case of bacteria, by histone-like proteins.

Bacterial chromosomes tend to be tethered to the plasma membrane of the bacteria. In molecular biology application, this allows for its isolation from plasmid DNA by centrifugation of lysed bacteria and pelleting of the membranes (and the attached DNA).

Prokaryotic chromosomes and plasmids are, like eukaryotic DNA, generally supercoiled. The DNA must first be released into its relaxed state for access for transcription, regulation, and replication.

Eukaryotes

Main article: Chromatin

See also: DNA condensation, Nucleosome, Histone, and Protamine

See also: Eukaryotic chromosome fine structure

Organization of DNA in a eukaryotic cell

Each eukaryotic chromosome consists of a long linear DNA molecule associated with proteins, forming a compact complex of proteins and DNA called chromatin. Chromatin contains the vast majority of the DNA in an organism, but a small amount inherited maternally can be found in the mitochondria. It is present in most cells, with a few exceptions, for example, red blood cells.

Histones are responsible for the first and most basic unit of chromosome organization, the nucleosome.

Eukaryotes (cells with nuclei such as those found in plants, fungi, and animals) possess multiple large linear chromosomes contained in the cell's nucleus. Each chromosome has one centromere, with one or two arms projecting from the centromere, although, under most circumstances, these arms are not visible as such. In addition, most eukaryotes have a small circular mitochondrial genome, and some eukaryotes may have additional small circular or linear cytoplasmic chromosomes.

The major structures in DNA compaction: DNA, the nucleosome, the 10 nm "beads-on-a-string" fibre, the 30 nm fibre and the metaphase chromosome

In the nuclear chromosomes of eukaryotes, the uncondensed DNA exists in a semi-ordered structure, where it is wrapped around histones (structural proteins), forming a composite material called chromatin.

Interphase chromatin

The packaging of DNA into nucleosomes causes a 10 nanometer fibre which may further condense up to 30 nm fibres. Most of the euchromatin in interphase nuclei appears to be in the form of 30-nm fibers. Chromatin structure is the more decondensed state, i.e. the 10-nm conformation allows transcription.

Heterochromatin vs. euchromatin

During interphase (the period of the cell cycle where the cell is not dividing), two types of chromatin can be distinguished:

• Euchromatin, which consists of DNA that is active, e.g., being expressed as protein.
• Heterochromatin, which consists of mostly inactive DNA. It seems to serve structural purposes during the chromosomal stages. Heterochromatin can be further distinguished into two types:
  • Constitutive heterochromatin, which is never expressed. It is located around the centromere and usually contains repetitive sequences.
  • Facultative heterochromatin, which is sometimes expressed.

Metaphase chromatin and division

See also: mitosis and meiosis

Human chromosomes during metaphase

Stages of early mitosis in a vertebrate cell with micrographs of chromatids

In the early stages of mitosis or meiosis (cell division), the chromatin double helix becomes more and more condensed. They cease to function as accessible genetic material (transcription stops) and become a compact transportable form. The loops of thirty-nanometer chromatin fibers are thought to fold upon themselves further to form the compact metaphase chromosomes of mitotic cells. The DNA is thus condensed about ten-thousand-fold.

The chromosome scaffold, which is made of proteins such as condensin, TOP2A and KIF4, plays an important role in holding the chromatin into compact chromosomes. Loops of thirty-nanometer structure further condense with scaffold into higher order structures.

This highly compact form makes the individual chromosomes visible, and they form the classic four-arm structure, a pair of sister chromatids attached to each other at the centromere. The shorter arms are called p arms (from the French petit, small) and the longer arms are called q arms (q follows p in the Latin alphabet; q-g "grande"; alternatively it is sometimes said q is short for queue meaning tail in French). This is the only natural context in which individual chromosomes are visible with an optical microscope.

Mitotic metaphase chromosomes are best described by a linearly organized longitudinally compressed array of consecutive chromatin loops.

During mitosis, microtubules grow from centrosomes located at opposite ends of the cell and also attach to the centromere at specialized structures called kinetochores, one of which is present on each sister chromatid. A special DNA base sequence in the region of the kinetochores provides, along with special proteins, longer-lasting attachment in this region. The microtubules then pull the chromatids apart toward the centrosomes, so that each daughter cell inherits one set of chromatids. Once the cells have divided, the chromatids are uncoiled and DNA can again be transcribed. In spite of their appearance, chromosomes are structurally highly condensed, which enables these giant DNA structures to be contained within a cell nucleus.

Human chromosomes

Chromosomes in humans can be divided into two types: autosomes (body chromosome(s)) and allosome (sex chromosome(s)). Certain genetic traits are linked to a person's sex and are passed on through the sex chromosomes. The autosomes contain the rest of the genetic hereditary information. All act in the same way during cell division. Human cells have 23 pairs of chromosomes (22 pairs of autosomes and one pair of sex chromosomes), giving a total of 46 per cell. In addition to these, human cells have many hundreds of copies of the mitochondrial genome. Sequencing of the human genome has provided a great deal of information about each of the chromosomes. Below is a table compiling statistics for the chromosomes, based on the Sanger Institute's human genome information in the Vertebrate Genome Annotation (VEGA) database. Number of genes is an estimate, as it is in part based on gene predictions. Total chromosome length is an estimate as well, based on the estimated size of unsequenced heterochromatin regions.

Chromosome	Genes	Total base pairs	% of bases
1	2000	247,199,719	8.0
2	1300	242,751,149	7.9
3	1000	199,446,827	6.5
4	1000	191,263,063	6.2
5	900	180,837,866	5.9
6	1000	170,896,993	5.5
7	900	158,821,424	5.2
8	700	146,274,826	4.7
9	800	140,442,298	4.6
10	700	135,374,737	4.4
11	1300	134,452,384	4.4
12	1100	132,289,534	4.3
13	300	114,127,980	3.7
14	800	106,360,585	3.5
15	600	100,338,915	3.3
16	800	88,822,254	2.9
17	1200	78,654,742	2.6
18	200	76,117,153	2.5
19	1500	63,806,651	2.1
20	500	62,435,965	2.0
21	200	46,944,323	1.5
22	500	49,528,953	1.6
X (sex chromosome)	800	154,913,754	5.0
Y (sex chromosome)	200	57,741,652	1.9
Total	21,000	3,079,843,747	100.0

Based on the micrographic characteristics of size, position of the centromere and sometimes the presence of a chromosomal satellite, the human chromosomes are classified into the following groups:

Group	Chromosomes	Features
A	1–3	Large, metacentric or submetacentric
B	4–5	Large, submetacentric
C	6–12, X	Medium-sized, submetacentric
D	13–15	Medium-sized, acrocentric, with satellite
E	16–18	Small, metacentric or submetacentric
F	19–20	Very small, metacentric
G	21–22, Y	Very small, acrocentric (and 21, 22 with satellite)

Karyotype

Main article: Karyotype

Karyogram of a human male

Schematic karyogram of a human, with annotated bands and sub-bands. It is a graphical representation of the idealized human diploid karyotype. It shows dark and white regions on G banding. Each row is vertically aligned at centromere level. It shows 22 homologous chromosomes, both the female (XX) and male (XY) versions of the sex chromosome (bottom right), as well as the mitochondrial genome (at bottom left).

Further information: Karyotype

In general, the karyotype is the characteristic chromosome complement of a eukaryote species. The preparation and study of karyotypes is part of cytogenetics.

Although the replication and transcription of DNA is highly standardized in eukaryotes, the same cannot be said for their karyotypes, which are often highly variable. There may be variation between species in chromosome number and in detailed organization. In some cases, there is significant variation within species. Often there is:

1. variation between the two sexes

2. variation between the germline and soma (between gametes and the rest of the body)

3. variation between members of a population, due to balanced genetic polymorphism

4. geographical variation between races

5. mosaics or otherwise abnormal individuals.

Also, variation in karyotype may occur during development from the fertilized egg.

The technique of determining the karyotype is usually called karyotyping. Cells can be locked part-way through division (in metaphase) in vitro (in a reaction vial) with colchicine. These cells are then stained, photographed, and arranged into a karyogram, with the set of chromosomes arranged, autosomes in order of length, and sex chromosomes (here X/Y) at the end.

Like many sexually reproducing species, humans have special gonosomes (sex chromosomes, in contrast to autosomes). These are XX in females and XY in males.

History and analysis techniques

See also: Argument from authority § Use in science

Investigation into the human karyotype took many years to settle the most basic question: How many chromosomes does a normal diploid human cell contain? In 1912, Hans von Winiwarter reported 47 chromosomes in spermatogonia and 48 in oogonia, concluding an XX/XO sex determination mechanism. In 1922, Painter was not certain whether the diploid number of man is 46 or 48, at first favouring 46. He revised his opinion later from 46 to 48, and he correctly insisted on humans having an XX/XY system.

New techniques were needed to definitively solve the problem:

1. Using cells in culture
2. Arresting mitosis in metaphase by a solution of colchicine
3. Pretreating cells in a hypotonic solution 0.075 M KCl, which swells them and spreads the chromosomes
4. Squashing the preparation on the slide forcing the chromosomes into a single plane
5. Cutting up a photomicrograph and arranging the result into an indisputable karyogram.

It took until 1954 before the human diploid number was confirmed as 46. Considering the techniques of Winiwarter and Painter, their results were quite remarkable. Chimpanzees, the closest living relatives to modern humans, have 48 chromosomes as do the other great apes: in humans two chromosomes fused to form chromosome 2.

Aberrations

Main article: Chromosome abnormality

In Down syndrome, there are three copies of chromosome 21.

Chromosomal aberrations are disruptions in the normal chromosomal content of a cell. They can cause genetic conditions in humans, such as Down syndrome, although most aberrations have little to no effect. Some chromosome abnormalities do not cause disease in carriers, such as translocations, or chromosomal inversions, although they may lead to a higher chance of bearing a child with a chromosome disorder. Abnormal numbers of chromosomes or chromosome sets, called aneuploidy, may be lethal or may give rise to genetic disorders. Genetic counseling is offered for families that may carry a chromosome rearrangement.

The gain or loss of DNA from chromosomes can lead to a variety of genetic disorders. Human examples include:

• Cri du chat, caused by the deletion of part of the short arm of chromosome 5. "Cri du chat" means "cry of the cat" in French; the condition was so-named because affected babies make high-pitched cries that sound like those of a cat. Affected individuals have wide-set eyes, a small head and jaw, moderate to severe mental health problems, and are very short.
• DiGeorge syndrome, also known as 22q11.2 deletion syndrome. Symptoms are mild learning disabilities in children, with adults having an increased risk of schizophrenia. Infections are also common in children because of problems with the immune system's T cell-mediated response due to an absence of hypoplastic thymus.
• Down syndrome, the most common trisomy, usually caused by an extra copy of chromosome 21 (trisomy 21). Characteristics include decreased muscle tone, stockier build, asymmetrical skull, slanting eyes, and mild to moderate developmental disability.
• Edwards syndrome, or trisomy-18, the second most common trisomy. Symptoms include motor retardation, developmental disability, and numerous congenital anomalies causing serious health problems. Ninety percent of those affected die in infancy. They have characteristic clenched hands and overlapping fingers.
• Isodicentric 15, also called idic(15), partial tetrasomy 15q, or inverted duplication 15 (inv dup 15).
• Jacobsen syndrome, which is very rare. It is also called the 11q terminal deletion disorder. Those affected have normal intelligence or mild developmental disability, with poor expressive language skills. Most have a bleeding disorder called Paris-Trousseau syndrome.
• Klinefelter syndrome (XXY). Men with Klinefelter syndrome are usually sterile, and tend to be taller than their peers, with longer arms and legs. Boys with the syndrome are often shy and quiet, and have a higher incidence of speech delay and dyslexia. Without testosterone treatment, some may develop gynecomastia during puberty.
• Patau Syndrome, also called D-Syndrome or trisomy-13. Symptoms are somewhat similar to those of trisomy-18, without the characteristic folded hand.
• Small supernumerary marker chromosome. This means there is an extra, abnormal chromosome. Features depend on the origin of the extra genetic material. Cat-eye syndrome and isodicentric chromosome 15 syndrome (or Idic15) are both caused by a supernumerary marker chromosome, as is Pallister–Killian syndrome.
• Triple-X syndrome (XXX). XXX girls tend to be tall and thin, and have a higher incidence of dyslexia.
• Turner syndrome (X instead of XX or XY). In Turner syndrome, female sexual characteristics are present but underdeveloped. Females with Turner syndrome often have a short stature, low hairline, abnormal eye features and bone development, and a "caved-in" appearance to the chest.
• Wolf–Hirschhorn syndrome, caused by partial deletion of the short arm of chromosome 4. It is characterized by growth retardation, delayed motor skills development, "Greek Helmet" facial features, and mild to profound mental health problems.
• XYY syndrome. XYY boys are usually taller than their siblings. Like XXY boys and XXX girls, they are more likely to have learning difficulties.

Sperm aneuploidy

Exposure of males to certain lifestyle, environmental and/or occupational hazards may increase the risk of aneuploid spermatozoa. In particular, risk of aneuploidy is increased by tobacco smoking, and occupational exposure to benzene, insecticides, and perfluorinated compounds. Increased aneuploidy is often associated with increased DNA damage in spermatozoa.

Number in various organisms

Main article: List of organisms by chromosome count

In eukaryotes

The number of chromosomes in eukaryotes is highly variable. It is possible for chromosomes to fuse or break and thus evolve into novel karyotypes. Chromosomes can also be fused artificially. For example, when the 16 chromosomes of yeast were fused into one giant chromosome, it was found that the cells were still viable with only somewhat reduced growth rates.

The tables below give the total number of chromosomes (including sex chromosomes) in a cell nucleus for various eukaryotes. Most are diploid, such as humans who have 22 different types of autosomes—each present as two homologous pairs—and two sex chromosomes, giving 46 chromosomes in total. Some other organisms have more than two copies of their chromosome types, for example bread wheat which is hexaploid, having six copies of seven different chromosome types for a total of 42 chromosomes.

Chromosome numbers in some plants Plant species # Thale cress (diploid) 10 Rye (diploid) 14 Einkorn wheat (diploid) 14 Maize (diploid or palaeotetraploid) 20 Durum wheat (tetraploid) 28 Bread wheat (hexaploid) 42 Cultivated tobacco (tetraploid) 48 Adder's tongue fern (polyploid) approx. 1,200

Chromosome numbers (2n) in some animals Species # Indian muntjac 6♀, 7♂ Common fruit fly 8 Pill millipede 30 Earthworm 36 Tibetan fox 36 Domestic cat 38 Domestic pig 38 Laboratory mouse 40 Laboratory rat 42 Rabbit 44 Syrian hamster 44 Guppy 46 Human 46 Hare 48 Gorilla 48 Chimpanzee 48 Domestic sheep 54 Garden snail 54 Silkworm 56 Elephant 56 Cow 60 Donkey 62 Guinea pig 64 Horse 64 Dog 78 Hedgehog 90 Goldfish 100–104 Kingfisher 132

Chromosome numbers in other organisms Species Large chromosomes Intermediate chromosomes Microchromosomes Trypanosoma brucei 11 6 ≈100 Domestic pigeon 18 – 59–63 Chicken 8 2 sex chromosomes 60

Normal members of a particular eukaryotic species all have the same number of nuclear chromosomes. Other eukaryotic chromosomes, i.e., mitochondrial and plasmid-like small chromosomes, are much more variable in number, and there may be thousands of copies per cell.

The 23 human chromosome territories during prometaphase in fibroblast cells

Asexually reproducing species have one set of chromosomes that are the same in all body cells. However, asexual species can be either haploid or diploid.

Sexually reproducing species have somatic cells (body cells) that are diploid [2n], having two sets of chromosomes (23 pairs in humans), one set from the mother and one from the father. Gametes (reproductive cells) are haploid [n], having one set of chromosomes. Gametes are produced by meiosis of a diploid germline cell, during which the matching chromosomes of father and mother can exchange small parts of themselves (crossover) and thus create new chromosomes that are not inherited solely from either parent. When a male and a female gamete merge during fertilization, a new diploid organism is formed.

Some animal and plant species are polyploid [Xn], having more than two sets of homologous chromosomes. Important crops such as tobacco or wheat are often polyploid, compared to their ancestral species. Wheat has a haploid number of seven chromosomes, still seen in some cultivars as well as the wild progenitors. The more common types of pasta and bread wheat are polyploid, having 28 (tetraploid) and 42 (hexaploid) chromosomes, compared to the 14 (diploid) chromosomes in wild wheat.

In prokaryotes

Prokaryote species generally have one copy of each major chromosome, but most cells can easily survive with multiple copies. For example, Buchnera, a symbiont of aphids has multiple copies of its chromosome, ranging from 10 to 400 copies per cell. However, in some large bacteria, such as Epulopiscium fishelsoni up to 100,000 copies of the chromosome can be present. Plasmids and plasmid-like small chromosomes are, as in eukaryotes, highly variable in copy number. The number of plasmids in the cell is almost entirely determined by the rate of division of the plasmid – fast division causes high copy number.

Energy medicine

From Wikipedia, the free encyclopedia

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

Practitioners performing at a Reiki share

Energy medicine is a branch of alternative medicine based on a pseudo-scientific belief that healers can channel "healing energy" into patients and effect positive results. The field is defined by shared beliefs and practices relating to mysticism and esotericism in the wider alternative medicine sphere rather than any unified terminology, leading to terms such as energy healing, vibrational medicine, and similar terms being used synonymously. In most cases, no empirically measurable "energy" is involved: the term refers instead to so-called subtle energy. Practitioners may classify their practice as hands-on, hands-off, or distant, wherein the patient and healer are in different locations. Many approaches to energy healing exist: for example, "biofield energy healing", "spiritual healing", "contact healing", "distant healing", therapeutic touch, Reiki, and Qigong.

Reviews of the scientific literature on energy healing have concluded that no evidence supports its clinical use. The theoretical basis of energy healing has been criticised as implausible; research and reviews supportive of energy medicine have been faulted for containing methodological flaws and selection bias, and positive therapeutic results have been determined to result from known psychological mechanisms, such as the placebo effect. Some claims of those purveying "energy medicine" devices are known to be fraudulent, and their marketing practices have drawn law-enforcement action in the U.S.

History

History records the repeated association or exploitation of scientific inventions by individuals claiming that newly discovered science could help people to heal. In the 19th century, electricity and magnetism were in the "borderlands" of science, and electrical quackery became rife. These concepts continue to inspire writers in the New Age movement. In the early 20th century, health claims for radio-active materials put lives at risk; recently, quantum mechanics and grand unification theory have provided similar opportunities for commercial exploitation. Thousands of devices claiming to heal via putative or veritable energy are used worldwide. Many are illegal or dangerous and are marketed with false or unproven claims. Several of these devices have been banned. Reliance on spiritual and energetic healing is associated with serious harm or death when patients delay or forego medical treatment.

Classification

The term "energy medicine" has been in general use since the founding of the non-profit International Society for the Study of Subtle Energies and Energy Medicine in the 1980s. Guides are available for practitioners, and other books aim to provide a theoretical basis and evidence for the practice. Energy medicine often proposes that imbalances in the body's "energy field" result in illness, and that by rebalancing the body's energy field, health can be restored. Some modalities describe treatments as ridding the body of negative energies or blockages in 'mind'; illness or episodes of ill health after a treatment are referred to as a 'release' or letting go of a 'contraction' in the body-mind. Usually, a practitioner will then recommend further treatments for complete healing.

The US-based National Center for Complementary and Integrative Health (NCCIH) distinguishes between health care involving scientifically observable energy, which it calls "Veritable Energy Medicine", and health care methods that invoke physically undetectable or unverifiable "energies", which it calls "Putative Energy Medicine":

• Types of "veritable energy medicine" include magnet therapy, colorpuncture, and light therapy. Medical techniques involving the use of electromagnetic radiation (e.g., radiation therapy or magnetic resonance imaging) are not considered "energy medicine" in the terms of alternative medicine.
• Types of "putative energy medicine" include biofield energy healing therapies that are claimed to direct or modulate "energies" to allow healing in the patient. This includes spiritual healing, psychic healing, therapeutic touch, healing touch, Hands of light, Esoteric healing, Magnetic healing (now a historical term not to be confused with magnet therapy), Qigong healing, Reiki, crystal healing, distant healing, intercessory prayer, and similar modalities. Concepts such as Qi (Chi), Prana, Innate Intelligence, Mana, Pneuma, vital fluid, Odic force, and orgone are among the many terms that have been used to describe these putative energy fields. This category does not include acupuncture, Ayurvedic medicine, chiropractic, moxibustion and other modalities where a physical intervention is used to manipulate a putative energy.

Polarity therapy founded by Randolph Stone is a kind of energy medicine based on the belief that a person's health is subject to positive and negative charges in their electromagnetic field. It has been promoted as capable of curing many human ailments ranging from muscular tightness to cancer; however, according to the American Cancer Society, "available scientific evidence does not support claims that polarity therapy is effective in treating cancer or any other disease."

Beliefs

A Reiki practitioner

There are various schools of energy healing, including biofield energy healing, spiritual healing, contact healing, distant healing, Pranic Healing, therapeutic touch, Reiki, and Qigong among others.

Spiritual healing occurs largely among practitioners who do not see traditional religious faith as a prerequisite for effecting cures. Faith healing by contrast takes place within a traditional or non-denominational religious context such as with some televangelists. The Buddha is often quoted by practitioners of energy medicine, but he did not practise "hands on or off" healing.

Energy healing techniques such as therapeutic touch have found recognition in the nursing profession. In 2005–2006, the North American Nursing Diagnosis Association approved the diagnosis of "energy field disturbance" in patients, reflective of what has been variously called a "postmodern" or "anti-scientific" approach to nursing care. This approach has been strongly criticised.

Believers in these techniques have proposed quantum mystical invocations of non-locality to try to explain distant healing. They have also proposed that healers act as a channel passing on a kind of bioelectromagnetism which shares similarities to vitalistic pseudosciences such as orgone or qi. Writing in the Journal of Bodywork and Movement Therapies, James Oschman introduced the concept of healer-sourced electromagnetic fields which change in frequency. Oschman believes that "healing energy" derives from electromagnetic frequencies generated by a medical device, projected from the hands of the healer, or by electrons acting as antioxidants. Beverly Rubik, in an article in the Journal of Alternative and Complementary Medicine, justified her belief with references to biophysical systems theory, bioelectromagnetics, and chaos theory that provide her with a "...scientific foundation for the biofield..." Drew Leder remarked in a paper in the same journal that such ideas were attempts to "make sense of, interpret, and explore 'psi' and distant healing." and that "such physics-based models are not presented as explanatory but rather as suggestive."

Physicists and sceptics criticise these explanations as pseudophysics – a branch of pseudoscience which explains magical thinking by using irrelevant jargon from modern physics to exploit scientific illiteracy and to impress the unsophisticated. Indeed, even enthusiastic supporters of energy healing say that "there are only very tenuous theoretical foundations underlying [spiritual] healing".

Scientific investigations

Distant healing

A systematic review of 23 trials of distant healing published in 2000 did not draw definitive conclusions because of the methodological limitations among the studies. In 2001 the lead author of that study, Edzard Ernst, published a primer on complementary therapies in cancer care in which he explained that though "about half of these trials suggested that healing is effective", the evidence was "highly conflicting" and that "methodological shortcomings prevented firm conclusions." He concluded that "as long as it is not used as an alternative to effective therapies, spiritual healing should be virtually devoid of risks." A 2001 randomised clinical trial by the same group found no statistically significant difference on chronic pain between distance healers and "simulated healers". A 2003 review by Ernst updating previous work concluded that the weight of evidence had shifted against the use of distant healing, and that it can be associated with adverse effects."

Contact healing

A 2001 randomised clinical trial randomly assigned 120 patients with chronic pain to either healers or "simulated healers", but could not demonstrate efficacy for either distance or face-to-face healing. A systematic review in 2008 concluded that the evidence for a specific effect of spiritual healing on relieving neuropathic or neuralgic pain was not convincing. In their 2008 book Trick or Treatment, Simon Singh and Edzard Ernst concluded that "spiritual healing is biologically implausible and its effects rely on a placebo response. At best, it may offer comfort; at worst, it can result in charlatans taking money from patients with serious conditions who require urgent conventional medicine."

Evidence base

Alternative medicine researcher Edzard Ernst has said that although an initial review of pre-1999 distant healing trials highlighted 57% of trials as showing positive results. Later reviews of non-randomised and randomised clinical trials conducted between 2000 and 2002 led to the conclusion that "the majority of the rigorous trials do not support the hypothesis that distant healing has specific therapeutic effects." Ernst described the evidence base for healing practices to be "increasingly negative". Many of the reviews were also under suspicion for fabricated data, lack of transparency, and scientific misconduct. He concluded that "[s]piritual healing continues to be promoted despite the absence of biological plausibility or convincing clinical evidence ... that these methods work therapeutically and plenty to demonstrate that they do not." A 2014 study of energy healing for colorectal cancer patients showed no improvement in quality of life, depressive symptoms, mood, or sleep quality.

Earthing

The Earthing Institute gathers researchers and therapists who believe that to maintain or regain good health, direct contact with Earth by removing floors, carpets, and especially shoes is necessary. Walking barefoot and sleeping on the ground are conceived as useful tools for achieving the "earthing" (or "grounding") of the body. It is claimed that thanks to earthing one would benefit from the "extraordinary healing power" of Nature through the transferral of electrons from the Earth's surface to the body: "a primordial and naturally stabilized electric reference point for all body biological circuits is created". According to its practitioners, Earthing has preventive and curative effects on chronic inflammation, aging-related disorders, cardiovascular diseases, diabetes, arthritis, autoimmune disorders, cancer, and even depression and autism spectrum disorders.

The concept of earthing has been criticized as pseudoscience by skeptics and the medical community. A review of the available literature on the subject was written by several people that are financially tied to the company espousing the practice of earthing. Steven Novella referred to the work as "typical of the kind of worthless studies designed to generate false positives—the kind of in-house studies that companies sometimes use so that they can claim their products are clinically proven."

Bioresonance therapy

Bioresonance therapy (including MORA therapy and BICOM) is a pseudoscientific medical practice in which it is proposed that electromagnetic waves can be used to diagnose and treat human illness.

History and method

Bioresonance therapy was invented (in Germany) in 1977 by Franz Morell and his son-in-law, engineer Erich Rasche. Initially, they marketed it as "MORA-Therapie", for MOrell and RAsche. Some of the machines contain an electronic circuit measuring skin-resistance, akin to the E-meter used by Scientology, which the bioresonance creators sought to improve; Franz Morell had links with Scientology.

Practitioners claim to be able to detect a variety of diseases and addictions. Some practitioners also claim they can treat diseases using this therapy without drugs, by stimulating a change of "bioresonance" in the cells, and reversing the change caused by the disease. The devices would need to isolate and pinpoint pathogens' responses from the mixture of responses the device receives via the electrodes. Transmitting these transformed signals over the same electrodes is claimed by practitioners to generate healing signals that have the curative effect.

Scientific evaluation

Lacking any scientific explanation of how bioresonance therapy might work, researchers have classified bioresonance therapy as pseudoscience. Some studies did not show effects above that of the placebo effect. WebMD states: "There is no reliable scientific evidence that bioresonance is an accurate indicator of medical conditions or disease or an effective treatment for any condition."

Proven cases of online fraud have occurred, with a practitioner making false claims that he could cure cancer, and that his clients did not need to follow the chemotherapy or surgery recommended by medical doctors, which can be life-saving. Ben Goldacre ridiculed the BBC when it reported as fact a clinic's claim that the treatment could stop 70% of clients smoking, a better result than any conventional therapy.

In the United States of America, the U.S. Food and Drug Administration (FDA) classifies "devices that use resistance measurements to diagnose and treat various diseases" as Class III devices, which require FDA approval before marketing. The FDA has banned some of these devices from the US market, and has prosecuted many sellers of electrical devices for making false claims of health benefits.

According to Quackwatch, the therapy is completely nonsensical and the proposed mechanism of action impossible.

Explanations for positive reports

There are several, primarily psychological, explanations for positive reports after energy therapy, including placebo effects, spontaneous remission, and cognitive dissonance. A 2009 review found that the "small successes" reported for two therapies collectively marketed as "energy psychology" (Emotional Freedom Techniques and Tapas Acupressure Technique) "are potentially attributable to well-known cognitive and behavioral techniques that are included with the energy manipulation." The report concluded that "[p]sychologists and researchers should be wary of using such techniques, and make efforts to inform the public about the ill effects of therapies that advertise miraculous claims."

There are primarily two explanations for anecdotes of cures or improvements, relieving any need to appeal to the supernatural. The first is post hoc ergo propter hoc, meaning that a genuine improvement or spontaneous remission may have been experienced coincidental with but independent from anything the healer or patient did or said. These patients would have improved just as well even had they done nothing. The second is the placebo effect, through which a person may experience genuine pain relief and other symptomatic alleviation. In this case, the patient genuinely has been helped by the healer – not through any mysterious or numinous function, but by the power of their own belief that they would be healed. In both cases, the patient may experience a real reduction in symptoms, though in neither case has anything miraculous or inexplicable occurred. Both cases are strictly limited to the body's natural abilities.

Positive findings from research studies can also result from such psychological mechanisms, or as a result of experimenter bias, methodological flaws such as lack of blinding, or publication bias; positive reviews of the scientific literature may show selection bias, in that they omit key studies that do not agree with the author's position. All of these factors must be considered when evaluating claims.

Academic publishing

From Wikipedia, the free encyclopedia

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

Scientific and technical journal publications per million residents of the world as of 2020

Academic publishing is the subfield of publishing which distributes academic research and scholarship. Most academic work is published in academic journal articles, books or theses. The part of academic written output that is not formally published but merely printed up or posted on the Internet is often called "grey literature". Most scientific and scholarly journals, and many academic and scholarly books, though not all, are based on some form of peer review or editorial refereeing to qualify texts for publication. Peer review quality and selectivity standards vary greatly from journal to journal, publisher to publisher, and field to field.

Most established academic disciplines have their own journals and other outlets for publication, although many academic journals are somewhat interdisciplinary, and publish work from several distinct fields or subfields. There is also a tendency for existing journals to divide into specialized sections as the field itself becomes more specialized. Along with the variation in review and publication procedures, the kinds of publications that are accepted as contributions to knowledge or research differ greatly among fields and subfields. In the sciences, the desire for statistically significant results leads to publication bias.

Academic publishing is undergoing major changes as it makes the transition from the print to the electronic format. Business models are different in the electronic environment. Since the early 1990s, licensing of electronic resources, particularly journals, has been very common. An important trend, particularly with respect to journals in the sciences, is open access via the Internet. In open access publishing, a journal article is made available free for all on the web by the publisher at the time of publication.

Both open and closed journals are sometimes funded by the author paying an article processing charge, thereby shifting some fees from the reader to the researcher or their funder. Many open or closed journals fund their operations without such fees and others use them in predatory publishing. The Internet has facilitated open access self-archiving, in which authors themselves make a copy of their published articles available free for all on the web. Some important results in mathematics have been published only on arXiv.

History

The Journal des sçavans (later spelled Journal des savants), established by Denis de Sallo, was the earliest academic journal published in Europe. Its content included obituaries of famous men, church history, and legal reports. The first issue appeared as a twelve-page quarto pamphlet on Monday, 5 January 1665, shortly before the first appearance of the Philosophical Transactions of the Royal Society, on 6 March 1665.

The publishing of academic journals has started in the 17th century, and expanded greatly in the 19th. At that time, the act of publishing academic inquiry was controversial and widely ridiculed. It was not at all unusual for a new discovery to be announced as a monograph, reserving priority for the discoverer, but indecipherable for anyone not in on the secret: both Isaac Newton and Leibniz used this approach. However, this method did not work well. Robert K. Merton, a sociologist, found that 92% of cases of simultaneous discovery in the 17th century ended in dispute. The number of disputes dropped to 72% in the 18th century, 59% by the latter half of the 19th century, and 33% by the first half of the 20th century. The decline in contested claims for priority in research discoveries can be credited to the increasing acceptance of the publication of papers in modern academic journals, with estimates suggesting that around 50 million journal articles have been published since the first appearance of the Philosophical Transactions. The Royal Society was steadfast in its not-yet-popular belief that science could only move forward through a transparent and open exchange of ideas backed by experimental evidence.

Early scientific journals embraced several models: some were run by a single individual who exerted editorial control over the contents, often simply publishing extracts from colleagues' letters, while others employed a group decision-making process, more closely aligned to modern peer review. It was not until the middle of the 20th century that peer review became the standard.

The COVID-19 pandemic hijacked the entire world of basic and clinical science, with unprecedented shifts in funding priorities worldwide and a boom in medical publishing, accompanied by an unprecedented increase in the number of publications. Preprints servers become much popular during the pandemic, the Covid situation has an impact also on traditional peer-review. The pandemic has also deepened the western monopoly of science-publishing, "by August 2021, at least 210,000 new papers on covid-19 had been published, according to a Royal Society study. Of the 720,000-odd authors of these papers, nearly 270,000 were from the US, the UK, Italy or Spain."

Publishers and business aspects

See also: Academic journal § Costs

In the 1960s and 1970s, commercial publishers began to selectively acquire "top-quality" journals that were previously published by nonprofit academic societies. When the commercial publishers raised the subscription prices significantly, they lost little of the market, due to the inelastic demand for these journals. Although there are over 2,000 publishers, five for-profit companies (Reed Elsevier, Springer Science+Business Media, Wiley-Blackwell, Taylor & Francis, and SAGE) accounted for 50% of articles published in 2013. (Since 2013, Springer Science+Business Media has undergone a merger to form an even bigger company named Springer Nature.) Available data indicate that these companies have profit margins of around 40% making it one of the most profitable industries, especially compared to the smaller publishers, which likely operate with low margins. These factors have contributed to the "serials crisis" – total expenditures on serials increased 7.6% per year from 1986 to 2005, yet the number of serials purchased increased an average of only 1.9% per year.

Unlike most industries, in academic publishing the two most important inputs are provided "virtually free of charge". These are the articles and the peer review process. Publishers argue that they add value to the publishing process through support to the peer review group, including stipends, as well as through typesetting, printing, and web publishing. Investment analysts, however, have been skeptical of the value added by for-profit publishers, as exemplified by a 2005 Deutsche Bank analysis which stated that "we believe the publisher adds relatively little value to the publishing process... We are simply observing that if the process really were as complex, costly and value-added as the publishers protest that it is, 40% margins wouldn't be available."

Crisis

Main article: Serials crisis

A crisis in academic publishing is "widely perceived"; the apparent crisis has to do with the combined pressure of budget cuts at universities and increased costs for journals (the serials crisis). The university budget cuts have reduced library budgets and reduced subsidies to university-affiliated publishers. The humanities have been particularly affected by the pressure on university publishers, which are less able to publish monographs when libraries can not afford to purchase them. For example, the ARL found that in "1986, libraries spent 44% of their budgets on books compared with 56% on journals; twelve years later, the ratio had skewed to 28% and 72%." Meanwhile, monographs are increasingly expected for tenure in the humanities. In 2002 the Modern Language Association expressed hope that electronic publishing would solve the issue.

In 2009 and 2010, surveys and reports found that libraries faced continuing budget cuts, with one survey in 2009 finding that 36% of UK libraries had their budgets cut by 10% or more, compared to 29% with increased budgets. In the 2010s, libraries began more aggressive cost cutting with the leverage of open access and open data. Data analysis with open source tools like Unpaywall Journals empowered library systems in reducing their subscription costs by 70% with the cancellation of the big deal with publishers like Elsevier.

Academic journal publishing reform

Main article: Academic journal publishing reform

Several models are being investigated, such as open publication models or adding community-oriented features. It is also considered that "Online scientific interaction outside the traditional journal space is becoming more and more important to academic communication". In addition, experts have suggested measures to make the publication process more efficient in disseminating new and important findings by evaluating the worthiness of publication on the basis of the significance and novelty of the research finding.

Scholarly paper

See also: Scientific literature § Scientific article, and Academic journal § Scholarly articles

In academic publishing, a paper is an academic work that is usually published in an academic journal. It contains original research results or reviews existing results. Such a paper, also called an article, will only be considered valid if it undergoes a process of peer review by one or more referees (who are academics in the same field) who check that the content of the paper is suitable for publication in the journal. A paper may undergo a series of reviews, revisions, and re-submissions before finally being accepted or rejected for publication. This process typically takes several months. Next, there is often a delay of many months (or in some fields, over a year) before an accepted manuscript appears. This is particularly true for the most popular journals where the number of accepted articles often outnumbers the space for printing. Due to this, many academics self-archive a 'preprint' or 'postprint' copy of their paper for free download from their personal or institutional website.

Some journals, particularly newer ones, are now published in electronic form only. Paper journals are now generally made available in electronic form as well, both to individual subscribers, and to libraries. Almost always these electronic versions are available to subscribers immediately upon publication of the paper version, or even before; sometimes they are also made available to non-subscribers, either immediately (by open access journals) or after an embargo of anywhere from two to twenty-four months or more, in order to protect against loss of subscriptions. Journals having this delayed availability are sometimes called delayed open access journals. Ellison in 2011 reported that in economics the dramatic increase in opportunities to publish results online has led to a decline in the use of peer-reviewed articles.

Categories of papers

See also: Academic journal § Types of article

An academic paper typically belongs to some particular category such as:

• Concept paper
• Research paper
• Case report or Case series
• Position paper
• Review article or Survey paper
• Species paper
• Technical paper

Note: Law review is the generic term for a journal of legal scholarship in the United States, often operating by rules radically different from those for most other academic journals.

Peer review

Main article: Academic peer review

Peer review is a central concept for most academic publishing; other scholars in a field must find a work sufficiently high in quality for it to merit publication. A secondary benefit of the process is an indirect guard against plagiarism since reviewers are usually familiar with the sources consulted by the author(s). The origins of routine peer review for submissions dates to 1752 when the Royal Society of London took over official responsibility for Philosophical Transactions. However, there were some earlier examples.

While journal editors largely agree the system is essential to quality control in terms of rejecting poor quality work, there have been examples of important results that are turned down by one journal before being taken to others. Rena Steinzor wrote:

Perhaps the most widely recognized failing of peer review is its inability to ensure the identification of high-quality work. The list of important scientific papers that were initially rejected by peer-reviewed journals goes back at least as far as the editor of Philosophical Transaction's 1796 rejection of Edward Jenner's report of the first vaccination against smallpox.

"Confirmatory bias" is the unconscious tendency to accept reports which support the reviewer's views and to downplay those which do not. Experimental studies show the problem exists in peer reviewing.

There are various types of peer review feedback that may be given prior to publication, including but not limited to:

• Single-blind peer review
• Double-blind peer review
• Open peer review

Rejection rate

The possibility of rejections of papers is an important aspect in peer review. The evaluation of quality of journals is based also on rejection rate. The best journals have the highest rejection rates (around 90–95%). American Psychological Association journals' rejection rates ranged "from a low of 35 per cent to a high of 85 per cent." The complement is called "acceptance rate".

Publishing process

The process of academic publishing, which begins when authors submit a manuscript to a publisher, is divided into two distinct phases: peer review and production.

The process of peer review is organized by the journal editor and is complete when the content of the article, together with any associated images, data, and supplementary material are accepted for publication. The peer review process is increasingly managed online, through the use of proprietary systems, commercial software packages, or open source and free software. A manuscript undergoes one or more rounds of review; after each round, the author(s) of the article modify their submission in line with the reviewers' comments; this process is repeated until the editor is satisfied and the work is accepted.

The production process, controlled by a production editor or publisher, then takes an article through copy editing, typesetting, inclusion in a specific issue of a journal, and then printing and online publication. Academic copy editing seeks to ensure that an article conforms to the journal's house style, that all of the referencing and labelling is correct, and that the text is consistent and legible; often this work involves substantive editing and negotiating with the authors. Because the work of academic copy editors can overlap with that of authors' editors, editors employed by journal publishers often refer to themselves as "manuscript editors". During this process, copyright is often transferred from the author to the publisher.

In the late 20th century author-produced camera-ready copy has been replaced by electronic formats such as PDF. The author will review and correct proofs at one or more stages in the production process. The proof correction cycle has historically been labour-intensive as handwritten comments by authors and editors are manually transcribed by a proof reader onto a clean version of the proof. In the early 21st century, this process was streamlined by the introduction of e-annotations in Microsoft Word, Adobe Acrobat, and other programs, but it still remained a time-consuming and error-prone process. The full automation of the proof correction cycles has only become possible with the onset of online collaborative writing platforms, such as Authorea, Google Docs, Overleaf, and various others, where a remote service oversees the copy-editing interactions of multiple authors and exposes them as explicit, actionable historic events. At the end of this process, a final version of record is published.

From time to time some published journal articles have been retracted for different reasons, including research misconduct.

Citations

Main article: Citation

Academic authors cite sources they have used, in order to support their assertions and arguments and to help readers find more information on the subject. It also gives credit to authors whose work they use and helps avoid plagiarism. The topic of dual publication (also known as self-plagiarism) has been addressed by the Committee on Publication Ethics (COPE), as well as in the research literature itself.

Each scholarly journal uses a specific format for citations (also known as references). Among the most common formats used in research papers are the APA, CMS, and MLA styles.

The American Psychological Association (APA) style is often used in the social sciences. The Chicago Manual of Style (CMS) is used in business, communications, economics, and social sciences. The CMS style uses footnotes at the bottom of page to help readers locate the sources. The Modern Language Association (MLA) style is widely used in the humanities.

Publishing by discipline

Natural sciences

Main articles: Scientific literature, Technical literature, and Medical literature

Shares of the top five STM publishers in 2010 and 2020

Scientific, technical, and medical (STM) literature is a large industry which generated $23.5 billion in revenue in 2011; $9.4 billion of that was specifically from the publication of English-language scholarly journals. The overall number of journals contained in the WOS database increased from around 8,500 in 2010 to around 9,400 in 2020, while the number of articles published increased from around 1.1 million in 2010 to 1.8 million in 2020.

Most scientific research is initially published in scientific journals and considered to be a primary source. Technical reports, for minor research results and engineering and design work (including computer software), round out the primary literature. Secondary sources in the sciences include articles in review journals (which provide a synthesis of research articles on a topic to highlight advances and new lines of research), and books for large projects, broad arguments, or compilations of articles. Tertiary sources might include encyclopedias and similar works intended for broad public consumption or academic libraries.

A partial exception to scientific publication practices is in many fields of applied science, particularly that of U.S. computer science research. An equally prestigious site of publication within U.S. computer science are some academic conferences. Reasons for this departure include a large number of such conferences, the quick pace of research progress, and computer science professional society support for the distribution and archiving of conference proceedings.

Since 2022, the Belgian web portal Cairn.info is open to STM.

Social sciences

Publishing in the social sciences is very different in different fields. Some fields, like economics, may have very "hard" or highly quantitative standards for publication, much like the natural sciences. Others, like anthropology or sociology, emphasize field work and reporting on first-hand observation as well as quantitative work. Some social science fields, such as public health or demography, have significant shared interests with professions like law and medicine, and scholars in these fields often also publish in professional magazines.

Humanities

Publishing in the humanities is in principle similar to publishing elsewhere in the academy; a range of journals, from general to extremely specialized, are available, and university presses issue many new humanities books every year. The arrival of online publishing opportunities has radically transformed the economics of the field and the shape of the future is controversial. Unlike science, where timeliness is critically important, humanities publications often take years to write and years more to publish. Unlike the sciences, research is most often an individual process and is seldom supported by large grants. Journals rarely make profits and are typically run by university departments.

The following describes the situation in the United States. In many fields, such as literature and history, several published articles are typically required for a first tenure-track job, and a published or forthcoming book is now often required before tenure. Some critics complain that this de facto system has emerged without thought to its consequences; they claim that the predictable result is the publication of much shoddy work, as well as unreasonable demands on the already limited research time of young scholars. To make matters worse, the circulation of many humanities journals in the 1990s declined to almost untenable levels, as many libraries cancelled subscriptions, leaving fewer and fewer peer-reviewed outlets for publication; and many humanities professors' first books sell only a few hundred copies, which often does not pay for the cost of their printing. Some scholars have called for a publication subvention of a few thousand dollars to be associated with each graduate student fellowship or new tenure-track hire, in order to alleviate the financial pressure on journals.

Open access journals

Main article: Open access journal

Under Open Access, the content can be freely accessed and reused by anyone in the world using an Internet connection. The terminology going back to Budapest Open Access Initiative, Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities, and Bethesda Statement on Open Access Publishing. The impact of the work available as Open Access is maximised because, quoting the Library of Trinity College Dublin:

• Potential readership of Open Access material is far greater than that for publications where the full-text is restricted to subscribers.
• Details of contents can be read by specialised web harvesters.
• Details of contents also appear in normal search engines like Google, Google Scholar, Yahoo, etc.

Open Access is often confused with specific funding models such as Article Processing Charges (APC) being paid by authors or their funders, sometimes misleadingly called "open access model". The reason this term is misleading is due to the existence of many other models, including funding sources listed in the original the Budapest Open Access Initiative Declaration: "the foundations and governments that fund research, the universities and laboratories that employ researchers, endowments set up by discipline or institution, friends of the cause of open access, profits from the sale of add-ons to the basic texts, funds freed up by the demise or cancellation of journals charging traditional subscription or access fees, or even contributions from the researchers themselves". For more recent open public discussion of open access funding models, see Flexible membership funding model for Open Access publishing with no author-facing charges.

Prestige journals using the APC model often charge several thousand dollars. Oxford University Press, with over 300 journals, has fees ranging from £1000-£2500, with discounts of 50% to 100% to authors from developing countries. Wiley Blackwell has 700 journals available, and they charge different amounts for each journal. Springer, with over 2600 journals, charges US$3000 or EUR 2200 (excluding VAT). A study found that the average APC (ensuring open access) was between $1,418 and US$2,727.

The online distribution of individual articles and academic journals then takes place without charge to readers and libraries. Most open access journals remove all the financial, technical, and legal barriers Archived 2021-05-06 at the Wayback Machine that limit access to academic materials to paying customers. The Public Library of Science and BioMed Central are prominent examples of this model.

Fee-based open access publishing has been criticized on quality grounds, as the desire to maximize publishing fees could cause some journals to relax the standard of peer review. Although, similar desire is also present in the subscription model, where publishers increase numbers or published articles in order to justify raising their fees. It may be criticized on financial grounds as well because the necessary publication or subscription fees have proven to be higher than originally expected. Open access advocates generally reply that because open access is as much based on peer reviewing as traditional publishing, the quality should be the same (recognizing that both traditional and open access journals have a range of quality). In several regions, including the Arab world, the majority of university academics prefer open access publishing without author fees, as it promotes equal access to information and enhances scientific advancement, a previously unexplored but crucial topic for the region's higher education. It has also been argued that good science done by academic institutions who cannot afford to pay for open access might not get published at all, but most open access journals permit the waiver of the fee for financial hardship or authors in underdeveloped countries. In any case, all authors have the option of self-archiving their articles in their institutional repositories or disciplinary repositories in order to make them open access, whether or not they publish them in a journal.

If they publish in a Hybrid open access journal, authors or their funders pay a subscription journal a publication fee to make their individual article open access. The other articles in such hybrid journals are either made available after a delay or remain available only by subscription. Most traditional publishers (including Wiley-Blackwell, Oxford University Press, and Springer Science+Business Media) have already introduced such a hybrid option, and more are following. The fraction of the authors of a hybrid open access journal that makes use of its open access option can, however, be small. It also remains unclear whether this is practical in fields outside the sciences, where there is much less availability of outside funding. In 2006, several funding agencies, including the Wellcome Trust and several divisions of the Research Councils in the UK announced the availability of extra funding to their grantees for such open access journal publication fees.

In May 2016, the Council for the European Union agreed that from 2020 all scientific publications as a result of publicly funded research must be freely available. It also must be able to optimally reuse research data. To achieve that, the data must be made accessible, unless there are well-founded reasons for not doing so, for example, intellectual property rights or security or privacy issues.

Growth

In recent decades there has been a growth in academic publishing in developing countries as they become more advanced in science and technology. Although the large majority of scientific output and academic documents are produced in developed countries, the rate of growth in these countries has stabilized and is much smaller than the growth rate in some of the developing countries. The fastest scientific output growth rate over the last two decades has been in the Middle East and Asia with Iran leading with an 11-fold increase followed by the Republic of Korea, Turkey, Cyprus, China, and Oman. In comparison, the only G8 countries in top 20 ranking with fastest performance improvement are, Italy which stands at tenth and Canada at 13th globally.^[

By 2004, it was noted that the output of scientific papers originating from the European Union had a larger share of the world's total from 36.6% to 39.3% and from 32.8% to 37.5% of the "top one per cent of highly cited scientific papers". However, the United States' output dropped from 52.3% to 49.4% of the world's total, and its portion of the top one percent dropped from 65.6% to 62.8%.

Iran, China, India, Brazil, and South Africa were the only developing countries among the 31 nations that produced 97.5% of the most cited scientific articles in a study published in 2004. The remaining 162 countries contributed less than 2.5%. The Royal Society in a 2011 report stated that in share of English scientific research papers the United States was first followed by China, the UK, Germany, Japan, France, and Canada. The report predicted that China would overtake the United States sometime before 2020, possibly as early as 2013. China's scientific impact, as measured by other scientists citing the published papers the next year, is smaller although also increasing. Developing countries continue to find ways to improve their share, given research budget constraints and limited resources.

Role for publishers in scholarly communication

There is increasing frustration amongst OA advocates, with what is perceived as resistance to change on the part of many of the established academic publishers. Publishers are often accused of capturing and monetising publicly funded research, using free academic labour for peer review, and then selling the resulting publications back to academia at inflated profits. Such frustrations sometimes spill over into hyperbole, of which "publishers add no value" is one of the most common examples.

However, scholarly publishing is not a simple process, and publishers do add value to scholarly communication as it is currently designed. Kent Anderson maintains a list of things that journal publishers do which currently contains 102 items and has yet to be formally contested from anyone who challenges the value of publishers. Many items on the list could be argued to be of value primarily to the publishers themselves, e.g. "Make money and remain a constant in the system of scholarly output". However, others provide direct value to researchers and research in steering the academic literature. This includes arbitrating disputes (e.g. over ethics, authorship), stewarding the scholarly record, copy-editing, proofreading, type-setting, styling of materials, linking the articles to open and accessible datasets, and (perhaps most importantly) arranging and managing scholarly peer review. The latter is a task that should not be underestimated as it effectively entails coercing busy people into giving their time to improve someone else's work and maintain the quality of the literature. Not to mention the standard management processes for large enterprises, including infrastructure, people, security, and marketing. All of these factors contribute in one way or another to maintaining the scholarly record.

It could be questioned though, whether these functions are actually necessary to the core aim of scholarly communication, namely, dissemination of research to researchers and other stakeholders such as policy makers, economic, biomedical and industrial practitioners as well as the general public. Above, for example, we question the necessity of the current infrastructure for peer review, and if a scholar-led crowdsourced alternative may be preferable. In addition, one of the biggest tensions in this space is associated with the question if for-profit companies (or the private sector) should be allowed to be in charge of the management and dissemination of academic output and execute their powers while serving, for the most part, their own interests. This is often considered alongside the value added by such companies, and therefore the two are closely linked as part of broader questions on appropriate expenditure of public funds, the role of commercial entities in the public sector, and issues around the privatisation of scholarly knowledge.

Publishing could certainly be done at a lower cost than common at present. There are significant researcher-facing inefficiencies in the system including the common scenario of multiple rounds of rejection and resubmission to various venues as well as the fact that some publishers profit beyond reasonable scale. What is missing most from the current publishing market, is transparency about the nature and the quality of the services publishers offer. This would allow authors to make informed choices, rather than decisions based on indicators that are unrelated to research quality, such as the JIF. All the above questions are being investigated and alternatives could be considered and explored. Yet, in the current system, publishers still play a role in managing processes of quality assurance, interlinking and findability of research. As the role of scholarly publishers within the knowledge communication industry continues to evolve, it is seen as necessary that they can justify their operation based on the intrinsic value that they add, and combat the perception that they add no value to the process.