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Cosmogony

Cosmogony is any model concerning the origin of the cosmos or the universe.

Scientific theories
In astronomy, cosmogony refers to the study of the origin of particular astrophysical objects or systems, and is most commonly used in reference to the origin of the universe, the Solar System, or the Earth–Moon system. The prevalent cosmological model of the early development of the universe is the Big Bang theory.

Sean M. Carroll, who specializes in theoretical cosmology and field theory, explains two competing explanations for the origins of the singularity, which is the center of a space in which a characteristic is limitless (one example is the singularity of a black hole, where gravity is the characteristic that becomes limitless—infinite).

It is generally thought that the universe began at a point of singularity, but among Modern Cosmologists and Physicists, a singularity usually represents a lack of understanding, and in the case of Cosmology/Cosmogony, requires a theory of quantum gravity to understand. When the universe started to expand, what is colloquially known as the Big Bang occurred, which evidently began the universe. The other explanation, held by proponents such as Stephen Hawking, asserts that time did not exist when it emerged along with the universe. This assertion implies that the universe does not have a beginning, as time did not exist "prior" to the universe. Hence, it is unclear whether properties such as space or time emerged with the singularity and the known universe.

Despite the research, there is currently no theoretical model that explains the earliest moments of the universe's existence (during the Planck epoch) due to a lack of a testable theory of quantum gravity. Nevertheless, researchers of string theory, its extensions (such as M-theory), and of loop quantum cosmology, like Barton Zwiebach and Washington Taylor, have proposed solutions to assist in the explanation of the universe's earliest moments. Cosmogonists have only tentative theories for the early stages of the universe and its beginning. The proposed theoretical scenarios include string theory, M-theory, the Hartle–Hawking initial state, emergent Universe, string landscape, cosmic inflation, the Big Bang, and the ekpyrotic universe. Some of these proposed scenarios, like the string theory, are compatible, whereas others are not.

Mythology

In mythology, creation or cosmogonic myths are narratives describing the beginning of the universe or cosmos.

Some methods of the creation of the universe in mythology include:

 * the will or action of a supreme being or beings,
 * the process of metamorphosis,
 * the copulation of female and male deities,
 * from chaos,
 * or via a cosmic egg.

Creation myths may be etiological, attempting to provide explanations for the origin of the universe. For instance, Eridu Genesis, the oldest known creation myth, contains an account of the creation of the world in which the universe was created out of a primeval sea (Abzu). Creation myths vary, but they may share similar deities or symbols. For instance, the ruler of the gods in Greek mythology, Zeus, is similar to the ruler of the gods in Roman mythology, Jupiter. Another example is the ruler of the gods in Tagalog mythology, Bathala, who is similar to various rulers of certain pantheons within Philippine mythology such as the Bisaya's Kaptan.

Compared with cosmology
In the humanities, the distinction between cosmogony and cosmology is blurred. For example, in theology, the cosmological argument for the existence of God (pre-cosmic cosmogonic bearer of personhood) is an appeal to ideas concerning the origin of the universe and is thus cosmogonical. Some religious cosmogonies have an impersonal first cause (for example Taoism).

However, in astronomy, cosmogony can be distinguished from cosmology, which studies the universe and its existence, but does not necessarily inquire into its origins. There is therefore a scientific distinction between cosmological and cosmogonical ideas. Physical cosmology is the science that attempts to explain all observations relevant to the development and characteristics of the universe on its largest scale. Some questions regarding the behaviour of the universe have been described by some physicists and cosmologists as being extra-scientific or metaphysical. Attempted solutions to such questions may include the extrapolation of scientific theories to untested regimes (such as the Planck epoch), or the inclusion of philosophical or religious ideas.

title: Cosmogony


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Gattaca

Gattaca is a 1997 American dystopian science fiction film written and directed by Andrew Niccol in his feature directorial debut. It stars Ethan Hawke and Uma Thurman with Jude Law, Loren Dean, Ernest Borgnine, Gore Vidal, and Alan Arkin appearing in supporting roles. The film presents a future society driven by eugenics where children are conceived through genetic selection to ensure they possess the best hereditary traits of their parents. The film centers on Vincent Freeman, played by Hawke, who was conceived outside the eugenics program and struggles to overcome genetic discrimination to realize his dream of going into space.

The film draws on concerns over reproductive technologies that facilitate eugenics, and the possible consequences of such technological developments for society. It also explores the idea of destiny and the ways in which it can and does govern lives. Characters in Gattaca continually battle both with society and with themselves to find their place in the world and who they are destined to be according to their genes.

The film's title is based on the letters G, A, T, and C, which stand for guanine, adenine, thymine, and cytosine, the four nucleobases of DNA. It was a 1997 nominee for the Academy Award for Best Art Direction and the Golden Globe Award for Best Original Score. A follow-up series was in development at Showtime, but has been cancelled as of 2023.

Plot
In the "not-too-distant" future, eugenics is common. A genetic registry database uses biometrics to classify those so created as "valids" while those conceived naturally and more susceptible to genetic disorders are known as "in-valids". Genetic discrimination is illegal, but in practice genotype profiling is used to identify valids to qualify for professional employment while in-valids are relegated to menial jobs.

Vincent Freeman was conceived naturally, and his genetic profile indicates a high probability of several disorders and an estimated lifespan of 30.2 years. His parents, regretting their decision, use genetic selection in conceiving their second child, Anton Jr. Growing up, the two brothers often play a game of "chicken" by swimming out to sea as far as possible, with the first one returning to shore considered the loser; Vincent always loses. Vincent dreams of a career in space travel, but is always reminded of his genetic inferiority. One day, Vincent challenges Anton to a game of chicken and beats him. Anton starts to drown and is saved by Vincent. Shortly after, Vincent leaves home.

Years later, Vincent works cleaning office spaces, including that of spaceflight conglomerate Gattaca Aerospace Corporation. He gets a chance to pose as a valid by using donated hair, skin, blood, and urine samples from former swimming star Jerome Eugene Morrow, who was paralyzed after being hit by a car. With Jerome's genetic makeup, Vincent gains employment at Gattaca and is assigned as a navigator for an upcoming mission to Saturn's moon Titan. To conceal his identity, Vincent must meticulously groom and scrub down daily to remove his own genetic material, pass daily DNA scanning and urine tests using Jerome's samples, and hide his heart defect.

When a Gattaca administrator is murdered a week before a possible launch, the police find one of Vincent's eyelashes near the crime scene, but can only identify it as from an "unregistered" in-valid, and thus launch an investigation to find who owns the eyelash. During this, Vincent becomes close to a co-worker, Irene Cassini, and falls in love with her. Though a valid, Irene has a higher risk of heart failure that will bar her from any deep space mission. Vincent also learns that Jerome's paralysis is self-inflicted; after placing silver in the Olympics, Jerome threw himself in front of a car. Jerome maintains that he was designed to be the best, yet somehow wasn't, and is suffering because of this.

Vincent repeatedly evades the grasp of the investigation. Finally, it is revealed that Gattaca's mission director Josef killed the administrator because he threatened to cancel the mission. Vincent learns that the detective who closed the case was his brother Anton, who consequently has discovered Vincent's presence. The brothers meet, and Anton warns Vincent about his illegal actions, but Vincent asserts that he has gotten to this position on his own merits. Anton challenges Vincent to a final game of chicken. As the two swim out at night, Vincent's stamina surprises Anton, so Vincent reveals that he won by not saving energy for the swim back. Anton turns back and begins to drown, but Vincent rescues him and swims them back to shore.

On the day of the launch, Jerome reveals that he has stored enough DNA samples for Vincent to last two lifetimes upon his return and gives him an envelope to open once in flight. After saying goodbye to Irene, Vincent prepares to board, but discovers there is a final genetic test, and he currently lacks any of Jerome's samples. He is surprised when Dr. Lamar, who oversees background checks, reveals that he knows Vincent has been posing as a valid. Lamar admits that his son looks up to Vincent and wonders whether his son, who is genetically selected, but "not all that they promised", could exceed his potential just as Vincent has. The doctor changes the test results, allowing Vincent to pass.

As the rocket launches, Jerome dons his swimming medal and immolates himself in his home's incinerator. Vincent opens the note to find a lock of Jerome's hair.

Cast

 * Ethan Hawke as Vincent Freeman, impersonating Jerome Eugene Morrow
 * Mason Gamble as young Vincent
 * Chad Christ as teenage Vincent
 * Uma Thurman as Irene Cassini
 * Jude Law as Jerome Eugene Morrow
 * Loren Dean as Anton Freeman
 * Vincent Nielson as young Anton
 * William Lee Scott as teenage Anton
 * Gore Vidal as Director Josef
 * Xander Berkeley as Dr. Lamar
 * Jayne Brook as Marie Freeman
 * Elias Koteas as Antonio Freeman
 * Maya Rudolph as delivery nurse
 * Blair Underwood as geneticist
 * Ernest Borgnine as Caesar
 * Tony Shalhoub as German
 * Alan Arkin as Detective Hugo
 * Dean Norris as cop on the beat
 * Ken Marino as sequencing technician
 * Cynthia Martells as Cavendish
 * Gabrielle Reece as Gattaca trainer

Production
The film was shot under the working title The Eighth Day, a reference to the seven days of creation in the Bible. However, by the time its release was scheduled for the fall of 1997, the Belgian film Le huitième jour had already been released in the US under the title The Eighth Day. As a result, the film was retitled Gattaca, which takes inspiration from the letters G, A, T, and C, derived from four of the nucleobases of DNA: guanine, adenine, thymine and cytosine.

Filming
The exteriors (including the roof scene) and some of the interior shots of the Gattaca complex were filmed at Frank Lloyd Wright's 1960 Marin County Civic Center in San Rafael, California. The speakers in the complex broadcast announcements both in Esperanto and English; Miko Sloper from the Esperanto League of North America went to the recording studio to handle the Esperanto part. The parking lot scenes were shot at the Otis College of Art and Design, distinguished by its punch card-like windows, located near Los Angeles International Airport. The exterior of Vincent Freeman's house was shot at the CLA Building on the campus of California State Polytechnic University, Pomona. Other exterior shots were filmed at the bottom of the spillway of the Sepulveda Dam, Culver City High School, and outside The Forum in Inglewood. The solar power plant mirrors sequence was filmed at the Kramer Junction Solar Electric Generating Station.

The film is noted for its unique use of color. Cinematographer Slawomir Idziak employed vibrant gold, green, and electric blue tones throughout the film, and shot the film in Super 35mm format, which adds an enlarged layer of grain.

Design
The movie uses a swimming treadmill in the opening minutes to punctuate the swimming and futuristic themes. The production design makes heavy use of retrofuturism; the futuristic electric cars are based on 1960s car models like Rover P6, Citroën DS19 and Studebaker Avanti.

Title sequence
The opening title sequence, created by Michael Riley, features closeups of body matter (fingernails and hair), which are later revealed to be from Vincent's daily bodily scourings, hitting the floor accompanied by loud sounds as the objects strike the ground. According to Riley, oversized models of the fingernails and hair were created for the effect.

Music and soundtrack
The score for Gattaca was composed by Michael Nyman, and the original soundtrack was released on October 21, 1997.

Box office
Gattaca was released in theaters on October 24, 1997, in the United States by Columbia Pictures and opened at number 5 at the box office; trailing I Know What You Did Last Summer, The Devil's Advocate, Kiss the Girls and Seven Years in Tibet. Over the first weekend the film brought in $4.3 million. It ended its theatrical run with a domestic total of $12.5 million against a reported production budget of $36 million.

Home media
Gattaca was released on DVD on July 1, 1998, and was also released on Superbit DVD. Special Edition DVD and Blu-ray versions were released on March 11, 2008. Both editions contain a deleted scene featuring historical figures like Einstein, Lincoln, etc., who are described as having been genetically deficient.

Gattaca was released on Ultra HD Blu-ray in 2021.

Critical response
Gattaca received positive reviews from critics. The film received an approval rating of 82% on Rotten Tomatoes based on 66 reviews, with a rating average of 7.1/10. The site's critical consensus states that "Intelligent and scientifically provocative, Gattaca is an absorbing sci-fi drama that poses important interesting ethical questions about the nature of science." On Metacritic, the film received "generally favorable reviews" with a score of 64 out of 100, based on 20 reviews. Roger Ebert stated, "This is one of the smartest and most provocative of science fiction films, a thriller with ideas." James Berardinelli praised it for "energy and tautness" and its "thought-provoking script and thematic richness."

Although critically acclaimed, Gattaca was not a box office success, but it is said to have crystallized the debate over the controversial topic of human genetic engineering. The film's dystopian depiction of "genoism" has been cited by many bioethicists and laypeople in support of their hesitancy about, or opposition to, eugenics and the societal acceptance of the genetic-determinist ideology that may frame it. In a 1997 review of the film for the journal Nature Genetics, molecular biologist Lee M. Silver stated that "Gattaca is a film that all geneticists should see if for no other reason than to understand the perception of our trade held by so many of the public-at-large".

Continuation
On October 30, 2009, Variety reported that Sony Pictures Television was developing a television adaptation of the feature film as a one-hour police procedural set in the future. The show was to be written by Gil Grant, who has written for 24 and NCIS. A Gattaca television series was revealed to be in development at Sony and Showtime in March 2023. It was intended to take place one generation after the events of the film. Howard Gordon and Alex Gansa were tapped as showrunners, and were also expected to serve as screenwriters alongside Craig Borten. Gordon, Gansa, Glenn Gellar, and actor Danny DeVito (who produced the film) would have served as executive producers. However, in June 2023, Showtime announced that they had abandoned plans to produce the show.

Influence on In Time
Writer-director Andrew Niccol has called his 2011 film In Time a "bastard child of Gattaca". Both films feature classic cars in a futuristic dystopia as well as a caste privilege schism which the protagonist challenges and which prejudices the authorities into neglecting a thorough investigation in favor of condemning the protagonist.

Political references
U.S. Senator Rand Paul used near-verbatim portions of the plot summary from the English Wikipedia entry on Gattaca in a speech at Liberty University on October 28, 2013, in support of Virginia Attorney General Ken Cuccinelli's campaign for Governor of Virginia. Paul said that abortion rights advocates are advancing eugenics in a manner similar to the events in Gattaca.

Transhumanism
In the 2004 democratic transhumanist book Citizen Cyborg, bioethicist James Hughes criticized the premise and influence of the film as fear-mongering, arguing:
 * 1) Astronaut-training programs are entirely justified in attempting to screen out people with heart problems for safety reasons;
 * 2) In the United States, people are already screened by insurance companies on the basis of their propensities to disease, for actuarial purposes;
 * 3) Rather than banning genetic testing or genetic enhancement, society should develop genetic information privacy laws, such as the U.S. Genetic Information Nondiscrimination Act signed into law on May 21, 2008, that allow justified forms of genetic testing and data aggregation, but forbid those that are judged to result in genetic discrimination. Citizens should then be able to make a complaint to the appropriate authority if they believe they have been discriminated against because of their genotype.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

title: Gattaca


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Human genome

The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are usually treated separately as the nuclear genome and the mitochondrial genome. Human genomes include both protein-coding DNA sequences and various types of DNA that does not encode proteins. The latter is a diverse category that includes DNA coding for non-translated RNA, such as that for ribosomal RNA, transfer RNA, ribozymes, small nuclear RNAs, and several types of regulatory RNAs. It also includes promoters and their associated gene-regulatory elements, DNA playing structural and replicatory roles, such as scaffolding regions, telomeres, centromeres, and origins of replication, plus large numbers of transposable elements, inserted viral DNA, non-functional pseudogenes and simple, highly repetitive sequences. Introns make up a large percentage of non-coding DNA. Some of this non-coding DNA is non-functional junk DNA, such as pseudogenes, but there is no firm consensus on the total amount of junk DNA.

Although the sequence of the human genome has been completely determined by DNA sequencing in 2022, it is not yet fully understood. Most, but not all, genes have been identified by a combination of high throughput experimental and bioinformatics approaches, yet much work still needs to be done to further elucidate the biological functions of their protein and RNA products (in particular, annotation of the complete CHM13v2.0 sequence is still ongoing ).

Size of the human genome
In 2003, scientists reported the sequencing of 85% of the entire human genome, but as of 2020, at least 8% was still missing. In 2021, scientists reported sequencing the complete female genome (i.e., without the Y chromosome). This sequence identified 19,969 protein-coding sequences, accounting for approximately 1.5% of the genome, and 63,494 genes in total, most of them being non-coding RNA genes. The genome consists of regulatory DNA sequences, LINEs, SINEs, introns, and sequences for which as yet no function has been determined. The human Y chromosome, consisting of about 62.5 x 106 base pairs from a different cell line and found in all males, was sequenced completely in January 2022.

The current version of the standard reference genome is called GRCh38.p14 (July 2023). It consists of 22 autosomes plus one copy of the X chromosome and one copy of the Y chromosome. It contains approximately 3.1 billion base pairs (3.1 Gb or 3.1 x 109 bp). This represents the size of a composite genome based on data from multiple individuals but it is a good indication of the typical amount of DNA in a haploid set of chromosomes. Most human cells are diploid so they contain twice as much DNA.

In 2023, a draft human pangenome reference was published. It is based on 47 genomes from persons of varied ethnicity. Plans are underway for an improved reference capturing still more biodiversity from a still wider sample.

While there are significant differences among the genomes of human individuals (on the order of 0.1% due to single-nucleotide variants and 0.6% when considering indels), these are considerably smaller than the differences between humans and their closest living relatives, the bonobos and chimpanzees (~1.1% fixed single-nucleotide variants and 4% when including indels).

Molecular organization and gene content
The total length of the human reference genome does not represent the sequence of any specific individual. The genome is organized into 22 paired chromosomes, termed autosomes, plus the 23rd pair of sex chromosomes (XX) in the female and (XY) in the male. These chromosomes are all large linear DNA molecules contained within the cell nucleus. The current version of the human reference genome includes one copy of each of the autosomes plus one copy of the two sex chromosomes (X and Y). The total amount of DNA is 3.1 billion base pairs (3.1 Gb).

Protein-coding genes
Protein-coding sequences represent the most widely studied and best understood component of the human genome. These sequences ultimately lead to the production of all human proteins, although several biological processes (e.g. DNA rearrangements and alternative pre-mRNA splicing) can lead to the production of many more unique proteins than the number of protein-coding genes.

The human genome contains somewhere between 19,000 and 20,000 protein-coding genes. These genes contain an average of 10 introns and the average size of an intron is about 6 kb (6,000 bp). This means that the average size of a protein-coding gene is about 62 kb and these genes take up about 40% of the genome.

Exon sequences consist of coding DNA and untranslated regions (UTRs) at either end of the mature mRNA. The total amount of coding DNA is about 1-2% of the genome.

Many people divide the genome into coding and non-coding DNA based on the idea that coding DNA is the most important functional component of the genome. About 98-99% of the human genome is non-coding DNA.

Non-coding genes
Noncoding RNA molecules play many essential roles in cells, especially in the many reactions of protein synthesis and RNA processing. Noncoding RNA include tRNA, ribosomal RNA, microRNA, snRNA and other non-coding RNA genes including about 60,000 long non-coding RNAs (lncRNAs). Although the number of reported lncRNA genes continues to rise and the exact number in the human genome is yet to be defined, many of them are argued to be non-functional.

Many ncRNAs are critical elements in gene regulation and expression. Noncoding RNA also contributes to epigenetics, transcription, RNA splicing, and the translational machinery. The role of RNA in genetic regulation and disease offers a new potential level of unexplored genomic complexity.

Pseudogenes
Pseudogenes are inactive copies of protein-coding genes, often generated by gene duplication, that have become nonfunctional through the accumulation of inactivating mutations. The number of pseudogenes in the human genome is on the order of 13,000, and in some chromosomes is nearly the same as the number of functional protein-coding genes. Gene duplication is a major mechanism through which new genetic material is generated during molecular evolution.

For example, the olfactory receptor gene family is one of the best-documented examples of pseudogenes in the human genome. More than 60 percent of the genes in this family are non-functional pseudogenes in humans. By comparison, only 20 percent of genes in the mouse olfactory receptor gene family are pseudogenes. Research suggests that this is a species-specific characteristic, as the most closely related primates all have proportionally fewer pseudogenes. This genetic discovery helps to explain the less acute sense of smell in humans relative to other mammals.

Regulatory DNA sequences
The human genome has many different regulatory sequences which are crucial to controlling gene expression. Conservative estimates indicate that these sequences make up 8% of the genome, however extrapolations from the ENCODE project give that 20 -40% of the genome is gene regulatory sequence. Some types of non-coding DNA are genetic "switches" that do not encode proteins, but do regulate when and where genes are expressed (called enhancers).

Regulatory sequences have been known since the late 1960s. The first identification of regulatory sequences in the human genome relied on recombinant DNA technology. Later with the advent of genomic sequencing, the identification of these sequences could be inferred by evolutionary conservation. The evolutionary branch between the primates and mouse, for example, occurred 70–90 million years ago. So computer comparisons of gene sequences that identify conserved non-coding sequences will be an indication of their importance in duties such as gene regulation.

Other genomes have been sequenced with the same intention of aiding conservation-guided methods, for exampled the pufferfish genome. However, regulatory sequences disappear and re-evolve during evolution at a high rate.

As of 2012, the efforts have shifted toward finding interactions between DNA and regulatory proteins by the technique ChIP-Seq, or gaps where the DNA is not packaged by histones (DNase hypersensitive sites), both of which tell where there are active regulatory sequences in the investigated cell type.

Repetitive DNA sequences
Repetitive DNA sequences comprise approximately 50% of the human genome.

About 8% of the human genome consists of tandem DNA arrays or tandem repeats, low complexity repeat sequences that have multiple adjacent copies (e.g. "CAGCAGCAG..."). The tandem sequences may be of variable lengths, from two nucleotides to tens of nucleotides. These sequences are highly variable, even among closely related individuals, and so are used for genealogical DNA testing and forensic DNA analysis.

Repeated sequences of fewer than ten nucleotides (e.g. the dinucleotide repeat (AC)n) are termed microsatellite sequences. Among the microsatellite sequences, trinucleotide repeats are of particular importance, as sometimes occur within coding regions of genes for proteins and may lead to genetic disorders. For example, Huntington's disease results from an expansion of the trinucleotide repeat (CAG)n within the Huntingtin gene on human chromosome 4. Telomeres (the ends of linear chromosomes) end with a microsatellite hexanucleotide repeat of the sequence (TTAGGG)n.

Tandem repeats of longer sequences (arrays of repeated sequences 10–60 nucleotides long) are termed minisatellites.

Transposable genetic elements, DNA sequences that can replicate and insert copies of themselves at other locations within a host genome, are an abundant component in the human genome. The most abundant transposon lineage, Alu, has about 50,000 active copies, and can be inserted into intragenic and intergenic regions. One other lineage, LINE-1, has about 100 active copies per genome (the number varies between people). Together with non-functional relics of old transposons, they account for over half of total human DNA. Sometimes called "jumping genes", transposons have played a major role in sculpting the human genome. Some of these sequences represent endogenous retroviruses, DNA copies of viral sequences that have become permanently integrated into the genome and are now passed on to succeeding generations.

Mobile elements within the human genome can be classified into LTR retrotransposons (8.3% of total genome), SINEs (13.1% of total genome) including Alu elements, LINEs (20.4% of total genome), SVAs (SINE-VNTR-Alu) and Class II DNA transposons (2.9% of total genome).

Junk DNA
There is no consensus on what constitutes a "functional" element in the genome since geneticists, evolutionary biologists, and molecular biologists employ different definitions and methods. Due to the ambiguity in the terminology, different schools of thought have emerged. In evolutionary definitions, "functional" DNA, whether it is coding or non-coding, contributes to the fitness of the organism, and therefore is maintained by negative evolutionary pressure whereas "non-functional" DNA has no benefit to the organism and therefore is under neutral selective pressure. This type of DNA has been described as junk DNA In genetic definitions, "functional" DNA is related to how DNA segments manifest by phenotype and "nonfunctional" is related to loss-of-function effects on the organism. In biochemical definitions, "functional" DNA relates to DNA sequences that specify molecular products (e.g. noncoding RNAs) and biochemical activities with mechanistic roles in gene or genome regulation (i.e. DNA sequences that impact cellular level activity such as cell type, condition, and molecular processes). There is no consensus in the literature on the amount of functional DNA since, depending on how "function" is understood, ranges have been estimated from up to 90% of the human genome is likely nonfunctional DNA (junk DNA) to up to 80% of the genome is likely functional. It is also possible that junk DNA may acquire a function in the future and therefore may play a role in evolution, but this is likely to occur only very rarely. Finally DNA that is deliterious to the organism and is under negative selective pressure is called garbage DNA.

Sequencing
The first human genome sequences were published in nearly complete draft form in February 2001 by the Human Genome Project and Celera Corporation. Completion of the Human Genome Project's sequencing effort was announced in 2004 with the publication of a draft genome sequence, leaving just 341 gaps in the sequence, representing highly repetitive and other DNA that could not be sequenced with the technology available at the time. The human genome was the first of all vertebrates to be sequenced to such near-completion, and as of 2018, the diploid genomes of over a million individual humans had been determined using next-generation sequencing.

These data are used worldwide in biomedical science, anthropology, forensics and other branches of science. Such genomic studies have led to advances in the diagnosis and treatment of diseases, and to new insights in many fields of biology, including human evolution.

By 2018, the total number of genes had been raised to at least 46,831, plus another 2300 micro-RNA genes. A 2018 population survey found another 300 million bases of human genome that was not in the reference sequence. Prior to the acquisition of the full genome sequence, estimates of the number of human genes ranged from 50,000 to 140,000 (with occasional vagueness about whether these estimates included non-protein coding genes). As genome sequence quality and the methods for identifying protein-coding genes improved, the count of recognized protein-coding genes dropped to 19,000–20,000.

In 2022, the Telomere-to-Telomere (T2T) consortium reported the complete sequence of a human female genome, filling all the gaps in the X chromosome (2020) and the 22 autosomes (May 2021). The previously unsequenced parts contain immune response genes that help to adapt to and survive infections, as well as genes that are important for predicting drug response. The completed human genome sequence will also provide better understanding of human formation as an individual organism and how humans vary both between each other and other species.

Although the 'completion' of the human genome project was announced in 2001, there remained hundreds of gaps, with about 5–10% of the total sequence remaining undetermined. The missing genetic information was mostly in repetitive heterochromatic regions and near the centromeres and telomeres, but also some gene-encoding euchromatic regions. There remained 160 euchromatic gaps in 2015 when the sequences spanning another 50 formerly unsequenced regions were determined. Only in 2020 was the first truly complete telomere-to-telomere sequence of a human chromosome determined, namely of the X chromosome. The first complete telomere-to-telomere sequence of a human autosomal chromosome, chromosome 8, followed a year later. The complete human genome (without Y chromosome) was published in 2021, while with Y chromosome in January 2022.

In 2023, a draft human pangenome reference was published. It is based on 47 genomes from persons of varied ethnicity. Plans are underway for an improved reference capturing still more biodiversity from a still wider sample.

Human reference genome
With the exception of identical twins, all humans show significant variation in genomic DNA sequences. The human reference genome (HRG) is used as a standard sequence reference.

There are several important points concerning the human reference genome:
 * The HRG is a haploid sequence. Each chromosome is represented once.
 * The HRG is a composite sequence, and does not correspond to any actual human individual.
 * The HRG is periodically updated to correct errors, ambiguities, and unknown "gaps".
 * The HRG in no way represents an "ideal" or "perfect" human individual. It is simply a standardized representation or model that is used for comparative purposes.

The Genome Reference Consortium is responsible for updating the HRG. Version 38 was released in December 2013.

Measuring human genetic variation
Most studies of human genetic variation have focused on single-nucleotide polymorphisms (SNPs), which are substitutions in individual bases along a chromosome. Most analyses estimate that SNPs occur 1 in 1000 base pairs, on average, in the euchromatic human genome, although they do not occur at a uniform density. Thus follows the popular statement that "we are all, regardless of race, genetically 99.9% the same", although this would be somewhat qualified by most geneticists. For example, a much larger fraction of the genome is now thought to be involved in copy number variation. A large-scale collaborative effort to catalog SNP variations in the human genome is being undertaken by the International HapMap Project.

The genomic loci and length of certain types of small repetitive sequences are highly variable from person to person, which is the basis of DNA fingerprinting and DNA paternity testing technologies. The heterochromatic portions of the human genome, which total several hundred million base pairs, are also thought to be quite variable within the human population (they are so repetitive and so long that they cannot be accurately sequenced with current technology). These regions contain few genes, and it is unclear whether any significant phenotypic effect results from typical variation in repeats or heterochromatin.

Most gross genomic mutations in gamete germ cells probably result in inviable embryos; however, a number of human diseases are related to large-scale genomic abnormalities. Down syndrome, Turner Syndrome, and a number of other diseases result from nondisjunction of entire chromosomes. Cancer cells frequently have aneuploidy of chromosomes and chromosome arms, although a cause and effect relationship between aneuploidy and cancer has not been established.

Mapping human genomic variation
Whereas a genome sequence lists the order of every DNA base in a genome, a genome map identifies the landmarks. A genome map is less detailed than a genome sequence and aids in navigating around the genome.

An example of a variation map is the HapMap being developed by the International HapMap Project. The HapMap is a haplotype map of the human genome, "which will describe the common patterns of human DNA sequence variation." It catalogs the patterns of small-scale variations in the genome that involve single DNA letters, or bases.

Researchers published the first sequence-based map of large-scale structural variation across the human genome in the journal Nature in May 2008. Large-scale structural variations are differences in the genome among people that range from a few thousand to a few million DNA bases; some are gains or losses of stretches of genome sequence and others appear as re-arrangements of stretches of sequence. These variations include differences in the number of copies individuals have of a particular gene, deletions, translocations and inversions.

Structural variation
Structural variation refers to genetic variants that affect larger segments of the human genome, as opposed to point mutations. Often, structural variants (SVs) are defined as variants of 50 base pairs (bp) or greater, such as deletions, duplications, insertions, inversions and other rearrangements. About 90% of structural variants are noncoding deletions but most individuals have more than a thousand such deletions; the size of deletions ranges from dozens of base pairs to tens of thousands of bp. On average, individuals carry ~3 rare structural variants that alter coding regions, e.g. delete exons. About 2% of individuals carry ultra-rare megabase-scale structural variants, especially rearrangements. That is, millions of base pairs may be inverted within a chromosome; ultra-rare means that they are only found in individuals or their family members and thus have arisen very recently.

SNP frequency across the human genome
Single-nucleotide polymorphisms (SNPs) do not occur homogeneously across the human genome. In fact, there is enormous diversity in SNP frequency between genes, reflecting different selective pressures on each gene as well as different mutation and recombination rates across the genome. However, studies on SNPs are biased towards coding regions, the data generated from them are unlikely to reflect the overall distribution of SNPs throughout the genome. Therefore, the SNP Consortium protocol was designed to identify SNPs with no bias towards coding regions and the Consortium's 100,000 SNPs generally reflect sequence diversity across the human chromosomes. The SNP Consortium aims to expand the number of SNPs identified across the genome to 300 000 by the end of the first quarter of 2001. Changes in non-coding sequence and synonymous changes in coding sequence are generally more common than non-synonymous changes, reflecting greater selective pressure reducing diversity at positions dictating amino acid identity. Transitional changes are more common than transversions, with CpG dinucleotides showing the highest mutation rate, presumably due to deamination.

Personal genomes
A personal genome sequence is a (nearly) complete sequence of the chemical base pairs that make up the DNA of a single person. Because medical treatments have different effects on different people due to genetic variations such as single-nucleotide polymorphisms (SNPs), the analysis of personal genomes may lead to personalized medical treatment based on individual genotypes.

The first personal genome sequence to be determined was that of Craig Venter in 2007. Personal genomes had not been sequenced in the public Human Genome Project to protect the identity of volunteers who provided DNA samples. That sequence was derived from the DNA of several volunteers from a diverse population. However, early in the Venter-led Celera Genomics genome sequencing effort the decision was made to switch from sequencing a composite sample to using DNA from a single individual, later revealed to have been Venter himself. Thus the Celera human genome sequence released in 2000 was largely that of one man. Subsequent replacement of the early composite-derived data and determination of the diploid sequence, representing both sets of chromosomes, rather than a haploid sequence originally reported, allowed the release of the first personal genome. In April 2008, that of James Watson was also completed. In 2009, Stephen Quake published his own genome sequence derived from a sequencer of his own design, the Heliscope. A Stanford team led by Euan Ashley published a framework for the medical interpretation of human genomes implemented on Quake's genome and made whole genome-informed medical decisions for the first time. That team further extended the approach to the West family, the first family sequenced as part of Illumina's Personal Genome Sequencing program. Since then hundreds of personal genome sequences have been released, including those of Desmond Tutu, and of a Paleo-Eskimo. In 2012, the whole genome sequences of two family trios among 1092 genomes was made public. In November 2013, a Spanish family made four personal exome datasets (about 1% of the genome) publicly available under a Creative Commons public domain license. The Personal Genome Project (started in 2005) is among the few to make both genome sequences and corresponding medical phenotypes publicly available.

The sequencing of individual genomes further unveiled levels of genetic complexity that had not been appreciated before. Personal genomics helped reveal the significant level of diversity in the human genome attributed not only to SNPs but structural variations as well. However, the application of such knowledge to the treatment of disease and in the medical field is only in its very beginnings. Exome sequencing has become increasingly popular as a tool to aid in diagnosis of genetic disease because the exome contributes only 1% of the genomic sequence but accounts for roughly 85% of mutations that contribute significantly to disease.

Human knockouts
In humans, gene knockouts naturally occur as heterozygous or homozygous loss-of-function gene knockouts. These knockouts are often difficult to distinguish, especially within heterogeneous genetic backgrounds. They are also difficult to find as they occur in low frequencies.

Populations with high rates of consanguinity, such as countries with high rates of first-cousin marriages, display the highest frequencies of homozygous gene knockouts. Such populations include Pakistan, Iceland, and Amish populations. These populations with a high level of parental-relatedness have been subjects of human knock out research which has helped to determine the function of specific genes in humans. By distinguishing specific knockouts, researchers are able to use phenotypic analyses of these individuals to help characterize the gene that has been knocked out.

Knockouts in specific genes can cause genetic diseases, potentially have beneficial effects, or even result in no phenotypic effect at all. However, determining a knockout's phenotypic effect and in humans can be challenging. Challenges to characterizing and clinically interpreting knockouts include difficulty calling of DNA variants, determining disruption of protein function (annotation), and considering the amount of influence mosaicism has on the phenotype.

One major study that investigated human knockouts is the Pakistan Risk of Myocardial Infarction study. It was found that individuals possessing a heterozygous loss-of-function gene knockout for the APOC3 gene had lower triglycerides in the blood after consuming a high fat meal as compared to individuals without the mutation. However, individuals possessing homozygous loss-of-function gene knockouts of the APOC3 gene displayed the lowest level of triglycerides in the blood after the fat load test, as they produce no functional APOC3 protein.

Human genetic disorders
Most aspects of human biology involve both genetic (inherited) and non-genetic (environmental) factors. Some inherited variation influences aspects of our biology that are not medical in nature (height, eye color, ability to taste or smell certain compounds, etc.). Moreover, some genetic disorders only cause disease in combination with the appropriate environmental factors (such as diet). With these caveats, genetic disorders may be described as clinically defined diseases caused by genomic DNA sequence variation. In the most straightforward cases, the disorder can be associated with variation in a single gene. For example, cystic fibrosis is caused by mutations in the CFTR gene and is the most common recessive disorder in caucasian populations with over 1,300 different mutations known.

Disease-causing mutations in specific genes are usually severe in terms of gene function and are rare, thus genetic disorders are similarly individually rare. However, since there are many genes that can vary to cause genetic disorders, in aggregate they constitute a significant component of known medical conditions, especially in pediatric medicine. Molecularly characterized genetic disorders are those for which the underlying causal gene has been identified. Currently there are approximately 2,200 such disorders annotated in the OMIM database.

Studies of genetic disorders are often performed by means of family-based studies. In some instances, population based approaches are employed, particularly in the case of so-called founder populations such as those in Finland, French-Canada, Utah, Sardinia, etc. Diagnosis and treatment of genetic disorders are usually performed by a geneticist-physician trained in clinical/medical genetics. The results of the Human Genome Project are likely to provide increased availability of genetic testing for gene-related disorders, and eventually improved treatment. Parents can be screened for hereditary conditions and counselled on the consequences, the probability of inheritance, and how to avoid or ameliorate it in their offspring.

There are many different kinds of DNA sequence variation, ranging from complete extra or missing chromosomes down to single nucleotide changes. It is generally presumed that much naturally occurring genetic variation in human populations is phenotypically neutral, i.e., has little or no detectable effect on the physiology of the individual (although there may be fractional differences in fitness defined over evolutionary time frames). Genetic disorders can be caused by any or all known types of sequence variation. To molecularly characterize a new genetic disorder, it is necessary to establish a causal link between a particular genomic sequence variant and the clinical disease under investigation. Such studies constitute the realm of human molecular genetics.

With the advent of the Human Genome and International HapMap Project, it has become feasible to explore subtle genetic influences on many common disease conditions such as diabetes, asthma, migraine, schizophrenia, etc. Although some causal links have been made between genomic sequence variants in particular genes and some of these diseases, often with much publicity in the general media, these are usually not considered to be genetic disorders per se as their causes are complex, involving many different genetic and environmental factors. Thus there may be disagreement in particular cases whether a specific medical condition should be termed a genetic disorder.

Additional genetic disorders of mention are Kallman syndrome and Pfeiffer syndrome (gene FGFR1), Fuchs corneal dystrophy (gene TCF4), Hirschsprung's disease (genes RET and FECH), Bardet-Biedl syndrome 1 (genes CCDC28B and BBS1), Bardet-Biedl syndrome 10 (gene BBS10), and facioscapulohumeral muscular dystrophy type 2 (genes D4Z4 and SMCHD1).

Genome sequencing is now able to narrow the genome down to specific locations to more accurately find mutations that will result in a genetic disorder. Copy number variants (CNVs) and single nucleotide variants (SNVs) are also able to be detected at the same time as genome sequencing with newer sequencing procedures available, called Next Generation Sequencing (NGS). This only analyzes a small portion of the genome, around 1–2%. The results of this sequencing can be used for clinical diagnosis of a genetic condition, including Usher syndrome, retinal disease, hearing impairments, diabetes, epilepsy, Leigh disease, hereditary cancers, neuromuscular diseases, primary immunodeficiencies, severe combined immunodeficiency (SCID), and diseases of the mitochondria. NGS can also be used to identify carriers of diseases before conception. The diseases that can be detected in this sequencing include Tay-Sachs disease, Bloom syndrome, Gaucher disease, Canavan disease, familial dysautonomia, cystic fibrosis, spinal muscular atrophy, and fragile-X syndrome. The Next Genome Sequencing can be narrowed down to specifically look for diseases more prevalent in certain ethnic populations.

Evolution
Comparative genomics studies of mammalian genomes suggest that approximately 5% of the human genome has been conserved by evolution since the divergence of extant lineages approximately 200 million years ago, containing the vast majority of genes. The published chimpanzee genome differs from that of the human genome by 1.23% in direct sequence comparisons. Around 20% of this figure is accounted for by variation within each species, leaving only ~1.06% consistent sequence divergence between humans and chimps at shared genes. This nucleotide by nucleotide difference is dwarfed, however, by the portion of each genome that is not shared, including around 6% of functional genes that are unique to either humans or chimps.

In other words, the considerable observable differences between humans and chimps may be due as much or more to genome level variation in the number, function and expression of genes rather than DNA sequence changes in shared genes. Indeed, even within humans, there has been found to be a previously unappreciated amount of copy number variation (CNV) which can make up as much as 5–15% of the human genome. In other words, between humans, there could be +/- 500,000,000 base pairs of DNA, some being active genes, others inactivated, or active at different levels. The full significance of this finding remains to be seen. On average, a typical human protein-coding gene differs from its chimpanzee ortholog by only two amino acid substitutions; nearly one third of human genes have exactly the same protein translation as their chimpanzee orthologs. A major difference between the two genomes is human chromosome 2, which is equivalent to a fusion product of chimpanzee chromosomes 12 and 13. (later renamed to chromosomes 2A and 2B, respectively).

Humans have undergone an extraordinary loss of olfactory receptor genes during our recent evolution, which explains our relatively crude sense of smell compared to most other mammals. Evolutionary evidence suggests that the emergence of color vision in humans and several other primate species has diminished the need for the sense of smell.

In September 2016, scientists reported that, based on human DNA genetic studies, all non-Africans in the world today can be traced to a single population that exited Africa between 50,000 and 80,000 years ago.

Mitochondrial DNA
The human mitochondrial DNA is of tremendous interest to geneticists, since it undoubtedly plays a role in mitochondrial disease. It also sheds light on human evolution; for example, analysis of variation in the human mitochondrial genome has led to the postulation of a recent common ancestor for all humans on the maternal line of descent (see Mitochondrial Eve).

Due to the lack of a system for checking for copying errors, mitochondrial DNA (mtDNA) has a more rapid rate of variation than nuclear DNA. This 20-fold higher mutation rate allows mtDNA to be used for more accurate tracing of maternal ancestry. Studies of mtDNA in populations have allowed ancient migration paths to be traced, such as the migration of Native Americans from Siberia or Polynesians from southeastern Asia. It has also been used to show that there is no trace of Neanderthal DNA in the European gene mixture inherited through purely maternal lineage. Due to the restrictive all or none manner of mtDNA inheritance, this result (no trace of Neanderthal mtDNA) would be likely unless there were a large percentage of Neanderthal ancestry, or there was strong positive selection for that mtDNA. For example, going back 5 generations, only 1 of a person's 32 ancestors contributed to that person's mtDNA, so if one of these 32 was pure Neanderthal an expected ~3% of that person's autosomal DNA would be of Neanderthal origin, yet they would have a ~97% chance of having no trace of Neanderthal mtDNA.

Epigenome
Epigenetics describes a variety of features of the human genome that transcend its primary DNA sequence, such as chromatin packaging, histone modifications and DNA methylation, and which are important in regulating gene expression, genome replication and other cellular processes. Epigenetic markers strengthen and weaken transcription of certain genes but do not affect the actual sequence of DNA nucleotides. DNA methylation is a major form of epigenetic control over gene expression and one of the most highly studied topics in epigenetics. During development, the human DNA methylation profile experiences dramatic changes. In early germ line cells, the genome has very low methylation levels. These low levels generally describe active genes. As development progresses, parental imprinting tags lead to increased methylation activity.

Epigenetic patterns can be identified between tissues within an individual as well as between individuals themselves. Identical genes that have differences only in their epigenetic state are called epialleles. Epialleles can be placed into three categories: those directly determined by an individual's genotype, those influenced by genotype, and those entirely independent of genotype. The epigenome is also influenced significantly by environmental factors. Diet, toxins, and hormones impact the epigenetic state. Studies in dietary manipulation have demonstrated that methyl-deficient diets are associated with hypomethylation of the epigenome. Such studies establish epigenetics as an important interface between the environment and the genome.

title: Human genome


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Fusor

A fusor is a device that uses an electric field to heat ions to a temperature in which they undergo nuclear fusion. The machine induces a potential difference between two metal cages, inside a vacuum. Positive ions fall down this voltage drop, building up speed. If they collide in the center, they can fuse. This is one kind of an inertial electrostatic confinement device – a branch of fusion research.

A Farnsworth–Hirsch fusor is the most common type of fusor. This design came from work by Philo T. Farnsworth in 1964 and Robert L. Hirsch in 1967. A variant type of fusor had been proposed previously by William Elmore, James L. Tuck, and Ken Watson at the Los Alamos National Laboratory though they never built the machine.

Fusors have been built by various institutions. These include academic institutions such as the University of Wisconsin–Madison, the Massachusetts Institute of Technology and government entities, such as the Atomic Energy Organization of Iran and the Turkish Atomic Energy Authority. Fusors have also been developed commercially, as sources for neutrons by DaimlerChrysler Aerospace and as a method for generating medical isotopes. Fusors have also become very popular for hobbyists and amateurs. A growing number of amateurs have performed nuclear fusion using simple fusor machines. However, fusors are not considered a viable concept for large-scale energy production by scientists.

Underlying physics
Fusion takes place when nuclei approach to a distance where the nuclear force can pull them together into a single larger nucleus. Opposing this close approach are the positive charges in the nuclei, which force them apart due to the electrostatic force. In order to produce fusion events, the nuclei must have initial energy great enough to allow them to overcome this Coulomb barrier. As the nuclear force is increased with the number of nucleons, protons and neutrons, and the electromagnetic force is increased with the number of protons only, the easiest atoms to fuse are isotopes of hydrogen, deuterium with one neutron, and tritium with two. With hydrogen fuels, about 3 to 10 keV is needed to allow the reaction to take place.

Traditional approaches to fusion power have generally attempted to heat the fuel to temperatures where the Maxwell-Boltzmann distribution of their resulting energies is high enough that some of the particles in the long tail have the required energy. High enough in this case is such that the rate of the fusion reactions produces enough energy to offset energy losses to the environment and thus heat the surrounding fuel to the same temperatures and produce a self-sustaining reaction known as ignition. Calculations show this takes place at about 50 million kelvin (K), although higher numbers on the order of 100 million K are desirable in practical machines. Due to the extremely high temperatures, fusion reactions are also referred to as thermonuclear.

When atoms are heated to temperatures corresponding to thousands of degrees, the electrons become increasingly free of their nucleus. This leads to a gas-like state of matter known as a plasma, consisting of free nuclei known as ions, and their former electrons. As a plasma consists of free-moving charges, it can be controlled using magnetic and electrical fields. Fusion devices use this capability to retain the fuel at millions of degrees.

Fusor concept
The fusor is part of a broader class of devices that attempts to give the fuel fusion-relevant energies by directly accelerating the ions toward each other. In the case of the fusor, this is accomplished with electrostatic forces. For every volt that an ion of ±1 charge is accelerated across it gains 1 electronvolt in energy. To reach the required ~10 keV, a voltage of 10 kV is required, applied to both particles. For comparison, the electron gun in a typical television cathode-ray tube is on the order of 3 to 6 kV, so the complexity of such a device is fairly limited. For a variety of reasons, energies on the order of 15 keV are used. This corresponds to the average kinetic energy at a temperature of approximately 174 million Kelvin, a typical magnetic confinement fusion plasma temperature.

The problem with this colliding beam fusion approach, in general, is that the ions will most likely never hit each other no matter how precisely aimed. Even the most minor misalignment will cause the particles to scatter and thus fail to fuse. It is simple to demonstrate that the scattering chance is many orders of magnitude higher than the fusion rate, meaning that the vast majority of the energy supplied to the ions will go to waste and those fusion reactions that do occur cannot make up for these losses. To be energy positive, a fusion device must recycle these ions back into the fuel mass so that they have thousands or millions of such chances to fuse, and their energy must be retained as much as possible during this period.

The fusor attempts to meet this requirement through the spherical arrangement of its accelerator grid system. Ions that fail to fuse pass through the center of the device and back into the accelerator on the far side, where they are accelerated back into the center again. There is no energy lost in this action, and in theory, assuming infinitely thin grid wires, the ions can circulate forever with no additional energy needed. Even those that scatter will simply take on a new trajectory, exit the grid at some new point, and accelerate back into the center again, providing the circulation that is required for a fusion event to eventually take place.

Losses
It is important to consider the actual startup sequence of a fusor to understand the resulting operation. Normally the system is pumped down to a vacuum and then a small amount of gas is placed inside the vacuum chamber. This gas will spread out to fill the volume. When voltage is applied to the electrodes, the atoms between them will experience a field that will cause them to ionize and begin accelerating inward. As the atoms are randomly distributed to begin, the amount of energy they will gain differs; atoms initially near the anode will gain some large portion of the applied voltage, say 15 keV. Those initially near the cathode will gain much less energy, possibly far too low to undergo fusion with their counterparts on the far side of the central reaction area.

The fuel atoms inside the inner area during the startup period are not ionized. The accelerated ions scatter with these and lose their energy, while ionizing the formerly cold atom. This process, and the scatterings off other ions, causes the ion energies to become randomly distributed and the fuel rapidly takes on a non-thermal distribution. For this reason, the energy needed in a fusor system is higher than one where the fuel is heated by some other method, as some will be "lost" during startup.

Real electrodes are not infinitely thin, and the potential for scattering off the wires or even capture of the ions within the electrodes is a significant issue that causes high conduction losses. These losses can be at least five orders of magnitude higher than the energy released from the fusion reaction, even when the fusor is in star mode, which minimizes these reactions.

There are numerous other loss mechanisms as well. These include charge exchange between high-energy ions and low-energy neutral particles, which causes the ion to capture the electron, become electrically neutral, and then leave the fusor as it is no longer accelerated back into the chamber. This leaves behind a newly ionized atom of lower energy and thus cools the plasma. Scatterings may also increase the energy of an ion which allows it to move past the anode and escape, in this example anything above 15 keV.

Additionally, the scatterings of both the ions, and especially impurities left in the chamber, lead to significant Bremsstrahlung, creating X-rays that carries energy out of the fuel. This effect grows with particle energy, meaning the problem becomes more pronounced as the system approaches fusion-relevant operating conditions.

As a result of these loss mechanisms, no fusor has ever come close to break-even energy output and it appears it is unable to ever do so.

The common sources of the high voltage are ZVS flyback HV sources and neon-sign transformers. It can also be called an electrostatic particle accelerator.

History
The fusor was originally conceived by Philo T. Farnsworth, better known for his pioneering work in television. In the early 1930s, he investigated a number of vacuum tube designs for use in television, and found one that led to an interesting effect. In this design, which he called the "multipactor", electrons moving from one electrode to another were stopped in mid-flight with the proper application of a high-frequency magnetic field. The charge would then accumulate in the center of the tube, leading to high amplification. Unfortunately it also led to high erosion on the electrodes when the electrons eventually hit them, and today the multipactor effect is generally considered a problem to be avoided.

What particularly interested Farnsworth about the device was its ability to focus electrons at a particular point. One of the biggest problems in fusion research is to keep the hot fuel from hitting the walls of the container. If this is allowed to happen, the fuel cannot be kept hot enough for the fusion reaction to occur. Farnsworth reasoned that he could build an electrostatic plasma confinement system in which the "wall" fields of the reactor were electrons or ions being held in place by the multipactor. Fuel could then be injected through the wall, and once inside it would be unable to escape. He called this concept a virtual electrode, and the system as a whole the fusor.

Design
Farnsworth's original fusor designs were based on cylindrical arrangements of electrodes, like the original multipactors. Fuel was ionized and then fired from small accelerators through holes in the outer (physical) electrodes. Once through the hole they were accelerated towards the inner reaction area at high velocity. Electrostatic pressure from the positively charged electrodes would keep the fuel as a whole off the walls of the chamber, and impacts from new ions would keep the hottest plasma in the center. He referred to this as inertial electrostatic confinement, a term that continues to be used to this day. The voltage between the electrodes needs to be at least 25 kV for fusion to occur.

Work at Farnsworth Television labs
All of this work had taken place at the Farnsworth Television labs, which had been purchased in 1949 by ITT Corporation, as part of its plan to become the next RCA. However, a fusion research project was not regarded as immediately profitable. In 1965, the board of directors started asking Harold Geneen to sell off the Farnsworth division, but he had his 1966 budget approved with funding until the middle of 1967. Further funding was refused, and that ended ITT's experiments with fusion.

Things changed dramatically with the arrival of Robert Hirsch, and the introduction of the modified Hirsch–Meeks fusor patent. New fusors based on Hirsch's design were first constructed between 1964 and 1967. Hirsch published his design in a paper in 1967. His design included ion beams to shoot ions into the vacuum chamber.

The team then turned to the AEC, then in charge of fusion research funding, and provided them with a demonstration device mounted on a serving cart that produced more fusion than any existing "classical" device. The observers were startled, but the timing was bad; Hirsch himself had recently revealed the great progress being made by the Soviets using the tokamak. In response to this surprising development, the AEC decided to concentrate funding on large tokamak projects, and reduce backing for alternative concepts.

Recent developments
George H. Miley at the University of Illinois reexamined the fusor and re-introduced it into the field. A low but steady interest in the fusor has persisted since. An important development was the successful commercial introduction of a fusor-based neutron generator. From 2006 until his death in 2007, Robert W. Bussard gave talks on a reactor similar in design to the fusor, now called the polywell, that he stated would be capable of useful power generation. Most recently, the fusor has gained popularity among amateurs, who choose them as home projects due to their relatively low space, money, and power requirements. An online community of "fusioneers", The Open Source Fusor Research Consortium, or Fusor.net, is dedicated to reporting developments in the world of fusors and aiding other amateurs in their projects. The site includes forums, articles and papers done on the fusor, including Farnsworth's original patent, as well as Hirsch's patent of his version of the invention.

Basic fusion

Nuclear fusion refers to reactions in which lighter nuclei are combined to become heavier nuclei. This process changes mass into energy which in turn may be captured to provide fusion power. Many types of atoms can be fused. The easiest to fuse are deuterium and tritium. For fusion to occur the ions must be at a temperature of at least 4 keV (kiloelectronvolts), or about 45 million kelvins. The second easiest reaction is fusing deuterium with itself. Because this gas is cheaper, it is the fuel commonly used by amateurs. The ease of doing a fusion reaction is measured by its cross section.

Net power
At such conditions, the atoms are ionized and make a plasma. The energy generated by fusion, inside a hot plasma cloud can be found with the following equation.

 * $$P_\text{fusion} = n_A n_B \langle \sigma v_{A,B} \rangle E_\text{fusion},$$

where
 * $$P_\text{fusion}$$ is the fusion power density (energy per time per volume),
 * n is the number density of species A or B (particles per volume),
 * $$\langle \sigma v_{A,B} \rangle$$ is the product of the collision cross-section σ (which depends on the relative velocity) and the relative velocity v of the two species, averaged over all the particle velocities in the system,
 * $$E_\text{fusion}$$ is the energy released by a single fusion reaction.

This equation shows that energy varies with the temperature, density, speed of collision, and fuel used. To reach net power, fusion reactions have to occur fast enough to make up for energy losses. Any power plant using fusion will hold in this hot cloud. Plasma clouds lose energy through conduction and radiation. Conduction is when ions, electrons or neutrals touch a surface and leak out. Energy is lost with the particle. Radiation is when energy leaves the cloud as light. Radiation increases as the temperature rises. To get net power from fusion it's necessary to overcome these losses. This leads to an equation for power output.

 * $$P_\text{out} = \eta_\text{capture} (P_\text{fusion} - P_\text{conduction} - P_\text{radiation}).$$

where:
 * η is the efficiency,
 * $$P_\text{conduction}$$ is the power of conduction losses as energy-laden mass leaves,
 * $$P_\text{radiation}$$ is the power of radiation losses as energy leaves as light,
 * $$P_\text{out}$$ is the net power from fusion.

John Lawson used this equation to estimate some conditions for net power based on a Maxwellian cloud. This became the Lawson criterion. Fusors typically suffer from conduction losses due to the wire cage being in the path of the recirculating plasma.

In fusors
In the original fusor design, several small particle accelerators, essentially TV tubes with the ends removed, inject ions at a relatively low voltage into a vacuum chamber. In the Hirsch version of the fusor, the ions are produced by ionizing a dilute gas in the chamber. In either version there are two concentric spherical electrodes, the inner one being charged negatively with respect to the outer one (to about 80 kV). Once the ions enter the region between the electrodes, they are accelerated towards the center.

In the fusor, the ions are accelerated to several keV by the electrodes, so heating as such is not necessary (as long as the ions fuse before losing their energy by any process). Whereas 45 megakelvins is a very high temperature by any standard, the corresponding voltage is only 4 kV, a level commonly found in such devices as neon signs and CRT televisions. To the extent that the ions remain at their initial energy, the energy can be tuned to take advantage of the peak of the reaction cross section or to avoid disadvantageous (for example neutron-producing) reactions that might occur at higher energies.

Various attempts have been made at increasing deuterium ionization rate, including heaters within "ion-guns", (similar to the "electron gun" which forms the basis for old-style television display tubes), as well as magnetron type devices, (which are the power sources for microwave ovens), which can enhance ion formation using high-voltage electromagnetic fields. Any method which increases ion density (within limits which preserve ion mean-free path), or ion energy, can be expected to enhance the fusion yield, typically measured in the number of neutrons produced per second. The ease with which the ion energy can be increased appears to be particularly useful when "high temperature" fusion reactions are considered, such as proton-boron fusion, which has plentiful fuel, requires no radioactive tritium, and produces no neutrons in the primary reaction.

Modes of operation

Fusors have at least two modes of operation (possibly more): star mode and halo mode. Halo mode is characterized by a broad symmetric glow, with one or two electron beams exiting the structure. There is little fusion. The halo mode occurs in higher pressure tanks, and as the vacuum improves, the device transitions to star mode. Star mode appears as bright beams of light emanating from the device center.

Power density
Because the electric field made by the cages is negative, it cannot simultaneously trap both positively charged ions and negative electrons. Hence, there must be some regions of charge accumulation, which will result in an upper limit on the achievable density. This could place an upper limit on the machine's power density, which may keep it too low for power production.

Thermalization of the ion velocities
When they first fall into the center of the fusor, the ions will all have the same energy, but the velocity distribution will rapidly approach a Maxwell–Boltzmann distribution. This would occur through simple Coulomb collisions in a matter of milliseconds, but beam-beam instabilities will occur orders of magnitude faster still. In comparison, any given ion will require a few minutes before undergoing a fusion reaction, so that the monoenergetic picture of the fusor, at least for power production, is not appropriate. One consequence of the thermalization is that some of the ions will gain enough energy to leave the potential well, taking their energy with them, without having undergone a fusion reaction.

Electrodes

There are a number of unsolved challenges with the electrodes in a fusor power system. To begin with, the electrodes cannot influence the potential within themselves, so it would seem at first glance that the fusion plasma would be in more or less direct contact with the inner electrode, resulting in contamination of the plasma and destruction of the electrode. However, the majority of the fusion tends to occur in microchannels formed in areas of minimum electric potential, seen as visible "rays" penetrating the core. These form because the forces within the region correspond to roughly stable "orbits". Approximately 40% of the high energy ions in a typical grid operating in star mode may be within these microchannels. Nonetheless, grid collisions remain the primary energy loss mechanism for Farnsworth–Hirsch fusors. Complicating issues is the challenge in cooling the central electrode; any fusor producing enough power to run a power plant seems destined to also destroy its inner electrode. As one fundamental limitation, any method which produces a neutron flux that is captured to heat a working fluid will also bombard its electrodes with that flux, heating them as well.

Attempts to resolve these problems include Bussard's Polywell system, D. C. Barnes' modified Penning trap approach, and the University of Illinois's fusor which retains grids but attempts to more tightly focus the ions into microchannels to attempt to avoid losses. While all three are Inertial electrostatic confinement (IEC) devices, only the last is actually a "fusor".

Radiation
Charged particles will radiate energy as light when they change velocity. This loss rate can be estimated for nonrelativistic particles using the Larmor formula. Inside a fusor there is a cloud of ions and electrons. These particles will accelerate or decelerate as they move about. These changes in speed make the cloud lose energy as light. The radiation from a fusor can (at least) be in the visible, ultraviolet and X-ray spectrum, depending on the type of fusor used. These changes in speed can be due to electrostatic interactions between particles (ion to ion, ion to electron, electron to electron). This is referred to bremsstrahlung radiation, and is common in fusors. Changes in speed can also be due to interactions between the particle and the electric field. Since there are no magnetic fields, fusors emit no cyclotron radiation at slow speeds, or synchrotron radiation at high speeds.

In Fundamental limitations on plasma fusion systems not in thermodynamic equilibrium, Todd Rider argues that a quasineutral isotropic plasma will lose energy due to Bremsstrahlung at a rate prohibitive for any fuel other than D-T (or possibly D-D or D-He3). This paper is not applicable to IEC fusion, as a quasineutral plasma cannot be contained by an electric field, which is a fundamental part of IEC fusion. However, in an earlier paper, "A general critique of inertial-electrostatic confinement fusion systems", Rider addresses the common IEC devices directly, including the fusor. In the case of the fusor the electrons are generally separated from the mass of the fuel isolated near the electrodes, which limits the loss rate. However, Rider demonstrates that practical fusors operate in a range of modes that either lead to significant electron mixing and losses, or alternately lower power densities. This appears to be a sort of catch-22 that limits the output of any fusor-like system.

Safety
There are several key safety considerations involved with the building and operation of a fusor. First, there is the high-voltage involved. Second, there are the x-ray and neutron emissions that are possible. Also there are the publicity / misinformation considerations with local and regulatory authorities.

Neutron source
The fusor has been demonstrated as a viable neutron source. Typical fusors cannot reach fluxes as high as nuclear reactor or particle accelerator sources, but are sufficient for many uses. Importantly, the neutron generator easily sits on a benchtop, and can be turned off at the flick of a switch. A commercial fusor was developed as a non-core business within DaimlerChrysler Aerospace – Space Infrastructure, Bremen between 1996 and early 2001. After the project was effectively ended, the former project manager established a company which is called NSD-Fusion. To date, the highest neutron flux achieved by a fusor-like device has been 3 × 1011 neutrons per second with the deuterium-deuterium fusion reaction.

Medical isotopes
Commercial startups have used the neutron fluxes generated by fusors to generate Mo-99, a precursor to Technetium-99m, an isotope used for medical care.

Patents

 * Bennett, W. H.,, February 1964. (Thermonuclear power).
 * P. T. Farnsworth,, June 1966 (Electric discharge — Nuclear interaction).
 * P. T. Farnsworth, . June 1968 (Method and apparatus).
 * Hirsch, Robert, . September 1970 (Apparatus).
 * Hirsch, Robert, . September 1970 (Generating apparatus — Hirsch/Meeks).
 * Hirsch, Robert, . October 1970 (Lithium-Ion source).
 * Hirsch, Robert, . April 1972 (Reduce plasma leakage).
 * P. T. Farnsworth, . May 1972 (Electrostatic containment).
 * R. W. Bussard, "Method and apparatus for controlling charged particles",, May 1989 (Method and apparatus — Magnetic grid fields).
 * R. W. Bussard, "Method and apparatus for creating and controlling nuclear fusion reactions",, November 1992 (Method and apparatus — Ion acoustic waves).

title: Fusor