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DNA profiling

DNA profiling (also called DNA fingerprinting and genetic fingerprinting) is the process of determining an individual's deoxyribonucleic acid (DNA) characteristics. DNA analysis intended to identify a species, rather than an individual, is called DNA barcoding.

DNA profiling is a forensic technique in criminal investigations, comparing criminal suspects' profiles to DNA evidence so as to assess the likelihood of their involvement in the crime. It is also used in paternity testing, to establish immigration eligibility, and in genealogical and medical research. DNA profiling has also been used in the study of animal and plant populations in the fields of zoology, botany, and agriculture.

Background
Starting in the 1980s, scientific advances allowed the use of DNA as a material for the identification of an individual. The first patent covering the direct use of DNA variation for forensics (US5593832A ) was filed by Jeffrey Glassberg in 1983, based upon work he had done while at Rockefeller University in the United States in 1981.

British geneticist Sir Alec Jeffreys independently developed a process for DNA profiling in 1985 while working in the Department of Genetics at the University of Leicester. Jeffreys discovered that a DNA examiner could establish patterns in unknown DNA. These patterns were a part of inherited traits that could be used to advance the field of relationship analysis. These discoveries lead to the first use of DNA profiling in a criminal case.

The process, developed by Jeffreys in conjunction with Peter Gill and Dave Werrett of the Forensic Science Service (FSS), was first used forensically in the solving of the murder of two teenagers who had been raped and murdered in Narborough, Leicestershire in 1983 and 1986. In the murder inquiry, led by Detective David Baker, the DNA contained within blood samples obtained voluntarily from around 5,000 local men who willingly assisted Leicestershire Constabulary with the investigation, resulted in the exoneration of Richard Buckland, an initial suspect who had confessed to one of the crimes, and the subsequent conviction of Colin Pitchfork on January 2, 1988. Pitchfork, a local bakery employee, had coerced his coworker Ian Kelly to stand in for him when providing a blood sample—Kelly then used a forged passport to impersonate Pitchfork. Another coworker reported the deception to the police. Pitchfork was arrested, and his blood was sent to Jeffreys' lab for processing and profile development. Pitchfork's profile matched that of DNA left by the murderer which confirmed Pitchfork's presence at both crime scenes; he pleaded guilty to both murders. After some years, a chemical company named Imperial Chemical Industries (ICI) introduced the first ever commercially available kit to the world. Despite being a relatively recent field, it had a significant global influence on both criminal justice system and society.

Although 99.9% of human DNA sequences are the same in every person, enough of the DNA is different that it is possible to distinguish one individual from another, unless they are monozygotic (identical) twins. DNA profiling uses repetitive sequences that are highly variable, called variable number tandem repeats (VNTRs), in particular short tandem repeats (STRs), also known as microsatellites, and minisatellites. VNTR loci are similar between closely related individuals, but are so variable that unrelated individuals are unlikely to have the same VNTRs.

Before VNTRs and STRs, people like Jeffreys used a process called Restriction Fragment Length Polymorphism (RFLP). This process regularly used large portions of DNA to analyze the differences between two DNA samples. RFLP was among the first technologies used in DNA profiling and analysis. However, as technology has evolved, new technologies, like STR, emerged and took the place of older technology like RFLP.

The admissibility of DNA evidence in courts was disputed in the United States in the 1980s and 1990s, but has since become more universally accepted due to improved techniques.

DNA extraction
When a sample such as blood or saliva is obtained, the DNA is only a small part of what is present in the sample. Before the DNA can be analyzed, it must be extracted from the cells and purified. There are many ways this can be accomplished, but all methods follow the same basic procedure. The cell and nuclear membranes need to be broken up to allow the DNA to be free in solution. Once the DNA is free, it can be separated from all other cellular components. After the DNA has been separated in solution, the remaining cellular debris can then be removed from the solution and discarded, leaving only DNA. The most common methods of DNA extraction include organic extraction (also called phenol chloroform extraction), Chelex extraction, and solid phase extraction. Differential extraction is a modified version of extraction in which DNA from two different types of cells can be separated from each other before being purified from the solution. Each method of extraction works well in the laboratory, but analysts typically select their preferred method based on factors such as the cost, the time involved, the quantity of DNA yielded, and the quality of DNA yielded.

RFLP analysis
RFLP stands for restriction fragment length polymorphism and, in terms of DNA analysis, describes a DNA testing method which utilizes restriction enzymes to "cut" the DNA at short and specific sequences throughout the sample. To start off processing in the laboratory, the sample has to first go through an extraction protocol, which may vary depending on the sample type or laboratory SOPs (Standard Operating Procedures). Once the DNA has been "extracted" from the cells within the sample and separated away from extraneous cellular materials and any nucleases that would degrade the DNA, the sample can then be introduced to the desired restriction enzymes to be cut up into discernable fragments. Following the enzyme digestion, a Southern Blot is performed. Southern Blots are a size-based separation method that are performed on a gel with either radioactive or chemiluminescent probes. RFLP could be conducted with single-locus or multi-locus probes (probes which target either one location on the DNA or multiple locations on the DNA). Incorporating the multi-locus probes allowed for higher discrimination power for the analysis, however completion of this process could take several days to a week for one sample due to the extreme amount of time required by each step required for visualization of the probes.

Polymerase chain reaction (PCR) analysis
The technique was developed in 1983 by Kary Mullis, PCR is now a common and important technique used in medical and biological research labs for a variety of applications.

PCR, or Polymerase Chain Reaction, is a widely used molecular biology technique to amplify a specific DNA sequence. Amplification is achieved by a series of three steps:

1- Denaturation : In this step, the DNA is heated to 95 °C to dissociate the hydrogen bonds between the complementary base pairs of the double-stranded DNA.

2-Annealing : During this stage the reaction is cooled to 50-65 °C. This enables the primers to attach to a specific location on the single -stranded template DNA by way of hydrogen bonding.

3-Extension : A thermostable DNA polymerase which is Taq polymerase is commonly used at this step. This is done at a temperature of 72 °C. DNA polymerase adds nucleotides in the 5'-3' direction and synthesizes the complementary strand of the DNA template.

STR analysis

The system of DNA profiling used today is based on polymerase chain reaction (PCR) and uses simple sequences.

From country to country, different STR-based DNA-profiling systems are in use. In North America, systems that amplify the CODIS 20 core loci are almost universal, whereas in the United Kingdom the DNA-17 loci system is in use, and Australia uses 18 core markers.

The true power of STR analysis is in its statistical power of discrimination. Because the 20 loci that are currently used for discrimination in CODIS are independently assorted (having a certain number of repeats at one locus does not change the likelihood of having any number of repeats at any other locus), the product rule for probabilities can be applied. This means that, if someone has the DNA type of ABC, where the three loci were independent, then the probability of that individual having that DNA type is the probability of having type A times the probability of having type B times the probability of having type C. This has resulted in the ability to generate match probabilities of 1 in a quintillion (1x1018) or more. However, DNA database searches showed much more frequent than expected false DNA profile matches.

Y-chromosome analysis
Due to the paternal inheritance, Y-haplotypes provide information about the genetic ancestry of the male population. To investigate this population history, and to provide estimates for haplotype frequencies in criminal casework, the "Y haplotype reference database (YHRD)" has been created in 2000 as an online resource. It currently comprises more than 300,000 minimal (8 locus) haplotypes from world-wide populations.

Mitochondrial analysis
mtDNA can be obtained from such material as hair shafts and old bones/teeth. Control mechanism based on interaction point with data. This can be determined by tooled placement in sample.

Issues with forensic DNA samples
When people think of DNA analysis, they often think about television shows like NCIS or CSI, which portray DNA samples coming into a lab and being instantly analyzed, followed by the pulling up of a picture of the suspect within minutes. However, the reality is quite different, and perfect DNA samples are often not collected from the scene of a crime. Homicide victims are frequently left exposed to harsh conditions before they are found, and objects that are used to commit crimes have often been handled by more than one person. The two most prevalent issues that forensic scientists encounter when analyzing DNA samples are degraded samples and DNA mixtures.

Degraded DNA
Before modern PCR methods existed, it was almost impossible to analyze degraded DNA samples. Methods like Restriction fragment length polymorphism (RFLP), which was the first technique used for DNA analysis in forensic science, required high molecular weight DNA in the sample in order to get reliable data. High molecular weight DNA, however, is lacking in degraded samples, as the DNA is too fragmented to carry out RFLP accurately. It was only when Polymerase Chain Reaction techniques were invented that analysis of degraded DNA samples were able to be carried out. Multiplex PCR in particular made it possible to isolate and to amplify the small fragments of DNA that are still left in degraded samples. When multiplex PCR methods are compared to the older methods like RFLP, a vast difference can be seen. Multiplex PCR can theoretically amplify less than 1 ng of DNA, but RFLP had to have a least 100 ng of DNA in order to carry out an analysis.

Low-Template DNA
Low-template DNA can happen when there is less than 0.1 ng of DNA in a sample. This can lead to more stochastic effects (random events) such as allelic dropout or allelic drop-in which can alter the interpretation of a DNA profile. These stochastic effects can lead to the unequal amplification of the 2 alleles that come from a heterozygous individual. It is especially important to take low-template DNA into account when dealing with a mixture of DNA sample. This is because for one (or more) of the contributors in the mixture, they are more likely to have less than the optimal amount of DNA for the PCR reaction to work properly. Therefore, stochastic thresholds are developed for DNA profile interpretation. The stochastic threshold is the minimum peak height (RFU value), seen in an electropherogram where dropout occurs. If the peak height value is above this threshold, then it is reasonable to assume that allelic dropout has not occurred. For example, if only 1 peak is seen for a particular locus in the electropherogram but its peak height is above the stochastic threshold, then we can reasonably assume that this individual is homozygous and is not missing its heterozygous partner allele that otherwise would have dropped out due to having low-template DNA. Allelic dropout can occur when there is low-template DNA because there is such little DNA to start with that at this locus the contributor to the DNA sample (or mixture) is a true heterozygote but the other allele is not amplified and so it would be lost. Allelic drop-in can also occur when there is low-template DNA because sometimes the stutter peak can be amplified. The stutter is an artifact of PCR. During the PCR reaction, DNA Polymerase will come in and add nucleotides off of the primer, but this whole process is very dynamic, meaning that the DNA Polymerase is constantly binding, popping off and then rebinding. Therefore, sometimes DNA Polymerase will rejoin at the short tandem repeat ahead of it, leading to a short tandem repeat that is 1 repeat less than the template. During PCR, if DNA Polymerase happens to bind to a locus in stutter and starts to amplify it to make lots of copies, then this stutter product will appear randomly in the electropherogram, leading to allelic drop-in.

MiniSTR analysis
In instances in which DNA samples are degraded, like if there are intense fires or all that remains are bone fragments, standard STR testing on those samples can be inadequate. When standard STR testing is done on highly degraded samples, the larger STR loci often drop out, and only partial DNA profiles are obtained. Partial DNA profiles can be a powerful tool, but the probability of a random match is larger than if a full profile was obtained. One method that has been developed to analyse degraded DNA samples is to use miniSTR technology. In the new approach, primers are specially designed to bind closer to the STR region.

In normal STR testing, the primers bind to longer sequences that contain the STR region within the segment. MiniSTR analysis, however, targets only the STR location, which results in a DNA product that is much smaller.

By placing the primers closer to the actual STR regions, there is a higher chance that successful amplification of this region will occur. Successful amplification of those STR regions can now occur, and more complete DNA profiles can be obtained. The success that smaller PCR products produce a higher success rate with highly degraded samples was first reported in 1995, when miniSTR technology was used to identify victims of the Waco fire.

DNA mixtures
Mixtures are another common issue faced by forensic scientists when they are analyzing unknown or questionable DNA samples. A mixture is defined as a DNA sample that contains two or more individual contributors. That can often occur when a DNA sample is swabbed from an item that is handled by more than one person or when a sample contains both the victim's and the assailant's DNA. The presence of more than one individual in a DNA sample can make it challenging to detect individual profiles, and interpretation of mixtures should be performed only by highly trained individuals. Mixtures that contain two or three individuals can be interpreted with difficulty. Mixtures that contain four or more individuals are much too convoluted to get individual profiles. One common scenario in which a mixture is often obtained is in the case of sexual assault. A sample may be collected that contains material from the victim, the victim's consensual sexual partners, and the perpetrator(s).

Mixtures can generally be sorted into three categories: Type A, Type B, and Type C. Type A mixtures have alleles with similar peak-heights all around, so the contributors cannot be distinguished from each other. Type B mixtures can be deconvoluted by comparing peak-height ratios to determine which alleles were donated together. Type C mixtures cannot be safely interpreted with current technology because the samples were affected by DNA degradation or having too small a quantity of DNA present.

When looking at an electropherogram, it is possible to determine the number of contributors in less complex mixtures based on the number of peaks located in each locus. In comparison to a single source profile, which will only have one or two peaks at each locus, a mixture is when there are three or more peaks at two or more loci. If there are three peaks at only a single locus, then it is possible to have a single contributor who is tri-allelic at that locus. Two person mixtures will have between two and four peaks at each locus, and three person mixtures will have between three and six peaks at each locus. Mixtures become increasingly difficult to deconvolute as the number of contributors increases.

As detection methods in DNA profiling advance, forensic scientists are seeing more DNA samples that contain mixtures, as even the smallest contributor can now be detected by modern tests. The ease in which forensic scientists have in interpenetrating DNA mixtures largely depends on the ratio of DNA present from each individual, the genotype combinations, and the total amount of DNA amplified. The DNA ratio is often the most important aspect to look at in determining whether a mixture can be interpreted. For example, if a DNA sample had two contributors, it would be easy to interpret individual profiles if the ratio of DNA contributed by one person was much higher than the second person. When a sample has three or more contributors, it becomes extremely difficult to determine individual profiles. Fortunately, advancements in probabilistic genotyping may make that sort of determination possible in the future. Probabilistic genotyping uses complex computer software to run through thousands of mathematical computations to produce statistical likelihoods of individual genotypes found in a mixture.

DNA profiling in plant:

Plant DNA profiling (fingerprinting) is a method for identifying cultivars that uses molecular marker techniques. This method is gaining attention due to Trade Related Intellectual property rights (TRIPs) and the Convention on Biological Diversity (CBD).

 Advantages of Plant DNA profiling:

Identification, authentication, specific distinction, detecting adulteration and identifying phytoconstituents are all possible with DNA fingerprinting in medical plants.

DNA based markers are critical for these applications, determining the future of scientific study in pharmacognosy.

It also helps with determining the traits (such as seed size and leaf color) are likely to improve the offspring or not.

DNA databases
An early application of a DNA database was the compilation of a Mitochondrial DNA Concordance, prepared by Kevin W. P. Miller and John L. Dawson at the University of Cambridge from 1996 to 1999 from data collected as part of Miller's PhD thesis. There are now several DNA databases in existence around the world. Some are private, but most of the largest databases are government-controlled. The United States maintains the largest DNA database, with the Combined DNA Index System (CODIS) holding over 13 million records as of May 2018. The United Kingdom maintains the National DNA Database (NDNAD), which is of similar size, despite the UK's smaller population. The size of this database, and its rate of growth, are giving concern to civil liberties groups in the UK, where police have wide-ranging powers to take samples and retain them even in the event of acquittal. The Conservative–Liberal Democrat coalition partially addressed these concerns with part 1 of the Protection of Freedoms Act 2012, under which DNA samples must be deleted if suspects are acquitted or not charged, except in relation to certain (mostly serious or sexual) offenses. Public discourse around the introduction of advanced forensic techniques (such as genetic genealogy using public genealogy databases and DNA phenotyping approaches) has been limited, disjointed, unfocused, and raises issues of privacy and consent that may warrant the establishment of additional legal protections.

The U.S. Patriot Act of the United States provides a means for the U.S. government to get DNA samples from suspected terrorists. DNA information from crimes is collected and deposited into the CODIS database, which is maintained by the FBI. CODIS enables law enforcement officials to test DNA samples from crimes for matches within the database, providing a means of finding specific biological profiles associated with collected DNA evidence.

When a match is made from a national DNA databank to link a crime scene to an offender having provided a DNA sample to a database, that link is often referred to as a cold hit. A cold hit is of value in referring the police agency to a specific suspect but is of less evidential value than a DNA match made from outside the DNA Databank.

FBI agents cannot legally store DNA of a person not convicted of a crime. DNA collected from a suspect not later convicted must be disposed of and not entered into the database. In 1998, a man residing in the UK was arrested on accusation of burglary. His DNA was taken and tested, and he was later released. Nine months later, this man's DNA was accidentally and illegally entered in the DNA database. New DNA is automatically compared to the DNA found at cold cases and, in this case, this man was found to be a match to DNA found at a rape and assault case one year earlier. The government then prosecuted him for these crimes. During the trial the DNA match was requested to be removed from the evidence because it had been illegally entered into the database. The request was carried out. The DNA of the perpetrator, collected from victims of rape, can be stored for years until a match is found. In 2014, to address this problem, Congress extended a bill that helps states deal with "a backlog" of evidence.

 DNA profiling databases in Plants:

 PIDS:

PIDS(Plant international DNA-fingerprinting system) is an open source web server and free software based plant international DNA fingerprinting system.

It manages huge amount of microsatellite DNA fingerprint data, performs genetic studies, and automates collection, storage and maintenance while decreasing human error and increasing efficiency.

The system may be tailored to specific laboratory needs, making it a valuable tool for plant breeders, forensic science, and human fingerprint recognition.

It keeps track of experiments, standardizes data and promotes inter-database communication.

It also helps with the regulation of variety quality, the preservation of variety rights and the use of molecular markers in breeding by providing location statistics, merging, comparison and genetic analysis function.

Considerations in evaluating DNA evidence
When using RFLP, the theoretical risk of a coincidental match is 1 in 100 billion (100,000,000,000) although the practical risk is actually 1 in 1,000 because monozygotic twins are 0.2% of the human population. Moreover, the rate of laboratory error is almost certainly higher than that and actual laboratory procedures often do not reflect the theory under which the coincidence probabilities were computed. For example, coincidence probabilities may be calculated based on the probabilities that markers in two samples have bands in precisely the same location, but a laboratory worker may conclude that similar but not precisely-identical band patterns result from identical genetic samples with some imperfection in the agarose gel. However, in that case, the laboratory worker increases the coincidence risk by expanding the criteria for declaring a match. Studies conducted in the 2000s quoted relatively-high error rates, which may be cause for concern. In the early days of genetic fingerprinting, the necessary population data to compute a match probability accurately was sometimes unavailable. Between 1992 and 1996, arbitrary-low ceilings were controversially put on match probabilities used in RFLP analysis, rather than the higher theoretically computed ones.

Evidence of genetic relationship
It is possible to use DNA profiling as evidence of genetic relationship although such evidence varies in strength from weak to positive. Testing that shows no relationship is absolutely certain. Further, while almost all individuals have a single and distinct set of genes, ultra-rare individuals, known as "chimeras", have at least two different sets of genes. There have been two cases of DNA profiling that falsely suggested that a mother was unrelated to her children.

Fake DNA evidence
The functional analysis of genes and their coding sequences (open reading frames [ORFs]) typically requires that each ORF be expressed, the encoded protein purified, antibodies produced, phenotypes examined, intracellular localization determined, and interactions with other proteins sought. In a study conducted by the life science company Nucleix and published in the journal Forensic Science International, scientists found that an in vitro synthesized sample of DNA matching any desired genetic profile can be constructed using standard molecular biology techniques without obtaining any actual tissue from that person.

Familial DNA searching
Familial DNA searching (sometimes referred to as "familial DNA" or "familial DNA database searching") is the practice of creating new investigative leads in cases where DNA evidence found at the scene of a crime (forensic profile) strongly resembles that of an existing DNA profile (offender profile) in a state DNA database but there is not an exact match. After all other leads have been exhausted, investigators may use specially developed software to compare the forensic profile to all profiles taken from a state's DNA database to generate a list of those offenders already in the database who are most likely to be a very close relative of the individual whose DNA is in the forensic profile.

Familial DNA database searching was first used in an investigation leading to the conviction of Jeffrey Gafoor of the murder of Lynette White in the United Kingdom on 4 July 2003. DNA evidence was matched to Gafoor's nephew, who at 14 years old had not been born at the time of the murder in 1988. It was used again in 2004 to find a man who threw a brick from a motorway bridge and hit a lorry driver, killing him. DNA found on the brick matched that found at the scene of a car theft earlier in the day, but there were no good matches on the national DNA database. A wider search found a partial match to an individual; on being questioned, this man revealed he had a brother, Craig Harman, who lived very close to the original crime scene. Harman voluntarily submitted a DNA sample, and confessed when it matched the sample from the brick. As of 2011, familial DNA database searching is not conducted on a national level in the United States, where states determine how and when to conduct familial searches. The first familial DNA search with a subsequent conviction in the United States was conducted in Denver, Colorado, in 2008, using software developed under the leadership of Denver District Attorney Mitch Morrissey and Denver Police Department Crime Lab Director Gregg LaBerge. California was the first state to implement a policy for familial searching under then-Attorney General Jerry Brown, who later became Governor. In his role as consultant to the Familial Search Working Group of the California Department of Justice, former Alameda County Prosecutor Rock Harmon is widely considered to have been the catalyst in the adoption of familial search technology in California. The technique was used to catch the Los Angeles serial killer known as the "Grim Sleeper" in 2010. It was not a witness or informant that tipped off law enforcement to the identity of the "Grim Sleeper" serial killer, who had eluded police for more than two decades, but DNA from the suspect's own son. The suspect's son had been arrested and convicted in a felony weapons charge and swabbed for DNA the year before. When his DNA was entered into the database of convicted felons, detectives were alerted to a partial match to evidence found at the "Grim Sleeper" crime scenes. David Franklin Jr., also known as the Grim Sleeper, was charged with ten counts of murder and one count of attempted murder. More recently, familial DNA led to the arrest of 21-year-old Elvis Garcia on charges of sexual assault and false imprisonment of a woman in Santa Cruz in 2008. In March 2011 Virginia Governor Bob McDonnell announced that Virginia would begin using familial DNA searches.

At a press conference in Virginia on 7 March 2011, regarding the East Coast Rapist, Prince William County prosecutor Paul Ebert and Fairfax County Police Detective John Kelly said the case would have been solved years ago if Virginia had used familial DNA searching. Aaron Thomas, the suspected East Coast Rapist, was arrested in connection with the rape of 17 women from Virginia to Rhode Island, but familial DNA was not used in the case.

Critics of familial DNA database searches argue that the technique is an invasion of an individual's 4th Amendment rights. Privacy advocates are petitioning for DNA database restrictions, arguing that the only fair way to search for possible DNA matches to relatives of offenders or arrestees would be to have a population-wide DNA database. Some scholars have pointed out that the privacy concerns surrounding familial searching are similar in some respects to other police search techniques, and most have concluded that the practice is constitutional. The Ninth Circuit Court of Appeals in United States v. Pool (vacated as moot) suggested that this practice is somewhat analogous to a witness looking at a photograph of one person and stating that it looked like the perpetrator, which leads law enforcement to show the witness photos of similar looking individuals, one of whom is identified as the perpetrator.

Critics also state that racial profiling could occur on account of familial DNA testing. In the United States, the conviction rates of racial minorities are much higher than that of the overall population. It is unclear whether this is due to discrimination from police officers and the courts, as opposed to a simple higher rate of offence among minorities. Arrest-based databases, which are found in the majority of the United States, lead to an even greater level of racial discrimination. An arrest, as opposed to conviction, relies much more heavily on police discretion.

For instance, investigators with Denver District Attorney's Office successfully identified a suspect in a property theft case using a familial DNA search. In this example, the suspect's blood left at the scene of the crime strongly resembled that of a current Colorado Department of Corrections prisoner.

Partial matches
Partial DNA matches are the result of moderate stringency CODIS searches that produce a potential match that shares at least one allele at every locus. Partial matching does not involve the use of familial search software, such as those used in the United Kingdom and the United States, or additional Y-STR analysis and therefore often misses sibling relationships. Partial matching has been used to identify suspects in several cases in both countries and has also been used as a tool to exonerate the falsely accused. Darryl Hunt was wrongly convicted in connection with the rape and the murder of a young woman in 1984 in North Carolina.

Surreptitious DNA collecting
Police forces may collect DNA samples without a suspect's knowledge, and use it as evidence. The legality of the practice has been questioned in Australia.

In the United States, where it has been accepted, courts often rule that there is no expectation of privacy and cite California v. Greenwood (1988), in which the Supreme Court held that the Fourth Amendment does not prohibit the warrantless search and seizure of garbage left for collection outside the curtilage of a home. Critics of this practice underline that this analogy ignores that "most people have no idea that they risk surrendering their genetic identity to the police by, for instance, failing to destroy a used coffee cup. Moreover, even if they do realize it, there is no way to avoid abandoning one's DNA in public."

The United States Supreme Court ruled in Maryland v. King (2013) that DNA sampling of prisoners arrested for serious crimes is constitutional.

In the United Kingdom, the Human Tissue Act 2004 prohibits private individuals from covertly collecting biological samples (hair, fingernails, etc.) for DNA analysis but exempts medical and criminal investigations from the prohibition.

England and Wales
Evidence from an expert who has compared DNA samples must be accompanied by evidence as to the sources of the samples and the procedures for obtaining the DNA profiles. The judge must ensure that the jury must understand the significance of DNA matches and mismatches in the profiles. The judge must also ensure that the jury does not confuse the match probability (the probability that a person that is chosen at random has a matching DNA profile to the sample from the scene) with the probability that a person with matching DNA committed the crime. In 1996 R v. Doheny

Juries should weigh up conflicting and corroborative evidence, using their own common sense and not by using mathematical formulae, such as Bayes' theorem, so as to avoid "confusion, misunderstanding and misjudgment".

Presentation and evaluation of evidence of partial or incomplete DNA profiles
In R v Bates, Moore-Bick LJ said:

"We can see no reason why partial profile DNA evidence should not be admissible provided that the jury are made aware of its inherent limitations and are given a sufficient explanation to enable them to evaluate it. There may be cases where the match probability in relation to all the samples tested is so great that the judge would consider its probative value to be minimal and decide to exclude the evidence in the exercise of his discretion, but this gives rise to no new question of principle and can be left for decision on a case by case basis. However, the fact that there exists in the case of all partial profile evidence the possibility that a 'missing' allele might exculpate the accused altogether does not provide sufficient grounds for rejecting such evidence. In many there is a possibility (at least in theory) that evidence that would assist the accused and perhaps even exculpate him altogether exists, but that does not provide grounds for excluding relevant evidence that is available and otherwise admissible, though it does make it important to ensure that the jury are given sufficient information to enable them to evaluate that evidence properly."

DNA testing in the United States
There are state laws on DNA profiling in all 50 states of the United States. Detailed information on database laws in each state can be found at the National Conference of State Legislatures website.

Development of artificial DNA
In August 2009, scientists in Israel raised serious doubts concerning the use of DNA by law enforcement as the ultimate method of identification. In a paper published in the journal Forensic Science International: Genetics, the Israeli researchers demonstrated that it is possible to manufacture DNA in a laboratory, thus falsifying DNA evidence. The scientists fabricated saliva and blood samples, which originally contained DNA from a person other than the supposed donor of the blood and saliva.

The researchers also showed that, using a DNA database, it is possible to take information from a profile and manufacture DNA to match it, and that this can be done without access to any actual DNA from the person whose DNA they are duplicating. The synthetic DNA oligos required for the procedure are common in molecular laboratories.

The New York Times quoted the lead author, Daniel Frumkin, saying, "You can just engineer a crime scene ... any biology undergraduate could perform this". Frumkin perfected a test that can differentiate real DNA samples from fake ones. His test detects epigenetic modifications, in particular, DNA methylation. Seventy percent of the DNA in any human genome is methylated, meaning it contains methyl group modifications within a CpG dinucleotide context. Methylation at the promoter region is associated with gene silencing. The synthetic DNA lacks this epigenetic modification, which allows the test to distinguish manufactured DNA from genuine DNA.

It is unknown how many police departments, if any, currently use the test. No police lab has publicly announced that it is using the new test to verify DNA results.

Researchers at the University of Tokyo integrated an artificial DNA replication scheme with a rebuilt gene expression system and micro-compartmentalization utilizing cell-free materials alone for the first time. Multiple cycles of serial dilution were performed on a system contained in microscale water-in-oil droplets.

Chances of making DNA change on purpose

Overall, this study's artificial genomic DNA, which kept copying itself using self-encoded proteins and made its sequence better on its own, is a good starting point for making more complex artificial cells. By adding the genes needed for transcription and translation to artificial genomic DNA, it may be possible in the future to make artificial cells that can grow on their own when fed small molecules like amino acids and nucleotides. Using living organisms to make useful things, like drugs and food, would be more stable and easier to control in these artificial cells.

On July 7, 2008, the American chemical society reported that Japanese chemists have created the world's first DNA molecule comprised nearly completely of synthetic components.

A nano-particle based artificial transcription factor for gene regulation:

Nano Script is a nanoparticle-based artificial transcription factor that is supposed to replicate the structure and function of TFs. On gold nanoparticles, functional peptides and tiny molecules referred to as synthetic transcription factors, which imitate the various TF domains, were attached to create Nano Script. We show that Nano Script localizes to the nucleus and begins transcription of a reporter plasmid by an amount more than 15-fold. Moreover, Nano Script can successfully transcribe targeted genes onto endogenous DNA in a nonviral manner.

Three different fluorophores—red, green, and blue—were carefully fixed on the DNA rod surface to provide spatial information and create a nanoscale barcode. Epifluorescence and total internal reflection fluorescence microscopy reliably deciphered spatial information between fluorophores. By moving the three fluorophores on the DNA rod, this nanoscale barcode created 216 fluorescence patterns.

Cases

 * In 1986, Richard Buckland was exonerated, despite having admitted to the rape and murder of a teenager near Leicester, the city where DNA profiling was first developed. This was the first use of DNA fingerprinting in a criminal investigation, and the first to prove a suspect's innocence. The following year Colin Pitchfork was identified as the perpetrator of the same murder, in addition to another, using the same techniques that had cleared Buckland.
 * In 1987, genetic fingerprinting was used in a US criminal court for the first time in the trial of a man accused of unlawful intercourse with a mentally disabled 14-year-old female who gave birth to a baby.
 * In 1987, Florida rapist Tommie Lee Andrews was the first person in the United States to be convicted as a result of DNA evidence, for raping a woman during a burglary; he was convicted on 6 November 1987, and sentenced to 22 years in prison.
 * In 1990, a violent murder of a young student in Brno was the first criminal case in Czechoslovakia solved by DNA evidence, with the murderer sentenced to 23 years in prison.
 * In 1992, DNA from a palo verde tree was used to convict Mark Alan Bogan of murder. DNA from seed pods of a tree at the crime scene was found to match that of seed pods found in Bogan's truck. This is the first instance of plant DNA admitted in a criminal case.
 * In 1994, the claim that Anna Anderson was Grand Duchess Anastasia Nikolaevna of Russia was tested after her death using samples of her tissue that had been stored at a Charlottesville hospital following a medical procedure. The tissue was tested using DNA fingerprinting, and showed that she bore no relation to the Romanovs.
 * In 1994, Earl Washington, Jr., of Virginia had his death sentence commuted to life imprisonment a week before his scheduled execution date based on DNA evidence. He received a full pardon in 2000 based on more advanced testing.
 * In 1999, Raymond Easton, a disabled man from Swindon, England, was arrested and detained for seven hours in connection with a burglary. He was released due to an inaccurate DNA match. His DNA had been retained on file after an unrelated domestic incident some time previously.
 * In 2000 Frank Lee Smith was proved innocent by DNA profiling of the murder of an eight-year-old girl after spending 14 years on death row in Florida, USA. However he had died of cancer just before his innocence was proven. In view of this the Florida state governor ordered that in future any death row inmate claiming innocence should have DNA testing.
 * In May 2000 Gordon Graham murdered Paul Gault at his home in Lisburn, Northern Ireland. Graham was convicted of the murder when his DNA was found on a sports bag left in the house as part of an elaborate ploy to suggest the murder occurred after a burglary had gone wrong. Graham was having an affair with the victim's wife at the time of the murder. It was the first time Low Copy Number DNA was used in Northern Ireland.
 * In 2001, Wayne Butler was convicted for the murder of Celia Douty. It was the first murder in Australia to be solved using DNA profiling.
 * In 2002, the body of James Hanratty, hanged in 1962 for the "A6 murder", was exhumed and DNA samples from the body and members of his family were analysed. The results convinced Court of Appeal judges that Hanratty's guilt, which had been strenuously disputed by campaigners, was proved "beyond doubt". Paul Foot and some other campaigners continued to believe in Hanratty's innocence and argued that the DNA evidence could have been contaminated, noting that the small DNA samples from items of clothing, kept in a police laboratory for over 40 years "in conditions that do not satisfy modern evidential standards", had had to be subjected to very new amplification techniques in order to yield any genetic profile. However, no DNA other than Hanratty's was found on the evidence tested, contrary to what would have been expected had the evidence indeed been contaminated.
 * In August 2002, Annalisa Vicentini was shot dead in Tuscany. Bartender Peter Hamkin, 23, was arrested, in Merseyside in March 2003 on an extradition warrant heard at Bow Street Magistrates' Court in London to establish whether he should be taken to Italy to face a murder charge. DNA "proved" he shot her, but he was cleared on other evidence.
 * In 2003, Welshman Jeffrey Gafoor was convicted of the 1988 murder of Lynette White, when crime scene evidence collected 12 years earlier was re-examined using STR techniques, resulting in a match with his nephew.
 * In June 2003, because of new DNA evidence, Dennis Halstead, John Kogut and John Restivo won a re-trial on their murder conviction, their convictions were struck down and they were released.
 * In 2004, DNA testing shed new light into the mysterious 1912 disappearance of Bobby Dunbar, a four-year-old boy who vanished during a fishing trip. He was allegedly found alive eight months later in the custody of William Cantwell Walters, but another woman claimed that the boy was her son, Bruce Anderson, whom she had entrusted in Walters' custody. The courts disbelieved her claim and convicted Walters for the kidnapping. The boy was raised and known as Bobby Dunbar throughout the rest of his life. However, DNA tests on Dunbar's son and nephew revealed the two were not related, thus establishing that the boy found in 1912 was not Bobby Dunbar, whose real fate remains unknown.
 * In 2005, Gary Leiterman was convicted of the 1969 murder of Jane Mixer, a law student at the University of Michigan, after DNA found on Mixer's pantyhose was matched to Leiterman. DNA in a drop of blood on Mixer's hand was matched to John Ruelas, who was only four years old in 1969 and was never successfully connected to the case in any other way. Leiterman's defense unsuccessfully argued that the unexplained match of the blood spot to Ruelas pointed to cross-contamination and raised doubts about the reliability of the lab's identification of Leiterman.
 * In November 2008, Anthony Curcio was arrested for masterminding one of the most elaborately planned armored car heists in history. DNA evidence linked Curcio to the crime.
 * In March 2009, Sean Hodgson—convicted of 1979 killing of Teresa De Simone, 22, in her car in Southampton—was released after tests proved DNA from the scene was not his. It was later matched to DNA retrieved from the exhumed body of David Lace. Lace had previously confessed to the crime but was not believed by the detectives. He served time in prison for other crimes committed at the same time as the murder and then committed suicide in 1988.
 * In 2012, a case of babies being switched, many decades earlier, was discovered by accident. After undertaking DNA testing for other purposes, Alice Collins Plebuch was advised that her ancestry appeared to include a significant Ashkenazi Jewish component, despite a belief in her family that they were of predominantly Irish descent. Profiling of Plebuch's genome suggested that it included distinct and unexpected components associated with Ashkenazi, Middle Eastern, and Eastern European populations. This led Plebuch to conduct an extensive investigation, after which she concluded that her father had been switched (possibly accidentally) with another baby soon after birth. Plebuch was also able to identify the biological ancestors of her father.
 * In 2016 Anthea Ring, abandoned as a baby, was able to use a DNA sample and DNA matching database to discover her deceased mother's identity and roots in County Mayo, Ireland. A recently developed forensic test was subsequently used to capture DNA from saliva left on old stamps and envelopes by her suspected father, uncovered through painstaking genealogy research. The DNA in the first three samples was too degraded to use. However, on the fourth, more than enough DNA was found. The test, which has a degree of accuracy acceptable in UK courts, proved that a man named Patrick Coyne was her biological father.
 * In 2018 the Buckskin girl (a body found in 1981 in Ohio) was identified as Marcia King from Arkansas using DNA genealogical techniques
 * In 2018 Joseph James DeAngelo was arrested as the main suspect for the Golden State Killer using DNA and genealogy techniques.
 * In 2018, William Earl Talbott II was arrested as a suspect for the 1987 murders of Jay Cook and Tanya Van Cuylenborg with the assistance of genealogical DNA testing. The same genetic genealogist that helped in this case also helped police with 18 other arrests in 2018.
 * In 2018, With the use of Next Generation Identification System's enhanced biometric capabilities, the FBI matched the fingerprint of a suspect named Timothy David Nelson and arrested him 20 years after the alleged sexual assault.

DNA evidence as evidence to prove rights of succession to British titles
DNA testing has been used to establish the right of succession to British titles.

Cases:
 * Baron Moynihan
 * Pringle baronets

title: DNA profiling


text:
Second Amendment Sisters

Second Amendment Sisters, Inc. (SAS) was a United States women's gun rights advocacy group that supported gun use for self defense and empowerment. According to a 2003 Los Angeles Times article, SAS was founded in December 1999 by five women who were "outraged" by the Million Mom March. The national organization closed in 2015, though individual state chapters continue to operate independently.

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

title: Second Amendment Sisters


text:
Alec Jeffreys

Sir Alec John Jeffreys, (born 9 January 1950) is a British geneticist known for developing techniques for genetic fingerprinting and DNA profiling which are now used worldwide in forensic science to assist police detective work and to resolve paternity and immigration disputes.

Jeffreys is Professor of Genetics at the University of Leicester, and became an honorary freeman of the City of Leicester on 26 November 1992. In 1994, he was knighted by Queen Elizabeth II for services to genetics.

Early life and education
Jeffreys was born into a middle-class family in Oxford, where he spent the first six years of his life until 1956 when the family moved to Luton, Bedfordshire. He says he inherited his curiosity and inventiveness from his father and paternal grandfather, who held a number of patents. When he was eight, his father gave him a chemistry set, which he enhanced over the next few years with extra chemicals, even including a small bottle of sulphuric acid. He says he liked making small explosions, but an accidental splash of the sulphuric acid caused a burn, which left a permanent scar on his chin (now under his beard). His father also bought him a Victorian-era brass microscope, which he used to examine biological specimens. At about 12, he made a small dissecting kit (including a scalpel, crafted from a flattened pin) which he used to dissect a bumblebee, but he got into trouble with his parents when he progressed to dissecting a larger specimen. One Sunday morning he found a deceased cat on the road while doing his paper round and took it home in his bag. He relates that he started to dissect it on the dining room table before Sunday lunch, causing a foul smell throughout the house after he ruptured its intestines.

Jeffreys was a pupil at Luton Grammar School and then Luton Sixth Form College. He won a scholarship to study at Merton College, Oxford on a four-year course, where he graduated in 1971 with first-class honours in biochemistry. Jeffreys completed his Doctor of Philosophy degree on the mitochondria of cultured mammalian cells, as a postgraduate student at the Genetics Laboratory at the University of Oxford.

Career and research
After finishing his doctorate, he moved to the University of Amsterdam, where he worked on mammalian genes as a research fellow, and then to the University of Leicester in 1977, where in 1984 he discovered a method of showing variations between individuals' DNA, inventing and developing genetic fingerprinting.

Genetic fingerprinting
Jeffreys says he had a "eureka moment" in his lab in Leicester after looking at the X-ray film image of a DNA experiment on 10 September 1984, which unexpectedly showed both similarities and differences between the DNA of different members of his technician's family. Within about half an hour, he continued, he realised the possible scope of DNA fingerprinting, which uses variations in the genetic information to identify individuals. The method has become important in forensic science to assist police detective work, and it has also proved useful in resolving paternity and immigration disputes. The method can also be applied to non-human species, for example in wildlife population genetics studies. Before his methods were commercialised in 1987, his laboratory was the only centre in the world that carried out DNA fingerprinting, and was consequently very busy, receiving inquiries from all over the globe.

Jeffreys's DNA method was first put to use in 1985 when he was asked to help in a disputed immigration case to confirm the identity of a British boy whose family was originally from Ghana. The case was resolved when the DNA results proved that the boy was closely related to the other members of the family, and Jeffreys saw the relief in the mother's face when she heard the results. DNA fingerprinting was first used in a police forensic test to identify the killer of two teenagers, Lynda Mann and Dawn Ashworth, who had been raped and murdered in Narborough, Leicestershire, in 1983 and 1986 respectively. Colin Pitchfork was identified and convicted of their murders after samples taken from him matched semen samples taken from the two dead girls. This turned out to be a specifically important identification; British authorities believe that without it an innocent man would have inevitably been convicted. Not only did Jeffreys' work, in this case, prove who the real killer was, but it exonerated Richard Buckland, initially a prime suspect, who likely would have spent his life in prison otherwise. The story behind the investigations is told in Joseph Wambaugh's 1989 best-selling book The Blooding: The True Story of the Narborough Village Murders and the murders and subsequent solving of the crimes was featured in Episode 4 of the first season of the 1996 American TV series Medical Detectives in which Jeffreys himself also appears. A further television mini-series based on these events was released in 2015, Code of a Killer. In 1992, Jeffreys's methods were used to confirm the identity for German prosecutors of the body of Josef Mengele, who had died in 1979, by comparing DNA obtained from a femur bone of his exhumed skeleton, with DNA from his mother and son, in a similar way to paternity testing.

DNA profiling
DNA profiling, based on typing individual highly variable minisatellites in the human genome, was also developed by Alec Jeffreys and his team in 1985, with the term (DNA fingerprinting) being retained for the initial test that types many minisatellites simultaneously. By focusing on just a few of these highly variable minisatellites, DNA profiling made the system more sensitive, more reproducible and amenable to computer databases. It soon became the standard forensic DNA system used in criminal case work and paternity testing worldwide.

The development of DNA amplification by the polymerase chain reaction (PCR) opened up new approaches to forensic DNA testing, allowing automation, greatly increased sensitivity, and a move to alternative marker systems. The most commonly used markers are now variable microsatellites, also known as short tandem repeats (STRs), which Jeffreys first exploited in 1990 in the Mengele case. STR profiling was further refined by a team of scientists led by Peter Gill at the Forensic Science Service in the 1990s, allowing the launch of the UK National DNA Database (NDNAD) in 1995. With highly automated and sophisticated equipment, modern-day DNA profiling can process hundreds of samples each day. Sixteen microsatellites, plus a marker for sex determination, are used with the current system developed for the NDNAD, giving a discrimination power of one in over a billion. Under British law, anyone arrested in England, Wales or Northern Ireland has their DNA profile taken and stored on the database whether or not they are convicted (different rules apply in Scotland). The national database in 2020 contained the DNA information of about 5.6 million people. Jeffreys has opposed the current use of DNA profiling, where the government has access to that database, and has instead proposed a database of all people's DNA, access to which would be controlled by an independent third party.

Awards and honours

 * 1986 – Elected a Fellow of the Royal Society (FRS)
 * 1989 – Press, Radio and TV awards for the Midlander of the Year, 1988, 1989
 * 1991 – Appointed as a Royal Society Research Professor.
 * 26 November 1992 – Honorary freeman of the City of Leicester.
 * 1994 – Knighted for services to genetics and to science and technology.
 * 1995 – Honorary member of the International Society for Forensic Genetics
 * 1996 – Albert Einstein World Award of Science.
 * 1998 – Australia Prize, 1998.
 * 1999 – Sir George Stokes Medal
 * 2003 – Association for Molecular Pathology Award for Excellence in Molecular Diagnostics
 * 2004 – Honorary doctorate awarded by the University of Leicester, where Jeffreys is a member of staff.
 * 2004 – Royal Medal of the Royal Society.
 * 2004 – Pride of Britain Award for Lifetime Achievement.
 * 2004 – Louis-Jeantet Prize for Medicine.
 * 2005 – Albert Lasker Award for Clinical Medical Research, jointly with Edwin Southern of the University of Oxford.
 * 2005 – United States National Academy of Sciences, elected member.
 * 2006 – Great Briton Award for the Greatest Briton of the year, winner in the category of Science and Innovation, as well as the overall winner.
 * 2006 – Dr A.H. Heineken Prize for Biochemistry and Biophysics.
 * 8 March 2007 – Honorary degree from King's College London.
 * 23 January 2008 – Graham Medal of the Glasgow Philosophical Society, awarded after he gave his lecture "DNA Profiling; Past, present and future", which was nominated as the Graham Lecture.
 * 16 November 2009 – Awarded Honorary Doctor of Science by the University of Huddersfield
 * 14 April 2010 – Awarded Edinburgh Medal
 * April 2010 – Officially opened the new Soar Valley College building in Leicester.
 * 21 February 2011 – Awarded ABRF Annual Award
 * 2012 – Officially opened the Sir Alec Jeffreys Building in Wakefield, West Yorkshire, the scientific support building for West Yorkshire Police and the wider Yorkshire and the Humber region.
 * 2014 – Copley Medal
 * 22 January 2014 – Honorary Doctor of Science Degree from De Montfort University.
 * 2017 – Member of the Order of the Companions of Honour

Personal life
Jeffreys met his future wife, Sue Miles, in a youth club in the centre of Luton, Bedfordshire, before he became a university student, and they married on 28 August 1971. Jeffreys has one brother and one sister; he and his wife have two daughters, born in 1979 and 1983.

title: Alec Jeffreys


text:
Batumi

Batumi (ბათუმი ), historically Batum or Batoum, is the second-largest city of Georgia and the capital of the Autonomous Republic of Adjara, located on the coast of the Black Sea in Georgia's southwest, 20 kilometers north of the border with Turkey. It is situated in a subtropical zone at the foot of the Caucasus. Much of Batumi's economy revolves around tourism and gambling (it is nicknamed "The Las Vegas of the Black Sea"), but the city is also an important seaport and includes industries like shipbuilding, food processing and light manufacturing. Since 2010, Batumi has been transformed by the construction of modern high-rise buildings, as well as the restoration of classical 19th-century edifices lining its historic Old Town.

Early history
Batumi is located on the site of the ancient Greek colony in Colchis called "Bathus" or "Bathys", derived from (βαθύς λιμεν, bathus limen; or βαθύς λιμήν, bathys limēn; lit. the 'deep harbour'). Under Hadrian (c. 117–138 AD), it was converted into a fortified Roman port and later deserted for the fortress of Petra founded in the time of Justinian I (c. 527–565). Garrisoned by the Roman-Byzantine forces, it was formally a possession of the kingdom of Lazica until being occupied briefly by the Arabs, who did not hold it; In 780 Lazica fell to kingdom of Abkhazia via a dynastic union; the latter led the unification of the Georgian monarchy in the 11th century.

From 1010, it was governed by the eristavi (ერისთავი, viceroy) of the king of Georgia. In the late 15th century, after the disintegration of the Georgian kingdom, Batumi passed to the princes (mtavari, მთავარი) of Guria, a western Georgian principality under the sovereignty of the kings of Imereti.

A curious incident occurred in 1444 when a Burgundian flotilla, after a failed crusade against the Ottoman Empire, penetrated the Black Sea and engaged in piracy along its eastern coastline until the Burgundians under the knight Geoffroy de Thoisy were ambushed while landing to raid Vaty, as Europeans then knew Batumi. De Thoisy was taken captive and released through the mediation of the emperor John IV of Trebizond.

Ottoman rule
In the 15th century in the reign of the prince Kakhaber Gurieli, the Ottomans conquered the town and its district but did not hold them. They returned to it in force a century later and inflicted a decisive defeat on the Georgian armies at Sokhoista. Batumi was recaptured by the Georgians several times, first in 1546 by prince Rostom Gurieli, who lost it soon afterwards, and again in 1609 by Mamia II Gurieli. In 1703, Batumi again became part of the Ottoman Empire. In the one-and-a-half century of Ottoman rule it grew into a provincial port serving the Empire's hinterlands on the eastern fringes of the Black Sea. After the Ottoman conquest, Islamization of the hitherto Christian region began but this was terminated and to a great degree reversed, after the area was annexed to Russian Imperial Georgia after the Russo-Turkish War of 1877–78.

Imperial Russian rule
It was the last Black Sea port annexed by Russia during the Russian conquest of that area of the Caucasus. In 1878, Batumi was annexed by the Russian Empire in accordance with the Treaty of San Stefano between Russia and the Ottoman Empire (ratified on 23 March). Occupied by the Russians on 28 August 1878, the town was declared a free port until 1886. It functioned as the center of a special military district until being incorporated in the Kutaisi Governorate on 12 June 1883. Finally, on 1 June 1903, with the Artvin Okrug, the Batum Okrug was established as the Batum Oblast and placed under the direct administration of the Viceroy of the Caucasus.

The expansion of Batumi began with the construction of the Batumi–Tiflis–Baku Transcaucasus Railway (completed in 1883 ), and the Baku–Batumi pipeline which opened in 1907. Henceforth, Batumi became the chief Russian oil port in the Black Sea. The population increased rapidly doubling within 20 years: from 8,671 inhabitants in 1882 to 12,000 in 1889. By 1902 the population had reached 16,000, with 1,000 working in the refinery for Baron Rothschild's Caspian and Black Sea Oil Company.

In the late 1880s and after, more than 7,400 Doukhobor emigrants sailed for Canada from Batumi, after the government agreed to let them emigrate. Quakers and Tolstoyans aided in collecting funds for the relocation of the religious minority, which had come into conflict with the Imperial government over its refusal to serve in the military and other positions. Canada settled them in Manitoba and Saskatchewan.

Russian Civil War, Soviet Union, and 1991 independence
During 1901, sixteen years prior to the October Revolution, Joseph Stalin, the future leader of the Soviet Union, lived in the city organizing strikes. On 3 March 1918, the Treaty of Brest-Litovsk gave the city back to the Ottoman Empire, confirmed in the Treaty of Batum of June 1918 between the Ottoman Empire and the new Democratic Republic of Georgia. As result of the end of World War I the British took control over Batumi from December 1918, who stayed until July 1920 when the city and province was transferred to the Democratic Republic of Georgia, which gave Adjara autonomy. In 1921 Kemal Atatürk ceded the northern part of Adjara, including Batumi, to the Bolsheviks who reconquered the Transcaucasian republics, on the condition that it be granted autonomy for the sake of the Muslims among Batumi's mixed population.

When Georgia regained its independence from the Soviet Union in 1991, Aslan Abashidze was appointed head of Adjara's governing council and subsequently held onto power throughout the unrest of the 1990s. While Abkhazia and South Ossetia areas attempted to break away from the Georgian state, Adjara remained an integral part of the republic. Instead, Abashidze turned Adjara into his personal fiefdom. In May 2004, he fled to Russia after mass protests in Batumi, which concluded the 2004 Adjara crisis.

Post-1991
Batumi today is one of the main port cities of Georgia. It has the capacity for 80,000-ton tankers to take materials such as oil that are shipped through Georgia from Central Asia. Additionally, the city exports regional agricultural products. Since 1995 the freight conversion of the port has constantly risen, with an approximate 8 million tons in 2001. The annual revenue from the port is estimated at between $200 million and $300 million.

Since the change of power in Adjara, Batumi has attracted international investors, and the prices of real estate in the city have trebled since 2001. In July 2007, the seat of the Constitutional Court of Georgia was moved from Tbilisi to Batumi to stimulate regional development. Several new hotels opened after 2009, first the Sheraton in 2010 and the Radisson Blu in 2011. The city features several casinos that attract tourists from Turkey, where gambling is illegal.

Batumi was host to the Russian 12th Military Base. Following the Rose Revolution, the central government pushed for the removal of these forces and reached an agreement in 2005 with Moscow. According to the agreement, the process of withdrawal was planned to be completed in 2008, but the Russians completed the transfer of the Batumi base to Georgia on 13 November 2007, ahead of schedule.

Climate

Batumi has a humid subtropical climate (Cfa) according to Köppen's classification. The city's climate is heavily influenced by the onshore flow from the Black Sea and is subject to the orographic effect of the nearby hills and mountains, resulting in significant rainfall throughout most of the year, making Batumi the wettest city in both Georgia and the entire Caucasus Region.

The average annual temperature in Batumi is approximately 14 °C. January is the coldest month with an average temperature of 7 °C. August is the hottest month, with an average temperature of 22 °C. The absolute minimum recorded temperature is -6 °C, and the absolute maximum is 40 °C. The number of days with daily temperatures above 10 °C is 239. The city receives 1958 hours of sunshine per year.

Batumi's average annual precipitation is 2435 mm. November is the wettest month with an average of 312 mm of precipitation, while May is the driest, averaging 84 mm. Batumi receives snow most years, but it is often limited in amount (accumulating snowfall of more than 30 cm is rare), and the number of days with snow cover for the year is 12. The average level of relative humidity ranges from 70 to 80%.

Subdivisions
According to the 31 March 2008, decision of the Batumi City Council, Batumi is divided into seven boroughs, those of:

 * Old Batumi (ძველი ბათუმის უბანი)
 * Rustaveli (რუსთაველის უბანი)
 * Khimshiashvili (ხიმშიაშვილის უბანი)
 * Bagrationi (ბაგრატიონის უბანი)
 * Aghmashenebeli (აღმაშენებლის უბანი)
 * Javakhishvili (ჯავახიშვილის უბანი)
 * Tamar (თამარის უბანი)
 * Boni-Gorodok (ბონი-გოროდოკის უბანი)
 * Airport (აეროპორტის უბანი)
 * Gonio-Kvariati (გონიო-კვარიათის უბანი)
 * Kakhaberi (კახაბრის უბანი)
 * Batumi Industrial (ბათუმის სამრეწველო უბანი)
 * Green Cape (მწვანე კონცხის უბანი)

Contemporary architecture
Batumi's skyline has been transformed since 2007 with remarkable buildings and monuments of contemporary architecture, including:
 * Radisson Blu hotel
 * Public Service Hall
 * Hilton Batumi
 * Leogrand

A large Kempinski hotel and casino is to open in 2013, a Hilton Hotel as well as a 47-storey Trump Tower is also planned. Alliance Privilege, a building compromising Marriot Hotel, Casino and serviced apartments is one of the contemporary buildings with unique architecture by the beach.

Novelty architecture
Novelty architecture in Batumi includes:
 * Sheraton Hotel, designed in the style of the Great Lighthouse at Alexandria, Egypt
 * Alphabetic Tower (145 m high), celebrating Georgian script and writing
 * Batumi Piazza, a mixed-used development in the form of an Italian piazza
 * Buildings designed in the style of a lighthouse, the Acropolis, and an upside-down White House

Main sights
Attractions include
 * Adjara State Museum
 * Aquarium
 * Batumi Botanical Garden
 * Circus
 * Former resort area along the Black Sea coast.

Tourist attractions

 * Batumi Boulevard
 * The statue of "Man and Woman" AKA "Ali and Nino" by Georgian artist, Tamara Kvesitadze
 * Batumi Botanical Gardens
 * Cafe Fantasy
 * Dancing Fountains, Batumi
 * Dolphinarium
 * Piazza Square
 * Panoramic Wheel
 * Astronomical clock
 * Argo Cable Car
 * 6 May Park
 * Europe Square
 * Alphabetic Tower
 * Batumi Sea Port
 * Miracle Park
 * Chacha Clock Tower (defunct)
 * Fountain of Neptun
 * Batumi Archeological Museum
 * Monument of Ilia Chavchavadze

Religion
Of the 4,970 inhabitants in 1872, about 4,500 were Muslim (Adjarians, Turks, Circassians, and Abkhazians). In the 1897 census, the Orthodox Christian population was 15,495 (mostly Slavs) while Muslims numbered 3,156, including some of whom were citizens of Turkey.

As of 2014, out of 152,839 inhabitants of Batumi, 68,7% is Eastern Orthodox Christian, and they primarily adhere to the national Georgian Orthodox Church. Muslims make up 25,3% of population, while there are also Catholic, Armenian Apostolic, Jehovah's Witness, Seventh-day Adventist, and Jewish communities.

The main places of worship in the city are:
 * Georgian Orthodox Cathedral of the Mother of God, and Saint Barbara Church
 * Catholic Church of the Holy Spirit
 * Saint Nicholas Church
 * Batumi Mosque
 * Batumi Synagogue

Culture
Batumi has 18 various museums, including State Art Museum of Adjara. Rugby Union club Batumi RC competes in the Pan-European Rugby Europe Super Cup and the Georgian Didi 10. Football club FC Dinamo Batumi play at the Batumi stadium.

A sculpture by Tamara Kvesitadze of two standing figures on the seashore shows the story first told in the 1937 Austrian novel, Ali and Nino, of lovers who are parted after World War I. Each day, the two figures move toward each other but never stay together. Ali, an Azerbaijani Muslim, falls in love with Georgian princess, Nino, but sadly, after they are finally able to get together, the war hits home and Ali is killed. It was installed in 2010.

Notable people
Notable people who are from or have resided in Batumi:

 * Irakli Alasania (*1973), Georgian politician, Minister of Defense
 * Herbert Backe (1896–1947), Reich Minister of Food in Nazi Germany
 * Ioseb Bardanashvili (*1948), composer
 * Khatia Buniatishvili (*1987), concert pianist
 * Odysseas Dimitriadis (1908–2005), Greek-Soviet music conductor
 * Roman Dolidze (*1988), mixed martial artist
 * Mary, Princess Eristavi (1888–1986), Georgian princess and model
 * , (1887–1978), writer
 * Devi Khajishvili (*1991), actor
 * Sopho Khalvashi (*1986), first Georgian entrant to the Eurovision Song Contest 2007
 * Mindia Khitarishvili (*1973), composer
 * Konstantin Meladze (*1963), composer and producer
 * Valery Meladze (*1965), singer
 * Katie Melua, singer
 * Lado Seidishvili (1931–2010), Georgian painter and poet
 * Joseph Stalin (1878–1953), General secretary of the Communist Party of the Soviet Union
 * Arkady and Boris Strugatsky (1925–1991 ; 1933–2012), science fiction authors
 * William Horwood Stuart (1857–1906), British diplomat who was murdered there in 1906
 * Sergei Yesenin (1895–1925), Russian lyrical poet
 * Fyodor Yurchikhin (*1959), astronaut
 * Lamara Chkonia (1930–2024), Georgian soprano

Transport
The city is served by Batumi Airport, one of three international airports in the country. A bike-sharing system named BatumVelo allows you to rent a bicycle on the street with a smart card.

The main types of public transport are buses, minibusses, and taxis. Batumi has modern electric buses. Using the service is possible by BATUMICARD, transit card, or debit/credit cards. Buses connect almost everywhere in the city.

The port of Batumi is on one of the routes of China's proposed Eurasian Land Bridge (part of the "New Silk Road"), which would see an eastern freight link to China via Azerbaijan and the Caspian Sea, and a western link by ferry to Ukraine and on to Europe.

Twin towns – sister cities
Batumi is twinned with:

 * 🇮🇹 Bari, Italy (1987)
 * 🇺🇸 Savannah, United States (1992)
 * 🇹🇷 Trabzon, Turkey (2000)
 * 🇦🇲 Vanadzor, Armenia (2006)
 * Volos, Greece (2007)
 * 🇺🇦 Yalta, Ukraine (2008)
 * 🇧🇬 Burgas, Bulgaria (2009)
 * 🇪🇸 Marbella, Spain (2010)
 * 🇹🇷 Kuşadası, Turkey (2010)
 * 🇹🇷 Ordu, Turkey (2011)
 * 🇺🇦 Ternopil, Ukraine (2011)
 * 🇮🇱 Ashdod, Israel (2011)
 * 🇺🇸 New Orleans, United States (2012)
 * 🇹🇷 Yalova, Turkey (2012)
 * 🇦🇿 Nakhchivan, Azerbaijan (2012)
 * 🇱🇻 Daugavpils, Latvia (2012)
 * 🇺🇦 Donetsk, Ukraine (2013)
 * 🇨🇿 Prague 1, Czech Republic (2013)
 * 🇪🇬 Sharm El Sheikh, Egypt (2014)
 * 🇨🇳 Ürümqi, China (2015)
 * 🇧🇾 Brest, Belarus (2015)
 * 🇨🇾 Paphos, Cyprus (2016)
 * 🇵🇱 Nysa, Poland (2017)
 * 🇧🇾 Mogilev, Belarus (2017)
 * 🇮🇱 Netanya, Israel (2018)
 * 🇵🇱 Wrocław, Poland (2019)
 * Constanța, Romania (2020)

title: Batumi


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Vltava

The Vltava (,  ; Moldau ) is the longest river in the Czech Republic, running southeast along the Bohemian Forest and then north across Bohemia, through Český Krumlov, České Budějovice, and Prague, and finally merging with the Elbe at Mělník. It is commonly referred to as the "Czech national river".

Etymology
Both the Czech name Vltava and the German name Moldau are believed to originate from the old Germanic words wilt ahwa 'wild water' (compare Latin aqua). In the Annales Fuldenses (872 AD) it is called Fuldaha; from 1113 AD it is attested as Wultha. In the Chronica Boemorum (1125 AD) it is attested for the first time in its Bohemian form, Wlitaua.

Course
The Vltava River is 430.3 km long and drains an area of 28,090 km2 in size, over half of Bohemia and about a third of the Czech Republic's entire territory.

The source of the Vltava River is in the Bohemian Forest (Šumava in Czech), which hills are the southern border of the Czech Republic with Austria and Germany. The Bohemian Forest has elevation of 800–1,400 metres. The river flows north across Bohemia, through Český Krumlov, České Budějovice and Prague. It merges with the Elbe River at Mělník, a town about 16 miles north of Prague. The waters ultimately drain to the North Sea.

The height difference from source to mouth is about 1016 m and the largest stream at the source is named Černý potok ("Black Brook") or Teplá Vltava ("Warm Vltava"). The Vltava itself originates by a confluence of two streams, the Teplá Vltava, which is longer, and the Studená Vltava ("Cold Vltava"), sourcing in Bavaria.

As it runs through Prague, the river is crossed by 18 bridges (including the Charles Bridge) and covers 31 km within the city. The water from the river was used for drinking until 1912 when the Vinohrady Water Tower ceased pumping operations, and is now a place to view the city. It is, however, the source of drinking water in case of failures of or repairs to the water supply from the Želivka and Kárané sources. The Podolí water processing plant is on standby for such cases with the long section of the river upstream of the Podolí plant under the stricter, second degree of pollution prevention regulations.

Along its course, the river receives many tributaries. The longest tributaries of the Vltava are listed in this table.

Navigation
Between the confluence with the Elbe at Mělník and Prague, the river is navigable by vessels of up to 1000 tonnes displacement. Most of the river upstream of Prague as far as České Budějovice is navigable by craft of up to 300 tonnes displacement, but such vessels cannot pass the dams at Orlík and Slapy, and are also restricted by a low bridge at Týn nad Vltavou. Work is planned to complete boat lifts, planned for but never completed, at the two dams, and to rebuild the bridge, in order for them to navigate throughout. Much smaller craft, of up to 3.5 tonnes displacement and under 3 m beam and 3 m air draft, can avoid these obstacles.

Upstream of České Budějovice, the river's section around Český Krumlov (specifically from Vyšší Brod to Boršov nad Vltavou) is a very popular destination for water tourism.

Dams
Nine hydroelectric dams have been built on the Vltava south of Prague to regulate the water flow and generate hydroelectric power, starting in the 1930s. Beginning at the headwaters, these are: Lipno, Lipno II, Hněvkovice, Kořensko, Orlík, Kamýk, Slapy, Štěchovice and Vrané. The Orlík Reservoir supports the largest reservoir on the Vltava by volume, while the Lipno Reservoir retains the largest reservoir by area. The Štěchovice Reservoir is built over the site of St John's Rapids.

The river also features numerous weirs that help mitigate its flow from 1172 m in elevation at its source near the German border to 155 m at its mouth in Mělník.

Floods
The Vltava basin has flooded multiple times throughout recorded history. Markers have been created along the banks denoting the water line for notable floods in 1784, 1845, 1890, 1940, and the highest of all in 2002.

In August of 2002, the basin was heavily affected by the 2002 European floods when the flooded river killed several people and caused massive damage and disruption along its length, including in Prague. It left the oldest bridge in Prague, Charles Bridge, seriously weakened, requiring years of work to repair.

Prague was again flooded in 2013. Many locations within the Vltava and Elbe basins were left under water, including the Prague Zoo, but metal barriers were erected along the banks of the Vltava to help protect the historic city centre.

References in culture and science
One of the best-known works of classical music by a Czech composer is Bedřich Smetana's Vltava, sometimes called The Moldau in English. It is from the Romantic era of classical music and is a musical description of the river's course through Bohemia.

Smetana's symphonic poem also inspired a song of the same name by Bertolt Brecht. An English version of it, by John Willett, features the lyrics Deep down in the Moldau the pebbles are shifting / In Prague three dead emperors moulder away.

The Vltava River has been used as the setting for a number of films, including the 1942 Czech drama The Great Dam. More recently, the Vltava has been used as a film location for such films as Amadeus in 1984 and Mission: Impossible in 1996.

A minor planet, 2123 Vltava, discovered in 1973 by Soviet astronomer Nikolai Stepanovich Chernykh, is named after the river.

In DC Comics, there's a country called Vlatava, which is the homeland of the villain Count Vertigo, an enemy of the Green Arrow. It's likely that this country is named after the Vltava.

title: Vltava


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Syenite

Syenite is a coarse-grained intrusive igneous rock with a general composition similar to that of granite, but deficient in quartz, which, if present at all, occurs in relatively small concentrations (< 5%). It is considered a granitoid. Some syenites contain larger proportions of mafic components and smaller amounts of felsic material than most granites; those are classed as being of intermediate composition.

The extrusive equivalent of syenite is trachyte.

Composition
The feldspar component of syenite is predominantly alkaline in character (usually orthoclase). Plagioclase feldspars may be present in small proportions, between 10% and 35% of the feldspar content. Such feldspars often are interleaved as perthitic components of the rock.

When ferromagnesian minerals are present in syenite at all, they usually occur in the form of amphibole (typically hornblende) and clinopyroxene. Biotite is rare, because in a syenite magma the formation of feldspar consumes nearly all the aluminium. However less Al-rich phyllosilicates may be included, such as annite.

Other common accessory minerals are apatite, titanite, zircon and other opaques.

Most syenites are either peralkaline with high proportions of alkali elements relative to aluminum, or peraluminous with a higher concentration of aluminum relative to alkali (predominantly K and Na) and earth-alkali (predominantly Ca) elements.

Partial melting
Syenites are products of alkaline igneous activity, generally formed in thick continental crustal areas, or in Cordilleran subduction zones. The formation of syenites can be theorized to be from the melt of granitic or igneous protolith to a fairly low degree of partial melting. This is required because potassium is an incompatible element and tends to enter a melt first, whereas higher degrees of partial melting will liberate more calcium and sodium, which produce plagioclase, and hence a granite, adamellite or tonalite.

At very low degrees of partial melting a silica undersaturated melt is produced, forming a nepheline syenite, where orthoclase is replaced by a feldspathoid such as leucite, nepheline or analcime.

Conversely in certain conditions, large volumes of anorthite crystals may precipitate from thoroughly molten magma in a cumulate process as it cools. This leaves a drastically reduced concentration of silica in the remainder of the melt. The segregation of the silica from the melt leaves it in a state that may favour syenite formation.

Fractional crystallization
Some syenites are also theorized to be the product of the fractional crystallization of basaltic magmas.

Occurrence
Syenite is not a common rock. Regions where it occurs in significant quantities include the following.
 * In the Kola Peninsula of Russia two giant nepheline syenite bodies exists making up the Lovozero Massif and the Khibiny Mountains. These syenites are part of the Kola Alkaline Province.
 * In North America syenite occurs in Arkansas and Montana. Regions in New England have sizable amounts, and in New York syenite gneisses occur. The "great syenite dyke" extends from Hanging Rock, South Carolina, through Taxahaw, South Carolina, to the Brewer and Edgeworth mine in Chesterfield, South Carolina. Syenite pebbles, containing fluorescent sodalite, were moved from Canada to Michigan by glaciers; these glacial erratic pebbles have been given the trade name "yooperlite". In other parts of the world, these types of rocks are known as sodalite-syenite and occur in Canada, India, other US states, Greenland, Malawi, and Russia.
 * In Europe syenite may be found in parts of Switzerland, Germany, Norway, Portugal, Sweden, Scotland, in Plovdiv, Bulgaria and in Ditrău, Romania.
 * In Africa there are syenite formations in Aswan, Egypt, and in Malawi in the Mulanje Mountain Forest Reserve. Syenite rock was used to make the Quay with Sphinxes.
 * In Australia syenite occurs as small intrusive bodies in nearly every state. In New South Wales, a large syenite intruded during the breakup of Gondwana in the Cretaceous.
 * Paatusoq and Kangerluluk fjords in southeastern Greenland, where a bay within the latter (Syenitbugt) and a headland (Syenitnæs) are named after the rock.

Etymology
The term syenite was originally applied to hornblende granite like that of Syene (now Aswan) in Egypt, from which the name is derived.

Episyenite
Episyenite (or epi-syenite) is a term used in petrology to describe veins, pods, or lenses of rock originally rich in silicon dioxide (SiO2) from which quartz has been severely depleted. This is often accompanied by strong enrichment in potassium and rare earth elements, leaving the altered rock a distinctive brick red color, or by albitization (enrichment in sodium), leaving the altered rock a conspicuous white color.

Episyenites are heterogenous in their properties, but all have experienced nearly complete disappearance of quartz at sub-solidus temperatures; that is, at temperatures below the melting point of the host rock. The formation of episyenites (episyenitization) typically takes place through leaching of quartz by mildly saline hydrothermal fluids, typically near a cooling intrusion. Because episyenitization usually takes place in granitoid rock and usually involves alkaline metasomatism (addition of alkali metal oxides to the rock) the result is a rock that has the mineral composition of an igneous syenite.

In addition to rare earth elements, episyenites may be important sources of uranium and other valuable metals.

Notable occurrences of episyenite are found in the Central Iberian Massif of Spain, in Cambrian to Ordovician beds of New Mexico and Colorado, Scandinavia, Brazil, and Ukraine.

title: Syenite


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Junk DNA

Junk DNA (non-functional DNA) is a DNA sequence that has no relevant biological function. Most organisms have some junk DNA in their genomes—mostly pseudogenes and fragments of transposons and viruses—but it is possible that some organisms have substantial amounts of junk DNA.

All protein-coding regions of genes are generally considered as functional elements in genomes. Additionally, non-protein coding regions such as genes for ribosomal RNA and transfer RNA, regulatory sequences controlling expression of those genes, elements of the genome involving origins of replication (in all species), centromeres, telomeres, and scaffold attachment regions (in eukaryotes) are generally considered as functional elements of genomes as well. (See Non-coding DNA for more information.)

It is difficult to determine whether other regions of the genome are functional or nonfunctional. There is considerable controversy over which criteria should be used to identify function. Many scientists have an evolutionary view of the genome and they prefer criteria based on whether DNA sequences are preserved by natural selection. Other scientists dispute this view or have different interpretations of the data.

The history of junk DNA
The idea that only a fraction of the human genome could be functional dates back to the late 1940s. The estimated mutation rate in humans suggested that if a large fraction of those mutations were deleterious then the human species could not survive such a mutation load (genetic load). This led to predictions in the late 1940s by one of the founders of population genetics, J.B.S. Haldane, and by Nobel laureate Hermann Muller, that only a small percentage of the human genome contains functional DNA elements (genes) that can be destroyed by mutation. (see Genetic load for more information)

In 1966 Muller reviewed these predictions and concluded that the human genome could only contain about 30,000 genes based on the number of deleterious mutations that the species could tolerate. Similar predictions were made by other leading experts in molecular evolution who concluded that the human genome could not contain more than 40,000 genes and that less than 10% of the genome was functional.

The size of genomes in various species was known to vary considerably and there did not seem to be a correlation between genome size and the complexity of the species. Even closely related species could have very different genome sizes. This observation led to what came to be known as the C-value paradox. The paradox was resolved with the discovery of repetitive DNA and the observation that most of the differences in genome size could be attributed to repetitive DNA. Some scientists thought that most of the repetitive DNA was involved in regulating gene expression but many scientists thought that the excess repetitive DNA was nonfunctional.

At about the same time (late 1960s) the newly developed technique of C0t analysis was refined to include RNA:DNA hybridization leading to the discovery that considerably less than 10% of the human genome was complementary to mRNA and this DNA was in the unique (non-repetitive) fraction. This confirmed the predictions made from genetic load arguments and was consistent with the idea that much of the repetitive DNA is nonfunctional.

The idea that large amounts of eukaryotic genomes could be nonfunctional conflicted with the prevailing view of evolution in 1968 since it seemed likely that nonfunctional DNA would be eliminated by natural selection. The development of the neutral theory and the nearly neutral theory provided a way out of this problem since it allowed for the preservation of slightly deleterious nonfunctional DNA in accordance with fundamental principles of population genetics.

The term "junk DNA" began to be used in the late 1950s but Susumu Ohno popularized the term in a 1972 paper titled "So much 'junk' DNA in our genome" where he summarized the current evidence that had accumulated by then. In a second paper that same year, he concluded that 90% of mammalian genomes consisted of nonfunctional DNA. The case for junk DNA was summarized in a lengthy paper by David Comings in 1972 where he listed four reasons for proposing junk DNA:

 * 1) some organisms have a lot more DNA than they seem to require (C-value paradox),
 * 2) current estimates of the number of genes (in 1972) are much less than the number that can be accommodated,
 * 3) the mutation load would be too large if all the DNA were functional, and
 * 4) some junk DNA clearly exists.

The discovery of introns in the 1970s seemed to confirm the views of junk DNA proponents because it meant that genes were very large and even huge genomes could not accommodate large numbers of genes. The proponents of junk DNA tended to dismiss intron sequences as mostly nonfunctional DNA (junk) but junk DNA opponents advanced a number of hypotheses attributing functions of various sort to intron sequences.

By 1980 it was apparent that most of the repetitive DNA in the human genome was related to transposons. This prompted a series of papers and letters describing transposons as selfish DNA that acted as a parasite in genomes and produced no fitness advantage for the organism.

Opponents of junk DNA interpreted these results as evidence that most of the genome is functional and they developed several hypotheses advocating that transposon sequences could benefit the organism or the species. The most important opponent of junk DNA at this time was Thomas Cavalier-Smith who argued that the extra DNA was required to increase the volume of the nucleus in order to promote more efficient transport across the nuclear membrane.

The positions of the two sides of the controversy hardened with one side believing that evolution was consistent with large amounts of junk DNA and the other side believing that natural selection should eliminate junk DNA. These differing views of evolution were highlighted in a letter from Thomas Jukes, a proponent of junk DNA, to Francis Crick on December 20, 1979:

"Dear Francis, I am sure that you realize how frightfully angry a lot of people will be if you say that much of the DNA is junk. The geneticists will be angry because they think that DNA is sacred. The Darwinian evolutionists will be outraged because they believe every change in DNA that is accepted in evolution is necessarily an adaptive change. To suggest anything else is an insult to the sacred memory of Darwin."

The other point of view was expressed by Roy John Britten and Kohne in their seminal paper on repetitive DNA.

"A concept that is repugnant to us is that about half of the DNA of higher organisms is trivial or permanently inert (on an evolutionary timescale)."

Junk DNA and non-coding DNA
There is considerable confusion in the popular press and in the scientific literature about the distinction between non-coding DNA and junk DNA.

According to an article published in 2021 in American Scientist:

"Close to 99 percent of our genome has been historically classified as noncoding, useless 'junk' DNA. Consequently, these sequences were rarely studied."

A book published in 2020 states:

"When it was first discovered, the nongenic DNA was sometimes called—somewhat derisively by people who did not know better—'junk DNA' because it had no obvious utility, and they foolishly assumed that if it was not carrying coding information it must be useless trash."

The common theme is that the original proponents of junk DNA thought that all non-coding DNA was junk and generally ignored. This claim has been attributed to a paper by David Comings in 1972 where he is reported to have said that junk DNA refers to all non-coding DNA. But Comings never said that. In that paper he discusses non-coding genes for ribosomal RNA and tRNAs and non-coding regulatory DNA and he proposes several possible functions for the bulk of non-coding DNA. In another publication from the same year Comings again discusses the term junk DNA with the clear understanding that it does not include non-coding regulatory sequences.

These statements have been criticized by numerous authors for distorting the history of junk DNA; for example: "It is simply not true that noncoding DNA has long been dismissed as worthless junk and that functional hypotheses have only recently been proposed - despite the frequency with which this cliché is repeated in media reports and in the introduction of far too many scientific studies." Some of the criticisms have been strong: "Revisionist claims that equate noncoding DNA with junk merely reveal that people who are allowed to exhibit their logorrhea in Nature and other glam journals are as ignorant as the worst young-earth creationists."

Since the 1960s, proponents of junk DNA were well aware of functional non-coding DNA and even discussed possible functions when new types of non-coding sequences were identified. For instance, the existence of functional non-coding DNA elements such as noncoding genes, regulatory sequences, origins of replication, and centromeres were well known in the late 1960s when the idea of junk DNA was being proposed. Many of the main supporters of junk DNA explicitly mentioned the importance of (non-coding) regulatory sequences and addressed the issue of whether regulatory sequences were a minor part of the functional genome or whether regulatory sequences took up most of the human genome. Early proponents of junk DNA did not base their arguments on ignorance; they based their arguments on what was known about genome sizes, gene duplication, mutational load, and population genetics. (See The history of junk DNA.)

Some have argued that the term "non-coding DNA" is unfortunate because it sounds like "nonsense sequence which does nothing at all." They suggest that this misleading phrase be replaced with "untranslated DNA."

Identifying function
The phrase "junk DNA" is debatable, and differing precise definitions (and associated approaches) provide wildly disparate estimates of its prevalence. Strong objections to the term "junk DNA" have prompted some to advocate for more neutral nomenclature, such as "nonfunctional DNA."

Proponents of junk DNA define "functional" DNA as DNA that is currently under purifying selection. For instance, Dan Gaur in his textbook "Molecular and Genome Evolution."

 * "Functional DNA refers to any segment in the genome whose selected-effect function is that for which it was selected and/or by which it is maintained. Most functional sequences are maintained by purifying selection."

This definition of "function" is called the maintenance function. Other similar definitions have been published but they all have in common the idea that junk DNA is DNA that does not have a function and this means that it is not under negative selective pressure. About 11% or less of the human genome is conserved and about 7% is under purifying selection.

Biochemical activity is another criterion that has been used to estimate functional elements. Biochemical activity includes whether a given locus is transcribed or whether it binds a transcription factor. In a series of papers published in 2012, the Encyclopedia of DNA Elements (ENCODE) project reported that detectable biochemical activity was observed in regions covering at least 80% of the human genome. These conclusions were promoted by a publicity campaign announcing the demise of junk DNA. The ENCODE conclusions were challenged in a series of publications over the next few years with some suggesting that many transcripts are spurious transcripts that do not necessarily come from functional regions of the genome. They also suggested that many transcription factor binding sites are nonfunctional sites that occur by chance in large genomes.

In 2014, ENCODE researchers responded that there are both limitations and advantages to the different approaches (genetic, evolutionary, biochemical) used to get estimates of functional elements. They agreed that biochemical activity by itself is not a reliable indicator of function and they did not repeat their earlier claim that 80% of the genome is functional. Their revised position is that the ENCODE data can be used to identify candidate elements that can be further examined to see if they are functional and that this contribution is "far more important than any interim estimate of the fraction of the human genome that is functional." The most recent attempt to define function using biochemical activity focuses on identifying which transcripts have a function and which transcription factor binding sites are true regulatory sequences. One way of distinguishing between true functional biochemical activity and spurious nonfunctional biochemical activity is to look for evidence of sequence conservation or purifying selection. Opponents of junk DNA argue that biochemical activity detects functional regions of the genome that are not identified by sequence conservation or purifying selection.

Some scientists have argued that functionality can only be assessed in reference to an appropriate null hypothesis. In this case, the null hypothesis would be that these parts of the genome are non-functional and have properties, be it on the basis of conservation or biochemical activity, that would be expected of such regions based on our general understanding of molecular evolution and biochemistry. According to these scientists, until a region in question has been shown to have additional features, beyond what is expected of the null hypothesis, it should provisionally be labelled as non-functional.

title: Junk DNA