User:GospodinovD/sandbox

History
Junk DNA as a term became popular in the 1960s. Junk DNA can be viewed as all regions of a genome which are neither functional nor deleterious. The very first mention of junk DNA was in a Carnegie institution publication, "It is much more difficult to imagine how the different DNA’s could act as templates for the similar RNA’s. This is the problem that can be avoided most easily by considering a large part of the DNA to be junk.” Another early mention of the term occurred in a 1963 paper by Charles Ehret and Gérard de Haller, entitled “Origin, development, and maturation of organelles and organelle systems of the cell surface in Paramecium”. In Ehret and Haller’s work the term was used once and simply to describe that not all DNA is, “competent genetic material”. The term was formalized in 1972 by Susumu Ohno, who spoke of mutations leading to pseudogenes to be what this junk DNA was . Another source for Ohno's theory was the observation that even closely related species can have widely different genome sizes (orders-of-magnitude), which had been dubbed the C-value paradox in 1971. According to T. Ryan Gregory, the term was first linked with non-coding DNA by David Comings who extended the classification of junk DNA to non-coding DNA in 1972 as well. Today junk DNA is used as a broad definition to any DNA sequence that does not in some capacity play a functional role in an organism’s development or physiology. This broader definition became the target of debate towards the quantity or existence of junk DNA mainly because of simplistic claims that this term implied uselessness and implying that current discoveries are revealing functions in junk DNA previously thought to not have any function.

Classification
The term junk DNA has been questioned on the grounds that it provokes a strong a priori assumption of total non-functionality and some have recommended using more neutral terminology such as "non-coding DNA" instead. This proposal occurred around the 1980s when junk DNA began to catch on in terms of use, this was described as, “trying to characterize all dogs as a single breed since non-coding DNA comes in many varieties like a dog comes in different species.” This blend of junk and non-coding is incorrect because junk DNA is defined as all regions of DNA that are neither functional nor deleterious while non-coding DNA is all regions of DNA do not encode a protein. The overlap being that if a protein is not encoded it might not enact change, however junk DNA can become junk RNA and junk proteins. Junk DNA is also defined as any stretch of DNA that is not necessary to preserve the fitness of the individual meaning it can be removed and the individual will not suffer, in the human genome this constitutes: 43% transposons and introns, 30% additional defective transposon sequences, 9% defective virus sequences, 5% pseudogenes, 2% extra repetitive DNA, and 0.01% mitochondrial DNA.

Since the late 1970s it has become apparent that the majority of non-coding DNA in large genomes finds its origin in the selfish amplification of transposable elements, of which W. Ford Doolittle and Carmen Sapienza in 1980 wrote in the journal Nature: "When a given DNA, or class of DNAs, of unproven phenotypic function can be shown to have evolved a strategy (such as transposition) which ensures its genomic survival, then no other explanation for its existence is necessary." The amount of junk DNA can be expected to depend on the rate of amplification of these elements and the rate at which non-functional DNA is lost. In the same issue of Nature, Leslie Orgel and Francis Crick wrote that junk DNA has "little specificity and conveys little or no selective advantage to the organism". Junk DNA is still a controversial wording for some who feel that it occurs mainly in popular science or in a colloquial way in scientific publications, and it has been suggested that its connotations may have delayed interest in the biological functions of non-coding DNA.

ENCODE Controversy
The Encyclopedia of DNA Elements (ENCODE) project uncovered, by direct biochemical approaches, that at least 80% of human genomic DNA has biochemical activity such as "transcription, transcription factor association, chromatin structure, and histone modification". The encode project had declared junk DNA no more, however others disagreed like Hurst, who compared the claim that these regions of junk DNA have function is similar to, “In a car collision with a pedestrian the car’s hood has the “function” of hurting the pedestrian and the pedestrian has the “function” of denting the car” that is to say these are not actual functions but merely byproducts of what happens Furthermore, the Onion test by T. Ryan Gregory which is usually enacted for such claims of function did receive a response from the head of the ENCODE project Ewan Birney who stated, “polyploidy and letting your repeats "go crazy" (bad piRNAs anyone) mean your genome can be v. big” which does not apply to the diploid onion.

Changes in Functionality

A new division of the genome was proposed having 4 distinct categories: Junk DNA that is not contributing to selection, garbage DNA that negatively impacts selection, Literal DNA which nucleotides are under selection, and Indifferent DNA which only the presence of the sequence is under selection. Some evidence indicate that some "junk DNA" sequences are sources for (future) functional activity in evolution through exaptation of originally selfish or non-functional DNA. Junk DNA is able to change functionality becoming functional DNA or turning harmful which is coined as garbage DNA. Graur et. al. coined the transformation of junk DNA to functional DNA as lazarus DNA after the biblical resurrection, and junk DNA transforming to a harmful garbage DNA was labeled zombie DNA.