Wikipedia / Wikipedia:Wiki Markup Language

Wiki Mark Up Language (WKML) is a group, started by Nick Irelan, that seeks to create an XML-based format for wikis so that the information they present may be used by third-party programs such as mashups.

This format should be created in a way that allows wikis to be syndicated similar to an RSS feed.

Request to define format and useful attributes

All editors with XML experience are welcome to comment on how they feel Wikipedia created content such as, but not limited to Infoboxes and Titles should be formatted.

What is the broadly defined structure of any given article?

All of the common parts of articles should receive special attention to make sure they can be worked with easily by a programmer. For example, the history section would probably be used a lot.

Title
Sections
Categories
Info boxes (?)

What are the broadly defined attributes of any given article?

Which, if any, attributes to the articles should be included in WKML?

Date created
Updates

Request to define discussion pages format

All editors with XML experience are welcome to comment on how they feel discussion pages should be formatted.

Basic principles: narrowly or broadly defined?

All xml formats represent a balance struck between two extremes: the format being defined very narrowly, and the format being defined very broadly. Each approach carries with it a series of advantages and challenges, and it is the job of a format designer to decide which approach's characteristics best suit the way that the format will be used.

Generally speaking, broadly defined formats are more usable, and in particular are more likely to be adopted. One of the reasons for the incredible success of RSS is that it is, eponymously, really simple, and easily expanded. The drawback of a broadly defined format is that it generally requires more work on the part of the developer when the consumer desires a specific application for a document. Consider the following two formats:

Narrow definition

 <biography>
   <name>George Washington</name>
   <content>George Washington was a...</content>
 </biography>

</wikiarticle>

Broad definition

 <content>George Washington was a...</content>

</wikiarticle>

Obviously, the second article can be about anything. This is an advantage in that it fits the extremely loosely-structured nature of Wikipedia, but a disadvantage in that it makes development for specific formats more difficult. Ultimately, defining narrow formats would require articles to conform to templates at the very least, which would drastically limit the scope of articles would could be exposed via WKML. Ultimately, a format which can be applied to any Wikipedia article, no matter how minimally or bizarrely defined, is probably the most appropriate approach. If infobox or template specific information is available, it should be used, but cannot be required.

How the format will be used

XML exists to be consumed or transformed. A XML document might be consumed by a database in the form of an updategram, which leads to an update of a record in a table, or it might be transformed into a more readable format in the case of an RSS reader.

A pure consumption of the XML involves direct coding against the format, which is typically very narrowly defined. It seems unlikely that much Wikipedia content would be used this way, so this leaves transformation as the end use of WKML.

One approach would be to simply utilize RSS. The problem with this approach is that RSS is probably too broad, and probably doesn't suit the encyclopedic nature of Wikipedia. Ultimately, if RSS was required for a mashup (an RSS feed of new pages, or changes to a page, for example), as long as WKML meets some minimal requirements, it can be transformed into RSS.

A hybrid approach

Indeed, one way to solve this problem of specificity versus simplicity would be separate formats divided along, for example, template lines, with a roll down to a generic article format. This approach has the further advantage that it need not be implemented immediately; a basic WKML format could be created and deployed for widespread use, and then later function as the rolldown format when more specific formats are created. Ultimately, whether the broad or narrow format of the article is used can be an attribute of the request, with the rolldown format as the default for backwards compatibility.

Open questions

Are article content and metadata documents separate or are they unified into a single document?

Content and history are definitely contained in the same document. Documents which represent previous revisions of the document are separate documents, retrieved by a separate syndication / service command.

What is the broadly defined structure of any given article? (Title, sections, ?)

The broadly defined structure is as follows:

root, containing a root document element and some document meta-info such as category information.
title
content sections
history
What are the broadly defined attributes of any given article?(Title, date created, further date questions feed back into question #1)

How will infoboxes be handled?

At this point, it's pretty clear that we have to renotate all of the infobox content.

How much and how will HTML be scrubbed from the content?

A general principle which might be helpful is that markup that affects presentation (such as font-strength (bold) or italicization) will be scrubbed without re-notation, while markup that affects actions, such as links, will be renotated in a format that we have to determine. One exception to this will be images, which may need to be renotated, or may simple pass through as is.

Proposed date format

Wikipedia Markup Language documents use the date format specified in the ISO standard document ISO 8601:1988(E). An important distinction:

Document node values or document attributes which are dates are subject to this standard, dates used in the content are not.

For example:

Standard applies

<wikiarticle linkback="Neuralizer" revisiondate="2007-01-01T16:28:49Z">

Standard does not apply

Brett Bretterson was born at 8:14 PM on Saturday, June 21st, 1954.

Differently grained attributes may require different formats specified within the standard, e.g., some dates may not require time. As per the standard, all times are UTC.

Examples

Highly developed article in XML format

(In Progress)

<wikiarticle title="DNA"> <template type="sprotect2" /> <template type="otheruses" /> <section id="7" title="Chemical modifications"> <section id="9" title="DNA damage"> <template type="further|<link type="internal">Mutation</link>" />

Many mutagens <link type="internal">intercalation (chemistry)|intercalate</link> into the space between two adjacent base pairs. These molecules are mostly polycyclic, <link type="internal">aromaticity|aromatic</link>, and planar molecules, and include <link type="internal">ethidium</link>, <link type="internal">proflavin</link>, <link type="internal">daunomycin</link>, <link type="internal">doxorubicin</link> and <link type="internal">thalidomide</link>. DNA intercalators are used in <link type="internal">chemotherapy</link> to inhibit DNA replication in rapidly-growing <link type="internal">cancer</link> cells. In order for an intercalator to fit between base pairs, the bases must separate, distorting the DNA strands by unwinding of the double helix. These structural modifications inhibit <link type="internal">transcription (genetics)|transcription</link> and <link type="internal">DNA replication|replication</link> processes, causing both toxicity and mutations. As a result, DNA intercalators are often <link type="internal">carcinogen</link>s, with <link type="internal">benzopyrene|benzopyrene diol epoxide</link>, <link type="internal">acridine</link>s, <link type="internal">aflatoxin</link> and <link type="internal">ethidium bromide</link> being well-known examples.

==Overview of biological functions== DNA contains the genetic information that allows living things to function, grow and reproduce. This information is held in the <link type="internal">DNA sequence|sequence</link> of pieces of DNA called <link type="internal">gene</link>s. Genetic information in genes is transmitted through complementary base pairing. For example, when a cell uses the information in a gene, the DNA sequence is copied into a complementary RNA sequence in a process called transcription. Usually, this RNA copy is then used to make a matching protein sequence in a process called translation. Alternatively, a cell may simply copy its genetic information in a process called DNA replication. The details of these functions are covered in other articles; here we focus on the interactions that happen in these processes between DNA and other molecules. <link type="internal">Image:RNA pol.jpg|thumb|left|300px|<link type="internal">T7 RNA polymerase</link> producing a mRNA (green) from a DNA template (red and blue). The protein is shown as a purple ribbon. combinations). These encode the twenty <link type="internal">list of standard amino acids|standard amino acids</link>. Most amino acids, therefore, have more than one possible codon. There are also three 'stop' or 'nonsense' codons signifying the end of the coding region; these are the TAA, TGA and TAG codons.

===Replication=== <template type="further|<link type="internal">DNA replication</link>" />

==Genes and genomes== <template type="further|<link type="internal">Cell nucleus</link>, <link type="internal">Gene</link>, <link type="internal">Non-coding DNA</link>" /> DNA is located in the <link type="internal">cell nucleus</link> of eukaryotes, as well as small amounts in <link type="internal">mitochondrion|mitochondria</link> and <link type="internal">chloroplast</link>s. In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the <link type="internal">nucleoid</link>. The DNA is usually in linear <link type="internal">chromosome</link>s in eukaryotes, and circular chromosomes in prokaryotes. In the <link type="internal">human genome</link>, there is approximately 3 billion base pairs of DNA arranged into 46 chromosomes. The genetic information in a genome is held within genes. A gene is a unit of <link type="internal">heredity</link> and is a region of DNA that influences a particular characteristic in an organism. Genes contain an <link type="internal">open reading frame</link> that can be transcribed, as well as <link type="internal">regulatory sequence</link>s such as <link type="internal">promoter</link>s and <link type="internal">enhancer (genetics)|enhancers</link>, which control the expression of the open reading frame.

In many <link type="internal">species</link>, only a small fraction of the total sequence of the <link type="internal">genome</link> encodes protein. For example, only about 1.5% of the human genome consists of protein-coding <link type="internal">exon</link>s, with over 50% of human DNA consisting of non-coding <link type="internal">repeated sequence (DNA)|repetitive sequences</link>. The reasons for the presence of so much <link type="internal">noncoding DNA|non-coding DNA</link> in eukaryotic genomes and the extraordinary differences in <link type="internal">genome size</link>, or <link type="internal">C-value</link>, among species represent a long-standing puzzle known as the "<link type="internal">C-value enigma</link>".

Some non-coding DNA sequences play structural roles in chromosomes. <link type="internal">Telomere</link>s and <link type="internal">centromere</link>s typically contain few genes, but are important for the function and stability of chromosomes. An abundant form of non-coding DNA in humans are <link type="internal">pseudogene</link>s, which are copies of genes that have been disabled by mutation. These sequences are usually just molecular <link type="internal">fossil</link>s, although they can occasionally serve as raw genetic material for the creation of new genes through the process of <link type="internal">gene duplication</link> and <link type="internal">divergent evolution|divergence</link>.

==Interactions with proteins== All the functions of DNA depend on interactions with proteins. These protein interactions can either be non-specific, or the protein can only bind to a particular DNA sequence. Enzymes can also bind to DNA and of these, the polymerases that copy the DNA base sequence in transcription and DNA replication are particularly important.

===DNA-binding proteins=== {|border="0" width=260px border="0" cellpadding="0" cellspacing="0" style="font-size: 85%; border: 1px solid #CCCCCC; margin: 0.3em;" |<link type="internal">Image:Nucleosome 2.jpg|260px</link> |- |<link type="internal">Image:Nucleosome_(opposites_attracts).JPG|260px</link> |} Interaction of DNA with <link type="internal">histone</link>s (shown in white, top). These proteins' basic amino acids (below left, blue) bind to the acidic phosphate groups on DNA (below right, red).

Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. Within chromosomes, DNA is held in complexes between DNA and structural proteins. These proteins organize the DNA into a compact structure called <link type="internal">chromatin</link>. In eukaryotes this structure involves DNA binding to a complex of small basic proteins called <link type="internal">histone</link>s, while in prokaryotes multiple types of proteins are involved. The histones form a disk-shaped complex called a <link type="internal">nucleosome</link>, which contains two complete turns of double-stranded DNA wrapped around its surface. These non-specific interactions are formed through basic residues in the histones making <link type="internal">ionic bond</link>s to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence. Chemical modifications of these basic amino acid residues include <link type="internal">methylation</link>, <link type="internal">phosphorylation</link> and <link type="internal">acetylation</link>. These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to <link type="internal">transcription factor</link>s and changing the rate of transcription. Other non-specific DNA-binding proteins found in chromatin include the high-mobility group proteins, which bind preferentially to bent or distorted DNA. These proteins are important in bending arrays of nucleosomes and arranging them into more complex chromatin structures.

A distinct group of DNA-binding proteins are the single-stranded DNA-binding proteins that specifically bind single-stranded DNA. In humans, replication protein A is the best-characterised member of this family and is essential for most processes where the double helix is separated, including DNA replication, recombination and DNA repair. These binding proteins seem to stabilize single-stranded DNA and protect it from forming <link type="internal">stem loop</link>s or being degraded by <link type="internal">nuclease</link>s.

As these DNA targets can occur throughout an organism's genome, changes in the activity of one type of transcription factor can affect thousands of genes. Consequently, these proteins are often the targets of the <link type="internal">signal transduction</link> processes that mediate responses to environmental changes or cellular differentiation and development. The specificity of these transcription factors' interactions with DNA come from the proteins making multiple contacts to the edges of the DNA bases, allowing them to "read" the DNA sequence. Most of these base interactions are made in the major groove, where the bases are most accessible.

===DNA-modifying enzymes=== ====Nucleases and ligases==== Nucleases are <link type="internal">enzyme</link>s that cut DNA strands by catalyzing the <link type="internal">hydrolysis</link> of the <link type="internal">phosphodiester bond</link>s. Nucleases that hydrolyse nucleotides from the ends of DNA strands are called <link type="internal">exonuclease</link>s, while <link type="internal">endonuclease</link>s cut within strands. The most frequently-used nucleases in <link type="internal">molecular biology</link> are the <link type="internal">restriction enzyme|restriction endonucleases</link>, which cut DNA at specific sequences. For instance, the EcoRV enzyme shown to the left recognizes the 6-base sequence 5'-GAT|ATC-3' and makes a cut at the vertical line. In nature, these enzymes protect <link type="internal">bacteria</link> against <link type="internal">phage</link> infection by digesting the phage DNA when it enters the bacterial cell, acting as part of the <link type="internal">restriction modification system</link>. In technology, these sequence-specific nucleases are used in <link type="internal">clone (genetics)|molecular cloning</link> and <link type="internal">DNA fingerprinting</link>.

Enzymes called <link type="internal">DNA ligase</link>s can rejoin cut or broken DNA strands, using the energy from either <link type="internal">adenosine triphosphate</link> or <link type="internal">nicotinamide adenine dinucleotide</link>. Ligases are particularly important in <link type="internal">lagging strand</link> DNA replication, as they join together the short segments of DNA produced at the <link type="internal">replication fork</link> into a complete copy of the DNA template. They are also used in <link type="internal">DNA repair</link> and <link type="internal">genetic recombination</link>.

====Topoisomerases and helicases==== <link type="internal">Topoisomerase</link>s are enzymes with both nuclease and ligase activity. These proteins change the amount of <link type="internal">DNA supercoil|supercoiling</link> in DNA. Some of these enzyme work by cutting the DNA helix and allowing one section to rotate, thereby reducing its level of supercoiling; the enzyme then seals the DNA break. Other types of these enzymes are capable of cutting one DNA helix and then passing a second strand of DNA through this break, before rejoining the helix. Topoisomerases are required for many processes involving DNA, such as DNA replication and transcription.

Helicases are proteins that are a type of <link type="internal">molecular motor</link>. They use the chemical energy in <link type="internal">adenosine triphosphate</link> to break the hydrogen bonds between bases and unwind a DNA double helix into single strands. These enzymes are essential for most processes where enzymes need to access the DNA bases.

====Polymerases==== Polymerases are enzymes that synthesise polynucleotide chains from <link type="internal">nucleoside triphosphate</link>s. They function by adding nucleotides onto the 3' <link type="internal">hydroxyl|hydroxyl group</link> of the previous nucleotide in the DNA strand. As a consequence, all polymerases work in a 5' to 3' direction. In the <link type="internal">active site</link> of these enzymes, the nucleoside triphosphate substrate base-pairs to a single-stranded polynucleotide template: this allows polymerases to accurately synthesise the complementary strand of this template. Polymerases are classified depending of the type of template they use.

In <link type="internal">DNA replication</link>, a DNA-dependent <link type="internal">DNA polymerase</link> make a DNA copy of a DNA sequence. Accuracy is vital in this process, so many of these polymerases have a <link type="internal">Proofreading#Proofreading in biology|proofreading</link> activity. Here, the polymerase recognizes the occasional mistakes in the synthesis reaction by the lack of base pairing between the mismatched nucleotides. If a mismatch is detected, a 3' to 5' <link type="internal">exonuclease</link> activity is activated and the incorrect base removed. In most organisms DNA polymerases function in a large complex called the <link type="internal">replisome</link> that contains multiple accessory subunits, such as the <link type="internal">DNA clamp</link> or <link type="internal">helicase</link>s.

RNA-dependent DNA polymerases are a specialised class of polymerases that copy the sequence of a RNA strand into DNA. They include <link type="internal">reverse transcriptase</link>, which is a <link type="internal">virus|viral</link> enzyme involved in the infection of cells by <link type="internal">retrovirus</link>es, and <link type="internal">telomerase</link>, which is required for the replication of <link type="internal">telomere</link>s. Telomerase is an unusual polymerase because it contains its own RNA template as part of its structure.

Transcription is carried out by a DNA-dependent <link type="internal">RNA polymerase</link> that copies the sequence of a DNA strand into RNA. To begin transcribing a gene, the RNA polymerase binds to a sequence of DNA called a <link type="internal">promoter</link> and separates the DNA strands. It then copies the gene sequence into a <link type="internal">messenger RNA</link> transcript until it reaches a region of DNA called the <link type="internal">terminator (genetics)|terminator</link>, where it halts and detaches from the DNA. As with human DNA-dependent DNA polymerases, RNA polymerase II, the enzyme that transcribes most of the genes in the human genome, operates as part of a large protein complex with multiple regulatory and accessory subunits.

==Genetic recombination== {|border="0" width=250px border="0" cellpadding="0" cellspacing="0" style="font-size: 85%; border: 1px solid #CCCCCC; margin: 0.3em;" |<link type="internal">Image:Holliday Junction cropped.png|250px</link> |- |<link type="internal">Image:Holliday junction coloured.png|250px</link> |} Structure of the <link type="internal">Holliday junction</link> intermediate in <link type="internal">genetic recombination</link>. The four separate DNA strands are coloured red, blue, green and yellow. <template type="further|<link type="internal">Genetic recombination</link>" /> <link type="internal">Image:Chromosomal Recombination.svg|thumb|250px|left|Recombination involves the breakage and rejoining of two chromosomes (M and F) to produce two re-arranged chromosomes (C1 and C2).</link>

A DNA helix does not usually interact with other segments of DNA, and in human cells the different chromosomes even occupy separate areas in the nucleus called "chromosome territories". This physical separation of different chromosomes is important for the ability of DNA to function as a stable repository for information, as one of the few times chromosomes interact is when they <link type="internal">genetic recombination|recombine</link>. Recombination is when two DNA helices break, swap a section and then rejoin. In eukaryotes this process usually occurs during <link type="internal">meiosis</link>, when the two sister <link type="internal">chromatid</link>s are paired together in the center of the cell. Recombination allows chromosomes to exchange genetic information and produces new combinations of genes, which increases the efficiency of <link type="internal">selection</link> and can be important in the rapid evolution of new proteins. Genetic recombination can also be involved in DNA repair, particularly in the cell's response to double-strand breaks.

The most common form of recombination is <link type="internal">chromosomal crossover|homologous recombination</link>, where the two chromosomes involved share very similar sequences. Non-homologous recombination can be damaging to cells, as it can produce <link type="internal">chromosomal translocation</link>s and genetic abnormalities. The recombination reaction is catalyzed by enzymes known as recombinases, such as <link type="internal">Cre recombinase</link>. In the first step, the recombinase creates a nick in one strand of a DNA double helix, allowing the nicked strand to pull apart from its <link type="internal">complementarity (molecular biology)|complementary</link> strand and <link type="internal">annealing (biology)|anneal</link> to one strand of the double helix on the opposite chromatid. A second nick allows the strand in the second chromatid to pull apart and anneal to the remaining strand in the first helix, forming a structure known as a cross-strand exchange or a <link type="internal">Holliday junction</link>. The Holliday junction is a tetrahedral junction structure which can be moved along the pair of chromosomes, swapping one strand for another. The recombination reaction is then halted by cleavage of the junction and re-ligation of the released DNA.

==Uses in technology== ===Forensics === <template type="further|<link type="internal">Genetic fingerprinting</link>" />

===Bioinformatics=== <template type="further|<link type="internal">Bioinformatics</link>" /> <link type="internal">Bioinformatics</link> involves the manipulation, searching, and <link type="internal">data mining</link> of DNA sequence data. The development of techniques to store and search DNA sequences have led to widely-applied advances in <link type="internal">computer science</link>, especially <link type="internal">string searching algorithm</link>s, <link type="internal">machine learning</link> and <link type="internal">database theory</link>. String searching or matching algorithms, which find an occurrence of a sequence of letters inside a larger sequence of letters, was developed to search for specific sequences of nucleotides. In other applications such as <link type="internal">text editor</link>s, even simple algorithms for this problem usually suffice, but DNA sequences cause these algorithms to exhibit near-worst-case behaviour due to their small number of distinct characters. The related problem of <link type="internal">sequence alignment</link> aims to identify <link type="internal">homology (biology)|homologous</link> sequences and locate the specific <link type="internal">mutation</link>s that make them distinct. These techniques, especially <link type="internal">multiple sequence alignment</link>, are used in studying <link type="internal">phylogenetics|phylogenetic</link> relationships and protein function. Data sets representing entire genomes' worth of DNA sequences, such as those produced by the <link type="internal">Human Genome Project</link>, are difficult to use without annotations, which label the locations of genes and regulatory elements on each chromosome. Regions of DNA sequence that have the characteristic patterns associated with protein- or RNA-coding genes can be identified by <link type="internal">gene finding</link> algorithms, which allow researchers to predict the presence of particular <link type="internal">gene product</link>s in an organism even before they have been isolated experimentally.

===DNA and computation === <template type="further|<link type="internal">DNA computing</link>" /> DNA was first used in computing to solve a small version of the directed <link type="internal">Hamiltonian path problem</link>, an <link type="internal">NP-complete</link> problem. <link type="internal">DNA computing</link> is advantageous over electronic computers in power use, space use, and efficiency, due to its ability to compute in a highly parallel fashion (see <link type="internal">parallel computing</link>). A number of other problems, including simulation of various <link type="internal">abstract machine</link>s, the <link type="internal">boolean satisfiability problem</link>, and the bounded version of the <link type="internal">travelling salesman problem</link>, have since been analysed using DNA computing. Due to its compactness, DNA also has a theoretical role in <link type="internal">cryptography</link>, where in particular it allows unbreakable <link type="internal">one-time pad</link>s to be efficiently constructed and used.

===History and anthropology=== <template type="further|<link type="internal">Phylogenetics</link> and <link type="internal">Genetic genealogy</link>" /> Because DNA collects mutations over time, which are then inherited, it contains historical information and by comparing DNA sequences, geneticists can infer the evolutionary history of organisms, their <link type="internal">phylogeny</link>. This field of <link type="internal">phylogenetics</link> is a powerful tool in <link type="internal">evolutionary biology</link>. If DNA sequences within a species are compared, <link type="internal">population genetics|population geneticists</link> can learn the history of particular populations. This can be used in studies ranging from <link type="internal">ecological genetics</link> to <link type="internal">anthropology</link>; for example, DNA evidence is being used to try to identify the <link type="internal">Ten Lost Tribes of Israel</link>.

DNA has also been used to look at modern family relationships, such as establishing family relationships between the descendants of <link type="internal">Sally Hemings</link> and <link type="internal">Thomas Jefferson</link>. This usage is closely related to the use of DNA in criminal investigations detailed above. Indeed, some criminal investigations have been solved when DNA from crime scenes has matched relatives of the guilty individual.

==History== <link type="internal">Image:Francis Crick.png|thumb|right|<link type="internal">Francis Crick</link></link> <link type="internal">Image:JamesWatson.jpg|thumb|<link type="internal">James D. Watson|James Watson</link> in the <link type="internal">Cavendish Laboratory</link> at the <link type="internal">University of Cambridge</link></link> <template type="further|<link type="internal">History of molecular biology</link>" /> DNA was first isolated by <link type="internal">Friedrich Miescher</link> who, in 1869, discovered a microscopic substance in the <link type="internal">pus</link> of discarded surgical bandages. As it resided in the nuclei of cells, he called it "nuclein".

In 1929 this discovery was followed by <link type="internal">Phoebus Levene</link>'s identification of the base, sugar and phosphate nucleotide unit. Levene suggested that DNA consisted of a string of nucleotide units linked together through the phosphate groups. However, Levene thought the chain was short and the bases repeated in a fixed order. In 1937 <link type="internal">William Astbury</link> produced the first <link type="internal">X-ray diffraction</link> patterns that showed that DNA had a regular structure.

In 1943, <link type="internal">Oswald Theodore Avery</link> discovered that <link type="internal">trait (biology)|traits</link> of the "smooth" form of the Pneumococcus could be transferred to the "rough" form of the same bacteria by mixing killed "smooth" bacteria with the live "rough" form. Avery identified DNA as this <link type="internal">transforming principle</link>. DNA's role in <link type="internal">heredity</link> was confirmed in 1953, when <link type="internal">Alfred Hershey</link> and <link type="internal">Martha Chase</link> in the <link type="internal">Hershey-Chase experiment</link> showed that DNA is the <link type="internal">genetic material</link> of the <link type="internal">T2 phage</link>.

Using <link type="internal">X-ray diffraction</link> data from <link type="internal">Rosalind Franklin</link> and the information that the bases were paired, <link type="internal">James D. Watson</link> and <link type="internal">Francis Crick</link> produced the first accurate model of DNA structure in 1953 in their article <link type="internal">Molecular structure of Nucleic Acids|The Molecular structure of Nucleic Acids</link>. Watson and Crick proposed the <link type="internal">central dogma of molecular biology</link> in 1957, describing how proteins are produced from <link type="internal">cell nucleus|nucleic</link> DNA. In 1962 Watson, Crick, and <link type="internal">Maurice Wilkins</link> jointly received the <link type="internal">Nobel Prize</link> in <link type="internal">Nobel Prize in Physiology or Medicine|Physiology or Medicine</link>.

In an influential presentation in 1957, Crick laid out the "Central Dogma", which foretold the relationship between DNA, RNA, and proteins, and articulated the "adaptor hypothesis". Final confirmation of the replication mechanism that was implied by the double-helical structure followed in 1958 through the <link type="internal">Meselson-Stahl experiment</link>. Further work by Crick and coworkers showed that the genetic code was based on non-overlapping triplets of bases, called codons, allowing <link type="internal">Har Gobind Khorana</link>, <link type="internal">Robert W. Holley</link> and <link type="internal">Marshall Warren Nirenberg</link> to decipher the <link type="internal">genetic code</link>. These findings represent the birth of <link type="internal">molecular biology</link>.

==References==

==Further reading== <list> <item> Clayton, Julie. (Ed.). 50 Years of DNA, Palgrave MacMillan Press, 2003. ISBN 978-1-40-391479-8</item> <item> Judson, Horace Freeland. The Eighth Day of Creation: Makers of the Revolution in Biology, Cold Spring Harbor Laboratory Press, 1996. ISBN 978-0-87-969478-4</item> <item> <link type="internal">Robert Olby|Olby, Robert</link>. The Path to The Double Helix: Discovery of DNA, first published in October 1974 by MacMillan, with foreword by Francis Crick; ISBN 978-0-48-668117-7; the definitive DNA textbook, revised in 1994, with a 9 page postscript.</item> <item> <link type="internal">Matt Ridley|Ridley, Matt</link>. Francis Crick: Discoverer of the Genetic Code (Eminent Lives) first published in June 2006 in the USA and then to be in the UK September 2006, by HarperCollins Publishers; 192 pp, ISBN 978-0-06-082333-7 <item> Rose, Steven. The Chemistry of Life, Penguin, ISBN 978-0-14-027273-4</item>. <item> Watson, James D. and Francis H.C. Crick. A structure for Deoxyribose Nucleic Acid (PDF). <link type="internal">Nature (journal)|Nature</link> 171, 737 – 738, <link type="internal">25 April</link> <link type="internal">1953</link>.</item> <item> Watson, James D. DNA: The Secret of Life ISBN 978-0-375-41546-3.</item> <item> Watson, James D. <link type="internal">The Double Helix|The Double Helix: A Personal Account of the Discovery of the Structure of DNA (Norton Critical Editions)</link>. ISBN 978-0-393-95075-5</item> </list> ==External links== <template type="Spoken Wikipedia|dna.ogg|2007-02-12" /> <template type="commonscat|DNA" /> *DNA from the beginning *Double helix: 50 years of DNA, <link type="internal">Nature (journal)|Nature</link> *Rosalind Franklin's contributions to the study of DNA *U.S. National DNA Day - watch videos and participate in real-time chat with top scientists *Genetic Education Modules for Teachers - DNA from the Beginning Study Guide *Listen to Francis Crick and James Watson talking on the BBC in 1962, 1972, and 1974 *Using DNA in Genealogical Research *DNA Interactive (requires <link type="internal">Adobe Flash</link>) *DNA: RCSB PDB Molecule of the Month *DNA under electron microscope *<template type="dmoz|Science/Biology/Biochemistry_and_Molecular_Biology/Biomolecules/Nucleic_Acids/DNA/|DNA" /> *DNA Articles - articles and information collected from various sources *<template type="McGrawHillAnimation|genetics|Dna%20Replication" /> *DNA coiling to form chromosomes

<category>DNA</category> <category>Genetics</category>

Stub Article in XML Format

  <title>Franklin Pierce High School</title>
  <categories>
     <category>Stub</category>
  </categories>
  <infobox type="Secondary school">
     <infoboxattribute>
        <name>name</name>
        <value>Franklin Pierce High School</value>
     </infoboxattribute>
     <infoboxattribute>
        <name>established</name>
        <value>1952</value>
     </infoboxattribute>
     <infoboxattribute>
        <name>city</name>
        <value>Tacoma</value>
     </infoboxattribute>
     <infoboxattribute>
        <name>state</name>
        <value>Washington</value>
     </infoboxattribute>
     <infoboxattribute>
        <name>country</name>
        <value>USA</value>
     </infoboxattribute>
     <infoboxattribute>
        <name>campus</name>
        <value>Suburban</value>
     </infoboxattribute>
     <infoboxattribute>
        <name>type</name>
        <value>Public secondary</value>
     </infoboxattribute>
     <infoboxattribute>
        <name>principal</name>
        <value>Eric Hogan</value>
     </infoboxattribute>
     <infoboxattribute>
        <name>grades</name>
        <value>9-12</value>
     </infoboxattribute>
     <infoboxattribute>
        <name>enrollment</name>
        <value>1,220 (2005)</value>
     </infoboxattribute>
     <infoboxattribute>
        <name>district</name>
        <value>Franklin Pierce School District</value>
     </infoboxattribute>
     <infoboxattribute>
        <name>mascot</name>
        <value>Cardinals</value>
     </infoboxattribute>
     <infoboxattribute>
        <name>colors</name>
        <value>Red and yellow</value>
     </infoboxattribute>
     <infoboxattribute>
        <name>website</name>
        <value><link type="external">http://www.fp.k12.wa.us/fphs/</link></value>
     </infoboxattribute>
  </infobox>
  
      Franklin Pierce High School in <link type="internal">Tacoma, Washington</link> is named after the fourteenth US President, <link type="internal">Franklin Pierce</link>, who was president when the Washington Territory was formed in 1853.
   
  
      <link type="internal">Advanced Placement</link> courses are offered in Calculus AB, Statistics, Chemistry (at Washington H.S.) and US History. Language classses offered are French, Spanish, Japanese, and American Sign Language.
   
  
      Clubs at FPHS are Drama Club, <link type="internal">FBLA</link>, <link type="internal">FFA</link>, <link type="internal">National Honor Society</link>, International Cultures Club, and Ski Club.
   
  
      Football, Golf, Cross Country, Volleyball, Soccer,Basketball, Wrestling, Tennis, Baseball, Fastpitch Softball, and Track.
      <link type="internal">Category:High schools in Washington</link>
      <link type="internal">Category:South Puget Sound League</link>
      <link type="internal">Category:Educational institutions established in 1952</link>
   
  <history>
     <revision type="minor">
        <version>106992867</version>
        <date>2007-02-09T20:45:00Z</date>
        <user>Quirkyperki</user>
        <description />
     </revision>
     <revision type="section">
        <version>106992539</version>
        <date>2007-02-09T20:43:00Z</date>
        <user>Quirkyperki</user>
        <description>(Created page with '{{Infobox Secondary school | name = Franklin Pierce High School | established = 1952 | city = Tacoma | state = Washington | country = USA | campus = Suburban | type...') </description>
     </revision>
  </history>

</wikiarticle>

Absolute minimum article in XML format

  <title>Neuralizer</title>
  
         A neuralizer is a fictional device portrayed in the 1991 movie, Men In Black.
         It is used to erase memories of people involved in encounters with extraterrestrials.
   
  <history />

</wikiarticle>