User talk:Thomas Wright Sulcer/sandbox7: Difference between revisions

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imported>Chris Day
(this quote implies that prokaryotes cannot do the same, but that is not true. The reporter got the wrong end of the stick here, I think.)
imported>Thomas Wright Sulcer
(possible future article)
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Temporary file: Intron; (possible suggestions for new material March 5, 2010)
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[[Image:DNA splicing introns off to make proteins.jpg|thumb|right|alt=Diagram showing how DNA is translated into proteins by splicing off introns.|When DNA makes a protein, introns are spliced off during this process, so only the exons remain.]]
(awaiting permission for cover of book to be uploaded)
An '''intron''' is the '''''int'''''ervening, non-coding sequence of [[nucleic acid]] that is between the '''''ex'''''pressed sequences ([[exon]]s) in a [[gene]]. It is removed from the primary [[RNA]] transcript by [[RNA splicing|splicing]] and is a common feature of [[eucaryote|eucaryotic]] genes. Introns are the spacer regions of DNA that separate the information-coding parts of a gene.<ref name=twsMAR02p>{{cite news
|author= Nicholas Wade
|title= As Scientists Pinpoint the Genetic Reason for Lactose Intolerance, Unknowns Remain
|quote= The authors of the new report say the two DNA units that switch off the lactase gene are in the 9th and 13th introns in a neighboring gene whose role strangely has nothing to do with lactose metabolism. Introns are the spacer regions of DNA that separate the information-coding parts of a gene. Because the cell cuts out and discards the introns when a gene is activated, these disposable pieces of DNA have long been ignored. Now it seems they play unexpected roles in gene control.
|publisher= The New York Times
|date= January 14, 2002
|url= http://www.nytimes.com/2002/01/14/us/scientists-pinpoint-genetic-reason-for-lactose-intolerance-unknowns-remain.html?pagewanted=1
|accessdate= 2010-03-02
}}</ref>


Generally introns are found in the [[DNA]] of more advanced species. Scientists believe that the only living creatures on earth billions of years ago were [[bacteria]] which belonged to a group called [[prokaryotes]].<ref name=twsMAR02m>{{cite news
Possible article title: "The Burr in the Garden of Eden (book)"
|author= Carl Zimmer
|title= From Bacteria to Us: What Went Right When Humans Started to Evolve?
|quote= Eukaryotes can do more with their genes, too. They can switch genes on and off in complex patterns to control where and when they make proteins. And they can make many proteins from a single gene. That is because eukaryote genes are segmented into what are called exons. Exons are interspersed with functionless stretches of DNA known as introns. Human cells edit out the introns when they copy a gene for use in building a protein. But a key ability is that they can also edit out exons, meaning that they can make different proteins from the same gene. This versatility means that eukaryotes can build different kinds of cells, tissues and organs, without which humans would look like bacteria.
|publisher= The New York Times
|date= January 3, 2006
|url= http://www.nytimes.com/2006/01/03/science/03zimm.html
|accessdate= 2010-03-02
}}</ref> But about two billion years ago, a group branched off from prokaryotes called [[eukaryotes]] which evolved into much more complex organisms including animals, plants, fungi, and some protozoans, and which had bigger and more complex DNA.<ref name=twsMAR02m/>


Why is the DNA more advanced? It's segmented. The DNA alternates between what are called [[exons]] and [[introns]]. This allows human cells to "edit out introns" when copying genes to build proteins, and lets cells make a wide variety of different proteins from the same gene.<ref name=twsMAR02m/> It is believed that the exons were functionless stretches whose only purpose was to break up stretches of exons, but this view has been questioned.<ref name=twsMAR02m/> Scientist Michael Lynch suspected the addition of introns into DNA was a harmful accident at first. When an intron was wedged into the middle of a gene, cells had to be able to recognize the boundaries and "skip over" the introns when making a protein.<ref name=twsMAR02m/> Lynch hypothesized that this first led to defective proteins, but that the overall effect of interspersed introns was a phenomenon called [[genetic drift]] which ultimately helped evolution, since it created new opportunities for adaptations to be successful.<ref name=twsMAR02m/>  
'''''The Burr in the Garden of Eden''''' is a [[science fiction]] [[book]] by author [[Hayford Peirce]]. Napoleon V, the "all-powerful Emperor of the United States of Europe," has to deal with four experimental time machines running amok in two different [[parallel]] [[universe|universes]] and con-artist "MacNair of MacNair" (the debonair hero of Peirce's ''Napoleon Disentimed'') gets involved.<ref name=twsMar14n>{{cite news
|title= The Burr in the Garden of Eden by Hayford Peirce (Paperback - May 2001)
|publisher= flipkart.com
|date=  May 2001
|url= http://www.flipkart.com/burr-garden-eden-hayford-peirce/1587152770-1sx3fdelje
|accessdate= 2010-03-14
}}</ref> Orgones are "going out all over [[Europe]]" and innocent subjects are "exploding at random" and [[Paris|Parisian]] party girls are demonstrating on the Champs-Elysee. The "Burr" refers to a fictionalized character based on the past American former vice president [[Aaron Burr]] who killed [[Alexander Hamilton]] in a real-life duel. The book is written in [[English]] has 252 pages and was released in 2001.<ref name=twsMar14n/>


There is no single mechanism for splicing an intron from the primary RNA transcript.  Introns are classified into four groups based on the mechanism of splicing.  In general splicing can be either autocatalytic or be catalyzed by a large complex of proteins know as the [[spliceosome]]. Splicing can also be viewed as a form of gene regulation since [[alternative splicing]] can result in different combinations of exons in the mature RNA transcript. In this way one gene can code for distinct open reading frames and hence has the potential to code for more than one protein.  
==[[Nibiru]] controversy==
Speculation about a possible end-of-the-world forecast known as [[2012]] is a pop culture hysteria phenomenon dismissed by scientists as "bunk." The hysteria was created by doomsayers that a possible planet named [[Niburu]] would collide with [[Earth]] on December 21st or 23rd in 2012 causing the destruction of mankind. There was speculation about the possible source of the controversy. It was noticed that the cover of ''The Burr in the Garden of Eden'' featured an image of [[Earth]] being struck by another large object, possibly planet Nibiru. The book was released in 2003, nine years before 2012. When asked whether there was any truth to rumors that his book was responsible for launching the 2012 hysteria, Peirce replied:
{{quote|It was probably the group sex scenes in which they are channeling Reichian orgones that caused all the problems. -- author [[Hayford Peirce]], March 2010.}}


The human DNA helix, if unraveled, would be about three feet long, and the sections of introns inside it have been referred to as "mostly chaotic" and an "indecipherable wilderness".<ref name=twsMAR02n>{{cite news
==Notes==
|title= DNA Evidence
* ISBN 1587152770
|quote= DNA probe analysis grew out of basic genetic research, with far different aims. A kind of serendipitous gift to police science, it takes advantage of a peculiarity within the human genetic code. Along the three feet of the double helix in each complete DNA molecule there exists, in addition to the tens of thousands of protein-coding genes, a so-far indecipherable wilderness called the intron. The intron, although it seems mostly chaotic, nevertheless contains certain repetitive sequences of the genetic alphabet, which geneticists sometimes call "stutters" or "burps."
* ISBN 13:9781587152771
|publisher= The New York Times
* ISBN 978-1587152771
|date= June 18, 2009
|url= http://topics.nytimes.com/topics/reference/timestopics/subjects/d/dna_evidence/index.html
|accessdate= 2010-03-02
}}</ref>
 
Sometimes the [[DNA]] that codes for introns is classified as [[junk DNA]] but this is an oversimplification since introns can contain functional RNA or DNA sequences; these include transfer RNA ([[tRNA]]) or microRNA ([[miRNA]]) sequences. In the chromosome, DNA sequences that code for an intron can also include enhancers that are important for gene expression.
 
The true role of introns is unclear but one hypothesis is that introns allow [[gene shuffling]] to occur, resulting in the creation of new exon combinations and novel proteins. The presence of an intron can also enhance gene expression since the process of RNA splicing seems to facilitate the trafficking of the mRNA out of the eucaryotic nucleus.
 
==Discoveries==
 
After completing the human genome in 2001, scientists found 22,000 genes, but noticed there were more than 100,000 different proteins. If each gene could make only one protein, then how could there be so many different proteins? A ''Washington Post'' reporter explained:
{{quote|When a gene is activated, it is first transcribed into an intermediate molecule called mRNA. The introns are clipped out and the exons spliced together, and the whole thing is then translated into the protein. Biologists used to think one gene produced one protein. Now it's clear that one gene can produce many different proteins. Under certain conditions, a cell clips out not only the intron fillers but also one or more of the exons. This is like taking a speech and removing many of the sentences. Done in different ways, it can produce many different messages.<ref name=twsMAR03vgff>{{cite news
|author= David Brown
|title= How Science Is Rewriting the Book on Genes
|publisher= Washington Post
|date= November 12, 2007
|url= http://www.washingtonpost.com/wp-dyn/content/story/2007/11/11/ST2007111101076.html
|accessdate= 2010-03-03
}}</ref>}}
 
Scientists think that about five percent of the human genome has a "message" of one sort or another, with a particular order of nucleotide letters (A, G, C, T) being of utmost importance in determining important aspects of a human's body chemistry. Any addition, deletion, or change can have a big effect, including death.<ref name=twsMAR03vgff/> Still, there are large stretches of genes which had been thought to have been "junk DNA" but is turning out to have an important role. These conserved "non-coding elements" include insulators, micro-RNAs, exon-splicing enhancers, e'-untranslated hairpins and other molecules which are "emerging from the shadows."<ref name=twsMAR03vgff/> They regulate the activity of genes that ''do'' make the proteins by turning them on and off, tweaking them, and coordinating the sequential action of their effects.<ref name=twsMAR03vgff/> And how these processes operate are important not only for geneticists, but for scientists who study evolution, since "more of evolution's survival-of-the-fittest battles occurred in writing the instruction manual for running the genes than in designing the genes themselves," according to a ''Washington Post'' report in 2007.<ref name=twsMAR03vgff/>
 
==The naming of intron==
The names ''intron'' and ''exon'' were described as "less catchy" but nevertheless "novel" names, and the naming was against a trend of using "dull and pedantic" impenetrable Latin names.<ref name=twsMAR02o>{{cite news
|author= Stephen S. Hall
|title= Scientists Find Catchy Names Help Ideas Fly
|quote= Novel though less catchy are the terms "intron" and "exon," used to distinguish different regions of the genetic material. It used to be thought that a stretch of DNA forming a gene was simply copied onto a strand of RNA, which directed synthesis of a protein.
|publisher= The New York Times
|date= October 20, 1992
|url= http://www.nytimes.com/1992/10/20/science/scientists-find-catchy-names-help-ideas-fly.html?pagewanted=all
|accessdate= 2010-03-02
}}</ref> In 1977, three scientists at a cafeteria in Basel, [[Switzerland]], discussed possible names. Dr. Walter Gilbert was credited for thinking up the name ''intron'', while Dr. Melvin Cohn coined the term ''exon'', although he was originally thinking of the large oil firm [[Exxon]]. Dr. Cohn explained:
{{quote|I was actually thinking of 'exxon' with two x's like the oil company -- it was a joke -- I was making fun of Gilbert because I didn't think those were the best possible terms. They were too slangy and didn't best describe what was going on.<ref name=twsMAR02o/>}}
Nevertheless, Dr. Gilbert wrote down the terms on a napkin, and both terms appeared in a 1978 commentary in the journal ''Nature''.<ref name=twsMAR02o/>
 
==Recent research involving introns==
 
According to one source, scientists are exploring ways of using data from introns when doing DNA analysis regarding police investigations. While each intron seems chaotic, there are repetitive sequences of the genetic alphabet sometimes called "stutters" or "burps" which can be analyzed.<ref name=twsMAR02n/> When multiple probes are used, it's possible to analyze introns in the DNA to identify its uniqueness and produce an identification "as reliable as a human fingerprint."<ref name=twsMAR02n/>
 
Scientists discovered that two DNA units that switch off the lactase gene are in "the 9th and 13th introns of a neighboring gene whose role strangely has nothing to do with lactose metabolism."<ref name=twsMAR02p/> Scientists are discovering that the spacer-regions in DNA called introns "play unexpected roles in gene control."<ref name=twsMAR02p/>
 
Researchers are studying the relationship between introns and gender-related differences in colon cancer.<ref name=twsMAR02q>{{cite news
|author= Reuters Health
|title= Gene effect on colon cancer differs by gender
|quote= The research team at the Keck School of Medicine in Los Angeles, headed by Dr. Heinz-Josef Lenz, studied two variant forms of EGFR. One of the variants involved a change at a spot called codon 497 and the other involved a change in an area known as intron 1.
|publisher= Reuters
|date= April 15, 2008
|url= http://www.reuters.com/article/idUSCOL24375320080502
|accessdate= 2010-03-02
}}</ref>
 
There are suggestions that the composition of a specific intron, a three-SNP haplotype in the intron 1 of OCA2, is related to "human eye color variation", and scientists believe two major genes and several minor ones which account for the "tremendous variation in human eye color."<ref name=twsMAR02r>{{cite news
|author= April Holladay
|title= Hazel is in the eye of the beholder; more on memory
|quote= D.L. Duffy, G.W. Montgomery, W. Chen, Z.Z. Zhao, L. Le, M.R. James, N.K. Hayward, N.G. Martin, R.A. Sturm. A three-SNP haplotype in the intron 1 of OCA2 explains most human eye color variation. American Journal of Human Genetics, 80: 241-252 (2007).
|publisher= USA Today
|date= 2007-03-19
|url= http://www.usatoday.com/tech/columnist/aprilholladay/2007-03-19-hazel-eye-memory_N.htm
|accessdate= 2010-03-02
}}</ref>
 
There was speculation that introns inside the dysbindin gene may have a role in [[schizophrenia]].<ref name=twsMAR02rxxx>{{cite news
|author= Nicholas Wade
|title= Schizophrenia May Be Tied To 2 Genes, Research Finds
|quote= Despite years of false leads, setbacks and unsustained claims, researchers hope they are now starting to close in on some of the genes that go awry in schizophrenia, a devastating mental disease that affects two million Americans... Dr. Straub found genetic variations in the dysbindin gene that were more common in the schizophrenic patients. Curiously, they are all in introns, the spacer regions of the DNA that lie between the working parts of the dysbindin gene. The Richmond team is not sure that any of the intron changes is the causative mutation of schizophrenia and is analyzing the working parts more closely.
|publisher= The New York Times
|date= July 4, 2002
|url= http://www.nytimes.com/2002/07/04/us/schizophrenia-may-be-tied-to-2-genes-research-finds.html?pagewanted=1
|accessdate= 2010-03-02
}}</ref>


==References==
==References==
{{Reflist}}
{{reflist}}

Revision as of 15:15, 15 March 2010

Temporary file:

(awaiting permission for cover of book to be uploaded)

Possible article title: "The Burr in the Garden of Eden (book)"

The Burr in the Garden of Eden is a science fiction book by author Hayford Peirce. Napoleon V, the "all-powerful Emperor of the United States of Europe," has to deal with four experimental time machines running amok in two different parallel universes and con-artist "MacNair of MacNair" (the debonair hero of Peirce's Napoleon Disentimed) gets involved.[1] Orgones are "going out all over Europe" and innocent subjects are "exploding at random" and Parisian party girls are demonstrating on the Champs-Elysee. The "Burr" refers to a fictionalized character based on the past American former vice president Aaron Burr who killed Alexander Hamilton in a real-life duel. The book is written in English has 252 pages and was released in 2001.[1]

Nibiru controversy

Speculation about a possible end-of-the-world forecast known as 2012 is a pop culture hysteria phenomenon dismissed by scientists as "bunk." The hysteria was created by doomsayers that a possible planet named Niburu would collide with Earth on December 21st or 23rd in 2012 causing the destruction of mankind. There was speculation about the possible source of the controversy. It was noticed that the cover of The Burr in the Garden of Eden featured an image of Earth being struck by another large object, possibly planet Nibiru. The book was released in 2003, nine years before 2012. When asked whether there was any truth to rumors that his book was responsible for launching the 2012 hysteria, Peirce replied:

‘ It was probably the group sex scenes in which they are channeling Reichian orgones that caused all the problems. -- author Hayford Peirce, March 2010. ’

Notes

References

  1. ↑ 1.0 1.1 The Burr in the Garden of Eden by Hayford Peirce (Paperback - May 2001), flipkart.com, May 2001. Retrieved on 2010-03-14.
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