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Junk DNA may not be so junky after all
EurekAlert ^ | March 23, 2006 | Johns Hopkins Staff

Posted on 03/29/2006 5:46:20 PM PST by DaveLoneRanger

Researchers develop new tool to find gene control regions

Researchers at the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins have invented a cost-effective and highly efficient way of analyzing what many have termed "junk" DNA and identified regions critical for controlling gene function. And they have found that these control regions from different species don't have to look alike to work alike.

The study will be published online at Science Express March 23.

The researchers developed a new system that uses zebrafish to test mammalian DNA and identify DNA sequences, known as enhancers, involved in turning on a gene. In studying RET, the major gene implicated in Hirschsprung disease and multiple endocrine neoplasia (MEN2), the team identified DNA sequences that can control RET but had not been identified using standard methods. Hirschsprung disease, also known as congenital megacolon, is a relatively common birth defect marked by bowel obstruction. MEN2 is an inherited predisposition to neuroendocrine cancers.

The notion that mutations in enhancers play a role in human disease progression has been difficult to confirm because usually enhancers are located in the 98 percent of the human genome that does not code for protein, termed non-coding DNA. Unlike DNA sequences that code for protein, non-coding DNA, sometimes referred to as "junk" DNA, follows few rules for organization and sequence patterns and therefore is more difficult to study.

"The difficulty with human genetic approaches to common disease is that we lack the power to precisely localize DNA sequences that are associated with disease, often leaving us immense stretches of DNA to look at," says one of the study's corresponding authors, Andy McCallion, Ph.D., an assistant professor in the McKusick-Nathans Institute. Most often one is limited to looking in the most obvious places, which may not yield the best results. "Until now," he says, "we've only been able to look under the lamplights for the car keys."

Traditionally, DNA sequences are thought to have to look similar to function similarly; this is how scientists identify genes in other species, a strategy best used for studying similar species. From an evolutionary standpoint, the last common ancestor of human and zebrafish lived more than 300 million years ago. Because DNA sequences in each species have changed over time, traditional methods of comparing DNA sequences between humans and zebrafish have failed to identify any potential enhancers around the RET gene because the DNA sequences differ too much.

That drove the Hopkins researchers to seek and develop this new system, by which virtually any DNA sequence can be tested for its ability to turn on a marker gene in zebrafish embryos. The system is a significant advance over current methods in this model species, allowing researchers to study more sequences in a shorter period of time. Using this, they identified several human enhancers able to control expression consistent with the zebrafish ret gene.

Zebrafish have become the ideal system for doing these types of large scale studies. They are small - only about a half inch in length - they grow quickly, and are relatively inexpensive to maintain compared to mice or rats. "Zebrafish are the only vertebrate embryo you can even think about doing this type of work in," says Shannon Fisher, M.D., Ph.D., the study's first author and an assistant professor in cell biology in Johns Hopkins' Institute for Basic Biomedical Sciences.

The researchers' next steps are further study of the RET enhancers they found to identify other mutations that might contribute to Hirschsprung disease and MEN2, and to entice other investigators to collectively build a database of human enhancers. "If there's one thing we've learned here, it's that we are not very good at recognizing enhancers. We just don't know what they look like," says Fisher. "We are anxious for others to use this technology on their favorite genes."


TOPICS: Constitution/Conservatism; Culture/Society; Extended News
KEYWORDS: bewarefrevolutionist; creatards; creation; creationism; creationist; creationists; creationuts; crevolist; dna; evolution; evolutionist; frevolutionist; id; intelligentdesign; junkdna
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According to the evolutionist site Talk Origins, "In human beings 90-97% of the DNA is "junk DNA" that does nothing (as best as can be determined.)"

Wikipedia claims junk DNA "is probably an evolutionary artifact that serves no present-day purpose."

Of course, "junk DNA" and "no present-day purpose" really mean "we don't know what function some DNA serves, so we'll call it junk DNA for now."

This ignorance is what led to saying the appendix is useless, or tonsils. (See: Do any vestigial organs exist in humans?)

As science progresses, new functions are being discovered for this "junk" DNA, and evolutionists are having to eat crow.

See also:

‘Junk’ DNA: evolutionary discards or God’s tools?

DNA: marvelous messages or mostly mess?

'Junk' DNA reveals vital role

UCSD Study Shows 'Junk' DNA Has Evolutionary Importance

'Junk' throws up precious secret

Introns Stump Evolutionary Theorists

When "Junk" DNA Isn't Junk

Junk DNA (again)

Vestigial Organs Q & A

1 posted on 03/29/2006 5:46:24 PM PST by DaveLoneRanger
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To: gobucks; mikeus_maximus; MeanWestTexan; JudyB1938; isaiah55version11_0; bondserv; Elsie; ...


You have been pinged because of your interest regarding matters of Creation vs. Evolution - from the young-earth Creationist perspective. Freep-mail me if you want on/off this list.


Still trying to figure out why my comment below the post used double-spacing...
2 posted on 03/29/2006 5:48:01 PM PST by DaveLoneRanger (*Burp* I just got done chewing up a liberal. http://www.freerepublic.com/focus/f-news/1583155/posts)
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To: DaveLoneRanger
kind of like a moron that takes an engine apart and puts it back together and has a bunch of extra pieces left over, ahh those are just "junk pieces" they weren't needed anyhow, the engineers just put them in there cause they like to waste money.
3 posted on 03/29/2006 5:49:29 PM PST by Echo Talon
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To: PatrickHenry; Junior

(( ping ))


4 posted on 03/29/2006 5:51:57 PM PST by Virginia-American
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To: DaveLoneRanger

Who ever said that tonsils are useless or vestigal? I've never heard that.


5 posted on 03/29/2006 5:53:46 PM PST by Virginia-American
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To: DaveLoneRanger
Some scientists are clearly liberals and they are endlessly amusing.
If they don't understand it it either doesn't exist, or it has no purpose.

"Such large returns of conjecture from such small investment of fact"

6 posted on 03/29/2006 5:54:53 PM PST by Publius6961 (Multiculturalism is the white flag of a dying country)
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To: Virginia-American

Gracias.


7 posted on 03/29/2006 5:56:26 PM PST by Junior (Identical fecal matter, alternate diurnal period)
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To: DaveLoneRanger

If we ever get to the point of being able to accurately manipulate genes, would it be then possible to slip someone like Alec Baldwin a "gene pill" so he grows a penis on his head?


8 posted on 03/29/2006 5:57:47 PM PST by Screamname (Tagline)
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To: Fasciitis; PatrickHenry

dna ping


9 posted on 03/29/2006 5:58:01 PM PST by adam_az (It's the border, stupid!)
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To: DaveLoneRanger

10 posted on 03/29/2006 6:02:27 PM PST by ElkGroveDan (California bashers will be called out)
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To: Screamname
would it be then possible to slip someone like Alec Baldwin a "gene pill" so he grows a penis on his head?

You mean another one?

11 posted on 03/29/2006 6:05:42 PM PST by Bernard Marx (Fools and fanatics are always certain of themselves, but the wise are full of doubts.)
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To: Virginia-American
Who ever said that tonsils are useless or vestigal?

Alot of doctors used to believe that, its why removing tonsils was so popular for so many years.

I lucked out, my doctor (while being arrogant) was right in his point that if it was useless, then it wouldn't be there, and told my mother the other doctors were just idiots for always removing them.

12 posted on 03/29/2006 6:07:37 PM PST by Sonny M ("oderint dum metuant")
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Comment #13 Removed by Moderator

To: DaveLoneRanger
“In studying RET, the major gene implicated in Hirschsprung disease and multiple endocrine neoplasia (MEN2), the team identified DNA sequences that can control RET but had not been identified using standard methods. Hirschsprung disease, also known as congenital megacolon, is a relatively common birth defect marked by bowel obstruction.”

Will they claim this is the “gay gene” now???

Really... I saw someone the other day here on FR (one of the usual suspects) allude to “junk DNA” as having something to do with homosexual perversions.

14 posted on 03/29/2006 6:18:07 PM PST by Sir Francis Dashwood (LET'S ROLL!)
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Comment #15 Removed by Moderator

To: Sonny M
A lot of doctors used to believe that, its why removing tonsils was so popular for so many years.

Bill Clinton was trying to win the Stanley Cup in tonsil hockey!

16 posted on 03/29/2006 6:22:01 PM PST by Sir Francis Dashwood (LET'S ROLL!)
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To: Syncretic
Yet again it is shown that the scientific community does not know what in the hell they are talking about.

The paper was written by members of the scientific community.

If they don't know what they're talking about, then nothing was shown.

Elementary logic is your friend.

17 posted on 03/29/2006 6:23:47 PM PST by Right Wing Professor
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To: DaveLoneRanger
Of course, "junk DNA" and "no present-day purpose" really mean "we don't know what function some DNA serves, so we'll call it junk DNA for now."

Some non-coding DNA clearly does have a purpose. Some equally clearly does not. Finding a purpose for 0.001% of it doesn't really do much to change the picture.

18 posted on 03/29/2006 6:26:36 PM PST by Right Wing Professor
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To: DaveLoneRanger
As science progresses, new functions are being discovered for this "junk" DNA, and evolutionists are having to eat crow.

Whether there's a lot or a little noncoding DNA has little effect on whether evolution is true or not. DNA sequences have their utility (coding sequences a GREAT utility, most noncoding sequences not so much), but DNA also exerts a cost. Just what those costs & benefits are will depend on the species, and could fall anywhere along the spectrum from strongly favoring no noncoding DNA to allowing vast amounts of the stuff.

Nature. 2004 Oct 21;431(7011):988-93. Related Articles, Links

Megabase deletions of gene deserts result in viable mice.

Nobrega MA, Zhu Y, Plajzer-Frick I, Afzal V, Rubin EM.

DOE Joint Genome Institute Walnut Creek, California 94598, USA.

The functional importance of the roughly 98% of mammalian genomes not corresponding to protein coding sequences remains largely undetermined. Here we show that some large-scale deletions of the non-coding DNA referred to as gene deserts can be well tolerated by an organism. We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis. Further detailed analysis of the expression of multiple genes bracketing the deletions revealed only minor expression differences in homozygous deletion and wild-type mice. Together, the two deleted segments harbour 1,243 non-coding sequences conserved between humans and rodents (more than 100 base pairs, 70% identity). Some of the deleted sequences might encode for functions unidentified in our screen; nonetheless, these studies further support the existence of potentially 'disposable DNA' in the genomes of mammals.


19 posted on 03/29/2006 6:28:20 PM PST by jennyp (WHAT I'M READING NOW: your mind)
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To: jennyp

That's interesting. They removed 2.3 megabases, which sounds impressive, but it's only one tenth of one percent of the mouse genome.

However, on the ID hypothesis, *I'd* think there would be *no* unused DNA.

But until we can get a better description of the hypothetical designer's abilities and aims and so forth, no-one knows what to expect from the ID hypothesis.


20 posted on 03/29/2006 6:38:37 PM PST by Virginia-American
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