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#1 deadlock

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Posted 03 September 2008 - 09:27 AM

New findings challenge beliefs about DNA

New studies show the 3 bn letters of the human genetic code toiling away at an array of previously invisible tasks

THE first concerted effort to understand the inner workings of the DNA molecule is overturning a host of long-held assumptions about the nature of genes and their role in human health and evolution. The new perspective reveals DNA to be a dauntingly complex operating system that processes many more kinds of information than previously appreciated.

The findings—from a project involving hundreds of scientists in 11 countries and detailed in 29 papers—confirm growing suspicions that the vast stretches of so-called “junk DNA” flanking hardworking genes are not junk at all. But the study goes further, indicating for the first time that the most of the three billion letters of the human genetic code are busily toiling at an array of previously invisible tasks.

The new work also overturns the conventional notion that genes are discrete packets of information arranged like beads on a thread of DNA. Instead, many genes physically overlap and share common stretches of molecular code. As with phone lines that carry many voices at once, that arrangement has prompted the evolution of complex switching, splicing and silencing mechanisms to sort out the interwoven messages.

One implication is that most genetic diseases come from errors in the DNA between genes rather than within the gene. Complicating the picture further, it turns out that genes and the DNA sequences that regulate their activity are often far apart along the 6-ft-long strands of DNA inside each cell. How they communicate is still largely a mystery.

“There’s a lot more going on than we thought,” said Francis Collins, director of the National Human Genome Research Institute, the part of the National Institutes of Health that financed most of the $42 million project.

“It’s like trying to read and understand a very complicated Chinese novel,” said Eric Green, the institute’s scientific director. “The take-home message is, ‘Oh my gosh, this is really complicated.”

The findings come from the Encyclopedia of DNA Elements project, nicknamed ENCODE. While much of the decades-long effort to understand DNA’s role in health and disease has been driven by scientists’ interest in particular genes, ENCODE focused on a representative 1 per cent of the genome. Using a variety of experimental and computational approaches, the researchers sought to catalogue absolutely everything going on there.

The 3 1/2-year effort was designed to see if it would be practical to study the entire genome in such depth—and to hasten development of cheaper tools to do so. So successful was ENCODE, Collins said, that the other 99 percent of the genome is now expected to be studied the same way for just $100 million.

Perhaps most surprising was how much of the human genome is at work at any given time, the scientists said. Researchers have long known that only about 2 per cent of human DNA is involved in making proteins, the molecular workhorses inside cells. That involves a two-step process in which a stretch of DNA—a gene—serves as a template to produce a strand of RNA, which is then used as a template to produce a protein.

Recent studies had shown that some snippets of DNA in between genes also get transcribed into RNA even though they do not go on to make protein.
Surprisingly, though, the new work shows that most of a cell’s DNA gets transcribed, raising big questions as to what all that RNA is doing.

“We are increasingly being forced to pay attention to our non-gene DNA sequences,” wrote John Greally, of the Albert Einstein College of Medicine in New York, in a commentary in the journal Nature, where one of the new reports was published on Thursday. The other 28 papers appear in Genome Research.

While the new view of the genome may at first complicate efforts to identify DNA stretches of prime medical interest, ENCODE is sure to help in the long run, said Michael Snyder of Yale University, another coordinator.

“Defining the functional elements helps us zoom in to look for differences in sequence that might relate to disease,” Snyder said.

New findings challenge beliefs about DNA

#2 scott

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Posted 08 September 2008 - 12:12 PM

Ok the Junk DNA theory was junk and absurd to have even been made in the first place. Just because you dont know what something does, doesnt mean its junk. Calling the unknown parts of DNA junk is like someone calling the engine of a car
junk, simply because he or she doesnt know how it works. Not knowing what something is, or does, never justifies by calling it junk. Calling something you dont understand junk is very juvenile, and ive always thought this way toward the evolutionist who called it junk.

I'm almost positive that in the future all parts of the DNA will be found out, as to what each function of its parts are. I'm also thankful that they are actually researching this instead of being naive and accepting it as junk. So I say thank you to all the scientist who put their hard work into researching this!

#3 A.Sphere

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Posted 08 September 2008 - 12:38 PM

New findings challenge beliefs about DNA

New studies show the 3 bn letters of the human genetic code toiling away at an array of previously invisible tasks

    THE first concerted effort to understand the inner workings of the DNA molecule is overturning a host of long-held assumptions about the nature of genes and their role in human health and evolution. The new perspective reveals DNA to be a dauntingly complex operating system that processes many more kinds of information than previously appreciated.

        The findings—from a project involving hundreds of scientists in 11 countries and detailed in 29 papers—confirm growing suspicions that the vast stretches of so-called “junk DNA” flanking hardworking genes are not junk at all. But the study goes further, indicating for the first time that the most of the three billion letters of the human genetic code are busily toiling at an array of previously invisible tasks.

      The new work also overturns the conventional notion that genes are discrete packets of information arranged like beads on a thread of DNA. Instead, many genes physically overlap and share common stretches of molecular code. As with phone lines that carry many voices at once, that arrangement has prompted the evolution of complex switching, splicing and silencing mechanisms to sort out the interwoven messages.

      One implication is that most genetic diseases come from errors in the DNA between genes rather than within the gene. Complicating the picture further, it turns out that genes and the DNA sequences that regulate their activity are often far apart along the 6-ft-long strands of DNA inside each cell. How they communicate is still largely a mystery.

        “There’s a lot more going on than we thought,” said Francis Collins, director of the National Human Genome Research Institute, the part of the National Institutes of Health that financed most of the $42 million project.

        “It’s like trying to read and understand a very complicated Chinese novel,” said Eric Green, the institute’s scientific director. “The take-home message is, ‘Oh my gosh, this is really complicated.”

      The findings come from the Encyclopedia of DNA Elements project, nicknamed ENCODE. While much of the decades-long effort to understand DNA’s role in health and disease has been driven by scientists’ interest in particular genes, ENCODE focused on a representative 1 per cent of the genome. Using a variety of experimental and computational approaches, the researchers sought to catalogue absolutely everything going on there.

          The 3 1/2-year effort was designed to see if it would be practical to study the entire genome in such depth—and to hasten development of cheaper tools to do so. So successful was ENCODE, Collins said, that the other 99 percent of the genome is now expected to be studied the same way for just $100 million.

          Perhaps most surprising was how much of the human genome is at work at any given time, the scientists said. Researchers have long known that only about 2 per cent of human DNA is involved in making proteins, the molecular workhorses inside cells. That involves a two-step process in which a stretch of DNA—a gene—serves as a template to produce a strand of RNA, which is then used as a template to produce a protein.

              Recent studies had shown that some snippets of DNA in between genes also get transcribed into RNA even though they do not go on to make protein.
          Surprisingly, though, the new work shows that most of a cell’s DNA gets transcribed, raising big questions as to what all that RNA is doing.

              “We are increasingly being forced to pay attention to our non-gene DNA sequences,” wrote John Greally, of the Albert Einstein College of Medicine in New York, in a commentary in the journal Nature, where one of the new reports was published on Thursday. The other 28 papers appear in Genome Research.

            While the new view of the genome may at first complicate efforts to identify DNA stretches of prime medical interest, ENCODE is sure to help in the long run, said Michael Snyder of Yale University, another coordinator.

“Defining the functional elements helps us zoom in to look for differences in sequence that might relate to disease,” Snyder said.

New findings challenge beliefs about DNA

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This is old news - circa 2007.

#4 A.Sphere

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Posted 08 September 2008 - 12:43 PM

Ok the Junk DNA theory was junk and absurd to have even been made in the first place.  Just because you dont know what something does, doesnt mean its junk. Calling the unknown parts of DNA junk is like someone calling the engine of a car
junk, simply because he or she doesnt know how it works.  Not knowing what something is, or does, never justifies by calling it junk.  Calling something you dont understand junk is very juvenile, and ive always thought this way toward the evolutionist who called it junk.

I'm almost positive that in the future all parts of the DNA will be found out, as to what each function of its parts are. I'm also thankful that they are actually researching this instead of being naive and accepting it as junk.  So I say thank you to all the scientist who put their hard work into researching this!

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Nope. Scientists have known for a long time that some non-coding DNA has function however there is pretty strong evidence that most of it does not. They have cut, removed, shuffled, and replaced "junk" DNA without any affect to the organism.

#5 scott

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Posted 08 September 2008 - 01:37 PM

Personnally I know its old news, I read about it a year ago before I even came to this site, just wanted to post what I thought about it.

Also if you truly think junk DNA should be labled junk DNA before its discovered what it is, then I would have to wonder if when you were younger, that you called the English language junk, simply because you didnt understand it.

And on another point that is truth, it was thought by evolutionist that it would simply be marvelous to call what they didnt understand junk, because it would fit nicely with the trial and error evolution that they believe. Simply because they knew that since no one else had an answer for the unanswered, they had one.

#6 ikester7579

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Posted 08 September 2008 - 04:55 PM

Ok the Junk DNA theory was junk and absurd to have even been made in the first place.  Just because you dont know what something does, doesnt mean its junk. Calling the unknown parts of DNA junk is like someone calling the engine of a car
junk, simply because he or she doesnt know how it works.  Not knowing what something is, or does, never justifies by calling it junk.  Calling something you dont understand junk is very juvenile, and ive always thought this way toward the evolutionist who called it junk.

I'm almost positive that in the future all parts of the DNA will be found out, as to what each function of its parts are. I'm also thankful that they are actually researching this instead of being naive and accepting it as junk.  So I say thank you to all the scientist who put their hard work into researching this!

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It falls in-line with the claims that our appendix had no real function, and therefore was a supposed organ that was not needed. And then was used in several debates to make God's creation look stupid. Why create things that are not needed, is what the evolutionists would say. To later find out that the appendix plays an important role in our immune system.

So junk DNA was used for the same reason. And the same logic of: Why would God create junk DNA? Here again the statement leaves the evolutionists with their foot in their mouths as they look stupid once again for making such a prediction, then having it proven wrong.

It kinda fits the verse that says: They thought themselves wise but became ....?

But you won't hear any apologies from their side of the issue because they can never be wrong. Theories are just an excuse that allows them to be wrong on so many levels, but yet look right anyway. Skate by with a scientific explanation that sounds more like a political dodge of the issues at hand.

I try not to stereotype people into one box, but it's hard not to when so many use the same arguments that get proven wrong. And then they act as if it never happened, or they never claimed that. It's like the two new movements to distance evolution from origins by making a new category called abiogenesis. So that the problems of origins can be pointed towards abiogenesis instead of evolution. The other movement s to steer evolution away from ever claiming we evolved from apes or chimps. And to only claim we have a common ancestor instead. When those claims can be looked up in text books that are not to many years old.

Switching ideas does not get science out of being wrong. It shows their inability to admit to being wrong, learning from it, and moving on. It's goes along the same pattern as ignoring or denying past history of wrong doings connected to the theory of evolution. History does not change just because some people decide to deny it or ignore it. And it has been proven that if we refuse to learn from our mistakes from past history, we will be doomed to repeat them.

#7 scott

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Posted 08 September 2008 - 05:12 PM

ikester, I totally agree. Its extremely hard to demonstrate this to someone who thinks they are never wrong. Time is pictured as evolutionist best friend, but as time goes, its gradually proving their assumptions wrong.

#8 deadlock

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Posted 09 September 2008 - 02:58 AM

This is old news -  circa 2007.

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And so what ? Isn´t it true anymore ?

#9 A.Sphere

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Posted 09 September 2008 - 07:50 AM

And so what ? Isn´t it true anymore ?

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Not what I meant - in bold face letters you have copied and pasted "New findings challenge beliefs about DNA" which leads the reader to assume that this was just printed. I wanted to clear up that it was old news.

#10 A.Sphere

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Posted 09 September 2008 - 07:53 AM

ikester, I totally agree.  Its extremely hard to demonstrate this to someone who thinks they are never wrong.  Time is pictured as evolutionist best friend, but as time goes, its gradually proving their assumptions wrong.

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Right - it is hard because you need to provide evidence. Scientist wanted to test their theory about what junk DNA is by removing it, reshuffling it, and etc and found no change to the organism. How would you have them test that? What other method exists? Scientists have strong evidence that much of DNA has no function.

#11 scott

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Posted 09 September 2008 - 08:14 PM

Offcourse if you take one cell from an animal, take what you suppose is junk DNA out of the cell, then put it back in, the animal will be just fine. Now assuming that they took the junk DNA out of an egg cell and a sperm cell, and then produced a completely unharmed animal, without any deffects then offcourse I stand corrected. If not, then they will need to try a little harder next time.

#12 A.Sphere

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Posted 09 September 2008 - 08:48 PM

Offcourse if you take one cell from an animal, take what you suppose is junk DNA out of the cell, then put it back in, the animal will be just fine.  Now assuming that they took the junk DNA out of an egg cell and a sperm cell, and then produced a completely unharmed animal, without any deffects then offcourse I stand corrected.  If not, then they will need to try a little harder next time.

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When I said removing, shuffling etc I meant that they have done both of those things independently. Meaning they have removed the DNA and nothing happened and so on.

#13 scott

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Posted 09 September 2008 - 09:01 PM

When I said removing, shuffling etc I meant that they have done both of those things independently.  Meaning they have removed the DNA and nothing happened and so on.

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So I am supposed to believe that they produced a kitten using only 2 percent DNA?
This is sketchy and hard to believe, maybe this isn't what you meant.

#14 CTD

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Posted 09 September 2008 - 09:55 PM

(I too, am fond of automotive analogies.)

Remove the brakes from a car and it'll run just fine.

Until...

#15 deadlock

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Posted 10 September 2008 - 03:17 AM

When I said removing, shuffling etc I meant that they have done both of those things independently.  Meaning they have removed the DNA and nothing happened and so on.

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The wheels of my car have 4 bolts, But they work fine with only three.Perhaps, is the fourth a junk-bolt ?

I have clients that use double-servers.The second just mirrors the first.Is the second one a Junk-Server ?

#16 A.Sphere

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Posted 10 September 2008 - 08:20 AM

So I am supposed to believe that they produced a kitten using only 2 percent DNA?
This is sketchy and hard to believe, maybe this isn't what you meant.

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They didn't remove all suspected junk DNA - just some of it.

#17 deadlock

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Posted 08 November 2008 - 02:29 AM

Right - it is hard because you need to provide evidence.  Scientist wanted to test their theory about what junk DNA is by removing it, reshuffling it, and etc and found no change to the organism.  How would you have them test that?  What other method exists?  Scientists have strong evidence that much of DNA has no function.

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The prediciton keeps on being fulfilled :

'Junk' DNA proves functional

More than 50 percent of human DNA has been referred to as "junk" because it consists of copies of nearly identical sequences. A major source of these repeats is internal viruses that have inserted themselves throughout the genome at various times during mammalian evolution.

Using the latest sequencing technologies, GIS researchers showed that many transcription factors, the master proteins that control the expression of other genes, bind specific repeat elements. The researchers showed that from 18 to 33% of the binding sites of five key transcription factors with important roles in cancer and stem cell biology are embedded in distinctive repeat families.

Over evolutionary time, these repeats were dispersed within different species, creating new regulatory sites throughout these genomes. Thus, the set of genes controlled by these transcription factors is likely to significantly differ from species to species and may be a major driver for evolution.

This research also shows that these repeats are anything but "junk DNA," since they provide a great source of evolutionary variability and might hold the key to some of the important physical differences that distinguish humans from all other species.

The GIS study also highlighted the functional importance of portions of the genome that are rich in repetitive sequences.

"Because a lot of the biomedical research use model organisms such as mice and primates, it is important to have a detailed understanding of the differences between these model organisms and humans in order to explain our findings," said Guillaume Bourque, Ph.D., GIS Senior Group Leader and lead author of the Genome Research paper.

"Our research findings imply that these surveys must also include repeats, as they are likely to be the source of important differences between model organisms and humans," added Dr. Bourque. "The better our understanding of the particularities of the human genome, the better our understanding will be of diseases and their treatments."

"The findings by Dr. Bourque and his colleagues at the GIS are very exciting and represent what may be one of the major discoveries in the biology of evolution and gene regulation of the decade," said Raymond White, Ph.D., Rudi Schmid Distinguished Professor at the Department of Neurology at the University of California, San Francisco, and chair of the GIS Scientific Advisory Board
.

"We have suspected for some time that one of the major ways species differ from one another – for instance, why rats differ from monkeys – is in the regulation of the expression of their genes: where are the genes expressed in the body, when during development, and how much do they respond to environmental stimuli," he added.

"What the researchers have demonstrated is that DNA segments carrying binding sites for regulatory proteins can, at times, be explosively distributed to new sites around the genome, possibly altering the activities of genes near where they locate. The means of distribution seem to be a class of genetic components called 'transposable elements' that are able to jump from one site to another at certain times in the history of the organism. The families of these transposable elements vary from species to species, as do the distributed DNA segments which bind the regulatory proteins."

Dr. White also added, "This hypothesis for formation of new species through episodic distributions of families of gene regulatory DNA sequences is a powerful one that will now guide a wealth of experiments to determine the functional relationships of these regulatory DNA sequences to the genes that are near their landing sites. I anticipate that as our knowledge of these events grows, we will begin to understand much more how and why the rat differs so dramatically from the monkey, even though they share essentially the same complement of genes and proteins."


Physorg

What is laughable in all this, is that JUNK DNA was evidence of evolution and now that it´s not JUNK anymore, it´s evidence of evolution.Eveything is evidence of evolution :lol:

#18 jason777

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Posted 08 November 2008 - 12:20 PM

Remember,to an evolutionist nothing makes sense but evolution,no evidence needed.

#19 BVZ

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Posted 09 November 2008 - 11:18 PM

Biologists say that most non-coding DNA has no function.

The discovery that some non-coding DNA DOES have a function requires biologists to rethink a few things.

Can someone please tell me how non-coding DNA that has a function is a problem for the theory of evolution?

#20 deadlock

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Posted 10 November 2008 - 05:45 AM

Biologists say that most non-coding DNA has no function.

The discovery that some non-coding DNA DOES have a function requires biologists to rethink a few things.

Can someone please tell me how non-coding DNA that has a function is a problem for the theory of evolution?

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Because of mutation.It´s expected that mutation, being a random process, leaves some garbage from ancient traits.And The bigger is the coding region, the greater is the genetic load.

For more details : Monkey-Man Hypothesis Thwarted by Mutation Rates




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