Study finds value in 'junk' DNA

October 17, 2008,

For about 15 years, scientists have known that certain "junk" DNA -- repetitive DNA segments previously thought to have no function -- could evolve into exons, which are the building blocks for protein-coding genes in higher organisms like animals and plants. Now, a University of Iowa study has found evidence that a significant number of exons created from junk DNA seem to play a role in gene regulation.

The findings, which increase understanding of how humans differ from other animals, including non-human primates, appear Oct. 17 in the open-access journal PLoS Genetics.

Nearly half of human DNA consists of repetitive DNA, including transposons, which can "transpose" or move around to different positions within the genome. A type of transposon called retrotransposons are transcribed into RNA and then reintegrated into the genomic DNA. The most common form of retrotransposons in the human genome are Alu elements, which have more than one million copies and occupy approximately 10 percent of the human genome.

"Alu elements are a major source of new exons. Because Alu is a primate-specific retrotransposon, creation of new exons from Alu may contribute to unique traits of primates, so we want to better understand this process," said the study's senior author Yi Xing, Ph.D., assistant professor of internal medicine and biomedical engineering, who holds a joint appointment in the University of Iowa Carver College of Medicine and the UI College of Engineering.

To study the impact of Alu-derived exons on human gene expression, the researchers used a high-density exon microarray. The technology has nearly six million probes for monitoring the expression patterns of all human exons. Using data generated by these microarrays, the scientists analyzed 330 Alu-derived exons in 11 human tissues. The team then identified a number of exons with interesting expression and functional characteristics.

"Hundreds of exons in the human genome were created from Alu elements. The whole-genome exon microarray allowed us to quickly identify exons that most likely contribute to the regulation of gene expression and function," said Lan Lin, Ph.D., University of Iowa postdoctoral fellow in internal medicine and the lead author of this study.

Analysis of one human gene, SEPN1, which is known to be involved in a type of muscular dystrophy, along with comparative data from chimpanzee and macaque tissues, suggested that the presence of a muscle-specific Alu-derived exon resulted from a human-specific change that occurred after humans and chimpanzees diverged evolutionarily.

"In this case, this exon is only expressed at a high level in the human muscle but not in any other human or non-human primate tissue, so this implies that the exon plays a functional role in muscle, and this role is human-specific," said Xing, who is also affiliated with University of Iowa Center for Bioinformatics and Computational Biology.

Source: University of Iowa

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27 comments

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markd7
3.4 / 5 (10) Oct 17, 2008
Can someone PLEASE bring this to the attention of the "intelligent design" wackos!
seversky
2.3 / 5 (8) Oct 17, 2008
How does this conflict with intelligent design?

I find it impossible to believe that any information storage and retrieval system can exist without design, and impossible to believe that design can come out of a truly random universe.
Geggamojja
3 / 5 (7) Oct 17, 2008
seversky, so you are basically saying that you don't understand the concept of evolution by natural selection. Maybe you should look it up.
D666
3.9 / 5 (9) Oct 17, 2008
I'd be willing to give the intelligent design people a bit of slack if they could come up with any evidence whatsoever of a designer. As it is, all we're getting is argument by disbelief, and it's disbelief by people who are ignorant of the basics of the subject.

I've sometimes thought that the best way to handle creationists might be to give them exactly what they want -- teach creationism in science class. But not just the christian version -- also the Hindu version, the Chinese version, the islamic version, every native american version you can find, etc. Compare the various creation myths and the writings that support them; contrast their complete lack of proof and unwillingness to test their beliefs with how science works; since this is now a valid educational subject, you could subject the bible to that same critical examination with probably devastating results; and most importantly -- have the science teacher do this, *without* any fundamentalists in the room to "correct" him. I'm thinking it may not go quite the way the creationists imagine it might.
seversky
2.3 / 5 (9) Oct 17, 2008
All life requires a coherent information system (DNA/RNA) to function and reproduce. I'm sure you are aware that the information system of even the simplest RNA-based organism is highly sophisticated.

Without going into the details (PM me if you care), the fact that this information system exists and serves a purpose requires that it was designed. If "junk" DNA does indeed serve a purpose, it demonstrates even further that it does not exist by accident.

It doesn't require intellectual suicide to believe in the existence of a designer.

By the way, Geggamojja, natural selection and intelligent design are not mutually exclusive.
Sophos
3 / 5 (3) Oct 17, 2008
I'm not sure what I believe but if some ultimate scientist created life wouldn't we eventually be able to understand it? And wouldn't the principles of physics still act on that life (i.e. random mutations?)
gmurphy
2.4 / 5 (5) Oct 17, 2008
seversky, the universe isn't random. it's built on well defined rules which facilitate the emergence of order. Of course initially everything was well scrambled but the distribution of energy throughout the universe facilitates the emergence of order. All life on our planet is simply the result of energy from the sun http://www.physor...868.html . Furthermore, it's an established observation that structure (emulating "design") can emerge from simple rule based systems http://en.wikiped...automata
seversky
3 / 5 (4) Oct 17, 2008
seversky, the universe isn't random. it's built on well defined rules which facilitate the emergence of order.


I agree.
itistoday
3 / 5 (2) Oct 17, 2008
I agree


Unfortunately (or fortunately), quantum mechanics disagrees with both of you.
seversky
2.3 / 5 (7) Oct 17, 2008
Unfortunately (or fortunately), quantum mechanics disagrees with both of you.


I have to disagree there. Quantum mechanics is revealing a reality that is more beautiful and intricately balanced than we could ever have imagined. Its paradoxes just demonstrate how limited we are in our 3-plus-1 dimensions.
math888
2.3 / 5 (6) Oct 17, 2008
For many years junk DNA was cited as evidence against design. It supposedly resulted from random events transforming a functional DNA segment into 'junk' - a leftover from evolution. The results of this and other studies showing that it's not 'junk' but has function effectively eliminate this argument against design.
Vovix
5 / 5 (1) Oct 17, 2008
>any information storage and retrieval system can exist without design

Learn Shannon's theory, plz. Information is everywhere. The ultimate its origin ("before the Big Bang") may be discussed or (un)believed, but since the BB everything seems to be going naturally.
D666
4.4 / 5 (7) Oct 17, 2008
the fact that this information system exists and serves a purpose requires that it was designed.


Simply not true. Saying it don't make it so.

If "junk" DNA does indeed serve a purpose, it demonstrates even further that it does not exist by accident.

Also not true.


It doesn't require intellectual suicide to believe in the existence of a designer.

Depends on whether your belief is conditional or absolute faith. If the latter, it is *by definition* intellectual suicide.


By the way, Geggamojja, natural selection and intelligent design are not mutually exclusive.


True in principle, but while there's vast evidence for natural selection (including but not limited to direct observation), there's no evidence for Intelligent Design, observational or otherwise. Making imperative statements like the two at the top doesn't prove anything. You have to *actually* show how your statements are logically inevitable. I've never yet seen an ID-advocate actually do so, although generally after producing several unsupported imperative statements, they will simply declare these to be a logical proof.

Unfortunately for you, since the physical laws of the universe very clearly *do* allow racheting up of complexity, as far as an intelligent designer is concerned, we have no need of that hypothesis.
itistoday
5 / 5 (3) Oct 18, 2008
I have to disagree there. Quantum mechanics is revealing a reality that is more beautiful and intricately balanced than we could ever have imagined. Its paradoxes just demonstrate how limited we are in our 3-plus-1 dimensions.


That's all wonderful but you said absolutely nothing there. Anyone who knows QM knows that true randomness plays a vital role in the universe.
seversky
not rated yet Oct 18, 2008
That's all wonderful but you said absolutely nothing there. Anyone who knows QM knows that true randomness plays a vital role in the universe.


Ah, I misunderstood your first post... you were talking about randomness and I was talking about rules.
seversky
not rated yet Oct 18, 2008
I should clarify. I think we're talking about 2 different kinds of randomness: the absence of predictability and the absence of adherence to a set of rules. Quantum Mechanics is built around the former, while my statement was referring to the latter.
itistoday
not rated yet Oct 18, 2008
seversky: Ah, in that case I agree. So far as recorded history has been able to tell, the laws of physics haven't changed (e.g. gravity attracts; when you drop a ball on Earth it falls "downwards", and always has).
k_m
1 / 5 (2) Oct 19, 2008
and maybe science is just figuring out how things work? WHY they work the way they do is philosophical at best.
fingersinterlaced
not rated yet Oct 19, 2008
There is a theory which states that if ever anyone discovers exactly what the Universe is for and why it is here, it will instantly disappear and be replaced by something even more bizarre and inexplicable.

There is another theory which states that this has already happened.
Douglas Adams
MVV
not rated yet Oct 19, 2008
If there is any design in the human body , we'll be searching for cosmic lawyers to field a suit for such a lousy work.

Now , on track again with the article , all this talk about this kind of dna starts for mislabeling that sections, for they are not "Junk" , it's simple we don't exactly know what they do, and since now we didn't catch them doing something usefull , it was assumed they were leftovers , so , junk.

If just they were called "mostly inactive and of unknown function" , we wouldn't be having any argument about design. But i suppose calling it Junk is more quick.
3lliot
not rated yet Oct 19, 2008
Has anyone ever considered that life itself might be its own 'strange attractor'?
kuczman
not rated yet Oct 19, 2008
http://www.physor...pix1835/
Reminder to the weak of mind, how life started on Earth. Mars lost its atmosphere early on so no surface evolution there it seems. But deep, underground who knows?
kuczman
not rated yet Oct 20, 2008
Has anyone ever considered that life itself might be its own 'strange attractor'?

Well, now you have started another endless debate.
Leading common folk right into creationists view of things. But rather than starting to disseminate it into right or wrong- I think this is the way the Universe works: from simple into complex and than self-concious.
3lliot
not rated yet Oct 20, 2008
I'm not a creationist... It's not a metaphysical idea really, it's just anti-entropic. A system with enough complexity leans towards order, rather than away from it. And let's face it, the universe after the big bang was an amazingly complex thing, it just had very little order. As it ages, the complexity doesn't increase, just the order in the complexity. Am I being contradictory?
Soylent
not rated yet Oct 20, 2008
All life requires a coherent information system (DNA/RNA) to function and reproduce. I'm sure you are aware that the information system of even the simplest RNA-based organism is highly sophisticated.


You're assuming that the simplest, most inefficient and uncompetitive RNA-based replicator that is thought to have started it all is still around; some 3.x billion years later while enduring though competition from its decendants. That's plainly unreasonable.

For all you and I know there could be many different combinations of RNA capable of catalysing their own replication in a suitable environment.
D666
4 / 5 (1) Oct 20, 2008

Now , on track again with the article , all this talk about this kind of dna starts for mislabeling that sections, for they are not "Junk" , it's simple we don't exactly know what they do, and since now we didn't catch them doing something usefull , it was assumed they were leftovers , so , junk.


I've never believed that the vast stretches of junk DNA were "just junk", so this revelation isn't much of a surprise. On the other hand, it's silly to swing all the way over to the other side now and say that since *some* of it apparently isn't junk, *all* of it must have some purpose. In fact there are lots of pieces of demonstratable junk or non-working DNA in the various genomes, most notably in cases where something that used to have a purpose now doesn't and has been deteriorating. A good example is the ice fish, which literally doesn't have haemoglobin in its blood. It does have a gene for haemoglobin, which is degenerate, i.e. has numerous errors in it, but is still recognizable the singer formerly known as haemoglobin gene. There are also gene sequences that are junk but not quite non-working, such as the stutter in the gene that causes Parkinson's.
MVV
not rated yet Oct 20, 2008

I've never believed that the vast stretches of junk DNA were "just junk", so this revelation isn't much of a surprise. On the other hand, it's silly to swing all the way over to the other side now and say that since *some* of it apparently isn't junk, *all* of it must have some purpose. In fact there are lots of pieces of demonstratable junk or non-working DNA in the various genomes, most notably in cases where something that used to have a purpose now doesn't and has been deteriorating. A good example is the ice fish, which literally doesn't have haemoglobin in its blood. It does have a gene for haemoglobin, which is degenerate, i.e. has numerous errors in it, but is still recognizable the singer formerly known as haemoglobin gene. There are also gene sequences that are junk but not quite non-working, such as the stutter in the gene that causes Parkinson's.


"Waste not..." seems to be nature motto. Any function that ever was usefull is packed , and in the rigth conditions , an unactivated dna strand could be reactivated. That we don't know how could something possibly be of use doesn't mean it can't be of use. I remember reading that some kind of Diabetes protects from frostbite , or something like that.

On the other side , current humans live long after their "certified" lifespan , thanks to drugs , controlled enviroment and so on , so Parkinsons , Alzehimer , etc are disorders rarely found on people under 35 years. We live long after nature has any use for us, so some of our "legacy code" gets corrupted or the safeguards relax.

We are not designed , but our grand-grandsons surely will.

Anyway , i regard your post as very accurate and to the point of the article. My respect.

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