Research team finds important role for junk DNA

News at Princeton ^ | 5/22/2009 | Kitta MacPherson

[SeekAndFind]

Scientists have called it "junk DNA." They have long been perplexed by these extensive strands of genetic material that dominate the genome but seem to lack specific functions. Why would nature force the genome to carry so much excess baggage?

Now researchers from Princeton University and Indiana University who have been studying the genome of a pond organism have found that junk DNA may not be so junky after all. They have discovered that DNA sequences from regions of what had been viewed as the "dispensable genome" are actually performing functions that are central for the organism. They have concluded that the genes spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow.

It all happens very quickly. Genes called transposons in the single-celled pond-dwelling organism Oxytricha produce cell proteins known as transposases. During development, the transposons appear to first influence hundreds of thousands of DNA pieces to regroup. Then, when no longer needed, the organism cleverly erases the transposases from its genetic material, paring its genome to a slim 5 percent of its original load.

"The transposons actually perform a central role for the cell," said Laura Landweber, a professor of ecology and evolutionary biology at Princeton and an author of the study. "They stitch together the genes in working form." The work appeared in the May 15 edition of Science.

In order to prove that the transposons have this reassembly function, the scientists disabled several thousand of these genes in some Oxytricha. The organisms with the altered DNA, they found, failed to develop properly.

Other authors from Princeton's Department of Ecology and Evolutionary Biology include: postdoctoral fellows Mariusz Nowacki and Brian Higgins; 2006 alumna Genevieve Maquilan; and graduate student Estienne Swart. Former Princeton postdoctoral fellow Thomas Doak, now of Indiana University, also contributed to the study.

Landweber and other members of her team are researching the origin and evolution of genes and genome rearrangement, with particular focus on Oxytricha because it undergoes massive genome reorganization during development.

In her lab, Landweber studies the evolutionary origin of novel genetic systems such as Oxytricha's. By combining molecular, evolutionary, theoretical and synthetic biology, Landweber and colleagues last year discovered an RNA (ribonucleic acid)-guided mechanism underlying its complex genome rearrangements.

"Last year, we found the instruction book for how to put this genome back together again -- the instruction set comes in the form of RNA that is passed briefly from parent to offspring and these maternal RNAs provide templates for the rearrangement process," Landweber said. "Now we've been studying the actual machinery involved in the process of cutting and splicing tremendous amounts of DNA. Transposons are very good at that."

The term "junk DNA" was originally coined to refer to a region of DNA that contained no genetic information. Scientists are beginning to find, however, that much of this so-called junk plays important roles in the regulation of gene activity. No one yet knows how extensive that role may be.

Instead, scientists sometimes refer to these regions as "selfish DNA" if they make no specific contribution to the reproductive success of the host organism. Like a computer virus that copies itself ad nauseum, selfish DNA replicates and passes from parent to offspring for the sole benefit of the DNA itself. The present study suggests that some selfish DNA transposons can instead confer an important role to their hosts, thereby establishing themselves as long-term residents of the genome.

[SeekAndFind]

Here is how Intelligent Design Theorists would read it see here : http://www.uncommondescent.com/intelligent-design/another-important-unexpected-role-for-junk-dna/ :

As predicted by Intelligent Design theorists “researchers from Princeton and Indiana University have found that junk DNA may not be so junky after all. They have discovered that DNA sequences from regions of what had been viewed as the “dispensable genome” are actually performing functions that are central for the organism.

The term “junk DNA” was originally coined (by Darwinian biologists) to refer to a region of DNA that (they wrongly concluded because of their philosophical committment) contained no genetic information. Scientists are beginning to find, (as predicted by Intelligent Design theorists), that much of this so-called junk plays important roles in the regulation of gene activity.

[wombtotomb]

As I posted the last time this story was on here, God doesn’t make junk!

[bgill]

Some have more junk in their trunk than others.

[chuck_the_tv_out]

"The term "junk DNA" was originally coined ..."

here are some other worthless coins:

[Mrs. Don-o]

This phrase struck me:

"The present study suggests that some selfish DNA transposons can instead confer an important role to their hosts, thereby establishing themselves as long-term residents of the genome."

I'm very ignorant about this, so I have to ask: is this the typical or routine way that genetic researchers refer to DNA particles, as "residents" of the "host" organism? It makes it sound as if the DNA transposons are interlopers, not actually a part of the organism as a whole.

Why wouldn't the author have put it this way:

"The present study suggests that so-called "selfish DNA transposons" in fact play an important role in the genome as a whole, thereby demonstrating that they essential to the well-being of the organism."

???

[syriacus]

Interesting! Thanks for posting this.

[Senator John Blutarski]

The illogicality of assuming that something is worthless simply because one fails to understand it is apparent here.

[BroJoeK]

"The term “junk DNA” was originally coined (by Darwinian biologists) to refer to a region of DNA that (they wrongly concluded because of their philosophical committment) contained no genetic information. Scientists are beginning to find, (as predicted by Intelligent Design theorists), that much of this so-called junk plays important roles in the regulation of gene activity."

You make a strained and strange argument here.

In the beginning of DNA analysis, biologists could see no function for certain genetic sequences, so someone gave those sections the catchy label "junk DNA." "Philosophical commitment" had nothing to do with it.

Now some of those same biologists, on further study, have found some (not all) "junk DNA" sequences actually do play important roles. Some new "Philosophical commitment" had nothing to do with the new findings.

And you claim this a "victory" for "intelligent design"?
I'd say it's a victory for science, and "intelligent design" like beauty, is in the eye of the beholder. ;-)

[SeekAndFind]

Well, a little history would be useful for us here since we are talking about scientific predictions based on one’s presuppositions ...

it is worth citing William Dembski from First Things, 1998, on Junk DNA:

. . . Consider the term “junk DNA.” Implicit in this term is the view that because the genome of an organism has been cobbled together through along, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as “junk” merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how “non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development.” Design encourages scientists to look for function where evolution discourages it.”

Now let’s cite the prediction made by the committed atheist and evolutionist, Richard Dawkins. As late as 2003 - 4, Mr Dawkins was still confidently asserting:

“Genomes are littered with nonfunctional pseudogenes, faulty duplicates of functional genes that do nothing, while their functional cousins (the word doesn’t even need scarequotes) get on with their business in a different part of the same genome. And there’s lots more DNA that doesn’t even deserve the name pseudogene. It too is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, ‘tandem repeats,’ and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself. . . . Creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudognes and junk tandem repeat DNA. [A Devil’s Chaplain, p. 98]

Looks like the despised ID thinkers (and the even more despised Creationists), are turning out to be right on the functionality of the so-called junk DNA; and on what evolutionary materialism led Mr Dawkins and others committed to his paradigm to erroneously perceive and expect!

[BroJoeK]

"Looks like the despised ID thinkers (and the even more despised Creationists), are turning out to be right on the functionality of the so-called junk DNA; and on what evolutionary materialism led Mr Dawkins and others committed to his paradigm to erroneously perceive and expect!"

I won't defend Dawkins, but I do defend science, as best I can.

Science today is a long way from yet saying that every single DNA "letter" has a definite use, or is something more than "junk DNA."

When that day comes, then I'll be most impressed. Until then, "junk DNA" is still out there, and seems to serve an extraordinarily useful purpose -- but not in controlling any organism.

The extraordinarily useful "purpose" of "junk DNA" turns out be: benefiting scientists by serving as a harmless place for the accumulation of random mutations.

And by counting up these mutations in related species, scientists can estimate how long it's been since their most recent common ancestor.

Now, to a guy like me, who firmly believes that God wants us to understand just what He did, and how He did it, these mutations in the "junk DNA" are miracles of God, and firm evidence of "Intelligent Design."

Of course, that's probably not quite what you had in mind, right? ;-)

[allmendream]

Junk is what you have up in the attic.

Garbage is what you throw out in the dumpster.

Biologists referred to non genetic or regulatory DNA as “junk” DNA, not “garbage” DNA.

Junk sits around in the attic mostly unused, but some stuff like transposons are there like a box marked “Christmas decorations” to be dragged out to be useful for special occasions.