Is this the end of "Junk" DNA?

[classical_hero]

http://www.sciencemag.org/content/337/6099/1159.summary

his week, 30 research papers, including six in Nature and additional papers published online by Science, sound the death knell for the idea that our DNA is mostly littered with useless bases. A decade-long project, the Encyclopedia of DNA Elements (ENCODE), has found that 80% of the human genome serves some purpose, biochemically speaking. Beyond defining proteins, the DNA bases highlighted by ENCODE specify landing spots for proteins that influence gene activity, strands of RNA with myriad roles, or simply places where chemical modifications serve to silence stretches of our chromosomes.

Or do old habits die hard?

[don_Durandal]

The only old habit that dies hard is how a combination of media cluelesness and misrepresentation aimed at an equally clueless public leads to people making wrong conclusion about the actual scientific facts.

See here:
http://www.forbes.com/sites/johnfarr...y-exaggerated/
http://arstechnica.com/staff/2012/09...tific-history/

[Sphere]

The best that can be said about these results is that they establish a lower bond of 20%. At least that much of the human genome is "junk" by any definition. They didn't actually find the function for 80% of the genome, they just established that it wasn't impossible for it to play a biological role. And as The Don shows from his well written sources, this value of 80% is mostly just a redefining of the definition of "functional DNA", and hasn't really expanded our understanding.

Even with this study, the safest assumption is still that the bulk of the human genome is some form of "junk" and doesn't play any active part in human biology.

[Aanker]

I find the ability of viruses to leave (for an organism) permanent modifications in the genome especially intriguing.

[Lord Baal]

I find the ability of viruses to leave (for an organism) permanent modifications in the genome especially intriguing.

Didn't you knew that? Geneticists use them all da time to inject DNA on specimens as far as I understand. Not that I really understand much of that. Astronomy and computers is my deal, not bioengineering.

[Aanker]

Didn't you knew that? Geneticists use them all da time to inject DNA on specimens as far as I understand. Not that I really understand much of that. Astronomy and computers is my deal, not bioengineering.

Of course I knew it. I just find the potential implications astonishing.

Gene therapy is an advancing field; in 2010 thalassemia was partially cured (not certain if the treatment was 100% effective) in a human specimen by the use of virus vectors.

When it comes to bioengineering, at least with bacteria, plasmids can be used.

[Phier]

In the end nothing of value was lost.

Anyone who gets their science news only from the popular press isn't exactly going to affect scientific progress. Now if this were a 'voting' issue it would be different, though I'm sure some creationists will twist this to continue to bamboozle the bamboozlable.

[Nutsack]

Is it possible that viruses have replicated by mixing their genetic code into other organisms, essentially becoming a part of it?

That might explain some of the junk DNA, although I'm sure there are better reasons.

[hellheaven1987]

Is it possible that viruses have replicated by mixing their genetic code into other organisms, essentially becoming a part of it?

Yap, in fact some virus can remain inactive in DNA until the condition is right.

That might explain some of the junk DNA, although I'm sure there are better reasons.

On the other hand I also think "junk" DNA may be a form of protective device against virus.

[Lord Baal]

Say what?? Hahahaha... I more or less get what you said. I was just joking on my first post.

[conon394]

Or do old habits die hard?

They do and usually not until there key pronates die and there ex graduate students loose funding...

In any case not as epic as the media would have, but a small victory for those who argue for a need to focus on the real complexity of the issue be in the Genome or in the interaction between Genes and Environment.

http://arstechnica.com/staff/2012/09...tific-history/

And as The Don shows from his well written sources

The funny thing is the Ars guy does the very thing he is pontificating about (I don't see a lot citation is that link). The fact is you could write a complete Mirror image article. I mean there are well funded, well established programs and experts in Genetics who simply don't talk to each other and would look and the same data with one saying black and the other white. The reality the conventional wisdom that filters down to Undergrad level or the science media is usually vociferously contested and always in flux in reality.

For example I would you could if you wanted find just as many well established well funded Geneticists who would likely say maybe Encode was a bit over the top but overall correct. Forbes looks to have been fishing for a story - if you are up on the Lit its easy to know who to call for a contrary opinion. I would also point out funding is a bitter ugly fight in US science and if you are excluded from Encode (and thus maybe other NIH funding since they tend to favor insiders or those who have proven track record or already large well connected operation etc) its easy to find dissenters.

[Logios]

I find the ability of viruses to leave (for an organism) permanent modifications in the genome especially intriguing.

This is one of the strongest driving forces of evolution, another is Transposons. By having non-coding DNA moving coding DNA areas apart some factors can be silenzed, and once in a blue moon this results in a more adaptable organism for the environment it is contained in. Radiation, UV light and mutagenic chemicals play only a minor role compared to this.

Is it possible that viruses have replicated by mixing their genetic code into other organisms, essentially becoming a part of it?

That might explain some of the junk DNA, although I'm sure there are better reasons.

Yes, that it how a lot of viruses actually work - at least those known as retroviruses.
And actually, you are right. Our genome contains a lot of DNA originating from viral infections in organisms eventually leading to human beings throughout the span of evolution.
http://en.wikipedia.org/wiki/Retrovirus

Spoiler Alert, click show to read: 

When retroviruses have integrated their own genome into the germ line, their genome is passed on to a following generation. These endogenous retroviruses (ERVs), contrasted with exogenous ones, now make up 5-8% of the human genome.[5] Most insertions have no known function and are often referred to as "junk DNA". However, many endogenous retroviruses play important roles in host biology, such as control of gene transcription, cell fusion during placental development in the course of the germination of an embryo, and resistance to exogenous retroviral infection. Endogenous retroviruses have also received special attention in the research of immunology-related pathologies, such as autoimmune diseases like multiple sclerosis, although endogenous retroviruses have not yet been proven to play any causal role in this class of disease.[6]

[Slaytaninc]

I'm not very scientifically minded, but I once imagined being wealthy just so I could finance research "just because"

[Adar]

Quite frankly, I don't believe in junk DNA as it just doesn't make sense for the genome to be unnecessarily large.

That being said the importance of different pieces is going to differ immensely. The majority of it is most likely only there as spacers when wrapping genes around histones and other low impact "value". And of course some sections might just not have been weeded out yet after viral infections or random mutations.

[Phier]

Quite frankly, I don't believe in junk DNA as it just doesn't make sense for the genome to be unnecessarily large.

That being said the importance of different pieces is going to differ immensely. The majority of it is most likely only there as spacers when wrapping genes around histones and other low impact "value". And of course some sections might just not have been weeded out yet after viral infections or random mutations.

A secondary "use" for junk DNA might be as primers for mutations and evolution itself. Many changes seem to require a neutral change or two prior to becoming a beneficial mutation. Perhaps the "junk" itself helps facilitate evolution in this respect.

[Aanker]

Anything that doesn't leave the carrier of "junk DNA" at a distinct disadvantage would take time to disappear from the genome. One could also assume that there comes an evolutional advantage in having some junk DNA that can mutate and code for functional, beneficial proteins (although those cases are rare).

[The Hedge Knight]

Anything that doesn't leave the carrier of "junk DNA" at a distinct disadvantage would take time to disappear from the genome. One could also assume that there comes an evolutional advantage in having some junk DNA that can mutate and code for functional, beneficial proteins (although those cases are rare).

Arguably Eukaryotes don't have a high selection pressure for losing DNA unlike bacteria/archea as Eukaryotes generally have an evolutionary stable strategy of being adaptable and specific allowing them to out compete others. Bacteria on the other hand are selected for a smaller genome as the primary method of bacterial competition is reproduction, a smaller DNA sequence allows for faster reproduction hence any bacteria that can drop part of its genome while remaining as efficient at surviving in a given situation will out generally compete others. Eukaryotes on the contrary predate one another and do not simply reproduce as fast as possible hence things like energy efficiency are selected for leading to a larger genome. This also allows eukaryotes to grow larger and occupy niches which bacteria cannot.

Saying the advantage is in the increased chance mutation to beneficial proteins strikes me as likely to be untrue, evolution has no foresight so it is not possible to select for a large quantity of unused DNA. It also seems unlikely that the chance of a random useful protein spontaneously forming from junk dna is high enough given the specificity of protein coding sequences to give any selective advantage.

[removeduser_4536284751384]

There are selection pressures on most creatures that select for DNA efficiency though. Sperm motility is directly related to the load of the DNA it carries.

[Aanker]

There are selection pressures on most creatures that select for DNA efficiency though. Sperm motility is directly related to the load of the DNA it carries.

On the other hand the presence of old viral remnants in the genome is counterindicative to the conclusion that would be made following the above assertion (whether true or not).

@THK: evolution has no foresight but the presence of non-coding "expendable" regions offers an advantage nonetheless, similar to how our nose was never "intended" as a rest for our future glasses but nonetheless offers the ability to wear such devices. In that sense, the junk DNA would offer an "unintended" advantage. However it seems unlikely that an organism would create spaces of unused DNA to be mutated.

[Elfdude]

A huge part of the junk DNA also comprises evolutionary remnants of currently inactive code which could be turned on if we were to change the activators. This is how we can make a bird with a toothy dinosaur snout.