Junk No More: ENCODE Project Nature Paper Finds "Biochemical Functions for 80% of the

[empirex]

Seems another prediction Intelligent Design got right

Junk No More: ENCODE Project Nature Paper Finds "Biochemical Functions for 80% of the Genome"

A groundbreaking paper in Nature reports the results of the Encyclopedia of DNA Elements (ENCODE) project, which has detected evidence of function for the "vast majority" of the human genome. Titled "An integrated encyclopedia of DNA elements in the human genome," the paper finds an "unprecedented number of functional elements," where "a surprisingly large amount of the human genome" appears functional. Based upon current knowledge, the paper concludes that at least 80% of the human genome is now known to be functional:

The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many

discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation.
(The ENCODE Project Consortium, "An integrated encyclopedia of DNA elements in the human genome," Nature, Vol. 489:57-74 (September 6, 2012)​

Read more here

 

[copacetic]

This should be interesting.

*popcorn*

 

[copacetic]

The accepted notion has been that 98 percent of the human genome is “noncoding DNA” – that is, not associated with encoding protein strings. If that figure were slashed to 20 percent, it would clearly be a genetic revolution.

Would it surprise any seasoned Register reader to think there’s more nuance in the story than appears at first glance? Of course not.

It boils down to defining what is “functional”. The layperson probably thinks “functional” DNA strings have a specific expression – that the functions discovered by ENCODE are, in other words, somehow analogous to the genes that give us blue eyes, red hair, that regulate melanin in the skin or whatever.

ENCODE, however, has used a much broader definition of function: if any specific biological activity could be tagged to a gene, it was described as functional. As Canadian biologist notes, that’s a broad stretch. It means that even being replicated counts as a “function” (that is, if this gene string gets copied accurately in the next copy of a human genome, it’s performed a function).

The authors of the Nature paper agree, in fact: they make the more conservative – and interesting – claim that a sizeable chunk (20 percent) of DNA thought to be inactive is actually involved in regulating that tiny proportion (two percent) of the human genome that actually encodes protein sequences.

Worst of all, according to sci-bloggers like Nick Matzke on his Panda’s Thumb blog: the inflated “80 percent” claim gives considerable aid and comfort to creationists. The study “provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called "junk" DNA”, says Evolution News, for example.

It would be a pity if this argument distracted attention from the real value of the ENCODE work: the human genome is a huge and complex beast, and the better it's catalogued and understood - including the "junk DNA" - the better our tools for battling genetic disease will become.

http://www.theregister.co.uk/2012/09/06/bio_boffin_bunfight/

 

[empirex]

It boils down to defining what is “functional”. The layperson probably thinks “functional” DNA strings have a specific expression – that the functions discovered by ENCODE are, in other words, somehow analogous to the genes that give us blue eyes, red hair, that regulate melanin in the skin or whatever.

ID has never ever restricted it to this strawman caricature.

I really have to stop myself from belly-laughing here:

Worst of all, according to sci-bloggers like Nick Matzke on his Panda’s Thumb blog: the inflated “80 percent” claim gives considerable aid and comfort to creationists. The study “provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called "junk" DNA”, says Evolution News, for example.

Yes, it's absolutely terrible that evidence continues to lead toward their predictions

But sweep these discoveries under the carpet, put your fingers in your ears, and let's wait and see what the next set of results provide..

 

[w1z4rd]

Lol @ this thread. So sloooooooooooooooooooooooooooooooow.

 

[Geriatrix]

"Functional". Therein lies the rub, doesn't it.
All those virus DNA chunks and bits of primate DNA thrown in there. Would that be functional too?

 

[Unhappy438]

This is obviously wrong , it doesn't say 90%

 

[copacetic]

I just want to make it clear that I don't remotely understand journal articles like that, nor do I pretend to.

What I do do though, is take with a huge pinch of salt any organization connected to the Discovery Institute.

Further, I couldn't be arsed 'debating' with creationists. Especially not those that have the attitude and tone of the OP of this thread.

 

[empirex]

"Functional". Therein lies the rub, doesn't it.
All those virus DNA chunks

Yes.

and bits of primate DNA thrown in there. Would that be functional too?

Which primate DNA?

 

[empirex]

I just want to make it clear that I don't remotely understand journal articles like that, nor do I pretend to.

What I do do though, is take with a huge pinch of salt any organization connected to the Discovery Institute.

Which organisation might that be?

Further, I couldn't be arsed 'debating' with creationists. Especially not those that have the attitude and tone of the OP of this thread.

Boohoo.

 

[w1z4rd]

empirex is the only person who posts worse sources than killadoob. Sorry killa, you are officially knocked off the top of the, "worst sources for news" ladder.

 

[empirex]

empirex is the only person who posts worse sources than killadoob. Sorry killa, you are officially knocked off the top of the, "worst sources for news" ladder.

Way to play the man, and not the evidence that ENCODE has revealed

 

[w1z4rd]

Way to play the man, and not the evidence that ENCODE has revealed

You mean the information presented by that intelligent design fake knock off of a biology website? Im not ganna waste time responding to that garbage. If you came with a half way intelligent argument I would consider it, but the stuff you post is You Magazine material. Not really in my league tbh. When you work your way up to Farmers Weekly level I might be more interested.

 

[empirex]

You mean the information presented by that intelligent design fake knock off of a biology website? Sure. Im not ganna waste time responding to that garbage. If you came with a half way intelligent argument I would consider it, but the stuff you post is You Magazine material. Not really in my league tbh. When you work your way up to Farmers Weekly level I might be more interested.

Nice

 

[copacetic]

Which organisation might that be?

Pardon, meant to say website, in this case Evolutionnews.org, which you posted an article from.

 

[Geriatrix]

Which primate DNA?

Those chunks that correspond with the chimp, orangutang, bonobo and baboon genome. And fruitbat. And field mouse. And slug.
Anyway. I'll forward this to a buddy of mine, he'll be delighted, he's always arguing about proof of Lord Brahma's creation. Coconuts will be thrown, I bet.

 

[empirex]

Pardon, meant to say website, in this case Evolutionnews.org, which you posted an article from.

Yeah, they reported on ENCODE's findings.

 

[empirex]

Those chunks that correspond with the chimp, orangutang, bonobo and baboon genome. And fruitbat. And field mouse. And slug.
Anyway. I'll forward this a buddy of mine, he'll be delighted, he's always arguing about proof of Lord Brahma's creation.

Yes, those regions as well, we share a lot of analogous regions.
Common designer, or common descent.... you decide.

 

[Geriatrix]

Yes, those regions as well, we share a lot of analogous regions.
Common designer, or common descent.... you decide.

It's interesting looking at big piles of data. Especially when it's a complex and interacting, feedback-loop-like system. Reminds me somewhat of cloud watching. There's a rabbit! There's a tokolosh!

 

[copacetic]

Yeah, they reported on ENCODE's findings.

No, they interpret ENCODE'S findings. There is a big difference.

As an aside: