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(The New York Times)   Junk DNA turns out to have actual value after assessment by Antiques Roadshow   (nytimes.com) divider line 58
    More: Spiffy, junk DNA, dark matter, DNA, Human Genome Project, educational assessment, Broad Institute, genetic conditions, Weill Cornell Medical College  
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3542 clicks; posted to Geek » on 05 Sep 2012 at 5:34 PM (1 year ago)   |  Favorite    |   share:  Share on Twitter share via Email Share on Facebook   more»



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2012-09-05 03:02:11 PM
Well sure, if it has a nice veneer.
 
2012-09-05 03:40:46 PM
The scientific theory of Intelligent Design predicted this. While Darwinists were claiming that "junk DNA" serves no purpose at all, but was just the leftover trash from millions of years of evolution, ID scientists predicted that function and purpose would be discovered in that region. That prediction is coming true.
 
2012-09-05 03:48:31 PM
"Drink More Ovaltine"......a crummy commercial!?!
 
2012-09-05 03:56:51 PM
Does Monica still have that damn blue dress??
 
2012-09-05 04:13:07 PM

SkinnyHead: The scientific theory of Intelligent Design predicted this. While Darwinists were claiming that "junk DNA" serves no purpose at all, but was just the leftover trash from millions of years of evolution, ID scientists predicted that function and purpose would be discovered in that region. That prediction is coming true.


Except for three things:
1) Evolutionists predicted agenic DNA had functional properties which were as yet unknown, they just simply don't do anything for encoding proteins
2) The regions of agenic DNA that are showing functional utility are still relatively small considering the vast swathe of DNA that is agenic
3) Evolutionists conducted the research while creationists have done approximately dick all except for say "Evolution isn't true"
 
2012-09-05 04:17:29 PM

Kome: 2) The regions of agenic DNA that are showing functional utility are still relatively small considering the vast swathe of DNA that is agenic


That point may need clarification: TFA says 80% of it is active and needed, which implies that based on our current knowledge 20% is not. If 20% of something is effectively unneeded or purposeless, the last thing that points to is deliberate, intelligently-guided creation. It points to a gradual and unguided modification process that has simply not excised the useless bits because while unnecessary they aren't deleterious enough to be selected out.
 
2012-09-05 04:43:57 PM
Big words, Kome. That's not gonna fly at all.
 
2012-09-05 04:48:05 PM

Calmamity: Big words, Kome. That's not gonna fly at all.


If there's any big word I used that Skinny is intimately familiar with, it's dick. The rest, though, you may have a point.
 
2012-09-05 05:01:21 PM
I, for one, never believed that "junk DNA" served no purpose. One of the common things that happens during evolution is elimination of DNA that does not provide an advantage to propagation and/or survival.
 
2012-09-05 05:01:45 PM

Kome: Kome: 2) The regions of agenic DNA that are showing functional utility are still relatively small considering the vast swathe of DNA that is agenic

That point may need clarification: TFA says 80% of it is active and needed, which implies that based on our current knowledge 20% is not. If 20% of something is effectively unneeded or purposeless, the last thing that points to is deliberate, intelligently-guided creation. It points to a gradual and unguided modification process that has simply not excised the useless bits because while unnecessary they aren't deleterious enough to be selected out.


The article says: "At least 80 percent of it is active and needed." It also states that "there are still parts of the genome that have not been figured out." Since most of it is active and needed, that suggests that all of it is active and needed.

Evolutionists have been saying that useless junk DNA falsifies intelligent design theory. They were wrong about that. And their Darwinian assumption that junk DNA is just leftover trash from millions of years of evolution has held back medical research. This is a big win for the scientific theory of Intelligent Design
 
2012-09-05 05:02:35 PM
The dna from my junk is worth something down at the sperm bank

/Wasn't that a song by sublime?
//down at the sperm bank-yank-yank-yank
 
2012-09-05 05:19:50 PM

SkinnyHead: Evolutionists have been saying that useless junk DNA falsifies intelligent design theory.


Not really. In a very real way, agenic DNA is only confirmatory evidence of evolution and neutral about creationism. Combined with the millions of other data points - from comparative anatomy, ecology, the fossil record, etc. - it all speaks to a natural and scientific explanation, i.e. evolution, and not to religious explanations, i.e. creationism.

And their Darwinian assumption that junk DNA is just leftover trash from millions of years of evolution has held back medical research.

Except the evolutionary biologists and evolutionary geneticists haven't said agenic DNA is leftover trash, merely "junk" in regards to coding for proteins. And consider that greater understanding of evolutionary biology has advanced medicine in leaps and bounds compared to before it was accepted, I'd say the biggest thing holding back medical research these days is the concerted effort by religious conservatives to ban the teaching of evolution in education, resulting in less students being interested in these topics and thus not going into the fields.

This is a big win for the scientific theory of Intelligent Design

How come you're the only creationist who says it's a scientific theory? Phillip Johnson has said there's no scientific theory of creationism yet. Michael Behe and William Dembski don't call it a fully outlined scientific theory, they only claim their (eminently falsified) claims of irreducible complexity and complex specified information are theoretical models with real world examples to support that (although, again, those examples have been shown to be made in gross error). To date, literally no creationist has put forward a full scientific theory about creationism. Hell, Behe admitted - under oath! - that in order for creationism as it is currently described to be science, the definition of science would have to be expanded to such a degree that astrology would be considered scientific.
 
2012-09-05 05:38:40 PM
..But if you HADN'T mutated those three chromosomes by huffing cut-rate air fresheners, you might have been able to keep your hair for an extra 5-7 years. But, since you did - balding.
 
2012-09-05 05:43:47 PM
I'd love to let her 'assess' my DNA, ifyaknowwhatImean.

2.bp.blogspot.com
 
2012-09-05 05:45:34 PM
All you need to know about intelligent design:

1.bp.blogspot.com 

It's a semantic Band-aid on the untenable position of teaching creationism in public classrooms. The end.
 
2012-09-05 05:47:46 PM
I think this is an appropriate image for this thread.

i457.photobucket.com
 
2012-09-05 05:52:01 PM

SkinnyHead: The scientific theory of Intelligent Design predicted this. While Darwinists were claiming that "junk DNA" serves no purpose at all, but was just the leftover trash from millions of years of evolution, ID scientists predicted that function and purpose would be discovered in that region. That prediction is coming true.


A broken clock is right twice a day.
 
2012-09-05 06:00:26 PM

Quantum Apostrophe: A broken clock is right twice a day.


However, without another way of telling time, you cannot know when that clock is correct, and as such it should be disregarded

/Also, ID did not predict that (It makes no predictions) and evolution doesn't disallow it. But Kome has already put it better
 
2012-09-05 06:01:54 PM
these scientists are very brilliant for their ability to reverse-engineer this design.
kudos.
yay science!
 
2012-09-05 06:15:26 PM

ricewater_stool: I, for one, never believed that "junk DNA" served no purpose. One of the common things that happens during evolution is elimination of DNA that does not provide an advantage to propagation and/or survival.


Only if having a streamlined genome is itself advantageous; which is usually only true in parasites. Yes there are energetic costs to carrying around extra DNA, as replicating it costs more, but for most organisms it just doesn't factor in. Plenty of organisms have huge genomes with lots of redundancy. Ciliates and Dinoflagellates are two prime examples.
 
2012-09-05 06:19:40 PM
I'm going through some of the papers now, but it is going to take a bit of doing (there are a lot). I would; however, point out a few things. One is that, IMO (and others) ENCODE is known for overstating things. Their evidence of "pervasive transcription across the entire genome" has been deconstructed by a few people since it was published. Their threshold for "this represents a novel transcript" is often quite low. Keep in mind that with deep sequencing (RNA-Seq) you can often get reads for transcripts with an average abundance of less than 1 copy per cell. Transcription is messy, and leaky, and we know there is a certain amount of noise expected from these processes by their very nature. Very, very low copy numbers of transcripts is consistent with that. Sometimes ENCODE likes to take that as a positive signal.

Secondly from reading the overview that 80% figure seems to be derived by including all base pairs within a certain distance of active chromatin marking, etc as being functional. Which is going to overstate your numbers by a lot. Known functional elements are pretty dispersed across the whole genome.
 
2012-09-05 06:20:11 PM
I got a huge collection of tissues fullof DNA over by my trashcan. My dog must know they have value because he takes then and hides them somewhere.
 
2012-09-05 06:23:33 PM

Kome: Except the evolutionary biologists and evolutionary geneticists haven't said agenic DNA is leftover trash, merely "junk" in regards to coding for proteins. And consider that greater understanding of evolutionary biology has advanced medicine in leaps and bounds compared to before it was accepted, I'd say the biggest thing holding back medical research these days is the concerted effort by religious conservatives to ban the teaching of evolution in education, resulting in less students being interested in these topics and thus not going into the fields.


Its also wrong to equate "non-coding" with Junk. Pseudogenes are junk. Repetitive elements are often junk. LINES, SINES, Alu repeats, retrotransposons, etc.

Hell going by the ENCODE overview data it looks like they are counting pseudogenes as functional in some cases:


The GENCODE project also annotated 11,224 pseudogenes, of which 863 were transcribed and associated with active chromatin


We know pseudogenes are often still transcribed until they degenerate to a certain point, but those transcripts undergo nonsense-mediated decay right away or produce non-functional protein that is immediately targeted for degradation. Thats not functional. Yes 863 cases is going to make up a small portion of their "80%" figure, but it is indicative of the types of things they may be lumping in to that functional category.
 
2012-09-05 06:40:50 PM
I'll also state I think these papers are exciting and I think ENCODE is producing some valuable data and resources for the genomics community, I know I'll be using lots of these databases in the near future in my own work. But I think some of the numbers are likely very inflated. Which is a shame. I think the amount of functional DNA that is currently unannotated is higher than what has already been annotated, but I doubt it is in the 80% range. Something like 62% of that BTW comes from the RNA category. Looking at the RNA paper now to see what their threshold for calling a transcript actually was.

If you use twitter there is an #ENCODE hashtag operational right now. Lots of scientists weighing in on the action. I'll post some links to blog posts here for those interested.
 
2012-09-05 06:42:40 PM

entropic_existence: If you use twitter there is an #ENCODE hashtag operational right now. Lots of scientists weighing in on the action. I'll post some links to blog posts here for those interested.


Yes plzkthx!!! I don't use twitter, and prefer in-depth blog posts to twitter posts anyway.
 
2012-09-05 06:43:48 PM

SkinnyHead: The scientific theory of Intelligent Design predicted this. While Darwinists were claiming that "junk DNA" serves no purpose at all, but was just the leftover trash from millions of years of evolution, ID scientists predicted that function and purpose would be discovered in that region. That prediction is coming true.


I took out the part I know for a fact is wrong. There is absolutely nothing scientific about the theory of ID.

I am curious if you can point to a major proponent of ID who has said that "junk DNA" serves a purpose.
 
2012-09-05 06:46:16 PM
It's where the aliens left their coding comments

//comments
 
2012-09-05 06:58:32 PM

SkinnyHead: Kome: Kome: 2) The regions of agenic DNA that are showing functional utility are still relatively small considering the vast swathe of DNA that is agenic

That point may need clarification: TFA says 80% of it is active and needed, which implies that based on our current knowledge 20% is not. If 20% of something is effectively unneeded or purposeless, the last thing that points to is deliberate, intelligently-guided creation. It points to a gradual and unguided modification process that has simply not excised the useless bits because while unnecessary they aren't deleterious enough to be selected out.

The article says: "At least 80 percent of it is active and needed." It also states that "there are still parts of the genome that have not been figured out." Since most of it is active and needed, that suggests that all of it is active and needed.

Evolutionists have been saying that useless junk DNA falsifies intelligent design theory. They were wrong about that. And their Darwinian assumption that junk DNA is just leftover trash from millions of years of evolution has held back medical research. This is a big win for the scientific theory of Intelligent Design


godofchances.files.wordpress.com

So that's your argument?
 
2012-09-05 07:01:00 PM

wiredroach: All you need to know about intelligent design:

[1.bp.blogspot.com image 563x422] 

It's a semantic Band-aid on the untenable position of teaching creationism in public classrooms. The end.


Funny how it's always implied that "you-know-who" is the intelligent designer, ain't it?
 
2012-09-05 07:02:25 PM

Kome: entropic_existence: If you use twitter there is an #ENCODE hashtag operational right now. Lots of scientists weighing in on the action. I'll post some links to blog posts here for those interested.

Yes plzkthx!!! I don't use twitter, and prefer in-depth blog posts to twitter posts anyway.


Dr. Ewan Birney, formerly the lead analysis coordinator for ENCODE has a blog post up here in the style of a Q&A for some of his more "skeptical" friends with a more nuanced view. He provides his own rational for some of the word choice/vocabulary they used in the publication(s), most of those rationale's I don't agree with him on but I get the point he is making. I just wish, especially for these large flashy-publications from massive consortia with a lot of scientific credibility, that they would be more nuanced in their pubs. Speaking as a scientists I don't want someone going with 80% over a 20-80% figure just because they think the latter is "too much" for someone to get without lots of explanation. The former leads itself to being taken out of context too easy.

It is also worth noting that intronic regions seem to be explicitly included in their functional category as they note that ~60% of the genome is currently exonic/intronic according to existing GENCODE standards. So it should put the 80% figure in more context, they aren't exactly using the same definitions as many other genome scientists for how to define functional regions, specifically the usual figure where 1.5-2% of the genome is thought to comprise all of the known, widely-agreed upon exons from protein-coding genes and a handful of well established non-coding RNAs.
 
2012-09-05 07:05:40 PM

Fano: wiredroach: All you need to know about intelligent design:

[1.bp.blogspot.com image 563x422] 

It's a semantic Band-aid on the untenable position of teaching creationism in public classrooms. The end.

Funny how it's always implied that "you-know-who" is the intelligent designer, ain't it?


Lord Voldemort? You must be reading different creationist websites.
 
2012-09-05 08:03:25 PM

colon_pow: these scientists are very brilliant for their ability to reverse-engineer this design.
kudos.
yay science!


To what "design" do you refer?
 
2012-09-05 08:05:50 PM

entropic_existence: Kome: Except the evolutionary biologists and evolutionary geneticists haven't said agenic DNA is leftover trash, merely "junk" in regards to coding for proteins. And consider that greater understanding of evolutionary biology has advanced medicine in leaps and bounds compared to before it was accepted, I'd say the biggest thing holding back medical research these days is the concerted effort by religious conservatives to ban the teaching of evolution in education, resulting in less students being interested in these topics and thus not going into the fields.

Its also wrong to equate "non-coding" with Junk. Pseudogenes are junk. Repetitive elements are often junk. LINES, SINES, Alu repeats, retrotransposons, etc.

Hell going by the ENCODE overview data it looks like they are counting pseudogenes as functional in some cases:


The GENCODE project also annotated 11,224 pseudogenes, of which 863 were transcribed and associated with active chromatin

We know pseudogenes are often still transcribed until they degenerate to a certain point, but those transcripts undergo nonsense-mediated decay right away or produce non-functional protein that is immediately targeted for degradation. Thats not functional. Yes 863 cases is going to make up a small portion of their "80%" figure, but it is indicative of the types of things they may be lumping in to that functional category.


You are attempting to actually analyze and understand the research. Creationists, however, will not do so prior to claiming the published research to validate their position.
 
2012-09-05 08:07:20 PM

wiredroach: All you need to know about intelligent design:

It's a semantic Band-aid on the untenable position of teaching creationism in public classrooms. The end.


See also: cdesign proponentsists

=Smidge=
 
2012-09-05 08:19:53 PM
And when the scientists were told how important the just DNA was, they smiles slightly and muttered flatly, "Wow, that's nice, I had no idea."
 
2012-09-05 08:20:05 PM

entropic_existence: ricewater_stool: I, for one, never believed that "junk DNA" served no purpose. One of the common things that happens during evolution is elimination of DNA that does not provide an advantage to propagation and/or survival.

Only if having a streamlined genome is itself advantageous; which is usually only true in parasites. Yes there are energetic costs to carrying around extra DNA, as replicating it costs more, but for most organisms it just doesn't factor in. Plenty of organisms have huge genomes with lots of redundancy. Ciliates and Dinoflagellates are two prime examples.


Well I am a bacteriologist, so there's my bias.
 
2012-09-05 08:29:29 PM

ricewater_stool: Well I am a bacteriologist, so there's my bias.


Yeah, bacteria/archaea don't really have introns, much in the way of intergenic regions, and I think even pseudogenes are pretty much unheard of. Totally different ball game when it comes to genome size, complexity, and organization in Eukaryotes.
 
2012-09-05 08:31:41 PM

entropic_existence: ricewater_stool: Well I am a bacteriologist, so there's my bias.

Yeah, bacteria/archaea don't really have introns, much in the way of intergenic regions, and I think even pseudogenes are pretty much unheard of. Totally different ball game when it comes to genome size, complexity, and organization in Eukaryotes.


Working in wheat and Barley myself at the moment, I've got pretty much nothing -but- intronic DNA. (These are huge fracking genomes)
 
2012-09-05 09:08:49 PM
The notion of "functiinality" was originally flawed in that there are several functions of dna besides coding for genes, for example:
- physical packaging and unpacking
- formation of complex structures involved in long distance transcriptional regulation
- absorption of potentially harmful UV light.

So you cant really say DNA is junk until you understand all of what it is doing anyway. And none of this has anything to do with evolution vs. creationism.
 
2012-09-05 09:09:28 PM
The only way you'll get DNA from my junk is to pry it from my warm, lotioned hand.
 
2012-09-05 09:33:11 PM

Fano: Funny how it's always implied that "you-know-who" is the intelligent designer, ain't it?


Yup...even if intelligent design held water the designer could be Jesus, or Allah, or Osiris, or Cthulhu, or.....
 
2012-09-05 10:03:16 PM
Just don't try to have it restored. That kills the value.
 
2012-09-05 11:13:53 PM

the_sidewinder: Quantum Apostrophe: A broken clock is right twice a day.

However, without another way of telling time, you cannot know when that clock is correct, and as such it should be disregarded

/Also, ID did not predict that (It makes no predictions) and evolution doesn't disallow it. But Kome has already put it better


Yeah, pretty much.
 
2012-09-05 11:23:22 PM
www.icanhasinternets.com

I would add "Well Played, God." But I guess He wasn't playing around at all. We were playing catch up.
 
2012-09-05 11:56:00 PM

meat0918: I think this is an appropriate image for this thread.

[i457.photobucket.com image 402x536]


Well, except that the Archaea probably came around much later. They presumably evolved from bacteria and are a transitional species between the bacteria and the eukaryotes.
 
2012-09-06 12:40:57 AM

treesloth: Just don't try to have it restored. That kills the value.


Right! If you clean that patina off, you are screwed and the appraiser will very politely insult you for it and make you feel like an idiot.
 
2012-09-06 12:50:12 AM

SkinnyHead: The scientific theory of Intelligent Design predicted this. While Darwinists were claiming that "junk DNA" serves no purpose at all, but was just the leftover trash from millions of years of evolution, ID scientists predicted that function and purpose would be discovered in that region. That prediction is coming true.


How can I tell you don't actually know what the "Darwinists" expected?

Strict Darwinians did not expect DNA to be nothing but "junk." Or maybe you don't know what a "Darwinian" even is.
 
2012-09-06 01:03:33 AM

SkinnyHead: The scientific theory of Intelligent Design predicted this. While Darwinists were claiming that "junk DNA" serves no purpose at all, but was just the leftover trash from millions of years of evolution, ID scientists predicted that function and purpose would be discovered in that region. That prediction is coming true.


Cite your sources. This isn't snarky. I'm being genuine.
 
2012-09-06 01:17:55 AM
Does the new batch of papers include proteomics and metabolismics or just transcripts? I'm eager for somebody to (try to) correlate them all and find that there is no relationship.

/sure as hell would make my data make more sense...
 
2012-09-06 01:42:39 AM

pivazena: Does the new batch of papers include proteomics and metabolismics or just transcripts? I'm eager for somebody to (try to) correlate them all and find that there is no relationship.

/sure as hell would make my data make more sense...


I believe that their data is just transcripts, any expressed RNA.

At the risk of inducing information overload, you can check out some of the data available on the UCSC Genome Browser.
 
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