13 replies to this topic

[ihatesnow]

http://news.yahoo.co...3lQHWsATirQtDMD

[xEva]

I never bought that "junk DNA" story. A program cannot exist without the instruction code, but it may exist without a data array, which DNA coding for specific proteins is. In fact, a data array without the instruction code on how to utilize these data is junk for virtue of being useless.

Back in the depths of time (well, circa 1970), all DNA that did not code for proteins or proximal regulatory elements (promoters and terminators) was tossed on the junk pile.

I don't understand what the guy you linked to is unhappy about. He links to even unhappier guy who insists that most of it is still junk. But to my POV, things have finally turned right: "... much of what has been called 'junk DNA' in the human genome is actually a massive control panel with millions of switches regulating the activity of our genes."

How else can it be? The main part of a program is the instruction code. And the way we are programmed seems non-modular, which is smart. It sort of has a 'printf' subroutine enclosed everywhere it is needed. Imagine if it was stated only in one place and then only be called when needed. Should a mutation happen in that one place, nothing would ever be 'printed'. If that's how our program is written then of course it would seem to have many repeats.

[Marios Kyriazis]

The study of transposons ('junk' DNA elements) is one of the most promising ways to fight aging and promote extreme lifespans. This can be aided by Synthetic Biology which can create artificial DNA elements that can intentionally regulate and modify gene expression.

[xEva]

The study of transposons ('junk' DNA elements) is one of the most promising ways to fight aging and promote extreme lifespans. This can be aided by Synthetic Biology which can create artificial DNA elements that can intentionally regulate and modify gene exp<b></b>ression.

Interesting. And how do transposons affect aging?

I thought environment modified gene expression.

Edited by xEva, 14 October 2012 - 09:59 PM.

[niner]

http://news.yahoo.co...3lQHWsATirQtDMD

Nice to finally see a slap-down to the ridiculous hype surrounding the ENCODE project. Another media fail for not doing better fact checking, and the ENCODE guys are not off the hook for their misleading press releases either.

[Marios Kyriazis]

The study of transposons ('junk' DNA elements) is one of the most promising ways to fight aging and promote extreme lifespans. This can be aided by Synthetic Biology which can create artificial DNA elements that can intentionally regulate and modify gene expression.

Interesting. And how do transposons affect aging?

I thought environment modified gene expression.

See the short paper below, discussing some aspects of this:


Transposable elements and longevity


by Andreas Apostolides


Based on theories proposed by Marios Kyriazis


This project is based on a hypothesis first proposed by Marios Kyriazis as part of his ELPIs theory. The hypothesis states that there are certain transposon (described below) in humans that either promote or repress longevity, and that it may be possible for us to enhance longevity by either increasing the function of those transposons that promote longevity or decreasing the function of those that repress it.


Transposons are DNA segments that have the ability to move within the genome either by being removed from one place and then integrated into another (these are called "DNA transposons"), or by first being transcribed into RNA and then reverse-transcribed into cDNA which is then integrated into another place of the genome (these are called "retrotransposons"). About 45% of the human genome consists of recognizable transposons (Lander, et al. 2001).


Because when they were first discovered it was believed that these elements code for no protein at all and have no effect on the expression of genes, they were initially considered as part of at~94%of DNA they used to call "junk DNA". This soon changed, however, as it begun being revealed that transposons, either readily after their integration in the genome or after minor nucleotide changes in their sequence,can acquire new functions leading to the expression of novel genes or affecting the expression of other genes.


Specifically, transposons can either offer themselves as protein-coding regions (either because they had been inserted inside a gene's exon, or due to more complex mechanisms that will not be described here), or they can affect the expression of nearby genes by offering themselves assplice sites, polyadenylation signals, or transcription regulatory elements such as promoters, transcription enhancers, transcription silencers, transcription inhibitors, etc (see Brosius, 1999, for many examples).Such phenomena, where elements acquire new functions, are called exaptations (seeGould and Vrba 1982)


It is already known that there are certain genes that promote and others that repress longevity (for example by increasing chances of development of certain diseases). It is also known, as discussed above, that transposons can contribute novel genes, or they can affect the expression of existing ones. The purpose of this project is to examine whether there are existing transposons that contribute to our longevity in a way described by Kyriazis' theory. Specifically, we are interested in:





Transposons that contribute to the expression of longevity genes


Transposons that inhibit the expression of mortality genes


For the time being we will concentrate on the first part: Transposons that contribute to the expression of longevity genes. This could be happening in various ways, but at first, we will be examining the following scenarios:





A transposon being a part of the protein-coding region a longevity gene


A transposon serving as a longevity gene's promoter


A transposon serving as a splice site that makes possible the creation of a longevity gene transcript


A transposon serving as apoly(A) signalthat makes possible the creation of a longevity gene transcript.

[xEva]

Thank you, mrszeta! So, it is still a hypothesis. Yes, reshuffling transposons should modify the gene expression. I recently saw a study to this effect, where removal of two chunks did not affect the viability, but did affect the gene expression. My understanding is that a change in the position of a gene within a DNA strand makes it more or less accessible for the "switches" the ENCODE press released talked about, which affects this gene transcription. But affecting longevity only? Why not also any other attribute?

Interesting that many people here linked to unhappy reviews of ENCODE work, while obviously no one had a chance to read the 30 papers that were released. As if a priori insisting that our DNA is mostly junk makes them happier, or perhaps feel smarter -? Psychologically, it is a strange stance. To say the least... and considering how little we still know.

With time we will learn how the program of life works. I find it fascinating comparing our hardware/software with it.



.

Edited by xEva, 15 October 2012 - 04:36 PM.

[niner]

Interesting that many people here linked to unhappy reviews of ENCODE work, while obviously no one had a chance to read the 30 papers that were released. As if a priori insisting that our DNA is mostly junk makes them happier, or perhaps feel smarter -? Psychologically, it is a strange stance. To say the least... and considering how little we still know.

I don't think you understand what we're complaining about. ENCODE made it sound like we all thought that everything that wasn't coding was "junk". We never thought that, and we've known about promoters, repressors, transposons and all the other stuff for decades. They presented a very misleading picture, and the media slavishly scooped it up and regurgitated it. It was a bad day for the public understanding of science. The Creationists and the ID people had a field day with it, though, which figures.

[xEva]

Thank you niner! I did understand it very well from the first link (that linked to the second). It is true that the public was misled to believe that most of our DNA is junk, but it could not be ENCODE's fault, because this notion was spread around long before they even started their decoding work. The second link, to which the first one refers, is by some authority in genetics who insists that at least 50% of our DNA is still junk and that's his grief with ENCODE, i.e. that they now misrepresent the situation by slanting it in the opposite direction.

IMHO what ENCODE did is let the public finally know the real situation. Why did this made some people unhappy? Especially since they have not even read the 30 reports yet. What if, after reading them, they would have to agree with ENCODE assessment?

PS
Their press release was addressed to the public, not specialists.

As a member of public, just reading the popular press on genetics, I had the impression that the geneticists indeed thought that most of out DNA was junk. I could not believe that no-one from the computer business would inform them that no program can exist consisting of just a data array. I am glad it is all cleared now.

Edited by xEva, 15 October 2012 - 07:39 PM.

[niner]

The ENCODE publicity barrage got it wrong in two ways. They falsely led people to believe that scientists (recently) thought ALL non-protein coding DNA was "junk", and the also let people get the wrong idea that it was ALL solved now. Neither is true. That's not letting the public know the real situation, it's letting them know the wrong situation.

[xEva]

Yes, niner, but put yourself in their shoes. What would you say? Sorry, dear public, you were misled and it is journalists fault... Or?.. The public did believe that geneticists thought that non-protein coding DNA was junk. How would you word the press release?

Instead of the announcement of a celebrated achievement, this could easily derail into a finger-pointing campaign. Whose fault, when... ENCODE did the right thing by simply stating that 'we thought that in the past but think differently now'. No finger-pointing, case closed. All can move on now.

I for one was elated by this news. For years I suffered cognitive dissonance because of this. Surely, I could not believe that geneticists were so stupid, but I could not dismiss what the press had been hummering into us for decades either. I simply avoided reading the literature, thinking that the dust had not settled in genetics yet. I did not want to pollute my head with another half-baked theory. I am very glad it all cleared now.

Edited by xEva, 16 October 2012 - 12:57 AM.

[niner]

I would say what was done and how it added to existing knowledge. But then it wouldn't have sounded like such a big deal. The dust in genetics was a lot more settled, a lot longer ago that you might have thought from the ENCODE media blitz. Generally speaking, it's a bad idea to try to understand science on the basis of mainstream media reports. There are a handful of decent science writers out there, but a lot of lousy ones.

[ymc]

Interesting that many people here linked to unhappy reviews of ENCODE work, while obviously no one had a chance to read the 30 papers that were released. As if a priori insisting that our DNA is mostly junk makes them happier, or perhaps feel smarter -? Psychologically, it is a strange stance. To say the least... and considering how little we still know.

I don't think you understand what we're complaining about. ENCODE made it sound like we all thought that everything that wasn't coding was "junk". We never thought that, and we've known about promoters, repressors, transposons and all the other stuff for decades. They presented a very misleading picture, and the media slavishly scooped it up and regurgitated it. It was a bad day for the public understanding of science. The Creationists and the ID people had a field day with it, though, which figures.

ENCODE says while 80% of genome has some functions. Only 10-15% is important enough to be highly conserved.

For example, while 62% of genome encodes long noncoding RNAs, only a small part of each long noncoding RNA has critical function.

I would say what was done and how it added to existing knowledge. But then it wouldn't have sounded like such a big deal. The dust in genetics was a lot more settled, a lot longer ago that you might have thought from the ENCODE media blitz. Generally speaking, it's a bad idea to try to understand science on the basis of mainstream media reports. There are a handful of decent science writers out there, but a lot of lousy ones.

I agree with this. Concepts of DNAse hypersensitive sites, histones, long noncoding RNA, Chromatin States, etc had been studied way before the latest crop of ENCODE papers.

What the ENCODE papers show is a genome-wide survey of these non protein coding elements which in itself is an admirable effort IMHO

[ymc]

The study of transposons ('junk' DNA elements) is one of the most promising ways to fight aging and promote extreme lifespans. This can be aided by Synthetic Biology which can create artificial DNA elements that can intentionally regulate and modify gene expression.

Transposons is just one of the many types of non protein coding elements (aka 'junk' elements). Some of them might affect aging but there are many other non protein coding elements that can do that as well.